bacteria and viruses

photo courtesy of renjith krishnan at

Our bodies have been proven to not be sterile, but instead are a literal war zone of viruses, bacteria, and microbes that are in competition. Yet, we can build resistance to these viruses and bacteria. In our bodies there are bacteria that exist for viruses. There are yeasts that exist to protect us. Everything we eat, everything we touch, what we drink, people who are close to us, smelling a fart, inhaling fake perfumes, all contribute to what is going on in our internal war zone. We are either strong and balanced, or in a declined state where we are susceptible to picking up every cough and sniffle from those around us.

“Because we’re bringing balance and competitive forces within the microbiome, it gives every species that’s coming in a chance. It also translates into fermented foods, because you end up with more diversity. You end up with the ability to assimilate, the ability to take in more nutrients from all the various foods you consume,” says microbiologist Kiran Krishnan. Krishnan is one of the elite scientists who worked on the Human Microbiome Project, studying the microbiome for the NIH which started back in 2017. Their findings have been phenomenal.

Due to these studies, we now know more than ever before, how these viruses work in our bodies and why one person is affected worse than another. We can build resistance to these viruses and bacteria to make us more resilient.

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Viruses, bacteria, and fungi are all part of the balance in the microbiome. The ecosystem of viruses in the human body is called the viome, the microbiota for the viruses. Krishnan says, “There’s lots of latent viruses in most of us. Most of us have been exposed to Epstein-Barr virus, Cytomegalovirus, Herpes Simplex, papillomavirus. Most of us have them all over our bodies, even in our cerebrospinal fluid.”

Epstein-Barr virus is classified as a common virus. The Mayo Clinic says antibodies have been detected in nearly every person by the time they turn 35. In healthy individuals it goes unseen. In those with weakened immune systems it generally consists of fatigue, headache, fever, sore throat, and swollen lymph nodes. It is spread through bodily fluids.

Cytomegalovirus is classified as a common virus that does not leave your body. In healthy individuals it is rarely noticed. In those with weakened immune systems it can cause great problems such as fever, fatigue, throat pain, and muscles aches. It is also spread through bodily fluids.

Herpes Simplex Virus is also known as a common virus often called herpes which can present as a blister or blisters on the mouth or genital region. A weakened immune system will cause it to flare. It is also spread through bodily fluids.

Papillomavirus is spread from skin to skin contact and appears as warts in many different areas and formations including common warts, genital warts, plantar warts, and flat warts.

Increasing Virus Transmission Risks

These are viruses that affect people when their resistance is low, their immune system isn’t strong. One of the main things known to lower our resistance is consumption of sugar and processed foods, combined with lack of sunlight and rest. It has been proven time and time again that the best way to strengthen the immune system is to eat real foods, in their most natural forms. This includes organically grown vegetables, pasture raised animals, fruit straight from the tree or vine when it’s ripe, and consuming water that is alive with minerals while absent of chemicals. A healthy immune system is the best defense as these viruses are spread easily from careless contact, where hygienic methods are not a concern. This includes washing your hands regularly, many times each day, as well as cleaning doorknobs, railings, cabinet knobs, handles, cell phones, TV remotes, and other items that come into regular human contact. Not doing these things increases the risk of virus transmission. 

Normal Virus Findings

Krishnan says, “There were a few studies on the cerebrospinal fluid, it’s loaded with herpes and papillomavirus in most people. Nothing is sterile in the body, nothing. What’s so interesting about bacteria and viruses is there’s competition and then there’s this whole phage area where there’s viruses specific for bacteria. Viruses are unique in that they don’t have any replication capability themselves so they kind of hijack our cellular mechanism to replicate themselves. Bacteria support our immune system in helping detect viruses.”

Specifically he says the bacteria, “Provide clues to our immune system to figure out how to detect not only a virus but a cell that’s infected by a virus. Imagine our immune system comes across an immune cell or a tissue cell that’s now infected with a virus, but on the outside of the cell it looks like our own tissue. It can’t really detect that cell has been infected.”

