Abstract
The vaginal microbiota, in particular Lactobacillus species, play an important role in female health through modulation of immunity, countering pathogens and maintaining a pH below 4.7. We report the isolation and genome sequence of Lactobacillus pentosus strain KCA1 (formally known as L. plantarum) from the vagina of a healthy Nigerian woman. The genome was sequenced using Illumina GA II technology. The resulting 16,920,226 paired-end reads were assembled with the Velvet tool. Contigs were annotated using the RAST server, and manually curated. A comparative analysis with the available genomes of L. pentosus IG1 and L. plantarum WCFS1 showed that over 15% of the predicted functional activities are found only in this strain. The strain has a chromosome sequence of 3,418,159 bp with a G+C content of 46.4%, and is devoid of plasmids. Novel gene clusters or variants of known genes relative to the reference genomes were found. In particular, the strain has loci encoding additional putative mannose phosphotransferase systems. Clusters of genes include those for utilization of hydantoin, isopropylmalate, malonate, rhamnosides, and genes for assimilation of polyglycans, suggesting the metabolic versatility of L. pentosus KCA1. Loci encoding putative phage defense systems were also found including clustered regularly interspaced short palindromic repeats (CRISPRs), abortive infection (Abi) systems and toxin-antitoxin systems (TA). A putative cluster of genes for biosynthesis of a cyclic bacteriocin precursor, here designated as pentocin KCA1 (penA) were identified. These findings add crucial information for understanding the genomic and geographic diversity of vaginal lactobacilli.
Publication types
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Comparative Study
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Research Support, Non-U.S. Gov't
MeSH terms
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Amino Acids / biosynthesis
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Bacteriocins / genetics
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Base Composition
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Base Sequence
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Female
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Gene Expression Regulation, Bacterial / genetics*
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Gene Transfer, Horizontal / genetics
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Genome, Bacterial / genetics*
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Humans
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Lactobacillus plantarum / genetics*
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Membrane Proteins / genetics
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Molecular Sequence Data
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Multigene Family / genetics
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Nigeria
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Phylogeny*
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RNA, Ribosomal, 16S / genetics
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Sequence Alignment
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Sequence Analysis, DNA
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Species Specificity
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Vagina / microbiology*
Substances
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Amino Acids
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Bacteriocins
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Membrane Proteins
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RNA, Ribosomal, 16S
Associated data
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GENBANK/AKAO01000001
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Grants and funding
This work was partly funded by the Academy of Sciences for the Developing World (TWAS) based in ITALY, under the RESEARCH GRANT AGREEMENT (RGA) No.09-017RG/BIO/AF/AC_G-UNESCOFR:3240230312, awarded to Dr. Kingsley C. Anukam of the Department of Medical Laboratory Science, School of Basic Medical Sciences, University of Benin, Nigeira. The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.