Meet the Microbiologist

Viral gastroenteritis around the world causes 200,000 deaths globally each year. Mary Estes talks about her work on 2 gastroenteritis-causing viruses, rotavirus and norovirus, and tells the story of her discovery of the first viral enterotoxin. She also describes how noroviruses have changed from human volunteer studies to studies using "miniguts," a system now used with many enteropathogenic microorganisms. Julie's Biggest Takeaways: Rotaviruses and noroviruses kill 200,000 people annually, despite an available rotavirus vaccine and current anti-infective measures. Rotavirus is generally associated with gastrointestinal disease in the very young and the very old, while norovirus infects people at all life stages. Rotavirus is so stable that even when viral samples are extremely dessicated by lyophilization, the samples remain perfectly infectious. Rotavirus stability is largely due to 3 concentric capsid cells. NSP4 is a rotavirus enterotoxin, and the first viral enterotoxin to be discovered. It affects the concentration of the intracellular calcium pools. By activating the calcium chloride channel, NSP4 forces chloride and water to be excreted, directly leading to diarrhea. NSP4 is secreted from infected cells and can also disrupt calcium concentrations of neighboring cells, amplifying the effect of a single infected cell. Rotarix® and RotaTeq® are 2 different attenuated rotavirus vaccines. One contains a single attenuated viral strain while the other contains 5 attenuated viral strains; both vaccines have high efficacy in developed countries and slightly lower efficacy in developing countries. Why vaccine efficacy is lower in developing countries is uncertain, with many hypotheses including microbiome-based effects under study now. Human enteroids, or "miniguts," offer insight into complex virus-cell interactions. These stem-cell derived miniguts can be generated from different types of animal stem cells, and the enteroids they become reflect the same host-barrier restriction as the animal of origin. The miniguts can be used to culture many sorts of viruses and other microorganisms, such as bacteria and protozoa. Links for this Episode: Mary Estes Website at Baylor College of Medicine Hyser J.M. et al. Rotavirus Disrupts Calcium Homeostasis by NSP4 Viroporin Activity. mBio. 2010. Crawford S.E. et al. COPII Vesicle Transport is Required for Rotavirus NSP4 Interaction with the Autophagy Protein LC3 II and Trafficking to Viroplasms. J Virology. 2019. Ettayebi K. et al. Replication of Human Noroviruses in Stem Cell-Derived Human Enteroids. Science. 2016. In J.G. et al. Human Mini-Guts: New Insignts into Intestinal Physiology and Host-Pathogen Interactions. Nat Rev Gastroenterol Hepatol. 2016. Finkbeiner S.R. et al. Stem Cell-Derived Human Intestinal Organoids as an Infection Model for Rotaviruses. mBio. 2012. Henning S.J. and Estes M.K. Women in Science: Hints for Success. Gastroenterology. 2015. Kapikian A.Z. et al. Visualization of a 27-nm Particle Associated with Acute Infectious Nonbacterial Gastroenteritis. Journal of Virology. 1972. HOM Tidbit: Smith K.N. The Iron Long was just an Engineer's Side Project. Forbes. 2019. HOM Tidbit: Ramirez M. Living Inside a Canister: Dallas Polio Survivor is One of Few People Left in U.S. Using Iron Lung. Dallas Morning Star. 2018.

The most abundant organism on Earth lives in its seas: the marine bacterium SAR11. Steve Giovannoni describes how the origins of SAR11 provided its name, and the ways that studying SAR11 have taught scientists about ocean ecology. He also discusses how the different depths of the ocean vary in their microbial compositions and what his big questions are in marine microbiology. Different depths of the ocean have different habitats, but the microbes vary continuously, based in part on light availability: Surface light facilitates photosynthesis by algal cells. These primary producers fix carbon for the entire ecosystem! Because nutrients are readily available, the cell concentration in surface waters can reach nearly 1,000,000 cells/ml. The twilight zone offers dim light. Microbes in this area mainly use carbon sources generated by the surface-dwelling microbes. Below a few hundred meters, cell concentrations drop to 10,000-100,000 cells/ml. The deep ocean has no light and the microbes that live here have significantly different biochemistries and metabolisms. SAR11 is small in both physical size and genome size (0.37–0.89 µm and 1.3 million base pairs, respectively). It is nevertheless the most abundant organism on the planet, with more than 1028 cells estimated to exist worldwide. These cells convert between 6-37% of the carbon fixed in the oceans daily. SAR11 in different niches have ecotypes with different specialties but look physically similar and have very similar genome sequences. Naturally, the most abundant cells in the ocean have the most abundant parasites: bacteriophages called pelagiphages infect SAR11 all over the world. SAR11 and pelagiphages are under constant evolution, though there doesn't seem to be a CRISPR system in the Pelagibacter genome; these bacteria largely use other mechanisms to evade phage infection. SAR11 is like a house with the lights on all the time, in that the cells constitutively express most metabolic genes. For example, SAR11 metabolizes dimethylsulfoniopropionate (DMSP) into dimethyl sulfide (DMS) and methanethiol (MeSH), which can be produced as soon as the cells are exposed to DMSP. While this may seem energetically expensive, the cells must capitalize on their encounters with this transient resource, often found only at low concentrations, and this capitalization requires the investment of protein production. The cost of metabolic gene regulation outweighs the benefits in this particular case. SAR11 and SAR202 are the poles on the spectrum of heterotrophic marine bacteria. SAR11 is very efficient at accessing and using the organic compounds that come from the phytoplankton (also called the labile organic matter). SAR202, found in the deeper part of the ocean, specializes in hard-to-access carbon compounds that other bacteria can't access. Links for This Episode MTM Listener Survey, only takes 3 minutes. Thanks! Stephen Giovannoni website at Oregon State University OSU High Throughput Microbial Cultivation Lab Carini P. et al. Discovery of SAR11 Growth Requirement for Thiamin's Pyrimidine Precursor and its Distribution in the Sargasso Sea. ISME J. 2014. Sun J. et al. The Abundant Marine Bacterium Pelagibacter Simultaneously Catabolizes Dimethylsulfoniopropionate to the Gases Dimethyl Sulfide and Methanethiol. Nature Microbiology. 2016. Moore E.R. et al. Pelagibacter Metabolism of Diatom-Derived Volatile Organic Compounds Imposes an Energetic Tax on Photosynthetic Carbon Fixation. Environmental Microbiology. 2019. HOM Tidbit: Sagan L. On the Origin of Mitosing Cells. 1967. HOM Tidbit: Cellmates (Radiolab podcast episode) ASM Article: The Origin of Eukaryotes: Where Science and Pop Culture Collide

Can a protein be contagious? Jason Bartz discusses his work on prion proteins, which cause spongiform encephalopathy and can be transmitted by ingestion or inhalation among some animals. He further discusses how prions can exist as different strains, and what techniques may help improve diagnosis of subclinical infections. Links for this Episode: Jason Bartz Creighton University website Holec SAM, Yuan Q, and Bartz JC. Alteration of Prion Strain Emergence by Nonhost Factors. mSphere. 2019. Yuan Q et al. Dehydration of Prions on Environmentally Relevant Surfaces Protects Them from Inactivation by Freezing and Thawing. Journal of Virology. 2018. Bartz JC. Prion Strain Diversity. Cold Spring Harbor Perspectives in Medicine. 2016. Bartz JC. From Slow Viruses to Prions PLoS Pathogens. 2016. Deleault NR, Harris BT, Rees JR, Supattapone S. Formation of native prions from minimal components in vitro. Proceedings of the National Academy of Sciences. 2007. Planet Money Episode 952: Sperm Banks

Microbial interactions drive microbial evolution, and in a polymicrobial infection, these interactions can determine patient outcome. Deb Hogan talks about her research on interkingdom interactions between the bacterium Pseudomonas and the fungus Candida, 2 organisms that can cause serious illness in cystic fibrosis patients' lung infections. Her research aims to better characterize these interactions and to develop better diagnostic tools for assessing disease progression and treatment. Links for this Episode: Deb Hogan Lab Website Demers EG et al. Evolution of Drug Resistance in an Antifungal-Naive Chronic Candida lusitaniae Infection. PNAS. 2018. Lewis KA et al. Ethanol Decreases Pseudomonas aeruginosa Flagella Motility through the Regulation of Flagellar Stators. Journal of Bacteriology. 2019. Gifford AH et al. Use of a Multiplex Transcript Method for Analysis of Pseudomonas aeruginosa Gene Expression Profiles in the Cystic Fibrosis Lung. Infection and Immunity. 2016. Grahl N et al. Profiling of Bacterial and Fungal Microbial Communities in Cystic Fibrosis Sputum Using RNA. mSphere. 2018. Microbiology Resource of the Month: The Aeminium ludgeri Genome Sequence HOM Tidbit: https://www.sciencedirect.com/science/article/pii/S0065216408705628 HOM Tidbit: The Frozen Potential of Microbial Collections

Why is C. diff such a serious disease and what are clinical microbiologists doing to improve patient outcomes with better diagnostic tools?

Many hospital-acquired bacterial infections are also drug-resistant. Amy Mathers describes her work tracking these bacteria to their reservoir in hospital sinks, and what tools allowed her team to make these discoveries. Mathers also discusses her work on Klebsiella, a bacterial pathogen for the modern era. Subscribe (free) on Apple Podcasts, Google Podcasts, Android, RSS, or by email. Julie's Biggest Takeaways Nosocomial infections are a type of opportunistic infection: one that wouldn't normally cause disease in healthy individuals. Once the immune system is compromised due to other infection or treatment, the opportunist bacteria take advantage of the conditions to grow to higher numbers and cause disease. How are different pathogens transmitted in the hospital? Previously, transmission was considered to occur from one patient to a second patient, perhaps via a healthcare worker. When patients from very different parts of the hospital began to come down with the same resistant strain of bacteria, without interacting through the same space or staff, researchers began to look at a different reservoir: the hospital wastewater. How does the bacteria get from the sink to the patients? The bacteria, existing in a biofilm in the pipe right below the drain, can be transferred in droplets when the water is run. These droplets can fall as far as 36 inches from the drain plate and can contaminate the sink bowl or patient care items next to the sink. Some of the solutions to decrease bacterial dispersion from hospital sinks are very simple: for example, offsetting the drain from the tap, which keeps the water from directly running onto the drain, helps decrease the force with which the water hits the drain and therefore decreases bacterial dispersion. The Sink Lab at University of Virginia couldn't replicate the bacterial growth patterns seen in the rest of the building; in particular, there were fewer protein nutrients that promoted bacterial growth. By setting up a camera observation of sink stations used in the hospital, the team realized that the waste thrown down the sink (extra soda, milk, soup, etc) was feeding the microbial biofilm. This helps the CRE in the biofilms in the sinks thrive. Links for This Episode MTM Listener Survey, only takes 3 minutes. Thanks! Amy Mathers website at University of Virginia The Sink Lab at UVA Kotay SM et al. Droplet- Rather than Aerosol-Mediated Dispersion is the Primary Mechanism of Bacterial Transmission from Contaminated Hand-Washing Sink Traps. Applied and Environmental Microbiology. 2018. Mather AJ et al. Klebsiella quasipneumoniae Provides a Windo into Carbapenemase Gene Transfer, Plasmid Rearrangements, and Patient Interactions within the Hospital Environment. Antimicrobial Agents and Chemotherapy. 2018. Kotay S et al. Spread from the Sink to the Patient: in situ Study Using Green Fluorescent Protein (GFP)-Expressing Escherichia coli to Model Bacteral Dispersion from Hand-Washuing Sink-Trap Reservoirs. Applied and Environmental Microbiology. 2016. Let us know what you thought about this episode by tweeting at us @ASMicrobiology or leaving a comment on facebook.com/asmfan. Send your stories about our guests and/or your comments to [email protected].

