PXD012725

PXD012725 is an original dataset announced via ProteomeXchange.

Title	Rapid Assay of Individual Microbiome responses to drugs data part2
Description	We developed an approach named Rapid Assay of Individual Microbiome (RapidAIM) to screen xenobiotics against individual microbiomes. To evaluate technical reproducibility, we tested 43 compounds against an individual's microbiome. The individual microbiome is cultured in triplicates in 96-well plates for 24 hours and the samples are then analyzed using a metaproteomics-based analytical approach to gain functional insight into the individual microbiomes responses following drug treatments.The tested compounds significantly affected overall microbiome abundance, microbiome composition and functional pathways at multiple taxonomic levels. The microbiome responses to berberine, metformin, diclofenac, fructooligosaccharide and most antibiotics were consistent among most individual microbiomes. Interestingly, most of our tested NSAIDs, statins, and histamine-2 blockers induced individually distinct responses. Our workflow offers an effective solution to systematically study the effects of many different compounds on individual microbiomes.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:06:08.499.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Leyuan Li
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationList	monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-02-15 01:55:40	ID requested
1	2020-05-26 17:12:24	announced
⏵ 2	2024-10-22 05:06:14	announced	2024-10-22: Updated project metadata.

10.1186/s40168-020-00806-z;

Li L, Ning Z, Zhang X, Mayne J, Cheng K, Stintzi A, Figeys D, RapidAIM: a culture- and metaproteomics-based Rapid Assay of Individual Microbiome responses to drugs. Microbiome, 8(1):33(2020) [pubmed]

curator keyword: Biological, Biomedical

submitter keyword: in vitro culture, drug,microbiome, metaproteomics

Daniel Figeys
contact affiliation	Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
contact email	dfigeys@uottawa.ca
lab head
Leyuan Li
contact affiliation	Universtiy of Ottawa
contact email	lli8@uottawa.ca
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/05/PXD012725

PRIDE project URI

• PRIDE
  1. PXD012725
     1. Label: PRIDE project
     2. Name: Rapid Assay of Individual Microbiome responses to drugs data part2