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Fish feed DNA can significantly influence gut microbiome studies. Analyzing feed and digesta revealed shared and unique microbial communities, highlighting a potential carry-over bias in research.

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Area of Science:

  • Aquatic microbiology
  • Fish nutrition
  • Gut microbiome research

Background:

  • The fish gut microbiome is increasingly studied, often using 16S rRNA gene sequencing.
  • Current methods analyze total DNA, including live and dead bacteria, from digesta.
  • Feed composition's microbial contribution is often overlooked, potentially biasing results.

Purpose of the Study:

  • To investigate the microbial DNA carry-over effect from feed to the Atlantic salmon gut microbiome.
  • To compare microbial communities in fish feed and intestinal digesta.
  • To assess the influence of feed-associated microbes on gut microbiome profiles.

Main Methods:

  • Analysis of 15 different fish feeds and corresponding Atlantic salmon intestinal digesta.
  • Microbial community profiling using 16S rRNA gene sequencing.
  • Comparative analysis to identify shared and unique microbial taxa.

Main Results:

  • Identified diverse "feed microbiomes" with shared taxa also found in digesta microbiomes.
  • Observed digesta-specific microbial enrichment, notably by Mycoplasma and Ruminococcaceae.
  • Findings support a model where feed microbiome DNA influences gut microbial profiles.

Conclusions:

  • Feed microbiome DNA carry-over is a significant factor affecting fish gut microbiome studies.
  • Future research should account for feed microbial DNA to avoid bias.
  • Understanding this influence is crucial for accurate fish gut health assessments.