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New collection of intestinal bacteria opens up research opportunities

When it comes to health, the intestines deserve special attention. Because in the intestine there is a large part of the immune cells in the entire body, which interact very closely with a large variety of microorganisms (the intestinal microbiota). This applies not only to humans, but also to many animals. A research team from the RWTH Aachen University Hospital led by Univ.-Prof. Dr. rer. nat Thomas Clavel, head of the functional microbiome research group at the Institute for Medical Microbiology at the RWTH Aachen University Hospital, has now for the first time described in detail the intestinal microbiome of pigs using cultivation and metagenomics. The study was published in the prestigious journal Nature Communications released.

In the intestines of mammals, one to two thirds of the prokaryotic diversity (organisms without a nucleus) have not yet been described. Knowledge of the microbiome is particularly important for the animal species that play a role in biomedical research and agriculture. In order to close this knowledge gap, Prof. Dr. rer. nat Thomas Clavel and his team analyzed the intestinal microbiota of pigs and cultivated and described many novel groups of bacteria (taxa) - and thus also the functions of these bacteria.

The resulting collection contains 110 species in 40 families and nine bacterial strains (Phyla). It provides taxonomic descriptions for 22 novel species and 16 genera. A meta-analysis of 16S rRNA amplicon sequence data and metagenome-assembled genomes reveals widespread and pig-specific species within Lactobacillus, Streptococcus, Clostridium, Desulfovibrio, Enterococcus, Fusobacterium as well as several new genera. Potentially important functions discovered in these organisms include a new fucosyltransferase, which opens up interesting biotechnological perspectives for the creation of synthetic oligosaccharides, and widespread gene clusters for the biosynthesis of sactipeptide-like peptides with potential antimicrobial properties.

This public collection now serves as the basis for experimental studies aimed at understanding the ecology of gut microbes as well as studying microbe-host interactions using in vitro and in vivo systems. In addition, the team is researching the use of synthetic isolate communities to improve animal health. This therapeutic method can be used in a form adapted to humans, for example as an alternative to fecal microbiota transplantation.

The strain collection, called “Pig intestinal bacterial collection” (PiBAC), is accessible at

The press release in English can be found here.

The publication in Nature Communications can be found here.