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

Nicholas Liao

Nat Commun. 2020 Dec 15;11(1):6389. doi: 10.1038/s41467-020-19929-w. | PubMed

David Wylensek1, Thomas C A Hitch1, Thomas Riedel2,3, Afrizal Afrizal1, Neeraj Kumar1,4, Esther Wortmann1, Tianzhe Liu5, Saravanan Devendran6,7, Till R Lesker8, Sara B Hernández9, Viktoria Heine10, Eva M Buhl11, Paul M D'Agostino5, Fabio Cumbo12, Thomas Fischöder10, Marzena Wyschkon2,3, Torey Looft13, Valeria R Parreira14, Birte Abt2,3, Heidi L Doden6,7, Lindsey Ly6,7, João M P Alves15, Markus Reichlin16, Krzysztof Flisikowski17, Laura Navarro Suarez18, Anthony P Neumann19, Garret Suen19, Tomas de Wouters16, Sascha Rohn18,20, Ilias Lagkouvardos4,21, Emma Allen-Vercoe14, Cathrin Spröer2, Boyke Bunk2, Anja J Taverne-Thiele22, Marcel Giesbers23, Jerry M Wells22, Klaus Neuhaus4, Angelika Schnieke4,17, Felipe Cava9, Nicola Segata12, Lothar Elling10, Till Strowig8,24, Jason M Ridlon6,7, Tobias A M Gulder5, Jörg Overmann2,3, Thomas Clavel25

  1. Functional Microbiome Research Group, RWTH University Hospital, Aachen, Germany.
  2. Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.
  3. German Center for Infection Research (DZIF), Partner site Hannover-Braunschweig, Braunschweig, Germany.
  4. ZIEL - Institute for Food & Health, Technical University of Munich, Freising, Germany.
  5. Chair of Technical Biochemistry, Technical University of Dresden, Dresden, Germany.
  6. Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology, Urbana, IL, USA.
  7. Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
  8. Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany.
  9. Laboratory for Molecular Infection Medicine Sweden (MIMS), Department of Molecular Biology, Umeå University, Umeå, Sweden.
  10. Laboratory for Biomaterials, Institute for Biotechnology and Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University, Aachen, Germany.
  11. Electron Microscopy Facility, Institute of Pathology, RWTH University Hospital, Aachen, Germany.
  12. Department CIBIO, University of Trento, Trento, Italy.
  13. National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA, USA.
  14. Department of Molecular and Cellular Biology, University of Guelph, Guelph, Canada.
  15. Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.
  16. PharmaBiome AG, Zurich, Switzerland.
  17. Chair of Livestock Biotechnology, Weihenstephan School of Life Science, Technical University of Munich, Freising, Germany.
  18. Institute of Food Chemistry, Hamburg School of Food Science, University of Hamburg, Hamburg, Germany.
  19. Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.
  20. Institute of Food Technolgy and Food Chemistry, Technische Universität Berlin, Berlin, Germany.
  21. Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Center of Marine Research, Heraklion, Greece.
  22. Host-Microbe Interactomics Group, Department of Animal Science, Wageningen University, Wageningen, The Netherlands.
  23. Electron Microscopy Center, Wageningen University, Wageningen, The Netherlands.
  24. Hannover Medical School, Hannover, Germany.
  25. Functional Microbiome Research Group, RWTH University Hospital, Aachen, Germany. tclavel@ukaachen.de.

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.

Presented By Thomas Hitch