Saturday, February 7, 2009

the ecosystem model of everything

(image of antiobiotc resistant Staphylococcus aureus subsp. aureus original here)

A flurry of recent news items and newly minted research consortia have drawn unprecedented attention to the nether world of microorganisms that exist within and upon us middle-of-the-universe humans. I've discussed this before. The most significant is the Human Microbiome Project, a multi-disciplinary research group with the goal of cataloging all the flora and fauna that lives in and on the human body. The research thus far makes it uncertain if this is even possible, but does open up an entirely new can of worms where the boundaries between humans and their environment are increasingly blurred.

One of the first papers to come out of this collaboration details the unique tribes of bacteria that dwell on the skin of your inner elbow (nytimes article here). The skin, in general is loaded with microorganisms, even after you wash there are approximately 1 million of these tiny creatures on every square centimeter of your body. For the most part these hitchhikers are commensulate, feasting on our dead skin cells in return for keeping us clean and moist. On the inner elbow a team of researchers sampled five people and found that everyone had 6 major tribes of bacteria in common, with a few specific tribes depending on the individual. This was good news for the researchers; it meant that developing a general model of human microorganism communities could be possible. A general model in turn could be used to detect abnormalities in an individual's microbiota and create a sort of standardized probiotic regimen that could correct deviations in the profile. Making us healthier and more resistant to the bacteria that make us sick. However, a separate group of researchers that focused on an area of the forearm a few inches away from the inner-elbow study had a very different outcome...

"We swabbed the forearm skin of six people. There were 12 arms. We found 182 species of microbes representing seven different phyla,” he said. “Recently, another group studied skin from the crook of the elbow, just a few centimeters away from the site of our study, and found an entirely different microbial population. In our studies, we found 91 different genera, but only five of them were present in all six individuals. Sixty-one were present in just one individual, indicating a very high level of intrahost variability. Further, we looked at the same individuals eight to 10 months later and found that their microbial populations were no more similar to their own arms than to somebody else’s arm.” original here

in another study at University of Colorado Boulder, researchers swabbed the hands of 51 undergraduates. They detected and identified more than 4,700 different bacteria species but only five species were shared among all participants. Even more surprising, the right and left palms of the same individual shared an average of only 17 percent of the same bacteria types.

This research suggests that everybody has a unique microbiotic "signature." This signature varies both in space on our bodies and in time as we move through new environments, seasons cycle, and our diet changes. Understanding how this signature is related to health, behavior, and our evolution as a species will help us understand each human not as an isolated organism acting in space, pursuing an individual agenda, but as complex and densely populated ecosystems that are in constant flux and flow, disturbances in the community creating moods, diseases, thought patterns, rashes, glow, love, tumors etc. Known as a superorganism, our human cells are outnumbered 10 to 1 by microbiotic partners, and we are constantly exchanging these creatures with our environment.

(photo of bacteria colonies on a cell, original here)

The primary tool that has unlocked this new mode of understanding is metagenomics. A rapid DNA/RNA sequencing technique that rather than amplifying an isolated genome to identify a single species, takes a large sample of many different genomes and parses out individual genes. A sort of gene frequency map for a given scoop of earth or skin swab, where function is defined not as a single organism but as a suite of genes that blur boundaries between organism and ecosystem.

This is a new way of thinking, where the individual is superceded by the community, where function can be found in an overall ecosystem genetic profile rather than trophic webs. What are the primary genes in this system and what function do those genes carry? A way of viewing the world as a series of concentrated microbial activity nodes, each node corresponding to a function or an organism. Co-evolution seems logical, but given the incredible variation between microbial communities on/in individuals a sort of human-as-garden (bacteria being the gardeners) seems more appropriate. We evolved the capability to play host to almost anything that comes along, and the first-come-first-served concept seems to play out nicely as our friendlies circle the wagons and battle back the invaders, who of course have another host (pig, goose, rat, etc) in which they are the good guys. In this light every plant and every animal is an ecosystem maintained by microorganisms. The genus/species model based on the individual is very poor resolution, akin to viewing Earth as a single species. To give some perspective, humans have approximately 4305 square feet of surface area that is speckled with microbiota at a density of (+/- 1,000,000) one million per square inch. If you were the size of an average bacteria, that would be like living on a planet 51 times the size of earth (a finger is the area west of the Mississippi) where everyone had 135 acres of prime real estate to call home. A strange world.

The implications are clearly far reaching, and I believe that in the next 50 years this mode of thinking will be highly instrumental in forging a new kind of eco-ethic, where humans are inextricably tied to their environment through the constant flow of microorganisms. A robust ecosystem keeps us (me and my flora/fauna) healthy, clean water keeps us healthy, living food keeps us healthy, but when the environment becomes toxic, or corrupt with antibiotics, and conditions shift to favor a different suite of microorganisms, we get sick, or angry, or depressed, or greedy, and we create a world that favors those creatures that are in us, so they grow stronger, multiply and spread. Good versus evil. The future will be a time where we learn how to live in harmony with the microorganisms, gathering beneficials to combat the superbugs we've bred, washing our crops with pest fighters, clothes designed to encourage not kill, energy from algae, fungi digesting our waste, a world where we fully embrace ourselves as ecosystems, not individuals.

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