Heat-Resistant Agglutinin 1 Is an Accessory Enteroaggregative Escherichia coli Colonization Factor

Enteroaggregative Escherichia coli (EAEC) is an important cause of acute and persistent diarrhea. The defining stacked brick adherence pattern of Peruvian EAEC isolate 042 has previously been attributed to aggregative adherence fimbriae II (AAF/II), which confer aggregative adherence on laboratory E. coli strains. EAEC strains also show exceptional autoaggregation and biofilm formation, other phenotypes that have hitherto been ascribed to AAF/II. We report that EAEC 042 carries the heat-resistant agglutinin (hra1) gene, also known as hek, which encodes an outer membrane protein. Like AAF/II, the cloned EAEC 042 hra1 gene product is sufficient to confer autoaggregation, biofilm formation, and aggregative adherence on nonadherent and nonpathogenic laboratory E. coli strains. However, an 042 hra1 deletion mutant is not deficient in these phenotypes compared to the wild type. EAEC strain 042 produces a classic honeycomb or stacked brick pattern of adherence to epithelial cells. Unlike wild-type 042, the hra1 mutant typically does not form a tidy stacked brick pattern on HEp-2 cells in culture, which is definitive for EAEC. Moreover, the hra1 mutant is significantly impaired in the Caenorhabditis elegans slow kill colonization model. Our data suggest that the exceptional colonization of strain 042 is due to multiple factors and that Hra1 is an accessory EAEC colonization factor.Enteroaggregative Escherichia coli (EAEC) was originally identified as the etiologic agent of persistent diarrhea in developing countries but is gaining increasing prominence for its role in a wider spectrum of diarrheal syndromes. EAEC strains have been implicated in acute as well as persistent diarrhea among adults and children (reviewed in references 25 and 40). A recent meta-analysis found that EAEC is significantly associated with disease in every group at high risk for diarrhea, including young children, human immunodeficiency virus-positive individuals, and visitors to developing countries (24). In addition to its association with disease in epidemiological studies in developing countries, EAEC has also been identified as a principal cause of diarrheal disease in Germany, the United Kingdom, and the United States (11, 26, 51).Aggregative adherence is the defining characteristic of EAEC (38). EAEC strains adhere to the intestinal epithelium, and to epithelial cells in culture, in a characteristic two-dimensional “stacked brick” fashion. The pattern features bacteria adhering to the eukaryotic surface, other bacteria, and the solid substratum. Four types of fimbriae have so far been documented as conferring aggregative adherence (4, 14, 17, 37). Two noncontiguous plasmid loci containing the complete complement of genes encoding aggregative adherence fimbriae I (AAF/I) or AAF/II are sufficient to confer aggregative adherence on nonadherent E. coli (14, 49). The plasmid bearing type IV pili found in Serbian EAEC outbreak strain C1096 are also sufficient to confer a weak aggregative adherence phenotype on E. coli K-12 (17). AAF additionally play an essential role in production of a superfluous EAEC-associated biofilm, which could account for the association of these strains with persistent diarrhea in epidemiological studies (46).Some categories of diarrheagenic pathogens have a conserved set of adhesins which allow them to overcome flushing across the intestinal epithelium. Typical enteropathogenic E. coli isolates, for example, all possess bundle-forming pili and the outer membrane adhesin intimin, whereas atypical enteropathogenic E. coli isolates possess intimin but not bundle-forming pili (reviewed in reference 10). EAEC strains, by contrast, are considerably heterogeneous. While many EAEC strains carry genes encoding one of the known aggregative adherence fimbriae, some EAEC do not harbor any known AAF even though they do demonstrate aggregative adherence (4, 7, 13, 14). This, and the presence of multiple adhesins in most mucosal colonizers (53), points to the likelihood of other EAEC adhesins. Imuta et al. recently implicated a TolC secreted factor in adherence (27), and Montiero-Neto et al. (33) described a 58-kDa nonstructural adhesin in O111:H12 EAEC. However, the former factor is only a contributor to aggregative adherence and the latter adhesin is not found in other EAEC. Overall, nonstructural EAEC adhesins have received little attention.The outer membrane protein Tia was originally characterized as an invasin and later shown to confer adhesive properties on enterotoxigenic E. coli (ETEC) (20, 21). Fleckenstein et al. (21) observed that a tia gene probe hybridized to DNA from non-ETEC strains, one of which was EAEC strain 042. As the Southern blot data published by Fleckenstein et al. showed bands of different intensities, as well as size, between ETEC strain {"type":"entrez-nucleotide","attrs":{"text":"H10407","term_id":"875229","term_text":"H10407"}}H10407, which carries tia, and EAEC strain 042, we hypothesized that the probe was recognizing a similar, rather than identical, gene (21).We have determined that EAEC strain 042 harbors a gene encoding the heat-resistant agglutinin 1 (hra1), a hemagglutinin originally reported from an O9:H10:K99 porcine ETEC strain. Hra1 has also been reported from uropathogenic E. coli strains and neonatal meningitis E. coli strain RS218, in which context it is otherwise known as Hek (19, 48). (The hek nomenclature was introduced after hra1, to delineate the form of the gene found in invasive human pathogens from that of a porcine isolate [19].) A role for the outer membrane protein Hra1/Hek in adherence by neonatal meningitis E. coli has recently been defined (19).Although hra1/hek has been reported from multiple pathogens, its role in colonization and virulence has only been conclusively studied in the neonatal meningitis E. coli strain RS218 (19). In this paper, we demonstrate that the EAEC hra1 gene is sufficient to confer colonization-associated phenotypes, including aggregative adherence and biofilm formation, on laboratory E. coli strains. Intriguingly, we find that although it confers these phenotypes on K-12 and is expressed in 042, hra1 is not required for in vitro colonization-associated phenotypes demonstrated by 042. The hra1 gene is, however, essential for the formation of a true stacked brick pattern in EAEC and for optimal in vivo colonization in a Caenorhabditis elegans model.     

Induction of Immune Responses in Mice after Oral Immunization with Recombinant Lactobacillus casei Strains Expressing Enterotoxigenic Escherichia coli F41 Fimbrial Protein

In an effort to develop a safe and effective vaccine for the prevention of enterotoxigenic Escherichia coli (ETEC) F41 infections, we have developed a surface antigen display system using poly-γ-glutamate synthetase A (PgsA) as an anchoring matrix. The recombinant fusion proteins comprised of PgsA and fimbrial protein of F41 were stably expressed in Lactobacillus casei 525. Surface localization of the fusion protein was verified by immunoblotting, immunofluorescence microscopy, and flow cytometry. Oral inoculation of recombinant L. casei 525 into specific-pathogen-free BALB/c mice resulted in significant mucosal immunoglobulin A (IgA) titers that remained elevated for >16 weeks. High levels of IgG responses in sera specific for F41 fimbriae were also induced, with prominent IgG1 titers as well as IgG2a and IgG2b titers. The helper T-cell (Th) response was Th2-cell dominant, as evidenced by increased mucosal and systemic interleukin-4-producing T cells and a concomitant elevation of serum IgG1 antibody responses. More than 80% of the mice were protected against challenge with a 2 × 10⁴-fold 50% lethal dose of standard-type F41 ({"type":"entrez-nucleotide","attrs":{"text":"C83919","term_id":"2706851","term_text":"C83919"}}C83919). The induced antibodies were important for eliciting a protective immune response against F41 infection. These results indicated that the use of recombinant L. casei 525 could be a valuable strategy for future vaccine development for ETEC.Enterotoxigenic Escherichia coli (ETEC) strains colonize the small intestine, secrete enterotoxins, and cause diarrhea. Colonization is facilitated by pili (fimbriae). Pili facilitate the adherence of ETEC to intestinal mucosa (27). Pilus adhesins that are known to be important in ETEC infections of neonatal animals are K88, K99, 987P, FY, and F41 (26, 28, 29, 38). F41 is less prevalent than K88, K99, or 987P and is usually accompanied by K99 (25). There is, however, strong suggestive evidence that F41 can mediate colonization by adhesion. Variants of a K99- and F41-positive porcine ETEC strain that have lost the K99 gene (29) and still carry the gene for and produce F41 are still virulent for newborn pigs (13).The previously conventional vaccine variability in levels of protective immunity may have been due to the lack of stimulation of appropriate mucosal immunity, since these vaccines were delivered parenterally. Mucosal immunization has proven to be an effective approach against the colonization of pathogens and their further spread to the systemic circulation (15, 34). Therefore, it is necessary to develop efficient and safe antigen vectors that will be able to trigger mucosal and systemic immune responses. One promising approach relies on the use of live bacterial vehicles (22). For mucosal immunization, lactic acid bacteria (LAB) are more attractive as delivery vehicles than other live vaccine vectors (e.g., Shigella, Salmonella, and Listeria spp.) (1, 3, 20, 21) because LAB are considered safe, they exhibit adjuvant properties, and they are weakly immunogenic (7, 9, 10, 12, 23, 41). In addition, extracellularly accessible antigens expressed on the surfaces of bacteria are better recognized by the immune system than those that are intracellular (18).It is now realized that the delivery of antigen to mucosal surfaces can induce a strong local immune response in mucosa-associated lymphoid tissue. For the surface display of antigens on Lactobacillus casei, we have developed an expression vector using the poly-γ-glutamate synthetase A (PgsA) gene product as an anchoring matrix. PgsA is a transmembrane protein derived from the poly-γ-glutamic acid synthetase complex (the PgsBCA system) of Bacillus subtilis (5, 6); in this system, the N terminus of the target protein was fused to the PgsA protein, and the resulting fusion protein was expressed on the cell surface (32). In this study, the F41 fimbrial gene of ETEC was inserted into the vector pHB:pgsA and displayed on the surface of L. casei. The oral vaccination of mice with the recombinant L. casei strain elicited systemic and mucosal immune responses. These immune responses against F41 provided protective immunity in mice challenged with virulent live infectious {"type":"entrez-nucleotide","attrs":{"text":"C83919","term_id":"2706851","term_text":"C83919"}}C83919 postimmunization. Moreover, we showed that mice orally immunized with recombinant L. casei anchoring F41 induced a Th2-type response to ETEC F41. The results of this study suggest a potential use for our surface expression system against other pathogens that are transmitted to mucosal systems.     

Longus,a Type IV Pilus of Enterotoxigenic Escherichia coli,Is Involved in Adherence to Intestinal Epithelial Cells

Enterotoxigenic Escherichia coli (ETEC) is the leading bacterial cause of diarrhea in the developing world, as well as the most common cause of traveler''s diarrhea. The main hallmarks of this type of bacteria are the expression of one or more enterotoxins and fimbriae used for attachment to host intestinal cells. Longus is a pilus produced by ETEC. These bacteria grown in pleuropneumonia-like organism (PPLO) broth at 37°C and in 5% CO₂ produced longus, showing that the assembly and expression of the pili depend on growth conditions and composition of the medium. To explore the role of longus in the adherence to epithelial cells, quantitative and qualitative analyses were done, and similar levels of adherence were observed, with values of 111.44 × 10⁴ CFU/ml in HT-29, 101.33 × 10⁴ CFU/ml in Caco-2, and 107.11 × 10⁴ CFU/ml in T84 cells. In addition, the E9034AΔlngA strain showed a significant reduction in longus adherence of 32% in HT-29, 22.28% in Caco-2, and 21.68% in T84 cells compared to the wild-type strain. In experiments performed with nonintestinal cells (HeLa and HEp-2 cells), significant differences were not observed in adherence between E9034A and derivative strains. Interestingly, the E9034A and E9034AΔlngA(pLngA) strains were 30 to 35% more adherent in intestinal cells than in nonintestinal cells. Twitching motility experiments were performed, showing that ETEC strains E9034A and E9034AΔlngA(pLngA) had the capacity to form spreading zones while ETEC E9034AΔlngA does not. In addition, our data suggest that longus from ETEC participates in the colonization of human colonic cells.Enterotoxigenic Escherichia coli (ETEC) is an important cause of infant diarrhea in developing countries, a leading cause of traveler''s diarrhea, and a reemergent diarrheal pathogen in the United States (1, 25, 29, 33, 38, 40, 41, 44, 51, 52, 55). ETEC strains were first recognized as a cause of diarrheal disease in animals, especially in piglets and calves, where the disease continues to cause lethal infection in newborn animals (3, 37). Studies of ETEC in piglets first elucidated the mechanisms of disease, including the presence of two plasmid-encoded enterotoxins. In humans, the clinical appearance of ETEC infection is identical to that of cholera, with severe dehydrating illness not commonly seen in adults (38, 46). DuPont et al. (12) subsequently showed that ETEC strains were able to cause diarrhea in adult volunteers. ETEC strains cause watery diarrhea similar to that caused by Vibrio cholerae through the action of two enterotoxins, the cholera-like heat-labile and heat-stable enterotoxins (LT and ST, respectively) (38). These strains may express an LT only, an ST only, or both LT and ST. To cause diarrhea, ETEC strains must first adhere to small bowel enterocytes, an event mediated by a variety of surface fimbrial appendages called colonization factor antigens (CFAs), coli surface antigens (CSs), and putative colonization factors (PCF) (22, 33, 38). Transmission electron microscopy (TEM) of ETEC strains typically reveals many peritrichously arranged fimbriae around the bacterium; often, multiple fimbrial morphologies can be visualized on the same bacterium (6, 19, 31, 38). ETEC strains also express the K99 fimbriae, which are pathogenic for calves, lambs, and pigs, whereas K88-expressing organisms are able to cause disease only in pigs (8). Human ETEC strains possess their own array of colonization fimbriae, the CFAs usually encoded in plasmids (10). Currently, more than 20 CFAs known in human ETEC infections have been described (17). The CFAs can be subdivided based on their morphological characteristics. Three major morphological varieties exist: rigid rods (CFA I), bundle-forming flexible rods (CFA III), and thin, flexible, wiry structures (CFA II and CFA IV) (7, 8, 26, 30, 49, 53, 54).A high proportion of human ETEC strains contain a plasmid-encoded type IV pilus (T4P) antigen (CS20) also called longus for its length (19, 21). Longus is a T4P composed of a repeating structural subunit called LngA of 22 kDa, and its N-terminal amino acid sequences shares similarities with the class B type IV pili. These pili include the CFA III pilin subunit CofA of ETEC, the toxin-coregulated pilin (TCP) of V. cholerae, and the bundle-forming pilin (BFP) found in enteropathogenic E. coli (EPEC) and in a small percentage in other Gram-negative pathogens (21, 23). The lngA gene, which encodes the longus pilus in ETEC strains, is widely distributed in different geographic regions such Bangladesh, Chile, Brazil, Egypt, and Mexico (23). Interestingly, the lngA gene has been observed in association with ETEC strain producers of LT and ST (23). Sequence analysis of the fimbrial genes provided insight into the evolutionary history of longus. It appears that the highly conserved nonstructural lngA genes evolved in a similar manner to that of housekeeping genes.Recently, another important adherence factor called E. coli common pilus (ECP) has been identified; it is composed of a 21-kDa pilin subunit whose amino acid sequence corresponds to the product of the yagZ (renamed ecpA) gene present in all E. coli genomes sequenced to date (47). ECP production was demonstrated in strains representing intestinal (enterohemorrhagic E. coli [EHEC], EPEC, and ETEC) and extraintestinal pathogenic E. coli as well as normal-flora E. coli.In this study we report that longus plays an important role in the adherence to colonic epithelial cells. In addition to mediating cell adherence, longus is also associated with other pathogenicity attributes exhibited by other Gram-negative pathogenic bacteria producing T4P, which can contribute in part to the virulence of ETEC.     

Rapid Microarray-Based Genotyping of Enterohemorrhagic Escherichia coli Serotype O156:H25/H?/Hnt Isolates from Cattle and Clonal Relationship Analysis

Since enterohemorrhagic Escherichia coli (EHEC) isolates of serogroup O156 have been obtained from human diarrhea patients and asymptomatic carriers, we studied cattle as a potential reservoir for these bacteria. E. coli isolates serotyped by agglutination as O156:H25/H−/Hnt strains (n = 32) were isolated from three cattle farms during a period of 21 months and characterized by rapid microarray-based genotyping. The serotyping by agglutination of the O156 isolates was not confirmed in some cases by the results of DNA-based serotyping as only 25 of the 32 isolates were conclusively identified as O156:H25. In the multilocus sequence typing (MLST) analysis, all EHEC O156:H25 isolates were characterized as sequence type 300 (ST300) and ST688, which differ by a single-nucleotide exchange in the purA gene. Oligonucleotide microarrays allow simultaneous detection of a wider range of EHEC-associated and other E. coli virulence markers than other methods. All O156:H25 isolates showed a wide spectrum of virulence factors typical for EHEC. The stx₁ genes combined with the EHEC hlyA (hlyA_EHEC) gene, the eae gene of the ζ subtype, as well as numerous other virulence markers were present in all EHEC O156:H25 strains. The behavior of eight different cluster groups, including four that were EHEC O156:H25, was monitored in space and time. Variations in the O156 cluster groups were detected. The results of the cluster analysis suggest that some O156:H25 strains had the genetic potential for a long persistence in the host and on the farm, while other strains did not. As judged by their pattern of virulence markers, E. coli O156:H25 isolates of bovine origin may represent a considerable risk for human infection. Our results showed that the miniaturized E. coli oligonucleotide arrays are an excellent tool for the rapid detection of a large number of virulence markers.Shiga toxin-producing Escherichia coli (STEC) strains comprise a group of zoonotic enteric pathogens (45). In humans, infections with some STEC serotypes may result in hemorrhagic or nonhemorrhagic diarrhea, which can be complicated by the hemolytic uremic syndrome (HUS) (32). These STEC strains are also designated enterohemorrhagic Escherichia coli (EHEC). Consequently, EHEC strains represent a subgroup of STEC with high pathogenic potential for humans. Although E. coli O157:H7 is the most frequent EHEC serotype implicated in HUS, other serotypes can also cause this complication. Non-O157:H7 EHEC strains including serotypes O26:H11/H−, O103:H2/H−, O111:H8/H10/H−, and O145:H28/H25/H− and sorbitol-fermenting E. coli O157:H− isolates are present in about 50% of stool cultures from German HUS patients (10, 42). However, STEC strains that cause human infection belong to a large number of E. coli serotypes, although a small number of STEC isolates of serogroup O156 were associated with human disease (7). Strains of the serotypes O156:H1/H8/H21/H25 were found in human cases of diarrhea or asymptomatic infections (9, 22, 25, 26). The detection of STEC of serogroup O156 from healthy and diseased ruminants such as cattle, sheep, and goats was reported by several authors (1, 11-13, 21, 39, 46, 50, 52). Additional EHEC-associated virulence genes such as stx, eae, hlyA_EHEC, or nlaA were found preferentially in the serotypes O156:H25 and O156:H− (11-13, 21, 22, 50, 52).Numerous methods exist for the detection of pathogenic E. coli, including genotypic and phenotypic marker assays for the detection of virulence genes and their products (19, 47, 55, 57). All of these methods have the common drawback of screening a relatively small number of determinants simultaneously. A diagnostic DNA microarray based on the ArrayTube format of CLONDIAG GmbH was developed as a viable alternative due to its ability to screen multiple virulence markers simultaneously (2). Further microarray layouts working with the same principle but different gene targets were developed for the rapid identification of antimicrobial resistance genes in Gram-negative bacteria (5) and for the rapid DNA-based serotyping of E. coli (4). In addition, a protein microarray for E. coli O serotyping based on the ArrayTube format was described by Anjum et al. (3).The aim of our study was the molecular genotyping of bovine E. coli field isolates of serogroup O156 based on miniaturized E. coli oligonucleotide arrays in the ArrayStrip format and to combine the screening of E. coli virulence markers, antimicrobial resistance genes, and DNA serotyping targets, some of which were partially described previously for separate arrays (2, 4, 5). The epidemiological situation in the beef herds from which the isolates were obtained and the spatial and temporal behavior of the clonal distribution of E. coli serogroup O156 were analyzed during the observation period. The potential risk of the isolates inducing disease in humans was assessed.     

