# Autochthonous and Allochthonous Gut Microbes May Work Together: Functional Insights from Farmed Gilthead Sea Bream (Sparus aurata)

## TL;DR

This study explores how resident and transient gut microbes in farmed sea bream interact and function differently, suggesting both are important for understanding fish gut health.

## Contribution

The study provides new insights into the functional cooperation between resident and transient gut microbes in fish, using a Bayesian network framework.

## Key findings

- Resident and transient bacterial communities in the gut of gilthead sea bream show distinct structures and compositions.
- Functional synergies exist between resident and transient bacteria, with each community specializing in different metabolic pathways.
- Resident bacteria are more stable and less affected by post-feeding time compared to transient bacteria.

## Abstract

The intestinal microbiome is highly complex in vertebrates, including farmed fish. Nevertheless, methodological approaches for its study are not standardized, and it remains unclear whether analyses should target bacteria adhered to the mucus (resident) and/or those in transit with the digesta (transient). In this study, both bacterial communities were examined in different gut sections, and resident bacteria were also assessed at various post-feeding times. Differences associated with gut region, and especially with post-feeding times for resident bacteria, were less pronounced, whereas we detected strong compositional differences between resident and transient communities. Numerous interactions between bacteria from both environments were identified. Additionally, many functional synergies appeared to occur, although each community showed specialization in several specific pathways. These results support the idea that resident and transient bacteria form distinct communities but may cooperate at a functional level, suggesting that both are relevant and should be considered separately in fish microbiome studies.

In fish gut microbiome studies, there are no standardized protocols regarding sampling region or post-feeding time, nor clear consensus on whether analyses should target resident (autochthonous) or transient (allochthonous) bacteria. This study examined the dynamics and interactions of both microbial communities in the anterior and posterior intestine of farmed gilthead sea bream and evaluated the resident microbiome at 24 and 48 h post-feeding. Microbial DNA was sequenced using the Oxford Nanopore Technology platform. Data were analyzed through statistical and discriminant approaches, as well as a Bayesian network framework to assess bacterial interactions. Transient communities showed higher richness and diversity, regardless of intestinal section, suggesting a more specialized and stable microbial environment in the mucus layer. The two communities differed markedly in structure and composition. Variations associated with intestinal region were less pronounced, particularly for autochthonous bacteria, and post-feeding fluctuations in the resident microbiome were minimal. Functionally, results indicated relevant synergies between communities. Protein metabolism pathways were enriched in autochthonous bacteria, whereas allochthonous microorganisms contributed mainly to bile acid and carbohydrate metabolism. Overall, resident and transient bacteria constitute distinct communities in the gut of gilthead sea bream, with numerous genera present in both but most being differentially represented and interconnected.