The pan-genome of Lactobacillus reuteri strains originating from the pig gastrointestinal tract

Wegmann, Udo, Mackenzie, Donald A., Zheng, Jinshui, Goesmann, Alexander, Roos, Stefan, Swarbreck, David, Walter, Jens, Crossman, Lisa C. and Juge, Nathalie (2015) The pan-genome of Lactobacillus reuteri strains originating from the pig gastrointestinal tract. BMC Genomics, 16. ISSN 1471-2164

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Abstract

Background Lactobacillus reuteri is a gut symbiont of a wide variety of vertebrate species that has diversified into distinct phylogenetic clades which are to a large degree host-specific. Previous work demonstrated host specificity in mice and begun to determine the mechanisms by which gut colonisation and host restriction is achieved. However, how L. reuteri strains colonise the gastrointestinal (GI) tract of pigs is unknown. Results To gain insight into the ecology of L. reuteri in the pig gut, the genome sequence of the porcine small intestinal isolate L. reuteri ATCC 53608 was completed and consisted of a chromosome of 1.94 Mbp and two plasmids of 138.5 kbp and 9.09 kbp, respectively. Furthermore, we generated draft genomes of four additional L. reuteri strains isolated from pig faeces or lower GI tract, lp167-67, pg-3b, 20-2 and 3c6, and subjected all five genomes to a comparative genomic analysis together with the previously completed genome of strain I5007. A phylogenetic analysis based on whole genomes showed that porcine L. reuteri strains fall into two distinct clades, as previously suggested by multi-locus sequence analysis. These six pig L. reuteri genomes contained a core set of 1364 orthologous gene clusters, as determined by OrthoMCL analysis, that contributed to a pan-genome totalling 3373 gene clusters. Genome comparisons of the six pig L. reuteri strains with 14 L. reuteri strains from other host origins gave a total pan-genome of 5225 gene clusters that included a core genome of 851 gene clusters but revealed that there were no pig-specific genes per se. However, genes specific for and conserved among strains of the two pig phylogenetic lineages were detected, some of which encoded cell surface proteins that could contribute to the diversification of the two lineages and their observed host specificity. Conclusions This study extends the phylogenetic analysis of L. reuteri strains at a genome-wide level, pointing to distinct evolutionary trajectories of porcine L. reuteri lineages, and providing new insights into the genomic events in L. reuteri that occurred during specialisation to their hosts. The occurrence of two distinct pig-derived clades may reflect differences in host genotype, environmental factors such as dietary components or to evolution from ancestral strains of human and rodent origin following contact with pig populations.

Item Type:	Article
Additional Information:	© 2015 Wegmann et al. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.
Uncontrolled Keywords:	lactobacillus reuteri,pig ,host-specificity ,comparative genomics ,clade-specific genes ,surface adhesins ,serine-rich repeat proteins ,auxiliary secretion system
Faculty \ School:	Faculty of Science > School of Biological Sciences
Depositing User:	Pure Connector
Date Deposited:	19 Dec 2015 07:24
Last Modified:	22 Oct 2022 00:32
URI:	https://ueaeprints.uea.ac.uk/id/eprint/55823
DOI:	10.1186/s12864-015-2216-7

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