Meet The Microbiologist
Who is microbiology? Meet the Microbiologist (MTM) introduces you to the people who discover, innovate and advance the field of microbiology. Go behind-the-scenes of the microbial sciences with experts in virology, bacteriology, mycology, parasitology and more! Share in their passion for microbes and hear about research successes and even a few setbacks in their field. MTM covers everything from genomics, antibiotic resistance, synthetic biology, emerging infectious diseases, microbial ecology, public health, social equity, host-microbe biology, drug discovery, artificial intelligence, the microbiome and more! From graduate students to working clinicians and emeritus professors, host, Ashley Hagen, Scientific and Digital Editor at the American Society for Microbiology, highlights professionals in all stages of their careers, gleaning wisdom, career advice and even a bit of mentorship along the way.
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Biorisk Assessment and Management With Saeed Khan
11/11/2024
Biorisk Assessment and Management With Saeed Khan
Saeed Khan, Ph.D., Head of the Department of Molecular Pathology at Dow diagnostic research and reference laboratory and President of the Pakistan Biological Safety Association discusses the importance and challenges of biosafety/biosecurity practices on both a local and global scale. He highlights key steps for biorisk assessment and management and stresses the importance of training, timing and technology. Ashley's Biggest Takeaways Adequate biosafety and biosecurity protocols depend on a thorough understanding of modern challenges, and scientists must be willing and able to respond to new technological threats appropriately. In the microbiology lab, the threat goes beyond the physical pathogen. Implications of genomics and cyber security must be built into biorisk management techniques, including data storage and waste management practices. Risk assessments involve evaluation of both inherent and residual risk. Inherent risk is linked to the pathogen. Residual risk varies according to the lab, equipment, employee, environment, etc. As a result, biosafety and biosecurity risks are constantly changing, and assessments must be repeated strategically and often. Khan recommended repeating a risk assessment whenever a key variable in the equation changes, i.e., new equipment, new employee, new pathogen. He also recommended (at minimum) conducting routine risk assessments every 6 months, or twice a year. Featured Quotes: “We need to have basic biosafety and biosecurity to stay away from these bugs and the modern challenges, like cyber biosecurity and genomics. These are the new areas, which are potential threats for the future, and where we need to train our researchers and students.” “Starting from simple hand washing or hand hygiene, the basic things we use are gloves, goggles and PPE to protect the workers, the staff and the patient from getting infected from the environment, laboratory or hospitals. These are the basic things, and it's very crucial, because if one is not using gloves in the lab or not wearing the lab coat, he or she may get infected from the sample, and the patient can get infected from the physician and doctors or nurse if they are not following the basic biosafety rules. These [things] are routinely important. Every day we should practice this.” “But there are [also] new challenges. Particularly in the microbiology lab, we [used to] think that once we killed the bacteria, then it's fine. But nowadays, it's not the way we should think about it. Though you kill the bacteria practically, it still has a sequence, [which] we call the genome, and if you have that information with you, you theoretically have the potential to recreate that pathogen… that can be used or maybe misused as well.” “[Working with] scripts of pathogens, like smallpox or the polioviruses, we call this synthetic biology. Different scientists are doing it for the right purposes, like for production of vaccines, to find new therapeutics, to understand the pathology of the diseases. But on [the other hand]—we call it dual use research of concern (DURC)—the same can be misused as well. That's why it's very important to be aware of the bugs that we are working with, and the potential of that pathogen or microbe, to the extent that can be useful or otherwise.” “So, we should be aware of the new concern of the technology, synthetic biology and DURC. These are new concepts—cyber, biosecurity and information security [are all] very much important these days. You cannot be relaxed being in the microbiology lab. Once we have identified a pathogen, declared a result to the patient and the physician, and it's been treated, we [still] need to be worried about waste management—that we discard that waste properly and we have proper inventory control of our culture. It should be safe in the locker or on in the freezers and properly locked, so we should not be losing any single tube of the culture, otherwise it may be misused.” Risk Assessment “The best word that you have used is risk assessment. So, it should gage the severity of the issue. We should not over exaggerate the risk, and we should not undermine the risk. Once the risk assessment been made, we can proceed.” “Right from the beginning of touching a patient or a sample of the patient until the end of discarding the sample, that is called biorisk management. It's a complete science that we need to be aware of—not in bits and pieces. Rather a comprehensive approach should be adopted, and each and every person in the organization should be involved. Otherwise, we may think [we are] doing something good, but someone else may spoil the whole thing, and it will be counterproductive at the end.” “We should involve each and every person working with us and the lab, and we should empower them. They should feel ownership that they are working with us, and they are [as] responsible as we are. So, this the whole process needs to be properly engaged. People must be engaged, and they should be empowered, and they should be responsible.” “Each and every lab has different weaknesses and strengths of their own, which play an important role in the risk assessment.” “There is inherent risk, which is linked with the pathogen, and there is another thing we call residual risk. So, residual risk everywhere and varies. Though the inherent risk may be the same, the residual risk is based on the training of the person, the lab facility that is available, the resources that labs have and the potential threats from the environment.” “It's not usually possible that you do a risk assessment every day. So, when you have different factors involving a new pathogen in your lab, you have new equipment in your in your lab, or some new employee in your lab—[a new] variable factor that is involved—you should [perform] the risk assessment. Otherwise, [a routine risk assessment] should [be done] twice a year, after 6 months.” “Training is important, and response time is very much crucial. And different technology plays a vital role, but the lack of technology should not be an excuse for not responding. There is always an alternative on the ground that you may do the risk assessment. And within the given resources and facility, we should mimic the technology and respond to any outbreaks or disease within our given resources.” Links for the Episode (video) Take the
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From Hydrothermal Vents to Cold Seeps: How Bacteria Sustain Ocean Life With Nicole Dubilier
09/27/2024
From Hydrothermal Vents to Cold Seeps: How Bacteria Sustain Ocean Life With Nicole Dubilier
Nicole Dubilier, Ph.D., Director and head of the Symbiosis Department at the Max Planck Institute for Marine Microbiology, has led numerous reserach cruises and expeditions around the world studying the symbiotic relationships of bacteria and marine invertebrates. She discusses how the use of various methods, including deep-sea in situ tools, molecular, 'omic' and imaging analyses, have illuminated remarkable geographic, species and habitat diversity amongst symbionts and emphasizes the importance of discovery-driven research over hypothesis-driven methods. Watch this episode: Ashley's Biggest Takeaways: In 1878, German surgeon, botanist and microbiologist, Heinrich Anton de Bary, first described symbiosis as the living together of two or more different organisms in close physical intimacy for a longer period of time. These relationships can be beneficial, detrimental or commensal, depending on the organisms involved. Microbial symbiosis research holds great potential to contribute to sustainable energy production and environmental health. Links for This Episode: Take the
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When Proteins Become Infectious: Understanding Prion Disease With Neil Mabbott
08/23/2024
When Proteins Become Infectious: Understanding Prion Disease With Neil Mabbott
From Bovine Spongiform Encephalopathy (BSE) to Creutzfeldt-Jakob disease (CJD), Neil Mabbott, Ph.D., has worked for nearly 2 decades on understanding the mechanisms by which prion proteins become infectious and cause neurological disease in humans and animals. He discusses the remarkable properties of prions and addresses complexities surrounding symptoms, transmission and diagnosis of prion disease.
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Trillion Dollar Microbes Make the Bioeconomy Go Round With Tim Donohue
05/28/2024
Trillion Dollar Microbes Make the Bioeconomy Go Round With Tim Donohue
Episode Summary —ASM Past President, University of Wisconsin Foundation Fetzer Professor of Bacteriologyand Director of the (GLBRC) calls genomics a game-changer when it comes the potential of microbes to create renewable resources and products that can sustain the environment, economy and supply chain around the world. He also shares some exciting new advances in the field and discusses ways his research team is using microorganisms as nanofactories to degrade lignocellulose and make a smorgasbord of products with high economic value. Take the Ashley's Biggest Takeaways: The bioeconomy can be broadly defined as the use of renewable resources, including microorganisms, to produce valuable goods, products and services. Microbes have the potential to create products that cannot be made by existing synthetic chemistry routes. Using raw, renewable resources to create a circular bioeconomy is beneficial to the environmental footprint, economic footprint and supply chain security around the globe. Links for This Episode: The theme of our Spring 2024 Issue of , our flagship member magazine is Microbes and the Bioeconomy: Greasing the Gears of Sustainability, launches this week and features an article based on this MTM conversation. If you are an ASM Member, check back on Wed., June 30 for the newly published content! Not a member? Consider , and begin exploring endless potential to boulster your career and network with professionals, like Donohue, in your field. . Heading to ? Check out this , including those discussing the use of algae for bioproduction and synthetic biology for natural product discovery. Learn more about the .
