Work

Hi-C Metagenome Deconvolution of Double-Crested Cormorant (Nannopterum auritum) Fecal Samples Demonstrates Feasibility of Linking Microbial Genomes, AMR Genes, and Mobile Elements in Avian Microbiomes

Year: 2026

Type: article

Abstract: The double-crested cormorant (Nannopterum auritum), a piscivorous bird endemic to North America, frequently forages in aquaculture ponds during migration and wintering, contributing to economic losses in catfish-producing regions of the southern United States. While interactions between cormorants and aquaculture systems are well documented, their associated microbial communities and genetic elements remain less characterized. In this exploratory study, Hi-C-enabled metagenomics was applied to fecal samples from two cormorants to generate a genome-resolved, descriptive analysis of gut microbial composition and to associate bacterial genomes with mobile genetic elements (MGEs), antimicrobial resistance genes (ARGs), and putative virulence-associated genes. Metagenome-assembled genomes (MAGs) included taxa reported in aquatic or animal-associated environments, including Edwardsiella tarda, Plesiomonas shigelloides, Clostridium perfringens, and Campylobacter volucris. ARGs were detected across multiple MAGs, with E. tarda harboring the greatest diversity. Hi-C-enabled linkage of plasmids and phages to putative hosts, providing structural insight into microbial organization. Analyses are descriptive (n = 2) and do not include statistical comparisons or diversity metrics. These findings demonstrate the utility of Hi-C for resolving gene–host associations and provide a framework for future studies of microbial connectivity in One Health contexts.

Source: Microorganisms

DOI: 10.3390/microorganisms14061198