Microbial Videos

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 recesses. 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.

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 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 interview, I talked with Dr. Salyers about the most influential teacher in her own life (you might be surprised to learn who that is), about whether antibiotic resistance is getting the kind of play it deserves, and about why the baboon vagina is an interesting study system.

Celsis as seen on 21st Century Business

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, D. 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 investigation, will be speaking at ASM s Biodefense and Emerging Diseases Research Meeting in Baltimore in February, where they ll present the facts about their contributions to the criminal investigation. 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.

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 is 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. 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: *Small Things Considered *The Loom by Carl Zimmer *Esos Pequenos Bichitos *Le blog des bacteries et de l'evolution *Aetiology *Microbiology Bytes *The Registry of Mushrooms in Works

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. There is also a video supplement that shows Proteopedia 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.

Nancy Keller is a Professor of Bacteriology and Medical Microbiology and Immunology at the University of Wisconsin-Madison. A mycologist, Dr. Keller works with a genus of fungi called Aspergillus – many of which are potent plant and human pathogens that produce deadly mycotoxins. Her research focuses on finding those aspects of Aspergillus species that make them effective as pathogens and toxin factories. Tiny fungi cause big problems for agriculture and human health, and the U.S. alone spends millions of dollars every year to fight the fungi that attack crops. Aspergillus fungi, in particular, cause a problem for crop plants themselves, but the bigger concern is the mycotoxins they produce: aflatoxin is one of the most potent naturally-occurring toxins ever discovered. What’s more, aflatoxin and other Aspergillus toxins are carcinogenic. The bottom line? Exposure to large amounts of these fungal toxins can kill you quickly, and exposure to small amounts can kill you slowly. On this episode, I talk with Dr. Keller about her work with Aspergillus, why we don’t even know how big the fungal toxin problem is, how reproduction and toxin-making are linked in these fungi, and how we may eventually use viruses as weapons against pathogenic fungi.

Daniel Lew is a professor of Pharmacology and Cancer Biology and of Genetics at the Duke University Medical Center in Durham, North Carolina. His research program focuses on cell cycle control in yeast, and how the cell cycle interacts with cell polarity. Yeast cells may look simple, but inside every little single-cell package lurks an intricate creature that senses and responds cunningly to its surroundings. Dr. Lew has uncovered many of the secrets of the tiny yeast, and since yeast bear a striking resemblance to human cells, some of these facts could help us eventually conquer our own problems with the cell cycle, including cancer – a kind of cell division gone wild. On this episode, Dr. Merry Buckley talks with Dr. Lew about how a yeast cell knows when to say “when” during budding, why he studies yeast at a medical school, and where his hard-to-discern accent really comes from (hint: it’s not a North Carolina accent).

Tony Maurelli is a professor of microbiology and immunology in the F. Edward Hébert School of Medicine at the Uniformed Services University of the Health Sciences in Bethesda, Maryland. Dr. Maurelli’s major research interest lies in the genetics of bacterial pathogenesis – the genetic nuts and bolts of how bacteria infect humans and make us sick. Dr. Maurelli’s work has uncovered “antivirulence genes” in Shigella flexneri, a major cause of dysentery and food borne illness. This is an interesting concept: antivirulence genes undermine pathogenicity, so they must be broken or dropped from the genome for a bacterium to take good advantage of a host and cause disease. These genes are a hindrance, so to become an effective pathogen, Shigella must stop using them. In this interview, Dr. Merry Buckley talks with Dr. Maurelli about antivirulence genes, whether the naming system for bacteria should be fixed, and his favorite microbe.

Stanley Falkow is a professor of Microbiology and Immunology at the Stanford School of Medicine. His research interests lie in bacterial pathogenesis – how bacteria cause infection and disease – and over the course of his career he has contributed fundamental discoveries to the field. Falkow received the Lasker prize this year for special achievement in medical science, and the Lasker Foundation calls him “one of the great microbe hunters of all time”. Molecular techniques (methods of analysis that rely on bacterial DNA) are now widely used for infectious disease diagnosis, thanks in large part to Falkow, who was among the first to apply an understanding of genes and virulence determinants to analyzing patient samples. He has published extensively in areas ranging from antibiotic resistance to food borne illness to microarrays. In this interview, Dr. Merry Buckley talks with Dr. Falkow about his prescient concerns about the dangers of using antibiotics as growth promoters in livestock, why Salmonella is so good at making you sick, and why students who are interested in science should follow their passion. From this point forward, MicrobeWorld listeners should be caught up with the "Best of" Meet the Scientist to date. Episodes will now come out on the regular Meet the Scientist schedule which is approximately every two weeks.

