Gut Check: How Short-Chain Fatty Acids Can Keep Your Brain in Shape

A happy baby sits in a high chair eating oatmeal, with a spoon in his mouth


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 3 of 4 in our Science of Happiness series, where we’ll learn: 

  • How the brain keeps itself calm and collected, 
  • What gut bacteria are in charge of that, and 
  • What foods can help improve brain functioning.

Our gut health report gives you deep insights into your baby's gut health. See a sample
Our gut health report gives you deep insights into your baby's gut health. See a sample

Short-chain fatty acids (SCFAs) are tiny but mighty compounds that keep your gut in tip-top shape. They are produced by good bacteria in your gut as they break down dietary fibers and resistant starch.

There’s plenty of evidence on the beneficial role that SCFAs play in gut health [1], [2]. And while the science is still developing, exciting new research suggests that SCFAs are key for brain health too [3]. So next time you give your little one some fiber-rich foods, know that you're doing their gut and brain a big favor by boosting those SCFAs.

The benefits of short-chain fatty acids in gut health and more

Plant-based foods contain fiber. Fiber is broken down by gut bacteria, and one of the end products of fiber digestion are SCFAs. The most common types of SCFAs are acetate, butyrate, and propionate [1].

Butyrate is especially important because it’s the favorite source of fuel for gut cells [4]. It also helps maintain a strong gut barrier [5], [6]. This prevents the leakage of unfriendly bacteria and inflammatory molecules from the gut to the bloodstream.

Even when SCFAs are produced in the gut, their beneficial effects go way beyond:

  • SCFAs regulate immune function
  • Reduce inflammation
  • Help control appetite
  • Keep blood sugar levels steady
  • Lower cholesterol and triglycerides in the blood
  • Stimulate the production of serotonin by gut cells [7], [8], [9], [10]

And new research suggests that SCFAs may also have beneficial effects on the brain, by either sending signals through the gut-brain axis or taking a direct route there [11]. 

Brain food: How short-chain fatty acids can keep your microglia happy and the blood-brain barrier strong

Did you know that your brain has its own special immune cells called microglia? These little guys are like the security guards of your nervous system, always on the lookout for trouble. They become activated by inflammatory stimuli and protect your brain against injury and infection [12].

But if microglias get too active, it can actually harm your brain instead of protecting it [13], [14].

Think of it like this: if a bad guy breaks into your house, you want the security to show up and take care of it. But if the security sticks around for too long and starts messing with your furniture, that's not good either. That's kinda what happens when microglia get too excited and start causing inflammation in your brain.

The good news is that some scientists think there may be a way to keep microglia in check—by feeding your gut microbes with fiber-rich foods. When gut bugs munch on fiber, they produce SCFAs. And guess what? A study on mice found out that adding fiber to the diet increased the production of SCFAs, which seemed to travel from the gut to the brain, where they helped keep microglia calm and collected [15].

Another study in mice suggests that SCFAs are also important for maintaining a strong blood-brain barrier [16]. The blood-brain barrier is like a protective wall that separates the blood in our body from our brain and spinal cord. It helps keep our brain safe from harmful things that might be in our bloodstream, while still allowing good things like nutrients and oxygen to pass through.

How to boost the production of short-chain fatty acids in your little one’s gut

SCFAs are formed when gut bacteria digest the fibers in food. So any plant-based food, especially those high in fiber, are good options to increase SCFAs production in your little one’s gut.

Here are some suggestions to boost SCFAs production: 

  • Offer a variety of fiber-rich foods: It's important to offer a variety of fruits, veggies, whole grains, and legumes. These foods are high in fiber and can promote the growth of beneficial gut bacteria that produce SCFAs. Some examples of high-fiber foods for babies include sweet potatoes, peas, avocados, and oatmeal.
  • Introduce fermented foods: Fermented foods contain beneficial probiotic bacteria that can help to improve gut health and promote the production of SCFAs. Some examples of fermented foods for babies include yogurt, kefir, sauerkraut, and pickles. Introduce these foods gradually and in small amounts to avoid digestive issues.
  • Avoid processed foods: Processed foods are typically low in fiber and can disrupt the balance of bacteria in your baby's gut. Instead, focus on whole, nutrient-dense foods that are minimally processed.

As we continue to explore short-chain fatty acids and their profound impact on gut and brain health, remember that nurturing your little one's gut microbiome with fiber-rich foods is a simple yet powerful way to support their cognitive development and overall well-being. 

Incorporating various plant-based foods into their diet and introducing fermented options can help foster a healthy gut environment where SCFAs thrive. 

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. 

Want to know more? Check out the final post in our series on serotonin's role in your body and mind, and how food could affect your mood.

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[1] C. Martin-Gallausiaux, L. Marinelli, H. M. Blottière, P. Larraufie, and N. Lapaque, “SCFA: mechanisms and functional importance in the gut,” Proc. Nutr. Soc., vol. 80, no. 1, pp. 37–49, Feb. 2021, doi: 10.1017/S0029665120006916.

