Microbiomes: The middle road to understanding

     "Western" medicine is excellent on the mechanics of the body -- replacing a hip, changing out a lens for the eye, insert a replacement cochlea, add an artificial replacement limb, and so forth. When it comes to working with the biochemistry of the body, it is more hit-and-miss and many discoveries have been serendipitous findings rather than the tail end of a focused search. Some aspects of interactions have been investigated and understood but, still, more from the point of view of mechanics -- receptacle points, chemical reactions, and enzymal subsystems.

     "Eastern" medicine has a longer history of treating the body, mind, and functioning as a holistic system -- recognizing that the mind (whatever that is), soul (whatever that is), and body all interact to make us live, react, and process life the way that we do. There is a tradition of building up longtime knowledge of the effects of various herbs, foods, and other substances with the way the body works. The manner in which such substances interact with the body are subsumed into spiritual, and traditional, teachings which often use words without specific "western" definitions.

     All approaches, and knowledge, can be of benefit.  Divisions between areas of knowledge are only useful for classification. "Western" medicine is becoming more interesting in energy aspects, such as chi. "Eastern" medicine is more allowing of the uses for engineering aspects of treating bodily ailments. Perhaps at some point, no divisions or classification will shine out.

     One area of development which is more in the "middle" of such development is research into the microbiomes of the body. As a recent "Gates Notes" blog indicated, a large percentage of our bodies are actually cells not directly part of the body. Most of such are beneficial and many are symbiotic. His blog emphasizes uses of pro- and prebiotics to help the microbiome in their tasks and provide a better symbiosis with the body. There are also books on microbiomes, a major tome of which is "I Contain Multitudes" by Ed Yong.

     Gates' blog emphasizes the role of the microbiome as applied to treatment of malnutrition. My own older blog on microbiomes (perhaps of interest to read, from May 25, 2015) covers some of the various important microbiomes -- including that on the skin which can provide a first point of defense for intruders into the body as well as the effect of the microbiomes may play with systemic diseases such as diabetes and asthma.

     I point out that a large problem with the transformation of our microbiomes is that manipulation can be very difficult to achieve. The upper digestive tract -- which should be the most direct route to the environment of the lower digestive tract, acting as a home for a major microbiome -- destroys most of any pre- or probiotics that try to enter via the route of ingestion. Substitution from the other direction (not necessarily for the squeamish) works much better but has the problem of being more of a "mallet" approach where it is not a manipulation but, rather, an attempt to conquer the old microbiome by a newer, hopefully healthier, microbiome.

     One side-effect of being aware of the existence of the microbiomes on, and inside, our bodies is that it has become much more obvious that it is wrong to say "kill all the bacteria" or "stop all the viruses". In fact, although antibiotics have been literal lifesavers to prevent major harm from bad bacteria, antibiotics may also contribute to more general illnesses (diabetes, arthritis, cancer, etc.) as a result of killing off helpful good bacteria.

     Note that there will never be ONE general population of microbiomes because each environment supports different situations. Someone who has rice as their principal food will support different creatures in their microbiome than someone who has wheat bread as their dominant food (and even different for those who have cola soft drinks as THEIR dominant calorie intake). A person living in near constant heat will have a different skin microbiome than someone who lives (or, with climate change, lived) in sub-freezing temperatures year-round.

     One of our challenges in this investigation is inventories. Just what viruses and bacteria are present in, and on, our bodies? What are their side-effects from living? What helps the good ones (which are typically dominant)? What hinders the specific bad ones (the methods we have do not discriminate well between beneficial inhabitants and those that are bad). We are aware that traditional uses of antibiotics are losing their usefulness as bacteria adapt to resist the medicines. Knowledge of our microbiomes will require us to understand well enough to tailor medicines against specific creatures rather than "all" creatures.

     After inventories -- knowing what, and what they do -- we need methods of manipulation. Pre-, pro-, and regular biotics might be encapsulated such that they only become vulnerable after the digestive process has completed its task of breaking down food into components. "Good" cultures could be maintained outside of the body and used to supplement existing microbiomes.

