Genome Sequence of Lactobacillus pentosus KCA1: Vaginal Isolate from a Healthy Premenopausal Woman
Genome Sequence of Lactobacillus pentosus KCA1: Vaginal Isolate from a Healthy Premenopausal Woman
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DOI：
10.1371/journal.pone.0059239
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发表时间：
2013-03-19
期刊：
影响因子：
3.7
通讯作者：
Siezen, Roland J.
中科院分区：
文献类型：
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作者：
Anukam, Kingsley C.;Macklaim, Jean M.;Siezen, Roland J.
阴道微生物群，特别是乳酸菌，通过调节免疫力、对抗病原体和维持 pH 值低于 4.7，在女性健康中发挥着重要作用。我们报告了从一名健康尼日利亚女性阴道中分离得到的戊糖乳杆菌 KCA1 菌株（正式名称为植物乳杆菌）并进行了基因组序列分析。使用 Illumina GA II 技术对基因组进行测序。使用 Velvet 工具组装所得的 16,920,226 个双端读数。使用 RAST 服务器对重叠群进行注释，并手动进行管理。与戊糖乳杆菌 IG1 和植物乳杆菌 WCFS1 的可用基因组的比较分析表明，超过 15% 的预测功能活性仅在该菌株中发现。该菌株染色体序列为3,418,159 bp，G+C含量为46.4%，不含质粒。发现了相对于参考基因组的新基因簇或已知基因的变体。特别地，该菌株具有编码额外的推定甘露糖磷酸转移酶系统的基因座。基因簇包括利用乙内酰脲、苹果酸异丙酯、丙二酸、鼠李糖苷的基因以及用于同化多聚糖的基因，表明戊糖乳杆菌 KCA1 的代谢多功能性。还发现了编码假定噬菌体防御系统的基因座，包括成簇的规则间隔短回文重复序列 (CRISPR)、流产感染 (Abi) 系统和毒素-抗毒素系统 (TA)。鉴定了用于生物合成环状细菌素前体的推定基因簇，此处指定为喷尿素 KCA1 (penA)。这些发现为了解阴道乳酸杆菌的基因组和地理多样性提供了重要信息。
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.