Short-Term Captivity Restructures the Gut Microbiome of Fundulus heteroclitus

Short-term captivity is widely used in experimental studies but may unintentionally alter host-associated microbiomes, potentially confounding biological interpretation of experimental outcomes. Here, we evaluated the effects of 35 days of captivity on the gut microbiome of Fundulus heteroclitus collected from Long Island Sound (Milford, CT, USA) using 16S rRNA gene sequencing. Comparisons between Field Control (FC) and short-term Captive Treatment (CT) groups revealed a marked reduction in microbial diversity under captive conditions. Observed richness decreased approximately five-fold (Field Control: 1026 features; Captive Treatment: 221 features), and Shannon diversity declined from 8.89 to 5.93. Beta diversity analyses based on UniFrac distances demonstrated clear separation between groups, indicating substantial shifts in community composition. Taxonomic profiling revealed reduced community complexity in captive fish, with increased dominance of Proteobacteria and loss of diverse environmental taxa. Predicted enrichment of pathways associated with stress response, altered respiration, and metabolic flexibility in captivity reflects inferred functional potential rather than direct functional activity. Given the use of pooled samples with limited biological replication, these findings should be interpreted as strong community-level patterns rather than population-level inference. Collectively, these results indicate that short-term captivity alters the F. heteroclitus gut microbiome.