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  • Selma Weerdenburg

Microbiota Mayhem: Exploring the links between antibiotics, gut health and autism

Updated: Feb 21

The effect of diet on behaviour and mood is something that has always fascinated me. No, not only because I love food, although it may be a factor ;). When I was in high school, I did a project about the positive effect of certain dietary changes on children with ADHD. We designed a diet that would increase certain neurotransmitters – like dopamine, noradrenalin and serotonin – in the brain. At this point, I had never heard about the microbiota and how these creatures form an essential link between nutrition and brain function. I couldn’t begin to imagine the effects these microbes can have on your behaviour and mood.

A few years later, I read the story about John Rodakis and his son with autism. His son started taking amoxicillin – an antibiotic that is commonly prescribed – when he came down with strep throat. To his surprise, John Rodakis also saw improvements in his son’s autism traits. The researcher John Rodakis is, he started looking for similar cases; he talked to many parents of children with autism spectrum disorder (ASD) who had observed changes in their child’s behaviour while taking antibiotics as well. Some described improvements, some worsening of traits. This all suggested a link between these antibiotics and ASD. However, at that time, little scientific evidence was available to explain this link.

Before I go into the research that followed John’s observation of his son, let’s first establish what the term autism spectrum disorder encompasses. Children with ASD struggle with social interactions and communication. They might have trouble understanding social cues and expressing themselves to others. They also might show specific repetitive behaviours typical to ASD, like body rocking or echoing the words of another. Many children with ASD also have restricted patterns of interests. For example, they might like playing with a specific toy in a very specific way. As you may have noticed, I used the word “might” in these sentences. The reason for this is that not all children with ASD are the same. ASD is a spectrum of different severities and different neurodevelopmental disorders, meaning some children struggle more with communication than others, and the same goes for the other autistic traits. Because of these big differences in children with ASD, understanding the cause of ASD is incredibly tricky. At present, there is still not much known about the biology of ASD, making it difficult to come up with effective treatment strategies.


In the early 1990s, researchers mostly thought ASD was all in your DNA. A role for bacteria? There was just too little evidence, turning the investigation into a sort of ‘cold case’ – despite some first evidence for a link between ASD, dysbiosis and a leaky gut.


Fortunately, John Rodakis didn’t let this lack of solid evidence stop him from studying what he saw in his son. To quote Rodakis: “If the history of science has taught us anything, it is that real breakthroughs do not occur until paradigms shift, and that that process can be messy and full of controversy.”


Let me explain what happened here. You may remember from the first post of this series that there are millions of tenants living in your body: your microbiota. They live inside your gut, especially in your intestine, but your body has this barrier of bricks – epithelial cells – preventing them from entering your blood. It is important that this barrier is strong enough to prevent the bacterial tenants from breaching it. The annoying fact is, however, that bacterial tenants have ways to influence the strength of the barrier, meaning if they see an opportunity, some bacteria can weaken the wall by taking out their pickaxes. Additionally, the dysregulated “police unit” – your immune system – seen in ASD can destroy the wall even further. This means that, as you’ll remember from the last article in this series, when the tenants are acting up, more metabolites, and even toxic substances, can enter your blood. Via the flow of your bloodstream, these metabolites can also reach your brain. This can lead to inflammation in the brain, something that is often seen in ASD, which I’ve also mentioned in the previous post.


Now let’s zoom in on the barrier. The epithelial cell “bricks” do a pretty good job, but on their own they don't form a solid wall. To prevent bacteria from entering your blood, you need cement gluing the bricks together. In place of actual cement, your intestine uses special proteins connecting the cells. There are many different groups of these proteins, but for this post, I will focus on my favourite ones: the tight junction proteins. As their name gives away, they form super tight connections between the bricks.

Delving deeper into this, bear with me, it gets even a little more complicated.

There is not just one type of tight junction protein between the bricks: a lot of different proteins make up a specific composition of cement – differing from person to person, from wall to wall. These different tight junctions can be divided into two groups: barrier forming junctions and pore forming junctions. The barrier forming junctions act as regular old cement: they completely close the gaps between the bricks. Thanks to them, metabolites – including the toxic ones – cannot reach your blood. They are even waterproof; water molecules cannot cross these junctions.

Pore forming junctions, on the other hand, tightly connect the cells but leave small gaps between the bricks, like arrow slits. Through these so-called pores, water and very small substances like metabolites can enter your blood. The leakiness of the wall can be regulated by the amounts of these proteins between the bricks. The more barrier forming cement is present, the stronger the wall. And vice versa, the more pore forming arrow slits, the more leaky the barrier is.

Researchers see a higher amount of pore forming junctions and less barrier forming junctions in the gut of children with ASD compared to children without ASD. This means that the barrier in the gut of ASD children is more leaky – in sciency words: the permeability is increased.

