MEASURING THE METABOLIC ACTIVITY OF THE HUMAN INTESTINAL MICROBIOTA USING STABLE ISOTOPES

ABSTRACT

The human intestinal microbiota is a complex biological system comprising a vast repertoire of microbes with considerable metabolic activity relevant to both bacterial growth and host health. Greater strides have been made in the analysis of microbial diversity than in the measurement of functional activity, particularly in vivo. Stable isotope probing offers a new approach by coupling measurements of metabolic activity with microbial identification. Using a low-enrichment labelling strategy in vitro, this study has identified metabolically-active bacterial groups using magnetic bead capture methodology and stable isotope ratio analysis. Using five probes (EUB338, Bac303, Bif164, EREC482 and Clep866), changes in the activities of key intestinal microbial groups were successfully measured by expoliting tracers of de novo RNA synthesis. Perturbation of the nutrient source with oligofructose generated changes in activity of bifidobacteria as expected, but also in the Bacteroides-Prevotella-group, Eubacterium rectale-Clostridium coccoides-group and the Clostridium leptum-subgroup. Changes in activity were also observed in response to media type. This study suggests that changes in the functional activity of the gut microbiota can be assessed using tracers of de novo nucleic acid synthesis combined with measurement of low isotopic enrichment in 16S rRNA. Such tracers potentially limit substrate bias because they are universally available to bacteria. This low enrichment labelling approach does not depend on the commercial availability of specific labelled substrates and can be more easily translated to in vivo probing experiments of the functional activity of the microbiota in the human gut.