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Rabies: The Diabolical Virus With Many Symptoms and Hosts With Rodney Rohde
05/07/2024
Rabies: The Diabolical Virus With Many Symptoms and Hosts With Rodney Rohde
, Regents’ Professor and Chair of the Medical Laboratory Science Program at Texas State University discusses the many variants, mammalian hosts and diverse neurological symptoms of rabies virus. Take the Ashley’s Biggest Takeaways: Prior to his academic career, Rohde spent a decade as a public health microbiologist and molecular epidemiologist with the and , and over 30 years researching rabies virus. While at the Department of Health Lab, Rohde worked on virus isolation using what he described as “old school” cell culture techniques, including immunoassays and hemagglutinin inhibition assays. He also identified different variants of rabies virus, using molecular biology techniques. Rohde spent time in the field shepherding oral vaccination programs that, according to passive surveillance methods have completely eliminated canine rabies in Texas. In the last 30-40 years, most rabies deaths in the U.S. have been caused by bats. Approximately 98% of the time rabies is transmitted through the saliva via a bite from a rabid animal. Post-exposure vaccination must take place before symptoms develop in order to be protective. Links for This Episode: . Rabies is an ancient, unpredictable and potentially fatal disease. Rohde and Charles Rupprecht, 2 rabies researchers, explain how to protect yourself. .
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Increasing Laboratory Capacity for TB Diagnosis With Aureliana Chambal
03/09/2024
Increasing Laboratory Capacity for TB Diagnosis With Aureliana Chambal
ASM's Young Ambassador, Aureliana Chambal, discusses the high incidence of tuberculosis in Mozambique and how improved surveillance can help block disease transmission in low resource settings. Ashley's Biggest Takeaways: Mozambique is severely impacted by the TB epidemic, with one of the highest incidences in Africa (368 cases/ 100,000 people in the population). Human-adapted members of the . These 7 lineages may vary in geographic distribution, and have varying impacts on infection and disease outcome. For decades, 2 reference strains have been used for TB lab research, H37Rv, which Chambal mentions, and Erdman. Both of these belong to TB Lineage 4. According to Chambal, the reference strains that we use for whole genome sequencing (worldwide) may be missing genes that are related the virulence (and/or resistance) of strains that are circulating in a given population and detected in clinical settings. Chambal is endeavoring to employ a new strain to control these analyses and better understand transmission dynamics in the community setting. Featured Quotes: The Schlumberger Foundation Faculty for the Future Fellowship is one of my proudest accomplishments for the 2023. I applied for this fellowship last year to pursue my Ph.D. It is a program that supports women coming from emerging and developing economies to pursue advanced research qualifications in science, technology, engineering and mathematics. I applied because I was looking to get more skills in microbiology, specifically tuberculosis, to pursue my Ph.D. at Nottingham Trent University. Pathway to Microbiology Research My trajectory is different because I have a bachelor’s in veterinary medicine. And during my undergrad, I always had more interest in the lab practice modules or disciplines. For the end of the [bachelor’s] project, I was looking to understand the anthelmintic effectiveness against the gastrointestinal parasites in goats. After I finished this project, I was looking to continue a related project, but unfortunately, I couldn't get work related to that.. In 2016, I applied for the National Institutes of Health of Mozambique, which is one of the biggest research institutions in my home country. That's when I was selected to work at the north region of Mozambique, specifically at the Nampula Tuberculosis Reference Laboratory. And then I moved to the public health laboratory as well, where I had the opportunity to work in the microbiology section. So, to be honest, my passion for microbiology started when I had the first contact with the TB lab, and then I couldn't separate myself from this area, tuberculosis. In 2016, I had the opportunity to receive a mentorship. Our lab, the TB lab of Nampula, received mentorship from the American Society for Microbiology. And we worked with Dr. Shirematee Baboolal; she was the mentor of our lab. The main idea of the program was to get the lab accredited and to build technical capacity in the lab. And to be honest, at the time, I didn't have much experience in lab techniques to detect or diagnosis tuberculosis. And I said to Dr. Shirematee, “I don't have much experience in this area, so, I don't know if I will be able to help you to accomplish these goals.” And she said, “If you want to learn, I can teach you, and you can be one of the best in this area.” And then we started training with her. It was very interesting. The passion she passed to us about microbiology—and tuberculosis, in particular—was one of the triggers for my passion in this area. So, to be honest, Dr. Shirematee Baboolal was one of the persons that triggered my interest from tuberculosis. So, I have to say thank you to her! Tuberculosis Genomic Diversity and Transmission Dynamics Mozambique is one of the higher burden countries of tuberculosis. So, our population is about 33 million people. And the case rate is high, it is approximately 360 per 100,000 people in the population, which is equivalent to over 110,000, which is equivalent 211,000 cases in the population. So, while I was working for the TB lab, I always had the desire to understand more about the transmission of the disease in the community. And I felt like I didn't have enough skills to do that; I didn't the tools to do that. And I said, “Okay, let me try to look to improve the skills.” That's why for my master's degree I tried to understand the genomic diversity of M. tuberculosis and see how we can see the gene content diversity within the lineage for which is the most spread lineage worldwide, and is predominant in Mozambique. Afterwards, I tried to expand to the other lineages. When I finished my master's degree, I felt that it was still missing something. I had the information about [TB] diversity, but I didn't get the point about transmission itself. That's why, when I went back and applied for my Ph.D., I structured my current project to specifically look at transmission and transmission clusters in the community. I'm trying to see how we can expand the gold standard of whole genome sequencing to try to make it applicable for all settings, including the low resources settings where most TB cases happen. So, M. tuberculosis itself doesn't have a lot of diversity between strains and within strains, because [strains] are very monomorphic. But you can find some genes that are different, specifically from the reference strain that we use, which is H37Rv. In the reference strain for M. tuberculosis, we saw is that many genes are missing—genes that are related to virulence. So, this information can be tricky, because it's the reference that we use worldwide to analyze our samples that come from whole genome sequencing. If we have genes missing, we are not [seeing] the complete information about the virulence of the bacterial strain that is circulating. So, my analysis was trying to understand how we can employ a new strain (that has at least most of the genes that are present in the other screens of the lineage) to control our analysis. Whole genome sequencing requires a lot of computational resources. So, the main idea is to try to extend that pipeline to make applicable to use in all settings. In Mozambique, we have whole genome sequencing equipment at the central level of the country, and the demand is high. But there is a queue for processing the samples. So, if we have a pipeline that [makes it so] anyone is able to analyze the data, we can have the results quick, and we can have more information for the public health sector. And with transmission studies, you can have a clearer idea of where the recent infection happened. We can see how many cases we have and when the transmission started. And then we can [try to] track and block the transmission. Involvement with ASM Young Ambassador Program So, I had the opportunity to hear about ASM’s Young Ambassador Program while I was working at the TB lab, in 2018. I spoke to Dr. Shirematee Baboolal and Dr. Maritza Urrego. And they told me about this position. Then, once I finished my masters [program], I applied for that position. I saw the requirements, and I felt like it was the right position for what I wanted to do for my community—to support the youth community and engage with my community back in Mozambique. I applied in 2020, and I got the position. And I have to say, it is one of the best things I have done so far. Because since the implementation of this program in Mozambique, I have interacted with students in schools and universities. We have developed a lot of workshops. I feel like I can contribute scientifically to improve their lives, to improve their academic lives. And recently, we launched a program called . We go to schools, in church, and we teach children about science, specifically microbiology. We use cartoons and paint microbes to explain the importance of the microbes for the community for our daily activities. And it's very interesting how they are engaged. I can feel that it's a way to develop the taste for science in the children. So, I'm very happy with this accomplishment. In this role of young ambassador, I feel like I can contribute to my community back home. I have so many ideas, so many dreams. I don't even know where to start! Because I have the ambitions to support my country back home. After I finish my Ph.D., I would like to create a robust technique that will help us to properly understand the [TB] transmission studies. So hopefully, with my Ph.D., I will be able to do that, or at least contribute something to support not only my country, but all low resources settings. And I would also like to be like to support some public health policies that can help us. Because we don't have like a strong component that involves the lab, the public health sector—I feel like everything is separated. We need to combine everything if we want to fight against tuberculosis. So, my desire is also to create a link between all these specific sites so we can make our fight against TB stronger. I want to continue [to drive] awareness about the support we need in low resource settings to control the fight against tuberculosis. Links for the Episode:
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Good Science, Bad Science and How to Make it Better with Ferric Fang and Arturo Casadevall
01/26/2024
Good Science, Bad Science and How to Make it Better with Ferric Fang and Arturo Casadevall
The scientific process has the power to deliver a better world and may be the most monumental human achievement. But when it is unethically performed or miscommunicated, it can cause confusion and division. Drs. Fang and Casadevall discuss what is good science, what is bad science and how to make it better. Get the book!
