16. We Need More Genes!

An organism’s genome contains all of the information necessary to produce a mature reproductive adult from a single fertilized cell. One of the most fascinating aspects of genetics is that every non-reproductive cell in your body that possesses DNA also possesses the entire genome. However, each cell has a very specific purpose and uses only the tiniest fraction of the available genetic information. The thousands of different kinds of cells in our bodies use different fractions of the genome, but the entire genome is being used in one way or another or at one time or another.

In that sense, the genome is like a vast library full of books and each person visiting the library is checking out different books on different subjects. No one has time to read the entire library and nor would doing so be of any particular value. When we go to the library, we typically want a very specific portion of the information for a very specific purpose. That’s essentially what the cells in our bodies do with the vast amount of information in the human genome.

Of course, when we were embryos, each embryonic cell was undifferentiated and it produced a lineage of daughter cells that would eventually have a particular vocation. While the embryonic cell was using very little of the genetic information, it would go on to produce a huge variety of daughter cells that collectively were going to use a large portion of the genomic information. With each subsequent cell division and overall growth of the embryo, the daughter cells began to follow certain pathways and differentiated into particular cell types. As they did so, less and less of the available genetic information was relevant to the pathway they were on.

Eventually, as each tissue and organ formed, the cells developed very specific functions and had access only to very specific portions of the genetic code. A carpenter does not need a syringe; a nurse does not need a hammer. Skin tissue does not need to rhythmically contract; heart tissue does not need to sense touch. Nonetheless, all cells may interact either directly or indirectly with many other and often very different cells as part of their normal function.

Given our physical and biochemical complexity, the human genome has surprisingly few genes, about 20,000, on our 23 chromosomes. Every one of us has exactly the same genes in the same places on the same chromosomes. What makes us different are the versions of the genes, the alleles, that each of us possesses that together make each of us into very distinct individuals. And because we have two copies of each chromosome, one from our mother and one from our father, the combination of the two alleles can create additional variation. We can express one allele or the other or both simultaneously. And often we have multiple genes for particular traits, like eye color, that add even more potential for variation. However, in many ways, it isn’t the genes or the alleles of the genes that are interesting, it’s the timing and intensity of the expression of the alleles and their interactions that can be mysterious.

The expression of a gene concerns the product that the gene codes for. For many years, geneticists thought that the phrase “one gene, one protein” reflected the way the cell decoded a gene to produce a protein and the role the protein played in the cell. That is, each gene is transcribed to produce a protein and the protein has a single job in the cell. The protein might be an enzyme that catalyzes a reaction or it might be a building block as the cell produces new structures.

It was recognized that the long string of amino acids that formed each protein would curl and fold to form a three-dimensional structure and that formed a fixed shape that was the activated protein. We now understand this is only true for some proteins and most proteins are much more complicated than that. For example, the biochemical conditions in the cell where the protein is being produced can determine how the amino acid string folds and different 3-D conformations of the same string of amino acids will result in enzymes with different metabolic functions. Or an enzyme may have more than one binding site, and therefore more than one function. Or, after performing one function, the shape of the enzyme can change to allow for a different function.

Enzymes can even split in two with each fragment taking on a new capacity. The mystery behind enzymatic proteins and their functions is the timing of when, where, how, and on what other molecules are they acting. Enzymes can even influence the decoding and therefore the expression of other DNA. That is, the magnitude of the expression of a gene can be influenced by not only the presence, but the abundance of other proteins.

The oxygen carrying molecule in our red blood cells is hemoglobin and is an example of alleles and the proteins they produce being turned on and turned off. Before we were born and still in utero, our bodies obtained oxygen from our mother’s blood. Mother’s blood doesn’t mix with the baby’s blood because the two are in separate circulatory systems, but the blood vessels in the placenta pass so closely that oxygen from mother’s blood diffuses into the baby’s blood.

This indirect access to oxygen works because the embryonic blood of the fetus has a higher affinity for oxygen than the adult blood of the mother and the oxygen moves easily from her system to the fetus. Our blood is made up of very small red blood cells that contain hemoglobin molecules, a complex molecule made up of four subunits of two different globin molecules. Embryonic blood is not the same as mother’s blood: the maturing embryo produces blood subunits made of two molecules each of alpha and gamma globins and mother’s adult blood is comprised of alpha and beta globins.[i]

Just before a baby is born, the composition of the hemoglobin shifts from embryonic to adult globins over the course of several months. In other words, the gene for the gamma globin protein is turned off (down-regulated) and the gene for the alpha globin protein is turned on (up-regulated) and this is somehow facilitated by changes in the physical and biochemical environment of the fetus.

