Small-sized microbes from rural groundwater showed antimicrobial resistance and resistome sharing with human microbiomes

Small-sized microbes (SMs) are widespread in groundwater; however, their implications for human health remain poorly understood. By employing multi-omics and culture techniques, we uncovered a substantial diversity of SMs in rural groundwater, demonstrating clear distinctions from large-sized fractions. SMs were dominated by pathogens represented by several Acinetobacter species, although they were typically considered as large-sized. SMs harbored 1136 antibiotic resistance genes (ARGs), and approximately 700 were transcriptionally active. Nearly 20% of metagenome-assembled genomes harbored ARGs, with 54 belonging to Acinetobacter, and therein a genome classified to Patescibacteria was detected harboring macrolides resistance mef(B). While SMs displayed lower antibiotic tolerance in groundwater, there were 62 species – including 17 pathogens – showing enhanced tolerance to ten antibiotics after resuscitation. The 653 shared ARGs and 42 homologs suggest resistome sharing between groundwater SMs and the gut microbiomes from local residents. These findings highlight the role of SMs as latent reservoirs for antimicrobial resistance. While small-sized microbes showed lower antibiotic resistance in groundwater, 62 species including 17 pathogens displayed enhanced tolerance to 10 antibiotics and 653 genes shared resistome with human gut microbiome of local residents, based on a field study at Bobai County, Southern China.