Genome Sequence of the Immunomodulatory Strain Bifidobacterium bifidum LMG 13195

In this work, we report the genome sequences of Bifidobacterium bifidum strain LMG13195. Results from our research group show that this strain is able to interact with human immune cells, generating functional regulatory T cells.     

Complete Genome Sequence of Probiotic Bifidobacterium animalis subsp. lactis Strain V9

Bifidobacterium animalis subsp. lactis strain V9 is a Chinese commercial bifidobacteria with several probiotic functions. It was isolated from a healthy Mongolian child in China. We present here the complete genome sequence of V9 and compare it to 3 other published genome sequences of B. animalis subsp. lactis strains. The result indicates the lack of polymorphism among strains of this subspecies from different continents.Bifidobacterium animalis subsp. lactis strain V9 was isolated from the feces of a healthy Mongolian child in China (5). It has shown a high level of tolerance to gastric acid and bile acids (5). This strain has been implemented in the industrial production of dairy starter cultures by Inner Mongolia Yili Industrial Group Company Limited, the largest dairy corporation in China.Whole-genome sequencing of B. animalis subsp. lactis V9 was performed with a combined strategy of 454 sequencing (8) and Solexa paired-end sequencing technology (2). Genomic libraries containing 7-kb inserts were constructed, and 325,824 paired-end reads and 67,177 single-end reads were generated using the GS FLX system, giving 36.0-fold coverage of the genome. A total of 96.0% of the reads were assembled into four large scaffolds, including 163 nonredundant contigs, using the 454 Newbler assembler (454 Life Sciences, Branford, CT). A total of 8,953,102 reads (2-kb library) were generated to reach a depth of 335-fold coverage with an Illumina Solexa Genome Analyzer IIx and mapped to the scaffolds using the Burrows-Wheeler Alignment (BWA) tool (7). The gaps between scaffolds were filled by sequencing PCR products using an ABI 3730 capillary sequencer. The analysis of the genome was performed as described previously (3, 4).The complete genome sequence of V9 contains a circular 1,944,050-bp chromosome, with a GC content of 60.5%. The genome size is slightly larger than the sequenced genome sizes of B. animalis subsp. lactis strains DSM 10140^T (1), Bl-04 (1), and AD011 (6) due to a unique insertion of 4,037 bp. The V9 genome contains 1,636 genes in total, including 1,572 coding genes, 4 rRNA operons, and 52 tRNAs.Comparison of the four B. animalis subsp. lactis genomes revealed nearly perfect synteny. AD011 is the most diverged strain, with more single nucleotide polymorphisms (SNPs) and indels than the other three strains. There are 197 SNPs in AD011, with 70 synonymous and 16 nonsynonymous SNPs, which means that there is only 1 SNP per 10 kb, indicating the high consistency within this subspecies. The other three strains are almost identical, with only 25 SNPs in V9, 13 SNPs in Bl-04, and 44 SNPs in DSM 10140^T. Strain V9 was isolated from the feces of a Mongolian child in Inner Mongolia, China, where traditional fermented milk has been consumed for thousands of years, and the other three strains were originally isolated from fecal samples (1, 6) or yogurt (1) in the United States of America, France, and Korea. The result indicated the lack of polymorphism among multiple lineages from different continents (1).Interestingly, compared to the other three sequenced B. animalis subsp. lactis strains, V9 has a large insertion, which encodes one putative transposase (BalV_1091) and two sugar metabolism-related proteins, an alpha-1,4-glucosidase (BalV_1092) and an ABC transporter solute-binding protein (BalV_1093). This insertion is a copy of the region at positions 1,860,164 to 1,864,073, which is commonly shared by all four B. animalis subsp. lactis strains.     

Genome Sequence of the Probiotic Bacterium Bifidobacterium animalis subsp. lactis AD011

Bifidobacterium animalis subsp. lactis is a probiotic bacterium that naturally inhabits the guts of most mammals, including humans. Here we report the complete genome sequence of B. animalis subsp. lactis AD011 that was isolated from an infant fecal sample. Biological functions encoded in a single circular chromosome of 1,933,695 bp, smallest among the completely sequenced bifidobacterial genomes, are suggestive of their probiotic functions, such as utilization of bifidogenic factors and a variety of glycosidic enzymes and biosynthesis of polysaccharides.     

