Meet the Microbiologist

Dr. Andrew Knoll is the Fisher Professor of Natural History in Harvard University’s Department of Organismic and Evolutionary Biology, where he studies ancient life, its impacts on the environment, and how the environment, in turn, shaped the evolution of life.  In recognition of the 200th anniversary of Charles’ Darwin’s birth and the 150th anniversary of the first printing of his book, “On the Origin of Species”, the American Society for Microbiology has invited Dr. Knoll to deliver the opening lecture, titled “Microbes and Earth History,” at the society’s general meeting in Philadelphia this year. Before the dinosaurs, before trees and leaves, before trilobites, there were microbes.  Vast, slimy layers of them covered the rocks and peppered the seas of the harsh, alien planet we now call Earth.  Those slimy cells were our ancestors, and they played a defining role in changing that once-barren moonscape into the world we see today: a planet covered with diverse, striving life, topped by an oxygen-rich atmosphere.  Dr. Knoll says he puts on his paleontologist’s hat and studies the fossil record to learn more about this ancient life, then he dons his geochemist’s hat to reconstruct Earth’s environmental history from the chemical signatures he finds in ancient sedimentary rocks.  He weaves these two stories together to figure out how life has transformed the planet and how the planet has influenced the course of evolution. In this interview, I talk with Dr. Knoll about what early earth must have looked like, his involvement with the Mars rover project, and how intelligent design concepts may well belong in high school curricula, but not in the context of science class.

Roberto Kolter is a professor of Microbiology andMolecular Genetics at Harvard’s Medical School.  Dr. Kolter’s research interests are broad, but he says his eclectic program boils down to an interest in the ecology and evolution of microbes, bacteria in particular, and on how these forces operate at the molecular level. Although he’s worked in a number of different systems, lately Dr. Kolter is spending a lot of time with Bacillus subtilis, a modest little bacterium that doesn’t get the headlines of a wicked pathogen like Salmonella or a useful industrial workhorse like yeast.  What it lacks in notoriety,  B. subtilis makes up for in usefulness.  According to Dr. Kolter, B. subtilis is an important source of industrial enzymes (as in laundry detergent) and, as a bacterial model, a prolific source of information on how some bacteria make spores and other diverse cell types.  This ability to form different kinds of cells is intriguing to Dr. Kolter: B. subtilis cells can wear any of a number of different hats, depending on what is needed at any given moment.  From spores to swimming cells to cells that wage chemical warfare on their neighbors, B. subtilis can do it all.  Dr. Kolter and his colleagues are looking at the how and the why of this multiplicity. In the interview, Dr. Merry Buckley talks with Dr. Kolter about what he finds interesting about B. subtilis, why we should start thinking about bacteria as multicellular organisms, and how he got involved in producing a book of poetry (poetry about microbes, that is). Dr. Kolter also provided the photography for the book Germ Stories by Arthur Kornberg. To see a full description and pricing details, click the ASM estore and pick up your copy today.

Dr. Ellen Jo Baron is a professor of pathology and director of clinical microbiology at Stanford University’s medical center in Palo Alto, California.  A co-author of the authoritative Manual of Clinical Microbiology, Dr. Baron and her staff in the clinical lab evaluate and advise in the development of new diagnostic technologies.  Dr. Baron has also volunteered her time as a microbiology advisor in numerous hospitals and clinics in developing countries since 1996. In a hospital, you have to be able to diagnose infections in order to treat patients, but hospitals in the developing world that are forced to get along with inadequate and ill-equipped microbiology labs have to treat infectious disease blindly, without full knowledge of which organism is to blame and which drugs will be most effective.  These missteps cost lives.  Dr. Baron, who normally works in a modern, fully-equipped western hospital, travels to hospitals and clinics in places like Cambodia and Nepal to train staff and organize clinical microbiology labs.  She says it’s not always feel-good work for her: cumbersome bureaucracy and lack of money and equipment are constant challenges.  But experiencing other cultures and getting out of her comfort zone help make the work rewarding. In this episode, Dr. Merry Buckley talks with Dr. Baron about her work at home and abroad, the kinds of problems she faces in under-resourced labs, and about how, as a result of her work in the developing world, she now knows more about sheep and goats than she ever really wanted to know.