How do medical professionals incorporate microbiome science into their patient care? Ami Bhatt discusses her research on the diversity within and between human gut microbiomes, and how this research is slowly and carefully being used to build new patient care recommendations. Subscribe (free) on Apple Podcasts, Google Podcasts, Android, RSS, or by email. Julie's Biggest Takeaways Although these terms are often used interchangeably, microbiome and microbiota represent distinct samples types: Microbiotarepresents all the organisms that live within a community: archaea, bacteria, viruses, and fungi. Microbiomeis the genomes or transcriptomes of these organisms. The gut microbiota may often be referred to as a single entity, but the gastrointestinal tract has many different niches. Alterations in pH, cell type, and the available nutrients provide different selective pressures for the microorganisms that reside in these conditions. By clustering small proteins based on similarity, Ami's group was able to identify over 4000 new families of small proteins from existing microbiome datasets. Some of these were found among all microbiome datasets while others were found only in human microbiomes, which provides a clue to their potential housekeeping versus host-microbe-interaction functionality, although the exact functions are still unknown. Outcomes for non-infectious diseases are affected by the gut microbiome. Ami and her colleagues have worked with transplant patients to understand what type of diversity and which strains play a role in best outcome for cancer therapy patients, such as patients receiving bone marrow transplants. Medical doctors are beginning to incorporate new patient care in light of new microbiome studies. Understanding the effects of the gut microbiome on human health have helped slowly change patient care in some settings. For example, doctors are reconsidering recommendations for immunocompromised people to stay away from fresh fruits and vegetables, a recommendation previously made due to the potential risk of patients exposure to pathogenic microbes. The benefit of a wide variety of fiber sources, which promote a diverse and robust microbiome, may turn out to outweigh this risk. Links for This Episode MTM Listener Survey, only takes 3 minutes. Thanks! Ami Bhatt lab website Brewster R. et al. Surveying Gut Microbiome Research in Africans: Toward Improved Diversity and Representation. Trends in Microbiology. Oct 1 2019. Sberro H. et al. Large-Scale Analyses of Human Microbiomes Reveal Thousands of Small, Novel Genes. Cell August 22 2019. Andermann T. et al. The Microbiome and hematopoietic Cell Transplantation: Past, Present, and Future. Biol Blood Marrow Transplant. July 1 2019. Bloomberg: Superbugs Deadlier Than Cancer Put Chemotherapy into Question Clinical Guide to Probiotic Products Available in USA HOM Tidbit: Rous P. A Sarcoma of the Fowl Transmissible by an Agent Separable from the Tumor Cells. Journal of Experimental Medicine. April 1 1911. ASM Article: A Brief History of Cancer Virology

Identified in the 1980s, Borrelia burgdorferi and other Lyme disease-associated spirochetes have since been found throughout the world. Jorge Benach answers questions about Lyme Disease symptoms, his role in identifying the causative bacterium, and his current research on multispecies pathogens carried by hard-bodied ticks. Julie's Biggest Takeaways Erythema migrans (the classic bullseye rash) is the most common manifestation that drives people to go see the doctor to be diagnosed with Lyme disease, but only about 40% of people diagnosed with Lyme disease experience erythema migrans. Lyme disease can progress to serious secondary manifestations. Why some patients experience these additional disease manifestations, but others do not, is one of the heaviest areas of study in Lyme disease. Though Borreliadoesn't have virulence factors that mediate tissue damage, it does avoid the immune system via antigenic variation. When the bacterium is first introduced into a new human host, that person's immune system generates reactions to the outer membrane components. These bacterial components change over time, leaving the immune response lagging behind and unable to clear the infection. Ixodesticks are the vector for Lyme disease and there are 3 stages in the Ixodestick life: Larvae: the stage during which the tick is most likely to become infected by feeding on a rodent. Nymph: the stage most likely to infect a person (due to their small size, they are less likely to draw attention while feeding). Adult: the stage when the tick develops into a sexual adult; females are most likely to be infected but because female ticks are large, most people will detect and pull out a feeding adult. Ticks feed for 2-4 days; removing a tick in the first 48 hours of attachment decreases the chance for transmission to the patient. Long Island is seeing anecdotal increases of Ambliomaticks (the Lone Star tick), which can transmit the human pathogen Ehrlichia. These anecdotal increases were one of the motivations behind a recently published survey of ticks and the human pathogens they carry. Links for This Episode MTM Listener Survey, it only takes 3 minutes. Thanks! Jorge Benach website at Renaissance School of Medicine Stony Brook University Sanchez-Vicente S. et al. Polymicrobial Nature of Tick-Borne Diseases. mBio. September 10 2019. Monzón J.D. et al. Populaiton and Evolutionary Genomics of Amblyomma americanum, and Expanding Arthropod Disease Vector. Genome Biol Evol. May 2016. ASM Article: The Bulls-Eye Rash of Lyme Disease: Investigating the Cutaneous Host-Pathogen Dynamics of Erythema Migrans Patient Zero podcast HOM Tidbit: Barbour A.G. and Benach J.L. Discovery of the Lyme Disease Agent. mBio. September 17 2019.

Influenza is famous for its ability to mutate and evolve but are mutations always the virus' friend? Jesse Bloom discusses his work on influenza escape from serum through mutation and how mutations affect influenza virus function and transmission. Subscribe (free) on Apple Podcasts, Google Podcasts, Android, RSS, or by email. Also available on the ASM Podcast Network app. Julie's Biggest Takeaways Influenza is famous for its ability to mutate and evolve through two major mechanisms: Antigenic drift occurs when a few mutations accumulate in the influenza genome and lead to seasonal changes. Antigenic shift occurs when two influenza strains recombine their genomes to form one previously unknown in human populations. Avian influenza has caused thousands of zoonotic cases, in which the virus is transmitted from birds to people. This causes serious disease but the virus doesn't easily pass from person-to-person, limiting how many people are affected. When a zoonotic case becomes easily transmissible between people, as is suspected occurred in the 1918 influenza pandemic, the outcome can be very serious for many, many people. During antigenic drift, the virus accumulates mutations randomly throughout its genome. Mutations in the hemagglutinin (HA) glycoprotein gene are the mutations most likely to affect the ability of antibodies to attach and block HA during viral infection of a new host cell. The circulating human H3N2 influenza A virus accumulates approximately 3-4 mutations annually within its HA gene, representing a 0.5-1% change. On average, it takes 5-7 years of these mutations accumulating until a viral strain can reinfect a previously infected person. The changes in the influenza sequence are responsible for waning immunity against the annually circulating strain. This was demonstrated when a flu strain from the 1950s was inadvertently reintroduced in the 1970s; older people who had previously been infected were protected against this exact same strain. Influenza viruses can escape from sera, which contains many different antibodies, similar to how they can escape from a single monoclonal antibody: through mutations in major antibody binding sites. However, the mutations that allow escape from one person's serum are different from the mutations that allow escape from another person's serum. This means the strains that escape one person's immune system may only be able to infect those with similar immunity. Links for This Episode MTM Listener Survey, only takes 3 minutes. Thanks! Jesse Bloom's lab website Guns Germs and Steel by Jared Diamond Lee J.M. et al. Mapping Person-to-Person Variation in Viral Mutations that Escape Polyclonal Serum Targeting Influenza Hemagglutinin.eLife. August 2019. Xue K.S. et al. Cooperating H3N2 Influenza Virus Variants are not Detectable in Primary Clinical Samples.mSphere. January 2018. Francis Arnold at ASM Microbe:Innovation by Evolution: Bringing New Chemistry to Life Let us know what you thought about this episode by tweeting at us @ASMicrobiology or leaving a comment on facebook.com/asmfan.

Graciela Lorca studies genetic systems to find positive and negative microbial interactions that lead to disease. She talks about her discovery of chemical inhibitors for the citrus greening disease bacterium, Liberibacter asiaticus,and how a specific strain of Lactobacillus johnsoniimodulates the immune system and may help prevent development of diabetes in people. Subscribe (free) on Apple Podcasts, Google Podcasts, Android, RSS, or by email. Also available on the ASM Podcast Network app. Julie's Biggest Takeaways Citrus greening disease, or huanglongbing, is a disease of citrus trees causing a major epidemic among citrus farmers around the world. The disease causes trees to sicken and eventually die, and is best diagnosed by PCR amplification of the bacterial DNA from the bacterium that causes the disease, Liberibacter asiaticus. Because the disease spreads through the tree at different rates, it's important that many samples be tested for accurate diagnosis. Quarantining the disease has proved difficult, as undiagnosed roots can transmit the disease if they are used to hybridize with canopy plants. The disease becomes even harder to contain under bad weather conditions: the high winds of recent hurricanes can scatter the insect vector, the Asian citrus psyllid, leading to infection of new orchards. Although L. asiaticuscan't be cultured, Graciela performed a screen on L. asiaticustranscription factors that were produced by E. coli. These were tested for inhibition by a chemical library, and discovered that a common treatment for gout, benzbromarone, inhibited protein activity. This discovery was confirmed using in vivoinfected plants and by expressing the gene in related bacterial species, Graciela and her team predict the protein plays a role in responding to osmotic stress. The protein target of the chemical differs widely between citrus greening disease and gout, but the protein-chemical interaction is similar enough to allow protein inhibition. Is there a link between the microbiome and diabetes? 10 years ago, Lactobacillus johnsoniican rescue animals that are predisposed to diabetes. L. johnsoniiinactivates a host enzyme, IDO, which regulates proinflammatory responses. Activated immune cells can travel to the pancreas and attack beta cells, leading to diabetes. Regulating the proinflammatory response by administering L. johnsoniias probiotics offers the opportunity to control development of diabetes in predisposed people. Links for This Episode MTM Listener Survey, only takes 3 minutes. Thanks! Graciela Lorca's lab website Pagliai F.A. et al. The Transcriptional Activator LdtR from 'Candidatus Liberibacter asiaticus' Mediates Osmotic Stress Tolerance. PLoS Pathogens. April 2014. Lai K.K., Lorca G.L. and Gonzalez C.F. Biochemical Properties of Two Cinnamoyl Esterases Purified from a Lactobacillus johnsonii Strain Isolated from Stool Samples of Diabetes-Resistant Rats. Applied and Environmental Microbiology. August 2009. Marcial G.E. et al. Lactobacillus johnsonii N6.2 Modulates the Host Immune Response: A Double-Blind, Randomized Trial in Healthy Adults. Frontiers in Immunology. June 2017. HOM Tidbit: Hartmann A., Rothballer M., and Schmid M. Lorenz Hiltner, a Pioneer in Rhisophere Microbial Ecology and Soil Bacteriology Research. Plant and Soil November 2008.

When a new biothreat or emerging infectious agent threatens, how are diagnostic protocols put into place? It's up to the Laboratory Response Network (LRN), a multipartner network of public health, clinical and other labs, to generate and distribute reagents, and provide training to detect these threats. Julie Villanueva, Chief of the Laboratory Preparedness and Response Branch at the CDC, talks about the LRN and how no two weeks on the job are alike. Subscribe (free) on Apple Podcasts, Google Podcasts, Android, RSS, or by email. Also available on the ASM Podcast Network app. Julie's Biggest Takeaways In the mid-1990s, the CDC joined public health representatives along with the Departments of Defense and Justice to determine the best way to prepare and respond to potential bioterrorism threats. The result was the Laboratory Response Network (LRN), founded in 1999. The LRN provides infrastructure to detect potential pathogens. Though first put into place to detect and prevent bioterror events, the LRN has also been able to detect infectious diseases that have emerged through other means. When a new disease emerges, there are typically no widely available tests to diagnose the disease. The CDC works hard to quickly develop diagnostic tests, validate the tests, manufacture the necessary reagents, and ship these out to the reference labs that are part of the LRN. This ensures that each lab can accurately reach the same result with the same sample. The laboratory response network requires more than just developing and deploying diagnostic tests. The LRN must also provide Training for LRN scientists. Proficiency testing to test the network. Reporting protocols for sending results. What diseases keep Julie up at night? A viral hemorrhagic fever is one, and microorganisms that evolve quickly and have high pathogenic potential, like influenza virus, is another. Featured Quotes "Our collaborations across other federal agencies like the FDA and the USDA are really important for us to stay on the cutting edge of what could be emerging." "Partnerships are so critical when managing an outbreak. There's never an outbreak that only affects one group of people...there are lots of different facets of an outbreak that need to be addressed and partnerships are critical for managing and trying to mitigate as much as possible." "The LRN primarily focuses on diagnostics, this is what the network really does. It's made to be able to detect biothreats and emerging infectious diseases in both clinical and environmental samples." "We're always looking at new technologies for faster, more sensitive, and more specific tests." "Every outbreak has been different in a different way, and I've learned something every time. I think that each outbreak has taught us a few things that work well within the network and a few things with which we can improve, and continued improvement is very important to us. For example, the Ebola outbreak in 2014-16 really highlighted the need for biosafety and biosecurity procedures all across not only the network but also our hospitals...we learn something different from every outbreak." Links for This Episode MTM Listener Survey, only takes 3 minutes. Thanks! The Laboratory Response Network(CDC website) HOM: The Origin of In Situ Hybridization- a Personal History

George F. Gao discusses how China CDC promotes global public health during outbreaks SARS and Ebola. He also talks about running a structural biology lab, the importance of both basic and translational research, and the most important discovery of the 20th century. Julie's Biggest Takeaways: China CDC was founded in 2001. Its experience with the SARS outbreak informed its response to the western Africa Ebola outbreak in 2014-2016, having learned that viruses don't care about national borders and can quickly become an international problem. Responding to any major outbreak serves both altruistic and selfish motives, since quelling the outbreak decreases the chance that the disease will continue to circulate, potentially reaching your country. Basic research is fundamental for many translational applications to improve human health. By measuring the mutation rate, for example, of a circulating virus, scientists can determine if previous isolates can be used to generate vaccines. The basic research that led to new nucleic acid sequencing techniques has many important applications! When asking other scientists what the most important discovery of the 20th century is, many biomedical scientists name the discovery of the double helix. George points out that bird migration patterns have influenced our understanding of avian diseases like the flu. This discovery led scientists to understand more about the annual transmission patterns of flu, highlighting the importance of interdisciplinary research. George has a foot in both basic and translational sciences and is an ardent supporter of both. The difficulty is in identifying basic research that has potential for application and providing opportunities to basic researchers to create companies and products based on their research. Another hurdles is collaborating and coordinating to ensure people talk to each other George lists the 4 Cs required to promote science, public health and societal development: Collaboration Cooperation Communication Competition Links for this Episode: George F. Gao Lab Website Gao GF and Feng Y. On the Ground in Sierra Leone. Science 2014. Carroll D et al. The Global Virome Project. Science 2018. Watts G. George F. Gao: Head of China CDC Signals a More Global Outlook. Lancet 2018. Forging the Path for Polio Vaccination: Isabel Morgan and Dorothy Horstmann

