Commensal or "live in" good microbes that support good health supply nutrients, metabolize indigestible compounds and defend our bodies against pathogenic colonization. A century ago, Elie Metchnikoff, a Russian embryologist, thought that good gut bacteria could combat against senility. Metchnikoff believed that the bacterial strains in buttermilk and yogurt could lengthen human longevity.
Another study in 2011 used germ free or gnotobiotic mice born into a sterile environment were immunized with central nervous system antigens that cause Multiple Sclerosis. Even though the mice were resistant to the pathogens when the mice were given common gut bacteria they developed the disease after immunization.
How and why did that happen?
70% of the immune cells in the body live in the intestine. These immune cells circulate throughout the body. The gut microbiota directs how the immune cells behave in other parts of the body. Microbes in the gut shed proteins, carbohydrates and other molecules that can leave the gut and play a role in either conjuring up or suppressing disease. Bacterial metabolites are present in many body tissues - lungs, amniotic fluid and breast milk.
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If these metabolites were not present my guess is that babies would not be able to acclimate to the external environment outside of the womb. There are high levels of enzymes in breast milk that prevent inflammatory responses in the infant. Bacteria found in breast milk is part of a distinct microbial community. Vaginal birth babies have more diverse microbial communities than babies delivered by Cesarean section.
In our culture, we have been busy trying to kill the very bacteria that is trying to keep us alive. Microbial colonization of the G.I. tract begins at birth. During the first several months of life this intestinal microbiome develops rapidly especially when infants move from breast milk to solid foods. The intestinal microbiome resembles that of an adult by two years of age and then it continues to develop during puberty and lactation.
How does the intestinal microbiome fit into celiac disease? Patients ask me every week about celiac disease, food allergies and food sensitivities ALL of which I test for. Celiac disease is when you are born without an enzyme to break down the proteins in gluten which includes: wheat, barley, rye and contaminated oats. I run celiac disease panels, test for the genetics behind celiac predisposition - HLA DQ2 and DQ8 and we test for immediate hypersensitivities or IgE allergies to several foods. Sometimes people test positive for celiac disease, but more often than not there are many false negatives. We get more information from the genetic testing as most are positive for DQ2 and or DQ8. When someone is positive for the genetics behind celiac we immediately remove all gluten and any known gluten-free cross reactive foods (quinoa, kamut, amaranth, sorghum, corn, tapioca etc.). Not everyone who has a genetic predisposition to celiac disease develops the condition as most develop the disease years after their first gluten exposure. Celiac disease, until recently, was the most under-diagnosed autoimmune disease.
Gluten is the smoking gun or environmental trigger. One of the top celiac researchers, Dr. Fasano and his team at John Hopkins, looked at the guts of 30 infants with positive genetic susceptibility to celiac disease between birth and two years. Interestingly, the intestinal microbiome of the predisposed infants matured more slowly and was less stable at 24 months than the control infants who had no genetic susceptibility to celiac disease. Genetically susceptible infants who were introduced to gluten at 6 months developed antibodies to gluten more than the infants who were introduced to gluten at 12 months. Fasano says, "Less than one percent of the bacteria that live with us in symbiosis has been cultured, it is the dark side of the moon."
Is there a window of susceptibility to disease? Celiac disease affects 5-10% of people worldwide and the incidence is higher in women. Some studies found gut microbiota was similar in young boys and girls and then differences began to emerge between the genders after puberty. Testosterone protects the gut microbes. This was proven in a study that linked elevated testosterone levels to beneficial gut microbes and strong protection against Type 1 diabetes.
The biggest environmental factor for creating the functional composition of the intestinal microbiome is the daily diet. That is why fermented foods are a critical component for our health. Yogurt, miso, soy products, kombucha, pickles, beet kvass and fermented vegetables are all making a comeback into the diet. Every culture has fermented foods.
Microorganisms in the gut share a similar structure with neuropeptides (proteins in the brain) that regulate our moods, behaviors and emotions. In biochemical terms similar structure is known as molecular mimicry and the body can't tell the difference between the structure of mimics and its own cells. Therein lies the problem because when our cells can't identify these microorganisms we produce antibodies that can attack the microorganisms and our own cells. Researchers believe this gut-brain axis is linked to neuropsychiatric disorders like: autism, depression and eating disorders.
The emerging field of studying the human gut or intestinal microbiome is called metagenomics. Researchers want to sequence the genetic richness of microbial communities to identify which strains are friendly or pathogenic, if any are antibiotic resistant and what is the function of the bacteria as a whole? They want to know which microbes are active, which ones are damaged and which ones respond to specific compounds.
The National Institute of Environmental Health Sciences has found that some microbes metabolize environmental toxicants like polycyclic aromatic hydrocarbons and heavy metals - arsenic. This information can be applied to human health and to clean up environmental disasters. Studying the microbiome will lead to new therapies for a number of immunological, metabolic and neurological diseases. It may be that children in the future will receive routine combinations of bacteria to prevent auto-immune diseases instead of vaccinations.
Second Nature patients take a functional comprehensive stool analysis to see what their microbiome is made of and how we can correct pathological differences. Lastly, did you know that 95% of the viral DNA in the human gut comes from plant viruses? Plant viruses do not cause disease or infections because they are not built to enter human cells. Researchers are busy studying plant viruses common in tobacco, cucumbers, tomatoes and peppers in human serum. It turns out that smokers have more antibodies to a tobacco plant virus than nonsmokers. This may highlight why smokers have a lower risk of some autoimmune and neurodegenerative diseases such as Parkinson's, Alzheimer disease and ulcerative colitis. I am not advocating that anyone take up any kind of smoking as your risk and incidence of certain cancers will skyrocket. Plant virus research may help illuminate more about molecular mimicry and answer questions about susceptibility to autoimmune and neurodegenerative diseases.
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