Finding a Balance Between Microbiome Health and Hand Hygiene

Does handwashing protect our health or does it damage our microbiome?

By Stephanie Oehler

Reports of high levels of E. coli bacteria in the Seine River before the 2024 Paris Olympics raised health concerns for athletes preparing to race through the river. Triathletes scrambled for solutions to boost their immune function. Some increased their intake of carbohydrates and probiotics before the games. American triathlete Seth Rider took a different approach— swearing off handwashing after using the bathroom. Rider was convinced that increasing his tolerance to pathogens before the games would provide him protection against bacteria in the Seine that could cause illness. 

Rider’s approach stemmed from a growing belief online that overdoing hygiene practices, such as handwashing, may disturb the microbiome and make it easier for people to get sick. This theory is gaining traction as the relationship between the human microbiome and the immune system becomes better understood.  Could exposing ourselves to pathogens by reducing hygiene improve the composition of our microbiomes and, therefore, strengthen our immune system’s defenses?

The Human Microbiome and Immune System

Microorganisms, including fungi, viruses, protists, and bacteria, can be found in almost every part of the human body. The collection of these microbes is referred to as the human microbiome. Most microorganisms support the human body in essential processes such as digestion and metabolism, brain function, and immunity. However, a small percentage of microbes, known as pathogens, can cause sickness under the right conditions.

A crucial breakthrough in microbiome research is the discovery that a greater diversity of microbes living in the body benefits human health. Hygiene practices are designed to kill microorganisms or remove them from surfaces. The majority of microbes, however, are either helpful or non-harmful to humans. This raises the question of whether frequent hygiene practices, such as hand washing and sanitation gel, are harmful to the human microbiome. 

Dr. John Toney, an Infectious Diseases Physician and Professor of Medicine at the University of South Florida Morsani College of Medicine finds flaw with this theory. “It’s a nice thought. We like to preserve our microbiome. However, there are reasons that we do hand hygiene,” he said.

History of Handwashing

Infection prevention is the primary rationale behind frequent handwashing. It’s why an “Employees must wash hands before returning to work” sign is hung in the restroom of almost every U.S. business. Handwashing has become so routine that most people don’t take the time to think about why they do it or what the world was like before it became a common practice. 

Handwashing has been a common religious ritual in Jewish, Islamic, and Christian cultures for thousands of years. However, it didn’t become a practice associated with disinfection until the mid-1850s with the work of medical workers and social reformers, such as Florence Nightingale.

Patients treated in hospitals dies at much higher rates than patients treated in their homes before advancements in hospital hygiene. Doctors did not routinely wash their hands in healthcare settings before discoveries made by two 19th-century physicians, Oliver Holmes and Ignáz Semmelweis, who found that postpartum infections decreased when doctors washed their hands before delivering babies.

In the 1980s, the CDC released a collection of federal hand-washing guidelines following a series of outbreaks of foodborne illnesses and hospital-acquired infections. 

The importance of hand hygiene in preventing the spread of infectious diseases was further emphasized in 2020 at the start of the COVID-19 pandemic. The global outbreak fueled global health handwashing campaigns as an initial method of reducing the spread of the virus, although contact transmission of COVID-19 was ultimately found to be much less important than respiratory spread.

Effectiveness of Hand Washing

Dr. Toney has been at the frontlines of every major infectious disease outbreak in the last 40 years, from HIV and MRSA to COVID-19. His recommendations and guidance for hospital infection control have had a critical effect on patients and staff for decades.

“When you’re touching public surfaces, you run the risk of not knowing what you’re being exposed to. Sure, there may be some harmless things in there, but there’s also the potential of really bad things,” Toney said.

Toney has seen firsthand how poor hygiene practices can contribute to the spread of infections in his 40 years in infectious diseases medicine. 

Poor hand hygiene practices can result in group A Strep or Staph aureus skin infections. “If you have, for example, small cuts on your hands, these are agents that, given the right chance, can cause infection,” Toney said. 

Handwashing is especially important following bathroom use as human waste contains high amounts of microbes. A gram of feces, equal in weight to a raisin, contains over a trillion microorganisms including bacteria such as Salmonella, Campylobacter, Staphylococcus, and E. coli and viruses such as Norovirus, and Hepatitis A.

GI tract infections and respiratory illnesses can be spread through poor hand hygiene practices, in addition to skin infections. Handwashing decreases the prevalence of diarrheal infections by 30 percent and the prevalence of respiratory illnesses, like colds, by 20 percent, according to the CDC.

Washing with soap and water helps lift and remove microbes from the skin. Surfactant chemicals in soap don’t directly kill the microbes, but rather cause the hand to become slippery, making it hard for any microbes to stick. 

Pathogenic bacteria on the hands following bathroom use can be spread to others without removal by handwashing. Handshaking and public surfaces such as doorknobs, tabletops, or handrails may serve as transmission routes for these bacteria to spread to others. People commonly touch their eyes, nose, and mouth or may have small cuts on their hands that may provide the right opportunity for infection. 

“If bacteria were the size of roaches, everybody would be washing their hands, because you’d see them. But we don’t see them,” Toney said. 

The Hygiene Hypothesis and Antibiotic Resistance

An overwhelming amount of evidence suggests that hand washing is effective at preventing the spread of pathogenic microbes. The effect of handwashing on the microbiome, however, offers a more nuanced perspective.

“It’s clear that the microbiome is very important for our health,” said Bruce Levin, an evolutionary microbiologist and Professor of Biology at Emory University. “We’re really dealing with two things with hygiene practices– one is avoiding pathogens and the other is trying to maintain the diversity of the microbiome.”

