2017 ; 27(8):
|Author||Jihyun Yu, Sojin Ahn, Kwondo Kim, Kelsey Caetano-Anolles, Chanho Lee, Jungsun Kang, Kyungjin Cho, Sook Hee Yoon, Dae-Kyung Kang, Heebal Kim|
|Affiliation||Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 08826, Republic of Korea|
|Title||Comparative Genomic Analysis of Lactobacillus plantarum GB-LP1 Isolated from Traditional Korean Fermented Food|
J. Microbiol. Biotechnol.2017 ; 27(8):
|Abstract||As probiotics play an important role in maintaining a healthy gut flora environment through
antitoxin activity and inhibition of pathogen colonization, they have been of interest to the
medical research community for quite some time now. Probiotic bacteria such as Lactobacillus
plantarum, which can be found in fermented food, are of particular interest given their easy
accessibility. We performed whole-genome sequencing and genomic analysis on a GB-LP1
strain of L. plantarum isolated from Korean traditional fermented food; this strain is well
known for its functions in immune response, suppression of pathogen growth, and antitoxin
effects. The complete genome sequence of GB-LP1 is a single chromosome of 3,040,388 bp with
2,899 predicted open reading frames. Genomic analysis of GB-LP1 revealed two CRISPR
regions and genes showing accelerated evolution, which may have antibiotic and antitoxin
functions. The aim of the present study was to predict strain specific-genomic characteristics
and assess the potential of this new strain as lactic acid bacteria at the genomic level using in
silico analysis. These results provide insight into the L. plantarum species as well as confirm
the possibility of its utility as a candidate probiotic.|
|Keywords||Lactobacillus plantarum GB-LP1, comparative genomics, probiotic, de novo assembly, antibiotic, glyoxylate reductase/hydroxypyruvate reductase|
Bäumler AJ, Sperandio V. 2016. Interactions between the microbiota and pathogenic bacteria in the gut. Nature 535:85-93.
Kostic AD, Xavier RJ, Gevers D. 2014. The microbiome in inflammatory bowel disease: current status and the future ahead. Gastroenterology 146: 1489-1499.
Virgin HW. 2014. The virome in mammalian physiology and disease. Cell 157: 142-150.
Goodrich JK, Waters JL, Poole AC, Sutter JL, Koren O, Blekhman R, et al. 2014. Human genetics shape the gut microbiome. Cell 159: 789-799.
Macfarlane S, Steed H, Macfarlane GT. 2009. Intestinal bacteria and inflammatory bowel disease. Crit. Rev. Clin. Lab. Sci. 46: 25-54.
Paolillo R, Carratelli CR, Sorrentino S, Mazzola N, Rizzo A. 2009. Immunomodulatory effects of Lactobacillus plantarum on human colon cancer cells. Int. Immunopharmacol. 9: 1265-1271.
Parvez S, Malik KA, Ah Kang S, Kim HY. 2006. Probiotics and their fermented food products are beneficial for health. J. Appl. Microbiol. 100: 1171-1185.
Shah N, Patel A, Ambalam P, Holst O, Ljungh A, Prajapati J. 2016. Determination of an antimicrobial activity of Weissella confusa, Lactobacillus fermentum, and Lactobacillus plantarum against clinical pathogenic strains of Escherichia coli and Staphylococcus aureus in co-culture. Ann. Microbiol. 66: 1137-1143.
Nomoto K. 2005. Prevention of infections by probiotics. J. Biosci. Bioeng. 100: 583-592.
Stewart PS, William Costerton J. 2001. Antibiotic resistance of bacteria in biofilms. Lancet 358: 135-138.
Eaton TJ, Gasson MJ. 2001. Molecular screening of Enterococcus virulence determinants and potential for genetic exchange between food and medical isolates. Appl. Environ. Microbiol. 67: 1628-1635.
Mah T-F, Pitts B, Pellock B, Walker GC, Stewart PS, O’Toole GA. 2003. A genetic basis for Pseudomonas aeruginosa biofilm antibiotic resistance. Nature 426: 306-310.
Morelli L. 2007. In vitro assessment of probiotic bacteria:from survival to functionality. Int. Dairy J. 17: 1278-1283.
Feil H, Feil WS, Chain P, Larimer F, DiBartolo G, Copeland A, et al. 2005. Comparison of the complete genome sequences of Pseudomonas syringae pv. syringae B728a and pv. tomato DC3000. Proc. Natl. Acad. Sci. USA 102: 11064-11069.
Singh G, Sharma D, Singh V, Rani J, Marotta F, Kumar M, et al. 2017. In silico functional elucidation of uncharacterized proteins of Chlamydia abortus strain LLG. Future Sci. OA 3: FSO169.
Siezen RJ, van Enckevort FH, Kleerebezem M, Teusink B. 2004. Genome data mining of lactic acid bacteria: the impact of bioinformatics. Curr. Opin. Biotechnol. 15: 105-115.
