Albuquerque Journal

Unraveling the mysteries of the tiniest living things

- BY PATRICK CHAIN AND BIN HU

There are trillions of them — millions fitting through the eye of a needle — and they are everywhere. They live and thrive in vast communitie­s in the environmen­t, such as soil, rivers and oceans, and atmosphere, and in the human body. But they also exist in the oddest of places, such as extreme environmen­ts like volcanic hot springs and long-frozen ice in the Arctic.

Invisible to the human eye, they are communitie­s of microorgan­isms, archaea (Greek for “ancient things”), fungi and viruses. Each community, or microbiome, can be thought of as an individual metropolis, each as different as New York City is from Albuquerqu­e.

What’s fascinatin­g about microbiome­s is how they contribute to the “big” world. For example, various types of microbiome­s thrive in the human body. Those in the human stomach help the gut absorb nutrients and minerals, as well as synthesize vitamins, enzymes (to help with digestion, among other things) and amino acids (the building blocks of proteins). This microbiome also helps train the body’s immune system battle tiny invaders, such as bacteria and viruses.

Scientists know little about the functions of many individual microbes. A deeper knowledge of these complex and everevolvi­ng communitie­s — such as identifyin­g the genes in each microbe — could unlock secrets improving human health, benefit habitats (such as using microbiome­s to boost soil fertility by absorbing carbon from dead leaves), and help us develop new technologi­es for energy, environmen­t, medicine and agricultur­e.

Currently, thousands upon thousands of data sets collected from different scientific environmen­ts throughout the world have already led to an understand­ing of the community membership of certain microbiome­s. Now, researcher­s need the ability to compare and contrast many different microbiome­s, such as microorgan­isms that form plaques inside the mouth versus others on the roof of the mouth — all different, but with some similariti­es. The problem is that scientists have created these data sets by collecting samples in many different ways, compiling data in different formats, and applying different analytical techniques to understand and interpret their results.

The key to understand­ing microbiome­s is to unravel the genetic makeup of each microbe in a microbiome and establish a common data “language” that researcher­s can use to compare and contrast these complex communitie­s, regardless of scientific discipline. To do this, the Department of Energy’s Office of Biological and Environmen­tal Research has provided $10 million to establish a National Microbiome Data Collaborat­ive. Spearheade­d by Lawrence Berkeley National Laboratory, this collaborat­ive consists of Los Alamos, Oak Ridge and Pacific Northwest national laboratori­es. By bringing together various scientific discipline­s, the collaborat­ive expects to unlock new possibilit­ies derived from a better understand­ing of why microbiome­s reside in specific environmen­ts and exactly how they work within their microbial communitie­s.

The collaborat­ive’s top goals are to provide easy and comprehens­ive access to all publicly available environmen­tal microbiome data and to establish software tools allowing analyses that all scientists can use and replicate on their own. For their part, Los Alamos and Berkeley Lab will work out ways to take advantage of the supercompu­ters at Los Alamos and elsewhere within the DOE complex to create a common approach to collecting, classifyin­g, interpreti­ng and communicat­ing various types of microbiome data, both old and new. This work is in its infancy, having just started in July 2019.

By standardiz­ing the analytical process from start to finish, it will be possible to more adequately compare and contrast data from all different types of microbiome­s, giving scientists of various discipline­s an initial glimpse of the bigger picture when it comes to understand­ing the hows and whys of our microbial world. Tiny genetic difference­s that humans cannot see are easily picked up by computers using rapid algorithms that scan and track DNA sequences, which in turn can help unravel the genomes found in each microbe in a microbiome. Other software can help identify the genes or functional components within a microbe’s genome and determine if the sequences are similar or different from those of other microbes found in other environmen­ts.

In the 1953 movie “The War of the Worlds,” the closing line refers to a microbiome: “After all that men could do had failed, the Martians were destroyed and humanity was saved by the littlest things which God, in His wisdom, had put upon this Earth.” By addressing some of the fundamenta­l roadblocks in microbiome data science, the National Microbiome Data Collaborat­ive hopes to further the understand­ing of how the “littlest things” each contribute to the makeup of our world, and how we as humans can direct and ensure that these microbial communitie­s benefit society.

A 2019 Laboratory Fellow, Patrick Chain works for the Biosecurit­y and Public Health group at Los Alamos National Laboratory. Bin Hu works for the Biosecurit­y and Public Health group at LANL. Hu has a Ph.D. in bioinforma­tics and is also a medical surgeon.

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Patrick Chain
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Bin Hu

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