Image: Courtesy the Alm Lab
Click to see the full microbiome tree. Image: Courtesy the Alm Lab

Low-cost genetic sequencing and high-powered computational methods now allow scientists to amass huge amounts of data on the makeup of individuals’ microbiomes, or the hundreds of species of microorganisms that call our bodies home. The goal is to use that data to learn more about the bacteria and other microbes that ordinarily help keep us healthy, but can lead to serious problems like inflammatory bowel disease when disrupted.

But how do you organize that information to have it make any sense?

Eric Alm and colleagues had the same question. “We wanted to figure out a way to quickly visualize all of that data,” says the associate professor of biological engineering and co-director of the Center for Microbiome Informatics and Therapeutics. Alm posed the question to his wife, Katherine Huang, a data-visualization specialist at the Broad Institute of Harvard and MIT, and eventually convinced her to write a computer program to do the visualization. “It was my Christmas present,” Alm says.

The program generates a microbiome “tree” for individuals participating in Alm lab research studies. Each tree, like that shown above, captures a variety of information, including the proportions of different microbes in an individual’s gut and how those microbes are related to each other. In the tree above, for example, each dot represents a different species of microbe. The dots’ colors correspond to the nine different phyla, or larger categories, these species fall under.

Read more about the founding of the new Center for Microbiome Informatics and Therapeutics in the Spring 2015 issue of Spectrum: “Microbiome Research: A New Frontier in Medicine


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  1. Constance Lai

    Thanks for committing to this research! When I lived in Europe in 1994-5, I was given prescriptions of probiotics made by Bayer (the aspirin maker) in order to replenish the good bacteria in my stomach. Here in the United States, the market is completely unregulated and the products on the market are sketchy at best. It is also very important to study how stress can change a microbiome as well, since that is how my microbiome became un-balanced in the first place.

  2. Jeff Rosner

    Katherine / Eric,
    Interesting view, but my feeling is that you have moved to a ‘middle ground’ of information that is neither scientifically precise, nor intuitively obvious. I am knowledgable in the genetics space (until recently CTO of the Genetics business at Life Technologies, formerly Applied Biosystems and now Thermo-Fisher). I believe that the community needs an approach to these informatics that is immediately intuitive to most working professionals, and eventually to the lay public. I assume from your diagram that the dots on the outer perimeter represent all the species detected and radially inward this collapses along standard taxonomic designations, but if that were my u-biome, I would want to know the relative fraction of each phylum present and the occurrence of any significant species known to have health outcome signatures. 

    …I am an MIT alum.

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