PXD017035

PXD017035 is an original dataset announced via ProteomeXchange.

Title	Simplified Human Intestinal Microbiota (SIHUMIx) LC-MS/MS dataset
Description	Many functions in host���microbiota interactions are potentially influenced by intestinal transit times, but little is known about the effects of altered transition times on the composition and functionality of gut microbiota. To analyze these effects, we cultivated the model community SIHUMIx in bioreactors in order to determine the effects of varying transit times (TT) on the community structure and function. After five days of continuous cultivation, we investigated the influence of different medium TT of 12 h, 24 h, and 48 h. For profiling the microbial community, we applied flow cytometric fingerprinting and revealed changes in the community structure of SIHUMIx during the change of TT, which were not associated with changes in species abundances. For pinpointing metabolic alterations, we applied metaproteomics and metabolomics and found, along with shortening the TT, a slight decrease in glycan biosynthesis, carbohydrate, and amino acid metabolism and, furthermore, a reduction in butyrate, methyl butyrate, isobutyrate, valerate, and isovalerate concentrations. Specifically, B. thetaiotaomicron was identified to be affected in terms of butyrate metabolism. However, communities could recover to the original state afterward. This study shows that SIHUMIx showed high structural stability when TT changed���even four-fold. Resistance values remained high, which suggests that TTs did not interfere with the structure of the community to a certain degree.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:00:01.931.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Nico Jehmlich
SpeciesList	scientific name: Erysipelatoclostridium ramosum DSM 1402; NCBI TaxID: 445974; scientific name: Anaerostipes caccae DSM 14662; NCBI TaxID: 411490; 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: Bacteroides thetaiotaomicron; NCBI TaxID: 818; scientific name: Blautia producta ATCC 27340 = DSM 2950; NCBI TaxID: 1121114; scientific name: Lactobacillus plantarum; NCBI TaxID: 1590;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2020-01-09 05:30:03	ID requested
1	2020-01-13 01:09:46	announced
⏵ 2	2024-10-22 05:00:04	announced	2024-10-22: Updated project metadata.

Sch, ä, pe SS, Krause JL, Engelmann B, Fritz-Wallace K, Schattenberg F, Liu Z, M, ü, ller S, Jehmlich N, Rolle-Kampczyk U, Herberth G, von Bergen M, Bioreactors. Microorganisms, 7(12):(2019) [pubmed]

10.3390/microorganisms7120641;

ProteomeXchange project tag: benchmarking, machine learning

curator keyword: Biological

submitter keyword: SIHUMIx, microbial community, bioreactor,In vitro model, intestinal microbiota, metaproteomics

Nico Jehmlich
contact affiliation	Helmholtz Centre for Environmental Research GmbH - UFZ Department of Molecular Systems Biology Permoserstra��e 15, 04318 Leipzig, Germany Phone +49 341 235 4767 nico.jehmlich@ufz.de, www.ufz.de
contact email	nico.jehmlich@ufz.de
lab head
Nico Jehmlich
contact affiliation	Helmholtz-Centre for Environmental Research - UFZ
contact email	nico.jehmlich@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/2020/02/PXD017035

PRIDE project URI

• PRIDE
  1. PXD017035
     1. Label: PRIDE project
     2. Name: Simplified Human Intestinal Microbiota (SIHUMIx) LC-MS/MS dataset