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.

AgResearch Ltd Grasslands Research Centre Palmerston North New Zealand

Anaerobic Fungi Network Kerkdriel Netherlands

Área de Microbiología Facultad de Ciencias Médicas Universidad Nacional de Cuyo Mendoza Argentina

Bavarian State Research Center for Agriculture Freising Germany

Bioenergy Group Agharkar Research Institute Pune India

Department of Applied Microbiology and Food Technology Research Institute for Bioscience and Biotechnology Kathmandu Nepal

Department of Biological Sciences University of Toronto Scarborough Toronto ON Canada

Department of Microbiology and Immunology Faculty of Pharmacy Cairo University Cairo Egypt

Department of Microbiology and Plant Pathology University of California Riverside Riverside CA USA

Department of Veterinary Medicine University of Sassari Sardinia Italy

Institute of Animal Physiology and Genetics Czech Academy of Sciences Prague Czechia

Langston University Langston OK USA

Oklahoma State University Department of Animal and Food Sciences Stillwater OK USA

Oklahoma State University Department of Microbiology and Molecular Genetics Stillwater OK USA

Prague Zoo Prague Czechia

Universität Innsbruck Faculty of Biology Department of Microbiology Innsbruck Austria

University of Milan Dept of Agricultural and Environmental Sciences Milan Italy

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