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.

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CDC Studies Microbial Ecology to Protect People from Infections

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  • Scientists study microbial ecology, the relationships between germ communities and people, animals, plants, the food supply, and more to better understand how germs influence health, keep balanced microbiomes, and protect people from infection.
  • Microbiomes are communicates of germs on our skin or in our gut. A balanced microbiome helps us fend off infections.
  • We use antibiotics, antifungals, and other therapeutics to kill harmful germs making us sick. However, at the same time, these drugs also kills the “good” germs that protect us.
  • This disrupts a microbiome’s natural balance, increasing risk for infection, including antimicrobial-resistant infections.
  • CDC research focuses on answering how to better protect our microbiomes. Learn more: www.cdc.gov/DrugResistance/Microbial-Ecology.

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.

Importance of Understanding Microbial Ecology

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

About Infections, Antibiotic/Antifungal Use, and Microbial Ecology

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.

Glossary of Terms

This glossary of terms provides the definition of scientific words related to microbial ecology.