Tiny Tummies, Big Brains: The Gut Microbiome and Cognitive Development in Infants

Two babies in diapers sit together happily eating watermelon


Happiness is a fundamental human emotion. And for most parents, seeing their babies smile, laugh, and engage with the world around them is a source of great joy and satisfaction. Accepting this premise, led us to ask: is there a link between food and mood? If parents want their children to experience joy, is there a way to amplify or even ensure happiness? 

Welcome to part 2 of 4 in our Science of Happiness series, where we’ll learn: 

  • What kind of development is happening in the first 2 years of life, 
  • What microbes in your gut are linked to better results, and 
  • How you can help feed those microbes with nourishing food for your gut and brain.
What foods should you introduce? Download our free 'Eat the Rainbow' guide. Get My Copy
What foods should you introduce? Download our free 'Eat the Rainbow' guide. Get My Copy

Baby Brains: Mini Supercomputers

Did you know that your little one's brain is growing super fast during the first two years of life? It's like they're building a supercomputer in there!

But here's something even cooler - The bacteria in your baby's gut might be helping with this brain-building process. Yup, studies with animals have shown that the gut microbiome is important for healthy brain function [1], [2]. And now, scientists are starting to think that the same may be true for cognitive development in infants [3].

So, what does this mean for you and your baby? Well, it's just another reason to make sure your little one is eating a healthy and balanced diet. That way, their gut bacteria can do their job and help your baby's brain reach its full potential.

Let’s dive into the science of infant cognitive development and what role gut microbes may play in this.

The first 2 years of life: a critical period for brain development

The first two years of your little one’s life is an exciting period full of incredible growth and development. During this time, your baby learns and achieves many new milestones: from rolling over to sitting up, and eventually taking their first steps. Not only will they be developing their physical abilities but also their cognitive, emotional, and social skills.

Your baby’s brain is growing and changing rapidly during the first two years of life:

  • Total brain volume increases by 101% in the first year of life and reaches 80-90% of adult volume by age 2.
  • Many new connections between neurons are being formed.
  • An area of the brain called white matter is being covered by myelin, a fatty substance that makes it easy for the brain to transmit information between neurons and to other parts of the body.
  • The volume of the cerebellum, a region of the brain that’s critical for movement coordination and balance, increases 240% during the first year of life [4].

The gut microbiome and infant cognitive development

Did you know that the tiny organisms living in your baby's gut can talk to their brain? Yep, they use something called the gut-brain axis to send messages back and forth.

Scientists are just starting to explore how the gut microbiome could be linked to cognitive development in infants. While many studies suggest that the right balance of microbes during the first few years of life is important for brain growth, it's important to note that these studies only show associations—not causation.

Basically, research has found that certain types of microbes are linked to better cognitive outcomes in little ones, but they can't say for sure if these microbes are the direct cause:

  • One study found that when Bacteroides bacteria dominate the gut microbiome at age 1, toddlers tend to have better language and cognitive skills at age 2. Another study found a similar connection, but only in boys [5], [6].
  • A different study found that lower levels of Bacteroides in a baby's gut at age 1 were associated with increased fear behavior [7].
  • In another study, scientists looked at toddlers who were flagged in a behavioral test at age 2 and found that most of them did not have Prevotella in their guts at age 1, unlike toddlers who passed the test [8].
  • Finally, researchers found that when babies have high levels of Bifidobacterium in their guts at 1-3 weeks old, they tend to be more outgoing and extroverted at age 1. On the other hand, high levels of unfriendly Klebsiella at this age were associated with less outgoing behavior at age 1 [9].

It also seems that the diversity of microbes (the different types of microbes) living in your little one’s gut also impacts their cognitive development. Diversity changes a lot during the first few years of life. Researchers have found that it's best for babies to have low diversity at first, but it should gradually increase as they start eating solid foods [10]. 

One study found that high diversity at age 1 was linked to less efficient processing of fear and emotion in the brain, while also being associated with better motor skills [11]. More studies are needed to confirm this.

Interestingly, at age 2, a higher diversity of gut microbes is linked to greater sociability in boys. This could mean that the types of bacteria in a child's gut could have different effects depending on their age and gender [12].

