Fish Gastrointestinal Microbiome Alterations Associated with Environmental and Host Factors

Gastrointestinal microbiota (GIM) play a crucial role in host physiology and are modulated by host biology, environmental conditions, and temporal dynamics. The GIM of two types of fishes, the redbreast sunfish (Lepomis auritus) and the bullhead catfish (Ameiurus spp.), from three streams over two seasons were sampled for host health (hepatosomatic index, Fulton’s condition factor), age, and additional environmental metadata. A total of 56 of these were fully analyzed using 16S rRNA amplicon sequencing and QIIME2. Specific taxonomic lineages were identified as significant with respect to observed differences between variables, including season, stream, and host taxonomic affiliation. The relative abundance of bacterial phyla varied significantly based on host type and between the three sites. However, the most significant effects for both relative abundance and alpha diversity metrics were seen when combining variables of site and season or host and season. Principal Component Analysis using weighted and unweighted Unifrac indicated the primacy of season in beta diversity analyses. Analysis of Compositions of Microbiomes (ANCOM) to identify taxa responsible for these differences revealed distinct amplicon sequence variants enriched by season, stream, host taxonomy, and host age. The larger picture emerging from these data suggests that there is a complex interplay between the host, season, and environment that shapes the structure of fish microbiota and associated host health.