Details zur Publikation
Kategorie Textpublikation
Referenztyp Zeitschriften
DOI 10.1016/j.isci.2024.111249
Lizenz creative commons licence
Titel (primär) Revealing taxonomy, activity, and substrate assimilation in mixed bacterial communities by GroEL-proteotyping-based stable isotope probing
Autor Klaes, S. ORCID logo ; Madan, S.; Deobald, D.; Cooper, M.; Adrian, L.
Quelle iScience
Erscheinungsjahr 2024
Department MEB
Band/Volume 27
Heft 12
Seite von art. 111249
Sprache englisch
Topic T7 Bioeconomy
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 i) it can be performed with a sample-independent database and ii) 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 2H-, 18O-, and 13C-labeled substrates. While 2H and 18O allowed assessing general activity, 13C enabled differentiation of substrate source and utilized metabolic pathways. GroEL-SIP offers fast and straightforward protein-SIP analyses of highly abundant families in mixed bacterial communities, but further work is needed to improve sensitivity, resolution, and database coverage.
dauerhafte UFZ-Verlinkung https://www.ufz.de/index.php?en=20939&ufzPublicationIdentifier=29849
Klaes, S., Madan, S., Deobald, D., Cooper, M., Adrian, L. (2024):
Revealing taxonomy, activity, and substrate assimilation in mixed bacterial communities by GroEL-proteotyping-based stable isotope probing
iScience 27 (12), art. 111249 10.1016/j.isci.2024.111249