Meet The Microbiologist - The Scientists Behind The Microbiology

In this episode I speak to Sallie "Penny" Chisholm, the Lee and Geraldine Martin Professor of Environmental Studies at MIT. Dr. Chisholm studies photosynthesis—the way life harnesses the energy of the sun. Plants carry out photosynthesis, but so do microbes in the ocean. Dr. Chisholm studies the most abundant of these photosynthetic microbes, a species of bacteria called Prochlorococcus.  There are a trillion trillion Prochlrococcus on Earth. Dr. Chisholm researches these microbial lungs of the biosphere, and how they produce oxygen on which we depend. Along with her scientific research, Dr. Chisholm is also the author of a new children's book, Living Sunlight: How Plants Bring The Earth To Life.

John Wooley is Associate Vice Chancellor of Research and Professor of Chemistry-Biochemistry and of Pharmacology at the University of California San Diego. Wooley is a leader in the young field of metagenomics: the science of gathering vast numbers of genes from the oceans, soils, air, and the human body. A generation ago biologist knew the sequences of a few thousand genes. Since then that figure has jumped to several million genes and it's only going to continue to leap higher in years to come. This wealth of data is allowing scientists to get answers to fundamental questions they rarely even asked a generation ago. They're starting to understand how thousands of species of microbes coexist in our bodies. They're investigating how hundreds of genes work together inside a single cell and they're starting to get a vision of the full diversity of the billions of proteins that life produces, what scientists sometimes call the protein universe. John Wooley has been at the center of this revolution, i

In this episode I talk with Paul Turner, an associate professor of ecology and evolutionary biology at Yale University.2009 saw the emergence of a new strain of H1N1 flu. Scientists soon determined that the virus had leaped from pigs to humans and then spread to millions of people. When viruses make this kind of leap it's a reason to worry. In 1918 when a strain of flu leapt from birds to humans, 50 million people died in a matter of months. So far the new H1N1 flu strain is behaving like a relatively ordinary flu. Still even ordinary flu is a matter of serious concern. Over 4,000 people in the US alone have died from the new H1N1 flu strain and scientists can't say for sure what it would take to turn this new strain into a global killer.It's a sobering reminder of how mysterious virus evolution remains. Over the past century a number of viruses have made the leap from animal host to humans including SARS and HIV and scientists worry that the next great plague may be a virus that we don't even k

Jonathan Eisen is a professor at the University of California, Davis Genome Center. Over the course of his career, he has pioneered new ways of sequencing microbial genomes and analyzing them. I talked to Eisen about some of the weirdest creatures he's studied, such as bacteria that only live on the bellies of worms at the bottom of the ocean, and how we may be able to exploit their genomes for our own benefit. We also discussed the new movement for open access to scientific literature, a subject that's a particular passion of Eisen, who is academic editor in chief at the open-access journal PLOS Biology.

Hazel Barton is the Ashland Professor of Integrative Science at Northern Kentucky. She explores some of the world's most remote caves to study the remarkable diversity of microbes that thrive in their dark rececesses. I spoke to Barton about how she first became captivated by these bizarre organisms, what it's like to do delicate microbiology when you're hip-deep in mud, and why she wants to explore caves on Mars in search of Martians.  

Dennis Bray is an active professor emeritus in both the Department of Physiology and Department of Neuroscience at the University of Cambridge. He studies the behavior of microbes--how they "decide" where to swim, when to divide, and how best to manage the millions of chemical reactions taking place inside their membranes. For Bray, microbes are tiny, living computers, with genes and proteins serving the roles of microprocessors. In this interview, I talked with Bray about his provocative new book, Wetware: A Living Computer Inside Every Cell.

Michael Cunliffe is a microbiologist in the Department of Biological Sciences at the University of Warwick in England. He studies the microbes that live in the thin layer of water at the very surface of the ocean. His research is shedding light on an ecosystem that's both mysterious and huge, spanning three-quarters of the surface of the planet. In this interview, I talked with Cunliffe about the discovery of this sea-surface ecosystem, and the influence it has over the Earth's climate.

Pratik Shah is a graduate student in the Department of Microbiology at the University of Mississippi Medical Center in Jackson, and he’s a 2009 recipient of ASM’s Raymond W. Sarber award, granted to recognize students for research excellence and potential.His research focuses on polyamines and polyamine biosynthesis and transport systems in Streptococcus pneumoniae.  He’s studying polyamines with the goal of finding potential targets for pneumococcal vaccines and prophylactic interventions against pneumococcal disease.  In this interview, I talked with Pratik about why polyamines may hold the key for new ways to combat pathogens, his plans for the future, and about advice he would give to young people considering grad school.