Complete Genome Sequence of the Endophytic Bacterium Burkholderia sp. Strain KJ006

Endophytes live inside plant tissues without causing any harm and may even benefit plants. Here, we provide the high-quality genome sequence of Burkholderia sp. strain KJ006, an endophytic bacterium of rice with antifungal activity. The 6.6-Mb genome, consisting of three chromosomes and a single plasmid, contains genes related to plant growth promotion or degradation of aromatic compounds.     

Complete Genome Sequence of the Pyrene-Degrading Bacterium Cycloclasticus sp. Strain P1

Cycloclasticus sp. strain P1 was isolated from deep-sea sediments of the Pacific Ocean and characterized as a unique bacterium in the degradation of pyrene, a four-ring polycyclic aromatic hydrocarbon (PAH). Here we report the complete genome of P1 and genes associated with PAH degradation.     

Complete Genome Sequence of Lactobacillus helveticus R0052, a Commercial Probiotic Strain

Lactobacillus helveticus R0052 is a commercially available strain that is widely used in probiotic preparations. The genome sequence consisted of 2,129,425 bases. Comparative analysis showed that it was unique among L. helveticus strains in that it contained genes encoding mucus-binding proteins similar to those found in Lactobacillus acidophilus.     

Complete Genome Sequence of the Copiotrophic Marine Bacterium Alteromonas macleodii Strain ATCC 27126T

The genome of Alteromonas macleodii strain ATCC 27126^T has been resequenced and closed into a single contig. We describe here the genome of this important and globally distributed marine bacterium.     

Complete Genome Sequence of Bifidobacterium longum JDM301

Bifidobacteria, known as probiotic bacteria, are high-G+C Gram-positive bacteria which naturally inhabit the human gastrointestinal tract and vagina. Recently, we completely sequenced Bifidobacterium longum JDM301, which is a widely used Chinese commercial strain with several probiotic properties.Bifidobacterium spp., which are considered model probiotic bacteria like Lactobacillus spp., play an important role in the stability of the intestinal microflora, the modulation of the immune response, and so on (6, 8). We determined the complete genome sequence of B. longum JDM301, which is commercially used in China as a probiotic strain, using the GS 20 system (454 Life Science Corporation) (7). A total of 192,888 reads with an average length of 210 bp were assembled into 112 contigs by the 454 assembly tool. Among these, 92 large contigs were larger than 500 bp. We determined the order of the largest contigs through BLAST analysis with the reference strain B. longum ATCC 15697 (GenBank accession number {"type":"entrez-nucleotide","attrs":{"text":"CP001095","term_id":"213522389","term_text":"CP001095"}}CP001095) (10) and arranged the others by multiplex PCR. Gaps were closed by sequencing gap-spanning PCR products or clones using ABI 3730 xl DNA sequencers. Primer design and sequence assembly were performed with the Phred/Phrap/Consed software package (2, 3).The complete genome of B. longum JDM301 is composed of a 59.8% G+C circular chromosome of 2,477,838 bp without any plasmid. The genome of JDM301 (2.48 Mb) is smaller than that of B. longum ATCC 15697 (2.83 Mb) and slightly larger than the complete genomes of B. longum NCC2705 (2.26 Mb; GenBank accession number {"type":"entrez-nucleotide","attrs":{"text":"AE014295","term_id":"58012118","term_text":"AE014295"}}AE014295) and DJO10A (2.38 Mb; GenBank accession number {"type":"entrez-nucleotide","attrs":{"text":"CP000605","term_id":"189427298","term_text":"CP000605"}}CP000605). The JDM301 genome contains 1,959 protein-coding genes, three rRNA operons, and 55 tRNA genes. There are four rRNA operons with two cascaded in the three reference B. longum strains, while there are three in JDM301. We resequenced the three regions containing rRNA operons in the genome of JDM301 and found no cascaded rRNA operon. However, the locations of the three rRNA operons in JDM301 are the same as in the other three B. longum strains. No complete prophages were found in the genome sequence, but 12 phage-related fragments were identified. The genome also contains 15 pseudogenes, which is evidence of the recent and ongoing genome reduction of lactic acid bacilli (9). In addition, 15 complete or disrupted insertion sequence (IS) elements were found in the entire genome, which were identified as 5 derivatives of ISBlo5, 3 complete copies of ISBlo3, and 7 other ISs or derivatives belonging to the IS256, IS3, IS21, and IS30 family elements, respectively. One of them, named ISBad1, was 98.08% identical to that of B. adolescentis, and the others have been reported in the B. longum NCC2705 genome (8).Genome analysis revealed 14 response regulators and 14 sensor histidine kinases throughout the JDM301 chromosome, which may suggest a less complex regulatory network in JDM301 than that in ATCC 15697 (10). JDM301 has been grown as a commercial strain in stable and rich nutritional medium for such a long time that the regulatory networks in the genome may degenerate slowly, which is required for responses to dynamic environmental cues in the gastrointestinal tract.A gene (for BLJ_1359) encoding a serpin (serine protease inhibitor) with 92.69% identity to that of NCC2705 (4) was found in the genome sequence. The serpin is a potential probiotic effector molecule, and it may contribute to the immunomodulation of this B. longum strain. As we know, modulation of the immune system is one of probiotic functions of lactic acid bacteria (5).As model probiotic bacteria, Bifidobacterium spp. attract more and more interest since the molecular mechanisms of their probiotic activities remain unclear to a large degree (11). On the other hand, the biosafety of probiotics has attracted more attention with their enlarged and wide applications in food and drug products (1). We believe that this work will bring us deeper insight into the probiotic activities and safety of the strain widely used in China.     

