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How a Cave in New Mexico Is Helping Scientists Understand Bacteria

Extremely drug-resistant bacteria have been found deep in New Mexico’s Lechuguilla Cave.

By Nathan Collins


Chandelier Ballroom in Lechuguilla Cave. (Photo: Wikimedia Commons)

Antibiotic-resistant bacteria are one of the most serious health threats we’re going to face in the years to come, according to the Centers for Disease Control and Prevention. It’s well-known that humans have contributed to the problem by overusing antibiotics, but two new studies in the journal Nature Communications highlight just how much we have left to figure out.

For one thing, how did bacteria resistant to 14 modern antibiotics end up in a New Mexico cave that hasn’t seen the light of day in four million years?

Yes, you read that right: In 2012, McMaster University biochemist Gerard Wright and his colleagues discovered bacteria in a 1,000-foot-deep section of New Mexico’s Lechuguilla Cave that, prior to it’s discovery in 1986, no human had ever set foot in. At the time, the team identified a range of bacteria that was resistant to a variety of drugs, including one drug, daptomycin, that’s only been on the market for about a decade and is used relatively rarely.

That drug resistance isn’t, on its face, so surprising. Penicillin-resistant bacteria were discovered before the drug was ever used to treat infections, and drug-resistant bacteria have been found in Incan mummies and Yukon permafrost. It’s not hard to see why: Many modern antibiotics derive from naturally occurring substances such as those that might be found in plants or even other bacteria, so it’s to be expected that some microorganisms evolved resistance to the active ingredients in modern drugs.

What’s surprising, Andrew Pawlowski, Wright, and their colleaguesreport in the new paper, is just how stubborn that drug resistance can be. The team focused on one particular bacteria they found in Lechuguilla Cave, known as Paenibacillus species LC231. Tests showed the bacteria was resistant to daptomycin and 25 more of the 40 antibiotics the team tested, even though humans have only recently explored the portions of the cave where the bacteria was found. Such stout resistance, the team found, was tied to 18 different genetic defenses—a substantial “reservoir of resistance elements” waiting to make their way into disease-causing bacteria.

That finding highlights the fact that antibiotic resistance is not something created by modern drug development. Instead, it’s been around—pervasive, in fact—for millions of years. What’s different today, Pawlowski and his team write, is that our misuse of antibiotics has allowed those drug-fighting elements to flourish.

In a second paper published today, Oriol Marimon, Miquel Pons, and some colleagues looked at one particular way E.coli bacteria defend themselves against both antibiotics and the body’s own antimicrobial defenses. Like many bacteria, E. coli can go into a dormant mode called a biofilm—a conglomeration of cells shrouded in a protective shell—when threatened. As a result, they won’t absorb antibiotics, rendering the drugs ineffective.

The way around this: oxygen. Ordinarily, biofilms form when bacteria themselves release a toxin in response to a threat; once the threat is gone, they release an antitoxin that dissipates the biofilm and reactivates individual bacterial cells.

Marimon, Pons, and their colleagues’ discovery is twofold: First, the E. coli antitoxin needs oxygen to work; second, E. coli biofilms form channels just the right size for oxygen molecules to penetrate—suggesting that simply adding oxygen to the environment around a biofilm could be an effective way to combat at least some bacterial infections.