Feeding your baby's gut microbes: a recipe for cognitive growth

Although we can’t guarantee your baby will become the next Einstein, research suggests that feeding their gut microbes with nutrient-dense foods could have a positive impact on their cognitive development.

Of course, there are many other factors at play here, like genetics, the environment, and family support. But if there’s something we can do to help our little ones, why not give it a go?

To keep those gut bugs happy and healthy, we should feed them with foods that are packed with nutrients. Here are some examples of foods that your baby's gut microbes might appreciate:

  • Whole grains
  • Fruits
  • Vegetables
  • Legumes
  • Nuts
  • Seeds

Curious about your baby’s gut? We now know healthier guts = healthier babies. Tiny Health’s revolutionary mess-free Baby Gut Health Test takes less than 5 minutes, and you’ll get a personalized report with actionable results so you can start taking steps towards optimal health. 

Ready to learn more? Read our next post on how the brain keeps itself calm and collected, what gut bacteria are in charge of that, and what foods can help improve brain functioning

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Download our FREE guide to Baby's First Foods

Includes a color-coded checklist to help your little one eat the rainbow, plus helpful tips for introducing solids and allergens


[1] R. Diaz Heijtz et al., “Normal gut microbiota modulates brain development and behavior,” Proc. Natl. Acad. Sci. U. S. A., vol. 108, no. 7, pp. 3047–3052, Feb. 2011, doi: 10.1073/pnas.1010529108.

[2] N. Sudo et al., “Postnatal microbial colonization programs the hypothalamic-pituitary-adrenal system for stress response in mice,” J. Physiol., vol. 558, no. Pt 1, pp. 263–275, Jul. 2004, doi: 10.1113/jphysiol.2004.063388.

[3] A. Jena et al., “Gut-Brain Axis in the Early Postnatal Years of Life: A Developmental Perspective,” Front. Integr. Neurosci., vol. 14, p. 44, 2020, doi: 10.3389/fnint.2020.00044.

[4] R. C. Knickmeyer et al., “A structural MRI study of human brain development from birth to 2 years,” J. Neurosci. Off. J. Soc. Neurosci., vol. 28, no. 47, pp. 12176–12182, Nov. 2008, doi: 10.1523/JNEUROSCI.3479-08.2008.

[5] A. L. Carlson et al., “Infant Gut Microbiome Associated With Cognitive Development,” Biol. Psychiatry, vol. 83, no. 2, pp. 148–159, Jan. 2018, doi: 10.1016/j.biopsych.2017.06.021.

[6] S. K. Tamana et al., “Bacteroides-dominant gut microbiome of late infancy is associated with enhanced neurodevelopment,” Gut Microbes, vol. 13, no. 1, Art. no. 1, Jan. 2021, doi: 10.1080/19490976.2021.1930875.

[7] A. L. Carlson et al., “Infant gut microbiome composition is associated with non-social fear behavior in a pilot study,” Nat. Commun., vol. 12, no. 1, Art. no. 1, Jun. 2021, doi: 10.1038/s41467-021-23281-y.

[8] A. Loughman et al., “Gut microbiota composition during infancy and subsequent behavioural outcomes,” EBioMedicine, vol. 52, p. 102640, Feb. 2020, doi: 10.1016/j.ebiom.2020.102640.

[9] M. Fox et al., “Development of the infant gut microbiome predicts temperament across the first year of life,” Dev. Psychopathol., pp. 1–12, undefined/ed, doi: 10.1017/S0954579421000456.

[10] R. E. Moore and S. D. Townsend, “Temporal development of the infant gut microbiome,” Open Biol., vol. 9, no. 9, Art. no. 9, Sep. 2019, doi: 10.1098/rsob.190128.

[11] W. Gao et al., “Gut microbiome and brain functional connectivity in infants-a preliminary study focusing on the amygdala,” Psychopharmacology (Berl.), vol. 236, no. 5, pp. 1641–1651, May 2019, doi: 10.1007/s00213-018-5161-8.

[12] L. M. Christian, J. D. Galley, E. M. Hade, S. Schoppe-Sullivan, C. Kamp Dush, and M. T. Bailey, “Gut microbiome composition is associated with temperament during early childhood,” Brain. Behav. Immun., vol. 45, pp. 118–127, Mar. 2015, doi: 10.1016/j.bbi.2014.10.018.