All kids can be moody at times, and childhood meltdowns can be very real and gruelling for everyone. However, some kids find it much easier to regulate their mood than others. And, it’s now thought that the balance of gut bacteria could play a role in extreme childhood tantrums and separation anxiety.

This article looks at why the gut microbiome can skew the brain to develop differently, affecting behaviour, learning as well as temperament. It explores how the right balance of gut bacteria can help children to be happier, brighter and more robust. Read on to learn more about important gut microbiome research that may be the clue to raising more resilient, better-regulated and well-grounded kids.

Just as our physical appearance is unique, so is our character and the way our mind is wired. We all interact with the world around us in our own very individual way and interpret our surroundings through our own personal lens. But what is it that forms our own individual temperament, emotional resilience, and style of learning?

Historically the debate has mainly surrounded the “Nature vs Nature” theories. However, it is now thought that the balance of bacteria in the gut microbiome may also influence a child’s character, temperament, and neurodevelopment. So, this is another piece in the puzzle to consider when you have a child who is struggling with their mental health, learning or behaviour.

Microbiome research has only been catching up in the last decade or so, and these studies have been accelerated as there is huge concern in the upsurge of mental health issues as well as learning differences and neurodiversity in children across the world. This is a trend over and above what can be easily explained by genetic factors and increase in awareness of these developmental differences.

It is now well established that gut microbes are key players in cultivating our brain neurotransmitters such as serotonin (happiness), dopamine (pleasure, satisfaction and motivation), norepinephrine (fight or flight), GABA (inner calm) and acetylcholine (learning and memory)– these are the building blocks that help to regulate mood, emotions, learning, memory and overall neurodevelopment. The different types of gut bacteria help to cultivate the brain hormones which are then sent along the vagus nerve to our brain. This is known as the gut-brain axis.

The Gut Bacteria That Feed The Brain

Gut Bacteria Neurotransmitter Building Block Neurotransmitter Action
Lactobacillus Acetylcholine
Learning and Memory
Inner Calm
Bifidobacterium GABA Inner Calm
Escherichia Norepinephrine
Fight or Flight
Pleasure, Satisfaction & Motivation
Streptococcus & Enterococcus Serotonin Happiness
Bacillus Norepinephrine
Fight or Flight
Pleasure, Satisfaction & Motivation


There are many factors which can influence the development of the microbiome in early childhood and here are some important pointers to consider.

Signs of An Out-of-Sync Gut

Most parents are obsessed with the contents of their little one’s nappies and baby and toddler poo can give you a clue if there is something out-of-sync in the microbiome, especially so after being weaned onto solid food.

If the poo contains undigested food, is very constipated, loose or irregular then there may be an imbalance in the gut microbiome. If the baby or toddler produces excess gas or regurgitates their feeds or has a sore tummy a lot of the time, then help maybe needed. Itchy rashes or constant gastric or viral infections may also mean the microbiome needs some extra support. Little ones who have been given antibiotics or reflux medications will find it harder to establish a healthy and diverse microbiome.

There are of course many other causes for all of these things, so it is important to speak to your GP or paediatrician if you have concerns. Also it is important to realise that the gut microbiome can still be out of balance even if the poo looks and smells very normal and digestion seems to be intact.

Birth & Baby Feeding Method

Birth method plays an important role in the development of a healthy and diverse gut microbiome, and it is thought that babies who have a vaginal delivery find it easier to build a more diverse microbiome at the start of life, compared with those delivered by caesarean section. Research has also found that babies born prematurely also need extra help with creating a healthy and diverse microbiome.

Equally babies who are breast fed will benefit from the diversity of the mother’s microbiome and the human milk oligosaccharides (HMO). However not every mother’s microbiome is equal and can also change easily due to stress, diet, lack of sleep and if antibiotics are needed. This is partly why breast milk varies so considerably in colour and consistency.

Even though most baby formula options are catching up in terms of microbiome support, these mainly only provide prebiotics in the form of galacto-oligosaccharides (GOS) which is a specific prebiotic that is derived from lactose. Prebiotics do help to feed the overall gut microbiome but HMO’s are more likely to increase microbial diversity.

Another factor to consider is that breast milk is not as diverse in microbes as it used to be. Over the last century human microbiome diversity has shrunk quite considerably, so it is thought that babies who are breastfed now, have less Bifidobacterium infantis in their bellies than the formula-fed babies 100 years ago. Bifidobacterium infantis is the key bacterium for preventing a build-up of pro-inflammatory bacteria and help to prevent childhood infections from becoming severe or life-threatening.

