Science Friday - Conflicting Directives Sow Confusion For NIH Workers | The Mycobiome

Episode Date: February 28, 2025

The acting head of the NIH reportedly pushed back against legal guidance to resume grant funding, leaving federal workers in the lurch. Also, though fungi make up a tiny part of the human microbiome, they play an important role in both the prevention and development of many diseases.Cuts And Conflicting Directives Sow Confusion For NIH WorkersJust over a month after President Trump’s inauguration, federal science in the US is in a state of disarray. Executive orders to halt grant funding at the National Institutes of Health (NIH) have faced court challenges. Last week, a federal judge extended a restraining order on a proposal to cap NIH grant funding for indirect costs, costs that experts say are critical to their work. But according to new reporting, staff within the NIH have been left without clear guidance about moving forward with those grants, with the NIH’s acting director reportedly pushing back against legal guidance from the agency’s lawyers to restart distribution of the funding.Host Flora Lichtman is joined by Katherine J. Wu, staff writer for The Atlantic, who reported on the turmoil at the NIH. They also talk about other science news of the week, including an update on the measles outbreak in Texas, how to see every planet in the solar system this week, and how scientists think runner Faith Kipeygon could be the first woman to break a four-minute mile.You’ve Heard Of The Microbiome—Welcome To The MycobiomeYou’ve heard of the microbiome, the community of bacteria, viruses, archaea parasites, and fungi that live in our bodies. But that last member of the group, fungi, get a lot less attention than the others. And perhaps that’s unsurprising. After all, bacteria outnumber fungi 999 to 1 in our guts.But now, scientists are beginning to piece together just how important fungi truly are. Disruption in the fungal balance can play a role in the development of Crohn’s disease, irritable bowel disease, celiac disease, colorectal cancer, some skin diseases, and more.Host Flora Lichtman talks with Dr. Mahmoud Ghannoum, microbiologist and professor at Case Western Reserve University’s School of Medicine, who has dedicated his career to studying the fungi in our bodies, and coined the term mycobiome over a decade ago.Transcripts for each segment will be available after the show airs on sciencefriday.com. Subscribe to this podcast. Plus, to stay updated on all things science, sign up for Science Friday's newsletters.

This is Science Friday. I'm Flora Lichten. Five weeks into the Trump presidency, federal science funding in the U.S. is in a state of confusion. Executive orders that have halted grant funding at the National Institutes of Health, the NIH, have faced court challenges. Last week, a federal judge lifted a freeze on some NIH funding. So is the NIH making new grants? What's the directive? It's opaque from the outside. Is it any clearer on the inside? Catherine Wu, staff writer for the Atlantic, talked to nearly a dozen former and current NIH officials to find out what's happening on the inside of the NIH campus. She's here to catch us up on that and other science stories of the week. Katie, welcome back to Science Friday. Always good to be here. So there's a lot going on, and you actually spoke to NIH workers about what it is like to try to do their jobs.

What did you find out? Yeah, I think it is fair to. say that this has been one of the worst five-week stretches in a lot of NIH officials' career. It is just a mess in there. I think they are battling a lot of really conflicting things. They are telling me that they are caught between their duty to their direct leaders, including their acting director, what is legal according to the literal law in this country, and their duty to the American public to protect and preserve and promote their health. Who is the acting director? Who's running the NIH show right now? Right. So for the past few weeks, it has been a flu researcher named Matt Memley, who was kind of picked out of a part of the NIH that does not typically yield acting directors. There actually usually is a deputy director who typically steps into that position when directors are in transition. But that didn't happen. And why was he picked?

