Challenges in Clinical Metaproteomics Highlighted by the Analysis of Acute Leukemia Patients with Gut Colonization by Multidrug-Resistant Enterobacteriaceae.

Détails

Ressource 1Télécharger: 30626002_BIB_F5CCD293B122.pdf (4993.14 [Ko])
Etat: Public
Version: Final published version
Licence: CC BY 4.0
ID Serval
serval:BIB_F5CCD293B122
Type
Article: article d'un périodique ou d'un magazine.
Collection
Publications
Institution
Titre
Challenges in Clinical Metaproteomics Highlighted by the Analysis of Acute Leukemia Patients with Gut Colonization by Multidrug-Resistant Enterobacteriaceae.
Périodique
Proteomes
Auteur(s)
Rechenberger J., Samaras P., Jarzab A., Behr J., Frejno M., Djukovic A., Sanz J., González-Barberá E.M., Salavert M., López-Hontangas J.L., Xavier K.B., Debrauwer L., Rolain J.M., Sanz M., Garcia-Garcera M., Wilhelm M., Ubeda C., Kuster B.
ISSN
2227-7382 (Print)
ISSN-L
2227-7382
Statut éditorial
Publié
Date de publication
08/01/2019
Peer-reviewed
Oui
Volume
7
Numéro
1
Langue
anglais
Notes
Publication types: Journal Article
Publication Status: epublish
Résumé
The microbiome has a strong impact on human health and disease and is, therefore, increasingly studied in a clinical context. Metaproteomics is also attracting considerable attention, and such data can be efficiently generated today owing to improvements in mass spectrometry-based proteomics. As we will discuss in this study, there are still major challenges notably in data analysis that need to be overcome. Here, we analyzed 212 fecal samples from 56 hospitalized acute leukemia patients with multidrug-resistant Enterobactericeae (MRE) gut colonization using metagenomics and metaproteomics. This is one of the largest clinical metaproteomic studies to date, and the first metaproteomic study addressing the gut microbiome in MRE colonized acute leukemia patients. Based on this substantial data set, we discuss major current limitations in clinical metaproteomic data analysis to provide guidance to researchers in the field. Notably, the results show that public metagenome databases are incomplete and that sample-specific metagenomes improve results. Furthermore, biological variation is tremendous which challenges clinical study designs and argues that longitudinal measurements of individual patients are a valuable future addition to the analysis of patient cohorts.
Mots-clé
clinical proteomics, data analysis, human gut microbiome, mass spectrometry, metaproteome, multi-omics, multidrug-resistant Enterobacteriaceae, proteomics
Pubmed
Open Access
Oui
Création de la notice
10/02/2019 16:43
Dernière modification de la notice
21/08/2019 7:11
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