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Using AI to Understand How the Gut-Brain Axis Points to Autism With James Morton
12/11/2023
Using AI to Understand How the Gut-Brain Axis Points to Autism With James Morton
Dr. James Morton discusses how the gut microbiome modulates brain development and function with specific emphasis on how the gut-brain axis points to functional architecture of autism. Watch James' talk from ASM Microbe 2023: Using AI to Glean Insights From Microbiome Data https://youtu.be/hUQls359Spo
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Atypical Metabolism of Leishmania and Other Parasitic and Free-Living Protists With Michael Ginger
10/31/2023
Atypical Metabolism of Leishmania and Other Parasitic and Free-Living Protists With Michael Ginger
Dr. Michael ginger, Dean of the School of Applied Sciences in the Department of Biological and geographical Science at the University of Huddersfield, in West Yorkshire, England discusses the atypical metabolism and evolutionary cell biology of parasitic and free-living protists, including Leishmania, Naegleria and even euglinids.
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IBS Biomarkers and Diagnostic Diapers With Maria Eugenia Inda-Webb
09/22/2023
IBS Biomarkers and Diagnostic Diapers With Maria Eugenia Inda-Webb
, Pew Postdoctoral Fellow working in the Synthetic Biology Center at MIT builds biosensors to diagnose and treat inflammatory disorders in the gut, like inflammatory bowel disease and celiac disease. She discusses how “wearables,” like diagnostic diapers and nursing pads could help monitor microbiome development to treat the diseases of tomorrow. Subscribe (free) on , , , , or by . Ashley's Biggest Takeaways Biosensors devices that engineer living organisms or biomolocules to detect and report the presence of certain biomarkers. The device consists of a bioreceptor (bacteria) and a reporter (fluorescent protein or light). Inda-Webb’s lab recently The work is focused on diagnosing and treating inflammatory bowel disease, but Inda-Webb acknowledged that that is a large research umbrella. The next step for this research is to monitor the use of the biosensor in humans to determine what chemical concentrations are biologically relevant and to show that it is safe for humans to ingest the device. It is believed that the gut microbiome in humans develops in the first 1000 days to 3 years of life. Early dysbiosis in the gut has been linked to disease in adulthood. However, we do not have a good way to monitor (and/or influence) microbiome development. Inda-Webb hopes to use biosensors in diapers (wearables) to monitor microbiome development and prevent common diseases in adulthood. In 2015, Inda-Webb became ASM’s first winner for her piece, “Harvest System.” Inda-Webb is the 2023 winner of the , which recognizes an early career investigator with distinguished research achievements that have improved our understanding of microbes in the environment, including aquatic, terrestrial and atmospheric settings. Learn More About Featured Quotes: We engineer bacteria to sense particular molecules of interest—what we call biomarkers—if they are associated with a disease. And then, we engineer a way that the bacteria will produce some kind of molecule that we can measure—what we call reporter—so that could be a fluorescent protein or light, like the one that we have in this device. The issue is that inflammation in the gut is really very difficult to track. There are no real current technologies to do that. That is like a black box. And so, most of what we measure is what comes out from the gut, and has its limitations. It doesn't really represent the chemical environment that you have inside, especially in areas where you're inflamed. So, we really needed technologies to be able to open a window in these areas. The final device that I am actually bringing here is a little pill that the patient would swallow and get into the gut. And then they engineer bacteria that the biosensors, will detect, let's say, nitrous oxide, which is a very transient molecule. And the bacteria are engineered to respond to that in some way—to communicate with the electronics that will wirelessly transmit to your cell phone. And from there, to the gastroenterologist. We make the bacteria produce light. If they sense nitrous oxide, they produce light, the electronics read that, and the [information] finally gets into your phone. Part of the challenge was that we needed to make the electronics very very tiny to be able to fit inside the capsule. And also, the amount of bacteria that we use also is only one microliter. And so, imagine one microliter of bacteria producing a tiny amount of light. Finally, the electronics need to be able to read it. So that has been also part of the challenge. In this case, you have 4 different channels. One is a reference, and then the other 3 are the molecule of your choice. So, for example, what we show in the paper here is that we can even follow a metabolic pathway. So, you can see one more molecule turn into the other one, then into the other one. I'm really excited about that. Because normally we kind of guess as things are happening, you know, but here you can see in real time how the different molecules are changing over time. I think that's pretty exciting for microbiologist. The immediate application would be for a follow up. Let's say the patient is going to have a flare, and so you could predict it more much earlier. Or there's a particular treatment, and you want to see what is happening [inside the gut]. But for me, as a microbiologist, one of the things I'm most excited about will be more in the longer term. One of my favorite experiments that I do with the students is the Winogradsky column, and everyone gets super excited. So, we all have nice feelings for that. And it’s basically a column where we asked the students to bring mud from a lake, for example, and then some sources of nutrients. And then, after 6months, you will see all the layers, which is super pretty—beautiful, nice colors. But actually, that gives the concept of how the microenvironment helps to define where, or how, bacteria build communities. And so, what I think this device is going to do is to help us identify what is this microenvironment and to characterize that. And then, from there, to know if [an individual’s] microbiome is leaning towards the disease state, or if it's already in a serious or dangerous situation, to think about treatments that can lead to a more healthy state. So, I would just say it's really to have a window into the gut, and to be able to give personalized treatment for the patient. So, one application: I was thinking, I'm from the Boston area. So, one problem we have is getting a tick bite, right? After that, you could actually have to go through a very traumatic, antibiotic regime. I would imagine, in that case, you could [use the biosensor to] get the baseline [measurement], and then if you need to take these antibiotics, the doctors can follow how your microbiome is responding to that. Because one of the problems is that antibiotics changed the oxidation level [in the gut], and that really affects a lot the microbiome. To that point, for example, I get to know patients that they were athletes, and then, after antibiotic treatment, they have serious problems with obesity. Their life gets really messed up in many ways. And so, what I'm thinking is, if we could monitor earlier, there are a lot of ways that we could prevent that. We could give antioxidants; we could change the antibiotic. There are things that I think the doctor could be able to do and still do the treatment that we know. And of course, [although] we talk a lot about how much trouble antibiotics are, for certain things, we still need [them]. [The multi-diagnostic diaper] is one of my pet projects. I really love it. So yeah, basically, the issue is that the microbiome develops in the first 3 years. People even say like, 1000 days, you know. But there's really no way to monitor that. And now we're seeing that actually, if the microbiome gets affected, there are a lot of diseases that you will see in adult life. So, if we will be able to monitor the microbiome development, I really believe that we'll be able to prevent many of the diseases of tomorrow. What happens is that babies wear diapers. So, I thought it was really a very good overlap. We call that “wearables,” you know, like devices that you can wear, and then from there, measure something connected with health. So, in the diaper, I was excited because—different from the challenge with the ingested device, which was so tiny—here, we don't have the limitation of space. So, we could measure maybe 1000 different biomarkers and see how that builds over time. We can measure so many things. One could be just toxic elements that could be in the environment. I try to do very grounded science, and so, my question is always, ‘what’s the actionable thing to do?’ So, I'm thinking if there was a lot of toxicity, for example, in the carpet, or in the environment where you live, those are the easiest things to change, right? Then also, other things connecting more with the metabolism. [Often] the parents don't know that the kid has metabolic issues. So, before that starts to build and bring disease, it would be best if you could detect it as early as possible. From there, with symbiotics, we are thinking there are a lot of therapies that could engineer bacteria to produce the enzymes that the kid can’t produce. We could also [develop] other products, like for example, a t-shirt to measure the sweat. I'm also thinking more of the milk. I'm very excited about how the milk helps to build the microbiome in the right way. And that that's a huge, very exciting area for microbiologists. And so, we could also have nursing pads that also measure [whether] the mother has the right nutrients. My family, my grandparents were farmers, and in Argentina, really the time for harvest is very important. You can see how the city and really the whole country gets very active. And at that time [during a course Inda-Webb was taking at Cold Spring Harbor] in this course, I could see that with yeast we were having a lot of tools that would allow us to be much more productive in the field. And I thought, ‘Oh, this feels like a harvest system for yeast.’ Yes. So that was how it [Inda-Webb’s winning agar artwork, ‘Harvest System’] came out. I really love the people. Here, [at 2023], I really found that how people are bringing so much energy and really wanted to engage and understand and just connect to this idea of human flourishing, right, giving value to something, and saying, ‘okay, we can actually push the limits of what we know.’ How beautiful is that? And you know, we can learn from that. That was very exciting. ASM Agar Art Contest Have you ever seen art created in a petri dish using living, growing microorganisms? That's agar art! ASM's annual Agar Art Contest is a chance for you to use science to show off your creative skills. Submissions Are Now Being Accepted! This year's contest theme is "Microbiology in Space." Head over to our to get all of the information about what you need to submit your entry. Submissions will be accepted until Oct. 28! Links for the Episode: Inda-Webb, et al. recent Nature publication: Let us know what you thought about this episode by tweeting at us or leaving a comment on .
