GEO DataSets

(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:

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

Type:

Other

17 related Platforms

199 Samples

Download data: BEDGRAPH, TXT, XLSX

(Submitter supplied) Inflammatory diseases of the gut are associated with increased intestinal oxygen concentrations and high levels of inflammatory oxidants, including hydrogen peroxide (H2O2) and hypochlorous acid (HOCl), which are antimicrobial compounds produced by the innate immune system. This contributes to dysbiotic changes in the gut microbiome, including increased populations of pro-inflammatory enterobacteria (Escherichia coli and related species) and decreased levels of health-associated anaerobic Firmicutes and Bacteroidetes. more...

Organism:

Limosilactobacillus reuteri

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26262

24 Samples

Download data: TXT

(Submitter supplied) Comparison of gene expression between L. reuteri DSM 17938 and L. reuteri DSM 17938::pocR mutant grown in semi-defined medium after 24h of growth at 37C in anaerobic condition. PocR is an AraC-like transcriptional regulator, and changes in gene expression between mutant and wild-type strains would indicate genes involved in the PocR regulon.

Organism:

Limosilactobacillus reuteri

Type:

Expression profiling by array

Platform:

GPL6366

6 Samples

Download data: GPR, TXT

(Submitter supplied) Lactobacillus reuteri 100-23 is an autochthonous inhabitant of the rodent gastrointestinal system that adheres to the non-secretory epithelium of the forestomach and forms biofilms. Microarray analysis of the expression profile of L. reuteri 100-23 cells harvested from the stomach of ex-Lactobacillus-free mice, compared to those of L. reuteri 100-23 in laboratory culture, revealed an in vivo upregulation of a urease gene cluster by greater than 50-fold. more...

Organism:

Limosilactobacillus reuteri subsp. rodentium

Type:

Expression profiling by array

Platform:

GPL10986

6 Samples

Download data: TXT

(Submitter supplied) Gene expression comparison of L. reuteri ATCC PTA 6475 grown (stationary phase) in a defined media with either glucose or sucrose as the carbon source, in anaerobic conditions at 37C.

Organism:

Limosilactobacillus reuteri

Type:

Expression profiling by array

Platform:

GPL7541

4 Samples

Download data: GPR

(Submitter supplied) Gene expression comparison of L. reuteri ATCC PTA 6475 and tetrahydrofolate synthase 2 mutant in MRS medium in anaerobic conditions at 37C.

Organism:

Limosilactobacillus reuteri

Type:

Expression profiling by array

Platform:

GPL7541

6 Samples

Download data: GPR

(Submitter supplied) Gene expression comparison of L. reuteri ATCC PTA 6475 and tetrahydrofolate synthase 1 in MRS medium in anaerobic conditions at 37C.

Organism:

Limosilactobacillus reuteri

Type:

Expression profiling by array

Platform:

GPL7541

7 Samples

Download data: GPR

(Submitter supplied) Autoinducer-2 (AI-2)-mediated quorum sensing has been extensively studied in relation to the regulation of microbial behaviour. There are however two potential roles for the AI-2 synthase (LuxS). The first is in the production of AI-2 and the second is as an enzyme in the activated methyl cycle where it catalyses the conversion of S-ribosylhomocysteine to homocysteine. The by-product of the reaction catalysed by LuxS is (S)-4,5-dihydroxy-2,3-pentanedione (DPD), which spontaneously forms the furanones known collectively as AI-2. more...

Organism:

Limosilactobacillus reuteri subsp. rodentium

Type:

Expression profiling by array

Platform:

GPL10986

8 Samples

Download data: TXT

(Submitter supplied) Sourdough is a very competitive and challenging environment for microorganisms. Usually, a stable microbiota composed of lactic acid bacteria (LAB) and yeasts comes to dominate this ecosystem. Although rich in carbohydrates, thus providing an ideal environment to grow, the low pH presents a particular challenge. The nature of the adaptation to this low pH was investigated for Lactobacillus plantarum IMDO 130201, an isolate from a laboratory wheat sourdough fermentation. more...

