The Importance of Healthy Gut Microbiome for Infants and Children

Most of our dietary habits and metabolic tendencies are built at a surprisingly early age. We tend to forget that our gut microbiome starts to get built as soon as we are born (1). In fact, some studies have found evidence that infants may not be born with sterile guts. (2,3) 

The Importance of Healthy Gut Microbiome for Infants and Children
Healthy microbiome for infants

Why Should We Care About Our Early Tendencies?

The microbial gut community plays an essential role in human health, and its composition during infancy - the first two years of life - has been associated with pediatric disorders. (4)

An increased relative abundance of specific types of bacteria has been linked to various inflammatory and metabolic diseases. Simultaneously, some strains of the same family as the ones associated with inflammation are shown to have positive effects on the body. One example is the Bacteroides bacteria which has been found to have anti-inflammatory activities. (5,6)

Studies that focus on microbial diversity and microbiota composition, also known as dysbiosis, reveal a relationship between intestinal diseases in infants and chronic illnesses such as Irritable Bowel Disease (IBS), as well as metabolic disorders including obesity. (7,8)

Effects of antibiotics on weight

The Effect of The Gut Microbiome Brain Axis on Health

There is increasing evidence that the gut microbiome impacts physical and mental health, and many metabolic disorders are associated with its disruption of it.

Food addiction is an abnormally intense appetite resulting from alterations of the brain-gut-microbiome axis. Normal eating behaviour is regulated through multiple hormones, neurotransmitters, and neural circuits; however, disruptions in reward and inhibitory mechanisms across the brain-gut-microbiome axis can lead to unrestrained cravings for food. (9)

Exposure to a range of early life events such as unhealthy nutrition, stress and antibiotics can alter Brain- Gut-Microbiome interactions and behaviours related to consumption, while long-term dietary choices like high fat or sugar Western diets result in suppressed feedback control over eating. (9,10)

Early-life experiences, combined with increased antibiotic intake and certain dietary patterns, can predispose an individual to food addiction. The presence of energy-dense foods in the contemporary food environment also promotes hedonic eating behaviours by impacting the brain’s dopamine levels and the gut's microbiome, metabolome, and immune system. (9, 11)

Probiotics for microbiome support

Black Seed Oil for Microbiome Regulation

Nigella sativa oil, a well-known folk remedy, is capable of inhibiting microbial growth such as the skin and gut microbiota Malassezia furfur, Candida albicans, and Staphylococcus aureus. These microorganisms can be pathogenic if overgrown, leading to disruption of the microbiome homeostasis.

A combination of high Thymoquinone and low Free Fatty Acid concentrations inhibited the growth of Malassezia furfur and antibiotic-resistant Candida albicans the most.

The antibacterial properties of Nigella sativa oil are effective in inhibiting Staphylococcus aureus; however, it seems another component may be responsible for its effect.

These findings suggest that Nigella sativa oil could be used as an alternative safe antimicrobial agent to help maintain microbiome balance and diversity. (12)

Researched Black Seed Oil Benefits

  • Supports the nervous system
  • Reduces metabolic syndrome
  • May control an allergic runny nose
  • Supports healthy hair growth
  • Reduces blood clotting
  • Soothes an irritated digestive tract
  • Regulates inflammatory cytokines
  • Regulates cholesterol levels
  • Enhances white blood cells
  • Can soothe stomach ulcers
  • Reduces insulin resistance
  • May results in significant improvements in mood
  • Has systemic antioxidant properties
  • May improve symptoms of rheumatoid arthritis
  • Significantly reduces Helicobacter pylori colonies in the stomach
  • May reduce pain in inflammatory bowel disease
  • Lowers oxidative stress for cancer patients
  • May improve viral infections
  • May improve symptoms of autoimmune diseases (13,14,15)
Black seed oil for gut health

Black Seed Oil For Immune Balance and Stress Support

In a study, that aimed to evaluate the protective effect of black seed oil, when it comes to acute stress, 35 total participants were recruited. The study aimed to evaluate the effects of a black seed and fish oil supplement combination on upper-respiratory tract infections and psychological state. During the 4-week supplementation period, subjects consumed either the oil blend or a placebo daily. (16)

Both subjective (e.g. POMS questionnaire, health log) and objective measures (saliva and fecal samples) were collected.


  • Significantly fewer respiratory infections
  • Better overall well-being
  • Higher omega-3 blood levels
  • Lower cortisol
  • Superior microbiome indices

These findings suggest that the combination of black cumin seed oil plus fish oil might improve immune system balance and overall well-being after mental/ emotional stress by impacting the microbiome and Gut-Immune-Axis. (16)

Black Seed Oil for C.Difficile

The Effect of Black Seed Oil On the Gut of Infants

Though black seeds have been used in food for thousands of years, black seed oil is considered a dietary supplement in North America. Luckily, black seed oil (depending on the thymoquinone concentration) tends to have a very high safety profile. Most black seed oil supplements are not labelled to be used by children. Thus, it is always important to consult a healthcare provider before considering using black seed oil for children as a special calculation for age, weight and medical condition has to be made.

A case report describes the successful use of black seed oil, bentonite clay, and probiotics - in treating a pediatric case of C. difficile. Following hospitalization and antibiotic treatment, a healthy two-year-old patient was found to have C. difficile symptoms.

Through a shared decision-making process, a treatment plan for the C.difficile infection was developed that included natural treatments.

