The Human Microbiome
The human microbiome, comprising trillions of microorganisms that inhabit our bodies, is increasingly recognized for its crucial role in maintaining overall health. Since the human microbiome project was launched in 2007 there has been an explosion of research studies into the importance of the gut microbiome not only for gut health. These microorganisms are involved in essential physiological processes such as immune function, digestion, neurodevelopment, and mental health – in the short and long-term. The gut microbiota regulates neurodevelopment through three pathways, the immune system, the nervous system, and the endocrine/hormone pathway, with overlaps and crosstalks in between the three pathways.
Dysbiotic microbiome markers have been found in children with autism, ADHD, and anxiety. A recent study showed that children with autism can be identified by looking at the composition of their microbiome. In addition a dysbiotic gut flora is associated with an increased risk of chronic diseases like cardiovascular disease, type 1 and 2 diabetes, obesity, autoimmune disease, and even cancer.
Whatever gut microbiome you child has around 2-3 years of age is what their immune system sets as a norm and will revert to after disruption of the microbiome by for example a course of antibiotics or a gastro-enteritis (diarrhoea). This means if a child has a beneficial gut flora by 3 years of age, they are at lower risk of developing autoimmune and other chronic illnesses, life-long. Therefore, establishing a healthy microbiome early in life is essential and one of the best predictors of long-term health, making it imperative to promote practices that support its development in children.
Specific lifestyle habits and interventions can either promote the growth of a healthy microbiome or harm it. There are so many opportunities from before birth through the first years of life to make positive choices for the microbiome, but unfortunately many routine (and often unnecessary) health interventions are harmful. This article aims at increasing your awareness of the impact of common healthcare interventions and lifestyle habits on the microbiome in the first years of life, and thus on life-long health outcomes.
One of the key strategies to enhance the microbiome in children begins during pregnancy. Eating an unprocessed, whole-foods, fibre-rich diet and supplementing with probiotics during pregnancy can significantly support the development of a healthy microbiome in the mother which is transferred to the infant during the birth process and later through close contact. Pregnant women should include probiotic-rich foods in their diets or consider high-quality probiotic supplements, in particular in the third trimester.
The mode of delivery plays a significant role in the establishment of an infant's microbiome. Infants born via vaginal delivery swallow their mother's vaginal microbiota, which colonizes their gut and boosts their immune system. Babies born vaginally have a microbiome rich in lactobacilli and bifidobacteria. In contrast, the microbiome of infants born via CS resembles the skin flora of the hospital staff – a highly inflammatory microflora. C-sections can of course save lives, but the C-section rates in all developed countries are far higher than the amount needed. Women need to be fully informed about the consequences of an elective C-section to make a truly informed decision about their birth choice. One can consider microbiota restoration techniques, such as vaginal seeding, for caesarean-delivered babies.
Breastfeeding is another critical factor. Breast milk contains prebiotics, probiotics, and human milk oligosaccharides (HMOs), that promote the establishment of a healthy, anti-inflammatory gut microbiome high in bifidobacteria and lactobacilli and aid in developing the infant's immune system. Exclusive breastfeeding for the first six months of life and continued breastfeeding along with solid foods for 2 years or beyond are recommended by WHO, Unicef, the American Academy of Pediatrics, and other peak health bodies, as it provides the optimal mix of nutrients and beneficial bacteria. Even just one bottle of formula changes the microbiome to one higher in E coli and inflammatory clostridia, and it can take up to 4 weeks of exclusive breastfeeding for the microbiome to recover from that one bottle. The longer a child is breastfed, the lower the risk of them developing allergies – one of the most common childhood illnesses.
Diet plays a fundamental role in microbiome development. A diet rich in fibre supports the growth of beneficial gut bacteria. Humans cannot digest fibre, but gut bacteria thrive on it. Every plant feeds a different type of gut bacteria, so the more different kinds of plant foods one consumes, the more diverse the microbiome will become. And the more diverse the microbiome, the healthier the person. Diets high in sugar and processed foods can promote the growth of harmful bacteria and yeast, disrupting the microbiome balance. Introducing a variety of fruits, vegetables, whole grains, and legumes in the early years promotes a healthy gut flora.
