About Harnessing Microbial Ecology for Public Health
Germs, or microbes, are found everywhere, including on and in people, animals, and the environment, where they exist in communities called microbiomes. People have their own microbiomes (e.g., on their skin, in the gut) that help maintain good health and protect people from infections.
CDC invests in research around microbial ecology, which looks at the relationships within and across these microbial communities to determine how germs interact with one another and their environment. Microbial ecology includes interactions with people, animals, plants, food, and surfaces (e.g., healthcare bed rails or counter tops), all of which can serve as sources, or reservoirs, of germs that can lead to infection. This innovative work helps scientists better understand the role of microbial ecology in human health and how to leverage its role to develop and implement life-saving tools.
Sometimes a microbiome can become unbalanced. For example, when a person takes antibiotics or antifungals, the drugs kill some germs that cause infections (pathogens) and beneficial germs that protect our body from infection. This results in an unbalanced microbiome.
Research has shown that therapeutics (treatments) focused on microbial ecology and protecting a person’s microbiome can protect people from infections, including healthcare-associated and antimicrobial-resistant infections, so that people live longer, healthier lives.
Although scientists know that microbial ecology plays important roles in maintaining human health, there are outstanding scientific questions. It is critical to understand the relationships and interactions within microbial communities to prevent infections and their spread, improve antibiotic and antifungal use, and slow the spread of antimicrobial resistance. Continued research will help public health scientists better understand microbial ecology treatment options to save lives.
As part of its AR Solutions Initiative, CDC invests in innovative research to better understand the microbiome, the role of microbial ecology in human health, and how to leverage these to develop and implement life-saving tools for prevention.
Microbial ecology studies the relationships of germs across many settings, including the diversity and abundance of germs within microbiomes. Knowing how germs behave and change, and how human behaviors drive the emergence and spread of pathogens, helps public health better anticipate, prevent, and treat infections and helps slow the spread of antimicrobial resistance.
Experts working in microbial ecology can help public health by studying the relationships between germs, including the factors (ecological pressure) that allow some germs to survive and multiply in a competitive environment, whereas other germs within the same species do not survive.
Germs of the same genus and species can differ by their strain type. These microbial strains are germs with similar genetics but with one or more different genetic traits. These different genetic traits can sometimes help the germ survive and multiply in certain environments. Some strains can be very harmful to humans. For example, the increase in fluoroquinolone antibiotic use in the late 1990s appears to have favored the spread of a fluoroquinolone-resistant strain of Clostridioides difficile, called strain 027. Strain 027 has been linked to more severe disease in patients that were infected, known as a hypervirulent strain.
The ability of germs to survive and multiply is referred to as microbial fitness, and those combined survival characteristics are known as a fitness profile. The fitness profile helps scientists understand how different strains and factors in the surrounding environment affect the ability of that strain to thrive. Scientists can compare a strain’s microbial fitness and the fitness profile to other strains within the same species and with other species in a microbial community.
Microbial fitness can be increased by traits like
- Antimicrobial resistance mechanisms
- Environmental persistence, the ability to withstand pressure that allows germs to persist and survive in an environment (e.g., host or a setting)
- Virulence, the increased ability to infect and multiply (i.e., cause disease) in a person
- Transmissibility, or spread, the increased ability to spread from person to person
A healthy microbiome is important for preventing infections and disease. An unbalanced microbiome can put people and animals at risk for infection. Pathogens, including resistant pathogens and C. difficile, can take over and multiply in unbalanced microbiomes. The body is less able to defend against infection. Infections caused by resistant germs are difﬁcult, and sometimes impossible, to treat.
For example, when a person takes antibiotics or antifungals, beneficial, health-promoting skin and/or gut bacteria or fungi are wiped out in addition to the pathogens, resulting in an unbalanced microbiome. It can take weeks to months for the beneficial bacteria or fungi to return. In the meantime, people can also spread the harmful pathogens to others, especially if the other person also has a disrupted microbiome.
People can also be colonized with germs—when germs are present on or in the body without symptoms of an infection. Colonization is a strong indicator of infection risk, and people who are colonized can unknowingly spread germs to others.
Germs can spread within healthcare facilities, communities, our food supply, and the environment. These settings can also serve as reservoirs for pathogens to survive and multiply. For example, hospital-room sink drains have been found to be a source of multidrug-resistant bacteria and fungi that cause severe infections in patients.
New microbial ecology therapies can help improve patient treatment and outcomes. More research is needed to better understand the connection between preventing infections and spread, antibiotic and antifungal use, microbial ecology, microbiomes, and antimicrobial resistance. This work will lead to addressing how to, for example, protect and restore the microbiome, tailor antibiotic and antifungal use for specific people, identify a person’s risk for colonization, and uncover germ reservoirs to prevent spread.
- Exploring New Approaches to Diagnose C. difficile Infections
- Tailoring Antibiotic Treatment for Patients with Cystic Fibrosis
- Manipulating the Human Microbiome for Precision Public Health: Prospects and Challenges
- Precision Public Health: Harnessing the Power of the Human Microbiome
- CDC Supports Microbiome Science to Advance Infection Prevention, Clinical Care, and Public Health, featuring a special issue of the Journal of Infectious Diseases (JID) on microbiome and antimicrobial resistance
This glossary of terms provides the definition of scientific words related to microbial ecology.
- Colonization: When a microbe is found on or in the body but does not cause symptoms or disease. Finding the microbe multiple times over time could represent persistent colonization.
- Diversity: The variety and composition of microbes present in a microbial community. Diversity can be evaluated at different levels (e.g., genus, species, strain, operational taxonomic units). Diversity can be measured using an index, such as alpha (within a community) or beta diversity (among two or more communities).
- Dominance: When a particular microbe makes up a large portion of a microbial community (e.g., 30%). An increased portion of a particular microbe may be associated with development of infection, sepsis, or other adverse outcomes.
- Ecological pressure: Any force(s) that impact living organisms (i.e., microbes) and/or their environment.
- Fitness: Any trait that allows a microbe at any taxonomic level (e.g., genus, species, strain) or a community of microbes to thrive in the environment.
- Infection: When a microbe (e.g., bacteria, fungus) causes disease in a living organism (host, e.g., people, animal).
- Microbes: Tiny living organisms, including bacteria and fungi, that can mostly only be seen with a microscope. Often referred to as germs.
- Microbial ecology: The study of the relationships and interactions within microbial communities (e.g., environment-host-microbe) within a defined space.
- Microbiome: A community of naturally occurring germs within a defined space, such as in and on our bodies. Microbial communities are found on our skin, and in our mouth, respiratory tract, urinary tract, and gut.
- Microbiota: Microbes living in a microbiome. Microbiota in our bodies can work together to keep us from getting sick.
- Microbial strain: Germs with similar genetics but with one or more different genetic traits. These different genetic traits can sometimes help the germ survive and multiply in certain environments.
- Strain selection: External pressure (e.g., antibiotic) applied to microbes. Microbes that withstand the pressure survive.
- Virulence: A measure of the ability or likelihood to cause disease.
- Virulence factor: A trait that allows a microbe to grow, multiply, and cause disease in a host (e.g., people, animal).