A Pilot Characterization of the Human Chronobiome
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Updated: Feb 17, 2026
Human Circadian Phenotyping and Diurnal Performance Testing in the Real World
Published on: April 7, 2020
Carsten Skarke1,2,3, Nicholas F Lahens4,5, Seth D Rhoades4
1Department of Systems Pharmacology and Translational Therapeutics, at the University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA. cskarke@pennmedicine.upenn.edu.
Abstract:
Physiological function, disease expression and drug effects vary by time-of-day. Clock disruption in mice results in cardio-metabolic, immunological and neurological dysfunction; circadian misalignment using forced desynchrony increases cardiovascular risk factors in humans. Here we integrated data from remote sensors, physiological and multi-omics analyses to assess the feasibility of detecting time dependent signals - the chronobiome - despite the "noise" attributable to the behavioral differences of free-living human volunteers. The majority (62%) of sensor readouts showed time-specific variability including the expected variation in blood pressure, heart rate, and cortisol. While variance in the multi-omics is dominated by inter-individual differences, temporal patterns are evident in the metabolome (5.4% in plasma, 5.6% in saliva) and in several genera of the oral microbiome. This demonstrates, despite a small sample size and limited sampling, the feasibility of characterizing at scale the human chronobiome "in the wild". Such reference data at scale are a prerequisite to detect and mechanistically interpret discordant data derived from patients with temporal patterns of disease expression, to develop time-specific therapeutic strategies and to refine existing treatments.
Insights
This study shows that the human chronobiome, or daily biological rhythms, can be detected in free-living individuals using various sensors and multi-omics. This research paves the way for personalized, time-specific medical treatments.
Area of Science:
- Chronobiology
- Human Physiology
- Microbiome Research
Background:
- Physiological functions, disease progression, and drug responses exhibit daily variations.
- Disruptions in circadian rhythms are linked to metabolic, immune, and neurological disorders, and increased cardiovascular risk.
Purpose of the Study:
- To assess the feasibility of detecting time-dependent signals (the chronobiome) in free-living humans amidst behavioral variability.
- To establish a scalable method for characterizing the human chronobiome in real-world settings.
Main Methods:
- Integration of data from remote sensors, physiological measurements, and multi-omics analyses (metabolome, oral microbiome).
- Analysis of temporal patterns in sensor readouts and biological samples from human volunteers.
Main Results:
- 62% of sensor data demonstrated time-specific variability, including blood pressure, heart rate, and cortisol levels.
- Temporal patterns were identified in the plasma (5.4%) and saliva (5.6%) metabolome, and in specific oral microbiome genera.
- Despite small sample size, the study confirms the feasibility of large-scale human chronobiome characterization.
Conclusions:
- The human chronobiome can be characterized "in the wild" using integrated data streams.
- This foundational data is crucial for identifying disease patterns, developing time-specific therapies, and optimizing treatments.
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