ArticlePLoS computational biology2014
A peptide-based method for 13C Metabolic Flux Analysis in microbial communities.
Article in PLoS computational biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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26 citing papers in PubMed, 56 citations in OpenAlex.
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- A pathogen-specific isotope tracing approach reveals metabolic activities and fluxes of intracellular Salmonella.PLoS biology · 2023Article
- Unravelling metabolic cross-feeding in a yeast-bacteria community usingMolecular systems biology · 2023Article
- Metabolic heterogeneity and cross-feeding within isogenic yeast populations captured by DILAC.Nature microbiology · 2023Article
- A Two-Compartment Fermentation System to Quantify Strain-Specific Interactions in Microbial Co-Cultures.Bioengineering (Basel, Switzerland) · 2023Article
- Review
- Retooling Microbiome Engineering for a Sustainable Future.mSystems · 2021Article
- Integrating Systems and Synthetic Biology to Understand and Engineer Microbiomes.Annual review of biomedical engineering · 2021Review
- Metabolic Modelling as a Framework for Metabolomics Data Integration and Analysis.Metabolites · 2020Review
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- Investigating metabolic interactions in a microbial co-culture through integrated modelling and experiments.Computational and structural biotechnology journal · 2020Article
- Common principles and best practices for engineering microbiomes.Nature reviews. Microbiology · 2019Review
- Synthetic microbial consortia for biosynthesis and biodegradation: promises and challenges.Journal of industrial microbiology & biotechnology · 2019Review
- Engineering microbial consortia by division of labor.Microbial cell factories · 2019Review
- Understanding and Engineering Distributed Biochemical Pathways in Microbial Communities.Biochemistry · 2019Review
- The Design of FluxML: A Universal Modeling Language forFrontiers in microbiology · 2019Article
- Microenvironmental regulation of cancer cell metabolism: implications for experimental design and translational studies.Disease models & mechanisms · 2018Review
- Cell-Type Specific Metabolic Flux Analysis: A Challenge for Metabolic Phenotyping and a Potential Solution in Plants.Metabolites · 2017Article
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Authors and funding
8 authors at 2 institutions in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
The study of intracellular metabolic fluxes and inter-species metabolite exchange for microbial communities is of crucial importance to understand and predict their behaviour. The most authoritative method of measuring intracellular fluxes, 13C Metabolic Flux Analysis (13C MFA), uses the labeling pattern obtained from metabolites (typically amino acids) during 13C labeling experiments to derive intracellular fluxes. However, these metabolite labeling patterns cannot easily be obtained for each of the members of the community. Here we propose a new type of 13C MFA that infers fluxes based on peptide labeling, instead of amino acid labeling. The advantage of this method resides in the fact that the peptide sequence can be used to identify the microbial species it originates from and, simultaneously, the peptide labeling can be used to infer intracellular metabolic fluxes. Peptide identity and labeling patterns can be obtained in a high-throughput manner from modern proteomics techniques. We show that, using this method, it is theoretically possible to recover intracellular metabolic fluxes in the same way as through the standard amino acid based 13C MFA, and quantify the amount of information lost as a consequence of using peptides instead of amino acids. We show that by using a relatively small number of peptides we can counter this information loss. We computationally tested this method with a well-characterized simple microbial community consisting of two species.
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