GEO DataSets

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

Organism:

Mus musculus; feces metagenome

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other; Expression profiling by array

Platforms:

GPL24116 GPL10787 GPL17021

72 Samples

Download data: BED, BIGWIG, CSV, TXT

(Submitter supplied) Crohn’s disease is a chronic, debilitating inflammatory bowel disease. Here we report a critical role for phospholipase C-β3 (PLC-β3) in intestinal homeostasis. In PLC-β3- deficient mice, exposure to oral dextran sodium sulfate induced lethality and severe inflammation in the small intestine. The lethality was due to PLC-3 deficiency in multiple non-hematopoietic cell types. PLC-β3 deficiency resulted in reduced Wnt/-catenin signaling, which is essential for homeostasis and regeneration of the intestinal epithelium. more...

Organism:

feces metagenome

Type:

Other

Platform:

GPL24116

26 Samples

Download data: CSV

(Submitter supplied) To examine potential changes of the intestinal microbiota in mice caused by repeated mild stress, we profiled bacteria and fungi in the mouse feces by sequencing the 16s v3v4 region and the ITS1-2 region.

Organism:

feces metagenome

Type:

Other

Platform:

GPL24116

28 Samples

Download data: TSV

(Submitter supplied) Background: Hypertension is one of the most common metabolic diseases in the elderly and its pathogenesis is associated with microbiota dysbiosis. Recent evidence suggests that oral microbiota dysbiosis is also an important factor in the development of hypertension. However, the relationship between hypertension and oral flora in the elderly has not been adequately investigated. Objective: The aim of this cross-sectional study was to investigate the structure of the oral microbiota and its correlation with hypertension in elderly hypertensive patients. more...

Organism:

human oral metagenome

Type:

Other

Platform:

GPL32222

206 Samples

Download data: TXT

(Submitter supplied) CYP monooxygenase-mediated conversion of LA to EpOMEs plays critical roles in the health effects of dietary LA, implicating a unique mechanistic linkage between dietary fatty acid intake and cancer risks.

Organism:

mouse gut metagenome

Type:

Other

Platform:

GPL21051

48 Samples

Download data: XLSX

(Submitter supplied) Early detection of spoilage microorganisms and food pathogens is of major importance in preventing food recalls and foodborne outbreaks. Although constant effort is invested in developing sensitive methods for rapid microbial detection, none of the current methods enables the detection of food pathogens within a few hours; therefore, development of innovative early-warning food-testing strategies are needed. more...

Organism:

food metagenome

Type:

Other

Platform:

GPL34170

145 Samples

Download data: CSV

(Submitter supplied) Fire disturbances are becoming more common, more intense, and further-reaching across the globe, with consequences for ecosystem functioning. Importantly, fire can have strong effects on the soil microbiome, including community and functional changes after fire, but surprisingly little is known regarding the role of soil fire legacy in shaping responses to recent fire. To address this gap, we conducted a manipulative field experiment administering fire across 32 soils with varying fire legacies, including combinations of 1-7 historic fires and 1-33 years since most recent fire. more...

Organism:

soil metagenome

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34803

39 Samples

Download data: CSV

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

Organism:

Mus musculus; feces metagenome

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL32080 GPL24247

71 Samples

Download data: MTX, TSV

(Submitter supplied) IL22 induces antimicrobial peptides which influnce microbiota. We used 16s rRNA gene sequencing (16s DNA-seq) to analyze the microbiota with Fc or IL-22Fc treatment.

Organism:

feces metagenome

Type:

Other

Platform:

GPL32080

63 Samples

Download data: XLSX

(Submitter supplied) Cellulose is the most abundant component of plant litter, which is critical for terrestrial carbon cycling. Nonetheless, it remains unknown how climate changes affect cellulose-decomposing microorganisms. Here, we carried out a multi-year litterbag experiment to examine cellulose decomposition undergoing +3°C warming in an Oklahoma tallgrass prairie, USA. GeoChip 5.0M was employed to detect microbial functional genes.

