GEO DataSets

(Submitter supplied) Sodium oligomannate (GV-971), an oligosaccharide drug approved in China for treating mild-to-moderate Alzheimer's disease (AD), was previously found to recondition the gut microbiota and limit altered peripheral Th1 immunity in AD transgenic mice. As a follow-up study, we here provide advances by pinpointing a Lactobacillus murinus strain that highly expressed a gene encoding a putative adhesin containing Rib repeats (Ribhigh-L.m.) that was particularly enriched in 5XFAD transgenic mice. more...

Organism:

Ligilactobacillus murinus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33917

6 Samples

Download data: CSV

(Submitter supplied) To investigate the subspecies level differences in the expression profiles of Streptococcus salivarius strains, we conducted the RNA sequencing analysis of Streptococcus salivarius strains.

Organism:

Streptococcus salivarius

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34965

24 Samples

Download data: TXT

(Submitter supplied) We found that biofilm formation ability of E. faecalis was impacted by surfactin. To further understand how E. faecalis responded to surfactin, we searched for differentially expressed genes between E. faecalis treated with or without surfactin using RNA-seq analysis.

Organism:

Enterococcus faecalis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL35064

2 Samples

Download data: XLSX

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Streptococcus agalactiae; Escherichia coli

Type:

Other; Expression profiling by high throughput sequencing

Platforms:

GPL25368 GPL28679 GPL29157

26 Samples

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(Submitter supplied) Bacterial CRISPR-Cas9 immune systems protect against foreign DNA. However, immune efficiency is constrained by Cas9 off-target effects and toxicity. Here, we demonstrate that CRISPR-Cas9 immunity is regulated by CovR, the major regulator of virulence in Group B Streptococcus, a pathobiont responsible for neonatal invasive infections. We show that CovR binds to and represses a distal promoter of the cas operon, embedding immunity in the virulence regulatory network. more...

Organism:

Streptococcus agalactiae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29157

18 Samples

Download data: TXT

(Submitter supplied) Bacterial CRISPR-Cas9 immune systems protect against foreign DNA. However, immune efficiency is constrained by Cas9 off-target effects and toxicity. Here, we demonstrate that CRISPR-Cas9 immunity is regulated by CovR, the major regulator of virulence in Group B Streptococcus, a pathobiont responsible for neonatal invasive infections. We show that CovR binds to and represses a distal promoter of the cas operon, embedding immunity in the virulence regulatory network. more...

Organism:

Escherichia coli; Streptococcus agalactiae

Type:

Other

Platforms:

GPL28679 GPL25368

8 Samples

Download data: XLSX

(Submitter supplied) Group A Streptococcus (GAS) is a human-adapted pathogen responsible for a variety of diseases. The GAS M1UK lineage has contributed significantly to the recently reported increases in scarlet fever and invasive infections, however the basis for its evolutionary success is not yet fully understood. During the transition to systemic disease, the M1 serotype is known to give rise to spontaneous mutations in the CovRS two-component transcriptional regulation system that confer a fitness advantage during invasive infections. more...

Organism:

Streptococcus pyogenes

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28678

12 Samples

Download data: TSV

(Submitter supplied) Single-molecule correlated chemical probing (smCCP) is an experimentally concise strategy for characterizing higher-order structural interactions in RNA. smCCP data yield rich, but complex, structural information on base pairing, conformational ensembles, and tertiary interactions. To date, through-space communication specifically measuring RNA tertiary structure has been difficult to isolate from structural communication reflective of other interactions. more...

Organism:

Enterococcus faecalis

Type:

Other

Platform:

GPL24867

15 Samples

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(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Serratia marcescens; Lactiplantibacillus plantarum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL30015 GPL33401 GPL34033

30 Samples

Download data: MTX, TSV, TXT

(Submitter supplied) A challenging task to reveal health and disease-associated microbiome signatures is to disentangle regulatory networks of microbes among themselves and with their host. Using the integrated Drosophila-commensal-pathogen model system, we here reported that Drosophila and commensal bacterium L. plantarum cooperated to compete with the opportunistic pathogen S. marcescens. At first, we found that Drosophila larvae and L. more...

Organism:

Serratia marcescens; Lactiplantibacillus plantarum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL33401 GPL30015 GPL34033

6 Samples

Download data: MTX, TSV

(Submitter supplied) A challenging task to reveal health and disease-associated microbiome signatures is to disentangle regulatory networks of microbes among themselves and with their host. Using the integrated Drosophila-commensal-pathogen model system, we here reported that Drosophila and commensal bacterium L. plantarum cooperated to compete with the opportunistic pathogen S. marcescens. At first, we found that Drosophila larvae and L. more...

Organism:

Lactiplantibacillus plantarum; Serratia marcescens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL30015 GPL33401 GPL34033

24 Samples

Download data: TXT

(Submitter supplied) Zn and Mn are essential micronutrients for many bacteria including Streptococcus pneumoniae. While Zn performs vital structural or catalytic roles in certain proteins, in excess, Zn can inhibit Mn uptake by S. pneumoniae and displace, but not functionally replace Mn from key enzymes including superoxide dismutase A (SodA). Here, we show that the Ccn small regulatory RNAs promote S. pneumoniae Mn uptake and resistance to the oxidative stress. more...

Organism:

Streptococcus pneumoniae TIGR4; Streptococcus pneumoniae D39

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL22373 GPL33901

18 Samples

Download data: XLSX

(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 mitis; Streptococcus mutans

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL34744 GPL34745 GPL34746

9 Samples

Download data: CSV, 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) 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