Elizabeth Edwards knows that nothing is simple or easy when it comes to cleaning up toxic waste, but Edwards, a professor of Chemical Engineering and Applied Chemistry at the University of Toronto, is looking for ways to harness microbes to do our dirty work for us.  Dr. Edward’s research focuses on the biodegradation of chlorinated solvents in the environment – the means by which microbes can actually make a living by eating our noxious waste. Chlorinated solvents like trichloroethylene (TCE), perchloroethylene (PCE), and others, have a sordid history in the environment.  They have long been used as degreasers and dry cleaning fluid, but before there were regulations about how to handle waste, manufacturers and dry cleaners dumped old, dirty solvents in evaporation ponds or out the back door of the facility.  Some of the fluid dumped this way evaporated, but since chlorinated solvents are both dense and recalcitrant, much of the liquid seeped straight down to the groundwater.  And stayed there.  Among other projects, Dr. Edwards is looking at the ability of mixed cultures of bacteria to break down these solvents in a step-wise process, with the expectation that we’ll eventually be able to treat the contamination at some sites with injections of microbes. In this interview, Dr. Merry Buckley talks with Dr. Edwards about why chlorinated solvents are such a difficult environmental problem, how working in environmental consulting for a time helped her realize where she wanted to focus her research, and why we might have to make some tough decisions when it comes to cleaning up the hundreds (thousands?) of solvent-contaminated sites in North America.

If you or someone you care about has ever had an antibiotic resistant infection, you know how dire that situation can be.  Stuart Levy, a professor of microbiology at Tufts University in Boston, has centered his research around the theme of antibiotic resistance and he says there are few antibiotics in the pipeline for use on that inevitable day when our current infection-fighters are finally overcome.  Dr. Levy is delivering the keynote address at ASM’s Biodefense and Emerging Diseases Research Meeting in Baltimore in February. Antibiotic resistance may not be making big headlines these days, but that’s not because the threat is any less serious than before.  Levy says he first became interested in antibiotics as a child, when he watched a course of antibiotics heal his twin brother, who suffered from an infection.  Later, as a researcher at the Pasteur Institute in Paris, France, he learned that bacteria can swap around the ability to resist antibiotics, and that failing to manage a small problem with resistance can have some serious consequences down the line. In this interview, I talked with Dr. Levy about his talk at the biodefense meeting, what antibiotic resistance has to do with biosecurity, and about why you should leave those bottles of antimicrobial soap on the shelves at the store.

Dr. Paul Keim is a professor of biological sciences at Northern Arizona University, in Flagstaff, where his research program focuses on microbial forensics and the genomic analysis of pathogenic bacteria.  As an expert in Bacillus anthracis, the bacterium responsible for anthrax, Dr. Keim participated in the FBI’s investigation into the anthrax letter attacks back in 2001. Microbial forensics is a field that developed in response to the twin threats of biological warfare and biological terrorism.  (What’s the difference between biological warfare and biological terrorism?  Both have the potential to reach beyond the site of the attack and both are a menace to innocent, unarmed citizens.  To me, there’s a fine line here.  But I digress.) Dr. Keim’s interest in microbial forensics arose out of his postdoctoral work at the University of Utah.  After this training in phage recombination and genomics, Dr. Keim applied what he had learned about bacterial genetics in a collaboration with scientists working on resolving and identifying the various strains of B. anthracis.  Fast forward to this past summer, when the F.B.I. revealed that Dr. Keim used his expertise on B. anthracis to help in the investigation that concluded a researcher at the U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID) perpetrated the anthrax attacks.  Dr. Keim, along with several other scientists who helped in the F.B.I.’s   In this podcast, I talked with Dr. Keim about his work with the F.B.I., whether the payoffs of bioterrorism research are worth the costs, and about how the plague (yes, the Black Death) made its way to North American shores and continues to sicken about a dozen people every year.

