GEO DataSets

(Submitter supplied) Here we report 16s rRNA data from environmental samples that include metal working fluid and air from a machine facility and lung tissue samples. Microbiota composition of environmental and lung tissue samples showed greater similarity between case samples than between control samples.

Organism:

uncultured bacterium

Type:

Other

Platform:

GPL22493

2 Samples

Download data: TXT

(Submitter supplied) The experiment was designed to test the interactions of Spartina alterniflora, its microbiome, and the interaction of the plant-microbe relationship with oil from the Deepwater Horizon oil spill (DWH). Total RNA was extracted from leaf and root microbiome of S. alterniflora in soils that were oiled in DWH oil spill with or without added oil, as well as those grown in unoiled soil with or without added oil. more...

Organism:

uncultured bacterium; Eukaryota; Viruses; synthetic construct; Archaea; Bacteria

Type:

Expression profiling by array

Platform:

GPL28373

24 Samples

Download data: TXT

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

Organism:

Mus musculus; uncultured bacterium

Type:

Expression profiling by array; Expression profiling by high throughput sequencing

Platforms:

GPL24769 GPL21163

56 Samples

Download data: TXT

(Submitter supplied) Dietary lipids favor the growth of the pathobiont Bilophila wadsworthia, but the relevance of this expansion in metabolic syndrome pathogenesis remains unknown. Here, we showed that B. wadsworthia synergize with HFD to promote higher inflammation, intestinal barrier dysfunction and bile acid dysmetabolism, leading to higher glucose dysmetabolism and hepatic steatosis. Host-microbiota transcriptomics analysis unraveled pathways, particularly butanoate metabolism, which may underlie the metabolic effects mediated by B. more...

Organism:

uncultured bacterium

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24769

29 Samples

Download data: TXT

(Submitter supplied) Salt marshes provide many key ecosystem services that have tremendous ecological and economic value. One critical service is the removal of fixed nitrogen from coastal waters, which limits the negative effects of eutrophication resulting from increased nutrient supply. Nutrient enrichment of salt marsh sediments results in higher rates of nitrogen cycling and, commonly, a concurrent increase in the flux of nitrous oxide, an important greenhouse gas. more...

Organism:

synthetic construct; uncultured bacterium; sediment metagenome

Type:

Other

Platform:

GPL24484

64 Samples

Download data: TXT

(Submitter supplied) Molecular analysis of dissimilatory nitrite reductase genes (nirS) was conducted using a customized microarray containing 165 nirS probes (archetypes) to identify members of sedimentary denitrifying communities. The goal of this study was to examine denitrifying community responses to changing environmental variables over spatial and temporal scales in the New River Estuary (NRE), NC, USA. Multivariate statistical analyses revealed three denitrifier assemblages and uncovered “generalist” and “specialist” archetypes based on the distribution of archetypes within these assemblages. more...

Organism:

uncultured bacterium; synthetic construct

Type:

Other

Platform:

GPL23374

8 Samples

Download data: TXT

(Submitter supplied) Sputum expectorated by the pulmonary tuberculosis patients still remains a primary diagnostic specimen. The expression pattern of mycobacteria in sputum will lead to an insight of bacterial adaptation at the most highly transmissible stage of infection and can also help in identifying newer diagnostic as well as drug targets. Further, the identification of crossreactive gene targets from the sputum samples of other lung diseases will help to find the diagnostic candidates which will be highly specific to pulmonary tuberculosis.

Organism:

Mycobacterium tuberculosis; uncultured bacterium

Type:

Expression profiling by array

Platform:

GPL4057

20 Samples

Download data: GPR, TXT

(Submitter supplied) Bacteriophage – host dynamics and interactions are important for microbial community composition and ecosystem function. Nonetheless, empirical evidence in engineered environment is scarce. Here, we examined phage and prokaryotic community composition of four anaerobic digestors in full-scale wastewater treatment plants (WWTPs) across China. Despite relatively stable process performance in biogas production, both phage and prokaryotic groups fluctuated monthly over a year of study period. more...

Organism:

Bacteria; Eukaryota; Viruses; Archaea; uncultured bacterium

Type:

Other

Platform:

GPL22866

48 Samples

Download data: TXT

(Submitter supplied) Xiangjiang River (Hunan, China) has been contaminated with heavy metal for several decades by surrounding factories. However, little is known about the influence of a gradient of heavy metal contamination on the diversity, structure of microbial functional gene in sediment. To deeply understand the impact of heavy metal contamination on microbial community, a comprehensive functional gene array (GeoChip 5.0) has been used to study the functional genes structure, composition, diversity and metabolic potential of microbial community from three heavy metal polluted sites of Xiangjiang River.

Organism:

uncultured bacterium; Archaea; Eukaryota; Viruses; Bacteria

Type:

Other

Platform:

GPL22263

9 Samples

Download data: TXT

(Submitter supplied) Samples of oil and production water were collected from five wells of the Qinghai Oilfield, China, and subjected to GeoChip hybridization experiments for microbial functional diversity profiling. Unexpectedly, a remarkable microbial diversity in oil samples, which was higher than that in the corresponding water samples, was observed, thus challenging previously believed assumptions about the microbial diversity in this ecosystem. more...

Organism:

uncultured bacterium; Bacteria

Type:

Other

Platform:

GPL18323

9 Samples

Download data: TXT

(Submitter supplied) The experiment at three long-term agricultural experimental stations (namely the N, M and S sites) across northeast to southeast China was setup and operated by the Institute of Soil Science, Chinese Academy of Sciences. This experiment belongs to an integrated project (The Soil Reciprocal Transplant Experiment, SRTE) which serves as a platform for a number of studies evaluating climate and cropping effects on soil microbial diversity and its agro-ecosystem functioning. more...

