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

Authors: WYLENSEK, DAVID - Aachen University; HITCH, THOMAS - Aachen University; RIEDEL, THOMAS - Technical University Of Braunschweig; AFRIZAL, AFRIZAL - Aachen University; KUMAR, NEERAJ - Technical University Of Munich; WORTMANN, ESTHER - Aachen University; LIU, TIANZHE - Technical University Dresden; DEVENDRAN, SARAVANAN - University Of Illinois; LESKER, TILL - Technical University Of Braunschweig; CUMBO, FABIO - University Of Trento, Italy; WYSCHKON, MARZENA - Technical University Of Braunschweig; Looft, Torey; PARREIRA, VALERIA - University Of Guelph; ABT, BIRTE - Technical University Of Braunschweig; AGOSTINO, PAUL - Technical University Dresden; DODEN, HEIDI - University Of Illinois; LY, LINDSEY - University Of Illinois; ALVES, JOAO - Brazil University; REICHLIN, MARKUS - Eth Zurich; FLISIKOWSKI, KRZYSZTOF - University Of Munich; NAVARRO SUAREZ, LAURA - University Of Hamburg; NEUMANN, ANTHONY - University Of Wisconsin; SUEN, GARRET - University Of Wisconsin; WELLS, JERRY - Wageningen University; WOUTERS, TOMAS DE - Eth Zurich; ROHN, SASCHA - University Of Hamburg; LAGKOUVARDOS, ILIAS - Technical University Of Munich; ALLEN-VERCOE, EMMA - University Of Guelph; NEUHAUS, KLAUS - Technical University Of Munich; SCHNIEKE, ANGELIKA - Technical University Of Munich; SEGATA, NICOLA - University Of Trento, Italy; STROWIG, TILL - Technical University Of Braunschweig; RIDLON, JASON - University Of Illinois; GULDER, TOBIAS - Technical University Dresden; OVERMANN, JORG - Technical University Of Braunschweig; CLAVEL, THOMAS - Aachen University

Submitted to: Nature Communications
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/2/2020
Publication Date: 12/15/2020
Citation: Wylensek, D., Hitch, T.C., Riedel, T., Afrizal, A., Kumar, N., Wortmann, E., Liu, T., Devendran, S., Lesker, T.R., Cumbo, F., Wyschkon, M., Looft, T.P., Parreira, V.R., Abt, B., Agostino, P.D., Doden, H.L., Ly, L., Alves, J.M., Reichlin, M., Flisikowski, K., Navarro Suarez, L., Neumann, A.P., Suen, G., Wells, J., Wouters, T., Rohn, S., Lagkouvardos, I., Allen-Vercoe, E., Neuhaus, K., Schnieke, A., Segata, N., Strowig, T., Ridlon, J.M., Gulder, T.A., Overmann, J., Clavel, T. 2020. A collection of bacterial isolates from the pig intestine reveals functional and taxonomic diversity. Nature Communications. 11. Article 6389. https://doi.org/10.1038/s41467-020-19929-w.
DOI: https://doi.org/10.1038/s41467-020-19929-w

Interpretive Summary: Bacteria that colonize the intestinal tracts of mammals are important for animal health, however many gut bacteria are still unknown, which impedes a full understanding of microbe-host interactions. Pork is the most consumed meat in the world and pigs are important in biomedical research, but knowledge about their gut microbiota is still scarce. Here we report new information about bacteria in the pig gut that can be cultured and can be used for future swine studies. We established a broad collection of cultured bacteria from the pig gut, which includes 112 species across 39 families and nine phyla. The taxonomic description of 38 previously uncharacterized bacteria is provided, including 21 novel species and 17 genera. Novel functions were detected in many of the bacteria, highlighting the importance of studies like these that provide insights into cultured gut bacteria. This culture collection has been made publicly accessible to support ongoing and future swine research, and is currently the largest publicly accessible collection of isolates from the pig gut.

Technical Abstract: Many gut bacteria are still unknown, which hampers full understanding of microbe-host interactions. Although pigs are very important animals in both biomedical research and agriculture, knowledge about their gut microbiota is still scarce despite a major impact on host physiology. Here we report new data on the cultured fraction of pig intestinal microbiomes and thereby open avenues for functional studies. We established the most comprehensive collection of cultured bacteria from the pig gut available to date, which includes 112 species across 39 families and nine phyla. The taxonomic description of 38 previously uncharacterized taxa is provided, including 21 novel species and 17 genera. Novel sactipeptides encoded by biosynthetic gene clusters within the genomes of 24 of these new taxa were discovered. Meta-analysis of 16S rRNA amplicon data and metagenome-assembled genomes identified prevalent and pig-specific species within Lactobacillus, Streptococcus, Clostridium, Desulfovibrio, Enterococcus, Fusobacterium, and several new genera described in this study. Metagenomic profiling predicted simplified communities represented by 23 most prevalent species that best mimicked the functional profile of fecal pig microbiomes. In vitro assays revealed a large number of strains that deconjugate primary bile acids, whilst one strain of the species Clostridium scindens produced secondary bile acids via dehydroxylation and showed host-specific functional adaptations to bile acid challenge. The resource is available at www.dsmz.de/pibac.