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Antibiotics wreak havoc on the gut. Can we kill the bad bugs and spare the good ones?

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Antibiotics wreak havoc on the gut. Can we kill the bad bugs and spare the good ones?

Inside every human is a thriving zoo of bacteria, fungi, viruses and other microscopic organisms collectively known as the microbiome. Trillions of microbes live in the digestive tract alone, a menagerie estimated to contain more than 1,000 species.

This ecosystem of tiny stuff affects our health in ways science is only beginning to understand, facilitating digestion, metabolism, the immune response and more. But when serious infection sets in, the most powerful antibiotics take a merciless approach, wiping out colonies of beneficial bacteria in the digestive tract and often prompting secondary health problems.

“Increasingly, researchers are recognizing the benefits of protecting the human gut microbiome, particularly because its integrity and diversity is linked to metabolic influences on mental health and physical health conditions,” said Dr. Oladele A. Ogunseitan, a professor of population health and disease prevention at UC Irvine.

Drug-resistant bugs are evolving faster than new medicines are being developed, rendering the current arsenal of medicines increasingly ineffective. But the more we understand about the microbiome, the clearer it is that we need antibiotics that are discerning in their targets.

With that goal in mind, a chemistry team at the University of Illinois Urbana-Champaign is experimenting with a compound that attempts to address both problems. The antibiotic, lolamicin, both successfully vanquished several drug-resistant pathogens in mice while sparing the animals’ microbiome. The results were published in the journal Nature.

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“Only recently has it been recognized that killing these [beneficial] bacteria is having many deleterious effects on patients,” said Paul J. Hergenrother, a chemistry professor at the University of Illinois Urbana-Champaign who co-led the study. “We have been interested for some time in finding antibiotics that would be effective without killing the good bacteria.”

The team set out to create an antibiotic that would both preserve the gut microbiome while targeting gram-negative bacteria, a particularly hardy category of superbugs. Encased in both an inner and outer membrane that antibiotics struggle to cross, gram-negative bacteria are resistant to most currently available therapies. They are responsible for the majority of the estimated 35,000 deaths in the U.S. each year from drug-resistant infections, according to the U.S. Centers for Disease Control and Prevention.

Worldwide, antimicrobial resistance kills an estimated 1.27 million people directly every year and contributes to the deaths of millions more.

Not all gram-negative bugs make us sick. Bacteria populations in the average human gut are roughly split between gram-negative and gram-positive types, said Kristen Munoz, a former doctoral student at the University of Illinois who co-led the study.

Broad spectrum antibiotics can’t tell which bugs to spare, she said. As a result, anything strong enough to treat a bad infection “is going to wipe out a good amount of your gut microbiome,” she said, even though they “aren’t doing anything wrong.”

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The team focused its search for a new drug on compounds that suppress the Lol system, which shuttles lipoproteins between the inner and outer membranes in gram-negative bacteria.

The Lol system’s genetic code looks different in harmful bacteria than it does in beneficial ones, which suggested to researchers that medicines that targeted the Lol system would be able to distinguish good bugs from bad ones.

The team designed multiple versions of these Lol-inhibiting compounds. When tested against 130 drug-resistant strains of Escherichia coli, Klebsiella pneumoniae and Enterobacter cloacae, one in particular proved especially potent.

They tested this antibiotic, which they named lolamicin, on mice that had been infected with drug-resistant strains of septicemia or pneumonia. All of the mice with septicemia survived after receiving lolamicin, as did 70% of the mice with pneumonia.

To measure the effect on gut bacteria, the researchers gave healthy mice either lolamicin, a placebo or one of two common antibiotics, amoxicillin and clindamycin. After collecting baseline stool samples, they sampled the animals’ poop seven, 10 and 31 days after treatment.

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Mice treated with amoxicillin or clindamycin had lower beneficial bacteria counts and less diversity of gut bacteria. In contrast, the guts of lolamicin-treated mice appeared largely the same.

“It was exciting to see that lolamicin did not really cause any changes in the microbiome, whereas the other clinically used antibiotics did,” Munoz said.

A disrupted microbiome can have immediate consequences for people battling infection. When beneficial microbes are decimated, dangerous bugs have fewer competitors and secondary infections can take hold.

Clostridium difficile is a notorious opportunistic pathogen, so the researchers did an experiment where they exposed mice treated with lolamicin, amoxicillin or clindamycin to C. difficile. The mice who took standard antibiotics were soon crawling with C. difficile. The lolamicin mice showed little to no infection.

