Microbiome composition of ocular surface in horses
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB47717 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR9530670.fastq.gz | Fastqsanger.gz | |||
| ERR9530671.fastq.gz | Fastqsanger.gz | |||
| ERR9530672.fastq.gz | Fastqsanger.gz | |||
| ERR9530673.fastq.gz | Fastqsanger.gz | |||
| ERR9530674.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 14 |
Similar Datasets
Project description:Differences of the intestinal microbiome between healthy horses and horses with colic
| PRJEB47719 | ENA
Project description:Ocular surface microbiome in dupilumab associated ocular surface disease
| PRJEB57775 | ENA
Project description:To determine if there is a core ocular surface microbiome and whether there are microbial community changes over time, the conjunctiva of 45 healthy subjects were sampled at three time points over three months and processed using culture-dependent and -independent methods. Contaminant taxa were removed using a linear regression model using taxa abundances in negative controls as predictor of taxa abundances in subject samples. Both cultured cell counts and sequencing indicated low microbial biomass on the ocular surface. No cultured species was found in all subjects at all times or in all subjects at any one time. After removal of contaminant taxa identified in negative controls using a statistical model, the most commonly detected taxon was Corynebacterium (11.1%). No taxa were found in all subjects at all times or in all subjects in any one time, but there were 26 taxa present in at least one or more subjects at all times including Corynebacterium and Streptococcus. The ocular surface contains a low diversity of microorganisms. Using culture dependent and independent methods, the ocular surface does not appear to support a substantial core microbiome. However, consistently present taxa could be observed within individuals suggesting the possibility of individual-specific core microbiomes.
| S-EPMC5575025 | biostudies-literature
Project description:Bovine Ocular Microbiome Raw sequence reads
| PRJNA578146 | ENA
Project description:Atypical myopathy (AM) is a severe rhabdomyolysis syndrome that occurs in grazing horses. Despite the presence of toxins in their blood, all horses from the same pasture are not prone to display clinical signs of AM. The objective of this study was to compare the blood metabolomic profiles of horses with AM clinical signs with those of healthy co-grazing (Co-G) horses. To do so, plasma samples from 5 AM horses and 11 Co-G horses were investigated using untargeted metabolomics. Metabolomic data were evaluated using unsupervised, supervised, and pathway analyses. Unsupervised principal component analysis performed with all detected features separated AM and healthy Co-G horses. Supervised analyses had identified 1276 features showing differential expression between both groups. Among them, 46 metabolites, belonging predominantly to the fatty acid, fatty ester, and amino acid chemical classes, were identified by standard comparison. Fatty acids, unsaturated fatty acids, organic dicarboxylic acids, and fatty esters were detected with higher intensities in AM horses in link with the toxins' pathological mechanism. The main relevant pathways were lipid metabolism; valine, leucine, and isoleucine metabolism; and glycine metabolism. This study revealed characteristic metabolite changes in the plasma of clinically affected horses, which might ultimately help scientists and field veterinarians to detect and manage AM. The raw data of metabolomics are available in the MetaboLights database with the access number MTBLS2579.
2021-08-31 | MTBLS2579 | MetaboLights
Project description:We undertook gene expression microarray experiments to identify genes that are differentially expressed in heaves-affected horses versus matched controls. Mediastinal (pulmonary-draining) lymph nodes were sterilely obtained from affected and control horses, dissected, and frozen at -80oC. RNA was extracted from these tissues for downstream applications. These experiments utilized a commercially available Agilent horse array that featured >43,000 probes on a 4x44k array format. Mediastinal lymph node RNA from seven heaves-affected horses was compared to matching RNA from healthy, normal control horses.
