GEO DataSets

(Submitter supplied) This work investigates the effects of a prebiotic mix containing lutein, zeaxanthin, and saffron, recognized for their anti-inflammatory properties, on ophthalmological and microbial parameters in neovascular AMD (nAMD) patients.

Organism:

human feces metagenome

Type:

Other

Platform:

GPL29470

60 Samples

Download data: FASTA, TSV

(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) Systemic sclerosis (SSc) is a complex and still unclear rare disease associated with fibrosis in multiple organs. Microbiota has recently emerged as an important environmental factor in SSc pathogenesis, either at gut, oral and skin level.

Organism:

human feces metagenome; human skin metagenome; human saliva metagenome

Type:

Other

Platforms:

GPL29470 GPL31025 GPL32156

78 Samples

Download data: FASTA, TXT

(Submitter supplied) This study demonstrates the usefulness of the API by generating a baseline gut microbiota profile of a healthy population and estimating reference intervals for the functional abundance of manually selected KEGG pathways. API facilitates microbiome research by providing dynamic and customizable tools for estimating reference intervals for gut microbiota functional abundances. Through the API, researchers can rapidly generate gut microbiota functional profiles of healthy populations to use as a baseline for comparison. more...

Organism:

human feces metagenome

Type:

Other

Platform:

GPL33296

57 Samples

Download data: TSV

(Submitter supplied) Objectives: Obstructive Sleep Apnea (OSA) is related to repeated upper airway collapse, intermittent hypoxia, and intestinal barrier dysfunction. The resulting damage to the intestinal barrier may affect or be affected by the intestinal microbiota. Methods: A prospective case-control was used, including 48 subjects from Sleep Medicine Center of Nanfang Hospital. Sleep apnea was diagnosed by overnight polysomnography. more...

Organism:

human feces metagenome

Type:

Other

Platform:

GPL29470

51 Samples

Download data: TXT

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

Organism:

human feces metagenome

Type:

Other

Platform:

GPL31937

102 Samples

Download data

(Submitter supplied) The role of gut microbiome dysbiosis in the pathogenesis of psoriasis has gained increasing attention in recent years. Secukinumab, targeting interleukin (IL)-17, has a promising efficacy in psoriasis treatment. However, it remains unclear the gut microbiota alteration and related functional changes caused by successful secukinumab therapy in psoriatic patients. In our study, we compared fecal microbiome profile between psoriatic patients after secukinumab successful treatment (AT) and the other two groups, psoriatic patients without therapy (BT) and healthy people (H), respectively by using next-generation sequencing targeting 16S ribosomal RNA. more...

Organism:

human feces metagenome

Type:

Other

Platform:

GPL31937

24 Samples

Download data

(Submitter supplied) The role of gut microbiome dysbiosis in the pathogenesis of psoriasis has gained increasing attention in recent years. Secukinumab, targeting interleukin (IL)-17, has a promising efficacy in psoriasis treatment. However, it remains unclear the gut microbiota alteration and related functional changes caused by successful secukinumab therapy in psoriatic patients. In our study, we compared fecal microbiome profile between psoriatic patients after secukinumab successful treatment (AT) and the other two groups, psoriatic patients without therapy (BT) and healthy people (H), respectively by using next-generation sequencing targeting 16S ribosomal RNA. more...

Organism:

human feces metagenome

Type:

Other

Platform:

GPL31937

78 Samples

Download data

(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; Enterococcus faecalis; Bacillus subtilis; Limosilactobacillus reuteri; Limosilactobacillus fermentum; human feces metagenome; Escherichia coli; Synechocystis sp. PCC 6803; Staphylococcus aureus; Bacillus amyloliquefaciens; Lactiplantibacillus plantarum; Cryptococcus neoformans; Caulobacter vibrioides

Type:

Other

17 related Platforms

199 Samples

Download data: BEDGRAPH, TXT, XLSX

(Submitter supplied) In previous study, patients with Diabetes Mellitus (DM) have high risk of active TB and LTBI. Here we report and compare 16S rRNA data of DM-LTBI and DM-nonLTBI in gut microbiota to identify differential candidates between the two groups. The results showed the differential genera have potential to predict the LTBI status in patients.

Organism:

human feces metagenome

Type:

Other

Platform:

GPL29470

130 Samples

Download data: TXT

(Submitter supplied) To compare the similarities and differences in species diversity of the gut microbiota between the patients with melasma and healthy subjects. The feces were collected for 16S rRNA sequencing analysis of the gut microbiota.

Organism:

human feces metagenome

Type:

Other

Platform:

GPL29470

17 Samples

Download data: FASTA, XLS

(Submitter supplied) Total DNA was extracted from stool specimens, amplified to collect amplicons of variable V3–V4 regions of the bacterial 16s rRNA gene and sequenced with MiSeq (2x300bp) Illumina platform.

