Episode Summary Sue Ishaq, Ph.D., Associate Professor of Microbiomes at the University of Maine, discusses how gut microbes transform seemingly inert plant compounds—like glucosinolates found in broccoli—into powerful anti-inflammatory agents such as sulforaphane. Her research dives into the fascinating interplay between diet, cooking methods and the diversity of the gut microbiota, revealing how these factors influence the body's ability to produce health-promoting molecules. Links for This Episode

• mSystems paper: Early life exposure to broccoli sprouts confers stronger protection against enterocolitis development in an immunological mouse model of inflammatory bowel disease.
• mSystems paper: Steamed broccoli sprouts alleviate DSS-induced inflammation and retain gut microbial biogeography in mice.
• Current Developments in Nutrition paper: Current knowledge on the preparation and benefits of cruciferous vegetables as relates to in vitro, in vivo, and clinical models of Inflammatory Bowel Disease.

Karl Matthews, Ph.D., Professor of Microbial Food Safety at Rutgers University, discusses ways to eliminate pathogens like Salmonella, E. coli O157:H7 and Listeria from fresh fruits and vegetables. He highlights the importance of preventative measures from farm to table, including the use of water antimicrobials, like chlorine, and photosensitizers, like curcumin.

Watch this episode: https://youtu.be/6Wkef9RyUVE

Ashley's Biggest Takeaways

• We consume billions of microorganisms in the food that we eat each day.
• Fresh fruits and vegetables that are not thermally processed are likely to carry a higher microbial load than cooked foods.
• Many of those microbes are not concerning to human health. However, when pathogens of human health concern are present, the food can become unsafe to eat.
• Scientists use many methods from pre-harvest through post-harvest to keep food free of human pathogens.
• Water antimicrobials, such as chlorine, and photodynamic inactivation using photosensitizers, such as curcumin, are 2 preventative measures that Matthews and colleagues are investigating.
• Curcumin is a natural chemical compound found in the turmeric plant. It is responsible for giving tumeric its yellow color.
• Curcumin is also a photosensitizer, meaning that it can absorb light energy and transfer it to another molecule to initiate chemical reactions that produce cytotoxic singlet oxygen.

Featured Quotes

When I look at [what makes fruits and vegetables safe to eat] as far as from a microbiological perspective, it's are they free of pathogens of human health concern? And so, we might think about organisms, such as Salmonella or the Shiga toxin producing E coli or Listeria. There are a number of processes and initiatives that are put into place, from the pre-harvest through post-harvest levels to try to ensure that the product is not contaminated with microorganisms of human health concern. Each day, we're consuming literally billions of microorganisms in the foods that we eat, and particularly the raw fruits and vegetables that we're eating that are not being thermally processed in any fashion by which you might reduce the microbial load. Oftentimes we think about the bacteria that might well be there. But we do know that there's viruses that could be present. There's certain type of protozoa that might be present. Many of us know of norovirus and the concerns associated with that particular pathogen. So, there's a multitude of microorganisms that might well be associated with fresh fruits and vegetables, but there's really a very limited number or types that are actually of concern from a human health standpoint. In my program, we're working on E. coli O157:H7, in particular. It's a certain serotype of E. coli, a diarrheagenic E. coli, what's also known as a Shiga toxin-producing E. coli. We work with Salmonella, and we work with Listeria monocytogenes, but there's other microorganisms, such as Campylobacter, Yersinia, Staphylococcus aureus. All of those types of pathogens can also be associated with foods—and different types of foods, at that—and be of concern to the general public—the consumer. If we look at a lot of the processing of foods that are taking place, not only here in the United States, but globally, many times, what will happen is they're utilizing some type of a water antimicrobial, and I stress that because, oftentimes, these antimicrobials are added to the water to control the microbial load in the water. So, ultimately, you're not basically putting on water and putting on a whole load of microorganisms along with it. And also, you can prevent cross contamination through that. Here in the U.S. and elsewhere, we'll often put additional chlorine into the water. So, let's say we're increasing the chlorine concentration to 20 parts per million, or 50 parts per million, or maybe in poultry processing, they're utilizing peracetic acid. These are 2 common antimicrobials that are being used. What we wanted to do is find out could we utilize some other types of methods that might well control microorganisms on the commodity itself? And that's where we started looking at photodynamic inactivation and coupling that with the use of a photosensitizer. And in this particular case, the photosensitizer we were using was curcumin. The reason for working with curcumin is that it's naturally used in foods as a food dye. It's also used as a flavoring agent, and so forth. So, it's there, and it's being used—not just in the U.S., but [also] globally. And we thought we would try to see if we utilize this compound, could we have an additive effect to it? If you apply certain wavelengths of light, you can inactivate microorganisms, but if you apply that wavelength to something like a photosensitizer type molecule (curcumin), you could generate singlet oxygen molecules. And those singlet oxygen molecules would act like little explosions on the cell membrane and basically blow it apart and, therefore, inactivate the organism. We looked at the ability of this to inactivate Listeria monocytogenes, Salmonella, as well as E. coli O157:H7, so these Shiga toxin-producing E. coli, and what we did indeed find is that it was very effective. We looked at it in comparison to peracetic acid use in the poultry industry, and we found it to be equivalent, at least to treatments that we were utilizing on poultry skin, with inactivation of the microorganisms, such as Listeria, on the poultry skin. So, it is really exciting.

