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‘Wee beasties’ inside us can help as well as hurt, says microbiome expert


Published November 3, 2014

“We tend to be scared of what we can’t see, so it used to be said that the only good microbe is a dead one. I’m here to promote the good ones.”
David Relman, Thomas C. and Joan M. Merigan Professor
Stanford University

There are monsters in our closets, invisible, lurking. Whether they’re zombies in “The Walking Dead,” or real-life viruses, we fear the invisible foe creeping up on us unawares. Are humans doomed to suffer from the things we cannot see?

Not necessarily, says noted microbiologist David Relman.

Relman, the Thomas C. and Joan M. Merigan Professor in the departments of Medicine, and Microbiology and Immunology at Stanford University, gave a fascinating and accessible presentation on Oct. 30 as part of the presidential “Critical Conversations” series. His talk, titled “Your Inner Self: The Human Microbiome in Health and Disease,” focused on his 15 years of research into the human microbiome — the collective group of microorganisms we all carry in and on our bodies. A panel discussion on understanding infectious diseases followed on Oct. 31.

Relman’s story began with a page from “Microbe Hunters,” Paul de Kruif’s classic book from high school biology class. In 1683, Anton van Leeuwenhoek, the “Father of Microbiology,” looked at scrapings from a colleague’s tooth under his microscope and spied squirming little organisms, calling them “animalcules” and “wee beasties.” At the time, these microbes we now know make us sick or help us heal were completely unknown, so humans looked to the spirit world to bring us good health — or put us in a pine box.

David Relman makes a point during the Friday panel discussion. In the background is Jean Wactawski-Wende, interim dean of the School of Public Health and Health Professions. Photo: Douglas Levere

Even centuries after van Leeuwenhoek’s discovery, microbes generally are viewed as threats and enemies that must be destroyed. The Ebola virus in Africa and the widespread use of antibacterials to “kill germs” are just two examples. But rather than shuddering with horror, Relman and a growing number of scientists believe that we should be thankful for the teensy organisms that share our lives, and work to better understand the roles they play in health and well-being.

“We tend to be scared of what we can’t see, so it used to be said that the only good microbe is a dead one,” Relman said, adding, “I’m here to promote the good ones.”

In front of a full auditorium on the South Campus, Relman laid out reasons why he believes the microbiome must be more thoroughly studied and understood as a potential cause of, and treatment for, modern global health problems, including obesity, malnutrition, irritable bowel disease, even cancer.

It turns out that an invisible army of microbes teem within each of us, all over and inside our bodies. In fact, human beings are made of more bacterial cells than human cells — 10 times more — as well as countless types of viruses, fungi, protozoans and other microscopic organisms. As humans evolved over the millennia, so have they, living in “colonies” throughout our bodies: in our mouths, in our guts, on our skin and elsewhere. These colonies, scientists now believe, have formed symbiotic relationships with their hosts, playing powerful, yet largely unknown roles in the everyday biological functions that determine whether a body thrives or dies.

Following the successful genetic mapping of the human microbiome in 2013 (a five-year effort called the Human Microbiome Project), we now recognize it as a “superorganism,” but much of the science is complex and yet to be done, Relman said during his keynote. Studying the microbiome requires sophisticated testing and analysis, including DNA sequencing and mass spectronomy.

According to Relman, this challenge is also an opportunity. Microbiologists and immunologists now are working with physicists, engineers and experts in other fields to unlock the microbiome’s secrets with the help of new advances in medical technology and data analysis, or “big data” (the topic of last fall’s Critical Conversations). Once we know more about the habitats, behaviors, triggers and dispersal of the microbiome, Relman believes we can better understand its impact on our digestion and nutrition, metabolic processes and immune responses. It also could answer how we process foreign chemicals and how our bodies grow and develop.

“We are one type of life among many, many others,” Relman said. “Nothing exists in isolation.”

Not even the monster under our beds.

Some more wacky facts about the human microbiome:

  • We are born without bacteria. Babies acquire most of their adult microbiota in the first three years, as their metabolic, cognitive, immune and digestive systems are developing. One of Relman’s landmark studies at Stanford involved tracking the growth and “restoration” of digestive microbes in the gut of newborn babies and their mothers, before and after receiving antibiotics. It showed general patterns of “disruption” and “recovery” of the gut microbes, but it’s still not known what causes varying degrees of each.
  • Microbial communities found in humans are not random, but are “well-organized and very site-specific.” They are also universal. All this means is that, for example, your gut bacteria have more in common with the gut bacteria of a person halfway around the world than with the bacteria in your own mouth.
  • So-called “probiotic” food additives might not have much health benefit. The body naturally breaks down the food we eat, using fermentation to produce compounds with probiotic and even antibacterial properties. But there is little proof so far, Relman said, that adding single species of probiotic bacteria to our bodies’ thousands of ancient species has any lasting effect. So much for the hype about yogurt.