Study points to how gut bacteria evolved host specificity

7th December 2015

The microbiota, the complex microbial community that we host in our gut, influences a number of different processes in our bodies, including metabolism and immunity. A change in the composition of the gut microbiota has been associated with a number of diseases. As we learn more about how these are linked, new possibilities arise for developing therapies based around restoring the composition of the microbial community to our benefit.  But to be effective, we need to understand how these bacteria colonise our gut – something we know little about.

Nathalie Juge from the Institute of Food Research has been studying this, focusing on bacteria associated with the mucus layer produced by the gut lining. Working in collaboration with The Genome Analysis Centre, the University of Nebraska Lincoln, and the University of Alberta, she has been studying the gut bacteria Lactobacillus reuteri. 

Dr Nathalie Juge

L. reuteri are commonly found in the microbiota of many different vertebrate animals, and have been well studied as a ‘model’ gut bacteria. By comparing the genomes of different strains of these bacteria, the researchers recently showed that during evolution, the bacteria diversified into different groups, or clades, and that these were specific to the host organism. This means that only rodent-specific L. reuteri could colonise mice, for example.

In a new study, published in the journal BMC Genomics Nathalie Juge and her team looked at L. reuteri strains found in pigs, to find out why these strains specifically colonise these animals.

“Such knowledge is important to gain as L. reuteri is one of the most dominant species in the porcine gastrointestinal tract and pig-derived strains of L. reuteri are used as probiotics to improve pig health and well-being, and potentially reduce the use of antibiotics” said Dr Juge.

The team completed the sequencing of a L. reuteri strain derived from a pig, which they used as reference. They then sequenced another 4 porcine isolates, and compared these to the reference genome. They also compared the pig genomes to genomes from L. reuteri strains from rodents and humans.

From their genomic analysis, they were able to show that there were two divergent clades within the pig L. reuteri that could clearly be differentiated from other organisms. The two clades appear to have evolved separately.

Having distinguished the differences on the genomic level, the researchers then tried to see what characterised the pig strains, to find clues to what might make them specific to pigs. They found a number of interesting genes that would encode proteins that would be expected to localise to cell surfaces, some of which also contained mucus-binding domains, or other adhesion proteins.

“Clearly, these genes provide a basis for future functional studies on the ecology of L. reuteri in the pig gastrointestinal tract,” said Dr Juge.

IFR is strategically supported by the Biotechnology and Biological Sciences Research Council (BBSRC).

You can read more about this study on the Gut Health and Food Safety blog


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. 16:1023 doi: 10.1186/s12864-015-2216-7

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