Bacteriophage are viruses that infect specific bacteria. Jeremy Barr discusses his discovery that phage interact with (but don't infect) mammalian epithelial cells. He explains how these different organisms: bacteria, bacteriophage, and the mammalian host, may exist in three-way symbioses. Subscribe (free) on Apple Podcasts, Google Podcasts, Android, RSS, or by email. Also available on the ASM Podcast Network app. Julie's Biggest Takeaways Jeremy's work as a postdoc focused on developing a protocol to clean phages for use in tissue culture. He and his advisor, Forest Rohwer, were asked to use this protocol to clean phages for a patient extremely sick with a multidrug-resistant Acinetobacter baumannii isolate. Within 24 hours, they used an experimental lab method to clean and purify phages that were used in an experimental procedure to treat a very sick person; phage therapy ultimately saved his life. Jeremy discovered that phages can pass through human epithelial cells by using a transwell system. Phage interaction with epithelial cells is not the same as an infection, since the phages cannot use mammalian molecular machinery to reproduce. Jeremy hypothesizes that the epithelial cells take up phage during active sampling from the gut, during which epithelial cells sample the environment to inform the immune system. Jeremy's work is building toward a model of tripartite symbioses. This includes symbiosis between bacteria and mammalian cells, between bacteria and bacteriophage, and between bacteriophage and mammalian cells. Bacteria can interact with mammalian cells to influence host cell signaling to their benefit, and Jeremy's hypothesis is that phage will be found to do the same. Building a gut-on-a-chip allowed Jeremy to study the interactions of phage with the gut in a controlled environment. The preliminary results suggest that the phage adapt to better adhere to the mucosal surfaces over time. Discovering the protein domains that phage use to stick to mucins opens up the possibility of using these domains in personalized therapeutics, by designing these into new phage or other therapeutics. Jeremy's 2 major pieces of advice for early career scientists: Follow what excites you! Find an aspect of biology that you're really passionate about and follow that. Find amazing mentors. Contact even people you don't directly work with, reach out to them and build your network. Links for This Episode MTM Listener Survey, only takes 3 minutes. Thanks! Jeremy Barr lab website The Perfect Predator by Steffanie Strathdee Gordillo Altamirano FL and Barr JJ. Phage Therapy in the Postantibiotic Era. Clin Microbiol Rev 2019. Nguyen S. et al. Bacteriophage Transcytosis Provides a Mechanism to Cross Epithelial Cell Layers. mBio 2017. Microbe information

Stanley Maloy discusses his career in Salmonella research, which started with developing molecular tools and is now focused on the role of Salmonella genome plasticity in niche development. He further talks about his role in science entrepreneurship, science education, and working with an international research community. Julie's Biggest Takeaways: Stanley's career began when transposon mutagenesis was a new, cutting-edge technique, and he found the best way to learn how to apply a new method was to jump in and try it. Antibiotic resistance has been a problem throughout Stanley's career. The future may hold new antimicrobials that aren't necessarily categorized as classical 'antibiotics,' but may offer precision therapy against specific infectious agents. Whatever the future holds, it won't be a single answer: Stanley sees many innovations necessary to deal with the future of antibiotic-resistant infections. Stanley's current research is in Salmonella genome plasticity and how genomic traits influence the bacterial niche. Where do traits like exotoxins or antibiotic resistance exist in the environment, and how are they transferred to new species to influence disease? Cases of Typhoid Fever in people without known exposure to another diseased person suggest there may be an environmental reservoir. What might it be? Stanley is a big proponent of scientist entrepreneurs and participates with the NSF Innovation Corps to promote early science start ups. In addition to creativity and the scientific process, one characteristic he encourages all entrepreneurs to develop is a good team spirit. Working collaboratively as a team is a very strong sign of success. Stanley believes in the importance of an international science communities, and he practices what he preaches: he works closely with the scientific community of Chile. He began in 1990 by teaching an intensive lab course about techniques, and has developed a decades-long relationship with this community. These relationships allow a dialog, and were the reason Stanley ultimately turned his focus to Salmonella Typhi from Salmonella Typhimurium. Links for this Episode: MTM Listener Survey, only takes 3 minutes! Thanks;) Stanley Maloy website at San Diego State University This Week in Microbiology #95: A Microbe Lover in San Diego National Science Foundation Innovation Corps Journal of Microbiology and Biology Education Call for Submissions for a Special Issue on diversity and inclusion. HOM Tidbit: A Large Community Outbreak of Salmonellosis Caused by Intentional Contamination of Restaurant Salad Bars

Cheese rinds contain microbial communities that are relatively simple to study in the lab while offering insight into other, more complex microbial ecosystems. Rachel Dutton discusses her work studying these cheese microbiomes, one of the few microbial ecosystem types where almost all of the microorganisms are culturable. Subscribe (free) on Apple Podcasts, Google Podcasts, Android, RSS, or by email. Also available on the ASM Podcast Network app. Julie's Biggest Takeaways The cheese microbiome makes a great study system because The communities are relatively simple (as few as 3 different microbial species) The microbial members are almost all culturable (in stark contrast to most microbial communities) The microbes colonize the cheese rind as a biofilm, which consists of the microbes and their secreted extracellular products. Like all biofilm communities, architecture and spatial structure are important for microbial interactions on cheese rinds, as are oxygen gradations, food access, and proximity to microbial neighbors. Rachel and her lab performed DNA sequencing on over 150 cheese samples from 10 countries to identify the microbes present on these rinds. By comparing these sequences to those they could grow in the lab (Rachel's lab makes "in vitro" cheese medium consisting of desiccated, autoclaved cheese), they realized almost all of the organisms identified by molecular means were present in their cultures. Does the cheese environment influence the microbial communities or do the microbial communities influence the cheese environment? Both! The pH, temperature, added salt and temperature act as knobs or dials that allow cheese makers to fine tune the final cheese product. Rachel was inspired to work on cheese after taking the Microbial Ecology course at Woods Hole, where the students spent a lot of time looking at the beautiful but complex interactions within microbial mats. Upon cutting open some Tomme de Savoie from a French colleague, she noted similarities between the microbial mat and the layered cheese rind Featured Quotes "The biofilm that colonizes the surface of the cheese has a lot to do with how the cheese ends up looking and smelling and tasting, and we actually eat this biofilm when we eat the cheese." "We're able to see that of all of the things that we identified by reasonable sequence abundance, we could also find them in culture. This told us that we were able to get a lot of these microbes in culture, which is not really possible in microbial ecosystems, but is one of the really strong advantages of working in the fermented food community." "We're looking at these interactions because they're happening on cheese and we can study them in the lab but they are things that are happening broadly across ecosystems, which I think is very exciting." "We've done some work on the succession of species over time. You have these very very reproducible successions over time, even though a lot of these cheeses are not inoculated with specific species; these are species that are coming in from the environment but they're very reproducible communities. There are some beautiful dynamics that happen and we're starting to look at the interactions between species that may be driving some of these dynamics." "We have this big need for model systems. One of the things I hope is that we'll have more people developing simple model systems for microbial ecology so we can compare results and see what the general principles are." Links for This Episode MTM Listener Survey, only takes 3 minutes! Thanks;) Rachel Dutton Lab Website Wolfe BE, Sutton JE, Santarelli M, and Dutton RJ. Cheese Rind Communities Provide Tractable Systems for in situ and in vitro Studies of Microbial Diversity. Cell 2014. Wolfe BE and Dutton RJ. Towards an ecosystems approach to cheese microbiology. Book chapter: Cheese and Microbes. ASM Press and Microbiology Spectrum (2014). Microbes After Hours: The Microbiology of Cheese (YouTube) Competition and Cooperation of Cheese Rind Microbes Exposed (The Scientist) Related: The Natural History of Cheese Mites HOM Tidbit: Peoria Historian Blog Post HOM Tidbit: Journal of Bacteriology Classic Spotlight: Crowd Sourcing Provided PenicilliumStrains for the War Effort

Most diagnostic tests look for a single microorganism, or at most a limited panel of microorganisms. Charles Chiu discusses his research on metagenomic sequencing as a diagnostic tool that can identify all potential pathogens in a given patient sample. Links for this Episode: MTM Listener Survey, only takes 3 minutes! Thanks;) Charles Chiu Profile at UCSF Chiu Lab at UCSF Validation of Metagenomic Next-Generation Sequencing Tests for Universal Pathogen Detection The Eukaryotic Gut Virome in Hematopoietic Stem Cell Transplantation: New Clues in Enteric Graft-Versus-Host Disease HOM Tidbit: Dochez and Avery. The Elaboration of Specific Soluble Substance by Pneumococcus during Growth. Journal of Experimental Medicine 1917. HOM Tidbit: Kozel and Burnham-Marusich. Point-of-Care Testing for Infectious Diseases: Past, Present, and Future. Journal of Clinical Microbiology 2017.

While searching for lignin-degrading soil microbes, Gautam Dantas discovered growth in an antimicrobial compound-containing control! He has since studied the resistance determinants (resistome) of soil and clinical samples to determine their similarities. Julie's Biggest Takeaways: Sequencing information is extremely useful for descriptive studies, but there's an increasing trend in microbiome studies to use the sequencing data as a basis for forming hypotheses. These hypotheses can then be tested by some variation of classical techniques, be in biochemical, culturing, animal models, etc. Surveying who is there helps scientists make testable predictions. Gautam's resistome research is built on the research of many, but especially inspired by: Gerry Wright, who proposed the presence of a resistome. The resistome is a collection of genetic determinants in a microbial group that allows phenotypic resistance against antimicrobial compounds. Julian Davies, who proposed the producer hypothesis. The producer hypothesis suggests that the same microorganisms that produce antimicrobials must also be the source of resistance, because they need to be able to protect themselves against the action of their own compounds. Gautam's discovery of antibiotic-eating microbes was completely serendipitous! As a postdoc, he was looking for lignin-degrading soil microbes and set up a culture with antibiotics as a negative control. To his surprise, there were some soil microbes that were able to grow - using the drugs as food! Samples from 3 different states were all able to support microbial life. The resistome of soil is very similar to the resistome of clinical samples, but the study design doesn't allow Gautam to conclude directionality: do the genes move from the clinic to the environment or from the environment to the clinic? This requires studying the resistomes over time, rather than the snapshot analyses this study generated. However, Gautam's group has received funding to do longitudinal studies, which will help scientists understand how resistance originates and then moves to new microbial communities. Context is very important for determining disease. A microbe may make one person but not another sick. Context can also be the genes carried by the microbe, and E. coli is a great example of this. Some E. coli are very good at causing UTIs but cause no disease when carried in the gut. Links for this Episode: Take the MTM listener survey (~3 min.) Gautam Dantas lab website Wright G.D. The Antibiotic Resistome. Expert Opinion in Drug Discovery. 2010. Davies J. and Davies D. Origins and Evolution of Antibiotic Resistance. MMBR. 2010. Bloomberg: Germ-Killing Brands Now Want to Sell You Germs HOM Tidbit: Recycling Metchnikoff: Probiotics, the Intestinal Microbiome and the Quest for Long Life

Pat Brown founded Impossible Foods with a mission to replace animals as a food production technology. Here, he discusses the ways microbial engineering helps produce the plant hemoglobin that provides the Impossible Burger's meaty qualities. Links for this episode: Take the MTM listener survey(~3 min.) The Microbial Reasons Why the Impossible Tastes So Good Impossible Foods The Conversation: What Makes the Impossible Burger Look and Taste Like Real Beef? Wired:The Impossible Burger: Inside the Strange Science of the Fake Meat that 'Bleeds' HOM Tidbit: Mendel's letters to von Nägeli HOM Tidbit:The Mendel-Nägeli Letters, circa 1866-73 (Scientific American)

CRISPR is a genome-editing tool, but what is its role in microbial biology and evolution? Joe Bondy-Denomy discusses his discovery of the first anti-CRISPR protein and the many unanswered questions surrounding CRISPR biology. Julie's Biggest Takeaways CRISPR is a bacterial immune system that identifies and destroys specific nucleotide sequences. These sequences are most commonly associated with foreign DNA from bacteriophage or plasmids. Bacterial acquisition of new CRISPR spacer sequences is fairly inefficient, and often a bacterium dies before acquiring and fending off a new phage infection. Only about 1 in a million cells emerge from a phage infection with a new spacer sequence, likely driven defective phages that act as a vaccine of sorts to provide spacer sequence material. 40% of bacteria and 85-90% of archaea have had some sort of CRISPR system detected in their genomic sequences. Most bacteria have Type I CRISPR system. This system includes different proteins that serve unique functions: one holds onto CRISPR RNA, one helps identify complementary sequences, and one cleaves the actual nucleotide sequence. The Type II CRISPR system has a single protein, Cas9, which performs all of these functions by itself. Because of its simplicity, this Type II CRISPR system has become widespread as a DNA manipulation tool. What are the inputs to CRISPR? How do bacterial cells turn CRISPR genes on and off? Do CRISPR systems serve any other regulatory functions? There are still a number of questions that need to be answered to understand the biological role of CRISPR systems. Take the MTM listener survey (~3 min.) Joe Bondy-Denomy UCSF Lab Website Rauch BJ. Inhibition of CRISPR-Cas9 with Bacteriophage Proteins. Cell 2017. Borges AL. Bacteriophage Cooperation Suppresses CRISPR-Cas3 and Cas9 Immunity. Cell 2018. Mendoza SD. A Nucleus-Like Compartment Shields Bacteriophage DNA from CRISPR-Cas and Restriction Nucleases. bioRxiv 2018. UCSF Sandler Fellows Program HOM Tidbit: Coming of Phage Celebrating the Fiftieth Anniversary of the First Phage Course

