Virulence associated genes in Streptococcus uberis
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ABSTRACT:
ORGANISM(S): Streptococcus uberis
PROVIDER: GSE63835 | GEO | 2016/12/31
SECONDARY ACCESSION(S): PRJNA269294
REPOSITORIES: GEO
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Project description:Streptococcus uberis is one of the principal causative agents of bovine mastitis. The organism is typically considered an environmental pathogen, however, recent studies also suggest possible host adaptation. In this study, two multilocus sequence typing (MLST) schemes and whole genome DNA microarrays were used to evaluate the degree and nature of genome flexibility between S. uberis strains. The 21 isolates examined in this study arise from a collection of 232 international isolates for which previous epidemiological and preliminary genotyping data existed. The microarray analysis resulted in an estimate of the core genome for S. uberis, consisting of 1530 ORFs, among 1855 tested, representing 82.5% of the S. uberis 0140J genome. The remaining ORFs were variable in gene content across the 21 tested strains. A total of 26 regions of difference (RDs), consisting of three or more contiguous ORFs, were identified among the variable genes. Core genes mainly encoded housekeeping functions, while the variable genes primarily fell within categories such as protection responses, degradation of small molecules, laterally acquired elements, and two component systems. Recombination detection procedures involving the MLST loci suggested S. uberis is a highly recombinant species, precluding accurate phylogenetic reconstructions involving these data. On the other hand, the microarray data did provide limited support for an association of gene content with strains found in multiple cows and/or multiple herds, suggesting the possibility of genes related to bovine transmissibility or host-adaptation. Keywords: comparative genomic hybridization
2009-09-13 | GSE12780 | GEO
Project description:Streptococcus uberis isolates from cases of bovine mastitis
| PRJNA795889 | ENA
Project description:Background Our objective was to compare mammary tissue gene expression profiles during a Streptococcus uberis (S. uberis) mastitis challenge between lactating cows subjected to dietary-induced negative energy balance (NEB; n = 5) and cows fed ad libitum to maintain positive energy balance (PEB; n = 5). The NEB cows were feed-restricted to 60% of calculated net energy for lactation requirements for 7 d, and cows assigned to PEB were fed the same diet for ad libitum intake. Five days after feed restriction, one rear mammary quarter of each cow was inoculated with 5,000 cfu of S. uberis (O140J). At 20 h post-inoculation, both the S. uberis-infected mammary quarters (i.e., YES) and non-infected rear quarters (i.e., NO) from all cows were biopsied for RNA extraction. Effect of S. uberis Intramammary Infection (IMI; YES vs NO) S. uberis IMI resulted in 2,102 oligos (1,939 annotated genes) differentially expressed genes (DEG; YES versus NO). Of these, 1,082 genes were up-regulated during IMI and were primarily involved with the immune response, e.g., IL6, TNF, IL8, IL10, SELL, LYZ, and SAA1. Genes down-regulated (1,020) included those associated with milk fat synthesis, e.g., LPIN1, LPL, CD36, and BTN1A1. Pathway analysis of all DEG indicated that IL-10 Signaling, IL-6 Signaling, and Glucocorticoid Receptor Signaling were among the top canonical pathways affected by infection. Interestingly, LXR/RXR Signaling was also a primary affected pathway, indicating a relationship between immune system response and metabolism during an IMI. Network analysis indicated that TNF had positive relationships (i.e. up-regulation) with genes involved with immune system function (e.g., CD14, IL8, IL1B, and TLR2) and negative relationships (i.e., down-regulation) with genes involved with lipid metabolism (e.g., GPAM, SCD, FABP4, CD36, and LPL) and antioxidant activity (SOD1). Results provided information into the early response factors associated with the innate immune response to S. uberis infection. Our study indicated that IMI challenge with S. uberis (strain O140J) elicited a strong transcriptomic response, leading to an overall up-regulation of genes involved in the innate immune response and a down-regulation of genes involved with lipid metabolism. Effect of NEB Within Infected Quarters (YES) Energy balance (NEB vs. PEB) resulted in 285 DEG (FDR ≤ 0.05), with 85 DEG up-regulated and 200 DEG down-regulated. Canonical pathways most affected by NEB were IL-8 Signaling (10 genes), Glucocorticoid Receptor Signaling (13), and NRF2-mediated Oxidative Stress Response (10). Among genes differentially expressed by NEB, Cell Growth and Proliferation (48) and Cellular Development (36) were the most enriched functions. Up-regulated genes included ANXA1, HMOX1, and HLAA; down-regulated