Microbiome (and virome)

God’s good created bacteria (and viruses) inside us

by Jonathan Sarfati

Many people ask, “Why would/did a loving God create nasty disease germs?” The big-picture answer is three-fold (with more information in the Related Articles below):

Rocky Mountain Laboratories, NIH–NIAID.

1. God did indeed create bacteria and viruses, during Creation Week. According to Exodus 20:8–11, God created the heavens, earth, and everything in them during the six normal-length days of creation week. This creation must logically include microscopic organisms such as bacteria and viruses. Today, with advanced science, we can see some of their amazing design features, and thus God’s creative brilliance.
2. Genesis 1 tells us seven times that God created things “good”, and when describing the finished product, everything was “very good”. This entails there was no disease in the finished creation. Therefore, even bacteria and viruses were created to be good. But Genesis 3 and Romans 8 inform us that disease, like death and other suffering, is the result of Adam’s Fall. So some bacteria and viruses became disease-causing after the Fall. However, even today, most are helpful.
3. God created some viruses to be beneficial to specific creatures. After the Fall, however, some viruses hopped to different creatures, including humans, and now cause diseases. E.g., influenza viruses were originally benign fowl viruses, and Ebola and coronaviruses were once benign bat viruses.

Human microbiome

Many are surprised that bacteria could be helpful, but our bodies are colonized inside and out by beneficial bacteria. For example, even the eye’s surface (the cornea) has a microbiome including the ‘good’ bacterium Corynebacterium mastitidis (C. mast). The eye is already very well protected by antimicrobial compounds in the designed tearing system. This bacterium stimulates a further immune response. Without C. mast, we would be much more vulnerable to fungal infections.¹

Trillions of bacteria inside us

Soon after a baby is born, his or her colon (large intestine) becomes loaded with trillions of bacteria. In fact:

Within the first year of life, an estimated 10¹³ to 10¹⁴ microbes/ml comprising 500–1,000 species colonize the gastrointestinal tract.²

Dr. Victor Padilla-Sanchez, PhD, Wikimedia Commons

Fortunately, God designed us with an immune system that keeps bacteria in their place, so the child doesn’t get sick. Even Adam and Eve would have needed an immune system before the Fall to distinguish their own cells (‘self’) from other cells (‘non-self’), even if the latter included non–disease-causing bacteria. For the entire life, a human colon contains trillions of bacteria.

It has been known for decades that we have enormous numbers of bacteria in our bodies. For a while, an urban myth persisted that there were ten bacterial cells for every human cell. But this 10–1 ratio was a back-of-the-envelope estimate made in 1972. Instead, a 2016 study showed that “the ratio is much closer to 1:1,” more like 1.3:1. To be specific, a ‘reference man’ of 70 kg (154 lb) aged 20–30 has about 3.8 × 10¹³ bacterial cells and 3.0 × 10¹³ human cells. Of the human cells, about 90%, mostly red blood cells and platelets, lack nuclei and mitochondria, leaving 3 × 10¹² nucleated cells. So the 10–1 ratio works only if we compare bacteria cell to nucleated human cells, but the initial claim concerned all cells.³ A 2018 study argued that the 1:3–1 ratio might lower still.²

However, bacteria are far smaller and less massive than human cells. Bacterial cells are about 0.2–10 microns in diameter, while animal cells are 10–100 microns (1 micron = 1 μm = 10⁻⁶ m).⁴ Since volume and mass are proportional to the diameter cubed, the total mass of bacteria in a 70-kg man is only about 0.2 kg.²

The microbiome is incredibly diverse. According to one estimate, we might have 1,000 different bacterial species in and on our bodies. If the average number of genes per species is 2,000, that would make 2 million genes—100 times as many as the ~20,000 human genes.

We need these bacteria!

Without the microbiome, we would not be able to digest certain foods as well. The bacteria also produce vitamins B and K. And they provide biofilm, a protective layer against harmful bacteria.

These bacteria inside our colon are so important that God designed us a bacterial safehouse: the appendix. The appendix is a small hidey-hole out of the way and has a lining that can nurture the good bacteria.

The appendix especially comes into play if our colon is cleared quickly. A bout of food poisoning or intestinal infection can clear out the microbiome. The appendix enables the bacteria to repopulate the colon quickly.

For too long, the appendix was regarded as a useless ‘vestige’ of evolution and was removed way too routinely. However, now we know that appendicectomy patients are deprived of this safehouse, so their colons are less protected. They suffer four times the rate of infection with the nasty bacterium Clostridium difficile and have increased rates of some types of cancer. This example is one of many where evolution has harmed medical practice.

