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

This Huberman Lab Essentials episode replays Andrew Huberman's conversation with Stanford microbiologist Justin Sonnenburg. Huberman introduces himself, calls himself "a true novice" on the topic and starts with the most basic question: what is the microbiome? Sonnenburg first sorts out the terms. "Microbiome" and "microbiota" are often used interchangeably for our microbial community, and he says he will switch between them. He also stresses that microbes are not only in the gut. They live in the nose, the mouth and on the skin, essentially "anywhere that the environment can get to in our body." Most of them, however, live in the distal gut and the colon.

He describes the community's density in concrete terms. Under a microscope, the microbes in gut contents are packed side to side and end to end. Microbes are thought to make up about 30% to 50% of fecal matter. The community holds trillions of cells, which in the gut probably belong to hundreds to a thousand species. Most are bacteria, but archaea, eukaryotes such as fungi, and viruses are also present. Bacteriophages, viruses that infect bacterial cells, outnumber the bacteria by roughly 10 to one and kill them, which sets up predator-prey dynamics within what he calls a "dense, complex, dynamic ecosystem."

It's a super dense bacterial community, almost like a biofilm.

Asked where an infant's microbes come from, Sonnenburg notes that some studies have looked for microbes in the womb and colonizing the fetus. He says this is debated, but overall it does not appear to be a big part of how colonization happens. Each newborn is therefore a new ecosystem.

It's like an island rising up out of the ocean that has no species on it, and suddenly there's this land rush for this open territory.

Because the microbiota is so malleable, early-life factors can push its development down different trajectories. His main example is birth mode. Infants born by C-section have gut microbiota that look more like human skin than like either the vaginal microbiota or the mother's stool microbiota. Other factors add to this: breastfeeding versus formula, whether the family has a pet, and antibiotic exposure. He cites animal studies showing that the microbes acquired early can send the immune system, metabolism or other parts of an organism's biology along "totally different developmental trajectories." The claim about lasting effects on biology is drawn from animal work, not from human trials described here.