Figure 3

NMDS ordination of microbial communities for days 4 to 9 of life. (A) This ordination was based on weighted UniFrac beta diversity and run with three dimensions in the vegan package of R, resulting in a stress of 4.06. Control samples are shown in black and NEC and non-NEC deaths are shown in red for those included in Cluster I or green for those samples included in Cluster II. Clusters of samples with similar microbial composition were systematically identified using the Ward minimum variance method. These clusters are labeled using roman numerals I through IV. All NEC cases were found in either Cluster I or Cluster II only. The samples from the two non-NEC deaths are also found in Cluster I. (B) Bars indicate the relative abundance of the ten most common genera in samples from individual infants, whose study numbers are noted on the horizontal axis. Samples are grouped according to case or control status and the cluster in which they were identified. NEC: necrotizing enterocolitis; NMDS: non-metric dimensional scaling.