Viruses

Almost all viruses are far smaller than even a bacterium. Their typical size of 20 to 300 nanometers (1 nanometer = 1 nm = 10⁻⁹ m) is below the wavelength of visible light, so they can’t be seen under a light microscope. An electron microscope is necessary to see them. The exception are giant viruses (aka giruses) of the phylum Nucleocytoviricota, which are about 500 nm in diameter (the wavelength of green light).

Viruses are not technically living creatures because they can’t reproduce independently. Rather, they hijack the reproductive machinery of real cells and force the infected cell to make many new viruses. The number of viruses each infected cell is forced to produce is called the burst size. Burst size depends on both the type of virus and type of cell. Each new virus is ready to infect a new cell and repeat the process. As a result, viruses multiply exponentially.

For example, the burst size is 10³ for the SARS-COV-2 that causes COVID-19.⁵ At peak infection, a patient has 10⁹–10¹¹ coronavirions with a total mass of 1–100 μg.⁶ Influenza viruses infecting human cells have an average burst size of about 6,000.⁷

While we often talk about ‘live’ viruses, they are more precisely called active viruses. And although people frequently talk about ‘killing’ viruses, it would be more technically precise to use the terms deactivating or destroying them.

Viruses interact with all types of organisms. There are even viruses that infect giant viruses, called virophages. On the other side, some organisms called virovores eat viruses. Virovory has been known for decades,⁸ and the protist Halteria, a type of single-celled non-bacterial creature, can live on a diet exclusively of viruses.⁹

Graham Beards, Wikimedia Commons

Also important are viruses that infect bacteria—bacteriophages. Bacteriophages were studied in depth a century ago, decades before they could be seen.

One of the early leaders was Félix d’Herelle (1873–1949), the inventor of the term ‘bacteriophage’. He showed that something must exist that was too small to be seen under a light microscope, could kill bacteria, and would reproduce only inside them. After diluting bacteriophages in a liquid solution, he showed that they killed discrete areas of bacteria. This experiment confirmed that the killer was not a poison but a discrete tiny particle.

Because bacteriophages kill specific types of bacteria, d’Herelle proposed that they could be wonder cures for bacterial diseases. But such ‘phage therapy’ was almost forgotten after antibiotics were developed. Now that antibiotic resistance, a non-evolutionary change, is a big problem, there is renewed interest in phage therapy.

How viruses help us

Like bacteria, viruses were created “very good”. And they have some useful functions even now in this fallen world. In fact, all life needs viruses. Tony Goldberg, an epidemiologist at the University of Wisconsin-Madison, explains:

If all viruses suddenly disappeared, the world would be a wonderful place for about a day and a half, and then we’d all die—that’s the bottom line.¹⁰

Viral functions include transporting genes among plants and animals, keeping soil fertile and water clean, regulating gases in the atmosphere, and killing cancer cells.¹¹

The human virome

We also have helpful bacteriophages living inside us, comprising the virome. They outnumber bacteria by at least 10 to 1. So all healthy humans have hundreds of trillions of viruses inside them. Their interactions with the bacteria are manyfold and important for human health. One review paper lists many important bacteriophage functions:¹²

1. The obvious one is that bacteriophages kill the bacteria they infect. But bacteria also have defence mechanisms. The attack and defence reach equilibrium, resulting in a stable population of both bacteria and viruses.
2. As can be seen from the electron micrograph, sometimes bacteriophages cover the bacterial surface. This helps cloak them so our immune system doesn’t eliminate them by mistake. The cloaking works both ways, protecting us from attack by our bacteria.
3. Our immune system has design features so they don’t attack the cloaking bacterial phages.
4. Our virome protects both us and our microbiome from invading harmful bacteria. Bacteriophages attach to bacteria with receptor-binding proteins (RBPs), which can be weapons against invaders. RBPs are being investigated as killers of antibiotic-resistant bacteria.

Conclusion

God created bacteria and viruses “very good”. After the Fall, some became extremely bad, causing illness and even death, sometimes by crossing from animals to humans. But even in this fallen world, many bacteria and viruses are still very good for us. A healthy human body has slightly more bacterial cells than human cells and over ten times as many viruses. Both our bodies and their bacterial and viral passengers have amazing design features that enable this beneficial co-existence.

Update

A 2023 paper published after this article estimates total body counts of ≈36 trillion human cells in a 70-kg male, ≈28 trillion in a 60-kg female, and ≈17 trillion in a 10yo 32-kg child.¹³ This paper also notes that cell size is inversely proportional to cell numbers, and that cells within a given size class contribute equally to the body’s total cellular biomass:

These data reveal a surprising inverse relation between cell size and count, implying a trade-off between these variables, such that all cells within a given logarithmic size class contribute an equal fraction to the body’s total cellular biomass. We also find that the coefficient of variation is approximately independent of mean cell size, implying the existence of cell-size regulation across cell types.^13,14

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