Cross-Sectional Analysis of the Microbiota of Human Gut and Its Direct Environment in a Household Cohort with High Background of Antibiotic Use

B.V.T. Ngoc, H.H. Bich, G. Galazzo, D.V.T. Viet, M. Oomen, T.N.N. Minh, H.T. Huy, H.R. van Doorn, H.F.L. Wertheim, J. Penders*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review


Comprehensive insight into the microbiota of the gut of humans and animals, as well as their living environment, in communities with a high background of antibiotic use and antibiotic resistance genes is scarce. Here, we used 16S rRNA gene sequencing to describe the (dis)similarities in the microbiota of feces from humans (n = 107), domestic animals (n = 36), water (n = 89), and processed food (n = 74) in a cohort with individual history of antibiotic use in northern Vietnam. A significantly lower microbial diversity was observed among individuals who used antibiotics in the past 4 months (n = 44) compared to those who did not (n = 63). Fecal microbiota of humans was more diverse than nonhuman samples and shared a small part of its amplicon sequence variants (ASVs) with feces from animals (7.4% (3.2-9.9)), water (2.2% (1.2-2.8)), and food (3.1% (1.5-3.1)). Sharing of ASVs between humans and companion animals was not associated with the household. However, we did observe a correlation between an Enterobacteriaceae ASV and the presence of extended-spectrum beta-lactamase CTX-M-group-2 encoding genes in feces from humans and animals (p = 1.6 x 10(-3) and p = 2.6 x 10(-2), respectively), hinting toward an exchange of antimicrobial-resistant strains between reservoirs.</p>
Original languageEnglish
Article number2115
Number of pages19
Issue number10
Publication statusPublished - 1 Oct 2021


  • microbiota
  • One Health
  • Vietnam
  • environmental microbiota
  • metagenomics
  • antibiotic resistance
  • DIET

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