What does too little sleep do to your gut?

Sleep deprivation may throw the balance of your gut microbiome out of kilter, but how large that effect is in humans remains uncertain. Several review studies conclude that insufficient sleep can disrupt the ratio of bacterial species in your gut. In animal research this effect was clearly visible: rats that slept too little lost some of the richness of bacterial species in their gut. In humans the picture is different: in one controlled study in which sleep was deliberately restricted, the composition of the gut microbiome did not change in any measurable way. That contradiction makes firm statements difficult.

One possible intermediate step is your body's stress system. Sleep deprivation activates that system, and that heightened stress response could disrupt the gut environment. At present this is still a hypothesis drawn from review literature, not a demonstrated mechanism in humans.

What may play a role over the longer term: a disrupted gut microbiome caused by sleep deprivation has been linked to a higher risk of overweight, diabetes and low-grade inflammation. In humans, a positive association has been found between the diversity of gut bacteria and an inflammatory protein involved in immune responses. But here too we are talking about associations, not a proven cause-and-effect chain.

The relationship also works in the other direction. A varied gut microbiome is associated with better sleep quality: people with greater diversity of gut bacteria slept more efficiently and for longer. Probiotics appear in some studies to improve sleep, although that evidence is still limited and small in scale.

Finally: in rat studies, sleep deprivation during pregnancy led in the offspring to a disrupted gut microbiome and higher levels of inflammatory proteins in the brain at adult age. Whether this also applies to humans is unknown; these are exclusively animal data.