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

• “Conditions of dysbiosis have been linked to circadian rhythm disruption, metabolic alterations, and release of neurotoxic products, all contributing to neurodegeneration.” [2023]
• “the gut microbiota can influence the host circadian rhythm by a variety of mechanisms including through interacting with the host immune system. The intricate and complex relationship between the microbiota and their host makes it challenging to disentangle host behaviors from bacterial circadian rhythms and clock mechanisms that might govern the daily oscillations observed in these microbial populations.” [2023]
• Homeostatic crosstalk among gut microbiome, hypothalamic and hepatic circadian clock oscillations, immunity and metabolism in response to different light-dark cycles: A multiomics study [2023]
• A ketogenic diet containing medium-chain triglycerides reduces REM sleep duration without significant influence on mouse circadian phenotypes [2023]
• “Misalignment of the clock can cause obesity, which is accompanied by reduced levels of the clock-controlled, rhythmic metabolite NAD⁺. Increasing NAD⁺ is becoming a therapy for metabolic dysfunction; however, the impact of daily NAD⁺ fluctuations remains unknown.” [2023]
• Circadian orchestration of host and gut microbiota in infection [2022]
• Crosstalk between circadian rhythms and the microbiota [2020]
• Gut microbiota as a transducer of dietary cues to regulate host circadian rhythms and metabolism [2021]
• Circadian rhythms and the gut microbiome synchronize the host’s metabolic response to diet [2021]
• Circadian Rhythms and Their Influence on Gastrointestinal and Hepatic Illnesses [2021]
• Circadian rhythms and the gut microbiota: from the metabolic syndrome to cancer [2020]
• Rhythmicity of the intestinal microbiota is regulated by gender and the host circadian clock [2015]
• Intersection of the Gut Microbiome and Circadian Rhythms in Metabolism [2020]

A few factoids from the above

Microbial deconjugation of bile salts	Unconjugated bile acids regulate the amplitude and periodicity of circadian gene expression in the ileum, colon, and liver
High-fat diet	Impaired central and hepatic circadian clock gene expression Dampened circadian oscillations of gut microbiota Altered microbial diversity
Time-restricted feeding	Increased 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 humans	Enhanced 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).