Genomic Investigation of Gut Microbiome Associations in Freshwater Fish Assemblages

Abundant and diverse groups of microorganisms, often referred to as the microbiome, occur in and on the bodies of vertebrates and perform a variety of functions crucial to host well-being. However, whether and how the microbiome influence the host species performance, niche partitioning, or species abundance in freshwater taxa still remain open questions. This research will investigate whether the gut microbiome in freshwater fishes contributes to the regulation of patterns of abundance and species diversity in local fish assemblages in the Meramec River watershed in southeastern Missouri. Fish and river water microbiome data will be generated using metagenomics techniques from field-collected samples to investigate the relative contributions of habitat and evolutionary history to fish gut microbiome assembly. Fish gut microbiome diversity will also be related to abundance of individuals in various fish species to investigate whether microbiome characteristics in individual species are related to overall assemblage structure. The proposed work will potentially provide fundamental insights regarding the influence of microorganisms on the abundance and diversity of vertebrate host species in freshwater systems.

Publications

Andres, K. J., Liu, B., Johnson, L. E., Kapuscinski, K. L., Moerke, A. H., Ling, F., & Knouft, J. H.
(2025). Life stage and vaccination shape the gut microbiome of hatchery-reared Atlantic salmon (Salmo salar) intended for river stocking. Aquaculture, 594, 741469. doi:10.1016/j.aquaculture.2024.741469

Liu, Z., Zhang, L., Knouft, J. H., & Ling, F. (2022). Meter-scale variation within a single transect demands attention to taxon accumulation curves in riverine microbiome studies. Frontiers of Environmental Science & Engineering, 16(5), 1-11. doi:10.1007/s11783-022-1543-6

Research Team

Fangqiong Ling, WashU (McKelvey School of Engineering)
Jason Knouft, Saint Louis University