Decoding whole bacteria neighborhoods– not just the hoodlums

This, ladies and gents, is our microbial future. Concentrating on whole communities rather than just bad actors. Sociomicrobiology. For a further update on this, see our manuscript “From Pasteur to CSI” here. 

Thanks to Michael Coren and Fast Company for this terrific article:

Decoding Genomes Of Microbe Ecosystems Could Deliver Untold Benefits


Because one microbe is never enough: Say hi to metagenomics.

germ art

“Microbes run the world. It’s that simple.” Those are the first words of a recent report on theongoing quest to sequence the DNA of the smallest of living things. These microbes live in communities, groups of tiny organisms–“intricate, balanced, and integrated entities that adapt swiftly and flexibly to environmental change”–which basically make life possible by regulating our environment, synthesizing food and nutrients, and mediating virtually every other biophysical process. Without them, human life would cease to exist. This only recently came to our full attention because humans have been limited to studying the handful of microbes one-by-one that grow well in the laboratory.

Metagenomics — meta means “beyond,” if you’ve forgotten your ancient Greek–overcomes these barriers by analyzing the aggregate DNA of microscope communities and mapping their genetic blueprints and collective functions, something never possible before. If you think it’s easy, scramble together thousands of jigsaw puzzles in single box (while blindfolded) and rearrange those millions of pieces into a coherent pictures (you may remove your blindfold now).

In the old days, circa 1990, unraveling the genetic blueprint of a single microscopic bug was a big, Nobel-prize winning deal. Polymerase chain reaction techniques were just getting busy revolutionizing our understanding of life by making it cheap and blazing fast to decode genomes. But these bugs don’t work individually. You need their whole community to see their true effect.

Today–after taking a few years to decode the nucleotides of parasites, fruit flies and our own species –scientists are racing to advance this next frontier of genetic exploration. The report, entitled “The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet,” lays out this new field (also in need of a new name) and proposes giving researchers the tools to study all the microbes in an environment simultaneously, offering a full view of the microbial community and its complex interactions. It proposes a Global Metagenomics Initiative that will “transform modern microbiology and lead to practical applications in medicine, agriculture, alternative energy, environmental remediation, and many others areas.”

The benefits to humans are myriad. Microbes can be deployed to eat away oil spills. A better understanding of how microbes work together could lead to faster diagnoses of diseases. By engineering the genes of microbes, they could be used to produce biofuels, medicines, even foods. And as we understand more how microbes work, it could be the first step to a greater of understanding of global environmental processes. Inside these microbes may even lay secrets to the path of our own evolution–all within the interactions of millions of little bugs, whose secrets have been closed to us until now.

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