2016-09-01 | E-GEOD-72645 | biostudies-arrayexpress
Project description:Capacity of exercise and performance is the most valuable in the horses. They have been selected for strength, speed, and indurance trait. Athletic pheno types are influenced markedly by environment, management, and training. However, it has long been accepted that there are underlying genetic factors. To determine altered mRNA expression in circulating leukocytes of horses induced by exercise. Healthy neutered male warmblood horses were subjected to indoor exercise (trotting with alternative cantering for 6o minutes). Peripheral blood was collected from the jugular vein before and after the exercise, and subsequently buffy coat leukocytes were isolated by centrifugation. Total RNAs was isolated. Cyanine 3-labeled cRNA (complementary RNA) was generated from Agilentâs Low RNA Input Linear Amplification kit with 500 ng total RNA. Labeled cRNA was applied microarray (Agilent technologies, 8x60K) using Agilentâs Gene Expression Hybridization Kit. The present study revealed a subset of mRNAs in equine peripheral blood leukocytes affected by exercise, providing background information for genes associated with exercise in warm-blood horses. Three healthy, gelding warmblood horses between 9 and 17 yr were selected. 6 samples were collected containing 3 samples before exercise and 3 samples after exercise
2015-12-24 | E-GEOD-76310 | biostudies-arrayexpress
Project description:IgE-binding monocytes are a rare peripheral immune cell type involved in the allergic response through binding of IgE on their surface. IgE-binding monocytes are present in both healthy and allergic individuals. We performed RNA sequencing to ask how the function of IgE-binding monocytes differs in the context of allergy. Using a large animal model of allergy, equine Culicoides hypersensitivity, we compared the transcriptome of IgE-binding monocytes in allergic and non-allergic horses at two seasonal timepoints: (i) when allergic animals were clinical healthy, in the winter “Remission Phase”, and (ii) during chronic disease, in the summer “Clinical Phase”. Most transcriptional differences between allergic and non-allergic horses occurred only during the “Remission Phase”, suggesting principal differences in monocyte function even in the absence of allergen exposure. F13A1, a subunit of fibrinoligase, was significantly upregulated at both timepoints in allergic horses. This suggested a role for increased fibrin deposition in the coagulation cascade to promote allergic inflammation. IgE-binding monocytes also downregulated CCR10 expression in allergic horses during the “Clinical Phase”, suggesting a defect in maintenance of skin homeostasis, which further promotes allergic inflammation. Together, this transcriptional analysis provides valuable clues into the mechanisms used by IgE-binding monocytes in allergic individuals.
2023-05-15 | GSE231427 | GEO
Project description:The major focus of Dr. Argueso's research is to characterize the carbohydrate portion of the different mucins expressed by the ocular surface epithelia as well as the enzymes involved with their synthesis, and to determine whether the alteration of mucin glycosylation is associated with ocular surface disease. Highly glycosylated mucins on the ocular surface (cornea and conjunctiva) are the first line of defense of the eye against injury and infection. Changes in O-glycosylation of mucins may cause ocular surface disorders, such as dry eye. Gene expression patterns in the conjunctival epithelium of three normal subjects were analyzed. The three subjects have the same ABO-blood-group. For each donor, conjunctival cells were obtained by impression cytology. Conjunctival impression cytology was performed on each eye two times with a one-week interval. Conjunctival cells obtained from each individual were pooled and the RNA isolated. All three samples were hybridized to the custom designed CFG GLYCOv2 glycogene array.
2011-03-02 | E-GEOD-27593 | biostudies-arrayexpress
Project description:Unlike other microbiomes of the body, the composition of the ocular surface microbiome (OSM) in children has yet to be thoroughly explored. Our goal was to evaluate the OSM in young infants and compare its composition to older children using both culture dependent and independent methodologies to assess for differences with age. Prospective, observational, cross-sectional study of children <18 years of age at a university-based institution. The mucosal surfaces of both eyes, nose and throat were swabbed with a forensic-quality swab. Half of the swab was plated for culture and the other half underwent 16S sequencing. Culture results and microbiome diversity were analyzed. Fifty patients (mean age 37 months, range 1-168 months) were enrolled. Forty-seven eyes of 30 patients had positive cultures; four eyes grew >1 species. Culture positive patients were older (43 vs. 29 months, P = 0.19). Additionally, older children had greater diversity than children under 6 months of age by 16S sequencing (P = 0.05). Staphylococcus species were predominant by culture (35/52 isolates) and by 16S sequencing. The OSM was fairly similar to the nose microbiome, whereas the throat microbiome differed significantly and had a higher abundance of Streptococcaceae (P = 0.001). The OSM is predominantly composed of Staphylococcus species in children, as demonstrated by both culture dependent and culture independent methods. Older children were more likely to have growth on culture and have more a complex bacterial milieu with 16S sequencing. 16S sequencing provides more robust information regarding the composition of the microbiomes than culture dependent methods.
| S-EPMC6269136 | biostudies-other