publication . Article . Other literature type . 2017

Phylogenomics and comparative genomics of Lactobacillus salivarius, a mammalian gut commensal

Hugh M.B. Harris; Maxence J. B. Bourin; Marcus J. Claesson; Paul W. O'Toole;
Open Access English
  • Published: 13 Jun 2017 Journal: Microbial Genomics, volume 3, issue 8 (eissn: 2057-5858, Copyright policy)
  • Publisher: Microbiology Society
  • Country: Finland
Abstract
The genus Lactobacillus is a diverse group with a combined species count of over 200. They are the largest group within the lactic acid bacteria and one of the most important bacterial groups involved in food microbiology and human nutrition because of their fermentative and probiotic properties. Lactobacillus salivarius, a species commonly isolated from the gastrointestinal tract of humans and animals, has been described as having potential probiotic properties and results of previous studies have revealed considerable functional diversity existing on both the chromosomes and plasmids. Our study consists of comparative genomic analyses of the functional and phy...
Subjects
free text keywords: Research Article, Systems Microbiology, Pangenome Analysis, Big-data Approaches, comparative genomics, Lactobacillus salivarius, bioinformatics, Plasmid, Genome, Bacteriocin, Biology, Replicon, Genetics, Phylogenomics, biology.organism_classification, Chromosome
57 references, page 1 of 4

Sun, Z, Harris, HM, Mccann, A, Guo, C, Argimón, S. Expanding the biotechnology potential of lactobacilli through comparative genomics of 213 strains and associated genera. Nat Commun. 2015; 6: 8322 [OpenAIRE] [PubMed] [DOI]

Salvetti, E, Torriani, S, Felis, GE. The genus Lactobacillus: a taxonomic update. Probiotics Antimicrob Proteins. 2012; 4: 217-226 [OpenAIRE] [PubMed] [DOI]

Slover, CM, Danziger, L. Lactobacillus: a review. Clinical Microbiology Newsletter. 2008; 30: 23-27 [OpenAIRE] [DOI]

Claesson, MJ, van Sinderen, D, O'Toole, PW. Lactobacillus phylogenomics – towards a reclassification of the genus. Int J Syst Evol Microbiol. 2008; 58: 2945-2954 [OpenAIRE] [PubMed] [DOI]

Zheng, J, Ruan, L, Sun, M, Gänzle, M. A genomic view of lactobacilli and pediococci demonstrates that phylogeny matches ecology and physiology. Appl Environ Microbiol. 2015; 81: 7233-7243 [OpenAIRE] [PubMed] [DOI]

Canchaya, C, Claesson, MJ, Fitzgerald, GF, van Sinderen, D, O'Toole, PW. Diversity of the genus Lactobacillus revealed by comparative genomics of five species. Microbiology. 2006; 152: 3185-3196 [OpenAIRE] [PubMed] [DOI]

Kant, R, Blom, J, Palva, A, Siezen, RJ, de Vos, WM. Comparative genomics of Lactobacillus. Microb Biotechnol. 2011; 4: 323-332 [OpenAIRE] [PubMed] [DOI]

Forde, BM, Neville, BA, O'Donnell, MM, Riboulet-Bisson, E, Claesson, MJ. Genome sequences and comparative genomics of two Lactobacillus ruminis strains from the bovine and human intestinal tracts. Microb Cell Fact. 2011; 10: S13 [OpenAIRE] [PubMed] [DOI]

Broadbent, JR, Neeno-Eckwall, EC, Stahl, B, Tandee, K, Cai, H. Analysis of the Lactobacillus casei supragenome and its influence in species evolution and lifestyle adaptation. BMC Genomics. 2012; 13: 533 [OpenAIRE] [PubMed] [DOI]

Cremonesi, P, Chessa, S, Castiglioni, B. Genome sequence and analysis of Lactobacillus helveticus. Front Microbiol. 2012; 3: 435 [OpenAIRE] [PubMed] [DOI]

Douillard, FP, Ribbera, A, Kant, R, Pietilä, TE, Järvinen, HM. Comparative genomic and functional analysis of 100 Lactobacillus rhamnosus strains and their comparison with strain GG. PLoS Genet. 2013; 9 [OpenAIRE] [PubMed] [DOI]

Smokvina, T, Wels, M, Polka, J, Chervaux, C, Brisse, S. Lactobacillus paracasei comparative genomics: towards species pan-genome definition and exploitation of diversity. PLoS One. 2013; 8 [OpenAIRE] [PubMed] [DOI]

Ojala, T, Kankainen, M, Castro, J, Cerca, N, Edelman, S. Comparative genomics of Lactobacillus crispatus suggests novel mechanisms for the competitive exclusion of Gardnerella vaginalis. BMC Genomics. 2014; 15 [OpenAIRE] [PubMed] [DOI]

Senan, S, Prajapati, JB, Joshi, CG. Comparative genome-scale analysis of niche-based stress-responsive genes in Lactobacillus helveticus strains. Genome. 2014; 57: 185-192 [OpenAIRE] [PubMed] [DOI]