Julie's Biggest Takeaways: Parasites are incredibly varied in many characteristics, including their size! Some are microscopic, while others are macroscopic and can be seen with the naked eye. Not just small macroscopic, although some worms at 35 cm can be considered quite large. Some tapeworms can reach 50 feet! Bobbi Pritt's blog started as an exercise to share the cases she observed while a student at the London School of Tropical Medicine. She wanted to share these cases with students back at the Mayo Clinic, but found the audience grew to include clinical parasitologists, microbiologists, and parasite-interested people worldwide. Part of its success relies on its succinctness: a short, digestible case study with the minimum information needed to make a diagnosis. Pritt's research focuses on developing molecular tests to detect microorganism RNA or DNA. Molecular tests can be used as a complementary diagnostic test or as the primary test, which can give healthcare workers definitive information to make therapeutic decisions much more quickly than a test that requires culturing the microorganism. A new bacterium that causes Lyme disease, Borellia mayonii, was found because the molecular tests that detect Borellia burgdorferi are flexible enough to detect multiple species and can differentiate between the different types of organisms. It was an astute technologist working at the bench who recognized the readout was slightly different than We did a tick drag, taking a white cloth and dragging it through vegetation. The Ixodes ticks that transmit Lyme disease will think the sheet is a host and will grab onto the sheet, allowing easy collection of a large number of ticks to test for bacterial presence. One of the outstanding questions in parasitology is the relationship of Blastocystis (formerly known as Blastocystis hominis but may actually be several species) to human health. Blastocystis lives in the intestinal tract and may cause irritable bowel-like syndrome. Definitive evidence on whether Blastocystis causes intestinal disease has yet to be presented, and there is a lot of opportunity for research in this area. Links for this Episode: Take the MTM Listener survey (~3 min.) Creepy Dreadful Wonderful Parasites (Bobbi Pritt's blog) ParasiteGal: Bobbi Pritt on Twitter Pritt B.S. et al. Identification of a Novel Pathogenic Borrelia species causing Lyme borreliosis with unusually high spirochaetaemia: a descriptive study. Lancet Infectious Disease. 2016. MTM Episode: Biofilms and Metagenomic Diagnostics in Clinical Infections with Robin Patel HOM Tidbit: Patrick Manson. On the Guinea Worm. British Medical Journal. Bobbi on This Week in Parasitism (TWiP)

How did discoveries made with bovine papillomavirus help scientists develop the human papillomavirus vaccine? Doug Lowy discusses his journey that began with basic research and led to the production of the HPV vaccine. Julie's Biggest Takeaways In the early 1950s, the U.S. was a high-incidence country for cervical cancer. Through application of screens using the Pap smear, doctors have been able to catch and excise suspicious tissue, leading to a significant drop in incidence. Cervical cancer remains high-incidence in low- and middle-income countries; in high-incidence countries, cervical cancer is the most common form of HPV-associated cancer. In the U.S., cervical cancer represents around 50% of the HPV-associated cancers, with others like penile, anal, and oropharyngeal cancers also represented. Henrietta Lacks, the woman from whom HeLa cells were derived, had a cervical adenocarcenoma caused by HPV-16. The viral DNA had integrated near the myc oncogene to generate high expression of this oncogene. The cell lines have been growing for decades but the epigenetic changes from HPV infection have led to a dependence of the cells on E6 and E7; if they are blocked or removed, the HeLa cells undergo apoptosis. Lowy's work on bovine papilloma virus (BPV) played a key role in development of the HPV vaccine. Other researchers attempting to generate a neutralizing response to the HPV capsid failed, but Lowy and his colleague Reinhard Kirnbauer had successfully achieved neutralization using BPV. By comparing HPV and BPV sequences, Lowy realized there was a single amino acid change in the HPV-16 strain that was being used as a lab standard strain; fixing this restored capsid self-assembly, led to immunogenicity and provided the basis for the HPV vaccine. HPV L1 capsid protein has a repeating structure that induces a very high level of immune protection. Protection is so high that it is sterilizing, meaning that exposed individuals prevent any infection, not just disease. This may serve as the basis for a new strategy, using repeating structures such as ferretin in vaccine development. The incubation between infection and development of cancer can take decades, and the vaccine has not been on the market long enough to assess a difference in cancer incidence. It has resulted in a decrease in cervical dysplasia, the endpoints used in cervical cancer screening via pap smear, but no cancer reduction has been observed yet. Links for this Episode: Harold zur Hausen Nobel Prize for association between HPV and cancer Lowy D. HPV Vaccination to Prevent Cervical Cancer and Other HPV-Associated Disease: From Basic Science to Effective Interventions. Journal of Clinical Investigation. Jan 2016. Schiller J. and Lowy D. Explanations for the High Potency of HPV Prophylactic Vaccines. Vaccine. August 6 2018. VAERS Vaccine Adverse Event Reporting System ASM Article: A Brief History of Cancer Virology JHU Press: Vaccines Did Not Cause Rachel's Autism

Burkholderia pseudomallei is an endemic soil-dwelling bacterium in southeast Asia, where it causes melioidosis. Direk Limmathurotsakul discusses his work to improve the official reporting numbers and how Julie's Biggest Takeaways: Melioidosis can present in a number of ways, such as sepsis, pneumonia, or abscesses. Because the symptoms are not specific, diagnosis requires isolation of the Burkholderia pseudomallei bacterium. Risk factors for disease include diabetes and exposure to the soil and water in which the bacterium lives. In 2012, only 4 people were officially reported to have died of melioidosis in Thailand, but microbiological records suggest the real number was closer to 696. Scientists like Direk worked with the government to improve reporting requirements and the numbers now reflect a more accurate assessment of the disease burden. More accurate official reporting can lead to more public health campaigns, resources, and support for both scientists and patients. Social media campaigns and a YouTube competition help to raise local awareness of melioidosis. The YouTube competition engages the community by allowing them to enter videos in their own dialect, which then inform others about how to minimize risk factors for melioidosis. The AMR Dictionary gives simple definitions to jargon surrounding the problem of antimicrobial resistance. The definitions are translated into multiple languages in ways that make sense with colloquialisms. For example, in Thai, many people refer to antibiotics as antiseptics or anti-inflammatory drugs, and the dictionary takes local use into consideration in its definitions. Links for this Episode: MTM Listener Survey Limmathurotsakul website at MORU Tropical Health Network Melioidosis.info Melioidosis: the Most Neglected Tropical Disease Antibiotic Footprint AMR Dictionary

When will the next disease outbreak occur? Why are some pests better at spreading disease than others? Disease Ecologist Barbara Han talks about her research that addresses these questions with computer modeling, as well as how modeling predictions can inform field and bench research. Take the listener survey: asm.org/mtmpoll Visit asm.org/mtm for all links and notes.

Why have scientists struggled to generate a protective HIV vaccine? Dan Barouch lays out the unique challenges and discusses the ongoing clinical trial with an adenovirus-based vaccine developed in his lab. Julie's Biggest Takeaways HIV poses unique and unprecedented challenges for vaccine development including: Viral diversity: extremely wide range of viral diversity. No natural precedent: No human has cleared HIV based on their immune responses. Unknown correlates of protection: scientists are unsure what immune responses are important to induce. Barouch's group uses a vaccine strategy comprised of computationally optimized mosaic HIV Env proteins, which represent pieces of the outermost glycoprotein, Env, that have been tied together in a way expected to generate protective immunity. Early data from animal and human trials suggests these mosaic antigens generate an immune response to a wider array of HIV types than previous vaccines. Clinical trials are ongoing to see if a strategy of mosaic antigen vaccination, followed by a boost with Env protein, is protective in people. Attenuated HIV hasn't been used as a vaccine strategy because of fears it could revert to a disease-causing form; similar fears have prevented a whole-killed virus platform for vaccine development. A clinical trial testing safety in 3 locations around the world demonstrated that this vaccine strategy in people elicited immune responses shown to be protective in animals. An efficacy trial is ongoing in sub-Saharan Africa, with results expected in 2021. The trial is double blinded: neither the doctor nor the patient know who was administered the candidate vaccine or who was administered the placebo. HIV latent infection causes complications in vaccine development because HIV latency is seeded early, possibly in the first few days of infection. Once latency is established, the individual is infected for life. Any low level of HIV infection in vaccinated people could potentially seed this latent infection. Quickly-seeded latency means immune responses must react extremely quickly. Featured Quotes "The challenges in the development of a prophylactic HIV vaccine are among the toughest challenges in biomedical and scientific research." "HIV poses unique challenges for vaccine development and truly unprecedented challenges that have never been posed before by vaccination. One such challenge is the viral diversity: HIV exists not as a single sequence, but as numerous different viral sequences — not only throughout the world, but also throughout regions, communities, and even within the same individual. So to create a vaccine against HIV, the immune responses have to be relevant for a vast diversity of viral sequences." "At what efficacy level would an HIV vaccine be licenced by both the industry partners as well as the government regulators in a particular country, and at what level of efficacy would it actually have a major public health impact? It's a moving target over time; it really depends on what the current state of the epidemic is at the time the vaccine is ready to be licensed." "It's critical to have high-quality research part of the clinical efficacy trials so that success or failure or something in between, that the HIV research field learns from it, and learns what worked well and what didn't work well, and how to make better vaccines moving forward." "I always encourage young scientists to pursue their dreams and to tackle hard problems. There's a lot of easy problems to solve but some of the hardest problems are the most impactful in the end." Links for This Episode MTM Listener Survey Barouch lab at the Center for Virology and Vaccine Research. MTM: Mark Connors. The Lancet: Evaluation of a Mosaic HIV-1 Vaccine in a Multicentre, Randomised, Double-Blide, Placebo-Controlled, Phase 1/2 a Clinical Trial (APPROACH) and in Rhesus Monkeys. The Lancet: A Step Forward for HIV Vaccines. Journal of Virology: Similar Epitope Specificities of IgG and IgA Antibodies Elicited by Ad26 Vector Prime, Env Protein Boost Immunizations in Rhesus Monkeys. PLoS One: First-in-Human Randomized, Controlled Trial of an oral, replicating adenovirus 26 vector vaccine for HIV-1. HOM Tidbit: I am the Berlin Patient: A Personal Reflection. HOM Tidbit: Doctor who cured Berlin Patient of HIV: 'We knew we were doing something very special'.

Erica Ollmann Saphire discusses her research on Ebola virus glycoprotein and the changing nature of structural biology. The Ebola virus glycoprotein sequence can vary up to 50% between Ebola virus species, presenting a challenge to develop pan-Ebola therapeutics or vaccines. Erica Ollmann Saphire discusses her work on antibodies that neutralize all Ebola virus species and the changing nature of the structural biology toolkit used to study them. Check out all our great podcasts at asm.org/podcast MTM Listener Survey: asm.org/mtmpoll Ollmann-Saphire Lab Site Protein Database Isolation of Potent Neutralizing Antibodies from a Survivor of the 2014 Ebola Virus Outbreak. Science 2016. Systemic Analysis of Monoclonal Antibodies against Ebola Virus GP Defines Features that Contribute to Proteciton. Cell 2018. Structural Basis of Pan-Ebolavirus Neutralization by a Human Antibody against a Conserved, yet Cryptic Epitope. mBio 2018. Tenacious Researchers Identify a Weakness in All Ebolaviruses. mBio 2018. HOM Tidbit: How "Lassa," a small Nigerian Town, was Stigmatized by having a Killer Virus Named after it.

