Shotgun Metagenomic Sequencing Reveals Functional Genes and Microbiome Associated with Bovine Digital Dermatitis

Abstract

Metagenomic methods amplifying 16S ribosomal RNA genes have been used to describe the microbial diversity of healthy skin and lesion stages of bovine digital dermatitis (DD) and to detect critical pathogens involved with disease pathogenesis. In this study, we characterized the microbiome and for the first time, the composition of functional genes of healthy skin (HS), active (ADD) and inactive (IDD) lesion stages using a whole-genome shotgun approach. Metagenomic sequences were annotated using MG-RAST pipeline. Six phyla were identified as the most abundant. Firmicutes and Actinobacteria were the predominant bacterial phyla in the microbiome of HS, while Spirochetes, Bacteroidetes and Proteobacteria were highly abundant in ADD and IDD. T. denticola-like, T. vincentii-like and T. phagedenis-like constituted the most abundant species in ADD and IDD. Recruitment plots comparing sequences from HS, ADD and IDD samples to the genomes of specific Treponema spp., supported the presence of T. denticola and T. vincentii in ADD and IDD. Comparison of the functional composition of HS to ADD and IDD identified a significant difference in genes associated with motility/chemotaxis and iron acquisition/metabolism. We also provide evidence that the microbiome of ADD and IDD compared to that of HS had significantly higher abundance of genes associated with resistance to copper and zinc, which are commonly used in footbaths to prevent and control DD. In conclusion, the results from this study provide new insights into the HS, ADD and IDD microbiomes, improve our understanding of the disease pathogenesis and generate unprecedented knowledge regarding the functional genetic composition of the digital dermatitis microbiome.

The cutaneous ecosystem: the roles of the skin microbiome in health and its association with inflammatory skin conditions in humans and animals

“…Fewer studies have described the skin microbiome using NGS in large animals, and no studies to date have characterized the skin microbiome inhabiting different skin surfaces in large animals. In ruminants, most attention has been given to describing the microbiome of digits (Table ), due to the high prevalence of digital dermatitis . The digits of bovine are highly diverse and Firmicutes, Spirochaetae, Bacteroidetes and Actinobacteria are the most predominant phyla.…”

“…In a metagenomic study, using shotgun sequencing, it was reported that cattle with DD had increased relative abundances of Spirochaetes, Bacteroidetes and Proteobacteria, in contrast to healthy feet which were colonized predominantly by Firmicutes and Actinobacteria . Treponema denticola and T. vincentii were the predominant bacterial species identified in both active and inactive DD.…”

Missing pieces of the puzzle to effectively control digital dermatitis

“…Despite a significant number of studies focused on elucidating the aetiology of DD, debate remains regarding the exact aetiology. Although fungal and viral aetiologies have been considered, the scientific community has largely agreed that these organisms are less likely to drive the disease process, and the field has focused its attention on bacterial organisms (Brandt et al., ; Krull et al., ; Rebhun, Payne, King, Wolfe, & Begg, ; Zinicola et al., ). For a detailed overview of the findings of this body of knowledge, readers are directed to the review articles referenced at the start of this manuscript; however, two consistent themes have emerged from these studies.…”

“…For a detailed overview of the findings of this body of knowledge, readers are directed to the review articles referenced at the start of this manuscript; however, two consistent themes have emerged from these studies. First, DD lesions are consistently associated with an abundant and diverse population of multiple species of treponemes (Evans et al., ; Krull et al., ; Zinicola et al., ). Second, these diverse treponeme populations exist as a portion of a much more diverse and complex bacterial community that comprises the total microbiota of the DD lesions.…”

“…Second, these diverse treponeme populations exist as a portion of a much more diverse and complex bacterial community that comprises the total microbiota of the DD lesions. Furthermore, the non‐treponemal constituents of the microbiota are not random and instead show association with the stage of lesion development (Krull et al., ; Zinicola et al., ). As described in more detail by Krull et al.…”