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ISME J. 2016 Apr;10(4):1002-14. doi: 10.1038/ismej.2015.177. Epub 2015 Oct 2.

Discordant temporal development of bacterial phyla and the emergence of core in the fecal microbiota of young children.

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Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland.
Department of Bacteriology and Immunology, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
Department of Maternal and Child Health, Gillings School of Global Public Health, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands.
Division of Gastroenterology and Hepatology, Department of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
Division of Gastroenterology, Rabin Medical Center, Beilinson Hospital, Petah Tikva, Israel.


The colonization pattern of intestinal microbiota during childhood may impact health later in life, but children older than 1 year are poorly studied. We followed healthy children aged 1-4 years (n=28) for up to 12 months, during which a synbiotic intervention and occasional antibiotics intake occurred, and compared them with adults from the same region. Microbiota was quantified with the HITChip phylogenetic microarray and analyzed with linear mixed effects model and other statistical approaches. Synbiotic administration increased the stability of Actinobacteria and antibiotics decreased Clostridium cluster XIVa abundance. Bacterial diversity did not increase in 1- to 5-year-old children and remained significantly lower than in adults. Actinobacteria, Bacilli and Clostridium cluster IV retained child-like abundances, whereas some other groups were converting to adult-like profiles. Microbiota stability increased, with Bacteroidetes being the main contributor. The common core of microbiota in children increased with age from 18 to 25 highly abundant genus-level taxa, including several butyrate-producing organisms, and developed toward an adult-like composition. In conclusion, intestinal microbiota is not established before 5 years of age and diversity, core microbiota and different taxa are still developing toward adult-type configuration. Discordant development patterns of bacterial phyla may reflect physiological development steps in children.

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