Genome sequences published outside of Standards in Genomic Sciences, January-March 2012

The purpose of this table is to provide the community with a citable record of publications of ongoing genome sequencing projects that have led to a publication in the scientific literature. While our goal is to make the list complete, there is no guarantee that we may have omitted one or more publications appearing in this time frame. Readers and authors who wish to have publications added to subsequent versions of this list are invited to provide the bibliographic data for such references to the SIGS editorial office.

Phylum Crenarchaeota

• Pyrobaculum strain 1860, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003098","term_id":"356640791","term_text":"CP003098"}}CP003098 [1]

Phylum Deinococcus-Thermus

• “Thermus sp.” Strain CCB_US3_UF1, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003126","term_id":"359289533","term_text":"CP003126"}}CP003126 (chromosome), {"type":"entrez-nucleotide","attrs":{"text":"CP003127","term_id":"359291781","term_text":"CP003127"}}CP003127 (plasmid) [2]

Phylum Proteobacteria

• “Achromobacter arsenitoxydans” SY8, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGUF00000000","term_id":"359366799","term_text":"AGUF00000000"}}AGUF00000000 [3]
• Acidovorax sp. Strain NO1, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGTS00000000","term_id":"363417938","term_text":"AGTS00000000"}}AGTS00000000 [4]
• Acinetobacter baumannii AB4857, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHAG00000000","term_id":"371492156","term_text":"AHAG00000000"}}AHAG00000000 [5]
• Acinetobacter baumannii AB5075, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHAH00000000","term_id":"371492114","term_text":"AHAH00000000"}}AHAH00000000 [5]
• Acinetobacter baumannii AB5256, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHAI00000000","term_id":"371492153","term_text":"AHAI00000000"}}AHAI00000000 [5]
• Acinetobacter baumannii AB5711, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHAJ00000000","term_id":"371492197","term_text":"AHAJ00000000"}}AHAJ00000000 [5]
• Aeromonas salmonicida, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGVO00000000","term_id":"356689990","term_text":"AGVO00000000"}}AGVO00000000 [6]
• Aggregatibacter actinomycetemcomitans RHAA1, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHGR00000000","term_id":"359757447","term_text":"AHGR00000000"}}AHGR00000000 [7]
• Agrobacterium tumefaciens 5A, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGVZ00000000","term_id":"358008163","term_text":"AGVZ00000000"}}AGVZ00000000 [8]
• Azoarcus sp. Strain KH32C, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AP012304","term_id":"358635055","term_text":"AP012304"}}AP012304, {"type":"entrez-nucleotide","attrs":{"text":"AP012305","term_id":"358639587","term_text":"AP012305"}}AP012305 [9]
• Burkholderia sp. Strain YI23, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003087","term_id":"357934279","term_text":"CP003087"}}CP003087 (Chromosome 1), {"type":"entrez-nucleotide","attrs":{"text":"CP003088","term_id":"357937049","term_text":"CP003088"}}CP003088 (Chromosome 2), {"type":"entrez-nucleotide","attrs":{"text":"CP003089","term_id":"357938589","term_text":"CP003089"}}CP003089 (Chromosome 3), {"type":"entrez-nucleotide","attrs":{"text":"CP003090","term_id":"357939954","term_text":"CP003090"}}CP003090 (plasmid BYI23_D), {"type":"entrez-nucleotide","attrs":{"text":"CP003091","term_id":"357941606","term_text":"CP003091"}}CP003091 (plasmid BYI23_E) {"type":"entrez-nucleotide","attrs":{"text":"CP003092","term_id":"357941997","term_text":"CP003092"}}CP003092 (plasmid BYI23_F) [10]
• Brucella suis VBI22, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003128","term_id":"358257303","term_text":"CP003128"}}CP003128, {"type":"entrez-nucleotide","attrs":{"text":"CP003129","term_id":"358259429","term_text":"CP003129"}}CP003129 [11]
• Comamonas testosteroni ATCC 11996, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHIL00000000","term_id":"371454882","term_text":"AHIL00000000"}}AHIL00000000 [12]
• “Commensalibacter intestini” A911^T, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGFR00000000","term_id":"353673384","term_text":"AGFR00000000"}}AGFR00000000 [13]
• Edwardsiella ictaluri, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP001600.1","term_id":"238867551","term_text":"CP001600.1"}}CP001600.1 [14]
• Enterobacter cloacae subsp. dissolvens SDM, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGSY00000000","term_id":"357435944","term_text":"AGSY00000000"}}AGSY00000000 [15]
• “Gluconobacter morbifer” G707^T, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGQV00000000","term_id":"356416073","term_text":"AGQV00000000"}}AGQV00000000 [16]
• Legionella dumoffii TEX-KL, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGVT00000000","term_id":"358009168","term_text":"AGVT00000000"}}AGVT00000000 [17]
• Legionella dumoffii NY-23, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGVU00000000","term_id":"358009167","term_text":"AGVU00000000"}}AGVU00000000 [17]
• Legionella pneumophila serogroup 12 Strain 570-CO-H, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003192","term_id":"364506764","term_text":"CP003192"}}CP003192 [18]
• Marinobacterium stanieri S30, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFPL00000000","term_id":"339778849","term_text":"AFPL00000000"}}AFPL00000000 [19]
• “Marinobacter manganoxydans” MnI7-9, sequence accession {"type":"entrez-nucleotide-range","attrs":{"text":"CP001978 to CP001980","start_term":"CP001978","end_term":"CP001980","start_term_id":"311692891","end_term_id":"311697125"}}CP001978 to CP001980 [20]
• Mesorhizobium alhagi CCNWXJ12-2T, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHAM00000000","term_id":"359256606","term_text":"AHAM00000000"}}AHAM00000000 [21]
• Mesorhizobium amorphae, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGSN00000000","term_id":"355545111","term_text":"AGSN00000000"}}AGSN00000000 [22]
• Methylomicrobium alcaliphilum 20Z, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"FO082060","term_id":"351716053","term_text":"FO082060"}}FO082060 and {"type":"entrez-nucleotide","attrs":{"text":"FO082061","term_id":"351720036","term_text":"FO082061"}}FO082061 [23]
• Mitsuaria sp. Strain H24L5A, sequence accession {"type":"entrez-nucleotide-range","attrs":{"text":"CAFG01000001 to CAFG01000607","start_term":"CAFG01000001","end_term":"CAFG01000607","start_term_id":"354809229","end_term_id":"354808623"}}CAFG01000001 to CAFG01000607 [24]
• Novosphingobium pentaromativorans US6-1, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGFM00000000","term_id":"357601355","term_text":"AGFM00000000"}}AGFM00000000 [25]
• Pantoea ananatis B1-9, sequence accession {"type":"entrez-nucleotide-range","attrs":{"text":"CAEI01000001 to CAEI01000169","start_term":"CAEI01000001","end_term":"CAEI01000169","start_term_id":"344197887","end_term_id":"344197719"}}CAEI01000001 to CAEI01000169 [26]
• Pantoea ananatis LMG 5342, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"HE617160","term_id":"365184443","term_text":"HE617160"}}HE617160 (chromosome), {"type":"entrez-nucleotide","attrs":{"text":"HE617161","term_id":"365188784","term_text":"HE617161"}}HE617161 (pPANA10) [27]
• Pantoea ananatis Strain PA13, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003085","term_id":"354986417","term_text":"CP003085"}}CP003085 and {"type":"entrez-nucleotide","attrs":{"text":"CP003086","term_id":"354685304","term_text":"CP003086"}}CP003086 [28]
• Pseudomonas aeruginosa, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFXI00000000","term_id":"343788111","term_text":"AFXI00000000"}}AFXI00000000 [29]
• Pseudomonas aeruginosa, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFXJ00000000","term_id":"343788109","term_text":"AFXJ00000000"}}AFXJ00000000 [29]
• Pseudomonas aeruginosa, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFXK00000000","term_id":"343788110","term_text":"AFXK00000000"}}AFXK00000000 [29]
• Pseudomonas chlororaphis GP72, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHAY01000000","term_id":"359757954","term_text":"gb||AHAY01000000"}}AHAY01000000 [30]
• Pseudomonas fluorescens F113, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003150","term_id":"359757955","term_text":"CP003150"}}CP003150 [31]
• Pseudomonas fluorescens Wayne 1R, sequence accession {"type":"entrez-nucleotide-range","attrs":{"text":"CADX01000001 to CADX01000090","start_term":"CADX01000001","end_term":"CADX01000090","start_term_id":"354924103","end_term_id":"354924014"}}CADX01000001 to CADX01000090 [32]
• Pseudomonas fluorescens Wood1R, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CAFF01000001","term_id":"354698772","term_text":"CAFF01000001"}}CAFF01000001 to {"type":"entrez-nucleotide","attrs":{"text":"CAFF01001437","term_id":"354697336","term_text":"CAFF01001437"}}CAFF01001437 [32]
• Pseudomonas psychrotolerans L19, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHBD00000000","term_id":"359372666","term_text":"AHBD00000000"}}AHBD00000000 [33]
• Pseudoalteromonas rubra ATCC 29570^T, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHCD00000000","term_id":"540289291","term_text":"AHCD00000000"}}AHCD00000000 [34]
• Pseudomonas stutzeri SDM-LAC, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGSX00000000","term_id":"357435965","term_text":"AGSX00000000"}}AGSX00000000 [35]
• Pseudoxanthomonas spadix BD-a59, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003093","term_id":"357433120","term_text":"CP003093"}}CP003093 [36]
• Rickettsia slovaca, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002428","term_id":"360041315","term_text":"CP002428"}}CP002428 [37]
• Salmonella enterica serovar Pullorum RKS5078, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003047","term_id":"357204415","term_text":"CP003047"}}CP003047 [38]
• Sinorhizobium meliloti CCNWSX0020, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGVV00000000","term_id":"359507569","term_text":"AGVV00000000"}}AGVV00000000 [39]
• Sphingobium sp. Strain SYK-6, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AP012222","term_id":"345135066","term_text":"AP012222"}}AP012222 and {"type":"entrez-nucleotide","attrs":{"text":"AP012223","term_id":"345138980","term_text":"AP012223"}}AP012223 [40]
• Sphingomonas sp. Strain PAMC 26605, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHIS00000000","term_id":"366040305","term_text":"AHIS00000000"}}AHIS00000000 [41]
• Stenotrophomonas maltophilia RR-10, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGRB00000000","term_id":"359757773","term_text":"AGRB00000000"}}AGRB00000000 [42]
• Strain HIMB30, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGIG00000000","term_id":"349602640","term_text":"AGIG00000000"}}AGIG00000000 [43]
• Taylorella equigenitalis, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003059","term_id":"347973256","term_text":"CP003059"}}CP003059 [44]
• Vibrio campbellii DS40M4, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGIE00000000","term_id":"358251732","term_text":"AGIE00000000"}}AGIE00000000 [45]
• Vibrio fischeri SR5, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHIH00000000","term_id":"371496097","term_text":"AHIH00000000"}}AHIH00000000 [46]
• Yersinia enterocolitica, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGQO00000000","term_id":"351780838","term_text":"AGQO00000000"}}AGQO00000000 [47]

Phylum Tenericutes

• Candidatus Mycoplasma haemominutum, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"HE613254","term_id":"357978897","term_text":"HE613254"}}HE613254 [48]
• Mycoplasma haemocanis strain Illinois, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003199","term_id":"363988676","term_text":"CP003199"}}CP003199 [49]
• Mycoplasma iowae, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGFP00000000","term_id":"349504222","term_text":"AGFP00000000"}}AGFP00000000 [50]
• Mycoplasma pneumoniae Type 2a Strain 309, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AP012303","term_id":"358640274","term_text":"AP012303"}}AP012303 [51]

Phylum Firmicutes

• Bacillus cereus F837/76, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003187","term_id":"364509831","term_text":"CP003187"}}CP003187 (chromosome) {"type":"entrez-nucleotide","attrs":{"text":"CP003188","term_id":"364515227","term_text":"CP003188"}}CP003188 (pF837_55kb), {"type":"entrez-nucleotide","attrs":{"text":"CP003189","term_id":"364515372","term_text":"CP003189"}}CP003189 (pF837_10kb) [52]
• Brevibacillus laterosporus Strain GI-9, sequence accession {"type":"entrez-nucleotide-range","attrs":{"text":"CAGD01000001 to CAGD01000061","start_term":"CAGD01000001","end_term":"CAGD01000061","start_term_id":"359745324","end_term_id":"359745264"}}CAGD01000001 to CAGD01000061 [53]
• Clostridium sporogenes PA 3679, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGAH00000000","term_id":"364889226","term_text":"AGAH00000000"}}AGAH00000000 [54]
• Enterococcus mundtii CRL1656, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFWZ00000000.1","term_id":"354620965","term_text":"AFWZ00000000.1"}}AFWZ00000000.1 [55]
• Geobacillus thermoleovorans CCB_US3_UF5, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003125","term_id":"359285645","term_text":"CP003125"}}CP003125 [56]
• Lactobacillus curvatus Strain CRL705, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGBU01000000","term_id":"354514905","term_text":"gb||AGBU01000000"}}AGBU01000000 [57]
• Lactobacillus rhamnosus ATCC 8530, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003094","term_id":"355393429","term_text":"CP003094"}}CP003094 [58]
• Lactobacillus rhamnosus R0011, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGKC00000000","term_id":"357540515","term_text":"AGKC00000000"}}AGKC00000000 [59]
• Lactococcus garvieae TB25, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGQX01000000","term_id":"359031556","term_text":"gb||AGQX01000000"}}AGQX01000000 [60]
• Lactococcus garvieae LG9, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGQY01000000","term_id":"359031592","term_text":"gb||AGQY01000000"}}AGQY01000000 [60]
• Lactococcus lactis subsp. cremoris A76, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003132","term_id":"358748197","term_text":"CP003132"}}CP003132 (chromosome), {"type":"entrez-nucleotide","attrs":{"text":"CP003136","term_id":"358750967","term_text":"CP003136"}}CP003136 (pQA505), {"type":"entrez-nucleotide","attrs":{"text":"CP003135","term_id":"358750954","term_text":"CP003135"}}CP003135 (PQA518), {"type":"entrez-nucleotide","attrs":{"text":"CP003134","term_id":"358750911","term_text":"CP003134"}}CP003134 (pQA549), {"type":"entrez-nucleotide","attrs":{"text":"CP003133","term_id":"358750841","term_text":"CP003133"}}CP003133 (pQA554) [61]
• Leuconostoc citreum LBAE C10, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CAGE00000000","term_id":"365487970","term_text":"CAGE00000000"}}CAGE00000000 [62]
• Leuconostoc citreum LBAE C11, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CAGF00000000","term_id":"365512054","term_text":"CAGF00000000"}}CAGF00000000 [62]
• Leuconostoc citreum LBAE E16, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CAGG00000000","term_id":"365528100","term_text":"CAGG00000000"}}CAGG00000000 [62]
• Leuconostoc mesenteroides subsp. mesenteroides Strain J18, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003101","term_id":"948298071","term_text":"CP003101"}}CP003101 [63]
• Paenibacillus peoriae Strain KCTC 3763^T, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGFX00000000","term_id":"359367787","term_text":"AGFX00000000"}}AGFX00000000 [64]
• Pediococcus acidilactici MA18/5M, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGKB00000000","term_id":"357540603","term_text":"AGKB00000000"}}AGKB00000000 [65]
• Pediococcus claussenii ATCC BAA-344^T, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003137","term_id":"361055534","term_text":"CP003137"}}CP003137 (chromosome), {"type":"entrez-nucleotide","attrs":{"text":"CP003138","term_id":"361057275","term_text":"CP003138"}}CP003138 (pPECL-1), {"type":"entrez-nucleotide","attrs":{"text":"CP003139","term_id":"361057278","term_text":"CP003139"}}CP003139 (pPECL-2), {"type":"entrez-nucleotide","attrs":{"text":"CP003140","term_id":"361057281","term_text":"CP003140"}}CP003140 (pPECL-3), {"type":"entrez-nucleotide","attrs":{"text":"CP003141","term_id":"361057302","term_text":"CP003141"}}CP003141 (pPECL-4), {"type":"entrez-nucleotide","attrs":{"text":"CP003142","term_id":"361057319","term_text":"CP003142"}}CP003142 (pPECL-5), {"type":"entrez-nucleotide","attrs":{"text":"CP003143","term_id":"361057355","term_text":"CP003143"}}CP003143 (pPECL-6), {"type":"entrez-nucleotide","attrs":{"text":"CP003144","term_id":"361057377","term_text":"CP003144"}}CP003144 (pPECL-7), {"type":"entrez-nucleotide","attrs":{"text":"CP003145","term_id":"380450589","term_text":"CP003145"}}CP003145 (pPECL-8) [66]
• Staphylococcus aureus M013, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003166","term_id":"359829121","term_text":"CP003166"}}CP003166 [67]
• Staphylococcus aureus subsp. aureus TW20, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"FN433596","term_id":"269939526","term_text":"FN433596"}}FN433596 [68]
• Weissella confusa LBAE C39-2, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CAGH00000000","term_id":"365549261","term_text":"CAGH00000000"}}CAGH00000000 [69]

