Television shows like the old Wild Kingdom or Nature Notes took us to remote places to view nature, nature being the living world not counting humans.
But nature is closer to us than we have traditionally thought. As early as 1683, Anton van Leeuwenhoek, the Dutch microscope maker, wrote a letter to the Royal Society in which he described the "animals in the scrurf of the teeth."
Van Leeuwenhoek reported that both our mouths and our gut contained microbes; he further observed that the ones he found in the mouth appeared to be different from those found in the gut. His observations were limited to organisms that could be seen using the tiny drops of glass that served as his microscopes. (Ursell, Metcalf, Parfrey, & Knight, 2012)
It was this view of nature, one filled with strange looking creatures, that came to be seen as a threat, especially when thanks to Louis Pasteur and Robert Koch we learned that we could become ill when some of these strange creatures got inside us. In school we learned that these microscopic organisms were really germs and that germs cause disease.
The cultural narrative since has been the war against germs. Medical scientists were microbe hunters who stalked and killed them. We work on keeping germs in check and therefore stock our homes with household and personal cleaning products that claim to "kill 99% of germs."
Since the birth of microbiology in the early 20th century, it has been known that our gut is home to microbes, but it wasn't until the revolution in genetic sequencing and data analysis techniques that we have begun to understand that far from having succeeded in the war on germs, our bodies actually resemble "microbe motels." The inhabitants of the microbe motel create our microbiome.
The modern technologies of genetic sequencing have made it possible to identify the living contents of the microbiome. The techniques can be used to examine data in a variety of ways such as time sequences so that the changes in the microbiome can be observed in real time.
The scale of our personal microbiome is staggering. There are from 10 to 100 trillion microbial cells living in each individual human's gut; that is, the microbial cells actually outnumber our human cells.
Even the diversity of the microbiome is astonishing. While there are on the order of 22,000 genes in the human genome, a catalog of the genes in the microbiome lists 3.3 million genes without counting any gene more than once.
As individuals, the genetic content of our individual microbiomes is more diverse than our human genome from individual to individual. While the genomes of individual humans are 99.9% similar to those of other individuals; the gut genome can be 80-90% different from individual to individual. (Ursell, Metcalf, Parfrey, & Knight, 2012)
How do we acquire our microbiome?
We acquire it at birth and its composition will vary by how the baby is delivered. A baby born by passing through the birth canal will have a microbiome that resembles the microbiome in the mother's birth canal. If the baby is born using C-section, its microbiome will resemble the microbiome of its mother's skin.
The interaction between the microbiome and its human host environment is clear.
As the baby matures, its microbiome will change. In one study, it was found that there were specific points at which the microbiome altered when the environment changed: ingesting breast milk, the development of a fever, the introduction of rice cereal, being fed formula and table food, antibiotic treatment, and the introduction of adult food. (Ursell, Metcalf, Parfrey, & Knight, 2012)
The sensitivity of the microbiome is shown by a study that found that when the baby transitions to an adult diet, the genes in the microbiome also transition to those associated with vitamin biosynthesis and the digestion of polysaccrides, showing the symbiosis between us and our microbiome. (Ursell et. al., 2012)
We provide an environment while the microbiome provides a number of benefits to our well-being. The evidence from the many projects that study the human microbiome is that it is inextricably linked to the host's microbia, digestion, and metabolism.
Thanks to our microbiome, we can digest things that would not be digestible if we relied solely on the human genome.
When diet changes, the microbial community changes and those changes are reflected back to the host and that these changes can show up in the space of a single day.
In a well-publicized study, it was reported that the microbiome plays a role in obesity.
New understandings about our microbiome have opened up new ways to think about health. Our current model of disease is top down: use an antibiotic to kill the germ.
Understanding the microbiome has opened a dramatically new approach from the bottom (literally) up.
To illustrate: there is a particularly difficult and dangerous bacteria named Clostridium difficile. According to the Centers for Disease Control, it affected a half a million Americans and caused 29,000 deaths in 2011. The disease is associated with the overuse of antibiotics with a quarter of all cases developing in hospitals and nursing homes. (Zimmer, 2016)
Because antibiotics are broad-spectrum, they kill not only the disease-causing organisms but they wipe out some portion of the "normal" microbes.
If the absence of the normal microbiome plays a role in allowing the C.difficile to cause havoc, then would it be possible to restore the normal biota by transplanting microbes from healthy guts? This was the thinking behind the work of Dr. Sahill Khanna at the Mayo Clinic. He and his colleagues isolated the spores from 50 different species of bacteria from the stool samples of healthy volunteers. The spores were put into pills and administered to 30 patients suffering from C.difficile. Twenty-nine of the patients recovered.
The reason for this dramatic result is only "sort of" understood.
The gut is a nice environment so that there is a lot of competition among microbes to live there. So one explanation is that the competition reduces the power of the harmful bacteria. Another explanation is that the competition reduces the power of the harmful bacteria. Another explanation is that there are microbes that feed on the bile acids secreted by the liver to help with the digestion of fat. It is known that those bacteria that feed on bile acids create by-products that are thought to slow the growth of the C. difficile. (Zimmer, 2016)
The challenge is to develop a mechanistic understanding for the changeability of the microbiome.
According to Ursell and colleagues, this will make it possible to create manipulations of the microbiome to improve health. (Ursell, Metcalf, Parfrey, & Knight, 2012)
Robertson-Albertyn, S., Hardee, E., & Stanley-Wall, N. R. (2016). Microbe Motels: An Interactive Method to Introduce the Human Microbiome. J Microbiol Biol Educ Journal of Microbiology & Biology Education, 17(2), 282-283. doi:10.1128/jmbe.v17i2.966
Ursell, L. K., Metcalf, J. L., Parfrey, L. W., & Knight, R. (2012). Defining the Human Microbiome. Nutr Rev Nutrition reviews, 70(Suppl 1), S38-S44. doi:10.1111/j.1753-4887.2012.00493.x
Zimmer, C. (2016c). Fecal Transplants Can Be Life-Saving, But How? New York Times.
Dr. John Holton
Dr. John Holton joined the S²TEM Centers SC in July of 2013, as a research associate with an emphasis on the STEM literature including state and local STEM plans from around the nation.