Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1202717 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR31825000_1.fastq.gz | Fastqsanger.gz | |||
| SRR31825000_2.fastq.gz | Fastqsanger.gz | |||
| SRR31825001_1.fastq.gz | Fastqsanger.gz | |||
| SRR31825001_2.fastq.gz | Fastqsanger.gz | |||
| SRR31825002_1.fastq.gz | Fastqsanger.gz |
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Project description:Stool metagenomes of healthy Chinese donors
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Project description:Epithelial Ovarian Cancer (EOC) is the leading cause of gynecologic cancer death. Despite many patients achieving remission with first-line therapy, up to 80% of patients will recur and require additional treatment. Retrospective clinical analysis of OC patients indicates antibiotic use during chemotherapy treatment is associated with poor overall survival. We assessed whether antibiotic (ABX) therapy would impact growth of EOC and sensitivity to cisplatin in murine models. Immune competent or compromised mice were given control or ABX containing water (metronidazole, ampicillin, vancomycin, and neomycin) before being intraperitoneally injected with murine EOC cells. Stool was collected to confirm microbiome disruption and tumors were monitored, and cisplatin therapy was administered weekly until endpoint. EOC tumor-bearing mice demonstrate accelerated tumor growth and resistance to cisplatin therapy in ABX treated compared with nonABX treatment. Stool analysis indicated most gut microbial species were disrupted by ABX treatment except for ABX resistant bacteria. To test for role of the gut microbiome, cecal microbiome transplants (CMTs) of microbiota derived from ABX or nonABX treated mice were used to recolonize the microbiome of ABX treated mice. nonABX cecal microbiome was sufficient to ameliorate the chemoresistance and survival of ABX treated mice indicative of a gut derived tumor suppressor. Mechanistically, tumors from ABX treated compared to nonABX treated mice contained a high frequency of cancer stem cells that were augmented by cisplatin. These studies indicate an intact microbiome provides a gut derived tumor suppressor and maintains chemosensitivity that is disrupted by ABX treatment.
2022-11-01 | GSE200025 | GEO
Project description:The rapid global rise of antimicrobial resistance (AMR) that increasingly invalidates conventional antibiotics has become a huge threat to human health. Although nanosized antibacterial agents have been extensively explored, they cannot sufficiently discriminate between microbes and mammals, which necessitates the exploration of other antibiotic-like candidates for clinical uses. Herein, two-dimensional boron nitride (BN) nanosheets are reported to exhibit antibiotic-like activity to AMR bacteria. Interestingly, BN nanosheets had AMR-independent antibacterial activity without triggering secondary resistance in their long-term use and displayed excellent biocompatibility in mammals. Surface proteome analysis coupled with molecular dynamic simulations and Bio-Layer Interferometry revealed that BN nanosheets could rapidly interact with the key surface proteins of cell division including FtsP, EnvC, and TolB, resulting in a specific antibacterial mechanism by impairment of Z-ring constriction in cell division. Notably, BN nanosheets had a potent antibacterial effect in a lung infection model by P. aeruginosa (AMR), displaying a two-fold increment of survival rate. Overall, these results suggested that BN nanosheets could be a promising nano-antibiotic to combat resistant bacteria and prevent AMR evolution.
2023-04-15 | PXD033277 | JPOST Repository
Project description:In this study, we have analyzed DNA methylation changes upon long-term culture and aging of MSC by using the HumanMethylation27 BeadChip assessing 27,578 unique CpG sites. Cells were taken from bone marrow aspirates from iliac crest (BM) of healthy donors or from the caput femoris (HIP) of elderly patients that received femoral head prosthesis.Overall, the methylation pattern was maintained throughout both long-term culture and aging but highly significant differences were observed at specific CpG sites. Notably, methylation changes in MSC were related in long-term culture and aging in vivo. Mesenchymal stromal cells (MSC) were isolated from human bone marrow as described before (Wagner et al., 2006, Exp Hematol, 34, 536-548; Wagner et al.,2008, PLoS One 21;3(5):e2213.; Wagner et al., PLoS One. 2009 Jun 9;4(6):e5846.) Cells were always replated when grown to confluency. A sample for DNA isolation was taken at every passage until the cells finally became senescent. For methylation profiles upon long-term culture we used the samples of early passage (P2) and senescent passage (PX). For methylation profiles upon aging we have only used the samples of passage 2 of younger and elderly donors. Gene expression data of these samples have been previously deposited unter GSE9593 and GSE12274.
