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Enrichment or depletion?: the impact of stool pretreatment on metaproteomic characterization of the human gut microbiota

Tanca, Alessandro and Palomba, Antonio and Pisanu, Salvatore and Addis, Maria Filippa and Uzzau, Sergio (2015) Enrichment or depletion?: the impact of stool pretreatment on metaproteomic characterization of the human gut microbiota. Proteomics (in press). ISSN 1615-9853. Article.

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DOI: 10.1002/pmic.201400573

Abstract

To date, most metaproteomic studies of the gut microbiota employ stool sample pretreatment methods to enrich for microbial components. However, a specific investigation aimed at assessing if, how, and to what extent this may impact on the final taxonomic and functional results is still lacking. Here, stool replicates were either pretreated by differential centrifugation (DC) or not centrifuged. Protein extracts were then processed by filter-aided sample preparation, single-run LC, and high-resolution MS, and the metaproteomic data were compared by spectral counting. DC led to a higher number of identifications, a significantly richer microbial diversity, as well as to reduced information on the nonmicrobial components (host and food) when compared to not centrifuged. Nevertheless, dramatic differences in the relative abundance of several gut microbial taxa were also observed, including a significant change in the Firmicutes/Bacteroidetes ratio. Furthermore, some important microbial functional categories, including cell surface enzymes, membrane-associated proteins, extracellular proteins, and flagella, were significantly reduced after DC. In conclusion, this work underlines that a critical evaluation is needed when selecting the appropriate stool sample processing protocol in the context of a metaproteomic study, depending on the specific target to which the research is aimed. All MS data have been deposited in the ProteomeXchange with identifier PXD001573 (http://proteomecentral.proteomexchange.org/dataset/PXD001573).

Item Type:Article
ID Code:10965
Status:In Press
Refereed:Yes
Uncontrolled Keywords:Differential centrifugation, gut microbiome, host, metaproteomics, microbiology, sample preparation
Subjects:Area 06 - Scienze mediche > MED/07 Microbiologia e microbiologia clinica
Divisions:002 Altri enti e centri di ricerca del Nord Sardegna > Porto Conte Ricerche, Alghero
001 Università di Sassari > 01-a Nuovi Dipartimenti dal 2012 > Scienze Biomediche
Publisher:Wiley
ISSN:1615-9853
Deposited On:11 Jun 2015 17:20

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