Project description: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.
2019-01-14 | PXD011515 | Pride
Project description:Metagenome assembly of PRJNA784430 data set (Deep-sea sediment metagenomes)
| PRJEB87677 | ENA
Project description:Metagenome assembly of PRJEB37497 data set (Lake Erken network metagenomes)
| PRJEB85613 | ENA
Project description:Metagenome assembly of PRJNA901668 data set (Mar Menor sediments metagenomes)
| PRJEB88160 | ENA
Project description:metagenome assembly of PRJNA473595 data set (Wolf lichen metagenomes and metatranscriptomes).
| PRJEB72392 | ENA
Project description:Metagenome assembly of PRJNA526329 data set (Mariana and Kermadec trench Metagenomes)
Project description:This data set contains 1376 mass spectrometry reads from root, rhizosphere and leaf sample of Populus Trichocarpa, as well as associated controls. This metabolomics data set was collected as part of a larger campaign which complements the metabolomics data with metagenome sequencing, transcriptomics, and soil measurement data.