PROKARYOTES
crossm Complete Genome Sequence of the Plasmid-Bearing Lactobacillus fermentum Strain SNUV175, a Probiotic for Women’s Health Isolated from the Vagina of a Healthy South Korean Woman Sunghee Lee,a,b Hyun Ju You,c,d,e Bomi Kwon,c GwangPyo Koa,b,c,e Center for Microbiome Therapeutics, KoBioLabs, Inc., Seoul, Republic of Koreaa; N-Bio, Seoul National University, Seoul, Republic of Koreab; Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, Republic of Koreac; Institute of Health and Environment, Seoul National University, Seoul, Republic of Koread; Center for Human and Environmental Microbiome, Seoul National University, Seoul, Republic of Koreae
ABSTRACT Lactobacillus fermentum SNUV175 has been identified as a probiotic
strain that inhibits pathogenic microorganisms related to women’s health. We present the complete genomic sequence of the strain L. fermentum SNUV175 isolated from the vagina of a South Korean woman. This genomic information may provide insight into the functional activity of this strain.
T
he composition of the vaginal microbiota is influenced by host genetics and plays a key role in host defense against bacterial vaginosis and pathogenic viral infections, such as human papillomavirus (HPV) and human immunodeficiency virus (HIV) (1–3). Among the microorganisms present in the vagina, Lactobacillus spp. help maintain an acidic environment and produce bacteriocins that inhibit potentially pathogenic microorganisms (4). In this study, the strain Lactobacillus fermentum SNUV175, isolated from the vagina of a healthy South Korean woman, showed functional properties in the treatment of vaginal infection caused by lactobacilli deficiency. Here, we present the complete genome sequence of this functional probiotic strain. In order to perform the complete genome sequencing of the strain L. fermentum SNUV175, massive sequencing technology was implemented using the PacBio platform (Pacific Biosciences, Menlo Park, CA, USA). A 20-kb library was constructed with purified DNA on a single-molecule real-time (SMRT) cell and was sequenced using P6-C4 chemistry with a data collection time of 4 h. The sequencing run provided a total of 125,532 reads with quality scores ⱖQ20. The number of bases was 805,055,752 bp. De novo assembly employed the default parameters of the Hierarchical Genome Assembly Process approach version 3 (HGAP3) (5). The single circular chromosome was 2,176,678 bp in size, with an estimated G⫹C content of 51.5% and around 276⫻ coverage. The three plasmids ranged between 29 and 33 kb in size: pSNU175-2 (33,413 bp; G⫹C content, 40.0%), pSNU175-3 (33,071 bp; G⫹C content, 39.6%), and pSNU175-3 (29,166 bp; G⫹C content, 43.8%). The assembled genome sequences were annotated using the Prokka annotation pipeline, version 1.11 (6), which predicted tRNA, rRNA, and mRNA genes. Putative gene products were then assigned to protein-coding genes (CDSs) based on their similarity to sequences in the respective database. Curated virulence factors and antibiotic resistance genes were estimated using IslandViewer3 (7) against the Virulence Factor Database (VFDB) (8) and the Comprehensive Antibiotic Resistance Database (CARD) (9). Volume 5 Issue 12 e00045-17
Received 24 January 2017 Accepted 25 January 2017 Published 23 March 2017 Citation Lee S, You HJ, Kwon B, Ko G. 2017. Complete genome sequence of the plasmidbearing Lactobacillus fermentum strain SNUV175, a probiotic for women’s health isolated from the vagina of a healthy South Korean woman. Genome Announc 5:e00045-17. https://doi.org/ 10.1128/genomeA.00045-17. Copyright © 2017 Lee et al. This is an openaccess article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to GwangPyo Ko,
[email protected].
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Lee et al.
The genome contains 2,272 CDSs, 59 tRNAs, and 15 rRNAs. The L. fermentum SNUV175 genome was compared with reference strain L. fermentum IFO3956 (GenBank accession no. AP008937.1) using the Rapid Annotations using Subsystems Technology (RAST) server (10). Through this comparison we detected 116 elements not present in the published strain L. fermentum IFO3956. No remarkable antibiotic resistance or virulence-associated genes were found. The analysis of the complete genome of L. fermentum SNUV175 may lead to deeper understanding of the mechanisms involved in its effect against bacterial vaginosis. Accession number(s). The results of this whole-genome project have been deposited at GenBank under the accession numbers CP019030 to CP019033. ACKNOWLEDGMENTS This project was supported by the National Research Foundation of Korea (NRF) (NRF-2015R1A2A1A10054078) and by the Korea Institute of Planning and Evaluation for Technology in Food, Agriculture, Forestry and Fisheries (IPET) through the High-ValueAdded Food Technology Development Program, funded by the Ministry of Agriculture, Food and Rural Affairs (MAFRA) (0534-20150013).
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6. Seemann T. 2014. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30:2068 –2069. https://doi.org/10.1093/bioinformatics/btu153. 7. Dhillon BK, Laird MR, Shay JA, Winsor GL, Lo R, Nizam F, Pereira SK, Waglechner N, McArthur AG, Langille MG, Brinkman FS. 2015. IslandViewer 3: more flexible, interactive genomic island discovery, visualization and analysis. Nucleic Acids Res 43:W104 –108. https://doi.org/ 10.1093/nar/gkv401. 8. Chen L, Xiong Z, Sun L, Yang J, Jin Q. 2012. VFDB 2012 update: toward the genetic diversity and molecular evolution of bacterial virulence factors. Nucleic Acids Res 40:D641– 645. https://doi.org/https://doi.org/ 10.1093/nar/gkr989. 9. McArthur AG, Waglechner N, Nizam F, Yan A, Azad MA, Baylay AJ, Bhullar K, Canova MJ, De Pascale G, Ejim L, Kalan L, King AM, Koteva K, Morar M, Mulvey MR, O’Brien JS, Pawlowski AC, Piddock LJ, Spanogiannopoulos P, Sutherland AD, Tang I, Taylor PL, Thaker M, Wang W, Yan M, Yu T, Wright GD. 2013. The Comprehensive Antibiotic Resistance Database. Antimicrob Agents Chemother 57:3348–3357. https://doi.org/10.1128/AAC.00419-13. 10. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. 2008. The RAST server: rapid annotations using subsystems technology. BMC Genomics 9:75. https://doi.org/10.1186/1471-2164-9-75.
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