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Microbiome Diurnal Rhythmicity and Its Impact on Host Physiology and Disease Risk


Microbiome Diurnal Rhythmicity and Its Impact on Host Physiology and Disease Risk

Samuel Philip Nobs et al. EMBO Rep.


Host-microbiome interactions constitute key determinants of host physiology, while their dysregulation is implicated in a wide range of human diseases. The microbiome undergoes diurnal variation in composition and function, and this in turn drives oscillations in host gene expression and functions. In this review, we discuss the newest developments in understanding circadian host-microbiome interplays, and how they may be relevant in health and disease contexts. We summarize the molecular mechanisms by which the microbiome influences host function in a diurnal manner, and inversely describe how the host orchestrates circadian rhythmicity of the microbiome. Furthermore, we highlight the future perspectives and challenges in studying this new and exciting facet of host-microbiome interactions. Finally, we illustrate how the elucidation of the microbiome chronobiology may pave the way for novel therapeutic approaches.

Keywords: circadian; diurnal; microbiome; rhythm.

Conflict of interest statement

EE is a paid consultant at DayTwo and BiomX. None of the work reviewed here is related to these or any other commercial entity.


Figure 1
Figure 1. The two‐tier hierarchical structure of mammalian circadian clocks
The gut microbiome undergoes diurnal changes in composition and function that are entrained by feeding rhythms. In turn, microbiome circadian fluctuations of the microbiome modulate circadian activity of peripheral mammalian clocks, both locally (right), through mucosal attachment, and systemically (left), through the production of metabolites.
Figure 2
Figure 2. Disruption of the circadian clock as a hallmark of modern lifestyle
Disruption of circadian microbiome fluctuations results in the establishment of an arrhythmic dysbiotic microbiome state, promoting the development or progression of several diseases, including metabolic syndrome, infections, and cancer.
Figure 3
Figure 3. Time constitutes an underappreciated but important dimension of host–microbiome interactions
A plethora of factors involving bacterial species, bacterial metabolites, and specific bacterial behaviors have been shown to affect host physiology, and at the same time, many of them have been demonstrated to exhibit circadian oscillations. Thus, the intersection of classical microbiome studies and temporal biology holds great potential for future investigation.

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