Inhibition of the Myotoxicity Induced by Bothrops jararacussu Venom and Isolated Phospholipases A2 by Specific Camelid Single-Domain Antibody Fragments

Antivenoms, produced using animal hyperimmune plasma, remains the standard therapy for snakebites. Although effective against systemic damages, conventional antivenoms have limited efficacy against local tissue damage. Additionally, the hypersensitivity reactions, often elicited by antivenoms, the high costs for animal maintenance, the difficulty of producing homogeneous lots, and the instability of biological products instigate the search for innovative products for antivenom therapy. In this study, camelid antibody fragments (VHH) with specificity to Bothropstoxin I and II (BthTX-I and BthTX-II), two myotoxic phospholipases from Bothrops jararacussu venom, were selected from an immune VHH phage display library. After biopanning, 28 and 6 clones recognized BthTX-I and BthTX-II by ELISA, respectively. Complementarity determining regions (CDRs) and immunoglobulin frameworks (FRs) of 13 VHH-deduced amino acid sequences were identified, as well as the camelid hallmark amino acid substitutions in FR2. Three VHH clones ({"type":"entrez-nucleotide","attrs":{"text":"KF498607","term_id":"558064687"}}KF498607, {"type":"entrez-nucleotide","attrs":{"text":"KF498608","term_id":"558064693"}}KF498608, and {"type":"entrez-nucleotide","attrs":{"text":"KC329718","term_id":"468362338"}}KC329718) were capable of recognizing BthTX-I by Western blot and showed affinity constants in the nanomolar range against both toxins. VHHs inhibited the BthTX-II phospholipase A₂ activity, and when tested for cross-reactivity, presented specificity to the Bothrops genus in ELISA. Furthermore, two clones ({"type":"entrez-nucleotide","attrs":{"text":"KC329718","term_id":"468362338"}}KC329718 and {"type":"entrez-nucleotide","attrs":{"text":"KF498607","term_id":"558064687"}}KF498607) neutralized the myotoxic effects induced by B. jararacussu venom, BthTX-I, BthTX-II, and by a myotoxin from Bothrops brazili venom (MTX-I) in mice. Molecular docking revealed that VHH CDRs are expected to bind the C-terminal of both toxins, essential for myotoxic activity, and to epitopes in the BthTX-II enzymatic cleft. Identified VHHs could be a biotechnological tool to improve the treatment for snake envenomation, an important and neglected world public health problem.     

Characterisation of the Bacterial and Fungal Communities Associated with Different Lesion Sizes of Dark Spot Syndrome Occurring in the Coral Stephanocoenia intersepta

The number and prevalence of coral diseases/syndromes are increasing worldwide. Dark Spot Syndrome (DSS) afflicts numerous coral species and is widespread throughout the Caribbean, yet there are no known causal agents. In this study we aimed to characterise the microbial communities (bacteria and fungi) associated with DSS lesions affecting the coral Stephanocoenia intersepta using nonculture molecular techniques. Bacterial diversity of healthy tissues (H), those in advance of the lesion interface (apparently healthy AH), and three sizes of disease lesions (small, medium, and large) varied significantly (ANOSIM R  = 0.052 p<0.001), apart from the medium and large lesions, which were similar in their community profile. Four bacteria fitted into the pattern expected from potential pathogens; namely absent from H, increasing in abundance within AH, and dominant in the lesions themselves. These included ribotypes related to Corynebacterium ({"type":"entrez-nucleotide","attrs":{"text":"KC190237","term_id":"441431659","term_text":"KC190237"}}KC190237), Acinetobacter ({"type":"entrez-nucleotide","attrs":{"text":"KC190251","term_id":"441431673","term_text":"KC190251"}}KC190251), Parvularculaceae (KC19027), and Oscillatoria ({"type":"entrez-nucleotide","attrs":{"text":"KC190271","term_id":"441431693","term_text":"KC190271"}}KC190271). Furthermore, two Vibrio species, a genus including many proposed coral pathogens, dominated the disease lesion and were absent from H and AH tissues, making them candidates as potential pathogens for DSS. In contrast, other members of bacteria from the same genus, such as V. harveyii were present throughout all sample types, supporting previous studies where potential coral pathogens exist in healthy tissues. Fungal diversity varied significantly as well, however the main difference between diseased and healthy tissues was the dominance of one ribotype, closely related to the plant pathogen, Rhytisma acerinum, a known causal agent of tar spot on tree leaves. As the corals’ symbiotic algae have been shown to turn to a darker pigmented state in DSS (giving rise to the syndromes name), the two most likely pathogens are R. acerinum and the bacterium Oscillatoria, which has been identified as the causal agent of the colouration in Black Band Disease, another widespread coral disease.     

