文章基本信息

标题：Metaproteomics method to determine carbon sources and assimilation pathways of species in microbial communities
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作者：Manuel Kleiner ; Xiaoli Dong ; Tjorven Hinzke 等
期刊名称：Proceedings of the National Academy of Sciences
印刷版ISSN：0027-8424
电子版ISSN：1091-6490
出版年度：2018
卷号：115
期号：24
页码：E5576-E5584
DOI：10.1073/pnas.1722325115
语种：English
出版社：The National Academy of Sciences of the United States of America
摘要：Measurements of stable carbon isotope ratios (δ¹³C) are widely used in biology to address questions regarding food sources and metabolic pathways used by organisms. The analysis of these so-called stable isotope fingerprints (SIFs) for microbes involved in biogeochemical cycling and microbiota of plants and animals has led to major discoveries in environmental microbiology. Currently, obtaining SIFs for microbial communities is challenging as the available methods either only provide low taxonomic resolution, such as the use of lipid biomarkers, or are limited in throughput, such as nanoscale secondary ion MS imaging of single cells. Here we present “direct protein-SIF” and the Calis-p software package ( https://sourceforge.net/projects/calis-p/ ), which enable high-throughput measurements of accurate δ¹³C values for individual species within a microbial community. We benchmark the method using 20 pure culture microorganisms and show that the method reproducibly provides SIF values consistent with gold-standard bulk measurements performed with an isotope ratio mass spectrometer. Using mock community samples, we demonstrate that SIF values can also be obtained for individual species within a microbial community. Finally, a case study of an obligate bacteria–animal symbiosis shows that direct protein-SIF confirms previous physiological hypotheses and can provide unexpected insights into the symbionts’ metabolism. This confirms the usefulness of this approach to accurately determine δ¹³C values for different species in microbial community samples.
关键词：Protein-SIP ; metaproteome ; microbial ecology ; microbiome ; Q Exactive