Researchers identify human bacteria clusters linked to the likelihood of acquiring the flu
A recent study administered by a team of professors and students within the School of Public Health and the Nicaragua Ministry of Health found that it may be easier to detect one’s susceptibility to influenza by simply looking at the bacteria present within the throat and nose.
Betsy Foxman, professor of epidemiology and a lead researcher on the project, said the team was interested in how contracting influenza makes it more likely for someone to get other diseases.
Foxman’s particular interest was how the microbiome, bacteria and other microbes that live in and on the human body might influence transmission. Aubree Gordon, assistant professor of epidemiology, researched factors that affect the susceptibility and transmission of influenza. By combining both of these areas of interest, Gordon designed a household transmission study to help gather samples and data to see how our ever-changing microbes affect our response to influenza.
Foxman said the project started with how influenza contraction affects transmission of other diseases.
“It started with the question, how come when you get influenza you might be more likely to get pneumonia off of strep pneumo and where does it come from?” Foxman said. “We thought that it would be great to look at what happens in a household transmission study. So when Dr. Gordon joined the faculty and I heard about her study and immediately went to her and asked if she would like to collaborate. So, it was opportunity plus interest.”
The longitudinal Nicaragua household transmission study took place between 2012 and 2014. In the study, members within a household of those affected by influenza were observed carefully for thirteen days to see if they would develop influenza.
About 710 bacterial samples were then collected at the initial date of the study and then 695 samples were gathered at the final date of the investigation.
After the study was complete, Foxman and her team carefully examined the samples of nose and throat bacteria collected from the initial enrollment and applied DNA sequencing to help identify the varying types of bacteria, which lead to the discovery of five diverse types of cluster communities.
Foxman said being able to study the microbiome was made easier thanks to the “miracle” of DNA sequencing.
“We can (now) take a sample and identify all of the bacteria that are living there without growing them individually,” Foxman said. “We sequence parts of their genomes and look relative to databases to see (which bacteria) is there and their relative abundance. Being able to do that allows us to look at these communities.”
After the sequencing, the team applied a clustering technique to group the data into clusters, or “community types,” which allowed them to see what groupings of bacteria appeared by looking at the similarities evident in the sequence.
By analyzing these clusters, Foxman and Gordon could see if these clusters predicted risk of influenza.'
“We discovered that individuals with a certain community type or certain microbiome are more susceptible to influenza,” Gordon said. “Right now, it is pretty preliminary, we’re learning so much about the microbiome. It looks like it affects your response to vaccines and your chances of getting certain diseases — particularly in the case of respiratory diseases. The first step is to see how it works and the interactions in the workplace.”
Foxman hopes to replicate the research in different geographic areas to better understand the mechanisms of the particular communities found in the Nicaraguan study.
“What we’re looking at now is using the data from the study to look at how the microbiome might affect shedding a virus and symptoms, and seeing if the microbiome that you have affects how sick you are and for how long,” Gordon said.
Ideally, the researchers would like to figure out how to manipulate the found communities to help prevent people from getting sick or transmitting influenza to others. But there is still much more to learn about the microbiome.
Public Health student Kyu Han Lee, a co-researcher on the project, acknowledges that microbiome research as a whole is still in the beginning stages.
“Microbiome research is still a baby,” Han Lee said. “We are developing methods and moving forward. What can happen with this is if we understand the relationship between the bacteria in our bodies and disease, then we can start thinking about preventative intervention that helps us avoid and reduce the risk of disease. The field is moving in that direction but a lot still needs to happen before we can access it and take action.”
Physicians change the microbiome each and every day by prescribing people with a series of antibiotics. In the future, Foxman predicts a potential microbiome pill that could hypothetically prevent influenza in those more susceptible. Although the flu vaccine is highly effective, it only reduces your risk of getting the disease by 40 to 60 percent.
According to the Centers for Disease Control and Prevention, more than 80,000 people died from the flu last flu season.
“People think ‘oh, the flu what's the big deal?’” Foxman said. “But the fact is a lot of people die of it every year — healthy, small children die every year. Antibiotics are miracle drugs, but they don’t always work because sometimes people are just too sick. We try to think we can treat everything, but sometimes we can’t. Perhaps our microbiomes can aid us in more ways than we think.”