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ProteomicsProteome-Level Functional Redundancy in the Human Gut Microbiome
Here, we quantify the proteome-level functional redundancy in the human gut microbiome using metaproteomics and network approaches.In particular, we used an ultra-deep metaproteomics approach based on high-pH reverse phase fractionation. The data analysis revealed high protein-level functional redun...
ORGANISM(S): human gut metagenome 
2023-06-08 | PXD027297 | Pride
Gut microbiome Network Functional redundancy Metaproteomics 
UnknownHypermethioninemia due to methionine adenosyltransferase I/III deficiency and brain damage.
Not available
S-EPMC11542214 | biostudies-literature
ProteomicsO-SaMPle: an optimized workflow for human salivary metaproteomic analysis reveals taxonomic and functional dysbiosis in IBD patients
We developed an Optimized Salivary MetaProteomic sample analysis workflow (O-SaMPle) to enrich salivary bacteria and reduce host-derived interferences for in-depth analysis of the oral metaproteome. This workflow integrates using selective microbial enrichment buffer and differential centrifugation...
ORGANISM(S): Human Oral Bacteria Ensemble 
PXD055269 |
ProteomicsA human gut microbiome treated in vitro with Diclofenac
One individual microbiome was cultured with or without the presence of diclofenac (an NSAID drug) in triplicates using RapidAIM assay.
ORGANISM(S): human gut metagenome 
2022-06-23 | PXD033624 | Pride
In vitro culture Drug treatment Human gut microbiome 
ProteomicsEffect of berberine analogues on functional profiles of human gut microbiomes
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...
ORGANISM(S): Escherichia coli Bacteria 
2020-07-21 | PXD015934 | Pride
Functionality Butyrate Gut microbiome Akkermansia Berberine Metaproteomics 
ProteomicsRapidAIM 2.0: a high-throughput assay to study functional response of human gut microbiome to xenobiotics
RapidAIM combines an optimized culturing model, which maintains the taxonomic and functional profiles of the human gut microbiome in vitro, and a high-throughput metaproteomics workflow to gain deep functional insights into microbiome responses. Here we exemplify the described RapidAIM 2.0 workflow ...
ORGANISM(S): human feces metagenome 
2025-08-31 | PXD035815 | Pride
In vitro culture Human gut microbiome Metaproteomics 
ProteomicsRapid Assay of Individual Microbiome responses to drugs part1
We developed an approach named Rapid Assay of Individual Microbiome (RapidAIM) to screen xenobiotics against individual microbiomes, and conducted a proof-of-concept (POC) study on the use of RapidAIM. We tested 43 compounds against five individual microbiomes. The individual microbiomes are culture...
ORGANISM(S): Escherichia coli 
2020-05-26 | PXD012724 | Pride
Drug Microbiome Metaproteomics In vitro culturing 
ProteomicsRapid Assay of Individual Microbiome responses to drugs data part2
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 plate...
ORGANISM(S): Escherichia coli 
2020-05-27 | PXD012725 | Pride
In vitro culture Drug Microbiome Metaproteomics 
ProteomicsSystematic Metaproteomic Mapping of Ex vivo Gut Microbiota Functional Responses to Therapeutic Drugs (3)
Some therapeutic compounds can influence our gut microbiota, but a comprehensive understanding of their impact on microbial systems ecology remains largely unexplored. This study examines the impact of 312 therapeutic compounds on metaproteomes of six ex vivo human gut microbiota, generating 4.6 mil...
ORGANISM(S): human gut metagenome 
2025-08-28 | PXD056968 | Pride
Gut microbiota Microbiome Drug response Functional redundancy Metaproteomics 
ProteomicsSystematic Metaproteomic Mapping of Ex vivo Gut Microbiota Functional Responses to Therapeutic Drugs (2)
Some therapeutic compounds can influence our gut microbiota, but a comprehensive understanding of their impact on microbial systems ecology remains largely unexplored. This study examines the impact of 312 therapeutic compounds on metaproteomes of six ex vivo human gut microbiota, generating 4.6 mil...
ORGANISM(S): human gut metagenome 
2025-08-28 | PXD056930 | Pride
Systems ecology Gut microbiome Metaproteomics Functional response 
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