Phylum Actinobacteria

• Corynebacterium casei, sequence accession {"type":"entrez-nucleotide-range","attrs":{"text":"CAFW01000001 to CAFW01000106","start_term":"CAFW01000001","end_term":"CAFW01000106","start_term_id":"356609265","end_term_id":"356606462"}}CAFW01000001 to CAFW01000106 [70]
• Corynebacterium glutamicum, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGQQ00000000","term_id":"658109743","term_text":"AGQQ00000000"}}AGQQ00000000 [71]
• Leucobacter chromiiresistens, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGCW00000000","term_id":"353529976","term_text":"AGCW00000000"}}AGCW00000000 [72]
• Mycobacterium abscessus, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGQU00000000","term_id":"353453148","term_text":"AGQU00000000"}}AGQU00000000 [73]
• Propionibacterium acnes ST9, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003195","term_id":"365742920","term_text":"CP003195"}}CP003195 [74]
• Propionibacterium acnes ST22, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003196","term_id":"365740656","term_text":"CP003196"}}CP003196 [74]
• Propionibacterium acnes ST27, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003197","term_id":"365738411","term_text":"CP003197"}}CP003197 [74]
• Saccharomonospora azurea SZMC 14600, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHBX00000000","term_id":"359740650","term_text":"AHBX00000000"}}AHBX00000000 [75]
• Streptomyces sp. Strain TOR3209, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGNH00000000","term_id":"359357427","term_text":"AGNH00000000"}}AGNH00000000 [76]
• Streptomyces sp. Strain W007, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGSW00000000","term_id":"364010697","term_text":"AGSW00000000"}}AGSW00000000 [77]

Phylum Spirochaetes

• Borrelia valaisiana VS116, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"ABCY02000001","term_id":"224510974","term_text":"ABCY02000001"}}ABCY02000001 (chromosome), {"type":"entrez-nucleotide","attrs":{"text":"CP001439","term_id":"224497263","term_text":"CP001439"}}CP001439 (plasmid Ip17), {"type":"entrez-nucleotide","attrs":{"text":"CP001437","term_id":"224497187","term_text":"CP001437"}}CP001437 (Ip25), {"type":"entrez-nucleotide","attrs":{"text":"CP001440","term_id":"224497290","term_text":"CP001440"}}CP001440 (plasmid Ip 28-3), {"type":"entrez-nucleotide","attrs":{"text":"CP001442","term_id":"224497476","term_text":"CP001442"}}CP001442 (plasmid Ip28-8), {"type":"entrez-nucleotide","attrs":{"text":"CP001436","term_id":"224497148","term_text":"CP001436"}}CP001436 (Ip 36), {"type":"entrez-nucleotide","attrs":{"text":"CP001433","term_id":"224496993","term_text":"CP001433"}}CP001433 (plasmid Ip 54), {"type":"entrez-nucleotide","attrs":{"text":"CP001438","term_id":"224497250","term_text":"CP001438"}}CP001438 (plasmid cp9), {"type":"entrez-nucleotide","attrs":{"text":"CP001432","term_id":"224496964","term_text":"CP001432"}}CP001432 (plasmid cp26), {"type":"entrez-nucleotide","attrs":{"text":"CP001441","term_id":"224497433","term_text":"CP001441"}}CP001441 (plasmid cp32-5), {"type":"entrez-nucleotide","attrs":{"text":"CP001434","term_id":"224497064","term_text":"CP001434"}}CP001434 (plasmid cp32-7), {"type":"entrez-nucleotide","attrs":{"text":"CP001435","term_id":"224497109","term_text":"CP001435"}}CP001435 (plasmid cp32-10) [78]
• “Borrelia bissettii” DN127, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002746","term_id":"342222012","term_text":"CP002746"}}CP002746 (chromosome), {"type":"entrez-nucleotide","attrs":{"text":"CP002756","term_id":"342223236","term_text":"CP002756"}}CP002756 (plasmid Ip12), {"type":"entrez-nucleotide","attrs":{"text":"CP002757","term_id":"342223270","term_text":"CP002757"}}CP002757 (plasmid Ip25), {"type":"entrez-nucleotide","attrs":{"text":"CP002758","term_id":"342223295","term_text":"CP002758"}}CP002758 (plasmid 28-3), {"type":"entrez-nucleotide","attrs":{"text":"CP002759","term_id":"342223320","term_text":"CP002759"}}CP002759 (plasmid Ip 28-4), {"type":"entrez-nucleotide","attrs":{"text":"CP002760","term_id":"342223351","term_text":"CP002760"}}CP002760 (Ip28-7), {"type":"entrez-nucleotide","attrs":{"text":"CP002761","term_id":"342223388","term_text":"CP002761"}}CP002761 (plasmid Ip54), {"type":"entrez-nucleotide","attrs":{"text":"CP002762","term_id":"342223459","term_text":"CP002762"}}CP002762 (plasmid Ip56), {"type":"entrez-nucleotide","attrs":{"text":"CP002755","term_id":"342223223","term_text":"CP002755"}}CP002755 (plasmid cp9), {"type":"entrez-nucleotide","attrs":{"text":"CP002747","term_id":"342222829","term_text":"CP002747"}}CP002747 (plasmid cp26), {"type":"entrez-nucleotide","attrs":{"text":"CP002749","term_id":"342222904","term_text":"CP002749"}}CP002749 (plasmid cp32-3), {"type":"entrez-nucleotide","attrs":{"text":"CP002750","term_id":"342222947","term_text":"CP002750"}}CP002750 (plasmid cp32-4), {"type":"entrez-nucleotide","attrs":{"text":"CP002751","term_id":"342222990","term_text":"CP002751"}}CP002751 (plasmid 32-5), {"type":"entrez-nucleotide","attrs":{"text":"CP002752","term_id":"342223034","term_text":"CP002752"}}CP002752 (plasmid cp32-6), {"type":"entrez-nucleotide","attrs":{"text":"CP002753","term_id":"342223077","term_text":"CP002753"}}CP002753 (plasmid cp32-7), CP0027554 (plasmid cp32-9), {"type":"entrez-nucleotide","attrs":{"text":"CP002748","term_id":"342222857","term_text":"CP002748"}}CP002748 (plasmid cp32-11) [78]
• Borrelia spielmanii A14S, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"ABKB02000001","term_id":"224514548","term_text":"ABKB02000001"}}ABKB02000001 (chromosome), {"type":"entrez-nucleotide","attrs":{"text":"CP001468","term_id":"224497637","term_text":"CP001468"}}CP001468 (plasmid Ip17), {"type":"entrez-nucleotide","attrs":{"text":"CP001471","term_id":"224497796","term_text":"CP001471"}}CP001471 (Ip28-3), {"type":"entrez-nucleotide","attrs":{"text":"CP001470","term_id":"224497745","term_text":"CP001470"}}CP001470 (plasmid Ip28-4), {"type":"entrez-nucleotide","attrs":{"text":"CP001465","term_id":"224497532","term_text":"CP001465"}}CP001465 (plasmid Ip28-2), {"type":"entrez-nucleotide","attrs":{"text":"CP001466","term_id":"224497566","term_text":"CP001466"}}CP001466 (plasmid Ip36), {"type":"entrez-nucleotide","attrs":{"text":"CP001464","term_id":"224497496","term_text":"CP001464"}}CP001464 (plasmid Ip38), {"type":"entrez-nucleotide","attrs":{"text":"CP001469","term_id":"224497671","term_text":"CP001469"}}CP001469 (plasmid Ip54), {"type":"entrez-nucleotide","attrs":{"text":"ABKB02000016","term_id":"224513758","term_text":"ABKB02000016"}}ABKB02000016, {"type":"entrez-nucleotide","attrs":{"text":"ABKB02000020","term_id":"224513743","term_text":"ABKB02000020"}}ABKB02000020 (plasmid cp9), {"type":"entrez-nucleotide","attrs":{"text":"CP001467","term_id":"224497607","term_text":"CP001467"}}CP001467 (plasmid cp26), {"type":"entrez-nucleotide","attrs":{"text":"ABKB02000026","term_id":"224513697","term_text":"ABKB02000026"}}ABKB02000026 (plasmid cp32-3), {"type":"entrez-nucleotide","attrs":{"text":"ABKB02000031","term_id":"224513641","term_text":"ABKB02000031"}}ABKB02000031 (plasmid 32-5), {"type":"entrez-nucleotide","attrs":{"text":"ABKB02000021","term_id":"224513736","term_text":"ABKB02000021"}}ABKB02000021 (plasmid cp32-12), {"type":"entrez-nucleotide","attrs":{"text":"ABKB02000014","term_id":"224513768","term_text":"ABKB02000014"}}ABKB02000014 (unidentified) [78]

Non-Bacterial genomes

• Aspergillus flavus, sequence accession {"type":"entrez-geo","attrs":{"text":"GSE32177","term_id":"32177"}}GSE32177 [79]
• Bacteriophage SPN3UB, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JQ288021","term_id":"378408798","term_text":"JQ288021"}}JQ288021 [80]
• Bamboo mitochondria, sequence accession {"type":"entrez-nucleotide-range","attrs":{"text":"JQ235166 to JQ235179","start_term":"JQ235166","end_term":"JQ235179","start_term_id":"372861916","end_term_id":"372861969"}}JQ235166 to JQ235179 [81]
• Boea hygrometrica chloroplast, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JN107811","term_id":"340549387","term_text":"JN107811"}}JN107811 [82]
• Boea hygrometrica mitochondrial, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JN107812","term_id":"340549473","term_text":"JN107812"}}JN107812 [82]
• Canine Picornavirus, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JN831356","term_id":"377826518","term_text":"JN831356"}}JN831356 [83]
• Chandipura virus (CHPV) CIN0327, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"GU212856.1","term_id":"309261828","term_text":"GU212856.1"}}GU212856.1 [84]
• Chandipura virus (CHPV) CIN0451, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"GU212857.1","term_id":"309261834","term_text":"GU212857.1"}}GU212857.1 [84]
• Chandipura virus (CHPV) CIN0751, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"GU212858.1","term_id":"309261840","term_text":"GU212858.1"}}GU212858.1 [84]
• Chandipura virus (CHPV) CIN0755, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"GU190711.1","term_id":"309099431","term_text":"GU190711.1"}}GU190711.1 [84]
• Chinese Porcine Parvovirus Strain PPV2010, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JN872448","term_id":"374676766","term_text":"JN872448"}}JN872448 [85]
• Common midwife toad megavirus, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JQ231222","term_id":"375281729","term_text":"JQ231222"}}JQ231222 [86]
• Dengue Virus Serotype 4, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JN983813","term_id":"372290533","term_text":"JN983813"}}JN983813 [87]
• Duck Tembusu Virus, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JF270480","term_id":"367465451","term_text":"JF270480"}}JF270480 [88]
• Duck Tembusu Virus, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JQ314464","term_id":"377824036","term_text":"JQ314464"}}JQ314464 [88]
• Duck Tembusu Virus, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JQ314465","term_id":"377824038","term_text":"JQ314465"}}JQ314465 [88]
• Emiliania huxleyi Virus 202, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"HQ634145","term_id":"356927554","term_text":"HQ634145"}}HQ634145 [89]
• Emiliania huxleyi Virus EhV-88, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JF974310","term_id":"347600450","term_text":"JF974310"}}JF974310 [89]
• Emiliania huxleyi EhV-201, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JF974311","term_id":"357972615","term_text":"JF974311"}}JF974311 [89]
• Emiliania huxleyi EhV-207, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JF974317","term_id":"347600924","term_text":"JF974317"}}JF974317 [89]
• Emiliania huxleyi EhV-208, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JF974318","term_id":"347601393","term_text":"JF974318"}}JF974318 [89]
• Glarea lozoyensis, sequence accession GUE00000000 [90]
• Nannochloropis gaditana, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGNI00000000","term_id":"366047505","term_text":"AGNI00000000"}}AGNI00000000 [91]
• Oryza sativa cv., sequence accession DRA000499 [92]
• Partetravirus, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JN990269","term_id":"374718987","term_text":"JN990269"}}JN990269 [93]
• Porcine Bocavirus PBoV5, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JN831651","term_id":"371449604","term_text":"JN831651"}}JN831651 [94]
• Porcine epidemic diarrhea virus, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JQ282909","term_id":"377824029","term_text":"JQ282909"}}JQ282909 [95]
• Pseudomonas aeruginosa lytic bacteriophage PA1Ø, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"HM624080","term_id":"315418954","term_text":"HM624080"}}HM624080 [96]
• Pseudomonas fluorescens phage OBP, sequence accesssion {"type":"entrez-nucleotide","attrs":{"text":"JN627160","term_id":"359842892","term_text":"JN627160"}}JN627160 [97]
• RNA Virus from Avocado, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JN880414","term_id":"371444768","term_text":"JN880414"}}JN880414 [98]
• Salmonella enterica Serovar Typhimurium Bacteriophage SPN1S, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JN391180","term_id":"370344404","term_text":"JN391180"}}JN391180 [99]
• Schistosoma haematobium, sequence accession PRJNA78265 [100]
• Schistosoma mansoni, sequence accession {"type":"entrez-protein","attrs":{"text":"ERP00038","term_id":"550209647","term_text":"ERP00038"}}ERP00038 [101]
• Stenopirates sp., sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JN100019","term_id":"340008214","term_text":"JN100019"}}JN100019 [102]
• T7-Like Virus, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JN651747","term_id":"374713556","term_text":"JN651747"}}JN651747 [103]
• Vibrio harveyi siphophage VHS1, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JF713456","term_id":"334898816","term_text":"JF713456"}}JF713456 [104]
• Tyrolean ice man, sequence accession ERP001144 [105]

     

Residues of Heat-Labile Enterotoxin Involved in Bacterial Cell Surface Binding

Enterotoxigenic Escherichia coli (ETEC) is a leading cause of traveler''s diarrhea worldwide. One major virulence factor released by this pathogen is the heat-labile enterotoxin LT, which upsets the balance of electrolytes in the intestine. After export, LT binds to lipopolysaccharide (LPS) on the bacterial surface. Although the residues responsible for LT''s binding to its host receptor are known, the portion of the toxin which mediates LPS binding has not been defined previously. Here, we describe mutations in LT that impair the binding of the toxin to the external surface of E. coli without altering holotoxin assembly. One mutation in particular, T47A, nearly abrogates surface binding without adversely affecting expression or secretion in ETEC. Interestingly, T47A is able to bind mutant E. coli expressing highly truncated forms of LPS, indicating that LT binding to wild-type LPS may be due primarily to association with an outer core sugar. Consequently, we have identified a region of LT distinct from the pocket involved in eukaryotic receptor binding that is responsible for binding to the surface of E. coli.Enterotoxigenic Escherichia coli (ETEC), a common etiologic agent behind traveler''s diarrhea, is also a significant cause of mortality worldwide (38). Many strains of ETEC elaborate a virulence factor called heat-labile enterotoxin or LT (34). LT is an AB₅ toxin, consisting of a single A subunit, LTA, and a ring of five B subunits, LTB (33). LTB mediates the toxin''s binding properties, and LTA ADP ribosylates host G proteins, increasing levels of cyclic AMP and causing the efflux of electrolytes and water into the intestinal lumen (27, 35). Each subunit of LT is translated separately from a bicistronic message and then transported to the periplasm, where holotoxin assembly spontaneously occurs (16). Subsequent export into the extracellular milieu is carried out by the main terminal branch of the general secretory pathway (31, 36).LT binds eukaryotic cells via an interaction between LTB and host gangliosides, primarily the monosialoganglioside GM₁ (35). The binding site for GM₁, situated at the interface of two B subunits, has been identified by crystallography (26). GM₁ binding can be strongly impaired by a point mutation in LTB that converts Gly-33 to an aspartic acid residue (37). LT is highly homologous to cholera toxin (CT), both in sequence and structure (7, 35), contributing to ETEC''s potentially cholera-like symptoms (39).Previous work in our lab has demonstrated that LT possesses an additional binding capacity beyond its affinity for host glycolipids: the ability to associate with lipopolysaccharide (LPS) on the surface of E. coli (20). LPS, the major component of the outer leaflet of the gram-negative outer membrane, consists of a characteristic lipid moiety, lipid A, covalently linked to a chain of sugar residues (30). In bacteria like E. coli, this sugar chain can be further divided into an inner core oligosaccharide of around five sugars, an outer core of four to six additional sugars, and in some cases a series of oligosaccharide repeats known as the O antigen. Lipid A itself cannot inhibit binding of soluble LT to cells containing full-length or truncated LPS, indicating that the LT-LPS interaction involves sugar residues on the surface of E. coli (19). The addition of the inner core sugar 3-deoxy-d-manno-octulosonic acid (Kdo) is the minimal lipid A modification required for LT binding, although longer oligosaccharide chains are preferred, and expression of a kinase that phosphorylates Kdo abrogates binding by LT (19). Competitive binding assays and microscopy with fluorescently labeled ETEC vesicles show that binding to GM₁ and LPS can occur at the same time, revealing that the binding sites are distinct (20, 23). In contrast to LT''s ability to bind to the surface of ETEC, CT (or LT, when expressed heterologously) cannot bind Vibrio cells, presumably because Kdo is phosphorylated in Vibrio spp. (5).As a result of the LT-LPS surface interaction, over 95% of secreted LT is found associated with E. coli outer membrane vesicles (OMVs), rather than being secreted solubly (20). OMVs are spherical structures, 50 to 200 nm in diameter, that are derived from the outer membrane but also enclose periplasmic components (24). As such, active LT is found both on the surface of an OMV and within its lumen (21). ETEC releases a large amount of OMVs (40), and these vesicles may serve as vehicles for delivery of LT to host cells.Recent work by Holmner et al. has uncovered a third binding substrate for LT: human blood group A antigen (17, 18). This interaction was noted previously as a novel binding characteristic of artificially constructed CT-LT hybrid molecules, but it has now been shown to occur with wild-type LT as well (17, 18). LTB binding to sugar residues in the receptor molecule occurs at a site that is separate from the GM₁-binding pocket, in the same region we proposed was involved in LPS binding (17, 19). While the severity of cholera disease symptoms has been linked to blood type (14), the effects of blood type on ETEC infection are less clear. However, it has been demonstrated that LT can use A antigen as a functional receptor in cultured human intestinal cells (11, 12), and one recent cohort study found an increased prevalence of ETEC-based diarrhea among children with A or AB blood type (29).We set out to generate a mutation in LT that reduces its LPS binding without adversely affecting its expression, secretion, or toxicity. In this work, we present the discovery of point mutations in LTB that impair its interactions with the bacterial surface. Examination of these mutations reveals an LPS binding pocket which shares residues with the blood sugar pocket. Binding studies of mutants to bacteria with truncated LPS provide a better understanding of the roles that inner and outer core sugars play in toxin binding, and expression, secretion, and toxicity studies demonstrate which mutant is a particularly good candidate for future research. These binding mutants may lead to further discovery of the role that surface binding plays in the pathogenesis associated with ETEC infection.     

