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The Balance Between "Good" and "Bad" Bacteria in the Human Body. An Expanded View of the Microbiome.

Updated: Feb 25


The microbiome of the earth shown in a lake, tree, and rocks

Some say that our microbiome contains both “good” and “bad” bacteria. Through study of the microbiome, many scientists are coming to understand this isn't necessarily true.


Trillions upon trillions of bacteria, fungi, viruses, parasites, and other microorganisms are found throughout our bodies. Our body is literally a wild ecosystem of interdependent microorganisms, many of which are crucial to our health. As a whole, this conglomerate of microorganisms is known as the "microbiome".


The microbiome is at the center of human health, both physical and mental. There are both "good" and "bad" bacteria, fungi, etc. found in all organs (even the brain), bodily fluids, epithelial tissues, and the skin (which is the body’s largest organ). We are literally covered in bacteria inside and out. But guess what? It's not gross. It's actually necessary. Without them, we would not exist.


Our gut microbiome contain helpful bacteria, such as Lactobacillus and Bifidobacteria, which are directly involved in the production of neurotransmitters dopamine, serotonin, and GABA. These are “happy chemicals” often associated with mental well-being.


But of course, there are also microorganisms that can be harmful, such as Candida albicans, a fungus that is crucial to the digestion of nutrients, but when it becomes overgrown it becomes a pathogenic fungus that is detrimental to physical and mental health.


It isn’t quite right to call bacteria “good” or “bad”

Here’s the thing that is often misunderstood in our current westernized “war on germs” paradigm. That is, it is not as simple as calling bacteria, fungi, or viruses “good” or “bad”. In some ways, it is perhaps more accurate to say there is balance and imbalance.


Just as is the case with the necessary Yin and Yang of life, we need both “good” and “bad” microorganisms in the ecosystem that is our human body. If we do not have the “bad” ones, then our immune system will not have anything to fight and adapt to, and it will become weak. We also need the “good” ones, as they support and instruct our immune system and many other systems.


According to Zach Bush MD, the issue comes in when the body is unable to adapt to the genetic input of a bacteria, virus, or fungi, or it does not contain enough other microorganisms to offset "harmful" species. Yes, certain microorganisms can cause suffering for your body, but if your body is equipped with the necessary biodiversity of the microbiome, strength of immunity, and biological adaptations, then these microorganisms may not even lead to any symptoms of sickness. Instead, they may lead to an increase in your body’s resilience.


Microorganisms such as bacteria and viruses become an issue when they overgrow and begin to take over - hence the imbalance that leads to symptoms. When the body is under stress from toxins, and the immune system is weakened, it can become incapable of successfully fighting off an infection. The body's sneezing, coughing, swelling, fever, etc. are all adaptations to fight off an infection. Through this process, your body detoxifies itself as your immune system learns to adapt to the genetic input of foreign invaders.


The very presence of these “bad” microorganisms requires the body to rise above and develop higher resiliency, leading to a resultantly stronger biological ecosystem and long-term, communally beneficial adaptation of the human species as a whole. As we each receive new genetic information from microorganisms, we continue to advance in our adaptations to their inputs, both as individuals and as a community.


So, am I saying you should go jump in a cesspool filled with harmful microorganisms or take a big ol' swig of Salmonella?


No, of course not. What are you nuts?


I'm simply saying that both commensal ("good") and opportunistic ("bad") species of bacteria or fungi, as well as viruses, are necessary for optimal human health. And in saying that, I think it is beneficial for us to understand that we do not need to be afraid of them.


Quorum Sensing

One incredible part of all of this is the function of quorum sensing. Quorum sensing is the communication that microorganisms (bacteria, fungi, viruses) use to pass along information. When one microorganism genetically adapts to something in its environment, it will pass along the information for that genetic adaptation, both to fellow bacteria/fungi of its own kind as well as bacteria/fungi of other species.


This is why we have new flu strains each year - they change. This is also why herbicides lose their function over time, rendering the result of resilient “super-weeds” that cannot be killed by toxic chemicals like RoundUp.


Nature adapts.


In this same way, we need viruses that pass along genetic information which causes our body to adapt and grow more resilient. Viruses carry with them packets of genetic inputs, and when adapted to properly they are actually helpful. Depending on the state of our immune system and our microbiome, we may either adapt or we may unfortunately experience inflammation that overwhelms our body, leading to severe sickness or death.


