Megan Murray has been in limbo. The Harvard University epidemiologist and infectious diseases doctor has grants from the U.S. National Institutes of Health to fund ongoing research on tuberculosis. Over decades, her work has produced insights on how TB spreads, how genetic and microbial characteristics interact in the disease and better ways to diagnose TB in people who don’t have symptoms. NIH told Murray in September that she would be getting a large new grant to study long-term lung damage from TB.
Yet between April and October, the agency didn’t give Harvard any money. Many of her colleagues and collaborators have had their grants cut or suspended. “Weirdly, my grant” Murray says, “was not terminated.” In principle, the money was restored in October, but the government shutdown meant she couldn’t spend it. Without money from NIH in hand, Murray was in a strange netherworld in which she both did and didn’t have research funding. Her scenario highlights the damage being done to biomedical research as labs get caught in battles between the Trump administration and academic institutions.
Harvard is just one of the universities that had its federal research funding threatened in 2025 as the Trump administration waged a campaign to reshape higher education according to the president’s agenda. In a post October 12 on his social media platform Truth Social, Trump wrote that “much of Higher Education has lost its way, and is now corrupting our Youth and Society with WOKE, SOCIALIST, and ANTI-AMERICAN Ideology.”
Murray was drawn into the fray when the administration froze $2.2 billion in NIH grants to Harvard researchers. The administration claimed that the university failed to protect students and faculty from antisemitism on campus. Harvard sued, and a federal judge ruled that the administration’s actions violated First Amendment rights to free speech, saying the government could not enforce these funding freezes or terminations. The government said it will appeal the ruling and is trying to ban Harvard from getting federal funds in the future.
Some universities have bowed to administration demands to keep federal funds flowing. In July, Columbia University agreed to pay $221 million to the federal government to settle antidiscrimination charges similar to those levied against Harvard and restore grant funding. Brown University and the University of Pennsylvania also struck deals with the administration, while several other universities have been locked in negotiations for months.
In October, the administration sent a compact to nine institutions — later extended to all colleges and universities — asking them to agree to provisions such as ending diversity, equity and inclusion programs, dismantling departments the administration deems hostile to conservative ideas, defining women according to certain biological characteristics, and limiting the number of foreign students. In exchange, the universities would get priority access to grant money. A refusal may lead to loss of federal benefits.
MIT was first to publicly reject the proposal on October 10; six other institutions followed MIT’s lead by the administration’s October 20 deadline. “Fundamentally, the premise of the document is inconsistent with our core belief that scientific funding should be based on scientific merit alone,” MIT president Sally Kornbluth wrote in a letter to U.S. Education Secretary Linda McMahon. Other schools may make different decisions. On October 27, the New College of Florida in Sarasota announced it would “happily be the first college in America to formally embrace and sign President Trump’s vision for higher education.”
The compact “seems to be trying to federalize our system of higher education and threaten academic freedom,” says Sarah Spreitzer, vice president and chief of staff for government relations for the American Council on Education. If it were implemented, grants would be given not based on merit decided through peer review, as they are now, but by “agreeing to change your governance structure, capping your international enrollment, freezing tuition prices.… How is that tied to your scientific capability?”
These unprecedented actions leave the door open for future administrations from either party to put their political stamp on higher education and science, Spreitzer says.
Murray is the lead researcher on grants supporting large consortia of scientists who examine the genetics and metabolism of people and of tuberculosis bacteria, trace social and nutritional factors that help the disease spread, and conduct studies with animals. Much of the money in Murray’s NIH grant supports research conducted in Peru, where tuberculosis affected 173 of every 100,000 people in 2023. TB is much more common there than in the United States, where only about 3 of every 100,000 people contracted the disease in 2023. That makes infection patterns and risk factors easier to study in Peru.
The Peruvian project has “been a very important, influential and high-value study for a number of years now,” says Richard Chaisson, an infectious diseases doctor at the Johns Hopkins University School of Medicine. “Everything that we learn there, we use here.” For instance, a large TB outbreak in Kansas that started in 2024 has infected 178 people, including 68 active cases as of October 17. “All the tools they’re using to diagnose and treat those people were studied overseas,” Chaisson says.
Part of Murray’s work done in Peru involved recruiting about 18,000 people for a study and collecting blood, saliva and bacteria samples from them. A later study involved samples from roughly 2,000 people.
A lab built inside a converted shipping container houses those irreplaceable samples in multiple freezers in Lima. The lab is owned and operated by Socios En Salud, the Peruvian arm of Partners in Health, an international nonprofit health care provider affiliated with Harvard. The lab was already dealing with the loss of funding from the U.S. Agency for International Development that the Trump administration cut earlier this year. Just over $400,000 is earmarked in Murray’s supplemental NIH grant for the work in Peru. Murray and colleagues couldn’t spend it during the shutdown, leading to worries that they wouldn’t have the resources to recontact 1,000 of those people who were previously cured of the bacterium that causes tuberculosis.
The plan is to conduct tests such as CT scans of the chest and several other expensive procedures to determine which of those people still have lung damage. Then the researchers will compare genetic data from the people and their bacteria, biomarkers in blood and saliva and other factors to see if any patterns can predict who is and isn’t likely to get debilitating lung damage.
“The faster we get back to them, the more likely it is that we’ll be able to find them,” Murray says of the participants. If they can’t be found, the samples they gave earlier would be useless for this study. “We have freezers full of incredibly valuable samples, and they cost money to run,” she says. Without Murray’s NIH grant money, the researchers and health care workers who conduct the screening may be laid off.
Such losses would be significant. No one has really studied TB’s long-term effects, says Maryline Bonnet, a medical epidemiologist at the French National Research Institute for Sustainable Development in Montpellier. “This is extremely important, because we realize now that maybe 50 percent of patients who are cured of the bacteria are living with existing lung disease, which affects significantly their quality of life.”
Murray spent much of 2025 scrambling to find a backup so that if she couldn’t recoup funds from the federal government, she wouldn’t put Harvard deeper in debt. She turned to private donors and nongovernmental organizations for help. She tried to get funding from philanthropy “to make sure the freezers aren’t unplugged, lights aren’t turned off and so that we don’t lose our staff who are incredibly well-trained.” But most charitable organizations can’t match NIH’s investment. And it is increasingly difficult to get funding for work done in other countries.
Labs such as Murray’s may survive in greatly pared-down form, but that could come at a cost to the United States’ economy and health, says Stephen Carpenter, an infectious diseases physician and immunology researcher at Case Western Reserve University in Cleveland. Each dollar NIH spends on research generated $2.56 in economic activity in 2024, according to advocacy group United for Medical Research. If President Trump’s requested cuts to the NIH budget are approved by Congress, 40 percent of that economic activity could be gone. Such deep cuts would slow the pace of developing new treatments for a wide variety of diseases, including tuberculosis.
What’s more, talented scientists may be lured to China, Europe or elsewhere, Carpenter says. “That would be a huge loss for us in innovation, for our intellectual property [and] therapeutics.”
Even though the Trump administration’s ire has been directed at Harvard, Murray says the situation felt a little personal. She hopes she would be seen as a good person who cares about her patients. “But [the administration] would say, ‘No. You’re an elitist university professor who does all these things we don’t like,’ ” she says.
“We’ve been trying to be good global citizens,” she added. “It’s weird to be told that that we’re evil because we’re doing those things.”