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ProteomicsLinking Intestinal Microorganisms to their Diet-derived Growth Substrates Using Protein Stable Isotope Fingerprinting (Protein-SIF)
The aim of this study was to directly link intestinal microorganisms to their diet-derived in vivo growth substrates using protein stable isotope fingerprinting (“Protein-SIF”)(Kleiner et al. 2018, PNAS 115(24)). We conducted studies in gnotobiotic mice (C57BL/6J) colonized with a community of 13 hu...
ORGANISM(S): Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482) Glycine max Faecalibacterium prausnitzii M21/2 Mus musculus (Mouse) Helianthus annuus (Common sunflower) Marvinbryantia formatexigens DSM 14469 Roseburia intestinalis L1-82 Gallus gallus (Chicken) [Clostridium] symbiosum WAL-14163 Bacteroides ovatus ATCC 8483 Escherichia coli HS Bos taurus (Bovine) Agathobacter rectalis DSM 17629 Beta vulgaris (Sugar beet) Akkermansia muciniphila ATCC BAA-835 Bacteroides caccae ATCC 43185 Barnesiella intestinihominis YIT 11860 Zea mays subsp. mays (maize) Bacteroides uniformis ATCC 8492 Collinsella aerofaciens ATCC 25986 
2024-12-16 | PXD046928 | Pride
1d-lc  mass spectrometry  ms/ms  metaproteomics  metaproteome  microbiota  microbiome  gut  intestinal  fecal  mouse  diet  protein-sif. 
ProteomicsMetaproteomics of the marine gutless oligochaete Olavius algarvensis and its symbionts to determine stable isotope fingerprints using Direct Protein-SIF
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 (PXD00...
ORGANISM(S): Olavius algarvensis Gamma 3 endosymbiont Chromatiales bacterium OalgGamma1 Olavius algarvensis Olavius algarvensis Delta 4 endosymbiont Olavius algarvensis Delta 1 endosymbiont Olavius algarvensis Gamma 1 endosymbiont Spirochaeta sp. ELBA 
2018-05-21 | PXD007510 | Pride
Lc-ms/ms Metaproteome Symbiosis Stable carbon isotope fingerprinting Metaproteomics Symbiont P-sif Protein-sif Stable isotopes 
ProteomicsProteomes of twenty bacterial, archaeal and eukaryotic species for bench marking of Direct Protein-SIF (stable carbon isotope fingerprinting proteomics)
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”. To benchmark this method, we measured twenty pure culture species using the Direct Protein-SIF method as w...
ORGANISM(S): Chlamydomonas reinhardtii Nitrososphaera viennensis Bacteria 
2018-05-21 | PXD006762 | Pride
Lc-ms/ms Stable carbon isotope fingerprinting Metaproteomics P-sif Protein-sif Stable isotopes 
ProteomicsProtein stable isotope fingerprinting (P-SIF): Chocolate Pots (Yellowstone) biomass
Protein stable isotope fingerprinting (P-SIF) is a method to measure the carbon isotope ratios of whole proteins separated from complex mixtures, including cultures and environmental samples. The goal of P-SIF is to expose the links between identity and function in microbial ecosystems by (i) determ...
ORGANISM(S): microbial mat metagenome 
2015-11-10 | PXD003119 | Pride
Lc-qtof-ms/ms Microbial mats Environmental proteomes Geobiology 
ProteomicsProtein stable isotope fingerprinting (P-SIF): Mahoney Lake (Canada) 7-m biomass
Protein stable isotope fingerprinting (P-SIF) is a method to measure the carbon isotope ratios of whole proteins separated from complex mixtures, including cultures and environmental samples. The goal of P-SIF is to expose the links between identity and function in microbial ecosystems by (i) determ...
ORGANISM(S): microbial mat metagenome 
2015-11-10 | PXD003125 | Pride
Lc-qtof-ms/ms Microbial mats Environmental proteomes Geobiology 
ProteomicsProtein stable isotope fingerprinting (P-SIF): Synechocystis sp. PCC6803 + Allochromatium vinosum DSM180 biomass mixture
Protein stable isotope fingerprinting (P-SIF) is a method to measure the carbon isotope ratios of whole proteins separated from complex mixtures, including cultures and environmental samples. The goal of P-SIF is to expose the links between identity and function in microbial ecosystems by (i) determ...
ORGANISM(S): Allochromatium vinosum (strain ATCC 17899 / DSM 180 / NBRC 103801 / NCIMB 10441 / D) (Chromatium vinosum) Synechocystis sp. PCC 6803 
2015-11-10 | PXD003150 | Pride
Chemostats Lc-qtof-ms/ms Photosynthetic species Culture studies 
ProteomicsProteomics and direct Protein-SIF of the bacterial ectosymbionts of the ciliate Kentrophoros sp. H
Kentrophoros ciliates are found worldwide in coastal marine sediment, and have an obligate symbiosis with sulfur-oxidizing Gammaproteobacteria called Candidatus Kentron. The genomes of different Kentron species suggest that they are chemolithoheterotrophs, producing new biomass from organic carbon s...
ORGANISM(S): Candidatus Kentron sp. H Kentrophoros sp. H 
2019-05-31 | PXD011616 | Pride
Kentrophoros Isola d' elba 1d-lc Thiotrophic symbiosis Candidatus kentron Ciliophora Mediterranean Metaproteomics Ciliate Metaproteome Gammaproteobacteria Protist Protein-sif Pampelonne beach 
ProteomicsMetaproteomics and direct Protein-SIF of the deep-sea mussel Bathymodiolus childressi and its bacterial symbionts
Bathymodiolus childressi is a species of deep-sea mussels found predominantly in the Gulf of Mexico. It colonizes cold seeps such as brine pool and oil seeps. The success of these animals in such environment is thought to be due to the symbiotic association of the mussel host with several species of...
ORGANISM(S): Bacteria Bathymodiolus childressi Archaea Viruses 
2020-02-27 | PXD008089 | Pride
Stable isotope fingerprinting Chemosynthetic symbiosis Stable carbon isotopes 2d-lc-ms/ms Bacteria-animal symbiosis Q exactive plus Methanotrophic symbionts Cold seeps Epsilonproteobacteria Calvin cycle 1d-lc-ms/ms 
ProteomicsMiddle Island Sinkhole microbial mat protein stable isotope fingerprinting
Metaproteomics data for a protein-stable isotope fingerprinting (P-SIF) study of phototrophic, sulfur-cycling benthic microbial mats in Middle Island Sinkhole, Lake Huron, USA
ORGANISM(S): Microbial Mat Metagenome (ncbitaxon:527640) 
2022-10-27 | MSV000090594 | MassIVE
TranscriptomicsA rapid and dynamic role for FMRP in the plasticity of adult neurons
Fragile X syndrome (FXS) is a neuro-developmental disorder caused by silencing Fmr1, which encodes the RNA-binding protein FMRP. Although Fmr1 is expressed in adult neurons, it has been challenging to separate acute from chronic effects of loss of Fmr1 in models of FXS. We have used the precision of...
ORGANISM(S): Drosophila melanogaster 
2025-03-15 | GSE241810 | GEO
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