Befriending Your Invisible Bacterial Organ

The Human Microbiome
Although unseen by the naked eye, these unique mechanisms constitute an entire invisible organ called the Human Microbiome whose evolution has far surpassed that of our own lenses. Comprised of trillions of bacterial bodies, this multi-functional environment consists of viruses, pathogens, and antibodies that are in a constant state of living and dying, executing essential functions like digestion, skin health, and even mental focus. The microbiome weighs roughly 1-3 pounds, working symbiotically to serve our most basic needs through its complex and previously unexplored interaction with our cell bodies.
Scientific Understanding
“Most of them aren’t your enemies, they’re essential allies that help you live and function.” – Rob Knight

At the Biofrontiers Institute at CU Boulder, Dr, Rob Knight and his team of researchers are hoping to magnify the meaning behind a healthy gut.
“The largest and most diverse populations in the human body live in our digestive system. Knowing who is in your gut provides a useful guide to what is going on in there. And it’s a very complex ecosystem, far more like a rainforest than a desert.”
Its greatest line of defense, our gut, which is home to the highest mass of bacteria responsible for their roles in essential functions such as dictating our metabolism and preventing pathogens from taking a toll on our system.

“It is like the government of a country, it is mission control. The biggest and most important, all happening in the gut in spades. They all seem to be regulating our metabolisms, how much energy we burn, and how much fat we store.”
In a recent article by the American Society for Microbiology, scientists Geraldine O. Canny and Beth McCormick discuss the residents in the intestinal wall:
“The microflora of the intestinal microenvironment as a unit has important protective, metabolic, and trophic functions. Resident bacteria serve a central line of resistance to colonization by exogenous microbes and thus assist in preventing the potential invasion (of pathogens). This protective function is known as the barrier effect or colonization resistance, and the bacteria have a number of important roles,” including their contribution to synthesizing certain vitamins like B12 and biotin which are necessary for proper growth.

They also discuss the importance of microbes found in our colon and their role in fermenting non-digestible carbohydrates, which are “key sources of energy in the colon. These non-digestible carbohydrates include large polysaccharides (i.e., resistant starches, pectins, and cellulose) and some oligosaccharides that escape digestion, as well as unabsorbed sugars and alcohols.”

The “endpoint” of this fermentation process being the formulation of short-chain fatty acids, chemical compounds that have a nourishing effect on the epithelium, the most basic type of connective tissue in the human body including our muscle and nervous tissue. 1.
Microbes can also be found literally right under our noses, assembling here to safeguard us from unwanted viruses or infections. Travel a few inches south to the ever-odorous underarm, where microbial life thrives, and here you’ll find an army equipped for a different type of battle. The armpit is host to bacteria that grows on sweat, producing anti-inflammatory, anti-bacterial bodies that shield our skin from invasive colonizing agents. As for our dry, desert regions like the limbs, a magnitude of bacterial organisms flourish here as well.

All together, we are uniquely post-marked with our own personalized map to health, a self-stamped, invisible “fingerprint” given immediately upon delivery. Each body contains its own brand of crucial antibodies, some even specific to only their host cell.
Current Research
So, what happens when our governing gut loses control of its mission?
At the San Francisco-based bio technical company, Second Genome, founders Corey Goodman and Paul DiLaura are on the forefront of developing revolutionary therapies in modern disease, exploring the diversity of the human gut, and taking their findings to the burgeoning market of microbial medicine. Given the long list of illnesses that are attributed to poor microbial health today, Second Genome’s major focus lies in the creating and isolating the bacterial components available in treating cases of Irritable Bowl Disease (IBD) and other causation-lead diseases like type 2 diabetes and Crohn’s disease. In John Gertner’s article in Fast Company, “Whats Lurking in Your Microbiome? Possibly a Cure for Disease”, he reviews the biotech duo and their recent studies not only on these bacterial cells, but the very “conversation” between our body and our microbiome:
“For centuries we have listened only to our bodies’ side of the exchange, but a host of new technologies allow us to listen to our bacteria’s, too.”