Dr. Kathryn Boor is a professor and chair in the Food Science department at Cornell University, where she’s director of the Food Safety Laboratory - a biosecurity level 2 laboratory that facilitates research on foodborne pathogens.  Her particular research interests lie in the “how” and “why” of pathogens and spoilage microbes in food.  Boor is also the director of the Milk Quality Improvement Program – a program funded by New York state to monitor and make recommendations to improve the quality of milk in the state. When I think about the complicated way dairy products come to be on the shelf in my grocery store – farmers use machinery to extract milk from an animal that lives in a barn or a field; the milk is piped through long tubes to a tank on a truck that conveys the product to a plant that processes and divvies it up; the bottles and packages are put on another truck and carted to the store – it seems like a wonder dairy is ever safe to eat.  But dairy is safe: CDC data indicate that less than 1% of foodborne illness outbreaks in the U.S. involve dairy products1 2 . Dr. Boor’s primary interest lies in Listeria monocytogenes, one of the few pathogens that is a problem in dairy, and most people who’ve heard of it associate it with unpasteurized soft cheese or cold cuts.  Listeriosis is not as common or familiar as some other foodborne illnesses, but it is more often fatal than salmonellosis or botulism, and in a pregnant woman even a mild case can be deadly for her fetus.  Dr. Boor’s research focuses on how this so-called “simple” organism is able to persist in some foods and overcome the stress of refrigeration and stomach acid to not only survive, but to make us really sick. In this interview, I asked Dr. Boor about how she came to this particular niche in science, whether pasteurization is any better than keeping milk from getting contaminated in the first place, and what her trained eye for food safety looks out for when she’s buying food.

Moselio Schaechter – known as Elio to his friends – is Distinguished Professor of Molecular Biology and Microbiology, Emeritus, at the Tufts University School of Medicine, and he’s currently an adjunct professor at San Diego State University and at the University of California at San Diego. Dr. Schaechter has had a long career in bacteriology and has authored or co-authored a number of text books, and is a former president of the American Society for Microbiology. He lives in sunny San Diego now, where he lectures, attends meetings, and writes his blog, “Small Things Considered”. If you want an example of the ways the internet has changed public discourse, look to the blogs - you’re reading one now, after all, and how many blogs did you read 10 years ago? Blogs give authors a bullhorn free from profit-driven publishers, provide people with ideas, and even build communities through reader discourse. To be sure, not every blog is interesting or even readable, but there are many bloggers out there working hard and stimulating some profound discussions. Those of us interested in the life microscopic are lucky to have Dr. Schaechter, who muses on the topics of interest to him and acts as host to other eminent scientists who write guest essays. With Small Things Considered, his goal is to express his own interest in various subjects while encouraging interest in others and kindling conversation and debate. In my interview with Dr. Schaechter, we talk about what he gets out of being a blogger, what makes for a successful blog, and about how mushroom hunting in xeric Southern California usually involves a lot of hunting and few mushrooms. Blogs and Websites mentioned in this episode include: The Loom by Carl Zimmer Esos Pequenos Bichitos Le blog des bacteries et de l’evolution Aetiology by Tara C. Smith Microbiology Bytes The Registry of Mushrooms in Works of Art

This is a video supplement to the audio podcast of Meet the Scientist episode 13 in which I interview Joel Sussman, Ph.D., a professor of structural biology at the Weizmann Institute of Science in Israel. The video shows Sussman's Proteopedia.org in action. It is narrated by Eran Hodis, the graduate student, who, together with Professors Jaime Prilusky and Joel L. Sussman developed Proteopedia at the Weizmann Institute of Science.

Joel Sussman, Ph.D. is a professor of structural biology at the Weizmann Institute of Science in Israel. In his research, Dr. Sussman is interested in elucidating the structures and functions of proteins, particularly those involved in the nervous system. He is also the lead scientist behind Proteopedia – a new online protein structure encyclopedia. Scientific endeavors have historically been a one-way street: an investigator or lab makes a discovery, then delivers the good news to the rest of the community via publication. Nowadays, computers and the internet are enabling easier and more seamless means of collaboration and communication. Proteopedia, with which Dr. Sussman is greatly involved, automatically gathers and compiles information from multiple curated sources of information, but its more revolutionary side is the wiki tool, which enables registered users to contribute information themselves. In this interview with Dr. Sussman, I talked with him about his work with acetylcholinesterase and “intrinsically unstructured proteins” and about Proteopedia – how it works and about the possibility of misinformation making its way onto the site. The video extra shows Proteopedia in action. It is narrated by Eran Hodis, the graduate student, who, together with Professors Jaime Prilusky & Joel L. Sussman developed Proteopedia at the Weizmann Institute of Science.