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Neutral Processes Dominate Microbial Community Assembly in Atlantic Salmon, Salmo salar.

C Heys1, B Cheaib2, A Busetti3

  • 1Institute of Behaviour, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom chloe.heys@glasgow.ac.uk bachar.cheaib@glasgow.ac.uk.

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|February 9, 2020
PubMed
Summary

This study analyzed the gut microbes of Atlantic salmon, revealing that most are transient in farmed fish. In wild salmon, host filtering increases with age, impacting microbial diversity and assembly processes.

Keywords:
aquaculturefishhost-microbemicrobial communitiesmicrobial ecologymicrobiome

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Area of Science:

  • Microbiome research
  • Aquatic ecology
  • Host-microbe interactions

Background:

  • Host-microbiome relationships are increasingly studied, yet the ecological processes driving microbiome assembly remain underexplored.
  • Understanding microbial colonization is crucial for Atlantic salmon, an important aquaculture species with increasing farmed-wild interactions.

Purpose of the Study:

  • To characterize the intestinal microbiota of farmed and wild Atlantic salmon.
  • To determine the balance of stochastic and deterministic processes in microbial community assembly.
  • To compare microbial community assembly between farmed and wild environments and across life stages.

Main Methods:

  • 16S rRNA gene MiSeq sequencing was used to analyze the intestinal microbiota of Atlantic salmon.
  • Neutral community models were applied to assess the roles of stochastic and deterministic processes.
  • Comparisons were made between gut compartments, life cycle stages, and farmed versus wild environments.

Main Results:

  • In farmed salmon, most gut microbes appear transient, with limited adaptation to the host environment.
  • Wild salmon exhibited declining microbial richness with age, suggesting increased host filtering.
  • Mycoplasma species were identified as a prominent, potentially adapted gut microflora in both environments.

Conclusions:

  • Stochastic processes significantly influence microbial community assembly in Atlantic salmon.
  • Host-specific filtering plays a greater role in shaping the microbiome of wild salmon as they mature.
  • Distinguishing between transient and resident microbes is essential for understanding microbiome function in this species.