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1.

Transcriptome analyses of aggregating Lactiplantibacillus plantarum

(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
Series
Accession:
GSE172351
ID:
200172351
2.

Cranberry proanthocyanidins and dietary oligosaccharides synergistically modulate Lactobacillus plantarum physiology

(Submitter supplied) Plant-based foods contain bioactive compounds such as polyphenols that resist digestion and potentially benefit the host through interactions with their gut microbiome. Based on previous observations, we hypothesized thatprobiotic Lactobacillus plantarum interact with cranberry polyphenols and dietary oligosaccharides to synergistically impact its physiology. In this study, L. plantarum ATCC BAA-793 was grown on dietary oligosaccharides including cranberry xyloglucans, fructooligosaccharides, and human milk oligosaccharidesin conjunction with proanthocyanidins (PACs) extracted from cranberry. more...
Organism:
Lactiplantibacillus plantarum
Type:
Expression profiling by high throughput sequencing
Platform:
GPL29328
22 Samples
Download data: CSV, TXT
Series
Accession:
GSE160565
ID:
200160565
3.

Characterization of Lactobacillus plantarum gene expression in the acidic conditions

(Submitter supplied) Characterization of Lactobacillus plantarum gene expression in the acididic conditions such as kimchi fermentation
Organism:
Lactiplantibacillus plantarum
Type:
Expression profiling by high throughput sequencing
Platform:
GPL23496
6 Samples
Download data: XLSX
Series
Accession:
GSE143834
ID:
200143834
4.

Transcriptional profile Lactobacillus plantarum WCFS1 : Hydroxytyrosol treated cells

(Submitter supplied) Whole genome transcriptional profiling was used to characterize the response of Lactobacillus plantarum WCFS1 human isolate during challenge with hydroxytyrosol. Twelve independent experiments were performed and mixed at random in groups of four for total of three RNA samples. Whole genome transcriptional profiling was used to characterize the response of Lactobacillus plantarum WCFS1 human isolate during challenge with hydroxytyrosol. more...
Organism:
Lactiplantibacillus plantarum
Type:
Expression profiling by array
Platform:
GPL22663
3 Samples
Download data: TXT
Series
Accession:
GSE90714
ID:
200090714
5.

Transcriptional profile Lactobacillus plantarum WCFS1 : Resveratrol treated cells

(Submitter supplied) Whole genome transcriptional profiling was used to characterize the response of Lactobacillus plantarum WCFS1 human isolate during challenge with resveratrol. Twelve independent experiments were performed and mixed at random in groups of four for total of three RNA samples. The transcriptional profile reveals a large reshape of nitrogen metabolism whic affects, among others, the pyridine and purine metabolisms as well as the metabolism of aminoacids related to thiol-specific oxidative stress response in this microorganism. more...
Organism:
Lactiplantibacillus plantarum
Type:
Expression profiling by array
Platform:
GPL22663
3 Samples
Download data: TXT
Series
Accession:
GSE89785
ID:
200089785
6.

Transcriptional profile Lactobacillus plantarum WCFS1 : Oleuropein treated cells

(Submitter supplied) Whole genome transcriptional profiling was used to characterize the response of Lactobacillus plantarum WCFS1 human isolate during challenge with oleuropein. Twelve independent experiments were performed and mixed at random in groups of four for total of three RNA samples. The transcriptional profile shows that Lactobacillus plantarum WCFS1 adapts its metabolic capacity to acquire certain carbohydrates and repress the expression of genes involved in fatty acid biosyntheis. more...
Organism:
Lactiplantibacillus plantarum
Type:
Expression profiling by array
Platform:
GPL22663
3 Samples
Download data: TXT
Series
Accession:
GSE90719
ID:
200090719
7.