This is just one way the expression of genes changes as the environment changes, whether the “environment” is in the cell, in the organ, or external to the body. The expression of the genes depends on the environment in which the genes are being used; the effect of the environment can be to turn them off or on or to moderate their expression. Thus, the phenotype of an organism depends on the environmental stimuli that affect the genome.

For example, plants will produce defensive chemicals after they have been attacked by an herbivore. After detecting the presence of a predator, water fleas (Daphnia) will produce sharply pointed defensive structures on their shells and tadpoles will develop more muscular tails. In humans, defensive antigens aren’t produced until after we are infected with a virus. The full development of our digestive system doesn’t occur until after we are exposed to and colonized by certain bacteria in our gut. It all comes AFTER because these changes represent responses to the environment.

Our Phenotypes are the result of the interaction between the Genotype and the Environment which is to say that our physical and physiological status depends on how our genetics are stimulated by the environment. (Evolutionary biologists abbreviate this interaction: P = G x E.) The constantly changing external world of living and nonliving factors forces our biological systems to react, to adjust, to compensate, in order to maintain a stable internal environment.

The homeostasis of our internal environment is critical to efficient functioning and is tightly regulated by many feedback systems that track inputs and stimuli and then respond accordingly. If we get too hot, we sweat and the evaporation of the sweat cools us. If we become dehydrated and our blood becomes more concentrated, we are stimulated to drink. These are our physiological reactions to the consequences of being in our environment.

We also interact with the living components of our external environment and some of those interactions are very close and intimate. Hundreds of species of bacteria and larger organisms live in the dozens of different locations and niches on our skin. Hundreds more species live in our mouth. Some species don’t live on us so much as we live near them and amongst them in our clothes and in our homes. We know very little about important interactions that may exist between those organisms and our biology, particularly with regard to the health of our skin and our oral, nasal, otic, vaginal, and anal cavities and orifices. And what we are now coming to understand is that our “environment” is not just the external world, but the internal world too, and sometime it’s hard to tell the difference.

The microbiota within us helps to regulate our internal environment. At the very least, the digestive microbiome controls the rate at which food materials move through us. In a broader sense, however, the internal microbiome filters and manages inputs from the external environment whether in the form of food materials or other microbial introductions. This filtering process is one that, for the most part, we lack as humans. Left to ourselves, it is unlikely our system could manage all that enters our bodies through our mouths as efficiently as we do with the help of our microbiome.

To a pathogenic bacterium, our bodies are a rich and untapped resource with a few antibiotic defenses, and any bacterium that overcomes those defenses will have won the bacterial sweepstakes. However, our microbiome is comprised of thousands of other species of bacteria that will compete for resources, dominate the different niches, and actively resist the colonization of other newly-arriving species whether they are pathogenic or not.

Under normal conditions, a healthy ecosystem is diverse, stable, resistant to change, and resilient in the face of change. This complexity acts as an incredibly strong filter preventing colonization by new bacteria. Dozens to hundreds of species attack the food materials moving though our intestine and they leave very little niche space for newcomers.[ii] The mucosal lining of the intestine is densely packed with colonies of many species that are finely adapted to the conditions there; very few novice species can gain a foothold.

The environmental conditions, from the entry to the large intestine at the cecum all the way to the exit at the anal sphincter, vary tremendously[iii] and each section of the colon is filled with bacteria that are well suited to those conditions. Thus, new bacterial introductions to the existing microbiome will go through a very extensive vetting process; a new colonist would have to be tolerant of the acidic environment of the stomach, resistant to the antimicrobial environment of the small intestine, and then be highly competitive for space on the intestinal lining or highly competitive for the food material moving through the colon.

In short, the environmental stimuli that result in the phenotype may be more correctly understood as the interaction of the two microbiomes that directly and indirectly stimulate the expression of the genotype. We are just now expanding our appreciation of the contribution of the internal microbiome to the intricacies of homeostasis of the human body. There is no question that the microbiome stimulates and helps develop the immune system, that it provides necessary nutrients to our bodies, that it defends us from pathogenic bacteria, and that it influences our physical and physiological development. There is also no question that our microbiome cannot survive without the human body to provide a very specific habitat. It is a true mutualistic relationship except that the microbiome is an entire community of perhaps a thousand species and they fill many different niches in that habitat we call our gut, and that together the human body and the microbiome create a very complex ecosystem.

We also know that the microbiome did not appear de novo in our digestive tract, but has developed over our lifetimes from the sterile environment of the newborn to the complex, interactive, self-regulating ecosystem of the adult person. However, we know very little about the assembly process and rates of colonization.

