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High Abundance of Escherichia During the Establishment of Fecal Microbiota in Brazilian Children

  • Environmental Microbiology
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Abstract

The sequence of bacterial events that occurs during the colonization of the gastrointestinal tract may affect the future health of the host. A clear understanding of the colonization process of the human neonatal gut in developing countries is lacking because the few available studies were mostly performed using culture techniques. Using molecular approaches, this study analyzed the fecal microbiota of children of low socioeconomic status in São Paulo, Brazil, during their first year of life. We collected fecal samples of healthy children at 3, 6, and 12 months of life. Total DNA was extracted directly from feces, and the bacteria-specific primers 27F-1492R were used to construct 16S rRNA libraries. Clones were randomly selected and partially sequenced. The main phylogenetic groups identified at 3 months were Streptococcus, unidentified bacteria, and Escherichia. At 6 months, Escherichia remained predominant, while the unidentified bacterial population increased significantly. At 12 months, a more complex composition of fecal microbiota was observed, represented by unidentified bacteria and microorganisms found at low rates at earlier ages. The genus Escherichia remained the most abundant microorganism (34 % relative abundance and 75 % prevalence). Principal component analysis (PCA) revealed changes in the composition of the microbiota at 6 months and an increase of diversity at 12 months of life. Bifidobacterium was identified by quantitative PCR (qPCR) and showed a high incidence in the microbiota at 3 months. The present results corroborate the global observation of inter-individual variability with an early establishment of microbial complexity at the end of the first year of life and highlight the presence of the Escherichia as abundant in microbiota composition of this group of children.

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Acknowledgements

Financial support—FAPESP 08/53959-5 and 2011/51196-7 (Fundação de Amparo à Pesquisa do Estado de São Paulo) to CRT.

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Authors and Affiliations

  1. Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil

    Carla R. Taddei, Fernanda F. Oliveira, Silvia T. Talarico, Elizabeth H. Takagi, Isabel I. Ramos Carvalho & Marina B. Martinez

  2. School of Arts, Science and Humanities, University of São Paulo, São Paulo, Brazil

    Carla R. Taddei

  3. Laboratory of Microbial Ecology, Oceanographic Institute, University of São Paulo, São Paulo, Brazil

    Rubens T. D. Duarte

  4. Department of Pediatrics, Medical School, University of São Paulo, São Paulo, Brazil

    Filumena M. S. Gomes

  5. Medical Institute Prof. Fernando Figueira, Recife, PE, Brazil

    Kátia Brandt

  6. Av. Prof. Lineu Prestes, 580, bl 17, Cidade Universitária, Butantã, 05508900, São Paulo, SP, Brasil

    Carla R. Taddei

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  1. Carla R. Taddei
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  2. Fernanda F. Oliveira
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Correspondence to Carla R. Taddei.

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Taddei, C.R., Oliveira, F.F., Duarte, R.T.D. et al. High Abundance of Escherichia During the Establishment of Fecal Microbiota in Brazilian Children. Microb Ecol 67, 624–634 (2014). https://doi.org/10.1007/s00248-014-0381-x

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