Extensive homologous recombination in classical swine fever virus: A re-evaluation of homologous recombination events in the strain AF407339

In this short report, the genome-wide homologous recombination events were re-evaluated for classical swine fever virus (CSFV) strain {"type":"entrez-nucleotide","attrs":{"text":"AF407339","term_id":"15488012","term_text":"AF407339"}}AF407339. We challenged a previous study which suggested only one recombination event in {"type":"entrez-nucleotide","attrs":{"text":"AF407339","term_id":"15488012","term_text":"AF407339"}}AF407339 based on 25 CSFV genomes. Through our re-analysis on the 25 genomes in the previous study and the 41 genomes used in the present study, we argued that there should be possibly at least two clear recombination events happening in {"type":"entrez-nucleotide","attrs":{"text":"AF407339","term_id":"15488012","term_text":"AF407339"}}AF407339 through genome-wide scanning. The reasons for identifying only one recombination event in the previous study might be due to the limited number of available CSFV genome sequences at that time and the limited usage of detection methods. In contrast, as identified by most detection methods using all available CSFV genome sequences, two major recombination events were found at the starting and ending zones of the genome {"type":"entrez-nucleotide","attrs":{"text":"AF407339","term_id":"15488012","term_text":"AF407339"}}AF407339, respectively. The first one has two parents {"type":"entrez-nucleotide","attrs":{"text":"AF333000","term_id":"13383931","term_text":"AF333000"}}AF333000 (minor) and {"type":"entrez-nucleotide","attrs":{"text":"AY554397","term_id":"49860681","term_text":"AY554397"}}AY554397 (major) with beginning and ending breakpoints located at 19 and 607 nt of the genome respectively. The second one has two parents {"type":"entrez-nucleotide","attrs":{"text":"AF531433","term_id":"22347661","term_text":"AF531433"}}AF531433 (minor) and {"type":"entrez-nucleotide","attrs":{"text":"GQ902941","term_id":"298113017","term_text":"GQ902941"}}GQ902941 (major) with beginning and ending breakpoints at 8397 and 11,078 nt of the genome respectively. Phylogenetic incongruence analysis using neighbor-joining algorithm with 1000 bootstrapping replicates further supported the existence of these two recombination events. In addition, we also identified additional 18 recombination events on the available CSFV strains. Some of them may be trivial and can be ignored. In conclusion, CSFV might have relatively high frequency of homologous recombination events. Genome-wide scanning of identifying recombination events should utilize multiple detection methods so as to reduce the risk of misidentification.     

Both STING and MAVS Fish Orthologs Contribute to the Induction of Interferon Mediated by RIG-I

Viral infections are detected in most cases by the host innate immune system through pattern-recognition receptors (PRR), the sensors for pathogen-associated molecular patterns (PAMPs), which induce the production of cytokines, such as type I interferons (IFN). Recent identification in mammalian and teleost fish of cytoplasmic viral RNA sensors, RIG-I-like receptors (RLRs), and their mitochondrial adaptor: the mitochondrial antiviral signaling (MAVS) protein, also called IPS-1, highlight their important role in the induction of IFN at the early stage of a virus infection. More recently, an endoplasmic reticulum (ER) adaptor: the stimulator of interferon genes (STING) protein, also called MITA, ERIS and MPYS, has been shown to play a pivotal role in response to both non-self-cytosolic RNA and dsDNA. In this study, we cloned STING cDNAs from zebrafish and showed that it was an ortholog to mammalian STING. We demonstrated that overexpression of this ER protein in fish cells led to a constitutive induction of IFN and interferon-stimulated genes (ISGs). STING-overexpressing cells were almost fully protected against RNA virus infection with a strong inhibition of both DNA and RNA virus replication. In addition, we found that together with MAVS, STING was an important player in the RIG-I IFN-inducing pathway. This report provides the demonstration that teleost fish possess a functional RLR pathway in which MAVS and STING are downstream signaling molecules of RIG-I. The Sequences presented in this article have been submitted to GenBank under accession numbers: Zebrafish STING ({"type":"entrez-nucleotide","attrs":{"text":"HE856619","term_id":"410810118","term_text":"HE856619"}}HE856619); EPC STING ({"type":"entrez-nucleotide","attrs":{"text":"HE856620","term_id":"410810120","term_text":"HE856620"}}HE856620); EPC IRF3 ({"type":"entrez-nucleotide","attrs":{"text":"HE856621","term_id":"410810122","term_text":"HE856621"}}HE856621); EPC IFN promoter ({"type":"entrez-nucleotide","attrs":{"text":"HE856618","term_id":"410810117","term_text":"HE856618"}}HE856618).     

