PXD017390

PXD017390 is an original dataset announced via ProteomeXchange.

Title	Human gut microbiome cultured over time responsed differently to drug stimulation
Description	In vitro gut microbiota models are often used to study drug-microbiome interaction. Similar to culturing individual microbial strains, the biomass accumulation of in vitro gut microbiota follows a logistic growth curve. Current studies on in vitro gut microbiome responses introduce drug stimulation during different growth stages, e.g. lag phase or stationary phase. However, in vitro gut microbiota in different growth phases may respond differently to a same stimuli. Therefore, in this study, we used a 96-deep well plate-based culturing model (MiPro) to culture the human gut microbiota. Metformin, as the stimulus, was added at the lag, log and stationary phases of growth. Microbiome samples were collected at different time points for optical density and metaproteomic functional analysis. Results show that in vitro gut microbiota responded differently to metformin added during different growth phases, in terms of the growth curve, alterations of taxonomic and functional compositions. The addition of drugs at log phase leads to the greatest decline of bacterial growth. Metaproteomic analysis suggested that the strength of the metformin effect on the gut microbiome functional profile was ranked as lag phase > log phase > stationary phase. Our results showed that metformin added at lag phase resulted in a significantly reduced abundance of the Clostridiales order as well as an increased abundance of the Bacteroides genus, which was different from stimulation during the rest of the growth phase. Metformin also resulted in alterations of several pathways, including energy production and conversion, lipid transport and metabolism, translation, ribosomal structure and biogenesis. Our results indicate that the timing for drug stimulation should be considered when studying drug-microbiome interactions in vitro.
HostingRepository	PRIDE
AnnounceDate	2022-03-01
AnnouncementXML	Submission_2022-03-01_08:02:45.531.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Leyuan Li
SpeciesList	scientific name: gut metagenome; NCBI TaxID: 749906;
ModificationList	monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF-X

Revision	Datetime	Status	ChangeLog Entry
0	2020-02-05 02:25:10	ID requested
⏵ 1	2022-03-01 08:02:46	announced

Hao Z, Li L, Ning Z, Zhang X, Mayne J, Cheng K, Walker K, Liu H, Figeys D, Gut Microbiota to Metformin. J Am Soc Mass Spectrom, 31(7):1448-1458(2020) [pubmed]

submitter keyword: microbiome, drug, 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

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PRIDE project URI

• PRIDE
  1. PXD017390
     1. Label: PRIDE project
     2. Name: Human gut microbiome cultured over time responsed differently to drug stimulation