Globally, half a billion people are employed in animal agriculture and are directly exposed to the associated microorganisms. However, the extent to which such exposures affect resident human microbiomes is unclear. Here we conducted a longitudinal profiling of the nasal and faecal microbiomes of 66 dairy farmers and 166 dairy cows over a year-long period. We compare farmer microbiomes to those of 60 age-, sex- and ZIP code-matched people with no occupational exposures to farm animals (non-farmers). We show that farming is associated with microbiomes containing livestock-associated microbes; this is most apparent in the nasal bacterial community, with farmers harbouring a richer and more diverse nasal community than non-farmers. Similarly, in the gut microbial communities, we identify more shared microbial lineages between cows and farmers from the same farms. Additionally, we find that shared microbes are associated with antibiotic resistance genes. Overall, our study demonstrates the interconnectedness of human and animal microbiomes.

全球有 5 亿人从事畜牧业并直接接触相关微生物。然而，此类暴露对人类常驻微生物组的影响程度尚不清楚。我们对 66 名奶农和 166 头奶牛在一年内的鼻腔和粪便微生物组进行了纵向分析。我们将农民的微生物组与 60 名年龄、性别和邮政编码匹配且没有职业接触农场动物的人（非农民）的微生物组进行了比较。我们证明农业与含有牲畜相关微生物的微生物组有关；这在鼻腔细菌群落中最为明显，农民比非农民拥有更丰富、更多样化的鼻腔群落。同样，在肠道微生物群落中，我们发现同一农场的奶牛和农民之间有更多共同的微生物谱系。此外，我们发现共享微生物与抗生素抗性基因有关。总的来说，我们的研究证明了人类和动物微生物组的相互关联性。