We are used to going to the doctor for our wellness check-up and having some routine lab tests. This screening happens in all ages. While stool samples are occasionally collected, they are usually done in response to an illness like infectious diarrhea or blood in the stool. It is very possible that stool samples may become part of the wellness checkup as we learn more about the microorganisms found in the gastrointestinal (GI) tract.
The stool microbiome is a community of microorganisms, including bacteria, fungi, viruses and other single-cell organisms lacking a nucleus found in the gut. It also includes the genetic material of the microorganism present in the gut.
Trillions of tiny microbes help the body get nutrients from food, fight off infections and much more. The GI tract is divided into anatomical pieces and each piece has different functions. One part absorbs more vitamins, other parts more protein or fats. Certain microorganisms secrete chemicals that can react with the muscle and nerves to slow the movement (motility) of the gut while others can secrete chemicals that speed up the gut. Some secrete chemicals that can help the gut lining absorb the nutrients from the stool.
The nervous system of the intestines is connected to the brain and the brain can play a role in regulating both GI motility and appetite. Part of the brain receives signals from hormones and nerve pathways that help determine fullness or hunger. Other areas of the brain can use sight, smell, social situations and feelings to influence or ignore hunger/fullness signals.
Increasing evidence has found that functional abdominal pain disorders may be caused by disorders of the Gut-Brain interaction in childhood. There is constant communication that exists between the brain and the nerves which may cause pain in the GI tract and/or the rest of the body. This disorder does not develop in one day but can take months or even years for the disorder to develop.
The cause of the pain is not known exactly but it is associated with stress, changes in the bacteria that live in the gut, a family history of gut-brain reactions and disordered movement of the GI tract, suggesting genetics. Each child is different and different causes may have similar symptoms.
It has long been known that children with autistic behaviors tend to have an increased incidence of GI complaints. A recent study measured behaviors of autism with identified bacteria of their microbiome. The study measured the frequency of the identified behaviors, measured the types of bacteria in their stools, treated those particular bacteria and had a decrease in these behaviors. While not a cure it is suggestive that the secretions of these bacteria contribute to their behaviors.
Another study measured clusters of bacteria in infancy and childhood and also measured behaviors over time. Certain troublesome behaviors were found to be associated with either an abundance of particular bacteria or a low level of another bacteria.
Soon, stool samples may be routine in wellness checks.
By Sally Robinson, MD
Keeping Kids Healthy
University of Texas Medical Branch (UTMB)
Published July 2025