Insights into the pan-genome of L. reuteri strains originating from pig

A paper from Nathalie Juge‘s Group at the Institute of Food Research (IFR) was published this week in the open-access Journal BMC Genomics.  The study described in this paper builds up from a successful collaboration between IFR, TGAC, University of Nebraska Lincoln (USA), and University of Alberta (Canada) on the ecological processes that mediate host-specificity of the vertebrate gut symbiont Lactobacillus reuteri1-3Nathalie Juge who led this work commented about the study: “Such knowledge is important to gain as L. reuteri is one of the most dominant species in the porcine GI tract and pig-derived strains of L. reuteri are used as probiotics to improve pig health and well-being.”

Nathalie Juge 2015

Dr Nathalie Juge

Below Nathalie blogs about the study which will provide a basis for future functional studies on the ecology of L. reuteri in the pig gastrointestinal tract:

L. reuteri colonises the gastrointestinal (GI) tract of a wide variety of vertebrate species and represents an excellent model to elucidate mechanisms of host-microbial symbiosis in vertebrates. We previously showed that that L. reuteri has diversified into distinct phylogenetic clades which are to a large degree host-specific1. Recently we demonstrated the mechanisms underlying host specificity of rodent L. reuteri strains in gnotobiotic mice3. However, how L. reuteri strains colonise the GI tract of pigs was so far unknown.

Genome conservation in the six pig strains of L. reuteri. From top to bottom, the Mauve-alignment backbone of the draft genome sequences is shown as follows: I5007, ATCC 53608, lp167-67, pg-3b, 20-2 and 3c6. Blocks of sequence conservation are denoted by burgundy lines, whilst blocks as calculated by Mauve are shown in alternating colours

Genome conservation in the six pig strains of L. reuteri. From top to bottom, the Mauve-alignment backbone of the draft genome sequences is shown as follows: I5007, ATCC 53608, lp167-67, pg-3b, 20-2 and 3c6. Blocks of sequence conservation are denoted by burgundy lines, whilst blocks as calculated by Mauve are shown in alternating colours.

In order to achieve this, we first completed the genome sequence of L. reuteri ATCC53608 (for which we previously obtained a draft genome1) which was then used as a reference genome in our comparative analyses with genomes from rodent and human L. reuteri isolates. 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 the porcine strain I5007.

Together with previous phylogenetic analyses based on a small set of housekeeping genes, this in-depth genomic analysis highlighted two divergent clades within L. reuteri pig strains that can be differentiated from other L. reuteri lineages.

We believe that several surface proteins, some with mucus-binding domains or other repeated domains found associated with adhesins3,4, as being pig clade-specific may contribute to the characteristic host-specificity of L. reuteri strains, and ultimately to the clustering of strains away from other L. reuteri lineages. Clearly, these genes provide a basis for future functional studies on the ecology of L. reuteri in the pig GI tract.

References:

Wegmann U, MacKenzie DA, Zheng J, Goesmann A, Roos S, Swarbreck D, Walter J, Crossman LC, Juge N. The pan-genome of Lactobacillus reuteri strains originating from the pig gastrointestinal tract. BMC Genomics. 16 (2015) 1023.

1Heavens, D., Tailford L.E., Crossman, L., Jeffers, F., Mackenzie, D.A., Caccamo, M., and Juge N. Genome sequence of a vertebrate gut symbiont Lactobacillus reuteri ATCC 53608. J Bacteriol. 193 (2011) 4015-6.

2Frese SA, Benson AK, Tannock GW, Loach DM, Kim J, Zhang M, Oh PL, Heng NCK, Patil PB, Juge N, MacKenzie DA, Pearson BM, Labidus A, Dalin E, Tice H, Goltsman E, Land M, Hauser L, Ivanova N, Kyrpides NC and Walter J. The evolutions of host specialization in the vertebrate gut symbiont Lactobacillus reuteri. PLoS Genet 7 (2011) e1001314.

3Frese SA, Mackenzie DA, Peterson DA, Schmaltz R, Fangman T, Zhou Y, Zhang C, Benson AK, Cody LA, Mulholland F, Juge N, Walter J. Molecular characterization of host-specific biofilm formation in a vertebrate gut symbiont. PLoS Genet. 9 (2013) e1004057.

4Mackenzie DA, Jeffers F, Parker ML, Vibert-Vallet A, Bongaerts RJ, Roos S, Walter J, Juge N. Strain-specific diversity of mucus-binding proteins in the adhesion and aggregation properties of Lactobacillus reuteri. Microbiology 156 (2010) 3368-78

 

 

 

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The programme receives funding from the BBSRC - Biotechnology and Biological Sciences Research Council and involves leading researchers from the Institute of Food Research, Imperial College, University of East Anglia and St. Mark's Hospital and Academic Institute

Institute of Food ResearchImperial College LondonUniversity of East AngliaSt. Mark's Hospital and Academic InstituteBBSRC - Biotechnology and Biological Sciences Research Council