title: The pan-genome of Lactobacillus reuteri strains originating from the pig gastrointestinal tract.
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.
authors.affiliation: The Gut Health and Food Safety Programme, Institute of Food Research, Norwich Research Park, Norwich, NR4 7UA, UK. udo.wegmann@ifr.ac.uk.
authors.forename: Udo
authors.initials: U
authors.lastname: Wegmann
authors.affiliation: The Gut Health and Food Safety Programme, Institute of Food Research, Norwich Research Park, Norwich, NR4 7UA, UK. donald.mackenzie@ifr.ac.uk.
authors.forename: Donald A
authors.initials: DA
authors.lastname: MacKenzie
authors.affiliation: State Key Lab of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China. elon1133@qq.com.
authors.forename: Jinshui
authors.initials: J
authors.lastname: Zheng
authors.affiliation: Bioinformatics and Systems Biology, Justus-Liebig-Universität, Gießen, 35392, Germany. alexander.goesmann@computational.bio.uni-giessen.de.
authors.forename: Alexander
authors.initials: A
authors.lastname: Goesmann
authors.affiliation: Department of Microbiology, Swedish University of Agricultural Sciences, Uppsala, S-750 07, Sweden. stefan.roos@slu.se.
authors.forename: Stefan
authors.initials: S
authors.lastname: Roos
authors.affiliation: The Genome Analysis Centre, Norwich Research Park, Norwich, NR4 7UH, UK. david.swarbreck@tgac.ac.uk.
authors.forename: David
authors.initials: D
authors.lastname: Swarbreck
authors.affiliation: Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2R3, Canada. jwalter1@ualberta.ca.|Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E1, Canada. jwalter1@ualberta.ca.
authors.forename: Jens
authors.initials: J
authors.lastname: Walter
authors.affiliation: School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK. l.crossman@uea.ac.uk.|SequenceAnalysis.co.uk, NRP Innovation Centre, Norwich, NR4 7UG, UK. l.crossman@uea.ac.uk.
authors.forename: Lisa C
authors.initials: LC
authors.lastname: Crossman
authors.affiliation: The Gut Health and Food Safety Programme, Institute of Food Research, Norwich Research Park, Norwich, NR4 7UA, UK. nathalie.juge@ifr.ac.uk.
authors.forename: Nathalie
authors.initials: N
authors.lastname: Juge
mesh_terms: D000818:Animals; D001425:Bacterial Outer Membrane Proteins / Q000235:genetics; D058947:Bacterial Secretion Systems / Q000235:genetics; D001435:Bacteriophages; D001481:Basal Metabolism / Q000235:genetics; D002876:Chromosomes, Bacterial; D041981:Gastrointestinal Tract / Q000382:microbiology; D023061:Gene Order; D022761:Gene Transfer, Horizontal; D040342:Genetic Structures; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing; D054884:Host-Pathogen Interactions; D052200:Limosilactobacillus reuteri / Q000235:genetics* / Q000302:isolation & purification / Q000378:metabolism / Q000821:virology; D005810:Multigene Family; D010802:Phylogeny; D011544:Pseudogenes; D013552:Swine
chemical_list: D001425:Bacterial Outer Membrane Proteins; D058947:Bacterial Secretion Systems