GEO DataSets

(Submitter supplied) Extracellular vesicles (EVs) are released by most cell types and are implicated in several biological and pathological processes, including multiple sclerosis (MS). In this study we performed RNA sequencing to analyze the diversity of microorganisms by assignment of reads using different taxa profilers. To diminish the risk of false positive biases derived from sample handling, we performed a similar analysis on EVs derived from known cultured bacterial species, as well as artificially-generated samples. more...

Organism:

Lactobacillus acidophilus; Homo sapiens; synthetic construct; Bifidobacterium animalis subsp. lactis

Type:

Expression profiling by high throughput sequencing

4 related Platforms

15 Samples

Download data: CSV

(Submitter supplied) Lacticaseibacillus rhamnosus Lcr35 is a well-known bacterial strain whose efficiency in preventing recurrent vulvovaginal candidiasis has been largely demonstrated in clinical trials. The presence of sodium thiosulfate (STS) has been shown to enhance its ability to inhibit the growth of C. albicans strains. In this study, we confirmed that Lcr35 has a fungicidal effect not only on the planktonic form of C. more...

Organism:

Lacticaseibacillus rhamnosus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33752

9 Samples

Download data: TXT

(Submitter supplied) Carbapenem-resistant Acinetobacter baumannii (CRAB) is a recognized nosocomial pathogen with limited therapeutics options. Lactic acid bacteria (LAB) constitute a promising therapeutic alternative. Here we aimed to study the antibacterial properties of a collection of LAB strains using phenotypic and transcriptomic analysis against A. baumannii clinical strains. One strain, Lacticaseibacillus rhamnosus CRL 2244, exerts a strong inhibitory capacity on A. more...

Organism:

Acinetobacter baumannii; Lacticaseibacillus rhamnosus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL28641 GPL33555

6 Samples

Download data: TXT

(Submitter supplied) We obtained L. kefiri (JCM5818) and L. kefiranofaciens (JCM6985) from the Japan Collection of Microorganisms (JCM). Bacteria were grown together at two different temperatures of 30C and 37C profiled for transcriptomics, metabolomics, and proteomics.

Organism:

Lentilactobacillus kefiri; Lactobacillus kefiranofaciens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33335

20 Samples

Download data: TXT

(Submitter supplied) To characterize the effect of lactic acid on the L. plantarum growth and adaptation, we investigated the transcriptome under hydrochloride (HCl) or lactic acid at the early stage of the growth.

Organism:

Lactiplantibacillus plantarum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32583

6 Samples

Download data: TXT

(Submitter supplied) Extracellularly released particles, including membrane vesicles, have increasingly been recognized as important for bacterial community functions and host-interaction processes, but their compositions and functional roles differ between species and also between strains of the same species. In this study, we have determined the composition of membrane vesicles and protein particles identified in the cell-free pellets of two strains of Apilactobacillus kunkeei, a defensive symbiont of honeybees. more...

Organism:

Apilactobacillus kunkeei

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32344

6 Samples

Download data: CSV, GFF

(Submitter supplied) The microbiome has revealed itself as a key player in health and disease. To better understand its role, in addition to microbial diversity, it is important to understand species-specific activity and gene expression. While metatranscriptomics investigates mRNA abundance2, it does not inform about faster post-transcriptional regulation3. Although prokaryotic translation is a common target for antibiotics, a direct measurement of microbiome ribosome dynamics remains inaccessible. more...

Organism:

Escherichia coli; Synechocystis sp. PCC 6803; Staphylococcus aureus; Bacillus amyloliquefaciens; Lactiplantibacillus plantarum; Cryptococcus neoformans; Caulobacter vibrioides; Segatella copri; Alistipes finegoldii; Hoylesella timonensis; compost metagenome; Enterococcus faecalis; Bacillus subtilis; Limosilactobacillus reuteri; Limosilactobacillus fermentum; human feces metagenome; Listeria monocytogenes; Saccharomyces cerevisiae; Salmonella enterica; Parabacteroides merdae

Type:

Other

17 related Platforms

199 Samples

Download data: BEDGRAPH, TXT, XLSX

(Submitter supplied) Malolactic fermentation (MLF) positively influences the quality of the wine, and it occurs as a result of a lactic acid bacteria’s metabolism, mainly of the Oenococcus oeni species. However, delays and halting of MLF are frequent problems in the wine industry. This is mainly because O. oeni’s development is inhibited by different kinds of stress. Even though the sequencing of the genome of the PSU-1 strain of O. more...

Organism:

Oenococcus oeni

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32828

2 Samples

Download data: TXT

(Submitter supplied) We applied total RNA sequencing of Lactobacillus fermentum strain GR1008 and GR1009 and compare the differentially expressed genes. This study aimed to find out the underlying mechanims for the differential morphology of the two strains.

