IBM sees big opportunity in sequencing microbes

We're trained to think microbes are bad. But researchers are gathering this week to discuss uses of massive ecosystems of the micro-organisms, many of which are beneficial.

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Researchers from around the world, and many industries, are gathering today at IBM Research in San Jose, Calif., to discuss the many opportunities presented by being able to sequence microbes found just about anywhere, from supermarkets to farms to subway systems. IBM Research

SAN JOSE, Calif.--We've been trained to think that bacteria and microbes are dangerous, disease-causing organisms we should fear. But there's actually plenty to like about them, and plenty of economic opportunity to explore.

Starting Tuesday at the IBM Almaden Research Center, scores of scientists and others will be gathering for a two-day symposium called "Sequence the City: Metagenomics in the Era of Big Data." The goal? To discuss the many ways that understanding the broad utility of bacteria and micro-organisms can help understand human health.

Part of a project known as the Almaden Institute, the work is part of a large effort to spread the study of "microbiomes" beyond medicine to other industries, including agriculture, food safety, counter-terrorism, forestry, forensics, retail, public utilities, and others.

According to James Kaufman, a research manager at the Almaden Research Center, the move to study metagenomics -- the study of systems of micro-organisms -- came from what he called a tipping point in big data. As more and more government-funded institutions study organisms and bacteria, they've collected more information about them, and submitted much of their work to centralized databases. "So there's a growing library of genomes across the field of life," Kaufman said. "That made possible metagenomics."

The result: We can now look at and understand whole ecosystems at the bacterial level. One example of how that manifests is what IBM refers to as the Human Microbiome Project. According to an IBM document, that's about characterizing "microbial communities found at multiple human body sites to discover correlations between changes in the microbiome with changes in human health."

The thing to realize, Kaufman said, and that could be a game changer for a wide range of industries, is that "we're swimming in ecosystems, and some of these bacteria are helpful...Instead of saying, 'Is there West Nile Virus in this mosquito, you could take samples from mosquitoes and tell me everything that's in there. That's possible because we have a growing database of knowledge about genomes of [nearly] everything."

Kaufman explained that in recent years, as scientists have submitted their research, there is now a central library of about 3,000 complete bacterial genomes, and between 30,000 and 40,000 complete virus genomes. And those numbers are growing quickly because it has become so inexpensive to sequence genomes. "We're anticipating," Kaufman said, "that with the costs of sequencing dropping, it will be routine to sequence anything and everything."

That could include, he added, houses, factories, restaurants, even whole cities.

But analyzing all this data requires significant computing power, and that's where IBM thinks it has a role to play an in the ecosystem of industries seeking opportunity in the data. Big Blue thinks it can offer computation as a service. "That's what's inspiring us to do this institute," Kaufman explained.

Many applications

As this work moves forward, IBM imagines a host of potential partners, or customers. Cities, for example, may want to know about the micro-organisms that collect on subway turnstiles, while any number of people may be interested in what is on paper money. Sequencing the city is about sequencing the everyday life of a person, the company believes.

One thing that is certain to happen as the work progresses is that companies that are not in life-sciences fields will want, more and more, to understand the impact of micro-organisms. For example, food is made from biological components -- plants and animals -- and there's lots of biology involved in its production.

But supermarket giant Safeway would never have been considered a life-sciences company. Yet, a company like that has a huge interest in understanding the presence of bacteria in its products, and which are good, and which are harmful. Similarly, agricultural companies have a big interest in learning which micro-organisms can be used to promote the growth of their crops. Too, plenty of foods, like beer, wine, and yogurt, are made using microbes.

This kind of work is not entirely new, but the scientists who will be gathering at IBM Research this week are grappling with one conundrum: they don't know what they don't know. So a big topic of conversation, and a big part of what IBM would like to see advanced, is "the ability to do metagenomics on the scale of a city or the world....That will depend on software services available in the cloud," Kaufman said. "It has to be cheap, easy, and accessible from anywhere. That's what we're really good at."

And to IBM research staff member Robert Prill, it's important for people to understand that "the world is not a scary place just because it's inhabited in every nook and cranny by microbes....You can have a community of microbes that live on anything, and it could be completely benign. But understanding that community can help you understand [any] industry better, whether it's food, or transportation," or something else.

Indeed, Prill said, while the spread of diseases like avian flu has generated an societal instinct to get rid of bacteria, "the blanked killing of microbes on your hand [might] not necessarily be beneficial."

Added Kaufman, "Some of these microbes can actually protect us, so you might want to think twice before you steam clean the house."

 

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