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17. Here's The Rub: BUGS help BIGS stay relevant

Updated: Jun 23, 2021

From an evolutionary biology point of view, exchanges with the environment (or at least an influx) would provide valuable information to the microbiome about the external environment and could help to optimize digestive efficiency and responsiveness to new food material. The capacity of the microbiota to respond to new food materials is based on previous experience. That is, we have the genetic capacity to digest basic food components (simple carbohydrates, fats/lipids, protein), but as BIGs we do not have the capacity to respond rapidly to significant changes in our environment without help from the BUGs.

The microbiota is a large and diverse collection of BUGs with a vast genetic profile and rapid reproductive potential. The more species diverse the microbiota is and the more genetically diverse it is, the greater the potential for being able to manage new food materials and to adjust to them in a relatively short period of time.

While BIGs cannot adapt rapidly and cannot easily adjust to environmental conditions with which there is no prior evolutionary experience (such as a very different source of food), the bacteria associated with the food or the same environment may be able to make rapid adjustments for us. Our evolutionary past, involving thousands of years of living in a particular region and eating the foods of that region, has molded our digestive ability and in some cases very specifically.[i] It very likely takes thousands of years for such adaptations in humans to take place, and so it is also a survival imperative to have the capacity for rapid adjustment. Our microbiome provides that.

Humans have the genetic capacity for handling a range of food types, but there is no way to anticipate sudden changes or novel food materials and the human system does not have unlimited capacity. Thus, most animals and especially all omnivores (such as ourselves) possess diverse microbiomes that can very likely adjust to manage new food material. The possession of the microbiome is itself an adaptation because it keeps us alive, healthy, and reproductive. The more capable our microbiome is, the healthier we are. In a bacterial sense, being capable in means diverse and up-to-date with respect to the surrounding environment and the stream of food materials moving into and through the body.

A bacterial community that is up-to-date and relevant is one that is regularly challenged by the environment and that, by necessity, means interactions between the internal and external worlds. The movement of bacteria into our digestive microbiome from the external microbiome is the movement of environmental information. New species and new genotypes of current species represent genetic information because those new colonists possess different genes and alleles.

If those genetic additions confer new traits, different responsiveness, or new digestive capacity, then the microbiome is more capable relative to the flow of food materials that is being consumed by the host organism. This in turn would accelerate responsiveness and shorten response time when new food materials are encountered in the large bowel and thereby lead to less digestive distress and more efficient digestion.

We have to assume that certain foods would facilitate this important and necessary flow of information to the microbiome. New food materials, with which we might need some digestive assistance, are almost certain to be indigestible plant materials and secondary plant compounds (because we are fully capable of managing basic fats, proteins, and carbohydrates). Of course, ingesting uncooked meat carries a very high risk of introducing pathogens so the sources of additions to the microbiome probably are from plant materials.

Fresh fruits and vegetables would be a likely source of new colonists because cooking and processing plant materials would essentially sterilize the foods and eliminate microbes (except those associated with spoilage). We can predict that a diet of highly processed and easily digested foods would not assist in the flow of new information just as we know that low fiber diets with very little plant material will reduce microbial diversity in the gut.

In contrast, diets high in novel and unusual fresh plant material may create digestive difficulties because of a different balance of celluloses, chitins, lignins, pectins, and some kinds of starch. In addition, plants produce a huge variety of toxins to prevent herbivory in the form of phenols, alkaloids, and terpenes. These compounds are particularly important because many of them have antibacterial qualities or interfere with chemical breakdown by microbes. An inexperienced digestive tract may lack the microbial diversity necessary to adjust to such new foods, but because humans do eat a tremendous variety of plant types around the world, we can safely predict that gut microbes that specialize on or are tolerant of these plants do exist.

If the microbiome does not receive regular information and maintain high genetic diversity, its resilience in the face of change may be compromised.[ii] Ecological research strongly suggests that less diverse systems are less resilient, but we should also expect that out-of-date and isolated systems are less resilient too. For example, a person on a very specific and low diversity diet is not actively challenging the digestive microbiome and can potentially lose diversity, especially with periodic flushing of the system due to diarrhea events or antibiotic use.

Such a low diversity digestive system would lose resilience and potentially would be less resistant to pathogenic colonizers and more prone to disease. Indeed, the increasing frequency of stubborn Clostridium difficile (C.


diff) infections is directly related to the use of antibiotics that reduce species diversity and invasion resistance in the gut and invite opportunistic infections and dominance.

In summary, given what we know and are learning about the importance of a healthy and stable internal microbiome to our health, we must predict that such stability is based on ecological and evolutionary principles, as are all other processes governing living things. An important part of that stability is active, vital, and frequent exchanges between ecosystems. We should certainly expect the discovery of interesting nuances concerning these ecosystem interactions, but the vitality of the internal ecosystem will be predictably dependent to some degree on the vitality of the external ecosystem.

Whether this dependence is a long-term function or also has short-term aspects, and


whether that changes over one’s lifetime, will be a fascinating avenue of research. Given the importance of the microbiome to the human system, we know that this symbiotic interaction has existed for millions of years and the stability of the microbiome, its ability to recover quickly, its close relationship with our physiology, and its dependence on our internal environment all reflect an evolutionarily significant link to our ability to survive.

Basically, we are very likely protected from short-term fluctuations in the environment because of our microbiome, but the microbiome is also reliant on a flow of information from the environment for its and our long-term health.



Based on principles and evidence, I think we must conclude that the health of our personal ecosystem depends in a very real way on the health of the external ecosystem. Damage to the internal microbiome has an effect on our health and we are just beginning to realize the implications. But perhaps just as important is that damage to the external ecosystem,


particularly to the external microbiome, will have an effect on the internal microbiome because of the loss of potentially important genetic information. The destruction or simplification of our ecosystems, or the loss of ecosystem components, may very well have ramifications that we can’t anticipate specifically, but which we can predict generally.

By simplifying our external world, we are losing genetic information in the form of microbial species that may be necessary for our long-term health. Just as losing one or a few species from a diverse ecosystem may not have obvious dramatic effects because there are additional species to fill the roles of the lost species, the repeated loss of species will result eventually in loss of ecological functions when no species remain to fill certain niches. Such losses result in wholesale shifts in the attributes of the ecosystem. Some of those losses may not be tolerable.


[i] In Food, Genes, and Culture (2013, Island Press) Gary Paul Nabhan writes about the tight link between cultures and their foods and give special attention to the idea that not only did humans adapt over long periods to the foods of the ethnic region, but in some cases the foods are necessary for general health. More specifically, some types of foods that are not part of the culture may be unhealthy because there is no adaptive history with them. [ii] An imperfect analogy is that of virus protection on your computer. When virus protection is out of date, the computer is naïve relative to external threats. Updated virus protection is essentially new information about the outside world that protects the computer from invasion and damage.


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