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Think Fungus Early: Preventing Angioinvasion Via Early Detection With Gary Procop
09/01/2023
Think Fungus Early: Preventing Angioinvasion Via Early Detection With Gary Procop
Dr. Gary Procop, CEO of the American Board of pathology and professor of pathology at the Cleveland Clinic, Lerner School of Medicine discusses the importance of early detection and diagnosis in order to prevent fungal invasion leading to poor outcomes, particularly in immunocompromised patients. He emphasizes the importance of thinking fungus early, shares his passion for mentoring and talks about key updates in the recently released 7th Edition of Larone’s Medically Important Fungi. Ashley's Biggest Takeaways Many invasive fungal infections are angiotrophic, meaning they actually grow toward, and into, blood vessels. Once the fungus has penetrated the blood vessel, the blood essentially clots, causing tissue downstream from the blood clot to die (infarction). When tissues that have been excised are viewed under the microscope, hyphal elements can be seen streaming toward or invading through the wall of the blood vessels. Once the clot forms, those hyphal elements can be seen in the center of the blood vessel where only blood should be. Antifungals cannot be delivered to areas where the blood supply has stopped. Therefore, treatment requires a combined surgical and medical approach, and the process is very invasive. Early detection can prevent these bad outcomes by allowing antifungal treatment to be administered before angioinvasion occurs. Links for the Episode: Expand your clinical mycology knowledge with the recently released Written by a new team of authors, Lars F. Westblade, Eileen M. Burd, Shawn R. Lockhart and Gary W. Procop, this updated edition continues the legacy of excellence established by founding author, Davise H. Larone. Since its first edition, this seminal text has been treasured by clinicians and medical laboratory scientists worldwide. The 7th edition carries forward the longstanding tradition of providing high-quality content to educate and support the identification of more than 150 of the most encountered fungi in clinical mycology laboratories. Get your copy today with $1 flat rate shipping within the U.S. or ASM members enjoy 20% off at checkout using the member promo code. Let us know what you thought about this episode by tweeting at us or leaving a comment on .
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Moldy Skin, Invasive Aspergillosis and the Rise of Candida auris With Shawn Lockhart
07/28/2023
Moldy Skin, Invasive Aspergillosis and the Rise of Candida auris With Shawn Lockhart
From antifungal resistance to disaster microbiology and tales of visible mold growing across the skin of patients following a tornado in Joplin, Missouri, Dr. Shawn Lockhart, Senior Clinical Laboratory Advisor in the Mycotic Diseases Branch at the CDC talks all things fungi—complete with references to pop TV shows and the recently released 7th Edition of Larone’s Medically Important Fungi. Links mentioned: (Use code: MCR20 at checkout for 20% off)
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Microbial Flavor Profiles for Bread and Wine Production With Kate Howell
07/14/2023
Microbial Flavor Profiles for Bread and Wine Production With Kate Howell
, Associate Professor of Food Chemistry at the University of Melbourne, Australia discusses how microbes impact the flavor and aroma of food and beverages and shares how microbial interactions can be used to enhance nutritional properties of food and beverage sources. Ashley's Biggest Takeaways Saccharomyces means sugar-loving fungus. Humans have similar olfactory structures and mechanisms as insects and are similarly attracted to fermenting or rotting fruits produced by Saccharomyces. Research has shown that insects (and humans) prefer yeasts that produce more esters and aromatic compounds. Palm wine is a product that is made from sap collected from palm trees (palm sap) across the tropical band of the world. Fruity flavors appear to be less important to persistence of Saccharomyces strains in an Indonesian palm wine fermentation. This may be because palm wine fermentation is very quick, generally 1-3 days often, with a maximum of 5 days for fermentation to be conducted. Wineries, on the other hand, ferment annually (one fermentation per year/vintage), when the grapes are right. Grape wine fermentations can take 7 days to 2 weeks to complete. So different selections likely take place between the 2 fermentation products. Featured Quotes: When we start drawing our lens on how microbes produce food for humans, we're coopting a process that happens quite naturally. Here I'll start off talking about Saccharomyces cerevisiae, the main fermenting yeast in food and beverage production, because it's one of the most studied organisms and was the first eukaryote to be sequenced. Saccharomyces cerevisiae, as the name implies, loves sugar, and it flourishes when there's a lot of sugar in the environment. Where is sugar found? In fruits, and that's done quite deliberately, because fruits develop sugars and flavors and aromas to attract a birds or insects or anything else that can carry their seeds elsewhere for dispersal. Now, Saccharomyces lies dormant in the environment in a spore before it encounters a sugar-loving environment. And then it replicates very quickly and tends to dominate fermentation. Humans have coopted that into our kitchens, into our meals, into our lives, and we use that process to produce food. As Saccharomyces starts to use this sugar, it balances up its metabolism. And as it does this, it produces aromas. These aromas have a lot of important characteristics. Humans love them, but insects also love them too. I've been interested in the yeasts that are found naturally in sourdough starters. Sourdough is a really interesting system. Because you've got yeast and bacteria interacting with one another. One of the things we are collaborating on with colleagues in France at Inrae, Dr. Delphine Sicard, is to understand some of the non-Saccharomyces yeasts that are naturally occurring in sourdough starters. So here we're looking at a collection of a yeast called Kazachstania humilis and trying to understand how it has adapted to the sourdough environment, how its sustained over time and how different global populations differ to one another. And this, of course, is of interest to the baking industry because not only do artisanal bakers have sort of an undiscovered wealth of biodiversity in their starters, baking companies also have an interest in using different sorts of flavors and bread for the commercial markets. The connection between a chemical profile and a person’s sensory preference isn't something that's complete and direct. So, in every method that we use, there's always caveats, but we try to correlate it. Let's start off with the chemical characterization. We use headspace sampling, analytical chemistry, separation with gas chromatography and identification with mass spectrometry. And we use different 2-dimensional methods to be able to understand what the very small compounds are, and to be able to identify them. We can semi-quantify these to be able to make comparisons between different fermentations. We know from wine fermentations and understanding preferences of wine that, in some cases, a particular increase, or an abundance of a particular compound, can be extremely attractive. And that might depend on the style of wine. What we've discovered through this process is that different people prefer different flavors. Makes sense, doesn't it? We like different things. But some really interesting results from our lab, show that people from different cultural backgrounds have different preferences. And here we're using here in Melbourne, I'm very lucky to work with some very talented postdocs and Ph.D. students from China, who have very different preferences for wine than an Australian does. Of course, Australians are quite heterogeneous in their in their cultural diversity as well. But there's certain flavors that our Chinese colleagues tend to prefer. So we decided to investigate this a little bit more. So for this study, we recruited wine experts from Australia, actively working in the wine industry, and also wine experts from China, working in the wine industry, and brought them to campus and ask them to rate their preferences on particular aromas and flavor characteristics that they noted in a panel of wines. These were very high-quality wines. We knew with wine experts, we couldn't just give them our loved wines, for example, which can be a little bit patchy quality wise. We asked them to rate their preferences, and then we collected saliva samples. The saliva samples were really