The Wonderful World of Bacteria in Your Body

by Dr. Elizabeth Mitchell on August 26, 2014
Featured in Answers in Depth


The “superorganism” that you are testifies to the superlative wisdom of our Creator God.

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Your body is home to trillions of fellow travelers—bacteria and other microorganisms that make up your microbiome. Most are not enemies. In fact, God designed them to be your friends.

This fascinating world of microbes that God created has remained largely hidden for 6,000 years. Now that DNA sequencing has made it possible to detect and characterize microbes that are difficult to culture, scientists can appreciate the scope of the microbial ecosystems living throughout the world and inside each of us.

Scientists have coined the term superorganism for the human body, because an estimated 90% of the cells in your body are not your own but rather belong to this microbiome. The term microbiome can refer to all microorganisms that live in a particular place—such as your mouth, skin, or intestines—or to the combined genetic material of all the microbes inhabiting an ecosystem. (The reason for this second definition should become clear in a moment.)

Molecular geneticist Dr. Georgia Purdom of Answers in Genesis explains that the microorganisms populating you supply your needs, crowd out unwanted microbes, influence your immune system, and interact with you in ways until recently never imagined:

Although humans have trillions of body cells, our bodies also harbor trillions of bacterial cells. Many believe that the number of bacterial cells far exceeds the number of body cells making us more bacteria than human! These bacteria are “good” and work in conjunction with our bodies to break down nutrients, synthesize vitamins, control the growth of “bad” bacteria, and perform many other functions that we are just now beginning to understand.
human microbiome

Different sorts of bacteria live in different places in and on the body. Exposure to antibiotics and many other factors can alter a person’s bacterial landscape, sometimes upsetting the ability of the microbiome to protect us. Pictured on this chart, Helicobacter pylori is commonly found in the stomach. It may be asymptomatic, but it can bind to stomach surface cells in some people, and 80-90% of gastric and duodenal ulcers are associated with this bacterium. Image by Tom Dunne, adapted from I. Cho and M. Blaser, Nature Reviews Genetics 13:260, via American Scientist.1

Where They Live and What They Do

By learning more about “who” lives in you in sickness and in health and what they are doing, medical scientists hope to recruit microbial aid to help the body fight not just infections but also noninfectious diseases and conditions ranging from premature birth to cancer.

The human placenta, for instance, hosts an assortment of bacteria similar to those in the mouth. These may well contribute to the normal progress of pregnancy, provide useful metabolites to the fetus, influence the development of the fetal immune system, and either promote or prevent premature labor—depending on the composition of the bacterial population. Research in this area is ongoing, and Baylor College of Medicine maternal-fetal medicine specialist Dr. Kjersti Aagaard says, “These discoveries could lead to rapid breakthroughs in not only identifying women at risk for preterm birth, but developing new and worthwhile strategies to prevent preterm birth.”3

A recent article in American Scientist, “The Superorganism Revolution,” not only explains that different bacteria predominate in different parts of your body—which is observable—but makes unobservable assumptions about how they got there in an evolutionary past:

The human microbiome is not a single continuous ecosystem. Instead, it has evolved and differentiated to occupy five reasonably distinct body habitats: the skin, the nose, the mouth, the lower gastrointestinal tract, and the vagina. Each of these major habitats is, in turn, further subdivided. Thus, the microbial community inhabiting the lining of the cheeks differs significantly from the one that inhabits dental plaque. (emphasis ours)

The American Scientist author leaps from the observable importance of these bacteria to unobservable assumptions about a deep evolutionary past and potential evolutionary future:

These bacteria are not simply squatters or unavoidable hitchhikers picked up as we move through a world crowded with microbes. Rather, they influence our health, digestion, metabolism, and response to medicines, not to mention our survival and evolution. The discovery of the human microbiome, the collection of microbial ecosystems that colonize virtually every external and internal body surface, has forever changed how we see ourselves. These bacteria shape our biology from birth to the grave. They are part of us. (emphasis ours)

Where Did They Come From?

God created everything, including the many kinds of microorganisms, about 6,000 years ago and called the world He created “very good.” The more scientists learn about microbiomes, the more we can appreciate the functions for which God made these invisible organisms. When things go wrong in this sin-cursed world, some microbes become pathogenic. (Learn more in “The Genesis of Pathogenic E. coli”) By and large, however, most microbes remain friendly, meeting our needs as God intended.

Microorganisms cannot up sticks and migrate to new places when environments become inhospitable. Therefore, God designed them to adapt to changing conditions so they can fulfill the roles for which He created them. Dr. Purdom calls them “master adapters.” (Be on the lookout for Dr. Purdom’s article about this in an upcoming issue of Answers magazine.)

