How to Enhance Your Gut Microbiome for Brain & Overall Health

The episode opens with the host, who introduces himself as Andrew Huberman, a professor of neurobiology and ophthalmology at Stanford School of Medicine, setting out the subject: how the gut influences the brain and how the brain influences the gut. He separates two everyday senses of a "gut feeling": knowing something without knowing how you know it, and an actual bodily sensation in the gut that pushes you to think, feel or act, perhaps moving toward or away from something.

He says the focus is the biology of gut feelings, not their psychology. The gut talks to the brain in two ways: directly, through neurons, and indirectly, by changing the body's chemistry, which reaches the brain and affects how it works. The signals also run the other way. According to the host, the brain affects how fast food is digested and the chemistry of the whole digestive tract, and states such as stress, social challenge or happiness shift that chemistry, which then changes how the brain works.

The gut microbiome links these ideas. He describes it as the trillions of bacteria living along the digestive tract that strongly affect metabolism, immune function and brain function. He promises practical tools for keeping up or improving gut health. He also presents the episode as standalone, though it doubles as a primer for an upcoming conversation with Stanford's Dr. Justin Sonnenburg, whom he calls a world expert on the gut microbiome. He notes the podcast is separate from his teaching and research roles at Stanford.

He describes the gut-brain exchange as an ongoing "dance" that usually happens below conscious awareness. It becomes noticeable with a stomachache, with food that doesn't agree with you, or with food that feels delicious through the whole body, so brain and body seem to share one perception. He extends the framing to social life: the gut reacts when you meet someone you dislike, and when you meet someone you'd like to spend more time with.

The host calls the gut and brain a biological circuit. Its stations pass signals along a chain, and the circuit runs in both directions.

It's a two-way street between gut and brain.

His first correction is to the word "gut." People tend to equate it with the stomach, but in gut-brain signaling and microbiome research it means the whole digestive tract, from start to finish. He says many of the neurons that signal to specific brain regions, and that trigger the release of neurochemicals such as dopamine or serotonin, sit in the small and large intestines, not the stomach. These signals can push you toward or away from particular foods, interactions and behaviors. He adds that taste receptors and neurons line the entire digestive tract.

"Brain" is shorthand too. The brain and spinal cord form the central nervous system. So do the neural retinas, the light-sensing tissue at the back of the eyes, which he describes as the only parts of the brain outside the cranial vault. Everything else belongs to the peripheral nervous system. He stresses this split because, in his account, the gut reaches the brain mainly through peripheral nerve cells in the gut and elsewhere in the body, whose signals cross into the central nervous system.

So actually your eyes are part of your brain.

The host describes the digestive system as a tube running from mouth to anus. Sphincters along it close off some chambers from others. Acidity, or pH, also changes along the tube, and he argues this creates separate microenvironments where particular microbiota thrive or fail. So the gut is not a single stomach with one chemistry but a chain of chambers, and your behavior and experiences can shift which bacteria do well in each.

He gives a sense of scale and structure. Stretched out with all its curves and turns removed, the tract would be about nine meters long. The hollow inside is the lumen. Over much of the tract, the walls are not smooth but have bumps and grooves, which he compares to the folds of the brain. These are covered by a mucosal lining with tiny hair-like microvilli that push contents along. Microbiota live in the lumen, among the microvilli, and in small niches where particular organisms grow best. He admits this may sound gross, but says many of these organisms are good for the gut and send good signals to the brain.

According to the host, the microbiome starts forming at birth. He lists several factors he says strongly affect it:

C-section versus vaginal birth; who handled the newborn and how much skin contact there was; whether the baby was premature; whether there were pets at home; whether the child was allowed to play in the dirt or eat snails, or was instead kept in a very antiseptic environment.

He says these experiences shaped the gut's microenvironments and what is best or worst for them. In this section he states the early-life effects without describing specific studies, and says he will discuss data on pets and skin contact later.

The host separates two terms. The microbiota are the bacteria themselves. The microbiome covers the bacteria plus all the genes they make, some of which he says affect all of us. He estimates people carry about two to three kilograms of these bacteria, which he converts to more than six pounds.

Under a microscope, he says, they are fairly simple organisms. Some stay put in the mucosal lining, on microvilli or in niches, while others move around, and together they fill the lumen. On the head of a pin you could fit "many, many hundreds, if not thousands or more." He explains the wide range by the fact that the bacteria vary in size and in whether they move.

About 60% of your stool, as unpleasant as that might be to think about, is made up of live and dead microbacteria.

The population turns over constantly. Bacteria are born and die off, and some stay for long periods while others are excreted. Which ones you make, and how many stay or leave, depends on gut chemistry and, he says, very strongly on what you eat and don't eat.

Diet is not the only input, the host says. Microbes also reach the digestive tract through the mouth, breathing, kissing and skin contact. He calls who we interact with, and the environment we're in, a major factor, including contact with animals. His examples are deliberately broad: people who talk or breathe on you, handshakes, kissing, romantic partners, and pets such as dogs, cats, lizards or rats. He says "there's absolutely no question" that pets affect the microbiome, though this section doesn't present the data behind that claim.

He then presents two opposing views of what the microbiome is for. A neurobiologist, he says, would almost certainly answer that it exists to affect brain function. Microbiologist friends flip it around:

Well, maybe the brain and nervous system are there to support the microbiome. It's the other way around.

He adds a caveat about agency. As far as we know, the microbes don't know what they're doing. We don't know whether they have consciousness, and although that can't be ruled out, he calls it pretty unlikely. Either way, they exploit the different environments along the digestive tract.

Beyond living in the gut for their own purposes, the microbiota help with digestion, according to the host. Many of their genes are involved in fermentation and in digesting particular nutrients, and he says diet can change the enzymes the microbiome produces. From this he reasons that someone lacking certain digestive microbiota would struggle to digest certain foods. He frames this as an inference ("it stands to reason"), not a demonstrated finding.