Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Proteomics of biphenyl labelling study

ABSTRACT: protein based stable isotope probing was performed for identifying microorganisms actually responsible for biphenyl biodegradation in soil environment.

INSTRUMENT(S): LTQ Orbitrap

ORGANISM(S): Soil Metagenome

SUBMITTER: Songcan Chen

LAB HEAD: Florin Musat

PROVIDER: PXD023646 | Pride | 2022-02-16

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	A1.Target.fasta	Fasta
	A4d-1.idXML	Other
	A4d-1_181026212317.raw	Raw
	A4d-2.idXML	Other
	A4d-2_181026234903.raw	Raw

Items per page:

1 - 5 of 36

Publications

Novel clades of soil biphenyl degraders revealed by integrating isotope probing, multi-omics, and single-cell analyses.

Chen Song-Can SC Budhraja Rohit R Adrian Lorenz L Calabrese Federica F Stryhanyuk Hryhoriy H Musat Niculina N Richnow Hans-Hermann HH Duan Gui-Lan GL Zhu Yong-Guan YG Musat Florin F

The ISME journal 20210611 12

Most microorganisms in the biosphere remain uncultured and poorly characterized. Although the surge in genome sequences has enabled insights into the genetic and metabolic properties of uncultured microorganisms, their physiology and ecological roles cannot be determined without direct probing of their activities in natural habitats. Here we employed an experimental framework coupling genome reconstruction and activity assays to characterize the largely uncultured microorganisms responsible for ...[more]

PMID: 34117322

Similar Datasets

Unravelling metabolic cross-feeding in a yeast-bacteria community using 13C proteomics

Project description:Cross-feeding is fundamental to the diversity and function of microbial communities. However, identification of cross-fed metabolites is often challenging due to the universality of metabolic and biosynthetic intermediates. Here, we use 13C isotope tracing in peptides to elucidate cross-fed metabolites in cocultures of Saccharomyces cerevisiae and Lactococcus lactis. The community was grown on lactose as the main carbon source with either glucose or galactose fraction of the molecule labelled with 13C. Data analysis allowing for the possible mass-shifts yielded hundreds of peptides for which we could assign both species identity and labelling degree. The labelling pattern showed that the yeast utilized galactose and, to a lesser extent, lactic acid shared by L. lactis as carbon sources. While the yeast provided essential amino acids to the bacterium as expected, the data also uncovered a complex pattern of amino acid exchange. The identity of the cross-fed metabolites was further supported by metabolite labelling in the co-culture supernatant, and by diminished fitness of a galactose-negative yeast mutant in the community. Together, our results demonstrate the utility of 13C-based proteomics for uncovering microbial interactions.

2023-02-07 | PXD019952 | Pride

Identification of syntrophic acetate-oxidizing bacteria in anaerobic digesters

Project description:Inhibition of the anaerobic digestion process through accumulation of volatile fatty acids (VFA) is a recurring problem which is the result of unbalanced growth between acidogenic bacteria and methanogens. A speedy recovery is essential for an establishment of a feasible economical biogas productions. Yet, little is known regarding the organisms participating in the recovery. In this study the organisms involved in the recovery were studied using protein-stable isotope probing (Protein-SIP) and mapping this data onto a binned metagenome. Under acetate-accumulated simulating conditions a formation of 13C-labeled CO2 and CH4 was detected immediately after the addition of [U-13C]acetate, indicative of a high turnover rate of acetate. Several labeled peptides were detected in protein-SIP analysis. These 13C-labeled peptides were mapped onto a binned metagenome for improved taxanomical classification of the organisms involved. The results revealed that Methanosarcina and Methanoculleus were actively involved in acetate turnover, as were five subspecies of Clostridia and one Bacteroidetes. The organisms affiliating with Clostridia and Bacteroidetes all contained the FTFHS gene for formyltetrahydrofolate synthetase, a key enzyme for reductive acetogenesis; indicating that these organisms are possible syntrophic acetate-oxidizing bacteria (SAOB) that can facilitate acetate consumption via syntrophic acetate oxidation coupled with hydrogenotrophic methanogenesis (SAO-HM). This study represents the first study applying protein-SIP for analysis of complex biogas samples, a promising method for identifying key microorganisms involved in specific pathways.

