Journal Article

Comparative Metagenomics and Population Dynamics of the Gut Microbiota in Mother and Infant

Parag A. Vaishampayan, Jennifer V. Kuehl, Jeffrey L. Froula, Jenna L. Morgan, Howard Ochman and M. Pilar Francino

in Genome Biology and Evolution

Published on behalf of Society for Molecular Biology and Evolution

Volume 2, issue , pages 53-66
Published in print January 2010 |
Published online January 2010 | e-ISSN: 1759-6653 | DOI:

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  • Bioinformatics and Computational Biology
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Colonization of the gastrointestinal tract (GIT) of human infants with a suitable microbial community is essential for numerous aspects of health, but the progression of events by which this microbiota becomes established is poorly understood. Here, we investigate two previously unexplored areas of microbiota development in infants: the deployment of functional capabilities at the community level and the population genetics of its most abundant genera. To assess the progression of the infant microbiota toward an adult-like state and to evaluate the contribution of maternal GIT bacteria to the infant gut, we compare the infant’s microbiota with that of the mother at 1 and 11 months after delivery. These comparisons reveal that the infant’s microbiota rapidly acquires and maintains the range of gene functions present in the mother, without replicating the phylogenetic composition of her microbiota. Microdiversity analyses for Bacteroides and Bifidobacterium, two of the main microbiota constituents, reveal that by 11 months, the phylotypes detected in the infant are distinct from those in the mother, although the maternal Bacteroides phylotypes were transiently present at 1 month of age. The configuration of genetic variants within these genera reveals populations far from equilibrium and likely to be undergoing rapid growth, consistent with recent population turnovers. Such compositional turnovers and the associated loss of maternal phylotypes should limit the potential for long-term coadaptation between specific bacterial and host genotypes.

Keywords: Bacteroides; Bifidobacterium; gut microbiota; community genomics; bacterial population genetics

Journal Article.  8368 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology ; Evolutionary Biology ; Genetics and Genomics

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