Locust bean gum derived galacto-manno-oligosaccharides utilization by Lactobacillus plantarum WCFS1

(Submitter supplied) In order to understand LBG derived galacto-manno-oligosaccharides utilization by a probiotic bacterium, Lactobacillus plantarum WCFS1, we have grown Lactobacillus plantarum WCFS1 (in duplicates) till mid log phase (OD600nm ~0.5, 10 h) in carbon free MRS (de Man, Rogosa Sharpe ) media containing either galacto-manno-oligosaccharides, mannose, glucose or galactose (1% w/v) as the sole carbon source.
Organism:
Lactiplantibacillus plantarum WCFS1
Type:
Expression profiling by array
Platform:
GPL25372
8 Samples
Download data: TXT
Series
Accession:
GSE117591
ID:
200117591
8.

Response of Lactobacillus plantarum WCSF1 to the Gram-negative pathogen-associated quorum sensing molecule N-3-oxododecanoyl homoserine lactone.

(Submitter supplied) The bacterial quorum sensing (QS) phenomenon has been well studied since its discovery and has traditionally been considered to include signaling pathways recognized exclusively within either Gram-positive (Gm+) or Gram-negative (Gm-) bacteria. The Gm+ bacteria are known to utilize quorum sensing pathways mediated by various small autoinducing peptides (AIP), while the Gm- bacteria use small molecules known collectively as acyl-homoserine lactones (AHL). more...
Organism:
Lactiplantibacillus plantarum
Type:
Expression profiling by high throughput sequencing
Platform:
GPL25957
36 Samples
Download data: TXT
Series
Accession:
GSE124050
ID:
200124050
9.

How Lactobacillus plantarum Shapes its Transcriptome in Response to Contrasting Habitats

(Submitter supplied) Triplets of Lactobacullus plantarum strains were isolated from nine contrasting habitats. Without any passage through other culture media, isolation and cultivation were on model media that strictly reproduced the chemical and physical conditions and stressors of the habitats of origin. Here, we demonstrated how L. plantarum regulates and shapes its transcriptome in response to contrasting habitats. more...
Organism:
Lactiplantibacillus plantarum
Type:
Expression profiling by high throughput sequencing
Platform:
GPL25156
36 Samples
Download data: TXT
Series
Accession:
GSE115448
ID:
200115448
10.

Trascriptomic profiles of Lactobacillus plantarum strains isolated from cheeses

(Submitter supplied) Analysis of Lactobacillus plantarum stains isolated from different cheese type
Organism:
Lactiplantibacillus plantarum
Type:
Expression profiling by high throughput sequencing
Platform:
GPL23496
12 Samples
Download data: TXT
Series
Accession:
GSE101169
ID:
200101169
11.

Transcriptional profile Lactobacillus plantarum WCFS1 : olive oil (OO) treated cells

(Submitter supplied) Whole genome transcriptional profiling was used to characterize the response of Lactobacillus plantarum WCFS1 human isolate during challenge with olive oil (OO). Twelve independent experiments were performed and mixed at random in groups of four for total of three RNA samples. The transcriptional profile reveals the downregulation of processes associated with rapid growth and the induction of stress-related pathways indicating the involvement of the stringent response. more...
Organism:
Lactiplantibacillus plantarum WCFS1; Lactiplantibacillus plantarum
Type:
Expression profiling by array
Platform:
GPL15934
3 Samples
Download data: TXT
Series
Accession:
GSE89534
ID:
200089534
12.

Global transcriptional responses to oxidative stress conditions in lactobacillus plantarum

(Submitter supplied) Bacteria cope with and adapt to stress by modulating gene expression in response to specific environmental cues. In this study the transcriptional response of lactobacillus plantarum CAUH2 to oxidative stress conditions was investigated via RNA-seq. The work provides detailed insights into the mechanisms through which L. plantarum responds to oxidative stress conditions and increases understanding of bacterial adaptation in natural and industrial settings.
Organism:
Lactiplantibacillus plantarum
Type:
Expression profiling by high throughput sequencing
Platform:
GPL23496
6 Samples
Download data: TXT, XLSX
Series
Accession:
GSE99096
ID:
200099096
13.