Organism:

human feces metagenome

Type:

Other

Platform:

GPL29470

74 Samples

Download data: CSV, FASTA, TSV

(Submitter supplied) Given the gut microbiota involve aging processing, we performed comparative analysis of gut bacteriophage between older and young subjects using next-generation sequencing (NGS). In our previous study, we found that the Ruminococcaceae is higher in aged subjects comparing to young one. To identify the bacteriophage targeting to the Ruminococcaceae, we also access the composition of phage in the Ruminococcaceae (ATCC, TSD-27) after incubated with human stool samples. more...

Organism:

human feces metagenome

Type:

Other

Platform:

GPL31937

8 Samples

Download data: XLSX

(Submitter supplied) We report the use of high-throughput sequencing technology to detect the microbial composition and abundance of human feces after in vitro co-fermentation with citrus peel flavonoid extracts. The genomic DNA was obtained by the QIAamp PowerFecal DNA Kit. Then, the DNA samples were sent to Biomarker Bio-Tech (Beijing, China) for V3-V4 region of the 16S rDNA gene high-throughput sequencing with an Illumina MiSeq platform. more...

Organism:

human feces metagenome

Type:

Other

Platform:

GPL31937

112 Samples

Download data: TXT

(Submitter supplied) The intestinal microbiome has been associated with response to immune checkpoint inhibitors (ICI) in humans, and causally implicated in ICI responsiveness in animal models. Therapeutic augmentation of the microbiome in ICI recipients is being investigated in multiple ongoing human clinical trials. We conducted an early phase clinical trial of a cultivated, orally-delivered 30-species microbial consortium (microbial ecosystem therapeutic-4, MET4) designed for co-administration with ICIs and assessed safety, tolerability and ecological responses in patients with advanced solid tumors.

Organism:

human feces metagenome

Type:

Other

Platform:

GPL29470

170 Samples

Download data: CSV

(Submitter supplied) Gut microbial profiling of uterine fibroids (UFs) patients comparing control subjects. The gut microbiota was examined by 16S rRNA quantitative arrays and bioinformatics analysis. The goal was to reveal alterations in the gut microbiome of uterine fibroids patients.

Organism:

human gut metagenome; synthetic construct; human feces metagenome

Type:

Other

Platform:

GPL32019

85 Samples

Download data: TXT

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

Organism:

Homo sapiens; Caenorhabditis elegans; Drosophila melanogaster; Saccharomyces cerevisiae; human feces metagenome

Type:

Other

Platforms:

GPL30425 GPL30426 GPL24106

8 Samples

Download data: TAR, TSV

(Submitter supplied) Pseudouridine (Ψ) is an abundant mRNA modification in the mammalian transcriptome, but its function has remained elusive due to the difficulty of transcriptome-wide mapping. We develop nanopore native RNA sequencing for quantitative Ψ analysis that utilizes native content training, machine learning model prediction, and single read coordination. We find interferon inducible Ψ modifications in the interferon stimulated gene transcripts, consistent with a role of Ψ in the efficacy of mRNA vaccines.

Organism:

Caenorhabditis elegans; Homo sapiens; Saccharomyces cerevisiae; human feces metagenome; Drosophila melanogaster

Type:

Other

Platform:

GPL30426

1 Sample

Download data: TSV

(Submitter supplied) Pseudouridine (Ψ) is an abundant mRNA modification in the mammalian transcriptome, but its function has remained elusive due to the difficulty of transcriptome-wide mapping. We develop nanopore native RNA sequencing for quantitative Ψ analysis that utilizes native content training, machine learning model prediction, and single read coordination. We find interferon inducible Ψ modifications in the interferon stimulated gene transcripts, consistent with a role of Ψ in the efficacy of mRNA vaccines.

Organism:

Caenorhabditis elegans; Homo sapiens; human feces metagenome; Saccharomyces cerevisiae; Drosophila melanogaster

Type:

Other

Platforms:

GPL30425 GPL24106

7 Samples

Download data: TAR

(Submitter supplied) In rodents, brown adipose tissue (BAT) contributes to whole body energy expenditure and low BAT activity is related to hepatic fat accumulation, partially attributable to the gut microbiome. Little is known of these relationships in humans. In adults (n=60), we assessed hepatic fat and cold-stimulated BAT activity utilizing magnetic resonance imaging and the gut microbiome with 16S sequencing. We transplanted gnotobiotic mice with feces from humans to assess the transferability of BAT activity and NAFLD through the microbiome. more...

Organism:

feces metagenome; human feces metagenome

Type:

Other

Platforms:

GPL29470 GPL24116

82 Samples

Download data: CSV