“This is clearly a high-anxiety moment,” says former US National Institutes of Health (NIH) director Monica Bertagnolli, who finished her term on 17 January. Since her departure, an onslaught of directives from the administration of US President Donald Trump, a Republican, have sown bewilderment and anxiety throughout the US scientific community, including at the NIH, where research-grant reviews and all external communications have been halted.

Many researchers fear that this tumult will continue if the US Senate confirms Robert F. Kennedy Jr as head of the NIH’s parent agency, the US Department of Health and Human Services. Kennedy has a long history of opposing vaccination and making false claims about the cause of AIDS. He has vowed to “make America healthy again”, in part by overhauling US health agencies to focus on chronic diseases and environmental toxins.

As Kennedy sits for his confirmation hearings this week, Bertagnolli, who was appointed by former Democratic president Joe Biden, spoke to Nature about Kennedy’s norm-shattering ideas, the upheaval at the NIH — the world’s largest public funder of biomedical research — and her biggest fears for the future.

What do you make of the Trump administration’s pause on grant-review meetings and external communications at health agencies, including the NIH?

It’s not unusual for an incoming administration to take a pause until they get their new people in place. But what has heightened anxiety is the expressed mandate of this administration to completely overhaul health. There are so many people that depend on the efficient and responsible functioning of NIH.

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What are the biggest challenges for the agency moving forwards?

Everybody recognizes that when science is under attack, that’s really a big detriment to the agency and to people. It’s great to have discussions about the uses or priorities of science, but anti-science is harmful to us all. To think we would eliminate vaccination is frankly frightening. There’s no question that diseases that existed in my lifetime are gone because of vaccinations, and we don’t want them back.

There’s growing appetite from Congress to reform the NIH, which has 27 institutes and centres. Some proposals call for nearly halving that number. Where do you hope these reforms land?

It’s never a bad idea to take a look at any large, complicated organization and ask if we’re performing optimally and if there are changes that are needed.

There are two components of the NIH structure to remember: it has to serve science really well, and it has to serve those who participate in the research, people who benefit from the research and advocates who care about a particular disease. One of the reasons I would be reluctant to completely collapse all these institutes and centres is that those advocates have, over time, developed these visible institutes as a focal point — as an open door for them.

Kennedy has floated the idea of replacing 600 employees at the NIH. What do you make of that proposal?

It certainly wouldn’t be what I would do, because I will say that the work that I was able to achieve as director argues very strongly against that. I could have all the great ideas in the world, but without the team to accomplish them, they don’t go anywhere.

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Kennedy has campaigned on a platform to ‘Make America Healthy Again’ (MAHA) by tackling the root causes of chronic diseases, removing toxic substances from the environment and combatting corporate corruption. Do you see opportunity in this campaign?

Those ideas that you just articulated are absolutely critical. I take issue with saying that they’ve been ignored by the [previous] team. One of the ways that we had been thinking about that is looking at cross-cutting biological programmes [that] underlie many diseases — the link between obesity and inflammation, for example. We’ve been focusing on these common fundamental pathways and uncovering them to identify someone at risk for developing chronic disease early, and combatting it before it happens.