GEO DataSets

(Submitter supplied) We used RNA-Seq to assess how the presence/absence of the RD2 pathogenicity island influences global gene expression in a serotype M28 GAS isolate following exposure to human plasma for 15 mins and for 60 mins

Organism:

Streptococcus pyogenes

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24912

12 Samples

Download data: XLSX

(Submitter supplied) Our group recently transcriptomically characterized coculture growth between Streptococcus mutans and several species of commensal streptococci (Rose et al, 2023; Choi et al 2024). One interaction that stood out was with Streptococcus mitis ATCC 49456, which completely inhibited the growth of S. mutans during biofilm formation. This is due to abudant hydrogen peroxide production by S. mitis ATCC 49456, 3-5x higher than other oral commensal streptococci we have worked with. more...

Organism:

Streptococcus mutans; Streptococcus mitis

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL34744 GPL34745 GPL34746

9 Samples

Download data: CSV, XLSX

(Submitter supplied) Staphylococcus aureus is a major human pathogen of the skin. The global burden of diabetes is high, with S. aureus being a major complication of diabetic wound infections. We investigated how the diabetic environment influences S. aureus skin infection and observed an increased susceptibility to infection in mouse models of both type I and type II diabetes. A dual gene expression approach was taken to investigate transcriptional alterations in both the host and bacterium after infection. more...

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24034

8 Samples

Download data: XLS

(Submitter supplied) Bacteria have developed multiple strategies, such as sporulation, to cope with environmental stress. Non-sporulating bacteria, however, may “hibernate” into a so-called viable but non-culturable (VBNC) state, where they are no longer able to grow in standard culture media and thus become undetectable by conventional growth-based methods. VBNC pathogens pose a significant risk for human and animal health as they can “wake up” back into a vegetative and virulent state. more...

Organism:

Listeria monocytogenes EGD-e

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33865

6 Samples

Download data: TSV

(Submitter supplied) Interrogating Staphylococcus aureus transcriptional changes in the presence or absence of glycosaminoglycans, specifically heparin.

Organism:

Staphylococcus aureus subsp. aureus NCTC 8325

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33368

12 Samples

Download data: CSV

(Submitter supplied) Staphylococcus aureus is a pulmonary pathogen associated with substantial human morbidity and mortality. As vaccines targeting virulence determinants have failed to be protective in humans, other factors are likely involved in pathogenesis. Here we analysed transcriptomic responses of human clinical isolates of S. aureus from initial and chronic infections. We observed upregulated collagenase and proline transporter gene expression in chronic infection isolates. more...

Organism:

Staphylococcus aureus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26273

8 Samples

Download data: CSV, TXT

(Submitter supplied) Most bacteria are surrounded by a peptidoglycan cell wall composed of glycan strands held together by short peptide crosslinks. There are two major types of crosslinks, termed 4-3 and 3-3 based on the amino acids involved. 4-3 crosslinks are created by penicillin-binding proteins (PBPs), while 3-3 crosslinks created byL,D-transpeptidases (LDTs). In well studied bacteria 3-3 crosslinks comprise only about 10% of the total and are not essential. more...

Organism:

Clostridioides difficile

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32868

6 Samples

Download data: XLSX

(Submitter supplied) Purpose: The purpose of this study is to clarify the response of Clostridium perfringens ATCC 13124 to host polysaccharide. Methods: Clostridium perfringens ATCC 13124 cells were cultured anaerobically in a medium containing Minimal medium-like condition Poor + medium, medium in which hyaluronic acid or mucin was added to Poor + medium. Total RNA was extracted from bacterial cells by the Hot-Phenol method. more...

Organism:

Clostridium perfringens ATCC 13124

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33655

3 Samples

Download data: XLSX

(Submitter supplied) Previous studies on RNase R have highlighted significant effects of this ribonuclease in several processes of Streptococcus pneumoniae biology. In this work we show that elimination of RNase R results in overexpression of most of genes encoding the components of type II fatty acid biosynthesis (FASII) cluster. We demonstrate that RNase R is implicated in the turnover of most of transcripts from this pathway, affecting the outcome of the whole FASII cluster, and ultimately leading to changes in the membrane fatty acid composition. more...

Organism:

Streptococcus pneumoniae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23152

4 Samples

Download data: TXT

(Submitter supplied) Streptococcus dysgalactiae subspecies equisimilis (SDSE) is a Gram-positive bacterial pathogen that infects humans and is closely related to group A streptococcus (GAS). Compared to GAS, far less is known about SDSE pathobiology. Increased rates of invasive SDSE infections have recently been reported in many countries. One SDSE emm type, stG62647, is known to cause severe diseases, including necrotizing soft-tissue infections, endocarditis, and osteoarticular infections. more...

