Probiotics first 1,000 days

Probiotics for the first 1,000 days

The more we uncover about the ecosystem of bacteria residing in us, the more it becomes evident that nurturing and supporting the good bacteria in our gut can have positive effects on our health and development. Addressing the health and diversity of the microbiome is now recognised as crucial to our development from as early as preconception.

Research now supports the pivotal role of micro-organisms in fertility, conception, pregnancy, and infancy, and it has been proposed that the period from conception to 2 years of age accounts for 70% of an individual’s future health.1 It also represents a critical window of opportunity to help support early childhood growth and development2 and to safeguard health in later years.

Probiotics are suggested to be an important tool to ensure an optimal conception state, pregnancy progression, infant development, and child maturation1 and have been shown to positively affect the microbiome over this crucial timeframe.

What is our microbiome?

Our bodies provide a home for a vast range of micro-organisms, including bacteria, fungi an d viruses. Collectively, these are known as the human microbiota. Our microbiome is the collection of genomes from all the micro-organisms and are specific to each person. Some micro-organisms are disease-causing, and others only become detrimental to our health if they are able to proliferate. Others can be beneficial to the body in many ways. In a healthy person, these micro-organisms are balanced and coexist peacefully.

How does the microbiota benefit our health?

The commensal bacteria in our microbiota help to keep us healthy in many ways. They help to support immunity, regulate hormones, digest our food, and synthesise vitamins. They also provide a physical barrier, protecting us against foreign pathogens through competitive exclusion and the production of antimicrobial substances.3

Why are the first 1,000 days so important?

The gut microbiota develops rapidly leading up to the second year of infancy, playing a crucial role in laying down the foundations for health.

Intervention during this timeframe is important as human plasticity (the body’s ability to adjust) decreases through age.1 As the assembly and maturation of the microbiota has largely occurred by the age of 2-3, strategies to target the gut microbiota after this period may have less impact.

The assembly of micro-organisms during early life plays a critical role in immune, endocrine, metabolic, and other host developmental pathways.2 If these important pathways are disrupted by unfavourable conditions, such as the poor microbiota of the mother, Caesarean section, formula feeding, antibiotic use, poor diet etc the course of infant growth can be disturbed. We can see therefore that potential lifelong complications can lie ahead.

Why is there now an increased need for probiotics?

The types of disease that are now prevalent, and are increasing, are chronic conditions such as cancer, obesity, diabetes, and autoimmune conditions – all notably having an inflammatory component. The change in the composition of our microbiome is likely contributing to this increase.

Factors that are having detrimental effects on our internal ecology include medications, Westernised diet, chronic stress, C-section/formula feeding, and the overuse of antibiotics. For example, research has demonstrated that antibiotics given during the first two years of life can increase the risk of eczema, food allergy, asthma, obesity, and inflammatory bowel disease in later life. Furthermore, Caesarean section births are becoming increasingly common. In Europe, Caesarean section rates have increased by 14% and here in the UK, they have increased from one in five to one in four.4,5 Conversely, breastfeeding statistics have decreased. Just 48.2 per cent of mothers now breastfeed their babies 6-8 weeks after birth, according to data from Public Health England.6


Statistics published by the NHS have shown that as many as one in seven couples in the UK struggle to conceive. Given the influence of our microbiota on fundamental processes, such as the digestion and absorption of nutrients, hormone regulation, synthesis of vitamins, and immunity, an unhealthy microbiome is likely to impact on fertility at a basic level. A lack of beneficial bacteria for example, has been associated with inflammation, of which infertility correlates with. In support, research has shown that Lactobacilli-dominated endometrial and vaginal microbiomes are greatly associated with positive reproductive outcome.7,8

From the point of conception, the microbiota of the mother can impact on the growth of the foetus and impact on pregnancy outcomes. The preconception period (although not included in the first 1, 000 days), may also provide a window in which to focus on optimising the maternal microbiome with probiotics with a view to supporting the healthy growth of the foetus in the future.


