Boxplots of proportional abundances in routine swabs of a) <i>Staphylococcus</i>, b) <i>Corynebacterium</i> II, c) <i>Moraxella</i> II, d) unclassified Flavobacteriaceae I, e) <i>Streptococcus</i> I, f) <i>Moraxella</i> I.

<p>Boxplots of proportional abundances in routine swabs of a) <i>Staphylococcus</i>, b) <i>Corynebacterium</i> II, c) <i>Moraxella</i> II, d) unclassified Flavobacteriaceae I, e) <i>Streptococcus</i> I, f) <i>Moraxella</i> I.</p

Heatmap of pneumococcal serotypes detected in culture per infant.

<p>The mean number of types acquired per child over the study period is 7.4.</p

Proportional abundances of a) <i>Corynebacterium</i> II, b) <i>Dolosigranulum</i>, c) <i>Staphylococcus</i>, d) <i>Streptococcus</i> I, grouped by the presence/absence of cocolonisers.

<p>There is some support for the observation that <i>Dolosigranulum</i> is negatively associated with <i>Streptococcus pneumoniae</i> in the squat distributions seen in (d) however <i>Corynebacterium</i> II does not appear to play a part in that interaction.</p

NMDS plot based on Jaccard distance (a-c) and Bray-Curtis dissimilarity (d-f), coloured according to age.

<p>a) and d) show 50% ellipses and centroids of the first 12 months of life as an overlay on the full 24-month dataset, while b) and e) show ellipses for 13–24 months overlaid on the full 24-month dataset. Ellipses and datapoints are presented in corresponding colours. Significant OTUs driving the ordination (p<0.0001 and with vector length >0.25) are shown in d) and f). Increasing age is significantly correlated with both x and y axis.</p

Optimization of high-throughput 16S rRNA gene amplicon sequencing: an assessment of PCR pooling, mastermix use and contamination

Supplementary materials for "Optimisation of high-throughput 16S rRNA gene amplicon sequencing: an assessment of PCR pooling, mastermix use and contamination", as described in Microbial Genomics, including:Supplementary FiguresSupplementary TablesSupplementary Methods and ResultsCARRIAGE study authorship listENA accession numbers and sample metadataSTORM guidelines checklistTaxonomy tables</p

Microbiota profile of one child from 1–24 months of age.

<p>Swabs taken during a pneumonia episode are highlighted by boxes. Where cultured, pneumococcal serotype in the sample is indicated in the top pane. OTUs are colour grouped by phylum: Actinobacteria (orange), Bacteroidetes (yellow), Firmicutes (green), Proteobacteria (blue).</p