Your microbiome, virome, and DNA

Pathogens, Pathogens; Everywhere Pathogens

I have always marveled at the mindset of germophobes—as if you could somehow escape pathogens. To be a germophobe:

  • You have not looked though a microscope recently.
  • You have a limited knowledge of bacteriology and virology.
  • You have paid no attention to the studies about the human microbiome and the human virome making the news over the last couple of years.
  • You think of all numbers over a billion as simply “many”.
  • Believe all the ads you see on television for antiseptic products promising to keep you pathogen free.
  • You deny the very essence of your own existence (as will be explained).

Let me explain

Bacteria

There are some 30,000 formally named species of bacteria that have been isolated in laboratories as pure cultures and for which the physiology has been investigated. But that’s just one drop in a rainstorm. When you add in the species not formally named, the number is probably closer to a billion.1 Dykhuizen D. “Species Numbers in Bacteria.” Proc Calif Acad Sci. 2005 Jun 3;56(6 Suppl 1):62-71. But remember, we are only talking about species of bacteria, not individual bacterium. When you consider that there are trillions and trillions of individual bacterium in each of those species (well, at least many of them), then the numbers start to get really interesting. In fact, the number of bacteria on earth is estimated to be 5,000,000,000,000,000,000,000,000,000,000. This is five million trillion trillion, or 5 x 10 to the 30th power.2 Christine Lehman. “How Many Bacteria Live on Earth?” Sciencing. April 24, 2017. (Accessed 25 Apr 2021.)

It is estimated that of all these bacteria, only about 10,000 microbial species interact with the human ecosystem.3 News Releases. “NIH Human Microbiome Project defines normal bacterial makeup of the body.” NIH June 13, 2012. (Accessed 25 Apr 2021.) Moreover, only about 500 to 1,000 of those species live in the human gut. Unlike for bacteria species as a whole, researchers calculate they have identified between 81 and 99 percent of all microorganismal genera in healthy adults.

Although most bacteria are harmless or often beneficial, some are pathogenic, with fewer than a hundred species seen to cause infectious diseases in humans. In fact, a great proportion of bacteria in the human ecosystem are beneficial. The flora within the guts of humans makes digestion possible. Soil bacteria drive the process of decomposition. If bacteria were not present, our ecosystem would collapse.

When it comes to bacteria, scientists have only recently begun to quantify the microbiome, discovering that it is inhabited by at least 38 trillion bacteria.4 Sender R, Fuchs S, Milo R. “Revised Estimates for the Number of Human and Bacteria Cells in the Body.” PLoS Biol. 2016 Aug 19;14(8):e1002533 More intriguing, perhaps, is that bacteria are not the most abundant microbes that live in and on our bodies. That award goes to viruses—by a cosmological mile.

Viruses

It is estimated there are 10 viruses for every bacterium on Earth. An estimated 10 nonillion (10 to the 31st power) individual viruses exist on earth. That is one for every star in the universe 100 million times over.5 No authors listed. “Microbiology by numbers.” Nat Rev Microbiol. 2011 Sep;9(9):628. , 6 Dirk Schulze-Makuch. “There Are More Viruses on Earth Than There Are Stars in the Universe.” Air & Space. March 17, 2020. (Accessed 25 Apr 2021.)  If you lined them all up, that line would be 10 million light years long! To put that in more earthly terms, it has been estimated that each day, more than 700 million viruses, mainly of marine origin, are deposited from Earth’s atmosphere onto every square meter of our planet’s surface.7 Reche I, D’Orta G, Mladenov N, Winget DM, Suttle CA. “Deposition rates of viruses and bacteria above the atmospheric boundary layer.” ISME J. 2018 Apr;12(4):1154-1162. As Katherine Wu writes in National Geographic,8 Katherine J. Wu. “There are more viruses than stars in the universe. Why do only some infect us?” National Geographic. April 15, 2020. (Accessed 25 Apr 2021.) “Viruses infiltrate every aspect of our natural world, seething in seawater,9 Katherine J. Wu. “Scientists just found 200,000 new marine viruses. Here’s why that matters.” NOVA. April 25 2019. (Accessed 25 April 2021.) drifting through the atmosphere,10 Mindy Weisberger. “Billions of Viruses Are Falling to Earth Right Now (But That Isn’t Why You Have the Flu).” LiveScience. February 07, 2018. (Accessed 25 Apr 2021.) and lurking in miniscule motes of soil.11 Joanne B. Emerson. “Soil Viruses: A New Hope.” mSystens. 2019. vol. 4, no. 3. Generally considered non-living entities,12 Nigel Brown. “Are viruses alive?” Microbiology Society. 10 May 2016. (Accessed 25 Apr 2021.) these pathogens can only replicate with the help of a host, and they are capable of hijacking organisms from every branch of the tree of life—including a multitude of human cells.

