Black soil metaproteomics
Ontology highlight
ABSTRACT:
ORGANISM(S): Bacteria
SUBMITTER: 
Zhigang Wang
PROVIDER: PXD011337 | iProX | Thu Oct 11 00:00:00 BST 2018
REPOSITORIES: iProX
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Ak16WZG_Control1.raw | Raw | |||
| Ak16WZG_Control2.raw | Raw | |||
| Ak16WZG_Control3.raw | Raw | |||
| Ak16WZG_DBP1.raw | Raw | |||
| Ak16WZG_DBP2.raw | Raw |
Items per page: 5 1 - 5 of 9 |
Similar Datasets
Project description:The present study focuses on the use of a metaproteomic approach to analyse Black Extrinsic Tooth Stains, a specific type of pigmented extrinsic substance, in a cohort of 96 Children. Metaproteomics is a powerful emerging technology that successfully enabled human protein and bacterial identification of this specific dental biofilm using mass spectrometry. 1600 bacterial proteins were identified in black stains (BS) samples and 2058 proteins in dental plaque (DP) samples whereas 607 and 582 human proteins identified in (BS and DP, respectively). 132 genera bacteria in black stains and dental plaque were identified using phylopeptidomic analysis, showing prevalence of Rothia, Kingella, Nesseria and Pseudopropionibatcterium in black stains samples. We additionally confirmed the metaproteomic approach by performing 16S rRNA. In this work, we showed an interesting diversity of the microbiota and proteome including significant difference between Black stain and dental plaque samples.
2024-07-25 | PXD029245 | Pride
Project description:Soils are a huge reservoir of organic C, and the efflux of CO2 from soils is one of the largest fluxes in the global C cycle. Out of all natural environments, soils probably contain the greatest microbial biomass and diversity, which classifies them as one of the most challenging habitats for microbiologists (Mocali and Benedetti, 2010). Until today, it is not well understood how soil microorganisms will respond to a warmer climate. Warming may give competitive advantage to species adapted to higher temperatures (Rinnan et al., 2009). The mechanisms behind temperature adaptations of soil microbes could be shifts within the microbial community. How microbial communities will ultimately respond to climate change, however, is still a matter of speculation. As a post-genomic approach in nature, metaproteomics allows the simultaneous examination of various protein functions and responses, and therefore is perfectly suited to investigate the complex interplay between respiration dynamics, microbial community architecture, and ecosystem functioning in a changing environment (Bastida et al., 2012). Thereby we will gain new insights into responses to climate change from a microbial perspective. Our study site was located at 910 m a.s.l. in the North Tyrolean Limestone Alps, near Achenkirch, Austria The 130 year-old mountain forests consist of Norway spruce (Picea abies) with inter-spread of European beech (Fagus sylvatica) and silver fir (Abies alba). Three experimental plots with 2 × 2 m warmed- and control- subplots were installed in 2004. The temperature difference between control and warmed plots was set to 4 °C at 5 cm soil depth. Soil was warmed during snow-free seasons. In order to extract proteins from forest soil samples, the SDS–phenol method was adopted as previously described by Keiblinger et al. (2012). Protein extractions were performed from each subplot soil samples. The abundance of protein-assigned microbial phylogenetic and functional groups, were calculated based on the normalized spectral abundance factor (NSAF, Zybailov et al., 2006).
2022-03-14 | PXD004428 | Pride
Project description:The experiments were performed to elucidate the enigmatic enzymatic formation of the pungent principle, piperine, from black pepper (Piper nigrum L.), the world´s most popular spice. Based a differential RNA-Seq approach including immature fruits, flowers, and leaves, the gene encoding piperine synthase, encoding a BAHD-type acyltransferase and several other candidate genes encoding various enzymatic functions in the biosynthetic pathway were identified. Recombinant piperine synthase and additional promiscuous piperamide synthases were used to facilitate the microbial production of a broad range of medicinally relevant piperamides. Subsequent investigations will also include the identification of enzymatic steps in the phenylpropanoid pathway and the amino acid derived biosynthesis of piperidine Based on the assumption that piperine encoding genes are highly expressed shortly before the slope of piperine accumulation reaches its maximum, RNA from greenhouse grown black pepper plants was extracted from young fruits at two different stages of development, flowers, and leaves were harvested for a differential RNA-Seq approach. Candidate transcripts associated with piperine biosynthesis were identified by comparative transcript abundance and sequence annotation tools.