2010-05-14 | E-GEOD-17448 | biostudies-arrayexpress
Project description:Clinical follow-up of Ebola virus disease (EVD) survivors revealed a persistence of clinical symptoms and higher risk of mortality. Long-term analyses of the immune and inflammatory profiles of EVD survivors are currently lacking. Here, we evaluate gene expression profiles in 26 Guinean Ebola virus disease survivors (EBOV_S) and 33 Healthy donnors (HD). We show a persistent increase of several biomarkers of inflammation, immune activation and gut tissue damage in EBOV_S compared to healthy donors living in the same area. Gene expression profiling in blood revealed a significant enrichment in genes associated with antiviral responses in EBOV_S.
2020-05-25 | GSE143549 | GEO
Project description:In this study, we have analyzed DNA methylation changes upon long-term culture and aging of MSC by using the HumanMethylation27 BeadChip assessing 27,578 unique CpG sites. Cells were taken from bone marrow aspirates from iliac crest (BM) of healthy donors or from the caput femoris (HIP) of elderly patients that received femoral head prosthesis.Overall, the methylation pattern was maintained throughout both long-term culture and aging but highly significant differences were observed at specific CpG sites. Notably, methylation changes in MSC were related in long-term culture and aging in vivo.
2010-02-04 | GSE17448 | GEO
Project description:Healthy full-term infants stool Raw sequence reads
| PRJNA562650 | ENA
Project description:Longitudinal transcriptome analysis for invsetigation of the effect of long-term oxygen therapy in COPD
2018-10-29 | GSE111790 | GEO
Project description:The most common long-term problems after rectal surgery are bowel problems. These problems can include needing to pass bowel movements a lot, loose or mushy stools, inability to fully clear your bowels, and/or poor control of gas and stool. The investigators believe that a major cause of these problems is too much bacteria in the bowel and treatment with antibiotic tablets will hopefully help improve these bowel problems. In order to test this idea, the Colorectal Surgery Service of Memorial Sloan Kettering Cancer Center is sponsoring a clinical trial. This trial will compare the antibiotic rifaximin and a placebo (a harmless tablet that has no effect) in the treatment of these bowel problems. Following this we will attempt to see if another antibiotic metronidazole also helps to treat these bowel problems. Both Metronidazole and rifaximin are well established drugs that have minimal side effects.
| 2106018 | ecrin-mdr-crc
Project description:<p><strong>Background</strong></p><p>Antibiotic treatment has a well-established detrimental effect on the gut bacterial composition, but effects on the fungal community are less clear. Bacteria in the lumen of the gastrointestinal tract may limit fungal colonization and invasion. Antibiotic drugs targeting bacteria are therefore seen as an important risk factor for fungal infections and induced allergies. However, antibiotic effects on gut bacterial-fungal interactions, including disruption and resilience of fungal community compositions, were not investigated in humans. We analysed stool samples collected from 14 healthy human participants over three months following a 6-day antibiotic administration. We integrated data from shotgun metagenomics, metatranscriptomics, metabolomics, and fungal ITS2 sequencing. </p><p><strong>Results</strong></p><p>While the bacterial community recovered mostly over three months post treatment, the fungal community was shifted from mutualism at baseline to competition. Half of the bacterial-fungal interactions present before drug intervention had disappeared three months later. During treatment, fungal abundances were associated with the expression of bacterial genes with functions for cell growth and repair. By extending the metagenomic species approach, we revealed bacterial strains inhibiting the opportunistic fungal pathogen Candida albicans. We demonstrate in vitro how C. albicans pathogenicity and host cell damage might be controlled naturally in the human gut by bacterial metabolites such as propionate or 5-dodecenoate.</p><p><strong>Conclusions</strong></p><p>We demonstrate that antibacterial drugs have long-term influence on the human gut mycobiome. While bacterial communities recovered mostly 30-days post antibacterial treatment, the fungal community was shifted from mutualism towards competition.</p><p><br></p><p><strong>Linked data:</strong></p><p>Metagenomics has been submitted to NCBI SRA repository as projects PRJNA573821, PRJNA573905 and PRJNA579284.</p>
2020-09-28 | MTBLS1846 | MetaboLights