“Yet, most of the time, our species manages to live in this virus-filled world relatively free of illness. The reason has less to do with the human body’s resilience to disease than the biological quirks of viruses themselves, says Sara Sawyer, a virologist and disease ecologist at the University of Colorado Boulder. These pathogens are extraordinarily picky about the cells they infect, and only an infinitesimally small fraction of the viruses that surround us actually pose any threat to humans.”

So, how many of these viruses interact with humans?

Biologists estimate that 380 trillion viruses are living on and inside your body right now—10 times the number of bacteria. Some can cause illness, but many simply coexist with you.13 David Pride. “Viruses Can Help Us as Well as Harm Us.” Scientific American. December 1, 2020. (Accessed 25 Apr 2021.) Collectively, they are known as the human virome. But the overwhelming number of these viruses are not the dangerous ones you commonly hear about, like those that cause the flu or the common cold or COVID-19. In fact, many of these viruses infect the harmful bacteria that live inside you and on your skin, thus protecting you by destroying them.

All in all, out of the millions and millions of different species of viruses in the world, only about 200 virus species are known to cause disease in humans.

And Then There’s DNA

So, what have we learned so far?

  • Viruses and Bacteria exist in numbers greater than we can count—or even imagine.
  • They exist all around us in everything we touch, walk on, bathe in, and breathe.
  • They are unavoidable.
  • The vast majority are totally indifferent to our existence and have nothing to do with us.
  • That said, many are beneficial to our existence.
  • Only an infinitesimally small percentage are harmful.

And if all that is not enough to freak out our germophobic readers, what we are about to discuss should seal the deal.

  • Bacteria and humans have been swapping DNA for millennia.14 Gray MW. “Mitochondrial evolution.” Cold Spring Harb Perspect Biol. 2012 Sep 1;4(9):a011403.
  • About 8–10 percent of human DNA comes from virus DNA inserted into our genomes in the distant past, in many cases into the genomes of our pre-human ancestors millions of years ago (or when God created the creatures of the earth, if you prefer). Most of these viral genes come from retroviruses, RNA viruses that insert DNA copies of their own genes into our genomes when they infect cells.15 News Release. “Genes from ‘fossil’ virus in human DNA found to be active.” UW Medicine. November 4, 2019. (Accessed 25 Apr 2021.)
  • Human cells make up only 43% of the body’s total cell count. The rest are microscopic colonists. In other words, more than half your body is not human.

Virus DNA

When viruses infect us, they can embed small chunks of their genetic material in our DNA. Although infrequent, the incorporation of this material into the human genome has been happening since the dawn of humankind. As a result of this ongoing process, viral genetic material makes up nearly 10 percent of the modern human genome. Over time, the vast majority of viral invaders populating our genome have mutated to the point that they no longer lead to active infections. But they are not entirely dormant.

Sometimes, these stowaway sequences of viral genes can contribute to the onset of diseases such as cancer and Alzheimer’s. They can also make their hosts susceptible to infections from other viruses. However, scientists have identified numerous cases of viral hitchhikers bestowing crucial benefits on their human hosts—from protection against disease to shaping important aspects of human evolution, such as the ability to digest starch.

Bacteria DNA

Mitochondria are separate little organelles located in every cell of your body. Their primary role is to supply energy to the cell in which they reside. In effect they are little ATP energy factories. In addition, they also play a role in other cellular processes such as signaling, cellular differentiation, and cell death, as well as the control of the cell cycle and cell growth. To put this in simple terms, not a single cell in your body would be alive without mitochondria and the bacterial DNA governing them.

And what does this have to do with bacteria? As it turns out, the genomes inside your mitochondria are not the same as the DNA in the cell nucleus (the DNA you inherited from your mother and father). In fact, mitochondrial DNA is vastly different, showing substantial similarity to bacterial genomes. The theory is that somewhere back in time, “a deal was struck.” Animal cells agreed to “incorporate” bacteria into their cellular structure — to provide a safe home for the bacteria — in exchange for which the bacteria would perform a number of important jobs necessary for the maintenance of those cells.  Is that cool or what?

