Drivers of ecological assembly in the hindgut of Atlantic Cod fed a macroalgal supplemented diet

Keating, C. , Bolton-Warberg, M., Hinchcliffe, J., Davies, R., Whelan, S., Wan, A.H.L., Fitzgerald, R.D., Davies, S.J., Smith, C.J. and Ijaz, U.Z. (2022) Drivers of ecological assembly in the hindgut of Atlantic Cod fed a macroalgal supplemented diet. npj Biofilms and Microbiomes, 8, 36. (doi: 10.1038/s41522-022-00296-x) (PMID:35508464) (PMCID:PMC9068720)

Abstract

It is difficult to disentangle the many variables (e.g. internal or external cues and random events) that shape the microbiota in the gastrointestinal tract of any living species. Ecological assembly processes applied to microbial communities can elucidate these drivers. In our study, farmed Atlantic cod (Gadus morhua) were fed a diet of 10% macroalgae supplement (Ulva rigida [ULVA] or Ascophyllum nodosum [ASCO] or a non-supplemented control diet [CTRL]) over 12 weeks. We determined the influence of ecological assembly processes using a suite of null-modelling tools. We observed dissimilarity in the abundance of common OTUs over time, which was driven by deterministic assembly. The CTRL samples showed selection as a critical assembly process. While dispersal limitation was a driver of the gut microbiome for fish fed the macroalgae supplemented diet at Week 12 (i.e., ASCO and ULVA). Fish from the ASCO grouping diverged into ASCO_N (normal) and ASCO_LG (lower growth), where ASCO_LG individuals found the diet unpalatable. The recruitment of new taxa overtime was altered in the ASCO_LG fish, with the gut microbiome showing phylogenetic underdispersion (nepotistic species recruitment). Finally, the gut microbiome (CTRL and ULVA) showed increasing robustness to taxonomic disturbance over time and lower functional redundancy. This study advances our understanding of the ecological assembly and succession in the hindgut of juvenile Atlantic cod across dietary treatments. Understanding the processes driving ecological assembly in the gut microbiome, in fish research specifically, could allow us to manipulate the microbiome for improved health or resilience to disease for improved aquaculture welfare and production.

• Item Type: Articles
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Keating, Dr Ciara and Ijaz, Dr Umer and Smith, Professor Cindy
• Authors: Keating, C., Bolton-Warberg, M., Hinchcliffe, J., Davies, R., Whelan, S., Wan, A.H.L., Fitzgerald, R.D., Davies, S.J., Smith, C.J., and Ijaz, U.Z.
• College/School: College of Medical Veterinary and Life Sciences > School of Biodiversity, One Health & Veterinary Medicine; College of Science and Engineering > School of Engineering > Infrastructure and Environment
• Journal Name: npj Biofilms and Microbiomes
• Publisher: Nature Research
• ISSN: 2055-5008
• ISSN (Online): 2055-5008
• Copyright Holders: Copyright © 2022 The Authors
• First Published: First published in npj Biofilms and Microbiomes 8: 36
• Publisher Policy: Reproduced under a Creative Commons License

Project Code	Award No	Project Name	Principal Investigator	Funder's Name	Funder Ref	Lead Dept
170256		Understanding microbial community through in situ environmental 'omic data synthesis	Umer Zeeshan Ijaz	Natural Environment Research Council (NERC)	NE/L011956/1	ENG - Infrastructure & Environment