Organism:

soil metagenome; uncultured soil microorganism; decomposition metagenome

Type:

Other

Platform:

GPL33589

48 Samples

Download data: TXT

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

Organism:

mouse gut metagenome; Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL32553 GPL24247

26 Samples

Download data

(Submitter supplied) Ulcerative colitis (UC) is a complex immune-mediated inflammatory disease. In recent years, the incidence of UC has increased rapidly, however, its exact etiology and mechanism are still unclear. Based on the definite anti-inflammatory and antibacterial activities of Sanguisorba officinalis L., we studied its monomer methyl gallate (MG). In this study, we employed flow cytometry and detected nitric oxide production, finding MG regulated macrophage polarization and inhibited the expression of proinflammatory cytokines in vitro. more...

Organism:

mouse gut metagenome

Type:

Other

Platform:

GPL32553

17 Samples

Download data: TXT

(Submitter supplied) The biodegradable polymer poly-β-hydroxybutyrate (PHB) is a promising carbon source for biological mitigation of nitrogen pollution, a significant problem in aquaculture that physical and chemical methods have not provided a comprehensive solution. Here we investigated the impact of PHB on the zero-water-change largemouth bass culture by 30- and 40-day experiments. PHB loaded into the filter circulation pump at 4g L-1, optimum value determined by the first experiment, significantly reduced the levels of nitrate by 99.65%, nitrite by 95.96%, and total nitrogen by 85.22% compared to the control without PHB. more...

Organism:

wastewater metagenome

Type:

Expression profiling by array

Platform:

GPL34479

6 Samples

Download data: TXT

(Submitter supplied) Here, we applied a microarray-based metagenomics technology termed GeoChip 5.0 to examined functional gene structure of microbes in three biomes, including boreal, temperate and tropical area.

Organism:

uncultured soil microorganism; soil metagenome

Type:

Other

Platform:

GPL29739

120 Samples

Download data: TXT

(Submitter supplied) The gut microbiota plays an important role in host health. Microbiota dysbiosis has been implicated in the global epidemic of Metabolic Syndrome (MetS) and could impair host metabolism by noxious metabolites. It has been well established that the gut microbiota is shaped by host immune factors. However, the effect of T cells on the gut microbiota is yet unknown. Here, we performed a metagenomic whole-genome shotgun sequencing (mWGS) study of the microbiota of TCRb-/- mice, which lack alpha/beta T cells.

Organism:

feces metagenome

Type:

Other

Platform:

GPL33160

14 Samples

Download data: TSV

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

Organism:

Mus musculus; feces metagenome

Type:

Other; Expression profiling by high throughput sequencing

Platforms:

GPL24116 GPL19057 GPL24247

32 Samples

Download data

(Submitter supplied) To examine the microbiota abundance difference, we performed fecal 16s sequencing of wild type, TCRb-/-, TCRb-/- co-housed with WT and TCRb-/- receiving WT T cells.

Organism:

feces metagenome

Type:

Other

Platform:

GPL24116

19 Samples

Download data: RDS

(Submitter supplied) Background: Alcohol misuse, binge drinking pattern, and gender-specific effects in the middle-aged population has been clearly underestimated. In the present study, we focused on understanding gender-specific effects of alcohol exposure on the gut-liver axis and the role of gut microbiota in modulating gender-specific responses to alcohol consumption. Methods: Fifty-two-week-old female and male C57BL/6 mice were fasted for 12 h, and then administered a single oral dose of ethanol (EtOH) (6 g/kg). more...

Organism:

mouse gut metagenome

Type:

Other

Platform:

GPL34367

11 Samples

Download data: CSV

(Submitter supplied) Background: Lung is the largest mucosal area of the human body and directly connected to the external environment, facing microbial exposure and environmental stimuli. Therefore, studying the internal microorganisms of the lung is crucial for a deeper understanding of the relationship between microorganisms and the occurrence and progression of lung cancer. Methods: Tumor and adjacent nontumor tissues were collected from 38 lung adenocarcinoma patients and used nanopore sequencing technology to sequence the 16s full-length sequence of bacteria, and combining bioinformatics methods to identify and quantitatively analyze microorganisms in tissues, as well as to enrich the metabolic pathways of microorganisms. more...

Organism:

metagenomes

Type:

Other

Platform:

GPL34320

74 Samples

Download data: TXT

(Submitter supplied) The study critically evaluate the results of 16S targeted amplicon sequencing performed on the total DNA collected from healthy donors’ blood samples in the light of specific negative controls.

Organism:

Mus musculus; human blood metagenome; Escherichia coli

Type:

Other

Platforms:

GPL34159 GPL16085 GPL16417

15 Samples

Download data: FASTA, TSV, TXT