In Vitro Metabolic Labeling of Intestinal Microbiota for Quantitative Metaproteomics

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• 作者：Xu Zhang ; Zhibin Ning ; Janice Mayne ; Shelley A. Deeke ; Jennifer Li ; Amanda E. Starr ; Rui Chen ; Ruth Singleton ; James Butcher ; David R. Mack ; Alain Stintzi ; Daniel Figeys
• 刊名：Analytical Chemistry
• 出版年：2016
• 出版时间：June 21, 2016
• 年：2016
• 卷：88
• 期：12
• 页码：6120-6125
• 全文大小：436K
• 年卷期：0
• ISSN：1520-6882

文摘

Intestinal microbiota is emerging as one of the key environmental factors influencing or causing the development of numerous human diseases. Metaproteomics can provide invaluable information on the functional activities of intestinal microbiota and on host–microbe interactions as well. However, the application of metaproteomics in human microbiota studies is still largely limited, in part due to the lack of accurate quantitative intestinal metaproteomic methods. Most current metaproteomic microbiota studies are based on label-free quantification, which may suffer from variability during the separate sample processing and mass spectrometry runs. In this study, we describe a quantitative metaproteomic strategy, using in vitro stable isotopically (¹⁵N) labeled microbiota as a spike-in reference, to study the intestinal metaproteomes. We showed that the human microbiota were efficiently labeled (>95% ¹⁵N enrichment) within 3 days under in vitro conditions, and accurate light-to-heavy protein/peptide ratio measurements were obtained using a high-resolution mass spectrometer and the quantitative proteomic software tool Census. We subsequently employed our approach to study the in vitro modulating effects of fructo-oligosaccharide and five different monosaccharides on the microbiota. Our methodology improves the accuracy of quantitative intestinal metaproteomics, which would promote the application of proteomics for functional studies of intestinal microbiota.