Good germs lurk in gross places | Science News for Students

Good germs lurk in gross places

The secret superpowers of poop, dog drool and snot
Oct 5, 2017 — 7:53 am EST
muddy dog

Dogs bring dirt into our homes. And that can be a good thing, scientists find. Kids that grow up in homes with dogs can be healthier. Pets are just one unexpected source of health-promoting germs.


Everybody poops. But we don’t usually like to talk about it. “Normally we flush it down the toilet and get away from it as fast as we possibly can,” observes Ari Grinspan. But, he adds, “there is a richness and goodness associated with poop.”

Grinspan knows what he’s talking about. He is a doctor at Mount Sinai Medical Center in New York City. And he regularly uses poop as medicine. The procedure, called a fecal transplant, isn’t for everyone. But “in the right patient, in the right setting,” he says, poop can improve a person’s health.

Ari Grinspan performs a fecal transplant at Mount Sinai Medical Center in New York City. Here, he injects fecal material directly into a patient’s intestines, or bowels. Some transplants use a tube placed down a person’s throat. Or patients may swallow the fecal material in pills or a special drink.
Mount Sinai Health System

That’s because human feces contain trillions of bacteria. These tiny germs live inside all of us, forming communities called microbiomes (My-kro-BY-ohms). Each microbiome is a miniature ecosystem full of different species. These communities exist on our skin, in our noses and elsewhere, especially in our guts. In a healthy person, these bugs cause no harm. They even can help keep the body healthy.

Sometimes, though, dangerous microbes invade or take over. When bad guys overrun the community, they may cause an infection. Or they might make chemicals that harm other systems in the body. In both cases, the human host will suffer.

In many human diseases, the gut microbiome is out of whack. Getting it back to normal might treat or even cure the disease. And one way to do that is to put into the sick person’s intestines a sample of good germs from the feces of a healthy person.

Poop isn’t the only disgusting substance with the potential to promote health. A team of researchers in Canada has found that dogs are good for babies’ health — not because they’re cute and lovable, but because they’re dirty. When babies grow up around dog drool, fur and muddy paw prints, they develop healthier gut microbiomes. And a German research team probing people’s noses found a surprise in the microbiome there. It was a brand-new antibiotic. ‘Snot bad!

From yellow soup to poop milkshakes

The healing power of poop is not a new idea. In 4th-century China, a doctor named Ge Hong described treating diarrhea with an unusual concoction. It was a drink made from the feces of a healthy person. This so-called “yellow soup” remained a part of Chinese medicine for centuries. 

However, Western medicine has only fully accepted the technique as treatment for one condition. That’s a potentially deadly infection called Clostridium difficile. It causes diarrhea and extreme pain in the gut. Years of research have shown that a fecal transplant is a safe and effective cure for this disease. In the United States, doctors aren’t allowed to use fecal transplants to treat anything else. The only exception is if they are testing treatments as part of a human trial. 

But in Australia, the rules are different. Thomas Borody is a doctor there who founded the Centre for Digestive Diseases in Sydney. He has been giving people fecal transplants for various conditions, including C. difficile infection, since the late 1980s. Early on, he was one of a handful of doctors experimenting with the procedure. “I’ve been laughed at for a long time,” he says. But he continued to perform fecal transplants anyway. He’s done thousands of them. “A lot of things are gross in medicine,” he says. People who are sick don’t care if a treatment is icky. They just want to get better.

Borody has treated illnesses called Crohn’s disease and colitis. In these conditions, the intestines swell with inflammation and may bleed. People may have diarrhea, constipation or painful cramps. Many doctors consider both conditions to be incurable. But many of Borody’s patients feel cured and stay off treatment for years. Other doctors who once scoffed at him are starting to change their minds, he says.

Still, stories from individual patients aren’t solid proof that the technique works. Researchers are still studying whether fecal transplants can help people with these conditions.

