Meet The Microbiologist - The Scientists Behind The Microbiology

Dr. Wun-Ju Sheih, worked as a pathologist and infectious diseases expert with the CDC from 1995-2020. He recounts his experiences conducting high risk autopsies on the frontlines of outbreaks including Ebola, H1N1 influenza, monkeypox and SARS-CoV-1 and 2. He also addresses key questions about factors contributing to the (re)emergence and spread of pathogens and discusses whether outbreaks are becoming more frequent or simply more widely publicized. Ashley’s Biggest Takeaways: • Pathologists are a group of medical doctors serving behind the line of the daily hospital activities. • Pathology service can be divided into atomic pathology and clinical pathology. The field covers all the laboratory diagnostic work in the hospital, and clinical microbiology or medical microbiology is actually a subdivision within the clinical pathology service. • Usually, a pathologist working in a hospital will examine and dissect tissue specimens from surgery or biopsy. • The pathologist also performs autopsies as requested to de

Dr. Linden Hu, Vice Dean for Research at Tufts University in Boston Massachusetts and Paul and Elaine Chervinsky Professor in Immunology, discusses new and ongoing research pertaining to the prevention, treatment and diagnosis of human Lyme disease. He also discusses some of the key unanswered questions about Lyme, such as how B. burgdorferi adapts to different hosts and environments and why some patients have been known to exhibit persistent symptoms even after treatment.   Links mentioned: Webinar - Vector-Borne Disease in a Changing Climate https://asm.org/Webinars/Vector-Borne-Disease-in-a-Changing-Climate The Bulls-Eye Rash of Lyme Disease: https://asm.org/Articles/2018/April/going-skin-deep-investigating-the-cutaneous-host-p Pfizer and Valneva Initiate Phase 3 Study of Lyme Disease Vaccine Candidate VLA15 https://www.pfizer.com/news/press-release/press-release-detail/pfizer-and-valneva-initiate-phase-3-study-lyme-disease Could This Treatment Prevent Chronic Lyme Disease? https://news.northeastern.e

Dr. Mark O. Martin, Associate professor of biology at the University of Puget Sound in Tacoma, Washington is a distinguished educator with a well-known social media presence. He discusses how he became interested in microbiology and what drives his varied research foci, including #Microbialcentricity, bacterial predation, bioluminescence, tardigrades, microbial midwives and more. In the process, he delves into his passion for using art and other creative approaches to facilitate learning in the classroom, and shares some experience-driven wisdom about building confidence in STEM. Links for this Episode: Vertically transmitted microbiome protects eggs from fungal infection and egg failure https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-021-00104-5 The effects of Sceloporus virgatus cloacal microbiota on the growth of pathogenic fungi https://soundideas.pugetsound.edu/summer_research/426/ Sex-specific asymmetry within the cloacal microbiota of the striped plateau lizard, Sceloporus virgatus

Dr. Elizabeth Dinsdale, Matthew Flinders Fellow in Marine Biology in the College of Science and Engineering at Flinders University in Adelaide, Australia, uses genomic techniques to investigate the biodiversity of microbial communities in distinct ecological niches, including coral reefs, kelp forest and shark epidermis. She discusses how shotgun metagenomics is being used to characterize the architecture of microbial communities living in the thin layer of underlying mucus on shark’s skin, and how understanding the function of these microbes is providing clues to important host-microbe interactions, including heavy metal tolerance. Ashley’s Biggest Takeaways: Sharks belong to a subclass of cartilaginous fish called elasmobranchs and are unique in that their epidermises are covered in dermal denticles—overlapping tooth-like structures that reduce drag and turbulence, helping the shark to move quickly and quietly through the water. These dermal denticles are sharp (if you’re going to pet a shark, make sure you

Dr. Mallory Choudoir, microbial ecologist and evolutionary biologist at the University of Massachusetts Amherst shares how she leverages microbial culture collections to infer ecological and evolutionary responses to warming soil temperatures. She discusses complexities of the soil microbiome and microbial dispersal dynamics, and introduces fundamental concepts about the intersection between microbes and social equity. Ashley’s Biggest Takeaways: Microbial culture collections are fundamental resources, serving as libraries where diverse species of microbes are identified, characterized and preserved in pure, viable form. Culture collections ensure conservation of species diversity and sustainable use of the collected microbes. For soil microbiologists, like Mallory Choudoir, culture collections provide the opportunity to connect patterns of genomic variation and microbial physiology to the conditions under which a particular microbe was isolated. Soil is a complex environment from the perspective of a microbe

