Challenges in Clinical Metaproteomics Highlighted by the Analysis of Acute Leukemia Patients with Gut Colonization by Multidrug-Resistant Enterobacteriaceae.
clinical proteomics
data analysis
human gut microbiome
mass spectrometry
metaproteome
multi-omics
multidrug-resistant Enterobacteriaceae
proteomics
Journal
Proteomes
ISSN: 2227-7382
Titre abrégé: Proteomes
Pays: Switzerland
ID NLM: 101621966
Informations de publication
Date de publication:
08 Jan 2019
08 Jan 2019
Historique:
received:
31
10
2018
revised:
20
12
2018
accepted:
03
01
2019
entrez:
11
1
2019
pubmed:
11
1
2019
medline:
11
1
2019
Statut:
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.
Identifiants
pubmed: 30626002
pii: proteomes7010002
doi: 10.3390/proteomes7010002
pmc: PMC6473847
pii:
doi:
Types de publication
Journal Article
Langues
eng
Subventions
Organisme : Bundesministerium für Bildung und Forschung
ID : 031L0089
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