Dataset Information

InfectERA: Challenges in clinical metaproteomics highlighted by the analysis of acute leukemia patients with gut colonization by multidrug-resistant Enterobacteriaceae

ABSTRACT: 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) colonization using metagenomics and metaproteomics. This is one of the largest clinical metaproteomic studies to date and the first 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 addition to the analysis of patient cohorts.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Feces

DISEASE(S): Acute Leukemia

SUBMITTER: Julia Woortman

LAB HEAD: Bernhard Kuster

PROVIDER: PXD011515 | Pride | 2019-01-14

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	02401_A02_P026075_B00_A00_R1.raw	Raw
	02401_A03_P026083_B00_A00_R1.raw	Raw
	02401_A05_P026102_B00_A00_R1.raw	Raw
	02401_A06_P026110_B00_A00_R1.raw	Raw
	02401_A07_P026118_B00_A00_R1.raw	Raw

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Publications

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

Rechenberger Julia J Samaras Patroklos P Jarzab Anna A Behr Juergen J Frejno Martin M Djukovic Ana A Sanz Jaime J González-Barberá Eva M EM Salavert Miguel M López-Hontangas Jose Luis JL Xavier Karina B KB Debrauwer Laurent L Rolain Jean-Marc JM Sanz Miguel M Garcia-Garcera Marc M Wilhelm Mathias M Ubeda Carles C Kuster Bernhard B

Proteomes 20190108 1

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 mu ...[more]

PMID: 30626002

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