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Fungal microbiomes are determined by host phylogeny and exhibit widespread associations with the bacterial microbiome.

Harrison, Xavier A and McDevitt, Allan D and Dunn, Jenny C and Griffiths, Sarah M and Benvenuto, Chiara and Birtles, Richard and Boubli, Jean P and Bown, Kevin and Bridson, Calum and Brooks, Darren R and Browett, Samuel S and Carden, Ruth F and Chantrey, Julian and Clever, Friederike and Coscia, Ilaria and Edwards, Katie L and Ferry, Natalie and Goodhead, Ian and Highlands, Andrew and Hopper, Jane and Jackson, Joseph and Jehle, Robert and da Cruz Kaizer, Mariane and King, Tony and Lea, Jessica MD and Lenka, Jessica L and McCubbin, Alexandra and McKenzie, Jack and de Moraes, Bárbara Lins Caldas and O'Meara, Denise B and Pescod, Poppy and Preziosi, Richard F and Rowntree, Jennifer K and Shultz, Susanne and Silk, Matthew J and Stockdale, Jennifer E and Symondson, William OC and de la Pena, Mariana Villalba and Walker, Susan L and Wood, Michael D and Antwis, Rachael E (2021) Fungal microbiomes are determined by host phylogeny and exhibit widespread associations with the bacterial microbiome. Proceedings of the Royal Society B: Biological Sciences, 288 (1957). p. 20210552. ISSN 0962-8452

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Abstract

Interactions between hosts and their resident microbial communities are a fundamental component of fitness for both agents. Though recent research has highlighted the importance of interactions between animals and their bacterial communities, comparative evidence for fungi is lacking, especially in natural populations. Using data from 49 species, we present novel evidence of strong covariation between fungal and bacterial communities across the host phylogeny, indicative of recruitment by hosts for specific suites of microbes. Using co-occurrence networks, we demonstrate marked variation across host taxonomy in patterns of covariation between bacterial and fungal abundances. Host phylogeny drives differences in the overall richness of bacterial and fungal communities, but the effect of diet on richness was only evident in the mammalian gut microbiome. Sample type, tissue storage and DNA extraction method also affected bacterial and fungal community composition, and future studies would benefit from standardized approaches to sample processing. Collectively these data indicate fungal microbiomes may play a key role in host fitness and suggest an urgent need to study multiple agents of the animal microbiome to accurately determine the strength and ecological significance of host-microbe interactions.

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