Bacterial genes, like all genes, can mutate—undergo changes in DNA sequence and consequently sometimes changes in the proteins produced by those genes. Microorganisms commonly transfer genetic information between themselves. This is called horizontal gene transfer. (This is the reason the microbiome can also be thought of as all the microbial genetic material in an ecosystem.) By multiplying rapidly, bacterial populations can take advantage of helpful mutations in their genes as well as genes that they receive from other microorganisms.

Most microbes remain helpful and occupy vital niches throughout the physical and biological worlds.

Microbial Library

The American Scientist article asserts that the library of collective microbial genomes in humans are “the result of billions of natural experiments that have been unfolding over the past 3 billion years.” Believing that the genetic information in microorganisms evolved through natural processes, the author writes, “Effectively, the microbiome is the creator and custodian of a repository of evolved information, potentially shared by every member of the microbiome.” (emphasis ours)

Because microbes can exchange genetic information, the American Scientist article credits microbiomes with preserving evolved information through the eons so that it hasn’t had to evolve again and again. “This trading of genetic information obeys neither lines of descent nor rules of shared ancestry. To a surprising extent, it enables bacteria to acquire functional genetic information in response to environmental change without having to evolve it de novo.

Not only does the author think 3 billion years of evolution built the microbial library but that, because bacteria reproduce so rapidly, evolution is ongoing— “Individual species and the microbiome itself can evolve within a single host. . . . Bound as humans’ perceptions are by our own experience, we have trouble imagining the evolutionary changes unfolding within us. But for our bacterial partners, a human lifetime is deep time.” Similarly, researchers investigating the placental microbiome write, “Over the past 4 million or so years, hominids have coevolved with their microbiomes as physiologic communities composed of distinct body site niches.”4

But are these valid statements? No. Speciation of bacteria, as exemplified in “The Wonderfully Made Design of the Skin and Its Microbiome,” is not evolution in the molecules-to-man sense. Furthermore, evolutionary scientists are in the habit of assuming that whenever complex biological systems—like microbiomes and humans—work well together, they “coevolved.” But coexistence of systems that work well together does not demonstrate that those systems came into being through the interaction of random natural evolutionary processes. Rather the complexity of a symbiotic system should make us realize a wise and merciful Designer planned it, or at least question the survivability of each organism during this supposed blind, purposeless co-evolution that molecules-to-man evolution requires.

Ever-Adapting, Never Evolving

Most microbes remain helpful and occupy vital niches throughout the physical and biological worlds—including the many niches inside our bodies. This is a testimony to the wisdom of our Creator and a reminder of the original “very good” world God created. Yet for all their ability to exploit helpful mutations and pass genes between themselves, microbes do not evolve the genetic information to become new kinds of organisms. Dr. Purdom explains that these microorganisms in us and around us are doing exactly what God designed them to do:

Our bodily bacteria or microbiome changes and adapts as we grow and are exposed to different environments both internally and externally. However, these are not the types of changes that result in the bacteria changing into a completely different kind of organism. The author of the article explains that the bacteria in our microbiome typically have very short generation times and so over a human lifetime experience “deep time.” But even with this deep time they never change into anything else—all remain bacteria (even the few that turn into pathogens) and most still work in conjunction with our bodies just as God designed them to do.

Because we live in a fallen world, many of God’s great designs go “bad,” mirroring in a metaphorical sense the disobedience of mankind. Thus, pathogens and pathogenicity develop. Sometimes for instance a population of “good” bacteria take advantage of a deleterious mutation and begin causing disease. In other cases, “good” microorganisms fail to keep the population of other “good” microorganisms in check and lead to problems. Nevertheless, more we learn about how the genomes of bacteria, with their rapid reproductive processes, are able to adapt to changing conditions—through the natural selection of favorable mutations and exploitation of genetic information acquired from other microbes through horizontal gene transfer—the more we should marvel at the wonderful microscopic world our wise Creator built within the world we can see.

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  1. Robert L. Dorit, “The Superorganism Revolution,” American Scientist 102, no. 5 (September–October 2014): 330, doi:10.1511/2014.110.330.
  2. Obstetricians have long noticed a link between periodontal disease, such as gingivitis, and premature birth. Because it appears the bacteria from the gums may travel via the blood to seed the placenta even in normal pregnancy, it is possible that the pathogenic population in diseased gums increase the risk of premature labor. This is an area of ongoing research and no firmly applicable conclusions for prevention and intervention have yet been reached. From K. Aagaard et al., “The Placenta Harbors a Unique Microbiome,” Science Translational Medicine 6 (2014): 237ra65, doi: 10.1126/scitranslmed.3008599.
  3. Charles Q. Choi, “Microbes Lurking in Placenta Also Found in Your Mouth,” LiveScience, May 21, 2014,
  4. Kjersti Aagaard et al., “The Placenta Harbors a Unique Microbiome,” Science Translational Medicine 6 (2014): 237ra65, doi:10.1126/scitranslmed.3008599.


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