Figure 2

Cladograms generated by LEfSe indicating differences in taxa between hospitals in samples from weeks 1 and 2. The central yellow dot in each cladogram represents kingdom; each successive circle is one step lower phylogenetically (phylum, class, order, family, and OTU). Regions in red indicate taxa that were enriched in 2010 compared to those in 2011, while regions in green indicate taxa that were enriched in 2011 compared to those in 2010. (A) Week 1 sample from hospital 1. In 2010, samples were enriched for Firmicutes, with a shift in microbiota towards an increase in Proteobacteria in 2011. (B) Week 1 sample from hospital 2. In 2010, infants at hospital 2 were enriched in Proteobacteria, while in 2011, they were enriched in Firmicutes. (C) Week 2 sample from hospital 1. Only OTU level differences were detectable between 2010 and 2011. (D) Week 2 sample from hospital 2. In 2010, samples were enriched for Proteobacteria. In 2011, the infant microbiota were enriched in Firmicutes, particularly, in Bacilli.