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 D’Agostino, Fabio Cumbo, Thomas Fischöder, Marzena Wyschkon, Torey Looft, Valeria R. Parreira, Birte Abt, Heidi L. Doden, Lindsey Ly, João M. P. Alves, Markus Reichlin, Krzysztof Flisikowski, Laura Navarro Suarez, Anthony P. Neumann, Garret Suen, Tomas 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 and Thomas Clavel ()
Additional contact information
David Wylensek: Functional Microbiome Research Group, RWTH University Hospital
Thomas C. A. Hitch: Functional Microbiome Research Group, RWTH University Hospital
Thomas Riedel: Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures
Afrizal Afrizal: Functional Microbiome Research Group, RWTH University Hospital
Neeraj Kumar: Functional Microbiome Research Group, RWTH University Hospital
Esther Wortmann: Functional Microbiome Research Group, RWTH University Hospital
Tianzhe Liu: Chair of Technical Biochemistry, Technical University of Dresden
Saravanan Devendran: Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology
Till R. Lesker: Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research
Sara B. Hernández: Laboratory for Molecular Infection Medicine Sweden (MIMS), Department of Molecular Biology, Umeå University
Viktoria Heine: Laboratory for Biomaterials, Institute for Biotechnology and Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University
Eva M. Buhl: Electron Microscopy Facility, Institute of Pathology, RWTH University Hospital
Paul D’Agostino: Chair of Technical Biochemistry, Technical University of Dresden
Fabio Cumbo: Department CIBIO, University of Trento
Thomas Fischöder: Laboratory for Biomaterials, Institute for Biotechnology and Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University
Marzena Wyschkon: Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures
Torey Looft: National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture
Valeria R. Parreira: Department of Molecular and Cellular Biology, University of Guelph
Birte Abt: Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures
Heidi L. Doden: Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology
Lindsey Ly: Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology
João M. P. Alves: Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo
Markus Reichlin: PharmaBiome AG
Krzysztof Flisikowski: Chair of Livestock Biotechnology, Weihenstephan School of Life Science, Technical University of Munich
Laura Navarro Suarez: Institute of Food Chemistry, Hamburg School of Food Science, University of Hamburg
Anthony P. Neumann: Department of Bacteriology, University of Wisconsin-Madison
Garret Suen: Department of Bacteriology, University of Wisconsin-Madison
Tomas Wouters: PharmaBiome AG
Sascha Rohn: Institute of Food Chemistry, Hamburg School of Food Science, University of Hamburg
Ilias Lagkouvardos: ZIEL - Institute for Food & Health, Technical University of Munich
Emma Allen-Vercoe: Department of Molecular and Cellular Biology, University of Guelph
Cathrin Spröer: Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures
Boyke Bunk: Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures
Anja J. Taverne-Thiele: Host-Microbe Interactomics Group, Department of Animal Science, Wageningen University
Marcel Giesbers: Electron Microscopy Center, Wageningen University
Jerry M. Wells: Host-Microbe Interactomics Group, Department of Animal Science, Wageningen University
Klaus Neuhaus: ZIEL - Institute for Food & Health, Technical University of Munich
Angelika Schnieke: ZIEL - Institute for Food & Health, Technical University of Munich
Felipe Cava: Laboratory for Molecular Infection Medicine Sweden (MIMS), Department of Molecular Biology, Umeå University
Nicola Segata: Department CIBIO, University of Trento
Lothar Elling: Laboratory for Biomaterials, Institute for Biotechnology and Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University
Till Strowig: Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research
Jason M. Ridlon: Microbiome Metabolic Engineering Theme, Carl R. Woese Institute for Genomic Biology
Tobias A. M. Gulder: Chair of Technical Biochemistry, Technical University of Dresden
Jörg Overmann: Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures
Thomas Clavel: Functional Microbiome Research Group, RWTH University Hospital

Nature Communications, 2020, vol. 11, issue 1, 1-26

Abstract: 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.

Date: 2020
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DOI: 10.1038/s41467-020-19929-w

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