A metagenomics approach to characterize the footrot microbiome in Merino sheep

In the Portuguese Alentejo region, Merino sheep breed is the most common breed, reared for the production of meat, dairy, and wool. Footrot is responsible for lameness, decreased animal welfare, and higher production losses, generating a negative economic impact. The disease is caused by Dichelobacter nodosus that interacts with the sheep foot microbiome, to date largely uncharacterized. In fact, Dichelobacter nodosus is not able to induce footrot by itself being required the presence of a second pathogen known as Fusobacterium necrophorum. To understand and characterize the footrot microbiome dynamics of different footrot lesion scores, a whole meta-genome sequencing (WMGS) approach was used. Foot tissue samples were collected from 212 animals with different degrees of footrot lesion scores, ranging from 0 to 5. Distinct bacterial communities were associated with feet with different footrot scores identifying a total of 63 phyla and 504 families. As the severity of footrot infection increases the microorganisms' diversity decreases triggering a shift in the composition of the micro -biome from a dominant gram-positive in mild stages to a dominant gram-negative in the severe stages. Several species previously associated with footrot and other polymicrobial diseases affecting the epidermis and pro-voking inflammatory responses such as Treponema spp., Staphylococcus spp., Streptococcus spp. and Campylobacter spp. were identified proliferating along with the lesions' severity. Although these bacteria are not able to initiate footrot, several evidences have been described supporting their association with the severity and incidence in-crease of footrot lesions caused by Dichelobacter nodosus and Fusobacterium necrophorum. Further investigation is required to establish the roles of particular taxa and identify which of them play a role in the disease process and which are opportunistic pathogens.

Automated summary

In the Portuguese Alentejo region, the Merino sheep breed is commonly reared for meat, dairy, and wool production. Footrot, caused by Dichelobacter nodosus and Fusobacterium necrophorum, leads to lameness and economic losses. Meta-genome sequencing revealed distinct bacterial communities associated with different footrot lesion scores, with a shift from gram-positive to gram-negative dominance as severity increases. Species such as Treponema spp., Staphylococcus spp., Streptococcus spp., and Campylobacter spp. were found proliferating alongside lesion severity, indicating their association with footrot incidence and severity.