# Exploring Bird Gut Microbiota Through Opportunistic Fecal Sampling: Ecological and Evolutionary Perspectives

## TL;DR

This study shows that bird gut microbiota can be studied using noninvasive fecal samples, revealing links to diet, habitat, and bird traits.

## Contribution

The study demonstrates the feasibility of using opportunistic fecal sampling to explore avian gut microbiota in wetland ecosystems.

## Key findings

- Fecal microbiota composition varied significantly with bird traits like trophic guild and body length.
- Environmental factors such as habitat location and pond surface influenced bacterial composition.
- The potential pathogen Campylobacter was more common in peri-urban sites.

## Abstract

Wetland ecosystems are facing alarming rates of destruction and degradation, posing significant challenges for avian populations reliant on these habitats. Bird health is closely linked to the composition of their intestinal microbiota, which is primarily influenced by local conditions, primarily through diet. Building on our previous work identifying dietary variations among bird populations in marshes within a Ramsar site along the Somme and Avre rivers (France), this pilot study aimed to assess the relevance of using fecal samples collected from the ground to characterize avian intestinal microbiota via 16S rRNA metabarcoding. We hypothesized that this noninvasive sampling method would capture how bird traits and environmental factors shape fecal microbiota composition. Sampling was conducted during the breeding season at seven locations (six within the Ramsar site and one on its outskirts) spanning rural or peri‐urban environments. A total of 52 fecal samples from nine bird species or families, predominantly waterbirds, were analyzed for bacterial composition. At the phylum level, Firmicutes and Proteobacteria were predominant, with the relative abundance of genera such as Clostridium, Rothia, Bacillus, Caldilinea and Pseudomonas varying among bird species. The potential enteropathogen Campylobacter was primarily detected in samples from peri‐urban sites. Multivariate analyses revealed significant variations in bacterial composition associated with bird trophic guild, ecology, body length, pond surface and habitat location. Additionally, a weak correlation was observed between host phylogeny and microbiota composition. Although the limited sample size, particularly for some species, constrains the robustness of these findings, the observed trends align with ecological expectations. This study highlights the potential of opportunistically collected fecal samples as a low‐impact tool for exploring the relationship between bird gut microbiota and their habitat.

Wetland degradation threatens bird populations, and their intestinal microbiota composition is influenced by local conditions, particularly diet. This pilot study used fecal samples collected from the ground to assess avian gut microbiota via 16S rRNA metabarcoding, revealing significant variations linked to bird traits and environmental factors. Despite limitations in sample size, the findings support the use of noninvasive fecal sampling as a valuable tool for studying bird microbiota in relation to habitat.