SDSU microbiologists identify bacteria that could one day speed food production, biofuel creation and vaccine development

It started with a simple statement by Scott Kelley’s former graduate adviser. What followed was an eye-opener about the place you go to get clean.

Just beyond the rubber ducky in your “disinfected” bathroom, your shower curtain plays host to a staggering array of bacteria. Most are harmless, but some are opportunists — waiting to prey upon bathers with compromised immune systems.

Scott Kelley examines a shower curtain sample.

“We found a rainforest of biodiversity on your shower curtain,” said Kelley, now an assistant professor of microbiology at San Diego State University. “There are a few things in there that could be problematic for people with HIV, young children and older folks.”

Wake-up call

Kelley’s findings were a wake-up call for how little is known about indoor environments.

Knowledge about the germs lurking in houses, offices and the other places we spend our days is scant due, in part, to a prior reliance on culture-based techniques.

Traditionally, researchers take a swab of something, and use a particular medium (food) to grow what they suspect is in their sample. There could be millions of different bacteria in the sample that all need different energy sources to propagate and be identified, but if the right medium isn’t used, most won’t grow. Culture-based methods restrict researchers to known organisms, leaving the true diversity of the bacterial world undiscovered.

Kelley and his colleagues specialize in DNA-based detection techniques, through which a sample’s DNA can be busted open to reveal every organism inside.

“We can get the stuff that won’t grow on the plate,” Kelley said. “We can use differences in the genetic code to figure out what’s what, and what they’re doing in the environment.”

Bacteria samples from the SDSU
Children's Center grow in liquid media.

Using this breakthrough method, Kelly has been taking samples from daycare centers, hospitals and airplanes to see what kind of bugs live in our indoor environments, how they migrate from place to place and how we can stop them from making us sick.

So far, among the immense diversity of organisms he has found, few are pathogens, or harmful bacteria, and those can be eradicated with proper sanitation.

The softer side of germs

The germ hunter’s mission isn’t always to search and destroy. Part of the value in discovering the immense variety of bacteria uncovered using DNA techniques is to see how they function in the ecosystem and how those functions carried out on a larger scale could help make our lives better.

“People are doing it in every environment imaginable, from undersea volcanoes to shower curtains to hot springs,” Kelley said. “They are finding a huge diversity of things; new organisms that could help in dentistry, with diseases; there are all sorts of bugs in the environment that we had no idea were there.”

Many bacteria help us every day; in fact, we couldn’t live without some of them. They help us digest our food and absorb micronutrients; they serve as the primary food source in the oceans and they eat the greenhouse gas methane, among other things.

But microbiologists have hardly begun to tap the potential of microorganisms.

Experts see a role for bacteria in the manufacture of biofuels, like ethanol, at an accelerated rate; the conversion of sewage into energy; the production of food; the capture of carbon dioxode from the atmosphere; the creation of resilient enzymes that could be used to treat cancer; even in the quest for healthier teeth.

“There are so many bacteria we could potentially use that are undiscovered,” Kelley said. “We don’t yet know the diversity, so we don’t know all of the possibilities.”

At the source

Richard Bizzoco studies a heat-resistant thermophile.

Researchers are chipping away at it, though. And some, like SDSU molecular biologist Richard Bizzoco, are heading straight for the extremes of the spectrum to find the most useful bacteria.

He searches for new, heat tolerant (thermophillic) bacteria in underground locations, where little work has been done to identify and classify resident microorganisms.

“We know that most thermophiles grow best between 50 to 70 degrees Celsius,” said Wendy Gutierrez, an undergraduate researcher who grows and extracts DNA from organisms in Bizzoco’s laboratory. “Non-thermophiles usually grow at 20 to 37 degrees Celsius.”

Thermophiles thrive in "extreme" environments,
like Old Faithful at Yellowstone National Park.
Photo courtesy of Richard Bizzoco.

There are only a few places to obtain samples that originate underground without tainting them; Bizzoco focuses on steam vents found in volcanic regions of Hawaii and hot springs in environments like Yellowstone National Park, both considered to be extreme habitats for microorganisms.

“The more extreme a habitat, the fewer organisms exist there. So the complexity of an ecosystem can be somewhat limited,” he said.

Since these extremophiles are simpler, more concentrated and hardier than their non-extreme counterparts, they can be subjected to a wider variety of experiments in the lab. As a result, they have enormous potential for producing disease-fighting enzymes, filling in evolutionary blanks and accelerating commercial processes in lucrative ways.

“There are lots of high-temperature enzymes that have been introduced because of the thermophiles that have been identified,” Bizzoco said. “Last year, we discovered two new types of motility flagellae with new structural features. Well, maybe one day those could be used for airplanes. I’m not joking. Or, what if we could introduce the genes for winemaking into a thermophillic organism; then it would be really easy to carry out fermentation. You could make lots of money.”

In fact, the very DNA-based techniques, used by Bizzoco and Kelley are dependent on a heat-resistant enzyme derived from a thermophile discovered at Yellowstone.

Give the bugs a break

Until researchers discover all of the organisms that fight illness, and their nemeses, that cause it, proper cleaning of shower curtains and surfaces in indoor environments should take care of pathogens, while your immune system does its job to ward off the rest.

Other than that, Kelley encourages giving the bugs a break.

“If you think all bacteria are bad, man, you’re completely mistaken.”

Related information

• SDSU Biology Department
• SDSU Center for Microbial Sciences
• CDC - Stopping Germs
• Yellowstone National Park

Credits

• Story by Lauren Coartney
• Graphics by John Signer
• Photographs by Tom Farrington, Instructional Technology Services
• Edited by Coleen Geraghty