Genomic Regions Conserved in Lineage II Escherichia coli O157:H7 Strains

Populations of the food- and waterborne pathogen Escherichia coli O157:H7 are comprised of two major lineages. Recent studies have shown that specific genotypes within these lineages differ substantially in the frequencies with which they are associated with human clinical disease. While the nucleotide sequences of the genomes of lineage I strains E. coli O157 Sakai and EDL9333 have been determined, much less is known about the genomes of lineage II strains. In this study, suppression subtractive hybridization (SSH) was used to identify genomic features that define lineage II populations. Three SSH experiments were performed, yielding 1,085 genomic fragments consisting of 811 contigs. Bacteriophage sequences were identified in 11.3% of the contigs, 9% showed insertions and 2.3% deletions with respect to E. coli O157:H7 Sakai, and 23.2% did not have significant identity to annotated sequences in GenBank. In order to test for the presence of these novel loci in lineage I and II strains, 27 PCR primer sets were designed based on sequences from these contigs. All but two of these PCR targets were found in the majority (51.9% to 100%) of 27 lineage II strains but in no more than one (<6%) of the 17 lineage I strains. Several of these linage II-related fragments contain insertions/deletions that may play an important role in virulence. These lineage II-related loci were also shown to be useful markers for genotyping of E. coli O157:H7 strains isolated from human and animal sources.Enterohemorrhagic Escherichia coli is associated with diarrhea, hemorrhagic colitis, and hemolytic-uremic syndrome in humans (31). E. coli serotype O157:H7 predominates in epidemics and sporadic cases of enterohemorrhagic E. coli-related infections in the United States, Canada, Japan, and the United Kingdom (12). Cattle are considered the most important reservoir of E. coli O157:H7 (10, 24, 37, 41), and foods contaminated with bovine feces are thought to be the most common source of human infection with this pathogen (27, 33). The two most important virulence factors of the organism are the production of one or more Shiga toxins (Stx) (6, 20, 32) and the ability to attach to and efface microvilli of host intestinal cells (AE). Stx genes are encoded by temperate bacteriophage inserted in the bacterial chromosome, and genes responsible for the AE phenotype are located on the locus of enterocyte effacement (LEE) as well as other pathogenicity islands (4, 17). All E. coli O157:H7 strains also possess a large plasmid which is thought to play a role in virulence (10, 40, 42).Octamer-based genome scanning (OBGS) was first used to show that E. coli O157 strains from the United States and Australia could be subdivided into two genetically distinct lineages (21, 22, 46). While both E. coli O157:H7 lineages are associated with human disease and are isolated from cattle, there is a bias in the host distribution between the two lineages, with a significantly higher proportion of lineage I strains isolated from humans than lineage II strains. Several recent studies have shown that there are inherent differences in gene content and expression between populations of lineage I and lineage II E. coli O157:H7 strains. Lejeune et al. (26) reported that the antiterminator Q gene of the stx₂-converting bacteriophage 933W was found in all nine OBGS lineage I strains examined but in only two of seven lineage II strains, suggesting that there may be lineage-specific differences in toxin production. Dowd and Ishizaki (9) used DNA microarray analysis to examine expression of 610 E. coli O157:H7 genes and showed that lineage I and lineage II E. coli O157:H7 strains have evolved distinct patterns of gene expression which may alter their virulence and their ability to survive in different microenvironments and colonize the intestines of different hosts (9, 28, 38).The observations of lineage host bias have been supported and extended by studies using a six-locus-based multiplex PCR termed the lineage-specific polymorphism assay (LSPA-6) (46). However, Ziebell et al. (48) have recently shown that not all LSPA-6 types within lineage II are host biased; e.g., LSPA-6 type 211111 isolation rates from humans and cattle were significantly different from those of other lineage II LSPA-6 types. Therefore, a clearer definition is required of not only the differences between lineages but also the differences among clonal groups within lineages.The genome sequences of two E. coli O157:H7 strains, Sakai and EDL933 (14, 36), have been determined; however, both of these strains are of lineage I, and there are presently no completed and fully annotated genome sequences available for lineage II strains. In our laboratory, comparative studies utilizing suppression subtractive hybridization (SSH) and comparative genomic hybridization revealed numerous potential virulence factors that are conserved in lineage I strains and that are rare or absent in lineage II strains (42, 47). In this study, we have used SSH to identify genomic regions present in E. coli O157:H7 lineage II strains that are absent from lineage I strains. We wished to examine the distribution of these novel gene segments in E. coli O157:H7 strains and gain insight into their origins and functions. We also attempted to identify molecular markers specific to lineage II strains as well as other markers that would be useful in the genetic subtyping or molecular fingerprinting of E. coli O157:H7 strains in population and epidemiological studies (25). This information may be helpful in the identification of genotypes of the organism associated with specific phenotypes of both lesser and greater virulence (29).     

Genome sequences published outside of Standards in Genomic Sciences, October �C November 2011

The purpose of this table is to provide the community with a citable record of publications of ongoing genome sequencing projects that have led to a publication in the scientific literature. While our goal is to make the list complete, there is no guarantee that we may have omitted one or more publications appearing in this time frame. Readers and authors who wish to have publications added to subsequent versions of this list are invited to provide the bibliographic data for such references to the SIGS editorial office.

• Phylum Crenarchaeota
• Thermoproteus tenax, strain Kra1, DSM 2078^T sequence accession {"type":"entrez-nucleotide","attrs":{"text":"FN869859","term_id":"350274033"}}FN869859 [1]
• Phylum Euryarchaeota
• Haloarcula hispanica CGMCC 1.2049, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002921","term_id":"343781660"}}CP002921 (chromosome I), {"type":"entrez-nucleotide","attrs":{"text":"CP002922","term_id":"343784702"}}CP002922 (chromosome II), and {"type":"entrez-nucleotide","attrs":{"text":"CP002923","term_id":"343785159"}}CP002923 (plasmid pHH400) [2]
• Methanococcus maripaludis, strain X1 (unculturable) sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002913","term_id":"339903450"}}CP002913 [3]
• Phylum Proteobacteria
• Acinetobacter baumannii strain 1656-2, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP001921","term_id":"322506180"}}CP001921 [4]
• Arcobacter butzleri strain ED-1, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AP012047","term_id":"345468266"}}AP012047, {"type":"entrez-nucleotide","attrs":{"text":"AP012048","term_id":"345470425"}}AP012048, and {"type":"entrez-nucleotide","attrs":{"text":"AP012049","term_id":"345473271"}}AP012049 [5]
• Brucella suis strain 1330, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002997","term_id":"343381878"}}CP002997 and {"type":"entrez-nucleotide","attrs":{"text":"CP002998","term_id":"343384001"}}CP002998 [6]
• Campylobacter fetus subsp. venerealis NCTC 10354, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFGH01000000","term_id":"342326654"}}AFGH01000000 [7]
• “Chromobacterium sp.” strain C-61, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CAEE01000001","term_id":"344197715"}}CAEE01000001 to {"type":"entrez-nucleotide","attrs":{"text":"CAEE01001118","term_id":"344196598"}}CAEE01001118 [8]
• Cronobacter sakazakii strain E899, sequence accession {"type":"entrez-protein","attrs":{"text":"AFMO00000000","term_id":"333956885"}}AFMO00000000 [9]
• “Desulfovibrio sp.” strain A2, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGFG01000000","term_id":"347520603"}}AGFG01000000 [10]
• “Erythrobacter sp.” strain NAP1, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"NZ_AAMW00000000","term_id":"85710750"}}NZ_AAMW00000000 [11]
• Escherichia coli strain XH140A, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFVX01000000","term_id":"342364931"}}AFVX01000000 [12]
• Escherichia coli strain XH001, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFYG01000000","term_id":"344195679"}}AFYG01000000 [13]
• Haemophilus haemolyticus strain {"type":"entrez-nucleotide","attrs":{"text":"M19107","term_id":"1059793989"}}M19107, sequence accession {"type":"entrez-protein","attrs":{"text":"AFQN00000000","term_id":"341956667"}}AFQN00000000 [14]
• Haemophilus haemolyticus strain {"type":"entrez-nucleotide","attrs":{"text":"M19501","term_id":"147422"}}M19501, sequence accession {"type":"entrez-protein","attrs":{"text":"AFQO00000000","term_id":"341951174"}}AFQO00000000 [14]
• Haemophilus haemolyticus strain {"type":"entrez-nucleotide","attrs":{"text":"M21127","term_id":"1015602694"}}M21127, sequence accession {"type":"entrez-protein","attrs":{"text":"AFQP00000000","term_id":"341951709"}}AFQP00000000 [14]
• Haemophilus haemolyticus strain {"type":"entrez-nucleotide","attrs":{"text":"M21621","term_id":"189206"}}M21621, sequence accession {"type":"entrez-protein","attrs":{"text":"AFQQ00000000","term_id":"341955662"}}AFQQ00000000 [14]
• Haemophilus haemolyticus strain {"type":"entrez-nucleotide","attrs":{"text":"M21639","term_id":"1036032350"}}M21639, sequence accession {"type":"entrez-protein","attrs":{"text":"AFQR00000000","term_id":"341956942"}}AFQR00000000 [14]
• Idiomarina sp.” strain A28L, sequence accession {"type":"entrez-nucleotide-range","attrs":{"text":"AFPO01000001 to AFPO01000028","start_term":"AFPO01000001","end_term":"AFPO01000028","start_term_id":"336283061","end_term_id":"336280888"}}AFPO01000001 to AFPO01000028 [15]
• Ketogulonicigenium vulgare” strain WSH-001, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002018","term_id":"343461404"}}CP002018 (chromosome), {"type":"entrez-nucleotide","attrs":{"text":"CP002019","term_id":"343464001"}}CP002019 (plasmid pKVU_100), and {"type":"entrez-nucleotide","attrs":{"text":"CP002020","term_id":"343464245"}}CP002020 (plasmid pKVU_200) [16]
• Methylobacter tundripaludum strain SV96, sequence accession {"type":"entrez-protein","attrs":{"text":"AEGW00000000","term_id":"344263587"}}AEGW00000000 [17]
• Pseudogulbenkiania sp.” strain NH8B, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AP012224","term_id":"345641016"}}AP012224 [18]
• Pseudomonas aeruginosa NCGM1179, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"DF126593","term_id":"346055306"}}DF126593 through {"type":"entrez-nucleotide","attrs":{"text":"DF126613","term_id":"346061544"}}DF126613 [19]
• Pseudomonas putida strain B001, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CAED01000001","term_id":"344196578"}}CAED01000001 to {"type":"entrez-nucleotide","attrs":{"text":"CAEE01000262","term_id":"344197454"}}CAEE01000262 [20]
• Pseudomonas putida strain B6-2, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGCS01000000","term_id":"1026254431"}}AGCS01000000 [21]
• Pseudomonas stutzeri CGMCC 1.1803, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002881","term_id":"338799449"}}CP002881 [22]
• Ralstonia solanacearum phylotype IB, strain Y45, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFWL01000000","term_id":"343176764"}}AFWL01000000 [23]
• Rheinheimera sp.” strain A13L, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFHI01000001","term_id":"335881665"}}AFHI01000001 through {"type":"entrez-nucleotide","attrs":{"text":"AFHI01000072","term_id":"335877953"}}AFHI01000072 [24]
• Sphingobium yanoikuyae strain XLDN2-5, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFXE01000000","term_id":"345099327"}}AFXE01000000 [25]
• Vibrio cholerae strain Amazonia, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFSV01000000","term_id":"341584524"}}AFSV01000000 [26]
• Phylum Firmicutes
• Bacillus coagulans strain XZL4, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFWM01000000","term_id":"343381451"}}AFWM01000000 [27]
• Bacillus megaterium strain WSH-002, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003017","term_id":"345441867"}}CP003017 (chromosome), plasmids {"type":"entrez-nucleotide","attrs":{"text":"CP003018","term_id":"345447048"}}CP003018 (plasmid pBME_100), {"type":"entrez-nucleotide","attrs":{"text":"CP003019","term_id":"345447118"}}CP003019 (plasmid pBME_200), and {"type":"entrez-nucleotide","attrs":{"text":"CP003020","term_id":"345447130"}}CP003020 (plasmid pBME_300) [28]
• Bacillus pumilus strain S-1, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGBY00000000","term_id":"346722060"}}AGBY00000000 [29]
• “Desulfosporosinus sp.” strain OT, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGAF01000000","term_id":"344330753"}}AGAF01000000 [30]
• Lentibacillus jeotgali strain Grbi, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGAV01000000","term_id":"345115115"}}AGAV01000000 [31]
• Leuconostoc carnosum KCTC 3525, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"BACM01000000","term_id":"338736686"}}BACM01000000 [32]
• Listeria ivanovii subsp. ivanovii strain PAM 55, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"FR687253","term_id":"346980581"}}FR687253 [33]
• Paenibacillus riograndensis strain SBR5, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGBD01000000","term_id":"345128217"}}AGBD01000000 [34]
• Sporolactobacillus inulinus strain CASD, sequence accession {"type":"entrez-protein","attrs":{"text":"AFVQ00000000","term_id":"823094357"}}AFVQ00000000 [35]
• Streptococcus pseudopneumoniae strain IS7493, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002925","term_id":"341932553"}}CP002925 and {"type":"entrez-nucleotide","attrs":{"text":"CP002926","term_id":"341934784"}}CP002926 [36]
• Streptococcus salivarius strain 57.I, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002888","term_id":"339291081"}}CP002888 and {"type":"entrez-nucleotide","attrs":{"text":"CP002889","term_id":"339293023"}}CP002889 [37]
• Streptococcus salivarius strain M18, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGBV01000000","term_id":"345528121"}}AGBV01000000 [38]
• Streptococcus suis SS12, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002640","term_id":"353733193"}}CP002640 [39]
• Streptococcus suis D9, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002641","term_id":"353735273"}}CP002641 [39]
• Streptococcus suis D12, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002644","term_id":"353737348"}}CP002644 [39]
• Streptococcus suis ST1, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002651","term_id":"353739427"}}CP002651 [39]
• Weissella thailandensis strain fsh4-2, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"HE575133","term_id":"341819811"}}HE575133 through {"type":"entrez-nucleotide","attrs":{"text":"HE575182","term_id":"341821297"}}HE575182 [40]
• Phylum Tenericutes
• Mycoplasma anatis strain 1340, sequence accession {"type":"entrez-protein","attrs":{"text":"AFVJ00000000","term_id":"341579585"}}AFVJ00000000 [41]
• Mycoplasma capricolum subsp. capripneumoniae strain M1601, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AENG01000000","term_id":"1067112011"}}AENG01000000 [42]
• Mycoplasma putrefaciens Type strain KS1, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003021","term_id":"343956693"}}CP003021 [43]
• Corynebacterium pseudotuberculosis strain PAT10, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002924","term_id":"341823823"}}CP002924 [44]
• Phylum Actinobacteria
• Bifidobacterium animalis subsp. lactis strain BLC1, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003039","term_id":"447219159"}}CP003039 [45]
• Bifidobacterium breve strain DPC 6330, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFXX01000000","term_id":"347344070"}}AFXX01000000 [46]
• Brachybacterium squillarum strain M-6-3, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGBX01000000","term_id":"346317973"}}AGBX01000000 [47]
• “Citricoccus sp.” strain CH26A, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFXQ01000000","term_id":"344198218"}}AFXQ01000000 [48]
• Corynebacterium glutamicum strain S9114, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFYA01000000","term_id":"344046353"}}AFYA01000000 [49]
• Dietzia alimentaria strain 72, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGFF01000000","term_id":"347366987"}}AGFF01000000 [50]
• Mycobacterium colombiense CECT 3035, sequence accession {"type":"entrez-protein","attrs":{"text":"AFVW00000000","term_id":"400333858"}}AFVW00000000 [51]
• Mycobacterium tuberculosis NCGM2209, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"DF126614","term_id":"358229918"}}DF126614 and {"type":"entrez-nucleotide","attrs":{"text":"DF126615","term_id":"358233644"}}DF126615 [52]
• Rhodococcus erythropolis strain XP, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGCF01000000","term_id":"345896954"}}AGCF01000000 [53]
• Serinicoccus profundi MCCC 1A05965^T, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFYF00000000","term_id":"345107103"}}AFYF00000000 [54]
• Phylum Spirochaetes
• Leptospira interrogans, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP001221","term_id":"353456277"}}CP001221 (CI), {"type":"entrez-nucleotide","attrs":{"text":"CP001222","term_id":"353459699"}}CP001222 (CII) [55]
• Phylum Bacteroidetes
• Bacteroides faecis Type strain MAJ27^T, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGDG01000000","term_id":"347014739"}}AGDG01000000 [56]
• Bizionia argentinensis, Type strain JUB59^T sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFXZ01000000","term_id":"344049519"}}AFXZ01000000 [57]
• Flavobacterium branchiophilum strain FL-15, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"FQ859183","term_id":"345528129"}}FQ859183 [58]
• “Flavobacteriaceae” strain S85, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFPK00000000","term_id":"339778866"}}AFPK00000000 [59]
• Phylum Thermotogae
• “Thermotoga sp.” strain RQ2, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP000969","term_id":"170175310"}}CP000969 [60]

Non-Bacterial genomes

• Aspergillus kawachii IFO 4308, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"DF126447","term_id":"358365263"}}DF126447 through {"type":"entrez-nucleotide","attrs":{"text":"DF126592","term_id":"358376882"}}DF126592, BACL01000001 through BACL01001641, {"type":"entrez-nucleotide","attrs":{"text":"AP012272","term_id":"354548779"}}AP012272 [61]
• Cajanus cajan pigeonpea, sequence accession PRJNA72815 [62]
• Coxsackievirus A22, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JN542510","term_id":"354682107"}}JN542510 [63]
• Gordonia phage GRU1, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JF923797","term_id":"356471393"}}JF923797 [64]
• Gordonia phage GTE5, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JF923796","term_id":"356471300"}}JF923796 [64]
• Heterocephalus glaber naked mole rat, sequence accession {"type":"entrez-protein","attrs":{"text":"AFSB00000000","term_id":"351716052"}}AFSB00000000, {"type":"entrez-nucleotide","attrs":{"text":"AFSB01000000","term_id":"351581530"}}AFSB01000000 [65]
• Human Adenovirus Prototype 17, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"HQ910407","term_id":"324105303"}}HQ910407 [66]
• Macaca mulatta lasiota rhesus macaque, sequence accession {"type":"entrez-protein","attrs":{"text":"AEHL00000000","term_id":"355786683"}}AEHL00000000 [67]
• Macaca mulatta mulatta rhesus macaque, sequence accession {"type":"entrez-protein","attrs":{"text":"AEHK00000000","term_id":"355710505"}}AEHK00000000 [67]
• Porcine epidemic diarrhea virus, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JN547228","term_id":"351630105"}}JN547228 [68]

     

Genome sequences of Bacteria and Archaea published outside of Standards in Genomic Sciences, June �C September 2011

The purpose of this table is to provide the community with a citable record of publications of ongoing genome sequencing projects that have led to a publication in the scientific literature. While our goal is to make the list complete, there is no guarantee that we may have omitted one or more publications appearing in this time frame. Readers and authors who wish to have publications added to this subsequent versions of this list are invited to provide the bibliometric data for such references to the SIGS editorial office.

