Take-aways from the Human Microbiome Project

Research on the human microbiome is hot – both in top-flight journal publications and popular press coverage. Although we know that many diseases and health conditions are associated with altered microbiota, we don’t know if the changes contribute to onset of the disease or are the result of the disease.

I attended the Gut Microbiota for Health meeting (Barcelona, Spain, March 13-15).  Check out the program and session videos. Amid lectures describing the state-of-the science, I began wondering what take-aways we have from this expanding body of science on the human microbiome. A recurring theme revolves around the benefit of acquiring or nurturing a diversified colonizing microbiota, which has the potential to make you healthier and help you resist getting sick. This is consistent with macro- communities, where diversity is related to resilience (ability to recover from a perturbation). Aside from a few pathogens that we know to discourage, scientists can’t (yet?) recommend the healthiest microbial composition. But what emerges frequently from this research is that reduced microbial diversity (or number of microbial genes) is associated with many different diseases or suboptimal health conditions. Here’s my list of practical recommendations which aim to increase the diversity of microbes colonizing your gut, with potential positive outcomes for your health:

  • Consume fermented foods to at least transiently bolster the live microbes in your gut.
  • Consume washed raw fruits and vegetables (not raw milk or meat) and ingest the environmental microbes associated with them. (If you have difficulties digesting raw vegetables, this isn’t a good idea for you.)
  • Consider consuming probiotic-containing foods or supplements. Unlike the gut microbiome studies, which are mostly associative, many probiotics have been tested in controlled trials and shown to have health benefits, including a plethora of gut-associated benefits (Ritchie and Romanuk 2012). Some probiotics can bolster gut barrier function – a porous gut barrier is associated with many disease conditions.
  • Consume adequate levels of a diverse array of fibers (including prebiotics).
  • Consume a diverse diet.
  • Don’t take antibiotics unless they are necessary.
  • Wash hands instead of sanitize.
  • Live on a farm, or at least have a friendly dog or two. It seems especially beneficial for babies, as they are more likely to grow up free of a multitude of allergic or immune system disorders.
  • Breast feed your baby – live microbes are contained in breast milk, along with a rich supply of oligosaccharides that appear to function solely to enrich the right bacteria in your baby.
  • Avoid elective Cesarean births – about 15% of births medically require C-section, but about 30% of U.S. births are C-section. If one is medically necessary, talk to your pediatrician about swabbing the newborn with mom’s vaginal flora, as per gut microbiota expert’s Rob Knight and Maria Gloria Dominguez Bello
  • For recurrent C. difficile disease, fecal microbial transplants may provide a solution. They are currently investigational, but being researched for other conditions, too. (OpenBiome is a stool bank in Boston, as a resource for clinicians and researchers.)
  • And for the curious: The American Gut Project is a crowd sourced research project where for a donation of $99 you can get your microbiota assayed and see where your microbial diversity falls relative to others in the project.

Quote from New York Times:

At dinner, Knight told me that he was sufficiently concerned about such an eventuality that, when his daughter was born by emergency C-section, he and his wife took matters into their own hands: using a sterile cotton swab, they inoculated the newborn infant’s skin with the mother’s vaginal secretions to insure a proper colonization.

Quote from New York Academy of Sciences:

Dominguez-Bello is conducting a study in Puerto Rico in which babies born via C-section are immediately swabbed with their mother’s vaginal secretions; these babies will be followed for years, and compared to those born vaginally and those born via C-section without swabbing. If significant differences between the babies are detected, she hopes that swabbing will one day become mainstream practice, or that more women will learn about the importance of the human microbiome and opt for vaginal birth when possible.