ORIGINAL RESEARCH article
Front. Microbiol.
Sec. Terrestrial Microbiology
Volume 16 - 2025 | doi: 10.3389/fmicb.2025.1626799
This article is part of the Research TopicTrigger the Microbiome Changes in Foods via Metagenomic Technologies: From Diagnostic to Potential Changes in Product Safety or Quality Risk ProfilesView all 4 articles
Shotgun Metagenomics Reveals Antibiotic Resistome Dynamics and Metabolic Specialization in Fungal-Dominated Microbiomes
Provisionally accepted
- Department of Materials and Chemical Engineering, Shanxi, China
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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 Saccharomyces cerevisiae, and exhibited elevated carbohydrate metabolism, aligning with the ecological role of fermentative fungi. Conversely, QFJ samples displayed higher bacterial diversity, particularly Firmicutes and Proteobacteria, and were enriched in lipid and amino acid metabolism pathways. Striking differences were also observed in ARG profiles. QFJ samples harbored greater ARG abundance, particularly genes conferring resistance to beta-lactams, aminoglycosides, and tetracyclines, indicating higher resistance potential and possible horizontal gene transfer activity. 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.
Keywords: Metagenomics, Fungi, Microbial genome, antibiotic resistance, Metabolism
Received: 25 May 2025; Accepted: 02 Sep 2025.
Copyright: © 2025 Zhao, Qiao, Wang, Xiong, Wang, Su and Guo. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Xin Zhao, Department of Materials and Chemical Engineering, Shanxi, China
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