2016-05-11 | PXD002996 | Pride

Metaproteomic analyses of microbial community from ancient permafrost

Project description:It remains challenging to study the viability and metabolic activity of microorganisms buried in ancient permafrost. We coupled aspartic acid racemization assay with metaproteomics to constraint the microbial activity of indigenous microbial community entrappped in permafrost sediment over 100 kyr ago.

2021-09-09 | PXD022683 | Pride

Mediterranean grassland soil C-N compound turnover is mediated by genomically novel organisms, depth stratified, and rainfall dependent

Project description:integrated soil metagenomics and metaproteomics to study grassland soil microbial communities

2019-03-27 | PXD013110 | Pride

2014 Panama soil proteomics - Community proteogenomics reveals the systemic impact of phosphorus availability on microbial functions in tropical soil

Project description:integrating metagenomics and metaproteomics to study microbial communities that have undergone long-term P addition experiment

2018-01-08 | PXD005910 | Pride

Sipros Ensemble Improves Database Searching and Filtering for Complex Metaproteomics

Project description:Complex microbial communities can be characterized by metagenomics and metaproteomics. However, metagenome assemblies often generate enormous, and yet incomplete, protein databases, which undermines the identification of peptides and proteins in metaproteomics. This challenge calls for increased discrimination of target identifications from decoy identifications by database searching and filtering algorithms in metaproteomics. Sipros Ensemble was developed here for metaproteomics using an ensemble approach to addressing this challenge.

2018-02-09 | PXD007587 | Pride

Angelo soil proteomics - Proteogenomic analyses indicate bacterial methylotrophy and archaeal heterotrophy are prevalent below the grass root zone

Project description:integration of metagenomics, metaproteomics, and metabolomics to study soil microbial community.

2016-12-23 | PXD004965 | Pride

Proteomics on extracellular fractions of polyphosphate accumulating organisms from wastewater treatment plant

Project description:Polyphosphate accumulating organisms are responsible for enhanced biological phosphate removal from wastewater, where they grow embedded in a matrix of extracellular polymeric substances. Little is known about the composition and dynamics of those proteins and their production by the different microorganisms. Tomás-Martínez et al., (2022) studied the turnover of proteins and polysaccharides in extracellular polymeric fractions of an enrichment culture of polyphosphate accumulating organisms using an anaerobic-aerobic sequencing batch reactor simulating EBPR conditions. Finally, the carbon source was switched to 13C-labelled acetate to study the protein turnover. Samples were collected at the end of each aerobic phase.

2022-12-25 | PXD036522 | Pride

Stable Isotope Probing Deuterium LC-MS/MS

Project description:Competition between commensal and pathogenic microbes for monosaccharides derived from mucus layer O-glycans as nutrient sources has been proposed as a mechanism by which the gut microbiota counteracts pathogen colonization. However, our understanding of the microbial interactions that determine competition for these sugars in complex microbial communities, and how to exploit such information to develop therapies, is limited. Here, we employed heavy water (D2O)-based activity labeling followed by automated Raman-Activated Cell Sorting of active (D-labeled) cells and metagenomics to identify mouse gut commensals that forage on O-glycan monosaccharides. Sequencing of cell-sorted fractions revealed members of the underexplored family Muribaculaceae as major mucin monosaccharide foragers, followed by members of Lachnospiraceae, Rikenellaceae and Bacteroidaceae families. We further show that the ability of these organisms to forage on mucosal sugars is well-supported by the presence of partial or complete catabolism pathways for O-glycan utilization in their genomes. Remarkably, administration of a 5-member bacterial consortium based on identified sialic acid and N-acetylglucosamine utilizers results in limited access of the gut pathogen Clostridioides difficile to mucosal sugars and in impaired pathogen colonization of antibiotic-treated mice. Our findings underscore the value of using targeted approaches to identify organisms performing key functions in the gut and to rationally design effective probiotic mixtures.

2020-09-09 | PXD015215 | Pride

MAA-SIP biomethanisation with hydrogen addition

Project description:By using metagenome resolved protein stable isotope probing (protein-SIP) through incubations of identical reactors with 13C labelled bicarbonate over a period of 48 hours, the study aims to map differences in the metabolic behaviour of the microbial community during anaerobic digestion.

2021-12-05 | PXD027519 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data