Abigail Salyers is a Professor of Microbiology and the G. William Arends Professor of Molecular and Cell Biology at the University of Illinois at Urbana-Champaign, and her research focuses on the ecology of microorganisms in the human body and the comings and goings of antibiotic resistance genes, particularly genes in Bacteroides species.  Dr. Salyers is ASM’s 2009 Graduate Microbiology Teaching Awardee.  If you’ve ever tried teaching or mentoring, you know it’s not always easy, but for an eminent scientist, teaching at the undergraduate or graduate level must be incredibly difficult.  After all, once you reach a certain level of knowledge in any field, it can be hard to relate your knowledge to people who know relatively little about it.  Dr. Salyers has tackled 100-level biology courses with as many as 300 students, taught one-on-one at the lab bench, and been an instructor at an intensive summer course in microbial diversity, all while rising to the top of her field in research.  In this int

Arthur Guruswamy is a clinical microbiologist in Virginia’s Department of General Services Division of Consolidated Laboratory Services and the winner of ASM's Scherago-Rubin Award in recognition of an outstanding, bench-level clinical microbiologist.  His particular interest lies in mycobacterial and fungal diseases, including tuberculosis.  In his work, Mr. Guruswamy places a lot of emphasis on helping others.  A while back, he traveled to his native Sri Lanka to train clinic staff in the use of a rapid, low tech method for identifying cases of tuberculosis.  Using this method has probably saved many lives, since staff Mr. Guruswamy trained can now treat their patients quickly and avoid the three to four week wait for culture results.  Mr. Guruswamy is also involved in ASM’s Minority Mentoring Program so he can offer younger scientists the kind of assistance he says he got from other ASM members back at the beginning of his own career, when he arrive in the United States with less than $50 in

Dr. Frances Arnold is a professor of Chemical Engineering and Biochemistry at the California Institute of Technology (most of us know it as Caltech).  Dr. Arnold’s research focuses on evolutionary design of biological systems, an approach she is currently applying to engineer cellulases and cellulolytic enzymes for manufacturing biofuels.  This country’s energy security can look pretty bleak when you think about it: the need to address global warming, strife in oil-rich nations, and depletion of fossil fuels combine to paint an uncertain future, and although ethanol has a lot of friends in Iowa and D.C., ethanol isn’t going to end our energy woes.  In the future, our energy supply will probably be cobbled together from a number of different fuels and sources.  Dr. Arnold is interested in engineering microbes that can grant us a biofuel that packs more of a caloric punch than ethanol.  She likes isobutanol, which can be converted into a fuel that’s more like the hydrocarbons we currently put into

Stanley Plotkin is Professor Emeritus at the Wistar Institute and the University of Pennsylvania, Philadelphia.  A renowned vaccinologist, Dr. Plotkin is, perhaps, best known for developing a highly successful vaccine for rubella back in 1968.  We are still using the same vaccine 40 years later.  Dr. Plotkin has been honored with the inaugural Maurice Hilleman / Merck Award for his lifetime of dedication to vaccinology.  For most people, rubella amounts to a bad rash and a crummy week, but for a fetus, the risks from infection are extremely serious.  The rubella virus inhibits tissue growth in infected fetuses, often resulting in profound birth defects collectively referred to as congenital rubella syndrome.  Dr. Plotkin developed the rubella vaccine in the wake of a rubella pandemic in 1964, during which he estimates that about 1 in 100 women in his home city of Philadelphia came down with rubella.  Nationwide, thousands of babies were born with congenital rubella syndrome in the wake of the ou

Christine Biron is the chair of the Department of Molecular Microbiology and Immunology at Brown University in Providence, and she focuses her research program on the mechanisms of the innate immune system – the body’s system of non-specific munitions for fighting off pathogens.  Dr. Biron is also a newly elected fellow of the American Academy of Microbiology. When a pathogen gets on or in your body, your innate immune system is on the front lines, working against the pathogen is a non-specific manner.  In research, the innate immune system got short shrift for a long time, and only in the last 10 or 20 years has the field picked up momentum.  Dr. Biron says back when she was in graduate school “the innate immune system wasn’t thought to be very cool”, but she says the field is fast-moving today, in part because of some major discoveries involving Type-1 interferons, natural killer cells, and an increased appreciation of a wider range of antigen processing cells that link the innate and adaptive i

Joseph DeRisi is a Professor of Biochemistry and Biophysics at the University of California, San Francisco and a Howard Hughes Medical Institute Investigator. His research focuses on two distinct areas: malaria and new viral pathogen discovery.  Dr. DeRisi is this year’s recipient of the Eli Lilly and Company Research Award, granted in recognition of fundamental research of unusual merit in microbiology or immunology by an individual on the threshold of his or her career. Discovering new viral pathogens seems like exciting work, and DeRisi has lots of ideas for prospecting.  In one recent success with their viral microarray, his group recently helped identify the virus responsible for a devastating disease among rare parrots and other birds: proventricular dilatation disease, or PDD, has been recognized for 30 years, but veterinarians didn’t know the cause or how to control it.  Now that DeRisi’s group has pinpointed Avian Bornavirus as the culprit and sequenced its genome, therapies and contro