The Epigenomic Landscape of Prokaryotes

(Submitter supplied) DNA methylation is an important regulator of genome function in the eukaryotes, but it is currently unclear if the same is true in prokaryotes. While regulatory functions have been demonstrated for a small number of bacteria, there have been no large-scale studies of prokaryotic methylomes and the full repertoire of targets and biological functions of DNA methylation remains unclear. Here we applied single-molecule, real-time sequencing to directly study the methylomes of 232 phylogenetically diverse prokaryotes. more...
Organism:
Lactococcus lactis subsp. lactis; Lactiplantibacillus plantarum; Lachnobacterium bovis; Clostridium perfringens ATCC 13124; Methanocaldococcus jannaschii DSM 2661; Methylorubrum extorquens AM1; Thermoplasma volcanium GSS1; Acidobacteriaceae bacterium TAA 166; Mycoplasmopsis bovis PG45; Methanospirillum hungatei JF-1; Actinobacillus succinogenes 130Z; Fervidobacterium nodosum Rt17-B1; Bifidobacterium longum subsp. infantis ATCC 15697 = JCM 1222 = DSM 20088; Staphylothermus marinus F1; Thermoanaerobacter sp. X514; Xenorhabdus nematophila ATCC 19061; Dyadobacter fermentans DSM 18053; Streptosporangium roseum DSM 43021; Pedobacter heparinus DSM 2366; Rhizobium etli CIAT 652; Meiothermus ruber DSM 1279; Planctopirus limnophila DSM 3776; Methanothermus fervidus DSM 2088; Sebaldella termitidis ATCC 33386; Methanohalophilus mahii DSM 5219; Aminobacterium colombiense DSM 12261; Acidobacteriaceae bacterium KBS 146; Pseudomonas stutzeri RCH2; Frankia sp. DC12; Pontibacter actiniarum DSM 19842; Thermobacillus composti KWC4; Marinithermus hydrothermalis DSM 14884; Bernardetia litoralis DSM 6794; Desulfobacca acetoxidans DSM 11109; Rikenella microfusus DSM 15922; Echinicola vietnamensis DSM 17526; Orenia marismortui DSM 5156; Sporocytophaga myxococcoides DSM 11118; Niabella soli DSM 19437; Sinorhizobium medicae WSM1115; Hippea alviniae EP5-r; Hippea sp. KM1; Sphingomonas melonis C3; Methylophilaceae bacterium 11; bacterium JKG1; Thioalkalivibrio sp. ARh3; Thiomonas sp. FB-6; Oxalobacteraceae bacterium AB_14; Solidesulfovibrio cf. magneticus IFRC170; Desulfotignum balticum DSM 7044; Methylobacterium sp. EUR3 AL-11; Bryobacter aggregatus MPL3; Ruminococcus albus AD2013; Eubacterium sp. AB3007; Ruminococcaceae bacterium AE2021; Lachnospiraceae bacterium AC2031; Selenomonas ruminantium AC2024; Peptostreptococcaceae bacterium VA2; Ruminococcus sp. HUN007; Streptococcus equinus; Salmonella enterica subsp. arizonae serovar 62:z4,z23:-; Xylella fastidiosa Temecula1; Acetivibrio thermocellus ATCC 27405; Rhodopseudomonas palustris CGA009; Neisseria meningitidis FAM18; Thermoplasma