Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Microbial remineralization of particulate organic carbon in the ocean’s twilight zone

ABSTRACT: we characterized the microbial communities and proteomes of POC collected from the twilight zone at three contrasting sites in the northwest Pacific Ocean using a metaproteomic approach.Particle-attached bacteria, Alteromonadales, Rhodobacterales and Enterobacteriales, were the major remineralizers of POC in the twilight zone.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Alteromonadales

SUBMITTER: He Yanbin

LAB HEAD: Siqi Liu

PROVIDER: PXD014630 | Pride | 2021-03-24

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	P10_1_1.raw	Raw
	P10_1_10.raw	Raw
	P10_1_2.raw	Raw
	P10_1_3.raw	Raw
	P10_1_4.raw	Raw

Items per page:

1 - 5 of 482

Similar Datasets

Extracellular vesicles isolated from the descending colon of pediatric patients with inflammatory bowel disease and control patients

Project description:Characterizing the proteomic profile of extracellular vesicles isolated from the descending colon of pediatric patients with inflammatory bowel disease and control participants

2018-09-11 | PXD007959 | Pride

Human gut microbiome cultured over time responsed differently to drug stimulation

Project description:In vitro gut microbiota models are often used to study drug-microbiome interaction. Similar to culturing individual microbial strains, the biomass accumulation of in vitro gut microbiota follows a logistic growth curve. Current studies on in vitro gut microbiome responses introduce drug stimulation during different growth stages, e.g. lag phase or stationary phase. However, in vitro gut microbiota in different growth phases may respond differently to a same stimuli. Therefore, in this study, we used a 96-deep well plate-based culturing model (MiPro) to culture the human gut microbiota. Metformin, as the stimulus, was added at the lag, log and stationary phases of growth. Microbiome samples were collected at different time points for optical density and metaproteomic functional analysis. Results show that in vitro gut microbiota responded differently to metformin added during different growth phases, in terms of the growth curve, alterations of taxonomic and functional compositions. The addition of drugs at log phase leads to the greatest decline of bacterial growth. Metaproteomic analysis suggested that the strength of the metformin effect on the gut microbiome functional profile was ranked as lag phase > log phase > stationary phase. Our results showed that metformin added at lag phase resulted in a significantly reduced abundance of the Clostridiales order as well as an increased abundance of the Bacteroides genus, which was different from stimulation during the rest of the growth phase. Metformin also resulted in alterations of several pathways, including energy production and conversion, lipid transport and metabolism, translation, ribosomal structure and biogenesis. Our results indicate that the timing for drug stimulation should be considered when studying drug-microbiome interactions in vitro.

2022-03-01 | PXD017390 | Pride

Evaluating in vitro culture medium of mouse gut microbiome

Project description:The mice stool samples were collected for culturing with different medium for understanding the role of different medium component on the microbiome.

2018-06-15 | PXD006808 | Pride

Evaluating the protein extraction methods for gut metaproteomics

Project description:Human stool samples were collected, microbial cells were harvested and subjected to protein extraction using different protocols for metaproteomics analyses. The protein extraction methods differ from the usage of different lysis buffer (SDS, urea and commercially available B-Per reagent), bead beating, ultrasonication and heating. The impacts of different protein extraction methods on metaproteomics results were evaluated with multiple criteria including protein yields, peptide identifications, taxonomic compositions and functional compositions.

2017-07-17 | PXD005969 | Pride

Deep gut metaproteomics - A deep metaproteomics approach for the study of human microbiomes

Project description:Stool samples were collected from 4 children and subjected to deep gut metaproteomics analysis for in-depth understanding the functional compositions of human gut mcirobiome.

2017-08-10 | PXD005619 | Pride

Pediatric IBD MLI metaproteomics

Project description:Mucosal-luminal interface (MLI) samples were collected from a cohort of children with new-onset IBD and microbial cells were harvested and processed for metaproteomic analysis. Deep metaproteomics data analysis was then performed for better understanding the MLI microbiota functions in the development of pediatric IBD.

2018-08-03 | PXD007819 | Pride

Hunam gut microbiome metaproteomcis in LP1

Project description:The samples of gut micorbiota were collected in "Lunar Palace 365" experiment. The "Lunar Palace 365" experiment was a 370-day, multicrew, closed experiment carried out in a ground-based experimental BLSS platform named Lunar Palace 1. Deep metaproteomics data analysis was then performed for better understanding the role of gut micorbiota in mood regulation.

2023-05-10 | PXD027661 | Pride

An in vitro model maintaining taxon-specific functional activities of the gut microbiome

Project description:We developed and validated a 96-deep well plate-based culturing model named Mipro to maintain individuals’ microbiomes. The Mipro model quintupled viable bacteria count while maintained the functional and compositional profiles of individuals’ gut microbiomes.

2019-08-16 | PXD013600 | Pride

Complete list of canonical post-transcriptional modifications in Bacillus subtilis ribosome.

Project description:Using bottom-up oligonucleotide LC-MS/MS in combination with stable isotope labeling, chemical derivatization, and bioinformatics variable modification search, a total of 25 modifications were mapped to the sequences of 16S and 23S RNA in B. subtilis. 10 modification sites, previously identified by others using alternative methods were independently confirmed using targeted MS/MS data analysis. Modification types, namely base/ribose methylation, pseudouridines and dihydrouridine, and modification positions are fully consistent with prior experimental evidence and agree well with modifications that were annotated in E. coli and other bacteria species.

2024-08-06 | PXD050367 | Pride

Lysine acetylation of microbiome

Project description:This project study and comprehensively characterize the lysine acetyltion in the human gut microbiome using antibody-based enrichment strategry and Orbitrap mass spectrometer. The technique has also been applied to study the microbiome in pediatric Crohn's disease and control subjects in order to understand the functional alterations of microbiome in IBD.

2020-07-08 | PXD013427 | 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