The gut microbiome is a complex subject. Amanda Fronk’s article “Inside Micropolis” in the Fall 2018 issue of BYU Magazine is a nice distillation of some of the basics. All quotations in this post are from that article, with bullets to separate different passages.

First, just to persuade you of the importance of gut bacteria, consider the effects of transplanting gut bacteria from one creature to another by transplanting poop:

• Consider this: Five years ago, Chinese researcher Liping Zhao and his team at Shanghai Jiao Tong University caused some mice in their lab to transform from healthy to obese in a matter of weeks, putting on four times the grams as their cage mates on a similar diet. How did they do it? By transplanting bacteria from the gut of a 385-pound, morbidly obese human.

• … Clostridium difficile is a pathogenic bacteria that causes severe diarrhea and can lead to death. It often occurs after intense courses of antibiotics, which leaves the intestines susceptible to infection. “It’s hard to get rid of. There aren’t good [traditional] treatments,” says Chaston. He calls its cure—a fecal microbiota transplant—“the hallmark of microbiome treatment.” The transplant involves giving “an unhealthy person a healthy person’s poop,” Chaston explains. “We don’t know what’s in it. We just know that they get better.” Some 90 percent of transplant recipients recover, often within mere hours of the transplant.

Here are some theories about how gut bacteria could affect health:

• Researchers aren’t sure exactly how Enterobacter cloacae B29 or any other bacterium causes obesity, but there are theories. One is that certain bacteria are masterful at squeezing calories from food.

• Another idea is connected to the endotoxins that some bacteria release into the bloodstream. At high levels, these endotoxins can cause septicemia and often death, but at very low levels, it could lead to chronic inflammation throughout the body. What does that have to do with obesity? “Inflammation affects insulin signaling,” says Bridgewater. “And if insulin response isn’t working right, then people can be storing fuel that they should be burning.”

• Bacteria also appear to play a part in mental illnesses like anxiety and depression. How can your intestines have anything to do with mental illness? First off, “90 percent of the serotonin in our body is actually made in the gut,” says Bridgewater. Serotonin is one of the key neurotransmitters our body uses to keep us emotionally balanced. And second, the vagus nerve, one of the biggest in the body, runs from the brain to the gut’s 100 million neurons.

The article has some reasonable advice for improving the health of gut microbiomes: let kids eat dirt (literally), eat greens consistently, reduce stress, and be careful in using antibiotics that could kill good gut bacteria. It also has a table listing characteristics of some important types of gut bacteria that I won’t try to retail.

Besides trying to identify antibiotics that kill bad gut bacteria but leave good gut bacteria unharmed, there are bacteria-killing viruses called “phages” that might be able to target bad gut bacteria while sparing good gut bacteria.

Overall, although there is plenty of evidence that the gut microbiome matters a lot, we are only beginning to understand what the gut microbiome does and all the interventions that might improve it. One thing that will make progress slower is that there are a huge number of different types of bacteria that can live in the human gut and the portfolio of different bacteria in given individuals vary enormously. Stay tuned for many more scientific results about the human gut microbiome in the coming years.

For annotated links to other posts on diet and health, see:

• Miles Kimball on Diet and Health: A Reader's Guide