Global survey of gut microbes uncovers 18 new bacterial species and clues to antibiotic resistance
Researchers examined scat from hundreds of animals around the world and pinpointed genes that could fuel drug-resistant infections.
One day in 2015, Joseph Manson placed in his refrigerator the colon of a wild turkey he’d just hunted near his small farm in South Carolina. A physics professor at Clemson University, he’d been recruited by his daughter, Abigail Manson, a scientist at the Broad Institute of MIT and Harvard, to help in a global study she was participating in to discover new species of gut bacteria. She’d wondered if any of the cows or chickens her father raised or the wild animals he hunted might carry some new variants of Enterococcus bacteria, a type of microbe found in the gut of all land animals on the planet and a leading cause of drug-resistant infections in humans.
He mailed a bit of the wild turkey’s waste to Massachusetts, where his daughter and her collaborators discovered that the bird had carried in its bowels a never-before-seen type of bacteria. To recognize Joseph’s contributions of dozens of animal fecal samples to the study, the research team named the bacteria Enterococcus mansonii, an unlikely distinction for a physicist and farmer.
The microbe is just one of 18 new species of Enterococcus discovered by the team, led by researchers at the Broad Institute and Massachusetts Eye and Ear. The researchers analyzed hundreds of scat, soil, and other samples that were collected from an unexplored peak in Nepal, a remote trail in Uganda, and many more places across the globe by an international team of scientists and elite adventurers.
The new species they found expand the genus diversity of known enterococcal strains by more than 25 percent and add unprecedented detail to this microbial family tree. In the new microbes’ DNA, the researchers found hundreds of novel genes that may offer clues to how enterococci are able to resist antibiotic treatment and thrive in the hospital environment. The findings could one day help monitor the emergence of new drug-resistant threats or highlight possible ways to prevent or treat those infections.
The work appears in Proceedings of the National Academy of Sciences (PNAS).
“Our results are part of a multi-phase effort to understand the origins of a major hospital pathogen through the lens of its long-term evolution over hundreds of millions of years,” said co-senior author Ashlee Earl, director of the Bacterial Genomics Group and an institute scientist at the Broad.
“Over the past 30 years, many of the most problematic bacteria have become increasingly resistant to antibiotics and this is now reaching crisis proportions,” said co-senior author Michael Gilmore, chief scientific officer at Mass Eye and Ear, director of the Infectious Disease Institute at Harvard Medical School, and an associate member at the Broad. “Our findings may improve understanding of how resistance genes spread to hospital bacteria and threaten human health.”
A microbial menagerie
The new study builds on an earlier effort by the team to explore the origins of antibiotic-resistant bacteria, which revealed that enterococci arose from an ancestral microorganism that dates back 450 million years, when animals first began crawling onto land. Since then, these bacteria have evolved to be able to survive in harsh conditions, including hospitals despite frequent disinfection. Enterococci are now one of the leading causes of drug-resistant bacterial infections, a public health menace that in 2019 was directly responsible for 1.27 million deaths globally.
In the current study, the Gilmore and Earl groups aimed to broadly survey the diversity of genes present across all kinds of enterococci. “Enterococci are found in almost every land animal on the planet,” said Abigail Manson, a co-author on the new study and a senior computational group leader at the Broad. “Understanding what genes are capable of living in the genus as a whole is really crucial to identifying what threats we could be facing in the future in hospitals.”
To conduct such a survey, the researchers created the Enterococcal Diversity Consortium, an international group of scientists and adventurers tasked with sampling the gut microbes of as many animals from as many places across the globe as possible. Their thorough survey included remote trails, peaks, and other areas untouched by humans, which they reasoned could harbor bacteria that naturally carry genes conferring drug-resistant traits. Those genes could one day be transferred to enterococcal species already residing in humans, leading to new “superbug” strains that cause untreatable infections.
The team collected specimens from a diverse menagerie including penguins migrating through sub-Antarctic waters; Kemp’s Ridley sea turtles stranded on the New England coast; wild duiker and elephants from Uganda; dragonflies, butterflies, ground beetles, and other insects from diverse locales; kestrel and vultures from Mongolia; wallabies, swans, and wombats from Australia; and zoo animals and wild birds from Europe. In addition to recruiting her dad’s help, Abigail Manson and her children gathered droppings from chickens on a Cape Cod farm and from geese resting in a field. To procure more exotic specimens, members of Adventure Scientists, a non-profit group of outdoor enthusiasts who assist with data collection in remote places, ascended an unexplored peak in Nepal to collect fresh scat from Himalayan blue sheep and traversed remote trails in Afghanistan to gather droppings from donkeys and marmots.
Adventure Scientist Stevie Anna Plummer holds water and scat samples collected in 2016 during an expedition to an unexplored peak in the Himalayas.
Adventure Scientist Lonnie Dupre collecting a scat sample from the high altitude Himalayan blue sheep in the Tsum Valley, Nepal, in 2016.
Over several years, consortium members sent to Gilmore’s lab nearly 600 specimens, mostly insects or scat, which resulted in 430 distinct bacterial cultures. Gilmore’s group analyzed these, along with more than 400 pre-existing enterococcal cultures, using a PCR-based method they developed that examines one highly variant gene to distinguish likely novel species.
They next sent notable cultures to the Broad Institute, where Earl’s group worked with the Broad’s Genomics Platform and Microbial ‘Omics Core to sequence the microbes’ genomes, which her team then analyzed. They identified 18 new species of enterococci — bringing the total number of known enterococcal species to more than 80 — in addition to one novel species of a related bacteria called Vagococcus found in an infected porpoise. Most of the new species were named for pre-eminent researchers who study enterococcal biology, but a few were named for individuals who contributed specimens, such as Joseph Manson.
Bacterial family tree
Genetic analysis of the new and existing enterococcal species allowed the team to expand the microbe’s family tree and refine its branches, or clades, yielding clues to how certain species are able to colonize particular hosts. For example, members of one clade have particularly small genomes that lack genes for amino acid biosynthesis, a hallmark of adaptation to mammalian hosts. Species in another clade carry large genomes that include genes necessary for producing the essential vitamin B12, indicating that they do not need their hosts to provide it.
The novel enterococcal species were found in specimens from farm chickens, dragonflies, butterflies, wild turkeys, cockroaches, ground beetles, sea turtles, and a salmon-crested cockatoo. The new species carried hundreds of novel genes, including those that produce toxins that would be harmful to humans if the microbes or their genes ever made their way to the human gut.
Notably, the greatest diversity of species occurred in arthropods, which include insects, crustaceans, centipedes, millipedes, spiders, and other arachnids. In the project’s next phase, the researchers are tapping into the unexplored diversity of enterococci in insects by amassing and analyzing an even larger collection of gut microbes.
“Insects have a wide range of diets and host environments, so we think that’s where a lot of the remaining diversity lies, as a potential reservoir of resistance genes,” said Abigail Manson. “In the next phase, we’ll continue to hunt for genetic novelty that could pose the next threat in hospitals, in addition to exploring the very roots of antibiotic resistance itself.”
Funding
This work was supported in part by the Harvard-wide Program on Antibiotic Resistance, Research to Prevent Blindness, and the National Institutes of Health.
Paper cited
Schwartzman J, et al. Global diversity of enterococci and description of 18 previously unknown species. Proceedings of the National Academy of Sciences. 121 (10) e2310852121. Feb. 27, 2024.