We pull back the curtain as former show hosts Merry Buckley and Carl Zimmer talk Meet the Scientist origins, favorite interviews and microbial topics. Julie's Biggest Takeaways: Though the show started before podcasts were as popular as they are now, this didn't pose a problem for Merry or Carl when soliciting guests - scientists were happy to have their work featured and to discuss their research. Inviting guests may involve bringing in a mix of experienced and early-career researchers, but both Merry and Carl agreed that the science is the major deciding factor when selecting guests. The ability to steer away from technical jargon and to use accessible, everyday analogies is one of the features shared by favorite guests. Carl uses the example of Bonnie Bassler, who explains bacterial quorum sensing as a communication mechanism. Delving into the personal motivations and experiences of guests can be tough, even when these experiences relate to science. Merry uses Abigail Salyers' claim of the English teacher who supported her through her high-school pregnancy and Julie uses Ilaria Capua's experience when falsely accused of trafficking viruses for money. Scientists can make themselves more visible to scientists and nonscientists by promoting their research on social media, particularly on Twitter. Links for this Episode: MTM Listener Survery Merry Buckley on twitter Carl Zimmer website Carl Zimmer on TWiV She has her Mother's Laugh

How does an engineer approach microbial genetics? cworks with microbes of all kinds to optimize metabolic and agricultural systems. Here he discusses his work with Rhodobacter to make biofuels and for membrane protein expression, with Agrobacterium and plant pathogenic viruses to make drought-resistant plants, and with Clostridium and yeast cocultures for lignocellulose digestion. Take the listener survey at asm.org/mtmpoll Full shownotes at asm.org/mtm Links for this Episode: Wayne Curtis Lab site at Penn State University PLoS One: Molecular Cloning, Overexpression, and Characerization of a Novel Water Channel protein from Rhodobacter sphaeroides Protein Expression and Purification: Advancing Rhodobacter sphaeroides as a Platform for Expression of Functional Membrane Proteins Biotechnology for Biofuels: Consortia-Mediated Bioprocessing of Cellulose to Ethanol with a symbiotic Clostridium phytofermentans/Yeast Co-Culture HOM Tidbit: Genentech "Cloning Insulin" blog HOM Tidbit: Genentech press release announcing insulin cloning

Over the course of a few decades, scientists have learned how insect endosymbiont bacteria affects insect reproduction and have used this understanding to control mosquito-born diseases. Seth Bordenstein talks about his research on the insect endosymbiont Wolbachia, human-microbiome interactions, and how the ecosystem of a host and its microbes can be refered to as a holobiont. Take the listener survey at asm.org/mtmpoll Links for this Episode: Bordenstein Lab at Vanderbilt University mSystems: Getting the hologenome concept right: an eco-evolutionary framwork for hosts and their microbiomes. PLoS Biology: Gut microbiota diversity across ethnicities in the United States. PNAS: One prophage WO gene rescues cytoplasmic incompatibility in Drosophila melanogaster. Discover the Microbes within! The Wolbachia Project HOM Tidbit: Studies on Rickettsia-Like Micro-Organisms in Insects (1924 paper from Hertig and Wolbach)

Christine Foreman explains how microbes can survive and grow on glaciers, and what we can learn from microbes in glacier ice cores. Take the MTM listener (that's you!) survey asm.org/mtmpoll it only take 3 minutes. Thanks! Julie's Biggest Takeaways Liquid inclusions between ice crystals create a vein-like network that allow microbes to survive between the ice crystals. Microbes living in glaciers have to adapt to a number of extreme environments: low water, low nutrients, extreme cold, and 6 months each of full sun or complete darkness mean there are many adaptive requirements to live in glaciers. Air bubbles trapped in ice cores provide data on the atmosphere 40,000 or 100,000 years ago. Using very old samples like these can inform scientists about the precipitation, temperature, and major cataclysmic events that occured at those time periods. Because so many researchers share ice core samples, a research group like Foreman's will often get a very small sample, as low as 7 ml, for a particular time period. Given that there are only 100 to 10,000 cells per ml, that is not a lot of sample to work with! Aggregation of life, including microbial biofilms, changes the absorption of solar radiation. A clear, white surface radiates back as much as 90% of the solar radiation, but as aggregates form, they allow more of the solar radiation to be trapped. This in turn can increase microbial metabolic activity and allow even more microbial growth, leading to a feedback loop that increases absorption of solar energy and loss of glacial surfaces. Subscribe (free) on Apple Podcasts, Google Podcasts, Android, RSS, or by email. Also available on the ASM Podcast Network app.

A very small proportion of people infected with HIV do not develop AIDS. Mark Connors talks about 2 patient populations that his lab studies, the elite controllers and the elite neutralizers, who control HIV infection with their respective T cell or B cell responses. Connors hopes his work on killer T cells and broadly neutralizing antibodies will help scientists develop better HIV therapies or an effective HIV vaccine. Links for This Episode: Mark Connors labsite at NIAID Immunity article: Identification of a CD4-binding-site antibody to HIV that evolved near-pan neutralization breadth. Immunity commentary: Class II-restricted CD8s: New lessons violate old paradigms. Science article: Trispecific broadly neutralizing HIV antibodies mediate potent SHIV protection in macaques. Imagining an HIV-Free Future (Smithsonian Worlds AIDS Day Event (Live Dec 4th at 6:45pm) HOM Tidbit: 12 Diseases that Changed Our World MTM Listener Survey

In the early 2000s, Andrew Read predicted that non-sterilizing vaccines would lead to more virulent disease. He was able to test his hypothesis with the real-world example of Marek's disease, a disease of chickens. Read tells the story of his discovery, and talks about his work on myxoma virus. Take the MTM Listener Survey Subscribe (free) on Apple Podcasts, Google Podcasts, Android, RSS, or by email. Also available on the ASM Podcast Network app. Julie's Biggest Takeaways: Every chicken on the market is vaccinated against Marek's disease. Infection with Marek's disease causes tumors on the bird and can lead to direct death, or condemnation of a flock requiring their culling. Birds are vaccinated with a live, attenuated virus, and there have been 3 vaccine iterations. The first used a related herpesvirus isolated from turkeys, while the second vaccine added a second virus strain. Each of these vaccines conferred protection for about 10 years, after which the disease began popping up again. The 3rd generation vaccine added yet another serotype - this additional strain is a mutant strain of the chicken-infecting serotype - and has been effectively protecting chickens since the 1990s. Chickens do not get sterilizing immunity from the Marek's disease vaccine; they can be infected by the wild-type virus, but the vaccine prevents infected animals from having disease symptoms. These asymptomatically infected animals can still shed the virus. Contrast this to human immunity from many of our vaccines, such as measles or smallpox vaccines, in which our immune response stops the virus from entering our cells and therefore blocks virus replication. Vaccination inhibits strains with lower virulence more than strains with higher virulence. This fact, combined with asymptomatic infection, means that although the infected birds don't show disease symptoms, they are more likely to be shedding more virulent (or 'hot') strains. This generates selection for these hot strains that wouldn't normally be successful. Without vaccination, host strains kill the host too quickly to allow viral replication and transmission to occur; Vaccines allow these hot strains to propagate. Vaccine resistance is much more rare than antibiotic or antimicrobial resistance. This is due to a number of factors, including the diversity of microbial population being acted upon (small with initial infection, large when treated with antimicrobial drugs). Vaccines are much more evolution-proof for these reasons. Purposeful release of myxoma virus during the 1950s in Australia killed between 10 and 100 million animals, or 99.9% of the rabbit population. Frank Fenner followed the virus and surviving rabbit populations and discovered that myxoma viruses that were too virulent were less likely to be transmitted, because they killed the host too quickly. He also showed that the small surviving number of rabbits were more resistant to viral infection. The arms race between the two has generated a virus so immunosuppressive that Read's group has found the currently circulating myxoma virus has changed the way it kills its host: the virus disables the rabbit immune system and allows the rabbit's own microbiome to cause invasive bacterial disease.

A recent Nipah virus outbreak in Kerala, India, was halted due to improved detection capabilities. G. Arunkumar tells the story of his involvement. Host: Julie Wolf Take the MTM Listener Survey Subscribe (free) on Apple Podcasts, Google Podcasts, Android, RSS, or by email. Also available on the ASM Podcast Network app. Julie's Biggest Takeaways: Because bats are the normal reservoir, Nipah virus outbreaks appear to be seasonal, with an increase in cases coinciding with the spring, when the bat reproduction season is. Once a person is infected through direct contact with the virus, the virus is transmitted person-to-person through respiratory droplets. Family clusters combined with the right incubation time acted as a clue that a Nipah virus outbreak had begun. Molecular tests improved virus detection during the 2018 Nipah outbreak because patients presented symptoms within a few days, which was too short for them to have developed antibodies. Molecular tests allowed identification of infected patients within days. Previous outbreaks have taken weeks to months, or even years, to identify the infectious virus. A single crossover event in the recent Nipah outbreak led to person-to-person transmission within the 22 additional individuals. Hospital infection control practices are important to reduce transmission to healthcare workers and hospital attendants. Featured Quotes: "Most of the Nipah outbreaks, you find a lot of hospital transmission from the infected patient to healthcare workers, the other patients in the ward as well as the patient attendants." "The only virus that can cause encephalitis in a family cluster is Nipah. With other encephalitis viruses like herpes or Japanese encephalitis virus, you don't see family clusters." "Nipah virus is a level 4 pathogen, so the cultivation can be only done in a level 4 laboratory. But molecular tests allow you to test for it at a lower level laboratory, such as a BSL-3 lab, because you inactivate the virus. You are only focusing on RNA. The risk can be reduced." "When you use serological diagnosis, the antibodies are detectable only after 8-10 days after onset of illness. Nipah is a very, very acute, serious fatal disease. Many people may die before they develop antibody. So we need to use a combination of real-time PCR and antibody." "This is the first time in the history of Nipah that the diagnosis was done in country. All the previous diagnoses were done at CDC Atlanta." Links for This Episode: Department of Virus Research at Manipal Academy of Higher Education Journal of Clinical Microbiology Review on Nipah virus ASM Global Impact Report HOM Tidbit: NPR piece interviewing K. B. Chua and others HOM Tidbit: Science article first describing Nipah virus

Robin Patel discusses her work on prosthetic joint infections and how metagenomics is changing infectious disease diagnostic procedures. Take the listener survey: asm.org/mtmpoll Julie's Biggest Takeaways: The term antimicrobial resistance can mean many things. Although acquisition of genetic elements can lead to drug resistance, so can different growth lifestyles of bacteria; the same bacteria growing in liquid culture may be more susceptible to a drug than those bacteria growing on a biofilm. Lifestyle and genetics can intertwine, however, when bacteria growing as a biofilm exchange resistance genes through horizontal gene transfer. How do bacteria reach an implanted surface, such as on a prosthetic joint, to cause infection? It may rarely occur during surgery, if even a single bacterium reaches the joint surface despite the sterile conditions; alternatively, it could occur through hematogenous spread (through the blood) after the surgery is over. Most infections are believed to be seeded at the time of implantation. While scientists don't perform teeny, tiny implants in animal models of infection, the materials are placed in animal bone to mimic as similar an immune response as possible. Targeted metagenomics and shotgun metagenomics are both being developed clinically. Targeted metagenomics looks at one specific gene found in a number of species, such as the 16S ribosomal RNA gene. Shotgun metagenomic looks at all DNA present, and requires a lot more cleaning up to eliminate human genomic material, which is the major sequence of any human-derived sample.

To eliminate malaria, you have to stop transmission, and that's what Carolina Barillas-Mury hopes to do. Her work on the interaction of the malaria parasite Plasmodium falciparum may lead to a transmission-blocking vaccine. She explains how, and discusses the co-evolution of malaria, mosquitos, and man. Take the listener survey: asm.org/mtmpoll Julie's Biggest Takeaways: When born, babies carry antibodies from their mothers, which may protect them through passive immunity; additionally, babies are more easily protected from mosquito exposure by placing them under bed netting. As they grow, children become more active, and their passive immunity concurrently wanes. They may be exposed to mosquitoes carrying malaria parasites and their still-developing immune systems aren't able to keep the parasites from replicating, leading to more severe disease, including cerebral malaria. The Culicines and Anopholines are two major groups of mosquitoes that carry disease. The culicines have recently spread around the world, but the Anopholines species moved from Africa into South America one hundred million years ago, but malaria only moved into the New World a few hundred years ago with the slave trade. The relationship between the mosquitoes and malaria parasites has been evolving much longer in Africa than it has been with the specific population of mosquitoes in South America - one of the reasons why the disease is less devastating in South America. The 'invisibility gene,' pfs47, is expressed in the banana-shaped ookinete and helps the malaria parasite to avoid detection by the mosquito immune system. The pfs47 malarial gene is adapted for the localized mosquito populations from the same region as the parasite; if an African mosquito is infected with a South American parasite, the parasite is more likely to be recognized and killed than if the African mosquito is infected with an African parasite. The most immunogenic proteins in parasites may produce an immune response, but this immune response may not block infection. New vaccines are concentrating on where antibodies bind, to ensure there is a biological effect of the immune response, and this is why Barillas-Mury has used a modified Pfs47 protein to generate immune responses, rather than its native form. Links for this Episode: Carolina Barillas-Mury NIAID website NPJ Vaccines: Antibody Targeting of a Specific Region of Pfs47 Blocks Plasmodium falciparum Malaria Transmission. PLoS One: Molecular Analysis of Pfs47-Mediated Plasmodium Evasion of Mosquito Immunity. PNAS: Plasmodium Evasion of Mosquito Immunity and Global Malaria Transmission: The Lock-and-Key Theory. HOM Tidbit: History of the Discovery of the Malaria Parasites and their Vectors MTM Listener Survey

How do researchers study a new pathogen? Stanley Perlman talks about how virus researchers studied SARS and MERS after they emerged, what they learned, and why there are no more cases of SARS. He also discusses his work on a coronavirus model of multiple sclerosis. We want to hear from you! Please take our listener survey. Julie's Biggest Takeaways: Coronaviruses have the largest RNA genomes, with up to 40 kB of sequence, but why their genomes is so big is unclear - their genomes don't seem to code for more genes than viruses with smaller genomes. Before the SARS coronavirus outbreak in 2002, few severe human infectious coronaviruses were known, but the several coronaviruses had been identified that cause serious disease in animals such as pigs, cats, and cows. Where did SARS go? SARS coronavirus had to cross into people and mutate for better infectivity, and when infecting people, it caused a lower respiratory disease. Quarantining SARS patients is extremely effective because the symptoms coincide with infectivity, and spread of SARS was quenched by strict use of quarantine. Quarantine is less effective for diseases like influenza or measles, because patients are contagious before showing symptoms. Because of its low person-to-person transmission, there's very small possibility of major outbreaks from large gatherings such as the Hajj. MERS acts more like an opportunistic infection, and its transmission among people has been mostly among immunocompromised or otherwise sick people in the hospital. By the time patients present with multiple sclerosis, it may be 20 years after an inciting event that triggers the disease. By using a murine coronavirus inciting event for neuron demyelinization in mice, the role of the immune system in this process can be interrogated. Scientists may not understand the exact cause of MS in people, but this model helps them to understand how different immune cells contribute to disease.