Peter Hotez talks about the global impact and historical context of neglected tropical diseases. He also highlights important developments in mass drug administration and vaccine research and shares why he chose to publish the third edition of Forgotten People, Forgotten Diseases during the COVID-19 pandemic. Ashley's Biggest Takeaways Neglected Tropical Diseases (NTDs) are chronic and debilitating conditions that disproportionately impact people in low- and middle-income countries (LMICs).  Many of these diseases are parasitic, such as hookworm infection, schistosomiasis and chagas disease; however, in recent years, several non-parasitic infections caused by bacteria, fungi and viruses, as well as a few conditions that are not infections, including snake bite and scabies (an ectoparasitic infestation), have been added to the original NTD framework (established in the early 2000s).  What do most NTDs have in common? High prevalence. High mortality; low morbidity. Disabling. Interfere with people’s ability to

Rita Colwell has made major advances in basic and applied microbiology, largely focused on Vibrio cholerae. She describes several lines of evidence for the environmental niche of the bacterium, as well as her work to predict and prepare for cholera outbreaks. Colwell closes with her thoughts on why it’s a great time to be a microbiologist.

Denise Akob discusses her studies of microbial communities of contaminated and pristine environments using life science and earth science techniques. She discusses how to figure out “who’s there,” how to optimize select natural microbial activities, and her career path into government research. Julie’s Biggest Takeaways: Biogeomicrobiology straddles the life science and earth science fields. This is a growing area of research in the academic setting as well as in the private sector, where one can contribute to hydrogeology or bioremediation efforts.   What happens on the surface when extracting resources like natural gases? Wastewater from hydraulic shale fracking, or fracking, can contaminate microbes. Preliminary data suggests that microbes that thrive in that wastewater can be a fingerprint for surface contamination, and this is one of the areas of active research in Akob’s lab. Additionally, microbes can respond to contaminants to remove that risk and remediate the spills. One trip to the field can provid

How does tick biology influence their ability to transmit disease? Marshall Bloom explains the role of the tick salivary glands in Powassan virus transmission and the experiments that led to this discovery. He also provides a historical background for the Rocky Mountain Labs in Hamilton, Montana, and talks about the 3 elements to consider when working with potentially harmful biological agents. Subscribe (free) on Apple Podcasts, Google Podcasts, Android, RSS or by email. Julie’s Biggest Takeaways There are 3 elements to consider when working with potentially harmful biological agents: Biosafety: protecting the laboratory workers from the infectious agents in the lab. Biocontainment: protecting the community by keeping the infectious agent contained within the facility. Bioassurity: protecting the individual by ensuring those working with infectious agents are capable to do so. You need 4 bites of an APPLE for full lab safety, for work in labs from high school level through biosafety level 4: A: Administ

What kinds of microorganisms can degrade oil? How do scientists prioritize ecosystems for bioremediation after an oil spill? Joel Kostka discusses his research and the lessons from the Deepwater Horizon oil spill that will help scientists be better prepared for oil spills of the future. Links for this Episode: Joel Kostka Lab Website Kostka J. et al. Hydrocarbon-Degrading Bacteria and the Bacterial Community Response in Gulf of Mexico Beach Sands Impacted by the Deepwater Horizon Oil Spill. Applied and Environmental Microbiology. 2011. Shin B. et al. Succession of Microbial Populations and Nitroget-Fixation Associated With the Biodegradation of Sediment-Oil-Agglomerates Buried in a Florida Sandy Beach. Scientific Reports. 2019. Bociu I. Decomposition of Sediment-Oil-Agglomerates in a Gulf of Mexico Sandy Beach. Scientific Reports. 2019. Overhold W.A. et al. Draft Genome Sequences for Oil-Degrading Bacterial Strains from Beach Sands Impacted by the Deepwater Horizon Oil Spill. Genome Announcements. 2013. G

