Plasmid mediated colistin resistance found in the U.S.

"When antibiotics first came out, nobody could have imagined we’d have the resistance problem we face today. We didn’t give bacteria credit for being able to change and adapt so fast." -Bonnie Bassler

Antibiotic resistant superbugs have dominated health-related news recently, warning of an impending post-antibiotic apocalypse where current antibiotics are no longer effective. Though it is true that antimicrobial resistance is increasing quickly and the effectiveness of many antibiotics is dwindling, much of what has been reported recently about a colistin resistant bacteria isolated in the U.S. may not be completely true. (more…)


Sourdough, an incubator for microbial symbiosis

"Blues is to jazz what yeast is to bread. Without it, it's flat." - Carmen McRae, jazz musician

History of sourdough

Sourdough bread and other fermented foods have been around for centuries. The oldest leavened bread was excavated in Switzerland, dating from 3500 BCE. However, the oldest evidence of leavening was recorded by the Egyptians possibly when flatbread dough was left out and colonized by wild yeasts and bacteria. Throughout most of human history, sourdough was the source of leavening and the use of baker's yeast (Saccharomyces cerevisiae) did not occur until the 19th century. For more detail about this history of sourdough, visit The Sourdough School. (more…)


Metropolitan Microbes: Microbiomes of Indoor Environments

In recent years, the human microbiome has gotten a lot of press. We have read about how our gut microbes affect our eating habits, immune system and mind. But what about the microbes that surround us indoors? We spend most of our time indoors, at home, in our cars, in offices and other buildings. We interact with these "built environments" (BE) extensively, leaving microbes from our skin on the surfaces we touch and also acquiring microbes that are already present on these surfaces. Airborne microbes from the outdoors or from humans also accumulate on these surfaces and travel throughout our indoor spaces. In a recent paper from the Caporaso lab, the individual factors that affect the microbiome of BEs were explored. (more…)


Microbe of the month: Helicobacter pylori

The first Microbe of the Month is Helicobacter pylori, my favorite bacterium during my graduate school years.

Discovery of Helicobacter pylori

Stomach ulcers were traditionally thought to be caused by stress. However, in 1982 Barry Marshall and Robin Warren discovered that the bacterium Helicobacter pylori (H. pylori for short) is actually the cause of these ulcers. These scientists found that almost all stomach biopsies from patients with gastric ulcers also contained this helical shaped bacteria (hence the name Helicobacter). Barry and Marshall's discovery was met with much skepticism at the time. Desperate to prove that H. pylori was indeed the cause of gastric ulcers, Marshall drank a culture of H. pylori and developed gastric ulcers that were accompanied by H. pylori in his gastric biopsies. He then cured himself of the infection by taking antibiotics. For this discovery Marshall and Warren were awarded the Novel Prize in Physiology or Medicine in 2005. (more…)


Welcome to the microbial menagerie, a blog dedicated to exploring the diverse microbial "menagerie" around us and their vast impact on the biosphere. The aim of this site is to develop a collection of unique microbes and microbial roles that we often do not think about: microbes in food, how microbes influence and transform the environment, how innovation can be shaped by microbes, etc.

In the initial stages of the blog, there will be series of posts with common themes as well as posts about recent methodological advances or commenting exciting publications that have recently been published. Series will include:

(1) Microbiome Monday: This series will focus on the microbiome, the community of organisms that reside in an environmental niche. For example, the human gut microbiome (the microorganisms that reside in the gut) is estimated to account for up to 3 pounds of our body weight (i.e. we carry 3 pounds of bacteria in our gut!) and may possibly have positive and negative effects on digestion and propensities for certain diseases. Many other environments have an associated microbiome. For example, microbial communities colonizing coral or soil have immense impacts on the plants that inhabit these environments.

(2) Foodie Friday: Many of the foods we eat exist because of microbes. The unique flavors of cheese depend on microbial communities that live on cheese, beer and wine are created by microbial fermentations, bread is dependent on yeasts. The Foodie Friday series aim to elucidate how microbes create these food products.

(3) Microbe of the month: Each month, a unique microbe will be chosen to feature. There are really no criteria for the microbe of the month, just something that is either newly discovered or just very peculiar. If there is a microbe you would like me to write a post on a certain microbe, please let me know!