acidophilum DSM 1728; Hydrogenovibrio crunogenus XCL-2; Chloroflexus aggregans DSM 9485; Thermosipho melanesiensis BI429; Shewanella woodyi ATCC 51908; Bradyrhizobium elkanii USDA 76; Dinoroseobacter shibae DFL 12 = DSM 16493; Parabacteroides distasonis ATCC 8503; Anoxybacillus flavithermus WK1; Escherichia coli str. K-12 substr. MG1655; Capnocytophaga ochracea DSM 7271; Haloterrigena turkmenica DSM 5511; Palaeococcus ferrophilus DSM 13482; Acetivibrio thermocellus DSM 1313; Treponema caldarium DSM 7334; Treponema succinifaciens DSM 2489; Caldithrix abyssi DSM 13497; Calidithermus chliarophilus DSM 9957; Cohnella panacarvi Gsoil 349; Methylobacterium sp. 10; Xanthobacter sp. 91; Geopsychrobacter electrodiphilus DSM 16401; Hydrogenovibrio marinus DSM 11271; Nocardia sp. BMG111209; Klebsiella oxytoca BRL6-2; Polaribacter sp. Hel_I_88; Methylohalobius crimeensis 10Ki; Streptomyces sp. WMMB 714; Ruminiclostridium josui JCM 17888; Alteromonas sp. ALT199; Aminiphilus circumscriptus DSM 16581; Caldicoprobacter oshimai DSM 21659; Geovibrio sp. L21-Ace-BES; Microbacterium sp. KROCY2; Thermogemmatispora carboxidivorans; Acidobacterium ailaaui; Ruminococcus flavefaciens AE3010; Selenomonas ruminantium AB3002; Butyrivibrio sp. FCS014; Polycyclovorans algicola TG408; Clostridium sp. KNHs205; Lachnospiraceae bacterium AC2029; Enterococcus faecalis 68A; Butyrivibrio sp. AE3004; Teredinibacter purpureus; Enterococcus gallinarum; Clostridium algidicarnis; Pyrococcus horikoshii OT3; Methylocystis sp. LW5; Agrobacterium fabrum str. C58; Persephonella; Mastigocladopsis repens PCC 10914; Neisseria gonorrhoeae FA 1090; Clostridioides difficile 630; Thiobacillus denitrificans ATCC 25259; Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150; Sulfurimonas denitrificans DSM 1251; Sulfolobus acidocaldarius DSM 639; Flavobacterium psychrophilum JIP02/86; Methanocorpusculum labreanum Z; Cronobacter; Pseudarthrobacter chlorophenolicus A6; Joostella marina; Saccharomonospora viridis DSM 43017; Verrucomicrobia bacterium LP2A; Thermanaerovibrio acidaminovorans DSM 6589; Meiothermus silvanus DSM 9946; Corynebacterium aurimucosum ATCC 700975; Zymomonas mobilis subsp. pomaceae ATCC 29192; Klebsiella aerogenes FGI35; Cellulophaga algicola DSM 14237; Flexistipes sinusarabici DSM 4947; Sulfurospirillum barnesii SES-3; Gillisia limnaea DSM 15749; Spirochaeta thermophila DSM 6578; Ruminococcus sp. NK3A76; Spirochaeta africana DSM 8902; Holophaga foetida DSM 6591; Salmonella enterica subsp. enterica serovar Paratyphi B str. SPB7; Acetivibrio clariflavus 4-2a; Thermacetogenium phaeum DSM 12270; Methylophilus sp. 5; Arthrobacter sp. 31Y; Methylophilus sp. 42; Methylotenera