You may know that beer is fermented, but did you know making chocolate requires a fermentation step? Kevin Verstrepen discusses how his lab optimizes flavor profiles of the yeast used in this fermentation step, and explains how yeast was domesticated before microorganisms had been discovered. Take the MTM listener survey, we want to hear from you. Thanks! Julie's Biggest Takeaways: Microbes are used to ferment foods, but they do more than just add ethanol or carbon dioxide: their metabolic byproducts add flavors and aromas that are an essential part of the fermented food. In cocoa bean fermentation, the yeast that are part of the initial fermentative microbial population control the development of the subsequent microbial populations and the quality of the final product. How the volatile flavor compounds generated during fermentation survive the roasting step remains unclear. Heat can destroy these labile compounds, but Kevin thinks the compounds were able to survive roasting because they become embedded in lipids (fat) of the cocoa beans. Similar compounds produced during bread rising are destroyed during baking, possibly because there is less fat to protect these molecules. Mixing data science and beer: a computer scientist in the Verstrepen lab analyzed the flavor profiles of several hundred beers, which were also analyzed by a trained tasting panel. The goal is to link the chemistry to the aroma, which requires complex algorithms due to the integration of hundreds of flavor molecules. A spontaneous hybridization between Saccharomyces cerevisiae, the normal fermentative yeast, and S. eubayanus, a cold-tolerant yeast, resulting in a hybrid that can ferment at colder temperatures, as is required for brewing lager beers. There are 2 lineages that are used by most breweries, and while different characteristics have evolved over time, the genetic bottleneck limits characteristic diversity. The Verstrepen lab made several crosses between these two species and selected for hybrids that generated those with desirable characteristics. Molecular means can determine the offspring that are most likely to confer desired characteristics, but the commercial yeasts are not specifically genetically manipulated to this end. Domesticated yeast have different characteristics than their wild counterparts. Domesticated yeasts have lost the ability to use certain sugars, but have gained abilities associated with their use; beer yeasts use maltose at much higher rates, for example. When the origins are traced using molecular methods, it goes back to medieval times. How to domesticate an organism that hasn't been identified? Brewers have long transferred sediment from one batch of beer into new batches, which is how selection for human-desired characteristics began. Wine yeasts, which are not passaged but are likely inoculated from the same vineyard annually, show less domestication than the beer yeast.

How can the humble zebrafish teach us about the human microbiome? John Rawls discusses the benefits of using animal models Take the MTM Listener Survey Julie's Biggest Takeaways: Zebrafish and other model animals provide opportunities to understand host-microbe interactions. Zebrafish are particularly useful for imaging studies, due to their translucent skin and the ease of in vivo microscopy. This allows zebrafish to be used to in studies of spatial architecture or longitudinal studies (imaging the same fish specimen over time) in ways that other model organisms can't be. Zebrafish get their first microbes from their mother, just like mammals! The chorion, a protective coating that surrounds the zebrafish embryo, is seeded with microbes from passing through the cloaca of the female zebrafish. Surface-sterilizing this chorion allows researchers to generate germ-free animals that are very useful for microbiome studies. A gut epithelial transcription factor is regulated by a signal from the gut microbiota, and this signaling interaction is conserved among all vertebrates. The transcription factor itself, HNF4, is found in both complex and simple animals, like the sea sponge, and may serve a long-conserved function in regulating interactions between animals and their microbiota. Enteroendocrine cells release hormones based on specific chemical cues, but they can also interact with the nervous system. This makes them an important part of the gut-brain system, and the power of in vivo imaging has made zebrafish a great model for better understanding their function. Specific members of the microbiome specifically stimulate these EECs, sending signals up the vagus nerve to the brain. Featured Quotes: "We know that the zebrafish functionality of its intestine is very similar to what one encounters in the mouse or human intestine and we and others have been able to translate our findings from zebrafish studies into human biology." On genomic studies that have found similar transcription profiles in zebrafish, stickleback fish, mice, and humans: "This suggested that there is a core transcriptome that gut epithelial cell use in different vertebrate species that haven't shared an ancestor in 420 million years!" Comparing fish and mouse: "Genes regulated by microbiota in these respective hosts display a lot of overlap. Many of the same signaling pathways and metabolic processes are affected by microbiotas in different hosts in similar ways." "There's been a lot of interesting research documenting the role of the intestinal microbiome in promoting harvest of dietary nutrients we consume. Much of that literature has been focused on the events that occur in the distal intestine, in the colon, where recalcitrant carbohydrates and proteins that make it that far, many of which we are unable to digest, are made available to the colonic microbiome, members of which are able to digest and degrade them to things such as short chain fatty acids, which we can consume." "Eventually, we'll have some strong candidates in terms of specific bacterial strains or communities or factors or pharmacologic agents that could be used to affect dietary fat absorption or metabolism. We're still a long ways away from that." "One of the fascinating things about developmental biology is that the only way you get a viable animal is if the different tissues and the different cells within the body are coordinating amongst themselves for energy, for nutrients, for oxygen, et cetera. As you're building an animal and as you're sustaining an animal, the different tissues have to cooperate. When that doesn't happen, when tissues or cells become selfish or don't play by the rules, you get things like cancer and other diseases as well...when I began learning about the field of microbiome science and some of the work that was coming out from that field, it sounded to me like the microbiome was going to be a really important part of that. Not only can we think of the microbiome as a 'microbial organ,' as it is sometimes called, and therefore worthy of consideration within the context of developmental biology, but also the influence of the microbiome on any one tissue is going to modify its need and its ability to cooperate within the integrated system." Links for this Episode: John Rawls' lab website More amazing zebrafish images from the Rawls lab Duke University Microbiome Center Genome Research article on HNF4 regulation Cell Host and Microbe article on microbial influence on fatty acid absorption

Gemma Reguera discusses her studies of Geobacter pili, which transfers electrons to iron oxide and other minerals, and can be used for new biotech applications. Host: Julie Wolf Subscribe (free) on Apple Podcasts, Google Podcasts, Android, RSS, or by email. Also available on the ASM Podcast Network app. Julie's Biggest Takeaways: Geobacter sulferreducans, a bacterium that "breathes" rust, is the lab representative of the genus Geobacter that dump electrons onto rust. These specialized microbes use minerals like manganese oxide and iron oxide (also known as rust) for respiration in both terrestrial and aquatic sediments. Although many species are strict anaerobes, a few species can grow under microaerophilic conditions, in which the bacteria will respire the oxygen to eliminate its toxic effects on the cell. Iron oxide respiration relies on the Geobacter pili, a simple structure composed of a single peptide repeat. The pili concentrate on one side of the bacterial cell, where they connect the cell with the iron oxide to release the electrons that have been accumulating. The pili immediately depolymerize and retract, shedding the mineral before returning into the cell. Mass-producing pilin subunits in E. coli took a bit of trouble shooting, but now Reguera and her colleagues can make them on a much larger scale, which bodes well for expanding tests into electronic applications. Commercialization grants address the "valley of death," the chasm between the technologies developed at the bench and the scale of production necessary for industrialization. Geobacter can bind and reduce many minerals using their pili, including uranium and other toxic heavy metals like lead and cobalt. Using Geobacter pili in agricultural soils or aquaculture waters may help remove these contaminants and improve the health of these ecosystems. Featured Quotes: "I remember when I started as a microbiology student, I think I underappreciated the role that electrons and the movement of electrons play in microbiology." "There is absolutely not a single process in living organisms that is not energized by the movement of electrons." "The Earth didn't have oxygen for the first 2 billion years, if not longer - and there was life! On Earth! Those early organisms were really great at finding minerals, metals, just about anything other than oxygen to dump their electrons, continue to grow, and to colonize the Earth." "When you start comparing the structure and the amino acid composition of this subunit to any other known bacterial pilins, you really see 2 remarkable changes: one of them is the pilin of Geobacter is very small. the second is that little stick has aromatic amino acids. When the sticks come together to make the filament, they cluster very close to each other and create like a staircase for the electrons to move fast. It's like a magic combination in which you have the right structural reduction and the right amino acids to really fit like a puzzle to create paths for electrons." "What has always motivated me is learning something new." Links for This Episode: Gemma Reguera lab website Gemma Reguera interview on "People Behind the Science" HOM: Thirty-Second Annual Meeting of the Society of American Bacteriologists HOM: Barney Cohen: An Appreciation (Bacteriological Reviews memorial)

Why do Legionnaire's Disease outbreaks occur mostly in the summer? What is the connection of the Flint change in water source and Legionella outbreaks in the area? Michele Swanson discusses her work on Legionella pneumophila and her path from busy undergraduate to ASM President. Julie's Biggest Takeaways: Legionella pneumophila is a waterborne microbe that lives in fresh water and can colonize water systems of the built environment. Colonization of cooling systems, like those used in air conditioning systems, can lead to contaminated water droplets that can cause disease. Legionella are very adaptable to different environment, but scientists don't have great models to determine the exact preferences of the bacterium. After Flint switched water sources from lake to the Flint river, a chemical that prevents corrosion was omitted from the water treatment. This led to lead in the water, which was detected in pediatric patients. An increase of legionella cases in the two years also occurred, and the question was whether the outbreak was related to the shift in water chemistry. Michele joined a team of water engineers, epidemiologists and sociologists to answer this question, and the team found an association between low chlorine levels and high risk of legionella disease. Across the globe, more than 80% of disease is associated with L. pneumophila serogroup 1. The serogroup is based on the bacterial lipopolysaccharide (LPS) structure, which in this strain is very hydrophobic and may allow this serogroup to withstand a higher degree of desiccation than other strains. A urine-based diagnostic test works well, but only to detect serogroup 1. The strain isolated from patients of the Flint outbreak were serogroup 6, as were Legionella isolated from the homes of Flint residents. Featured Quotes: "Amoeba are very good at digesting bacteria, eating them for food, but Legionella, because it's been under this severe selective pressure of the amoeba, they've evolved tools to allow them not only to survive within the amoeba but to replicate within the vacuole of the amoeba." "We now have equipment that throws water into the air and gives [Legionella] a new opportunity to be ingested by a macrophage. It can then deploy the same tricks it uses to grow inside amoeba to grow inside the macrophage." "[Human infection] is a tragedy for the patient, but also for the microbe...humans are a dead-end for the bacterium." "I was really delighted to be recruited to work with this interdisciplinary team on a public health crisis here in my home state. It has opened my eyes to a much more complex pathway and I just feel really privileged in this stage in my career to be able to turn my attention to these larger public health issues." "People want to hear encouragement; we have a tendency to compare ourselves to those who are 5-10 years ahead of us. Encouragement really is valuable." Links for this Episode: Michele Swanson at the University of Michigan mBio: Prevalence of infection-competent Legionella pneumophila within premise plumbing within southeast Michigan PNAS: Assessment of the Legionnaire's disease outbreak in Flint, Michigan Microbial Sciences blog post: Examining Flint: New research highlights lack of Legionella public policy ASM membership

How is Toxoplasma gondii, a protozoan that causes neuro-invasive disease, transmitted as a foodborne pathogen? Why are cats important in transmitting Toxoplasma infection? Anita Koshy answer these questions and talks about her research on the latest Meet the Microbiologist. Julie's Biggest Takeaways: The primary host for T. gondii is cats, in which the protozoan can undergo sexual reproduction. Why cats? No one knows, in part because there isn't a good in vitro system to study cat epithelial cell interactions with T. gondii. Most warm-blooded animals, including birds, can be infected with Toxoplasma. Intermediate hosts can pass Toxoplasma from one to another if one eat these tissue cysts, explaining why Toxoplasma can be a foodborne pathogen. In healthy individuals, the immune response clears most fast-growing cells (tachyzoites) but some protozoans convert to a slow-growing cell form (bradyzoites). In people, these bradyzoites form cysts predominantly in the brain, the heart and the skeletal muscle. Some serological studies suggest a tie between Toxoplasma infection and brain disorders, but these are less definitive than causative studies in mice. Populations with high Toxoplasma or low Toxoplasma prevalence don't see a correlative incidence of disorders such as schizophrenia or Alzheimer's disease. Featured Quotes: "When we talk about neuroinfectious diseases, we're talking about the diseases that cause symptoms. Those that can get into the central nervous system and those that cause symptomatic disease are the same." "A parasite is sitting there dormant or maybe reactivating every so often and the immune system comes in and deals with that reactivation. But when you lack an immune system, all of a sudden when that parasite reactivates, there is no longer this immune system that will come in and clear it out." "What we don't know is whether reactivation occurs preferentially in the brain. There is evidence from HIV patients of inflammation of the heart or inflammation of the skeletal tissue - but those weren't the symptoms that presented, which were of the brain. Did reactivation happen in the brain, or did it occur elsewhere and the parasite was able to travel to the brain and there's no longer an immune system to clear it out?" Links for this Episode: Koshy Lab Site Sea Otter Infection with Toxoplasma Rats Infected with T. gondii Lose Their Aversion to Cat Urine HOM Tidbit: The History of Toxoplasma gondii Bill Hutchinson obituary

