PXD016242

PXD016242 is an original dataset announced via ProteomeXchange.

Title	Integrated meta-omic analysis of a lignocellulose-degrading microbial community
Description	Microbial communities that degrade lignocellulosic biomass are typified by high levels of species- and strain-level complexity, as well as synergistic interactions between both cellulolytic and non-cellulolytic microorganisms. Here we deconvoluted a highly efficient cellulose-degrading and methanogenic consortium (SEM1b) that is co-dominated by Clostridium (Ruminiclostridium) thermocellum and multiple heterogenic strains affiliated to C. proteolyticus. A time-series analysis was performed over the entire lifetime span of the microbial community and comprised of metagenomic, metatranscriptomic, metabolomics, metaproteomic and 16S rRNA gene analysis for 8 time points, in triplicate. Metagenomic analysis of SEM1b recovered metagenome-assembled genomes (MAGs) for each constituent population, whereas in parallel two novel strains of C. proteolyticus were isolated and sequenced. Both the recovered MAGs and the isolated strains were used as a database for further functional meta-omics. Absolute quantitative metatranscriptomics was performed thanks the spike-in of an in vitro transcribed RNA as an internal standard and label-free quantification was used for the metaproteomic analysis. The present dataset has been used for several publications. The first aim of the project was to characterize the interactions between uncultured populations in a lignocellulose-degrading community. Furthermore, because of the in-depth multi-omics characterization of the community, the dataset was used to develop new approaches for meta-omics integration as well as to assess the protein-to-RNA ratio of multiple microbial populations simultaneously. Modifications of multi-omics toolkits allowed us to assess the linearity between transcriptome and proteome for each population over time and reveal deeper functional-related trends and integrative co-dependent metabolisms that drive the overall phenotype of microbial communities.
HostingRepository	PRIDE
AnnounceDate	2020-08-21
AnnouncementXML	Submission_2020-09-27_23:53:03.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Magnus Arntzen
SpeciesList	scientific name: Methanothermobacter thermautotrophicus; NCBI TaxID: 145262; scientific name: Tepidimicrobium xylanilyticum; NCBI TaxID: 1123352; scientific name: Acetomicrobium mobile; NCBI TaxID: 97477; scientific name: Tepidanaerobacter acetatoxydans; NCBI TaxID: 499229; scientific name: [Clostridium] stercorarium; NCBI TaxID: 1510; scientific name: Coprothermobacter proteolyticus; NCBI TaxID: 35786; scientific name: Ruminiclostridium thermocellum; NCBI TaxID: 1515;
ModificationList	2-pyrrolidone-5-carboxylic acid (Gln); monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue; deamidated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2019-11-12 02:44:57	ID requested
1	2020-08-21 05:24:54	announced
⏵ 2	2020-09-27 23:53:04	announced	2020-09-28: Updated publication reference for PubMed record(s): 32948758.

Delogu F, Kunath BJ, Evans PN, Arntzen M Ø, Hvidsten TR, Pope PB, Integration of absolute multi-omics reveals dynamic protein-to-RNA ratios and metabolic interplay within mixed-domain microbiomes. Nat Commun, 11(1):4708(2020) [pubmed]

submitter keyword: metaproteomics, microbial community

Phil Pope
contact affiliation	Faculty of Chemistry, Biotechnology and Food Science Norwegian University of Life Sciences Post Office Box 5003 1432, Ås Norway
contact email	phil.pope@nmbu.no
lab head
Magnus Arntzen
contact affiliation	Norwegian University of Life Sciences
contact email	magnus.arntzen@nmbu.no
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/08/PXD016242

PRIDE project URI

• PRIDE
  1. PXD016242
     1. Label: PRIDE project
     2. Name: Integrated meta-omic analysis of a lignocellulose-degrading microbial community