Temporal metagenomic read-abundance profiles from MetaPhlan analyses of bacterial species. Relative abundance of paired-end reads that were classified at bacterial species-level based on clade-specific marker genes from 3,000 reference genomes . pH at the different time points is shown in white text inside the bar graph. No pH measurement was available for 48 hrs (N/A). Numbers of estimated bacterial species from MetaPhlan analyses are shown inside the bar graph (No. sp.).