Design of tandem genes cluster and expression vector for biosynthesis of soybean isoflavones

A tandem gene cluster CHS-CHI-IFS (rIFS) for secondary metabolites of plant isoflavones was constructed by using the chalcone synthase (CHS), chalcone isomerase (CHI), and isoflavone synthase (IFS) (GenBank accession numbers {"type":"entrez-nucleotide","attrs":{"text":"EU526827","term_id":"170783761","term_text":"EU526827"}}EU526827, {"type":"entrez-nucleotide","attrs":{"text":"EU526829","term_id":"170783765","term_text":"EU526829"}}EU526829, {"type":"entrez-nucleotide","attrs":{"text":"EU526830","term_id":"170783767","term_text":"EU526830"}}EU526830) in a single recombination event with the pET22b vector. The resulting expression vector pET-rIFS was heterogeneously expressed. The highlights of the vector include ease of handling, high efficiency and universal application among diverse plant species. To the best of our knowledge, this is the first attempt at developing a novel method of constructing tandem gene cluster for future research involving secondary metabolism of isoflavones and isoflavones engineering.Key words: Isoflavones biosynthesis, Novel method, Secondary metabolism, Tandem gene cluster     

Detection of Wolbachia pipientis, including a new strain containing the wsp gene,in two sister species of Paraphlebotomus sandflies,potential vectors of zoonotic cutaneous leishmaniasis

Individual, naturally occurring Phlebotomus mongolensis and Phlebotomus caucasicus from Iran were screened for infections with the maternally inherited intracellular Rickettsia-like bacterium Wolbachia pipientis via targeting a major surface protein gene (wsp). The main objective of this study was to determine if W. pipientis could be detected in these species. The sandflies were screened using polymerase chain reaction to amplify a fragment of the Wolbachia surface protein gene. The obtained sequences were edited and aligned with database sequences to identify W. pipientis haplotypes. Two strains of Wolbachia were found. Strain Turk 54 (accession {"type":"entrez-nucleotide","attrs":{"text":"EU780683","term_id":"212725653","term_text":"EU780683"}}EU780683) is widespread and has previously been reported in Phlebotomus papatasi and other insects. Strain Turk 07 (accession {"type":"entrez-nucleotide","attrs":{"text":"KC576916","term_id":"499068248","term_text":"KC576916"}}KC576916) is a novel strain, found for first time in the two sister species. A-group strains of W. pipientis occur throughout much of the habitat of these sandflies. It is possible that Wolbachia is transferred via horizontal transmission. Horizontal transfer could shed light on sandfly control because Wolbachia is believed to drive a deleterious gene into sandflies that reduces their natural population density. With regard to our findings in this study, we can conclude that one species of sandfly can be infected with different Wolbachia strains and that different species of sandflies can be infected with a common strain.     

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]

     

Prevalence,antimicrobial resistance profile,and characterization of multi-drug resistant bacteria from various infected wounds in North Egypt