interesting. We looked at 2 different aspects. We looked at the proteins that were present in the saliva samples. And we also looked at the oral microbiome. So the salivary microbiome—the bacteria, in particular—that are present. We found some really interesting things. And this has sparked a big area in our lab. So while the main enzymatic activities in the different groups of participants were quite similar—so esterase activity, Alpha amylase activity were similar—we found that there was a difference in the abundance of proline rich proteins and other potential flavor carrying compounds. Now, this is quite speculative. We'd like to know why this is the case. And so we're delving a little bit further into this area. What we do know though is that the abundances, especially if these proline rich proteins, is correlated with how people perceive the stringency. Now stringency is one of those characteristics in wine which is quite difficult to appreciate. It’s a lack of drying characteristic on the tongue and in the mouth and oral cavity. Some people find it quite attractive, others don't. But we found that the abundance of these polyproline-rich proteins correlates with stringency. This is, in fact, found in other studies because proline-rich proteins interact with polyphenols in the wine, and precipitate, which changes the sensation of astringency in the oral cavity. So here we've got a nice link to protein abundance and how people perceive flavor. But we're talking about microbiology, so maybe I should delve into the microbiological aspects of these studies as well. In that particular study that I'm referring to, we used wines that were naturally fermented, and that's the other variability that we need to consider when we think about wines from different areas. So, a natural fermentation, in a wine sense, is the grapes are harvested, and whatever microflora is present on the grapes will just ferment, and we often don't know what the main fermenting parties are. But if you contrast that with a majority of commercial wine that's produced, mainly in Australia, but also worldwide, it's inoculated with a selected strain of Saccharomyces or maybe 2 selected strains of Saccharomyces, and that tends to produce a fairly similar flavor profile, regardless of region. So, you can flatten out geographical characteristics and indications of flavor by inoculating a particular strain of yeast to ferment. That's not true with a natural fermentation, because that's conducted by the yeasts, and also the bacteria which just happened to be in the environment. So, I agree with you there is a lot of regional variation with wine flavor. And we can correlate that with regional diversity of yeast, but only if the wines are naturally fermented not if they're inoculated with a selected strain. Links for the Episode: and Their Potential Antioxidant Activities. Frozen, canned or fermented: Let us know what you thought about this episode by tweeting at us or leaving a comment on .
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AncientBiotics With Steve Diggle and Freya Harrison
06/02/2023
AncientBiotics With Steve Diggle and Freya Harrison
Dr. Steve Diggle, ASM Distinguished Lecturer and Microbiology Professor at the Georgia Institute of Technology in Atlanta, Georgia and Dr. Freya Harrison, Associate Microbiology Professor at the University of Warwick in Coventry, U.K., discuss the science behind medieval medical treatments and the benefits of interdisciplinary research. Ashley's Biggest Takeaways Diggle and Harrison met in Oxford, where Harrison was finishing up her Ph.D. and Diggle was doing background research for his work studying evolutionary questions about quorum sensing. When Diggle began searching for a postdoc, Harrison, who had been conducting an independent fellowship at Oxford and studying social evolution, applied. The AncientBiotics Consortium is a group of experts from the sciences, arts and humanities, who are digging through medieval medical books in hopes of finding ancient solutions to today’s growing threat of antibiotic resistance. The group’s first undertaking was recreation and investigation of the antimicrobial properties of an ancient eyesalve described in Bald’s Leechbook, one of the earliest known medical textbooks, which contains recipes for medications, salves and treatments. The consortium found that the eyesalve was capable of killing MRSA, a discovery that generated a lot of media attention and sparked expanded research efforts. The group brought data scientists and mathematicians into the consortium (work driven by Dr. Erin Connelly from the University of Warwick). Together, the researchers began scouring early modern and medieval texts and turning them into databases. The goal? To mathematically data mine these recipes see which ingredients were very often or non-randomly combined in ancient medical remedies. The group recently published work showing synergistic antimicrobial effects of acetic acid and honey. They are also working to pull out the active compounds from Bald’s eyesalve and make a synthetic cocktail that could be added to a wound dressings. A 1,000-Year-Old . : the return to maggots and leeches to treat ailments. A case study of the . Phase 1 safety trial of . Sweet and sour synergy: combined with medical-grade honeys. Let us know what you thought about this episode by tweeting at us or leaving a comment on .
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Sending Yeast to the Moon With Jessica Lee
05/05/2023
Sending Yeast to the Moon With Jessica Lee
Dr. Jessica Lee, scientist for the Space Biosciences Research Branch at NASA’s AIMS Research Center in Silicon Valley uses both wet-lab experimentation and computational modeling to understand what microbes really experience when they come to space with humans. She discusses space microbiology, food safety and microbial food production in space and the impacts of microgravity and extreme radiation when sending Saccharomyces cerevisiae to the moon. Ashley's Biggest Takeaways Lee applied for her job at NASA in 2020. Prior to her current position, she completed 2 postdocs and spent time researching how microbes respond to stress at a population level and understanding diversity in microbial populations. She has a background in microbial ecology, evolution and bioinformatics. Model organisms are favored for space research because they reduce risk, maximize the science return and organisms that are well understood are more easily funded. Unsurprisingly, most space research does not actually take place in space, because it is difficult to experiment in space. Which means space conditions must be replicated on Earth. This may be accomplished using creative experimental designs in the wet-lab, as well as using computational modeling. Links for the Episode: Register for . Add “,” to your ASM Microbe agenda. Let us know what you thought about this episode by tweeting at us or leaving a comment on .
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Invisible Extinction: The Loss of Our Microbes with Maria Gloria Dominguez-Bello and Martin Blaser
04/13/2023
Invisible Extinction: The Loss of Our Microbes with Maria Gloria Dominguez-Bello and Martin Blaser
Dr. Maria Gloria Dominguez-Bello, Henry Rutgers Professor of Microbiome and Health and director of the Rutgers-based New Jersey Institute for Food, Nutrition and Health, and Dr. Martin Blaser, Professor of Medicine and Pathology and Laboratory Medicine and director of the Center for Advanced Biotechnology and Medicine at Rutgers (NJ) discuss the importance of preserving microbial diversity in the human microbiome. The pair, whose research was recently featured in a documentary The Invisible Extinction, are on a race to prevent the loss of ancestral microbes and save the bacteria that contribute to human health and well-being. Links for the Episode: (documentary) (book) Missing Microbes: (article) (YouTube)
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The Self-Experimentation of Barry Marshall
02/07/2023
The Self-Experimentation of Barry Marshall
Dr. Robert Gaynes, distinguished physician and professor of infectious diseases at Emory University, joins Meet the Microbiologist for the 3rd , and final, episode in a unique 3-part segment, in which we share stories about the life and work of medial pioneers in infectious diseases. Here we discuss the career of Dr. Barry Marshall, the Australian physician who is best known for demonstrating in a rather unorthodox way that peptic ulcers are caused by the bacterium, Helicobacter pylori. Gaynes is author of Germ Theory: Medical Pioneers in Infectious Diseases, the 2nd edition of which will publish in Spring 2023. All 3 scientists highlighted in this special MTM segment are also featured in the upcoming edition of the book.
