Imagine Magazine - Johns Hopkins - September/October 2013 - (Page 26)

Our Second Genome by Rob Knight, PhD, and Daniel McDonald While our genomes may be 99.9 percent the same, our gut microbiomes can be 100 percent different. NIBSC/SCIENCE SOURCE Escherichia coli bacteria in culture. False-colored scanning electron micrograph of E. coli bacteria grown in tissue culture (magniﬁcation: x10,000). E. coli is one of the best-known bacteria that live in the human intestinal tract, so we may think of it as prevalent, but it is actually a rare member of the gut of most people. We just think of it as common because it is very good at growing in a Petri dish. In graduate school, Rob Knight was interested in microbes that live in extreme environments, like hydrothermal vents. But he realized that the human body is full of extreme environments from a microbial perspective, and that the communities of microbes that make their home in us are as fascinating as anything in the world outside our bodies. Now a professor of chemistry and biochemistry at the BioFrontiers Institute at the University of Colorado, Knight is a pioneer in the study of the microbiome and how it affects health and disease. N o man is an island. From a microbial perspective, each of us is more like an archipelago. The palm of the hand is an entirely different environment from the surface of a tooth or a tonsil or an intestine, but each of those parts of our body is densely populated with its own microbial inhabitants. We are each like our own Galapagos Islands—a collection of adjacent habitats with very different environments, each with its own community of organisms adapted to life in that locale. The 100 trillion or so microbial cells that thrive in and on us outnumber our own cells by as many as 10 to 1, although collectively they weigh only a few pounds. The fact that microscopic creatures live on us has been known for over 300 years, since the invention of the microscope. Until recently, our ability to study our co-inhabitants was limited by the fact that only a few percent of them can be grown in a Petri dish. Much has been learned about those microbes and their importance in human health and disease. But with the vast majority invisible to analysis, even basic questions—such as how many different species live on us, how diverse they are genetically, and which of them are common to all humans and which are unique to an individual—were unanswerable. In recent years new methods of identifying microbes based on their DNA have emerged, and many important questions can now be answered without growing them in culture. Innovations in molecular techniques, sequencing technology, and computational tools have made it possible to analyze vast amounts of DNA sequence data from diverse microbial communities, and to compare the communities within a single individual, across individuals, across time, and across species. In particular, the cost of DNA sequencing has decreased by a factor of about a million in the past decade. It’s an incredible time to be interested in microbes.

Table of Contents for the Digital Edition of Imagine Magazine - Johns Hopkins - September/October 2013

Imagine Magazine - Johns Hopkins - September/October 2013
Contents
Bridging the Gap
The War on Cancer
Teen Researchers on the Forefront of Medicine
Ancient Medicine Meets Modern Technology
Innovations in Medicine
Wherever Help Is Needed
Summer in the Lab
Our Second Genome
The Defi nition of Determination

Imagine Magazine - Johns Hopkins - September/October 2013