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Eczema and the Infant Microbiome

Written by
Clare Carrick ANutr (BHSc Nutrition and Health Promotion)

Scientifically reviewed by
Dr Fathalla Ali, PhD (Paediatrics)


What is eczema?

Eczema is a chronic inflammatory rash that often starts early in life (1). Its prevalence is on-the-rise, particularly in more affluent parts of the world, and this has prompted increased research into the risk and potential protective factors (1, 2). Eczema can be extremely itchy, affecting the infant’s quality of life, and causing added stress for parents. Eczema has no known cure, and is likely caused by a combination of genes and environmental factors (1). Whilst treatment has traditionally focused on topical ointments and creams, interest has grown regarding the role that gut health plays in eczema development (1).


The Gut Microbiome and Eczema

The gut microbiome is an important consideration in eczema development because it helps to shape and regulate the developing immune system (2). Comparisons of the microbiomes of babies with eczema, to those without eczema, have displayed compositional differences (2). Although it’s difficult to prove a causal relationship, studies have shown that these differences in gut microbiome composition are often evident before eczema onset, supporting the significance of the gut microbiome in the development of eczema (3). 


Birth order seems to have a significant impact on the composition of the microbiome (3) In fact, the lower the ‘birth order number’ (e.g. first- or second-born), the  greater the abundance of a bacterial strain called Clostridium cluster I, and the more likely these children are to develop eczema and allergic disease (3). This association has been supported by studies, which have found that babies with an increased number of the Clostridia strain Hungatella hathewayi, were more likely to develop eczema than those with lower levels of this strain (4). Although the reasons for this are not entirely understood, and birth order is obviously not a modifiable risk factor, these results do point to the importance of gut microbiome in the development of eczema (3). 


Numerous studies have also shown that a less diverse gut microbiome is associated with a greater risk of developing eczema (5). But how do we encourage a more diverse gut microbiome in our children? A number of environmental factors may influence the diversity of the infant gut microbiome in their early years (2).



The presence of the strain B. fragilis, a bacteria more abundant in breastfed babies, appears to lower the incidence of eczema development (6). Current recommendations are to breastfeed if possible (6). If not possible, a formula supplemented with prebiotics and/or probiotics may help to prevent eczema development (6).


Mode of Delivery

Gut dysbiosis can already be observed in caesarean-born infants within their first few days of life, along with a lower rate of microbial diversity (7). These disturbances in the composition of caesarean-born babies’ gut microbiomes have been shown to persist until at least two years of age (7). Caesarean delivery has been associated with an increase in eczema and allergic disease, however it is still not understood exactly why this is. One prominent theory is that the gut microbiome colonisation a baby acquires from a vaginal birth, which more closely resembles the mother’s vaginal microbiota, may lower the baby’s risk of developing eczema more successfully than a caesarean-section-associated gut microbiome, which more closely resembles the mother’s skin microbiome (4, 6).


Antibiotic Use

Antibiotic use can significantly alter the composition of the gut microbiome. (6) The use of antibiotics in the first few years of life has been associated with reduced microbial diversity and an increased incidence of eczema (7, 8).


Starting Solids

Be sure to offer your infant a wide variety of plant foods once they are old enough to eat solids. These help to encourage a diverse gut microbiome (9).


Own a Pet and Get Out in Nature

Exposing your child to as many different microbes, from the soil in your garden, to your animals own microbiomes, will increase the chances of your child developing a diverse gut microbiome (9).



The developing infant gut microbiome may play an important role in the prevention of eczema development in infants. Being aware of the factors affecting gut diversity, such as breastfeeding, mode of delivery, and antibiotic use, can help to reduce the likelihood of your baby developing eczema. 

Keywords: Eczema, Microbiome, Immunity, Breastfeeding, Mode of delivery


  1. 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. 
  2. Chan CW, Wong RS, Law PT, Wong CL, Tsui SK, Tang WP, Sit JW. Environmental factors associated with altered gut microbiota in children with eczema: a systematic review. International journal of molecular sciences. 2016 Jul;17(7):1147. 
  3. Penders J, Gerhold K, Stobberingh EE, Thijs C, Zimmermann K, Lau S, Hamelmann E. Establishment of the intestinal microbiota and its role for atopic dermatitis in early childhood. Journal of Allergy and Clinical Immunology. 2013 Sep 1;132(3):601-7. 
  4. Chan CW, Leung TF, Choi KC, Tsui SK, Wong CL, Chow KM, Chan JY. Association of early‐life gut microbiome and lifestyle factors in the development of eczema in Hong Kong infants. Experimental Dermatology. 2021 Jan 12. 
  5. Abrahamsson TR, Jakobsson HE, Andersson AF, Björkstén B, Engstrand L, Jenmalm MC. Low diversity of the gut microbiota in infants with atopic eczema. Journal of allergy and clinical immunology. 2012 Feb 1;129(2):434-40.
  6. Ta LD, Chan JC, Yap GC, Purbojati RW, Drautz-Moses DI, Koh YM, Tay CJ, Huang CH, Kioh DY, Woon JY, Tham EH. A compromised developmental trajectory of the infant gut microbiome and metabolome in atopic eczema. Gut microbes. 2020 Nov 9;12(1):1801964.
  7. Cukrowska B, Bierła JB, Zakrzewska M, Klukowski M, Maciorkowska E. The relationship between the infant gut microbiota and allergy. The role of Bifidobacterium breve and prebiotic oligosaccharides in the activation of anti-allergic mechanisms in early life. Nutrients. 2020 Apr;12(4):946.
  8. Ahmadizar F, Vijverberg SJ, Arets HG, de Boer A, Lang JE, Garssen J, Kraneveld A, Maitland‐van der Zee AH. Early‐life antibiotic exposure increases the risk of developing allergic symptoms later in life: a meta‐analysis. Allergy. 2018 May;73(5):971-86. 3. 
  9. Durack J, Lynch . The Gut Microbiome: relationships with disease and opportunities for therapy. J Exp Med. 2019;216(1):20-40.

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