Complete Genome Sequence of Lactobacillus fermentum CECT 5716, a Probiotic Strain Isolated from Human Milk

Lactobacillus fermentum is a heterofermentative lactic acid bacterium and is frequently isolated from mucosal surfaces of healthy humans. Lactobacillus fermentum CECT 5716 is a well-characterized probiotic strain isolated from human milk and, at present, is used in commercial infant formulas. Here, we report the complete and annotated genome sequence of this strain.Breast milk is the best food for neonates because it provides a unique combination of nutrients and bioactive compounds, ensuring correct growth and development of the infant. In addition, it also contains probiotic bacteria (4, 5). In a previous study, we isolated Lactobacillus fermentum CECT 5716 from such biological fluid (3). Subsequent studies revealed that this strain was a good probiotic candidate since it reached high survival rates when exposed to gastrointestinal tract-like conditions, showed a strong adherence to intestinal cells, stimulated the expression of mucin-encoding genes, produced antimicrobial compounds, and displayed in vivo and in vitro immunomodulatory and antibacterial properties against pathogenic bacteria (1, 5, 7). L. fermentum CECT 5716 showed a beneficial effect in a murine model of intestinal inflammation, reducing the inflammatory response and the intestinal damage (2). In addition, consumption of this strain enhances the response to influenza vaccination in healthy volunteers and reduces the incidence of influenza-like illness (8).In order to interrogate the genome sequence of Lactobacillus fermentum CECT 5716 with regard to its probiotic properties, the complete genome sequence was determined by a whole-genome shotgun strategy using 454 pyrosequencing technology (454 Life Sciences, Banford, CT). The initial draft assembly provided by 454 Life Sciences was based on 193,362 pyrosequencing reads with an average read length of 250 nucleotides which assembled into 1,343 contigs. Sequence reads were assembled automatically with the Life Sciences GS FLX (Newbler) program. The genome sequence of Lactobacillus fermentum IFO 3956 (6) was used to order these contigs into large scaffolds. The assembling process was relatively complex due to the 83 transposase-encoding regions that were found in the CECT 5716 genome.The complete genome of Lactobacillus fermentum CECT 5716 consists of a circular chromosome of 2,100,449 bp, with a GC content of 51.49%, and has no plasmid. Its chromosome contains 1,109 predicted protein-encoding genes, 54 tRNA-encoding genes, and 20 rRNA-encoding genes. The comparison of the CECT 5716 and IFO 3956 genomes revealed that they were highly similar, with the exception of 16 protein-encoding genes that are present in CECT 5716 but not in IFO 3956. Among them, there are putative enzymes involved in the metabolism of purines (allantoinase, GMP oxidoreductase, GMP synthase), amino acids (serine-pyruvate transaminase, 3 glutamate synthases), lipids (acyltransferase), and carbohydrates (mannose-6-phosphate isomerase).     