Organism:

Limosilactobacillus fermentum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30868

2 Samples

Download data: XLS

(Submitter supplied) RNA-Seq was used to compare the transcriptome of Streptococcus mutans UA159 during growth alone in monoculture, in coculture with Streptococcus gordonii DL1, Streptococcus sanguinis SK36 or Streptococcus oralis 34, and in a quadculture containing all four species. Individual cultures of commensal species Streptococcus gordonii DL1, Streptococcus sanguinis SK36 and Streptococcus oralis 34 were sequenced as well. more...

Organism:

Streptococcus gordonii; Streptococcus sobrinus; Lacticaseibacillus casei; Streptococcus mutans UA159; Streptococcus sanguinis; Streptococcus mutans; Streptococcus oralis; Corynebacterium matruchotii

Type:

Expression profiling by high throughput sequencing

11 related Platforms

33 Samples

Download data: CSV, XLSX

(Submitter supplied) Transcriptional profiling of Lactobacillus brevis UCCLBBS124 and UCCLBBS449 comparing control strain grown in MRS broth with strains growing in different stress conditons (5 % EtOH, pH4 or 30 ppm iso-a-acids).This study aimed to evaluate how certain Lb. brevis isolates are adapted so as to allow them to survive and grow in beer.

Organism:

Levilactobacillus brevis

Type:

Expression profiling by array

Platform:

GPL26808

12 Samples

Download data: TXT

(Submitter supplied) We report the transcriptome profile of the Lactobacillus plantarum NMM.1 treated by 5 μg/mL deoxynivalenol-3-glucoside (D3G),aiming to search for some different expression genes and pathways to reveal the change caused by D3G.

Organism:

Lactiplantibacillus plantarum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30863

6 Samples

Download data: TXT

(Submitter supplied) RIP-seq analysis to identify SpyCas9 and LrhCas9 bound RNAs using co-immunoprecipitation and sequencing.

Organism:

Escherichia coli; Lacticaseibacillus rhamnosus

Type:

Other

Platforms:

GPL21222 GPL30159

12 Samples

Download data: WIG

(Submitter supplied) Quorum sensing (QS) in bacteria has been a well studied cellular communication phenomenon for decades. In recent years, such systems have been repurposed for the use of biosensors in both cellular and cell-free contexts as well as for inducible protein expression in non-traditional chassis organisms. Such biosensors are particularly intriguing when considering the association between the pathogenesis of some bacteria and the QS signaling intermediates. more...

Organism:

Lactiplantibacillus plantarum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25957

6 Samples

Download data: CSV

(Submitter supplied) This study was aimed to further illustrate the expression files of REN between glucose and raffinose in MRS broth. Transcriptomic analysis combined with mutants of the key genes based on homologous recombination technology indicated that galA1 gene cluster plays an important role in raffinose metabolism. Gene rafP and galA1 are responsible for raffinose transport and α-galactoside hydrolysis, followed by galactose hydrolysis by galKTE and sucrose hydrolysis by scrB. more...

Organism:

Ligilactobacillus salivarius

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30124

6 Samples

Download data: XLS

(Submitter supplied) To determine whether osmotic pressure affects the translation efficiency of Lactobacillus rhamnosus, the ribosome profiling assay was performed to analyze the changes in translation efficiency in L. rhamnosus ATCC 53103. Under osmotic stress, differentially expressed genes (DEGs) involved in fatty acid biosynthesis and metabolism, ribosome, and purine metabolism pathways were co-regulated with consistent expression direction at translation and transcription levels. more...

Organism:

Lacticaseibacillus rhamnosus GG

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL30958 GPL30959

6 Samples

Download data: TXT

(Submitter supplied) Background: Of the many neurotransmitters in humans, gamma-aminobutyric acid (GABA) shows potential for improving several mental health indications such as stress and anxiety. The microbiota-gut-brain axis is an important pathway for GABAergic effects, as microbially-secreted GABA within the gut can affect host mental functionhealth outcomes. Understanding the molecular characteristics of GABA production by microbes within the gut can offer insight to novel therapies for mental health. more...

Organism:

Levilactobacillus brevis

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30477

40 Samples

Download data: CSV, GFF

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

Organism:

synthetic construct; Lacticaseibacillus casei

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL27609 GPL30169

17 Samples

Download data

(Submitter supplied) In the present study we characterized the sRNA profile of Lactobacillus casei BL23 using conventional and mDOT-seq approaches. In total 307 potential sRNAs were identified, 28 of which were validated by Northern hybridization. As a major portion of predicted sRNAs were shown to be conserved among the related species of Lactobacillus casei group (LCG), the results obtained in this study could serve as a valuable resource for achieving a better understanding of LCG physiology or even improving their applications in industry and medicine.

Organism:

Lacticaseibacillus casei

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30169

9 Samples

Download data: TSV

(Submitter supplied) The transcriptome of L. plantarum strains that aggregate was compared with non-aggregating strains

Organism:

Lactiplantibacillus plantarum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30015

11 Samples

Download data: CSV, TXT