The Good Gut: Taking Control of Your Weight, Your Mood, and Your Long-term Health

by Justin Sonnenburg

The hydra, a microscopic animal that lives in ponds, has only a mouth. That means that ingested food and excreted waste share the same opening. Now our “tube” doesn’t seem so shabby, right?

(The large intestine contains about 10,000 times more bacteria per teaspoon than the small intestine.)

To get a sense of what a fully functional microbiota might look like, we can look to the last remaining full-time hunter-gatherers in Africa, the Hadza. They live in the cradle of human evolution, the Great Rift Valley of Tanzania, home to some of the most ancient remains of our human ancestors dating back millions of years. Their diet and microbiota provides the closest modern-day approximation to that of our ancestors who lived before the advent of agriculture.

Those who have studied the Hadza estimate they consume between 100 to 150 grams of fiber per day. To put these numbers into context, Americans typically eat only 10 to 15 grams of fiber per day.

Evidence is thus mounting that the Western microbiota contains a less diverse collection of microbes compared with the microbiota of people who don’t consume much, if any, processed foods,

Each species of microbe within your microbiota has its own genetic code, or genome. The collection of genes encoded within all microbes is called your microbiome, a second genome. Just as your human genome is uniquely yours (with the exception of identical siblings) no two gut microbiotas are identical.

Every time a human cell divides, the genetic material from the entire human genome contained within that cell (roughly twenty-five thousand genes) needs to be replicated. We profit from microbial genes that perform a variety of functions that our genome cannot. For example, the microbial genomes provide the ability to convert otherwise indigestible food into key molecules that regulate many aspects of our biology, from

The germ theory of disease was a highly novel concept at the time because the prevailing scientific thought was that human diseases were caused by miasmas—foul-smelling poisonous air from rotting organic matter. This belief in disease-causing miasmas drove decisions about sanitation.

Five hundred extra calories per day may be required to produce enough breast milk for one child. By comparison, pregnancy only requires an extra three hundred calories per day.

That’s right, one of the main ingredients in breast milk is not digestible by the infant who’s drinking it. Why would a mother put precious energy into making something her baby can’t use? The answer is that HMOs aren’t for feeding the baby, they’re to provide sustenance for his microbiota. The microbiota, with its collection of 25 million genes, has the capacity to digest and extract energy from HMOs. The lactating mom is not just providing for her baby, she is also whipping up dinner for the 100 trillion bacterial guests her baby is hosting.

A calorie uptake system that is dependent on the composition of the microbiota would explain the weight gain seen in antibiotic-treated farm animals and may even explain why antibiotic use in children has mirrored rising obesity rates.

Based on the original observation that allergies were less prevalent in children with many siblings, the hygiene hypothesis suggested that children of large families were exposed to more sickness within their household, and so their immune system was occupied fighting infections and didn’t have “time” to overreact to pollen or gluten and cause problems.

The vast majority of microbes we encounter are not destined to cause disease, but they do tickle the immune system in different ways; it continually revs its engine, albeit in largely unnoticed ways, at microbes that land upon, transit through, or live within us. These mild mini immune responses depend upon regular interactions with microbes and are part of maintaining a healthy immune system.

Is it possible to determine which microbes are best for promoting a healthy immune system and create the ultimate “immune boosting” probiotic supplement? A pill of beneficial bacteria that would create the perfectly balanced immune system, one that quickly fights off infection yet leaves pollen or peanuts alone, is just what we need, right? Unfortunately, the complexity of the mucosal immune system makes this possibility seem more like science fiction than science.

and regulation that govern drug approval. By avoiding a drug categorization, probiotics can bypass scrutiny by the FDA, whose primary concern with these products is safety rather than effectiveness. But because probiotics are not drugs, the FDA prohibits claims on the labels that would indicate they treat disease.

Prebiotics are food-derived compounds, usually long chains of linked sugar molecules known as complex carbohydrates or polysaccharides—a purified form of dietary fiber—that are not absorbed or metabolized by the host (us) and therefore provide nourishment to the bacteria in the colon.

In Haiti some people eat bon bons de terre, which are earth cookies made with butter, sugar, and dirt. According to the Diagnostic and Statistical Manual of Mental Disorders, dirt consumption is abnormal, even though it has been practiced for hundreds of years.

Perhaps the lack of dirt in the diet of people living in the hygienic industrialized world is problematic, and probiotics from soil offer a way to recapture evolutionarily important interactions.

However, the microbiota must rely upon anaerobic metabolism, or fermentation, to generate energy and create important molecules without oxygen. The second challenge these microbes face is the speed at which this metabolism must take place. Food moves through our digestive tract rapidly, and a competitive ecosystem forces bacteria to quickly consume any available passing nutrients. The strategy utilized by the most prevalent human gut-residing bacteria to solve these problems is rapid fermentation of MACs, one of the most abundant forms of energy within the colon.

The most commonly manufactured fermentation products in the gut are short-chain fatty acids (SCFAs). SCFAs provide humans with a small amount of calories salvaged from plant carbohydrates which, without microbial digestion, would have no caloric value.

The term “dietary fiber” has been given multiple definitions by different official groups. Some of these definitions include fermentation by the microbiota, similar to our definition of MACs, while other definitions are indifferent to the microbiota. The potential confusion about the term “dietary fiber” is compounded by the lack of standard methods used to measure dietary fiber in food.

MACs are the carbohydrates found in a variety of plants, like fruits, vegetables, legumes, and grains, that are fermented by the microbiota.

While you can try to mitigate antibiotic damage by taking probiotics after treatment, the fact remains that we still don’t know how to effectively return a microbiota to its exact pre-antibiotic state.

There are four main tenets of a microbiota-friendly diet. The first is to consume foods that are rich in dietary MACs.

A second important facet of a microbiota-friendly diet is to consume meat in limited quantities. Red meat contains the chemical L-carnitine, which certain microbes in the gut can convert to trimethylamine (TMA), which then gets oxidized into trimethylamine-N-oxide (TMAO). Regular meat-eaters have more TMAO than vegans or vegetarians. High levels of TMAO increase the risk of strokes, heart attacks,

The third pillar of a microbiota-friendly diet is limiting saturated fat intake.

The final component of a microbiota-friendly diet is consuming beneficial microbes, or probiotics.