Channeling the Microbiome

The new discipline of sociomicrobiology is revealing life’s struggle tooth and nail—and gut.

By | May 25, 2011

ANDRZEJ KRAUZEThis year,’s annual question asked scientists “What scientific concept would improve everybody’s cognitive toolkit?” Stewart Brand’s wonderfully articulate response begins by recalling Carl Woese’s estimate that bacteria make up 80 percent of Earth’s biomass:

Microbes run our atmosphere. They also run much of our body. The human microbiome in our gut, mouth, skin, and elsewhere, harbors 3,000 kinds of bacteria with 3 million distinct genes. (Our own cells struggle by on only 18,000 genes or so.)…This biotech century will be microbe enhanced and maybe microbe inspired….Confronting a difficult problem we might fruitfully ask, “What would a microbe do?”

No surprise that the originator of the Whole Earth Catalog and cofounder of one of the Internet’s first robust communities, “The WELL” (Whole Earth ’Lectronic Link), would invoke the emerging field of “sociomicrobiology.” Pioneered by my one of my doctoral advisors at Cornell, E. Peter Greenberg (now at the University of Washington), this discipline uses the term quorum sensing—broadly defined as a decision-making process used by decentralized groups to coordinate behavior—to describe the biochemistry and molecular biology of environmental sensing and communication in bacteria. Of particular interest are the mechanisms by which bacteria switch from a nomadic existence to life in a biofilm, where living en masse helps them survive the action of antibiotics.

This might be an example of 'consilience' at its most basic level.

How bacteria employ stratagems rivaling those seen in the TV drama The Sopranos, is posited in a 2009 paper by Eduardo Rocha’s research group—“Horizontal gene transfer (HGT) of the secretome drives the evolution of bacterial cooperation and virulence” (Curr Biol, 19:1683-91, 2009). As explained by F1000 evaluators Jeremy Van Cleve and Steven Frank, HGT converts cheating strains that are attempting to steal secreted proteins into cooperating ones via mobile elements such as plasmids and phages. A more recent analysis by Rocha and colleagues, of 110 prokaryotic genomes and a few thousand of their defined protein families, showed that HGT—as opposed to gene duplication and mutations—accounted for 80 to 90 percent of the resulting protein evolution (PLoS Genet, 7:e1001284, 2011). This might be an example of “consilience”—defined by William Whewell in the mid-19th century as a “jumping together” of many independent sources to coordinate a particular pattern—at its most basic level.

To learn more about bacterial social behavior in small populations, under conditions that more accurately mimic those that exist in real life, Jason Shear and Marvin Whiteley developed ingenious protein-based microstructures that trap individual cells and limit the size of their colony’s expansion (see Hidden Jewel). This and other approaches on the drug discovery front, some of which are reported in Glenn Tillotson and Gayatri Vedantam’s feature article on Clostridium difficile, are helping to elucidate how we humans can remain on friendly terms with our microbiota.

And in this issue’s Critic-at-Large essay, H. Steven Wiley opines that we macrobiota might learn a lot from the social interactions of microbial communities. Increased specialization in biology research has led to necessary dependencies, while scarce resources have led to more competition, similar to the stresses we study in microbial communities. Might it be possible to create pockets of resistance by balancing the equation through cooperation and horizontal information exchange?

An interview with developmental biologist Peter A. Lawrence of Cambridge University, entitled “The Heart of Research is Sick,” was recently published in the UK magazine Lab Times. Lawrence points out that at its core, science must be about the discovery process, which may not be selected for in a highly competitive environment that rewards the most aggressive individuals and tends to diminish the efforts of younger scientists and women.

As F1000 Member Helen Skaer notes in her evaluation of the interview, Lawrence’s thoughts on the origins and consequences of these problems make thought-provoking reading. And as with all great scientific questions, she writes, “the solutions really lie in our hands.” We might look inside ourselves, to the microbiotic grandmasters of evolution, to find some answers.

Sarah Greene

Correction: The surname of Marvin Whiteley was misspelled as Whitely in the original version of this article. The Scientist regrets the error.

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