Multi-drug resistant (MDR) bacteria associated with wounds are extremely escalating. This study aims to survey different wounds in Alexandria hospitals, North Egypt, to explore the prevalence and characteristics of MDR bacteria for future utilization in antibacterial wound dressing designs. Among various bacterial isolates, we determined 22 MDR bacteria could resist different classes of antibiotics. The collected samples exhibited the prevalence of mono-bacterial infections (60%), while 40% included poly-bacterial species due to previous antibiotic administration. Moreover, Gram-negative bacteria showed dominance with a ratio of 63.6%, while Gram-positive bacteria reported 36.4%. Subsequently, the five most virulent bacteria were identified following the molecular approach by 16S rRNA and physiological properties using the VITEK 2 automated system. They were deposited in GenBank as Staphylococcus haemolyticus MST1 ({"type":"entrez-nucleotide","attrs":{"text":"KY550377","term_id":"1304487819","term_text":"KY550377"}}KY550377), Pseudomonas aeruginosa MST2 ({"type":"entrez-nucleotide","attrs":{"text":"KY550378","term_id":"1304487820","term_text":"KY550378"}}KY550378), Klebsiella pneumoniae MST3 ({"type":"entrez-nucleotide","attrs":{"text":"KY550379","term_id":"1304487821","term_text":"KY550379"}}KY550379), Escherichia coli MST4 ({"type":"entrez-nucleotide","attrs":{"text":"KY550380","term_id":"1304487822","term_text":"KY550380"}}KY550380), and Escherichia coli MST5 ({"type":"entrez-nucleotide","attrs":{"text":"KY550381","term_id":"1304487823","term_text":"KY550381"}}KY550381). In terms of isolation source, S. haemolyticus MST1 was isolated from a traumatic wound, while P. aeruginosa MST2 and E. coli MST4 were procured from hernia surgical wounds, and K. pneumoniae MST3 and E. coli MST5 were obtained from diabetic foot ulcers. Antibiotic sensitivity tests exposed that K. pneumoniae MST3, E. coli MST4, and E. coli MST5 are extended-spectrum β-lactamases (ESBLs) bacteria. Moreover, S. haemolyticus MST1 belongs to the methicillin-resistant coagulase-negative staphylococcus (MRCoNS), whereas P. aeruginosa MST2 exhibited resistance to common empirical bactericidal antibiotics. Overall, the study provides new insights into the prevalent MDR bacteria in Egypt for further use as specific models in formulating antibacterial wound dressings.     

High Prevalence and Significant Association of ESBL and QNR Genes in Pathogenic Klebsiella pneumoniae Isolates of Patients from Kolkata, India

Pathogenic Klebsiella pneumoniae, resistant to beta-lactam and quinolone drugs, is widely recognized as important bacteria causing array of diseases. The resistance property is obtained by acquisition of plasmid encoded bla_TEM, bla_SHV, bla_CTX-M, QNRA, QNRB and QNRS genes. The aim of this study was to document the prevalence and association of these resistant genes in K. pneumoniae infecting patients in India. Approximately 97 and 76.7 % of the 73 K. pneumoniae isolates showed resistance towards beta-lactam and quinolone drugs respectively. Bla genes were detected in 74 % of K. pneumoniae isolates; with prevalence in the following order: bla_TEM > bla_SHV > bla_CTXM. QNR genes were detected in 67 % samples. Chi-square analysis revealed significant association between presence of bla and qnr genes in our study (P value = 0.000125). Sequence analysis of some bla_TEM, bla_SHV, bla_CTX-M and QNRB PCR products revealed presence of bla_TEM1 (GenBank accession: {"type":"entrez-nucleotide","attrs":{"text":"JN193522","term_id":"343796760","term_text":"JN193522"}}JN193522), bla_TEM116 ({"type":"entrez-nucleotide","attrs":{"text":"JN193523","term_id":"343796762","term_text":"JN193523"}}JN193523 and {"type":"entrez-nucleotide","attrs":{"text":"JN193524","term_id":"343796764","term_text":"JN193524"}}JN193524), bla_SHV11, bla_CTXM72 variants ({"type":"entrez-nucleotide","attrs":{"text":"JF523199","term_id":"329024835","term_text":"JF523199"}}JF523199) and QNRB1 ({"type":"entrez-nucleotide","attrs":{"text":"JN193526","term_id":"343796802","term_text":"JN193526"}}JN193526 and {"type":"entrez-nucleotide","attrs":{"text":"JN193527","term_id":"343796804","term_text":"JN193527"}}JN193527) in our samples.     

