Two ecospecies of Helicobacter pylori — named ‘Hardy’ and ‘Ubiquitous’ — co-existed in the stomachs of modern humans since before they left Africa and were dispersed around the world by human migrations, according to new research.
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Tourrette et al. found that Indigenous people in Siberia and North and South America are infected by two distinct types of Helicobacter pylori. Image credit: sjs.org / CC BY-SA 3.0.
First discovered in 1983, Helicobacter pylori disturbs the stomach lining during long-term colonization of its human host, with sequelae including ulcers and gastric cancer.
Numerous Helicobacter pylori virulence factors have been identified, showing extensive geographic variation.
In the new study, Dr. Elise Tourette from the Shanghai Institute of Immunity and Infection and colleagues used an unprecedented collection of 6,864 Helicobacter pylori genomes from around the world to investigate the spread of the bacteria.
They unexpectedly found a highly distinct variant of Helicobacter pylori that they termed the Hardy ecospecies, which arose hundreds of thousands of years ago and spread around the world with humans.
They proposed that the ecospecies is specialized to live in the stomachs of people whose diet principally consists of meat or fish, i.e., carnivores.
Thus, the genetic variation found in the bacteria in our stomachs today can inform us what our ancestors ate.
“Our diverse global sample allowed us to have a better understanding of the history of Helicobacter in humans, which confirmed previous findings that these bacteria were already passengers in our stomachs when we left Africa more than 50,000 years ago,” Dr. Tourette said.
“However, we also identified something surprising, in the form of a new ecospecies of Helicobacter, which we called Hardy.”
“It differs from the common type, which we called Ubiquitous, in more than 100 genes.”
“The Hardy ecospecies turns out to be exceptionally informative about what the bacteria need to do to survive in our stomach, but also, more fundamentally, about how diversity is maintained in bacteria.”
“Most humans living today are omnivores or vegetarians, which means that a substantial proportion of our diet consists of plant material,” said Dr. Daniel Falush, also from the Shanghai Institute of Immunity and Infection.
“However, in some parts of the world, plant material has historically been unavailable for large parts of the year and people relied heavily on fish or meat for sustenance.”
“So far, the Hardy ecospecies has only been identified in humans from these Indigenous populations, in locations such as Siberia and Northern Canada.”
“It has also been found in tigers and cheetahs in zoos, due to an ancient host jump, and has key genetic differences that could adapt it to the conditions found in a carnivore’s stomach.”
“This association is particularly intriguing because our analysis also implies that both ecospecies accompanied humans since the origin of our species in Africa more than 200,000 years ago.”
“If the ecospecies is indeed adapted to carnivores, then it implies that the humans that spread out across the world often did not eat much plant matter, even when it was available to them.”
By analyzing Helicobacter pylori genomes from around the world, the researchers found that the first modern humans were infected by two distinct types of the bacterium, Hardy and Ubiquitous.
Both ecospecies spread out of Africa during the early migrations of humans, getting as far as South America.
The Ubiquitous ecospecies has been found in all human populations sampled to date, but the Hardy ecospecies has only been sampled from a small number of Indigenous populations, implying it might have gone extinct in many locations on its migration path.
However, one African lineage of Hardy strains made a host jump to big cats and has been isolated from cheetahs, lions, and tigers in zoos.
Understanding why the ecospecies can coexist in some populations but not others promises to shed light on our prehistory and on the substantial burden of gastric disease that we still suffer from today.
“Our results also show that highly distinct adaptive strategies can arise and be maintained stably within bacterial populations, even in the presence of continuous genetic exchange between strains,” the scientists said.
The findings were published in the journal Nature.
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E. Tourrette et al. An ancient ecospecies of Helicobacter pylori. Nature, published online October 16, 2024; doi: 10.1038/s41586-024-07991-z
