The Microbiome Circadian Rhythms

This is different than the body’s Circadian Rhythms. My experience is that it depends on the probiotic — some probiotics taken at bed time will drop me into deep sleep within 10 minutes; other probiotics taken at the same time will keep me wide wake until 3am in the morning — bummer. Why, the probiotic produces enzymes which interacts with the body and the mind. The enzymes vary between probiotics.

This posts reviews some of the literature and attempts to improve mine, and hopefully yours, understanding of the Circadian Rhythm of bacteria with it’s impact on when certain supplements and probiotics should be taken during the day.

There exists a bidirectional circadian interaction between the host and its gut microbiota, and potential circadian orchestration of both host and gut microbiota in response to invading pathogens. In this review, we summarize what is known about these intestinal microbial oscillations and the relationships between host circadian clocks and various infectious agents (bacteria, fungi, parasites, and viruses), and discuss how host circadian clocks prime the immune system to fight pathogen infections as well as the direct effects of circadian clocks on viral activity 

Circadian orchestration of host and gut microbiota in infection [2022]

This may account for items like night-sweats, for example, my sleeping body temperature is much higher than my usual daytime temperature.

The Literature

A few factoids from the above

Microbial deconjugation of bile saltsUnconjugated bile acids regulate the amplitude and periodicity of circadian gene expression in the ileum, colon, and liver
High-fat dietImpaired central and hepatic circadian clock gene expression
Dampened circadian oscillations of gut microbiota
Altered microbial diversity
Time-restricted feedingIncreased gut microbial diversity
Reduced total cholesterol and triglyceride levels
Altered light-dark cycle and mutation of the Clock gene [Bmal1]Microbiota dysbiosis: increase in proinflammatory bacteria and decrease in anti-inflammatory bacteria
Causes dysbiosis 
Germ-free mice receiving stool from jet-lagged humansEnhanced weight gain -Higher blood glucose levels after oral glucose challenge

Some Basic Visuals

The following illustrate the difference between day time and night time. “The endogenous clock anticipates the daily fluctuation in the risk of infection inducing a stronger immune response at the beginning of the active phase of the  light/dark cycle“. One common immune response is histamine / mast cells. This is seen in this study The Circadian Clock Drives Mast Cell Functions in Allergic Reactions [2018] which states: Allergic conditions such as asthma or allergic rhinitis have historically shown circadian bias as the severity of symptoms is exacerbated between midnight and morning time and exhibits prominent 24-h variation.

Needless to day (I hope needless), microbiome samples should be taken at the same time of day and preferable on the same day of the week (since shifts between a work day and a day of rest could be significant).