Feed microbiome: confounding factor affecting fish gut microbiome studies

Abstract

There is an increasing interest in the impact of feed on the fish gut microbiome. Most of the studies are based on sequencing the bacterial housekeeping gene 16S rRNA from extracted total DNA, including resident and non-resident live bacteria as well as dead bacteria. It has not been a common practice to include the feed as control, although it contains various nutritious ingredients that microorganisms can use before or after feed preparation. Thus, study designs using digesta as a proxy for the intestinal microbiome raise the concern that composition of the gut microbiome might be biased by carry-over of microbial DNA from the feed itself. Here we report analysis of 15 feeds and representative intestinal digesta of Atlantic salmon (Salmo salar) from five independent case studies. This allowed us to identify “feed microbiomes” that were microbially diverse and shared taxa with digesta microbiomes. Digesta-specific microbiomes were identified, though they were mainly enriched by a few taxa, such as Mycoplasma and Ruminococcaceae. Overall, findings are consistent with a model wherein gut microbial profiles are to a different degree influenced by bacterial DNA present in the feed itself through a “feed microbiome” carry-over effect.

Genetics and Nutrition Drive the Gut Microbiota Succession and Host-Transcriptome Interactions through the Gilthead Sea Bream (Sparus aurata) Production Cycle

“…This finding probably indicates that GS fish do not need to change the composition of their gut microbiota to a high extent to modify their microbial activity to cope with changes in diet composition. It must be noted that the microbial composition of feeds and their potential influence in gut microbiome [ 86 ] was not determined; however, our present results are in accordance with metatranscriptomic analyses that highlighted that the metabolic plasticity of microbiota is higher for the PROGENSA ® offspring in fish families selected for fast growth [ 24 ]. Moreover, this functional feature involved changes in both bacteria and fungi transcripts, which highly enlarges the catalogue of microbial functions in the fish intestine.…”

Relationship between gut microbiota and Chinook salmon (Oncorhynchus tshawytscha) health and growth performance in freshwater recirculating aquaculture systems

“…A typical characteristic of all these bacterial orders is their preference for an anaerobic environment like that found in fish intestines, suggesting that most bacteria detected in fish guts represent symbionts and commensals instead of a passive collection of water bacteria ( Sullam et al, 2012 ). It should be noted that some of these genera, such as Geobacillus , are feed-associated based on their thermophilic growth temperature requirements that range from 35 to 75°C ( Zarkasi et al, 2016 ; Karlsen et al, 2022 ). Additionally, the gut microbial communities detected in our study mainly represent the allochthonous microbiota, which are passing through the lumen with food and digesta ( Romero et al, 2014 ).…”

Potential of shrimp waste meal and insect exuviae as sustainable sources of chitin for fish feeds

“…The extended error bar graph and statistical analysis were made using STAMP bioinformatics software. can contain genetic material from animal and plant species that were used in its formulation, as well as the microbes associated to those ingredients (Karlsen et al, 2022). Although microbial contaminants may be killed by the high temperature during feed extrusion process, their DNA fragments may remain.…”