Metabolic reconstitution of germ-free mice by a gnotobiotic microbiota varies over the circadian cycle

Introduction

The gut microbiota is currently considered a key regulator of host energy metabolism [1]. In the absence of a microbiota, mice accumulated less fat [2] and were protected from obesity induced by certain types of high-fat diets [3–5]. Several mechanisms have been proposed to explain this phenomenon and its relationship to metabolic imbalances [6]. These include endocrine regulation of food intake [7,8], additional energy liberated by the microbiota from dietary fibers [9], alterations in bile acid profiles [10,11], inflammatory responses induced by some members of the microbiota [12], and induction of thermogenesis in adipose tissue [13–15]. However, given the complexity of a complete microbiota and its interactions with the host, validating any of these theories and identifying causal relationships remains a major experimental challenge [16,17].

Gnotobiotic mice, colonized with a simplified microbiota made up of defined species, have become a major tool to identify potential mechanisms of interaction between the microbiota and host [18–20]. Such approaches can generate a mechanistic understanding of how external factors (i.e., diet, infection) act on the different microbiota members individually and at a community level [21,22]. A widely used example, the OligoMM12, is a gnotobiotic consortium of 12 cultivable mouse-derived strains representing the major 5 bacterial phyla in the murine gut [23]. It is reproducible between facilities [24] and extensive data now exist on the metabolism of individual species and their metabolic interactions with each other [25–28]. Understanding how and to what extent, this gnotobiotic microbiota reconstitutes the metabolic phenotype of conventional mice is therefore of broad relevance for microbiota research.

Circadian variations in microbiota function adds an extra layer of complexity to metabolic interactions between the host and the microbiota. Circadian feeding is a major driver of microbiota composition [29,30]. The luminal concentration of fermentation products such as short-chain fatty acids (SCFAs) shows a dramatic circadian oscillation linked both to food intake and to intestinal motility [31]. Microbiota-derived molecules are known to influence host nutrient absorption [32] and host metabolic gene expression [33,34]. However, much of our current knowledge is derived from indirect calorimetry measurements made over a time period shorter than 24 h [2,3,35,36]. Measurements of the same host–microbiota system, if taken at different time points in the circadian cycle of metabolism, could therefore be wrongly interpreted...