Instead of introducing sugary cereal as a weaning food, children benefit from “baby-led weaning” where they are – once developmentally ready, i.e. able to sit and interested in food, offered unprocessed, whole foods they can pick up with their own hands and feed themselves. Another benefit of baby-led weaning is that children can stop eating when they feel full, rather than being spoon-fed when no longer hungry. This has been shown to reduce the risk of obesity.
Playing in dirt and exposure to pets, particularly dogs (who are by nature dirty), can also be beneficial. Interaction with pets has been shown to diversify the microbiome and reduce the risk of allergies and asthma – training the immune system from early on. Promoting safe and regular play in nature and interaction between children and pets can significantly enhance microbiome diversity.
On the other hand, certain factors can negatively impact the development of a healthy microbiome and should be avoided. Overuse of antibiotics and reflux medications can disrupt the balance of gut bacteria, leading to dysbiosis. While antibiotics are sometimes necessary, they should be prescribed judiciously. Most ear infections and all viral infections – the most common causes for antibiotic prescriptions in the first years - resolve without antibiotics. In fact, a course of antibiotics increases the risk of developing another bout of otitis media within 3 months.
Up to 10% of infants are treated with reflux medications. These reduce the acidity of stomach secretions and thus make the reflux painless. But they do not address the underlying causes of infant reflux – which is most commonly cow’s milk protein intolerance. 90% of infants’ reflux resolves within 3 weeks when all non-human milk is removed from their and their breastfeeding mother’s diet. PPIs or protein pump inhibitor medications for reflux have serious long-term consequences: the acidity in the stomach is essential to kill off pathogens that are swallowed; to absorb essential nutrients like iron, B12, zinc, and calcium; and they are of course needed to digest food. Thus PPIs increase the risk of gastro-enteritis (diarrhoea), a dysbiotic gut flora, nutrient deficiencies, and food allergies as half-digested proteins are presented to the immune system and trigger reactions. PPIs are even associated with an increased risk of fractures in children – probably due to poor absorption of calcium. There are simple and effective strategies to treat infants with reflux: Hold your baby upright for 30 minutes after feeds to let gravity do its job; avoid non-human dairy; skin-to-skin contact increases endorphin levels which reduce pain and inflammation; probiotics can promote gastric emptying and peristalsis to reduce pressure on the stomach.
Exposure to chemicals such as cleaning products, pesticides, and other environmental toxins can also harm the gut microbiome.
Promoting a healthy microbiome from infancy until the unique gut flora of a child is established by age 2-3 years, and of course beyond then, is essential for optimal development and long-term immune, physical, and mental health. Beneficial practices such as probiotic supplementation during pregnancy, vaginal birth when possible, breastfeeding, an unprocessed, varied, fibre-rich diet, and interaction with pets help to create a healthy, diverse microbiome in your child. At the same time, it is important to avoid the overuse of antibiotics, PPIs, exposure to harmful chemicals, excessive hygiene, and highly processed foods and sugar. It is not difficult and will support the development of a strong foundation for lifelong health.
References:
Recent studies on the microbiome and its impact on health and development:
Bidell MR, Hobbs ALV, Lodise TP. Gut microbiome health and dysbiosis: A clinical primer. Pharmacotherapy. 2022 Nov;42(11):849-857. doi: 10.1002/phar.2731. Epub 2022 Oct 7. PMID: 36168753; PMCID: PMC9827978.
Wang Q, Yang Q, Liu X. The microbiota-gut-brain axis and neurodevelopmental disorders. Protein Cell. 2023 Oct 25;14(10):762-775. doi: 10.1093/procel/pwad026. PMID: 37166201; PMCID: PMC10599644.
Whelan K, Bancil AS, Lindsay JO, Chassaing B. Ultra-processed foods and food additives in gut health and disease. Nat Rev Gastroenterol Hepatol. 2024 Jun;21(6):406-427. doi: 10.1038/s41575-024-00893-5. Epub 2024 Feb 22. PMID: 38388570.
Capra ME, Decarolis NM, Monopoli D, Laudisio SR, Giudice A, Stanyevic B, Esposito S, Biasucci G. Complementary Feeding: Tradition, Innovation and Pitfalls. Nutrients. 2024 Mar 4;16(5):737. doi: 10.3390/nu16050737. PMID: 38474864; PMCID: PMC10934571.