The lab hopes to one day take lolamicin or a version of it to clinical trials, Hergenrother said. (Munoz received her doctorate last year and now works as a scientific analyst in Los Angeles.) Yet these are still early days for the drug. While the concept of a discerning antibiotic is a welcome development, it must clear significant barriers before it could make a difference for patients.

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“Distinguishing a quote-unquote ‘bad bug’ from a quote-unquote ‘good bug’ is not always as straightforward as it may seem,” said Dr. Sean Spencer, a Stanford University gastroenterologist and physician scientist who was not involved with the research.

Some beneficial bugs in the gut bear a striking genetic resemblance to harmful pathogens, he said. Others are benign in some contexts and dangerous in others: “In a critically ill individual, a good bug can do bad things.”

Years can pass between a new antibiotic’s proof of concept and its entry to the market, and the vast majority never make it to the end of that pipeline. It’s also not clear how easily or how quickly bacteria will develop resistance, which is perhaps the most formidable obstacle that lolamicin or any new antibiotic faces.

“One of the biggest problems is that bacteria are so smart. You can tackle one particular protein system or protein target in bacteria, but they will quickly find a resistance mechanism,” Munoz said. “They just have so many inherent mechanisms to overcome antibiotics.”

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What’s in a Name? For These Snails, Legal Protection

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What’s in a Name? For These Snails, Legal Protection

The sun had barely risen over the Pacific Ocean when a small motorboat carrying a team of Indigenous artisans and Mexican biologists dropped anchor in a rocky cove near Bahías de Huatulco.

Mauro Habacuc Avendaño Luis, one of the craftsmen, was the first to wade to shore. With an agility belying his age, he struck out over the boulders exposed by low tide. Crouching on a slippery ledge pounded by surf, he reached inside a crevice between two rocks. There, lodged among the urchins, was a snail with a knobby gray shell the size of a walnut. The sight might not dazzle tourists who travel here to see humpback whales, but for Mr. Avendaño, 85, these drab little mollusks represent a way of life.

Marine snails in the genus Plicopurpura are sacred to the Mixtec people of Pinotepa de Don Luis, a small town in southwestern Oaxaca. Men like Mr. Avendaño have been sustainably “milking” them for radiant purple dye for at least 1,500 years. The color suffuses Mixtec textiles and spiritual beliefs. Called tixinda, it symbolizes fertility and death, as well as mythic ties between lunar cycles, women and the sea.

The future of these traditions — and the fate of the snails — are uncertain. The mollusks are subject to intense poaching pressure despite federal protections intended to protect them. Fishermen break them (and the other mollusks they eat) open and sell the meat to local restaurants. Tourists who comb the beaches pluck snails off the rocks and toss them aside.

A severe earthquake in 2020 thrust formerly submerged parts of their habitat above sea level, fatally tossing other mollusks in the snail’s food web to the air, and making once inaccessible places more available to poachers.

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Decades ago, dense clusters of snails the size of doorknobs were easy to find, according to Mr. Avendaño. “Full of snails,” he said, sweeping a calloused, violet-stained hand across the coves. Now, most of the snails he finds are small, just over an inch, and yield only a few milliliters of dye.

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Video: This Parrot Has No Beak, But Is at the Top of the Pecking Order

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Video: This Parrot Has No Beak, But Is at the Top of the Pecking Order

new video loaded: This Parrot Has No Beak, But Is at the Top of the Pecking Order

Bruce, a disabled kea parrot, is missing his top beak. The bird uses tools to keep himself healthy and developed a jousting technique that has made him the alpha male of his group.

By Meg Felling and Carl Zimmer

April 20, 2026

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Contributor: Focus on the real causes of the shortage in hormone treatments

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Contributor: Focus on the real causes of the shortage in hormone treatments

For months now, menopausal women across the U.S. have been unable to fill prescriptions for the estradiol patch, a long-established and safe hormone treatment. The news media has whipped up a frenzy over this scarcity, warning of a long-lasting nationwide shortage. The problem is real — but the explanations in the media coverage miss the mark. Real solutions depend on an accurate understanding of the causes.

Reporters, pharmaceutical companies and even some doctors have blamed women for causing the shortage, saying they were inspired by a “menopause moment” that has driven unprecedented demand. Such framing does a dangerous disservice to essential health advocacy.

