{"doi":"10.1101/2022.06.13.495811","title":"Elucidating dynamic anaerobe metabolism with Live Cell HRMAS <sup>13</sup> C NMR and genome-scale metabolic modeling","abstract":"Abstract Anaerobic microbial metabolism drives critical functions within global ecosystems, host-microbiota interactions, and industrial applications, yet remains ill-defined. Here we advance versatile approaches to elaborate dynamic metabolism in living cells of obligate anaerobes, using the pathogen Clostridioides difficile , an amino acid and carbohydrate-fermenting Clostridia . High-Resolution Magic Angle Spinning (HRMAS) Nuclear Magnetic Resonance (NMR) spectroscopy of C. difficile grown with uniformly labeled 13 C substrates informed dynamic flux balance analysis (dFBA) of the pathogen’s genome-scale metabolism. Predictions identified metabolic integration of glycolytic and amino acid fermentation pathways at alanine’s biosynthesis, to support efficient energy generation, maintenance of redox balance, nitrogen handling, and biomass generation. Model predictions advanced an approach using the sensitivity of 13 C NMR spectroscopy to simultaneously track cellular carbon and nitrogen flow, from [U- 13 C]glucose and [ 15 N] leucine, confirming the formation of [ 13 C, 15 N]alanine. We illustrate experimental and computational approaches to elaborate complex anaerobic metabolism for diverse applications.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2022,"id":303585,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":1,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9462,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2022-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":558633,"name":"Brintha P. Girinathan","orcid":"0000-0003-4920-0014","position":1,"is_corresponding":false},{"id":558634,"name":"Johann Peltier","orcid":"0000-0003-3207-9465","position":2,"is_corresponding":false},{"id":996042,"name":"Pamela Altamirano Silva","orcid":null,"position":3,"is_corresponding":false},{"id":558640,"name":"Bruno Dupuy","orcid":"0000-0001-7176-8453","position":4,"is_corresponding":false},{"id":912443,"name":"Isabella H. Muti","orcid":"0000-0002-5216-2306","position":5,"is_corresponding":false},{"id":240339,"name":"Craig R. Malloy","orcid":"0000-0001-5077-0642","position":6,"is_corresponding":false},{"id":580249,"name":"Leo L. Cheng","orcid":"0000-0001-5975-5406","position":7,"is_corresponding":false},{"id":298482,"name":"Lynn Bry","orcid":"0000-0002-8792-8527","position":8,"is_corresponding":false},{"id":863132,"name":"Aidan Pavao","orcid":"0000-0002-7516-6633","position":0,"is_corresponding":true}],"reference_count":46,"raw_metadata":null,"created_at":"2026-07-19T00:32:24.307938Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}