The Good Gut Summary (7/10) — Unearned Wisdom

Sud Alogu
6 min readMay 2, 2022


T he Good Gut by Justin Sonnenburg is about the human microbiome, what it is, why it is important, and what we can do to keep it healthy.

The species of bacteria and fungi that colonize the gut may determine our interactions with the environment, protecting us from or predisposing us to the development of allergy and autoimmunity. They may protect us from or predispose us to becoming obese or diabetic. They may inhibit or intensify inflammation in the body. They may interact with artificial sweeteners to cause insulin resistance and weight gain in some individuals. They may even influence mental function and emotional wellness.Grains and wheat are not necessarily bad. Gluten sensitivity seems to be most prominent in North America. China doesn’t have that problem.

The real culprit may be changes in the microbiome. Four factors have contributed to this over the past few decades:

1) increasing consumption of industrialized, processed foods, 2) widespread use of antibiotics, 3) the alarming rise in Caesarean deliveries, now accounting for one in every three births, and 4) the decline in breast-feeding. 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. Like DNA, no two microbiomes are identical.

Japanese have microbes that digest seaweed, while Americans don’t.

When an infectious germ invades our body, an army of immune cells are mobilized to fight back against the opposing microbe. If you undercooked chicken (laden with Salmonella), these pathogenic bacteria go through your digestive system, where they can penetrate the cells that line your intestine. The cells of this lining release a storm of molecules (cytokines) — which form a molecular SOS to your body’s immune system.

Immune cells rapidly reply to the cry for help, homing in on the site of the invasion to confront the enemy. Ultimately, B cells and T cells, the foot soldiers of the immune system, work with numerous other specialized infection-fighting cells to rid your body of the offending intruders.

Since you are the host of this internal war, you feel fever and achiness.

Over the past several decades it is the view of the immune system as a heavily armed military force that has largely guided scientific research in the field of immunology.

But recently, we have learned that microbiota are more complex than that. The immune system isn’t just an army ready to fight invasions, it has a diplomatic character. It interacts with symbiotic microbes through more peaceful efforts. Like global politics, the more peaceful efforts by the immune system are a daily effort, and these battles are much less frequent during crises.

Sometimes, a détente is reached, and during that time, relations become strained. Your immune system, either within your gut or elsewhere, will react very differently to a true assault by an invader. The immune system at this point is poised to zip into action, mounting a vigorous response. But in cases where détente isn’t reached, the immune system can reach a heightened state of readiness, making it more likely to overreact to perceived threats (that are not real). The results of this overreaction can range from a minor allergy to a painful ulcerated colon.


In 1989, David Strachan proposed the hygiene hypothesis, which suggested that hay fever and atopy (skin allergy) in the industrial world is a result to reduced exposure of infectious agents.

He suggested that the human immune system evolved to fight off many disease-causing microbes in food, water, and the overall environment each day.

The human immune system had (and has) a full-time job ridding the body of the never-ending onslaught of disease-causing microbes.

But thanks to antibiotics, sanitized drinking water, and sterilized food, we encounter far fewer microbes, reducing our immune system’s workload to part-time.

The original observation was that there was a negative correlation between allergies and children of large families, which suggests that encountering more microbes preoccupies the immune system (which has no time to overreact to pollen or gluten and cause problems).

The hygiene hypothesis has developed to include the finding that children living in farms had fewer allergies than children living in clean, affluent households. While there is still debate about the many factors that can undermine the hygiene hypothesis, it’s clear that the prevalence of autoimmune diseases correlates with how well the population reduces its exposure to microbes.

Sanitizing our environment, and eradicating microbes with antibiotics, has been incredibly successful in reducing the incidence of infectious diseases in our society. Unfortunately, the untargeted attack on disease-causing microbes has inflicted much collateral damage to the beneficial microbes caught in the crossfire.

Does this mean we should be sick more often to keep our immune system from overreacting? No. Autoimmune diseases seem more related to increase in cleanliness rather than decreased infection. Most microbes we encounter aren’t destined to cause disease, but continually adds appropriate stress to the immune system. (antifragile)

The modern environment and food are becoming more sanitized, so less exposure to microbes to occupy immune system. Antibacterial soaps and alcohol-based sanitizers are everywhere. More separation from soil due to Western lifestyle. More antibiotics and antibacterial chemicals not only limit exposure to harmless bacteria, but also increases prevalence of microbes resistant to these chemicals.

And more exposure to superbugs (found in hospital and factory-prepared ground beef) sets off a vicious spiral. As we learn about contaminated salad mixes or hamburgers, we double down on microbial eradication, which fuel the rise of immune-related diseases.

While it is clearly important to minimize our exposure to dangerous microbes, is there a way to safely regain interactions with beneficial environmental microbes without risking serious infectious diseases?

Some bacteria falls in the grey zone.

Exposure to microbes would be a good idea (example: soil through home gardening).

Fermented foods is another good idea (example: yogurt, pickles) or probiotic granola bars.

There are many probiotic supplements but we don’t which are really helpful. Few go through rigorous selection process.

Next to probiotics, there are prebiotics which are forms of dietary fiber which act as food for probiotics (ex: garlic, onions, Jerusalem artichokes, and most fruits and vegetables). Synbiotics combine probiotics and prebiotics (ex: yogurt + banana).

In the future, specific strains of probiotics will be refined but until then, it’s best to rely on natural foods.

A poor microbiome has been associated with weight gain.

Antibiotics should be used carefully.

The vast majority of antibiotics are taken orally, regardless of where pathogenic bacteria are causing the problem. At first glance, this may make sense. For example after swallowing an antibiotic, some will be absorbed into the bloodstream and eventually circulate to the ear and kill the earache-causing bug. But this body wide distribution of the drug puts all bacteria in and on your body in the line of fire. The oral route in particular puts your gut microbes directly in the drug’s crosshairs. And because most antibiotics are designed to kill many different bacterial species, each dose results in significant collateral damage to the microbiota. For some individuals it can take months for the gut microbes to recover, and during that time the risk of diarrheal illness skyrockets. Don’t worry, we’re not advocating licking your entire home to clean it. But maybe using antibacterial household cleaners or bleach is equivalent to boiling pacifiers as far as our health is concerned. A more microbe-friendly approach to cleaning is to use less-toxic cleaners such as vinegar, castile soap, and lemon juice, which will allow increased exposure to microbes and may lessen the risk of the misfiring immune system that is plaguing the Western world.

Originally published at on May 2, 2022.



Sud Alogu

In search of truth and deception.