Bruce Rittmann, the Director of the Center for Environmental Biotechnology at the Biodesign Institute of Arizona State, focuses his efforts on reclaiming contaminated water and producing renewable energy using microbes. He was elected to the National Academy of Engineering in 2004 and credited with pioneering development of biofilm fundamentals and contributing to their widespread use in the bioremediation of contaminated ecosystems. His research combines many disciplines of science, including engineering, microbiology, biochemistry, geochemistry and microbial ecology. Formerly with Northwestern University, Rittmann is also a leader in the development of the Membrane Biofilm Reactor, an approach that uses bacteria to destroy pollutants in water. The Membrane Biofilm Reactor is especially effective for removing perchlorate from drinking water, and it is being launched commercially. In this podcast, Merry Buckley talks with Dr. Rittmann about the biofilm reactor process, the electricity hiding in our wastewater, and how we may some day grow fuel on the roofs of buildings.

David Relman is a Professor of Medicine and of Microbiology and Immunology at Stanford University, and his research program focuses on the human microbiome – the microbial communities of bacteria, viruses, and other organisms that thrive on and in the human body. Since Louis Pasteur first deduced that microbes are to blame for infectious disease, doctors and scientists alike have mostly seen infection as warfare between a pathogen and the human body. Dr. Relman sees things a little differently. To him, the complex communities of microbes that line our skin, mouths, intestines, and other orifices are also involved in this battle, interacting with pathogens and with our bodies, and these interactions help determine how a fracas plays out.In this interview, Dr. Merry Buckley asks Dr. Relman about our personal ecosystems of microbes, whether we’ll ever be able to understand and predict what these communities do, and about the sometimes distressing effects of oral antibiotics on our guts. They also talked about whether being MTV’s Rock Doctor back in the 1990’s had an impact on his other professional pursuits.

Ute Hentshel is a professor of chemical ecology at the University of Würzburg in Germany. Her research focuses on characterizing the microbial communities associated with marine sponges, the diversity of these symbionts and their activities. On this episode, Dr. Merry Buckley talks with Ute Hentschel about her research on the microbes that live on and in sea sponges – those squishy, colorful residents of coral reefs. Dr. Hentschel describes some of the utterly unique microbes that are only found in sponges, what those microbes get from living in a sponge hotel, and why it’s nice to have a study site in the Bahamas.

Brett Finlay is a professor in the Michael Smith Laboratories, and the Departments of Biochemistry and Molecular Biology, and Microbiology and Immunology at the University of British Columbia. His research program focuses on E. coli, how it interacts with the cells of the human gut, and mouse models of E. coli-like infections. Dr. Finlay will speak at the conference on Beneficial Microbes in San Diego this October, where he’ll describe the results of some of his latest research, which examines how E. coli infections effect the microbes that live in our guts. Sadly, outbreaks of Escherichia coli infections in this country are common – just this summer a huge E. coli outbreak in Oklahoma sickened nearly 300 people and sent 67 of them to the hospital. Clearly, in an outbreak, not everyone is effected equally. When lots of people are exposed to E. coli, why do some of those people walk away unharmed while others wind up in the I.C.U.? Dr. Finlay would say part of the answer, at least, probably lies in which microbes live in our intestine. In this podcast, I talked with Dr. Finlay about why we have so many different kinds of microbes in our guts, what happens to them when E. coli strikes, and why we have a long way to go before probiotics offer help – and not just hope.

Seth Darst is a professor of Molecular Biophysics at the Rockefeller University in New York city, where his research centers on RNA polymerase, the enzyme at the heart of a cell’s ability to make protein from a set of DNA instructions. In this interview, Merry talks with Dr. Darst about how he got his start in research, whether computers will eventually be able to predict complex protein structures, and why eager young scientists shouldn’t miss their chance at postdoctoral training.

Ralph Tanner, a professor of microbiology at the University of Oklahoma, focuses his research on anaerobes in the environment and putting those bacteria to use in industry. He develops useful microbial catalysts for biofuel production from sustainable crops and has extended our knowledge of microbial diversity by isolating a number of new genera and species with novel physiologies. He helped define the phylogeny of bacteria. In this podcast, I talk with Dr. Tanner about his work producing biofuels from burnt plant material, the future of biofuels in the U.S., whether bacterial systematics might be forced to change in light of new research on recombination, and about his approach to teaching microbiology.