The Microbiome and Sleep: Can the Gut Microbiome Help with Chronic Insomnia?

Sleep disorders affect many people and can take a heavy toll on daily life. A common form is chronic insomnia: persistent difficulty falling asleep or staying asleep. Sleep aids can help in the short term, but they rarely resolve the underlying sleep problems.

Their long-term use is limited due to the development of tolerance, risks of dependence, and possible cognitive side effects. Cognitive behavioral therapy is the first-line treatment for chronic insomnia. However, not everyone responds well to it, and it is not readily available everywhere. Therefore, the question remains as to what other options are available to help people with chronic insomnia.

The exact nature of the relationship between the microbiome and sleep remains unclear. A human study investigated this question.

What was done?

A total of 80 people with chronic insomnia were randomly assigned to either a treatment group or a control group. The 40 people in the treatment group first received a two-day course of antibiotic therapy. After a two-day break, they underwent a fecal microbiota transplant (FMT). For this, they took 60 capsules containing gut microbiota from healthy donors without sleep disorders. After two weeks, they took another 20 capsules. In addition, half of the treatment group and half of the control group each received a synbiotic containing the two bacterial species Lactobacillus helveticus and Bifidobacterium longum, as well as 3 grams of inulin per day, for six weeks.

Before the start of treatment and approximately one month after its completion, sleep was objectively assessed using polysomnography in both groups. This comprehensive examination in a sleep laboratory records various bodily functions during sleep and measures, among other things, sleep efficiency and nighttime wake times. In addition, participants completed questionnaires regarding their subjectively perceived sleep quality before the start of the study and at 1, 2, 3, and 6 months.

What was the outcome?

Overall, the objectively measured sleep parameters improved more significantly in the group that received the FMT-based treatment protocol than in the control group.

After one month, polysomnography revealed higher sleep efficiency and less time spent awake after falling asleep in the treatment group compared to the control group. Surprisingly, however, the questionnaires at that point showed no clear difference between the groups, as both groups subjectively rated their sleep problems as having improved. This underscores the importance of a placebo control group: the expectation of sleeping better as a result of participating in the study may have influenced the subjective assessment.

However, after 2, 3, and 6 months, the group that had received an FMT rated their sleep quality higher in the questionnaires than the control group. After half a year, however, the difference between the groups was smaller than in the preceding months. This could indicate a waning effect. Since the polysomnography was repeated only after one month, it is not possible to say whether the objective sleep measures also deteriorated again later on.

Interestingly, not all participants in the treatment group responded to the same degree. A total of 14 out of 38 participants were classified as responders because their objectively measured sleep efficiency had improved by at least 20%.

The additional administration of the synbiotic showed no clear additional effect on sleep efficiency.

What do the results mean for medicine?

In the field of microbiome and sleep research, the results provide initial clinical evidence that an FMT-based treatment protocol, preceded by antibiotic therapy, may improve sleep quality in patients with chronic insomnia.

There may be several reasons why not all individuals responded to the same degree. One possible explanation is that the transplanted gut microbiota may establish itself more effectively in some individuals than in others. However, the researchers were unable to demonstrate that the microbiome of the responders changed more significantly or in a more targeted manner after treatment than that of the non-responders. Nevertheless, it is conceivable that the original microbiome influences how well a person responds to treatment. It is also possible, however, that chronic insomnia has different causes in different individuals and that a microbiome-based approach therefore cannot help everyone equally.

After six months, the difference in subjectively perceived sleep quality was still noticeable, but smaller than after 2 and 3 months. One possible explanation could be that the transplanted gut microbiota could not be sustained long-term without suitable living conditions . However, this is merely speculation, as the study did not examine either lifestyle habits or the microbiome after six months.

The study therefore provides an important initial indication. However, further studies are needed to determine whether FMT-based approaches can be used safely and effectively to treat chronic insomnia.

The Microbiome and Sleep: What Does This Mean for Everyday Life?

An intriguing question is whether a microbiome-friendly lifestyle can help people sleep better. However, the study does not directly answer this question. The study examined people diagnosed with chronic insomnia who received intensive treatment consisting of antibiotic pretreatment and FMT. This is a significant medical intervention affecting the gut microbiome and is not comparable to changes in diet or exercise in everyday life.
Synbiotics showed no effect in this study. However, this does not mean that they have no influence on sleep in general:

Only this specific combination was tested over a limited period of time and without any additional lifestyle interventions. Further studies are needed to determine whether diet, exercise, and other habits can influence sleep quality through the microbiome.

What do we learn from this?

The study provides new evidence of a link between the microbiome and sleep. The gut microbiome may play a significant role in sleep quality in cases of chronic insomnia. The exact mechanism behind this and the extent to which we can influence it have not yet been fully elucidated.
Given the importance of sleep for our health, however, it already makes sense today to adopt a lifestyle that also supports the microbiome, as the study provides initial evidence of a link between the gut microbiome and sleep quality.

Source:

Gao T, Liu X, Mi W, et al. Fecal microbiota transplantation-based treatment protocol for chronic insomnia: A randomized, double-blind, placebo-controlled trial. J Intern Med. Published online July 22, 2026. https://doi.org/10.1111/joim.70137