Gut microbiota development during infancy: Impact of introducing allergenic foods.

Affiliation

Marrs T(1), Jo JH(2), Perkin MR(3), Rivett DW(4), Witney AA(5), Bruce KD(6), Logan K(7), Craven J(7), Radulovic S(1), Versteeg SA(8), van Ree R(9), McLean WHI(10), Strachan DP(3), Lack G(7), Kong HH(2), Flohr C(11).
Author information:
(1)Paediatric Allergy Research Group, Department of Women and Children's Health, School of Life Course Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom; Children's Allergies Department, Guy's and St Thomas' NHS Foundation Trust, St Thomas' Hospital, Lambeth, United Kingdom.
(2)Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Md.
(3)Population Health Research Institute, St George's, University of London, London, United Kingdom.
(4)Department of Natural Sciences, Manchester Metropolitan University, Manchester, United Kingdom.
(5)Institute for Infection and Immunity, St George's, University of London, London, United Kingdom.
(6)Molecular Microbiology Research Laboratory, Pharmaceutical Science Division, King's College London, London, United Kingdom.
(7)Paediatric Allergy Research Group, Department of Women and Children's Health, School of Life Course Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom.
(8)Experimental Immunology, Amsterdam University Medical Center, Amsterdam, The Netherlands.
(9)Experimental Immunology, Amsterdam University Medical Center, Amsterdam, The Netherlands; Department of Otorhinolaryngology, Amsterdam University Medical Center, Amsterdam, The Netherlands.
(10)Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, United Kingdom.
(11)Unit for Population-Based Dermatology Research, St John's Institute of Dermatology, School of Basic and Medical Biosciences, King's College London, London, United Kingdom. Electronic address: [Email]

Abstract

BACKGROUND: The gut microbiota potentially plays an important role in the immunologic education of the host during early infancy. OBJECTIVE: We sought to determine how the infant gut microbiota evolve during infancy, particularly in relation to hygiene-related environmental factors, atopic disorders, and a randomized introduction of allergenic solids. METHODS: A total of 1303 exclusively breast-fed infants were enrolled in a dietary randomized controlled trial (Enquiring About Tolerance study) from 3 months of age. In this nested longitudinal study, fecal samples were collected at baseline, with additional sampling of selected cases and controls at 6 and 12 months to study the evolution of their gut microbiota, using 16S ribosomal RNA gene-targeted amplicon sequencing. RESULTS: In the 288 baseline samples from exclusively breast-fed infant at 3 months, the gut microbiota was highly heterogeneous, forming 3 distinct clusters: Bifidobacterium-rich, Bacteroides-rich, and Escherichia/Shigella-rich. Mode of delivery was the major discriminating factor. Increased Clostridium sensu stricto relative abundance at 3 months was associated with presence of atopic dermatitis on examination at age 3 and 12 months. From the selected cases and controls with longitudinal samples (n = 70), transition to Bacteroides-rich communities and influx of adult-specific microbes were observed during the first year of life. The introduction of allergenic solids promoted a significant increase in Shannon diversity and representation of specific microbes, such as genera belonging to Prevotellaceae and Proteobacteria (eg, Escherichia/Shigella), as compared with infants recommended to exclusively breast-feed. CONCLUSIONS: Specific gut microbiota characteristics of samples from 3-month-old breast-fed infants were associated with cesarean birth, and greater Clostridium sensu stricto abundance was associated with atopic dermatitis. The randomized introduction of allergenic solids from age 3 months alongside breast-feeding was associated with differential dynamics of maturation of the gut microbial communities.