Molecular Identification of Cryptosporidium viatorum Infection in a Patient Suffering from Unusual Cryptosporidiosis in West Bengal,India

In this study, we have collected and screened a total of 268 stool samples from diarrheal patients admitted to an Infectious disease hospital in Kolkata for the presence of Cryptosporidium spp. The initial diagnosis was carried out by microscopy followed by genus specific polymerase chain reaction assays based on 70 kDa heat shock proteins (HSP70). DNA sequencing of the amplified locus has been employed for determination of genetic diversity of the local isolates. Out of 268 collected samples, 12 (4.48%) were positive for Cryptosporidium spp. Sequences analysis of 70 kDa heat shock proteins locus in 12 Cryptosporidium local isolates revealed that 2.24% and 1.86% of samples were showing 99% to 100% identity with C. parvum and C. hominis. Along with the other 2 major species one recently described globally distributed pathogenic species Cryptosporidium viatorum has been identified. The HSP70 locus sequence of the isolate showed 100% similarity with a previously described isolate of C. viatorum (Accession No. {"type":"entrez-nucleotide","attrs":{"text":"JX978274.1","term_id":"441431305","term_text":"JX978274.1"}}JX978274.1, {"type":"entrez-nucleotide","attrs":{"text":"JX978273.1","term_id":"441431303","term_text":"JX978273.1"}}JX978273.1, and {"type":"entrez-nucleotide","attrs":{"text":"JN846706.1","term_id":"385399407","term_text":"JN846706.1"}}JN846706.1) present in GenBank.     

Vasorelaxin: A Novel Arterial Smooth Muscle-Relaxing Eicosapeptide from the Skin Secretion of the Chinese Piebald Odorous Frog (Odorrana schmackeri)

The defensive skin secretions of amphibians are a rich resource for the discovery of novel, bioactive peptides. Here we report the identification of a novel vascular smooth muscle-relaxing peptide, named vasorelaxin, from the skin secretion of the Chinese piebald odorous frog, Odorrana schmackeri. Vasorelaxin consists of 20 amino acid residues, SRVVKCSGFRPGSPDSREFC, with a disulfide-bridge between Cys-6 and Cys-20. The structure of its biosynthetic precursor was deduced from cloned skin cDNA and consists of 67 amino acid residues encoding a single copy of vasorelaxin (vasorelaxin, accession number: {"type":"entrez-nucleotide","attrs":{"text":"HE860494","term_id":"429534177","term_text":"HE860494"}}HE860494). Synthetic vasorelaxin caused a profound relaxation of rat arterial smooth muscle with an EC₅₀ of 6.76 nM.     

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]

     

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]

     

Phenotypic Assessment of Probiotic and Bacteriocinogenic Efficacy of Indigenous LAB Strains from Human Breast Milk

Breast milk is the combination of bioactive compounds and microflora that promote newborn’s proper growth, gut flora, and immunity. Thus, it is always considered the perfect food for newborns. Amongst their bioactives, probiotic communities—especially lactic acid bacteria (LAB)—are characterized from breast milk over the first month of parturition. In this study, seven LAB were characterized phenotypically and genotypically as Levilactobacillus brevis BDUMBT08 ({"type":"entrez-nucleotide","attrs":{"text":"MT673657","term_id":"1863149999"}}MT673657), L. gastricus BDUMBT09 ({"type":"entrez-nucleotide","attrs":{"text":"MT774596","term_id":"1873222494"}}MT774596), L. paracasei BDUMBT10 ({"type":"entrez-nucleotide","attrs":{"text":"MT775430","term_id":"1874262304"}}MT775430), L. brevis BDUMBT11 ({"type":"entrez-nucleotide","attrs":{"text":"MW785062","term_id":"2009762994"}}MW785062), L. casei BDUMBT12 ({"type":"entrez-nucleotide","attrs":{"text":"MW785063","term_id":"2009820773"}}MW785063), L. casei BDUMBT13 ({"type":"entrez-nucleotide","attrs":{"text":"MW785178","term_id":"2010296340"}}MW785178), and Brevibacillus brevis M2403 ({"type":"entrez-nucleotide","attrs":{"text":"MK371781","term_id":"1548854744"}}MK371781) from human breast milk. Their tolerance to lysozyme, acid, bile, gastric juice, pancreatic juice, and NaCl and potential for mucoadhesion, auto-aggregation, and co-aggregation with pathogens are of great prominence in forecasting their gut colonizing ability. They proved their safety aspects as they were negative for virulence determinants such as hemolysis and biofilm production. Antibiogram of LAB showed their sensitivity to more than 90% of the antibiotics tested. Amongst seven LAB, three isolates (L. brevis BDUMBT08 and BDUMBT11, and L. gatricus BDUMBT09) proved their bacteriocin producing propensity. Although the seven LAB isolates differed in their behavior, their substantial probiotic properties with safety could be taken as promising probiotics for further studies to prove their in vivo effects, such as health benefits, in humans.     

