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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 × 10 -3 and p = 2.6 × 10 -2 , respectively), hinting toward an exchange of antimicrobial-resistant strains between reservoirs.

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