Liu W-H, Yang C-H, Lin C-T, Li S-W, Cheng W-S, Jiang Y-P, et al. 2015. Genome architecture of Lactobacillus plantarum PS128, a probiotic strain with potential immunomodulatory activity. Gut Pathog. 7: 22.
Chin C-S, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, et al. 2013. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat. Methods 10: 563-569.
Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, et al. 2008. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9: 75.
Bose T, Haque MM, Reddy C, Mande SS. 2015. COGNIZER:a framework for functional annotation of metagenomic datasets. PLoS One 10: e0142102.
Carver T, Thomson N, Bleasby A, Berriman M, Parkhill J. 2009. DNAPlotter: circular and linear interactive genome visualization. Bioinformatics 25: 119-120.
Richter M, Rossello-Mora R. 2009. Shifting the genomic gold standard for the prokaryotic species definition. Proc. Natl. Acad. Sci. USA 106: 19126-19131.
Kim KM, Sung S, Caetano-Anollés G, Han JY, Kim H. 2008. An approach of orthology detection from homologous sequences under minimum evolution. Nucleic Acids Res. 36: e110.
Löytynoja A , Goldman N. 2 008. P hylog eny-aware g ap placement prevents errors in sequence alignment and evolutionary analysis. Science 320: 1632-1635.
Talavera G, Castresana J. 2007. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst. Biol. 56: 564-577.
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. 2013. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol. Biol. Evol. 30: 2725-2729.
Carver TJ, Rutherford KM, Berriman M, Rajandream M-A, Barrell BG, Parkhill J. 2005. ACT: the Artemis comparison tool. Bioinformatics 21: 3422-3423.
Yang Z. 2007. PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24: 1586-1591.
Grissa I, Vergnaud G, Pourcel C. 2007. CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res. 35: W52-W57.
Wolf YI, Makarova KS, Yutin N, Koonin EV. 2012. Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer. Biol. Direct 7: 46.
Zhang Z-Y, Liu C, Zhu Y-Z, Wei Y-X, Tian F, Zhao G-P, et al. 2012. Safety assessment of Lactobacillus plantarum JDM1 based on the complete genome. Int. J. Food Microbiol. 153:166-170.
Hacker J, Carniel E. 2001. Ecological fitness, genomic islands and bacterial pathogenicity. EMBO Rep. 2: 376-381.
Roberts AP, Kreth J. 2014. The impact of horizontal gene transfer on the adaptive ability of the human oral microbiome.
Wiedenbeck J, Cohan FM. 2011. Origins of bacterial diversity through horizontal genetic transfer and adaptation to new ecological niches. FEMS Microbiol. Rev. 35: 957-976.
Allali N, Afif H, Couturier M, Van Melderen L. 2002. The highly conserved TldD and TldE proteins of Escherichia coli are involved in microcin B17 processing and in CcdA degradation. J. Bacteriol. 184: 3224-3231.
Yang S-C, Lin C-H, Sung CT, Fang J-Y. 2014. Antibacterial activities of bacteriocins: application in foods and pharmaceuticals. Front. Microbiol. 5: 241.
Claud EC, K eeg an KP, B rulc JM, L u L, B artels D , Glass E, et al. 2013. Bacterial community structure and functional contributions to emergence of health or necrotizing enterocolitis in preterm infants. Microbiome 1: 20.
Glenn K, Smith KS. 2015. Allosteric regulation of Lactobacillus plantarum xylulose 5-phosphate/fructose 6-phosphate phosphoketolase (Xfp). J. Bacteriol. 197: 1157-1163.
Pan Y, Ni R, Deng Q, Huang X, Zhang Y, Lu C, et al. 2013. Glyoxylate reductase/hydroxypyruvate reductase: a novel prognostic marker for hepatocellular carcinoma patients after curative resection. Pathobiology 80: 155-162.
Duan X, Hu S, Zhou P, Zhou Y, Liu Y, Jiang Z. 2014. Characterization and crystal structure of a first fungal glyoxylate reductase from Paecilomyes thermophila. Enzyme Microb. Technol. 60: 72-79.
Knight J, Wood KD, Lange JN, Assimos DG, Holmes RP. 2016. Oxalate formation from glyoxal in erythrocytes. Urology 88: 226.e11-226.e15.
Abratt VR, Reid SJ. 2010. Oxalate-degrading bacteria of the human gut as probiotics in the management of kidney stone disease. Adv. Appl. Microbiol. 72: 63-87.
Lahm A, Paolini C, Pallaoro M, Nardi M, Jones P, Neddermann P, et al. 2 007. Unraveling the h idden catalytic activity of vertebrate class IIa histone deacetylases. Proc. Natl. Acad. Sci. USA 104: 17335-17340.
Tanaka Y, Kasahara K, Hirose Y, Murakami K, Kugimiya R, Ochi K. 2013. Activation and products of the cryptic secondary metabolite biosynthetic gene clusters by rifampin resistance (rpoB) mutations in actinomycetes. J. Bacteriol. 195: 2959-2970.