CHICAGO—Up to 45% of the species in the microbiome show substantial diurnal, seasonal and regional variations in gut microbiota at the population level, according to a global analysis presented at Digestive Disease Week 2023.

Diurnal variations in the gut microbiome already have been demonstrated at the level of individual patients, but this is the first large study of globally collected samples, and the results were to some degree unexpected, according to the senior author Amir Zarrinpar, MD, PhD, an assistant professor and researcher in the Division of Gastroenterology and Hepatology at the University of California, San Diego.

“The oscillations we identified demonstrate that the gut microbiome is very dynamic on a population basis,” Dr. Zarrinpar said. 

Of nearly 20,000 human stool samples obtained from the American Gut Project (AGP), the world’s largest repository, 18,219 met the study criteria for analysis, including a time stamp for the hour of the day and the day of year when the sample was collected, according to Ana Carolina Dantas Machado, PhD, a researcher working on Dr. Zarrinpar’s lab, who reported the findings at the meeting (abstract 395).

The samples were provided by centers in multiple countries from 2013 through 2019. No more than 10 samples were obtained from any one patient. The samples were evaluated with a technique called cosinor-based rhythmometry, a method to look for patterns in non-stationary data that is well suited to look for changes over short or long time periods.

On the basis of this analysis, “both diurnal and seasonal gut microbiome rhythms were present in the AGP dataset,” Dr. Machado reported. Overall, 57% of phyla evaluated in the stool displayed diurnal cycling. Even after controlling for several variables, specific patterns of diurnal cycling were detected in more than 30% of organisms. For example, populations of Acinetobacter species on a population basis peaked in the evening whereas populations of Synergistes peaked in the morning. 

Seasonal patterns overall were region-specific, with some regional differences in gut microbiome fluctuations being independent of season.

For attempting to understand microbiome composition in the context of disease, the population-based fluctuations “have large implications,” said Dr. Zarrinpar. In addition to the effort to connect dysbiosis to risk of specific diseases, these fluctuations might explain susceptibility to seasonal diseases, such as upper respiratory infections or allergies.

This “new information is important,” agreed Gary D. Wu, MD, a professor of gastroenterology at the University of Pennsylvania, in Philadelphia. Dr. Wu said the strengths of this study include the sample size and the value of evidence showing daily and seasonal gut microbiome fluctuations at a population level. He said that while diurnal and seasonal variations are likely an important part of the puzzle in understanding the gut microbiome, “It is very plausible that significant factors that influence the gut microbiome at an individual level will have a greater effect than the influence of diurnal or seasonal variations, but this will require further investigation.”

—Ted Bosworth

Dr. Dantas Machado reported no relevant financial relationships. Dr. Wu reported financial relationships with AbbVie, Biocodex, Danone, Intercept and Nestle. Dr. Zarrinpar reported a financial relationship with Endure Biotherapeutics.