Microbiome Blues in E

April 1, 2015

By M tanner

Many  bacteria live in and on me—I’ve always known that. But when I learned that bacteria make up 90% of the cells in my body, it made me feel so sucio, so unclean.

I went through my day, realizing for the first time that I am entertaining 100 trillion houseguests who never go home. And who lack all sense of decorum. I know that, technically speaking, bacteria are asexual. But then I read: “one special type of pilus found in ‘male’ strains of E coli is involved in conjugation, with the transfer of DNA from donor to recipient, probably accomplished through its core.” Why the quotation marks around ‘male’? Sounds like a typical guy to me.

I’ve always liked to think of myself as a eukaryote, the kind of standup, biped guy whose cells all have a nucleus. A member in good standing of the kingdom Animalia, the phylum Chordata, the class Mammalia, the order of Primates, the family Hominidae, the genus Homo, and the species Sapiens. Einstein’s species, the crown of creation.

Now I see myself as one of Car & Driver’s 10 best in the bacteria class, with a refined, roomy interior (30 linear feet of gastrointestinal tract); a beguiling, sporty exterior (20 square feet of skin); and an eagerness to romp. Looking at my reflection in the bathroom mirror I don’t see just me any longer. I’m trying to determine whether the man in the mirror is overall more gram-negative or anaerobic.

There is much about bacteria to admire. They have a lot of seniority: 3.5 billion years, compared with Homo’s 2 million. They reproduce (and mutate) in minutes, where it takes us 40 weeks. They produced the oxygen that makes our existence possible. There is no actual malice behind even their most horrendous infections. And most bacteria cause no trouble.

When I cut my finger, I do what everyone does. I put my finger in my mouth and clean off the blood with my tongue. There are 100 million bacteria in every milliliter of saliva. If Streptococcus salivarium were pathogenic, we’d all be dead.

The bacterial population of the gaps between our teeth is huge. How do I not get endocarditis every time I launch a diaspora with a strand of dental floss?

Everyone has heard of the serial killers E coli, Staph aureus, Strep pneumoniae, and M tuberculosis, but our heroes are unsung. No virgins strew rose petals in the paths of the benign, commensal bacteria holding down spots that could otherwise be occupied by superbugs producing the dreaded New Delhi metallo-beta-lactamase-1. I only recently learned the names of the Firmicutes and Bacteroidetes, benign anaerobes that make up over 98% of our bacteria.

On further reflection I feel better about the 10-to-1 situation. They only weigh three pounds. And it’s not like there are ten of them loitering in every one of my cells. There are strict divisions between the body’s sterile and microbial regions. Bacteria are confined to the skin, the gastrointestinal tract, the nose, the ears, and the vagina. The vital organs—heart, liver, kidneys, and brain—are sterile. Likewise, many bodily fluids–blood, urine, cerebrospinal fluid, and amniotic fluid—are sterile or close to it. That’s why I get mad when the border is crossed. Really mad.

I know I shouldn’t. Nobel laureate Joshua Lederberg wrote in 2005 that we should “supercede the twentieth-century metaphor of war for describing the relationship between people and infectious agents. A more ecologically-informed metaphor, which includes the germs’-eye view of infection, might be more fruitful.” Yes, but in the hospital I can’t get myself to be all ecologically minded when my patient has a fever of 105 and shaking chills.

Ask If My Hands Are Clean (poster by the elevators at Bellevue Hospital)

lunchtime. I’m walking across the Bellevue atrium when a strange man comes up to me.


Are your hands clean?


I beg your pardon?


Are your hands squeaky clean?


Do I know you?


No, but I know you. You’re a doctor. I’ve seen you around the clinic for years. You ride a bike to work.


Do you also happen to know the name of my first childhood pet?


Huh? That sign over there says “Ask if my hands are clean.” So I’m just doing what it says. Are your hands clean?


May I ask? What is your diagnosis?


Obsessive-compulsive disorder. So! Are they clean?


That’s a complex question. Have you heard of Stanley Falkow?




He’s a microbiologist at Stanford. Stanley Falkow wrote: “The world is covered with a fine patina of feces.”


That’s disgusting.


Disgusting but true, my friend. I rode 4 miles on my bike this morning through the streets of Manhattan, holding handlebar grips that I’ve never washed.


