PXD015934

PXD015934 is an original dataset announced via ProteomeXchange.

Title	Effect of berberine analogues on functional profiles of human gut microbiomes
Description	The understanding of the effects of compounds on the gut microbiome is limited and in particular we don’t know whether structurally similar compounds have similar or distinct effects on the gut microbiome. Here we selected berberine (BBR), an isoquinoline quaternary alkaloid, and sixteen structural analogues, and evaluated their effects on in vitro cultured individual gut microbiomes. The responses of the individual microbiomes were evaluated by metaproteomic profiles and by assessing butyrate production. BBR and eight analogues led to changes in proteins involved in microbial defense and stress responses, and enrichment of proteins from Verrumicrobia, Proteobacteria and Bacteroides phyla. It also led to a decrease in proteins from the Firmicutes phylum and its Clostridiales order which correlated to decrease proteins involved in the butyrate production pathway and butyrate concentration. Three of the compounds, Sanguinarine, Chelerythrine and Ethoxysanguinarine activated bacterial protective mechanisms, enriched Proteobacteria, increased opacity proteins and markedly reduced butyrate production. Dihydroberberine had a similar function to BBR in enriching the Akkermansia genus. In addition, it showed less overall adverse impacts on the functionality of the gut microbiome, including a better maintenance of the butyrate level. Our study shows that ex vivo microbiome assay can assess differential regulating effects of compounds with subtle differences and reveals that compound analogues can have distinct effects on the microbiome.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:09:34.082.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; scientific name: Bacteria; NCBI TaxID: NCBITaxon:2;
ModificationList	carbamoylated residue; acetylated residue
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2019-10-21 01:45:20	ID requested
1	2020-07-20 22:22:37	announced
⏵ 2	2024-10-22 05:09:36	announced	2024-10-22: Updated project metadata.

10.1080/19490976.2020.1755413;

Li L, Chang L, Zhang X, Ning Z, Mayne J, Ye Y, Stintzi A, Liu J, Figeys D, Berberine and its structural analogs have differing effects on functional profiles of individual gut microbiomes. Gut Microbes, 11(5):1348-1361(2020) [pubmed]

submitter keyword: functionality, butyrate,gut microbiome, Akkermansia, berberine, metaproteomics

Daniel Figeys
contact affiliation	Faculty of Medicine, University of Ottawa
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. PXD015934
     1. Label: PRIDE project
     2. Name: Effect of berberine analogues on functional profiles of human gut microbiomes