genes included NOTCH1 and CCND1. Regarding immune response, HLAA was up-regulated due to NEB, whereas the majority of genes involved in immune response were down-regulated (e.g., AKT1, IRAK1, MAPK9, and TRAF6). Results helped identify mechanisms affected by dietary-induced NEB that may be associated with the impairment of immune function and increased risk of mastitis in cows experiencing postpartal NEB. Effect of NEB Within Non-Infected Quarters (NO) Energy balance (NEB vs. PEB) resulted in 278 DEG within non-infected rear mammary quarters. Up-regulated DEG most affected by NEB (genes = 180) included genes involved in lipid metabolism and amino acid metabolism. The down-regulated DEG most affected by NEB (n = 98) included genes involved in carbohydrate metabolism, anti-inflammatory response, and apoptosis. Among genes up-regulated, Ingenuity Pathway Analysis® identified Lipid Metabolism (8), Molecular Transport (14), and Small Molecule Biochemistry (15) as some of the most enriched molecular functions. Genes down-regulated by NEB were associated with Cell Growth and Proliferation (21) and Cell Death (18). Results indicate that dietary induced-NEB alters genes primarily associated with cellular metabolism, proliferation, and tumorigenesis but no candidate genes were identified as being associated with risk of disease.
2009-10-26 | GSE15344 | GEO
Project description:Salvia is an important genus from the Lamiaceae with approximately 1000 species distributed globally. Several Salvia species are commercially important because of their medicinal and culinary properties. We report the construction of the first fingerprinting array for Salvia species enriched with polymorphic and divergent DNA sequences and demonstrate the potential of this array for fingerprinting several economically important members of this genus. In order to generate the Salvia Subtracted Diversity Array (SDA), a Suppression Subtractive Hybridization (SSH) was performed between a pool of ten Salvia species and a pool of non-angiosperm and angiosperms (excluding the Lamiaceae) to selectively isolate Salvia-specific sequences. A total of 285 subtracted genomic DNA (gDNA) fragments were amplified and arrayed. DNA fingerprints were obtained for fifteen Salvia genotypes including three that were not part of the original subtraction pool. Hierarchical cluster analysis indicated that the Salvia-specific SDA was capable of differentiating closely related species of S. officinalis and S. miltiorrhiza and was also able to reveal genetic relationships consistent with geographical origins. Species-specific features were also found for S. elegans, S. officinalis, S. sclarea, S. przewalskii and S. runcinata.
2013-07-31 | E-GEOD-39403 | biostudies-arrayexpress
Project description:Supplementation of a Saccharomyces cerevisiae fermentation product modulates dairy cows health by reducing incidence and severity of mastitis, one of the most common and economically important diseases of the dairy industry. However, mechanisms remain unclear. We conducted a comprehensive molecular analysis, along with physiological data, on dairy cows supplemented for 45 days with NutriTek, a commercially available S. cerevisiae fermentation product, and then subjected to a mastitis challenge . NutriTek supplementation improved cow’s responses to a mastitis challenge by stimulating influx of immune cells to the mammary gland , enhancing their bactericidal capacity, and protecting mammary tissues from the side effect of an immune response allowing faster and more complete recovery from milk production drop
2020-12-01 | GSE149194 | GEO
Project description:Streptococcus uberis isolate:Mastitis breast milk Genome sequencing
| PRJNA1165460 | ENA
Project description:To identify the expression of lncRNA in cow mammary glands infected with different pathogens, we used our custom lncRNA gene chip to explore expression of lncRNA from three Chinese cows. Compared with the control individual, a total of 629 and 139 lncRNAs showed significant different expression in mammary gland infected with S. aureus, and S. uberis, respectively. In addition, we found 3610, and 720 pairs of lincRNA/proteinencoding genes showing a highly significant correlated expression in mammary gland infected with S. aureus and S. uberis, respectively. Else, 309 and 98 pairs of lincRNA/proteinencoding genes showing a highly significant cis-regulation in mammary gland infected with S. aureus and S. uberis, respectively. Some of the lincRNAs expressed in mammary gland are located within quantitative trait loci for mastitis resistance. Our study first provides a glimpse into the lncRNA content of bovine mammary gland and will facilitate future experimental studies to unravel the function of these molecules. It may prove useful to elucidate their effects on mechanisms underlying the genetic variability of mastitis resistance.