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The Career of Tony Fauci
12/22/2022
The Career of Tony Fauci
Dr. Robert Gaynes, distinguished physician and professor of infectious diseases at Emory University, joins Meet the Microbiologist for the 2nd episode in a unique 3-part series, in which we share the impact of scientists at the heart of various paradigm shifts throughout scientific history. Here we discuss the life and career of Tony Fauci, the scientist who has been recognized as America’s Top Infectious Diseases Doctor and “voice of science” during the COVID-19 pandemic. Ashley's Biggest Takeaways Fauci was born in Brooklyn, New York. He was a 2nd generation American whose parents came from Italy. Fauci’s father was a pharmacist in Brooklyn and was very influential in his life. During high school, Fauci worked behind the counter at the family pharmacy and even delivered prescriptions by bicycle. He attended a Jesuit high school in Manhattan, and attended the College of Holy Cross. After college, Fauci attended Cornell Medical School in Manhattan, which was his first choice of medical school. Fauci graduated first in his class in medical school in the mid 1960’s, right in the midst of the Vietnam War. During that time, after completing their initial residency training, virtually all doctors were drafted into one of the military services or the U.S. Public Health Service. Fauci accepted into the NIH program within the U.S. Public Health Service, where he acquired training and a fellowship in Clinical Immunology and Infectious Diseases. Fauci became the Director of the National Institute of Allergy and Infectious Disease (NIAID) in 1984. Fauci served as advisor to 7 U.S. presidents, including Ronald Regan, George H.W. Bush, Bill Clinton, George W. Bush, Barack Obama, Donald Trump and Joe Biden. 15 years after the creation of PEPFAR, Fauci reported, in the New England Journal of Medicine, that PEPFAR funded programs had provided antiretroviral therapy to 13.3 M people, averted 2.2 M perinatal HIV infections and provided care for more than 6.4 M orphans and vulnerable children.
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Françoise Barré-Sinoussi's Discovery of HIV
11/19/2022
Françoise Barré-Sinoussi's Discovery of HIV
Dr. Robert Gaynes, distinguished physician and professor of infectious diseases at Emory University, joins Meet the Microbiologist for a unique episode, in which we share the story of Françoise Barré-Sinoussi, the French, female scientist who discovered HIV and found herself at the heart of one of the most bitter scientific disputes in recent history. Subscribe (free) on , , , , or by . Ashley's Biggest Takeaways The U.S. Centers for Disease Control and Prevention (CDC)’s Morbidity and Mortality Weekly Report first reported on a cluster of unusual infections in June of 1981, which would become known as AIDS. Evidence suggested that the disease was sexually transmitted and could be transferred via contaminated blood supply and products, as well as contaminated needles, and could be passed from mother to child. All hemophiliacs of this generation acquired AIDS (15,000 in the U.S. alone). The fact that the microbe was small enough to evade filters used to screen the clotting factor given to hemophiliacs indicated that the etiologic agent was a virus. AIDS patients had low counts of T-lymphocytes called CD4 cells. By 1993, the most likely virus candidates included, a relative of hepatitis B virus, some kind of herpes virus or a retrovirus. Howard Temin discovered reverse transcriptase, working with Rous sarcoma in the 50s and 60s. His work upset the Central Dogma of Genetics, and at first people not only did not believe him, but also ridiculed him for this claim. Research conducted by David Baltimore validated Temin’s work, and Temin, Baltimore and Renato Dulbecco shared the Nobel Prize for the discovery in 1975. Robert Gallo of the U.S. National Institute of Health (NIH), discovered the first example of a human retrovirus—human T-cell lymphotropic virus (HTLV-1). Françoise Barré-Sinoussi worked on murine retroviruses in a laboratory unit run by Luc Montagnier, where she became very good at isolating retroviruses from culture. In 1982, doctors gave lab Montagnier’s lab a sample taken from a with generalized adenopathy, a syndrome that was a precursor to AIDS. Barré-Sinoussi began to detect evidence of reverse transcriptase in cell culture 2 days after the samples were brought to her lab. Barré-Sinoussi and Luc Montagnier were recognized for the discovery of HIV with the 2008 Nobel Prize in Physiology or Medicine. Links for the Episode: From the ancient worlds of Hippocrates and Avicenna to the early 20th century hospitals of Paul Ehrlich and Lillian Wald to the modern-day laboratories of François Barré-Sinoussi and Barry Marshall, Germ Theory brings to life the inspiring stories of medical pioneers whose work helped change the very fabric of our understanding of how we think about and treat infectious diseases. The second edition of Germ Theory, which will include chapters on Françoise Barré-Sinoussi, Barry Marshall and Tony Fauci, will publish in Spring 2023.
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Permafrost with Devin Drown
10/28/2022
Permafrost with Devin Drown
Episode Summary Dr. Devin Drown, associate professor of biology and faculty director of the Institute of Arctic Biology Genomics Core at the University of Alaska Fairbanks, discusses how soil disturbance gradients in the permafrost layer impact microbial communities. He also explains the larger impacts of his research on local plant, animal and human populations, and shares his experience surveilling SARS-CoV-2 variants in Alaska, where he and colleagues have observed a repeat pattern of founder events in the state. Ashley's Biggest Takeaways Permafrost is loosely defined as soil that has been frozen for 2 or more years in a row. Some permafrost can be quite young, but a lot of it is much older—1000s of years old. This frozen soil possesses large storage capacity for walking carbon and other kinds of nutrients that can be metabolized by microbes as well as other organisms living above the frozen ground. About 85% of the landmass in Alaska is underlined by permafrost. Some is continuous permafrost, while other areas of landmass are discontinuous permafrost—locations where both unfrozen soil and frozen soil are present. As this frozen resource is thawing as a result of climate change, it is releasing carbon and changing soil hydrology and nutrient composition, in the active layer in the soil surrounding it. Changes in the nutrients and availability of those nutrients are also likely changing the structure of the microbial communities. Drown and team are using a combination of traditional (amplicon sequencing) and 3rd generation (nanopore) next sequencing (NGS) techniques to characterize the microbes and genes that are in thawing permafrost soil. Featured Quotes: “Globally, we've seen temperatures increase here in the Arctic. Changes in global temperatures are rising even faster, 2-3 times, and I've heard recent estimates that are even higher than that.” “These large changes in temperatures are causing direct impacts on the thaw of the permafrost. But they're also generating changes in other patterns, like increases in wildfires. We just had a substantial wildfire season here in Alaska, and those wildfires certainly contribute to additional permafrost thaw by sometimes removing that insulating layer of soil that might keep that ground frozen, as well as directly adding heat to the to the soil.” “There are other changes that might be causing permafrost thaw, like anthropogenic changes, changes in land use patterns. As we build and develop roads into areas that haven't been touched by humans in a long time. We're seeing changes in disruption to permafrost.” “Some people are quite interested in what might be coming out of the permafrost. We might see nutrients, as well as microorganisms that are moving from this frozen bank of soil into the active layer.” “We're using next generation sequencing techniques to characterize not only who is in these soils, but also what they're doing.” “I started as a faculty member in 2015. As I moved up to Alaska, I got some really great advice from a postdoctoral mentor that said, make sure you choose something local. I'm fortunate enough that I have access to permafrost thaw gradient, that's effectively in the backyard of my office.” “Just a few miles from campus, we have access to a site that's managed by the Army Corps of Engineers. They have a cold regions group up here that runs a more famous permafrost tunnel. So they've dug a deep tunnel into the side of a hill that stretches back about 40,000 years into permafrost. They also have a great field site that has an artificially induced permafrost thaw gradient, and a majority of our published work has been generated by taking soil cores from that field site.” “Maintaining that cold chain, whether it’s experimental reagents or experimental samples, is a challenge for everyone. We're collecting active layer soil—the soil directly beneath our feet—so that's not at terribly extreme temperatures. But we do put it in coolers immediately upon extracting from the from the environment. Then we can bring it back to our lab where we can freeze it if we're going to use it for later analysis, or we can keep it at appropriately cool temperatures, if we're going to be working with the microbial community directly.” “We were most interested in looking for microbes that might have impacts on the above ground. ecosystem. So when we were characterizing the microbial community, we were doing that because we also wanted to link it to above ground changes.” “Changes in vegetation that might be driven by changes in microorganisms would certainly have an impact on the wildlife that are that are present at the site. So, just as an example, if we see a decrease in berries that might be present, that might decrease the interest from animals that rely on that [food source]. And so we might see changes in who's there.” “Outside of my research, we've seen changes in the types of plants present across northern latitudes. So different willows, for instance, are moving farther north, and that is leading animals, like moose, to move farther north. And so we might see changes in those kinds of patterns directly as a result of the microorganisms as well.” “We're really working to expand our efforts to move to other kinds of disturbances. I mentioned wildfires before, these are an important source of disturbance for boreal forest ecosystems. We have a project here in the interior, looking at the impacts of wildfires on microbial communities and how [these disturbances] might be changing the functional potential of microbial communities.” Let us know what you thought about this episode by tweeting at us or leaving a comment on .
