AUTHOR=Wampach Linda , Heintz-Buschart Anna , Hogan Angela , Muller Emilie E. L. , Narayanasamy Shaman , Laczny Cedric C. , Hugerth Luisa W. , Bindl Lutz , Bottu Jean , Andersson Anders F. , de Beaufort Carine , Wilmes Paul TITLE=Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life JOURNAL=Frontiers in Microbiology VOLUME=8 YEAR=2017 URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2017.00738 DOI=10.3389/fmicb.2017.00738 ISSN=1664-302X ABSTRACT=
Perturbations to the colonization process of the human gastrointestinal tract have been suggested to result in adverse health effects later in life. Although much research has been performed on bacterial colonization and succession, much less is known about the other two domains of life, archaea, and eukaryotes. Here we describe colonization and succession by bacteria, archaea and microeukaryotes during the first year of life (samples collected around days 1, 3, 5, 28, 150, and 365) within the gastrointestinal tract of infants delivered either vaginally or by cesarean section and using a combination of quantitative real-time PCR as well as 16S and 18S rRNA gene amplicon sequencing. Sequences from organisms belonging to all three domains of life were detectable in all of the collected meconium samples. The microeukaryotic community composition fluctuated strongly over time and early diversification was delayed in infants receiving formula milk. Cesarean section-delivered (CSD) infants experienced a delay in colonization and succession, which was observed for all three domains of life. Shifts in prokaryotic succession in CSD infants compared to vaginally delivered (VD) infants were apparent as early as days 3 and 5, which were characterized by increased relative abundances of the genera