Fig. 5

Iteration on the Human Microbiome probe pool to achieve optimal depletion of infant stool samples for metatranscriptomic analysis. A Percentage of reads mapping to eukaryotic and prokaryotic rRNAs vs coding sequences following depletion of infant stool RNA samples 4–33 months of age using Ribo-Zero Plus and HMv1 probes (Left). Bacterial rRNA depletion (LSU & SSU) efficiency using HMv1 vs HMv2, a modified probe set supplemented with 42 additional probes targeting Bifidobacterium bifidum rRNA for three infant samples which had suboptimal depletion with the HMv1 probes is shown in the inset on lower right. B Alpha diversity (Shannon index) and metatranscriptomic taxonomic profiles for HMv1 depleted stool samples from infants and children aged 4 to 33 months. C Differential gene expression in young (< 6 month of age) vs older infants (> 20 months) across major metabolic groups (carbohydrate metabolism, cell wall and motility). D Table showing carbohydrate and amino acid metabolism genes with large changes in relative expression in infants (< 6 months) versus young children (> 20 months). Positive effect size values correlate with increased expression in infants while negative values correlate with increased expression in > 20 month children