It is well known that eating fruits, vegetables and whole grains are important for good health because they contain dietary fiber and other healthy substances1. The dietary fiber can be fermented by healthy bacteria in our gut to produce short chain fatty acids (acetic, propionic and butyric acids) that help the neuroendocrine immune system and help make vaccines more successful2. At the same time, eating sugar, high fructose corn syrup, meat, saturated or trans fats and drinking sweetened beverages is unhealthy, partly because it helps to produce an unhealthy gut microbiome. That is, the human body is an ecosystem that contains not just eukaryotic cells (sometimes just called human cells), but also bacteria and archaea (prokaryotic cells), as well as viruses, fungi, yeasts and protozoa3. In fact, the bacteria in our gut contain far more protein-coding genes (millions) than the ‘human’ cells that contain a little over 20,000 protein-coding genes, located in two pairs of 23 chromosomes4,5. Despite all these genes in our healthy cells, it just takes a few genes from bacteria (such as MRSA, or methicillin resistant Staphylococcus aureus) that are resistant to almost all antibiotics to kill a patient6,7. Antibiotic-resistant bacteria are in mass-produced beef, pork and other livestock. These unfortunate animals are often given antibiotics throughout their lives to prevent infection caused by living ankle-deep in their own fecal material caused by chronic diarrhea, which is caused by the antibiotics continually killing most of the bacteria in the animals’ guts8. So, the goals of this article are to describe the deep ecology of the human body, the importance of our microbiome in our health, disease and global climate change, as well as ways that diet can affect the microbiome.

The human body is a deep ecosystem

Systems thinkers realize that Mother Earth (or Gaia) is an ecosystem in which humans are just one of many equal parts9,10. This concept of a deep ecology has been extended into modern medicine. We now understand that there is also a deep ecology in the human body. That is, our bodies contain not just ‘human’ cells, but also Bacteria, Archaea and Eukarya that are essential for life. Even though most of the bacteria in our bodies are located in our gut, there are also bacteria, yeasts and viruses in our skin, mouth, mucosal surfaces, anus, genitals, lungs and even human milk. Although many people think that all viruses are bad for human health, they are not. There are many viruses that infect bacteria that are bad for us and may even kill us. Such viruses can help prevent pathological bacteria from growing in our bodies.

The holistic view of health that comes from systems thinking considers us to be holobionts with a hologenome that includes all the viruses and cells in our body, along with their genomes. So, when I’m asked “Why don’t you have your DNA tested? Don’t you want to know what you are, such as 100% European?”. My answer is “No, I already know what I am. I’m nearly 100% American because almost 100% of the bacteria in my body came from American genes produced by food grown in the Americas (including Mexico)”. Moreover, when I read articles that tell how Artificial Intelligence may someday be able to create a virtual person by scanning all the contents of one’s brain, I have to ask, “Which brain are you talking about?”. Our gut microbiome is a huge part of the enteric nervous system (the nervous system in our gastrointestinal tract), which has been called our second brain11. Moreover, our hormones and our immune system have strong influences on our health and personality. The brain and the rest of our nervous system can’t be separated from our endocrine and immune systems, except in textbooks. That’s why the term neuroendocrine immune system is used. It is all one interconnected system.

The importance of the microbiome in human health

Our microbiomes and hormones should work together to maintain a healthy neuroendocrine immune system3. This inter-kingdom system has been called microbial endocrinology. The gut microbiome is part of the gastrointestinal system, which has the highest concentration of immune cells in the human body. In a healthy gut, bacteria keep our immune response balanced. The natural (commensal) bacteria inhibit immune responses against them, while directing immune cells towards pathogenic (disease causing) bacteria that can enter the body. When the gut microbiome is healthy and functioning properly, it helps to maintain a tight epithelial layer that forms an important barrier. However, a diet of mass-produced meat, processed foods, saturated and trans fats, sugar, high fructose corn syrup and sweetened beverages can cause unhealthy bacteria to flourish, while disrupting the structure and function of the epithelial barrier. This barrier can leak when damaged, permitting pro-inflammatory compounds (lipopolysaccharides) to enter the body and cause smoldering inflammation, which can lead to many fatal diseases. On the other hand, healthy bacteria produce short chain fatty acids (SCFAs) that suppress inflammation and cancer3.