So I can't say for sure. I'm not in the brain. with the people who did the actual selection, but the rumor mill suggests that it was for largely political ideology reasons. Matt Memley gained some note of fame a few years ago when he emailed Anthony Fauci criticizing COVID vaccine mandates, and that became public. He publicly critiqued the idea of COVID vaccines reportedly refused the shot himself, at least in 2021. And he's also gotten sort of chummy with Jay Baticharia, who is Trump's nominee to lead the NIH next. And I was made aware that he submitted a DEI statement for an internal review at the agency where he called the term DEI offensive and demeaning. Okay. So is the NIH making grants right now? Like, what is the state of

grant making? Oh, gosh. I think the answer is sort of question mark. And I think that's actually a pretty fair assessment. I mean, normally we see tens of thousands of grants come out of the NIH every year. And there is still kind of a trickle. It's been happening in fits and spurts. It's been really, really stop and go at the agency since basically the end of January. But it is nowhere near the typical cadence that is necessary to support biomedical research in this country and frankly abroad. So the big issue here is that they have been told by their leaders, including Emily, and the folks at the Department of Health and Human Services, which oversees the NIH. But they are not to be issuing grants, and that is to be in compliance with President Trump's recent state of executive orders, including ones on DEI, gender, foreign aid, environmental justice.

Basically, the agency is not supposed to be funding grants that would violate those orders. But they've also been told by federal judges, it's not legal to be withholding those federal funds. We allocated those funds to you as a country, and you are supposed to be giving them out. So it is a total and complete mess. And what about – are there sort of competing directives within the NIH? So within the NIH, I would say that if you are looking to leadership, the message has largely been the same. Okay. Hold off. We're figuring things out.

We're trying to do our best to comply with President Trump's wishes. But I think the mixed messaging really comes from the fact that their leaders are telling them one thing. But these are also government workers. They, of course, you know, find the letter of the law very important. And all around them is this swirl of, you know, federal court orders that are saying, no, you really need to get back to business as usual to comply with the law. That is the most important thing. You must unpause things immediately.

And what about the NIH lawyers? What are they saying? Well, the NIH lawyers are certainly experts. in the law and they have been advising leadership, yeah, please follow those court orders. If they're telling you to unpause and get back to grantmaking, that is what you need to do. That is what is what is most legally advisable. And at worst, if they continue to violate some of these court orders, they could be held in contempt, they could be prosecuted as criminals. But I think people are really unsure what to do. If their leadership is telling them one thing, their lawyers are telling

them another thing, HSS is telling them kind of something else. Court orders are saying yet another thing, it's a mess. I mean, some people appear to have resigned over this mess. Is this also happening at other agencies, NSF, EPA? I believe this has been happening to some degree at every federal agency that you could name. But I think what makes NIH particularly special is the size of its budget, which is about $47 billion a year. And the fact that their pause has probably been one of the most prolonged and severe. You know, just for sake of comparison, the National Science Foundation, NSF, they resumed a decent degree of grantmaking as early as February 2nd. Things are by no means completely perfect and running smoothly over there.

But just for comparison, I think that shows that federal agencies are handling this very, very differently depending on their leadership, depending on who is overseeing that particular agency, and likely, you know, what staff internal to the agency are attempting to accomplish in this mess. Let's talk about the measles outbreak in Texas. What's the state of that? It is not great. As of this week, we have hit triple digits in terms of the number of confirmed cases. An unvaccinated kid has died amid the outbreak, which is the first measles death that the country has recorded in over a decade. It's incredibly tragic. I mean, this is a dire situation. This is one of the bigger outbreaks that we've had in recent years. And I'm already hearing experts talking about. the fact that this could be an outbreak if it continues to grow and size and the deaths continue, this could be something that could lose the country. It's elimination status for musals, which we declared in the year 2000. I need a break from our planet for a second. It's a pretty

special weekend for stargazers, right? Yeah, absolutely. I fully agree. Life on Earth is super stressful right now. I am constantly trying to look elsewhere. And tonight, I mean, I need to sort of check if my zone of habitation is in the right spot, but for some lucky people, if they have the right stargazing equipment, they can look upward and may be able to see all seven of the other planets in our solar system. Oh, the planetary parade. Yes. And I will say, like having some degree of what's called planetary alignment, which is, you know, being able to see more than one planet up in the sky at any given time isn't like super rare. But to have all seven of the other members, of the solar system up there at once and potentially visible. That's pretty cool.

