There may be more genes in the collective human microbiome than stars in the observable universe, and at least half of these genes appear to be unique to each individual, according to researchers at the Harvard Medical School and Joslin Diabetes Center.
The study is the first to include DNA samples from bacteria residing in the mouth and the gut, as previous studies have focused on one or the other. Even so, the researchers said, the work marks only the beginning of efforts to analyze the human microbiome’s entire genome.
“Ours is a gateway study, the first step on what will likely be a long journey toward understanding how differences in gene content drive microbial behavior and modify disease risk,” said Braden Tierney, first author and graduate student at Harvard Medical School.
The human microbiome includes trillions of bacteria—most harmless, many beneficial, and some causing disease. Changes in bacterial count and content have been linked to the development of conditions ranging from caries and gut infections to chronic inflammatory bowel disease, diabetes, and multiple sclerosis.
Most research has focused on mapping the types of bacteria that inhabit our bodies to determine whether and how the presence of a given species might affect disease risk. By contrast, the new study looks at the genes that make up the various species and strains.
Studying bacterial species alone will only provide partial clues into their role in disease and health, the researchers said. Given that genetic content varies greatly between the same microbes, understanding how and whether individual microbial genes affect disease risk is just as important, the researchers said.
“Just like no two siblings are genetically identical, no two bacterial strains are genetically identical either,” said coauthor Chirag Patel, PhD, assistant professor of biomedical informatics at the Harvard Medical School’s Blavatnik Institute.
“Two members of the same bacterial strain could have markedly different genetic makeup, so information about bacterial species alone could mask critical differences that arise from genetic variation,” said Patel.
Cataloging the array of microbial genes could inform the design of precision-targeted treatments, said senior coauthor Alex Kostic, PhD, assistant professor of microbiology at the Harvard Medical School and an investigator at the Joslin Diabetes Center.
“Such narrowly targeted therapies would be based on the unique microbial genetic makeup of a person rather than on a bacterial type alone,” said Kostic.
Profiling the unique genes that make up a person’s microbiome also could act as a form of microbial fingerprinting that provides valuable clues about past exposures to different pathogens or environmental influences as well as disease predispositions, Kostic added.
To estimate the number of microbial genes in the human body, the researchers gathered all publicly available DNA sequencing data on human oral and gut microbiomes. They analyzed the DNA of about 3,500 human microbiome samples, with 1,400 obtained from people’s mouths and 2,100 from people’s guts.
There were nearly 46 million bacterial genes in the 3,500 samples, with about 24 million in the oral microbiome and 22 million in the gut microbiome. More than half of all the bacterial genes, 23 million, occurred only once, rendering them unique to the individual.
The researchers called these unique genes “singletons.” Of the 23 million singletons, 11.8 million came from oral samples, and 12.6 million came from intestinal samples. These singletons also appeared to behave differently from other genes, performing different functions.
Commonly shared genes appeared to be involved in basic functions critical to the microbes day to day survival, such as the consumption and breakdown of enzymes, energy conversion, and metabolism.
Unique genes carried out more specialized functions such as gaining resistance against antibiotics and other pressures and helping to build a microbe’s protective cell wall, which shields it from external assaults.
These findings, the researchers said, suggest that singleton genes are key parts of a microbe’s evolutionary survival kit.
“Some of these unique genes appear to be important in solving evolutionary challenges,” Tierney said. “If a microbe needs to become resistant to an antibiotic because of exposure to drugs or suddenly faces a new selective pressure, the singleton genes may be the wellspring of genetic diversity the microbe can pull from to adapt.”
The fuel behind this gene diversity remains the subject of further research, the researchers said, but they believe there are at least two important drivers of genetic variation.
One is the microbes’ propensity to freely swap DNA material with their neighbors, or horizontal gene transfer. To test this hypothesis, the researchers performed a special type of analysis that detects the shared molecular content between two organisms.
To their surprise, the researchers found little evidence that horizontal gene transfer was a main source of genetic uniqueness. Less than 1% of unique genes detected in oral samples and just under 2% of those found in the gut appeared to have arisen through this gene exchange.
Therefore, the researchers hypothesize, another more powerful driver of genetic diversity could be the bacteria’s ability to evolve their DNA rapidly in response to changes in the host environment.
The study was not designed to detect the precise environmental changes that drive this variation, but examples of such changes may include the type of food a person consumes, what medication is used, lifestyle choices, environmental exposures, and physiologic changes, including upregulation and downregulation in various host genes or whether a person develops a disease.
Finally, the researchers said that there could be around 232 million genes in the collective human microbiome, though another estimate yielded a total comparable to the number of atoms in the universe. Patel said that the true number may be unknowable.
“Whatever it may be, we hope that our catalog, along with a searchable web application, will have many practical uses and seed many directions of research in the field of host-microbe relationships,” Patel said.
The study was published by Cell Host & Microbe.