Gut Bacteria and Insomnia: A Two-Way Street?

Insomnia is one of the most common sleep issues worldwide, affecting millions of people each year. While stress, hormones, and lifestyle are well-recognized factors, research is now exploring another possible player: your gut bacteria.

A study published in General Psychiatry (August 2025) examined whether specific gut bacteria might increase—or decrease—the risk of insomnia. The results are fascinating but raise as many questions as they answer.

What Did the Study Find?

• Researchers identified 41 bacterial groups linked to insomnia.

• 14 bacterial groups were associated with a higher risk of insomnia.

• 8 bacterial groups were linked to a lower risk.

• People with insomnia also had reduced levels of some gut bacteria and elevated levels of others.

• Importantly, the connection seems bidirectional: gut bacteria may affect sleep, but insomnia may also shift the gut microbiome.

Cause or Correlation?

The researchers used a method called Mendelian randomization, which aims to strengthen causal inferences from genetic and microbiome data. They suggested some bacterial groups may causally influence insomnia risk.

However, outside experts remain cautious. Stress, diet, and lifestyle can influence both the gut and sleep. As Dr. Charlene Gamaldo of Johns Hopkins noted, stress alone can shift gut bacteria and is also a major insomnia trigger. This raises the possibility that gut and sleep changes are driven by shared upstream factors rather than one directly causing the other.

Why This Matters for You

Even if the science isn’t fully settled, your gut microbiome is dynamic—it changes with what you eat, your stress levels, and your health status. This means it’s a modifiable target for improving sleep and overall wellbeing.

When working with a naturopathic doctor, several tests can help make the gut–sleep connection more personal:

 Functional Tests

• GI-MAP stool test – measures gut bacteria balance, pathogens, and inflammation.

• OAT (Organic Acids Test) – assesses metabolic byproducts that reflect gut microbiome activity, nutrient status, and detox capacity.

• NutraVal – a comprehensive panel combining organic acids, amino acids, fatty acids, and oxidative stress markers to highlight nutrient and biochemical imbalances.

• DUTCH test – evaluates cortisol rhythms, melatonin, sex hormones, and metabolites. Since hormones strongly regulate sleep–wake cycles, this test adds another dimension to understanding insomnia.

 Conventional Serum Labs: Although less specific, basic bloodwork provides context and a “whole-body terrain” view:

• CBC (Complete Blood Count) – screens for anemia, immune health.

• CRP & ESR – markers of inflammation that may impact sleep.

• eGFR & liver enzymes – assess detox and clearance capacity.

• Lipids & glucose challenge – reflect cardiometabolic health, often linked to poor sleep.

Together, these tests create a comprehensive picture: functional labs zoom in on the microbiome, hormones, and metabolism, while serum labs provide a wider lens on the terrain in which your gut and nervous system operate.

The Bottom Line

It’s too early to say that gut bacteria cause insomnia. But the evidence is growing that your microbiome, hormones, and overall systemic health are deeply interconnected.

By combining gut-focused testing (GI-MAP, OAT), nutrient and metabolic testing (NutraVal), hormone mapping (DUTCH), and foundational serum labs, you can better understand how your body’s systems interact—and where to intervene.

If you’re struggling with sleep, exploring your gut, hormones, and systemic health together may open the door to more restorative rest.

References

1. Shi, S. et al. General Psychiatry, August 12, 2025.

2. Patrice Wendling. “Specific Gut Bacteria Linked to Insomnia.” Medscape Medical News, August 15, 2025.

3. Gamaldo, C., Johns Hopkins Center for Sleep and Wellness – Commentary, 2025.

4. Saito, J., American Academy of Sleep Medicine – Commentary, 2025.