Borody believes fecal transplants could treat a host of conditions. Autism is one of them. People with autism often have trouble speaking and interacting socially. Many also have constipation and other gut problems. Sidney Finegold is a doctor at the VA Greater Los Angeles Healthcare System in California. He found two types of gut bacteria that might be tied to certain cases of autism. He did a study showing that an antibiotic, which kills bacteria, could temporarily lessen autism symptoms.

But antibiotics destroy good bacteria as well as bad. In contrast, Borody thinks, a fecal transplant might kill bad bacteria while bringing in good ones. To test this, he and his colleagues recruited 18 children with autism. They treated each of them with purified fecal bacteria.

“We gave it to them in a chocolate drink,” says Borody. But don’t barf just yet. The team carefully screened donors and their stools for disease. Next, they mixed the poop with purified salt water. Then they filtered out everything potentially harmful (or smelly). The result was an odorless, tasteless liquid packed with healthy bacteria. Then they mixed in a chocolate flavoring.

eating yogurt
 Drinking a poop milkshake may sound disgusting, but you probably already eat similar bacteria. Yogurt often contains some of the same bacteria that are in poop. “But no one cares,” says Thomas Borody. 

Kids drank this concoction daily for eight weeks. During and after the treatment, parents filled out questionnaires on their kids’ symptoms. Gut conditions (such as constipation) improved, they reported. Some symptoms of autism seemed to improve as well.

The researchers published the results in January in the journal Microbiome. However, “it was a very, very small study,” notes Grinspan. He was not involved in the trial. Also, he points out, all children with autism received the same treatment. In a future study, the researchers should give some kids a fake treatment, called a placebo (Pla-SEE-bo), he says. This could help show whether any improvements are really due to the poop therapy, not just to the kids’ or parents’ expectations.

Birthing fluid and dog drool

Doctors such as Grinspan and Borody use fecal transplants to repair a microbiome gone bad. It would be even better, however, if people never fell sick in the first place. So what’s the secret to keeping your gut microbiome healthy? There are likely many factors. But researchers know that a baby’s first experiences can matter a lot.

Birth is a messy affair. There are blood, fluids and plenty of germs. During a baby’s trip through the birth canal, microbes from its mom’s body hop on board. They move into the baby’s gut. Even before birth, microbes from mom may sneak into her baby. In general, the more bacteria, the merrier.

“A baby needs to be exposed to microbes,” says Anita Kozyrskyj. She works at the University of Alberta in Edmonton, Canada. As a pediatric epidemiologist (Ep-ih-dee-me-OL-oh-gist), she studies patterns of disease among children. Exposure to microbes trains a baby’s immune system to fight bad germs and leave good ones alone. It also helps build up a diverse, healthy community of microbes in the baby’s body.

Missing out on microbes may affect a baby’s’ future health. For example, babies born in a procedure called a C-section never travel through a mom’s birth canal. Instead, a doctor cuts into the mother’s belly to remove the baby. Later in life, these babies may be more likely to have asthma, food allergies and obesity.

One team of researchers in New York City tried something unusual. (Okay, it’s also a little gross.) After a C-section, they swabbed each of four babies with fluid from its mom’s birth canal. This helped make the babies’ microbiomes more similar to those of babies born naturally, they found. This was a very small, early study. Still, notes Kozyrskyj, who was not involved, the results seem promising.

dogging mom
Studies have found that even having a dog in the home during pregnancy can confer some health benefits to the baby.

Her team is now looking at another common source of microbes: dogs and other furry pets. In a large group of 746 families with new babies, they looked at which families owned furry pets before and after the baby’s birth. They compared the gut microbiomes of babies from these families to those from families without furry pets.

Gut microbes, you’ll recall, come out in poop. To find out what kinds of microbes had moved into these babies’ guts, Kozyrskyj’s team had a messy job to do. They collected poopy diapers at each home.

