Abstract
BackgroundLactobacillus 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.ResultsTo 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.ConclusionsThis 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2216-7) contains supplementary material, which is available to authorized users.
Highlights
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
Together with previous phylogenetic analyses based on a small set of housekeeping genes, the genomic analysis highlights two divergent clades within L. reuteri pig strains that can be differentiated from other L. reuteri lineages
No genes were identified that were conserved among all pig isolates and specific to this host, we identified genes specific for and conserved among strains from the two pig phylogenetic lineages IV and V, with high rates of homology among strains
Summary
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. The gastrointestinal (GI) tract of vertebrates is colonised by a complex microbial community dominated by bacteria referred to as the gut microbiota. By having a profound influence on vertebrate physiology, metabolism, and immune functions, the gut microbiota plays important roles in the health of the host [1, 2]. These associations open avenues for the development of therapies that aim to restore the ecosystem, but their implementation requires a mechanistic understanding about the ecological principles that shape and regulate microbial communities [3, 4]. A more transient colonisation of the human GI tract by L. reuteri is likely to be mediated by mucus-binding adhesins (as discussed below), resulting in a relatively low prevalence in the human population even this species is still considered to be autochthonous in humans [5, 6]
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
