Microbiome: passenger or vehicle?

Remember how you learned in BIO 101 that many fluids in the human body are normally sterile? And you know how you laugh with condescension when someone dares to question this dogma? After all, we know that the gut and the skin are full of microorganisms, but the lung? The bladder? This is inconceivable, heretical!

Well, actually, this, like many other dogmas that seemed like God's word at the time, has been broken open by some very interesting research emerging from multiple laboratories around the world. I was first stopped in my tracks about a year ago, while listening to an NPR story in my car and learning that the number of bugs we carried on and in us was about 10-times greater than the number of our own cells. Then, in a farm house in Cornwall a couple of weeks ago, while on vacation, I read an article in an October 2009 issue of Eureka, The Times monthly science magazine, which once again made me ponder our sojourns in life, the bacteria that cohabitate with us. And finally, today I saw this story in yesterday's NYT, which galvanized me into writing action. This grabbed me in particular:

Scientists are even discovering ecosystems in our bodies where they weren’t supposed to exist. Lungs have traditionally been considered to be sterile because microbiologists have never been able to rear microbes from them. A team of scientists at Imperial College London recently went hunting for DNA instead. Analyzing lung samples from healthy volunteers, they discovered 128 species of bacteria. Every square centimeter of our lungs is home to 2,000 microbes.

It grabbed me for two reasons:
1). I am a lung doctor, and a lot of the research that I do centers around lung infections. One type of this infection, ventilator-associated pneumonia or VAP, is the subject of much scrutiny by policy makers and payers, and is emerging as a quality indicator. There are many challenging issue in VAP, not the least of which is its treatment: because it is likely to be caused by an antibiotic resistant organism, and because at least one-half of all cases of suspected VAP never grows out a specific microbe, the recommended empiric treatment is with broad-spectrum drugs. The clinician treads a fine line between undertreating the patient at the expense of increased mortality or overtreating and promoting antibiotic resistance.
2). I have already written here about my thoughts on evidence and how we tend to approach our knowledge with the arrogance that blinds us to the possibility of being either under-informed or plain wrong. Well, here is the case where we were so convinced of what we knew, yet it was plain wrong! With the scientific skepticism and appropriate tools we are learning something completely opposite to what we thought we knew.

Taking this line of thinking one step further, can we now conceive of the possibility that what we expose our bodies to actually plays a role in our long-term health? To be specific, I mean something as simple as food and the way our food is produced. Monoculture and food engineering have become staples of our food production. Animals are raised in CAFOs in conditions requiring them to be on antibiotics to ward off infections and to help with growth. Additionally, to leverage the subsidized and abundant corn supply, food animals are forced into diets completely unnatural to them. Cows, for example, evolved over millennia to be ruminants meant to eat grass and hay, are fed a corn-based grain diet, which, by altering their gut environment, makes them much more likely to carry toxigenic E. coli. Although there is much nay-saying about whether antibiotics (and hormones, by the way), are passed on to humans through meat or milk, I have never seen any convincing scientific evidence to the contrary. So, if we eat meat that is microbiologically altered, and may also be exposed to antimicrobial residues that may in turn change our own native microbiome, is it possible that at least some of the emerging health issues are due to the travesty of monoculture production?

I am not saying that I have all the answers -- clearly, this research has a long way to go to establish causal pathways and potential points of intervention. But let's exercise our common sense and at least ask the questions. Do it early and often. And let's please agree that there is a certain burden of proof here that resides with the food production oligopoly. Oh, yeah, and let's not forget to continue limiting the use of antibiotics in human health too. And have a little bit of dirt... for lunch... every day...