versatilis 79; Psychrilyobacter atlanticus DSM 19335; Prevotella sp. 10(H); Methylotenera sp. 73s; Acidovorax sp. JHL-3; Gillisia sp. JM1; Cellulomonas sp. KRMCY2; Clostridium sp. ASBs410; Polaromonas sp. EUR3 1.2.1; [Ruminococcus] gnavus AGR2154; Levilactobacillus brevis AG48; Pediococcus acidilactici AGR20; Exiguobacterium chiriqhucha; Prevotella sp. HUN102; Flavimarina sp. Hel_I_48; Lachnospiraceae bacterium AC2012; Clostridioides mangenotii LM2; Exiguobacterium aurantiacum DSM 6208; Exiguobacterium acetylicum DSM 20416; Exiguobacterium oxidotolerans JCM 12280; Exiguobacterium antarcticum DSM 14480; Methylobacter tundripaludum 21/22; Lachnoclostridium phytofermentans KNHs2132; Staphylococcus epidermidis AG42; Butyrivibrio sp. AE3003; Teredinibacter turnerae; Escherichia coli CFT073; Salmonella bongori NCTC 12419; Treponema denticola ATCC 35405; Akkermansia muciniphila ATCC BAA-835; Phaeobacter inhibens DSM 17395; Actinosynnema mirum DSM 43827; Staphylococcus aureus subsp. aureus USA300_TCH1516; Sphaerobacter thermophilus DSM 20745; Veillonella parvula DSM 2008; Streptobacillus moniliformis DSM 12112; Sedimentitalea nanhaiensis DSM 24252; Sediminispirochaeta smaragdinae DSM 11293; Hirschia baltica ATCC 49814; Coraliomargarita akajimensis DSM 45221; Syntrophothermus lipocalidus DSM 12680; Syntrophobotulus glycolicus DSM 8271; Bacillus subtilis subsp. spizizenii str. W23; Phocaeicola salanitronis DSM 18170; Nitratifractor salsuginis DSM 16511; Cellulophaga lytica DSM 7489; Asinibacterium sp. OR53; Solitalea canadensis DSM 3403; Patulibacter minatonensis DSM 18081; Acetobacterium woodii DSM 1030; Nocardia sp. BMG51109; Halomicrobium katesii DSM 19301; Nitriliruptor alkaliphilus DSM 45188; Methylophilus sp. 1; Pseudomonas aeruginosa NCAIM B.001380; Kangiella aquimarina DSM 16071; Pelobacter seleniigenes DSM 18267; Thiomicrospira pelophila DSM 1534; Desulfurobacterium sp. TC5-1; Bacteroides sp. 14(A); Clostridium sp. 12(A); Hydrogenovibrio kuenenii DSM 12350; Leptolyngbya sp. PCC 6406; Maribacter sp. Hel_I_7; Desulfospira joergensenii DSM 10085; Tolumonas lignilytica; Cellvibrionaceae bacterium 1162T.S.0a.05; [Clostridium] methoxybenzovorans SR3; [Clostridium] indolis DSM 755; Desulforegula conservatrix Mb1Pa; Oceanicola sp. HL-35; Algoriphagus marincola HL-49; Desulfohalovibrio reitneri; Alicyclobacillus macrosporangiidus CPP55; Sediminibacter sp. Hel_I_10; Hydrogenovibrio sp. MA2-6; Pseudobutyrivibrio ruminis HUN009; Lachnoclostridium phytofermentans KNHs212; Robinsoniella sp. KNHs210
Type:
Methylation profiling by high throughput sequencing
228 related Platforms
237 Samples
Download data: CSV, GFF
Series
Accession:
GSE69872
ID:
200069872
14.

