Shotgun metagenomics reveals antibiotic resistome dynamics and metabolic specialization in fungal-dominated microbiomes.

Background: Metagenomics offers a culture-independent framework for comprehensively characterizing microbial communities by directly extracting and sequencing DNA from environmental samples. In this study, we employed high-throughput metagenomic sequencing to explore microbial communities inhabiting fungal-rich environments, emphasizing taxonomic composition, functional potential, and antibiotic resistance gene (ARG) dynamics. Methods: Six samples from two distinct groups (HFJ and QFJ) were subjected to Illumina-based shotgun sequencing, followed by rigorous quality control, taxonomic classification, KEGG-based functional annotation, and ARG identification via the CARD database. Comparative analysis revealed stark contrasts between the two groups. Results: HFJ samples were dominated by eukaryotic taxa, particularly Conclusion: Our results reveal distinct microbial, functional and resistome profiles in fungal-rich versus bacterial-rich fermentation environments. Fungal dominance correlated with lower bacterial diversity and a reduced abundance of certain ARGs, whereas bacterial-rich samples exhibited higher diversity and ARG prevalence. These correlations generate the hypothesis that fungal dominance may suppress bacterial growth or ARG dissemination; however, causal relationships cannot be inferred from our cross-sectional data. The study highlights the potential of metagenomic surveillance to elucidate ecological niches that influence bacterial diversity and resistance dynamics.