Premature Infant Gut Escherichia In-Situ Physiological-Condition Community

A premature infant gut microbiome study that combines metagenomic and metatranscriptomic sequencing to probe the in situ physiological conditions experienced by Escherichia spp. in four premature infants (two of whom developed necrotizing enterocolitis, NEC). Twenty fecal samples spanning 4-6 time points per infant were analyzed using sample-specific metagenome-assembled genomes (MAGs) as references for transcript mapping, and a "diametric ratio" method that compares transcript ratios of genes with opposite transcription responses to eliminate biases related to organism abundance. Diametric ratios of genes associated with low oxygen levels were significantly higher in samples from infants later diagnosed with NEC than in samples without NEC, and the method extends to other physiological conditions such as nitric oxide exposure and osmotic pressure.