2016-09-01 | GSE66491 | GEO
Project description:Our objectives were to compare gene expression profiles in neutrophils (PMN) during a Streptococcus uberis mastitis challenge between lactating cows subjected to feed restriction to induce negative energy balance (NEB; n = 5) and cows fed ad libitum to maintain positive energy balance (PEB; n = 5). The NEB cows were feed-restricted to 60% of calculated net energy for lactation requirements for 7 d, whereas PEB cows were fed the same diet for ad libitum intake. After 5 d of feed restriction, one rear mammary quarter of each cow was inoculated with 5,000 cfu of Streptococcus uberis (strain O140J). Blood PMN were isolated at 24 h post-inoculation from all cows for RNA extraction and microarray analysis. NEB resulted in 94 differentially expressed genes compared with PEB. Of these, 51 genes were down-regulated, including genes involved with antigen presentation (HLADRA and HLAA), respiratory burst (SOD1), and the pro-inflammatory response (TNFA and IRAK-1). The most affected genes up-regulated by NEB (n = 43) included IL1R2 and IL6, toll-like receptors (TLR2 and TLR4), and THY1. Network analysis by Ingenuity Pathway Analysis ® revealed that TNFA was associated with the expression of numerous differentially expressed genes involved with immune response in NEB cows compared with PEB cows. Energy balance alters PMN expression of several genes involved with immune response, which provides new information on transcriptomic mechanisms associated with post-partal NEB and immune response during early lactation. Briefly, 10 multiparous Holstein cows in PEB and past peak lactation were used for this study. The NEB cows were feed-restricted to 60% of calculated NEL requirements for 7 d, whereas PEB cows were fed the same diet for ad libitum intake. After 5 d of feed restriction, one rear mammary quarter of each cow was inoculated with 5,000 cfu of Streptococcus uberis (strain O140J). Blood PMN were isolated at 24 h post-inoculation from all cows. A 13,257-oligonucleotide (70-mers) array was used for transcript profiling. Cy3- and Cy5 labelled cDNA from PMN and a reference standard were used for hybridizations. All samples were hybridized to duplicate slides with reverse labeling (20 microarrays total).
2010-05-16 | E-GEOD-15364 | biostudies-arrayexpress
Project description:Our objectives were to compare gene expression profiles in neutrophils (PMN) during a Streptococcus uberis mastitis challenge between lactating cows subjected to feed restriction to induce negative energy balance (NEB; n = 5) and cows fed ad libitum to maintain positive energy balance (PEB; n = 5). The NEB cows were feed-restricted to 60% of calculated net energy for lactation requirements for 7 d, whereas PEB cows were fed the same diet for ad libitum intake. After 5 d of feed restriction, one rear mammary quarter of each cow was inoculated with 5,000 cfu of Streptococcus uberis (strain O140J). Blood PMN were isolated at 24 h post-inoculation from all cows for RNA extraction and microarray analysis. NEB resulted in 94 differentially expressed genes compared with PEB. Of these, 51 genes were down-regulated, including genes involved with antigen presentation (HLADRA and HLAA), respiratory burst (SOD1), and the pro-inflammatory response (TNFA and IRAK-1). The most affected genes up-regulated by NEB (n = 43) included IL1R2 and IL6, toll-like receptors (TLR2 and TLR4), and THY1. Network analysis by Ingenuity Pathway Analysis ® revealed that TNFA was associated with the expression of numerous differentially expressed genes involved with immune response in NEB cows compared with PEB cows. Energy balance alters PMN expression of several genes involved with immune response, which provides new information on transcriptomic mechanisms associated with post-partal NEB and immune response during early lactation.
2009-12-25 | GSE15364 | GEO