Organism:

uncultured bacterium; Bacteria

Type:

Other

Platform:

GPL21402

81 Samples

Download data: TXT

(Submitter supplied) The protocol to test the preservation capabilities was based on a standardized procedure using the ECSIM, a chemostat-based fermentation system establishes to maintain microbiota. The initial fresh stool sample (1 g) was first cultivated in 5 mL, then 100 mL and then 1 L of a standard artificial gut medium and then either immediately tested in the P-ECSIM or preserved for 3 and 6 months with cryoprotectants before being next used for inoculation of the P-ECSIM. more...

Organism:

human gut metagenome; uncultured bacterium

Type:

Other

Platform:

GPL16731

15 Samples

Download data: TXT

(Submitter supplied) Wastewater treatment plants use a variety of bioreactor types and configurations to remove organic matter and nutrients. Little is known regarding the effects of different configurations and within-plant immigration on microbial community dynamics. Previously, we found that the structure of ammonia-oxidizing bacterial (AOB) communities in a full-scale dispersed growth activated sludge bioreactor correlated strongly with levels of NO2- entering the reactor from an upstream trickling filter (Wells et al 2009). more...

Organism:

Archaea; uncultured archaeon; uncultured bacterium; Bacteria

Type:

Other

Platform:

GPL15537

11 Samples

Download data: CEL

(Submitter supplied) This study in rats was designed to investigate whether whole rhye (WR) can influence the metabolism of n-3 and n-6 long-chain fatty acids (LCFA) and gut microbiota composition. For 12 weeks, rats were fed a diet containing either 50% WR or 50% refined rye (RR). Total bacterial DNA was extracted from fecal and cecal samples (n=5 per group). 16S PCR amplification was performed to assess the microbial diversity at the family level using the HuGChip. more...

Organism:

uncultured bacterium; human gut metagenome

Type:

Expression profiling by array

Platform:

GPL20773

30 Samples

Download data: TXT

(Submitter supplied) To study whether and how soil nitrogen conditions affect the ecological effects of long-term elevated CO2 on microbial community and soil ecoprocess, here we investigated soil microbial community in a grassland ecosystem subjected to ambient CO2 (aCO2, 368 ppm), elevated CO2 (eCO2, 560 ppm), ambient nitrogen deposition (aN) or elevated nitrogen deposition (eN) treatments for a decade. Under the aN condition, a majority of microbial function genes, as measured by GeoChip 4.0, were increased in relative abundance or remained unchanged by eCO2. more...

Organism:

Bacteria; uncultured bacterium

Type:

Other

Platform:

GPL17437

48 Samples

Download data: TXT

(Submitter supplied) Aeolian soil erosion, exacerbated by anthropogenic perturbations, has become one of the most alarming processes of land degradation and desertification. By contrast, dust deposition might confer a potential fertilization effect. To examine how they affect topsoil microbial community, we conducted a study GeoChip techniques in a semiarid grassland of Inner Mongolia, China. We found that microbial communities were significantly (P<0.039) altered and most of microbial functional genes associated with carbon, nitrogen, phosphorus and potassium cycling were decreased or remained unaltered in relative abundance by both erosion and deposition, which might be attributed to acceleration of organic matter mineralization by the breakdown of aggregates during dust transport and deposition. more...

Organism:

Bacteria; Eukaryota; Viruses; uncultured bacterium; Archaea

Type:

Other

Platform:

GPL19950

30 Samples

Download data: TXT

(Submitter supplied) Microbial communities in the rhizosphere make significant contributions to crop health and nutrient cycling. However, their ability to perform important biogeochemical processes remains uncharacterized. Important functional genes, which characterize the rhizosphere microbial community, were identified to understand metabolic capabilities in the maize rhizosphere using GeoChip 3.0-based functional gene array method.

Organism:

uncultured bacterium; Bacteria

Type:

Genome variation profiling by array

Platform:

GPL19187

6 Samples

Download data: TXT

(Submitter supplied) Despite the global importance of forests, it is virtually unknown how their soil microbial communities adapt at the phylogenetic and functional level to long term metal pollution. Studying twelve sites located along two distinct gradients of metal pollution in Southern Poland revealed that both community composition (via MiSeq Illumina sequencing of 16S rRNA genes) and functional gene potential (using GeoChip 4.2) were highly similar across the gradients despite drastically diverging metal contamination levels. more...

Organism:

Bacteria; uncultured bacterium

Type:

Genome variation profiling by array

Platform:

GPL18982

12 Samples

Download data: TXT

(Submitter supplied) Due to its high altitude and extreme climate conditions, the Tibetan plateau is a region vulnerable to the impact of climate changes and anthropogenic perturbation, thus understanding how its microbial communities function may be of high importance. Here, we report a study to profile soil microbial structural genes, which infers functional roles of microbial communities, aiming to explore potential microbial responses to climate changes and anthropogenic perturbation. more...

Organism:

Bacteria; uncultured bacterium

Type:

Genome variation profiling by array

Platform:

GPL17437

63 Samples

Download data: TXT

(Submitter supplied) Soil transplant serves as a proxy to simulate climate change in realistic climate regimes. Here, we assessed the effects of climate warming and cooling on soil microbial communities, which are key drivers in Earth’s biogeochemical cycles, four years after soil transplant over large transects from northern (N site) to central (NC site) and southern China (NS site) and vice versa. Four years after soil transplant, soil nitrogen components, microbial biomass, community phylogenetic and functional structures were altered. more...

Organism:

uncultured bacterium; Bacteria

Type:

Genome variation profiling by array

Platform:

GPL17825

54 Samples

Download data: TXT