# Gut Microbiota Response in Meagre (Argyrosomus regius) Subjected to a Plant-Based Nutritional Challenge

## TL;DR

This study explores how the gut microbiota of meagre fish responds to plant-based diets and identifies low-abundance bacteria as potential indicators of nutritional stress.

## Contribution

The study identifies low-abundance gut bacteria as potential biomarkers for nutritional stress in meagre fish under plant-based diets.

## Key findings

- The gut microbiota of meagre remained dominated by Firmicutes across all diets.
- Low-abundance taxa like Thermoactinomycetales and Kroppenstedtia increased in fish on plant-based diets.
- These low-abundance bacteria may serve as biomarkers for gut health in aquaculture.

## Abstract

Gut microbiota has a major influence on fish health, affecting both the immunological and nutritional status of farmed species. In this study, the objective was to examine how the gut microbiota of meagre (Argyrosomus regius) responds to diets containing low to very low levels of fishmeal and fish oil, replaced with plant-based ingredients, and to then use this information to help identify potential biomarkers of the fish’s nutritional status. To achieve this, fish were fed three different diets: a traditional control diet, a low fishmeal/fish oil diet, and a very low fishmeal/fish oil diet. Both gut contents and gut lining were then analyzed using next-generation sequencing. Results showed that the main bacterial groups did not change with diet and that the microbiota of meagre was consistently dominated by Firmicutes. However, several low-abundance taxa increased in the fish that were fed the more challenging diets, suggesting that these taxa may be sensitive indicators of nutritional stress. Overall, these findings suggest that low-abundance bacteria could serve as useful markers of gut health in meagre that may support future research in aquaculture nutrition.

The gut plays a central role in fish nutrition, immunity, and overall health, making it key in aquaculture research. The microbiota, crucial to gut function, is increasingly studied as an indicator of health and nutritional status. This study characterized the gut microbiota of juvenile meagre (Argyrosomus regius) (initial weight 4.6 ± 0.4 g) fed for seven weeks on diets in which fishmeal (FM) and fish oil (FO) were replaced by increased proportions of plant-based ingredients, with the aim of identifying microbial profiles associated with nutritional challenge. Fish were fed a FM/FO control diet (CTRL; 55.1% FM, 11.3% FO), a low FM/FO diet (CD; 15% FM, 7% FO), or a very low FM/FO diet (ED; 5% FM, 5% FO). Next-generation sequencing analysis of gut mucosa and digesta revealed no significant differences in alpha or beta diversity among different dietary groups. Firmicutes dominated all samples, particularly Bacilli, Mycoplasmatales, Mycoplasmataceae, and Mycoplasma. Significant differences were only observed in low-abundance taxa (<1%), with higher abundance of Thermoactinomycetales (p = 7.71 × 10−4), Thermoactinomycetaceae (p = 7.71 × 10−4), Kroppenstedtia (p = 1.70 × 10−3), and Pseudogracilibacillus (p = 0.039) in challenged groups. This study highlights the potential of low-abundance microbial groups as targets to establish gut health biomarkers in fish.