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

Scholey, Rachel; Evans, Nicholas J.; Blowey, Roger; Massey, Jonathan; Murray, Richard D.; Smith, Robert F.; Ollier, William; Carter, Stuart

doi:10.1016/j.tvjl.2013.03.008

Cited by 23 publications

(31 citation statements)

References 45 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The host immune response was investigated through the mRNA expression of a panel of six inflammatory genes likely to have a role in skin immune responses in sheep and cattle235455. Surprisingly, in the context of foot disease, no differential expression of IL1β, IL6, CXCL8 and IL17 was identified in ID and footrot compared to healthy samples.…”

Section: Discussionmentioning

confidence: 99%

A distinct bacterial dysbiosis associated skin inflammation in ovine footrot

Maboni

Blanchard

Frosth

et al. 2017

Sci Rep

View full text Add to dashboard Cite

Ovine footrot is a highly prevalent bacterial disease caused by Dichelobacter nodosus and characterised by the separation of the hoof horn from the underlying skin. The role of innate immune molecules and other bacterial communities in the development of footrot lesions remains unclear. This study shows a significant association between the high expression of IL1β and high D. nodosus load in footrot samples. Investigation of the microbial population identified distinct bacterial populations in the different disease stages and also depending on the level of inflammation. Treponema (34%), Mycoplasma (29%) and Porphyromonas (15%) were the most abundant genera associated with high levels of inflammation in footrot. In contrast, Acinetobacter (25%), Corynebacteria (17%) and Flavobacterium (17%) were the most abundant genera associated with high levels of inflammation in healthy feet. This demonstrates for the first time there is a distinct microbial community associated with footrot and high cytokine expression.

show abstract

Section: Discussionmentioning

confidence: 99%

A distinct bacterial dysbiosis associated skin inflammation in ovine footrot

Maboni

Blanchard

Frosth

et al. 2017

Sci Rep

View full text Add to dashboard Cite

show abstract

“…There is a general dermal thickening in lesion development that is accompanied by varying degrees of infiltration of inflammatory cells (neutrophils and eosinophils) and changes in local cytokine concentrations (Refaai et al., ). Similarly, gene expression in skin biopsies from five bovine DD lesions and five healthy bovine feet was compared using RNA‐Seq technology (Scholey et al., ). They demonstrated changes in cytokine expression (especially interleukin 1β being upregulated in DD lesions) and changes in expression of several other keratin or keratin‐associated genes.…”

Section: Immune Responses To Infectionmentioning

confidence: 99%

Missing pieces of the puzzle to effectively control digital dermatitis

Orsel

Plummer

Shearer

et al. 2017

Transbound Emerg Dis

View full text Add to dashboard Cite

Since the first report of bovine digital dermatitis (DD) in 1974, there is a large body of the literature published; however, effective prevention and control of the disease remain elusive. Although many aspects of the pathogenesis of DD have been investigated, even some of the most basic questions such as the aetiology of this disease remain under debate. Treponema spp. have been strongly associated with DD lesions and occur in abundance in advanced lesions; however, efforts to induce disease with pure cultures of these organisms have been largely underwhelming and inconsistent. Furthermore, although the disease has been presented for several decades, there is limited scientific evidence regarding effective treatment of DD. Apparent discrepancies between effectiveness in vitro and in vivo have challenged the scientific community to identify new potential treatment options. With no treatment resulting in a 100% cure rate, the current expectation is manageable control, but prospects for the eradication of the disease are unlikely using current approaches. In order to develop more effective approaches to control DD on-farm, there is a critical need for a deeper understanding regarding the causation, ecology, transmission and treatment of this disease. In this article, we attempt to provide insights into specific research needs related to DD in order to assist the industry, researchers, pharmaceutical companies and research sponsors with decision-making and identified research gaps.

show abstract

“…The raw data with the accession number GSE41732 was obtained from the GEO database and analysed with the GeneTiles software package. Comparing the differential expression data from Scholey et al 2013 (Scholey et al 2013 ), we could not validate all transcripts, since 23 % of the transcripts are retired and are not available anymore, due to the updated version of the Bos taurus 4.0 Ensembl annotation to the COW UMD3.1 Ensembl annotation. All other transcripts could be validated.…”

Section: Resultsmentioning

confidence: 99%

“…To date, we have only found 1 publication in PubMed describing RNAseq analysis of the host after a bacterial infection in vivo other than in zebrafish (Scholey et al 2013 ). The data of Scholey et al 2013 (Scholey et al 2013 ), describing the bovine digital dermatitis (BDD, an infectious foot disease), was used to compare the host response in the cow and zebrafish. The raw data with the accession number GSE41732 was obtained from the GEO database and analysed with the GeneTiles software package.…”

Section: Resultsmentioning

confidence: 99%

“…Finally, we wanted to include a comparison with whole organism infection data in other vertebrate species. Unfortunately, there are still few available RNAseq data for this that can be mapped on Ensembl genome data; and as a result, we have only been able to compare our zebrafish infection data with the RNAseq data from a bovine digital dermatitis (BDD) model as published by Scholey et al 2013 (Scholey et al 2013 ). However, the results are sufficient to show that our approach makes also such interspecies comparisons of RNAseq datasets very easy and this can quickly lead to conclusions on conserved immune responses, even in comparisons between very different fish and mammalian infection models.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Analysis of RNAseq datasets from a comparative infectious disease zebrafish model using GeneTiles bioinformatics

Veneman

Sonneville²,

Kolk

et al. 2014

Immunogenetics

View full text Add to dashboard Cite

We present a RNA deep sequencing (RNAseq) analysis of a comparison of the transcriptome responses to infection of zebrafish larvae with Staphylococcus epidermidis and Mycobacterium marinum bacteria. We show how our developed GeneTiles software can improve RNAseq analysis approaches by more confidently identifying a large set of markers upon infection with these bacteria. For analysis of RNAseq data currently, software programs such as Bowtie2 and Samtools are indispensable. However, these programs that are designed for a LINUX environment require some dedicated programming skills and have no options for visualisation of the resulting mapped sequence reads. Especially with large data sets, this makes the analysis time consuming and difficult for non-expert users. We have applied the GeneTiles software to the analysis of previously published and newly obtained RNAseq datasets of our zebrafish infection model, and we have shown the applicability of this approach also to published RNAseq datasets of other organisms by comparing our data with a published mammalian infection study. In addition, we have implemented the DEXSeq module in the GeneTiles software to identify genes, such as glucagon A, that are differentially spliced under infection conditions. In the analysis of our RNAseq data, this has led to the possibility to improve the size of data sets that could be efficiently compared without using problem-dedicated programs, leading to a quick identification of marker sets. Therefore, this approach will also be highly useful for transcriptome analyses of other organisms for which well-characterised genomes are available.Electronic supplementary materialThe online version of this article (doi:10.1007/s00251-014-0820-3) contains supplementary material, which is available to authorized users.

show abstract

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

Cited by 23 publications

References 45 publications

A distinct bacterial dysbiosis associated skin inflammation in ovine footrot

A distinct bacterial dysbiosis associated skin inflammation in ovine footrot

Missing pieces of the puzzle to effectively control digital dermatitis

Analysis of RNAseq datasets from a comparative infectious disease zebrafish model using GeneTiles bioinformatics

Contact Info

Product

Resources

About