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9. The Microbiome: What's The Flux?

We are not born with a microbiome; we begin to acquire it from our mothers and our environment at birth and as a continuous process over the course of our lives. At birth, a baby is essentially washed with his or her mother’s vaginal bacterial community, which appears to be important as an early protection from less friendly bacteria. The infant is also exposed to the mother’s colonic bacteria just beause of proximity to her anus. This is also important because those bacteria are going to be essential for proper digestion.

These initial sources of bacteria are in strong contrast to babies born by Caesarean delivery whose first encounter with bacteria is from the skin of the mother which is a bacterial community unrelated to the digestion of food or the immune system.[i] Many of those bacteria are also more closely related to disease-causing bacteria.

Upon birth, our digestive system is not yet functioning, having never received solid food from the mouth, and it will slowly be activated with the introduction of breast milk. The presence of many species of useful gut bacteria in breast milk, such as streptococci, staphylococci and lactobacilli, implies that the naïve gut is transformed almost immediately as the baby begins breast-feeding. These bacteria appear to be transferred from the mother’s gut to the mammary glands while the mother is in labor. This movement makes sense because the infant has not yet been introduced to food and the digestive system has not been stimulated, the presence of undigested lactose from breast milk will require very particular bacteria.

Lactose intolerance is a common but transient problem in newborns and may be one cause of infant colic. That is, the lactobacilli that break down lactose sugar generate lactic acid in both the small intestine and the colon and unfortunately may produce gas that causes discomfort in babies unless other bacteria are present to consume the lactic acid. However, lactobacilli also produce hydrogen peroxide, which inhibits the growth of the common intestinal fungi, Candida, which in turn can be transformed from commensal to pathogenic (candidiasis) for people with compromised immune systems.[ii] Thus, the baby is gaining both an ability to consume lactose sugar from mom and a protection from other bacteria that are not yet welcome in the digestive tract.

As children age and begin to eat more complex food, especially foods containing plant fiber and indigestible solids, the bacteria community grows and shifts. Breast milk bacteria become less abundant while other species become much more common. As adults, the diet will shift the abundance and diversity of the bacterial community depending on the proportions of lactose-rich dairy products or fiber-rich vegetable material or highly processed grains. How much influence the infant and juvenile diets will have on the diversity and stability of the adult bacterial community is still completely unknown.

As the digestive tract matures and is colonized by increasing numbers of the mother’s microbiome, certain bacteria will interact with the lining of the colon and help to form a protective barrier. This barrier is a mucus layer with dense colonies of the protective bacterial species and it prevents other bacteria from coming in direct contact with the colon. This prevents dangerous bacteria from penetrating the gut tissue and causing infections or invading other organs and tissues.

These protective bacteria, in turn, seem to be mediated by the presence of an antibody, provided by the mother but also produced later by the infant, called immunoglobin A which helps regulate the abundance of beneficial bacteria.[iii] Thus, the baby’s body works with beneficial bacteria to keep the majority of the microbiome isolated in the colon.

The colonization of the baby, particularly via the digestive tract, may have implications for later health. The diversity, abundance, and balance of the bacterial species of the colon are a function of our personal history as well as a function of the food we eat.[iv] The ability of the bacteria to manage our indigestible food, to maintain their populations, and to avoid being dominated by invasive species may be a persistent characteristic that depends on the conditions of our childhood. For example, a diet with a large proportion of calories from sugary drinks (high digestibility) will necessarily contain lower quantities of foods with low digestibility. If the foods we eat are the foods we feed friendly bacteria in our colon, a diet of highly digestible foods leaves very little for the bacterial community to feed on.

When we are healthiest, we are feeding ourselves well, but also feeding our mutualists and keeping them healthy. In turn they provide services to us that influence our health in others ways. The presence of certain bacterial groups is strongly related to the presence sugars while other groups are related to proteins and fats, and therefore the quality of food we eat determines the abundance and dominance of different bacterial groups.[v]


The Beer-Fries-Chicken Diet

What happens when we eat a very simplified diet and for long period of time? We have to assume that a diet of French fries, fried chicken, and light beer (or soda) is probably not sufficiently complex to support the diversity one would find in a digestive tract receiving a more traditional diet that is high in unprocessed plants. French fries are carbohydrates (potato starch) and oil, fried chicken is protein and fats, light beer is alcohol and some carbohydrates, and the diet lacks fiber altogether. The different food materials are digested (broken down chemically) at different rates.

In humans, simple carbs and fats are easy to digest and this takes place in the small intestine where they are absorbed quickly while digestion of the more complex proteins begins in the stomach and is completed in the small intestine. Fats, simple carbs, and proteins are completely digested in the small intestine and little if any of that material arrives intact to the large intestine. On a beer-fries-chicken diet, none of the food makes it to the large intestine no matter how fast it moves through the small intestine.

The transit time of food through the small intestine is typically less than two hours.[vi] Foods with materials such as bone, gristle, and cellulose fiber cannot be digested in such a short amount of time and therefore those materials enter the large intestine more or less intact. This is the food for the microbiome.

On the beer-fries-chicken diet, the bacterial composition of the microbiome would shift dramatically to the few species that can survive on the meager supply of food materials. As the food supply is simplified, the composition of the microbiome would be simplified and diversity would decrease. The restructured bacterial community would be genetically less genetically diverse as well.