How do arboviruses evolve as they pass between different hosts? Greg Ebel discusses his research on West Nile virus evolution and what it means for viral diversity. He also talks about using mosquitos’ most recent blood meal to survey human health in a process called xenosurveillance. Julie’s Biggest Takeaways: Mosquitoes and other arthropods have limited means of immune defense against infection. One major defense mechanism is RNA interference (RNAi). RNAi uses pieces of the West Nile viral genome to select against the viral genome, which helps select for broadly diverse viral sequences. The more rare a viral genotype, the more likely it is to escape negative selection inside the mosquito host, allowing this viral sequence to increase in frequency.  West Nile virus passes largely between birds and mosquitos. Culex mosquitos tend to prefer birds, and this leads to an enzootic cycle for the virus passing between birds and mosquitos. The viral life cycle inside the mosquito has several important steps:  The vi

How can the intricate relationship between soil microbiota and plants be managed for improved plant health? Linda Kinkel discusses new insights into the plant rhizosphere and the ways that some Streptomyces isolates can protect agricultural crops against bacterial, fungal, oomycete, and nematode infections. Julie’s Biggest Takeaways: The soil microbiome is extremely dynamic, with boom-and-bust cycles driven by nutrient fluxes, microbial interactions, plant-driven microbial interactions, and signaling interactions. Finding the source of these boom-and-bust cycles can help people to manage the microbiome communities and produce plant-beneficial communities for agricultural purposes.  Rhizosphere soil is soil closely associated with the root and is distinct from rhizoplane soil that directly touches the root. The endophytic rhizosphere are those microbes that get inside the root. Many scientists view these communities as a continuum rather than sharply delineated. Plants provide necessary carbon for the largely

Pathogenic E. coli are different than lab-grown or commensal E. coli found in the gut microbiome. Alfredo Torres describes the difference between these, the method his lab is using the develop vaccines against pathogenic E. coli, and how this same method can be used to develop vaccines against Burkholderia infections. Julie’s Biggest Takeaways: coli plays many roles inside and outside the scientific laboratory: Laboratory E. coli strains used by scientists to study molecular biology. Commensal E. coli strains contribute to digestion and health as part of the intestinal microbiome. Pathogenic E. coli strains have acquired factors that allow them to cause disease in people The pathogenic E. coli associated with diarrheal disease are the ones named for their O-antigen and flagellar H-antigen, such as O157:H7. There are about 30 E. coli strains with various combinations of O-H factors known to cause diarrheal disease in people.  The E. coli Shiga toxin (though not the bacterium itself) can pass through the ep

Does the fetus have a microbiome? How does the placenta prevent infection? Carolyn Coyne talks about placental structure and biology, and why studying the maternal-fetal interface remains a critical area of research. Julie’s Biggest Takeaways: The placenta forms within 3-5 days post conception as a single layer of cells surrounding the fertilized embryo. These cells differentiate and develop into more complex structures. Very few microbes cause fetal disease. Of those that do, the disease-causing microorganisms are diverse and can lead to serious congenital defects or even death of a developing fetus. These microbes are largely grouped into the TORCH (now TORCH-Z) microorganisms: Toxoplasma gondii Other (a variety of different bacteria and viruses) Rubella Cytomegalovirus Herpesviruses Zika virus The fetus is immunologically immature and unable to protect itself. Some of the maternal immunological molecules (such as maternal antibodies) cross the placenta to protect the fetus, but that only happens during l

Are there drugs that can treat coronaviruses? Timothy Sheahan talks about his drug discovery work on a compound that can inhibit all coronaviruses tested so far, and tells how his career path  took him to pharmaceutical antiviral research and then back to academia. Julie’s Biggest Takeaways: Even though the MERS-CoV was discovered as a human pathogen in 2012, it was likely percolating as a disease agent for a long time before that. Banked camel serum provides evidence that the virus had been circulating in camels for several decades prior. Differentiated ex vivo lung cultures allow study of virus infection in a 3D model representation for studying viral infection, including target cell types of both MERS-CoV and SARS-CoV. SARS-CoV prefers ciliated epithelial cells Ace2 MERS-CoV prefers nonciliated epithelial cells DPP4 Coronavirus disease in people takes place over a course of about 2 weeks. In mice, the disease is similar, but progression is faster, taking about 1 week.  The drug remdesivir (RDV) is a nucl

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

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 signi

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 Bacteri

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