Links for This Episode

• ​​​​​​Preventing Foodborne Outbreaks Starts in the Field.
• Influences of photosensitizer curcumin on microbial survival and physicochemical properties of chicken during storage.

Michael Lynch, Ph.D., Director of the Center for Mechanisms of Evolution at Arizona State University and Vaughn Cooper, Ph.D., professor of Microbiology and Molecular Genetics at the University of Pittsburgh, School of Medicine, examine the origins and trajectory of early microbial life (EML) and discuss the collaborative report between the American Academy of Microbiology and the Gordon and Betty Moore Foundation, which explores the journey of life on Earth, from non-living chemical compounds to early unicellular life, to the vast diversity of organisms we see today. This episode is brought to you by the American Academy of Microbiology, a think tank at American Society for Microbiology and the Gordon and Betty Moore Foundation, which has been dedicated to advancing scientific discovery for the past 25 years.

Links for This Episode:

• Project Report Early Microbial Life: Our Past, Present and Future.
• Article: The Great Oxidation Event: How Cyanobacteria Changed Life.
• MTM Podcast: From Hydrothermal Vents to Cold Seeps: How Bacteria Sustain Ocean Life With Nicole Dubilier.
• Take the MTM listener survey!

Sally Bornbusch, Ph.D., is an NSF postdoctoral fellow in biology conducting microbial ecology research in animal care and conservation at the Smithsonian National Zoo & Conservation Biology Institute. She discusses how FMTs are being used to mitigate health concerns in wild animals in captivity, shares key findings about the milk microbiome from the Smithsonian milk repository, the largest collection of exotic animal milks in the world, and explains the science behind eating poo (Coprophagia).

Links for This Episode

• Why Do Animals Eat Poop? (And Why It Might Be a Good Thing).
• Faeces as food: a framework for adaptive nutritional coprophagy in vertebrates.
• Even Monkeys Should Eat Their Vegetables.
• Take the MTM listener survey!

Dev Mittar, Ph.D., Scientific Director of the ASM Health Scientific Unit discusses the use of metagenomic next generation sequencing to develop agnostic diagnostic technology, giving scientists and clinicians alike, a tool to diagnose any infectious disease with one single test. He also discusses how the ASM Health Unit is empowering scientists and leveraging microbial science innovations to address critical global health challenges and improve lives worldwide.

Ashley's Biggest Takeaways

• The Division of Research, Innovation and Ventures is a small entrepreneurial arm of BARDA that takes on early-stage projects with high potential of turning into medical countermeasures.
• Prior to his role as Scientific Director for ASM Health, Mittar worked as a health scientist and program officer at DRIVe, where he focused on advancing high-impact science.
• He is particularly passionate about his work to develop agnostic diagnostics—a single test that uses metagenomic next generation sequencing to identify any pathogen from 1 clinical sample.
• Mittar discusses applications for this technology in surveillance (pandemic preparedness), variant detection, AMR and clinical settings (diagnosing complicated infections where etiology is not clearly defined).
• He also shares how a recent bout with illness emphasized the value and potential of this technology to save money, time, pain and suffering of the patient.
• Agnostic diagnostics can also help prevent the overuse/misuse of antibiotics, which are key factors in the spread of antimicrobial resistance.
• Furthermore, when this technology is coupled with the use of metatranscriptomics, it can provide information about the patient's immune profile that can be helpful in developing personalized treatment strategies, as opposed to a one-size-fits-all approach.
• ASM is organizing around 3 scientific units, ASM Health, ASM Mechanism Discovery and ASM Applied and Environmental Microbiology.
• These units will empower researchers and scientists to use science make a difference in the world and provide a forum for them to come together to shape the future of the field.