I read that it won't happen again until 2040. Yeah. So if this is your jam, I would definitely get in there. You're going to be waiting a long time. Okay, let's move on to one of my favorites from the week. A glass brain. Tell us all about it. Oh, yes. So if you are an archaeology nerd, you may already know about this glass brain that was uncovered from the region that was, you know, seriously impacted by the Mount Vesuvius eruption 2,000 years ago. And I do want to note that this isn't quite in Pompeii, but it's adjacent to Pompeii. But basically, researchers a few years ago found what looked to be nerve tissue that had glossified. What happened this week as researchers came out with a paper that suggested a new explanation for,

how the brain tissue could have glassified. And the big problem before is to get glass, you need to heat something very, very quickly and then cool it very, very quickly. That's typically what happens with like the molten sediment that we use to make like the glass we see in our homes. But that wouldn't have happened very easily with an eruption like this. So the researchers said, well, maybe it wasn't all the like thick volcanic debris. You're picturing when you picture an eruption. Maybe in advance of that, this super hot cloud of ash hit the, this poor guy who was lying down in his bed, glassified his brain, and then dissipated really quickly because it was just ash. It could move really quickly. And that's how the super fast heating

and cooling happened in that short time frame. All right. I'm lacing up my running shoes. Well, in my case, my slow, slow jogging shoes for our last story. Researchers have crunched the numbers and think that Kenyon Runner, Faith Kipiagan could break the four-minute mile. Is this a big deal? Oh, it would be a huge deal. So no woman has a woman has. been recorded doing this, a man broke the record, well, multiple men have broken the record as early as the 1950s. But to have a woman break this record as well would be not only just another amazing feat of human performance, but I would also hope would be really inspiring to people across the gender spectrum, just to think like this is not one of those things where, oh, a man can do

it, but a woman can't. I think that's an incredibly important message to send. So the idea here is, I I mean, she is close, but also not close. Her record is four minutes and seven point six four seconds. And to non-runners, that may not sound like a lot, but to people who are sprinters, that is a huge chasm to be breaching. And so people have been really skeptical that this could happen. I mean, she currently holds the world record for a woman. So she is an incredible candidate, but it would be really tricky. What these researchers are saying is what might be the trick is to have really strategically, placed pace setters during a race to basically be in front of her and in back of her to reduce drag. So, you know, the force that would be working against her from like wind resistance

and all that stuff. But if you have strategically paste people, you're basically able to draft off of those people and run to your maximum ability without having to battle as many external forces as you otherwise would. What did Faith have to say about this? So I believe she was interviewed by the New York Times on this. And I think she called it interesting. I don't think she really wanted to, I suspect she didn't really want to guarantee that this was going to happen or not. But she seemed to be very gracious. I mean, if someone did this modeling study on me, which they definitely wouldn't because I'm the world's slowest runner, I would also say it was intriguing, but like TBD on what's going to happen next.

Thanks, Katie. Thanks for joining us today. Thanks so much for having me. Catherine Wu is a staff writer at the Atlantic. Before we go, Next Friday is the stand-up for science rally in Washington, D.C. and across the country, are you planning to go? Tell us about it. How far are you traveling? Is there a crowded van involved? And why are you going? Call us or text us at 646-767-6532. That's 646-66-7-6532. After the break, you've heard of the microbiome, but how about the mycobiome? A researcher makes the case for why the fungus among us is vital to our health. Bacteria and fungi, they interact together and they play together.