Interestingly it appears from studies that babies with more abundant Bifidobacterium species in their gut are more likely to be more settled and are easier to soothe. And this research has found that babies who are easier to soothe are less likely to develop anxiety, depression and cognitive problems later on in life. This is maybe because Bifidobacteria are thought to shape the neural circuits in a baby’s brain by promoting synapse formation and microglial function, which I will unpack in more detail below.

It is thought that composition and function of the intestinal microflora starts from birth; this becomes more established once the baby is weaned onto solid foods from around 6 months old, and gradually stabilises and develops into a more adult-like pattern at around the time of the toddler years. This is why it is particularly important to feed little babies and toddlers a healthy diet with a broad range of fruit, vegetables, nuts, seeds, wholegrains and cultivated foods such as kefir and yoghurt during their first three years of life.

Between birth and 12 months, the brain doubles in size and it triples in size by the age of three, where it is then nearly adult size. This rapid brain development is because of increased myelination and synaptic connections, driven by the infant’s sensory-motor experiences and diversity in the gut microbiome.

The First Six Months

Interestingly, the first six months when a baby is exclusively fed breast or formula milk, is a key stage for neurodevelopment and is when most of the brain synapses are formed. A healthy balance of bacteria in the gut microbiome as well as play, nonverbal expression, and routine problem-solving also stimulate the formation of synaptic linkages which form the basis for future cognitive, social, and behavioural performance.

It is a key stage for helping to regulate the nervous system and general demeanour and it is thought that a child’s behaviour and risk for depressive and anxiety type outcomes may be influenced at this stage. Working on a healthy gut microbiome at this point in a baby’s development is thought to affect cognition, arousal, attention and memory. It may also help with spatial learning.

It’s also a time when the majority of the brain’s microglia are being formed, which are the “housekeepers” in the brain keeping everything shipshape and ordered. Microglia are sensitive to changes in the gut microbiome and receive signals from the vagus nerve to regulate neuroimmune activity and brain function.

And it’s the time when most of the myelination in the brain occurs, and it’s the myelin sheath that sends electrical impulses quickly and efficiently along the nerve cells. This in turn helps to regulate the peripheral and central nervous systems. Increasing myelination allows the baby to reach their developmental milestones such as lifting their head, reaching out, rolling over and crawling, and eventually walking and running. Again, recent research has found that an imbalanced gut microbiome can influence the rate of myelination.

Six Months to Three

It is recommended to introduce solid food to a baby from around four to six months. And the period of time between being weaned and a child’s third birthday is the window of opportunity to help develop the gut microbiome further by feeding your child a wide range of fruits, vegetables, ground up nuts and seeds, pulses, wholegrains, herbs and spices.

It is when the central nervous system is maturing, and the brain synapses are at their most abundant. After the age of three, synaptic pruning starts which is a natural process that occurs in the brain between early childhood and adulthood and reduces the number of synapses by around 50% by the teen years.

From age 6 months to three years is the time when the neurons in the brain are most neuroplastic which means they can adapt and change. This is the time when the neurons are most adaptable in response to diet changes and it the best opportunity to nourish your child’s brain through food.

This is also a period of time when smell and taste preferences are established, so the more smells and tastes you expose your child to during this time, the more likely they are going to enjoy a broader range of foods over time.

Tips for Supporting a Child’s Microbiome

  • If a baby is born via caesarean section or has been exposed to antibiotics within the first six months, consider supplementation with a Bifidobacterium-based beneficial bacteria.
  • Expose them to fresh air as much as possible and keep your house well ventilated.
  • Spend as much time outside and once they are on the move encourage time playing, crawling, rolling and running in grass and even in the mud.
  • Avoid ultra-processed convenience ready-made foods, white flour and refined sugars.
  • Aim to feed the “rainbow” of fruits and vegetables a day and aim for a minimum of “5 a day”. Find clever ways to get more into your kids via smoothies, ice lollies or grated/blended into muffins, waffles and pancakes.
  • Bolster up the diet with pulses, wholegrains, nut butters and ground nuts and seeds.
  • Vitamin D and Omega 3 help to nourish a healthy microbiome.
  • Aim for variety of food as much as possible.
  • Consider fermented or cultured foods such as live yoghurt, kefir, apple cider vinegar and miso.

The great news is that even if you are reading this when your kids are older, it’s now well-established that it’s never too late to work on the gut microbiome and eating habits can be changed over time (even if this seems painfully slow!). Since a child’s brain is still developing until their mid-twenties there is still plenty of time to re-set their gut bugs and this might even influence their learning, behaviour and developmental trajectory.

Lucinda Recommends

BioCare Baby Infantis Powder
Natures Aid Bio360 Kidz Pro-5
Baba West Bifikalm Multibiotic Relief


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