Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8666150_1.fastq.gz | Fastqsanger.gz | |||
| SRR8666150_2.fastq.gz | Fastqsanger.gz | |||
| SRR8666151_1.fastq.gz | Fastqsanger.gz | |||
| SRR8666151_2.fastq.gz | Fastqsanger.gz | |||
| SRR8666152_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Metagenomic sequencing of mice with different treatments: Mice were randomly divided into donor control group (Donor + MRS), constipation model group (STC + MRS), or a Lactobacillus acidophilus treated group (STC + La): A humanized mouse model was established by intragastric administration of fecal bacterial liquid from healthy donors or STC patients on alternate days, followed by continuous administration of Lactobacillus acidophilus in treatment group. Finally, the feces of each group of mice were collected, and the intestinal microbial communities of the mice were analyzed through metagenomic sequencing. 16S rRNA sequencing of mice before and after the use antibiotics: Before and after treating the mice with antibiotics, the mice's feces were collected for 16s rRNA sequencing respectively.
2026-03-11 | E-MTAB-16505 | biostudies-arrayexpress
Project description:In this study we investigated whether gut microbiota profile of Italian healthy volunteers could differ based on their geaographical origin. To this purpose, fecal samples were collected from 31 healthy individuals living in 3 different italian regions (Lombardy, North; Lazio, Center; Apulia, South) and their respective microbiota profiles were analyzed employing 16S metagenomic sequencing method. This study identifies differences in the gut microbiota content and richness among individuals with the same ethnicity coming from three different Italian regions.
2026-01-08 | E-MTAB-8136 | biostudies-arrayexpress
Project description:Chronic acid suppression by proton pump inhibitor (PPI) has been hypothesized to alter the gut microbiota via a change in intestinal pH. To evaluate the changes in gut microbiota composition by long-term PPI treatment. Twenty-four week old F344 rats were fed with (n = 5) or without (n = 6) lansoprazole (PPI) for 50 weeks. Then, profiles of luminal microbiota in the terminal ileum were analyzed. Pyrosequencing for 16S rRNA gene was performed by genome sequencer FLX (454 Life Sciences/Roche) and analyzed by metagenomic bioinformatics.
2015-04-14 | E-GEOD-67800 | biostudies-arrayexpress
Project description:Primary outcome(s): Metagenomic analysis and Metabolome analysis of Intestinal flora before, 2weeks, 1months, 3months, 6months, 12months
| 2636430 | ecrin-mdr-crc
Project description:Next-Generation-Sequencing (NGS) technologies have led to important improvement in the detection of new or unrecognized infective agents, related to infectious diseases. In this context, NGS high-throughput technology can be used to achieve a comprehensive and unbiased sequencing of the nucleic acids present in a clinical sample (i.e. tissues). Metagenomic shotgun sequencing has emerged as powerful high-throughput approaches to analyze and survey microbial composition in the field of infectious diseases. By directly sequencing millions of nucleic acid molecules in a sample and matching the sequences to those available in databases, pathogens of an infectious disease can be inferred. Despite the large amount of metagenomic shotgun data produced, there is a lack of a comprehensive and easy-use pipeline for data analysis that avoid annoying and complicated bioinformatics steps. Here we present HOME-BIO, a modular and exhaustive pipeline for analysis of biological entity estimation, specific designed for shotgun sequenced clinical samples. HOME-BIO analysis provides comprehensive taxonomy classification by querying different source database and carry out main steps in metagenomic investigation. HOME-BIO is a powerful tool in the hand of biologist without computational experience, which are focused on metagenomic analysis. Its easy-to-use intrinsic characteristic allows users to simply import raw sequenced reads file and obtain taxonomy profile of their samples.