Links for This Episode

• Learn More About ASM's Scientific Units.
• Join the Conversation on ASM Connect, our online community platform.
• Browse Volunteer Opportunities.
• Become an ASM Member.
• Register for ASM Microbe 2025.

Episode Summary Afreenish Amir, Ph.D., Antimicrobial Resistance (AMR) Project Director at the National Institute of Health in Pakistan, highlights significant increases in extensively drug-resistant typhoid and cholera cases in Pakistan and discusses local factors driving AMR in Asia. She describes the development and implementation of a National Action Plan to combat AMR in a developing country, emphasizing the importance of rational antimicrobial use, surveillance and infection control practice. Ashley's Biggest Takeaways

• AMR is a global and One Health issue.
• Pakistan has a huge disease burden of AMR.
• Contributing factors include, but are not limited to, overcrowding, lack of infection control practices, poor waste management practices and over-the-counter prescription practices.
• Promoting the rational use of antimicrobials is imperative at all levels—from tertiary care to primary care practitioners.
• Typhoid and cholera are high-burden infections in Pakistan, with typhoid being a year-round issue and cholera being seasonal.
• A holistic approach, involving various sectors and disciplines, is necessary in order to address the global AMR threat.
• Amir highlights the need for better communication and collaboration to bridge gaps and build trust between different organizations.

Featured Quotes: I've been working at the National Institutes of Health for the last 7 years now. So, I've been engaged in the development and the implementation of the national action plan on AMR, and that gave me the opportunity to explore the work in the field of antimicrobial resistance. Reality of AMR in Pakistan [Pakistan] is an LMIC, and we have a huge disease burden of antimicrobial resistance in the country right now. A few years back, there was a situational analysis conducted, and that has shown that there is presence of a large number of resistant pathogens within the country. And National Institutes of Health, they have started a very standardized surveillance program based upon the global antimicrobial use and surveillance system back in 2017. And [those datasets have] generated good evidence about the basic statistics of AMR within the country. So, for example, if I talk about the extensively drug-resistant typhoid, typhoid is very much prevalent in the country. Our data shows that in 2017 there were 18% MDR typhoid cases through the surveillance data. And in 2021 it was like 60%. So that has shown that how the resistance has increased a lot. A number of challenges are associated with this kind of a thing, overcrowded hospitals, poor infection prevention and control (IPC) measures. So, there is AMR within the country—there's a huge burden—and we are trying to look for the better solutions. Local Factors Driving AMR Bacteria, they do not know the borders. We have a close connection with the other Asian countries, and we have a long border connected with the 2 big countries, which are Afghanistan and India and Bangladesh and China. So, we see that it's not limited to 1 area. It's not regional. It's also a history of travel. When the people travel from one area to the other, they carry the pathogen as a colonizer or as a carrier, and they can infect [other] people. So, it's really connected, and it's really alarming as well. You never know how the disease is transmitted, and we have the biggest example of COVID—how things have spread from 1 country to the other, and how it has resulted in a massive pandemic. AMR is similar. We have seen that it's not limited to 1 region. We are part of this global community, and we are contributing somehow to the problem. First, I'll talk about the health care infrastructure. We do have the capacities in the hospitals, but still, there's a huge population. Pakistan is a thickly populated country. It's a population of around 241 million. And with the increasing population, we see that the infrastructure has not developed this much. So now the existing hospitals are overcrowded, and this has led to poor infection control practices within the hospitals. The staff is not there. In fact, ID consultants are not available in all the hospitals. Infection control nurses are not available in all the hospitals. So, this is one of the main areas that we see, that there is a big challenge. The other thing that can contribute is the poor waste management practices. Some of the hospitals—private and public sectors—they are following the waste management guidelines—even the laboratories. But many of the hospitals are not following the guidelines. And you know that AMR is under one health. So, whatever waste comes from the hospital eventually goes to the environment, and then from there to the animal sector and to the human sector. [Another big] problem that we are seeing is the over-the-counter prescription of antimicrobials. There is no regulation available in the country right now to control the over-the-counter prescription of antibiotics. They are easily available. People are taking the antibiotics without a prescription from the doctors, and the pharmacist is giving the patients any kind of medicine. And either it is effective/not effective, it's a falsified, low-quality antibiotic for how long in duration antibiotic should be taken. So, there are multiple of things or reasons that we see behind this issue of AMR. Rational Use of Antimicrobials It is a complex process how we manage this thing, but what we are closely looking at in the country right now is that we promote the rational use of antimicrobials at all levels—not only at the tertiary care levels, but also at the general practitioner level. They are the first point of contact for the patients, with the doctors, with the clinicians. So, at this point, I think the empirical treatment needs to be defined, and they need to understand the importance of this, their local antibiograms, what are the local trends? What are the patterns? And they need to prescribe according to those patterns. And very recently, the AWaRE classification of WHO, that is a big, big support in identifying the rational use of antimicrobials—Access, Watch and Reserve list—that should be propagated and that should be understood by all the general practitioners. And again, I must say that it's all connected with the regulations. There should be close monitoring of all the antibiotic prescriptions, and that can help to control the issue of AMR. National Action Plan on AMR So, when I joined NIH, the National Election plan had already been developed. It was back in 2017, and we have a good senior hierarchy who has been working on it very closely for a long period of time. So, the Global Action Plan on AMR, that has been our guiding document for the development of the national action plan on AMR, and we are following the 5 strategic objectives proposed in the global action plan. The five areas included:

1. The promotion of advocacy and awareness in the community and health care professionals.
2. To generate evidence through the data, through the surveillance systems.
3. Generation of support toward infection prevention and control services IPC.
4. Promoting the use of antimicrobials both in the human sector and the animal sector, but under the concept of stewardship, antimicrobial consumption and utilization.
5. Invest in the research and vaccine and development.

So, these are some of the guiding principles for us to develop the National Action Plan, and it has already been developed. And it's a very comprehensive approach, I must say. And our institute has started working on it, basically towards recreating awareness and advocacy. And we have been successful in creating advocacy and awareness at a mass level. Surveillance We have a network of Sentinel surveillance laboratories engaged with us, and they are sharing the data with NIH on a regular basis, and this is helping NIH to understand the basic trends on AMR and what is happening. And eventually we plan to go towards this case-based surveillance as well, but this is definitely going to take some time because to make people understand the importance of surveillance, this is the first thing. And very recently, the Institute and country has started working towards the hospital acquired infection surveillance as well. So, this is a much-needed approach, because the lab and the hospital go hand in hand, like whatever is happening in the lab, they eventually reach the patients who are in the hospitals. Wastewater surveillance is the key. You are very right. Our institute has done some of the work toward typhoid and cholera wastewater surveillance, and we were trying to identify the sources where we are getting these kinds of pathogens. These are all enteric pathogens. They are the key source for the infection. And for the wastewater surveillance mechanism, we can say that we have to engage multiple stakeholders in this development process. It's not only the laboratory people at NIH, but we need to have a good epidemiologist. We need to have all the water agencies, like the public health engineering departments, the PCRWR, the environmental protection agencies who are working with all these wastewater sites. So, we need to connect with them to make a good platform and to make this program in a more robust fashion. Pathogens and Disease Burdon For cholera and typhoid within Pakistan, I must say these are the high burden infections or diseases that we are seeing. For typhoid, the burden is quite high. We have seen a transition from the multidrug-resistant pathogens to the extensively drug-resistant pathogens, which now we are left with only azithromycin and the carbapenems. So, the burden is high. And when we talk about cholera, it is present in the country, but many of the times it is seasonal. It comes in during the time of the small zone rains and during the time of floods. So, every year, during this time, there are certain outbreaks that we have seen in different areas of the country. So, both diseases are there, but typhoid is like all year long—we see number of cases coming up—and for cholera, it's mainly seasonal. Capacity Building and ASM's Global Public Health Programs

Capacity building is a key to everything, I must say, [whether] you talk about the training or development of materials. I've been engaged with ASM for quite some time. I worked to develop a [One Health] poster in the local language to create awareness about zoonotic diseases. So, we have targeted the 6 zoonotic diseases, including the anthrax, including the Crimean-Congo hemorrhagic fever and influenza. And we have generated a very user-friendly kind of layout in the local language, trying to teach people about the source of transmission. What are the routes of transmission, if we talk about the CCHF? And then how this can be prevented. So, this was one approach. And then I was engaged with the development of the Learnamr.com. This is online platform with 15 different e-modules within it, and we have covered different aspects—talking about the basic bacteriology toward the advanced, standardized methods, and we have talked about the national and global strategies [to combat] AMR, One Health aspects of AMR, vaccines. So, it's a huge platform, and I'm really thankful to ASM for supporting the program for development. And it's an online module. I have seen that there are around more than 500 subscribers to this program right now, and people are learning, and they are giving good feedback to the program as well. We keep on improving ourselves, but the good thing is that people are learning, and they are able to understand the basic concepts on AMR.

