Scientists Raise Alarm About Threats to the Human Microbiome – The Invisible Extinction

This article by Stephanie Emma Pfeffer appeared originally January 3, 2023 in Yahoo! Entertainment as Scientists Raise Alarm About Threats to the Human Microbiome in New Documentary The Invisible Extinction

The Invisible Extinction

The human gut microbiome — bacteria and other microorganisms living in our gut that are essential for our survival — are endangered. Overuse of antibiotics, elective C-sections and processed foods are just some of the factors that are killing off these bacteria that we need to live healthy lives.

In the new documentary film The Invisible Extinction, Dr. Martin Blaser and Dr. Gloria Dominguez-Bello go on a quest to save the microbiome. They spoke with PEOPLE about the important work they are doing to better understand and preserve this essential part of life.

What is a microbiome and why is it so important?

Dr. Martin Blaser: The microbiome is all the microbes that live in and on the human body. It performs essential functions for us. It helps us digest our food. It makes vitamins. It protects us against invaders. It trains our immune system. So when we eat, we are nourishing both our human cells and also our microbial cells. Most of them are in the gut, but there are also microbes on our skin, mouth and the vagina.

Where did it originate?

Dr. Gloria Dominguez-Bello:  We co-evolved with it. Every living complex organism on earth, including animals and plants, has associated microbes because bacteria was the first form of life on Earth. We have always co-evolved with bacteria. The microbiome is a name for the diverse microbes that have co-evolved with hosts (in this case, humans).

Why do you study the microbiomes of people who live in the Amazon?

Dr. Gloria Dominquez-Bello: These are peoples that are only now starting to be exposed to urban practices and medicine. So these are survivors, because you can imagine the mortality in places where there’s no medicine. You fall from a tree, you are dead. You break a leg, you are dead. One of every 10 mothers that are in labor, one mother or baby dies. So if you survive, you are really a survivor.

And these are healthy people because the unhealthy ones have died. So we are very interested in understanding their microbiome. And what we find is that they have much higher diversity. In general, diversity is a marker for health. The more diverse the microbiome, the healthier the ecosystem. We study them to understand what functions are lost in urban areas where the microbiome is at risk.

How are stool samples used in the clinic?

Dr. Martin Blaser: Here’s one example: There’s a bad infection called C. diff that involves the gastrointestinal tract. The microbes in the gut are very abnormal and can get out of control. It kills more than 20,000 people a year in the United States. And a number of years ago, it was found that if you gave those sick people healthy, normal poop back into their system — known as a fecal matter transplant — those people could be cured. It established the principle that if you can normalize the microbiome, you can cure a disease. And so, people have been trying that for many other diseases, including inflammatory bowel disease, multiple sclerosis, liver diseases, diabetes and autism as well.

Tell us more about the possible link between the microbiome and autism.

Dr. Martin Blaser: We know that the rate of autism has gone up dramatically over the last 80 years. And it’s a disease of early life — it manifests within the first couple years. And so we are interested in the idea that the early life microbiome, as it forms, has a connection with the brain. We know that the microbiome is talking to the brain. And so, a number of investigators have been interested in the idea that maybe an abnormal early life gut microbiome is having an altered conversation with the brain, and it’s changing brain development.


Why are antibiotics such a problem?

Dr. Martin Blaser: Antibiotics can disrupt the microbiome by inhibiting or destroying the growth of good bacteria that we need to live. And the average child in the United States, by the time they’re two, gets almost three courses of antibiotics. By the time they’re 10, they’ve gotten 10 courses of antibiotics. But the more courses of antibiotics, the more likely a child is to develop illnesses like asthma, allergies, diabetes, obesity and autism.

It’s been long recognized in the medical profession that we’re overusing antibiotics. The CDC has estimated that about a third of all antibiotic uses are unnecessary, but many scientists believe is much higher. Take ear infections, for example. We know that viruses cause 70 to 80% of all the ear infections. Those are viral infections that do not need antibiotics. But when kids go to the doctor for an ear infection, a huge percentage walk out of the doctor’s office with a prescription for an antibiotic.

Why are C-sections part of this story?

Dr. Gloria Dominquez-Bello: If a baby is born via elective C-section, with no water breaking, they are not exposed to the mother’s microbiome in the vagina. But we have shown that if we normalize, at least partially, the microbiome of a baby that is born by elective C-section by rubbing them with gauze soaked in fluid with their mother’s microbiome, we can normalize the mouth microbiome of the baby during the first year of life. Are we protecting kids against asthma, against Type 1 diabetes, against celiac disease, allergies, obesity by doing this? We are doing a 5-year clinical trial to find out.

How does processed food play a role in the microbiome?

Dr. Gloria Dominquez-Bello: The single most important component of the diet to feed the microbiome is fiber. Fibers are not digestible by our enzymes. So these indigestible component of the diet is super important for us because it feeds our microbiome. In processed food they take out digestible elements like fibers. They make the food much more dense in calories. It’s sweeter. It’s saltier. And it’s fattier. So basically, it is very unhealthy and lacks fiber, which negatively impacts the microbiome.

What can we do about this problem?

Dr. Martin Glaser: People should not be pressuring their doctor to give them antibiotics because there is a cost involved. They need to go to a doctor not to get a prescription, but to get a careful examination and an evaluation. The doctor may say, “Okay, this is really severe. You need an antibiotic,” or “This isn’t too bad. Let’s give it some time and see what happens.” And if the doctor prescribes the antibiotic, they should say, “Are you certain that we need it? Could we do without getting an antibiotic this time and wait a while?” And societally, we have to develop better diagnostic tests so we can tell if a child has a viral infection or a bacterial infection. We have to develop new antibiotics that are narrow spectrum, that don’t have a lot of collateral damage that are killing every bacterium inside. And then of course they should try to eat more fiber and fewer processed foods, and think carefully about having an elective C-section.

What do scientists hope to achieve? 

Dr. Gloria Dominquez-Bello: We need to preserve the current biodiversity of microbes in humans of everywhere. And this is true also for the environment. We are making a complete mess of biodiversity, including microbial. Microbes are essential in every ecosystem, not only in humans or animals or plants, but also in the oceans. The whole thing is linked together by impact of human activities. We need to preserve microbes because they really modulate functions of Earth. They modulate the climate. They modulate everything. They modulate our own gene expression. So there has to be more of that effort to preserve microbial biodiversity, to restore, because we will need restoration. And the damage is not going to stop suddenly, unfortunately.

The Invisible Extinction opens in NY and LA on January 6 and will be available On Demand.