You haven’t? I use Purell 20 times a day. I love these Purell dispensers they’ve placed all over the hospital.


I bet you do. You might want to back off on the Purell. Have you heard of Dr. Martin Blaser?


Oh yeah, he was on Jon Stewart.


He wrote: “What’s wrong with good old soap and water?” So let’s say I walk into the hospital with 10 billion bacteria on my hands, and that Purell, if the claim on the label is true, kills 99.99% of them. That still leaves a million bacteria on my hands. The whole notion of getting out of the shower and being “squeaky clean” is a joke. You haven’t been squeaky clean since you were bunking with a placenta. But don’t be blue. The bacteria you acquired on that ride down your mom’s birth canal are actually helping you.


Can you write me a prescription for a good colon cleanser?


Why don’t you take that up with your primary care physician?

Most of Our DNA is Bacterial

Martin Blaser, in his book Missing Microbes: How the Overuse of Antibiotics Is Fueling Our Modern Plagues, maintains that antibiotics, modern hygiene, and overreliance on Caesarean section have disrupted our microbiota and led to the proliferation of type 1 diabetes, asthma, obesity, and celiac disease. But I found this even more disturbing:

…your microbes and mine have millions of unique genes, and a more current estimate is 2 million. Your human genome, by comparison, has about 23,000 genes. In other words, 99 percent of the unique genes in your body are bacterial, and only about 1 percent are human…”

This brought to mind the classic passage from Richard Dawkins’s The Selfish Gene about the Replicators (self-copying molecules, DNA):

Now the Replicators swarm in huge colonies, safe inside gigantic lumbering robots, sealed off from the outside world, communicating with it by tortuous indirect routes, manipulating it by remote control. They are in you and in me; they created us, body and mind; and their preservation is the ultimate rationale for our existence. They have come a long way, those replicators. Now they go by the name of genes, and we are their survival machines.

Shared Decision Making I

I walk out of the hospital and suddenly feel like driving to Jones Beach. But is it really I who want to go to the beach? Or is it that erogenous zone on my 30 trillion Y chromosomes–the DNA sequence responsible for the atavistic tendency of the Tanner males to drift toward potential Tanner-germinators–that wants to go to the beach and “I”, the lumbering robot, the survival machine, who will just be just handling the driving and tolls?


Shared Decision Making II

My wife and I are at our neighborhood restaurant for our anniversary. “Let me tell you about tonight’s dessert specials,” our waiter says. “We have an orange soufflé topped off with Grand Marnier sauce, a citrus tart drizzled with pomegranate compote, and, lastly, a chocolate mousse. It is scandalous.’’

Carlo Maley of UCSF believes that our cravings for certain foods are bacterial in origin. The brain may be sterile, but it is subject to remote control. A neural impulse originating in my abdomen zooms up the vagus nerve to my hypothalamus and I can almost make out the words of a dull chant: “Order the mousse! Get the mousse!” Without too much deliberation I tell the waiter: “We’ll have the mousse. Two spoons, please.”

Microbiome Blues

It’s not that bad being bossed around by my bacteria. I don’t even notice it. I’m worth more to them alive than dead, so our interests are pretty much aligned. We’re so intertwined that it’s like a marriage. At various times bacteria are our friends, our enemies, and our bosses. Servants too: every time I prescribe human insulin for a patient, E coli have done the heavy lifting. Our behavior is an amalgam of many forces, and our microbiome is part of the mix. What really determines our daily choices? Hormones? Our parents? Our past experiences? Our genes? Our bacterial genes? The configuration of the planets on the day we were born? When we don’t have a good explanation for something we tend to put all our bad explanations together and call it “multifactorial.”

It’s bedtime. I brush my teeth and gargle with Listerine, which kills 99% of odor-causing bacteria. The other 1%, however, will be at it all night. Then I wash my hands one last time and say the Lavabo, from Psalm 26. Said fast, it takes 15 seconds—the amount of time we doctors are supposed to spend washing our hands:

“I wash my hands in innocence, O Lord. Giving voice to my thanks and marveling at your miraculous universe. O Lord I love the house in which you dwell, the tenting place of your glory. Gather not my soul with those of sinners, nor with men of blood my life. On their hands are crimes and their right hands are full of bribes. But I walk in integrity. Redeem me and have pity on me.”

Dr. Michael Tanner is Executive Editor of Clinical Correlations


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