Measure Catabolism: Real-time shifts in microbial metabolism through online pressure measurements

Abstract

Microbial activity is often inferred from cell density measurements; however, biomass formation is merely an indirect, cumulative result of metabolism, known as anabolism. Microbial activity is more accurately indicated by energy conservation or catabolism. This is especially true under low or no-growth conditions, where anabolism remains constant, and shifts in catabolic fluxes go unnoticed with biomass measurements alone. In anaerobic and gas-based metabolic processes, net gas exchange is linked to energy conservation, and catabolism can then be quantified through headspace measurements. We introduce a sealed-vial, non-invasive workflow that uses high-resolution headspace pressure measurements to estimate gas exchange rates and catabolic reactions, enabling real-time visualisation of metabolic shifts throughout an entire batch cultivation cycle. The method was applied to carbon monoxide (CO) fermentations of three Clostridium autoethanogenum strains (JA1-1, LAbrini, and LAbrini_mut) cultivated in serum bottles. Two of them were indistinguishable by OD-derived max. Pressure-derived gas uptake rates resolved multiple exponential phases of gas consumption and identified specific shifts in the metabolism, consistent with transitions from mixotrophic to autotrophic growth. Small but significant differences in terminal headspace pressure were detected, providing an experimentally accessible end-state parameter for phenotypic characterisation that would be obscured by routine intrusive headspace sampling. Finally, pressure-derived catabolic rates further enabled estimates of relative product formation during the main autotrophic phase. The strains were successfully characterised and distinguished by identifying several exponential phases of gas consumption and their rates, as well as differences in the final absolute pressure threshold. This provided phenotypic characterisation and insights not obtainable from OD measurements alone. The work establishes a practical framework for catabolism-resolved microbial characterisation in sealed batch vials through high-resolution online pressure (gas exchange). The assumption that pressure measurements correlate with CO2 and catabolic rates is sensitive to solubility/buffering and temperature/vapour effects, but these limitations are addressable through controls and complementary analytics.