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To Catch a Virus with Marie Landry and John Booss
10/17/2022
To Catch a Virus with Marie Landry and John Booss
Dr. Marie Landry, Professor of Laboratory medicine and Infectious Diseases at Yale University School of Medicine and Dr. John Booss, former National Director of Neurology for the Department of Veteran’s Affairs discuss the past, present and future of diagnostic virology. These proclaimed coauthors walk us through the impact of some of the most significant pathogens of our time in preparation for the launch of their 2nd edition of “To Catch a Virus,” a book that recounts the history of viral epidemics from the late 1800s to present in a gripping storytelling fashion. Ashley's Biggest Takeaways Coauthoring a book requires having great respect for the opinions of the person you are working with. The first human disease shown to be viral in nature was yellow fever, but for quite some time, the mode of disease transmission remained mysterious. In early 1881, Carlos Finlay of Cuba suggested that the disease could be spread by mosquitoes and significantly advanced the field. It wasn’t until polio was discovered in the early 1900s that scientists determined that viruses could also be transmitted by and animals. The ability to grow virus in tissue culture was another huge advancement in the field of diagnostic virology, which eventually led to the development of the Salk inactivated polio vaccine (IPV). Although he did not seek the spotlight for his work, Walter Roe, was a bright, hardworking (and one of John’s favorite) virologist, who made important advances in tissue culture, researched the role of retroviruses in animal cancer and discovered adenoviruses. As a result of the COVID-19 pandemic, the clinical laboratory played a central role in public health. The importance of a laboratory diagnosis became more evident and next generation sequencing moved further into the clinical lab. Featured Quotes: “Advice that was given to me way back when I started on my first book is that you have to write about something you're passionate about. You have to really believe in the topic because otherwise it'll come across as superficial and artificial. So the very first step is do you really believe in, [and in the case of writing a book, that means] believe in what you're writing about.” – Booss. “Science is often projected as a steady stream of advances one after the other. But there is a certain amount, I think, of arbitrary choice at each step. And it's also true for for writing a book.” – Booss “In putting the book together, there are obviously major events that occurred in virology, major crises that move the field forward, an interplay, really, of the scientific advances, the clinical need of the crisis at hand and some very remarkable people. One highlight of this book is the way it does focus on individuals and their stories and how they contributed to that progress.” -Landry “When [pathogens] spread from a local area to a larger area geopolitical area or even globally, they become pandemic.” Polio “The most compelling virus that I can think of in my youth was obviously polio. So when I was a small child, polio was causing epidemics every summer, at the end of which, between 20 and 30,000 children in the United States were left either paralyzed or dead. So this was it really struck fear into parents hearts.” – Landry “And then came the oral polio vaccine. We lined up, and it was a very, very painless way to be immunized. So that was a tremendous success story, we've come very close to eliminating polio, because of a number of reasons it hasn't happened.” - Landry “There was a case recently of paralytic polio in New York, in an unvaccinated person. And I hope this is a wake-up call, we really thought we were about to eliminate before COVID. And then with those disruptions and others, there's been a little resurgence, but I hope that it will be accomplished soon.” -Landry COVID-19 “It's amazing how much the world did change. International economies collapsed. whole societies shut down. The education and socialization of children came to a screeching halt. As schools close, whole chasms of inequality opened up or were revealed. And also the poor and marginalized people were the ones who suffered most. And the U.S. cultural divisions interfered with attempts to block the disease. So that by 2022, the U.S. was unique in having over 1 million deaths. We lead unfortunately led the world in that regard.” – Booss “Sometimes we need a crisis to move us forward. And we saw this with the new vaccine platforms, especially the mRNA vaccine.” Let us know what you thought about this episode by tweeting at us or leaving a comment on . Links From yellow fever and smallpox, to polio, AIDS and COVID-19, To Catch a Virus guides readers through the mysterious process of catching novel viruses and controlling deadly viral epidemics— and the detective work of those determined to identify the culprits and treat the infected. The new edition will be released October 15, 2022, available at
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Outbreak Detection with Wun-Ju Shieh
10/01/2022
Outbreak Detection with Wun-Ju Shieh
Dr. Wun-Ju Shieh, 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 determine or confirm the cause of death. • Serving as first a clinician in Taiwan and then a pathologist in the United States has provided Shieh with the unique experience of evaluating patients from both the outside-in and the inside-out! • Even when a major outbreak of a known etiologic agent is taking place, confirmatory diagnosis is necessary for subsequent quarantine, control and prevention of the outbreak. • During major disease outbreaks, other pathogens do not go away, and we must simultaneously facilitate their timely diagnosis to ensure effective patient treatment and care. • SARS-CoV-2 appears to be transmitted more easily than SARS-CoV-1. One possible explanation for this is that the amount of viral load appears to be the highest in the upper respiratory tract of those with COVID-19, shortly after the symptoms develop. This indicates that people with COVID-19 may be transmitting the virus early in infection, just as their symptoms are developing…or even before they appear or without symptoms. • SARS-CoV-1 viral loads peak much later in the illness. • Asymptomatic transmission is rarely seen with SARS-CoV-1 infection. • Almost 99% of SARS-CoV-1 patients developed prominent fever when they started to carry infectivity. Temperature monitoring was therefore, very effective at detecting sick patients and facilitating prompt quarantining procedures, which effectively contained/minimized transmission of the virus. • This was not as effective for SARS-CoV-2, despite early attempts at temperature. monitoring. • SARS-CoV-2 was much harder to contain both because of the milder display of host symptoms and the demonstration of higher viral transmissibility.