     Whatever emphasis is taken, our bodies ARE indeed houses for many. Some religious scriptures may refer to our bodies as temples and occupational spaces for the gods. We need good neighbors within our bodies as well as in the outside world between people. Finding methods of understanding these interior worlds of interacting cells may be as difficult as understanding of the outer world but both can be of great benefit and worth the effort;

Our Bodies are Houses with many Rooms

   When we think of our bodies, we think of all of the various parts that built up from that original egg and sperm that started the process of dividing, growing, and specializing. From that beginning, we end up with a set of systems which allows us to stand, move, breathe, eat, and do the other functions of everyday living. These systems work together to make it possible for us to live and reproduce.

   But, our bodies are NOT just composed of the cells that were created as part of growing and life. Our bodies provide an environment for many other living organisms -- some hostile but many of great benefit to our everyday lives. For many years, medical researchers have just noted the facts of their existence (and, sometimes, blindly tried to eliminate them) and had no real idea of just how they interact with the rest of our bodily functions. This is now changing and active research is being done. Note that this research is still young in experience and knowledge and many interactions and functions are still unknown.

   An organism can exist anywhere within our body but we will focus on four areas that are of specific interest. These include the interior cell, the skin, the mouth, and the digestive tract. Within the interior cells exists organisms called the mitochondria (one of such is called a mitochondrion). While these "organelles" are an important mechanism to supply energy to the human cell (and, thus, to the human body), they also have many other functions within the body.

   The mitochondrion reproduces independently from the other cells of the human body. It exists only within the egg (and not the sperm) and thus, inheritance of the mitochondria within a body is based on maternal lineage (mother to child). The separation between egg and sperm and its independent reproduction gives it a likelihood of being considered an endosymbiont. In other words, at some point in the past the mitochondria took up residence within human (and other animals) cells and act as cooperative parts of the cell.

   On the surface of the skin (even the very "cleanest" of skin), exists a wonderland of tiny animals, bacteria, and other living creatures. The exact interplay between these creatures and their environment (the skin) is still to be fully understood but it is recognized that they do play a part in keeping the body from being invaded by unwelcome visitors. Of course, within this dermal ecosystem is the possibility of undesirable inhabitants -- such as fungus that creates "athlete's foot".

   There is a large difference between the mitochondria living peacefully within the cell and the exposed environment of the skin -- a large, direct, interaction with the exterior world. Showers, baths, perfume, makeup, dirt, and so forth will affect the living environment on the skin. How does it affect it? We don't really know but two people (let's say they are identical twins to make this simpler) who have different exterior living environments, diets, and exterior habits will have different sets of creatures (or, at least, different proportions) on the skin -- which is likely to affect some aspect of health and protection from exterior invasion.

   Our mouths harbor a large collection of bacteria and other living matter. This environment can be altered by both external and internal processes. Cleaning teeth and gums can reduce the amount of bacteria and their by-products. Blood sugar levels (especially relevant to those with diabetes) can alter the number and type of bacteria living in the mouth. (Note that brushing, diet, gum health, and blood sugar levels can all change the smell of your breath.) Many oral bacteria have potentially bad effects -- but controllable -- and, presently, few beneficial effects are known.

   The area of symbiosis of greatest present interest is the world of the digestive tract. Although it has long been known that interior bacteria can be directly involved with digestion -- for example, termites have special bacteria that allow them to digest cellulose (wood fiber) -- it was not known that the same was true with humans and other animals. It turns out that the composition of the neighborhoods of our digestive system can affect hormones, immune system, metabolism, allergies, blood sugar levels (not just insulin and sugar), mood, and other matters.

   Just how, and what, makes a difference is still unknown but the knowledge that it makes a difference is truly exciting -- in reality the addition of an entirely new bodily system. This infant study, of course, gives rise to much speculation and marketing of things believed to make a difference -- such as probiotics which are supposed to enhance positive groups of bacteria within the digestive system. Little is known for certain but it is an additional, important, area to understand for better health and activity.