What Is Gut Microbiota? 

Gut microbiota is a complex “ecosystem” consisting of over 100 trillion microorganisms living inside our digestive tract, primarily in the colon (1). The most abundant members of this community are anaerobic bacteria. In addition to bacteria, there are also yeasts, viruses, and other microbes in smaller quantities (2).

Interestingly, each person has a unique “microbial fingerprint.” A child’s gut microbiota composition is influenced by age, genetics, environment, and diet. Even during the fetal stage, children begin acquiring microbiota from amniotic fluid and the placenta. As their diet evolves, so does their gut microbiota—transitioning from a simple community dominated by anaerobic bacteria to a more complex and diverse ecosystem capable of synthesizing vitamins and digesting polysaccharides.

Children’s gut microbiota contains many genes related to amino acid degradation, vitamin synthesis, and inflammation—distinct from adults, whose microbiota is more associated with inflammation and obesity. Overall, the gut microbiota undergoes continuous and resilient development throughout life (2). 

Benefits of a Balanced Gut Microbiota and How It Works 

A balanced gut microbiota means a rich diversity and an ideal ratio of beneficial to harmful microbes. The optimal ratio is approximately 85% beneficial bacteria to 15% harmful bacteria (3). When beneficial bacteria dominate, they help stabilize the gut environment and prevent the overgrowth of harmful microbes.

Here are the key benefits of a balanced gut microbiota: 

  • Supports digestion and nutrient absorption: 
    Dietary fiber and indigestible carbohydrates are fermented by beneficial bacteria in the gut. These bacteria act like “mini fermentation factories” (4), producing short-chain fatty acids (SCFAs) such as acetate, propionate, and butyrate, as well as other metabolites like serotonin and gamma-aminobutyric acid (GABA). SCFAs provide metabolic energy for colon epithelial cells and help reduce cholesterol. They are produced during the fermentation of prebiotics like inulin and fructo-oligosaccharides, promoting the growth of beneficial bacteria such as Bifidobacterium spp. and Lactobacillus spp. (5). Beneficial bacteria also play a role in synthesizing essential vitamins (K, biotin, folic acid, B12, pantothenic acid) and amino acids from urea or ammonia (2).
  • Promotes physical development and growth: 
    A healthy gut microbiota strengthens the intestinal epithelial barrier, enhancing nutrient absorption and metabolism—laying a solid foundation for optimal height and weight development in children (5).
  • “Trains” the immune system: 
    About 70–80% of the body’s immune cells are located in the gut (6). Microbes help the immune system distinguish between friendly bacteria and harmful pathogens. This training ensures balanced immune development, preventing overreactions to harmless substances (allergies) while preparing to fight real threats (4).
  • Protects against harmful agents: 
    A balanced gut microbiota acts as a biological shield. Beneficial bacteria compete for adhesion sites on the gut lining, leaving no room for harmful bacteria to settle and multiply (7). They also secrete natural antimicrobial substances (e.g., bacteriocins, lactic acid, peroxide) to inhibit pathogen growth (7). Additionally, beneficial bacteria consume nutrients, depriving harmful microbes of food and limiting their proliferation (8).
  • Improves mental health and brain development: 
    The gut and brain are closely connected via the gut–brain axis, with the vagus nerve serving as the main communication channel. The enteric nervous system is often called the “second brain” because it produces neurotransmitters similar to those in the brain, such as serotonin, dopamine, and GABA. These chemicals play vital roles in mood regulation, cognitive function, and reducing stress and anxiety. In fact, an estimated 90% of serotonin is produced in the digestive tract (9). 

Khoa học về hệ vi sinh đường ruột và lợi ích lên sức khỏe tổng thể của trẻ

Consequences and Symptoms of Gut Microbiota Imbalance in Children 

When the gut microbiota becomes imbalanced (also known as dysbiosis), beneficial bacteria are significantly reduced while harmful bacteria have the opportunity to overgrow, disrupting the harmony of the gut microbial ecosystem. Causes include overuse of antibiotics, an unbalanced diet (too much sugar and fat, lack of fiber), exposure to pollutants or disinfectants, and prolonged stress (4). This imbalance can lead to: 