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Lyme Disease Prevention and Treatment with Linden Hu
09/02/2022
Lyme Disease Prevention and Treatment with Linden Hu
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 The Bulls-Eye Rash of Lyme Disease: Pfizer and Valneva Initiate Phase 3 Study of Lyme Disease Vaccine Candidate VLA15 Could This Treatment Prevent Chronic Lyme Disease? Promising New Drug Would Eradicate Lyme While Leaving Gut Microbes Alone: A Tick’s Meal: Evidence That the Variable Regions of the Central Domain of VlsE Are Antigenic during Infection with Lyme Disease Spirochetes Distinct Roles for MyD88 and Toll-Like Receptors 2, 5, and 9 in Phagocytosis of Borrelia burgdorferi and Cytokine Induction
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Tardigrades and Microbial Midwives with Mark O. Martin
08/08/2022
Tardigrades and Microbial Midwives with Mark O. Martin
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 The effects of Sceloporus virgatus cloacal microbiota on the growth of pathogenic fungi Sex-specific asymmetry within the cloacal microbiota of the striped plateau lizard, Sceloporus virgatus Predatory Prokaryotes: An Emerging Research Opportunity (pdf) Carleton College #LuxArt 2019
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Shark Epidermis Microbiome with Elizabeth Dinsdale
05/20/2022
Shark Epidermis Microbiome with Elizabeth Dinsdale
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 go from the head to the tail to avoid getting cut!), and depending on the species of shark, may be more or less spread out across the epidermis. Where do microbes enter the story? Dermal denticles overlay a thin layer of mucus, which provides a distinctive environment for microbial life. Collecting microbial samples from underneath a shark’s dermal denticles is quite difficult, and the technique varies by shark species (shark size, water depth and ability to bite all factor into the equation). Liz’s team uses a specially designed tool that the group affectionately calls a “supersucker,” to create and capture a slurry of microbes and water for analysis. The team then uses shotgun metagenomics to identify and characterize the microbes in their collected samples. Sequencing has revealed biogeographical difference, as well as similarities in microbial architecture of whale sharks across the globe. There are 2 populations of whale sharks—one in the Atlantic Ocean and the other in the Indian Pacific Ocean. Samples collected from both populations have revealed that each individual whale shark, from within each aggregation, shares many of the same microbes. In fact, unlike algae which may share 1 to 2 microbial species, whale sharks share about 80% of microbes across every individual. Since many of the sharks don’t cross aggregations, Liz’s team is investigating the possibility of coevolution between microbes and hosts. Metagenomic sequencing also provides information about the function of the sequenced microbes. High presence of heavy metal-tolerant microbes has been found in the epidermis of all shark species that the team has analyzed. Sharks are known to carry high levels of heavy metals in their skin, muscle and even blood. However, muscle tissue samples contain lower concentrations than skin, indicating that there may be a density gradient in place, and raising questions about how microbes might be involved in this regulation. Is there a pathway by which the microbes metabolize and help to remove concentrations of heavy metals across the epidermis? Liz and her team are hoping to find out. Links: Elizabeth Dinsdale Tracking Pathogens via Next Generation Sequencing (NGS) Microbial Ecology of Four Coral Atolls in the Northern Line Islands Coral Research Metagenomic analysis of stressed coral holobionts Metagenomic analysis of the microbial community associated with the coral Porites astreoides
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Microbial Culture Collections and the Soil Microbiome with Mallory Choudoir
04/18/2022
Microbial Culture Collections and the Soil Microbiome with Mallory Choudoir
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. In order to coexist in such a biologically diverse environment, which consists of spatial heterogeneity, as well as heterogeneity in access to moisture and nutrients, microbes must evolve different strategies to survive as part of a stable community. Choudoir’s field site is based in the Harvard Forest Long Term Ecological Research Program's field site, where coils are buried and have been heating the forest soil to 5 degrees above ambient temperatures for nearly 30 years. The study allows Choudoir and colleagues to observe and evaluate long-term responses to chronic soil warming stress. This research is important because microbes function as resources to the health and well-being of ourselves and our planet. Understanding how microbes adapt to biotic and abiotic stresses can help inform future conservation strategies, biotechnological approaches and applications and equitable allocation of microbial resources. Visit for links mentioned
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Neglected Tropical Diseases and Pandemic Prevention With Peter Hotez
11/01/2021
Neglected Tropical Diseases and Pandemic Prevention With Peter Hotez
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 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 work productively. Impact child development and/or the health of girls and women. Occur in a setting of poverty and actually cause poverty because of chronic and debilitating effects. Hotez and his colleagues recognized that there is a uniqueness to the NTDs ecosystem, and they began putting together a package of medicines that could be given on a yearly or twice per year basis, using a strategy called Mass Drug Administration (MDA). This involved the identification of medicines that were being used on an annual basis in vertical control programs and combining those medications in a package of interventions that costs about $0.50 per person per year. “Throw in an extra 50 cents per person and we could double or triple the impact of public health interventions,” he explained. Emerging diseases, such as SARS-CoV-2, capture the attention of the public for obvious reasons. They pose an imminent threat to mankind. NTDs are not emerging infections, but they are ancient afflictions that have plagued humankind for centuries and, as a consequence, have had a huge impact on ancient and modern history. One of the reasons we have mainland China and Taiwan today may have been, in part, due to a parasitic infection, Schistosomiasis. Hotez and colleagues at the Texas Children’s Center for Vaccine Development have developed a COVID-19 vaccine, based on simple technology, similar to what is used for the Hepatitis B vaccine. They hope to release the vaccine for emergency use in resource poor countries like India and Indonesia. When asked about the timing of the publication of his book, the third edition of Forgotten People, Forgotten Diseases, Hotez acknowledged the difficulty of helping countries understand that NTDs have not gone away. COVID-19 is superimposed on top of them, and the pandemic has done a lot of damage in terms of NTD control. Although social disruption has interfered with the ability to deliver mass treatments, Hotez said that it has been gratifying to see that the USAID and their contractors have responded by putting out guidelines about how to deliver mass treatments with safe social distancing. “As a global society, we have to figure out how to walk and chew gum at the same time,” he said. “We’ve got to take care of COVID, but we really must not lose the momentum we’ve had for NTDs because the prevalence is starting to decline and we’re really starting to make an impact.”
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133: Vibrio cholerae with Rita Colwell
06/10/2021
133: Vibrio cholerae with Rita Colwell
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.
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132: Life Science and Earth Science and Biogeomicrobiology with Denise Akob
11/12/2020
132: Life Science and Earth Science and Biogeomicrobiology with Denise Akob
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 provide samples for years of analysis. From one sample, scientists can conduct: Microbiome studies through amplicon sequencing to understand population structures. Metagenomics studies to understand functional potential. Biochemical studies to understand active metabolic processes. Akob asks how to make natural microbial degraders happy. For example: acetylene, a triple-bonded carbon compound, can inhibit degradation of chlorinated solvents, a potent groundwater contaminant. By studying the microbes that use acetylene as a primary energy source (acetylenotrophs), this removes this inhibition caused by acetylene and the chlorinated solvent-degraders can increase their activity. Akob studies pristine environments to understand natural microbial communities. A cave she studied in Germany was ‘ultra pristine,’ discovered while building a highway. Understanding natural processes, such as the biomineralization promoted during stalagmite and stalactite formation helps scientists imagine how to use tehse processes in other applications. Links for this Episode: HOM Tidbit:
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131: Powassan virus and tick biology with Marshall Bloom
07/31/2020
131: Powassan virus and tick biology with Marshall Bloom
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 , , , or by . 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: Administration. Training, paperwork, etc. P: Personal protective equipment (PPE). Varies from gloves to positive pressure suits, depending on the microorganisms under study. PL: Laboratory procedures. Standard operating protocols. E: Engineering. Biosafety cabinets and labs that have protective features. Most of the vector-borne flaviviruses, including Powassan virus, don’t cause overt disease in the people they infect, so many people never know they’ve been infected. Without serological surveys, it’s difficult to know the full range of infected individuals versus those that develop serious disease. Serious disease often manifests in neurological symptoms such as encephalitis, with 10-15% mortality rate; half of those suffering neurological disease will continue to have serious sequelae for years. The Rocky Mountain Labs was once the world reference center for ticks: it held thousands of samples which represented the type species for the entire world. The tick salivary glands look like a bunch of grapes: the stem of the grapes is a series of branching ducts. The “grapes” at the end of the ducts are the acini, which is Latin for ‘little sac.’ These acini play a major role in tick feeding, and different types of acini play different functional roles: Type 1 acini: cells have no granules. Acini involved with fluid exchange. Type 2 and type 3 acini: cells with granules. Cells degranulate to release vasoactive compounds into tick saliva during feeding. Featured Quotes “The first isolation of Powassan virus was from a little boy in Powassan, Canada in 1958. If you look at the cases over the years, the numbers are going up, but compared to Lyme disease, they’re pretty low: there’s been less than 200 cases, all told.” “Amazingly, the Powassan virus can be transmitted in as little as 15 minutes….[and] a female tick can take days to get a full meal.” “I take a tick-centric view. If I can anthropomorphize, as my old friend Stanley Falkow used to say, he’d say ‘think like the microbe.’ The microbe doesn’t really care if we get sick or not. The microbe is just trying to make a living and survive.” “One of the really surprising things is that infected ticks can infect uninfected ticks, if they are feeding right next to each other. Ticks like to feed in groups: it’s called co-feeding. The virus can transferred really quickly, 15 min, which is way faster than the virus can go through a replication cycle. What that means to me is that the ticks are infecting each other….we want to investigate the role of co-feeding.” “If something sounds like fun or sounds important, and especially if something sounds fun AND important, then you should do it.” Links for this Episode: Amazon: by Esther Gaskins Price New York Times: Twitter thread from @BugQuestions: History of Microbiology Tidbit:
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