• Phylum Crenarchaeota
• Phylum Euryarchaeota
• Pyrococcus yayanosii CH1, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002779","term_id":"334899445","term_text":"CP002779"}}CP002779 [1]
• Methanocella paludicola, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AP011532","term_id":"282154984","term_text":"AP011532"}}AP011532 [2]
• Halorhabdus tiamatea, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFNT00000000","term_id":"543102264","term_text":"AFNT00000000"}}AFNT00000000 [3]
• Thermococcus sp. Strain 4557, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002920","term_id":"340808746","term_text":"CP002920"}}CP002920 [4]
• Phylum Chloroflexi
• Phylum Proteobacteria
• Ralstonia solanacearum strain Po82, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002819","term_id":"334194119","term_text":"CP002819"}}CP002819 (chromosome) and {"type":"entrez-nucleotide","attrs":{"text":"CP002820","term_id":"334197458","term_text":"CP002820"}}CP002820 (megaplasmid) [5
• Desulfovibrio alaskensis G20, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP000112","term_id":"78217452","term_text":"CP000112"}}CP000112 [6]
• Methylophaga aminisulfidivorans MP^T, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFIG00000000","term_id":"333790299","term_text":"AFIG00000000"}}AFIG00000000 [7]
• Acinetobacter sp. P8-3-8, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFIE00000000","term_id":"333463740","term_text":"AFIE00000000"}}AFIE00000000 [8]
• Sphingomonas strain KC8, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFMP01000000","term_id":"333609216","term_text":"gb||AFMP01000000"}}AFMP01000000 [9]
• Brucella pinnipedialis B2/94, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002078","term_id":"340558088","term_text":"CP002078"}}CP002078 and {"type":"entrez-nucleotide","attrs":{"text":"CP002079","term_id":"340560226","term_text":"CP002079"}}CP002079 [10]
• Salmonella enterica Serovar Typhimurium UK-1, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002614","term_id":"332986951","term_text":"CP002614"}}CP002614 (chromosome), {"type":"entrez-nucleotide","attrs":{"text":"CP002615","term_id":"332991407","term_text":"CP002615"}}CP002615 (plasmid) [11]
• Bordetella pertussis CS, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002695","term_id":"332380677","term_text":"CP002695"}}CP002695 [12]
• Alteromonas sp. Strain SN2, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002339","term_id":"332991508","term_text":"CP002339"}}CP002339 [13]
• Escherichia coli O104:H4, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFOB00000000","term_id":"340742082","term_text":"AFOB00000000"}}AFOB00000000 ({"type":"entrez-nucleotide","attrs":{"text":"LB226692","term_id":"753016073","term_text":"LB226692"}}LB226692) and {"type":"entrez-nucleotide","attrs":{"text":"AFPS00000000","term_id":"340736249","term_text":"AFPS00000000"}}AFPS00000000 (01-09591) [14]
• Acidithiobacillus caldus, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002573","term_id":"340554897","term_text":"CP002573"}}CP002573 (Chromosome), {"type":"entrez-nucleotide","attrs":{"text":"CP002574","term_id":"340557778","term_text":"CP002574"}}CP002574 (pLAtcm), {"type":"entrez-nucleotide","attrs":{"text":"CP002575","term_id":"340558034","term_text":"CP002575"}}CP002575 (pLAtc1), {"type":"entrez-nucleotide","attrs":{"text":"CP002576","term_id":"340558045","term_text":"CP002576"}}CP002576 (pLAtc2), {"type":"entrez-nucleotide","attrs":{"text":"CP002577","term_id":"340558059","term_text":"CP002577"}}CP002577 (pLAtc3) [15]
• Cupriavidus necator N-1, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002877","term_id":"338164315","term_text":"CP002877"}}CP002877 (chromosome 1), {"type":"entrez-nucleotide","attrs":{"text":"CP002878","term_id":"338167938","term_text":"CP002878"}}CP002878 (chromosome 2), {"type":"entrez-nucleotide","attrs":{"text":"CP002879","term_id":"338170382","term_text":"CP002879"}}CP002879 (pBB1), and {"type":"entrez-nucleotide","attrs":{"text":"CP002880","term_id":"338171767","term_text":"CP002880"}}CP002880 (pBB2) [16]
• Oligotropha carboxidovorans OM4, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002821","term_id":"336093334","term_text":"CP002821"}}CP002821 (OM4 chromosome), {"type":"entrez-nucleotide","attrs":{"text":"CP002822","term_id":"336096622","term_text":"CP002822"}}CP002822 (pHCG3b), {"type":"entrez-nucleotide","attrs":{"text":"CP002823","term_id":"336096746","term_text":"CP002823"}}CP002823 (pOC167B) [17]
• Oligotropha carboxidovorans OM5, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002826","term_id":"336096911","term_text":"CP002826"}}CP002826 (OM5 chromosome), {"type":"entrez-nucleotide","attrs":{"text":"CP002827","term_id":"336100253","term_text":"CP002827"}}CP002827 (pHCG3), and {"type":"entrez-nucleotide","attrs":{"text":"CP002828","term_id":"336100378","term_text":"CP002828"}}CP002828 (pOC167) [17]
• Pantoea ananatis LMG20103, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP001875","term_id":"326698716","term_text":"CP001875"}}CP001875 [18]
• Helicobacter bizzozeronii strain CIII-1, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"FR871757","term_id":"335332259","term_text":"FR871757"}}FR871757 (chromosome) and {"type":"entrez-nucleotide","attrs":{"text":"FR871758","term_id":"335334154","term_text":"FR871758"}}FR871758 (HBZ-1) [19]
• Vibrio anguillarum 775, sequence accession {"type":"entrez-nucleotide-range","attrs":{"text":"CP002284 to CP002285","start_term":"CP002284","end_term":"CP002285","start_term_id":"335340310","end_term_id":"335343122"}}CP002284 to CP002285 [20]
• Zymomonas mobilis subsp. pomaceae, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002865","term_id":"336293797","term_text":"CP002865"}}CP002865 (chromosome), {"type":"entrez-nucleotide","attrs":{"text":"CP002866","term_id":"336295481","term_text":"CP002866"}}CP002866 (p29192_1), {"type":"entrez-nucleotide","attrs":{"text":"CP002867","term_id":"336295515","term_text":"CP002867"}}CP002867 (p29192_2) [21]
• Agrobacterium sp. strain ATCC 31749, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AECL01000000","term_id":"333795931","term_text":"gb||AECL01000000"}}AECL01000000 [22]
• Xanthomonas spp. strain Xrc, sequence accesssion {"type":"entrez-nucleotide","attrs":{"text":"CP002789","term_id":"341934791","term_text":"CP002789"}}CP002789 [23]
• Xanthomonas spp. strain Xoc, sequence accesssion {"type":"entrez-nucleotide","attrs":{"text":"AAQN00000000","term_id":"94721237","term_text":"AAQN00000000"}}AAQN00000000 [23]
• Glaciecola sp. Strain 4H-3-7+YE-5, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002526","term_id":"332171715","term_text":"CP002526"}}CP002526 (chromosome) and {"type":"entrez-nucleotide","attrs":{"text":"CP002527","term_id":"332175949","term_text":"CP002527"}}CP002527 (plasmid) [24]
• Escherichia coli Strain HM605, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CADZ01000001","term_id":"335324271","term_text":"CADZ01000001"}}CADZ01000001 through {"type":"entrez-nucleotide","attrs":{"text":"CADZ01000154","term_id":"335324105","term_text":"CADZ01000154"}}CADZ01000154 [25]
• Salinisphaera shabanensis, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFNV00000000","term_id":"543113482","term_text":"AFNV00000000"}}AFNV00000000 [26]
• Methyloversatilis universalis FAM5^T, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFHG00000000","term_id":"333445722","term_text":"AFHG00000000"}}AFHG00000000 [27]
• Alicycliphilus denitrificans Strain BC, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002449","term_id":"317115299","term_text":"CP002449"}}CP002449 (chromosome), {"type":"entrez-nucleotide","attrs":{"text":"CP002450","term_id":"317119630","term_text":"CP002450"}}CP002450 (megaplasmid), {"type":"entrez-nucleotide","attrs":{"text":"CP002451","term_id":"317119756","term_text":"CP002451"}}CP002451 (plasmid) [28].
• Alicycliphilus denitrificans K601^T, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002657","term_id":"329308025","term_text":"CP002657"}}CP002657 (chromosome) and {"type":"entrez-nucleotide","attrs":{"text":"CP002658","term_id":"329312633","term_text":"CP002658"}}CP002658 (plasmid) [28]
• Oligotropha carboxidovorans Strain OM4, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002821","term_id":"336093334","term_text":"CP002821"}}CP002821 (chromosome), {"type":"entrez-nucleotide","attrs":{"text":"CP002822","term_id":"336096622","term_text":"CP002822"}}CP002822 (pHCG3b), {"type":"entrez-nucleotide","attrs":{"text":"CP002823","term_id":"336096746","term_text":"CP002823"}}CP002823 (pOC167B) [29]
• Oligotropha carboxidovorans Strain OM5, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002826","term_id":"336096911","term_text":"CP002826"}}CP002826 (chromosome), {"type":"entrez-nucleotide","attrs":{"text":"CP002827","term_id":"336100253","term_text":"CP002827"}}CP002827 (pHCG3), and {"type":"entrez-nucleotide","attrs":{"text":"CP002828","term_id":"336100378","term_text":"CP002828"}}CP002828 (pOC167) [29]
• Bradyrhizobiaceae strain SG-6C, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFOF01000000","term_id":"338235257","term_text":"gb||AFOF01000000"}}AFOF01000000 [30]
• Hyphomicrobium sp. Strain MC1, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"FQ859181","term_id":"337757426","term_text":"FQ859181"}}FQ859181 [31]
• Shewanella sp. Strain HN-41, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFOZ01000000","term_id":"335867028","term_text":"gb||AFOZ01000000"}}AFOZ01000000 [32]
• Myxococcus fulvus HW-1, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002830","term_id":"337255776","term_text":"CP002830"}}CP002830 [33]
• Nitrosomonas sp. Strain AL212, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"NC_015222","term_id":"325980881","term_text":"NC_015222"}}NC_015222 (chromosome), {"type":"entrez-nucleotide","attrs":{"text":"NC_015223","term_id":"325983714","term_text":"NC_015223"}}NC_015223 pNAL21201), {"type":"entrez-nucleotide","attrs":{"text":"NC_015221","term_id":"325980815","term_text":"NC_015221"}}NC_015221 (pNAL21202) [34]
• Ruegeria sp. Strain KLH11, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"ACCW00000000","term_id":"218703200","term_text":"ACCW00000000"}}ACCW00000000 [35]
• Acidovorax avenae subsp. avenae RS-1, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFPT01000000","term_id":"336283372","term_text":"gb||AFPT01000000"}}AFPT01000000 [36]
• Escherichia coli (ExPEC), sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFAT00000000","term_id":"338771881","term_text":"AFAT00000000"}}AFAT00000000 [37]
• Vibrio mimicus SX-4, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"ADOO01000000","term_id":"340396595","term_text":"gb||ADOO01000000"}}ADOO01000000 [38]
• Agrobacterium tumefaciens Strain F2, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFSD00000000","term_id":"338825258","term_text":"AFSD00000000"}}AFSD00000000 [39]
• Pasteurella multocida subsp. gallicida {"type":"entrez-nucleotide-range","attrs":{"text":"AFRR01000001 to AFRR01000489","start_term":"AFRR01000001","end_term":"AFRR01000489","start_term_id":"338220663","end_term_id":"338215299"}}AFRR01000001 to AFRR01000489 [40]
• Pseudomonas aeruginosa 138244, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AEVV00000000","term_id":"537462489","term_text":"AEVV00000000"}}AEVV00000000 [41]
• Pseudomonas aeruginosa 152504, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AEVW00000000","term_id":"557220721","term_text":"AEVW00000000"}}AEVW00000000 [41]
• Campylobacter jejuni strain 305, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"ADHL00000000","term_id":"315930937","term_text":"ADHL00000000"}}ADHL00000000 [42]
• Campylobacter jejuni strain DFVF1099, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"ADHK00000000","term_id":"315928465","term_text":"ADHK00000000"}}ADHK00000000 [42]
• Xanthomonas campestris pv. raphani strain 756C, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002789","term_id":"341934791","term_text":"CP002789"}}CP002789 [43]
• Xanthomonas campestris pv. raphani strain BLS256, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AAQN01000001","term_id":"94721236","term_text":"AAQN01000001"}}AAQN01000001 [43]
• Rickettsia heilongjiangensis, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002912","term_id":"340807448","term_text":"CP002912"}}CP002912 [44]
• Acidiphilium sp. Strain PM (DSM 24941), sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFPR00000000","term_id":"338209258","term_text":"AFPR00000000"}}AFPR00000000 [45]
• Pseudomonas putida Strain S16, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002870","term_id":"338835784","term_text":"CP002870"}}CP002870 [46]
• Acinetobacter lwoffii, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFQY01000000","term_id":"337752636","term_text":"gb||AFQY01000000"}}AFQY01000000 [47]
• Phylum Firmicutes
• Caldalkalibacillus thermarum strain TA2.A1, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFCE00000000","term_id":"334181820","term_text":"AFCE00000000"}}AFCE00000000 [48]
• Listeria monocytogenes Scott A, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFGI00000000","term_id":"332188986","term_text":"AFGI00000000"}}AFGI00000000 [49]
• Lactococcus garvieae 8831, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFCD00000000","term_id":"333218454","term_text":"AFCD00000000"}}AFCD00000000 [50]
• Natranaerobius thermophilus JW/NM-WN-LF, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP001034","term_id":"179349329","term_text":"CP001034"}}CP001034 (chromosome), {"type":"entrez-nucleotide","attrs":{"text":"CP001035","term_id":"179352354","term_text":"CP001035"}}CP001035 (plasmid) [51]
• Melissococcus plutonius ATCC 35311, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AP012200","term_id":"332369543","term_text":"AP012200"}}AP012200 (chromosome) and {"type":"entrez-nucleotide","attrs":{"text":"AP012201","term_id":"332371286","term_text":"AP012201"}}AP012201 (plasmid) [52]
• Lactobacillus buchneri NRRL B-30929, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002652","term_id":"329127738","term_text":"CP002652"}}CP002652 (chromosome), {"type":"entrez-nucleotide","attrs":{"text":"CP002653","term_id":"329130053","term_text":"CP002653"}}CP002653 (plasmid pLBU01), {"type":"entrez-nucleotide","attrs":{"text":"CP002654","term_id":"329130100","term_text":"CP002654"}}CP002654 (plasmid pLBU02), and {"type":"entrez-nucleotide","attrs":{"text":"CP002655","term_id":"329130119","term_text":"CP002655"}}CP002655 (plasmid pLBU03) [53]
• Lactobacillus kefiranofaciens ZW3 , sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002764","term_id":"333956887","term_text":"CP002764"}}CP002764 (chromosome), {"type":"entrez-nucleotide","attrs":{"text":"CP002765","term_id":"333958796","term_text":"CP002765"}}CP002765 (plasmid), and {"type":"entrez-nucleotide","attrs":{"text":"CP002766","term_id":"333958996","term_text":"CP002766"}}CP002766 (plasmid) [54]
• Bacillus megaterium strain QM B1551, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP001983","term_id":"294346812","term_text":"CP001983"}}CP001983 (chromosome), {"type":"entrez-nucleotide-range","attrs":{"text":"CP001984 to CP001990","start_term":"CP001984","end_term":"CP001990","start_term_id":"294351929","end_term_id":"294352220"}}CP001984 to CP001990 (plasmids pBM100 through pBM700) [55]
• Bacillus megaterium strain DSM319, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP001982","term_id":"294799901","term_text":"CP001982"}}CP001982 (chromosome) [55]
• Listeria monocytogenes serovar 4a strain M7, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002816","term_id":"336021869","term_text":"CP002816"}}CP002816 [56]
• Bacillus coagulans 2-6, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002472","term_id":"335366109","term_text":"CP002472"}}CP002472 [57]
• Streptococcus salivarius strain CCHSS3, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"FR873481","term_id":"338741860","term_text":"FR873481"}}FR873481 [58]
• Paenibacillus elgii B69, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFHW01000000","term_id":"332713477","term_text":"gb||AFHW01000000"}}AFHW01000000 [59]
• Lactobacillus pentosus MP-10, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"FR871759","term_id":"334880280","term_text":"FR871759"}}FR871759 through {"type":"entrez-nucleotide","attrs":{"text":"FR871848","term_id":"334883124","term_text":"FR871848"}}FR871848 [60]
• Leuconostoc pseudomesenteroides KCTC 3652, sequence accession AEOQ00000001 through AEOQ00001160 [61]
• Lactobacillus mali KCTC 3596, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"BACP01000001","term_id":"338747920","term_text":"BACP01000001"}}BACP01000001 through {"type":"entrez-nucleotide","attrs":{"text":"BACP01000122","term_id":"338747799","term_text":"BACP01000122"}}BACP01000122 [62]
• Paenibacillus polymyxa Type Strain ATCC 842^T, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFOX01000000","term_id":"335355762","term_text":"gb||AFOX01000000"}}AFOX01000000 [63]
• Streptococcus salivarius strain JIM8777, sequence accssion {"type":"entrez-nucleotide","attrs":{"text":"FR873482","term_id":"338744031","term_text":"FR873482"}}FR873482 [64]
• Lactobacillus cypricasei KCTC 13900, sequence accession {"type":"entrez-nucleotide-range","attrs":{"text":"BACS01000001 to BACS01000487","start_term":"BACS01000001","end_term":"BACS01000487","start_term_id":"338748625","end_term_id":"338748139"}}BACS01000001 to BACS01000487 [65]
• Lactobacillus zeae KCTC 3804, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"BACQ01000001","term_id":"338748035","term_text":"BACQ01000001"}}BACQ01000001 to BACQ101000113 [66]
• Listeria monocytogenes Serovar 4a Strain M7, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002816","term_id":"336021869","term_text":"CP002816"}}CP002816 [67]
• Lactobacillus salivarius GJ-24, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFOI00000000","term_id":"335351482","term_text":"AFOI00000000"}}AFOI00000000 [68]
• Lactobacillus johnsonii PF01, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFQJ01000000","term_id":"338762788","term_text":"gb||AFQJ01000000"}}AFQJ01000000 [69]
• Clostridium acetobutylicum DSM 1731, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002660","term_id":"336289872","term_text":"CP002660"}}CP002660 through {"type":"entrez-nucleotide","attrs":{"text":"CP002662","term_id":"336293787","term_text":"CP002662"}}CP002662 [70]
• Lactobacillus suebicus KCTC 3549, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"BACO01000000","term_id":"338746125","term_text":"dbj||BACO01000000"}}BACO01000000 [71]
• Brevibacillus laterosporus LMG 15441, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFRV00000000","term_id":"338776733","term_text":"AFRV00000000"}}AFRV00000000 [72]
• Lactobacillus salivarius NIAS840, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFMN00000000","term_id":"334308865","term_text":"AFMN00000000"}}AFMN00000000 [73]
• Bifidobacterium animalis subsp. lactis CNCM I-2494, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002915","term_id":"340364148","term_text":"CP002915"}}CP002915 [74]
• Megasphaera elsdenii, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"HE576794","term_id":"341821300","term_text":"HE576794"}}HE576794 [75]
• Lactobacillus versmoldensis KCTC 3814, sequence accession {"type":"entrez-nucleotide-range","attrs":{"text":"BACR01000001 to BACR01000102","start_term":"BACR01000001","end_term":"BACR01000102","start_term_id":"338748138","end_term_id":"338748037"}}BACR01000001 to BACR01000102 [76]
• Lactobacillus pentosus IG1, sequence accession {"type":"entrez-nucleotide-range","attrs":{"text":"FR874848 to FR874860","start_term":"FR874848","end_term":"FR874860","start_term_id":"339636574","end_term_id":"339639349"}}FR874848 to FR874860 [77]
• Alicyclobacillus acidocaldarius Strain Tc-4-1, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002902","term_id":"339287872","term_text":"CP002902"}}CP002902 [78]
• Streptococcus thermophilus Strain JIM8232, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"FR875178","term_id":"339277069","term_text":"FR875178"}}FR875178 [79]
• Streptococcus equi subsp. zooepidemicus Strain ATCC 35246, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002904","term_id":"338846021","term_text":"CP002904"}}CP002904 [80]
• Bacillus amyloliquefaciens XH7, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002927","term_id":"341825903","term_text":"CP002927"}}CP002927 [81]
• Leuconostoc kimchii Strain C2, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002898","term_id":"338851854","term_text":"CP002898"}}CP002898 [82]
• Lactobacillus malefermentans KCTC 3548, sequence accession {"type":"entrez-nucleotide-range","attrs":{"text":"BACN01000001 to BACN01000172","start_term":"BACN01000001","end_term":"BACN01000172","start_term_id":"338736862","end_term_id":"338736691"}}BACN01000001 to BACN01000172 [83]
• Weissella koreensis KACC 15510, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002900","term_id":"338855046","term_text":"CP002900"}}CP002900 [84]
• Phylum Tenericutes
• Mycoplasma bovis Strain Hubei-1, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002513","term_id":"338226653","term_text":"CP002513"}}CP002513 [85]
• Mycoplasma fermentans Strain M64, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"NC_014921","term_id":"319776738","term_text":"NC_014921"}}NC_014921 [86]
• Haloplasma contractile, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFNU00000000","term_id":"543107448","term_text":"AFNU00000000"}}AFNU00000000 [87]
• Mycoplasma ovipneumoniae Strain SC01, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFHO01000000","term_id":"336091059","term_text":"gb||AFHO01000000"}}AFHO01000000 [88]
• Phylum Actinobacteria
• Kocuria rhizophila P7-4, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFID00000000","term_id":"333463600","term_text":"AFID00000000"}}AFID00000000 [89]
• Streptomyces S4, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CADY01000000","term_id":"334306078","term_text":"emb||CADY01000000"}}CADY01000000 [90]
• Corynebacterium nuruki S6-4^T, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFIZ00000000","term_id":"333352007","term_text":"AFIZ00000000"}}AFIZ00000000 [91]
• Propionibacterium humerusii, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFAM00000000.1","term_id":"328908381","term_text":"AFAM00000000.1"}}AFAM00000000.1 [92]
• Strain JDM601, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002329","term_id":"333484608","term_text":"CP002329"}}CP002329 [93]
• Streptomyces sp. strain Tü6071, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFHJ01000000","term_id":"332514755","term_text":"gb||AFHJ01000000"}}AFHJ01000000 [94]
• Bifidobacterium breve UCC2003, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP000303","term_id":"339478266","term_text":"CP000303"}}CP000303 [95]
• Propionibacterium acnes, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002815","term_id":"335276409","term_text":"CP002815"}}CP002815 [96]
• Amycolicicoccus subflavus DQS3-9A1^T, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002786","term_id":"333479900","term_text":"CP002786"}}CP002786 (chromosome), {"type":"entrez-nucleotide","attrs":{"text":"CP002787","term_id":"333484458","term_text":"CP002787"}}CP002787 (plasmid pAS9A-1), and {"type":"entrez-nucleotide","attrs":{"text":"CP002788","term_id":"333484486","term_text":"CP002788"}}CP002788 (plasmid pAS9A-2). [97]
• Gordonia neofelifaecis NRRL B-59395, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AEUD01000000","term_id":"326199990","term_text":"gb||AEUD01000000"}}AEUD01000000 [98]
• Pseudonocardia dioxanivorans strain CB1190, sequence accession NC_015312-4 and CP002595-7 [99]
• Bifidobacterium longum subsp. longum KACC 91563, sequence accession {"type":"entrez-nucleotide-range","attrs":{"text":"CP002794 to CP002796","start_term":"CP002794","end_term":"CP002796","start_term_id":"338753582","end_term_id":"338755560"}}CP002794 to CP002796 [100]
• Streptomyces cattleya NRRL 8057, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"FQ859185","term_id":"337764029","term_text":"FQ859185"}}FQ859185 (chromosome) and {"type":"entrez-nucleotide","attrs":{"text":"FQ859184","term_id":"337762320","term_text":"FQ859184"}}FQ859184 (megaplasmid) [101]
• Rhodococcus sp. Strain R04, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFAQ01000000","term_id":"338230982","term_text":"gb||AFAQ01000000"}}AFAQ01000000 [102]
• Mycobacterium bovis BCG Moreau, sequence accession [103]
• Saccharopolyspora spinosa NRRL 18395, sequence accession [104]
• Mycobacterium tuberculosis CCDC5079, sequence accession [105]
• Mycobacterium tuberculosis CCDC5180, sequence accession [105]
• Amycolatopsis mediterranei S699, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002896","term_id":"340523290","term_text":"CP002896"}}CP002896 [106]
• Nesterenkonia sp. Strain F, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFRW01000000","term_id":"340539543","term_text":"gb||AFRW01000000"}}AFRW01000000 [107]
• Streptomyces xinghaiensis NRRL {"type":"entrez-nucleotide","attrs":{"text":"B24674","term_id":"2510184","term_text":"B24674"}}B24674^T, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFRP01000000","term_id":"339790456","term_text":"gb||AFRP01000000"}}AFRP01000000 [108]
• Phylum Chlamydiae
• Chlamydophila abortus variant strain LLG, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFHM01000000","term_id":"1154501422"}}AFHM01000000 [109]
• Chlamydia psittaci 6BC, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002586","term_id":"328914189","term_text":"CP002586"}}CP002586 (chromosome), {"type":"entrez-nucleotide","attrs":{"text":"CP002587","term_id":"328915192","term_text":"CP002587"}}CP002587 (plasmid) [110]
• Chlamydia psittaci Cal10, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AEZD00000000","term_id":"328815518","term_text":"AEZD00000000"}}AEZD00000000 (draft chromosome and plasmid) [110]
• Chlamydia trachomatis, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002024","term_id":"339460423","term_text":"CP002024"}}CP002024 [111]
• Phylum Spirochaetes
• Spirochaeta thermophila DSM 6192, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP001698","term_id":"306531442","term_text":"CP001698"}}CP001698 [112]
• Brachyspira intermedia, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002874","term_id":"343385146","term_text":"CP002874"}}CP002874 (chromosome) and {"type":"entrez-nucleotide","attrs":{"text":"CP002875","term_id":"343388016","term_text":"CP002875"}}CP002875 (plasmid) [113]
• Phylum Fibrobacteres
• Phylum Bacteroidetes
• Porphyromonas gingivalis TDC60, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AP012203","term_id":"333802964","term_text":"AP012203"}}AP012203 [114]
• Krokinobacter sp. strain 4H-3-7-5, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002528","term_id":"332168736","term_text":"CP002528"}}CP002528 [115]
• Lacinutrix sp. strain 5H-3-7-4, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002825","term_id":"334725715","term_text":"CP002825"}}CP002825 [115]
• Bacterium HQM9, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFPB00000000","term_id":"336042206","term_text":"AFPB00000000"}}AFPB00000000 [116]
• Anaerophaga sp. Strain HS1, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFSL00000000","term_id":"339506355","term_text":"AFSL00000000"}}AFSL00000000 [117]
• Capnocytophaga canimorsus Strain 5, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002113","term_id":"339901044","term_text":"CP002113"}}CP002113 [118]
• Mesoflavibacter zeaxanthinifaciens strain S86, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFOE00000000","term_id":"339831579","term_text":"AFOE00000000"}}AFOE00000000 [119]
• Phylum Verrucomicrobia
• Phylum Lentisphaerae
• Phylum Thermotogae
• Kosmotoga olearia Strain TBF 19.5.1, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP001634","term_id":"239505242","term_text":"CP001634"}}CP001634 [120]
• Domain Archaea
• "Candidatus Nitrosoarchaeum koreensis" MY1, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFPU00000000","term_id":"339521013","term_text":"AFPU00000000"}}AFPU00000000 [121]

