{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"submitter":["Klaes S"],"funding":["German Research Foundation","Helmholtz-Gemeinschaft","European Regional Development Fund","Helmholtz-Zentrum für Umweltforschung"],"pagination":["111249"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC11700628"],"repository":["biostudies-literature"],"omics_type":["Unknown"],"volume":["27(12)"],"pubmed_abstract":["Protein-based stable isotope probing (protein-SIP) can link microbial taxa to substrate assimilation. Traditionally, protein-SIP requires a sample-specific metagenome-derived database for samples with unknown composition. Here, we describe GroEL-prototyping-based stable isotope probing (GroEL-SIP), that uses GroEL as a taxonomic marker protein to identify bacterial taxa (GroEL-proteotyping) coupled to SIP directly linking identified taxa to substrate consumption. GroEL-SIP's main advantages are that (1) it can be performed with a sample-independent database and (2) sample complexity can be reduced by enriching GroEL proteins, increasing sensitivity and reducing instrument time. We applied GroEL-SIP to pure cultures, synthetic bicultures, and a human gut model using <sup>2</sup>H-, <sup>18<"],"journal":["iScience"],"pubmed_title":["Revealing taxonomy, activity, and substrate assimilation in mixed bacterial communities by GroEL-proteotyping-based stable isotope probing."],"pmcid":["PMC11700628"],"funding_grant_id":["GRK 2032/2"],"pubmed_authors":["Cooper M","Klaes S","Madan S","Deobald D","Adrian L"],"additional_accession":[]},"is_claimable":false,"name":"Revealing taxonomy, activity, and substrate assimilation in mixed bacterial communities by GroEL-proteotyping-based stable isotope probing.","description":"Protein-based stable isotope probing (protein-SIP) can link microbial taxa to substrate assimilation. Traditionally, protein-SIP requires a sample-specific metagenome-derived database for samples with unknown composition. Here, we describe GroEL-prototyping-based stable isotope probing (GroEL-SIP), that uses GroEL as a taxonomic marker protein to identify bacterial taxa (GroEL-proteotyping) coupled to SIP directly linking identified taxa to substrate consumption. GroEL-SIP's main advantages are that (1) it can be performed with a sample-independent database and (2) sample complexity can be reduced by enriching GroEL proteins, increasing sensitivity and reducing instrument time. We applied GroEL-SIP to pure cultures, synthetic bicultures, and a human gut model using <sup>2</sup>H-, <sup>18<","dates":{"release":"2024-01-01T00:00:00Z","publication":"2024 Dec","modification":"2026-04-08T19:53:24.383Z","creation":"2026-04-08T14:31:27.485Z"},"accession":"S-EPMC11700628","cross_references":{"pubmed":["39759010"],"doi":["10.1016/j.isci.2024.111249"]}}