Links for This Episode:

• Experts Discuss One Health in Pakistan: Biosafety Education Inside and Outside the Lab.

• Explore ASM's Global Public Health Programs.

• Download poster about zoonotic disease in English or Urdu.

• Progress on the national action plan of Pakistan on antimicrobial resistance (AMR): A narrative review and the implications.

• Global diversity and antimicrobial resistance of typhoid fever pathogens: insights from 13,000 Salmonella Typhi genomes.

• Wastewater based environmental surveillance of toxigenic Vibrio cholerae in Pakistan.

• Point Prevalence Survey of Antimicrobial Use in Selected Tertiary Care Hospitals of Pakistan Using WHO Methodology: Results and Inferences.

• Overcoming the challenges of antimicrobial resistance in developing countries.

• Take the MTM listener survey!

Manuel Martinez Garcia, Ph.D., a professor of microbiology in the Physiology, Genetics and Microbiology Department at the University of Alicante in Spain, paints a picture of what microbial life looked like thousands of years ago by analyzing microbial genomic signatures within ice cores collected from the Antarctic ice shelves in the 1990s.

Links for the Episode

• New avenues for potentially seeking microbial responses to climate change beneath Antarctic ice shelves – mSphere paper.
• Viruses under the Antarctic Ice Shelf are active and potentially involved in global nutrient cycles – Nature communications article.
• Manuel Martinez Garcia's Lab website.
• How stable is the West Antarctic Ice Shelf? – Press Release from Alfred Wegener Institute.
• Take the MTM listener survey!
• Watch this episode: https://youtu.be/CHCMO74_gIY

Ashley's Biggest Takeaways

• There is a unique habitat beneath Antarctic ice shelves, where microbes live without light and rely on unusual energy sources.
• Ice cores from these Antarctic ice shelves can preserve fossilized genomic records of microbial life from long ago.
• Comparing past and present samples can help us understand how microbial life is responding to environmental stressors, like temperature changes and acidification, over time.
• It can also provide key insights to changes in biodiversity.

Featured Quotes: Motivation for the Research

Ice shelves are like massive floating ice that are in Antarctica, mainly. They can be as big as, for example, France, the country. So, they are super big—they are enormous. And they can be as thick as, let's say, 1000 meters. So, this is a massive [piece of] ice that we have in our planet.

And beneath that massive ice, we can have a very peculiar and a special habitat in which microbes live without light. They have to manage, to thrive and reproduce, without using a standard energy like we have on the surface of the sea or in the forest, where we have light that is driving and providing the energy for the ecosystem. But in this case, these ecosystems are totally different.

[The ice shelves] are deep and interconnected. Basically, there are different oceanic currents, for example, there is one Circumpolar Current that surrounds Antarctica, and there are also other currents that basically go from the bottom to the surface, moving, you know, all the water masses.

The interesting part of this story is that every single second in our lives, this sea that is beneath the platform, the ice shelf, is frozen over and over, and then we have different layers of antiquity that preserve the microbes that are living in the ocean. So, for example, let's say, 1000 years ago, the sea water was frozen, and then we can find a layer beneath the Antarctica ice shelf, where these microbes are preserved and frozen. Basically, it's like a record—a library of microbes, fossil records of microbes—from the past ocean, from 1000 years ago until present, more or less.

And then we can go to these records, to these layers of frozen sea water, and pick these samples to somehow recover the genetic material of the microbes that were preserved and frozen 1000 years ago or 500 years ago, in the way that we can somehow reconstruct or build the genetic story of the microbes from the past, for example, pre-industrial revolution to present.

We need to think that microbes sustain the rest of the food web. So, they sustain of the rest of life in the ocean. They provide carbon for the rest of organisms, the fishes, whales [and other] big animals that we have in our oceans. And if the microbes are responding in a way that is not satisfactory, or in the way that we think can maintain the food web, this is kind of scary. And this is what we are trying to do: we are trying to go back to the past and see how the microbes are changing [genetically].

Sample Collection

We didn't collect the samples. [They were collected] back in the 90s, so, 40 years ago, by a German group led by the Alfred Wegener Institute, which is probably one of the most famous polar institutes in the world. They, basically, led an expedition, I think it was in 92, and they decided to go to this ice shelf in Antarctica, in the Filchner–Ronne Ice Shelf to collect these ice cores.

And then the surprise was when they were progressing in the drilling, they realized that on the top part of the ice core was fresh water, meteoric snow that was compacted forming the ice. But they realized that below that part, there was a sea water that was frozen. And then they thought that these samples were very interesting, because they somehow store material from the past, and they shipped these samples to Alfred Werner Institute in Bremerhaven in Germany.

