“To see an individual… as really an entire world in their own right… is a beautiful and wonderful idea.” — Ed Yong
What if your experiences with cannabis isn’t just in your brain—but in your gut?
The idea sounds absurd at first. But when you consider the trillions of bacteria, viruses (including phages), fungi, and other microorganisms living inside your body—collectively known as the microbiome—it begins to make a strange kind of sense. These microbes help digest your food, regulate inflammation, shape your immune system, and even tweak your mood. The gut sends more information to your brain, then any other organ, via the vagal nerve. And they may be talking to your endocannabinoid system (ECS)—the same network of receptors targeted by cannabis.
A 2025 review article by May Soe Thu, PhD, and colleagues, published in Biomedicine & Pharmacotherapy, dives into this very intersection, exploring how cannabinoids and gut bacteria influence each other in the context of health and disease. When paired with the perspective of science writer Ed Yong, who has long chronicled the rise of microbiome science, the emerging story becomes even more provocative: Our bodies are not solitary vessels—they’re ecosystems. And cannabis might be another microbial whisperer.
Gut Feelings: A Bidirectional Relationship
Dr. Thu examined nine studies—two clinical trials and seven observational studies—investigating how cannabis or cannabinoids like THC, CBD, and endocannabinoid-like molecules affect the human microbiota. Their results suggest a bidirectional interaction: cannabinoids can shift microbial populations, and microbes may influence how cannabinoids are absorbed, metabolized, and even how they affect the brain and body.
Our other guide for this subject is Ed Yong. He is someone who deeply understands the microbiome and sees animal biology very differently. Seeing us not as individuals—but as collectives.
This “collective” appears to respond to cannabinoids in specific, sometimes surprising ways. For example, the endocannabinoids anandamide (AEA) and oleoylethanolamide (OEA) are associated with increased levels of beneficial gut microbes like Faecalibacterium, Coprococcus, and Akkermansia muciniphila—all linked to anti-inflammatory effects and better metabolic health.
Clinical Snapshots: Where Microbes, Cannabinoids, and Disease Intersect
Inflammatory Bowel Disease (IBD)
In patients with IBD, cannabis may increase microbial diversity—often seen as a marker of gut health. One study found that in HIV-positive patients who used marijuana, the abundance of Prevotella (a bacterium often elevated in dysbiosis) was reduced in the rectal mucosa.
But causality is murky. Is cannabis restoring gut balance? Or are people with better gut health more likely to benefit from cannabis?
Yong offers a dose of skepticism from his Gizmodo interview:
“The majority of studies can’t tell us whether the changes in the micro biome are actually causing poor health, or are simply a consequence of them. There is evidence of a causal role for some conditions, but it is still not clear whether the micro biome is initiating the problems or simply perpetuating them.”
Mood, Mind, and the Gut–Brain Axis
The microbiome and ECS both play key roles in mood regulation, stress responses, and neuroinflammation. Cannabis use has been associated with shifts in gut bacteria linked to anxiety and depression—yet these shifts could be beneficial or harmful depending on dose, duration, and individual variation.
In people with cognitive impairment and chronic marijuana use, one study reported a lower Prevotella:Bacteroides ratio—a change also associated with altered mitochondrial function. This suggests cannabis might modulate not just the mind, but the microbiota-mitochondria conversation.
Again, Yong urges caution:
“There is this assumption that any change to the micro biome is necessarily bad…it’s still not clear whether loss of diversity is a bad thing, or to what extent it accounts for ailments of modern life, like allergies or autoimmune diseases.”
In most cases, we simply do not know if the changes are good or bad.
Obesity and the Cannabis Paradox
Cannabis users often report higher caloric intake—yet population studies show lower obesity rates and reduced diabetes prevalence. How?
One clue: cannabinoids like OEA appear to increase A. muciniphila, a bacterium that ferments fiber into beneficial short-chain fatty acids (SCFAs) and supports metabolic health. Thu et al. highlight this connection in a clinical trial of OEA supplementation in obese individuals, which led to a notable rise in this microbial ally.
Mechanisms: How Does Cannabis Affect the Microbiome?
Here’s what the Thu review and others propose:
- Cannabinoids regulate bacterial gene expression, modulating immune responses and short chain fatty acid (SCFA) production.
- Microbes influence cannabinoid receptor expression and may even produce ECS-like signaling molecules.
- Cannabis may reduce gut permeability (“leaky gut”), curbing systemic inflammation.
This kind of systemic cross-talk blurs the boundaries between plant, host, and microbe. In an interview with the National Institute of Health, Yong likens this complexity to ecology itself:
“Altering someone’s microbiome is as complicated as changing a rainforest or a coral reef.”
If that’s true, cannabis might be more like rainfall—sometimes healing, sometimes flooding—depending on the environment. Cannabinoid showers bring their own flowers, to paraphrase an old saying.
Do Gut Bacteria Enjoy Cannabis? Do Phages Get High?
These tongue-in-cheek questions highlight a deeper scientific curiosity: Are the effects of cannabis mediated purely through human cells—or are our microbes co-experiencing these effects? Do some bacteria flourish under THC exposure, while others wilt?
While we don’t yet know if bacteria “enjoy” cannabis, the review suggests that our microbial guests do respond—chemically, behaviorally, and perhaps adaptively. Some microbes might increase SCFA production in the presence of cannabinoids. Others might become more competitive or cooperative, subtly nudging our immune system or appetite in ways that echo through our bodies and brains.
And what about phages—viruses that prey on bacteria? Could they be influenced by host ECS changes, or by bacterial metabolites that stem from cannabinoid processing? No studies have answered this yet. But it’s not outlandish to wonder.
The Future: Personalizing Cannabis via the Microbiome
Imagine a future where your microbiome determines which cannabis formulation will work best for you. Or where gut-targeted prebiotics are used to boost the benefits—or reduce the side effects—of cannabinoids.
This is not science fiction. The Thu review calls for:
- Standardized cannabis preparations for research
- Micro biome-aware clinical trials
- Tracking microbial and ECS changes over time
Yong seems to support such an approach, if not a broader scope:
Conclusion: A Grander View of Life (and Medicine)
The cannabis–microbiome connection invites us to think differently—not just about health, but about selfhood. Are we individuals with minds and bodies, or are we walking ecosystems guided by unseen partners?
Cannabis doesn’t just act on neurons—it flows through the microbial forest inside us. And maybe, just maybe, your gut is part of the reason you reach for it.
As Yong so eloquently puts it:
“All the biology I grew up learning as a kid… is only a fraction of the true biology that exists.”
