GEO DataSets

(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) Comprehensive profiling of hormone-dependent breast cancer (HDBC) has identified hundreds of protein-coding alterations contributing to cancer initiation, but only a handful have been linked to endocrine therapy resistance, potentially contributing to 40% of relapses. If other mechanisms underlie the evolution of HDBC under adjuvant therapy is currently unknown. In this work, we employ integrative functional genomics to dissect the contribution of cis-regulatory elements (CREs) to cancer evolution by focusing on 12 megabases of non-coding DNA, including clonal enhancers, gene promoters, and boundaries of topologically associating domains. more...

Organism:

mixed DNA library; Homo sapiens

Type:

Other

Platforms:

GPL16791 GPL20301 GPL32000

68 Samples

Download data: FA, TXT

(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

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(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

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(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 GPL16417 GPL16085

15 Samples

Download data: FASTA, TSV, TXT

(Submitter supplied) Folic acid deficiency is common worldwide and is linked to intestinal flora imbalance. The intestinal microbial utilization of folic acid based on model animals faces the challenges of repeatability and individual variability. In this study, we built an in vitro fecal slurry culture model deficient in folic acid. We examined the effects of supplementation with different forms of folic acid (5-methyltetrahydrofolate and non-reduced folic acid) on the modulation of intestinal flora. more...

Organism:

human feces metagenome

Type:

Other

Platform:

GPL31937

96 Samples

Download data: TSV, TXT, XLS

(Submitter supplied) The neurotoxic effects and mechanisms of low-dose and long-term sulfamethoxazole (SMZ) exposure remain unknown. This study exposed zebrafish to environmental SMZ concentrations and observed behavioral outcomes. SMZ exposure increased hyperactivity and altered the transcript levels of 17 genes associated with neurological function. It impaired intestinal function by reducing the number of intestinal goblet cells and lipid content. more...

Organism:

feces metagenome

Type:

Other

Platform:

GPL24920

6 Samples

Download data: TXT, XLSX

(Submitter supplied) The gut and local esophageal microbiome progressively shift from healthy commensal bacteria to inflammatory-linked pathogenic bacteria in patients with gastroesophageal reflux disease, Barrett’s esophagus and esophageal adenocarcinoma (EAC). However, mechanisms by which microbial communities contribute to reflux-driven EAC remain incompletely understood and challenging to target. Herein, we utilized a rat reflux-induced EAC model to investigate targeting the gut microbiome-esophageal metabolome axis with cranberry proanthocyanidins (C-PAC) to inhibit EAC progression. more...

Organism:

rat gut metagenome

Type:

Other

Platform:

GPL24042

25 Samples

Download data: CSV

(Submitter supplied) Esophageal squamous cell carcinoma (ESCC) is characterized as a metabolic disorder characterized by lipid metabolic reprogramming. To investigate the regional characteristics of ESCC patients in Xinjiang Province, China, and lipid metabolism, in this study, we described the characteristics of the serum lipid composition in Kazakh ESCC patients by performing an integrated analysis of the transcriptome and lipidomic data. more...

Organism:

Homo sapiens; solid waste metagenome

Type:

Non-coding RNA profiling by array

Platform:

GPL30375

6 Samples

Download data: TXT