The ticktock of your gut microbiome

We all have an internal “master clock” that maintains a 24-hour rhythm. 

These so-called circadian rhythms drive many of the processes in your body, from hormone levels to energy levels and from sleep to hunger.

Virtually all multicellular lifeforms — including plants, fungi, insects, and mammals — have these daily rhythms.

But do bacteria have circadian rhythms, and does our gut microbiome follow circadian cycles? In this article, we’ll find out.

Circadian rhythms in bacteria

For many years, scientists assumed that bacteria wouldn’t follow circadian rhythms. 

Bacteria tend to live their entire life in less than 24 hours. So, experts presumed there would be little point in following a 24-hour clock if they were going to die before the first cycle ended. Which is a fair point.

However, in the 1980s, things changed. Much to everyone’s surprise, scientists found that communities of certain types of bacteria — cyanobacteria — do indeed have circadian rhythms.

These bacteria are photosynthetic, so they rely on sunlight to survive. Other bacteria — like most of those in your gut — would die if they were exposed to oxygen, so they live their lives without light.

So, are cyanobacteria the exception to the rule?

Scientists now think that some non-photosynthetic bacteria might also follow circadian rhythms. 

But at this stage, it’s not clear whether these bacteria can generate their own independent circadian rhythm. In other words, we don’t know if they have a master clock that runs on a 24-hour cycle.

So, does the gut microbiome have a circadian rhythm? Although each individual bacterium might only live for a few hours, the community of microbes in the gut persists for years.

And it’s becoming increasingly clear that your gut microbiome does follow a 24-hour cycle.

Your microbial gut clock

In your gut, there are trillions of bacteria, which are collectively called the gut microbiome. 

There’s growing evidence that gut bacteria are important for health. Consequently, scientists are spending a lot of time figuring out what they’re up to in there.

And some scientists are interested in how the gut microbiome changes across the day. Recent evidence suggests that it fluctuates in a 24-hour cycle. 

While one species of bacteria might be more abundant in the morning, another might be more numerous in the evening.

One study in mice, for instance, found that numbers of more than half of the gut bacteria species fluctuated in a 24-hour rhythm. 

They also showed that in humans, around 10% of species fluctuated in a daily rhythm.

So, everyone has a unique gut microbiome with hundreds of species present in varying amounts, and that unique microbiome may be significantly different at different times of the day.

What genes tell us

In the same study, the researchers looked at how bacterial genes ebbed and flowed across the day.

This is important because it gives us an idea of what the bacteria are doing at any given time. 

In mice, the researchers found that genes responsible for energy metabolism, DNA repair, and cell growth tended to be more active at night.

And during the day, genes involved in detoxification, movement, and sensing their environment were more abundant.

In humans, this was flipped on its head: Energy metabolism and protein production were more common during the day, and detoxification pathways were more active at night. 

This is probably because mice tend to be active at night, whereas humans are more active during the day.

These findings suggest that the gut microbiome might carry out different functions during different parts of the day.

How do bacteria follow our body clock?

If bacteria can’t maintain their own circadian rhythm, how do they follow ours?

Scientists are still trying to work this out. One theory is that some bacteria are sensitive to melatonin.

Melatonin is a hormone that’s most famous for its role in promoting sleep. Levels rise and fall across the day under the control of our body clock, and some is released into your gut. 

One study showed that at least one species of gut bacteria — Enterobacter aerogenes — is sensitive to melatonin. 

The authors found that the hormone promoted swarming behavior, where the bacteria move together in large groups.

Although melatonin may play a part in syncing bacteria to our body clock, experts believe our regular meal times might also help “train” our gut microbiome. 

For instance, one study found that when mice became obese, they lost much of the rhythmic changes in their gut bacteria. But when the researchers put the mice on a time-restricted eating plan, these rhythms partly returned.

Another study, led by scientists in Israel, backed this up. 

Among other findings, the researchers showed that feeding rhythms influence daily rhythms in the gut microbiome. 

They also found that when they destroyed the master clock in the animals’ brains, fluctuations in gut bacteria lost their rhythmic pattern. This suggests that bacteria’s regular cycles depend on their hosts’ cycles.

This particular study also helps us understand why these fluctuations might be important for health, as we’ll see below.

Does it matter?

As part of the Israeli research, the scientists investigated whether circadian disruptions might interfere with gut bacteria. 

To do this, they induced jet lag in human volunteers, putting their circadian rhythms out of sync. Then, they sampled their poop.

Next, they took the stool samples and transplanted them into germ-free mice. These are animals with no gut microbiome. 

The researchers showed that after the transplant, the mice developed poorer blood sugar responses and were more prone to weight gain.

The scientists also noted that when human participants were in a jet-lagged state, they had more Firmicutes

These bacteria, as the authors explain, “have been associated with a higher propensity for obesity and metabolic disease.”

Once the participants had recovered from jet lag, numbers of Firmicutes returned to normal.

This suggests that changes in human circadian rhythms can upset the balance of the microbiome and influence metabolic health. 

More research is needed, but this might be part of the reason why shift workers have a higher risk of type 2 diabetes than people who work the day shift.

And scientists have already noted links between the gut microbiome and diabetes. 

Some researchers are now investigating whether circadian fluctuations in bacteria matter for diabetes risk.

For instance, research on almost 2,000 people in Germany found that 13 species of bacteria with disrupted 24-hour rhythms were linked to type 2 diabetes. 

This work certainly doesn’t show that disrupting gut bacteria’s daily rhythms causes type 2 diabetes, but it suggests that gut microbiome fluctuations might play a role in metabolic health.

More to come

Modern life makes it more difficult for our circadian rhythms to keep a firm footing — we stay up long after the sun goes down, and we might eat at irregular times.

And it now seems likely that if our circadian rhythms are out of whack, our gut microbes’ cycles might be, too.

But at this stage, we don’t know how the ebb and flow of our gut bugs impact health.

Additionally, your gut microbiome isn’t just bacteria. There are viruses, fungi, archaea, and more. Do these organisms follow rhythms, too? And does it matter?

To get to grips with our gut microbiome's clock, scientists need to carry out much more research, especially in humans.

Only time will tell.


Arrhythmic gut microbiome signatures predict risk of type 2 diabetes. Cell Host & Microbe. (2020).

Circadian rhythms in rapidly dividing cyanobacteria. Science. (1997). 

Diet and feeding pattern affect the diurnal dynamics of the gut microbiome. Cell Metabolism. (2014). 

Evidence of circadian rhythms in non-photosynthetic bacteria? Journal of Circadian Rhythms. (2010). 

Human gut bacteria are sensitive to melatonin and express endogenous circadian rhythmicity. PLOS One (2016). 

Microbiome and diabetes: Where are we now? Diabetes Research & Clinical Practice. (2018). 

Night shift work, genetic risk, and type 2 diabetes in the UK Biobank. Diabetes Care. (2018). 

Transkingdom Control of Microbiota Diurnal Oscillations Promotes Metabolic Homeostasis. Cell. (2014).