# One Function, Many Faces: Functional Convergence in the Gut Microbiomes of European Marine and Freshwater Fish Unveiled by Bayesian Network Meta-Analysis

## TL;DR

This study explores how gut microbiomes of European marine and freshwater fish are shaped by diet, environment, and genetics, revealing a conserved core microbiota with key metabolic roles.

## Contribution

The study introduces a Bayesian network meta-analysis approach to uncover functional convergence in fish gut microbiomes despite taxonomic differences.

## Key findings

- A conserved core microbiota with central roles in key metabolic pathways was identified across species.
- Core-associated clusters showed strong positive interactions and distinct biomarkers across ecological contexts.
- The study highlights practical tools for monitoring intestinal health and supporting sustainable aquaculture.

## Abstract

To address the challenge of assessing how diet, environment, and genetics shape fish gut microbiota of different species, in this work we integrated taxonomic, functional, and network-based approaches. Analyzing sea bass, trout, and sea bream, we identified a conserved core microbiota with central hierarchical and functional roles participating significantly in key metabolic pathways. Despite taxonomic variability, core-associated clusters showed strong positive interactions and specific biomarkers across ecological contexts. These results provide a robust framework for monitoring intestinal health, defining welfare indicators, and supporting sustainable aquaculture through targeted strategies.

Intestinal microbiota populations are constantly shaped by both intrinsic and extrinsic factors, including diet, environment, and host genetics. As a result, understanding how to assess, monitor, and exploit microbiome–host interplay remains an active area of investigation, especially in aquaculture. In this study, we analyzed the taxonomic structure and functional potential of the intestinal microbiota of European sea bass and rainbow trout, incorporating gilthead sea bream as a final reference. The results showed that the identified core microbiota (40 taxa for sea bass and 20 for trout) held a central role in community organization, despite taxonomic variability, and exhibited a predominant number of positive connections (>60% for both species) with the rest of the microbial community in a Bayesian network. From a functional perspective, core-associated bacterial clusters (75% for sea bass and 81% for sea bream) accounted for the majority of predicted metabolic pathways (core contribution: >75% in sea bass and >87% in trout), particularly those involved in carbohydrate, amino acid, and vitamin metabolism. Comparative analysis across ecological phenotypes highlighted distinct microbial biomarkers, with genera such as Vibrio, Pseudoalteromonas, and Paracoccus enriched in saltwater species (Dicentrarchus labrax and Sparus aurata) and Mycoplasma and Clostridium in freshwater (Oncorhynchus mykiss). Overall, this study underscores the value of integrating taxonomic, functional, and network-based approaches as practical tools to monitor intestinal health status, assess welfare, and guide the development of more sustainable production strategies in aquaculture.