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ProteomicsKamrad et al Interspecies interactions drive proteome reorganization and emergent metabolism in gut bacteria"
Inter-species interactions shape the function and dynamics of microbial communities. Yet, the understanding of how these interactions influence the molecular physiology of interacting species remains surprisingly limited. Here, we assembled 104 synthetic pairwise co-cultures of 15 diverse gut bacter...
ORGANISM(S): Phocaeicola vulgatus Segatella copri Parabacteroides merdae Bacteroides uniformis Clostridium sporogenes Bacteroides thetaiotaomicron Bacteria Lactobacillus acidophilus [Clostridium] saccharolyticum Ruminococcus gnavus Lactobacillus gasseri Escherichia coli Collinsella aerofaciens Clostridioides difficile Klebsiella aerogenes Agathobacter rectalis 
2025-05-12 | PXD055395 | Pride
C. difficile Metaproteomics Microbiome 
ProteomicsBenchmark dataset relating to Kamrad et al "Interspecies interactions drive bacterial proteome reorganisation and emergent metabolism"
Three co-cultures containing gram-positive and -negative species at different ratios (1:1 to 1:9) were measured in quadruplicates, as well as the same number of corresponding mono-cultures. To isolate LC-MS matrix effects in the absence of biological proteome changes, we mixed mono-culture samples i...
ORGANISM(S): Bacteroides thetaiotaomicron Peptoclostridium difficile (strain 630) (Clostridium difficile) Agathobacter rectalis 
2026-02-02 | PXD072524 | Pride
Gut bacteria Synthetic communities Microbiome 
ProteomicsDifferential gene expression of cells located in the top and bottom of yeast colonies
Saccharomyces cerevisiae colonies were grown on synthetic minimal media containing 1% glucose. The top layer of cells was scraped off using a custom plastic guide and a cell scraper. The remaining bottom layer of cells was then washed off with water and proteomics samples were prepared from both lay...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2023-02-13 | PXD033395 | Pride
Dia Swath Colony Yeast 
ProteomicsDifferential gene expression of isotopically marked lysine producer and consumer subpopulations in yeast colonies
Genetically identical cells are known to differ in many physiological parameters such as growth rate and drug tolerance, but the source of such heterogeneity is often insufficiently understood. Exchange interactions between metabolite producing and consuming cells are believed to be one possible cau...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2023-02-13 | PXD037508 | Pride
Yeast Heterogeneity Dilac Colony 
ProteomicsDifferential gene expression of yeast colonies in response to lysine
Saccharomyces cerevisiae colonies were grown for 2 days on synthetic minimal media with 1% glucose, with and without 400uM lysine (5 colonies/biological replicates each). Whole colonies were then used for proteome profiling by SWATH-MS for differential gene expression analysis. A number of genes wer...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2023-02-13 | PXD030702 | Pride
Dia Swath Gene expression Lysine Colony Saccharomyces cerevisiae 
ProteomicsThe proteome landscape of genome-wide genetic perturbations
Despite the massive research efforts of the post-genomics era, a significant fraction of genes remain without functional annotation. Proteomics holds the promise to close significant gaps, but has only recently reached the scalability and precision of genome-scale studies. Here we combine large-scal...
ORGANISM(S): Saccharomyces Cerevisiae (ncbitaxon:4932) 
2022-08-15 | MSV000090136 | MassIVE
MetabolomicsImpact of low-calorie sweeteners on gut bacteria is modulated by commonly used xenobiotics

The gut microbiota is implicated in adverse effects associated with low-calorie sweeteners. Yet, the direct impact of sweeteners on gut bacteria has not been systematically assessed. Here we report interactions between 25 phylogenetically diverse gut bacterial strains and 39 commercially used swe...

2025-06-11 | MTBLS11480 | MetaboLights
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