New study examines the gut microbiome in Kleefstra syndrome

Can the gut microbiome be yet another piece of the complex phenotype of Kleefstra syndrome?;

This question was investigated by a new study from Radboud University Medical Center in the Netherlands, which systematically examined for the first time the composition of the gut microbiome in individuals with Kleefstra Syndrome and its relationship with gastrointestinal and behavioral characteristics.

The work, titled The role of the gut microbiota in patients with Kleefstra syndrome, published in American Journal of Medical Genetics Part B: Neuropsychiatric Genetics and included 23 individuals with Kleefstra syndrome and 40 family members.

The results showed differences in the gut microbial community between the two groups and some correlations with gastrointestinal and behavioral characteristics.

However, it is a first exploratory study. Her findings do not prove that microbiome changes cause Kleefstra symptoms, and most importantly, do not indicate that probiotics, specific diets, or other microbiome interventions can be used as a treatment for the syndrome.

What is the gut microbiome

The human gut hosts a vast number of microorganisms, mainly bacteria. The entirety of this microbial community is referred to as gut microbiome or gut microbiota.

In recent years, scientific interest in the so-called has increased significantly gut-brain axis, meaning the bidirectional communication between the gastrointestinal system and the central nervous system.

This communication is particularly complex and appears to involve the immune system, metabolic products of microorganisms, hormonal mechanisms, and neural pathways.

For this reason, the microbiome is now also being studied in various neurodevelopmental disorders.

Why researchers studied it in Kleefstra

Kleefstra syndrome is caused by the insufficient function of the EHMT1, of a gene with an important role in the regulation of gene expression and neurodevelopment.

Alongside intellectual and developmental disability and neuropsychiatric features, individuals with Kleefstra syndrome are also frequently reported to have gastrointestinal disorders.

Therefore, the researchers wanted to examine two main questions.

First, whether the composition of the gut microbiome of individuals with Kleefstra differs from that of people in their immediate family environment.

And secondly, if the differences observed in the microbiome are related to specific characteristics of the syndrome, such as gastrointestinal problems or the severity of certain behavioral symptoms.

23 individuals with Kleefstra and 40 family members

The study involved 23 individuals with molecularly confirmed Kleefstra syndrome, aged approximately 5 to 40 years, as well as 40 of their relatives.

The comparison group included 14 fathers, 16 mothers, and 10 siblings.

The selection of members of the same family as a comparison group is of particular interest.

Individuals living in the same family are more likely to share a similar environment and, to some extent, similar dietary habits. This can help researchers narrow down some of the many external factors that influence the gut microbiome.

Participants provided stool samples and the microbial composition was analyzed by 16S rRNA sequencing, a technique widely used for the study of bacterial communities.

At the same time, information was collected regarding diet, body mass index, medications, gastrointestinal symptoms, and behavioral characteristics.

The microbiome of individuals with Kleefstra showed differences

The researchers identified differences in both alpha diversity as much as in beta diversity of the microbiome.

In simpler terms, alpha diversity describes how rich and diverse the microbial community is within a single individual, while beta diversity examines how different the overall microbiome composition is between different people or groups.

In individuals with Kleefstra, microbial diversity was lower and the overall microbiome composition differed from that of their family members.

Indeed, the Kleefstra diagnosis explained approximately 3% of variation in the overall microbial community in this specific statistical model.

This percentage may seem small, but the microbiome is simultaneously affected by many factors, such as age, diet, body weight, medications, and the environment.

Lower presence of Coprococcus 3

When the researchers examined specific bacterial genera, one of the clearest findings concerned the Coprococcus 3.

Its relative abundance was significantly lower in individuals with Kleefstra compared to their family members. The finding is interesting because alterations in the genus Coprococcus have also been reported in other studies of neurodevelopmental or gastrointestinal conditions. However, this does not mean that the reduced presence of this specific bacterium causes Kleefstra Syndrome or any of its features.

The study can show a correlation. It cannot prove which is the cause and which is the effect.

An interesting connection to gastrointestinal problems

A second finding concerned the bacterial genus Merdibacter.

In participants who reported gastrointestinal problems, the relative abundance of Merdibacter was lower in individuals with Kleefstra compared to their family members. Interestingly, the opposite pattern was observed in participants without gastrointestinal complaints. This result indicates that the relationship between Kleefstra, the gastrointestinal system, and the microbiome may be more complex than a simple increase or decrease of specific bacteria.

Microbiome and behavioral traits

The researchers also examined whether differences in the microbiome were related to the severity of the behavioral characteristics of the participants with Kleefstra. For the assessment, among other things, the Child Behavior Checklist, CBCL. In the group of individuals with Kleefstra, the behavioral problem score correlated with the overall composition of the microbial community and explained approximately 7% of its differentiation.

At the same time, a greater abundance of certain bacterial groups was associated with greater severity of behavioral symptoms. Furthermore, in this specific group, more intense behavioral problems occurred more frequently in individuals who also reported gastrointestinal discomfort. This is an interesting finding, but it requires particularly careful interpretation. In individuals with limited verbal communication, gastrointestinal distress can sometimes be expressed through changes in behavior, restlessness, or irritability. On the other hand, there are many other factors that can simultaneously influence both behavior and the microbiome.

Therefore, the study does not prove that specific bacteria cause behavioral problems.

Does the type of genetic alteration in EHMT1 matter?;

Researchers also examined whether there were differences in the microbiome depending on the type of genetic alteration. The study included individuals with pathogenic variants of EHMT1 as well as individuals with smaller or larger deletions. No statistically significant relationship was identified between the type of genetic alteration and the composition of the microbiome. However, due to the small number of participants, it is not yet possible to rule out that such differences may exist.

What do these results really mean

This study presents for the first time evidence that the gut microbiome of individuals with Kleefstra syndrome may have certain distinct characteristics compared to that of their family members. At the same time, it shows potential correlations between microbial composition, gastrointestinal problems, and certain behavioral characteristics.

However, we do not know whether microbiome alterations are a cause, a consequence, or simply an accompanying feature of Kleefstra syndrome.

For example, the syndrome itself can affect diet, mobility, bowel function, medication use, and many other factors, which in turn can alter the microbiome. It is also possible that there is a bidirectional relationship. To distinguish between these possibilities, much larger and, above all, longitudinal studies are needed.