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<p>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 <i>Acinetobacter</i> 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 <i>Acinetobacter</i>, and therein a genome classified to <i>Patescibacteria</i> was detected harboring macrolides resistance <i>mef(B)</i>. 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.</p>

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

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2026年5月25日

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  • Fang-Zhou Gao,
  • Ping Li,
  • Zi-Chuan Huang,
  • Zi-Yin Chen,
  • Jia-Yi Zheng,
  • Hong Bai,
  • Liang-Ying He,
  • You-Sheng Liu,
  • Guang-Guo Ying

摘要

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.