Wild herbivorous mammals (genus Neotoma) host a diverse but transient assemblage of fungi

Fungi are often overlooked in microbiome research and, as a result, little is known about the mammalian mycobiome. Although frequently detected in vertebrate guts and known to contribute to digestion in some herbivores, whether these eukaryotes are a persistent part of the mammalian gut microbiome r...

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Bibliographic Details
Published in:Symbiosis (Philadelphia, Pa.) Pa.), 2022-05, Vol.87 (1), p.45-58
Main Authors: Weinstein, Sara B., Stephens, W. Zac, Greenhalgh, Robert, Round, June L., Dearing, M. Denise
Format: Article
Language:English
Subjects:
Biomedical and Life Sciences
Captivity
Developmental Biology
Diet
Digestive system
Ecology
Evolutionary Biology
Feces
Fungi
Gastrointestinal tract
Intestinal microflora
Life Sciences
Metagenomics
Microbiology
Microbiomes
Neotoma
Plant Sciences
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Summary:Fungi are often overlooked in microbiome research and, as a result, little is known about the mammalian mycobiome. Although frequently detected in vertebrate guts and known to contribute to digestion in some herbivores, whether these eukaryotes are a persistent part of the mammalian gut microbiome remains contentious. To address this question, we sampled fungi from wild woodrats ( Neotoma spp.) collected from 25 populations across the southwestern United States. For each animal, we collected a fecal sample in the wild, and then re-sampled the same individual after a month in captivity on a controlled diet. We characterized and quantified fungi using three techniques: ITS metabarcoding, shotgun metagenomics and qPCR. Wild individuals contained diverse fungal assemblages dominated by plant pathogens, widespread molds, and coprophilous taxa primarily in Ascomycota and Mucoromycota. Fungal abundance, diversity and composition differed between individuals, and was primarily influenced by animal geographic origin. Fungal abundance and diversity significantly declined in captivity, indicating that most fungi in wild hosts came from diet and environmental exposure. While this suggests that these mammals lack a persistent gut mycobiome, natural fungal exposure may still impact fungal dispersal and animal health.
ISSN:0334-5114
1878-7665
DOI:10.1007/s13199-022-00853-0