The mysteries of the poopy diaper

Researchers are looking to babies’ diapers to get to the bottom of how a healthy, efficient gut microbiome is generated.

The intestines of overactive ADHD dogs house a specific microbe population, reported Yliopisto magazine last autumn. A year earlier, the magazine had described a successful faecal microbiota transplantation: transplanting microbes from a healthy gut to that of a diarrhoea sufferer is an efficient means of treating the disease.

Doctors are becoming progressively more insistent in their recommendations that children should be protected from unnecessary drug treatments – also to protect the life growing inside them.

The microbes in the gut are increasingly linked to a variety of different ailments. They can explain ailments such as allergies, obesity or even depression. Some of the stories sound downright fantastical.

Even the researchers studying the microbiome admit that the picture they have drawn of the microbial life in the human intestine is drawn in the broadest of strokes at the moment. We do not know what combination of species we need to be healthy, or how the microbes are chosen for the microbiome.

The human gut is colonised in practically one fell swoop at birth. At first, an undifferentiated population of microbes spreads all over the baby’s body, and within a few weeks they begin to adapt to the circumstances of the various body parts. After birth, the factors shaping the microbiome include illnesses and medications, but also food, pets as well as the cleanliness and other circumstances in the home environment.


One of the giants of the field, Professor Willem de Vos, who works at the University of Helsinki, describes the microbiota as our second genome, comparing the microbial load to our genetic heritage. According to him, the combination of species is relatively permanent and unique.

But how can this idea of permanence be reconciled with the claim that poor diet or drugs could impair the life inside the intestines?

Docent Anne Salonen, immunologist, confirms that the extensive colonisation of the gut takes place in childhood.

 “We all have our characteristic microbiome, which is largely permanent. Food and other factors change the situation for individual bacteria, and can influence bacterial teams, i.e., networks of interdependent bacteria,” says Salonen.


In adults with robust microbiomes, bacterial invaders from the outside typically find it easiest to break in after repeated courses of antibiotics. Gut disorders should be taken seriously.

 “Even a change in an individual bacterium can have major health impacts. These issues should not be taken lightly,” emphasises Salonen.

She lists bifidobacteria, or lactobacilli, often found in probiotic supplements, as important protective microbes, along with microbes that produce butyric acid. Butyric acid is a short-chain fatty acid which seems to alleviate inflammation and the growth of cancer cells, firm the gut and reduce the creation of oxygen free radicals.

 “Butyric acid tastes bad and is unstable, so it must be produced on-site, so to speak.”

Salonen believes Faecalibacterium prausnitzii and other prolific producers of butyric acid will lead the next generation of probiotics, microbes which balance the gut and promote health.


However, Anne Salonen emphasises that the lack of a particular species of microbe is rarely the problem. There are many different bacteria attending to the various functions in the body, and it is not particularly important to the host which species is in charge of which function at any given time.

Studies have indicated that there are a few hundred bacterial species which could be classified as common, and seem to have colonised more than half of all people.

 “However, there are staggering differences between the number of species found in the gut of even perfectly healthy people.”

While the reasons for this variation are not yet understood, it is known that a particularly diverse gut microbiome may have thousand-fold the number of species that exist in a more homogenous intestine.

In addition to bacteria, the gut is rife with viruses and fungi. There are several different viruses for each bacterial species, but researchers are currently focusing on bacteria.

 “Bacteria have critical mass. Their metabolites are produced in the largest quantities, so their impact on people's health is the most significant,” explains Salonen.

Nevertheless, viruses certainly warrant further research.

 “The viruses infecting bacteria, or bacteriophages, have at the very least an indirect impact on humans. They are a part of the intestinal predator-prey cycle, and are partially responsible for regulating the amounts of the bacteria.”


Only species specialising in the human gut will make their homes there. This means that we must contract them from the faecal remnants of others in our species – as disgusting as that may sound. “In a way, childbirth itself is a kind of a faecal transplant.”

 “It would be good for the mother’s microbiome to be in good shape at the time of labour, so that the transplant will be as beneficial as possible. A probiotic eaten during pregnancy may well protect the child being born”, Salonen says.

One of the unsolved questions regarding the intestinal microbiota has to do with the moments before birth. It has traditionally been thought that a healthy uterus is free from microbes, and that the fetus develops in a sterile environment, but now some researchers are announcing findings of small quantities of bacteria in the intestines of fetuses.

 “This is a real bone of contention whenever microbiologists meet,” explains Docent Mikael Niku, who studies the development of the immune system.

Niku works as university lecturer at the Faculty of Veterinary Medicine and studies the intestinal microbes of cows, pigs and horses.

 “It's too early to say whether live microbes exist in the fetal intestine, but the microbiome of the mother or dam seems to have a profound impact on the development of the fetus’s immune system," Niku states.


Most of the bacteria we encounter do not become permanent residents of our gut. The array of species also depends on the kinds of bacteria our intestines are particularly hospitable to. According to Anne Salonen, the significance of the conditions in the gut is still a mystery.

The University of Helsinki and the Helsinki University Central Hospital have recently launched a study focusing on this topic, in which the microbiomes of babies are monitored for a few years.

The parents are tasked with collecting faecal samples from the diapers of their infants and making notes of any digestive issues or skin conditions of the child.

 “Our HELMi project focuses on the basics: how do the family's lifestyle and environmental factors shape the microbiome of the baby and which features of the microbiota are associated with childhood illnesses? We already have a great deal of information on the impacts of breastfeeding and antibiotics, but the role of environmental factors has never before been surveyed in such breadth," states Salonen.


The intention is to follow at least some of the children in the longer term, even though the current funding is intended for a two-year project.

 “It would be good to follow the subjects until adulthood, particularly if we want to gain information on a topic like obesity.”

Obesity is of particular interest to the researchers because the basic causality has been established quite reliably: disorders in the microbiota increase the risk of obesity. Other cases are still at the level where researchers can state that illnesses are connected to changes in the microbial species.

Salonen hopes that once researchers can better understand the natural development of the microbiota and its health impacts, we can begin to support the generation of a beneficial bacterial makeup through lifestyle choices.

 “Babies born prematurely or via C-section, treated with antibiotics or fed with formula are important target groups, as are babies with increased risk to contract an allergy or autoimmune diseases, or a tendency to gain excessive weight.” 

This article was published in Finnish in the Y/01/17 issue of Yliopisto magazine.