And half of the samples were stored for 40 years until I decided to contact the Institute and to propose this research. And I basically contacted the director of the Institute, and also the group of Frank Wilhelm, to propose the idea. And basically, I said, 'Hey, I think what you have in your research is a valuable material that that can provide interesting answers for climate change and microbiology.' And they say, 'Well, that's interesting. And we never thought about that.' And then we started a collaboration to dig into these questions.

Shipping the Ice Cores

We had a meeting after one of the first pandemic lockdowns, when they allow [me] to travel. I went to Bremerhaven to have a personal meeting with the team. And we decided to ship some samples to Spain.

They arrived frozen and very well packaged and preserved in an isolated container. But it was really surprising to see that that they were delivered in the same compartment with a dry ham. That was a that was a funny story!

Sample Preparation

When we received the samples, the first thing was to basically decontaminate the surface of the [ice]. Because when you unpackage, you have an ice core, pieces like a half meter. And then, we have to think that this ice core has been manipulated by different groups, different people. And you have to decontaminate the surface of the ice core in order to just have the center of the ice core for the for the investigation.

And basically, we adapted a protocol in order to make sure that we didn't have cross contamination from the rest of the from the surface.

So, what we did was we melted the center of the core—well, in fact, different parts of the core with different ages, from 1000 years old to 200 years old—and we melted in a very dedicated laminar flow hood that we have in a clean room. And then, we extracted the DNA from that piece. And in our case, the amount of DNA was so little that we had to amplify with some molecular techniques in order to have [enough] copies of this genetic material to do sequencing.

Sample Analysis

I will say that we are in the middle of the project. We had, like, 2 years ongoing for the project.

The most surprising was 2 things. One, in the sea water, beneath the Antarctic, we discovered a very autoctonos (indigenous) viral community that was quite different from the rest of the world, I will say, from the rest of the ocean. So, I think this viral community is quite adapted to infect the microbes that are living in this peculiar environment beneath the Antarctica ice shelf.

And these viruses were carrying some genes that we think are very important for microbes. We call these genes auxiliary metabolic genes. And these genes are very important because somehow the viruses provide these pieces of information, of DNA material, to microbes that are driving important ecological roles, like, for example, carbon fixation.

It's very important, because carbon fixation is probably the primary step in all ecosystems—to provide food for the rest of the organisms. And if this is altering, or we are altering it with different factors—like temperature increase, like melting of the ice—its going to change these patterns and the rate of carbon fixation. This is going to produce a deep impact for the rest of organisms.

We are still investigating, but we think that it's interesting to think that microbes that live in our ocean now are responding to stressing factors like increasing temperature and also acidification by different ways. In fact, it is unclear—it is a very hot topic and a very hot question—because we don't know for sure what the fate of these microbes in our oceans is going to be. For example, people think that we are going to lose biodiversity. There are some hypotheses that say that heterotrophy is going to be more predominant in the sea water. But it's unclear, because we don't really have fossil records that can compare the past to the present, and this is what we can provide, or at least potentially provide. We can say, 'Hey, we can go before the industrial revolution, before the CO2 increase, and try to compare series of different samples until the present in order to see if, for example, heterotrophy, or microbes that are heterotrophs, are more predominant in modern samples compared to unseen samples.

Episode Summary Mother-Son duo, Brenda Wilson, Ph.D., professor of microbiology and the Associate Director of Undergraduate Education in the School of Molecular and Cellular Biology at the University of Illinois at Urbana Champaign and Brian Ho, Ph.D., researcher and lecturer at the Institute of structural and molecular biology, a joint institute between the Department of structural and molecular biology at the University College of London and the Department of Biological Sciences at Birkbeck University of London discuss the inspiration and motivation for their recent book, Revenge of the Microbes: How Bacterial Resistance is Undermining the Antibiotic Miracle, 2nd Edition, emphasizing the global nature of AMR and providing a unique perspective on what is needed to solve it. Ashley's Biggest Takeaways:

• Dynamics surrounding the AMR crisis are complex and require an understanding of many different perspectives, including those of the farmers, health care professionals, pharmaceutical companies and individuals, in order to foster true and lasting global collaboration on the issue.
• Point-of-care diagnostics are critical to improving treatment decisions and reducing hospital costs.
• Better communication and education are needed in order to rebuild trust in scientists and institutions.
• Continuous research is necessary, as AMR will continue to evolve.
• Citizens are a key piece of the puzzle when it comes to pushing for change and supporting solutions to AMR.