Although a beer-fries-chicken diet is an extreme example, the modern Western Diet[vii] is even less complex than it once was and this has been part of the reason for the growth of the fad diet market. Soluble and insoluble fibers, lycopene, resveratrol, purple fruits and vegetables, antioxidants, omega 3 fatty acids, oats and whole grains, and so on, are all purported solutions to the problem of the modern highly-processed, nutritionally-depleted diet.

We eat more processed foods than ever before with many natural substances completely removed, and many other unnatural substances added in. The complexity of the materials reaching the large intestine has been greatly reduced. Processed foods and fast foods make up a diet that is very easily digested and with low amounts of slow-to-digest plant material. The typical human microbiome being fed the Western Diet is being starved and is less diverse compared to the typical microbiome of 50 years ago or that of people living in more traditional cultures.

While it’s very easy to increase the diversity of the gut microbiome by manipulating our diet, our concern should be for the influence that simplification has at critical periods in our lives. If a physiological process is changed, it can have important consequences for other processes in the body. That is, a direct change can have indirect and unforeseen effects.

Ecosystem ecologists use the phrase “cascading effects” to refer to the multiple indirect consequences that can follow an apparently simple change in an environment. For example, in humans, some people suffer from a genetic disorder called phenylketonuria (PKU) and are unable to process the amino acid phenylalanine in the food they eat. Without the necessary enzyme (phenylalanine hydroxylase) to break down phenylalanine, this amino acid builds up in their system to toxic levels and interferes with other metabolic processes.

If uncontrolled, PKU results in a variety of developmental disorders, including such seemingly unrelated problems as learning disabilities, hyperactivity, eczema, microcephaly, and unusually light-colored skin and hair. In part, this is because phenylalanine is broken down to the essential[viii] amino acid tyrosine, which is necessary for the production of neurotransmitters such as dopamine, epinephrine, and norepinephrine. Instead, the buildup of phenylalanine blocks the normal movement of other necessary amino acids in the brain and that hinders normal brain development.

Thus, the overabundance of a single compound in our system acts as a bottleneck and interferes with or prevents a multitude of other processes from occurring. People with PKU must modify their diets by eating foods low in phenylalanine and avoiding such things as diet soft drinks that are artificially sweetened with aspartame, which is composed of two amino acids, one of which is phenylalanine.

As our diet becomes more and more dominated by highly processed, easy to digest foods, we run the risk of starving certain mutualistic bacteria in our gut and causing long-term biochemical imbalances for ourselves. If children never have a healthy balance of foods that favor the gut microbiota, it is possible that their immune systems, their vitality, their growth and development, and other characteristics might be impaired. It’s possible they may suffer from infections more often during their life. In this sense, the quality of their food and not just the number of calories is a critical factor for long-term health and vitality.

The growing numbers of pediatric conditions requiring chronic medications appears to implicate a compromised microbiome from infancy. And the growing reliance on prescription medicines from childhood to adulthood may be affecting our microbiome in unknown ways. Thus, any actions we take that may alter the biochemistry of the intestine (and the rest of the body) should be considered in light of the health of the microbiome and this is particularly true of the young developing bodies of our children.

[i] Dominguez-Bello, Maria G., Elizabeth K. Costello, Monica Contreras, Magda Magris, Glida Hidalgo, Noah Fierer, and Rob Knight. (2010) "Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns." Proceedings of the National Academy of Sciences 107(26): 11971-11975. [ii] Martins N, Ferreira IC, Barros L, Silva S, Henriques M (2014). "Candidiasis: predisposing factors, prevention, diagnosis and alternative treatment". Mycopathologia. 177 (5-6): 223–240. [iii] Rogier, Eric W., Aubrey L. Frantz, Maria EC Bruno, Leia Wedlund, Donald A. Cohen, Arnold J. Stromberg, and Charlotte S. Kaetzel. (2014) "Secretory antibodies in breast milk promote long-term intestinal homeostasis by regulating the gut microbiota and host gene expression." Proceedings of the National Academy of Sciences 111(8): 3074-3079. [iv] Wu, G. D.; Chen, J.; Hoffmann, C.; Bittinger, K.; Chen, Y.-Y.; Keilbaugh, S. A.; Bewtra, M.; Knights, D.; Walters, W. A.; Knight, R.; Sinha, R.; Gilroy, E.; Gupta, K.; Baldassano, R.; Nessel, L.; Li, H.; Bushman, F. D.; Lewis, J. D. (2011). "Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes". Science. 334 (6052): 105–8. doi:10.1126/science.1208344 [v] Ibid. [vi] Kim, Seuk Ky, 1968. Small intestine transit time in the normal small bowel study. American Journal of Roentgenology, 104(3), pp.522-524. [vii] The Western diet is typified by high sugar and saturated fat content with low amounts of plant fiber as a direct consequence of the increasing proportion of highly processed foods. The sugar (carb) portion includes a great many calories from refined grains, especially wheat. [viii] There are 20 amino acids that together make up all proteins. Of those 20, our bodies can produce 11 and we do not need to consume in our diet. The remaining nine amino acids are considered “essential amino acids” and must be obtained through our food. People on diets lacking one or more essential amino acids (a form of malnutrition) will experience a variety of illnesses because of the inability to produce needed proteins. This is most often seen in infants and children on low protein diets in poverty-stricken regions, but has also been seen historically in adults on highly restricted diets such as the corn–based diet of the American south.


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