Diurnal and Seasonal Microbiome Fluctuations

Research from this year’s Digestive Disease Week (DDW) offers evidence that the microbiome is more dynamic than originally thought. Both diurnal and seasonal changes have been shown to cause fluctuations in the human gut microbiome, based on the time of day and season the samples were tested. The findings are based on over 20,000 stool samples from an international database and presented by Carolina Dantas Machado, PhD, the study’s lead author and a researcher in the laboratory of Amir Zarrinpar, MD, PhD, at the University of California, San Diego. Machado used data from the American Gut Project, one of the largest databases of microbiome data, to analyze the bacterial makeup of adult stool samples from countries around the world collected mostly between 2013 and 2019. They observed both diurnal and seasonal gut microbiome rhythms at various taxonomic levels. It was previously known that the bacteria that make up the human gut microbiome varies by person based on diet, environment and lifestyle, but it wasn’t shown until recently that the gut environment is highly variable and dynamic.

“The researchers reported that nearly 60% of certain related groups of bacteria had a 24 hour cycle as well as seasonal fluctuations with certain types of bacteria having one or two distinct patterns throughout the year.”

The researchers reported that nearly 60% of certain related groups of bacteria had a 24 hour cycle as well as seasonal fluctuations with certain types of bacteria having one or two distinct patterns throughout the year. Actinobacteria, a common group of bacteria found in the gut, was shown to have lower levels in the morning and higher levels at the end of day. This would make sense considering the gut environment is going to be very different in terms of water availability and pH levels during sleep versus after eating breakfast, mentioned Amir Zarrinpar, PhD, a co-author of the study and principal investigator at the University of California San Diego lab. Additionally, bacteria known as proteobacteria was shown to drop to lower levels in the winter months and increase throughout the year to its highest levels in the summer showing that similar fluctuations in bacterial levels are found seasonally. These findings could also offer a potential explanation why humans are more susceptible to colds and flu during specific months of the year, since the microbiome is known to influence immune response.

“The researchers of the study suggest that light, temperature, humidity and pollen exposure may have an effect on seasonal changes to the microbiome as well.”

Dr. Emeran Mayer echoed a similar sentiment, noting that “diurnal variations in the geometry of the gut microbiome in mice have previously been reported and since profound diurnal variations in the gut microbiome of the Hazda people in Africa have been described. In both cases, the main factor has been diurnal and seasonal variations of food intake,” Mayer told Medical News Today. He also mentioned that seasonal bacterial fluctuation may be due to changing elements of diet such as increased intake of fresh produce in the summertime as well as seasonal mood changes. Diet and sleep are also likely contributing factors to these fluctuations as sleep cycles and mealtimes shift around based on the solar cycle. The researchers of the study suggest that light, temperature, humidity and pollen exposure may have an effect on seasonal changes to the microbiome as well.

“Since the microbiome and immune systems are so interrelated, it’s worth looking further into the connections between the different gut bacterial fluctuations and disease as they may affect clinical decisions.”

Similarly to the microbiome, many diseases show seasonal variation such as allergies, respiratory infections, infectious diarrhea. Since the microbiome and immune systems are so interrelated, it’s worth looking further into the connections between the different gut bacterial fluctuations and disease as they may affect clinical decisions. Bacteria are key players in major functions necessary for overall human health and disease treatment and prevention including metabolizing the food we eat as well as certain drugs, solidifying the importance of understanding microbiome fluctuations for clinical decisions. Even though it’s still too early to base any actionable decisions on this research, it is important to consider these fluctuations when conducting microbiome research.


Juliette Frank is a recent UCLA graduate with a degree in Public Affairs and Food Studies. Her interests include the interrelation between food systems, digestive health, and the environmental impacts of food production. She believes the intersectionality of food has long been overlooked and is the key connection between the health of humans, animals, and the environment. She is passionate about reforming the food system as It is one of the most accurate determinants of the health inequities present in our society, making it one of the most effective places to start in healing the people and the planet from a long history of damage.