Abstract

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.

Highlights

  • Our knowledge about the gut microbiota of pigs is still scarce, despite the importance of these animals for biomedical research and agriculture

  • Cultivation of bacteria from the pig intestine has been sporadic, focusing mainly on pathogens or probiotic strains, with little effort placed on commensals

  • The diversity and occurrence in the pig intestine of the 110 selected species is summarized in Fig. 1 and a listing with detailed metadata is provided in Supplementary Data 1

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Summary

Introduction

Our knowledge about the gut microbiota of pigs is still scarce, despite the importance of these animals for biomedical research and agriculture. There has so far been no comprehensive study of cultured bacteria from the pig intestine, despite obvious added value: providing access to well-described bacterial strains will facilitate (i) functional studies to dissect microbe–host interactions underlying diseases in preclinical contexts, and (ii) intervention trials with defined cocktails of commensals as an alternative to antibiotics use. Such trials could influence enteric infection-associated postweaning diarrhoea that affect millions of pigs worldwide and is linked to the use of colistin, a last-resort antibiotic in human medicine[23,24]. A detailed survey of the ecological distribution of all taxa as well as new functional insights are presented

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