Ovine pedomics: the first study of the ovine foot 16S rRNA-based microbiome

Abstract

We report the first study of the bacterial microbiome of ovine interdigital skin based on 16S rRNA by pyrosequencing and conventional cloning with Sanger-sequencing. Three flocks were selected, one a flock with no signs of footrot or interdigital dermatitis, a second flock with interdigital dermatitis alone and a third flock with both interdigital dermatitis and footrot. The sheep were classified as having either healthy interdigital skin (H) and interdigital dermatitis (ID) or virulent footrot (VFR). The ovine interdigital skin bacterial community varied significantly by flock and clinical condition. The diversity and richness of operational taxonomic units was greater in tissue from sheep with ID than H or VFR-affected sheep. Actinobacteria, Bacteriodetes, Firmicutes and Proteobacteria were the most abundant phyla comprising 25 genera. Peptostreptococcus, Corynebacterium and Staphylococcus were associated with H, ID and VFR, respectively. Sequences of Dichelobacter nodosus, the causal agent of ovine footrot, were not amplified because of mismatches in the 16S rRNA universal forward primer (27F). A specific real-time PCR assay was used to demonstrate the presence of D. nodosus, which was detected in all samples including the flock with no signs of ID or VFR. Sheep with ID had significantly higher numbers of D. nodosus (10 4 -10 9 cells per g tissue) than those with H or VFR feet.

A distinct bacterial dysbiosis associated skin inflammation in ovine footrot

“…In healthy and ID feet the most abundant genera were Corynebacteria, Psychrobacter and Acinetobacter , while in footrot the most abundant genera were Mycoplasma, Corynebacteria, Psychrobacter and Treponema . However, these populations differ from a small study that was the first publication of the 16S based ovine foot microbiome, where Macrococcus, Peptostreptococcus and Corynebacteria were most abundant in healthy, Macrococcus and Corynebacteria were most abundant in ID and Macrococcus, Staphylococcus and Corynebacteria most abundant in footrot affected feet6. There are several factors that explain those differences, in our study the sample number was higher (40 healthy, 30 ID and 36 footrot versus 3 healthy, 2 ID, 1 footrot), each of our samples was from an individual foot and not pooled from all feet per sheep.…”

“…Increased proportions of Corynebacteria were also observed in canine atopic dermatitis34. Of the bacterial genera identified, Dichelobacter, Fusobacteria and Treponema all linked to ovine or bovine foot disease467810. Prevotella and Porphyromonas were isolated from footrot cases in goats35 and were recently reclassified from Bacteriodes melaninogenicus 36, a species regularly isolated from bovine interdigital necrobacillosis (bovine footrot)37.…”

“…Fusobacterium necrophorum, also a Gram negative bacterium, is attributed to play a role in the initiation of ID prior to D. nodosus infection1, and/or in the exacerbation of footrot lesions once it is established5. Other bacteria such as Treponema have also been detected in footrot cases, but its role in the disease process remains unclear678. A microbiota study, using a pyrosequencing approach, found 27 different bacterial genera in the ovine interdigital skin where Peptostreptococcus was the most abundant genus in healthy interdigital skin, Corynebacterium was mainly associated with ID and Staphylococcus was the most abundant read genus in footrot samples6.…”

“…Other bacteria such as Treponema have also been detected in footrot cases, but its role in the disease process remains unclear678. A microbiota study, using a pyrosequencing approach, found 27 different bacterial genera in the ovine interdigital skin where Peptostreptococcus was the most abundant genus in healthy interdigital skin, Corynebacterium was mainly associated with ID and Staphylococcus was the most abundant read genus in footrot samples6. A similar disease in cattle, bovine digital dermatitis (BDD), also presents a complex aetiology and is considered a polymicrobial disease910.…”

Targeting the Treponemal Microbiome of Digital Dermatitis Infections by High-Resolution Phylogenetic Analyses and Comparison with Fluorescent In Situ Hybridization

“…With the advent of high-throughput sequencing technologies, however, it is now possible to obtain high-resolution bacterial communities and to process large numbers of samples at an affordable price (29,30). In this study, we used 454 pyrosequencing to perform in-depth, phylogenetic analysis of 36 DD biopsy specimens that were removed from 10 different dairy herds in Spain.…”