A collection of bacterial isolates from the pig intestine reveals functional and taxonomic diversity

David Wylensek, Thomas C A Hitch, Thomas Riedel, Afrizal Afrizal, Neeraj Kumar, Esther Wortmann, Tianzhe Liu, Saravanan Devendran, Till R Lesker, Sara B Hernández, Viktoria Heine, Eva M Buhl, Paul M D'Agostino, Fabio Cumbo, Thomas Fischöder, Marzena Wyschkon, Torey Looft, Valeria R Parreira, Birte Abt, Heidi L DodenLindsey Ly, João M P Alves, Markus Reichlin, Krzysztof Flisikowski, Laura Navarro Suarez, Anthony P Neumann, Garret Suen, Tomas de Wouters, Sascha Rohn, Ilias Lagkouvardos, Emma Allen-Vercoe, Cathrin Spröer, Boyke Bunk, Anja J Taverne-Thiele, Marcel Giesbers, Jerry M Wells, Klaus Neuhaus, Angelika Schnieke, Felipe Cava, Nicola Segata, Lothar Elling, Till Strowig, Jason M Ridlon, Tobias A M Gulder, Jörg Overmann, Thomas Clavel

Research output: Contribution to journalArticlepeer-review

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.

Original languageEnglish (US)
Article number6389
Pages (from-to)6389
JournalNature communications
Volume11
Issue number1
DOIs
StatePublished - Dec 15 2020

Keywords

  • Aged, 80 and over
  • Animals
  • Bacteria/classification
  • Bile Acids and Salts/metabolism
  • Biodiversity
  • Clostridium/classification
  • Feces/microbiology
  • Female
  • Gastrointestinal Microbiome/genetics
  • Genes, Bacterial/genetics
  • Host Specificity
  • Humans
  • Intestines/microbiology
  • Male
  • Metagenome
  • Multigene Family
  • Phylogeny
  • RNA, Ribosomal, 16S
  • Swine/microbiology

ASJC Scopus subject areas

  • Physics and Astronomy(all)
  • Chemistry(all)
  • Biochemistry, Genetics and Molecular Biology(all)

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