GEO DataSets

(Submitter supplied) The purpose of this study was to explore the mechanism of aerobic decay of whole-plant corn silage and the effect of Neolamarckia cadamba essential oil on aerobic stability of whole-plant corn silage. Firstly, the dynamic changes of temperature, microbial community and metabolite content after aerobic exposure of whole-plant corn silage were determined, and the main microbial species and mechanism leading to aerobic spoilage of whole-plant corn silage were analyzed. more...

Organism:

silage metagenome

Type:

Other

Platform:

GPL33693

12 Samples

Download data: TXT

(Submitter supplied) Nucleic acids in wastewater provide a rich source of data for detection and surveillance of microbes. We have longitudinally collected 116 RNA samples from a wastewater treatment plant in Berlin/Germany, from March 2021 to July 2022, and 24 DNA samples from May to July 2022. We tracked human astroviruses, enteroviruses, noroviruses and adenoviruses over time to the level of strains or even individual nucleotide variations, showing how detailed human pathogens can be observed using wastewater. more...

Organism:

wastewater metagenome

Type:

Other

Platform:

GPL33283

239 Samples

Download data: FA, TSV

(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:

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

Type:

Other

17 related Platforms

199 Samples

Download data: BEDGRAPH, TXT, XLSX

(Submitter supplied) DNA methylation plays important roles in foreign DNA defense, mismatch repair, and gene regulation in prokaryotic genomes. Existing methods for DNA methylation detection using next-generation sequencing (NGS) are incapable of simultaneously detecting multiple types of DNA methylation. Here, we present nitrite treatment followed by sequencing (NT-seq), a sequencing method to simultaneously detect adenine and cytosine methylation. more...

Organism:

Helicobacter pylori; Escherichia coli; mixed culture metagenome

Type:

Methylation profiling by high throughput sequencing; Other

Platforms:

GPL30645 GPL21222 GPL30644

14 Samples

Download data: CSV

(Submitter supplied) The spread of antibiotic resistance genes (ARG) into agricultural soils, products, and foods severely limits the use of organic fertilizers in agriculture. In this study, experimental land plots were fertilized, sown, and harvested for two consecutive agricultural cycles using either mineral or three types of organic fertilizers: sewage sludge, pig slurry, or composted organic fraction of municipal solid waste. more...

Organism:

solid waste metagenome; feces metagenome; soil metagenome; sludge metagenome

Type:

Other

4 related Platforms

71 Samples

Download data: CSV, XLSX

(Submitter supplied) The available energy and carbon sources for prokaryotes in the deep ocean remain still largely enigmatic. Reduced sulfur compounds, such as thiosulfate, are a potential energy source for both auto- and heterotrophic marine prokaryotes. Shipboard experiments performed in the North Atlantic using Labrador Sea Water (~2000 m depth) amended with thiosulfate led to an enhanced prokaryotic dissolved inorganic carbon (DIC) fixation.

Organism:

seawater metagenome

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27409

7 Samples

Download data: TXT

(Submitter supplied) Drought represents a significant stress to microorganisms and is known to reduce microbial activity and organic matter decomposition in Mediterranean ecosystems. However, we lack a detailed understanding of the drought stress response of microbial decomposers. Here we present metatranscriptomic data on the physiological response of in situ microbial communities on plant litter to long-term drought in Californian grass and shrub ecosystems.

Organism:

leaf litter metagenome

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28389

41 Samples

Download data: CSV

(Submitter supplied) Background: The soil environment is responsible for sustaining most terrestrial plant life on earth, yet we know surprisingly little about the important functions carried out by diverse microbial communities in soil. Soil microbes that inhabit the channels of decaying root systems, the detritusphere, are likely to be essential for plant growth and health, as these channels are the preferred locations of new root growth. more...

Organism:

soil metagenome

Type:

Other

Platform:

GPL20780

18 Samples

Download data: FASTA, TXT

(Submitter supplied) Purpose: Deconstructing the soil microbiome into reduced-complexity functional modules represents a novel method of microbiome analysis. The goals of this study are to confirm differences in transcriptomic patterns among five functional module consortia. Methods: mRNA profiles of 3 replicates each of functional module enrichments of soil inoculum in M9 media with either 1) xylose, 2) n-acetylglucosamine, 3) glucose and gentamycin, 4) xylan, or 5) pectin were generated by sequencing using an Illumina platform (GENEWIZ performed sequencing). more...