The belief that over-sanitation and hygiene practices may dull the body’s immune function by limiting exposure to pathogens is not new. This idea can partially be traced back to the “Hygiene Hypothesis” proposed by Dr. David Strachan in a study published by the British Medical Journal in 1989. 

The rise of allergies and autoimmune diseases in highly developed countries is due to a lack of exposure to certain microorganisms due to the modernization of society, according to Strachan’s study.

“The hygiene hypothesis explains why autoimmune diseases, like multiple sclerosis, are more frequent in places that are cleaner,” Levin said. 

The National Health Council reports that more than 50 million Americans are affected by autoimmune diseases such as celiac disease, type 1 diabetes, multiple sclerosis, and inflammatory bowel disease (IBD). The prevalence of each of these conditions has increased over the last 40 years. The hygiene hypothesis brought about the concern that lower levels of microbial exposure through hygiene practices may be to blame for this increase. 

Studies demonstrate that skin microbiome diversity is lower after washing with soap and water. Research on the role of the skin microbiome diversity on human health is ongoing, however, lower levels of gut microbiome diversity are linked to several chronic diseases. Additionally, studies on germ-free mice– mice engineered to have no microbiome– show that certain immune cells and antibodies are greatly reduced without the help of beneficial microbes. 

“There’s definitely an argument to be made that being too clean can also have consequences for our health”, Levin said.

Levin received his PhD from the University of Michigan in 1967. Since then, he’s been at the frontlines of research developments related to bacteriophage therapy, the human gut microbiome, and antibiotic resistance. 

Antibiotic resistance occurs when germs develop the ability to survive in the presence of antibiotics that were once able to kill them. This poses a significant threat to human health. Over 2.8 million antimicrobial-resistant infections occur each year in the U.S., resulting in over 35,000 deaths, according to the CDC.

“Certainly, any time that you can avoid using antibiotics is beneficial,” said Levin. “The more antibiotics we are exposed to, the better bacteria become at resisting them”, he added.

Levin’s recent research focuses on modeling heteroresistance, a form of antibiotic resistance that is particularly dangerous. Heteroresistant pathogens initially seem sensitive to an antibiotic, but after exposure, they quickly develop resistance and treatment fails. 

Handwashing can play a significant role in fighting antibiotic resistance by reducing the number of antibiotics needed each year. Diarrhea-related illnesses and respiratory infections can be reduced significantly through hand hygiene practices. Antibiotics are frequently unnecessarily used for these conditions. Reducing the occurrence of these diseases can limit the need for antibiotics.

Additionally, antibiotic use greatly impacts the human gut microbiome. Studies show that even as little as three days of treatment with commonly prescribed antibiotics can reduce microbiota diversity. Handwashing may affect the composition of bacteria in the short term by directly killing bacteria living on the hands. However, in the long term, evidence may suggest that less antibiotic use due to good hygiene may offset this short-term loss of hand microbes.

Practicing Good Hygiene While Optimizing Microbiome Diversity

The delicate balance between maintaining hygiene practices and diversifying the microbiome can be confusing for the average person to navigate.

“I’ve heard the theory before that being too clean can be harmful to your health,” said Peyton Panos, an undergraduate student at Emory University. “I think it’s partially true, but we still have to worry about preventing the spread of illnesses.” 

In recent years, Panos has become more concerned with his microbiome and how to best nurture it. The lack of concrete guidance about maintaining microbiome health, however, causes him frustration. “There’s so much contradictory information out there. Some articles talk about how awesome fermented foods are, some say that red meat or vegetarian diets are the way to go,” Panos said. “I wish there was more of a general consensus on how to protect my microbiome.”

The science around diet and the microbiome is evolving. Toney emphasizes that safer methods of increasing bacterial exposure and preserving the gut microbiome should be used instead of foregoing handwashing. 

“The data around the effectiveness of over-the-counter pre- and probiotics is not very robust, so I don’t commonly recommend them,” Toney said. “Yogurt and kefir products are fine, but staying away from antibiotics unless you really need them is what will have the most significant effect.”

In terms of handwashing and disease prevention, Toney agrees that too much of a good thing can be bad, even with hand hygiene. “Too much [hand hygiene] is not necessarily a good thing either,” he said. “Alcohol-based hand gels, for example, work well, but can cause dry skin which increases the risk of getting a bacterial infection”, he added.

In terms of handwashing and the microbiome, Levin is adamant that overdoing hygiene practices may have consequences on the microbiome and lead to immune dysfunction or increased allergies. “We’re trying to avoid the pathogens, but we also want to prioritize the stability of the microbiome,” he said.

Experts agree that being intentional about when to handwash can prevent over- or under-washing, both of which can have negative effects. Handwashing should be done after activities that present an increased risk of exposure to pathogenic bacteria such as after going to the bathroom, touching garbage, or touching animals.

Additionally, data shows that quality over quantity is key with handwashing. Meta-analysis studies demonstrate that there is no advantage of hand washing more than 10 times/day compared to 5–10 times per day in terms of preventing respiratory or GI tract diseases. The CDC indicates that thoroughly lathering hands with a non-antibacterial soap under running water for 15-30 seconds is the most effective handwashing method. Studies have shown no benefit of using antibacterial soap and suggest that doing so may contribute to antibiotic resistance.

The science of microbiome health and the immune system will continue to evolve in years to come. In the meantime, infection disease experts and microbiologists agree that a balance can be found between maintaining optimal hygiene practices and microbiome diversity. 

“Should you wash your hands? Of course. But do you need to overdo it? The answer is no,” Toney said.