In fact, viewed through the lens of the genome it contains, the mitochondrion is of unquestioned bacterial ancestry, originating from within the bacterial phylum α-Proteobacteria (Alphaproteobacteria).16 Gray. The members of the class Alphaproteobacteria are highly diverse and possess few commonalities. The one thing they share, as do our mitochondria, is a now extinct common ancestor, protomitochondion.

Conclusion

When it comes to bacteria and viruses, we are pretty much in a “can’t live with ‘em’, can’t live without ‘em’ scenario.” Yes, a small number can make us sick and even kill us. But then, a small number can improve our health and quality of life. Additionally, some, are not just beneficial, they are necessary for our existence. We simply would not be alive without them—and we barely mentioned the soil bacteria and viruses essential for making our food grow.

For the purposes of our discussion, though the most important thing is that we cannot avoid them or kill them all. We need to find a way to coexist—defending ourselves against the harmful ones, while simultaneously encouraging and nurturing the beneficial ones. Now, to be clear, that does not mean that you no longer need to minimize contact with people who are highly infectious or that you stop washing your hands after going to the bathroom. Common sense still applies.

It just means that, in the real world, being a germophobe, unless you suffer from OCD or a similar condition, is simply an untenable position. There is no way to avoid all bacteria and viruses; it is simply not possible. Even if you were to lock yourself in a germ-free room for the rest of your life, you would still be bringing trillions and trillions of viruses and bacteria into the room with you by virtue of your very existence—including your microbiome, your virome, and your DNA. In other words: you need to protect yourself against the bad guys and live with the fact that you are going to be immersed in a sea of microbial entities (most of them neutral or even beneficial) for the rest of your life no matter what you do.

References

References
1 Dykhuizen D. “Species Numbers in Bacteria.” Proc Calif Acad Sci. 2005 Jun 3;56(6 Suppl 1):62-71.
2 Christine Lehman. “How Many Bacteria Live on Earth?” Sciencing. April 24, 2017. (Accessed 25 Apr 2021.)
3 News Releases. “NIH Human Microbiome Project defines normal bacterial makeup of the body.” NIH June 13, 2012. (Accessed 25 Apr 2021.)
4 Sender R, Fuchs S, Milo R. “Revised Estimates for the Number of Human and Bacteria Cells in the Body.” PLoS Biol. 2016 Aug 19;14(8):e1002533
5 No authors listed. “Microbiology by numbers.” Nat Rev Microbiol. 2011 Sep;9(9):628.
6 Dirk Schulze-Makuch. “There Are More Viruses on Earth Than There Are Stars in the Universe.” Air & Space. March 17, 2020. (Accessed 25 Apr 2021.)
7 Reche I, D’Orta G, Mladenov N, Winget DM, Suttle CA. “Deposition rates of viruses and bacteria above the atmospheric boundary layer.” ISME J. 2018 Apr;12(4):1154-1162.
8 Katherine J. Wu. “There are more viruses than stars in the universe. Why do only some infect us?” National Geographic. April 15, 2020. (Accessed 25 Apr 2021.)
9 Katherine J. Wu. “Scientists just found 200,000 new marine viruses. Here’s why that matters.” NOVA. April 25 2019. (Accessed 25 April 2021.)
10 Mindy Weisberger. “Billions of Viruses Are Falling to Earth Right Now (But That Isn’t Why You Have the Flu).” LiveScience. February 07, 2018. (Accessed 25 Apr 2021.)
11 Joanne B. Emerson. “Soil Viruses: A New Hope.” mSystens. 2019. vol. 4, no. 3.
12 Nigel Brown. “Are viruses alive?” Microbiology Society. 10 May 2016. (Accessed 25 Apr 2021.)
13 David Pride. “Viruses Can Help Us as Well as Harm Us.” Scientific American. December 1, 2020. (Accessed 25 Apr 2021.)
14 Gray MW. “Mitochondrial evolution.” Cold Spring Harb Perspect Biol. 2012 Sep 1;4(9):a011403.
15 News Release. “Genes from ‘fossil’ virus in human DNA found to be active.” UW Medicine. November 4, 2019. (Accessed 25 Apr 2021.)
16 Gray.

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