strains isolated from different communities. Microbial population dynamics can be strongly influenced by synergism and competition with coexisting microorganisms and through phage predation (Sandaa et al., 2009). The mobile element pool, which is generally excluded when analyzing isolates, can rapidly give rise to the genomic variation that underpins strain differentiation (Oliver et al., 2009).

Cultivation-independent genomic analyses of time-series samples provide a way to link shifts in population abundance to genetic characteristics that underlie physiological traits, such as virulence. Here, we analyzed human intestinal colonization during the neonatal period. We conducted a 16S rRNA gene-based survey of fecal samples collected daily during the first 3 wk of life of a premature infant and reconstructed and manually curated population genomic datasets for the dominant gut microorganisms in the third of three colonization phases. We chose to focus on the premature infant microbiome because, in addition to its medical relevance, the limited number of dominant bacterial species in the community allows for deep sequence coverage of multiple subpopulations.

Results and Discussion

Study Subject

We studied fecal samples from a female infant delivered by caesarean section at 28-wk gestation due to premature rupture of membranes. She was treated empirically with broad-spectrum antibiotics (ampicillin/gentamicin) for the first 7 d of life but did not receive antibiotics during the remainder of the study period. She received enteral feedings with maternal breast milk between the fourth and ninth days of life. Feedings were withheld between days 9 and 13 because of abdominal distension. On day 13, feedings were slowly resumed with artificial infant formula (Similac Special Care 20 cal/fl oz; Abbott Nutrition). She also received parenteral nutrition until caloric intake from enteral nutrition was adequate (day 28). She had no major illnesses during her hospitalization and was discharged to home at 64 d of life. Fecal samples were collected daily as available between days 5 and 21.

Day-to-Day Dynamics of Community Composition

Sequencing of amplified bacterial 16S rRNA genes (SI Materials and Methods and Table S1 A and B) from 15 fecal samples collected on different days during the first 3 wk revealed three distinct community configurations demarcated by rapid transitions. This finding is consistent with previously reported colonization patterns in term infants: relative stability over days to months punctuated by rapid compositional change (Koenig et al., 2010; Palmer et al., 2007). Marked shifts in abundant lineages around days 9 and 15 seemed to follow dietary adjustments. On days 5 through 9, communities were largely composed of Leuconostoc,

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