Understanding the role of the microbiome in health and disease is the new frontier in medicine.  The fact that there are 10 times more bacteria in our bodies than our own cells (with 100 times more bacterial DNA than human genetic material) is a bit mind-boggling (and nauseating if you are eating while reading this)!

The initial colonization of bacteria begins at birth, explain writers at Discover Magazine:

We inherit our microbiomes from our mother, picking up billions of them as we slide from her largely bacteria-free womb through her microbe-laden vagina. Being slathered in vaginal microbes might not seem like much of a treat but it’s vital for a newborn.

Babies end up with a very different portfolio of skin and gut bacteria depending on how they are delivered. Those who are born naturally harbour a more diverse array of bacteria, which resemble those in their mother’s vagina, including several species that are important for digestion. Those who are delivered by C-section are colonised by a less diverse array of bacteria, including some like Staphylococcus that are picked up from the hospital environment.


We are what we eat, and what we feed our microbiome might be the biggest factor of why different cultures with different dietary customs suffer from different health conditions.  In a long and fascinating article about the microbiome, Michael Pollan compares the diets and health of Westerners to natives of the Amazon:

Preliminary results indicate that a pristine microbiome — of people who have had little or no contact with Westerners — features much greater biodiversity, including a number of species never before sequenced, and, as mentioned, much higher levels of prevotella than is typically found in the Western gut. Dominguez-Bello says these vibrant, diverse and antibiotic-naïve microbiomes may play a role in Amerindians’ markedly lower rates of allergies, asthma, atopic disease and chronic conditions like Type 2 diabetes and cardiovascular disease.


Pollan says experts are worried about how antibiotics affect the microbiome adversely.  And it’s not just antibiotics that doctors prescribe to cure patients of infections caused by pathogenic bacteria:

These days Blaser is most concerned about the damage that antibiotics, even in tiny doses, are doing to the microbiome — and particularly to our immune system and weight. “Farmers have been performing a great experiment for more than 60 years,” Blaser says, “by giving subtherapeutic doses of antibiotics to their animals to make them gain weight.” Scientists aren’t sure exactly why this practice works, but the drugs may favor bacteria that are more efficient at harvesting energy from the diet. “Are we doing the same thing to our kids?” he asks. Children in the West receive, on average, between 10 and 20 courses of antibiotics before they turn 18. And those prescribed drugs aren’t the only antimicrobials finding their way to the microbiota; scientists have found antibiotic residues in meat, milk and surface water as well. Blaser is also concerned about the use of antimicrobial compounds in our diet and everyday lives — everything from chlorine washes for lettuce to hand sanitizers. “We’re using these chemicals precisely because they’re antimicrobial,” Blaser says. “And of course they do us some good. But we need to ask, what are they doing to our microbiota?” No one is questioning the value of antibiotics to civilization — they have helped us to conquer a great many infectious diseases and increased our life expectancy. But, as in any war, the war on bacteria appears to have had some unintended consequences.


Shelly Wegman focuses on the site where the largest number of bacteria thrive — the intestine:

A healthy gut flora is essential for the synthesis of enzymes and vitamins, it improves our immune system so we can fight infections. and it regulates metabolism. Changes in the gut mircobiome are linked to an increase in autoimmune diseases, irritable bowel syndrome, diabetes and obesity.

Our lifestyle choices determine the makeup of our gut bacteria. People who eat a diet higher in fried foods, processed foods and sugar tend to have more issues with inflammation, diabetes, obesity and infections, as do people with chronic stress and those who over-use antibiotics and non-steroidal anti-inflammatory medications.


Dr. Andrew Weil hopes that research into the microbiome will “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.


A registered dietician, Wegman offers these tips for a healthier microbiome:

How do we get a healthy gut?

• Choose carbohydrates from whole grains and starchy vegetables like oats, barley and winter squash.

• Cut back on processed foods, sweets, pastries, soft drinks and sweetened tea.

• Limit added sugar to a small serving of dark chocolate or a little honey in your tea.

• Eat foods that feed the good gut bacteria – garlic, onions, leeks, asparagus, artichokes, whole fruits, lentils, sauerkraut or kimchi or plain yogurt.


Read yesterday’s post, “The Universe Of Us” on The PediaBlog here.