The bacterial communities in the gastro-intestinal tract of animals and humans have a multitude of functions that can impact health, such as the metabolism of nutrients and interactions with the immune system. The composition of the gut microbiota is shaped by both intrinsic and extrinsic or environmental factors (e.g., diet and geography) (Spor et al., 2011; Gupta et al., 2017). The human-animal interface is an important element of our environment, and interactions between humans and animals are well-recognized as important determinants for public health. Especially when this relates to zoonoses, as up to 60% of human pathogens are of zoonotic origin (Rahman et al., 2020). Exposure to animals also includes exposure to their microbiomes. In recent years, studies have shown that contact with animals can have an influence on the microbiome of humans (Trinh et al., 2018; Mucci et al., 2022). Among others, influence on the diversity and composition of skin, nasal and gut microbiota has been described for people living together with pets or having occupational contact with livestock. Also, microbiome and resistome (i.e., all the antibiotic resistance genes in the gut ecosystem) components can be shared between humans and animals when in close contact (Sun et al., 2020; Yang et al., 2023; Mahmud et al., 2024). In the Netherlands, dairy farming is an important livestock sector with more than 15–000 dairy farms and 1.5 million dairy cattle in 2021 (CBS, 2025). Often, these are family owned farms, where contact of the farmer and family members with the dairy cattle is frequent. In previous studies from other countries, influence of contact with dairy cattle on the nasal and gut microbiome of humans has been described (Shukla et al., 2017; Mahmud et al., 2024). In this pilot study we aimed to compare the gut microbiome of participants from Dutch dairy farms with age and sex-matched control subjects from a population-wide study to determine the main drivers of the microbiome composition. This will help to elucidate the impact of occupational animal exposure on the human gut microbiome.

In this study, the faecal microbiome from 130 persons was determined; 65 participants from dairy farms (DF) and 65 controls. DF participants originated from 36 different farms (1–4 participants per farm). From the DF participants, 63% reported being a dairy farmer with the others being relatives (partner, parent or child), and one person reported being an employee. Most of the DF participants (92%) reported going into the cattle stables ≥ 1 time a day, and 82% reported daily physical contact with cattle. For the controls, no information on animal contact was available.

Alpha diversity of DF was lower compared to controls, both in the Shannon (p=0.0059) and Simpson index (p=0.0018), with no differences in the observed number of taxa (p=0.45, Figure 1A ). The overall microbiome composition of the DF participants was significantly different from the controls, assessed by the Bray Curtis dissimilarity index and Principal Coordinate Analysis (PCoA) (PERMANOVA p=0.001, Figure 1B ). Beta diversity analyses showed that the difference between DF participants and controls was driven largely (with 37% of variance explained by the first principal component) by the higher relative abundance of Prevotella and Prevotella_9 groups (p=2.8x10^-6, with amplicon sequence variants (ASV’s) further annotated as P. copri) ( Figures 1B, E ).

Looking at the ratio of Prevotella to Bacteroides in our study population, a clear gradient emerged, which was distinctive between DF participants and controls ( Figures 1C, D ). At the genus level, the other significant differences were a higher relative abundance of Bacteroides (p=0.0043), Faecalibacterium (p=0.0004) and Subdoligranulum in the controls (p=0.047, Figure 1E ).

We further investigated the influence of contact frequency (i.e., contact with cattle once a day or more, n=57 vs. once a week or less, n=8). Although group size was limited, we observed significant differences in both overall microbiome composition (PERMANOVA p=0.019, Figure 2A ) and in the relative abundance of Prevotella_9 between the groups (p=0.01, Figure 2B ). In the group with less contact with cattle, the relative abundance of Prevotella_9 was significantly lower.

In this study, we compared faecal microbiome composition between participants from Dutch dairy farms and control subjects. The alpha diversity of DF participants was lower than controls. Previous reports on farming and alpha diversity have been conflicting, as a study in Chinese pig farmers showed a higher diversity in control subjects, while a Dutch study on pig farmers and a US study on dairy farmers did not report differences compared to the control subjects (Sun et al., 2017; Van Gompel et al., 2020; Mahmud et al., 2024). While a lower microbial diversity has been associated with diseased states, in these cases, other than in our study, a lower diversity was observed together with an increased proportion of facultative anaerobes (e.g. Proteobacteria and Bacilli), often considered less desirable (Kriss et al., 2018).

Overall microbiome composition was significantly different between DF participants and controls. In contrast, in the study among US dairy farmers, no difference in overall microbiome composition was observed compared to controls (Mahmud et al., 2024).

Principal coordinate analysis showed that the main driver of the difference between DF and control microbiomes was the genus Prevotella. Members of the genus Prevotella are Gram-negative anaerobic bacteria, found in various animal hosts. In ruminants, Prevotella are a common feature of the gut microbiome (Henderson et al., 2015). Human gut microbiomes are often dominated by either Prevotella or Bacteroides (Gorvitovskaia et al., 2016), with Prevotella-dominated microbiomes more often found among non-Western populations. In addition, a high abundance of Prevotella, a fibre-degrading genus, is also associated with diets rich in fibres and complex carbohydrates (Tett et al., 2021). A limitation of our study was the lack of diet and other lifestyle information gathered from both DF participants and controls. The potential contribution of these factors, especially diet, to the Prevotella abundance remains to be determined. Potential associations of Prevotella with health and disease are currently still unclear, with conflicting reports linking this genus to both beneficial or detrimental health outcomes (Abdelsalam et al., 2023). It becomes more evident that there is also a link between Prevotella and animal contact, as higher Prevotella abundance was previously observed in a US study of dairy farmers, a Swiss study of pig farmers and associated with pet ownership in a Dutch cohort (Moor et al., 2021; Mahmud et al., 2024; Gacesa et al., 2022).

Differences in microbiome composition and Prevotella abundance were not only observed between DF participants and controls, but also between DF participants with frequent and less frequent contact with the dairy cattle. These findings suggest that the observed associations between dairy farming and gut microbiome are most likely a direct effect of (frequent) contact with dairy cattle, rather than other possible differences between DF and controls. In a previous study in pig farmers, common bacterial sequences, including Prevotella, were found in samples from the farmers, the pigs and air samples from the stables (Moor et al., 2021). The authors suggested that farmers took up aerosols with bacteria derived from the pigs. Other studies also reported overlap of sequences between humans and the animals they were in close contact with (Tan et al., 2020; Mahmud et al., 2024). Possibly, shared microbial lineages between the dairy cattle and DF participants, leading to a shift in microbiome composition, could be similarly explanatory for our findings. Unfortunately, we did not include samples from the dairy cattle in our study, as these samples were not suitably collected for microbiome analysis (e.g., to preserve nucleid acids or prevent the overgrowth of anaerobes). This could be a valuable addition for future studies as insight in shared sequences at farm-level would help further explain the microbiome diversity in dairy farmers.

In conclusion, we report an association between dairy farming and the gut microbiome of farmers and their family members, largely driven by Prevotella, and likely as a direct effect of contact with dairy cattle. Our results are an addition to previous studies and strengthen the knowledge about the influence of human-animal contact on the microbiome.