PXD002420

PXD002420 is an original dataset announced via ProteomeXchange.

Title	Shotgun metaproteomic profiling of biomimetic anaerobic digestion processes treating sewage sludge
Description	Two parallel anaerobic digestion lines were designed to match a "bovid-like" digestive structure. Each of the lines consisted of two Continuous Stirred Tank Reactors placed in series and separated by an acidic treatment step. The first line was inoculated with industrial inocula whereas the second was seeded with cow digestive tract contents. After three month of continuous sewage sludge feeding, samples were recovered for shotgun metaproteomic and DNA-based analysis. Strikingly, protein inferred and 16S rDNA tags based taxonomic community profiles were not fully consistent. Principal Component analysis however revealed a similar clustering pattern of the samples, suggesting that reproducible methodological and/or biological factors underlie this observation. The performances of the two digestion lines did not differ significantly and the cow derived inocula did not establish in the reactors. A low throughput metagenomic dataset (3.4x106 reads, 1.1 Gb) was also generated for one of the samples. It allowed a substantial increase of the analysis depth (increase of the spectral identification rate). For the first time, a high level of proteins expressed by members of the "Candidatus Competibacter" group is reported in an anaerobic digester, a key microbial player in environmental bioprocess communities.
HostingRepository	PRIDE
AnnounceDate	2015-08-12
AnnouncementXML	Submission_2015-08-12_03:17:06.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ariane Bize
SpeciesList	scientific name: anaerobic digester metagenome; NCBI TaxID: 1263854;
ModificationList	S-carboxamidoethyl-L-cysteine; acetylated residue; iodoacetamide derivatized residue; reduction of disulfide crosslink in cystine to two cysteines; L-methionine sulfoxide
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2015-06-24 01:30:17	ID requested
⏵ 1	2015-08-12 03:17:07	announced

Bize A, Cardona L, Desmond-Le Qu, é, m, é, ner E, Battimelli A, Badalato N, Bureau C, Madigou C, Chevret D, Guillot A, Monnet V, Godon JJ, Bouchez T, Shotgun metaproteomic profiling of biomimetic anaerobic digestion processes treating sewage sludge. Proteomics, 15(20):3532-43(2015) [pubmed]

curator keyword: Metaproteomics, Biological

submitter keyword: Candidatus Competibacter, anaerobic digestion, two-stage system, animal mimicry, cow digestive tracts, Q-Exactive

Théodore Bouchez
contact affiliation	Hydrosystems and bioprocesses unit research (HBAN), Environmental Technologies Department, Irstea, France
contact email	theodore.bouchez@irstea.fr
lab head
Ariane Bize
contact affiliation	Irstea
contact email	ariane.bize@irstea.fr
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/2015/08/PXD002420

PRIDE project URI

• PRIDE
  1. PXD002420
     1. Label: PRIDE project
     2. Name: Shotgun metaproteomic profiling of biomimetic anaerobic digestion processes treating sewage sludge