Second Genome hopes to generate “a system or “platform” for interpreting how elements of the microbiome are leading to disease, and how to intervene or prevent the disease… by analyzing samples of human cells and then creating vast and powerful databases for interpretation, the company can build “a high-resolution understanding” of what different types of bacteria are doing in a disease state and a wellness state.”
Goodman and DiLaura, bacterial “code-breakers”, translate the copious amount of dialogue being exchanged between our body’s first genome, our DNA, and our second, our bacterial makeup. Their research seeks to examine and clarify the cryptic languages of our human-to-bacterial structure by our “propensity for disease, our progression of disease, our flare-ups of disease” in order to establish a novel approach to treatment.
In Gertner’s article, he states that, “gut bacteria affects health in good and bad ways by producing secretions of proteins and metabolites—or what the executives at Second Genome call “bioactives.” These bioactives affect our bodies much like drugs. By 2012, Second Genome had focused on two efforts: (1) to identify, patent, and produce bioactives that mimic the secretions of healthful gut bacteria; and (2) to identify, patent, and produce bioactives that block the unhealthful effects of secretions of gut bacteria.”

In theory, such a product could be manufactured with precision and consistency like any other pharmaceutical; not incidentally, it could involve substances that, once swallowed, would stay in the gut rather than enter a patient’s circulatory system,” a crucial measure in FDA regulatory standards for allowing “bugs as drugs” onto the medical market.
Hundreds of common diseases are associated with the human microbiome, such as “inflammation, metabolic disease, autism, multiple sclerosis, psoriasis, skin disorders”,  while only several are both found to be correlational and causational.

“Obesity, type 2 diabetes, and IBDs such as ulcerative colitis and Crohn’s disease” are more the prevalent illnesses studied in recent scientific literature, and “accompanied by a large unmet need for therapeutics.”
After years of research, Gertner shares that Second Genome’s goal of creating a drug for IBD is a modest one amongst the company’s alternate project: tackling type 2 diabetes.

“The first drug, if effective, could affect hundreds of thousands of people; the second, millions.”
Knight and researchers worldwide are now studying the vast, unknown world of the Human Microbiome and discovering how that at life’s most basic level, bacteria in our gut may be informing our cells through a complex and archaic relationship, communicating with our nervous system, and perhaps even affecting our deepest, darkest drives.
“We humans have always been really concerned about the health of our bodies, but we haven’t always been that good at figuring out what parts are important. “Take the Ancient Egyptians for example. They were very careful to preserve the parts of their bodies that they knew they’d need in the afterlife: the heart, the liver, the intestines, and so forth. But there were other parts of the body they were somewhat less careful about. The brain for example, which essentially they just mushed up with metal or wooden tools, drained out through the nose, and threw away…Disregarding the microbiome is potentially as foolish as throwing the brain away as a useless organ.” –Dr. Rob Knight

For the first time, Rob Knight and his team at the Knightlab are exploring the possibilities of microbial medicine, “using genetic technologies to open a window into the world of microbial life.”

Institutes and universities nationwide are launching the bacterial brigade and pairing up to perform the largest interactive health project to date.The American Gut is comprised of over 35 expert scientists and universities world-wide, and is host to leading names in genomic research.

Jose Clemente and Antonio Gonzales, both major force behind the Knightlab’s success, continue to make huge strides in microbial reserach today from their new location at the University of California in San Diego. Clemente shares about their recent work at the Biomedical Research Facility and the necessity for establishing a scientific base of bacterial data today.

In a recent article written by Clemente and Gonzales, Our Microbial Selves: What Ecology Can Teach Us, they discuss how  using “well‐tested ecological theories” have allowed insight into “the microbial changes associated with normal development and human disease.”

“Focusing on diversity, biological drivers of community structure, spatial patterning and temporal dynamics,” the team studies the ecosystems of the body and certain “trends identified in communities” in hopes of building predictive models for personalized medicine.



To be continued…


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