The bacterial faecal microbiota shifts during the transition period in dairy cows

In dairy cows, the transition period around parturition is a critical period with the highest incidence of infectious and metabolic diseases compared to the rest of the lactation. Over the past few years, several studies have highlighted the central role of the microbiota in health and disease. In mammals, gut microbiota is typically studied by analysing faecal samples. In cattle, most research on the gastrointestinal microbiota has focused on the ruminal microbiota, while the composition and evolution of the faecal microbiota in transitioning dairy cows remain poorly studied. We aimed to describe the composition of the faecal bacterial microbiota in a large number of dairy cows around parturition on commercial farms. Faecal samples were collected three weeks before and one week after calving from a cohort of 411 Holstein dairy cows in their 2nd and 3rd lactations across 25 dairy herds. DNA was extracted from faeces, and the 16S rRNA gene (hypervariable region V3-V4) was sequenced after amplification.

A loss of microbial diversity was observed after calving, with no significant association with the lactation rank. The analysis identified different genera when comparing pre- and post-calving samples, indicating significant changes in the faecal microbiota of dairy cows after calving compared to the dry period, closer to calving. Among the major changes, Verrucomicrobiota were less abundant in the two unknown genera from the phylum after calving. In contrast, the proportion of Bifidobacterium was higher after than before calving.

Shifts in faecal microbiota around calving may be attributed to changes in diet composition, feed intake modifications, or physiological changes from the dry period to lactation. However, other factors such as genetic background and health factors may also influence the microbiota composition. This could be further investigated to identify biomarkers for predicting imbalances or identifying maladaptation to the lactation stage.