Abstract

In this study we investigated the microbial composition from neonates with necrotizing enterocolitis (NEC) Bell stadium IV. NEC is a serious bacterial infection in the intestine. It is not known if or which bacteria are responsible and which other factors triggers the infection in the intestine, but immaturity, premature birth and the diet are known to play a key role. In situ hybridization with a general bacterial 16S rRNA-targeting probe was used on 24 neonate’s tissue samples to visualize all bacteria in the borderline of the surgical removed formalin-fixed necrotic samples followed by Lacer Capture Microdissection (LCM). LCM offers the possibility to recover specific cells of interest from fixed intestinal tissue samples for downstream extraction of DNA and RNA from the host and the bacterial population. The isolated DNA was extracted and the relative number of bacteria was measured using a quantitative real-time PCR assay. A 16S rDNA clone library from 10 neonate was created, and the primarily data showed that the most frequent clones belong to Enterobacteria and Enterococcus. There were surprisingly few Lactobacillus and Clostridia clones and less than 0.1% of the clones belonged to the Bacteroidetes group. Instead many clones were found to belong to Actinobacteria, but none of these clones was Bifidobacterium.