Non-Bacterial genomes

• North-European Cucumber Cucumis sativus L., sequence accession {"type":"entrez-nucleotide-range","attrs":{"text":"FI132140-FI136208","start_term":"FI132140","end_term":"FI136208","start_term_id":"192759773","end_term_id":"192763063"}}FI132140-FI136208, {"type":"entrez-nucleotide-range","attrs":{"text":"GS765762-GS766880","start_term":"GS765762","end_term":"GS766880","start_term_id":"269146953","end_term_id":"269148071"}}GS765762-GS766880, {"type":"entrez-nucleotide-range","attrs":{"text":"GS815969-GS874855","start_term":"GS815969","end_term":"GS874855","start_term_id":"282718378","end_term_id":"282698342"}}GS815969-GS874855 [122]
• Castor bean Ricinus communis organelle genome, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JF937588","term_id":"339516144","term_text":"JF937588"}}JF937588(chloroplast), {"type":"entrez-nucleotide","attrs":{"text":"HQ874649","term_id":"322394252","term_text":"HQ874649"}}HQ874649 (mitochondria) [123]
• Stretch Lagoon Orbivirus Umatilla, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"HQ842619","term_id":"332713884","term_text":"HQ842619"}}HQ842619 through {"type":"entrez-nucleotide","attrs":{"text":"HQ842628","term_id":"332713902","term_text":"HQ842628"}}HQ842628 [124]
• Atlantic cod Gadus morhua, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CAEA01000001","term_id":"344901723","term_text":"CAEA01000001"}}CAEA01000001 through {"type":"entrez-nucleotide","attrs":{"text":"CAEA01554869","term_id":"344345641","term_text":"CAEA01554869"}}CAEA01554869 [125]
• Potato Solanum tuberosum L., sequence accession {"type":"entrez-nucleotide","attrs":{"text":"GS025503","term_id":"255349557","term_text":"GS025503"}}GS025503 through {"type":"entrez-nucleotide","attrs":{"text":"GS026177","term_id":"255350231","term_text":"GS026177"}}GS026177 [126]
• ΦCA82, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"HQ264138","term_id":"311336635","term_text":"HQ264138"}}HQ264138 [127]
• Paramecium caudatumreveals mitochondria, sequence accession NC001324 [128]
• bacteriophage IME08, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"NC_014260","term_id":"299778956","term_text":"NC_014260"}}NC_014260 [129]
• virus (ILTV), sequence accession HQ_630064 [130]
• Australian kangaroo Macropus eugenii, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"ABQO000000000","term_id":"377520186","term_text":"ABQO000000000"}}ABQO000000000 [131]
• Aichi virus, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"FJ890523","term_id":"260176795","term_text":"FJ890523"}}FJ890523 [132]
• "Candidatus Tremblaya princeps" Strain PCVAL, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002918","term_id":"340536387","term_text":"CP002918"}}CP002918 [133]

     

Prevalence and Impact of Bacteriophages on the Presence of Escherichia coli O157:H7 in Feedlot Cattle and Their Environment

The relationship between endemic bacteriophages infecting E. coli O157:H7 (referred to as “phage”) and levels of shedding of E. coli O157:H7 by cattle was investigated in two commercial feedlots in southern Alberta, Canada. Between May and November 2007, 10 pens of cattle were monitored by collection of pooled fecal pats, water with sediment from troughs, manure slurry from the pen floor, and rectal fecal samples from individual animals (20 per pen) at two separate times. Bacteriophages infecting E. coli O157:H7 were detected more frequently (P < 0.001) after 18 to 20 h enrichment than by initial screening and were recovered in 239 of 855 samples (26.5% of 411 pooled fecal pats, 23.8% of 320 fecal grab samples, 21.8% of 87 water trough samples, and 94.6% of 37 pen floor slurry samples). Overall, prevalence of phage was highest (P < 0.001) in slurry. Recovery of phage from pooled fecal pats was highest (P < 0.05) in May. Overall recovery did not differ (P > 0.10) between fecal grab samples and pooled fecal pats. A higher prevalence of phage in fecal pats or water trough samples was associated (P < 0.01) with reduced prevalence of E. coli O157:H7 in rectal fecal samples. There was a weak but significant negative correlation between isolation of phage and E. coli O157:H7 in fecal grab samples (r = −0.11; P < 0.05). These data demonstrate that the prevalence of phage fluctuates in a manner similar to that described for E. coli O157:H7. Phage were more prevalent in manure slurry than other environmental sources. The likelihood of fecal shedding of E. coli O157:H7 was reduced if cattle in the pen harbored phage.Bacteriophages are the most abundant biological entities on earth. An estimated 10³⁰ marine bacteriophages are harbored in the ocean, and they significantly influence microbial communities and function (27). As resistance is an increasing challenge in antimicrobial therapy, the antimicrobial nature of bacteriophages is being more intensively studied (13, 15). Bacteriophages naturally inhabit the mammalian gastrointestinal tract (1, 8), and Escherichia coli-infecting bacteriophages are commonly isolated from sewage, hospital wastewater, and fecal samples from humans and animals (3). Ruminants have been shown to shed up to 10⁷ bacteriophage per gram of feces (6), and in humans multiple types of bacteriophage exhibiting activity against E. coli have been isolated from a single fecal sample (7).E. coli O157:H7 is an important zoonotic bacterium carried asymptomatically by cattle and readily isolated from manure, manure slurry, and drinking water in dairies and feedlots (11, 24, 30). Additionally, E. coli O157:H7 shedding by cattle has a seasonal pattern, peaking in the summer months (2, 25). Bacteriophage strains that infect E. coli O157:H7 have also been isolated from animal feces and have shown lytic activity against this bacterium in vivo and in vitro (5, 23, 28, 31). In recent studies, such phages were shown to be widely distributed in cattle and in feces on the pen floor within feedlots (4, 18). However, the relationships between the presence of E. coli O157:H7-infecting bacteriophage in cattle and their environment and the shedding of this bacterium by cattle are largely undefined. Consequently, the aims of the present study were (i) to determine the prevalence of endemic E. coli O157:H7-infecting bacteriophage (referred to as “phage”) in feedlots over a 7-month period and (ii) to compare the presence of phage to the occurrence of E. coli O157:H7 in cattle and their environment.     

