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Love Me, Love My Microbiome


“What is a human being?” It’s an age-old question to which Justin Sonnenburg offers a unique answer. Each of us is, he says, “an elaborate vessel optimized for the growth and spread of our microbial inhabitants” - known collectively as our microbiome.

It has recently been my privilege to meet Justin, read his published research, and learn from his gut-centric view of human physiology. A professor of microbiology and immunology at Stanford, he is one of the world’s leading researchers of the microbiome. Nobel Laureate Joshua Lederberg coined the term a decade ago to collectively describe the 100 trillion microbes that live upon and (mostly) within us.

This roughly two-pound community outnumbers our human cells (that is, the ones with our unique DNA profile) 10-fold. Further, the number of genes in all of those microbes' genomes is roughly 100 times greater than the number in our human cell genome.

The healing potential that will come from a better understanding of this complex internal ecosystem is vast. Sonnenburg envisions a world in which "microbiota typing" becomes a standard part of medical care. Sophisticated analysis of urine and feces would reveal the unique makeup of a person's internal microbial community, which would in turn go a long way toward understanding why that person is sick, and what might make him or her well.

This matters because while human beings all have similar DNA profiles, our microbiomes are vastly different - as Sonnenburg has written, "the number of microbial species that are unique to an individual far exceeds the number that is shared from person to person."

This field is in its infancy, but preliminary findings indicate that our microbiomes are becoming increasingly unbalanced (the technical term is dysbiotic) due to:

  • Dietary change toward processed foods.
  • Increased exposure to powerful antibiotics from medical treatment and residues in foods.
  • Increased incidence of C-section deliveries, which deprives infants of exposure to vital microorganisms in the birth canal that "seed" the gut.

These changes may underlie increased incidence of a wide range of diseases and conditions; everything from allergy and autoimmunity to obesity, type 1 diabetes, asthma, gluten sensitivity, and even psychological and behavioral conditions.

A therapy called fecal microbiota transplantation (FMT) is an early, practical implication of research like Sonnenburg's. As the name suggests, it involves transplanting, via enema or nasogastric tube, fecal material from a healthy donor to a sick one. It's developing a remarkable track record of successfully treating patients infected with Clostridium difficile, a bacterium that resists antibiotic treatment and causes severe diarrhea linked to 14,000 American deaths each year. The first study to compare FMT to standard antibiotic treatment found that FMT cured 15 of 16 people of C difficile infection, while antibiotics cured only three of 13 and four of 13 in two other groups.

In short, this is a medical frontier that bears close attention. The real value of learning more about the microbiome isn't just the promise of better medical interventions such as FMT, but also in using its insights to inform the daily business of how we live and, especially, what we eat.

Regarding yourself as a superorganism means you realize that everything you consume is, technically, a "prebiotic"; that is, material that will either enhance, maintain or undermine the health of your microbiome. Three early research insights:

  • Unprocessed foods that are low in sugar support microbiome health.
  • Probiotic supplements may help repopulate a depleted microbial community, although more research is needed.
  • Increased consumption of fermented foods (such as plain yogurt with active cultures and sauerkraut) may also help in achieving and maintaining healthy gut microbiota.

I'll bring you more information about this vital medical frontier as it develops, but as we await further research, here is a nutrition plan that I believe optimizes the health of both the microbiome and its "vessel."

Andrew Weil, M.D.

Justin L. Sonnenburg, Michael A. Fischbach
Sci Transl Med. Author manuscript; available in PMC 2012 February 27.
Published in final edited form as: Sci Transl Med. 2011 April 13; 3(78): 78ps12. doi: 10.1126/scitranslmed.3001626
PMCID: PMC3287364

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