Organism:

Staphylococcus aureus; Enterococcus faecalis; Enterococcus hirae; Lactococcus lactis; Lacticaseibacillus casei; Lacticaseibacillus paracasei; Companilactobacillus farciminis; Limosilactobacillus fermentum; Fructilactobacillus sanfranciscensis; Bifidobacterium; Lacticaseibacillus rhamnosus; Enterococcus mundtii; Lentilactobacillus parabuchneri; Leuconostoc mesenteroides; Pediococcus acidilactici; Pediococcus pentosaceus; Enterococcus faecium; Levilactobacillus brevis; Lactobacillus helveticus; Lactiplantibacillus plantarum; Companilactobacillus alimentarius; Fructilactobacillus fructivorans; Leuconostoc citreum; Limosilactobacillus pontis; Lactobacillus crispatus; Lactiplantibacillus paraplantarum; Limosilactobacillus frumenti; Furfurilactobacillus rossiae; Oenococcus oeni; Streptococcus thermophilus; Lactobacillus acidophilus; Weissella confusa; Lentilactobacillus hilgardii; Latilactobacillus sakei; Brevibacterium linens; Companilactobacillus mindensis; Lentilactobacillus buchneri; Lactobacillus delbrueckii; Lactiplantibacillus pentosus; Lactobacillus gasseri; Limosilactobacillus reuteri; Lactobacillus amylovorus; Latilactobacillus curvatus; Lactobacillus johnsonii; Leuconostoc pseudomesenteroides; Enterococcus casseliflavus; Mammaliicoccus lentus; Limosilactobacillus panis; Companilactobacillus paralimentarius

Type:

Expression profiling by array

Platform:

GPL10874

10 Samples

Download data: TXT

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

Organism:

Limosilactobacillus reuteri

Type:

Expression profiling by array

Platforms:

GPL7541 GPL6366

36 Samples

Download data: GPR

(Submitter supplied) Comparison of gene expression between L. reuteri ATCC 55730 in LDMIII between early log phase (T8), late log phase (T12) or early stationary phase phase (T16) or late stationary phase (T24)

Organism:

Limosilactobacillus reuteri

Type:

Expression profiling by array

Platform:

GPL6366

18 Samples

Download data: GPR

(Submitter supplied) Comparison of gene expression between L. reuteri ATCC PTA 6475 in LDMIII between early log phase (T8), late log phase (T12) or early stationary phase phase (T16) or late stationary phase (T24)

Organism:

Limosilactobacillus reuteri

Type:

Expression profiling by array

Platform:

GPL7541

18 Samples

Download data: GPR

(Submitter supplied) Gene expression comparison of L. reuteri ATCC PTA 6475 and cyclopropane-fatty-acyl-phospholipid synthase mutant in MRS medium in anaerobic condition at 37C

Organism:

Limosilactobacillus reuteri

Type:

Expression profiling by array

Platform:

GPL7541

6 Samples

Download data: GPR

(Submitter supplied) Commensal (symbiont) bacteria form communities in various regions of the bodies of vertebrates. Phylogenetic analysis of gut communities is advanced, but the relationships, especially at the trophic level, between commensals that share gut habitats of monogastric animals have not been investigated to any extent. Lactobacillus reuteri strain 100-23 and Lactobacillus johnsonii strain 100-33 cohabit in the forestomach of mice. more...

Organism:

Limosilactobacillus reuteri subsp. rodentium

Type:

Expression profiling by array

Platform:

GPL10986

4 Samples

Download data: TXT

(Submitter supplied) Comparison of gene expression between L. reuteri ATCC PTA 6475 and PocR mutant grown in semi-defined medium after 24h of growth at 37C in anaerobic condition

Organism:

Limosilactobacillus reuteri

Type:

Expression profiling by array

Platform:

GPL7541

6 Samples

Download data: GPR

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

Organism:

Pediococcus acidilactici; Enterococcus faecalis; Enterococcus hirae; Lacticaseibacillus casei; Lactobacillus helveticus; Lactiplantibacillus pentosus; Limosilactobacillus reuteri; Limosilactobacillus fermentum; Latilactobacillus curvatus; Lactobacillus johnsonii; Leuconostoc citreum; Mammaliicoccus lentus; Lactobacillus crispatus; Lactiplantibacillus paraplantarum; Companilactobacillus paralimentarius; Limosilactobacillus frumenti; Leuconostoc mesenteroides; Oenococcus oeni; Staphylococcus aureus; Lactococcus lactis; Levilactobacillus brevis; Lactiplantibacillus plantarum; Lacticaseibacillus paracasei; Latilactobacillus sakei; Lacticaseibacillus rhamnosus; Enterococcus mundtii; Lentilactobacillus parabuchneri; Furfurilactobacillus rossiae; Streptococcus thermophilus; Lactobacillus acidophilus; Lentilactobacillus buchneri; Weissella confusa; Lactobacillus delbrueckii; Lentilactobacillus hilgardii; Lactobacillus gasseri; Companilactobacillus farciminis; Fructilactobacillus sanfranciscensis; Bifidobacterium; Leuconostoc pseudomesenteroides; Companilactobacillus mindensis; Pediococcus pentosaceus; Enterococcus faecium; Companilactobacillus alimentarius; Lactobacillus amylovorus; Fructilactobacillus fructivorans; Brevibacterium linens; Limosilactobacillus pontis; Enterococcus casseliflavus; Limosilactobacillus panis

