Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Evaluate gut microbiome biobanking

ABSTRACT: A rapid ex vivo microbiome assay and metaproteomics approach was used for rapid evaluation of the cultivability of bio-banked live microbiota, which shows minimal detrimental influences of long-term freezing in deoxygenated glycerol buffer on the cultivability of fecal microbiota.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Human Gut Metagenome

SUBMITTER: Xu Zhang

LAB HEAD: Daniel Figeys

PROVIDER: PXD028857 | Pride | 2022-02-16

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Publications

Evaluating live microbiota biobanking using an <i>ex vivo</i> microbiome assay and metaproteomics.

Zhang Xu X Walker Krystal K Mayne Janice J Li Leyuan L Ning Zhibin Z Stintzi Alain A Figeys Daniel D

Gut microbes 20220101 1

Biobanking of live microbiota is becoming indispensable for mechanistic and clinical investigations of drug-microbiome interactions and fecal microbiota transplantation. However, there is a lack of methods to rapidly and systematically evaluate whether the biobanked microbiota maintains their cultivability and functional activity. In this study, we use a rapid <i>ex vivo</i> microbiome assay and metaproteomics to evaluate the cultivability and the functional responses of biobanked microbiota to ...[more]

PMID: 35130123

Similar Datasets

Effect of Edurans secretome of human microbiome

Project description:A rapid ex vivo microbiome assay and metaproteomics approach was used for evaluating the impacts of E. durans derived secretome on a human gut microbiome cultured in vitro.

2024-01-31 | PXD040751 | Pride

Microbiome biomarkers for Improved Screening of Anal Cance

Project description:Anal cancer is a leading neoplasia in people with immune impartments populations, and the lack of an accurate screening test challenges its prevention. Because the bacteria living in the anal epithelium the anal microbiota seems to influence and be influenced by cancer development, specific patterns of anal microbes could help in the diagnosis of precancerous anal lesions. We aimed to discover microbial biomarkers of anal precancer in high-risk populations. We discovered 12 proteins, previously reported to be associated with cancer progression, that were more abundant in the anal bacterial from subjects with precancerous lesions.

2022-12-11 | PXD037268 | Pride

Microbiota biobanking using ice recrystalization inhibitor

Project description:This study use different ice recrystalization inhibitors (IRIs) for better storing live microbiota. We evaluated whether the addition of IRIs can improve the cultivibility of microbiome and maintain their resposnes to prebiotic kestose. Frozen or fresh microbiota were cultured with or without kestose for 24 hours, and microbiota samples were collected for metaproteomics analysis.

2023-02-07 | PXD034979 | Pride

Relating human gut metagenome and metaproteome

Project description:Gut microbiome research is rapidly moving towards the functional characterization of the microbiota by means of shotgun meta-omics. Here, we selected a cohort of healthy subjects from an indigenous and monitored Sardinian population to analyze their gut microbiota using both shotgun metagenomics and shotgun metaproteomics. We found a considerable divergence between genetic potential and functional activity of the human healthy gut microbiota, in spite of a quite comparable taxonomic structure revealed by the two approaches. Investigation of inter-individual variability of taxonomic features revealed Bacteroides and Akkermansia as remarkably conserved and variable in abundance within the population, respectively. Firmicutes-driven butyrogenesis (mainly due to Faecalibacterium spp.) was shown to be the functional activity with the higher expression rate and the lower inter-individual variability in the study cohort, highlighting the key importance of the biosynthesis of this microbial by-product for the gut homeostasis. The taxon-specific contribution to functional activities and metabolic tasks was also examined, giving insights into the peculiar role of several gut microbiota members in carbohydrate metabolism (including polysaccharide degradation, glycan transport, glycolysis and short-chain fatty acid production). In conclusion, our results provide useful indications regarding the main functions actively exerted by the gut microbiota members of a healthy human cohort, and support metaproteomics as a valuable approach to investigate the functional role of the gut microbiota in health and disease.

