What a stranded whale’s stomach tells us about the ocean’s invisible microbes
Pygmy sperm whales are among the most elusive animals on Earth. They spend their days in the deep ocean, diving hundreds of meters to hunt squid, surfacing only briefly, and traveling in small groups that are almost impossible to track. The species Kogia breviceps is known almost entirely from strandings, when, for reasons still poorly understood, individual whales wash ashore dead or dying on coasts around the world.
The southeastern United States sees a disproportionate share of these strandings. Over 20 years, from 1999 to 2020, researchers at Florida Atlantic University’s Harbor Branch responded to 59 pygmy sperm whale strandings along Florida’s coast. That tragedy is also a scientific opportunity: each stranding provides a rare glimpse into the biology of an animal that otherwise refuses to reveal itself.
In four of those whales, the researchers found something they did not expect, spiral-shaped bacteria in the stomach tissue, belonging to three previously unknown genotypes of Helicobacter. The discovery, published in the Journal of Wildlife Diseases (DOI: 10.7589/JWD-D-24-00204), opens questions that extend far beyond a single whale species.
The Helicobacter connection
Helicobacter is best known to medicine as the genus that causes peptic ulcers in humans, H. pylori, whose discovery earned Barry Marshall and Robin Warren the 2005 Nobel Prize. But Helicobacter species are not exclusive to humans. They have been found in dogs, cats, horses, and since 2000, in marine mammals.
The FAU team, led by veterinarian Annie Page and corresponding author Wendy Marks, identified three new Helicobacter genotypes in the stranded whales, which they named Kogia Helicobacter 1, 2, and 3. Two of these are genetically similar to known cetacean and human strains. The third, Kogia Helicobacter 3, belongs to a far more divergent lineage, one that suggests there may be many more Helicobacter species living in marine mammals than science has cataloged.
“Two of the genotypes are genetically similar to known Helicobacter species previously found in other cetaceans and in humans,” Marks said. “But Kogia Helicobacter 3 belongs to a more divergent lineage, which emphasizes the possibility that there are far more undiscovered bacteria in the ocean than we realize.”
A hidden burden of disease
All four whales that tested positive had visible gastric pathology: inflammation, ulcers, scarring, and nematode infestations. One whale also had colitis, suggesting the infection was not confined to the stomach. Helicobacter was not listed as the cause of death in any of the animals, but the consistent association with tissue damage raises an uncomfortable question: could chronic Helicobacter infection be a factor in the health of deep-diving whales that we simply have not been able to study?
In humans, H. pylori infection can persist for decades, causing chronic gastritis and increasing the risk of peptic ulcers and gastric cancer. In whales, the effects are harder to assess because the animals are almost never observed alive. Low energy, appetite loss, and regurgitation, symptoms seen in other captive marine mammals with Helicobacter, would be invisible in a free-ranging pygmy sperm whale.
If Helicobacter infections are widespread and cause chronic gastric disease, they could affect individual health, foraging efficiency, and ultimately population viability for a species that is already difficult to study and potentially vulnerable.
The value of the stranding network
The paper’s deeper contribution may be methodological. The 20 years of stranding response data that made these discoveries possible required a sustained institutional commitment, funding, trained personnel, and the willingness to respond to every call, knowing that most strandings would not produce novel findings.
“The research underscores the value of long-term marine mammal stranding response programs,” Page said. “Without the ability to study these stranded animals over decades, we never would have discovered these bacteria.”
The findings also highlight how much microbial diversity the ocean likely contains. The divergent lineage of Kogia Helicobacter 3 suggests that the Helicobacter genus in marine environments is more diverse than current databases reflect. Each stranded whale, it turns out, carries a microbial world inside it, one that we are only beginning to map.
Reference: Marks et al., “Novel Helicobacter genotypes in pygmy sperm whales stranded along the Florida coast,” Journal of Wildlife Diseases 62(1), 2026. DOI: 10.7589/JWD-D-24-00204.