Lactobacillus paracasei comparative genomics: towards species pan-genome definition and exploitation of diversity.

Lactobacillus paracasei is a member of the normal human and animal gut microbiota and is used extensively in the food industry in starter cultures for dairy products or as probiotics. With the development of low-cost, high-throughput sequencing techniques it has become feasible to sequence many diff...

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Autores principales:	Tamara Smokvina, Michiel Wels, Justyna Polka, Christian Chervaux, Sylvain Brisse, Jos Boekhorst, Johan E T van Hylckama Vlieg, Roland J Siezen
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/1726debd465341bf8c9814cc576eb417
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spelling	oai:doaj.org-article:1726debd465341bf8c9814cc576eb4172021-11-18T09:03:49ZLactobacillus paracasei comparative genomics: towards species pan-genome definition and exploitation of diversity.1932-620310.1371/journal.pone.0068731https://doaj.org/article/1726debd465341bf8c9814cc576eb4172013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23894338/?tool=EBIhttps://doaj.org/toc/1932-6203Lactobacillus paracasei is a member of the normal human and animal gut microbiota and is used extensively in the food industry in starter cultures for dairy products or as probiotics. With the development of low-cost, high-throughput sequencing techniques it has become feasible to sequence many different strains of one species and to determine its "pan-genome". We have sequenced the genomes of 34 different L. paracasei strains, and performed a comparative genomics analysis. We analysed genome synteny and content, focussing on the pan-genome, core genome and variable genome. Each genome was shown to contain around 2800-3100 protein-coding genes, and comparative analysis identified over 4200 ortholog groups that comprise the pan-genome of this species, of which about 1800 ortholog groups make up the conserved core. Several factors previously associated with host-microbe interactions such as pili, cell-envelope proteinase, hydrolases p40 and p75 or the capacity to produce short branched-chain fatty acids (bkd operon) are part of the L. paracasei core genome present in all analysed strains. The variome consists mainly of hypothetical proteins, phages, plasmids, transposon/conjugative elements, and known functions such as sugar metabolism, cell-surface proteins, transporters, CRISPR-associated proteins, and EPS biosynthesis proteins. An enormous variety and variability of sugar utilization gene cassettes were identified, with each strain harbouring between 25-53 cassettes, reflecting the high adaptability of L. paracasei to different niches. A phylogenomic tree was constructed based on total genome contents, and together with an analysis of horizontal gene transfer events we conclude that evolution of these L. paracasei strains is complex and not always related to niche adaptation. The results of this genome content comparison was used, together with high-throughput growth experiments on various carbohydrates, to perform gene-trait matching analysis, in order to link the distribution pattern of a specific phenotype to the presence/absence of specific sets of genes.Tamara SmokvinaMichiel WelsJustyna PolkaChristian ChervauxSylvain BrisseJos BoekhorstJohan E T van Hylckama VliegRoland J SiezenPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 7, p e68731 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Tamara Smokvina Michiel Wels Justyna Polka Christian Chervaux Sylvain Brisse Jos Boekhorst Johan E T van Hylckama Vlieg Roland J Siezen Lactobacillus paracasei comparative genomics: towards species pan-genome definition and exploitation of diversity.
description	Lactobacillus paracasei is a member of the normal human and animal gut microbiota and is used extensively in the food industry in starter cultures for dairy products or as probiotics. With the development of low-cost, high-throughput sequencing techniques it has become feasible to sequence many different strains of one species and to determine its "pan-genome". We have sequenced the genomes of 34 different L. paracasei strains, and performed a comparative genomics analysis. We analysed genome synteny and content, focussing on the pan-genome, core genome and variable genome. Each genome was shown to contain around 2800-3100 protein-coding genes, and comparative analysis identified over 4200 ortholog groups that comprise the pan-genome of this species, of which about 1800 ortholog groups make up the conserved core. Several factors previously associated with host-microbe interactions such as pili, cell-envelope proteinase, hydrolases p40 and p75 or the capacity to produce short branched-chain fatty acids (bkd operon) are part of the L. paracasei core genome present in all analysed strains. The variome consists mainly of hypothetical proteins, phages, plasmids, transposon/conjugative elements, and known functions such as sugar metabolism, cell-surface proteins, transporters, CRISPR-associated proteins, and EPS biosynthesis proteins. An enormous variety and variability of sugar utilization gene cassettes were identified, with each strain harbouring between 25-53 cassettes, reflecting the high adaptability of L. paracasei to different niches. A phylogenomic tree was constructed based on total genome contents, and together with an analysis of horizontal gene transfer events we conclude that evolution of these L. paracasei strains is complex and not always related to niche adaptation. The results of this genome content comparison was used, together with high-throughput growth experiments on various carbohydrates, to perform gene-trait matching analysis, in order to link the distribution pattern of a specific phenotype to the presence/absence of specific sets of genes.
format	article
author	Tamara Smokvina Michiel Wels Justyna Polka Christian Chervaux Sylvain Brisse Jos Boekhorst Johan E T van Hylckama Vlieg Roland J Siezen
author_facet	Tamara Smokvina Michiel Wels Justyna Polka Christian Chervaux Sylvain Brisse Jos Boekhorst Johan E T van Hylckama Vlieg Roland J Siezen
author_sort	Tamara Smokvina
title	Lactobacillus paracasei comparative genomics: towards species pan-genome definition and exploitation of diversity.
title_short	Lactobacillus paracasei comparative genomics: towards species pan-genome definition and exploitation of diversity.
title_full	Lactobacillus paracasei comparative genomics: towards species pan-genome definition and exploitation of diversity.
title_fullStr	Lactobacillus paracasei comparative genomics: towards species pan-genome definition and exploitation of diversity.
title_full_unstemmed	Lactobacillus paracasei comparative genomics: towards species pan-genome definition and exploitation of diversity.
title_sort	lactobacillus paracasei comparative genomics: towards species pan-genome definition and exploitation of diversity.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/1726debd465341bf8c9814cc576eb417
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Lactobacillus paracasei comparative genomics: towards species pan-genome definition and exploitation of diversity.

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