LncRNA‐AK137033 inhibits the osteogenic potential of adipose‐derived stem cells in diabetic osteoporosis by regulating Wnt signaling pathway via DNA methylation

ObjectivesBone tissue engineering based on adipose‐derived stem cells (ASCs) is expected to become a new treatment for diabetic osteoporosis (DOP) patients with bone defects. However, compared with control ASCs (CON‐ASCs), osteogenic potential of DOP‐ASCs is decreased, which increased the difficulty of bone reconstruction in DOP patients. Moreover, the cause of the poor osteogenesis of ASCs in a hyperglycemic microenvironment has not been elucidated. Therefore, this study explored the molecular mechanism of the decline in the osteogenic potential of DOP‐ASCs from the perspective of epigenetics to provide a possible therapeutic target for bone repair in DOP patients with bone defects.Materials and methodsAn animal model of DOP was established in mice. CON‐ASCs and DOP‐ASCs were isolated from CON and DOP mice, respectively. {"type":"entrez-nucleotide","attrs":{"text":"AK137033","term_id":"74205820","term_text":"AK137033"}}AK137033 small interfering RNA (SiRNA) and an {"type":"entrez-nucleotide","attrs":{"text":"AK137033","term_id":"74205820","term_text":"AK137033"}}AK137033 overexpression plasmid were used to regulate the expression of {"type":"entrez-nucleotide","attrs":{"text":"AK137033","term_id":"74205820","term_text":"AK137033"}}AK137033 in CON‐ASCs and DOP‐ASCs in vitro. Lentiviruses that carried shRNA‐{"type":"entrez-nucleotide","attrs":{"text":"AK137033","term_id":"74205820","term_text":"AK137033"}}AK137033 or {"type":"entrez-nucleotide","attrs":{"text":"AK137033","term_id":"74205820","term_text":"AK137033"}}AK137033 cDNA were used to knockdown or overexpress {"type":"entrez-nucleotide","attrs":{"text":"AK137033","term_id":"74205820","term_text":"AK137033"}}AK137033, respectively, in CON‐ASCs and DOP‐ASCs in vivo. Hematoxylin and eosin (H&E), Masson''s, alizarin red, and alkaline phosphatase (ALP) staining, micro‐computed tomography (Micro‐CT), flow cytometry, qPCR, western blotting, immunofluorescence, and bisulfite‐specific PCR (BSP) were used to analyze the functional changes of ASCs.ResultsThe DOP mouse model was established successfully. Compared with CON‐ASCs, {"type":"entrez-nucleotide","attrs":{"text":"AK137033","term_id":"74205820","term_text":"AK137033"}}AK137033 expression, the DNA methylation level of the sFrp2 promoter region, Wnt signaling pathway markers, and the osteogenic differentiation potential were decreased in DOP‐ASCs. In vitro experiments showed that {"type":"entrez-nucleotide","attrs":{"text":"AK137033","term_id":"74205820","term_text":"AK137033"}}AK137033 silencing inhibited the Wnt signaling pathway and osteogenic ability of CON‐ASCs by reducing the DNA methylation level in the sFrp2 promoter region. Additionally, overexpression of {"type":"entrez-nucleotide","attrs":{"text":"AK137033","term_id":"74205820","term_text":"AK137033"}}AK137033 in DOP‐ASCs rescued these changes caused by DOP. Moreover, the same results were obtained in vivo.ConclusionsLncRNA‐{"type":"entrez-nucleotide","attrs":{"text":"AK137033","term_id":"74205820","term_text":"AK137033"}}AK137033 inhibits the osteogenic potential of DOP‐ASCs by regulating the Wnt signaling pathway via modulating the DNA methylation level in the sFrp2 promoter region. This study provides an important reference to find new targets for the treatment of bone defects in DOP patients.