2021-07-26 | E-MTAB-9189 | biostudies-arrayexpress
Project description:Gliomas and brain metastases (BrM) are associated with poor prognosis, necessitating a deeper understanding of brain tumor biology and the development of effective therapeutic strategies. While our group and others have demonstrated microbial presence in various tumors, recent controversies regarding cancer-type-specific intra-tumoral microbiota emphasize the importance of rigorous, orthogonal validation. This prospective, multi-institutional study included a total of 243 samples from 221 patients, comprising 168 glioma and BrM samples and 75 non-cancerous or tumor-adjacent tissues. Using stringent fluorescent in situ hybridization, immunohistochemistry, and high-resolution spatial imaging, we detected intracellular bacterial 16S rRNA and lipopolysaccharides in both glioma and BrM samples, localized to tumor, immune, and stromal cells. Custom 16S and metagenomic sequencing workflows identified taxa associated with intra-tumoral bacterial signals in the tumor microenvironment; however, standard culture methods did not yield readily cultivable microbiota. Spatial analyses revealed significant correlations between bacterial 16S signals and anti-microbial and immunometabolic signatures at regional, neighborhood, and cellular levels. Furthermore, intra-tumoral 16S bacterial signals showed sequence overlap with matched oral and gut microbiota, suggesting a possible connection with distant communities. Together, these findings introduce microbial elements as a component of the brain tumor microenvironment and lay the foundation for future mechanistic and translational studies.
2025-08-13 | GSE305393 | GEO
Project description:Gliomas and brain metastases (BrM) are associated with poor prognosis, necessitating a deeper understanding of brain tumor biology and the development of effective therapeutic strategies. While our group and others have demonstrated microbial presence in various tumors, recent controversies regarding cancer-type-specific intra-tumoral microbiota emphasize the importance of rigorous, orthogonal validation. This prospective, multi-institutional study included a total of 243 samples from 221 patients, comprising 168 glioma and BrM samples and 75 non-cancerous or tumor-adjacent tissues. Using stringent fluorescent in situ hybridization, immunohistochemistry, and high-resolution spatial imaging, we detected intracellular bacterial 16S rRNA and lipopolysaccharides in both glioma and BrM samples, localized to tumor, immune, and stromal cells. Custom 16S and metagenomic sequencing workflows identified taxa associated with intra-tumoral bacterial signals in the tumor microenvironment; however, standard culture methods did not yield readily cultivable microbiota. Spatial analyses revealed significant correlations between bacterial 16S signals and anti-microbial and immunometabolic signatures at regional, neighborhood, and cellular levels. Furthermore, intra-tumoral 16S bacterial signals showed sequence overlap with matched oral and gut microbiota, suggesting a possible connection with distant communities. Together, these findings introduce microbial elements as a component of the brain tumor microenvironment and lay the foundation for future mechanistic and translational studies.
2025-08-12 | GSE305267 | GEO
Project description:Purpose: This study aims to compare and analyze the differences in bacterial community composition in fecal samples from mice treated with Control(DW), Vancomycin (VAN), Ampicillin (AMP), Neomycin (NEO), Metronidazole (MET), and a combination of all antibiotics (ALL, VANM) using 16S rRNA sequencing. Methods: Each antibiotics treated mice's fecal samples were collected and stored -80'c until analyzation. DNA was extracted using the NucleoSpin DNA Stool Kit (MACHEREY-NAGEL) following the manufacturer’s protocol. Metagenomic sequencing was performed on an Illumina MiSeq platform (Illumina), targeting the V3 and V4 regions of the 16S rRNA gene according to the manufacturer's instructions. PCR products were purified using AMPure XP beads, and sequencing adapters were added using the Nextera XT Index Kit (Illumina). The library was further purified with AMPure XP beads and quantified using automated electrophoresis with the TapeStation System (Agilent). Sequencing was performed using the MiSeq v3 reagent kit (Illumina), following the manufacturer’s protocol. Results: QIIME2 (v2023.02) was used to process and analyze 16S rRNA gene amplicon sequencing data, from sequence preprocessing to taxonomic classification. Paired-end sequences were merged and quality-filtered using Deblur. The resulting amplicon sequence variants (ASVs) were used for downstream analyses. Conclusions: Our study presents a comparative analysis of bacterial community composition in fecal samples from antibiotic-treated mice. We observed that microbiota composition varied distinctly depending on the type of antibiotic administered.
2026-01-28 | GSE291841 | GEO
Project description:Interventions: Case (colorectal cancer) group:a newly diagnosed colorectal cancer( CRC ) by colonoscopy and pathology;Control group:Clinically healthy volunteers with no symptoms or history of intestinal disease(e.g. colonic adenomatous polyps, CRC or inflammatory bowel disease)
Primary outcome(s): composition of gut microbiota;intestinal microbial phytase activity;16s rRNA metagenomic sequencing;diet surveys;phytic acid intake
Study Design: Case-Control study
| 2667847 | ecrin-mdr-crc