O' Donnell, MM, Harris, HM, Lynch, DB, Ross, RP, O'Toole, PW. Lactobacillus ruminis strains cluster according to their mammalian gut source. BMC Microbiol. 2015; 15: 80 [OpenAIRE] [PubMed] [DOI]

57 references, page 1 of 4
Abstract
The genus Lactobacillus is a diverse group with a combined species count of over 200. They are the largest group within the lactic acid bacteria and one of the most important bacterial groups involved in food microbiology and human nutrition because of their fermentative and probiotic properties. Lactobacillus salivarius, a species commonly isolated from the gastrointestinal tract of humans and animals, has been described as having potential probiotic properties and results of previous studies have revealed considerable functional diversity existing on both the chromosomes and plasmids. Our study consists of comparative genomic analyses of the functional and phy...
Subjects
free text keywords: Research Article, Systems Microbiology, Pangenome Analysis, Big-data Approaches, comparative genomics, Lactobacillus salivarius, bioinformatics, Plasmid, Genome, Bacteriocin, Biology, Replicon, Genetics, Phylogenomics, biology.organism_classification, Chromosome
57 references, page 1 of 4

Sun, Z, Harris, HM, Mccann, A, Guo, C, Argimón, S. Expanding the biotechnology potential of lactobacilli through comparative genomics of 213 strains and associated genera. Nat Commun. 2015; 6: 8322 [OpenAIRE] [PubMed] [DOI]

Salvetti, E, Torriani, S, Felis, GE. The genus Lactobacillus: a taxonomic update. Probiotics Antimicrob Proteins. 2012; 4: 217-226 [OpenAIRE] [PubMed] [DOI]

Slover, CM, Danziger, L. Lactobacillus: a review. Clinical Microbiology Newsletter. 2008; 30: 23-27 [OpenAIRE] [DOI]

Claesson, MJ, van Sinderen, D, O'Toole, PW. Lactobacillus phylogenomics – towards a reclassification of the genus. Int J Syst Evol Microbiol. 2008; 58: 2945-2954 [OpenAIRE] [PubMed] [DOI]

Zheng, J, Ruan, L, Sun, M, Gänzle, M. A genomic view of lactobacilli and pediococci demonstrates that phylogeny matches ecology and physiology. Appl Environ Microbiol. 2015; 81: 7233-7243 [OpenAIRE] [PubMed] [DOI]

Canchaya, C, Claesson, MJ, Fitzgerald, GF, van Sinderen, D, O'Toole, PW. Diversity of the genus Lactobacillus revealed by comparative genomics of five species. Microbiology. 2006; 152: 3185-3196 [OpenAIRE] [PubMed] [DOI]

Kant, R, Blom, J, Palva, A, Siezen, RJ, de Vos, WM. Comparative genomics of Lactobacillus. Microb Biotechnol. 2011; 4: 323-332 [OpenAIRE] [PubMed] [DOI]

Forde, BM, Neville, BA, O'Donnell, MM, Riboulet-Bisson, E, Claesson, MJ. Genome sequences and comparative genomics of two Lactobacillus ruminis strains from the bovine and human intestinal tracts. Microb Cell Fact. 2011; 10: S13 [OpenAIRE] [PubMed] [DOI]

Broadbent, JR, Neeno-Eckwall, EC, Stahl, B, Tandee, K, Cai, H. Analysis of the Lactobacillus casei supragenome and its influence in species evolution and lifestyle adaptation. BMC Genomics. 2012; 13: 533 [OpenAIRE] [PubMed] [DOI]

Cremonesi, P, Chessa, S, Castiglioni, B. Genome sequence and analysis of Lactobacillus helveticus. Front Microbiol. 2012; 3: 435 [OpenAIRE] [PubMed] [DOI]

Douillard, FP, Ribbera, A, Kant, R, Pietilä, TE, Järvinen, HM. Comparative genomic and functional analysis of 100 Lactobacillus rhamnosus strains and their comparison with strain GG. PLoS Genet. 2013; 9 [OpenAIRE] [PubMed] [DOI]

Smokvina, T, Wels, M, Polka, J, Chervaux, C, Brisse, S. Lactobacillus paracasei comparative genomics: towards species pan-genome definition and exploitation of diversity. PLoS One. 2013; 8 [OpenAIRE] [PubMed] [DOI]

Ojala, T, Kankainen, M, Castro, J, Cerca, N, Edelman, S. Comparative genomics of Lactobacillus crispatus suggests novel mechanisms for the competitive exclusion of Gardnerella vaginalis. BMC Genomics. 2014; 15 [OpenAIRE] [PubMed] [DOI]

Senan, S, Prajapati, JB, Joshi, CG. Comparative genome-scale analysis of niche-based stress-responsive genes in Lactobacillus helveticus strains. Genome. 2014; 57: 185-192 [OpenAIRE] [PubMed] [DOI]

O' Donnell, MM, Harris, HM, Lynch, DB, Ross, RP, O'Toole, PW. Lactobacillus ruminis strains cluster according to their mammalian gut source. BMC Microbiol. 2015; 15: 80 [OpenAIRE] [PubMed] [DOI]

57 references, page 1 of 4
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