Proteomics

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Metaproteomics of the marine gutless oligochaete Olavius algarvensis and its symbionts to determine stable isotope fingerprints using Direct Protein-SIF

ABSTRACT: We developed a method that allows measuring the stable carbon isotope composition of individual species in microbial communities using metaproteomics. We call this methods “Direct Protein-SIF”. We validated and tested the method extensively using pure cultures (PXD006762) and mock communities (PXD006118, https://www.ebi.ac.uk/pride/archive/projects/PXD006118). As a case study we applied Direct Protein-SIF to the Olavius algarvensis symbiosis. Olavius algarvensis is a marine worm that lives in shallow-water sediments off the coast of Elba, Italy. The worm has no digestive and excretory system, instead it harbors five bacterial symbionts that fulfill its nutritional and waste recycling needs (http://www.pnas.org/content/109/19/E1173.short). For this project we generated metaproteomes of 14 O. algarvensis individuals. A total of 18 LC-MS/MS runs were generated. For Direct Protein-SIF the data from all runs was combined. In this submission we are including the Direct Protein-SIF specific isotope pattern file as well as the .mzML files and PSM file required as input for the Direct Protein-SIF software (Calis-p). In addition to the Olavius algarvensis samples a protein reference material (MKH files) was measured. The respective .raw files and isotopic pattern files are available through project PXD006762 (see publication for details on how the reference material is used to calibrate the method).

INSTRUMENT(S): Q Exactive

ORGANISM(S): Olavius Algarvensis Gamma 3 Endosymbiont Olavius Algarvensis Chromatiales Bacterium Oalggamma1 Olavius Algarvensis Gamma 1 Endosymbiont Olavius Algarvensis Delta 4 Endosymbiont Spirochaeta Sp. Elba Olavius Algarvensis Delta 1 Endosymbiont

SUBMITTER: Manuel Kleiner  

LAB HEAD: Manuel Kleiner

PROVIDER: PXD007510 | Pride | 2018-05-21

REPOSITORIES: Pride

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Dataset's files

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1.mzML Mzml
1.raw Raw
11.mzML Mzml
11.raw Raw
12.mzML Mzml
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Publications

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

Kleiner Manuel M   Dong Xiaoli X   Hinzke Tjorven T   Wippler Juliane J   Thorson Erin E   Mayer Bernhard B   Strous Marc M  

Proceedings of the National Academy of Sciences of the United States of America 20180529 24

Measurements of stable carbon isotope ratios (δ<sup>13</sup>C) 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  ...[more]

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