Why Scientists Are Obsessing Over the Bugs in Our Stool

A more diverse microbiome is typically associated with better health. (Illustration Forest/Shutterstock)

Cultivating Our Gut Microbiome to Stifle Disease (Part 3)

In this series, we’ll share how the latest developments on this medical frontier are transforming our approaches to illness and offering new strategies to heal and prevent disease.
Previously: The roles that microbes play in the body have been linked to processes that appear protective against disease. When disease happens, the link is dysbiosis, or an improper balance of microorganisms, but the science is too new for many specific conclusions.

What specific bugs—bacteria, viruses, and fungi—in what precise amounts might you find in normal healthy human stool?

It’s an odd question, but important because it’s one of the few clues we have as to what is happening inside the gut microbiome. This microbial community plays several essential roles, from helping to create hormones to supplying the key components of our immune system. Unfortunately, it’s also notoriously difficult to study. One of the few glimpses we can get into its inner workings is by what comes out of us.

By the end of the year, researchers hope to use insights from stool to categorize the gut microbiome.

This new fecal standard will be compiled using stool samples from healthy donors representing omnivore and vegan diets—5,000 of each—that are pooled and homogenized. Afterward, they will undergo a newly developed process to make them shelf-stable.

Since the microbiome is so essential to our health, it’s important to have some benchmark to measure against. For instance, if we didn’t have an idea what healthy blood pressure is, we wouldn’t know when someone was at risk of severe disease from high blood pressure.

The new standard hopes to solve an inconsistency in science that now uses a dozen or more diverse “controls” for studies, says Scott Jackson, leader of the complex microbial systems group at the National Institute of Standards and Technology (NIST).

Ideally, this will translate into better diagnostic tools, lab tests, probiotics, and other gut-related products that are already flooding the consumer marketplace with no regulation or oversight. Currently, the U.S. Food and Drug Administration doesn’t approve tests or supplements, although many are available.

Part of the challenge facing scientists is that the perfect microbiome may no longer exist, because of the ubiquitous presence of various chemicals, processed foods, and the microbial effects of many drugs, cleaners, and herbicides.

There’s no guarantee the scientific and medical communities will universally adopt it.

The hope is this will be the first meaningful baseline in this emerging field of science that’s complex beyond comprehension. Even those performing microbiome studies can’t say what the benchmark for health really is.

“What is good? I don’t know. We don’t know. We can give you a field guide, cataloging organisms as we see them. What that means is relatively unanswered,” Dr. Neil Stollman, chairman of gastroenterology at Alta Bates Summit Medical Center, said in a presentation at a recent Malibu Microbiome Meeting.

Jackson told doctors at the Malibu Microbiome Meeting that the standard will be a “well-characterized human feces for the scientific community to reference against.”

Snapshot of Evolving Health

While most human microbiomes somewhat resemble one another, they are also incredibly diverse, with each person having a different number and balance of various microbes. Our internal ecosystem can also lose commensals (the good bacteria), suffer loss of diversity, and experience outgrowths, though the precise reasons aren’t well understood, Stollman said.

A more diverse microbiome is generally associated with better health outcomes. One study found that after several weeks of switching to a diet with more fermented foods, diversity improved. This reflects the plasticity in microbiome composition, which can be affected by everything from foods, to stress, to drugs.

For the most part, though, our microbiome is thought to be stable after going through rapid changes in our early microbiome development. That is, as long as the rest of our life is generally stable. One interesting study found that the gut ecosystem of American immigrants transformed to resemble a more Westernized microbiome after nine months of relocating here.

Other research has shown bacterial levels can also shift in response to exercise, sleep, and stress management strategies such as meditation.

The Good and Bad of Technology

Evolving technology allows scientists to observe the microbiome in detail like never before. It’s an intricate science that requires not only mapping out an incredible diversity of microbes, but then trying to figure out how each one works and what effects it may have. Metagenomics is one area of study focused on the sequencing and function of microbial DNA. Newer shotgun sequencing methods are becoming faster and offer more power to identify less abundant types of microbe.

There are dozens of DNA extraction kits, sequencing methods, and requisite software applications researchers rely on for this work. Any subtle deviation, such as equipment differences, can affect results, Jackson said.

The very act of studying such small and reactive organisms can affect how they behave. It’s a bit like a giant as tall as the sky trying to figure out how people live by tearing the roofs off their homes. It isn’t hard to imagine that the observations of such a giant could be affected by only looking in the biggest houses, or in the largest cities.

As NIST rolls out its new microbiome measurement, Jackson is quick to point out that researchers need to be sensitive to bias, which can creep into many stages of study.

“There’s bias in every step of this measurement process from how you collect and store your sample to how you analyze and interpret your results and everything in between,” he said. “At the end of the day … you have to ask yourself, how truly representative is this of my sample?”

Even the precise numbers of microbes in the gut is subject to debate after a group of scientists finally decide to fact-check the oft-quoted 100 trillion microbes statistic. The team at the Weizmann Institute of Science determined it may be about 39 trillion bacterial cells living among about 30 trillion human cells.

A Science Full of Unknowns

Stollman says it may turn out that stool testing is an inferior way to learn about the gut microbiome.

“It’s not a given that the bugs you poop out are the same bugs that are working hard for you in the lining of your colon,” he said.

While stool collection is the easiest way to assess the gut microbiome, studies suggest bugs from the rectum, large intestine, and small intestine all have variability. The ecology may even be different from one area of the colon to another.

Yet, there are companies that claim their stool analyses can offer information for precision health.

Dr. Ari Grinspan, associate professor of medicine and director of the fecal microbiota transplant program at Mount Sinai Hospital, told The Epoch Times that while there may be some value to such tests, the results often prematurely raise treatment expectations.

“When patients come into your office and they spent a lot of money on these test results and they come in and they say, ‘The answer’s in here somewhere, doc. What do I need to do, what probiotic blend, what do I need to eat to make me better?’” he said. “There’s just no clinical basis to do anything useful there.”

Tests might also unnecessarily raise fears. For instance, many people—especially those who work in health care settings—have low levels of Clostridioides difficile (c. diff) in their microbiome. Though it’s associated with a very dangerous infection that causes mortality in about 10 percent of the elderly who get it, c. diff may also be an asymptomatic colonizer.

In other words, Stollman said simply having low levels of c. diff isn’t worrisome in a healthy microbiome. Those who get sick often do so in a hospital environment—where it’s nearly impossible to disinfect for this hearty bug—chiefly when they are on antibiotics for another infection. The driving factor of a dangerous c. diff, and many other infections isn’t so much the bacteria as it is a dysbiotic microbiome.

Next: Researchers explain what dysbiosis is, the complications wrapped up in defining and diagnosing it, and the promising protocols for reversing it.

Read Part 1 Killing Bacteria with Antimicrobials and Antibiotics May Be Shortsighted, According to New Science About the Microbiome

Read Part 2– How the Gut Cures and Creates Disease

Important Notice: This article was also published at www.theepochtimes.com by Amy Denney where all credits are due.


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