Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

GNPS - Drug metabolism - Bacterial synthetic community

ABSTRACT: Bacterial culture with drugs acquired on Q Exactive with chromatographic separation on a Phenomenex polar C18 column (Kinetex 2.6 um, 150 x 2.1 mm). Reversed-phase, ESI positive.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Bacteria (ncbitaxon:2)

SUBMITTER: Pieter C. Dorrestein

PROVIDER: MSV000095331 | GNPS | Sun Jul 14 16:47:00 BST 2024

REPOSITORIES: GNPS

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Drug metabolism - Bacterial synthetic community

Project description:Bacterial culture with drugs acquired on Q Exactive with chromatographic separation on a Phenomenex polar C18 column (Kinetex 2.6 um, 150 x 2.1 mm). Reversed-phase, ESI positive.

2024-07-14 | MSV000095331 | MassIVE

20231123_ChemProp2_Non-targeted Metabolomics of Xenobiotic Biotransformations using synthetic gut bacterial community

Project description:ChemProp2 Dataset: Investigating potential biotransformations with a panel of 45 Drugs on Synthetic Community (Com20) to elucidate Drug-Microbiome-Host Dynamics

2023-12-05 | MSV000093571 | MassIVE

185-member bacterial synthetic community

Project description:A single bacterial genus maintains root development in a complex microbiome

| PRJNA543313 | ENA

Transcriptional Responses of M. tuberculosis to inhibitors of metabolism

Project description:Transcriptional profiling of M.tuberculosis was performed using 430 whole-genome microarrays to measure the effects of 75 different drugs, drug combinations or different growth conditions at various times relative to a sample of logarithmically growing MTb. Analysis of this data set revealed 150 underlying clusters of coordinately regulated genes as described in Boshoff et al., 2004. Keywords = Gene clusters Keywords = Mechanism of action Keywords = tuberculosis Keywords = antimycobacterial drugs Keywords = natural product Keywords = respiration

2004-09-01 | E-GEOD-1642 | biostudies-arrayexpress

Transcriptional Responses of M. tuberculosis to inhibitors of metabolism

2004-09-01 | GSE1642 | GEO

GNPS - 20231123_ChemProp2_Non-targeted Metabolomics of Xenobiotic Biotransformations using synthetic gut bacterial community

Project description:ChemProp2 Dataset: Investigating potential biotransformations with a panel of 45 Drugs on Synthetic Community (Com20) to elucidate Drug-Microbiome-Host Dynamics

2023-12-05 | MSV000093571 | GNPS

Ecological drivers of bacterial community assembly in synthetic phycospheres.

Project description:In the nutrient-rich region surrounding marine phytoplankton cells, heterotrophic bacterioplankton transform a major fraction of recently fixed carbon through the uptake and catabolism of phytoplankton metabolites. We sought to understand the rules by which marine bacterial communities assemble in these nutrient-enhanced phycospheres, specifically addressing the role of host resources in driving community coalescence. Synthetic systems with varying combinations of known exometabolites of marine phytoplankton were inoculated with seawater bacterial assemblages, and communities were transferred daily to mimic the average duration of natural phycospheres. We found that bacterial community assembly was predictable from linear combinations of the taxa maintained on each individual metabolite in the mixture, weighted for the growth each supported. Deviations from this simple additive resource model were observed but also attributed to resource-based factors via enhanced bacterial growth when host metabolites were available concurrently. The ability of photosynthetic hosts to shape bacterial associates through excreted metabolites represents a mechanism by which microbiomes with beneficial effects on host growth could be recruited. In the surface ocean, resource-based assembly of host-associated communities may underpin the evolution and maintenance of microbial interactions and determine the fate of a substantial portion of Earth's primary production.

| S-EPMC7035482 | biostudies-literature

Defined spatial structure stabilizes a synthetic multispecies bacterial community.

Project description:This paper shows that for microbial communities, "fences make good neighbors." Communities of soil microorganisms perform critical functions: controlling climate, enhancing crop production, and remediation of environmental contamination. Microbial communities in the oral cavity and the gut are of high biomedical interest. Understanding and harnessing the function of these communities is difficult: artificial microbial communities in the laboratory become unstable because of "winner-takes-all" competition among species. We constructed a community of three different species of wild-type soil bacteria with syntrophic interactions using a microfluidic device to control spatial structure and chemical communication. We found that defined microscale spatial structure is both necessary and sufficient for the stable coexistence of interacting bacterial species in the synthetic community. A mathematical model describes how spatial structure can balance the competition and positive interactions within the community, even when the rates of production and consumption of nutrients by species are mismatched, by exploiting nonlinearities of these processes. These findings provide experimental and modeling evidence for a class of communities that require microscale spatial structure for stability, and these results predict that controlling spatial structure may enable harnessing the function of natural and synthetic multispecies communities in the laboratory.

| S-EPMC2587551 | biostudies-literature

Characteristic molecular and proteomic signatures of drug-induced liver injury in a rat model

Project description:we assessed characteristic molecular and proteomic signatures in rat liver treated with drugs (pyrazinamide, ranitidine, enalapril, carbamazepine, and chlorpromazine) that are known to cause DILI in humans. In the present study, we assessed the characteristic gene expression signature for DILI in a rat model. Rats were administered representative drugs that are already known to induce DILI in humans and transcriptomic changes in rat liver were analyzed. The representative drugs, which induce three types (hepatocellular, mixed, and cholestatic) of DILI, that were used in this study were pyrazinamide (PZA, 150~1500 mg/kg), ranitidine (RAN, 209.5~2095 mg/kg), enalapril (ENA, 148.65~1486.5 mg/kg), carbamazepine (CBZ, 97.85~978.5 mg/kg), and chlorpromazine (CPZ, 7.1~71 mg/kg).

2013-08-16 | E-GEOD-49631 | biostudies-arrayexpress

In vitro interaction network of a synthetic gut bacterial community.

Project description:A key challenge in microbiome research is to predict the functionality of microbial communities based on community membership and (meta)-genomic data. As central microbiota functions are determined by bacterial community networks, it is important to gain insight into the principles that govern bacteria-bacteria interactions. Here, we focused on the growth and metabolic interactions of the Oligo-Mouse-Microbiota (OMM12) synthetic bacterial community, which is increasingly used as a model system in gut microbiome research. Using a bottom-up approach, we uncovered the directionality of strain-strain interactions in mono- and pairwise co-culture experiments as well as in community batch culture. Metabolic network reconstruction in combination with metabolomics analysis of bacterial culture supernatants provided insights into the metabolic potential and activity of the individual community members. Thereby, we could show that the OMM12 interaction network is shaped by both exploitative and interference competition in vitro in nutrient-rich culture media and demonstrate how community structure can be shifted by changing the nutritional environment. In particular, Enterococcus faecalis KB1 was identified as an important driver of community composition by affecting the abundance of several other consortium members in vitro. As a result, this study gives fundamental insight into key drivers and mechanistic basis of the OMM12 interaction network in vitro, which serves as a knowledge base for future mechanistic in vivo studies.

| S-EPMC8941000 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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