It turns out that living with a dog before or after birth is good for a baby’s microbiome. All that dog hair, drool and dirt help a baby develop a diverse community of germs. And a diverse microbiome is a healthier one. “Babies had many more species [of microbes] when dogs were around than when they were not,” says Kozyrskyj. Even if the family owned a furry pet during pregnancy but not after birth, the baby still showed benefits.

Previous studies had shown that babies who grow up around dogs and farm animals are less likely to develop allergies. The microbe diversity Kozyrskyj’s team found may help explain this fact. Cats do not seem to provide the same protection. But if you own a cat, don’t despair. Kozyrskyj suspects that dogs are better for the microbiome because they spend more time outside. So they track in germs from outdoors. A cat that goes outside a lot may offer similar benefits.

Nosing around

As Kozyrskyj’s team collected poopy diapers, another team of researchers was peering into people’s noses. No, they weren’t looking for juicy boogers. They wanted to learn about the nose microbiome, says Bernhard Krismer. He works at the University of Tübingen in Germany. As a microbiologist, he studies microbes and their communities. 

It turns out the nose is not an easy place to live, notes Krismer. Food for microbes is hard to come by. So bacteria that live there have to work hard to survive. One way is to kill off their neighbors. Krismer’s team discovered that one nose-dwelling bacterium does just that. Its name is a mouthful: Staphylococcus lugdunensis (STAF-uh-lo-KOK-us LUG-dun-EN-sis). This microbe makes a powerful bacteria-killing substance known as lugdunin. Last year, Krismer’s team described discovering this new antibiotic.

Staphylococcus aureus
These yellow blobs are cells of MRSA, a dangerous bacterium that resists most known antibiotics. But the bacterium S. lugdunensis naturally produces a substance that kills this superbug.
National Institute of Allergy and Infectious Diseases (NIAID)

“We were very surprised,” he recalls. His team had not expected to find an antibiotic. But they realized how important the discovery could be to medicine. People regularly use antibiotics to prevent or treat infections. You may take them for an ear infection. Or you may smear some on a cut or scrape. But many common antibiotics don’t work as well as they once did. That’s because some types of bacteria have become resistant. They have found ways to protect themselves against these drugs. (One factor driving this problem is that people use antibiotics too much, Krismer says. For example, you should only put antibiotic cream on a scrape if it’s already infected.)

Researchers have to keep developing new antibiotics to fight the resistant types (or strains). Lugdunin successfully kills the bacterium Staphylococcus aureus, which also lives in the human nose. A resistant strain of this bacterium, called MRSA, can cause a life-threatening infection.

You may already have lugdunin in your nose. Slugdunensis shows up naturally in one out of every 10 people. But even if you’re a carrier, you can’t use your boogers as a natural remedy. “Bad idea,” says Krismer. “The amount you can get by picking your nose is so low it wouldn’t help anything.” Plus, Slugdunensis itself can cause an infection if it grows out of control.

Krismer and his team hope to partner with a company to produce lugdunin for medical use. Most likely, they would make an antibiotic cream containing this substance.

Giving good germs more respect

The lugdunin discovery shows that our own bodies may be a rich source of new potential drugs. Other microbes living in the human body also likely produce powerful antibiotics. This type of activity could explain why fecal transplants work. A healthy human gut already contains substances that fight off bad bacteria. Even though doctors don’t yet know exactly what these substances are, they can use a fecal transplant to help sick patients.

Poop pills
Some patients take pills containing fecal material. Thomas Borody jokingly calls them “crapsules.” Swallowing such pills can be easier for patients than getting fecal material injected into their bowels.
Prathibha De Zoysa, Centre for Digestive Diseases, Sydney, Australia

Some people fear germs of all kinds. They scrub their hands and household surfaces regularly with germ-killing products. They teach their kids to avoid dirt or sanitize their hands after petting a dog or cat. But researchers are realizing that there’s such a thing as being too clean. The body needs a diverse community of microbes to stay healthy. “If a dog licks you, I would not use a sanitizer,” says Kozyrskyj. “You can wash it off with water.”