2017-07-19 | PXD005780 | Pride

Defining the microbial response to colitis through integrated host and microbiome profiling: Replication data set

Project description:This is a replication study of E-MTAB-3562 ( http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-3562/ ) and complementary transcription profiling data from the mouse hosts have also been deposited at ArrayExpress under accession number E-MTAB-3590 ( http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-3590/ )

2015-12-31 | E-MTAB-4082 | biostudies-arrayexpress

Deciphering Differential Gut Bacterial Drug Metabolism with Activity-Based Protein Profiling

Project description:Gut bacterial β-glucuronidases (GUS) promote the toxic side effects of therapeutics by reactivating drugs from their inactive glucuronide conjugates. It is increasingly clear that the interindividual variability of bacterial GUS-producing species in the gut microbiota contributes to differential drug responses. Indeed, the anticancer drug irinotecan exhibits variable clinical toxicity outcomes that have been linked to interindividual differences in the composition of the gut microbiota. However, identification of the specific GUS enzymes responsible for drug metabolism in the context of the complexity of the human fecal microbiota has not been achieved. Here we pinpoint the specific bacterial GUS enzymes that reactivate SN-38, the active metabolite of irinotecan, from complex human fecal microbiota samples with activity-based protein profiling (ABPP). We identify and quantify gut bacterial GUS enzymes from human feces with ABPP-enabled proteomics and then integrate this information with ex vivo kinetics to reveal the specific GUS enzymes responsible for the reactivation of SN-38. The same ABPP approach also reveals the molecular basis for differential gut bacterial GUS inhibition between human fecal samples. Taken together, this work provides an unprecedented pipeline to identify the specific bacterial GUS enzymes responsible for drug-induced GI toxicity from the complexity of human feces, which may serve as highly precise biomarkers of clinical outcomes for irinotecan and other therapeutics.

2019-12-03 | PXD014864 | Pride

Effects of 5 drugs on the human gut microbiome.

Project description:We processed a human stool sample and cultured the processed microbiome in vitro under anaerobic condition for 48 hours using the rapidAIM assay. The microbiome was treated with either azathioprine, ciprofolxacin, diclofenac, nicatidine, paracetamol or control DMSO. Each drug was used at three different concentrations. We compared these results to those acquired using MS1-only data.

2022-07-29 | PXD024845 | Pride

Specific Gut Microbial Enzymes Drive Colitis Promotion by Triclosan

Project description:Triclosan (TCS), an antimicrobial agent in thousands of consumer products, is a risk factor for colitis and colitis-associated colorectal cancer. While the intestinal toxicities of TCS require the presence of gut microbiota, the molecular mechanisms involved have not been defined. Here we show that intestinal commensal microbes mediate metabolic activation of TCS in the colon and drive its gut toxicology. Using a range of in vitro, ex vivo, and in vivo approaches, we identify specific microbial β-glucuronidase (GUS) enzymes involved and pinpoint molecular motifs required to metabolically activate TCS in the gut. Finally, we show that targeted inhibition of bacterial GUS enzymes abolishes the colitis-promoting effects of TCS, supporting the essential roles of specific microbial proteins in TCS toxicity. Our results define a mechanism by which intestinal microbes cause the gut toxicity of environmental chemicals and suggest a therapeutic approach to alleviate colitis and associated diseases.

2021-11-04 | PXD025887 | Pride

Effect of morphine treatment on microbiome in the context of microbial transplant.

Project description:Morphine causes microbial dysbiosis. In this study we focused on restoration of native microbiota in morphine treated mice and looked at the extent of restoration and immunological consequences of this restoration. Fecal transplant has been successfully used clinically, especially for treating C. difficile infection2528. With our expanding knowledge of the central role of microbiome in maintenance of host immune homeostasis17, fecal transplant is gaining importance as a therapy for indications resulting from microbial dysbiosis. There is a major difference between fecal transplant being used for the treatment of C. difficile infection and the conditions described in our studies. The former strategy is based on the argument that microbial dysbiosis caused by disproportionate overgrowth of a pathobiont can be out-competed by re-introducing the missing flora by way of a normal microbiome transplant. This strategy is independent of host factors and systemic effects on the microbial composition. Here, we show that microbial dysbiosis caused due to morphine can be reversed by transplantation of microbiota from the placebo-treated animals.

2016-06-01 | E-MTAB-3723 | biostudies-arrayexpress

Streamlined TMT labeling workflow for proteomics and metaproteomics

Project description:This study established a streamlined TMT labeling workflow that is readily compatible with high throughput proteomics and metaproteomics sample preparation. The method was then evaluated using two different sample types, microbiome and intestinal Caco-2 cell line, with TMT11plex mix reagents.

2023-02-07 | PXD034791 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data