Jennifer Gardy talks about whole-genome sequencing as a technique to address public health issues using genomic epidemiology. She talks about her research on TB and new DNA sequencing technologies, including her vision for microbial genetic sequencing as one piece of the puzzle in the future of public health. Julie's Biggest Takeaways: Whole-genome sequencing technologies are replacing older DNA technologies to identify relatedness between microbial isolates. The genome sequences help to identify epidemiological questions such as the origins of an outbreak. A pathogen's genome being passed person-to-person accrues small changes, similar to children playing telephone - except those children are scattered around the room, and you have to logically deduce the order in which the information was passed. DNA sequencing has moved forward faster than the upstream genomic preparation and downstream sequence analysis areas; Gardy expects advances in these 'bookend' areas to be breakthroughs of the future. The Ebola and Zika outbreaks were test cases for portable DNA sequencing technologies, but informative based on the different disease presentation: Ebola patients have high viral loads and thus a lot of genomic material, but Zika patients have much lower viral loads and it was much harder to get samples. Based on pathogen characteristics, DNA sequencing can identify the end of an outbreak. Gardy used sequencing to find that patients with TB, which can take years to develop into fulminant disease, had been infected years previous, and was able to see that transmission was no longer ongoing. Featured Quotes: "Genomics is really cool because instead of interviewing people about what happened in an outbreak, we're interviewing the pathogen!" "[Working at BCCDC] is a really nice ecosystem, where you can really see the results of your research changing public care policy and practice in real time, and that is incredibly rewarding." "The only prediction you can make about DNA sequencing is there's always going to be something new and different." "Depending on your use-case, sometimes you need to go after the whole genome and other times a targeted approach is more than enough." "I'm excited to see how this [microbial DNA sequencing] work fits in into an overall public health landscape. It's cool to sequence genomes and make some reports about transmission networks, but that's just one small part of a very big public health system that is trying to keep populations healthy. It requires so many different people, from nurses and doctors on the frontline to policy makers behind the scenes to social scientists who are interacting with patients or care providers to people that are understanding the economics of these things... when you start to see how these different pieces of the puzzle fit together, I think there's a lot of opportunities in the future for making microbial genomics just one piece of a large interdisciplinary puzzle of people that are working together across different fields to address a disease from multiple different angles." Links for This Episode: Jennifer Gardy's website Jennifer Gardy at UBC Nanopore Minion Alan Alda Center for Communicating Science Banff Science Communications HOM Tidbit: Albrecht Kossel, a Biographical Sketch

See the full shownotes at: asm.org/mtm Julie Pfeiffer tells the story of how she serendipitously found a role for the gut microbiota during polio virus infection, and how she and her lab discovered an important role for bacterial glycans in viral biology. She also talks about viral fitness strategies, and how RNA viruses and DNA viruses benefit from making different amounts of errors when copying their genomes. Julie's biggest takeaways: Determining the exact nature of the glycans that play these roles has been difficult because they are very complex. Aspects of lipopolysaccharide, chitin, and peptidoglycan are all sufficient to bind the viral capsid, but because of their structural complexity, it's difficult to pinpoint the exact molecular interaction. Bacterial glycan interactions with viruses benefit the virus in two ways: the virus can be delivered to a host cell it will infect, and the viral capsid is stabilized. Whether there is a benefit to the bacterium during these interactions is unknown, but is an active area of research in Julie's lab. Many viruses can be inactivated at body temperature or even room temperature if they prematurely release their genetic material. Polio viruses are simply a protein shell surrounding an RNA genome, and the capsid can 'breathe,' slightly changing its conformation. Sometimes, the genome is accidentally released, resulting in a viral dead end. Julie showed that bacterial glycans will lock the capsids into a conformation and prevent genome release from happening until the virus encounters a host cell. Julie is a proponent of clear communication, including with those working in similar fields, which she learned from her experience as a postdoctoral fellow. She and a postdoc in a different institution, Marco Vignuzzi, independently isolated a polio virus mutant that made fewer in genome replication. Both showed that the virus had a defect during mouse infection, indicating that the ability to introduce errors during genome replication is beneficial to viral fitness. Julie and Marco finally met at a viral evolution conference, after which they became close friends. Featured Quotes (in order of appearance): "I get more excited about a surprising result because it probably means there's some interesting underlying biology that couldn't be anticipated!" "We've done many gross experiments, so buyer beware; you've got to know what you're getting into [with a fecal-oral pathogen]." "The infectious unit may be more complicated than we think!" "Communicating with people you know working on similar things can be mutually beneficial for everyone: you both get credit; nobody gets scooped. It's win-win for sure." "The truth is most enteric viral infections are self limiting in most healthy individuals so you're much better off trudging through a day or two of gastrointestinal illness than blowing up your microbiota." Links for this episode Julie Pfeiffer website at UT Southwestern Medical Center Back-to-back Science publications from Golovkina and Pfeiffer PLOS Pathogens: The importance of model systems: Why we study a virus on the brink of global eradication Viruses and Cells Gordon conference (donate here) HOM Tidbit: Michael Underwood's A Treatise on the Diseases of Children

Pete Greenberg tells how bacteria can communicate based on cell density, a phenomenon he helped name quorum sensing. He talks about therapeutics based on quorum-sensing discoveries, and how studying bacterial interactions can be used to test ecological principles like cooperation and social cheating. Julie's biggest takeaways: Quorum sensing can be likened to an old-fashioned smoking room, where a few cigar smokers don't affect the air quality, but as more smokers enter the room, it becomes beneficial to the group to open the window: a changed behavior that benefits the group environment. Differentiating waste molecules from signaling molecules is important to define specific quorum sensing. The experimental evidence that shows that molecules serve as quorum sensing signals that allow bacteria to respond at high density comes from social engineering experiments to identify 'cheaters.' Quorum sensing results in changes in gene expression that benefit the community but not necessarily individual cells. An example is antibiotics, which when made by a single cell aren't at a high enough concentration to kill competitor microbes. As a group, all cells working together can produce a cloud of antibiotic that may be able to protect from competitors. The ability of microbes to receive or 'eavesdrop' on the signals produced may be cooperative, but is more likely competitive, giving the eavesdropper a competitive advantage by informing them about another species' presence. If you knock out quorum sensing, you get abnormal biofilms, but it doesn't ablate biofilms completely. Although a self-described disinterested high-school student, Greenberg signed up for a weekend field trip to get out of a test on a Friday. It was looking at animals in the intertidal bay of the Pacific Northwest that inspired him to be a biologist! Greenberg also credits his broad biology undergraduate training for preparing him to apply socioecology concepts to bacteria. Quorum sensing was originally called 'auto induction.' In the early 1990s, Greenberg was writing a minireview for the Journal of Bacteriology and wanted to think of a catchy title. As Greenberg remembers, coauthor Steve Winans explained the concept to his family, and his brother-in-law said "it's like the bacteria need a quorum" - the birth of the term 'quorum sensing.' Featured Quotes (in order of appearance): "So-called 'cheaters' don't respond to the signal, they've lost the ability to respond to the signal. The product that's useful for the common good any more. They don't pay the cost of cooperation but they can benefit by the cooperative activity of everyone else in the community...there's a fitness advantage for cheaters in this environment." "It's a real case of convergent evolution. It's important that the bacteria can do this, and these two really distinct types of [gram-positive and gram-negative] bacteria have evolved completely different mechanisms to perform quorum sensing." "I think of bacteria as a way to study what is called 'Darwin's dilemma.' If a cheater emerges among a population, it will have a fitness advantage over the population of cooperators. It should take over the population and ultimately cause the tragedy of the commons, where there are too many cheaters and not enough cooperators and the whole system collapses. Darwin's dilemma is: how is cooperation stabilized? We know it exists and it seems like it shouldn't - we can use bacteria to get at the rules." "I got interested in [quorum sensing] because it was so cool!" "I had this idea, as we began to unravel quorum sensing in these marine luminescent bacteria, that any idea in biology that's a good idea will occur more than once - but I didn't have any evidence of that. For 15 years, my lab and essentially one other lab, Mike Silverman's lab, were the only labs working on this. It was really the early 90s when our group and other groups started to realie that lots of bacteria do this. It's one of those fantastic oddesies. It's luck - luck and hard work, I guess. Hard work by the people in my lab as I sit around as watch!" "It's funny how a term can catch on and sort of crystallize a field! But somehow, it seemed to do that. I've gotten really into trying to think of catchy terms since then, and the latest one is 'sociomicrobiology,' which I introduced with Matt Parsek about 12 years ago and there's a burgeoning field called sociomicrobiology. I'm trying to think of another term now, before I retire!" Links for this episode Pete Greenberg lab at the University of Washington Pete Greenberg 2004 PNAS bio Journal of Bacteriology minireview: Quorum Sensing in Bacteria HOM: Woody Hastings memoriam ASM Podcasts Send your stories about our guests and/or your comments to [email protected].

Charlie Rice gives the history of learning to grow hepatitis C virus in culture, from pitfalls to hurdles and successes along the 20-year journey. He also talks about yellow fever virus, its vaccine, and the importance of curiosity-driven research

How are new diseases detected in a clinical microbiology lab? Melissa Miller talks about the time it takes to develop a test for a new disease (hint: it's getting shorter). She also shares her definition of 'point-of-care' diagnostics and explains the major trends for clinical microbiology labs. Host: Julie Wolf Subscribe (free) on iPhone, Android, RSS, or by email. You can also listen on your mobile device with the ASM Podcast app. Julie's biggest takeaways: Antibiograms are vital to understand the resistance characteristics of locally circulating disease strains. These help make empirical decisions for antibiotic therapy regimens before the susceptibility test results are available. New diseases require new diagnostic tests. How to determine how well new tests work once they're developed? Clinical microbiologists look to the sensitivity (how well does a test detect if a patient has a disease) and specificity (how often is the test negative if the patients doesn't have it) of the test. Having access to positive controls (that is, samples from a patient known to have the disease) can prove difficult in some settings, such as in North Carolina, where no Zika patients were admitted while the Zika virus test was being developed. When the HIV epidemic was beginning, it took several years after the HIV virus was identified to sequence its genome and use this for molecular testing. In 2002-2003, it took just over a month to get the SARS genome sequence for use in developing assays. It's even quicker today; within a week, we can have sequences from viruses around the world. Defining 'point-of-care' testing took an entire hour at a recent American Academy of Microbiology colloquium! Melissa's take: It's a test that can be done at or near to where the patient is. Point-of-care tests are exciting but can also pose challenges. A recent example is false-positive pertussis tests that were shown to be due to pertussis vaccine being administered nearby. Ensuring the tests are used safely and accurately will best serve healthcare workers and patients alike. Molecular diagnostics have two trends: one trend simplifies existing technologies into point-of-care tests. The other trend adds complexity, by applying next-generation sequencing techniques in a reproducible manner. Featured Quotes (in order of appearance): "Laboratorians are often in the basement or in a setting where they aren't visible to the healthcare team, but they're very vital to taking care of the patient." "When you're using laboratory-developed tests, the way it works in one laboratory may be very different from how it works in another laboratory." "The ultimate goal [of point-of-care testing] is to get a result that's actionable. We don't need to do tests that aren't going to result in a clinically actionable decision." "In many ways, the technology is ahead of where our quality assurance protocols are." "I think it's going to be very important in going ahead that we continue to have laboratorians involved in developing these point-of-care programs and consulting to these sites, helping to make sure that there are policies and procedures that ensure quality results for their patients." "It's one thing to do it in a research setting; we've collaborated with a number of folks using next generation sequencing. But to then move it to the clinical lab and have it be reproducible and have the quality at the level you need for a clinical lab is a completely different challenge." Links for this episode Melissa Miller University of North Carolina Website Division of Clinical Laboratory Science at University of North Carolina Searchable List of Clinical Laboratory Science Programs AAM Colloquium Report on Point-of-Care Testing CPEP Program Career Blog: Tips on becoming a clinical microbiology laboratory director HOM Tidbid: Papagrigorakis 2006 International Journal of Infectious Diseases report HOM Tidbit: Shapiro reply to Papagrigorakis report Send your stories about our guests and/or your comments to [email protected].

