Wisdom Wednesday: Human Microbiome Project

This study is an extension of the Human Genome Project we reviewed last Wednesday. It began in 2008 with a goal of determining how microbes are associated with health and disease.

The initial study involved 242 “healthy” U.S. participants. Over 5,000 samples were collected, taken from 15 sites on men and 18 on women. This included mouth, nose, skin, stool and vagina. All samples were analyzed using DNA sequencing.

Researchers found that bacterial cells outnumber human cells by 10:1. Bacterial genes may outnumber human genes by 100:1. A majority of the cells were bacterial but they also found archaea (single-celled organisms), yeasts/fungus, protozoa, helminths (worms) and virus.

The human gut alone contained 1,200-1,400 species of which only 24% have been named. Another 8% have been cultured but not named. The remaining 68% have no manes and have not been cultured. Over 600 of the bacterial species documented are common to the human race in general.

Microbes contribute more to human survival than human genes do. Bacterial protein coding genes are 360 times more abundant than human genes. Microbial activities can be shared between different species. Diet, medications, and disease state can change composition and equilibrium and the microbial balance returns to a new norm that is often dysfunctional over time.

The initial colonization should be at birth. Afterward, they enter the body through ingestion of food or liquids, through the respiratory system, through a break in the skin and into the blood supply or through genital and anal openings.

The mother’s lifelong history of health will set the stage for postpartum delivery of the microbial “fingerprint”. Negative factors in this delivery are antibiotic use, GMO foods, birth control, vaccinations, stress and microbial health.



Passage through the birth canal introduces the baby to bacteria from the vaginal canal and anus. The dominant species is Lactobacillus. C-section babies miss this initial inoculation but often end up with Streptococcus, Pseudomonas, and/or Clostridium difficile from the hospital surfaces. Instead of lactose-digesting bacteria, they pick up Proteobacteria. These bacteria are sebum and mucus-loving bacteria that are less able to breakdown the complex sugars in mom’s milk. This results in a greater propensity for development of allergies, eczema and obesity. The average rate of C-section in the United States is just over 35%. It is now the most common abdominal surgery.

My Take:
Much of this data was presented by Dr. Ronda Nelson at the seminar I attended two weeks ago on Understanding the Microbiome. The emphasis this week in on the importance of prenatal health of the mother and having a vaginal delivery whenever possible.

I recommend that women looking to conceive clean up their diet and supplement 5-MTHF, fish oil, methylcobalamin, and vitamin D as a minimum for at least six months prior to trying to become pregnant. Ideally, both prospective parents seek nutritional evaluation and improve their health for a year or two prior to conception.

The Bottom Line:
If you are unable to have a vaginal delivery, vaginal swabbing is an alternative. Breast feeding is ideal and you can provide an infant probiotic to bridge the gap. Avoid antibiotic exposure and instill healthy eating habits for the child as they transition to whole food.