Neutral processes dominate microbial community assembly in Atlantic salmon, Salmo salar

Heys, C. , Cheaib, B. , Busetti, A., Kazlauskaite, R., Maier, L., Sloan, W.T. , Ijaz, U.Z. , Kaufmann, J., McGinnity, P. and Llewellyn, M.S. (2020) Neutral processes dominate microbial community assembly in Atlantic salmon, Salmo salar. Applied and Environmental Microbiology, 86(8), e02283-19. (doi: 10.1128/AEM.02283-19) (PMID:32033945) (PMCID:PMC7117918)

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Abstract

In recent years a wealth of studies have examined the relationships between a host and its microbiome across diverse taxa. Many studies characterise the host microbiome without considering the ecological processes that underpin microbiome assembly. In this study, the intestinal microbiota of Atlantic salmon, Salmo salar, sampled from farmed and wild environments was first characterised using 16s rDNA MiSeq sequencing analysis. We used neutral community models to determine the balance of stochastic and deterministic processes that underpin microbial community assembly and transfer across lifecycle stage and between gut compartments. Across gut compartments in farmed fish, neutral models suggest that most microbes are transient with no evidence of adaptation to their environment. In wild fish, we find declining taxonomic and functional microbial community richness as fish mature through different lifecycle stages. Alongside neutral community models applied to wild fish, we suggest declining richness demonstrates an increasing role for the host in filtering microbial communities that is correlated with age. We find a limited subset of gut microflora adapted to the farmed and wild host environment among which Mycoplasma sp. are prominent. Our study reveals the ecological drivers underpinning community assembly in both farmed and wild Atlantic salmon and underlines the importance of understanding the role of stochastic processes such as random drift and small migration rates in microbial community assembly, before considering any functional role of the gut microbes encountered.

Item Type:Articles
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Kazlauskaite, Raminta and Cheaib, Dr Bachar and Heys, Dr Chloe and Llewellyn, Dr Martin and Busetti, Dr Alessandro and Ijaz, Dr Umer and Sloan, Professor William
Authors: Heys, C., Cheaib, B., Busetti, A., Kazlauskaite, R., Maier, L., Sloan, W.T., Ijaz, U.Z., Kaufmann, J., McGinnity, P., and Llewellyn, M.S.
College/School:College of Medical Veterinary and Life Sciences > Institute of Biodiversity Animal Health and Comparative Medicine
College of Science and Engineering > School of Engineering > Infrastructure and Environment
Journal Name:Applied and Environmental Microbiology
Publisher:American Society for Microbiology
ISSN:0099-2240
ISSN (Online):1098-5336
Published Online:07 February 2020
Copyright Holders:Copyright © 2020 Heys et al.
First Published:First published in Applied and Environmental Microbiology 86(8): e02283-19
Publisher Policy:Reproduced under a Creative Commons License

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Project CodeAward NoProject NamePrincipal InvestigatorFunder's NameFunder RefLead Dept
173483A microbial basis for Atlantic Salmon energeticsMartin LlewellynBiotechnology and Biological Sciences Research Council (BBSRC)BB/P001203/1LS - Animal Biology
170256Understanding microbial community through in situ environmental 'omic data synthesisUmer Zeeshan IjazNatural Environment Research Council (NERC)NE/L011956/1ENG - Infrastructure & Environment