Veterinarian and epidemiologist Mathew Muturi tells how a Rift Valley Fever outbreak led to implementation of One Health-based policies. Muturi talks about his One Health training and its applications for health and biopreparedness. Julie's Biggest Takeaways: One Health Simple communication between experts helps facilitate implementation of one health in public systems. Sitting experts in human and animal health in the same office allows easier communication between these different health sectors. One Health policies involving close collaboration between animal and human healthcare workers were first implemented in Kenya in response to the threat of avian influenza, but were discontinued after the threat waned. Human cases of Rift Valley Fever, due to spillover from a livestock outbreak, led to the discovery that these collaborative policies could prevent other outbreaks as well, and the policies were reinstated. Zoonotic diseases can often be the most overlooked. Officials of countries where endemic diseases are present may have preparedness plans for serious cases but may overlook something endemic like brucellosis. There are 42 subtribes in Kenya, including diverse languages, religions, and beliefs. Public health interventions do their best to align the local beliefs of the people to minimize risk of pathogen exposure. Featured Quotes: "One health is not a new concept; it's an old concept that explains the health of humans, animals, and the environment is interconnected. It's a concept that plays out in everyday life." "One of the reasons One Health has been able to be successful in Kenya, and that I suggest to other countries wishing to implement this program, is the sitting together, talking together. Make sure that you work together, see each other - I don't think communication works well enough if it's on an ad hoc basis. The thing that has worked for us is sitting together." "The most important aspect of One Health is the fact that that it's impossible to control diseases that come from animals only by focusing on humans. It's like trying to concentrate on putting out fires without ascertaining where the fires are coming from." "Endemic diseases, despite the fact that they're ever-present, are often the most ignored." "A lot of the risk practices are cultural, and cultural change is very slow." "The value of One Health is much more than the investment required to put into it. It's one of the few things I've seen actually work in implementation of disease control strategies, in surveillance and in general disease control. It's worked for Kenya and I believe it can work for all other countries." Links for the episode: Republic of Kenya Zoonotic Disease Unit Prioritization of Zoonotic Diseases in Kenya, 2015. Plos One.

Dave Rasko uses comparative bacterial genomics to find DNA sequences that influence virulence or antibiotic resistance. Dave talks about his studies of E. coli, Acinetobacter baumanii, and B. anthracis, and the state of bacterial genomics past, present, and future. Host: Julie Wolf Subscribe (free) on iPhone, Android, RSS, or by email. You can also listen on your mobile device with the ASM Podcast app. Julie's biggest takeaways: Genome sequencing speed has significantly increased: The first bacterial genome sequenced, Haemophilus influenzae, took about 10 years to complete. The first organism with two sequenced genomes was Helicobacter pylori, published in 1999, and the first organism with three published genomes was Escherichia coli. Rasko's initial project at TIGR to sequence 11 E. coli genomes took about 2 years. Today, Rasko's lab can sequence 500 genomes in about five days. In E. coli, up to half of the genome can differ between two strains. The core genome is the collection of genes that will be shared among all isolates of a particular species. Core gene conservation varies among species and is important to consider in analyses for one's species of interest. Working on the Amerithrax investigation was unlike many other scientific inquiries for many reasons, including that the Federal Bureau of Investigation only gave the scientists involved the information pieces necessary to conduct their studies. Rasko and collaborators sequenced the genomes of spores within the samples, and found that the morphology of the colonies that grew were associated with genetic differences between the spores within the sample, linking phenotype and genotype. While comparative genomics can provide a lot of information, there are some phenomena that will always require further study. For example, Rasko is researching isolates of A. baumanii and Klebiella pneumoniae that quickly develop drug resistance when grown in sub-inhibitory drug concentrations. The genomic sequences of resistant or susceptible strains show no difference in DNA sequence, suggesting the phenotype is due to transcriptional changes. Featured Quotes (in order of appearance) "Genomics is fun in that we can hypothesize all day long, every day. It's really the start of a lot of very very hard work figuring out why." "There's a lot of DNA pieces that we don't fully understand how they moved, where they moved, where they came from. In some cases, there's evidence to say where they came from; in terms of G-C content and coding biases, we can make some assumptions, but in the grand scheme of things, we have no idea where they're coming from! In some cases, we'll see them dominant throughout a lineage, and in some cases we'll see them in sporadic isolates around the entire phylogenetic tree. . .We all thought genomics was going to solve so many problems, and it's really just made it more difficult!" "Plasmids tend to be mobile and exchangeable, and the pieces tend to be - I tend to think of them as legos, in the fact that you can put a plasmid together in a bunch of different ways." "I think a lot of conventional PCR fails and people assume that it's because it's negative, and not necessarily that it fails because of diversity." "Many microbiologists think of that colony on a plate as a clone. I force the people in my group to think about it a little differently, because it's really what I like to call 'genome space'. They're not all the same; bacteria are constantly evolving. There's changes all the time, some of them are positive, some of the are negative, the negative ones get lost, the positive ones unusually become dominant - and then there's lots of neutral changes that just kind of hang out." "Genomes really normalized everything. Before that, there were certain labs that could clone and there were certain labs that could sequence, and it was a little bit restrictive to the elite labs who had those resources. Now with the genome sequences out there, everyone was starting from the same place." "You really have to understand your organism to make the bioinformatics work." Links for this episode Rasko lab at the University of Maryland FBI summary of Amerithrax investigation 2011 PNAS report on B. anthracis comparative genomics Bugs N the 'hood HOM Tidbit: Stanley Falkow gives both video history and written history of plasmid biology Save on Microbe 2018, use code: asmpod Send your stories about our guests and/or your comments to [email protected].

Bill Jacobs talks about developing mycobacterial genetic tools and using them to discover ways to shorten TB treatment. He also talks about the SEA-PHAGES program that allows high-school students to participate in phage discovery. Host: Julie Wolf Subscribe (free) on iPhone, Android, RSS, or by email. You can also listen on your mobile device with the ASM Podcast app. Julie's biggest takeaways: The challenges of working with an easily aerosolized bacterium are aided by complementary studies on a noninfectious relative. M. smegmatus doesn't colonize mammals and grows slower, giving researchers the opportunity to acclimate themselves to working with mycobacterial cultures. Jacobs was the first scientist to introduce DNA into M. tuberculosis using a phasmid - part plasmid, part mycobacterial phage. The first phage came from Jacobs' dirt yard in the Bronx, so he named it BxB1 for the Bronx Bomber. Another phage, TM4, became the workhorse phasmid when Jacobs cloned an E. coli cosmid sequence into a nonessential part of the phage genome. It replicates in E. coli as a plasmid but becomes a phage inside Mycobacteria, facilitating manipulation. The shuttle phasmids allowed transposon delivery to make transposon libraries, and the creation of gene knockouts. To this day, we use Ziehl-Neelsen staining to differentiate acid-fast mycobacteria from gram-positive or gram-negative bacteria - the mycolic acids on the outer part of the envelope make up some of the longest microbial lipid chains. But mycobacteria can regulate its acid-fast positive or negative status; the acid-fast negative organisms are a persistent population that are often ignored inside of patients. 99.99% of M. tuberculosis bacteria are not persistent, but the last 0.1% have entered into a persistent state expressing many stress proteins that help them become refractory to killing. A normal course of antibiotic chemotherapy for patients is six months. If infected with a strain resistant to the two frontline drugs, that time goes up to two years. The problem is even greater in extremely multidrug resistant (XDR) strains. What we really need is a way to understand persistence and a way to shorten chemotherapy. That's why were were absolutely amazed when we discovered that cysteine with isoniazid completely sterilizes Mtb cultures in vitro and in vivo! The culture is sterilized because the bacteria can't form persisters. Vitamin C co-treatment with antibiotics may lead to a shortened course of therapy for TB treatment. Neutralizing antibodies to the herpesvirus glycoprotein have been the dogma for protecting from herpes. Jacobs and his colleagues discovered that a vaccine based on a glycoprotein-knockout virus confers sterilizing immunity not through neutralizing antibodies but through antibody-dependent cell cytoxicity (ADCC). This ADCC response may also be important to develop a more effective TB vaccine. Featured Quotes (in order of appearance): "You'll never know how bad your aseptic technique is until you start working with tuberculosis!" "I think part of the reason I had the opportunity to develop genetics for TB - it's not like it wasn't important to do - but a lot of people were disappointed when working with the organism." "We're about to take TB genetics to where yeast genetics is." "One of the tubicle bacilli's greatest powers or one of its most important phenotypes is that it has the ability to persist, which means it has the ability to tolerate killing effectors, either killing by the immune system or killing by bactericidal drugs." "I took students to the Bronx Zoo, and over by the zebra pen, I sniffed and said 'I smell a phage!' In fact, that's not crazy - anyone who plants flowers knows what good soil smells like, and in the good soil, you're smelling the bacteria that live in the soil, the Streptomyces and Mycobacteria. I reached down and grabbed that dirt, and when we went back to work we isolated BxE1." "I've never met a phage I wasn't excited about!" "I now believe that most pathogens do not 'want' ADCC antibodies to be made, and they have immune evasion strategies where they skew the immune response to get the wrong antibodies. Since the time we published our first paper, numerous groups have shown that correlates of protection for HIV, for influenza, and for Zika, turn out to be ADCC antibodies." "Genetics is the mathematics of biology!" Links for this episode Bill Jacobs lab site NYTimes story on 1993 rapid diagnostic test using luciferase AACJournal: Vitamin C potentiates the killing of Mycobacterium tuberculosis by the first-line tuberculosis drugs isoniazid and rifampicin in mice Cell: Origins of highly mosaic mycobacteriophage genomes SEA-PHAGES program eLife: Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity mBio: Dual-reported mycobacteriophages (Φ2DRMs) reveal preexisting Mycobacterium tuberculosis persistent cells in human sputum Tuberculosis - Its cause, cure an

Ilaria Capua talks about running an internationally renowned animal influenza lab, and her time spent in the Italian Parliament. Accused of virus trafficking as part of a national scandal, she has since cleared her name and speaks here about the importance of scientific credibility and reputation.

Most bacteria live a sedentary lifestyle in community structures called biofilms. Vaughn Cooper tells us what bacterial biofilms are, why biofilms differ from test tube environments, and how long-term evolution experiments combined with population genomics are teaching us how bacteria really work. He also discusses using hands-on bacterial evolution activities to introduce high schoolers to future STEM possibilities. Host: Julie Wolf Subscribe (free) on iPhone, Android, RSS, or by email. You can also listen on your mobile device with the ASM Podcast app. Julie's biggest takeaways: Cells in a biofilm shift to dedicate their resources to protection rather than reproduction. This allows biofilms to be innately more resistant to antibiotics than those growing in planktonic culture. One of the least-understood parts of a biofilm cycle is the dispersal stage. What cues or signals influence some biofilm-embedded cells to leave? This is a vital part of biofilm formation, since these dispersal cells can eventually attach to a new surface and restart the process of forming a biofilm. The bead system of biofilm propagation allows Vaughn and his colleagues to study the long-term evolution of biofilms. This system, combined with population genomics, allows the study of all the different genetic changes within the population. Traditional genetic screens compare libraries of mutants to see which survive under different conditions. Rather than on libraries of mutant strains, evolution works on random mutants that arise naturally. The accessibility of sequencing technologies has changed the way scientists study evolution, as now the mutations can be found as they form, rather than being seeded into the initial mutant library screen. High schoolers using nonpathogenic bacteria can study evolution in action by developing new colony morphologies. Work with high schoolers and their teachers has shown students who do hands-on learning do better on standardized tests and that girls, especially, express higher interest in technology and an interest in STEM careers after a 1-2 week project. Featured Quotes (in order of appearance) "From a perspective of an ecologist and evolutionary biologist, this is what captivated me about biofilms: that instantly in the process of forming a biofilm, the environment becomes heterogeneous. Different cells that are clone mates are experiencing different selective pressures." "The hypothesis that we've been testing for the last 15 years or so is that biofilms in and of themselves may generate ecological and heritable evolutionary diversity in really short periods of time." "In describing the wrinkled Pseudomonas colonies that can stem from biofilm cells: "I think they look like hydrangeas, and some look more like doilies. I think they're captivating and pretty charismatic as far as microbes go." "The average bacteria picked from any environment does an unbelieveably good job of protecting its genetic material. The per-cell mutation rate, per-genome, per-generation rate is about 1 in 1000 cells. So a bacterial cell needs to divide about 1000 times to create a single mutant. That means that mutations are actually relatively scarce, but bacterial populations are extraordinarily immense. If you grow a single cell to 108 cells, you've got about 105 new mutations. That's a pretty large number. Some of them, maybe a handful, maybe 1/100 of those 105 mutations, which would be about 1000, would be beneficial. Then selection will act on them, and the better ones will rise more quickly because they make more progeny. And that's evolution in action!" "Increasingly, we're using evolution to teach us about how the organism works." "I'm not saving lives with any of our studies on microbes in biofilm-associated infections just yet. We are seeing how they change in these infection and how they become more drug resistant. That's great, and I think that's a valuable contribution. But when we can encourage hundreds of high schoolers to really consider careers in the life sciences or mathematics or engineering, we're changing lives." Links for this episode Vaughn Cooper University of Pittsburgh website Rich Lenski Long-Term Evolution Experiment ASM video Journal of Bacteriology cover featuring Pseudomonas colonies Journal of Bacteriology report on the evolution of Pseudomonas biofilm diversity Journal of Bacteriology tribute to Bill Costerton Bill Costerton YouTube interview Send your stories about our guests and/or your comments to [email protected].