When I hear microbiome, I think of the billions and billions of bacteria that call my body home. But the microbiome is more diverse than that. It includes viruses and parasites and fungi. And that last group doesn't always get a lot of attention. Partially, it's a numbers thing. Fungi are outnumbered by bacteria about 1,000 to 1,000 to. one in the microbiome. But even if they're a smaller sliver of the population, according to my next guest, that does not meet our fungal friends and foes are less important. When your fungal feng shui

is off, things can go afoul. Fungi can play a role in Crohn's disease, irritable bowel, celiac diseases, colorectal cancer, and more. Our next guest has been banging the drum for fungi for many years. Over a decade ago, he coined the term mycoboom to shine a spot. light on these misunderstood mycelium. Dr. Mahmoud Ghanoum is a microbiologist and professor at Case Western Reserve University's School of Medicine based in Cleveland, Ohio. Welcome to Science Friday. Thank you for having me. Let's start with the basics. How do you define the microbiome? As you mentioned, in our body, there are microbes that live in and on our body, on the skin, in our God, all over the place. One important community of these microbes is the microbiome.

And as you know, my ecology is the study of fungus. So we coined the term mycoboom to refer to the fungi that live in our body. No one had coined that term before. Nobody had coined this term before us. And really it came from the fact that for many, many years, I worked with fungus. And I always knew that bacteria and fungi, they interact together and they play together. So about 15 years ago, when people were talking about the microbiome, they talk about bacteria, I told them, no, no, no, you really need to talk about fungi as well, or the fungus that live in our body.

And that's where I thought it would be a good idea to differentiate the bacteriome. which is the bacteria from the microbiome, which is the fungus. Did it work? Did people heed your call? You know, it's so funny you ask this question. For a long time, people did not listen. I wrote an article 2010 that we should look at both of these communities and nobody listened. 2016, I also wrote another article in the scientists saying the microbiome,

basically the ignored kingdom. And lo and behold, I published a paper after that to look at the microbes that live in the gut of Crohn's disease patients. And I showed that not only bacteria is there, but also fungi are there. And they really interact together and they help each other. After this, people start reaching out to me asking about the fungal community. And really they needed guidance, how we can help them to rebalance. And that's where people start to take lily the microbiome into consideration. In fact, 2021, also the National Institute of Health opined at that time to say, yes, we really need

to look at not just bacteria, but about the other communities on there. And that's really pleased me tremendously because it took them a decade, but they figured it out at the end. Well, how do fungi and bacteria interact with each other in the microbiome? What happens when they are together, you can imagine they are not like in suspension. They stick together. They adhere to the tissue in our gut, okay, the gut lining, for example. And then what they do, they start secreting some chemicals or metabolites that can change their behavior. In fact, to give you a specific example, we found that E. coli and Syracia marcisans are two bacteria. They interacted with Candidatropicalis, which is a fungi, and they formed what we call biofilm.

You know what a biofilm? It's like the plaque in our teeth. I was just going to say, yes, I know about it from my teeth. Exactly. But nobody described them in our gut how they interact together to really cause our issues with Crohn's disease, for example. And a biofilm in your gut, what should I be picturing? The best way to imagine a biofilm, it's like a yellow. Inside this yellow, you have m&Ms or raisins, okay? You're speaking my language, Mahmood. So you have the yellow is the matrix. Matrix is what these raisins and bugs inside the gelo produce.

It's made of carbohydrates, proteins, some DNA, and it becomes like a cover or an area which protects these organisms. Not only this, when they interact together these bacteria and fungi, we showed in animal models as well as in vitro or test tube experiments that the shape of the candida changes. So if you have a plat or biofilm of candida alone, it's in the shape of yeast like baker's yeast, okay? When you put them together with the E. coli and syracia,

they form what you call filaments or hyphae or like thread-like material. And what happens, these thread-like material, they start to poke holes in our gut lining. And that's why we have leaky gut, and they are protected from antibiotics or antifungals because of the matrix, which we talked about the yellow, as well as they are protected against our immune cells. You find the immune cells are unable to go in and kill these bad bugs. Wow, so they're working together in some cases. Yes. You know, we hear a lot about how antibiotics wreak havoc on our microbiome.

