Our knowledge about the gut microbiota of pigs is still scarce, despite the importance of these animals for biomedical research and agriculture. Here, we present a collection of cultured bacteria from the pig gut, including 110 species across 40 families and nine phyla. We provide taxonomic descriptions for 22 novel species and 16 genera. Meta-analysis of 16S rRNA amplicon sequence data and metagenome-assembled genomes reveal prevalent and pig-specific species within Lactobacillus, Streptococcus, Clostridium, Desulfovibrio, Enterococcus, Fusobacterium, and several new genera described in this study. Potentially interesting functions discovered in these organisms include a fucosyltransferase encoded in the genome of the novel species Clostridium porci, and prevalent gene clusters for biosynthesis of sactipeptide-like peptides. Many strains deconjugate primary bile acids in in vitro assays, and a Clostridium scindens strain produces secondary bile acids via dehydroxylation. In addition, cells of the novel species Bullifex porci are coccoidal or spherical under the culture conditions tested, in contrast with the usual helical shape of other members of the family Spirochaetaceae. The strain collection, called ‘Pig intestinal bacterial collection’ (PiBAC), is publicly available at www.dsmz.de/pibac and opens new avenues for functional studies of the pig gut microbiota.

The community of microorganisms inhabiting the intestine of mammals are referred to as the gut microbiome and are known to influence the health of their host. Despite extensive work in the last decades, we still know remarkably little about their diversity and the molecular mechanisms underlying interactions with the host. After reviewing the main methods used to analyse gut microbiomes, we summarize data on the structural and functional diversity of the microbial ecosystem in pigs and also highlight the potential of cultivation and applications based on the use of minimal bacterial consortia.

Intake of Western diet stimulates bile acid (BA) production and their conversion to secondary BAs by 7α-dehydroxylating (7αDH+) bacteria in the colon. Increased levels of 7αDH+ bacteria and the secondary BA deoxycholic acid (DCA) have been associated with sporadic colorectal cancer (CRC). However, causal proof of their tumour-promoting effects under detrimental dietary conditions is lacking. Therefore, we performed feeding studies in a transgenic pig model of CRC combined with multi-omics analyses and gnotobiotic mouse studies. Western diet worsened the disease phenotype inAPC1311/+pigs. This was accompanied by increased levels of DCA and colonic epithelial cell proliferation, which was counteracted by using the bile acid-scavenging drug colestyramine. Using a gnotobiotic mouse model of CRC, we demonstrate that colonization with different 7αDH+ bacterial isolates increased colonic tumour loads. These complementary approaches present clear evidence for the causal role of microbiome-derived DCA production in CRC, opening avenues for future preventive strategies.