Type:

Expression profiling by array

Platform:

GPL5459

34 Samples

Download data: TXT

(Submitter supplied) Lactic acid bacteria (LAB) are of industrial importance in the production of fermented foods, among which sourdough-derived products. Despite their limited metabolic capacity LAB contribute considerably to important characteristics of fermented foods, among which extended shelf-life, microbial safety, improved texture, and enhanced organoleptic properties. Thanks to the considerable amount of LAB genomic information that became available during the last years, transcriptome, and by extension meta-transcriptome studies, are the exquisite research approaches to study whole ecosystem gene expression into more detail. more...

Organism:

Pediococcus pentosaceus; Enterococcus faecium; Lactiplantibacillus plantarum; Lactobacillus gasseri; Companilactobacillus alimentarius; Lactobacillus amylovorus; Fructilactobacillus fructivorans; Enterococcus casseliflavus; Limosilactobacillus panis; Furfurilactobacillus rossiae; Streptococcus thermophilus; Enterococcus faecalis; Lactobacillus acidophilus; Lacticaseibacillus casei; Weissella confusa; Lentilactobacillus hilgardii; Companilactobacillus farciminis; Fructilactobacillus sanfranciscensis; Bifidobacterium; Brevibacterium linens; Limosilactobacillus pontis; Companilactobacillus mindensis; Oenococcus oeni; Staphylococcus aureus; Enterococcus hirae; Lactococcus lactis; Lactiplantibacillus pentosus; Lacticaseibacillus paracasei; Latilactobacillus sakei; Limosilactobacillus fermentum; Lacticaseibacillus rhamnosus; Enterococcus mundtii; Companilactobacillus paralimentarius; Lentilactobacillus parabuchneri; Leuconostoc mesenteroides; Pediococcus acidilactici; Levilactobacillus brevis; Lentilactobacillus buchneri; Lactobacillus delbrueckii; Lactobacillus helveticus; Limosilactobacillus reuteri; Latilactobacillus curvatus; Lactobacillus johnsonii; Leuconostoc citreum; Leuconostoc pseudomesenteroides; Mammaliicoccus lentus; Lactobacillus crispatus; Lactiplantibacillus paraplantarum; Limosilactobacillus frumenti

Type:

Expression profiling by array

Platform:

GPL5459

9 Samples

Download data: TXT

(Submitter supplied) Lactic acid bacteria (LAB) are of industrial importance in the production of fermented foods, among which sourdough-derived products. Despite their limited metabolic capacity LAB contribute considerably to important characteristics of fermented foods, among which extended shelf-life, microbial safety, improved texture, and enhanced organoleptic properties. Thanks to the considerable amount of LAB genomic information that became available during the last years, transcriptome, and by extension meta-transcriptome studies, are the exquisite research approaches to study whole ecosystem gene expression into more detail. more...

Organism:

Leuconostoc mesenteroides; Oenococcus oeni; Pediococcus acidilactici; Streptococcus thermophilus; Levilactobacillus brevis; Lentilactobacillus buchneri; Lactobacillus delbrueckii; Lactobacillus helveticus; Limosilactobacillus reuteri; Latilactobacillus curvatus; Lactobacillus johnsonii; Leuconostoc citreum; Leuconostoc pseudomesenteroides; Mammaliicoccus lentus; Lactobacillus crispatus; Lactiplantibacillus paraplantarum; Enterococcus faecalis; Lactobacillus acidophilus; Lacticaseibacillus casei; Weissella confusa; Lentilactobacillus hilgardii; Companilactobacillus farciminis; Fructilactobacillus sanfranciscensis; Bifidobacterium; Brevibacterium linens; Limosilactobacillus pontis; Limosilactobacillus frumenti; Companilactobacillus mindensis; Enterococcus hirae; Lactococcus lactis; Lactiplantibacillus pentosus; Lacticaseibacillus paracasei; Latilactobacillus sakei; Lactobacillus amylovorus; Limosilactobacillus fermentum; Limosilactobacillus panis; Lacticaseibacillus rhamnosus; Enterococcus mundtii; Companilactobacillus paralimentarius; Lentilactobacillus parabuchneri; Pediococcus pentosaceus; Staphylococcus aureus; Enterococcus faecium; Lactiplantibacillus plantarum; Lactobacillus gasseri; Companilactobacillus alimentarius; Fructilactobacillus fructivorans; Enterococcus casseliflavus; Furfurilactobacillus rossiae

Type:

Expression profiling by array

Platform:

GPL5459

9 Samples

Download data: TXT

(Submitter supplied) Lactic acid bacteria (LAB) are of industrial importance in the production of fermented foods, among which sourdough-derived products. Despite their limited metabolic capacity LAB contribute considerably to important characteristics of fermented foods, among which extended shelf-life, microbial safety, improved texture, and enhanced organoleptic properties. Thanks to the considerable amount of LAB genomic information that became available during the last years, transcriptome, and by extension meta-transcriptome studies, are the exquisite research approaches to study whole ecosystem gene expression into more detail. more...

