Wednesday, February 25, 2015

The Human Microbiome: Cleaning it Up (Part 1)

Through the Human Genome Project, completed in 2003, scientists finally sequenced and mapped the 23,000 genes of the human body. After this world-changing feat, the scientific community has begun the arduous task of identifying the genetic makeup of the non-human genetic forms in our body. You didn’t misread that… according to the National Institutes of Health (NIH), 90% of cells in the human body are not human. Advances in DNA technologies have birthed an amazing new field of research called metagenomics, allowing comprehensive examination of the microbial communities in and on our bodies. As a result, the Human Microbiome Project (also referred to as the Human Metagenome Project) was initiated in 2007.

The Project is a global initiative with multiple countries participating, whose aim is to characterize microbial communities found at multiple human body sites and to look for correlations between changes in the microbiome and human health. They are doing this by studying the human microbiome. Simply defined, the human microbiome is the total inclusion of every microorganism living in, on, and perhaps even around the human body. It not only encompasses the trillions of microorganisms themselves (bacteria, fungi, yeast, protozoa, and other viruses); it also includes all the combined genetic material of those microorganisms. This genetic material – both the “good” and the “bad” – makes up the building blocks of our DNA that live on our skin and in our nose, mouth, esophagus, lungs, intestines, genitals, etc.

The microbiome is a gift from the mother. When babies are delivered through the birthing canal, they are exposed to their mother’s microbiome, giving their brand new immune system a leg up on cesarean-birthed babies. According to Dr. David Perlmutter, in his new book, Brain Maker, statistics suggest there is an increased risk of disease for infants born by cesarean section. The rate of autism is doubled, Celiac Disease increases 80%, adult obesity increases 50%, Type 1 diabetes increases 70% and ADHD is tripled. Clearly, our healthy germs are critical for our mental and physical health.

Amazingly (or maybe not so amazingly), different diets, families, cultures, and places of residence are reflected in variances in the human microbiome. A study, published in Nature, indicates that changes can happen incredibly fast in the human gut—within three or four days of a big shift in what we eat. Our microbiome is continually adapting to a changing environment.

MarĂ­a Gloria Dominguez-Bello, a microbiologist at New York University, is studying the gut microbiome of hunter gatherers in the Amazon in order to determine what a clean microbiome would look like. “We want to see how the human microbiota looks before antibiotics, before processed food, before modern birth… These samples are really gold.” She is finding that these samples have much greater biodiversity and higher levels of prevotella bacteria… than in the West. Interestingly, these Amerindians have much lower rates of allergies, asthma, atopic disease and chronic diseases.

A Fine Balance
Within our microbiome lies an ecosystem with thousands of species of microbes (microorganisms, especially disease-causing bacteria) living in the cells and tissues of the human body. It is estimated that the combined microorganisms and microbial cells that live inside or on the body outnumber human cells by about ten to one! There are approximately 100 trillion microbial cells in the human microbiota (all the microbes of a particular site, in this case the human body); the human gut alone contains 40,000 bacterial species. It is not surprising that our microbiota influences our health. The symbiotic bacteria in our microbiome can be considered good bacteria, those that benefit us. These bacteria – “the good guys” – escort out the “bad bacteria” and rid the body of digested food and inflammatory molecules. There are also compensatory bacteria, which can be considered neutral; however, these so-called “neutral” organisms can be influenced into becoming good or bad. There are also potential pathogenic microbes (aka pathogens – bacteria capable of causing disease) and we all have them in our bodies. They include popular offenders like Candida, E-coli, and H-pylori, just to name a few. Microbes become pathogenic when they are not kept in check.

Our microbe DNA outnumbers our human DNA 99:1. Pathogens and symbiotic bacteria work and live together, making a sticky, slimy protective matrix in the gut and sinuses called biofilm. The biofilm is like a city where the microbes live, eat and multiply. It is a complex structure that includes channels where food is transported in and waste is transported out. The sticky matrix also helps protect the bad microbes from antibiotics, antifungals, and our immune system. They also communicate via quorum sensing, a sophisticated stimulus/response system that allows them to alert each other of an adversarial event. Pathogens respond and protect themselves, sometimes through mutation, multiplying and becoming more resistant.

In spite of such an overwhelming majority of potential offenders, our microbiome inhabitants coexist on basically friendly terms… that is, until imbalances in the body disrupt the natural order of things.