So, when pharmaceutical companies developed antibiotics, they often included special coatings for the capsules or tablets to protect them and prevent them from being released into the gut. The goal is to prevent the antibiotics from reaching the healthy gut bacteria and killing them. It would be highly undesirable to kill all the healthy bacteria in the gut.

So, I was especially disturbed when I read an advertisement for a dietary supplement containing nanosilver (very small, nanometer sized particles of silver) that supposedly kills all bacteria. If this statement were true, nanosilver would be deadly if taken internally. Moreover, nanosilver may cause cancer and is especially toxic to immature blood cells in bone marrow that can lead to leukemia and lymphoma12. Since nanosilver is manufactured and used in large quantities, it presents a special environmental problem. “Companies put it into socks, toothbrushes, washing machines, vacuum cleaners and other items. Sometimes adding the special silver is promoted as a defense against bacteria that might make people sick. Other times, it’s more about neutralizing bacteria that cause stinky feet or smelly breath. At last count, more than 400 consumer products contained this form of silver” 12. Not only humans, but also plants and animals need healthy commensal bacteria to survive. Even though some people are thinking of using nanosilver as a wide spectrum antibiotic, this may be a terrible idea. We need our gut microbiome to stay healthy. In addition, “Scientists warn that the more nanosilver that enters the environment, the greater the chance that microbes will learn how to resist it. Silver is a big line of defense against microbes. We don’t want to waste this weapon on socks” 12.

Perhaps the largest effect of microorganisms on human health is on the global climate13. This includes not just bacteria, but also archaea, phytoplankton, diatoms and even viruses. They affect the lives of all higher life forms. For example, there is a symbiotic bacterium (Snodgrassella alvi) in the guts of honey bees. Researchers have recently engineered a version of this bacterium that can protect honey bees from the deadly, parasitic Varroa mites14. The goal is to stop the widespread collapse of honey bee colonies.

In addition, some microorganisms produce greenhouse gases, while others consume them. Phytoplankton emit dimethylsulfide, which is converted to sulfates, which promote the condensation of clouds. Moreover, the atmosphere contains about 1022 microbial cells. They can aggregate and form aerosols. A recent consensus statement by eminent scientists warned that “the impact of climate change will depend heavily on responses of microorganisms” 13.

In contrast, a recent article showed that aerosols generated by pollution may be attenuating global warming to a greater extent than was thought previously15. This might suggest that if we decrease industrialization and pollution, that global warming could accelerate16. Some people even suggest that it is already too late – that hope is lost – that false hope can prevent us from preparing for the worst. That is, we should switch to a palliative, end of life paradigm. We should focus on living fully, pursue excellence and love. The author even wrote “Earth could lose all life”16. However, this ignores the roles of phytoplankton in the oceans and bacteria in the atmosphere, which also produce aerosols.

We should also remember that bacteria and archaea exist in extreme environments at the bottom of the ocean. It is quite unlikely that they will become extinct as the global climate changes13. Moreover, if people give up hope and assume that they only have a short time to live they might throw caution to the wind. They might feel that they might as well consume as much as possible as fast as possible and possibly even take drugs like opioids, which are given at the end of life in hospice care to make the dying person as comfortable as possible. So, I agree with Robert J. Burrowes who wrote in a recent article “There is also a significant body of evidence that human extinction is now inevitable; that is, it cannot be prevented no matter what we do. Obviously, I hope I am wrong (and I will be doing everything I can to make it so)”17.

