Background The importance of the microbiome to the health of preterm infants is increasingly recognised. Much of the data on microbiome development in preterm infants is from 15–30 years ago: infants, nursery practices, infection control measures and antibiotic use are now very different.

Objective To describe gut colonisation in modern preterm infants (<32 weeks) in comparison to existing data and explore differences in infants developing necrotising enterocolitis (NEC).

Methods The first stool, and weekly stool was collected as routine surveillance from birth to 8 weeks. A standard operating procedure was developed to identify the maximum numbers of species and strains of organisms present by standard culture.

Results 100 stools came from 38 infants, median gestational age 27 weeks (23–32 weeks), birth weight 895 g (520–1850 g). 35 received breast milk, 29 received fluconazole prophylaxis. Stools grew a median of three separately identifiable species/strains of organisms (range 0–8). The commonest organism was CONS (40% of stools, 55% of babies). Only six infants were ever colonised with lactobacilli, 1 with bifidobacteria and none with fungi. Eight infants had NEC (4 surgical). Those with NEC had more Enterococci (75% vs 23%) and Klebsiella (62% vs 32%).

Conclusions Compared to historical data we identified less species diversity, more colonisation with coagulase negative staphylococci, less lacto- and bifidobacteria, and no fungi. Infants developing NEC had different colonisation patterns. Current exposures on NICU result in a significantly abnormal microbiome and may predispose to NEC.