Featured Quotes:

Wilson: "I'll start with actually my Ph.D., which is talking about bacterial antibiotic biosynthesis. And so, I did some work in that arena, but since then, I've actually been working on bacterial protein toxins. These are very potent eukaryotic modulators that when bacteria get into the host, they release these proteins that are very large, that are able to interact with very specific cells. They actually get inside the cells—into the cytosol—and then they affect various signaling pathways in the host that can go anywhere from killing the cell to modulating some of the processes that the cell undertakes, even differentiating them and causing cancer. So, one of my main focuses in my lab has always been to understand the structure and function of these toxins, to understand how they affect the eukaryotic cell system. And then now that we know a lot about them, we're actually moving more into the direction of trying to basically use them as biologics. We have some platforms that we call bacterial toxin inspired drug delivery, where we're using the mechanisms of how they work and their exquisite specificities to be able to actually use them for therapeutic applications." Ho: "I got my start doing molecular genetics, actually, with John Mekalanos at Harvard, and I was kind of at the ground floor of the seminal work looking at the Type VI secretion system. And so, I got a front row seat to the kind of discovery and a lot of the initial understanding of the system. And I've kind of taken that work and expanded beyond it to look at kind of the ways different bacteria interact with each other within microbial communities. So my current work is looking at both DNA conjugation as well as the type six antagonism, and how the bacterial interactions kind of work together to build a larger population dynamics and interface with like the hosts that kind of house a your microbial communities." Antimicrobial Resistance Wilson: "In 2005 [when the first edition of Revenge of the Microbes was written], there was very little activity or understanding about antibiotic resistance and how important it was. Outside of the field, doctors were encountering it. But oftentimes what was happening is they just said, 'Oh, well, we'll just find another drug, you know.' And pharmaceutical companies, they were recognizing that there was a problem, and they would go off trying to hunt for new ones. And then right around the late 90s, there was a big impetus, because they thought, 'Oh, we, we have a miracle here, because we now do complete genomes. We can get out the comparative genomics and all the high throughput things, all the animations,' and that this would lead to many more new discoveries. And I think the pharmaceutical companies were very disappointed, and they started backing out of what they deemed a huge commitment. Two decades later, people already were starting to get aware, at least in the field, and even the industry and the physicians. People were getting aware, but I think that they were stumbling, because of their silos, in trying to get interactions with each other. And I think part of it was that they felt that, 'Oh, we can try to solve it ourselves.' And in reality, this is a problem that that is concerning everyone, and everyone is contributing to it. Everyone has to find a solution to help, and we need to have more synergy. There have to be more interactions, and we have to do this at a much more global scale. And so that was sort of what, what we thought when we first started the [2nd edition of the book, Revenge of the Microbes]." Ho: "At that point, I was just starting my new faculty position, and so I started having to teach students directly. And a lot of students were coming in and giving their presentation on their research proposal or project that they have, and they very adamantly declared the reason why we have antibiotic resistance. 'The problem is because doctors are over prescribing antibiotics.' And I'm scratching my head—a little like, 'Hmm, that's a really confident statement that you're making.' Next student comes in and they're talking about, 'Oh, it's all the farmers that are overusing antibiotics and causing the problem.' And then the next student comes in like, "Oh, the greedy corporations or pharmaceutical industry is trying to milk us for everything, and antibiotics are not profitable enough.' And, and I'm sitting here listening to the students who have a very narrow perspective. And clearly, they're getting it from whoever is teaching their classes. And so, it feels like every single perspective at every single stage, they only see things through their own eyes, and can't understand what the broader perspective is and why you have all these various different problems, and I guess we call them stakeholders in the thing. It is that that every different angle has its own personal motivations. Corporations do need to have money and persist to exist. Doctors, if you encounter a patient that is dying, well, you have a moral compulsion to actually treat them. And farmers having their livestock, well, their livelihood is at stake if they don't have their animals survive, right? And so, what I think was really important that we wanted to do is present the problem of antibiotic resistance and the way it works and why it's an issue, but also convey different perspectives on it, so that if people can kind of understand where everybody else is coming from, we can come together and have a more unified perspective, or understanding, at least, so that you're not thinking that everybody is this malicious actor, and you can actually work together to come with up with a complete solution." Wilson: "The first book, was very important, because you needed to get people's attention right, right? But we got the attention. So, now let's come up with a plan! And we don't have a good plan. People are making progress. People are moving in the directions that need to be moved, coming up with alternatives, coming up with, you know, even financial solutions, to some extent. They're not enough, still, and it's going to take a global community to come forward and buy in to the problem. And I think we still have a large sector of our whole global community that are not really fully aware of what really this problem entails. They hear on the media and the news, 'Oh, the crisis is here. We're in danger.' And then a year later, they say, 'Well, what happened? Nothing's happened.' It hasn't impacted their lives yet, right? Or at least not in a way that they've noticed. And I think this is why we need more awareness. We need to get the word out there. We need to actually start having folks that make some of the big decisions, both financially, regulatory and other types of things, like education." Ho: "One really big problem I think that COVID introduced us to, is that it's not just that we have to convince everybody it's important, but we have to also get people, in general, the population, to trust us. You know, that there is a problem. There's been a kind of an erosion in the trustworthiness, or trust in the institutions that we relied upon that are responsible for keeping everybody safe and healthy. And I think a big part of that is also communication education, that the populace needs to be better educated, but the communication level of people in charge, as well as researchers like us—we need to speak to the people in a way that people can understand." Wilson: "We're not saying that we have a solution, but we do have some directions that, in many areas, have started, and we feel that they need more support. And we're hoping that folks that are reading the book actually appreciate that aspect of it, and then start realizing that, 'Hey, I'm part of this solution too.' It can be very little—being mindful of making sure that we have clean water, making sure that we have food security, making sure that we stay healthy and, therefore, we don't have as many infections, right? Just little things like that that we can actually do as individuals, that as a whole population, will actually contribute to improving the situation. Then, of course, we have to support our leaders in making some of the decisions. We have to let them know that we care about this. And I think at this stage, what we're hoping is that we can maybe encourage some folks to take a citizen stand on this, to ask questions, to start going and probing and saying, 'Hey, congress person, what are you doing about this?' And maybe just start the dialog. This is all we're doing, is starting a dialog."