Organism:

Streptococcus dysgalactiae subsp. equisimilis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34696

114 Samples

Download data: TXT, XLSX

(Submitter supplied) Lactobacillus johnsonii, a Gram-positive, gut bacterium is well studied for its several health-beneficial properties. This

Organism:

Lactobacillus johnsonii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34689

16 Samples

Download data: TXT

(Submitter supplied) Group B Streptococcus (GBS) is a pathobiont responsible for invasive infections in neonates and in the elderly. The transition from a commensal to an invasive pathogen relies on the timely regulation of a set of virulence factors. In this study, we characterized the role of the SaeRS two-component system in GBS pathogenesis. Loss-of-function mutations in the SaeR response regulator decrease virulence in mouse models of invasive infection . more...

Organism:

Streptococcus agalactiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29157

12 Samples

Download data: TXT

(Submitter supplied) Staphylococcus aureus is responsible for a substantial number of invasive infections globally each year. These infections are problematic because they are frequently recalcitrant to antibiotic treatment. Antibiotic tolerance, the ability of bacteria to persist despite normally lethal doses of antibiotics, contributes to antibiotic treatment failure in S. aureus infections. To understand how antibiotic tolerance is induced, S. more...

Organism:

Staphylococcus aureus

Type:

Other

Platform:

GPL19006

21 Samples

Download data: WIG, XLSX

(Submitter supplied) The glycopeptide vancomycin is a drug of choice for the treatment of severe non-gastrointestinal infections with members of Bacillus cereus sensu lato. Recently, sporadic detection of vancomycin resistant phenotypes emerged, mostly for agar diffusion testing. The food packaging isolate BC70 displayed a pseudo-resistant phenotype for vancomycin in both Etest and disk diffusion. In this work, we used RNA-Seq on the nanopore platform to study differentially expressed genes in BC70 cells, which were able to actively move into the inhibition zone during vancomycin susceptibility testing using Etest and therefore appeared to be resistant. more...

Organism:

Bacillus cereus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34081

4 Samples

Download data: CSV

(Submitter supplied) Staphylococcus aureus (Sa) and Acinetobacter baumannii (Ab) are frequently co-isolated from polymicrobial infections that are severe and recalcitrant to therapy. Here, we apply a combination of wet-lab experiments and in silico modeling to unveil the intricate nature of the Ab/Sa interaction using both, representative laboratory strains and strains co-isolated from clinical samples. This comprehensive methodology allowed uncovering Sa's capability to exert a partial interference on Ab by the expression of phenol-soluble modulins. more...

Organism:

Staphylococcus aureus subsp. aureus USA300; Acinetobacter baumannii A118

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL34012 GPL29525

16 Samples

Download data: TXT, XLSX

(Submitter supplied) Cell-cell communication systems enable populations to regulate behavior via modifications in gene expression. In Gram-positive bacteria, these systems are often composed of secreted, signaling peptides that disperse across the population and interact with cognate transcriptional regulators. While cells generally possess multiple such systems, there is a gap in knowledge regarding molecular mechanisms that coordinate these systems to allow for optimization of phenotypic responses. more...

Organism:

Streptococcus pneumoniae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28680

8 Samples

Download data: CSV

(Submitter supplied) Bacterial vaginosis (BV), a common syndrome characterized by Lactobacillus-deficient vaginal microbiota, is associated with adverse health outcomes. BV often recurs after standard antibiotic therapy in part because antibiotics promote microbiota dominance by Lactobacillus iners instead of Lactobacillus crispatus, which has more beneficial health associations. Strategies to promote L. crispatus and inhibit L. more...

Organism:

Lactobacillus gasseri; Lactobacillus jensenii; Lactobacillus crispatus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL34635 GPL34636 GPL34634

36 Samples

Download data: FASTA, TSV, TXT

(Submitter supplied) To investigate the rapid adaptation mechanism of Bacillus thuringiensis in an alkaline environment, we have employed whole genome microarray expression profiling as a discovery platform to identify the difference of gene expression between normal condition and alkaline condition.

Organism:

Bacillus thuringiensis

Type:

Expression profiling by array

Platform:

GPL17384

6 Samples

Download data: TXT

(Submitter supplied) Symbiotic interactions between humans and our communities of resident gut microbes (microbiota) play many roles in health and disease. Some gut bacteria utilize mucus as a nutrient source and can under certain conditions damage the protective barrier it forms, increasing disease susceptibility. We investigated how Ruminococcus torques—a known mucin-degrader that remains poorly studied despite its implication in inflammatory bowel diseases (IBDs)— degrades mucin glycoproteins or their component O-linked glycans to understand its effects on the availability of mucin-derived nutrients for other bacteria. more...

Organism:

[Ruminococcus] torques VIII-239

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34352

6 Samples

Download data: GFF, XLSX

(Submitter supplied) Lactococcus lactis is a lactic acid bacterium of major importance for food fermentation and biotechnological applications. The ability to manipulate its genome quickly and easily through competence for DNA transformation would accelerate its general use as a platform for a variety of applications. Natural transformation in this species requires the activation of the master regulator ComX. However, the growth conditions that lead to spontaneous transformation, as well as the regulators that control ComX production, are unknown. more...

Organism:

Lactococcus lactis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34188

6 Samples

Download data: TXT, XLSX