Fig. 1

Overview of the preterm infant gut microbiota phases and properties. a The decision tree for classifying a microbiota sample into one of the three phases. b A composition bar chart with each sample grouped by phases 1–3 (P1–P3) from left to right. Green, gray, orange, and blue represent Bacilli, Gammaproteobacteria, Clostridia, and Bacteroidia, respectively. c Bar charts representing the average weighted UniFrac distance between consecutive samples of each individual infant. The bars are grouped into three major categories from left to right according to the initial phase of the consecutive samples being assessed. Each bar within a category corresponds to the phase of the second consecutive sample. The height of the bar indicates the average dissimilarity between consecutive samples of the corresponding phases, with exact values included in the table below the graph. d Bar charts indicating the transition probability between consecutive samples within an individual. The groupings and bars within each group indicate the phases of the first and second sample of a pair of consecutive samples, respectively, and are ordered as described in c. Transition probabilities are included in the table below the graph. e The distribution of samples over corrected gestational age in weeks. The dashed line separates the samples into early (< 34 weeks PMA) and late period (≥ 34 weeks PMA), based on functional variance of microbiota composition across all 81 individuals. f Bar charts showing the average composition of the samples in each phase at the genus level, with prominent genera labeled. For two Enterobacteriacaea and one Clostridiacaeae, the genus could not be determined and the family is indicated instead (See Additional file 2: Comment on Figure 3F). Lines connecting segments between phases indicate that the segment represents the same genus in each bar. A complete list of the genera represented here and their relative abundances can be found in Additional file 4: Table S3