After 4 days of combined therapy, no C. difficile was detected via stool immunoassay. (18)

These results indicate though gentle and supportive of healthy microbial diversity, black seed oil can have powerful effects against unhealthy gut bacteria; however, caution should be taken when considering such options, as consulting a healthcare practitioner for serious conditions is always recommended, especially for infants. It is always best to be on the safe side when it comes to infant/ child health.

Further clinical trials that evaluate the side effects, immune response, and rate adverse effects of black seed oil should be conducted to better conduct the proper use of black seed oil from traditional medicine to modern naturopathic medicine. Further research May also find new, and innovative ways to utilize the benefits of black seed oil as an injunctive treatment for the pediatric population.

How to Reset The Gut Microbiome of Children?

  • Get a high-quality probiotic supplement
  • Make sure that children are having fermented foods with every meal
  • Include pre-biotic foods such as asparagus, onions and garlic in children’s meals
  • Make sure that children are eating minimal amounts of sugar, flour, processed foods and high-fructose corn syrup
  • Keep in mind that children need a lot of greens, berries and colourful plants
  • For children suffering from issues with weight and digestion, consult a healthcare practitioner who can investigate food intolerances, heal the gut, discourage the growth of unhealthy gut microbiomes and build an environment in which healthy gut microbes can flourish.
  • Remember that putting in the effort to build a healthy body in infancy and childhood can significantly improve the health of tomorrow’s adults!
Dr Jewel Alfoure  – Naturopathic Doctor at Enerex Botanicals


Dr Jewel is a dedicated Doctor of Naturopathic Medicine who is known for her unwavering passion and commitment to delivering evidence-based natural medicine with a compassionate touch

Visit Dr Jewel's Education Hub

Article References

  1. Gaufin T, Tobin NH, Aldrovandi GM. The importance of the microbiome in pediatrics and pediatric infectious diseases. Current opinion in pediatrics. 2018 Feb;30(1):117.
  2. Stinson LF, Boyce MC, Payne MS, Keelan JA. The not-so-sterile womb: evidence that the human fetus is exposed to bacteria prior to birth. Frontiers in microbiology. 2019:1124.
  3. Vael C, Desager K. The importance of the development of the intestinal microbiota in infancy. Current opinion in pediatrics. 2009 Dec 1;21(6):794-800.
  4. Jiang F, Meng D, Weng M, Zhu W, Wu W, Kasper D, Walker WA. The symbiotic bacterial surface factor polysaccharide A on Bacteroides fragilis inhibits IL-1β-induced inflammation in human fetal enterocytes via toll receptors 2 and 4. PLoS One. 2017 Mar 9;12(3):e0172738.
  5. .Zheng H, Liang H, Wang Y, Miao M, Shi T, Yang F, Liu E, Yuan W, Ji ZS, Li DK. Altered gut microbiota composition associated with eczema in infants. PloS one. 2016 Nov 3;11(11):e0166026.
  6. Gerritsen J, Smidt H, Rijkers GT, de Vos WM. Intestinal microbiota in human health and disease: the impact of probiotics. Genes & nutrition. 2011 Aug;6:209-40.
  7. Brown K, DeCoffe D, Molcan E, Gibson DL. Diet-induced dysbiosis of the intestinal microbiota and the effects on immunity and disease. Nutrients. 2012 Aug 21;4(8):1095-119.
  8. Osadchiy V, Martin CR, Mayer EA. The gut–brain axis and the microbiome: mechanisms and clinical implications. Clinical Gastroenterology and Hepatology. 2019 Jan 1;17(2):322-32.
  9. Foster JA, Neufeld KA. Gut–brain axis: how the microbiome influences anxiety and depression. Trends in neurosciences. 2013 May 1;36(5):305-12.
  10. Foster JA, Rinaman L, Cryan JF. Stress & the gut-brain axis: regulation by the microbiome. Neurobiology of stress. 2017 Dec 1;7:124-36.
  11. Ogen-Shtern N, Margarita Y, von Oppen-Bezalel L. Antimicrobial activity by a unique composition of cold pressed Nigella sativa seed (black cumin) oil. Food Sci Nutr Res. 2021;4(2):1-9.
  12. Kooti W, Hasanzadeh-Noohi Z, Sharafi-Ahvazi N, Asadi-Samani M, Ashtary-Larky D. Phytochemistry, pharmacology, and therapeutic uses of black seed (Nigella sativa). Chinese journal of natural medicines. 2016 Oct 1;14(10):732-45.
  13. Kooti W, Hasanzadeh-Noohi Z, Sharafi-Ahvazi N, Asadi-Samani M, Ashtary-Larky D. Phytochemistry, pharmacology, and therapeutic uses of black seed (Nigella sativa). Chinese journal of natural medicines. 2016 Oct 1;14(10):732-45.
  14. Srinivasan K. Cumin (Cuminum cyminum) and black cumin (Nigella sativa) seeds: traditional uses, chemical constituents, and nutraceutical effects. Food quality and safety. 2018 Mar;2(1):1-6.
  15. Talbott SM, Talbott JA. Black Cumin Seed Oil Plus Fish Oil Combination Modulates Gut-Immune-Axis. EC Nutrition. 2022;17:18-27.
  16. Kuiper GA, van Prehn J, Ang W, Kneepkens F, van der Schoor S, de Meij T. Clostridium difficile infections in young infants: case presentations and literature review. IDCases. 2017 Jan 1;10:7-11.
  17. Littman E, Winningham N, Carson TB, Hidalgo IM. Black Seed Oil, Bentonite Clay, and Probiotics: A Comprehensive Holistic Cure for Clostridium difficile Infection in a 2-Year-Old Female Child. Case Reports in Infectious Diseases. 2022 May 29;2022.

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