JOURNAL OF BACTERIOLOGY, Sept. 2011, p. 5034 0021-9193/11/$12.00 doi:10.1128/JB.05601-11 Copyright © 2011, American Society for Microbiology. All Rights Reserved.
Vol. 193, No. 18
Genome Sequence of Lactobacillus ruminis SPM0211, Isolated from a Fecal Sample from a Healthy Korean䌤 Sunghee Lee,1 Yong-Joon Cho,2 Anne Hayoung Lee,1 Jongsik Chun,2 Nam-Joo Ha,3 and GwangPyo Ko1* Department of Environmental Health and Institute of Health and Environment, Graduate School of Public Health,1 and School of Biological Sciences and Chunlab, Inc.,2 Seoul National University, 151-742 Seoul, South Korea, and Department of Pharmacy, Sahmyook University, 139-742 Seoul, South Korea3 Received 17 June 2011/Accepted 29 June 2011
Lactobacillus ruminis SPM0211 is a potential probiotic strain that shows antimicrobial activity against emerging pathogens. Here we present the draft genomic sequence of L. ruminis SPM0211, isolated from a fecal sample from a healthy Korean and describe both the common and unique features of this strain. related L. ruminis strains was done as described previously (2). Similar to L. ruminis strain ATCC 25644 (NCBI genome project accession number PRJNA31499), SPM0211 possesses genes for phosphotransferase system family lactose/cellobiose porter component IIA, a DNA/RNA helicase, an anaerobic ribonucleosidetriphosphate reductase-activating protein, and a cell wall surface protein. However, we also found SPM0211-specific genes, including those encoding an ABC multidrug transporter ATPase, a phage antirepressor, a phage (prophage) protein, a 6-phosphobeta-galactosidase, and a urease. In summary, we report here the genomic sequence of L. ruminis SPM0211. Further analysis of these data will provide valuable information on this potential probiotic strain that can inhibit pathogenic drug-resistant microorganisms and provide effects beneficial to the host. Nucleotide sequence accession numbers. The 12 contig sequences of L. ruminis SPM0211 have been deposited in GenBank under accession numbers AFOJ01000001 to AFOJ01000012.
Lactobacillus, one of five genera of lactic acid bacteria, is a genus of Gram-positive facultative anaerobic or microaerophilic bacteria that are widely used for dairy production and fermentation (e.g., yogurt, cheese, and kimchi) (3). This microbe plays important roles in human health via several mechanisms, including strengthening of the intestinal barrier, modulation of the immune response, and antagonism to pathogens, through either the production of antimicrobial compounds or competition for mucosal binding sites (4, 6, 7). Lactobacillus ruminis SPM0211 is a potential probiotic strain isolated from a fecal sample from a healthy Korean (8). Among its phenotypic characteristics is inhibition of the growth of antibioticresistant pathogens, including intermediately vancomycin-resistant Staphylococcus aureus and vancomycin-resistant enterococci. Here, we present the draft genomic sequence of L. ruminis SPM0211. This is the second report of an L. ruminis genomic sequence. The genomic sequence of SPM0211 was determined using the Roche/454 genome sequencer FLX Titanium system with pairedend libraries (432,803 reads, a total of 89.2 Mb) (5). To correct homopolymeric sequencing errors, additional sequence data (34,108,328 reads, a total of 3,342.8 Mb) with a 100-bp read length were generated using an Illumina IIx genome analyzer (1); a total of 1,581-fold sequence data coverage was achieved. De novo assembly was carried out using GS de novo Assembler 2.5 (Roche) and CLC Genomics Workbench 4.5.1 (CLC Bio), which resulted in 12 contigs. Gaps between the contigs were filled by sequencing of the PCR products using an ABI 3730 Capillary Sequencer (Applied Biosystems). The SPM0211 genome contains 2,172,227 bp and has an average G⫹C content of 43.74%. It contains six rRNA operons and codes for 58 tRNAs and 2,335 protein-coding sequences. A comparative genomic analysis of both the test and closely
This project was supported by grants from the National Research Foundation of the Korean Ministry of Education, Science, and Technology, Republic of Korea (2010-0029113). REFERENCES 1. Bentley, D. R., et al. 2008. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456:53–59. 2. Chun, J., et al. 2009. Comparative genomics reveals mechanism for short-term and long-term clonal transitions in pandemic Vibrio cholerae. Proc. Natl. Acad. Sci. U. S. A. 106:15442–15447. 3. Lee, S. H., N. Y. Park, and W. J. Choi. 1999. Changes of the lactic acid bacteria and selective inhibitory substances against homo and hetero lactic acid bacteria isolated from kimchi. Korean J. Appl. Microbiol. Biotechnol. 27:410–414. [In Korean.] 4. Marco, M. L., S. Pavan, and M. Kleerebezem. 2006. Towards understanding molecular modes of probiotic action. Curr. Opin. Biotechnol. 17:204–210. 5. Margulies, M., et al. 2005. Genome sequencing in microfabricated highdensity picolitre reactors. Nature 437:376–380. 6. Saxelin, M., S. Tynkkynen, T. Mattila-Sandholm, and W. M. de Vos. 2005. Probiotic and other functional microbes: from markets to mechanisms. Curr. Opin. Biotechnol. 16:204–211. 7. Ventura, M., et al. 2009. Genome-scale analyses of health-promoting bacteria: probiogenomics. Nat. Rev. Microbiol. 7:61–71. 8. Yun, J. H., et al. 2005. Identification of Lactobacillus ruminus SPM0211 isolated from healthy Koreans and its antimicrobial activity against some pathogens. Arch. Pharm. Res. 28:660–666.
* Corresponding author. Mailing address: Department of Environmental Health and Institute of Health and Environment, Graduate School of Public Health, Seoul National University, 599 Gwanak-ro, Gwanak-gu, Seoul, South Korea. Phone: 82.2.880.8479. Fax: 82.2.745.9104. E-mail:
[email protected]. 䌤 Published ahead of print on 8 July 2011.
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