期刊
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
卷 115, 期 24, 页码 E5576-E5584出版社
NATL ACAD SCIENCES
DOI: 10.1073/pnas.1722325115
关键词
Protein-SIP; metaproteome; microbial ecology; microbiome; Q Exactive
资金
- Office of Science of the US Department of Energy [DE-AC02-05CH11231]
- Campus Alberta Innovation Chair Program
- Canadian Foundation for Innovation
- North Carolina State Chancellor's Faculty Excellence Program Cluster on Microbiomes and Complex Microbial Communities
- DAAD fellowship by the German Academic Exchange Service
- Natural Sciences and Engineering Research Council (NSERC) of Canada through a Banting fellowship
- NSERC undergraduate student research award
- NSERC Discovery grant
- International Microbiome Center
- Government of Canada through Genome Canada
- Government of Alberta through Genome Alberta
- Genome Prairie
- Research Manitoba
- Genome Quebec
- Canada First Research Excellence Fund
Measurements of stable carbon isotope ratios (delta C-13) 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 delta C-13 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 delta C-13 values for different species in microbial community samples.
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