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Review
. 2023 Nov 10;24(22):16169.
doi: 10.3390/ijms242216169.

Studying the Human Microbiota: Advances in Understanding the Fundamentals, Origin, and Evolution of Biological Timekeeping

Adam Siebieszuk  1 , Monika Sejbuk  2 , Anna Maria Witkowska  2
Affiliations
Review

Studying the Human Microbiota: Advances in Understanding the Fundamentals, Origin, and Evolution of Biological Timekeeping

Adam Siebieszuk et al. Int J Mol Sci. .

Abstract

The recently observed circadian oscillations of the intestinal microbiota underscore the profound nature of the human-microbiome relationship and its importance for health. Together with the discovery of circadian clocks in non-photosynthetic gut bacteria and circadian rhythms in anucleated cells, these findings have indicated the possibility that virtually all microorganisms may possess functional biological clocks. However, they have also raised many essential questions concerning the fundamentals of biological timekeeping, its evolution, and its origin. This narrative review provides a comprehensive overview of the recent literature in molecular chronobiology, aiming to bring together the latest evidence on the structure and mechanisms driving microbial biological clocks while pointing to potential applications of this knowledge in medicine. Moreover, it discusses the latest hypotheses regarding the evolution of timing mechanisms and describes the functions of peroxiredoxins in cells and their contribution to the cellular clockwork. The diversity of biological clocks among various human-associated microorganisms and the role of transcriptional and post-translational timekeeping mechanisms are also addressed. Finally, recent evidence on metabolic oscillators and host-microbiome communication is presented.

Keywords: TTFL; biological clock; cellular timekeeping; circadian rhythm; evolution; metabolic oscillations; microbiome; peroxiredoxins.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Visual representation of three different models describing the origins of Eukarya. CHIMERA—eukaryotes emerging as an evolutionary combination of bacterial and archaeal characteristics.
Figure 2
Figure 2
Overview of the different types of biological clocks in living organisms.
Figure 3
Figure 3
Visual representation of the diversity of structures, functionalities, and activities of peroxiredoxins under normal and acute oxidative stress conditions. A generalized model of redox relay signaling and the circadian cyclical variation in the abundance of peroxiredoxins is illustrated.
Figure 4
Figure 4
Key factors influencing the evolution of biological clocks: 1. The evolution of early Earth was shaped by constantly alternating periods of light and dark. Sunlight acted as the initial “zeitgeber”. 2. Primordial life forms had to cope and adapt to fluctuating nutrient availability and locally low aerobic conditions. Minimal (but significant) levels of oxidants were created abiotically through various photochemical and nonphotochemical processes.
Figure 5
Figure 5
Key factors influencing the evolution of biological clocks.
Figure 6
Figure 6
The bidirectional relationship between the microbiota and the host.
See this image and copyright information in PMC

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