Microbial Me

Bacteroides trichoides, one of the many species of bacteria that live in the human intestine (CDC image)
One of the most fascinating aspects of the biological world is the phenomenon of mutualism – two or more different species living together so that each organism benefits. I have blogged about this topic before (here, here, and here), and I discuss it quite a bit in my science texts. Technically, it is a subcategory of symbiosis, where two or more organisms live together. If all organisms benefit from this living arrangement, we call it mutualism. If one benefits and the others are not harmed, we call it commensalism. If one benefits and another is harmed, we call it parasitism.

Many scientists consider mutualism (and symbiosis as a whole) to be a fairly uncommon thing in nature. Sure, you can find some organisms that help each other out from time to time, but overall, nature is about organisms “battling it out” for survival. Nothing could be further from the truth! While organisms do compete against one another in nature, they also help each other quite a bit. As George D. Stanley, Jr wrote a few years ago in the journal Science:1

Symbiosis is the most relevant and enduring biological theme in the history of our planet.

Indeed, symbiosis (and mutualism in particular) is incredibly common throughout creation, and nothing makes that more apparent than a study of the microbiological communities that live in each one of us.

The journal Science recently published a review article discussing the microbes that live in people, and it is incredibly fascinating. As the article states:2

…we now know that almost every environmentally exposed surface of our bodies is teeming with symbiotic microbes.

Indeed, we have microbes living in our mouth, our airways, our intestines, our skin, and virtually any other part of our anatomy that comes into contact with the outside world. And “teeming” is definitely the right word to use. A healthy human body harbors ten times as many bacterial cells as it has human cells!

Not only is the sheer number of microbes in our bodies impressive, their variety is astounding! There are 1,000 to 1,150 different species of bacteria that are found in human bodies across the world, and a single individual will generally harbor about 160 of them! This seems to indicate that there is some “matchmaking” that goes on between microbes and the people who harbor them. While I might benefit from one set of microbes because of my genetic makeup and environment, you might benefit from a different set, given your genetic makeup and your environment.

Speaking of genetics, the article also made this shocking statement:

Recent efforts to sequence the bacterial genomes of the microbiota (known as the microbiome) have begun to reveal its genetic identity and suggest that our microbiome contains more than 150 times as many nonredundant genes as in the human genome.

Think about that for a moment. Humans have somewhere between 20,000 and 25,000 genes. Now imagine counting the genes in the bacteria we harbor. If several bacteria all have the same gene, even if they are from different species, you count that as only one gene. If you count the bacterial genes in this way, you will find about three million unique bacterial genes in each person. To me, that is truly astounding!

So what do all these microbes do for us? They have profound effects on our immune system. Some of them directly help us fight off disease by secreting chemicals that ward off pathogens. Others help to shape our immune system by altering certain receptors on our cells, affecting the proliferation of certain immune cells, and instructing our immune systems to be more tolerant of non-pathogenic microbes. The microbes in our intestines also help us make use of certain foods that we would otherwise not be able to digest, because they make digestive enzymes that we cannot make.

Interestingly enough, even though the article in Science discusses the profound immune system benefits that people receive from their microbiome, the authors continually refer to most of the microbes as “commensal.” This is probably the reigning view in the scientific community right now, but it is almost certainly incorrect. If the majority of microbes in our bodies were commensal, we would derive no benefits from them. The fact that there seem to be a host of benefits from our microbiome and the fact that the species mix in one person’s microbiome can be quite different from the species mix in another person’s microbiome indicate that the vast majority of organisms in a person’s microbiome are mutalistic. They derive benefits from us, and we derive benefits from them.

In other words, we were made for each other!


1. George D. Stanley, Jr, “Photosymbiosis and the Evolution of Modern Coral Reefs,”Science, 312:857-858, 2006.
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2. Yun Kyung Lee and Sarkis K. Mazmanian, “Has the Microbiota Played a Critical Role in the Evolution of the Adaptive Immune System?,”Science, 330:1768-1773, 2010.
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10 thoughts on “Microbial Me”

  1. Dr. Wile, thank you for the interesting article. You mention the microbiota that benefit the body: what about the “warfare” that happens with the normal microbial community when a pathogenic microbe enters the human body? I know the human body is wonderfully designed to combat infection; one would assume the microbes would also fight the invader…


    1. Thanks for the question, Scott. I am not familiar with any studies that discuss direct conflicts between the members of a healthy person’s microbiome and pathogens. There are, however, some preventive measures. Many species in the microbiome, for example, secrete substances (like lactic acid and bacteriocins) that discourage colonization by pathogens. As I understand it, they don’t do this in response to pathogens. They just do it as a matter of course. In addition, the members of the healthy microbiome tend to spread out, making it difficult for pathogens to even find a place to colonize. However, I have not read anything to suggest that species in the microbiome act like our B-cells and T-cells, actually attacking pathogens once they are encountered.

      Of course, studies of the mammalian microbiome are still relatively new. Thus, it is very possible that such warfare happens but has not yet been characterized.

    1. Dana, I think the rampant use of antibiotics and topical sanitizers can only have negative effects on the microbiome and human health as a whole. There are some studies that are by no means definitive but nevertheless provide evidence that the rise in certain autoimmune diseases is the result of us not having the proper microbiome, in part due to the overuse of antibiotics.

      As is the case with everything else in medicine, it is all about managing risk. If you have a severe infection that threatens some kind of long-term damage, then using an antibiotic makes perfect sense. Using an antibiotic as a PREVENTATIVE, however, seems to be asking for trouble, given our symbiotic relationship with our microbiome.

  2. I have 2 responses to this…

    First my usual, snarky response to one part in particular..

    “you will find about three million unique bacterial genes in each person. To me, that is truly astounding!”

    To me, this is truly disgusting! You have a sick sense of “astounding.”

    Second, the rarely seen Black Sheep comment that actually reflects interest in said topic…

    Thanks for defining the three subcategories of symbiosis. While I know you will find this practically impossible to believe, I was recently having a discussion with someone about symbiosis and I wasn’t aware of the term commensalism. We discussed one thing being either beneficial to or harmful to another, but didn’t know what the proper term for something that benefits from another, without harming it…. except perhaps freeloader, but that didn’t seem appropriate.

    1. Actually, Black Sheep, I think “freeloader” is an excellent term. Also, don’t you think it’s possible for something to be BOTH disgusting AND astounding?

  3. I guess I should rephrase – freeloader didn’t seem appropriate for the exact specimens we were discussing.

    I guess I’ll concede that something could be both disgusting and astounding. For example, come allergy season I am both rather astounded and disgusted by the amount of mucus my body manages to produce. (See, on most blogs, I would consider that to be sharing too much, but here it seems totally appropriate.)

    1. You are correct, Black Sheep. While the reigning scientific view is that most of the bacteria that live in and on us are commensal, it is almost certainly incorrect. As such, “freeloader” isn’t the correct term here.

      The mucus information is, of course, perfectly appropriate for this blog! Thanks for sharing.

  4. Dr. Wile,

    Thanks for the article! A question that immediately comes to my mind is: if the bacteria depend on us for survival and we depend on them, why are they not considered just other cells of one multicellular creature, namely, us! Why are they classified as other organisms if there is such an inter-dependence? Why are they not classified the same as our red blood cells, and etc.?

    1. Thank you for your comment! Remember that all of your cells have the same DNA. That’s what makes them a part of you. That DNA is not only distinct from other species, it is distinct from other people, unless you are a part of a set of identical twins, triplets, etc.

      So the bacteria, protozoa, and fungi that live in and on you are not a part of your body because they each have fundamentally different DNA.

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