How diet can affect the gut microbiome

Diet affects our gut microbiome from birth and possibly even while we are fetuses16. In other words, it is quite likely that our mothers’ wombs do contain bacteria that can be transferred to the fetus17, although this is still somewhat controversial20. Certainly, there are bacteria in the mother’s vagina and in her skin. Babies delivered vaginally develop a gut microbiome that resembles their mother’s vagina. In contrast, babies born by C-section that doesn’t rupture the placental membrane develop a microbiome that resembles their mother’s skin. Once the baby is born, breastfeeding can help the baby develop a healthy microbiome, since mother’s milk contains bacteria that stimulate the growth of beneficial microbial communities. The mother’s diet affects her microbiome and the types of bacteria that are in her breast milk.

The microbiota of most adults has been assigned to three predominant variants, or enterotypes. They have different amounts of three dominant genera: Bacteroides, Prevotella and Ruminococcus. The relative abundance of these genera is the basis for classifying the human gut microbiome into three enterotypes:

1) abundant Bacteroides;
2) few Bacteroides but abundant Prevotella;
3) an abundance of Ruminococcus.

Each of these genera has a different function in nutrition and metabolism21.

Their relative abundance can be affected by diet. The enterotype dominated by Bacteroides occurs mostly when people consume relatively large amounts of protein and animal fats. The Prevotella enterotype is linked to carbohydrate metabolism and a vegetarian diet. Moreover, bacteria produce important nutrients that our eukaryotic cells can’t make for themselves. For example, some species of healthy gut bacteria can ferment dietary fiber to produce very healthy SCFAs. Some people have less biodiversity in their gut microbiomes (known as low gene count (LGC)) than others (known as high gene count (HGC)). The LGC microbiota tends to be dominated by Bacteroides species and have fewer bacteria that make butyric acid. In contrast, LGC people tend to have more relatively unhealthy Firmicutes species, as well as a higher incidence of obesity and metabolic syndrome. Despite the well-known health benefits of consuming dietary fiber, almost 90% of all the people in the USA don’t consume the dietary reference intake amount for fiber (38 grams per day for men and 25 grams per day for women). This is unfortunate, because proper growth and development of a healthy gut microbiome is essential for producing a healthy neuroendocrine immune system22.

So, please remember that an inactive lifestyle, overconsumption of red meat, saturated and trans fats as well as sugar can lead to obesity. For example, a program of moderate exercise increased biodiversity in the Firmicutes phylum in participants of the American Gut Project23. Exercise has been shown to improve the gut microbiome and produce more butyrate, with significant health benefits23,24.

A diet rich in red meat tends to increase the levels of Fusobacterium nucleatum, which causes DNA damage and genomic instability within developing tumors22. Also, F. nucleatum stimulates inflammation and can protect tumors from proper immunosurveillance and destruction. This increases the risk of colorectal cancer.

In contrast, vegan and vegetarian diets can decrease the risk of not just cardiovascular diseases, but also autoimmune diseases and many types of cancer, as well as metabolic syndrome and diseases linked to it, including neurodegenerative diseases. Also, F. prausnitzii, the most abundant bacterium in the intestines of healthy adults, was more abundant in vegans than in vegetarians. This species has an especially strong protective role in preventing metabolic disease (obesity). Its level is lower in people who have intestinal disorders, inflammation, obesity and type-2 diabetes22.

The gut microbiome of obese diabetics is quite different than that of healthy, lean people. The composition of the gut microbiota has been linked to metabolic syndrome, obesity and chronic smoldering inflammation22. The microbiota of obese people is less diverse and has a lower ratio of Bacteroidetes to Firmicutes, with an increased abundance of potentially inflammatory Proteobacteria. They also have more local and systemic inflammation.