The problem with trying to create a sterile environment

The highest determinant of human health and strength of immunity is the degree of biodiversity (biological variety) in the microbiome. We need many, many different species of both “good” and “bad” species of bacteria and fungi in our system so that they can balance one another out and bring our cells a variety of inputs so they can adapt to the environment.


The trouble is that we live in a highly “sterilized” and toxin-filled environment in westernized society. This has led to a mass and tragic death of many diverse species of microorganisms that we once relied on for our immune health, which has lead to many of the chronic illnesses and severe mental illness we are now experiencing.


Without this biodiversity of bacteria and fungi in our bodies, we cannot adapt to the changing world and our body cannot behave harmoniously with the environment. As we have a microbiome, so does earth and nature. Without connection to this ecosystem of holy biodiversity, we experience a depletion of our resilience and become disconnected in more ways than one.


We have separated ourselves from nature. We have left the forests and jungles for steril, chemical laden office buildings. We spray antiseptic and antibacterial solutions on everything, thinking we are keeping ourselves “safe”. In reality, we are simply destroying the biodiversity of our environment and giving rise to more resilient, opportunistic (“bad”) microorganisms which have the opportunity to grow out of control because there aren’t enough other microorganisms to keep their population in check with healthy, natural competition.


I don’t say this to promote a “doomsday” mentality or suggest that we all sing kumbaya and rejoin nature in our loin cloths (though that does sound fun). Rather, I believe that our current circumstances are a divine call to action. Many of us have abandoned mother nature, and in so doing we have cut ourselves off from her healing capabilities. If we can respect her again by spending time in her, partaking of foods that are closer to the way we once ate, and actually caring about her longevity through being less wasteful, then we can experience the healing power of nature’s microbiome once more.


Without struggle, there is no need for transformation. Without opposition and suffering, how would we know we need to change our ways? There is reason and purpose for the state of our earth and our chronic illness. It is God’s and the earth’s sign to us that we need to change. The same way as suffering can be a sign that we are being too selfish or that there is some circumstance that we need to use our power to overcome, the current state of westernized society’s health is a call for each of us to change the way we do things. It is an opportunity, not a destructive ending of humanity.


Achieving the balance between “good” & “bad”

It is said by Dr. Josh Axe in his book Eat Dirt that a proper balance between “good” and “bad” species of bacteria is around 85% “good” and 15% “bad”. When this balance is achieved, our overall well-being is increased. We can increase biodiversity and achieve more proper balance of our microbiome by doing the following things:


Get out in nature

Spending time in nature and in the ocean is one of the most healing things we can do. This is because nature has its own microbiome, the most ancient one there is. Unfortunately, toxins like herbicides, pesticides, and petrochemicals have defiled nature and led to the death and imbalance of much of earth’s biodiversity, but we can still experience the healing properties of nature in many areas.


Feel free to touch the plants, walk barefoot in the dirt, swim in the ocean - heck, hug a tree! We expose ourselves to the many microorganisms in nature through breath and touch, inviting in new genetic adaptations for higher resilience and well-being.


Get away from toxic foods

Cutting out foods and toxins that defile and alter the health of our gut microbiome, such as conventional dairy, meat, wheat, and sugar can enable the biodiversity within our body to grow. This will lead to better physical, mental, and spiritual health.


Switch over to natural cleaning products

Switching from conventional to natural cleaning products, such as Puracy or Better Life can lead to a healthier microbiome and immune system. This is because you are no longer exposing yourself to toxins that cause inflammation in your body and brain, and you’re getting away from antibacterials which kill all bacteria in your body.


Natural cleaning products use many natural “antimicrobials”. These are compounds such as plant oils or “essential oils” that are non-toxic to the body when we breathe them in or touch them to our skin. Remember that the skin is absorbent and what we touch enters our bloodstream.


Coming in contact with antibacterials here or there is fine, so don’t be overwhelmed by the concept of always avoiding them. Your body can handle some adversity. Minimizing our exposure can be helpful to maintain a healthy biodiversity of our microbiome and decrease our exposure to chemicals that cause inflammation in the body and brain. Inflammation is an underlying condition for chronic physical and mental illness.