Links for the Episode:

• The 2nd Edition of Revenge of the Microbes, details the intricacies of the antibiotic-microbe arms race. Beginning with a historical perspective on antibiotics and their profound impact on both modern medicine and present-day society. It also examines the practices and policies driving the discovery and development of new antibiotics, what happens to antibiotics once they are released into the environment, how antibiotic-resistant bacteria evolve and spread and the urgency for finding alternative approaches to combating infections. For anyone interested in antimicrobial resistance (AMR), this is a completely approachable 360-degree view of a very complex topic. Get your copy of Revenge of the Microbes today!
• Want to get involved and spread the word about AMR? Become an ASM Advocate
• Bacterial Pathogenesis: a Molecular Approach
• Take the MTM listener survey!

Joseph James, biologist at the U.S. Environmental Protection Agency, discusses his career trajectory and the creation of Binning Singletons, a unique mentorship program built on peer-to-peer networking at scientific meetings and conferences and was first implemented in 2019 at ASM Microbe.

Links for the Episode Binning Singletons and Peer-to-Peer Networking

• Learn more about Binning Singletons.
• Contact Joe James: [email protected]
• Follow Binning Singletons on Bluesky.
• Binning Singletons: Mentoring through Networking at ASM Microbe 2019—mSphere article.
• Binning Singletons: Tackling Conference Networking When You Don't Know Anyone—Guest post on Addgene Blog.
• Mastering a Mentoring Relationship as the Mentee—asm.org article that James says has really helped him explain Binning Singletons as a coaching form of mentorship.
• Mapping a Mentoring Roadmap and Developing a Supportive Network for Strategic Career Advancement—article on developing networks of mentors, another area Binning Singletons tries to address.
• #FEMSmicroBlog: Networking at Online Conferences (for Early Career Scientists).
• Take the MTM listener survey!

James' Research

• Dietary lead modulates the mouse intestinal microbiome: Subacute exposure to lead acetate and lead contaminated soil.
• In situ differences in nitrogen cycling related to presence of submerged aquatic vegetation in a Gulf of Mexico estuary.
• Quantifying stream periphyton assemblage responses to nutrient amendments with a molecular approach.
• Analysis of Bacterial Communities in Seagrass Bed Sediments by Double-Gradient Denaturing Gradient Gel Electrophoresis of PCR-Amplified 16S rRNA Genes.
• Use of composite data sets for source-tracking enterococci in the water column and shoreline interstitial waters on Pensacola Beach, Florida.

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

• ASM Guidelines for Biosafety in Teaching Laboratories
• Pakistan Biological Safety Association
• Training to be a Biosafety Professional (video)
• Take the MTM listener survey!