Hello and welcome to Healthbeat's weekly report on stories shaping public health in the United States.

I am Dr. Jay K. Varma, a physician, epidemiologist, and public health expert currently serving as chief medical officer at Fedcap, a national nonprofit focused on economic mobility and well-being for vulnerable communities. Views expressed here are my own.

Antibiotics are one of the most important inventions of the 20th century. They made it safer for humans to do virtually every normal activity: breathe air, drink water, eat food, and have sex. In fact, we depend on antibiotics so much that we now face a vexing situation: We need to start taking fewer antibiotics, and we need to start making more of them.

In this week’s report, I review a new research finding that even a single course of antibiotics may disturb our body, the over-prescribing of antibiotics by dentists, and new Food and Drug Administration action to address a shortage of one of our oldest antibiotics: penicillin.

Do antibiotics harm your body?

A large new study published in Nature Medicine this month offers some of the most compelling evidence that antibiotics could cause lasting harm to our gut microbiome. The gut microbiome is the dense, diverse community of bacteria that live in our intestines and help with digestion, nutrition, and immunity. 

Researchers in Sweden linked prescription records from 14,979 adults to data about each adult’s microbiome (specifically fecal metagenomics data) to study the question: Does antibiotic use in the past eight years show up in the gut microbiome today? The answer was, “Yes.”

First, associations between antibiotic use and lower gut microbiome diversity were detectable for antibiotics whether they were taken within the past year, one to four years earlier, or four to eight years earlier.

Second, the effects varied sharply by drug class: Clindamycin was the most damaging, with each course taken in the past year associated with an average of 47 fewer gut species detected. Each course of fluoroquinolones was associated with 20 to 21 fewer species. Standard penicillins, by contrast, showed minimal or no association. (More on penicillin below.) The gut, it seems, has a long memory for antibiotics.

I routinely have to convince patients (as well as friends and relatives) why they do not need antibiotics for their runny nose, benign skin rash, or upset stomach. Often they become frustrated, believing that I am somehow gatekeeping a precious and harmless resource that will relieve their symptoms. One way that I try to assuage them is to explain all the ways that antibiotics could actually hurt, not help, them.

Antibiotics can wipe out protective bacteria in the gut, increasing the risk of Clostridioides difficile (C. diff), which kills nearly 30,000 people in the United States annually, as well as Salmonella and other foodborne bacteria. Repeated antibiotic use has also been linked to an increased risk of obesity, type 2 diabetes, cardiovascular disease, and colorectal cancer — all potentially through microbiome disruption.

The effects are also not limited to the gut microbiome. Another study just published in Nature highlighted potential risks to the respiratory tract microbiome when doctors inappropriately prescribe a “Z-pack” to patients with Covid. 

Whenever we prescribe a drug, we are balancing harms and benefits. The benefit of antibiotics outweighs the harms for many infections — both to cure infections that you currently have and for infections you might get after a high-risk exposure.

Whenever a doctor tells a patient that a conventional therapy could harm them, we run a risk that we will frighten them away from taking a medication that could save their lives. (Look at this bizarre and inappropriate statement recently from FDA Commissioner Marty Makary that he would only give his young child antibiotics if he was "on his deathbed or suffering.")

The value of studies like the one in Nature Medicine is to help all of us — patients and providers alike — ensure we use antibiotics only when they are truly needed.

Is your dentist prescribing too many antibiotics?

I recently experienced a version of this problem myself. In February, I had to get urgent dental work done, and the dentist prescribed me a week of amoxicillin after the procedure.

I went straight to the medical literature to review the evidence for whether antibiotics are proven to prevent infection and promote healing after the specific procedure I had done. The answer was: There is no evidence of benefit, but it is standard practice by many dentists.

Journalist Liz Szabo has just written an illuminating three-part series about dentists over-prescribing antibiotics. She describes how dentists wrote 27.3 million antibiotic prescriptions in 2025 and that 80% of preventive dental antibiotics are inappropriate, meaning they are prescribed to patients before or after procedures where there is no evidence of benefit.

The second most commonly prescribed antibiotic by dentists is clindamycin, the antibiotic found in the Nature Medicine study to have the most severe impact on the microbiome and a drug that carries a black-box warning — the FDA's strongest caution — for its risk of causing life-threatening C. diff infections.

In addition to the risks to individual patients, every unnecessary antibiotic prescription accelerates the evolution of bacteria that can evade our drugs. Drug-resistant infections already cause an estimated 5 million deaths worldwide each year, a number that is growing as pathogens evolve new ways to survive in the presence of antibiotics. 

Changing the behavior of health care providers — whether they are dentists, physicians, or others — is hard. What we learn in our training, even if it’s incorrect, often becomes our default practice for life. With opioids, it took a national crisis, widespread legislation, and mandatory continuing education before dental opioid prescribing meaningfully declined. 

The rise of the anti-vaccine movement may also further increase antibiotic use. One of the best ways we have to prevent antibiotic use is to prevent infections in the first place by taking recommended vaccines.

And, in case you're wondering, I did not take the antibiotics my dentist prescribed, and, so far, my teeth are OK.

We have a dangerous shortage of penicillin

Of course, infectious diseases are still a major public health problem, and antibiotics are often life-saving. What we try to teach clinicians is to prescribe the right drug for the right bug at the right dosage for the right time.

That is, make sure you know what bacterial infection the patient has, then prescribe an antibiotic that is specifically targeted to kill that bacteria using the correct dosage for the least amount of time necessary.

What happens, however, when the right drug is not available? And that drug happens to be one of the oldest and most useful antibiotics we have?

One of the most common sexually transmitted infections in the United States is syphilis, and, unlike many other bacteria, it remains uniquely susceptible to plain old penicillin, specifically a long-acting injectable form called Bicillin L-A (benzathine penicillin G). 

Syphilis rates in the United States have been rising sharply, particularly in pregnant women in whom untreated syphilis can lead to stillbirth, organ damage, and death of the fetus. No other antibiotic can reliably substitute for Bicillin L-A. 

Unfortunately, only a handful of manufacturers worldwide are willing to produce an old drug that is not very profitable. As syphilis cases increase, the United States has been experiencing recurrent supply shortages of Bicillin L-A.

The shortage has gotten so acute that the FDA has authorized the temporary importation of a version of benzathine penicillin called Lentocilin, made by a Portuguese company not normally licensed to sell in the United States. (Interestingly, the only U.S. company willing to import Portuguese penicillin was the Mark Cuban Cost Plus Drug Co., a venture by the billionaire entrepreneur aimed at lowering consumer drug prices.)

On March 10, the Centers for Disease Control and Prevention issued guidance to health departments across the country explaining how to use Lentocilin and urging them to conserve the remaining domestic supply of Bicillin L-A.

It’s a difficult paradox that I have to warn both about the danger of excess antibiotic use and the loss of access to antibiotics. Antibiotics are fundamentally a public good, and, as with other public goods, their supply is limited.

When we act as if supply is unlimited — prescribing them too much and for the wrong reasons — we degrade a resource we all need.

ICYMI

Here’s a recap of the latest reporting from Healthbeat:

• Measles: Spring break travel risks spread of measles throughout U.S.

• Health funding: NYC health department submits budget plan while bracing for federal cuts 

• Global public health: How to win the war of narratives

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Until next week,

Jay