If the vaginal microbiota is unbalanced and deficient in beneficial bacteria it may contribute to pregnancy complications, which can include premature birth and miscarriage.9 Antibiotic use during pregnancy for instance, has been associated with low birth weight.10 Studies have shown that probiotics have exhibited favourable effects on pregnancy-related conditions such as preeclampsia, gestational diabetes and preterm birth.11 It has recently been suggested that probiotic consumption during pregnancy could even affect the composition of human milk oligosaccharides (HMOs) in breastmilk.1

Mode of Delivery

During childbirth, the vaginal microbiota plays an important part in colonising the child during delivery through the birth canal, where the child is exposed to a complex range of micro-organisms. Ideally, this includes plenty of beneficial bacteria. However, maternal health during pregnancy can affect the quality and diversity of microbes passed on. Probiotics can therefore be beneficial in these circumstances. For example, one study demonstrated that consumption of the commensal bacteria L. rhamnosus GG by the mother affected faecal Bifidobacterium transfer and composition during early infancy.12 A separate study determined that treating expectant mothers with L. rhamnosus GG confers this strain to the newborn infant, with its presence documented for as long as 24 months.13 Lactobacillus rhamnosus GG has further research supporting its use for common infections, antibiotic-associated diarrhoea and acute gastroenteritis in infants.14

Many studies have demonstrated that the microbiome of children born by Caesarean section has less diversity and beneficial bacteria than those born naturally.15-16 A recent study in the UK looked at the gut bacteria of over 600 babies born either vaginally or via Caesarean-section. It was found that there were large differences in bacteria between the two delivery modes. Those born vaginally had higher levels of beneficial bacteria (in particular, Bifidobacteria) than those born via C-section.17 Those born via C-section are also more prone to opportunistic bacteria. Further studies show that children born via C-section are at a higher risk of food allergy, asthma, diabetes, and obesity.


After the birth, commensal bacteria colonise the infant. If conditions have not been ideal throughout pregnancy or delivery, supporting the infant microbiota after the birth may be a significant period in which probiotic interventions could be effective. Furthermore, probiotics might have an important role to help counteract the use of antibiotics administered during early life or during the pregnancy/birth. The subsequent two years therefore signifies a chance of targeted support to improve healthy composition of the microbiome. For instance, it has been shown that probiotic interventions soon after the birth can significantly increase weight and prevent infection. Systematic reviews of different studies suggest that the administration of certain probiotics to premature infants reduces the incidence of necrotising enterocolitis, with resultant significant improvements in survival rates.18

It is estimated that 75% of brain growth occurs during the first few years of life, and this uses approximately 50% of an infant’s energy.2 It is crucial therefore that children can digest and absorb their food adequately to support this. Probiotics can support the microbiota and thus help to aid digestion and increase nutrient absorption.


The intestinal microbiome of infants requires a high proportion of Bifidobacteria during the first year of life to aid in the digestion of milk. Breast milk harbours a diverse microbiota, plus nutrients that encourage the proliferation of health-promoting bacteria. For example, prebiotic HMOs are specifically metabolised by bacteria in the infant gut, strongly favouring the proliferation of bifidobacteria.1 It has been estimated that 25–30% of the infant bacterial microbiota originates from breast milk.2

If there is insufficient Bifidobacteria in the gut, harmful microbes have an increasing chance of proliferating, which can cause well-known symptoms typical in babies, such as colic, allergies and digestive issues. Probiotics have been shown to decrease these symptoms in infants. Babies who are breastfed have a lower chance developing allergies and are less likely to develop diabetes or become obese in later life.19,20


At the weaning stage, the introduction of solid foods instigates a rapid surge in different micro-organisms, which helps to create a more mature microbiome. The increased exposure to different foods can change the composition of the infant’s microbiome to one that can be beneficial to their health, or one that may increase the risk for poor development and health. Poor diet can, therefore, be especially detrimental to the development of the microbiome at this stage. In situations where unsuitable bacteria are able to colonise through lack of beneficial bacteria, even harmless stimuli such as antibiotics, food components, or harmless bacteria can cause inflammation. This may lead to conditions such as allergy and inflammatory bowel disease.21 Including a probiotic at this stage can help to populate and rebalance the gut with beneficial bacteria.

