Human microbiome a complex system
Most of us growing up in the 20th century have established a certain discomfort with bacteria. Those with even the slightest obsessive-compulsive tendency absolutely detest the idea of “germs” being an ever-present component of our environment. Talk to many American housewives and they will say theirs is an on-going battle against the forces of darkness, that being the bacteria that reside all around us.
As science has advanced in its understanding and knowledge of our planet and our place in it, physicians and scientists have become more comfortable with the concept that particular bacteria are an essential part of the balance so critical to the biological world. Nowhere is that more evident than in an examination of the microbiota.
This term refers to the aggregate of microorganisms residing on or in many human tissues and biofluids, including the skin, uterus, ovarian follicles, lung, saliva, oral mucosa, conjunctiva, biliary and gastrointestinal tracts. The human microbiome refers specifically to the genes these cells harbor. They include bacteria, archaea (a primitive one-celled organism), fungi, protists and viruses. Though micro-organisms can also live on the human body, they are typically excluded from this definition.
The human body is host to a huge number of these microscopic creatures. The most current data estimates that the average human body is inhabited by as many non-human cells as human cells. The human microbiota consists of 10-100 trillion symbiotic microbial cells harbored by each person, with most of these being bacteria residing in the gut.
There are 500-1000 different species of microbes in our gut. We initially get this microbiome from the womb, the delivery process and breastfeeding, but this changes throughout our life. Very importantly, our diet rapidly alters our microbiome over our lifespan. The acquisition of microbiota continues over the first few years of life, as an infant’s GI tract microbiome begins to resemble that of an adult as early as 1 year of life
As a generalization, microorganisms can have different types of relationships with their host. Some microorganisms that colonize humans are commensal, meaning they co-exist without harming humans, while others have a mutualistic relationship where both benefit.
Conversely, some non-pathogenic microorganisms can harm human hosts via the metabolites they produce but otherwise do not directly attack the host. Some microorganisms perform tasks known to be beneficial to us, the host. Perhaps not surprising, the role of most of them is not well understood. Those that are expected to be present, and aren’t normally disease-causing, are often referred to as “normal flora.”
Evolution has selected for a specialized community of microbes that thrive in the warm, enriched and stable environment of the human intestinal tract. Surprisingly, gut microbes and their human host share much of the same metabolic machinery.
Apparently, bacteria have great influence over which food items we can absorb and use, and how much energy their human host is able to extract from its diet. The interaction between the human microbiota and the environment is dynamic, with human microbes flowing freely onto the surfaces we interact with, on an everyday basis.
We do not know enough about how these organisms function within us, but we know that a balanced microbiome promotes good health. When your microbiome goes out of balance, many diseases can be associated. It can be argued that there are very few conditions where the role of the microbiome is not relevant, and its discovery will have to change the way we look at disease. Indeed, disease may sometimes result not only from the presence of a “bug” but, instead, from an imbalance in the indigenous microbial community. This concept demands significantly greater evaluation in future.
As for evidence, let me present a recent study which provided two groups of individual swith two very different diets. One was a high-protein diet (lots of meat), while the second was high-fiber (fruits, vegetables, grains, and beans). Bacterial analysis showed what each group ate had a huge and rapid effect on their gut bacteria.
Each developed the bacteria that would help them digest that particular type of food. Consequently, the consumption of a diet rich in refined flour, sugar, unhealthy fats, additives, preservatives, artificial sweeteners or too much meat does not promote gut health, because those ingredients feed exactly the wrong kind of bacteria.
Not surprisingly, we don’t yet know what constitutes a balanced microbiome. Some species seem to be protective but there are undoubtedly complex interactions between the different species, some known and some not, which are essential for a healthy microbiome.
And some of the commensal bacteria may be important for some functions and others for different ones. Clearly, it is not as simple as eating probiotics like yogurt (which still may be helpful). Instead, do everything you can to preserve the natural microbiome, best achieved by eating a diverse diet.
Will science create the studies that will allow us to gain a better understanding of the important role that the microbiome plays in nutrition and health? The current system for developing research studies focuses primarily on disease. It seems dietary interventions have an impact on health because of their effect on the microbiome (especially probiotics). Studying healthy populations is different than studying disease, yet these efforts have been lacking due a dearth of funding for research on health. The National Institute of Health funds disease research, not health research, and the food industry does not currently have the funds to do large-scale clinical trials, the kind that are needed to substantiate health claims. Certainly not like the pharmaceutical industry does.
In closing, some recommendations can be made: don’t kill off your microbial diversity with processed foods and factory-farmed meats. Take antibiotics only when necessary. Eat as many vegetables as possible and indulge a bit in traditionally produced cheeses, which are rich in microbes. Eat more pre-biotic foods (like artichokes, garlic, beans, oats, onions and asparagus) as well as probiotic foods, which include sauerkraut, kim chi, kombucha and pickled vegetables.
Having an abundance of different species is very important to health and well-being. A good microbiome richness is associated with greater ability to deal with stressors such as infections or poor diet. Reduced microbiome richness will result from a restricted diet, ageing, diets low in plant fiber, and the overuse of antibiotics. These changes in the microbiome seem to be associated with various disease processes, certainly obesity, insulin resistance and poor cholesterol profiles. The take home message of the day? Take care of your microbiome and it will take care of you!
Editor’s note: Dr. Conway McLean is a physician practicing foot and ankle medicine in the Upper Peninsula, with a move of his Marquette office to the downtown area. McLean has lectured internationally on wound care and surgery, being double board certified in surgery, and also in wound care. He has a sub-specialty in foot-ankle orthotics. Dr. McLean welcomes questions or comments email@example.com.