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ProteomicsA metabolic labeling strategy for relative protein quantification in Clostridioides difficile
Clostridioides difficile (formerly Clostridium difficile) is a Gram-positive, spore-forming pathogen which cases drug-induced Clostridioides difficile-associated diseases in hospitals worldwide. A detailed analysis of the proteome may provide new targets for drug development or therapy strategies to...
ORGANISM(S): Peptoclostridium difficile (strain 630) (Clostridium difficile) 
2018-10-25 | PXD010279 | Pride
Proteomics Relative protein quantification Mass spectrometry Metabolic labeling Clostridioides difficile 
ProteomicsCommunity context reshapes microbial proteomes and reduces functional overlap
Microbial coexistence in complex communities requires mechanisms that minimize competition and optimize resource use. Here, we show that bacteria modulate protein abundance in response to specific community members, reducing functional redundancy and promoting metabolic complementarity. Using synthe...
ORGANISM(S): Anaerobutyricum hallii DSM 3353 Faecalibacterium prausnitzii Roseburia intestinalis L1-82 Marvinbryantia formatexigens DSM 14469 Megasphaera elsdenii DSM 20460 Butyrivibrio fibrisolvens DSM 3071 Xylanibacter ruminicola 
2026-02-19 | PXD071838 | Pride
Microbial productivity Proteomics Gut microbiome Synthetic communities 
ProteomicsLFQ values with shared and unique peptides - Community context reshapes microbial proteomes and reduces functional overlap
Microbial coexistence in complex communities requires mechanisms that minimize competition and optimize resource use. Here, we show that bacteria modulate protein abundance in response to specific community members, reducing functional redundancy and promoting metabolic complementarity. Using synthe...
ORGANISM(S): Anaerobutyricum hallii DSM 3353 Faecalibacterium prausnitzii Marvinbryantia formatexigens DSM 14469 Roseburia intestinalis L1-82 Butyrivibrio fibrisolvens DSM 3071 Megasphaera elsdenii DSM 20460 Xylanibacter ruminicola 
2026-02-19 | PXD073583 | Pride
ProteomicsMetaproteome plasticity sheds light on the ecology of the rumen microbiome and its connection to host traits
The arsenal of genes that microbes express reflect the way in which they sense their environment. We have previously reported that the rumen microbiome composition and its coding capacity are different in animals having distinct feed efficiency states, even when fed an identical diet. Here, we revea...
ORGANISM(S): Bos taurus (Bovine) 
2022-08-25 | PXD033418 | Pride
Feed efficient animal Rumen metaproteome Rumen microbiome Lc-ms/ms 
ProteomicsScaffold_pairwise, single and consortia
The bacterial strains P. ruminicola ATCC 19189, M. elsdenii DSM 20460, B. fibrisolvens DSM 3071, E. hallii DSM 3353, R. intestinalis DSM 14610, M. formatexigens DSM 14469 and F. prausnitzii DSM 17677 were cultivated as single cultures, in pairwise cultures and full consortia. Bacteria were grown ana...
ORGANISM(S): Anaerobutyricum hallii DSM 3353 Faecalibacterium prausnitzii Marvinbryantia formatexigens DSM 14469 Roseburia intestinalis L1-82 Butyrivibrio fibrisolvens DSM 3071 Megasphaera elsdenii DSM 20460 Xylanibacter ruminicola 
2026-02-19 | PXD072222 | Pride
Microbial productivity Proteomics Gut microbiome Synthetic communities 
ProteomicsCharacterization of outer membrane vesicles of Aggregatibacter actinomycetemcomitans serotypes a, b and c and their interactions with human neutrophils
Aggregatibacter actinomycetemcomitans (Aa) is a Gram-negative oral pathogen associated with periodontitis and systemic diseases. Seven serotypes of Aa are known, with serotypes a, b and c being most prevalent worldwide. Interestingly, isolates belonging to serotypes a, b and c present differences in...
ORGANISM(S): Aggregatibacter actinomycetemcomitans (Actinobacillus actinomycetemcomitans) (Haemophilus actinomycetemcomitans) 
2025-12-02 | PXD040447 | Pride
Aggregatibacter actinomycetemcomitans Omvs Outer membrane vesicles Neutrophils Proteome 
ProteomicsSpring phytoplankton bloom in the North Sea during the 2020 spring bloom between 29th April and 11th May (sampling twice a day for 5th, 6th and 7th May 2020 at 7 AM and 9 PM)
The dataset represents the proteome analysis of eight sampling dates during the phytoplankton bloom at the island of Helgoland in the North Sea at the long-term research station ‘Kabeltonne’ (54˚11.3′N, 7˚54.0′E) in 2020. Samples for comparing short-term proteome dynamics were collected for three co...
ORGANISM(S): unclassified Bacteria (miscellaneous) 
2025-06-10 | PXD055396 | Pride
Metaproteomics Phytoplankton bloom 
ProteomicsBeyond difficile: three novel toxin B-producing Clostridioides species from human patients with diarrhea (spore proteome)
Clostridioides difficile infection (CDI), caused by strains producing toxin B (TcdB), poses a significant global health threat. While C. difficile exhibits substantial diversity, functional studies have focused on a limited number of isolates, overlooking other genomospecies within the genus. We des...
ORGANISM(S): Clostridioides sp. 
2026-05-06 | PXD066931 | Pride
Omics Clostridioides sp. nov. C. difficile Tcdb Taxonomy Spore proteome Pathogenesis 
ProteomicsAlgae-dominated metaproteomes uncover cellular adaptations to life on the Greenland Ice Sheet
Eukaryotic algae-dominated microbiomes thrive on the Greenland Ice Sheet (GrIS) in harsh environmental conditions, including low temperatures, high light, and low nutrient availability. Chlorophyte algae bloom on snow, while streptophyte algae dominate bare ice surfaces. Empirical data about the cel...
ORGANISM(S): unclassified Bacteria (miscellaneous) algae metagenome 
2025-08-21 | PXD057047 | Pride
Greenland ice sheet Snow algae Metaproteomics Glacier ice algae 
ProteomicsSpatial constraints drive amylosome-mediated resistant starch degradation by Ruminococcus bromii in the human colon
Degradation of complex dietary fibers by gut microbes is essential for colonic fermentation, short-chain fatty acid production, and microbiome function. Ruminococcus bromii is the primary resistant starch (RS) degrader in humans, which relies on the amylosome, a specialized cell-bound enzymatic comp...
ORGANISM(S): Ruminococcus bromii L2-63 
2025-11-02 | PXD060149 | Pride
Cryo-et Cell-associated proteome Structure Cohesin Dockerin 
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