Intestinal Barrier

In healthy infants, beneficial bacteria in the gut plays an important part in maintaining the integrity of the intestinal barrier. The intestinal barrier plays a crucial role in many aspects of health. It acts by allowing nutrients in and keeping invading pathogens out. Failure to support and protect the intestinal barrier can lead to intestinal permeability (leaky gut) and subsequent impaired immunity. As a result, the risk of allergies and other inflammatory conditions increases. The findings of one study found that probiotic supplementation in children may help to stabilise the intestinal barrier function and decrease gastrointestinal symptoms.22


Not all probiotic strains are suitable or relevant to the baby microbiome. It is important therefore to select a probiotic that is safe, effective, and specific to the requirements. For example, research on Bifidobacterium animalis has shown it helps to support intestinal/gastrointestinal health in infants aged 2 months and older and could promote a favourable gut flora. It has also been shown to help relieve abdominal discomfort, such as bloating and constipation. Bifidobacterium infantis Rosell has been shown to compete with pathogens for adhesion to epithelial cells, increase mucin expression in the small intestine and reduce pro-inflammatory cytokines in infants.23-26

Collectively, there is much research that supports the nurturing of the microbiome to ensure proper development of the child. In all periods discussed, from conception through to infancy, probiotics may prove a beneficial addition in the first 1000 days by providing a targeted intervention in a crucial window of opportunity to support the microbiome.

If you have questions regarding the topics that have been raised, or any other health matters, please do contact me (Helen) by phone or email at any time.
01684 310099

Amanda Williams and the Cytoplan Editorial Team


    1. White paper, First 1.000 Days Women’s & infant health
    2. Robertson, R. C. et al. (2019) “The Human Microbiome and Child Growth – First 1000 Days and Beyond,” Trends in Microbiology. Elsevier Ltd, pp. 131–147.
    3. Cash, H. L. et al. (2006) “Symbiotic bacteria direct expression of an intestinal bactericidal lectin,” Science. American Association for the Advancement of Science, 313(5790), pp. 1126–1130
    4. Betrán, A. P. et al. (2016) “The Increasing Trend in Caesarean Section Rates: Global, Regional and National Estimates: 1990-2014,” PLOS ONE. Edited by H. Zeeb. Public Library of Science, 11(2), p. e0148343.
    5. Wise, J. (2018) “Alarming global rise in caesarean births, figures show,” BMJ (Clinical research ed.). NLM (Medline), 363, p. k4319.
    6. Breastfeeding at 6 to 8 weeks after birth: annual data (online) Available at: [Accessed 17th October 2020]

