Creative Minds: The Human Gut Microbiome’s Top 100 Hits

Michael Fischbach

Michael Fischbach

Microbes that live in dirt often engage in their own deadly turf wars, producing a toxic mix of chemical compounds (also called “small molecules”) that can be a source of new antibiotics. When he started out in science more than a decade ago, Michael Fischbach studied these soil-dwelling microbes to look for genes involved in making these compounds.

Eventually, Fischbach, who is now at the University of California, San Francisco, came to a career-altering realization: maybe he didn’t need to dig in dirt! He hypothesized an even better way to improve human health might be found in the genes of the trillions of microorganisms that dwell in and on our bodies, known collectively as the human microbiome.

Continue reading

Snapshots of Life: Portrait of a Bacterial Biofilm

Colony of Pseudomonas aeruginosa

Credit: Scott Chimileski and Roberto Kolter, Harvard Medical School, Boston

In nature, there is strength in numbers. Sometimes, those numbers also have their own unique beauty. That’s the story behind this image showing an intricate colony of millions of the single-celled bacterium Pseudomonas aeruginosa, a common culprit in the more than 700,000 hospital-acquired infections estimated to occur annually in the United States. [1]. The bacteria have self-organized into a sticky, mat-like colony called a biofilm, which allows them to cooperate with each other, adapt to changes in their environment, and ensure their survival.

In this image, the Pseudomonas biofilm has grown in a laboratory dish to about the size of a dime. Together, the millions of independent bacterial cells have created a tough extracellular matrix of secreted proteins, polysaccharide sugars, and even DNA that holds the biofilm together, stained in red. The darkened areas at the center come from the bacteria’s natural pigments.

Continue reading

Cool Videos: Battling Bad Biofilms

Metabolomics of Bacterial BiofilmsPeriodically, I’ve posted some of the winners of the video competition to celebrate the Tenth Anniversary of the NIH Common Fund. After an intermission of several months, our scientific film fest is back to take another bow. This cool animation shows what some NIH-funded researchers are doing to address a serious health threat: hospital-acquired infections. Such infections can lead to hard-to-heal wounds, such as the foot sores that can trouble people with diabetes, and pressure ulcers in the elderly.

The stubbornness of such wounds owes, in part, to the infection-causing bacteria joining forces to improve their chances of survival within the injury. These microbes literally stick together to form microbial communities, called biofilms, that can resist antibiotics and evade our immune defenses. This strength in numbers has researchers pondering strategies that target the entire biofilm in innovative ways. One promising possibility involves exploiting metabolomics, which tracks the products produced by the bacterial troublemakers, and may provide new perspectives on how to battle this increasingly common healthcare problem.

The video was made by the laboratory of Mary Cloud Ammons at Montana State University in Bozeman. Ammons, who receives research support through the NIH Common Fund to study bacterial metabolomics, describes her work in this way: “The sixth leading cause of death in the United States is the result of hospital-acquired infections, which often result in nonhealing wounds colonized by communities of bacteria call biofilms. The research in our lab aims to uncover the mechanisms at the root of the deviation from the normal healing process that results in the development of chronic wounds. These metabolomic studies identify specific metabolite profiles that may be associated with pathogenicity in the chronic wound and could potentially be used in novel noninvasive diagnostics.”


Ammons Lab (Montana State University, Bozeman)

Ammons NIH Project Information (NIH RePORTER)

Common Fund (NIH)