Be Good to Your Microbes, You’re Probably Stuck With Them

For better or worse, gut microbes form long-lasting communities.

Posted Jul 28, 2020

You got your first microbes as a birthday present from your mother. The earliest of them came from the birth canal and were followed up by microbe-laden breast milk. Over time, you became the proud possessor of trillions of microbes, called your microbiota. If you were a c-section or formula-fed baby, your microbiota may have been sub-par, but all is not lost. That’s because when you were about 1,000 days old, that starter set gave way to a microbiota that was proficient with solid food. It established a core group of microbes that likely remains with you today.

Scott Anderson
Gut microbes are tolerated until they leak out.
Source: Scott Anderson

It’s hard to disrupt your microbiota, and for a good reason: it developed along with you. It is custom crafted to work with your unique genes and immune system.

That immune system is a marvel of complexity, always on a knife’s edge between friendly and hostile. Early on, it figures out which cells belong to you so that it won’t try to kill them. Problems learning this lesson can lead to the misery of autoimmunity, where your immune system attacks your own cells. Your immune system also learns to accept your current microbiota, giving them a pass too. As far as it is concerned, these established microbes may as well be human. That’s an incredibly tight bond to have with such radically different organisms. It is not dogs, but germs that seem to be humanity’s best friend.

At around 1,000 days, the window for accepting new bacteria closes. From then on, foreign bacteria will trigger an immune attack. At that point, your microbiota — for better or worse — is essentially set in stone. Or more properly, mucus.

Why do we go through such a rigamarole to form a partnership with a bunch of tiny microbes? It has a lot to do with the relative evolutionary speed of humans and microbes. A human gene can take thousands of years to evolve, but microbes can do it in minutes. Simply put, microbes run evolutionary circles around us. That means that fast-changing microbes, like antibiotic-resistant E. coli, leave us entirely unprepared.

The answer that animals came up with to deal with this problem was bold, if risky: We recruited our own set of microbes to act as our protectors. In return for a warm, wet home with a continuous buffet, our microbial conscripts protect us from the ubiquitous pathogens in the environment. They are the first line of defense against a microbial attack, being faster and more capable than our own immune system. It takes a germ to fight a germ.

Much of that microbiota is in the form of a biofilm, a multi-cellular mashup of bacteria, viruses, and fungi that form a miniature city, complete with plumbing and polymer “buildings” that protect its inhabitants. It acts as a fortress, protecting them — and us — from intruders. It’s surprisingly tough, which can be bad or good. In the form of plaque on your teeth, it’s a problem. But a healthy biofilm may be a lifesaver in the gut.

Some of these bacteria produce fatty acids like butyrate, a substance that both nourishes and protects the cells lining your gut. Some produce neurotransmitters which may affect your mood. Others, like Eubacterium limosum, prevent the formation of damaging molecules like TMA that are associated with atherosclerosis. Centenarians have higher levels of E. limosum, evidence of how important good microbes can be.

If you were gifted a good set of bacteria, they will be your friends and protectors for life. Their populations will fluctuate with various life factors like diet, exercise, stress, and sleep. But a core set of microbes remains quite stable and stubborn, even after traumatic microbe-killing events like food poisoning or heavy-duty antibiotics. If, on the other hand, you lost the microbe lottery and have a lousy microbiota, you may be plagued for life by gut diseases like irritable bowel syndrome, Crohn’s, celiac, colitis, and others.

These diseases all seem to involve a so-called “leaky gut." Guts are normally permeable; that’s how you absorb nutrients from your food. But larger leaks can be damaging, allowing bacteria to break through the gut lining and enter your bloodstream. That's how inflammation starts. If the leaks continue, you can end up with systemic inflammation — the root of almost all chronic diseases. Systemic inflammation can even affect how you deal with diseases like COVID-19: If you are already compromised by inflammation, it can be harder to fight off viral infections.

A bad microbiota can induce anxiety and depression, the major causes of disability in the world. Chronic inflammation is significantly associated with mood problems and may be a part of how we deal with potentially infectious disease. The desire of sick people to curl up alone in bed is likely a good way to avoid spreading disease. It’s a built-in form of social distancing.

The sheer stubbornness of your gut microbes means that these diseases can be hard to shake. So should you give up trying to fix it? No! Just because you can’t change it permanently, doesn’t mean you can’t treat it.

For instance, Professor John Cryan and Dr. Ted Dinan of University College Cork in Ireland have found that certain probiotics and prebiotics can improve mood. They call them “psychobiotics” and the concept represents a revolution in psychiatry. In the process of improving mood, psychobiotics can help to heal the gut lining and therefore mitigate dozens of other chronic diseases.

You may be able to take psychobiotics as a supplement, or simply boost the ones that you already have by feeding them fiber. Fiber comes from vegetables like onions, beans, artichokes, and asparagus. Avoid foods that are highly processed, because they may encourage the growth of potential pathogens and precipitate a leaky gut. Some people find that probiotics in the form of fermented foods like yogurt, kefir, and sauerkraut are also helpful to balance their gut bacteria. Surprisingly, exercise is also good for your gut bacteria. Scientists don't know exactly why but the impact is significant.

If all else fails, there is one well-researched way to completely reboot your microbiota: a fecal transplant. It is just as appetizing as it sounds, but to someone who is suffering or dying from a bad gut, it can be miraculous. Doctors first dose your microbiota with powerful antibiotics, then they use a kind of poop enema to reintroduce a microbiota from a healthy person.

For many patients, the results are blessedly rapid. Because your microbes affect your emotions, many patients have reported a lift in their mood.

That means as well as checking out the physical health of a donor, it might be wise to check their mental health also. There are caveats in today’s COVID-19 environment: Not all fecal supplies have been checked for coronavirus. But hang in there; the science is too compelling to ignore and the safety of the procedure continues to improve.

In short, the microbes you established in childhood are still there, so be good to them. In a trillion ways, they will return the favor.