Metaproteomics method to determine carbon sources and assimilation pathways of species in microbial communities

Proceedings of the National Academy of Sciences of the United States of America
Manuel KleinerMarc Strous

Abstract

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 st...Continue Reading

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Nov 18, 2017·Nature Communications·Manuel KleinerMarc Strous

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Citations

Dec 19, 2019·MBio·Tjorven HinzkeStephanie Markert
Sep 19, 2019·Nature Communications·Jackie K ZorzMarc Strous
Jun 27, 2019·MBio·Brandon K B SeahHarald R Gruber-Vodicka
Apr 10, 2019·Proceedings of the National Academy of Sciences of the United States of America·Oliver JäckleHarald R Gruber-Vodicka
Mar 7, 2019·Frontiers in Microbiology·Tjorven HinzkeManuel Kleiner
Dec 12, 2020·Frontiers in Microbiology·Krisztián LacziKatalin Perei
Mar 3, 2021·Critical Reviews in Microbiology·Faizan Ahmed SadiqHao Zhang
Jun 18, 2019·Current Opinion in Biotechnology·Mary Jo KirisitsAmeet J Pinto
Mar 13, 2021·Frontiers in Bioengineering and Biotechnology·Bashar Amer, Edward E K Baidoo
Apr 17, 2021·Frontiers in Microbiology·Maria GrimmKatharina Riedel
Jun 19, 2021·Annual Review of Plant Biology·Christine V HawkesLars Hestbjerg Hansen
Jun 30, 2021·The ISME Journal·Ling-Dong ShiHe-Ping Zhao

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Datasets Mentioned

BETA
PXD003626
PXD006762
PXD007510

Software Mentioned

PRIDE
ProteoWizard
IRMS
Calis
mzML
isotopicPattern
Proteome Discoverer
VSMOW
MSConvertGUI
p )

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