We know the first bacteria to enter the digestive system of the newborn are oral, vaginal, and anal bacteria of the mother plus additional important bacteria from her breast milk. Those bacteria begin the process of colonization of the digestive system, they aid in the breakdown of complex molecules, and their presence in the digestive tract facilitates further colonization by creating a low-oxygen environment that is more appropriate for other species.

The eventual “biogeography” of the digestive system results in oxygen dependent species living toward the front end of the digestive tract and those favoring very low oxygen environments occupying the back end of the digestive tract. Of course, this process of colonization is made more complex with the consumption of solid and slow-to-digest food as this becomes the primary resource for the later arriving bacteria. These bacteria are introduced to the baby in different ways, but from the external environment.

Obviously, the mother, father, and siblings create a bacterial environment that introduces appropriate bacteria to the newborn. The baby’s gut microbiome will strongly resemble those of the family regardless of their genetic similarity. Other bacteria will be introduced through contact with other people, places, and things in the environment, including the food the growing child eats. This process of adding diversity will continue for several years and will be highly dynamic over the course of a lifetime.

Our understanding of the P = G x E equation has to be expanded to include an appreciation of the contribution of both the external microbial environment and ever-increasing diversity and complexity of the internal microbiota. Thus, in terms of digestion, immunology, metabolism, and some developmental processes, we have to acknowledge that the environment we experience is greatly influenced by two microbiomes that interact with each other such that the Environment (E) = MBexternal x MBinternal or we can abbreviate that to E = MB2.

The two ecosystems cannot be separated; the internal microbiome is highly dependent on the external system for inputs, but the external microbiome in the near vicinity of each person (e.g., the household) is also influenced by the internal microbiome.

Given the recent discoveries of the intense and intricate interactions between human physiology and the gut microbiome and the dependence of the internal microbiome on colonization by the external microbiome and the fact that these interactions begin at birth can continue until death... we are faced with the realization that we know less than we thought about how our bodies work on their own. The studies of germ-free laboratory animals have clearly shown abnormal intestinal development and altered immunological capacity in the absence of gut bacteria. The implications for humans are under intense investigation, but what isn’t in doubt is the essential requirement of gut microbes for what we consider normal human development and health.[iv]

If E = MB2 does represent a true statement concerning the importance of microbial ecosystems on genetic expression in humans, then as part of our quest for understanding our health, we have to reconsider our personal orientation to the external world. While evidence is rapidly mounting that the internal microbiome is of unquestionable importance for internal homeostasis and health in humans, it will also become impossible to argue that the internal environment should be considered in any way separate from or disconnected to the external environment. Although the mature gut appears to have a very diverse and stable microbiota and the appendix may act as an emergency reservoir,[v] the flux of bacteria from the external environment is likely to play an important role in keeping the internal microbiota up-to-date and relevant. While we do not have any estimates of rates of exchange between the two worlds, researchers are now turning their attention to the role of our food in supplying bacteria to the gut microbiome.[vi]

[i] The alpha and beta globins are 3-dimensional proteins that form a complex structure around an iron molecule. The iron molecule binds to oxygen and this is how oxygen is transported through the body. One red blood cell contains about 250 million hemoglobin units and an adult circulatory system may contain 25 trillion red blood cells. [ii] And obviously, the opposite is also true. People with very simplified microbiomes will be much less resistant to invasion and colonization by new microbes. And this implies that such individuals will be more prone to new and recurrent diseases. [iii] Gregory P. Donaldson, A. Melanie Lee, Sarkis K. Mazmanian. 2016. Gut biogeography of the bacterial microbiota. Nature Reviews: Microbiology 14:20-32 [iv] Felix Sommer, Fredrik Bäckhed. 2013. The gut microbiota – masters of host development and physiology. Nature Reviews: Microbiology 11:227-237. [v] R. Randal Bollinger, Andrew S. Barbas, Errol L. Bush, Shu S. Lin, William Parker. 2007. Biofilms in the large bowel suggest an apparent function of the human vermiform appendix. Journal of Theoretical Biology 249:826-831. [vi] In particular, the American Gut portion (led by Dr. Rob Knight) of the Human Food Project (led by Dr. Jeff Leach) seeks to understand the influence of diet (and many other variables) on the microbiome. With a large enough dataset, it should be possible to find strong relationships between specific dietary choices and microbial diversity. While this doesn’t measure microbe flux with the external environment, it will add tremendously to the very little we know about the dietary influences on the human microbiome.