Switch over to natural cosmetic products

Switching from conventional to natural cosmetics can be extremely helpful as well. Whatever we put directly on our skin absorbs and enters the bloodstream. If we use chemicals on our bodies, this can cause inflammation in the body and brain, as these chemicals travel.


Products such as Dr. Bronners and Dr. Squatch are toxin-free, work well, and smell good. Some of Dr. Squatch’s scents honestly work great for women too, so don’t think they’re all just for men.


Eating organic fruits and veggies.

Organic fruits and veggies (especially those grown locally or from your own garden) have a microbiome of their own. They’re also loaded with phytonutrients that are antioxidant and anti-inflammatory, which promote physical and mental health like nothing else can.


Eating fermented foods

Eating fermented foods fills your gut with probiotic species such as Lactobacillus and Bifidobacteria, leading to better production of hormones and neurotransmitters, better digestion and absorption of nutrients, and more.


Biodiversity is what is important

By treating our bodies and environments more in the way God and nature intended, we can experience vibrant health and relief from anxiety and depression.


When we have a diverse, healthy microbiome, our body can properly absorb nutrients, produce neurotransmitters and hormones, flush out toxins, and maintain strong immunity.


When we have a balance of different species of both commensal (“good”) bacteria and opportunistic (“bad”) bacteria in our body, then they can keep one another in proper check.


Without the “bad” (opportunistic) bacteria, our “good” (commensal) bacteria would have nothing to keep them strong, struggling against other forces that cause them to adapt and become more resilient. We need exposure to viruses, bacteria, and microdoses of natural adversity to keep our immune system strong, as the gut microbiome is at the center of immunity.


Without “good” bacteria, “bad” bacteria take over the body, forming colonies that overwhelm the system and act out of self-preservation and the incessant instinct for proliferation, rather than a contribution to the well-being of the whole system. This is why these “bad” bacteria are technically referred to as opportunistic, because given the opportunity they will take over the system.


For instance, Candida albicans is well-known for its destructive potential in creating severe digestive issues, fatigue, anxiety, and depression. But Candida albicans has always been present in our bodies. It is a highly necessary fungi that promotes normal digestion and nutrient absorption. It is also necessary for keeping other microorganisms from overpopulating the gut and also for breaking down and consuming the physical body after death (one of the fundamental roles of fungi in general).


Candida only loses its normally helpful nature when specific conditions such as gut dysbiosis, a weakened immune system, and increased intestinal permeability (“leaky gut”) are present. Candida feeds on sugar, so consuming a diet filled with these (as the westernized diet is) can yield an overgrowth of the otherwise harmless and helpful Candida.


It is in circumstances like this that Candida forgets its part in the whole of the ecosystem of the gut and body. It begins to become “self-centered” in a fashion, consuming as much sugar as it can get its hands on, transforming into a biofilm that invades and overtakes the gut. It creates a network among those of its own kind, ignoring the overall balance, proliferating, and hiding in the gut to ensure its own survival. At the same time, it digests sugars, fermenting them and producing neurotoxins that can travel up the vagus nerve into the brain, causing fatigue, anxiety, and depression.


From micro to macro

Just as there is necessary “good” and “bad” in microorganisms, it is the same with life.


It is fascinating to take this from the micro to the macro level of consideration. Just as Candida albicans can become destructive when it is fed too many inflammatory foods like dairy, sugar, and wheat, so too can we become self-centered and destructive when we live a life filled with too much pleasure and self-centeredness. We can forget our part in the whole, disconnecting from others, hoarding attention, possessions, and love all to ourselves, believing that there isn’t enough to go around.


When we act in fear, pride, or anger we begin to forget God and forget other human beings. The same way that cancer comes from a disconnection of cell communication, leading to development of cells that feel completely “alone” and begin proliferating excessively on their own to create their own structure separate from the plan of the rest of the body, we can become a cancer of sorts when we forget God and our fellow human beings.


Life necessarily entails both joy and suffering. Without joy, we feel empty. Without suffering, we cannot learn, grow, and rise above. We need both “good” and “bad” in order to experience the depth of life. Suffering - physically, mentally, or spiritually - is not simply an ailment of agony, but a sign of the need for change, an opportunity to deepen our perspective on life, or a chance to gain compassion for ourselves and others.


We can see purpose in both the light and dark of life, as we center our lives on serving God and our fellow human beings, trusting that He has the answers and will make manifest the purpose in our suffering.


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