  • Digestive Disorders: Widespread use of antibiotics can eliminate many beneficial gut bacteria, reducing microbial diversity (11). This also decreases the production of beneficial metabolites like SCFAs, disrupting bowel movements and water absorption—leading to diarrhea or constipation (11). Children with irritable bowel syndrome or functional constipation often experience dysbiosis, resulting in excessive gas, bloating, and abnormal stools (12).
  • Weakened Immune Health and Increased Risk of Infections: The gut microbiota acts as a “coach” for the immune system. When disrupted, the immune system may become confused—less effective at fighting pathogens and more prone to mistakenly attacking harmless substances. This makes children more susceptible to infections (e.g., respiratory infections, bacterial diarrhea) and autoimmune conditions (e.g., IBS, eczema) (13). Additionally, the lack of signals from beneficial bacteria reduces IgA antibody production in the gut lining—weakening the “protective armor” and lowering resistance to pathogens. Some studies also link early dysbiosis to a higher risk of severe infections later in life (11).
  • Higher Risk of Allergic Reactions and Chronic Inflammation: Children with conditions like eczema, asthma, allergic rhinitis, or food allergies often have less diverse and imbalanced gut microbiota compared to healthy peers (14). Allergic children typically lack key beneficial bacteria (e.g., Bifidobacterium, Lactobacillus) and have an excess of opportunistic bacteria (e.g., Clostridium, Staphylococcus) (14). Prolonged dysbiosis is also associated with chronic inflammatory diseases such as Crohn’s disease and ulcerative colitis.
  • Increased Risk of Obesity and Metabolic Disorders: Gut microbiota imbalance is linked to the development and progression of obesity and metabolic disorders, including diabetes, insulin resistance, and early signs of metabolic syndrome. Chronic low-grade inflammation in the gut can disrupt hunger signals and impair the body’s regulation of sugar and fat (15).
  • Associated with Neurodevelopmental Disorders: Significant differences exist in the gut microbiota of children with developmental disorders such as autism compared to neurotypical children. Children on the autism spectrum often have fewer butyrate-producing bacteria (a beneficial SCFA for brain health) and more pro-inflammatory bacteria in the gut (2).

In conclusion, understanding the gut microbiota helps parents confidently and safely supplement beneficial bacteria for their children. However, nurturing a healthy gut microbiota goes beyond probiotics—it also requires a fiber-rich diet (prebiotics), an active lifestyle, and limiting antibiotic overuse. Today’s nutritional products often combine Probiotics (e.g., BB12™, LGG™) and Prebiotics (e.g., Inulin, FOS, GOS, HMO, HMP…)—a powerful synergy that supports gut microbiota balance and overall health.

Dr. Nguyễn Thị Ngọc Thanh, Specialist Level I – Nutrition Center, An Khang General Clinic  

Reference

Thursby E, Juge N. Introduction to the human gut microbiota. Biochem J. 2017 May 16;474(11):1823-1836. Link

Saeed NK, Al-Beltagi M, Bediwy AS, El-Sawaf Y, Toema O. Gut microbiota in various childhood disorders: Implication and indications. World J Gastroenterol. 2022 May 14;28(18):1875-1901. Link

Nutrition Society of Malaysia. Get to know you gut microbiota. Probiotics education programme. Link

Saadaoui M and Khodor SA (2023) The Human Microbiome and Its Role in Keeping Us Healthy. Front. Young Minds. 11:1322449. Link

Hemarajata P, Versalovic J. Effects of probiotics on gut microbiota: mechanisms of intestinal immunomodulation and neuromodulation. Therap Adv Gastroenterol. 2013 Jan;6(1):39-51. Link

Wiertsema SP, van Bergenhenegouwen J, Garssen J, Knippels LMJ. The Interplay between the Gut Microbiome and the Immune System in the Context of Infectious Diseases throughout Life and the Role of Nutrition in Optimizing Treatment Strategies. Nutrients. 2021 Mar 9;13(3):886. Link

Sarita, B., Samadhan, D., Hassan, M. Z., & Kovaleva, E. G. (2025). A comprehensive review of probiotics and human health-current prospective and applications. Frontiers in Microbiology, 15, 1487641. Link

Yang, Q., Hu, Z., Lei, Y., Li, X., Xu, C., Zhang, J., ... & Du, X. (2023). Overview of systematic reviews of probiotics in the prevention and treatment of antibiotic-associated diarrhea in children. Frontiers in Pharmacology, 14, 1153070. Link

Harward Health Publishing. Probiotics may help boost mood and cognitive function. March 22, 2023. Link

Zhang YJ, Li S, Gan RY, Zhou T, Xu DP, Li HB. Impacts of gut bacteria on human health and diseases. Int J Mol Sci. 2015 Apr 2;16(4):7493-519. Link

Wurm J, Curtis N and Zimmermann P (2024) The effect of antibiotics on the intestinal microbiota in children - a systematic review. Front. Allergy 5:1458688. Link

Avelar Rodriguez D, Popov J, Ratcliffe EM, Toro Monjaraz EM. Functional Constipation and the Gut Microbiome in Children: Preclinical and Clinical Evidence. Front Pediatr. 2021 Jan 20;8:595531. Link

Shaheen WA, Quraishi MN, Iqbal TH. Gut microbiome and autoimmune disorders. Clin Exp Immunol. 2022 Aug 19;209(2):161-174. Link

Pantazi AC, Mihai CM, Balasa AL, Chisnoiu T, Lupu A, Frecus CE, Mihai L, Ungureanu A, Kassim MAK, Andrusca A, Nicolae M, Cuzic V, Lupu VV, Cambrea SC. Relationship between Gut Microbiota and Allergies in Children: A Literature Review. Nutrients. 2023 May 29;15(11):2529. Link 15. He P, Shen X and Guo S (2023) Intestinal flora and linear growth in children. Front. Pediatr. 11:1252035. Link