    1. Moreno, I. and Simon, C. (2019) “Deciphering the effect of reproductive tract microbiota on human reproduction,” Reproductive Medicine and Biology. John Wiley and Sons Ltd, pp. 40–50.
    2. Babu, G. et al. (2017) “Comparative study on the vaginal flora and incidence of asymptomatic vaginosis among healthy women and in women with infertility problems of reproductive age,” Journal of Clinical and Diagnostic Research. Journal of Clinical and Diagnostic Research, 11(8), pp. DC18–DC22.
    3. Donders, G. G. et al. (2009) “Predictive value for preterm birth of abnormal vaginal flora, bacterial vaginosis and aerobic vaginitis during the first trimester of pregnancy,” BJOG: An International Journal of Obstetrics and Gynaecology. BJOG, 116(10), pp. 1315–1324.
    4. Vidal, A. C. et al. (2013) “Associations between antibiotic exposure during pregnancy, birth weight and aberrant methylation at imprinted genes among offspring,” International Journal of Obesity. Int J Obes (Lond), 37(7), pp. 907–913.
    5. Isolauri, E. et al. (2015) “Role of probiotics in reducing the risk of gestational diabetes,” Diabetes, Obesity and Metabolism. Blackwell Publishing Ltd, pp. 713–719.
    6. Effect of Maternal Consumption of Lactobacillus GG on Transfer and Establishment of Fecal Bifidobacterial Microbiota in Neonates | Request PDF (2006). Available at: (Accessed: October 18, 2020).
    7. Schultz, M. et al. (2004) “Administration of oral probiotic bacteria to pregnant women causes temporary infantile colonization,” Journal of Pediatric Gastroenterology and Nutrition. J Pediatr Gastroenterol Nutr, 38(3), pp. 293–297.
    8. Hojsak, I. et al. (2018) “Guidance on the use of probiotics in clinical practice in children with selected clinical conditions and in specific vulnerable groups,” Acta Paediatrica, International Journal of Paediatrics. Blackwell Publishing Ltd, pp. 927–937.
    9. Korpela, K. et al. (2018) “Probiotic supplementation restores normal microbiota composition and function in antibiotic-treated and in caesarean-born infants,” Microbiome. BioMed Central Ltd., 6(1), p. 182.
    10. Moya-Pérez, A. et al. (2017) “Intervention strategies for cesarean section- induced alterations in the microbiota-gut-brain axis,” Nutrition Reviews. Oxford University Press, 75(4), pp. 225–240.
    11. Shao, Y. et al. (2019) “Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth,” Nature. Nature Publishing Group, 574(7776), pp. 117–121.
    12. Anderson, S. (2015) “Probiotics for preterm infants: A premature or overdue necrotizing enterocolitis prevention strategy?,” Neonatal Network. Springer Publishing Company, 34(2), pp. 83–101.
    13. Tamburini, S. et al. (2016) “The microbiome in early life: Implications for health outcomes,” Nature Medicine. Nature Publishing Group, pp. 713–722.
    14. Pannaraj, P. S. et al. (2017) “Association between breast milk bacterial communities and establishment and development of the infant gut microbiome,” JAMA Pediatrics. American Medical Association, 171(7), pp. 647–654.
    1. Microbiome: The first 1,000 days – Harvard Health Blog – Harvard Health Publishing (2019). Available at: (Accessed: October 17, 2020).
    3. Basturk A. et al. (2016) ‘Efficacy of synbiotic, probiotic, and prebiotic treatments for irritable bowel syndrome in children: A randomized controlled trial’, Turk J Gastroenterol, 27 pp. 439- 43.
    4. Işlek et al. (2014) ‘The role of Bifidobacterium lactis B94 plus inulin in the treatment of acute infectious diarrhoea in children’, Turk J Gastroenterol, 25 pp. 628-33 3.
    5. Hojsak I, Fabiano V, Pop TL, et al. (2018) ‘Guidance on the use of probiotics in clinical practice in children with selected clinical conditions and in specific vulnerable groups’, Acta Paediatr, 107(6) pp. 927-937 4.
    6. Cazzola et al. (2010) ‘Efficacy of a symbiotic supplementation in the prevention of common winter diseases in children: a randomized, double-blind, placebo-controlled pilot study’, Th Adv in Res Dis,

Last updated on 26th July 2022 by cytoffice


3 thoughts on “Probiotics for the first 1,000 days

  1. Unfortunately the reference list is incomplete. This omission creates problems because the accurate recording of appropriate and authoritative evidence is necessary to the robustness of any scientific report/article. This said, the article offers a good introduction to this highly complex area.

    1. Thank you for noticing this. Please can you point us to where you feel references ae incomplete and we can amend the list accordingly?

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