@article{da20629ecb254f2796cc4402aeac870d,
title = "A collection of bacterial isolates from the pig intestine reveals functional and taxonomic diversity",
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.",
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",
author = "David Wylensek and Hitch, {Thomas C A} and Thomas Riedel and Afrizal Afrizal and Neeraj Kumar and Esther Wortmann and Tianzhe Liu and Saravanan Devendran and Lesker, {Till R} and Hern{\'a}ndez, {Sara B} and Viktoria Heine and Buhl, {Eva M} and {M D'Agostino}, Paul and Fabio Cumbo and Thomas Fisch{\"o}der and Marzena Wyschkon and Torey Looft and Parreira, {Valeria R} and Birte Abt and Doden, {Heidi L} and Lindsey Ly and Alves, {Jo{\~a}o M P} and Markus Reichlin and Krzysztof Flisikowski and Suarez, {Laura Navarro} and Neumann, {Anthony P} and Garret Suen and {de Wouters}, Tomas and Sascha Rohn and Ilias Lagkouvardos and Emma Allen-Vercoe and Cathrin Spr{\"o}er and Boyke Bunk and Taverne-Thiele, {Anja J} and Marcel Giesbers and Wells, {Jerry M} and Klaus Neuhaus and Angelika Schnieke and Felipe Cava and Nicola Segata and Lothar Elling and Till Strowig and Ridlon, {Jason M} and Gulder, {Tobias A M} and J{\"o}rg Overmann and Thomas Clavel",
note = "Funding Information: We are grateful to Franziska Klann, Simone Severitt, and Carola Berg from the Leibniz Institute DSMZ (Braunschweig, Germany) for their support with genome sequencing, to Caroline Ziegler from the ZIEL - Institute for Food & Health (Freising, Germany) for technical help with amplicon and genome sequencing, to Steffen and Viola L{\"o}bnitz from the Chair of Livestock Biotechnology (Technical University of Munich, Germany) for their support with animal care and sampling, to Fred and Ingrid de Martines of Perth Pork Products Ltd., Ontario, for access to wild boars, to Prof. Eckhard Wolf and Dr. Andreas Blutke from the Ludwig-Maximilians-Universit{\"a}t M{\"u}nchen for the access to samples from the MIDY Pig Biobank, and to Prof. Aharon Oren from The Hebrew University of Jerusalem for precious help with Latin bacterial names. Metagenomic data processing was supported by resources at the RWTH Compute Cluster under project rwth2608. T.C. received funding from the Boehringer Ingelheim Foundation and from the Deutsche Forschungsgemeinschaft (DFG; German Research Foundation) in form of an individual grant (no. CL481/2-1 within Priority Program SPP1656) and as part of Collaborative Research Center (CRC) 1371 (project no. 395357507). Funding from the DFG was also granted to J.O. (OV20/26-1) and T.A.M.G. (CRC1371, project 395357507; GU1233/1-1; GU1233/6-1 within SPP2002).",
year = "2020",
month = dec,
day = "15",
doi = "10.1038/s41467-020-19929-w",
language = "English (US)",
volume = "11",
pages = "6389",
journal = "Nature communications",
issn = "2041-1723",
publisher = "Nature Publishing Group",
number = "1",
}