The effects of the gut microbiome on human health

While an unhealthy gut microbiome can cause diseases, including cancer, a healthy gut microbiome can act as your personal oncologist and help prevent cancer21. Bacteria in the gut produce SCFAs and other metabolites that help prevent cancer. The most abundant SCFAs are acetic, propionic and butyric acids, which exist as the negatively charged anions called acetate, propionate and butyrate at the physiological pH of about 7.3. They account for about 90% of all the SCFAs and are present in a mole ratio of about 13:4:3. Butyrate is especially important. It is the main source of energy for cells in the colon. It helps protect against colorectal cancer. Butyrate is also essential for maintaining mucosal integrity, while modulating intestinal inflammation and promoting genome stability.

Non-digestible carbohydrates in dietary fiber are fermented by healthy bacteria in the gut to produce the SCFAs22. Butyrate and propionate are especially important in preventing cancer. Butyrate and propionate also induce the differentiation of important immune cells that help to control inflammation. In addition, some gut bacteria contain enzymes that catalyze the biotransformation of dietary phenolic compounds that act as antioxidants. This includes daidzein (in soybeans), which is metabolized into equol, which has been linked to a decreased risk of breast and prostate cancer in Asian women and men.

The composition of the gut microbiota can also affect health indirectly by influencing one’s state of mind, including happiness, sadness and depression22. That is, stress and anxiety can change the function of the gut and its microbiota. Several bacteria in the gut can influence neural development, complex behaviors and nociception. So, the concept of “state of the gut” has been proposed to take the place of or augment the concept of state of mind. Moreover, we can truly have a “gut feeling”. So, changing the gut microbiota through therapeutic intervention may eventually be used to treat gastrointestinal and affective disorders.

When the gut microbiome is healthy and functioning properly, there is a tight epithelial junction that forms a colonic, ileal, jejunal and gastric barrier22. The intestinal lumen acts as a barrier against bacteria and food antigens. However, gut microbiome dysbiosis (imbalance) can disrupt the structure and function of the barrier. This can cause pro-inflammatory biochemicals like lipopolysaccharides (LPS) to leak out of the gut and cause smoldering (low-grade) inflammation.

There is an undeniable link between the brain, the gut and the immune system22. When the cerebral cortex decides that an individual is under a stressful situation, it can give that person a ‘nervous stomach’. This can also lead to an imbalanced immune system. So, the gut microbiota can interact with the neuroendocrine system to play important roles in anxiety, depression, IBS (irritable bowel syndrome), autism spectrum disorders, Parkinson’s disease and multiple sclerosis, many of which are influenced by peripheral immune system homeostasis. The gut microbiota is also important in the development of a healthy, well-balanced neuroendocrine system. When the hypothalamic-pituitary-adrenal (HPA) axis is stimulated, it can change the composition of the gut microbiome. Depression has been associated with a dysregulation in the HPA axis. Resolution of episodes of depression has been associated with normalizing the HPA axis. Microbiota can also activate neuronal stress circuits by activating pathways in the vagal nerve. A combination of exposure to antibiotics and stress caused an increase in the abundance of unhealthy bacteria as well as a decrease in healthy bacteria as well as an increase in healthy bacteria. Proper serotonin signaling is also important for good brain function. So, it is noteworthy that over 90% of human serotonin is found in the intestines. Also, bacterial infections can increase stress and anxiety.

The microbiome also affects the brain through epigenetic mechanisms22. Biochemicals produced by gut Bacteria can affect chromatin plasticity within their host’s brain. This then leads to changes in gene transcription in neurons that can change the behavior of the host. Moreover, the microbiota is an important mediator of interactions between genes and the environment. That is, the microbiota is an epigenetic entity. So, the fields of neuro-epigenetics and microbiology are converging at many levels and leading to important interdisciplinary studies to better understand this interaction.

In conclusion, our gut microbiome has been called our second brain11 and personal oncologist3. For our second brain and inner oncologist to function properly, it’s important to eat plenty of dietary fiber, whole grains, beans, nuts and legumes, as well as fresh fruits and vegetables. It’s also important to avoid eating sugar, high fructose corn syrup, meat (especially beef), saturated or trans fats and drinking sweetened beverages.


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