When Professor Dr Maria Gloria Dominguez-Bello travels to the Amazon jungle and tells villagers the reason for her visit, their first response is often laughter.
“Did you come all this way just to see my poop?” they ask.
The microbial ecologist did – no humour intended – and she has been doing it for more than 20 years.
She and husband Prof Dr Martin J. Blaser, both scientists at Rutgers University in New Jersey, United States, are the stars of a new documentary called Invisible Extinction.
The documentary describes their years of research on how modern diet and medicine are disrupting our internal colonies of bacteria and other microbes, i.e. the human microbiome.
The microbiome has been a hot topic for well over a decade, as they and other researchers continue to identify connections between the loss of “good” bacteria and a variety of human diseases, such as obesity, certain cancers and autoimmune disorders.
Yet, the science of how to reverse these problems remains in its infancy.
That’s the message that the couple hopes to convey in the film, which premiered March 24 (2022) at a Copenhagen film festival.
They are racing to identify which kinds of bacteria are essential to human health, and how they might be restored through the use of targeted probiotics and other treatments.
The couple think the faecal samples from the Amazon are a big part of the solution, as they are teeming with microbes that have yet to be altered by antibiotics or sugary, low-fibre Western diets, Prof Dominguez-Bello tells filmmakers Steven Lawrence and Sarah Schenck.
“We seek answers in places where the problem hasn’t yet begun,” says the Henry Rutgers Professor of Microbiome and Health.
No screenings of the documentary have been scheduled yet in the US, but the filmmakers are on the hunt for a streaming service.
Modern practices
In the meantime, the two scientists are helping to create the Microbiota Vault: a secure, subzero repository to preserve the full richness of the microbiome, including species found in the oral and faecal samples from the Amazon.
A pilot phase storage facility has already been set up in Switzerland, and it could someday be a source of treatments, Prof Blaser said recently before flying to Denmark for the film premiere.
“One day,” he said, “we will probably be giving back bacteria to children just to restore the ancient organisms that they have lost.”
In their research, the couple explore how a variety of modern practices can alter the micro- biome, such as diet, the overuse of antibiotics, delivering babies by caeserean section, and the use of infant formula in lieu of breastfeeding.
The answer, they say, is not to reject drugs, caeserean sections and other elements of modern medicine, as all can save lives.
The key is to use them only when appropriate, so as to minimise collateral damage to the microbiome.
When antibiotics are overused, for example, not only do the drugs wipe out beneficial bacteria (along with the disease-causing pathogens for which they are designed), they also clear the way for any drug-resistant microbes to take hold.
The overuse of antibiotics is often portrayed as a problem of the developing world, where the drugs are sometimes administered without a prescription, says Prof Blaser, a physician and author of the book Missing Microbes, which explores many of the same themes.
But the holder of the Henry Rutgers Chair of the Human Microbiome cautioned that the drugs are overused in developed countries too.
He cited a 2018 study that found Spain and Greece were among the top antibiotic users per capita, and a 2014 study by researchers at Children’s Hospital of Philadelphia in the US, who found that some paediatric practices prescribed twice as many antibiotics as others – a difference that could not be explained by the patients’ medical histories or demographic factors.
The Rutgers professor of Medicine and Pathology & Laboratory Medicine is candid about his family’s own experience with apparent overuse of the drugs.
In the film, he speaks with Genia Blaser, his adult daughter from a previous marriage, about her diagnosis of coeliac disease.
She suffered repeated ear infections as a child and underwent many rounds of antibiotics, as was common practice.
Years later, she was treated with powerful antibiotics after contracting a foodborne illness in Peru.
Prof Blaser thinks the drugs contributed to her coeliac condition, disrupting her immune system so that it reacts to foods containing gluten.
“To me, that combination of those early childhood antibiotics and those later antibiotics, that’s kind of what led you to this problem,” he tells her. “Which of course I feel terrible about.”
Among Prof Blaser’s research specialities is a common bacterium called Helicobacter pylori, which causes ulcers.
When that connection was proven years ago, some physicians argued that the microbe should be eliminated in everyone.
Not so, according to Prof Blaser’s research.
These bacteria are present in many people’s microbiomes with no ill effects, and they appear to have a protective effect against certain cancers.
Dietary impact
Sometimes Prof Blaser and his wife conduct studies together, other times independently.
Prof Dominguez-Bello, a native of Caracas, Venezuela, comes at the problem through the lens of urbanisation and economic development, studying differences in the microbiome across rural, small-town and big-city environments in South America.
Once, during a trip to the Amazon, she even studied the impact of diet on her own microbiome.
She and four colleagues had arranged with the locals to stay in their village and eat their food.
That meant fruits, vegetables, some fish and occasional game meat, but nothing like the fatty, juicy varieties on North American grocery shelves.
“It’s so hard,” she said. “It’s like chewing the sole of a shoe.”
After a month on the Amazon diet, all had lost weight.
And as Prof Dominguez-Bello predicted, before-and-after faecal samples revealed that their microbiomes had changed too, although the impact was less dramatic for the five adults than for the two children who came on the trip.
Certain types of bacteria became more abundant in the guts of all seven, whereas the children’s microbiomes saw gains not only in abundance, but also in diversity.
After a month, analysis of the children’s faeces revealed types of bacteria that had not been there before.
“We gained on evenness,” Prof Dominguez-Bello said. “They gained richness.”
It was just a small sample, yet the results were consistent with earlier research suggesting that the human microbiome is more plastic or flexible early in life.
Still, none of the changes were permanent once the visitors returned to their usual diet and other habits back home.
More work needed
Restoring one’s microbial diversity is harder than it sounds.
One option is a faecal transplant – a technique that has helped some patients battle infections caused by the bacterium Clostridium difficile.
But research is needed to develop a more targeted approach for treating other conditions, Prof Blaser said.
Another option is the oral supplements called probiotics.
Yet more work is needed there too, as many current products are more about marketing than scientific substance, he said.
So the research continues, with a strong emphasis on communication.
In the Amazon, for example, Prof Dominguez-Bellow takes pains to teach villagers about her mission, bringing explanatory posters and microscopes so that they can see the microbes in question.
She also works with local scientists to set up labs and microbe collection facilities.
“The times that rich countries went to poor countries and extracted things, those days are over,” she said.
“We have to train them, educate them and empower them.”
The result, she and Prof Blaser hope, will be better for the long-term health of all. – By Tom Avril/The Philadelphia Inquirer/Tribune News Service
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