The Complete Genome Sequence of the Plant Growth-Promoting Bacterium Pseudomonas sp. UW4

The plant growth-promoting bacterium (PGPB) Pseudomonas sp. UW4, previously isolated from the rhizosphere of common reeds growing on the campus of the University of Waterloo, promotes plant growth in the presence of different environmental stresses, such as flooding, high concentrations of salt, cold, heavy metals, drought and phytopathogens. In this work, the genome sequence of UW4 was obtained by pyrosequencing and the gaps between the contigs were closed by directed PCR. The P. sp. UW4 genome contains a single circular chromosome that is 6,183,388 bp with a 60.05% G+C content. The bacterial genome contains 5,423 predicted protein-coding sequences that occupy 87.2% of the genome. Nineteen genomic islands (GIs) were predicted and thirty one complete putative insertion sequences were identified. Genes potentially involved in plant growth promotion such as indole-3-acetic acid (IAA) biosynthesis, trehalose production, siderophore production, acetoin synthesis, and phosphate solubilization were determined. Moreover, genes that contribute to the environmental fitness of UW4 were also observed including genes responsible for heavy metal resistance such as nickel, copper, cadmium, zinc, molybdate, cobalt, arsenate, and chromate. Whole-genome comparison with other completely sequenced Pseudomonas strains and phylogeny of four concatenated “housekeeping” genes (16S rRNA, gyrB, rpoB and rpoD) of 128 Pseudomonas strains revealed that UW4 belongs to the fluorescens group, jessenii subgroup.     

Complete Genome Sequence of Mycoplasma wenyonii Strain Massachusetts

Mycoplasma wenyonii is a hemotrophic mycoplasma that causes acute and chronic infections in cattle. Here, we announce the first complete genome sequence of this organism. The genome is a single circular chromosome with 650,228 bp and G+C% of 33.9. Analyses of M. wenyonii genome will provide insights into its biology.     

Genome Sequence of Hydrogenophaga sp. Strain PBC, a 4-Aminobenzenesulfonate-Degrading Bacterium

Hydrogenophaga sp. strain PBC is an effective degrader of 4-aminobenzenesulfonate isolated from textile wastewater. Here we present the assembly and annotation of its genome, which may provide further insights into its metabolic potential. This is the first announcement of the draft genome sequence of a strain from the genus Hydrogenophaga.     

Complete genome sequence of Bifidobacterium bifidum S17

Here, we report on the first completely annotated genome sequence of a Bifidobacterium bifidum strain. B. bifidum S17, isolated from feces of a breast-fed infant, was shown to strongly adhere to intestinal epithelial cells and has potent anti-inflammatory activity in vitro and in vivo. The genome sequence will provide new insights into the biology of this potential probiotic organism and allow for the characterization of the molecular mechanisms underlying its beneficial properties.     