Organism:

Staphylococcus aureus; Lactococcus lactis; Lactiplantibacillus plantarum; Lactobacillus gasseri; Lacticaseibacillus paracasei; Companilactobacillus alimentarius; Enterococcus casseliflavus; Lentilactobacillus parabuchneri; Furfurilactobacillus rossiae; Pediococcus acidilactici; Pediococcus pentosaceus; Enterococcus faecalis; Enterococcus faecium; Lacticaseibacillus casei; Weissella confusa; Lactobacillus helveticus; Companilactobacillus farciminis; Fructilactobacillus fructivorans; Fructilactobacillus sanfranciscensis; Bifidobacterium; Brevibacterium linens; Limosilactobacillus pontis; Lactobacillus crispatus; Lactiplantibacillus paraplantarum; Limosilactobacillus frumenti; Enterococcus hirae; Lactiplantibacillus pentosus; Lactobacillus amylovorus; Limosilactobacillus fermentum; Lactobacillus johnsonii; Mammaliicoccus lentus; Limosilactobacillus panis; Lacticaseibacillus rhamnosus; Enterococcus mundtii; Companilactobacillus paralimentarius; Leuconostoc mesenteroides; Oenococcus oeni; Streptococcus thermophilus; Lactobacillus acidophilus; Levilactobacillus brevis; Lentilactobacillus buchneri; Lactobacillus delbrueckii; Lentilactobacillus hilgardii; Limosilactobacillus reuteri; Latilactobacillus sakei; Latilactobacillus curvatus; Leuconostoc citreum; Leuconostoc pseudomesenteroides; Companilactobacillus mindensis

Type:

Expression profiling by array

Platform:

GPL5459

7 Samples

Download data: TXT

(Submitter supplied) Lactic acid bacteria (LAB) are of industrial importance in the production of fermented foods, among which sourdough-derived products. Despite their limited metabolic capacity LAB contribute considerably to important characteristics of fermented foods, among which extended shelf-life, microbial safety, improved texture, and enhanced organoleptic properties. Thanks to the considerable amount of LAB genomic information that became available during the last years, transcriptome, and by extension meta-transcriptome studies, are the exquisite research approaches to study whole ecosystem gene expression into more detail. more...

Organism:

Pediococcus pentosaceus; Enterococcus faecium; Companilactobacillus alimentarius; Lactobacillus amylovorus; Fructilactobacillus fructivorans; Brevibacterium linens; Limosilactobacillus pontis; Enterococcus casseliflavus; Limosilactobacillus panis; Leuconostoc mesenteroides; Oenococcus oeni; Staphylococcus aureus; Lactococcus lactis; Levilactobacillus brevis; Lactiplantibacillus plantarum; Lacticaseibacillus paracasei; Latilactobacillus sakei; Lacticaseibacillus rhamnosus; Enterococcus mundtii; Lentilactobacillus parabuchneri; Furfurilactobacillus rossiae; Streptococcus thermophilus; Lactobacillus acidophilus; Lentilactobacillus buchneri; Weissella confusa; Lactobacillus delbrueckii; Lentilactobacillus hilgardii; Lactobacillus gasseri; Companilactobacillus farciminis; Fructilactobacillus sanfranciscensis; Bifidobacterium; Leuconostoc pseudomesenteroides; Companilactobacillus mindensis; Pediococcus acidilactici; Enterococcus faecalis; Enterococcus hirae; Lacticaseibacillus casei; Lactobacillus helveticus; Lactiplantibacillus pentosus; Limosilactobacillus reuteri; Limosilactobacillus fermentum; Latilactobacillus curvatus; Lactobacillus johnsonii; Leuconostoc citreum; Mammaliicoccus lentus; Lactobacillus crispatus; Lactiplantibacillus paraplantarum; Companilactobacillus paralimentarius; Limosilactobacillus frumenti

Type:

Expression profiling by array

Platform:

GPL5459

9 Samples

Download data: TXT