Hidden beneath the Red Sea, the Coral Probiotics Village is home to a bustling community of sea critters and scientists. Underwater street signs mark pathways for scuba-diving researchers to navigate the reef. On Nemo Street, microbial ecologist Raquel Peixoto holds a syringe close to some coral and presses the plunger, releasing around seven strains of bacteria into the water. 

The goal, Peixoto later explains, is to restore a healthy microbiome to a reef thrown out of whack by coral diseases, triggered by pollution, ocean acidification, and warming waters. 

“We are causing the problem [that is] affecting these microbiomes,” says Peixoto, of the King Abdullah University of Science and Technology in Thuwal, Saudi Arabia. “So we need to try to restore it, or at least to protect it to be as similar as what it was before.”

The potential of probiotics

In the coral village, Peixoto is testing to see if a carefully curated dose of probiotics – bacteria that are beneficial to its host – could help reduce the bleaching diseases that are killing tropical reefs from the Caribbean to Australia at an alarming rate. A growing cohort of microbiologists believe that beneficial bacteria, already commonly used as nutritional supplement and agricultural fertilizer, might help not just corals but also many other at-risk animals and plants. Led by Peixoto, a global group of 25 experts made the argument in a perspective piece published in Nature Microbiology last year.

The concept of probiotics for wildlife has only been around for roughly a decade, so scientists are still teasing out which bacteria to use as they study the cascades of microbial interactions in both the host species and environment. But with extinctions looming, researchers are hurrying to test probiotics on everything from farmed Norwegian salmon to honeybees. So far, most of the tests have been confined to labs, though there have been some small-scale field tests, too. 

In 2019, for example, probiotic expert Gregor Reid mixed sugar and three strains of Lactobacillus bacteria to treat diseased honey bees in Ontario, Canada. A couple weeks later, larvae from treated hives had significantly fewer pathogens than those from untreated hives. He thinks other combinations of probiotics may be even more effective and is eager to explore the possibilities at a time when bee populations are declining.

“The bees are dying off,” says Reid. “And the day they die off, we’re toast as a species.”

Frogs are in a similar boat: In recent years, hundreds of frog species around the world have been ravaged by the Batrachochytrium dendrobatidis (Bd) fungus. In 2011, scientists caught frogs in the Sierra Nevada Mountains that hadn’t yet been exposed to Bd and bathed some in water with a naturally-occurring bacteria, and the rest in pond water. A year later, they returned to the site and couldn’t find any of the untreated frogs, but 39 percent of probiotic-treated individuals were recovered, indicating that the probiotics had at least some effect. 

Disease ecologist Molly Bletz of the University of Massachusetts at Amherst, who studies frogs from Madagascar, has also shown that some microbes resist Bd in the lab. “It’s complicated,” she sums up, “but with glimmers of hope.” 

One complication is that there are so many potentially beneficial bacteria to choose from, depending on the species being treated and its particular environmental risks. Bletz has cataloged over 7,000 amphibian microbes – and scientists aren’t limiting themselves to just the host’s resident microbes. “If it’s a species that is super-susceptible to the disease, maybe they just don’t have the right bacteria,” says Bletz. So in other cases – like Reid’s bees, which received bacteria harvested from a healthy woman’s urethra way back in 1980 – scientists are experimenting with foreign strains. 

Despite all the potential treatment variations, biotechnologist Gabriele Berg, a coauthor of the Nature Microbiology piece, says the fundamental practices for microbial interventions are similar. “If it is in our gut, or if it is in the rhizosphere [plant roots], or if it is on the nose of a bat,” she says, “the rules and the principles are the same.” 

Recognizing these commonalities, Peixoto, Berg, and other microbial researchers have joined forces to outline safe steps for any probiotic intervention, whether it be in corals or frogs. Their framework, included in the 2022 paper, calls for careful selection of probiotic strains and consideration of environmental impacts, among other recommendations. 

A carefully considered call to action

It’s essential that experts reach a consensus on ethical and safety considerations of these treatments before the technologies are widely used, says Rachel Backer, an independent scientific consultant based in Vancouver who has researched plant-microbe interactions in hops and cannabis. 

What could go wrong if probiotics are let loose in an ecosystem is the kind of question that keeps her up at night, she says.

“These are complex products to regulate, because they’re just inherently complex,” says Backer, who was not a signatory on the paper. She argues that the indiscriminate use of antibiotics in agriculture is a precedent to consider. Antibiotics were initially seen as a miracle for livestock farmers, Backer says, but their overuse has led to pollution and antimicrobial resistance.  “If we keep making the same mistake over and over of not considering these things, it becomes pretty indefensible,” she says. 

Peixoto notes that probiotics typically don’t last forever (unless they colonize a host, which can happen). And though she acknowledges the risks, she argues that doing nothing is also indefensible. Corals, for instance, have an alarming prognosis; a recent report projected that 70 to 90% of live coral would disappear by 2050. Her team is working tirelessly, applying probiotics three times a week to the underwater coral village, while developing an automatic dispenser that can spray probiotics from the comfort of home. Peixoto knows that it’s optimistic to be already increasing the efficiency of various treatments when there has been so little field testing. But she sees no other option. 

“We don’t have time. We can’t develop these things one at a time,” Peixoto says. “When you’re talking about terminal patients… this is urgent.”