BioProject

Premature infants are at a high risk of developing necrotising enterocolitis. A microbial element of the condition has been confirmed, however exact aetiology remains enigmatic and ‘typical’ microbiota development remains undefined. To characterise establishment of the severely preterm infant gut microbiota we employed targeted sequencing of the bacterial 16S rRNA gene. Sample types included oral and endotracheal swabs, stool and breast milk, collected from 7 patients over the first 2 months, postnatally (n = 158 samples). Propidium monoazide treatment was combined with targeted sequencing of the V4 region of the 16S rRNA gene to identify viable bacterial communities. Significantly lower alpha diversity was observed in stool than upstream mucosae (P < .005). Homogenising dispersal of dominant taxa was identified across all body-sites within the first week of life and persisted throughout the sampling period for all infants. Beta diversity was lowest immediately following birth and between proximal sampling sites. Oral microbiota showed the greatest similarity to stool (R2 = .73, P < 0.05), however the composition of stool microbiotas diverged from upstream mucosae over time (67% at WoL 1 vs 20% at WoL 8). We suggest a temporal pattern of gut microbiota development where speciation and divergence increase over time.