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Clinical metagenome

ABSTRACT: Microbiota of digital dermatitis lesions from Brazilian dairy cattle

PROVIDER: PRJNA369034 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR5209060.fastq.gz	Fastqsanger.gz
	SRR5209070.fastq.gz	Fastqsanger.gz
	SRR5209080.fastq.gz	Fastqsanger.gz
	SRR5209090.fastq.gz	Fastqsanger.gz
	SRR5209100.fastq.gz	Fastqsanger.gz

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Identifying host pathogenic pathways in bovine digital dermatitis by RNA-Seq analysis of lesions

Project description:Digital dermatitis is a painful foot disease compromising welfare in dairy cattle. The disease has a complex multibacterial aetiology, but little is known about its pathogenesis. In this study, gene expression in skin biopsies from five bovine digital dermatitis lesions and five healthy bovine feet was compared using RNA-Seq technology. Differential gene expression was determined after mapping transcripts to the Btau 4.0 genome. Pathway analysis identified gene networks involving differentially expressed transcripts. Bovine digital dermatitis lesions had increased expression of mRNA for a2-macroglobulin-like 1, a protein potentially involved in bacterial immune evasion and bacterial survival. There was increased expression of keratin 6A and interleukin 1b mRNA in bovine digital dermatitis lesions, but reduced expression of most other keratin and keratin-associated genes. There was little evidence of local immune reactions to the bacterial infection present in lesions. Ten samples were processed; five normal skin biopsies from the hind foot skin and five digital dermatitis lesions (large (>2cm) red raw in appearance).

2013-03-26 | E-GEOD-41732 | biostudies-arrayexpress

Identifying host pathogenic pathways in bovine digital dermatitis by RNA-Seq analysis of lesions

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Continuous activation of the IL-17F driven inflammatory pathway in acute and chronic digital dermatitis lesions in dairy cattle

Project description:Objectives of the present study were to get a deeper insight into the course of the inflammatory pathways of digital dermatitis lesions in dairy cattle by investigating the gene expression patterns throughout the different clinical stages (M0 to M4.1) of the disease. Normal skin samples (M0) were used as a reference for comparing the gene expression levels in the other M-stages through RNA Seq-technology.

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Targeting the treponemal microbiome of digital dermatitis infections by deep coverage pyrosequencing

Project description:We examined 36 biopsies taken from digital dermatitis lesions of Holstein cows. The target was the V3 -V4 variable region of 16S rRNA using Treponema specific primers. We identified 20 different taxa of Treponema using this approach. Phylogenetic study of the Treponema taxa found in digital dermatitis lesions of Holstein cows.

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Project description:Skin lesions from Digital Dermatitis Metagenome

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Profiling the proteolytic dysfunction in digital dermatitis in cattle and the therapeutic use of a non-antimicrobial matrix metalloproteinase inhibitor

Project description:ABSTRACT Digital dermatitis (DD) is a painful inflammatory skin disease affecting the digital regions of cattle feet, linked to pathogenic Treponemes spp. This condition imposes a substantial economic burden on the cattle industry attributable to lameness and subsequent production inefficiencies. Currently, there is an absence of fully effective therapeutics for DD, and the underlying mechanisms governing the skin's inflammatory response remain largely unknown. This study elucidated the proteomic signature in the foot skin of cattle manifesting active DD lesions subjected to topical treatment with a non-antimicrobial metalloprotease inhibitor, CMC2.24 or the routinely used antibiotic treatment, oxytetracycline (OTC). The results demonstrated that active, non-healing ulcerative DD lesions exhibited persistent infiltration of inflammatory leukocytes alongside a proteomic profile characterized by enrichment in neutrophil degranulation-related pathways and elevated activity of matrix metalloproteinases (MMPs), which likely exacerbates cutaneous inflammation and ulceration. Treatment with OTC accelerated the cornification of DD lesions; however, these lesions still exhibited distinct inflammatory characteristics, which included sustained elevated levels of S100A8, a molecule known to promote neutrophil aggregation and reactive oxygen species (ROS) generation. Conversely, the MMP inhibitor CMC2.24 effectively mitigated active DD lesions by attenuating ROS production and keratinization pathways. Furthermore, CMC2.24 inhibited interleukin-1 beta (Il-1β) secretion in both bovine and murine macrophages challenged with DD-associated Treponemas spp. These data indicate a pro-inflammatory proteomic profile in DD lesions, highlighting that a non-antimicrobial MMP inhibitor could effectively reduce foot skin inflammation relative to conventional OTC treatment.

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Project description:Microbiota from Bovine digital dermatitis lesions targeted loci

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Continuous activation of the IL-17F driven inflammatory pathway in acute and chronic digital dermatitis lesions in dairy cattle

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