RASCAL Is a New Human Cytomegalovirus-Encoded Protein That Localizes to the Nuclear Lamina and in Cytoplasmic Vesicles at Late Times Postinfection

The products of numerous open reading frames (ORFs) present in the genome of human cytomegalovirus (CMV) have not been characterized. Here, we describe the identification of a new CMV protein localizing to the nuclear envelope and in cytoplasmic vesicles at late times postinfection. Based on this distinctive localization pattern, we called this new protein nuclear rim-associated cytomegaloviral protein, or RASCAL. Two RASCAL isoforms exist, a short version of 97 amino acids encoded by the majority of CMV strains and a longer version of 176 amino acids encoded by the Towne, Toledo, HAN20, and HAN38 strains. Both isoforms colocalize with lamin B in deep intranuclear invaginations of the inner nuclear membrane (INM) and in novel cytoplasmic vesicular structures possibly derived from the nuclear envelope. INM infoldings have been previously described as sites of nucleocapsid egress, which is mediated by the localized disruption of the nuclear lamina, promoted by the activities of viral and cellular kinases recruited by the lamina-associated proteins UL50 and UL53. RASCAL accumulation at the nuclear membrane required the presence of UL50 but not of UL53. RASCAL and UL50 also appeared to specifically interact, suggesting that RASCAL is a new component of the nuclear egress complex (NEC) and possibly involved in mediating nucleocapsid egress from the nucleus. Finally, the presence of RASCAL within cytoplasmic vesicles raises the intriguing possibility that this protein might participate in additional steps of virion maturation occurring after capsid release from the nucleus.Cytomegalovirus (CMV) is a highly prevalent betaherpesvirus that can cause severe multiorgan disease in immunocompromised individuals (45). The ability of this virus to infect an exceptionally wide variety of different cell types substantially contributes to pathogenesis (5, 68). CMV tropism is largely determined by a finely tuned interplay between cellular and viral factors, many of which act at the earliest stages of infection (30, 68). We recently showed that the cellular protein vimentin is required for efficient onset of infection in primary human foreskin fibroblasts (HF). Interestingly, the degree of reliance on the presence and integrity of vimentin intermediate filaments is dependent on the virus strain, with the broadly tropic strain TB40/E being more negatively affected than the HF-adapted, attenuated strain AD169 (44).Serial passage of clinical isolates in HF or in endothelial cells (EC) has produced strains with different tropisms. The attenuated strains AD169 and Towne were developed as vaccine candidates by propagation in HF for more than 50 (AD169) and 125 (Towne) serial passages (19, 53, 61). During this process, both strains, compared to clinical isolates, accumulated multiple mutations and genomic deletions, resulting in the loss of more than 19 open reading frames (ORFs) (8). The number of serial passages in HF of another commonly used strain, Toledo, has been more moderate (19, 54, 58). This, however, did not prevent the emergence of numerous genomic mutations, including the inversion of an ∼15-kb fragment (8, 16, 56). As a consequence of these changes, productive infections by AD169, Towne, and Toledo are largely restricted to HF. In contrast, propagation of clinical isolates in EC has yielded a series of strains with more-intact genomes and broader tropisms, such as TB40/E, VHL/E, and FIX (VR1814) (25, 60, 71). These strains retain the ability to grow in a wider variety of cell types, including EC, epithelial cells, and dendritic cells (DC), in addition to HF (23, 28, 59, 60, 68).The UL128, UL130, and UL131A gene products were recently identified as essential mediators of CMV infection of EC and epithelial cells (26, 72, 73) and of virus transfer from infected EC to monocyte-derived DC (23). Each of these proteins is independently required for the broader tropisms of EC-propagated CMV isolates (63, 64), and the presence of mutations affecting their functionality has been directly linked to the inability of AD169, Towne, and Toledo to initiate productive infections in EC and epithelial cells (26, 72, 73).We have shown that mature Langerhans-type DC differentiated in vitro from CD34⁺ hematopoietic progenitor cells are highly permissive to direct infection with TB40/E or VHL/E, with 48 to 72% of cells in culture expressing the viral immediate-early genes IE1 and IE2 at 48 h postinfection (hpi) (28). In contrast, only 2 to 5% and 0% of mature Langerhans cells were IE1/IE2 positive after exposure to Towne and Toledo, respectively. However, productive infection was detected in 12 to 17% of cells infected with AD169, despite the fact that this strain lacks expression of the UL131A gene as a consequence of a frameshift mutation (26). These results suggested the existence of additional viral genes with products involved in mediating tropisms for specific cell types, such as DC. To identify possible candidates, we compared the amino acid sequence of each ORF found in the genome of TB40-BAC4, a sequenced clone of the TB40/E strain in a bacterial artificial chromosome (BAC) (GenBank accession number {"type":"entrez-nucleotide","attrs":{"text":"EF999921","term_id":"157779983","term_text":"EF999921"}}EF999921) (69), to the sequence of each ORF found in AD169 and AD169-BAC (accession numbers {"type":"entrez-nucleotide","attrs":{"text":"X17403","term_id":"59591","term_text":"X17403"}}X17403 and {"type":"entrez-nucleotide","attrs":{"text":"AC146999","term_id":"38093733","term_text":"AC146999"}}AC146999) (10, 49), Towne and Towne-BAC (accession numbers {"type":"entrez-nucleotide","attrs":{"text":"FJ616285","term_id":"222354438","term_text":"FJ616285"}}FJ616285, {"type":"entrez-nucleotide","attrs":{"text":"AC146851","term_id":"37654163","term_text":"AC146851"}}AC146851, and {"type":"entrez-nucleotide","attrs":{"text":"AY315197","term_id":"124303521","term_text":"AY315197"}}AY315197) (17, 18, 49), and Toledo-BAC (accession number {"type":"entrez-nucleotide","attrs":{"text":"AC146905","term_id":"37777314","term_text":"AC146905"}}AC146905) (49). The product of a putative ORF, originally identified by Murphy et al. and named conserved ORF 29 (c-ORF29) (49), was considered of particular interest because the amino acid sequence of the putative protein encoded by Toledo and Towne was extended by 79 residues compared to the putative protein encoded by TB40/E and AD169. This led to our speculation that that the extended version might result in a nonfunctional version of the c-ORF29-encoded protein. We thus focused our studies on the products of this ORF.Here, we show for the first time that CMV c-ORF29 encodes a protein expressed at early to late times postinfection (p.i.) and localizes to the nuclear rim in peculiar invaginations of the nuclear lamina and in cytoplasmic vesicular structures at late times p.i. Based on this localization pattern, we named this gene product nuclear rim-associated cytomegaloviral protein, or RASCAL. Surprisingly, no difference was observed in the distributions of RASCAL during infection of HF with TB40/E or Towne, suggesting that the intracellular trafficking of this protein is not affected by the presence of the additional residues at the C terminus of RASCAL from strain Towne (RASCAL_Towne). Ectopic expression of RASCAL in human embryo kidney 293T (HEK293T) cells further revealed that this protein requires the presence of the nuclear egress complex (NEC) member UL50 to reach the nuclear rim, while coimmunoprecipitation (co-IP) assays provided evidence for the existence of an interaction between RASCAL and UL50. These findings suggest that RASCAL may be a new component of the NEC with possible roles in remodeling the nuclear lamina during nucleocapsid egress from the nucleus.     

Heterologous Expression of Tulip Petal Plasma Membrane Aquaporins in Pichia pastoris for Water Channel Analysis

Water channels formed by aquaporins (AQPs) play an important role in the control of water homeostasis in individual cells and in multicellular organisms. Plasma membrane intrinsic proteins (PIPs) constitute a subclass of plant AQPs. TgPIP2;1 and TgPIP2;2 from tulip petals are members of the PIP family. In this study, we overexpressed TgPIP2;1 and TgPIP2;2 in Pichia pastoris and monitored their water channel activity (WCA) either by an in vivo spheroplast-bursting assay performed after hypo-osmotic shock or by growth assay. Osmolarity, pH, and inhibitors of AQPs, protein kinases (PKs), and protein phosphatases (PPs) affect the WCA of heterologous AQPs in this expression system. The WCA of TgPIP2;2-expressing spheroplasts was affected by inhibitors of PKs and PPs, which indicates that the water channel of this homologue is regulated by phosphorylation in P. pastoris. From the results reported herein, we suggest that P. pastoris can be employed as a heterologous expression system to assay the WCA of PIPs and to monitor the AQP-mediated channel gating mechanism, and it can be developed to screen inhibitors/effectors of PIPs.The movement of water across cell membranes has long been thought to occur by free diffusion through the lipid bilayer. However, the discovery of the membrane protein CHIP28 in red blood cells has suggested the involvement of protein channels (29), and it is now well established that transmembrane water permeability is facilitated by aquaporins (AQPs), water channel proteins that are found in bacteria, fungi, plants, and animals (1, 7, 13, 24). AQPs contain six transmembrane α-helices and five connecting loops, and both the N and C termini are located in the cytosol. The monomers assemble into tetrameric complexes, with each monomer forming an individual water channel (11, 14, 24, 33). Apart from the exceptions of AQP11 and AQP12 from mice, as described by K. Ishibashi (15), AQPs have two signature Asn-Pro-Ala motifs, which are located in the second intracellular and the fifth extracellular loops, B and E.While 13 different AQPs have been identified in mammals (16), more than 33 AQP homologues have been discovered in plants (6, 17, 30). Plant AQPs fall into four subclasses: (i) the plasma membrane (PM) intrinsic proteins (PIPs), which are localized in the PM; (ii) the tonoplast intrinsic proteins (TIPs), which are localized in the vacuolar membranes; (iii) the nodulin-26-like intrinsic proteins; and (iv) the small basic intrinsic proteins (24). In Arabidopsis and maize, there are 13 PIPs, which can be divided further into two subfamilies, PIP1 and PIP2 (6, 17).The functions and mechanisms of regulation of plant AQPs have been extensively investigated (7, 13, 18, 24). There have been several reports on the water channel activity (WCA) of specific AQPs and their regulation by protein phosphorylation (3, 4, 8, 12, 18, 25, 32, 33). It has been shown that the WCA of the PIP2 member SoPIP2;1 from spinach is regulated by phosphorylation at two Ser residues (19, 33).The physiologically interesting temperature-dependent opening and closing of tulip (Tulipa gesneriana) petals occur concomitantly with water transport and are regulated by reversible phosphorylation of an undefined PIP (4, 5). Recently, four PIP homologues were isolated from tulip petals, and their WCAs have been analyzed by heterologous expression in Xenopus laevis oocytes (3). It has been shown that the tulip PIP TgPIP2;2 (DDBJ/EMBL/GenBank accession no. {"type":"entrez-nucleotide","attrs":{"text":"AB305617","term_id":"196259707","term_text":"AB305617"}}AB305617) is ubiquitously expressed in all organs of the tulip and that TgPIP2;2 is the most likely of the TgPIP homologues to be modulated by the reversible phosphorylation that regulates transcellular water transport and mediates petal opening and closing (3, 4). However, while the members of the PIP2 subfamily are characterized as water channels (6), TgPIP2;1 (DDBJ/EMBL/GenBank accession no. {"type":"entrez-nucleotide","attrs":{"text":"AB305616","term_id":"196259705","term_text":"AB305616"}}AB305616) shows no significant WCA in the oocyte expression system (3). There is growing interest in research on AQPs due to their crucial roles in the physiology of plants and animals (1, 16, 21-24, 26-28, 36). The assay of AQP channel activity is usually performed using either a X. laevis oocyte expression system (29) or a stopped-flow light-scattering spectrophotometer (35), both of which are not widely available. Furthermore, the complexity of these methods and requirement of expertise limit their high-throughput applications. In contrast, a Pichia pastoris expression system is simple to use, inexpensive, and feasible and can be used in high-throughput applications. Although a P. pastoris expression system has been shown to assay the WCA of a TIP (9), extensive research is necessary with other AQPs such as PIPs or AQPs present in intragranular membranes to establish whether this assay system can be used to characterize a water channel and study its regulation mechanisms. With this in view, in the study reported herein, TgPIP2;1 and TgPIP2;2 have been heterologously expressed in P. pastoris, and their WCAs have been assayed. The effects of several factors, such as osmolarity, pH, and inhibitors of protein kinases (PKs) and protein phosphatases (PPs), on the WCA of the recombinant P. pastoris have been investigated. Based on the results, we demonstrate that the P. pastoris heterologous expression system can be used to rapidly characterize PIP channels, to monitor the effects of mutations, and to score the effects of inhibitors and abiotic factors.     

rhs Genes Are Potential Markers for Multilocus Sequence Typing of Escherichia coli O157:H7 Strains

DNA sequence-based molecular subtyping methods such as multilocus sequence typing (MLST) are commonly used to generate phylogenetic inferences for monomorphic pathogens. The development of an effective MLST scheme for subtyping Escherichia coli O157:H7 has been hindered in the past due to the lack of sequence variation found within analyzed housekeeping and virulence genes. A recent study suggested that rhs genes are under strong positive selection pressure, and therefore in this study we analyzed these genes within a diverse collection of E. coli O157:H7 strains for sequence variability. Eighteen O157:H7 strains from lineages I and II and 15 O157:H7 strains from eight clades were included. Examination of these rhs genes revealed 44 polymorphic loci (PL) and 10 sequence types (STs) among the 18 lineage strains and 280 PL and 12 STs among the 15 clade strains. Phylogenetic analysis using rhs genes generally grouped strains according to their known lineage and clade classifications. These findings also suggested that O157:H7 strains from clades 6 and 8 fall into lineage I/II and that strains of clades 1, 2, 3, and 4 fall into lineage I. Additionally, unique markers were found in rhsA and rhsJ that might be used to define clade 8 and clade 6. Therefore, rhs genes may be useful markers for phylogenetic analysis of E. coli O157:H7.Escherichia coli O157:H7 was first described in 1983 as the causative agent of a food-borne outbreak attributed to contaminated ground beef patties (35), and it has subsequently emerged as a very important food-borne pathogen. Diseases caused by E. coli O157:H7, such as hemorrhagic colitis and hemolytic uremic syndrome, can be very severe or even life-threatening. Cattle are believed to be the main reservoir for E. coli O157:H7 (5, 15, 41), although other animals may also carry this organism (6, 21). Outbreaks are commonly associated with the consumption of beef and fresh produce that come into contact with bovine feces or feces-contaminated environments, such as food contact surfaces, animal hides, or irrigation water (12, 21, 30, 38).It is well-established that strains of E. coli O157:H7 vary in terms of virulence and transmissibility to humans and that strains differing in these characteristics can be distinguished using DNA-based methods (22, 29, 42). For example, octamer-based genome scanning, which is a PCR approach using 8-bp primers, provided the first evidence that there are at least two lineages of O157:H7, termed lineage I and lineage II (22). Strains classified as lineage I are more frequently isolated from humans than are lineage II strains (42). A later refinement of this classification system was coined the lineage-specific polymorphism assay (LSPA), which classified strains based upon the amplicon size obtained using PCRs targeting six chromosomal regions of E. coli O157:H7 and assigned a six-digit code based upon the pattern obtained (42). Most strains of lineage I grouped into LSPA type 111111, while the majority of lineage II strains fell into LSPA types 211111, 212111, and 222222. More recently, it was suggested that LSPA type 211111 strains comprise a separate group called lineage I/II (45).To gain greater insight into the recent evolution of E. coli O157:H7, a method that is more discriminatory than the LSPA method is desirable. Multilocus sequence typing (MLST) is a method that discriminates between strains of a bacterial species by identifying DNA sequence differences in six to eight targeted genes. Satisfactory MLST schemes exist for other bacterial pathogens (28, 43); however, due to the lack of sequence variations in previously targeted gene markers in E. coli O157:H7 (13, 33), MLST approaches for subtyping this pathogen have been more difficult to develop. More recently, high-throughput microarray and sequencing platforms have been used to identify hundreds of single nucleotide polymorphisms (SNPs) that are useful for discriminating between strains of E. coli O157:H7 during epidemiologic investigations and for drawing phylogenetic inferences (11, 20, 29, 44). Particularly noteworthy, Manning et al. (29) developed a subtyping scheme based upon the interrogation of 32 putative SNP loci. This method separated 528 strains into 39 distinct SNP genotypes, which were grouped into nine statistically supported phylogenetic groups called clade 1 through clade 9. By analyzing the rates of hemolytic uremic syndrome observed in patients infected with strains of clades 2, 7, and 8, it was also concluded that clade 8 strains are more virulent to humans than other strains (29).One drawback of current DNA sequence-based subtyping schemes for E. coli O157:H7 is that they require screening of at least 32 SNP loci. We were interested in asking whether a simpler approach that targets a few informative gene markers could be developed for rapid strain discrimination and phylogenetic determination. A recent analysis of E. coli genomes predicted that rearrangement hot spot (rhs) genes are under the strongest positive selection of all coding sequences analyzed (34). Therefore, we hypothesized that these genes would display significant sequence variations for subtyping O157:H7 strains. The rhs genes were first discovered as elements mediating tandem duplication of the glyS locus in E. coli K-12 (26); however, their function remains unknown. There are nine rhs genes within the genome of the prototypical E. coli O157:H7 strain Sakai, and these genes are designated rhsA, -C, -D, -E, -F, -G, -I, -J, and -K (see Table S1 in the supplemental material) (16). Three of these nine rhs genes, rhsF, -J, and -K, were previously studied by Zhang et al. (44), and a number of SNPs were identified among these genes. However, no studies have been conducted to comprehensively investigate rhs genes as markers in an MLST scheme for subtyping E. coli O157:H7.The primary purpose of the present study was to investigate whether there are sufficient DNA sequence variations among rhs genes to develop an MLST approach for subtyping E. coli O157:H7. In this study, a greater level of DNA sequence variation was observed among rhs genes than in gene markers targeted in previous studies (13, 33). Furthermore, phylogenetic analysis using these rhs genes generally agreed with the established lineage and clade classifications of O157:H7 strains defined previously. We also wanted to determine whether there is a correlation between the lineage classification of O157:H7 strains (42) and the recently proposed clade classification (29). The present study reports evidence that O157:H7 strains from clade 8 are classified as lineage I/II, which is a different lineage from well-studied E. coli O157:H7 outbreak strains, such as EDL933 and Sakai. Therefore, we suggest that outbreaks of O157:H7 are caused by two lineages of this pathogen, lineage I and lineage I/II.     

Genome sequences published outside of Standards in Genomic Sciences, March-April 2012

The purpose of this table is to provide the community with a citable record of publications of ongoing genome sequencing projects that have led to a publication in the scientific literature. While our goal is to make the list complete, there is no guarantee that we may have omitted one or more publications appearing in this time frame. Readers and authors who wish to have publications added to subsequent versions of this list are invited to provide the bibliographic data for such references to the SIGS editorial office.