Organism:

soil metagenome

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20780

15 Samples

Download data: GFF, TXT

(Submitter supplied) Regulatory small RNAs (sRNAs) represent a major class of regulatory molecules that play large-scale and essential roles in many cellular processes across all domains of life. Microbial sRNAs have been primarily investigated in a few model organisms and little is known about the dynamics of sRNA synthesis in natural environments, and the roles of these short transcripts at the community level. Analyzing the metatranscriptome of a model extremophilic community inhabiting halite nodules (salt rocks) from the Atacama Desert, sampled over two years with different weather conditions, with SnapT – a new sRNA annotation pipeline – we discovered hundreds of intergenic (itsRNAs) and antisense (asRNAs) sRNAs expressed.

Organism:

halite metagenome

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27449

45 Samples

Download data: GFF, TXT

(Submitter supplied) We demonstrate the feasibility of total RNA-SIP in experiments where microbes from a hydrocarbon-contaminated aquifer were studied in microcosms with 13C-labelled-toluene to understand their adaptation to the simultaneous availability of low levels of different electron acceptors. SIP successfully resolved the involvement of microaerobic vs. aerobic and anaerobic populations. Under microoxic, nitrate-amended conditions hydrocarbon degradation was actually stimulated, but transcripts of denitrification showed no signs of 13C-labelling. more...

Organism:

aquifer metagenome

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27730

29 Samples

Download data: BIOM, TXT

(Submitter supplied) We reported the microbial communities in the biofilm anoxic-oxic-MBR system operated with different carbon source types.

Organism:

wastewater metagenome

Type:

Other

Platform:

GPL27052

6 Samples

Download data: PDF, TXT

(Submitter supplied) We reported the microbial communities in wastewater between conventional membrane bioreactor (MBR) system and biofilm MBR system using Illumina sequencing.

Organism:

wastewater metagenome

Type:

Other

Platform:

GPL27052

3 Samples

Download data: PDF, TXT

(Submitter supplied) We investigated a contaminant-degrading microbial community by sequencing total RNA (without rRNA depletion) from microcosms containing sediment from a hypoxic contaminated aquifer fed with isotopically labeled toluene.

Organism:

aquifer metagenome

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL25546

8 Samples

Download data: HDF5, TXT

(Submitter supplied) This study evaluated the ammonium oxidizing communities (COA) associated with a potato crop (Solanum phureja) rhizosphere soil in the savannah of Bogotá (Colombia) by examining the presence and abundance of amoA enzyme genes and transcripts by qPCR and next-generation sequence analysis. amoA gene abundance could not be quantified by qPCR due to problems inherent in the primers; however, the melting curve analysis detected increased fluorescence for Bacterial communities but not for Archaeal communities. more...

Organism:

soil metagenome

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL20780

3 Samples

Download data: TXT

(Submitter supplied) Total bacterial DNA was isolated from water and sediment samples from a local watershed and 16S rRNA sequences were analyzed using the Illumina MiSeq v3 platform in order to generate snapshots of bacterial community profiles.

Organism:

riverine metagenome

Type:

Other

Platform:

GPL20996

56 Samples

Download data: XLSX

(Submitter supplied) Contaminated aquifer (Dusseldorf-Flinger, Germany) templates extracted from 5 sediment depths ranging between 6.4 and 8.4 m below ground and over 3 years of sampling were amplified for amplicon pyrosequencing using the primers Ba27f (5’-aga gtt tga tcm tgg ctc ag-3’) and Ba519r (5’- tat tac cgc ggc kgc tg-3’), extended as amplicon fusion primers with respective primer A or B adapters, key sequence and multiplex identifiers (MID) as recommended by 454/Roche. more...

Organism:

aquifer metagenome

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL26069

15 Samples

Download data: FASTA

(Submitter supplied) The characterization of microbial community structure via 16S rRNA gene profiling has been greatly advanced in recent years by the application of amplicon pyrosequencing. The possibility of barcode-tagged sequencing of templates gives the opportunity to massively screen multiple samples from environmental or clinical sources for community details. However, an on-going debate questions the reproducibility and semi-quantitative rigour of pyrotag sequencing and, as in the early days of genetic community fingerprinting, pros and cons are continuously provided. more...

Organism:

environmental samples; environmental samples; aquifer metagenome; environmental samples; Aliivibrio fischeri

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL15200 GPL26069 GPL15201

21 Samples

Download data: FASTA, TXT