Transcriptional profile Lactobacillus plantarum WCFS1 : 1.5mM gallic acid (GA) treated cells

(Submitter supplied) Whole genome transcriptional profiling was used to characterize the response of Lactobacillus plantarum WCFS1 human isolate during challenge with 1.5 mM gallic acid (GA). Twelve independent experiments were performed and mixed at random in groups of four for total of three RNA samples. The transcriptional profile reveals a massive induction of genes involved in transport and decarboxilation of gallic acid.
Organism:
Lactiplantibacillus plantarum; Lactiplantibacillus plantarum WCFS1
Type:
Expression profiling by array
Platform:
GPL15934
3 Samples
Download data: TXT
Series
Accession:
GSE63728
ID:
200063728
15.

Transcriptional profile Lactobacillus plantarum WCFS1: 15 mM gallic acid (GA) treated cells

(Submitter supplied) Whole genome transcriptional profiling was used to characterize the response of Lactobacillus plantarum WCFS1 human isolate during challenge with gallic acid (GA). Twelve independent experiments were performed and mixed at random in groups of four for total of three RNA samples. The transcriptional profile reveals a massive induction of genes involved in transport and decarboxilation of gallic acid.
Organism:
Lactiplantibacillus plantarum; Lactiplantibacillus plantarum WCFS1
Type:
Expression profiling by array
Platform:
GPL15934
3 Samples
Download data: TXT
Series
Accession:
GSE56997
ID:
200056997
16.

From transcriptomics to phenomics to reveal adaptation response of Lactobacillus plantarum C2 in plant substrates

(Submitter supplied) The aim of the study was to determine biological relevance of differentially expressed genes in Lactobacillus plantarum C2 during fermentation of plant substrates. Whole-transcriptome analysis based on customized microarray profiles has been used to determine altered transcription patterns in L. plantarum C2.
Organism:
Lactiplantibacillus plantarum
Type:
Expression profiling by array
Platform:
GPL20099
8 Samples
Download data: TXT
Series
Accession:
GSE68188
ID:
200068188
17.

Identification of genes regulated by L-lactate and by DL-lactate in Lactobacillus plantarum

(Submitter supplied) L. plantarum is known to possess an L-lactate inducible lactate racemase activity (Goffin et al. 2005. J. Bacteriol. 187:6750). In the present study, microarrays were used in order to identify all genes that are up-regulated by L-lactate, but not by a racemic mixture of D- and L-lactate.
Organism:
Lactiplantibacillus plantarum; Lactiplantibacillus plantarum WCFS1
Type:
Expression profiling by array
Platform:
GPL4318
2 Samples
Download data: TXT
Series
Accession:
GSE43518
ID:
200043518
18.

Transcriptional profile Lactobacillus plantarum WCFS1 : p-coumaric acid (p-CA) treated cells

(Submitter supplied) Whole genome transcriptional profiling was used to characterize the response of Lactobacillus plantarum WCFS1 human isolate during challenge with p-coumaric acid (p-CA). Twelve independent experiments were performed and mixed at random in groups of four for total of three RNA samples. The transcriptional profile reveals a massive induction of genes involved in stress resistance and detoxification-related functions and a global shutdown of growth-associated processes.
Organism:
Lactiplantibacillus plantarum; Lactiplantibacillus plantarum WCFS1
Type:
Expression profiling by array
Platform:
GPL15934
3 Samples
Download data: TXT
Series
Accession:
GSE40126
ID:
200040126
19.

Comparative analysis of bacterial transcriptome using DNA microarray and next generation sequencing technologies

(Submitter supplied) Validation of Lactobacillus plantarum WCFS1 transcriptome profile using RNA sequencing (direct cDNA sequencing and 3'-UTR sequencing) in comparison with DNA microarray as a reference platform.
Organism:
Lactiplantibacillus plantarum
Type:
Expression profiling by array
Platform:
GPL13984
4 Samples
Download data: TXT
Series
Accession:
GSE35754
ID:
200035754
20.

Genome-wide prediction and validation of σ70 promoters in Lactobacillus plantarum WCFS1

(Submitter supplied) Background: In prokaryotes, sigma factors are essential for the targeting of the transcription machinery to promoters. Various sigma factors have been described that recognize and bind to specific DNA sequence motifs in promoter sequences. The canonical sigma factor σ70 is commonly involved in transcription of the cell's general housekeeping genes, which is mediated by the conserved σ70 promoter sequence motifs. more...
Organism:
Lactiplantibacillus plantarum; Lactiplantibacillus plantarum WCFS1
Type:
Expression profiling by genome tiling array
Platforms:
GPL15385 GPL15386
6 Samples
Download data: TXT
Series
Accession:
GSE36898
ID:
200036898
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