Journal: Cell

Article Title: Quantifying the varying harvest of fermentation products from the human gut microbiota

doi: 10.1016/j.cell.2025.07.005

Figure Lengend Snippet: (A) Major fermentation pathways that promote energy synthesis (ATP) and ensure redox balance during anaerobic growth. Colored circles indicate the number of carbon atoms in the corresponding molecules (details on metabolism with full stoichiometry in , ). (B) Experimental setup to determine nutrient uptake and fermentation product release. Samples taken at multiple time points throughout steady exponential growth (Bi) were analyzed for metabolite concentration using HPLC (Bii). With this data, we calculated linear concentration trends with bacterial density (Biii) to quantify per biomass uptake and excretion. Further details in . (C) Taxonomic classification of the 22 gut microbiota species characterized. Numbers indicate in percentage the typical fraction of bacterial biomass these species and their taxonomic groups represent in healthy individuals (samples from Schirmer et al. and Integrative Human Microbiome Project [iHMP] Research Network Consortium ). (D and E) Per biomass glucose/maltose uptake and fermentation product excretion for growth in YCA medium. Error bars denote SD of three biological replicates for sugar uptake and total fermentation product secretion, respectively. Dashed lines indicate averages of all measured species. (F) Balance of carbon content in taken-up carbohydrates and excreted fermentation products. Mismatched carbon balances for E. coli , R. bromii , and F. saccharivorans likely reflect the utilization of other media components as carbon sources; for B. hydrogenotrophica , the imbalance is likely due to acetogenesis. For E. siraeum , carbohydrate uptake is higher than the range shown (27.3 mmol maltose/g, stars in D and E). (G) Species averaged uptake and excretion rates in different media (YCA, BHIS, ϵ , γ ). Error bars denote SD of species-to-species variation. (H) Dependence of fermentation product excretion and carbohydrate uptake on pH. Changes for shifts in pH by 1 unit are based on linear regressions of measured values ( and ). Range of the horizontal axes was chosen to reflect the average uptake and excretion ranges determined in (D) and (E). See also , , and .

Article Snippet: Eubacterium siraeum , DSMZ , DSM 15702.

Techniques: Concentration Assay