PXD047410

PXD047410 is an original dataset announced via ProteomeXchange.

Title	High-throughput screening of effects of 90 xenobiotics on the Simplified Human Gut Microbiota Model (SIHUMIx): A Metaproteomic and Metabolomic Study
Description	The human gut microbiota is a complex microbial community with critical functions for the host, including the transformation of various chemicals. While effects on microorganisms has been evaluated using single-species models, their functional effects within more complex microbial communities remain unclear. In this study, we investigated the response of a simplified human gut microbiota model (SIHUMIx) cultivated in an in vitro bioreactor system in combination with 96 deep-well plates after exposure to 90 different xenobiotics, comprising 54 plant protection products and 36 food additives and dyes, at environmentally relevant concentrations. We employed metaproteomics and metabolomics to evaluate changes in bacterial abundances, the production of Short Chain Fatty Acids (SCFAs), and the regulation of metabolic pathways. Our findings unveiled significant changes induced by 23 out of 54 plant protection products and 28 out of 36 food additives across all three categories assessed. Notable highlights include azoxystrobin, fluoroxypyr, and ethoxyquin causing a substantial reduction (log2FC <-0.5) in the concentrations of the primary SCFAs: acetate, butyrate, and propionate. Several food additives had significant effects on the relative abundances of bacterial species; for example, acid orange 7 and saccharin led to a 75% decrease in Clostridium butyricum, with saccharin causing an additional 2.5-fold increase in E. coli compared to the control. Furthermore, both groups exhibited up- and down-regulation of various pathways, including those related to the metabolism of amino acids such as histidine, valine, leucine, and isoleucine, as well as bacterial secretion systems and energy pathways like starch, sucrose, butanoate, and pyruvate metabolism. This research introduces an efficient in vitro technique that enables high-throughput screening of the structure and function of a simplified and well-defined human gut microbiota model against 90 chemicals using metaproteomics and metabolomics. We believe this approach will be instrumental in characterizing chemical-microbiota interactions especially important for regulatory chemical risk assessments.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:31:32.114.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Victor Castaneda-Monsalve
SpeciesList	scientific name: Erysipelatoclostridium ramosum DSM 1402; NCBI TaxID: 445974; scientific name: Bifidobacterium longum NCC2705; NCBI TaxID: 206672; scientific name: Clostridium butyricum DSM 10702; NCBI TaxID: 1316931; scientific name: Escherichia coli str. K-12 substr. MG1655; NCBI TaxID: 511145; scientific name: Blautia producta ATCC 27340 = DSM 2950; NCBI TaxID: 1121114; scientific name: Anaerostipes caccae; NCBI TaxID: 105841; scientific name: Bacteroides thetaiotaomicron; NCBI TaxID: 818; scientific name: Lactobacillus plantarum; NCBI TaxID: 1590;
ModificationList	No PTMs are included in the dataset
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2023-11-30 09:20:54	ID requested
1	2024-02-21 22:06:19	announced
⏵ 2	2024-10-22 06:31:32	announced	2024-10-22: Updated project metadata.

10.3389/FMICB.2024.1349367;

submitter keyword: microbiome-mediated toxicity, metabolomics, chemical-microbe interaction, chemical screening,SIHUMIx, metaproteomics

Nico Jehmlich
contact affiliation	Groupd leader Microbiome Biology research group Helmholtz-Centre for Environmental Research - UFZ
contact email	nico.jehmlich@ufz.de
lab head
Victor Castaneda-Monsalve
contact affiliation	Helmholtz Centre for Environmental Research (UFZ)
contact email	victor.castaneda@ufz.de
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/2024/02/PXD047410

PRIDE project URI

• PRIDE
  1. PXD047410
     1. Label: PRIDE project
     2. Name: High-throughput screening of effects of 90 xenobiotics on the Simplified Human Gut Microbiota Model (SIHUMIx): A Metaproteomic and Metabolomic Study