When gut permeability is increased in this way, that means that stuff from your gut can pass the brick wall into your blood more easily - including metabolites made by microbes, as I mentioned in last week’s blog article. Among these metabolites are molecules that mess with the police department, your immune system, and neuroactive molecules – chemicals that can affect decisions made by the landlord, your brain.

So, why is this a problem in children with ASD and not in all children? In the early 21st century, scientists started to dig deeper into the role of the gut microbiota in ASD. Researchers found dysbiosis – a big difference in the composition of the microbial community – specifically in children with ASD. It is hypothesized that this disruption in the community, the leakiness of the gut and changes in the brain are connected. Microbiota can change the leakiness of the gut. When the gut is leaky, the imbalances in the gut, lead to imbalances in, for example, neurotransmitter systems and your immune system, which can have substantial effects on your brain.

Regardless of exactly what is cause, what is effect, and what is correlation, one thing is for sure: in ASD, we see a dysregulation of the immune system in the brain: the brain’s police unit is over-activated. In the brain, there are two types of star-shaped cells that play a key role in the regulation of the immune system: microglia and astrocytes. Microglia act as patrol officers – they maintain public order by responding to emergencies – while astrocytes are more like crime analysts, analysing suspicious activities and assisting patrol officers in strategic planning and resource allocation.

Normally, these star-shaped cells work together to suppress inflammation in the brain – it’s their job to ensure the brain's stability. However, in ASD, these cells change jobs. Instead of preventing the situation from getting out of hand, they start stimulating chaos. By doing so, they trigger what scientists call neuroinflammation. When this escalated inflammation in the brain stays on, it can damage the brain. On top of that, brain inflammation is not the only process the police cells influence. These star-shaped cells also regulate neuronal function and connectivity – the very wiring of your brain. In other words, when their activity changes, your behaviour changes. As the little bacterial tenants in the gut can influence the police unit, they might just be the culprits in this scenario!

Back to the story of John Rodakis: the antibiotics his son took are designed to target and eliminate bacteria, including those in the gut. By eliminating part of the tenants, the composition of the microbial community changes. Since each microbiome is unique and each antibiotic targets different bacterial tenants, the effects of taking antibiotics can vary from gut to gut, from brain to brain. In Rodakis’ son, the antibiotics may have eliminated some bad microbes, leaving behind a serene society. As microbes influence processes in the brain, this shift in the community affected his behaviour as well. In this case, it improved his autistic traits, but as I mentioned earlier, this effect is not seen in all children with ASD. In some cases, an antibiotic might cause an uprising of the bad bugs, leading to autistic traits getting even worse. Therefore, more research is needed into the effect of microbe-affecting substances like antibiotics, as well as prebiotics, probiotics and dietary supplements, before we can start using them to treat ASD.


The discovery of dysbiosis in the microbiota of children with ASD gives researchers a lot of new information about what happens in the bodies of these children. However, we are still far from understanding how ASD develops. In this series, so far, I described four main things we know. Firstly, we know that the immune system is overactivated in ASD. Secondly, the microbiome is disturbed. Thirdly, the barrier function of the intestines is affected. And lastly, connections in the brain are different. But which of these is cause and which is effect

Let’s compare it to ice cream and drowning. Researchers see an increase in drowning deaths when ice cream sales increase. When only taking into account these two observations, your conclusion could be that ice cream consumption leads to an increased risk of drowning. However, you cannot be sure eating ice cream causes drowning. To be certain, you need to do more research, and you may find out that the real cause is hot weather; on a hot day, more people eat ice cream, and more people go swimming, which increases the risk of drowning. Two observations in ASD, for example, are the rebellious microbiota and an overactivated police unit. These observations can have a cause-effect relationship, but there might be another link, like the hot weather. Researchers are not yet sure whether the acting up of tenants could be causing an overactivity in the brain’s police unit, or if it is the other way around: changes in the brain leading to a weakened barrier, changing the microbiota community. Future research will have to provide more clarity on this relationship.

A follow-up question researchers ask is: “Can we use the microbiota as a target for treatment of ASD?” It would be groundbreaking if we can achieve the same effect John Rodakis saw in his son in other children as well. But as you have probably figured out from this post, the microbiota form a complex and sensitive community, and way more research is needed before we find a potential new treatment. In the upcoming post, we'll explore how researchers can study the biology of ASD and new treatment options. Prepare for a challenge, because this type of research might be more difficult than you think.


As I’m not a native English speaker, I used Chat GPT for checking grammar and asking for synonyms. This helped me improve my language and find the right words in English to convey what I wanted to explain to you. 


I’m extremely grateful to Alex for all her help throughout my project. I could not have embarked on this blog writing journey without her feedback, enthusiasm and guidance. I am also thankful to Kristin Denzer for her mentorship as my Honours coordinator and for her feedback on my writing. Lastly, I would like to extend my sincere thanks to Lucía Peralta Marzal, my lab supervisor, for the amazing internship experience that laid the foundation for this project and for her insightful feedback on my writing.

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