Exploring Microbial Dark Matter to Fight Antibiotic Resistance

While it may sometimes take calamitous headlines about a death caused by a drug-resistant infection, societal awareness of the problem of antibiotic resistance seems to be increasing. Fortunately, many of the factors responsible for the deteriorating situation have been identified, such as the ubiquitous use of antibiotics on healthy livestock to encourage rapid animal growth or the inability to create a new class of effective antibiotics. What’s more, the World Health Organization published recently a list of the 12 families of bacteria that are believed to pose the greatest threat to human health. Our founder, Dr. Rita Colwell, even spoke this week at an American Society of Microbiology conference dedicated to the topic of antibiotic resistance mitigation about assessing microbiomes in complex ecosystems. Despite having such well-defined targets and well-informed experts, the solutions remain far from simple.


As has been cited extensively, the overwhelming majority, about 99 percent, of soil microbes cannot be cultivated and studied in laboratories. That means most of the microbial material living in the environment is effectively microbial dark matter. This post, though, we’ll discuss one clever solution to this confounding problem, and illustrate its powerful potential.


Given that researchers have not been able to pinpoint why most bacteria cannot be cultured in a lab setting, Dr. Slava Epstein of Northeastern University and some of his colleagues took the insightful step of developing a product that can capture samples of bacteria from soil while still allowing them to grow in their natural settings. Known as iChip, the device uses two semipermeable membranes to trap soil samples, and uses a diffusion chamber to connect to the soil environment. This technology has enabled researchers to grow colonies of bacteria that could not be cultivated for study previously.


What’s exciting is that this innovation is continuing to bear meaningful fruit in the form of novel antibiotic candidates, such as teixobactin, a new class of antibiotics that targets gram-positive pathogens. To underscore this breakthrough, consider that even though 40 new antibiotics were in clinical development for the U.S. as of late last year, most of them are much like the antibiotics in use today, meaning they are not necessarily the game-changers for which researchers are hunting. The role of the iChip cannot be overstated given that teixobactin was discovered in a soil sample taken from a grass field in the state of Maine.


When you add metagenomics and advances in sequencing technology to antibiotics discovery efforts, keeping pace with the ever-evolving microbial targets that threaten our health begins to seem possible. Given the urgency and danger of the situation, the science community needs to use every tool it can - and some luck wouldn’t hurt.