Grinspan agrees that it’s a good idea to avoid using antibacterial soaps. These products destroy good bacteria along with the bad. He also says, “I tell my kids that playing in the dirt is okay.”

Next time you flush the toilet, pet a dog or blow your nose, think of the good germs growing in and on your body. Then wash your hands — but stick to regular soap.

Power Words

(more about Power Words)

antibacterial     Having properties that tend to destroy or limit the growth or reproduction of bacteria.

antibiotic     A germ-killing substance, usually prescribed as a medicine (or sometimes as a feed additive to promote the growth of livestock). It does not work against viruses.

asthma     A disease affecting the body’s airways, which are the tubes through which animals breathe. Asthma obstructs these airways through swelling, the production of too much mucus or a tightening of the tubes. As a result, the body can expand to breathe in air, but loses the ability to exhale appropriately. The most common cause of asthma is an allergy. Asthma is a leading cause of hospitalization and the top chronic disease responsible for kids missing school.

autism     (also known as autism spectrum disorders ) A set of developmental disorders that interfere with how certain parts of the brain develop. Affected regions of the brain control how people behave, interact and communicate with others and the world around them. Autism disorders can range from very mild to very severe. And even a fairly mild form can limit an individual’s ability to interact socially or communicate effectively.

bacteria     (singular: bacterium) Single-celled organisms. These dwell nearly everywhere on Earth, from the bottom of the sea to inside other living organisms (such as plants and animals).

bug     The slang term for an insect. Sometimes it’s even used to refer to a germ.

carrier     (in medicine) A person or organism that has become infected with an infectious disease agent, but displays no symptoms.

chemical     A substance formed from two or more atoms that unite (bond) in a fixed proportion and structure. For example, water is a chemical made when two hydrogen atoms bond to one oxygen atom. Its chemical formula is H2O. Chemical also can be an adjective to describe properties of materials that are the result of various reactions between different compounds.

Clostridium difficile     A bacterium that releases one or more toxins, which can attack the lining of the intestines. This microbe can trigger colitis and severe diarrhea — conditions that can kill. In just the United States, C. difficile infections kill an estimated 14,000 people each year.

constipation     Difficulty defecating because the stool is too dense or because the intestinal tract does not contract sufficiently to efficiently move wastes through it.

diarrhea     (adj. diarrheal) Loose, watery stool (feces) that can be a symptom of many types of microbial infections affecting the gut.

disorder     (in medicine) A condition where the body does not work appropriately, leading to what might be viewed as an illness. This term can sometimes be used interchangeably with disease.

diversity      (in biology) A range of different life forms.

epidemiologist     Like health detectives, these researchers figure out what causes a particular illness and how to limit its spread.

factor     Something that plays a role in a particular condition or event; a contributor.

feces     A body's solid waste, made up of undigested food, bacteria and water. The feces of larger animals are sometimes also called dung.

germ     Any one-celled microorganism, such as a bacterium or fungal species, or a virus particle. Some germs cause disease. Others can promote the health of more complex organisms, including birds and mammals. The health effects of most germs, however, remain unknown.

host      (in biology and medicine) The organism (or environment) in which some other thing resides. Humans may be a temporary host for food-poisoning germs or other infective agents.

immune system     The collection of cells and their responses that help the body fight off infections and deal with foreign substances that may provoke allergies.

infection     A disease that can spread from one organism to another. It’s usually caused by some type of germ.

inflammation     (adj. inflammatory) The body’s response to cellular injury and obesity; it often involves swelling, redness, heat and pain. It also is an underlying feature responsible for the development and aggravation of many diseases, especially heart disease and diabetes.

journal     (in science) A publication in which scientists share their research findings with experts (and sometimes even the public). Some journals publish papers from all fields of science, technology, engineering and math, while others are specific to a single subject. The best journals are peer-reviewed: They send all submitted articles to outside experts to be read and critiqued. The goal, here, is to prevent the publication of mistakes, fraud or sloppy work.

