Development of the Microbiota and Associations With Birth Mode, Diet, and Atopic Disorders in a Longitudinal Analysis of Stool Samples, Collected From Infancy Through Early Childhood
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Background & aims Establishment of the gastrointestinal microbiota during infancy affects immune system development and oral tolerance induction. Perturbations in the microbiome during this period can contribute to development of immune-mediated diseases. We monitored microbiota maturation and associations with subsequent development of allergies in infants and children.Methods We collected 1453 stool samples, at 5, 13, 21, and 31 weeks postpartum (infants), and once at school age (6-11 years), from 440 children (49.3% girls, 24.8% born by cesarean delivery; all children except for 6 were breastfed for varying durations; median 40 weeks; interquartile range, 30-53 weeks). Microbiota were analyzed by amplicon sequencing. Children were followed through 3 years of age for development of atopic dermatitis; data on allergic sensitization and asthma were collected when children were school age.Results Diversity of fecal microbiota, assessed by Shannon index, did not differ significantly among children from 5 through 13 weeks after birth, but thereafter gradually increased to 21 and 31 weeks. Most bacteria within the Bacteroidetes and Proteobacteria phyla were already present at 5 weeks after birth, whereas many bacteria of the Firmicutes phylum were acquired at later times in infancy. At school age, many new Actinobacteria, Firmicutes, and Bacteroidetes bacterial taxa emerged. The largest increase in microbial diversity occurred after 31 weeks. Vaginal, compared with cesarean delivery, was most strongly associated with an enrichment of Bacteroides species at 5 weeks through 31 weeks. From 13 weeks onward, diet became the most important determinant of microbiota composition; cessation of breastfeeding, rather than solid food introduction, was associated with changes. For example, Bifidobacteria, staphylococci, and streptococci significantly decreased on cessation of breastfeeding, whereas bacteria within the Lachnospiraceae family (Pseudobutyrivibrio, Lachnobacterium, Roseburia, and Blautia) increased. When we adjusted for confounding factors, we found fecal microbiota composition to be associated with development of atopic dermatitis, allergic sensitization, and asthma. Members of the Lachnospiraceae family, as well as the genera Faecalibacterium and Dialister, were associated with a reduced risk of atopy.Conclusions In a longitudinal study of fecal microbiota of children from 5 weeks through 6 to 11 years, we tracked changes in diversity and composition associated with the development of allergies and asthma.
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Changes in gut microorganism composition and metabolic function caused by environment, diet, disease or medical intervention such as antibiotics are related to changes in immune response and airway homeostasis.
“Changes in gut microorganism composition and metabolic function caused by the environment, diet, disease or medical intervention (such as antibiotics) are related to changes in the immune response and airway homeostasis (31,32).”
From The Role of Gut Microbiota in Lung Cancer: From Carcinogenesis to Immunotherapy (2021) · cites this paper as [31]
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- Authors
- Galazzo, G., van Best, N., Bervoets, L., Dapaah, I. O., Savelkoul, P. H., Hornef, M. W., Hutton, E. K., Morrison, K., Holloway, A. C., McDonald, H., Ratcliffe, E. M., Stearns, J. C., Schertzer, J. D., Surette, M. G., Thabane, L., Mommers, M., Lau, S., Hamelmann, E., & Penders, J.
- Affiliations
- Maastricht University Medical Centre (NL)
- Universitätsklinikum Aachen (DE)
- Charité – Universitätsmedizin Berlin (DE)
- Bielefeld University (DE)
- Corresponding author
- Penders, John
- ORCID
- Venue
- Gastroenterology
- Publisher
- Elsevier BV
- Published
- 2020-05
- Volume
- 158
- Issue
- 6
- Pages
- 1584-1596
- ISSN
- 0016-5085 (ISSN-L)
- OpenAlex
- W2999444201
- Cited by
- 308
- References
- 59
- Citations by year
- 2026: 40 · 2025: 55 · 2024: 57 · 2023: 54 · 2022: 45 · 2021: 43 · 2020: 14
- FWCI
- 12.50
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Gastroenterology (publishedVersion)
- PubMed (publishedVersion)
- Research Publications (Maastricht University) (publishedVersion, other-oa)
- Pure Amsterdam UMC (publishedVersion, other-oa)
- Amsterdam UMC (VU Amsterdam) - Institutional Repository (publishedVersion)
- Research Publications (Maastricht University) (submittedVersion, other-oa)
- Data Archiving and Networked Services (DANS) (submittedVersion)
- Funders
- Bundesanstalt für Landwirtschaft und Ernährung
- Deutsche Forschungsgemeinschaft
- Joint Programming Initiative A healthy diet for a healthy life
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Health Sciences › Nursing › Nutrition and Dietetics › Infant Nutrition and Health
- Life Sciences › Agricultural and Biological Sciences › Food Science › Probiotics and Fermented Foods
- Keywords
- infant gut microbiota, microbiota maturation, mode of delivery, cesarean section, breastfeeding, infant nutrition, atopic dermatitis, allergen sensitization, asthma, Lachnospiraceae, Bacteroides, Firmicutes, Bacteroidetes, microbial diversity, oral tolerance, immune system development, early childhood, fecal samples, microbial biomarkers, atopic diseases
- MeSH terms
- Gastrointestinal Microbiome, Asthma, Bacteria, Breast Feeding, Cesarean Section, Child, Child Development, Dermatitis, Atopic, Feces, Female, Follow-Up Studies, Humans, Infant, Longitudinal Studies, Male, RNA, Ribosomal, 16S, Confounding Factors, Epidemiologic, Immunity, Mucosal
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Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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