The Body

Uh-oh! Our Good Gut Bugs May Be Going Extinct!

Flipping through The Whole-Body Microbiome, we learned this.

Girl With The Gourd - Yevgenia Nayberg

Flipping through The Whole-Body Microbiome, we learned this.

When you alter your diet, such as switching to a high-fiber/low-fat diet, changes in the microbiome can be detected within three days. It has been suggested that changes in diet can account for over half (57 percent) of the variation in the microbiome in a person, while genetic variation accounts for only 12 percent. One great example of how the gut microbiome adapts to diet comes from Japan. We know that a specific microbial enzyme, beta-porphyranase, breaks down a component of seaweed, glycans, and is found in marine microbes. It turns out that this enzyme is also found in a certain microbe, Bacteroides plebeius, in the gut microbiomes of Japanese people, but not in North American microbiomes. It seems that eating non-sterile seaweed, as many Japanese do, enabled the transfer of the gene encoding the enzyme from an ocean-dwelling microbe to resident members of the Japanese human microbiome, who passed this around Japan, thereby enhancing the population’s digestion of seaweed.

The case of seaweed is a specific illustration of how food consumption uniquely altered a community’s microbiome. By extension, there is concern that broad dietary changes across the general population will cause us, as humans, to lose the microbes that we evolved with.

In a series of intriguing experiments, Dr. Justin Sonnenberg of Stanford University showed that we may be doing serious, irreparable damage to our collective human microbiome. First, he fed “humanized” mice (i.e., germ-free mice colonized with human fecal microbes) a diet rich in plant fiber for six weeks. Next, he fed half of the mice a low-fiber (Western) diet for seven weeks, followed by a high-fiber diet for another six weeks. The control group remained on the high-fiber diet the whole time. The mice were bred, and this was repeated for each subsequent generation.

What Sonnenberg and his team found was quite disturbing. At first, the changes in the gut microbiome accompanying the diet change were partly reversible in a single generation. (One-third of the original species did not fully recover.) But then, with each subsequent generation, a low-fiber diet caused a further decrease in microbial diversity. After four generations (that would be your great-grandchildren), no length of time on a high-fiber diet could recover the microbes that break down fiber. However, researchers could restore the high-fiber microbes by a fecal transfer of normal microbes to the depleted animals.

Collectively, this suggests that we are driving to extinction the microbes that digest high amounts of fiber.

Collectively, this suggests that we are driving to extinction the microbes that digest high amounts of fiber, as society continues its low-fiber/high-simple-sugar diet—and these microbes produce SCFA, short chain fatty acids, which are critical to health. This effect could compound over just a few generations to the point of becoming irreversible, thus ending our relationship with the beneficial microbes that were so integral to our successful evolution. Losing the diversity and abundance of our ancestors’ gut flora could have a negative impact on health and well-being, making us more susceptible to gastrointestinal disorders, other diseases, and dysbiosis.

Perhaps the diverse gut microbiomes characteristic of centenarians and semi-supercentenarians will become impossible to achieve in the future, which could detrimentally affect our prospects for longevity. Scientists are now considering the possibility that we biobank feces from our grandparents for the health of future generations. It may also be important to incorporate high levels of fiber into our lifestyles if we want to save essential gut microbes before it’s too late.

—B. Brett Finlay PhD and Jessica M. Finlay PhD

Note: “Ridiculously Healthy Elderly People Have the Same Gut Microbiome as Thirty-Year-Olds”

This 2017 headline in Science Daily immediately drew our attention to a study involving over 1,000 “very healthy” Chinese people aged 3 to over 100. What researchers found was that the gut microbes in the healthy elderly participants were similar to microbes found in healthy individuals decades younger. When kept in good health, it seemed, the gut microbiome could remain robust for over a century. Is this a potential fountain of youth?

Adapted from The Whole-Body Microbiome, by B. Brett Finlay PhD and Jessica M. Finlay PhD. Published in January 2019 by The Experiment.