Melanie Cushion holds down two jobs: she’s a research career scientist at the Veterans Administration Medical Center in Cincinnati, Ohio, and she’s also professor and associate chair for research in the department of internal medicine at the University of Cincinnati College of Medicine.  Dr. Cushion focuses her research on the fungus, Pneumocystis carinii, which is a harmless commensal for most people, but a deadly pathogen for others.  Pneumocystis carinii was shrouded in obscurity for many years until its fifteen minutes in the spotlight came in the 80’s, when, unfortunately, an outbreak of Pneumocystis pneumonia prefigured the AIDS epidemic.  Large numbers of previously healthy homosexual men in California became deathly ill with Pneumocystis pneumonia, and doctors knew something unusual (later found to be HIV) was going on.  Dr. Cushion says Pneumocystis pneumonia is an opportunistic infection: it strikes individuals with immune systems too weak to fend it off.  This explains why it was –

Ian Orme is a professor in the Department of Microbiology, Immunology, and Pathology at Colorado State University, and his research focuses on the immune response to tuberculosis (TB) – a bacterial disease that most often infects the lungs. He's speaking at the American Society for Microbiology's Conference for Undergraduate Educators (ASMCUE). In the U.S., TB seems like a thing of the past. Here, public health measures and medical care have all but wiped out the threat from this infection. But worldwide, the WHO says there were 9.2 million new TB cases in 2006 alone, and each person with TB infects an average of 10 to 15 people with the TB bacterium every year. These are just some of the reasons Dr. Orme is delivering a talked titled “Tuberculosis: Why Now Is a Good Time to Leave the Planet” at ASMCUE. He admits leaving the planet isn’t a practical suggestion, but he wants to raise awareness of the disease and he’s not afraid to stir the pot a little. Orme and his group not only study the imm

Parisa Ariya is a professor in the Department of Atmospheric and Oceanic Sciences and the Chemistry Department at McGill University in Montreal.  Dr. Ariya works mostly in atmospheric chemistry, but she’s also done a good deal of work with bioaerosols and airborne microorganisms.  She’ll deliver a talk at the ASM General Meeting in May titled Bioaerosols: Impact on Physics and Chemistry of the Atmosphere. Bioaerosols – microscopic clumps of microorganisms and organic debris – arise through any of a number of mechanisms.  The scientific community has come full circle on the idea of microorganisms in the atmosphere, according to Dr. Ariya.  Back in the early days of microbiology it was widely recognized that the air is full of living, breathing microbes, but once our understanding of atmospheric chemistry and physics matured, the roles of microbes in atmospheric processes were marginalized.  Thanks, in part, to Dr. Ariya’s work, the activities and functions of bioaerosols are getting new attention.

Jeff Bender is a professor of veterinary public health at the University of Minnesota, and his research interests lie in the intersection of animal health and human health, including animal-borne diseases of humans, food safety, and antibiotic resistant pathogens in animals.  Dr. Bender will speak on “Methicillin-resistant Staphylococcus aureus ( MRSA) in Veterinary Practice” at the American Society for Microbiology’s General Meeting in Philadelphia this May. To a microorganism, vertebrates can all look pretty similar.  Dr. Bender’s work focuses on pathogens that can make themselves at home in both human bodies and the bodies of our pets and livestock.  Outbreaks of bacterial illnesses from meat products are well publicized these days, but the pathogens we have in common with animals don’t just travel in one direction.  We humans can pass organisms and diseases to our animals, too.  Dr. Bender says pets treated at veterinary clinics, for example, have come down with painful MRSA skin infections the

Jo Handelsman is a professor at the University of Wisconsin, where she’s a member of the Department of Plant Pathology and chair of the Department of Bacteriology. Dr. Handelsman’s research focuses on microbial communities – their composition, how they’re structured, and how they work. Thanks to her work to improve the quality of undergraduate education, Dr. Handelsman is this year’s recipient of the American Society for Microbiology’s Carski Foundation Undergraduate Teaching Award. Dr. Handelsman has been at the cutting edge of microbial science for years. After a long time spent studying the teeming communities of microorganisms that dwell in soil, Handelsman has pared down her focus to some arguably simpler neighborhoods: the guts of insects. Handelsman applies molecular methods to identify the strains and genes present in bug guts and combines this knowledge with other information about these environments to learn what these communities might be doing. Handelsman also takes a particular inter

David Knipe is the Higgins Professor of Microbiology and Molecular Genetics at Harvard Medical school. A virologist, Dr. Knipe focuses his research efforts on the herpes simplex virus 2 (HSV-2) – the virus we have to thank for genital herpes. An astonishing 20% of Americans have been infected with HSV-2, and whether they’ve had a recognizable outbreak of sores or not, they can still carry the virus. Once you contract the HSV-2 it lays low in your nerve cells, waiting for the right moment to create watery blisters that eventually burst and release more virus particles. Dr. Knipe is interested in how the cells lead these two, very different lives: quiet and quiescent inside the nerve cell and loud and lytic in the epithelium on the surface of the body. Genital herpes is no picnic, but the effects of HSV-2 infection are worst in people with depressed immune systems and in newborns; babies who pick up the virus during birth may suffer from neurological damage, brain damage, or even death. There is no