lugdunin     A germ-killing (antibiotic) substance produced by bacteria in the nose known as Staphylococcus lugdunensis.

microbe     Short for microorganism. A living thing that is too small to see with the unaided eye, including bacteria, some fungi and many other organisms such as amoebas. Most consist of a single cell.

microbiology     The study of microorganisms, principally bacteria, fungi and viruses. Scientists who study microbes and the infections they can cause or ways that they can interact with their environment are known as microbiologists.

microbiome     The scientific term for the entirety of the microorganisms — bacteria, viruses, fungi and more — that take up permanent residence within the body of a human or other animal.

MRSA     An abbreviation for methicillin-resistant Staphylococcus aureus. Methicillin is a widely used antibiotic. Staph aureus is a bacterium that can cause boils, food poisoning, toxic-shock syndrome and more. These bacteria sicken (and sometimes kill) by releasing potent natural poisons into the body, called toxins.

obesity     (adj. obese) Extreme overweight. Obesity is associated with a wide range of health problems, including type 2 diabetes and high blood pressure.

placebo     A substance that has no therapeutic effect, used as a control in testing new drugs.

questionnaire     A list of identical questions administered to a group of people to collect related information on each of them. The questions may be delivered by voice, online or in writing. Questionnaires may elicit opinions, health information (like sleep times, weight or items in the last day’s meals), descriptions of daily habits (how much exercise you get or how much TV do you watch) and demographic data (such as age, ethnic background, income and political affiliation).

resistance     (as in drug resistance) A drop in the effectiveness of a drug to cure a disease, usually a microbial infection. (as in disease resistance) The ability of an organism to fight off disease.

sanitizer     Some product that can removing substances, usually germs, that can spread disease.

species     A group of similar organisms capable of producing offspring that can survive and reproduce.

Staphylococcus aureus     (also known as staph) A species of bacteria that is responsible for a number of serious human infections. It can cause surface abscesses, or boils. If it gets into the bloodstream, where it can be carried throughout the body, it may also cause pneumonia and infections of the joints or bones.

stool     (in medicine) Another name for feces.

strain     (in biology) Organisms that belong to the same species that share some small but definable characteristics. For example, biologists breed certain strains of mice that may have a particular susceptibility to disease. Certain bacteria or viruses may develop one or more mutations that turn them into a strain that is immune to the ordinarily lethal effect of one or more drugs.

symptom     A physical or mental indicator generally regarded to be characteristic of a disease. Sometimes a single symptom — especially a general one, such as fever or pain — can be a sign of any of many different types of injury or disease.

transplant     (in medicine) The replacement of a tissue or an organ with that from another organism. It is also a term for the material that will be transplanted.

trillion     A number representing a million million — or 1,000,000,000,000 — of something.

Western     (n. the West)  An adjective describing nations in Western Europe and North America (from Mexico northward). These nations tend to be fairly industrialized and to share generally similar lifestyles; levels of economic development (incomes); and attitudes toward work, education, social issues and government.


Journal:​ H.M. Tun et al. Exposure to household furry pets influences the gut microbiota of infants at 3–4 months following various birth scenarios. Microbiome. Vol. 5, April 6, 2017. doi: 10.1186/s40168-017-0254-x.

Journal:​ ​​D.W. Kang et al. Microbiota Transfer Therapy alters gut ecosystem and improves gastrointestinal and autism symptoms: an open-label study. Microbiome. Vol. 5, January 23, 2017. doi: 10.1186/s40168-016-0225-7.

Journal:​ ​​A. Zipperer et al. Human commensals producing a novel antibiotic impair pathogen colonization. Nature. Vol. 535, July 28, 2016. doi: 0.1038/nature18634.

Journal:​ M.G. Dominguez-Bello et al. Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer. Nature Medicine. Vol. 22, published online February 1, 2016. doi: 10.1038/nm.4039.