Characterization of the footrot microbiome in Portuguese sheep breeds through metagenomics

Description

Abstract (English)

Introduction: In the Alentejo region Merino sheep are 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 the bacteria Dichelobacter nodosus that interacts with the sheep foot microbiome, to date largely uncharacterized. To understand and characterize the footrot microbiome dynamics,of different footrot affection scores, a whole metagenome sequencing (WMGS) approach was used.

Materials and methods: Tissue samples from affected feet were collected from 212 animals with different footrot degrees of lesion severity, ranging from 0 to 5. DNA was extracted from each sample and used in WMGS. The sequence dataset was analysed with a classic metagenomics approach to characterize and quantify the composition of the microbial community present in each sample. The reads of each sample were taxonomically classified and the abundance of each species identified was estimated in order to perform a differential abundance analysis between the samples with different footrot infection degrees.

Results and discussion: 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 microbiome from a dominant gram-positive in mild stages to a dominant gram-negative in the severe stages. The diminished diversity is accompanied by the increased abundances, as the disease progressed, of D. nodosus and Fusobacterium necrophorum (which plays a role as an opportunistic and is considered as a secondary pathogen), along with several species previously associated with footrot and other polymicrobial diseases affecting the epidermis and provoking inflammatory responses such as Treponema spp., Staphylococcus spp., Streptococcus spp. and Campylobacter spp. Although these bacteria are not able to initiate footrot, several evidences have been described supporting their association with the severity and incidence increase of footrot lesions caused by D. nodosus and F. necrophorum.

Conclusions: These results confirm the involvement of D. nodosus and F. necrophorum as two of the main species related with footrot infection. In this work were also identified a set of key-species that differentiate mild and severe footrot infection stages. Although further investigation is required to establish the roles of particular taxa, our results provided significant information to better understand diseases pathogenesis representing an important contribution for the analysis of the microbiome in animal welfare research.