Essentials: How to Build, Maintain & Repair Gut Health | Dr. Justin Sonnenburg

**Andrew Huberman** (0:00)
Welcome to Huberman Lab Essentials, where we revisit past episodes for the most potent and actionable science-based tools for mental health, physical health and performance. I'm Andrew Huberman, and I'm a professor of neurobiology and ophthalmology at Stanford School of Medicine. And now for my discussion with Dr. Justin Sonnenburg. Justin, thanks so much for being here.

**Justin Sonnenburg** (0:22)
Great to be here.

**Andrew Huberman** (0:23)
I am a true novice when it comes to the microbiome. So, I'd like to start off with a really basic question, which is, what is the microbiome?

**Justin Sonnenburg** (0:34)
I think, you know, just to start off with clarifying terminology, microbiome and microbiota quite often are used to refer to our microbial community interchangeably. And I'll probably switch between those two terms today. The other important thing to realize is that these microbes are not just in our gut, but they're all over our body. They're in our nose. They're in our mouths. They're on our skin. They're in basically anywhere that the environment can get to in our body, which includes inside our digestive tract, of course, is colonized with microbes. And the vast majority of these are in our distal gut and in our colon. And so this is the gut microbiota or gut microbiome. And the density of this community is astounding. You start off with a zoomed out view and you see something that looks like fecal material, the digesta inside the gut. And you zoom in and you start to get to the microscopic level and see the microbes. They are just packed side to side, end to end. It's a super dense bacterial community, almost like a biofilm. To the point where it's thought that around 30% of fecal matter is microbes, 30 to 50%. So it's an incredibly dense microbial community. We're talking of trillions of microbial cells. And all those microbial cells, if you start to get to know them and see who they are, break out in the gut probably to hundreds to a thousand species. Most of these are bacteria, but there are a lot of other life forms there. There are archaea, which are little microbes that are bacteria-like, but they're different. There are eukaryotes. So we commonly think of eukaryotes in the gut as something like a parasite, but there are eukaryotes, there are fungi, there are also little viruses. There are these bacteriophages that infect bacterial cells.
And those actually outnumber the bacteria like 10 to 1 So they're just everywhere there, they kill bacteria. And so there's these really interesting predator-prey interactions. But overall, it's just this really dense, complex, dynamic ecosystem.

**Andrew Huberman** (2:54)
Are microbiota seen in newborns? In other words, where do they come from? And dare I ask, what direction do they enter the body?

**Justin Sonnenburg** (3:03)
There have been some studies that have looked at whether there are microbes in the womb and microbes colonizing the fetus. And there's some debate about this, but overall, it looks like that's not a big part of the equation of microbial colonization. And so each time an infant is born, it's this new ecosystem. It's like an island rising up out of the ocean that has no species on it. And suddenly, there's this like land rush for, you know, this open territory. There also are a lot of different trajectories that developmental process can take because our microbiota is so malleable and so plastic.
And those trajectories can be affected by all sorts of factors in early life. So an example is whether an infant is born by C-section or born vaginally. Infants that are born by C-section actually have a gut microbiota that looks more like human skin than it does like either the birth canal, the vagina microbiota or the mother's stool microbiota. Compound on top of that whether you're breastfed or formula fed, whether your family has a pet or doesn't have a pet, whether you're exposed to antibiotics, there are all these factors that really can change that developmental process and really change your microbial identity eventually in life. We know from animal studies that depending upon the microbes that you get early in life, you can send the immune system or metabolism of an organism or other parts of their biology in totally different developmental trajectories. So what microbes you're colonized with early in life can really change your biology.

**Andrew Huberman** (4:46)
How do I know if my microbiome is healthy or unhealthy?

**Justin Sonnenburg** (4:49)
Context matters a lot. What's healthy for one person or one population may not be healthy for another person or population. And I will say that there's no single answer to this, but there's some really important considerations. Perhaps the best way to start talking about this is to go back to the inception of the Human Microbiome Project, which was this program that NIH started. They invested a lot of money in 2008, 2009, for really propelling the field of gut microbiome research. It was becoming evident at that point that this was not just a curiosity of human biology, that it was probably really important for our health. Through those studies, we really started to get the image that there is this tremendous individuality in the gut microbiome.