And I think, when I think of that, I think about the effects to bacteria. But has modern medicine changed our fungal makeup? Yes, definitely. You know, you will laugh at this. I am an old man. Now I am 75 next May. I did my PhD or doctorate 50 years ago. Okay?

The 50 years ago, my project was how antibiotics and steroids can affect candidate. In other words, when you use an antibiotic, what happens, you kill not only the bad bugs or the bad germs that are causing disease. We kill also the beneficial one, which keeps Canada under control. Okay? So that's why when you use an antibiotic, definitely it wreak havoc in your gut balance. You know, we hear about these good bacteria. Are there good fungi?

Yes, certainly. Thank you for asking this question because a lot of the time people think of fungus. our bad thing. Apart from the mushrooms, of course, people love those. Now, we have good fungi or good yeast like Saccharomycese service. You remember, Saccharomycese servici is what we use to bake our bread and make beer. And we found in healthy people, we have high level of this good yeast or good fungus. Wait, if you're healthy, you have a high level of bread making and beer making yeast in your Yes, yes. Do we know what these good fungi are doing? Yes, we know, of course. Remember, I mean, fungi, I know a lot about fungus, okay? So what they do, they can control the ability of Candida to grow.

And Candida is like the fungus we know is associated with like yeast infections and thrush. We don't want that one out of control. We don't want that out of control. But I love the word you said out of control. Why? Because if you look at people in general, healthy people, or you have maybe 50 to 70% of us have candida in their gut. If it is at low abundance, it's no problem. We can take care of it because the good guys can keep Canada under control. The problem starts when we kill these good guys. This gives Canada the opportunity to overgrow. And lo and behold, will it overgrows, believe it. it or not, what it does, it keeps the good guys down. So as if we killed the policeman and we keep

the policeman under control. That is not good for us. Okay. So the beer bread fungus keeps the bad guys under control. What I'm hearing you say is that this is an argument for drinking more beer and eating more bread. Unfortunately, biology is not as simple as this. I agree with you. Having a beer is great. So you don't want to take the message from me here that go and drink about five, six beers in a night. So yes, having little alcohol is good, but not too much of it. Do we have to worry about antifungal resistance, the way that we worry about antibacterial resistance? Certainly. I tell you something, you are asking good questions. I'm praising you now. Don't butter me up. I know what you're doing here. You know why? Because you touched on

the topic now, which now is becoming hot. The antifungal We all know about the antibacterial resistant. It's time to think antifungal resistance. There was a new fungi that caused infection in the skin discovered in India, which is resistant, highly resistant to thirbinophen, one of the major drugs we used to treat nail infections. And lo and behold, we are starting to see it in the US as well.

And there was big interest from the CDC asking people to submit applications to understand what is the extent of really spread in the U.S. I tell you, this is an area that needs to be addressed because in addition to antibacterial resistant, we have now antifungal resistant. Why do you think the microbiome has been overlooked for so long? You know, because for a long time, we did not have a lot of fungal infections. Okay, it was mainly bacteria. But what happens, we change medicine, the way we practice medicine.

I'll give you a simple example. When you have cancer, you are treated with chemotherapy, radiation, and all this stuff. And guess what happens? You lower the immunity of the patient. And when a patient has low immunity, this gives the opportunity for fungi to cause infection. That's why we call it opportunistic infection. They take the opportunity when somebody's immunity is weak, it's started. And that's why now we are seeing more fungal infection than we used to see, let's say, 40, 50 years ago.

And so now people are paying attention. I hope so. Thank you so much for this fascinating conversation. You are most welcome. It's a pleasure to talk to you. Dr. Mahmoud Ghanoum, microbiologist and professor at Case Western Reserve University's School of Medicine based in Cleveland, Ohio. And that is about all we have time for. Lots of folks helped make the show happen, including Jordan Smudjik, Charles Bergquist, George Harper, John Dancosky. I'm Flora Lickman. Thanks for listening.