The goal is to assist the body in identifying them through support that feeds the overall raising of the balance. This is best done through the methods listed above, as well as building probiotics in the human body. Different foods, as well as probiotic strains, feed these to create balance. Spore forming bacteria such as Baccillus endospores through pattern recognition receptors in the immune system, “Will flag our own cells that are infected with viruses so our immune system will recognize them,” Krishnan says.

Keeping Viruses Maintained Within

“The upregulation of pattern recognition receptors are done by the commensal bacteria. Certain microbes within the commensal bacteria do a much better job of alerting and up regulating these pattern recognition receptors so your immune system sees it more visibly. One of the things the spores do in the system is they continually up regulate these pattern recognition receptors so if there’s any minute change on the outside of the cell, there’s a remainder of the viral coat from the virus going in, your immune system has a better chance of seeing it, alerting their immune system much better.”

Put in layman’s terms, people who have a balance of bacteria in their microbiome are much better protected, and fair better when exposed to a virus, than those who do not. If this were true it would mean healthier people who get exposed to a virus never show symptoms of the virus. This has, in fact, been seen with the coronavirus as well as the seasonal flu, year after year.

Yet, instead of building diversity in the gut microbiome, creating a strong immune system, we see a different approach. Building resistance to these viruses and bacteria proves to be the most effective method. Peter Doshi, postdoctoral fellow at Harvard University, published a study in The British Journal of Medicine showing the flu is approached by, “Marketing vaccine by marketing disease.”

Doshi keenly points out, “Promotion of influenza vaccines is one of the most visible and aggressive public health policies today. This enormous growth has not been fueled by popular demand but instead by a public health campaign. Closer examination of influenza vaccine policies shows that although proponents employ the rhetoric of science, the studies underlying the policy are often of low quality, and do not substantiate officials’ claims. The vaccine might be less beneficial and less safe than has been claimed, and the threat of influenza appears overstated.”

Even more interestingly is his study was published in 2013.

Building Resilience

Krishnan says the best objective is to build your resilience by creating different bacteria in the gut, in order to be one of the people who don’t show symptoms when they have a virus. He says, “There are some species of bacteria that act as antigen receptor cells, which is really in effect a bonafied immune cell in your system. One of the other aspects is using probiotics and your gut bacteria to protect you from infection is our macrophages and dendritic cells. They are our immune soldiers that are circulating all throughout our body looking for problematic things. They’re in our nose, our brain, everywhere. They are fed by butyrate, short chain fatty acids. If we don’t have adequate butyrate in our gut we are hindering these very important immune circulators.”

Diversity can be created through real foods, as well as home fermented probiotic foods (click here to read more). Krishnan also recommends a spore forming probiotic like this one. These methods are best known for building resistance to these viruses and bacteria,

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*Nourishing Plot is written by Becky Plotner, ND, traditional naturopath, CGP, D.PSc. who sees clients in Rossville, Georgia. She is a Board Certified Naturopathic Doctor, through The American Naturopathic Medical Association and works as a Certified GAPS Practitioner who sees clients in her office, Skype and phone. She has been published in Wise Traditions, spoken at two Weston A. Price Conferences, Certified GAPS Practitioner Trainings, has been on many radio shows, television shows and writes for Nourishing Plot. She serves on the GAPS Board of Directors and has recently been named “The GAPS Expert” by Dr. Natasha and will serve teaching other Certified GAPS Practitioners proper use of the GAPS protocol. Since her son was delivered from the effects of autism (Asperger’s syndrome), ADHD, bipolar disorder/manic depression, hypoglycemia and dyslexia, through food, she continued her education specializing in Leaky Gut and parasitology through Duke University, finishing with distinction. She is a Chapter Leader for The Weston A. Price Foundation. [email protected]

“GAPS™ and Gut and Psychology Syndrome™ are the trademark and copyright of Dr. Natasha Campbell-McBride. The right of Dr. Natasha Campbell-McBride to be identified as the author of this work has been asserted by her in accordance with the Copyright, Patent and Designs Act 1988.



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