Additional file 1: of A microbiome case-control study of recurrent acute otitis media identified potentially protective bacterial genera

Questionnaire completed by families recruited to the study. (PDF 28 kb

Additional file 9: of A microbiome case-control study of recurrent acute otitis media identified potentially protective bacterial genera

Figure S5. Procrustes analysis of left and right ear samples. The dataset includes both MEF and MER samples in left/right ear pairs from the same child. Samples with less than 1499 reads are excluded. The p-value is non-parametric and is based on 999 Monte Carlo simulations. (PNG 91 kb

Additional file 3: of A microbiome case-control study of recurrent acute otitis media identified potentially protective bacterial genera

Table S1. Full taxonomy of all OTUs identified in this study. Taxonomy is from the SILVA database, v123 for QIIME. Taxonomy assigned to OTUs by UCLUST v1.2.22q within QIIME v1.9.1 (assign_taxonomy.py). (XLSX 13 kb

Additional file 5: of A microbiome case-control study of recurrent acute otitis media identified potentially protective bacterial genera

Figure S2. Procrustes analysis of raw and rarefied datasets. The rarefied dataset was subsampled at a threshold of 1499 reads per sample. The raw dataset excluded samples below this depth. P-values are non-parametric and are based on 999 Monte Carlo simulations. (PNG 174 kb

Additional file 6: of A microbiome case-control study of recurrent acute otitis media identified potentially protective bacterial genera

Figure S3. Beta diversity PCoA in the nasopharynx of cases and controls, sorted by other covariates. Case and control nasopharyngeal samples shown in Fig. 3 are coloured by other covariates. NA refers to samples where the covariate was not applicable or was missing (not given or recorded “unknown”) and the number represents individual samples. (PDF 564 kb

Additional file 11: of A microbiome case-control study of recurrent acute otitis media identified potentially protective bacterial genera

Table S4. All correlations between OTUs determined by SparCC. Correlations within each sample type are listed in separate sheets. This includes correlations between all possible pairs of OTUs found in the samples. P-values are non-parametric and were calculated as the proportion of times a correlation coefficient more extreme than the observed correlation coefficient occurred in 100 simulated datasets. (XLSX 443 kb

Additional file 10: of A microbiome case-control study of recurrent acute otitis media identified potentially protective bacterial genera

Figure S6. Procrustes analysis of MEF and MER samples. The dataset includes pairs of MEF and MER samples from the same ear of the same child. Samples with less than 1499 reads are excluded. The p-value is non-parametric and is based on 999 Monte Carlo simulations. (PNG 80 kb

Additional file 2: of A microbiome case-control study of recurrent acute otitis media identified potentially protective bacterial genera

Figure S1. Diagrammatic overview of the 16S rRNA gene data analysis pipeline. Names of the software or tools used are in red. The SILVA database replaced the default taxonomy database in QIIME (GreenGenes) as GreenGenes 13_8 version does not discriminate between Alloiococcus and Dolosigranulum. (PDF 366 kb

Additional file 8: of A microbiome case-control study of recurrent acute otitis media identified potentially protective bacterial genera

Figure S4. Beta diversity PCoA in the samples from the cases, sorted by other covariates. Samples from the cases shown in Fig. 5 are coloured by other covariates. NA refers to samples where the covariate was not applicable or was missing (not given or recorded “unknown”) and the number represents individual samples (multiple samples per child). (PDF 392 kb

Additional file 7: of A microbiome case-control study of recurrent acute otitis media identified potentially protective bacterial genera

Table S3. Complete list of significantly differentially abundant OTUs determined by metagenomeSeq. All differentially abundant OTUs between a) MEF and MEF; b) MEF and NPS; c) MER and NPS; d) ECS and MEF are shown with their log fold change, p-values and mean and median abundance. OTUs in bold/grey are those above the selected threshold of at least 0.35% mean or median abundance in at least one group, and were present in both sets of samples where applicable. Set 1 refers to the set of samples were the left or right ear was chosen at random; these numbers are reported in results. Set 2 refers to the set of samples where the opposite ear was chosen; these results were only used for validation of the differentially abundant OTUs from Set 1. (XLSX 29 kb