[2] D. Parada Venegas et al., “Short Chain Fatty Acids (SCFAs)-Mediated Gut Epithelial and Immune Regulation and Its Relevance for Inflammatory Bowel Diseases,” Front. Immunol., vol. 10, p. 277, 2019, doi: 10.3389/fimmu.2019.00277.

[3] M. E. Caetano-Silva, L. Rund, N. T. Hutchinson, J. A. Woods, A. J. Steelman, and R. W. Johnson, “Inhibition of inflammatory microglia by dietary fiber and short-chain fatty acids,” Sci. Rep., vol. 13, no. 1, p. 2819, Feb. 2023, doi: 10.1038/s41598-022-27086-x.

[4] D. R. Donohoe et al., “The microbiome and butyrate regulate energy metabolism and autophagy in the mammalian colon,” Cell Metab., vol. 13, no. 5, pp. 517–526, May 2011, doi: 10.1016/j.cmet.2011.02.018.

[5] L. Peng, Z.-R. Li, R. S. Green, I. R. Holzman, and J. Lin, “Butyrate enhances the intestinal barrier by facilitating tight junction assembly via activation of AMP-activated protein kinase in Caco-2 cell monolayers,” J. Nutr., vol. 139, no. 9, pp. 1619–1625, Sep. 2009, doi: 10.3945/jn.109.104638.

[6] L. Zheng et al., “Microbial-Derived Butyrate Promotes Epithelial Barrier Function through IL-10 Receptor-Dependent Repression of Claudin-2,” J. Immunol. Baltim. Md 1950, vol. 199, no. 8, pp. 2976–2984, Oct. 2017, doi: 10.4049/jimmunol.1700105.

[7] R. Corrêa-Oliveira, J. L. Fachi, A. Vieira, F. T. Sato, and M. A. R. Vinolo, “Regulation of immune cell function by short-chain fatty acids,” Clin. Transl. Immunol., vol. 5, no. 4, p. e73, Apr. 2016, doi: 10.1038/cti.2016.17.

[8] A. Haghikia et al., “Propionate attenuates atherosclerosis by immune-dependent regulation of intestinal cholesterol metabolism,” Eur. Heart J., vol. 43, no. 6, pp. 518–533, Feb. 2022, doi: 10.1093/eurheartj/ehab644.

[9] G. Frost et al., “The short-chain fatty acid acetate reduces appetite via a central homeostatic mechanism,” Nat. Commun., vol. 5, p. 3611, Apr. 2014, doi: 10.1038/ncomms4611.

[10] C. S. Reigstad et al., “Gut microbes promote colonic serotonin production through an effect of short-chain fatty acids on enterochromaffin cells,” FASEB J. Off. Publ. Fed. Am. Soc. Exp. Biol., vol. 29, no. 4, pp. 1395–1403, Apr. 2015, doi: 10.1096/fj.14-259598.

[11] M. E. Caetano-Silva, L. Rund, N. T. Hutchinson, J. A. Woods, A. J. Steelman, and R. W. Johnson, “Inhibition of inflammatory microglia by dietary fiber and short-chain fatty acids,” Sci. Rep., vol. 13, no. 1, p. 2819, Feb. 2023, doi: 10.1038/s41598-022-27086-x.

[12] I. C. M. Hoogland, C. Houbolt, D. J. van Westerloo, W. A. van Gool, and D. van de Beek, “Systemic inflammation and microglial activation: systematic review of animal experiments,” J. Neuroinflammation, vol. 12, p. 114, Jun. 2015, doi: 10.1186/s12974-015-0332-6.

[13] S. T. Dheen, C. Kaur, and E.-A. Ling, “Microglial activation and its implications in the brain diseases,” Curr. Med. Chem., vol. 14, no. 11, pp. 1189–1197, 2007, doi: 10.2174/092986707780597961.

[14] S. Isik, B. Yeman Kiyak, R. Akbayir, R. Seyhali, and T. Arpaci, “Microglia Mediated Neuroinflammation in Parkinson’s Disease,” Cells, vol. 12, no. 7, p. 1012, Mar. 2023, doi: 10.3390/cells12071012.

[15] M. E. Caetano-Silva, L. Rund, N. T. Hutchinson, J. A. Woods, A. J. Steelman, and R. W. Johnson, “Inhibition of inflammatory microglia by dietary fiber and short-chain fatty acids,” Sci. Rep., vol. 13, no. 1, p. 2819, Feb. 2023, doi: 10.1038/s41598-022-27086-x.

[16] V. Braniste et al., “The gut microbiota influences blood-brain barrier permeability in mice,” Sci. Transl. Med., vol. 6, no. 263, p. 263ra158, Nov. 2014, doi: 10.1126/scitranslmed.3009759.