2021-04-28 | E-MTAB-9029 | biostudies-arrayexpress
Project description:Optimisation of DNA-protein co-extraction from the thin microbial biofilm inhabiting marine plastic debris for meta-omics and comparative metaproteomics analysis.
2023-06-20 | MSV000092214 | MassIVE
Project description:Metaproteomics approach was used to investigate the microbial community and diversity of the infant gut to identify different key proteins with metabolic functional roles in the microbiomes of healthy and atopic dermatitis infants in a Thai population-based birth cohort.
2020-09-06 | PXD021324 | JPOST Repository
Project description:In this study we characterize microbial community features on the surface of Indian Ocean. 11 samples were collected from Indian Ocean and subjected for quantitative metaproteomics analysis for taxonomic and functional analysis. Our results suggested that metabolic tuning at metaproteomics levels enabled microbial community to sustain stable when subjected to environmental perturbations in the oligotrophic ocean.
2023-05-10 | PXD016285 | Pride
Project description:Hallmarks of cystic fibrosis (CF) are increased viscosity of mucus and impaired mucociliary clearance within the airways due to mutations of the cystic fibrosis conductance regulator gene. This paves the way for the colonization by microbial pathogens and the concomitant establishment of chronic infections leading to lung tissue damage, reduced lung function, and to decreased life expectancy. Although microbial infections play a key role during disease progression, only a few studies investigated the pathophysiology of the microbial community in vivo so far. Moreover, no CF study so far applied metaproteomics, a powerful approach to unravel molecular mechanisms of microbial infection, mainly reasoned due to (I) the challenging processability of inhomogeneous, viscous, slimy sputum, and (II) the high number of human proteins masking comparably low abundant microbial proteins. Consequently, we developed a reliable, reproducible and widely applicable protocol for sputum processing, microbial enrichment, and subsequent metaproteomics analyses with a focus on microbial pathogens overcoming the aforementioned challenges. Metaproteomics data were complemented and validated by 16S sequencing, metabolomic as well as microscopic analyses. In total, we processed 21 CF sputum samples and selected three for detailed metaproteome analysis. The number of bacterial proteins/protein groups increased from 199-425 to 392-868. Moreover, our data suggest that the arginine deiminase pathway and multiple proteases and peptidases identified from various bacterial genera are so far underappreciated in their contribution to the CF pathophysiology. By providing a standardized and effective protocol for sputum processing and microbial enrichment, our study represents an important basis for future studies investigating the physiology of microbial pathogens in CF in vivo – an important prerequisite for the development of novel antimicrobial therapies against mucoviscidosis.
2021-11-03 | PXD025134 | Pride
Project description:This is the first metaproteomics-based featuring of the microbial community harbured in the traditional raw milk Caprino Nicastrese cheese
2023-03-11 | PXD032280 | Pride
Project description:Sensitive models of climate change impacts would require a better integration of multi-omics approaches that connect the abundance and activity of microbial populations. Here, we show that climate is a fundamental driver of the protein abundance of microbial populations (metaproteomics), yet not their genomic abundance (16S rRNA gene amplicon sequencing), supporting the hypothesis that metabolic activity may be more closely linked to climate than community composition.
2022-03-01 | PXD009773 | Pride
Project description:Custom made functional gene micoarray (E-FGA) consisting of 13,056 mRNA-enriched anonymus microbial clones from dirverse microbial communities to profile microbial gene transcript in agricultural soils with low and high flux of N2O. A total of 96 genes displayed expression that differed significantly between low and high N2O emitting soils. Creation and validation of an cDNA microarray from environmental microbial mRNA, to use as a monitoring tool for microbial gene expression
2010-08-05 | GSE23422 | GEO