Complete Genome Sequence of Mycoplasma hyorhinis Strain HUB-1

Mycoplasma hyorhinis is generally considered a swine pathogen yet is most commonly found infecting laboratory cell lines. An increasing body of evidence suggests that chronic infections with M. hyorhinis may cause oncogenic transformation. Here, we announce the complete genome sequence of M. hyorhinis strain HUB-1.Mycoplasma hyorhinis is generally considered to be a swine pathogen causing lung lesions, inflammation in the chest and abdominal lining, and arthritis (8). This agent also frequently contaminates laboratory cell cultures, impinging on many aspects of biological research (3). Recent studies have demonstrated that M. hyorhinis infections induce a malignant phenotype in human prostate (7) and gastric (4) cells, suggesting that M. hyorhinis infections are associated with oncogenic transformation. These properties of M. hyorhinis have increased its profile to researchers. The complete genome sequence of this microbe has yet to be determined.We sequenced the genome of M. hyorhinis strain HUB-1, a pathogenic strain isolated from the respiratory tract of swine. Whole-genome sequencing was performed by combining GS FLX (6) and Solexa paired-end sequencing technologies (1). Genomic libraries containing 3-kb inserts were constructed, and 308,604 reads (79.7% paired end) were produced using the GS FLX system, giving 65.9-fold coverage of the genome. About 93.4% of reads were assembled into one large scaffold using Newbler software (454 Life Sciences, Branford, CT). A total of 822,579 reads were generated using an Illumina Solexa Genome Analyzer IIx and were mapped to the scaffold using the Burrows-Wheeler alignment (BWA) tool (5). Gaps were filled by local assembly of the Solexa/Roche 454 reads or by sequencing PCR products by using an ABI 3730 capillary sequencer. Open reading frames containing more than 30 amino acid residues were predicted using Glimmer 3.0 (2) and verified by comparison with six other closely related genome sequences.The complete genome of M. hyorhinis HUB-1 consists of an 839,615-bp single circular chromosome with an average G+C content of 25.88%. A total of 654 protein-encoding genes are predicted. The average protein size is 364 amino acids, and the mean coding percentage is 85.2%. The genome includes 30 tRNA genes, and only a single copy of the 16S-23S rRNA operon can be found. The 5S rRNA operon is separate from the 16S-23S rRNA operon. Protein secretion occurs through a truncated membrane protein secretion system, consisting of SecA, SecD, SecY, PrsA, DnaK, Tig, and LepA. Additionally, 20 pseudogenes, which become truncated or inactivated, are identified in the genome.M. hyorhinis contains a special variable lipoprotein (Vlp) system that constitutes its major coat protein (9) and provides a mutational strategy for evasion of the host immune system. Different M. hyorhinis strains carry a variable number of vlp genes (9). M. hyorhinis HUB-1 is characterized to contain seven vlp genes displayed in the order 5′-vlpD-vlpE-vlpF-insertion sequence (IS)-vlpG-vlpA-IS-vlpB-vlpC-3′.This is the first complete genome sequence of M. hyorhinis, and its availability will provide a better-defined genetic background for future studies of gene expression and regulation.     

Complete Genome Sequence of an Uncultured Bacterium of the Candidate Phylum Bipolaricaulota

Microbiology - Bacteria of the candidate phylum Bipolaricaulota, previously known as OP1 and Acetothermia, have been identified in various terrestrial and marine ecosystems as a result of molecular...     

Complete Genome Sequence of Streptococcus thermophilus Strain MN-ZLW-002

Streptococcus thermophilus MN-ZLW-002 was originally isolated from traditionally fermented Chinese dairy products. One of the strain-dependent characteristics of this bacterium is its ability to produce exopolysaccharides (EPSs). This study determined and analyzed the genome sequence of MN-ZLW-002. Its complete genome comprised 2,046 genes and 1,848,520 nucleotides with an average GC content of 39%. The EPS cluster of MN-ZLW-002 includes 25 open reading frames (ORFs), and some results indicate a horizontal gene transfer between MN-ZLW-002 and other lactic acid bacteria (LAB).     

Genome Sequence of the Solvent-Producing Bacterium Clostridium carboxidivorans Strain P7T