Phylum Euryarchaeota

• Halococcus hamelinensis, sequence accession PRJNA80845 [1]
• “Methanocella conradii” HZ254, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003243","term_id":"379319823","term_text":"CP003243"}}CP003243 [2]
• Thermococcus litoralis NS-C, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHVB00000000","term_id":"374743520","term_text":"AHVB00000000"}}AHVB00000000 [3]

Phylum Crenarchaeota

• Candidatus Nitrosopumilus salaria” BD31, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AEXL00000000","term_id":"386807666","term_text":"AEXL00000000"}}AEXL00000000 [4]
• Candidatus Nitrosoarchaeum limnia, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHJG00000000","term_id":"367466343","term_text":"AHJG00000000"}}AHJG00000000 [5]

Phylum Deinococcus-Thermus

• Deinococcus gobiensis, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002536","term_id":"324314064","term_text":"CP002536"}}CP002536 [6]

Phylum Proteobacteria

• Aggregatibacter actinomycetemcomitans strain ANH9381, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003099","term_id":"365745154","term_text":"CP003099"}}CP003099 [7]
• Alishewanella jeotgali, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHTH00000000","term_id":"374571619","term_text":"AHTH00000000"}}AHTH00000000 [8]
• Enterobacter aerogenes KCTC 2190, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002824","term_id":"334732565","term_text":"CP002824"}}CP002824 [9]
• Escherichia coli O104:H4, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFOB02000092","term_id":"340739517","term_text":"AFOB02000092"}}AFOB02000092 [10]
• Helicobacter pylori strains 17874, sequence accession PRJNA76569 [11]
• Helicobacter pylori strains P79, sequence accession PRJNA76567 [11]
• Janthinobacterium sp. Strain PAMC 25724, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHHB00000000","term_id":"372292151","term_text":"AHHB00000000"}}AHHB00000000 [12]
• Klebsiella oxytoca KCTC 1686, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003218","term_id":"365906294","term_text":"CP003218"}}CP003218 [13]
• Klebsiella pneumoniae subsp. pneumoniae HS11286, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003200","term_id":"364515570","term_text":"CP003200"}}CP003200 (chromosome), {"type":"entrez-nucleotide","attrs":{"text":"CP003223","term_id":"365803686","term_text":"CP003223"}}CP003223 (plasmid pKPHS1), {"type":"entrez-nucleotide","attrs":{"text":"CP003224","term_id":"365803828","term_text":"CP003224"}}CP003224 (plasmid pKPHS2), {"type":"entrez-nucleotide","attrs":{"text":"CP003225","term_id":"365803989","term_text":"CP003225"}}CP003225 (plasmid pKPHS3), {"type":"entrez-nucleotide","attrs":{"text":"CP003226","term_id":"365804142","term_text":"CP003226"}}CP003226 (plasmid pKPHS4), {"type":"entrez-nucleotide","attrs":{"text":"CP003227","term_id":"365804147","term_text":"CP003227"}}CP003227 (plasmid pKPHS5), {"type":"entrez-nucleotide","attrs":{"text":"CP003228","term_id":"365804153","term_text":"CP003228"}}CP003228 (plasmid pKPHS6) [14]
• Oceanimonas sp. GK1, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003171","term_id":"372983507","term_text":"CP003171"}}CP003171 [15]
• “Pseudogulbenkiania ferrooxidans” Strain 2002, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"NZ_ACIS01000000","term_id":"224827334","term_text":"ref||NZ_ACIS01000000"}}NZ_ACIS01000000 [16]
• Pseudomonas extremaustralis 14-3b, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHIP00000000","term_id":"371721769","term_text":"AHIP00000000"}}AHIP00000000 [17]
• Pseudomonas sp. Strain PAMC 25886, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHHC00000000","term_id":"372002201","term_text":"AHHC00000000"}}AHHC00000000 [18]
• Psychrobacter, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHVZ00000000","term_id":"375126956","term_text":"AHVZ00000000"}}AHVZ00000000 [19]
• Rahnella sp. Strain Y9602, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002505","term_id":"321165934","term_text":"CP002505"}}CP002505 [20]
• Rhizobium sp. Strain PDO1-076, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHZC00000000","term_id":"375058045","term_text":"AHZC00000000"}}AHZC00000000 [21]
• Rhodospirillum photometricum DSM122, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"HE663493","term_id":"378401447","term_text":"HE663493"}}HE663493 [22]
• “Rickettsia sibirica sibirica”, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHIZ00000000","term_id":"374669031","term_text":"AHIZ00000000"}}AHIZ00000000 [23]
• Rickettsia sibirica subsp. mongolitimonae strain HA-91, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHZB00000000","term_id":"375318263","term_text":"AHZB00000000"}}AHZB00000000 [24]
• Salmonella enterica subsp. enterica Serotype Enteritidis Strain LA5, sequence accession [25]
• Salmonella enterica subsp. enterica Serotype Senftenberg Strain SS209, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CAGQ00000000","term_id":"379987603","term_text":"CAGQ00000000"}}CAGQ00000000 [26]
• Salmonella enterica subsp. enterica Serovar Typhi P-stx-12, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003278","term_id":"374352002","term_text":"CP003278"}}CP003278 (chromosome) and {"type":"entrez-nucleotide","attrs":{"text":"CP003279","term_id":"374356693","term_text":"CP003279"}}CP003279 (plasmid) [27]
• Sphingomonas echinoides ATCC 14820, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHIR00000000","term_id":"366040205","term_text":"AHIR00000000"}}AHIR00000000 [28]
• Strain HIMB55, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGIF00000000","term_id":"374304583","term_text":"AGIF00000000"}}AGIF00000000 [29]
• Vibrio harveyi CAIM 1792, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHHQ00000000","term_id":"374671508","term_text":"AHHQ00000000"}}AHHQ00000000 [30]
• Wolbachia Strain wAlbB, sequence accession {"type":"entrez-nucleotide-range","attrs":{"text":"CAGB01000001 to CAGB01000165","start_term":"CAGB01000001","end_term":"CAGB01000165","start_term_id":"371933004","end_term_id":"371931774"}}CAGB01000001 to CAGB01000165 [31]
• Xanthomonas axonopodis pv. punicae Strain LMG 859, sequence accession {"type":"entrez-nucleotide-range","attrs":{"text":"CAGJ01000001 to CAGJ01000217","start_term":"CAGJ01000001","end_term":"CAGJ01000217","start_term_id":"372556075","end_term_id":"372551622"}}CAGJ01000001 to CAGJ01000217 [32]

Phylum Tenericutes

• Mycoplasma hyorhinis Strain GDL-1, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003231","term_id":"367460291","term_text":"CP003231"}}CP003231 [33]

Phylum Firmicutes

• Bacillus subtilis, sequence accession BGSCID 3A27 through BGSCID 28A4 [34]
• Clostridium difficile Strain CD37, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHJJ00000000","term_id":"371930118","term_text":"AHJJ00000000"}}AHJJ00000000 [35]
• Clostridium perfringens, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFES00000000","term_id":"380306484","term_text":"AFES00000000"}}AFES00000000 [36]
• Lactobacillus fructivorans KCTC 3543, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AEQY00000000","term_id":"316986063","term_text":"AEQY00000000"}}AEQY00000000 [37]
• Lactococcus lactis IO-1, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AP012281","term_id":"374672113","term_text":"AP012281"}}AP012281 [38]
• Lactobacillus plantarum strain NC8, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGRI00000000","term_id":"376011245","term_text":"AGRI00000000"}}AGRI00000000 [39]
• Paenibacillus dendritiformis C454, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHKH00000000","term_id":"374393106","term_text":"AHKH00000000"}}AHKH00000000 [40]
• Paenibacillus sp. Strain Aloe-11, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGFI00000000","term_id":"374477730","term_text":"AGFI00000000"}}AGFI00000000 [41]
• “Peptoniphilus rhinitidis” 1-13^T, sequence accession {"type":"entrez-nucleotide-range","attrs":{"text":"BAEW01000001 to BAEW01000056","start_term":"BAEW01000001","end_term":"BAEW01000056","start_term_id":"374722129","end_term_id":"374722074"}}BAEW01000001 to BAEW01000056 [42]
• Streptococcus macedonicus ACA-DC 198, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"HE613569","term_id":"372283141","term_text":"HE613569"}}HE613569 and {"type":"entrez-nucleotide","attrs":{"text":"HE613570","term_id":"372285142","term_text":"HE613570"}}HE613570 [43]
• Staphylococcus aureus VC40, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003033","term_id":"374362062","term_text":"CP003033"}}CP003033 [44]
• Streptococcus infantarius subsp. infantarius Strain CJ18, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003295","term_id":"374681091","term_text":"CP003295"}}CP003295 (chromosome), {"type":"entrez-nucleotide","attrs":{"text":"CP003296","term_id":"374682963","term_text":"CP003296"}}CP003296 (plasmid) [45]
• Streptococcus macedonicus ACA-DC 198, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"HE613569","term_id":"372283141","term_text":"HE613569"}}HE613569 (chromosome), {"type":"entrez-nucleotide","attrs":{"text":"HE613570","term_id":"372285142","term_text":"HE613570"}}HE613570 (plasmid pSMA198) [46]

Phylum Actinobacteria

• Actinoplanes sp. SE50/110, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003170","term_id":"359832573","term_text":"CP003170"}}CP003170 [47]
• Amycolatopsis sp. Strain ATCC 39116, sequence accession [48]
• Nocardia cyriacigeorgica GUH-2, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"FO082843","term_id":"374843763","term_text":"FO082843"}}FO082843 [49]
• Salinibacterium sp., sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHWA00000000","term_id":"375323651","term_text":"AHWA00000000"}}AHWA00000000 [50]
• Streptomyces acidiscabies 84-104, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHBF00000000","term_id":"372137622","term_text":"AHBF00000000"}}AHBF00000000 [51]

Non-Bacterial genomes

• Bluetongue Virus Serotype 2, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AJ783905","term_id":"70907482","term_text":"AJ783905"}}AJ783905 (Seg-6) and {"type":"entrez-nucleotide","attrs":{"text":"JQ681257","term_id":"383932043","term_text":"JQ681257"}}JQ681257 (Seg-1), {"type":"entrez-nucleotide","attrs":{"text":"JQ681257","term_id":"383932043","term_text":"JQ681257"}}JQ681257 (Seg-1), {"type":"entrez-nucleotide","attrs":{"text":"JQ681258","term_id":"383932045","term_text":"JQ681258"}}JQ681258 (Seg-2), {"type":"entrez-nucleotide","attrs":{"text":"JQ681259","term_id":"383932047","term_text":"JQ681259"}}JQ681259 (Seg-3), {"type":"entrez-nucleotide","attrs":{"text":"JQ681260","term_id":"383932049","term_text":"JQ681260"}}JQ681260 (Seg-4), {"type":"entrez-nucleotide","attrs":{"text":"JQ681261","term_id":"383932051","term_text":"JQ681261"}}JQ681261 (Seg-5), {"type":"entrez-nucleotide","attrs":{"text":"JQ681262","term_id":"383932053","term_text":"JQ681262"}}JQ681262 (Seg-7), JQ6812563 (Seg-8), JQ6812564 (Seg-9), to {"type":"entrez-nucleotide","attrs":{"text":"JQ681265","term_id":"383932059","term_text":"JQ681265"}}JQ681265 (Seg-10) [52]
• Virus Serotype 1, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AJ585111","term_id":"118420282","term_text":"AJ585111"}}AJ585111 (Seg-2), {"type":"entrez-nucleotide","attrs":{"text":"AJ586659","term_id":"47826214","term_text":"AJ586659"}}AJ586659 (Seg-6), {"type":"entrez-nucleotide","attrs":{"text":"JQ282770","term_id":"383215071","term_text":"JQ282770"}}JQ282770 (Seg-1), {"type":"entrez-nucleotide","attrs":{"text":"JQ282771","term_id":"383215073","term_text":"JQ282771"}}JQ282771 (Seg-3), {"type":"entrez-nucleotide","attrs":{"text":"JQ282772","term_id":"383215075","term_text":"JQ282772"}}JQ282772 (Seg-4), {"type":"entrez-nucleotide","attrs":{"text":"JQ282773","term_id":"383215077","term_text":"JQ282773"}}JQ282773 (Seg-5), {"type":"entrez-nucleotide","attrs":{"text":"JQ282774","term_id":"383215079","term_text":"JQ282774"}}JQ282774 (Seg-7), {"type":"entrez-nucleotide","attrs":{"text":"JQ282775","term_id":"383215081","term_text":"JQ282775"}}JQ282775 (Seg-8), {"type":"entrez-nucleotide","attrs":{"text":"JQ282776","term_id":"383215083","term_text":"JQ282776"}}JQ282776 (Seg-9), and {"type":"entrez-nucleotide","attrs":{"text":"JQ282777","term_id":"383215085","term_text":"JQ282777"}}JQ282777 (Seg-10) [52]
• Chloroplast genome of Erycina pusilla, sequence accession JF_746994 [53]
• Danio rerio, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JQ434101","term_id":"384872525","term_text":"JQ434101"}}JQ434101 [54]
• Enterococcal Bacteriophage SAP6, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JF731128","term_id":"343411857","term_text":"JF731128"}}JF731128 [55]
• Eubenangee virus, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JQ070376","term_id":"383513837","term_text":"JQ070376"}}JQ070376 through {"type":"entrez-nucleotide","attrs":{"text":"JQ070385","term_id":"383513855","term_text":"JQ070385"}}JQ070385 [56]
• Fujian/411-like viruses, sequence accession {"type":"entrez-nucleotide-range","attrs":{"text":"CY087969 to CY088568","start_term":"CY087969","end_term":"CY088568","start_term_id":"380506411","end_term_id":"380507803"}}CY087969 to CY088568 [57]
• Hantavirus Variant of Rio Mamoré Virus, Maripa Virus, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JQ611712","term_id":"384382977","term_text":"JQ611712"}}JQ611712 (segment S), {"type":"entrez-nucleotide","attrs":{"text":"JQ611713","term_id":"384382979","term_text":"JQ611713"}}JQ611713 (segment M), and {"type":"entrez-nucleotide","attrs":{"text":"JQ611714","term_id":"384382981","term_text":"JQ611714"}}JQ611714 (segment L) [58]
• Pata virus, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JQ070386","term_id":"383513857","term_text":"JQ070386"}}JQ070386 through {"type":"entrez-nucleotide","attrs":{"text":"JQ070395","term_id":"383513875","term_text":"JQ070395"}}JQ070395 [59]
• Porcine Circovirus 2, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JQ413808","term_id":"383215164","term_text":"JQ413808"}}JQ413808 [60]
• Porcine Reproductive and Respiratory Syndrome Virus, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JQ326271","term_id":"382929416","term_text":"JQ326271"}}JQ326271 [61]
• Streptococcus mutans Phage M102AD, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"DQ386162","term_id":"88698119","term_text":"DQ386162"}}DQ386162 [62]
• Tilligery virus, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JQ070366","term_id":"383513817","term_text":"JQ070366"}}JQ070366 through {"type":"entrez-nucleotide","attrs":{"text":"JQ070375","term_id":"383513835","term_text":"JQ070375"}}JQ070375 [63]

     

Transmission and infectious dose of Escherichia coli O157:H7 in swine

Escherichia coli O157:H7 is only occasionally isolated from healthy swine, but some experimentally infected animals will shed the organism in their feces for at least 2 months. Potential explanations for the paucity of naturally occurring infections in swine, as compared to cattle, include a lack of animal-to-animal transmission so that the organism cannot be maintained within a herd, a high infectious dose, or herd management practices that prevent the maintenance of the organism in the gastrointestinal tract. We hypothesized that donor pigs infected with E. coli O157:H7 would transmit the organism to naïve pigs. We also determined the infectious dose and whether housing pigs individually on grated floors would decrease the magnitude or duration of fecal shedding. Infected donor pigs shedding <10⁴ CFU of E. coli O157:H7 per g transmitted the organism to 6 of 12 naïve pigs exposed to them. The infectious dose of E. coli O157:H7 for 3-month-old pigs was approximately 6 × 10³ CFU. There was no difference in the magnitude and duration of fecal shedding by pigs housed individually on grates compared to those housed two per pen on cement floors. These results suggest that swine do not have an innate resistance to colonization by E. coli O157:H7 and that they could serve as a reservoir host under suitable conditions.Escherichia coli O157:H7 and other serotypes of Shiga toxigenic E. coli (STEC) cause an estimated 110,000 cases of human illness yearly in the United States (26). Most cases are thought to occur as a result of the ingestion of contaminated food or water, although direct contacts with animals and person-to-person transmission have also been documented (4). Cattle are considered to be the major reservoir of STEC, and the prevalence of E. coli O157:H7 in the U.S. herd ranges from 2 to 28%, depending on the culture techniques used, the age of the animals, and the season in which samples are collected (10, 12, 15, 17, 29, 33). E. coli O157:H7 has also been recovered from other ruminants such as deer (22, 30) and sheep (24). E. coli O157:H7 has occasionally been isolated from nonruminant animals such as wild birds (32) and raccoons (18), but the bulk of the data suggests that the prevalence of STEC is greater in ruminants than it is in other animals.In the last several years, there have been reports that E. coli O157:H7 has been isolated from healthy swine in Japan, The Netherlands, Sweden, Canada, Norway, and the United States (11, 13, 19, 20, 27; C. L. Gyles, R. Friendship, K. Ziebell, S. Johnson, I. Yong, and R. Amezcua, Proc. 2002 Congr. Int. Pig Vet. Soc., abstr. 191). The prevalence of the organism in these studies is generally low (0.1 to 6%), and no human outbreaks have been specifically traced back to pork, although sausage containing both beef and pork was implicated as the source of human infection in at least one outbreak (28). In Chile, the prevalence of E. coli O157:H7 reported from pigs (10.8%) was greater than that reported from cattle (2.9%), suggesting that swine may be an important source of this organism in some countries (3). Previously, we have shown that some market-weight pigs experimentally infected with E. coli O157:H7 will shed the organism for at least 2 months (2). These animals do not become clinically ill, and the magnitude and duration of fecal shedding of E. coli O157:H7 are reminiscent of those seen in experimentally infected ruminants (6, 7). This suggests that swine have the biological potential to emerge as a reservoir for E. coli O157:H7 and other STEC strains pathogenic for humans. In order for swine to serve as a reservoir host, not only must the organism colonize the gastrointestinal tract of individual animals, it must also be transmitted from colonized animals to naïve animals to be maintained within the herd. In addition, the infectious dose must be of such a magnitude that a natural infection could be perpetuated within the herd. We hypothesized that E. coli O157:H7 would be transmitted from infected donor pigs to naïve pigs at levels that could be sustained in a natural infection. In addition, we determined the infectious dose of in vitro-grown E. coli O157:H7 for 3-month-old pigs and determined whether housing pigs individually on raised decks or in groups on cement floors affected the magnitude and duration of fecal shedding in infected animals.(A preliminary report of this work was presented at the International Symposium on Shiga Toxin-Producing E. coli, Kyoto, Japan, 2000, and Edinburgh, Scotland, 2003.)