Targeting the treponemal microbiome of digital dermatitis infections by deep coverage pyrosequencing
ABSTRACT: 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.
Modern pyrosequencing technology allows for a more comprehensive approach than traditional Sanger sequencing for elucidating the etiology of bovine digital dermatitis. We sought to describe the composition and diversity of treponemes in digital dermatitis lesions by using deep sequencing of the V3 and V4 hypervariable regions of the 16S rRNA gene coupled with species-level taxonomic identification. Treponema-specific 16S rRNA gene PCRs and pyrosequencing were performed on biopsy specimens origin ...[more]
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).
Project description:Here we report 16s rRNA data in patients with Rheumatoid Artrhitis as compared with patients with sarcoidosis and healthy volunteers. Our data shows that the BAL microbiota of RA patients was significantly less diverse and abundant when compared to healthy controls, but similar to sarcoidosis patients. This distal airways dysbiosis was attributed to the reduced presence of several genus (i.e., Actynomyces and Burkhordelia) as well as reported periodontopathic taxa, including Treponema, Prevotella and Porphyromonas. While multiple clades correlated with local and systemic levels of autoantibodies, the genus Pseudonocardia and various related OTUs were the only taxa overrepresented in RA BAL and correlated with higher disease activity and erosions. Overall design: 16S rRNA was quantified and sequenced (MiSeq) from lung BAL of control, RA, and sarcoid patients. The amplicons from a total of 58 samples are barcoded and the barcodes are provided in the complete_metadata.txt file.
Project description:The benefit of treatment in mild to moderate cases of E. coli mastitis in dairy cows remains a topic of discussion. We investigated the effect of intramammary treatment with Cefapirin + Prednisolone compared to Cefapirin only on gene expression profiles in experimentally induced E. coli mastitis. Five midlactating Holstein Friesian cows were challenged with 100 CFU in 3 quarters and treated with Cefapirin only in one quarter and the combination of Cefaprirn and Prednisolne in another quarter at 4, 12, 24 and 36h post challenge. After 24h (n=2) or 48h (n=3) post challenge cows were sacrificed and mammary gland tissue was collected from each quarter. From each cow total RNA of one non challenged quarter, one challenged not treated quarter, on Cefapirin treated and one Cefapirin + Prednisolone treated quarter was subjected to microarray analysis. Data were analyzed separately for the two sample time points
Project description:Data from one animal from B9_B12 group (Cow 31) were not taken into account for the liver samples Treated animals were compared to control (non supplemented cows) Twenty four multiparous Holstein cows were assigned to 6 blocks of 4 animals according to their 305-d milk production during the previous lactation to one of the following treatments: injections saline 0.9% NaCl (Ctl); folic acid (B9); vitamin B12 (B12) or folic acid and vitamin B12 (B9_B12). Biopsies of hepatic (foie for liver) and mammary (mam for mammary gland) tissues were taken from these 24 cows. Microarray analyses were performed on samples from both tissues for 3 animals per treatment in CTL, B9 and B9_B12 and for 4 animals in B12 treatment. Data for hepatic tissue of animal 31 (group B9_B12) were not included. For both tissues, treated animals were compared to control.
Project description:Analysis of key genes and gene networks determining milk productivity of the dairy HF cows Transcriptomes were compared of in the mammary glands of the healthy lactating Holstein Friesian cows of the high- (average 11097 kg milk/lactation) and low- (average 6956 kg milk/lactation) milk yield.
Project description:Feed restriction and L-carnitine infusion are known to affect the liver metabolism of dairy cows. In the present experiment the effects on liver transcriptome of feed restriction and L-carnitine abomasal infusion and the interaction of the two in mid-lactation Holstein dairy cows was assessed. Data clearly indicated a lack of transcriptomics effect by L-carnitine but a strong effect due to feed restriction. The functional analysis identified a overall reduction of cholesterol synthesis and oxidative phosphorylation and data suggested an increase flux toward gluconeogenesis and fatty acid oxidation. The liver biopsy was performed after 14 days of treatment in 8 Holstein dairy cows in a 2 x 2 factorial arrangment with 5 days washout between treatments. A dye-swap reference design (reference = mixture of RNA from several bovine tissues) was used.
Project description:Early embryonic development is enhanced in Holstein cows fed diets enriched in specific polyunsaturated fatty acids. However, the molecular mechanisms affected by specific polyunsaturated fatty acids during early embryonic development in cattle are poorly understood. Therefore, our objective was to evaluate the maternal effects of diets enriched in linoleic or α-linolenic acid on transcriptome profiling of in vivo bovine pre-implantation embryos. Overall design: Non-lactating Holstein cows were blocked by parity and body weight, and assigned to one of three diets supplemented with rolled oilseeds: canola (n=8, high in oleic acid; control; CAN), sunflower (n=7, high in linoleic acid; SUN) or flax (n=8, high in α-linolenic acid; FLX). n is the number of maternal cows involved in each group. After a minimum of 35 d diet adaptation, ovarian status was synchronized and superstimulated by follicle-stimulating hormone treatments. Cows were artificially inseminated twice, 12h apart, with semen of the same sire. Once initiated, cows remained on the same diet until the end of the experiment.
Project description:In this study, the profile of mastitis-induced differential gene expression in the mammary tissue of Chinese Holstein cattle was investigated by Gene-Chip microarray and bioinformatics Our experiments included RNA samples was isolated from the mammary tissue of adult Chinese Holstein cows during late lactation with (n=3) and without (n=3) mastitis
Project description:Transcriptional profiling in vivo in bovine secretory tissue from healthy (H) mammary gland and during infections with coagulase-negative Staphylococci (CoNS) and coagulase-positive Staphylococci (CoPS). The aim of this study was to examinate the global gene expression profiles of mammary gland tissues of infected and healthy (control) cows. Transcriptomes were compared of in the mammary glands of Holstein Friesian cows in two experiments, (H) vs (CoNS) cows and (H) vs (CoPS).