Clostridium carboxidivorans strain P7^T is a strictly anaerobic acetogenic bacterium that produces acetate, ethanol, butanol, and butyrate. The C. carboxidivorans genome contains all the genes for the carbonyl branch of the Wood-Ljungdahl pathway for CO₂ fixation, and it encodes enzymes for conversion of acetyl coenzyme A into butanol and butyrate.Clostridium carboxidivorans strain P7^T (equivalent to ATCC BAA-624^T and DSM 15243^T) is an obligate anaerobe that can grow autotrophically with H₂ and CO₂ or CO (fixing carbon via the Wood-Ljungdahl pathway), or it can grow chemoorganotrophically with simple sugars (1). Acetate, ethanol, butanol, and butyrate are end products of metabolism.For slow-growing strict anaerobes such as Clostridium carboxidivorans, genome sequencing provides a rapid theoretical characterization of its metabolism compared to traditional methods. We isolated and amplified genomic C. carboxidivorans DNA using the Wizard genomic DNA purification kit (Promega, Madison, WI) and the REPLI-g kit (Qiagen). A single shotgun pyrosequencing run using a Genome Sequencer FLX system (454 Life Sciences, Branford, CT) resulted in 429,680 high-quality reads (mean read length, 231.6 bp) that were assembled using Newbler software (454 Life Sciences) into 225 contigs >500 bp long. Paired-end sequencing produced 111,154 reads (mean read length, 256.3 bp). Assembly of the paired-end and shotgun reads produced 73 scaffolds containing 216 large contigs with a mean sequence depth of 16.33 reads. PCR amplification and Sanger sequencing were conducted, followed by scaffold assembly using Sequencher (Gene Codes, Ann Arbor, MI). The 4.4-Mb final assembly has 33 scaffolds containing 69 contigs with a Phred-equivalent quality score of 40 or above (accuracy, >99.99%) (GenBank accession no. {"type":"entrez-nucleotide","attrs":{"text":"ADEK00000000","term_id":"295883218","term_text":"ADEK00000000"}}ADEK00000000).The sequence was annotated using Annotation Engine (J. Craig Venter Institute) and manually curated using Manatee (http://manatee.sourceforge.net/). The genome has 29.7% G+C content and contains 4,174 protein-coding sequences, 3 rRNA operons, 1 tmRNA (dual tRNA-like and mRNA-like nature), 6 noncoding RNAs (ncRNAs), and 48 tRNA genes. (6). Comparison of 16S rRNA genes showed that C. carboxidivorans is closely related to Clostridium scatologenes ATCC 25775^T (97% sequence identity) and Clostridium drakei type strain SL1^T (99% sequence identity). C. carboxidivorans shares 94% 16S rRNA sequence identity with Clostridium ljungdahlii (4.6 Mb), another solventogenic species.Pathway analyses indicated that C. carboxidivorans is similar to other anaerobic acetogens, such as Moorella thermoacetica (8), in having an incomplete reductive tricarboxylic acid (TCA) cycle where fumarate reductase is absent. Like other acetogenic clostridia, C. carboxidivorans uses the Wood-Ljungdahl pathway for fixing carbon dioxide to organic carbon via acetyl coenzyme A (acetyl-CoA) (5). Two of these genes encode carbon monoxide dehydrogenase (CODH) and acetyl-CoA synthase (ACS), which form a complex to catalyze the carbonyl branch of the pathway for carbon fixation and acetyl-CoA production. C. carboxidivorans has genes that encode phosphotransacetylase and acetate kinase for converting acetyl-CoA into acetate, yielding ATP (2).C. carboxidivorans is unique among other known acetogenic clostridia because it can fix carbon via the Wood-Ljungdahl pathway and convert acetyl-CoA into butanol, which is more energy dense than ethanol. Both C. carboxidivorans and Clostridium acetobutylicum encode NADPH-dependent butanol dehydrogenase (74% identity) to convert acetyl-CoA into butanol (3, 4), but C. acetobutylicum cannot fix CO₂ or CO into acetyl-CoA. Conversely, C. ljungdahlii can fix CO and CO₂, but it lacks butanol dehydrogenase and cannot convert acetyl-CoA into butanol. Therefore, P7 includes beneficial properties of both these industrially important strains. The genome sequence of C. carboxidivorans P7 could potentially accelerate research allowing its industrial application for biofuel production or to enable some of its pathways to be used directly in synthetic biology for biofuel production.     

Draft Genome Sequence of the Cyanide-Utilizing Bacterium Pseudomonas fluorescens Strain NCIMB 11764

We report here the 6.97-Mb draft genome sequence of Pseudomonas fluorescens strain NCIMB 11764, which is capable of growth on cyanide as the sole nitrogen source. The draft genome sequence allowed the discovery of several genes implicated in enzymatic cyanide turnover and provided additional information contributing to a better understanding of this organism''s unique cyanotrophic ability. This is the first sequenced genome of a cyanide-assimilating bacterium.