Predicting the Future with Dirty Diapers

Microbiome research is booming right now, with more and more evidence that our personal health and environment are shaped and influenced by the microbes we harbor and encounter. One area of study I find particularly interesting is how the microbiome we acquire at birth affects our long-term health.

A flood of new findings have emerged related to infant microbiome research, leaving parents like me scratching their heads about whether the secrets to our children’s future health may exist in the seemingly endless stream of dirty diapers we change.

The human microbiome evolves and develops in utero and then during and after delivery is colonized by bacteria encountered during exposure to the external environment. The initial composition of microbes an infant is populated with influences their lifelong microbiome signature and can be influenced by many factors along the way, including the microbiome community of the mother, use of antibiotics or other antibacterial substances, breastfeeding, C-section birth. These variables have been correlated with disruption of the infant microbiome and associated with differences in cognitive development and the development of disease, such as asthma and allergies.

In general, these correlations are discovered by taking a fecal sample from an infant and analyzing the DNA sequences of the bacteria present. The microbiome composition of the individual is then compared against different individual characteristics (such as presence or absence of a disease) at the time of the sample and/or at later points in time. Finally researchers look for statistically significant patterns among individuals with similar characteristics or microbiome communities. This type of study can reveal associations between the microbiome and individual traits, but further experiments are needed to show causation.

Brain Development

The first study to show an association between cognitive development and the microbiome was published recently by a team at the UNC School of medicine. Fecal samples from one-year-olds were collected and analyzed, then divided into three groups based on similar microbiome compositions. One year later, children were given a series of test to measure cognitive performance.

The researchers found that babies with higher levels of Bacteroides scored better than children in the other groups. The scientists were surprised to find that these infants also had less diverse gut microbiomes. This was the opposite of what the researchers had hypothesized, since many other studies have found correlations between low gut diversity and negative health outcomes. They concluded that there is probably not a single ideal microbiome, but different optimal microbe communities for different health outcomes.

An important caveat is that this study does not indicate exactly how bacteria are influencing brain development. It is possible that the bacteria are directly communicating with the brain via chemical signals. On the other hand, the bacteria may just be an indicator of some other factor important for brain development, like nutrient levels.


A research team looking at data from the Canadian Health Infant Longitudinal Development (CHILD) study found that acquiring four types of bacteria (Faecalibacterium, Lachnospira, Veillonella, Rothia—dubbed FLVR) by the age of 3 months offered infants protection against developing asthma. The study revealed a “window of opportunity” where gut bacteria play a role in the development of asthma during the first few months of human life.

The researchers also found that newborn mice inoculated with FLVR bacteria decreased the severity of asthma in adulthood. These results offer the promise of developing a test to predict asthma risk in infants as well as probiotic treatments to prevent asthma.


Using data from the same CHILD study, a different research team revealed a connection between infant gut bacteria and the development of food sensitivities. Infants that had lower gut microbiome diversity at 3 months of age, including higher levels of Enterobacteriaceae and lower levels of Bacteroidaceae were more likely to develop food sensitivities by the age of 1.

The scientists found this association was still present, even after controlling for type of delivery (vaginal/C-section), breastfeeding and exposure to antibiotics (which have all been shown to affect the makeup of infant microbiomes). Although this information may eventually lead to new methods of preventing or treating allergies, the study does not indicate if the food sensitivities will actually develop into food allergies when the children are grown.

Influence of Delivery, Feeding and Antibiotics

There have been a number or studies correlating C-section delivery to health outcomes later in life, such as asthma, obesity and allergies. Research related to the impact of environmental factors on infant gut microbiome development showed differences in the types of bacteria that colonize babies delivered vaginally versus via C-section.

This and other studies have led some to conclude that the mode of delivery influences the microbiome, which in turn contributes to the development of disease. Some medical researchers took this idea a step further and tested a method to transfer bacteria that reside in the birth canal to babies born by C-section, as a possible prophylactic against the development of an unhealthy microbiome.

At this point, the available research does not prove that C-sections disrupt the microbiome to the extent that individual health is affected later in life. There is a lot of speculation that the conditions that lead to a C-section occurring, and happen as a result, may be influencing the microbiome rather than the surgical delivery itself (see this study on breastfeeding after C-section).

The effects of prevalent antibiotic use on the microbiome have been another area of focus, and the effect in infants has been investigated. This study showed that children who received multiple courses of antibiotics prior to age 3 had less diverse gut microbiomes. This leads to questions about what effect our society’s widespread use of antibacterial soaps and cleaners has on the microbiome.


Although definitive research about what exactly determines the bacterial makeup of an infant’s microbiome and how information about an individual’s microbiome translates to predicting or preventing long-term health outcomes is still needed, there are some important conclusions that can be drawn from many of these microbiome studies.

It appears that the infant gut microbiome at age one is roughly synonymous to its adult counterpart. This means that any interventions probably need to occur in infants to cause significant and lasting shifts in the composition of microbiome communities.

Another important lesson is that, while it is clear the human microbiome (in particular, the bacteria that inhabit the gut) affects and is affected by individual health, the complexity of the symbiosis between humans and bacteria make it difficult to remain anything but agnostic to suggestions that decisions made by doctors or parents are to blame for a child’s health later in life. Many of these studies put readers at risk of assuming that correlation equals causation, and there is simply not enough evidence to conclude that.

In other words, I’m going to remain hopeful about what my children may be able to find out from their own baby’s diapers—but I’m not going to worry about what the diapers I’m changing portend for their future.

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Darcia is a Science Writer at Promega. She earned her BS in Secondary Education at the University of Wisconsin Oshkosh, with minors in Biology and Spanish, and her MS in Biotechnology at the University of Wisconsin Madison. She is passionate about sharing scientific knowledge with all audiences, including her family and friends—whether they have solicited the lesson or not! In her free time, Darcia enjoys playing volleyball, eating delicious food and cheering for the Chicago Cubs.

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