# Hoof, Vaginal and Milk Microbiota Alterations in Dairy Cows with Foot Rot

## TL;DR

Foot rot in dairy cows causes changes in bacteria not just in the hoof but also in the udder and vagina, suggesting broader health impacts.

## Contribution

This study is the first to show microbiota changes in hoof, udder, and vaginal samples of cows with foot rot.

## Key findings

- Foot rot is linked to increased anaerobic and harmful bacteria in hoof, vaginal, and milk samples.
- Fusobacterium and Clostridium were more abundant in affected cows, with lower microbial diversity and stability.
- Integrated management of hoof, udder, and reproductive health may improve cow welfare and productivity.

## Abstract

Foot rot is a common infectious hoof disease that causes pain and lameness in dairy cows and can reduce milk production and overall performance. This study aimed to determine whether cows with foot rot show changes in the bacterial communities not only on the hoof but also in the udder and the vagina. Our results showed that foot rot was associated with clear shifts in the bacteria found in hoof swabs, vaginal swabs, and milk. In affected cows, the abundance of anaerobic bacteria and other potentially harmful bacteria increased, and the stability of the bacterial community decreased. These findings suggest that foot rot may not be only a local hoof problem and that herd management should consider its broader effects on cow health. Strengthening prevention and early control of hoof disease, while paying attention to udder health and reproductive health, may help improve animal welfare and farm productivity.

Foot rot is a major infectious cause of lameness in dairy cows and can severely compromise production performance and animal welfare. However, it remains unclear whether foot rot is accompanied by microbiota alterations beyond the hoof, particularly in the vagina and milk. We conducted a case–control study of 24 Holstein cows (12 with clinical foot rot and 12 healthy controls). Hoof swabs, milk, and vaginal swabs were collected and analyzed using 16S rRNA gene amplicon sequencing, alongside quantitative PCR. Microbial community composition differed between cows with foot rot and healthy controls across hoof (R2 = 0.26), vaginal (R2 = 0.072), and milk (R2 = 0.16) samples (Bray–Curtis, PERMANOVA, p < 0.001). Simpson diversity was lower in the hoof and vaginal microbiota (p < 0.05) but not in milk (p = 0.13). Differential abundance analysis identified enrichment of Fusobacterium in hoof and vaginal samples (p < 0.001), and absolute qPCR confirmed a higher vaginal load of Fusobacterium necrophorum in cows with foot rot (p < 0.05). Milk samples from foot rot cows showed enrichment of Clostridium and Porphyromonas. Co-occurrence network analysis revealed reduced microbial connectivity in foot rot-affected cows (average degree: 4.98 vs. 6.70) and increased network fragmentation (14 vs. 9 modules), suggesting lower ecosystem stability. Overall, foot rot was associated with microbiota shifts across the hoof, vagina, and milk, highlighting the potential value of integrated management strategies that consider extra-hoof microbial alterations.