In this narrative, there has been unprecedented demand, and it is explained in part by the Food and Drug Administration’s recent removal of the “black-box warning” from estradiol patches’ packaging. That inaccurate (and, quite frankly, terrifying) label had been required since a 2002 announcement overstated the link between certain menopause hormone treatments and breast cancer. Right-sizing and rewording the warning was long overdue. But the trouble with this narrative is that even after the black-box warning was removed, there has not been unprecedented demand.

Around 40% of menopausal women were prescribed hormone treatments in some form before the 2002 announcement. Use plummeted in its aftermath, dipping to less than 5% in 2020 and just 1.8% in 2024. According to the most recent data, the number has now settled back at the 5% mark. Unprecedented? Hardly. Modest at best.

Nor is estradiol a new or complex drug; the patch formulation has existed for decades, and generic versions are widely manufactured. There is no exotic ingredient, no rare supply chain dependency, no fluke that explains why women are suddenly being told their pharmacy is out of stock month after month.

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The story is far more an indictment of the broken insurance industry: market concentration, perverse incentives and the consequences of allowing insurance companies to own the pharmacy benefit managers that effectively control drug access for the majority of users. Three companies — CVS Caremark, Express Scripts and OptumRx — manage 79% of all prescription drug claims in the United States. Those companies are wholly owned subsidiaries of three insurance behemoths: CVS Health, Cigna and UnitedHealth Group, respectively. This means that the same corporation that sells you your insurance plan also decides which drugs get covered, at what price, and whether your pharmacy can stock them. This is called vertical integration. In another era, we might have called it a cartel. The resulting problems are not unique to hormone treatments; they have affected widely used medications including blood thinners, inhalers and antibiotics. When a low-cost generic such as estradiol — a medication with no blockbuster profit margins and no patent protection — runs into friction in this system, the friction is not random. It is structural. Every decision in that chain is filtered through the same corporate profit motive. And when the drug in question is an off-patent estradiol patch that has negligible profit margins because of generic competition but requires logistical investment to keep consistently in stock? The math on “how much does this company care about ensuring access” is not complicated.

Unfortunately, there is little financial incentive to ensure smooth, consistent access. There is, however, significant financial incentive to steer patients toward branded alternatives, or simply to let supply tighten — because the companies aren’t losing much profit if sales of that product dwindle. This is not a conspiracy theory: The Federal Trade Commission noted this dynamic in a report that documented how pharmacy benefit managers’ practices inflate costs, reduce competition and harm patient access, particularly for independent pharmacies and for generic drugs.

Any claim that the estradiol patch shortage is meaningfully caused by more women now demanding hormone treatments is a distraction. It is also misogyny, pure and simple, to imply that the solution to the shortage is for women’s health advocates to dial it down and for women to temper their expectations. The scarcity of estradiol patches is the outcome of a broken system refusing to provide adequate supply.

Meanwhile, there are a few strategies to cope.

  • Ask your prescriber about alternatives. Estradiol is available in multiple formulations, including gel, spray, cream, oral tablet, vaginal ring and weekly transdermal patch, which is a different product from the twice-weekly patch and may be more consistently available depending on manufacturer and region.
  • Consider an online pharmacy. Many are doing a good job locating and filling these prescriptions from outside the pharmacy benefit manager system.
  • Call ahead. Patch shortages are inconsistent across regions and distributors. A call to pharmacies in your area, or a broader geographic radius if you’re able, can locate stock that your regular pharmacy doesn’t have.
  • Consider a compounding pharmacy. These sources can sometimes meet needs when commercially manufactured products are inaccessible. The hormones used are the same FDA-regulated bulk ingredients.

Beyond those Band-Aid solutions, more Americans need to fight for systemic change. The FTC report exists because Congress asked for it and committed to legislation that will address at least some of the problems. The FDA took action to change the labeling on estrogen in the face of citizen and medical experts’ pressure; it should do more now to demand transparency from patch manufacturers.

Most importantly, it is on all of us to call out the cracks in the current system. Instead of repeating “there’s a patch shortage” or a “surge in demand,” say that a shockingly small minority of menopausal women still even get hormonal treatments prescribed at all, and three drug companies control the vast majority of claims in this country. Those are the real problems that need real solutions.

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Jennifer Weiss-Wolf, the executive director of the Birnbaum Women’s Leadership Center at New York University School of Law, is the author of the forthcoming book When in Menopause: A User’s Manual & Citizen’s Guide. Suzanne Gilberg, an obstetrician and gynecologist in Los Angeles, is the author of “Menopause Bootcamp.”

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