Patterns and determinants of the global herbivorous mycobiome

Casey H. Meili, Adrienne L. Jones, Alex X. Arreola, Jeffrey Habel, Carrie J. Pratt, Radwa A. Hanafy, Yan Wang, Aymen S. Yassin, Moustafa A. TagElDein, Christina D. Moon, Peter H. Janssen, Mitesh Shrestha, Prajwal Rajbhandari, Magdalena Nagler, Julia M. Vinzelj, Sabine M. Podmirseg, Jason E. Stajich, Arthur L. Goetsch, Jerry Hayes, Diana Young, Katerina Fliegerova, Diego Javier Grilli, Roman Vodička, Giuseppe Moniello, Silvana Mattiello, Mona T. Kashef, Yosra I. Nagy, Joan A. Edwards, Sumit Singh Dagar, Andrew P. Foote, Noha H. Youssef () and Mostafa S. Elshahed ()
Additional contact information
Casey H. Meili: Oklahoma State University, Department of Microbiology and Molecular Genetics
Adrienne L. Jones: Oklahoma State University, Department of Microbiology and Molecular Genetics
Alex X. Arreola: Oklahoma State University, Department of Microbiology and Molecular Genetics
Jeffrey Habel: Oklahoma State University, Department of Microbiology and Molecular Genetics
Carrie J. Pratt: Oklahoma State University, Department of Microbiology and Molecular Genetics
Radwa A. Hanafy: Oklahoma State University, Department of Microbiology and Molecular Genetics
Yan Wang: University of Toronto Scarborough
Aymen S. Yassin: Cairo University
Moustafa A. TagElDein: Cairo University
Christina D. Moon: Grasslands Research Centre
Peter H. Janssen: Grasslands Research Centre
Mitesh Shrestha: Research Institute for Bioscience and Biotechnology (RIBB)
Prajwal Rajbhandari: Research Institute for Bioscience and Biotechnology (RIBB)
Magdalena Nagler: Universität Innsbruck, Faculty of Biology, Department of Microbiology
Julia M. Vinzelj: Universität Innsbruck, Faculty of Biology, Department of Microbiology
Sabine M. Podmirseg: Universität Innsbruck, Faculty of Biology, Department of Microbiology
Jason E. Stajich: University of California, Riverside
Arthur L. Goetsch: Langston University
Jerry Hayes: Langston University
Diana Young: Bavarian State Research Center for Agriculture
Katerina Fliegerova: Institute of Animal Physiology and Genetics Czech Academy of Sciences
Diego Javier Grilli: Universidad Nacional de Cuyo
Roman Vodička: Prague Zoo
Giuseppe Moniello: University of Sassari
Silvana Mattiello: University of Milan, Dept. of Agricultural and Environmental Sciences
Mona T. Kashef: Cairo University
Yosra I. Nagy: Cairo University
Joan A. Edwards: Anaerobic Fungi Network
Sumit Singh Dagar: Agharkar Research Institute
Andrew P. Foote: Oklahoma State University, Department of Animal and Food Sciences
Noha H. Youssef: Oklahoma State University, Department of Microbiology and Molecular Genetics
Mostafa S. Elshahed: Oklahoma State University, Department of Microbiology and Molecular Genetics

Nature Communications, 2023, vol. 14, issue 1, 1-18

Abstract: Abstract Despite their role in host nutrition, the anaerobic gut fungal (AGF) component of the herbivorous gut microbiome remains poorly characterized. Here, to examine global patterns and determinants of AGF diversity, we generate and analyze an amplicon dataset from 661 fecal samples from 34 mammalian species, 9 families, and 6 continents. We identify 56 novel genera, greatly expanding AGF diversity beyond current estimates (31 genera and candidate genera). Community structure analysis indicates that host phylogenetic affiliation, not domestication status and biogeography, shapes the community rather than. Fungal-host associations are stronger and more specific in hindgut fermenters than in foregut fermenters. Transcriptomics-enabled phylogenomic and molecular clock analyses of 52 strains from 14 genera indicate that most genera with preferences for hindgut hosts evolved earlier (44-58 Mya) than those with preferences for foregut hosts (22-32 Mya). Our results greatly expand the documented scope of AGF diversity and provide an ecologically and evolutionary-grounded model to explain the observed patterns of AGF diversity in extant animal hosts.

Date: 2023
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DOI: 10.1038/s41467-023-39508-z

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