Additional file 1 of Highly abundant core taxa in the blow within and across captive bottlenose dolphins provide evidence for a temporally stable airway microbiota

Additional file 1: Fig. S1. Shows a scatterplot of the technical contaminant zOTUs of control samples (‘TRUE’ in green) and dolphins blow zOTUs (‘FALSE’ in red). The R package decontam determined 157 technical contaminants which were then deleted from the 81 dolphin blow samples. Fig. S2. Shows a histogram of the technical contaminant zOTUs of control samples (bars on the left) and dolphins blow zOTUs (bars on the right). The R package decontam determined 157 technical contaminants which were then deleted from the 81 dolphin blow samples. The figure shows the bimodal division between dolphin zOTUs and technical control zOTUs. Fig. S3. Rarefaction curves of dolphin blow samples. The majority of samples was sampled to saturation. Fig. S4. Rarefaction curves of pool water samples. The majority of samples was sampled to saturation. Fig. S5. Shows a scatterplot of the contaminant zOTUs of pool water samples (‘TRUE’ in green) and dolphins blow zOTUs (‘FALSE’ in red). The R package decontam determined 520 water contaminants which were then deleted from the 81 dolphin blow samples. Fig. S6. Shows a histogram of the water contaminant zOTUs of pool water samples (bars on the left) and dolphins blow zOTUs (bars on the right). The R package decontam determined 520 water contaminants which were then deleted from the 81 dolphin blow samples. The figure shows the bimodal division between dolphin zOTUs and water zOTUs. Fig. S7. Shows the alpha diversity parameter, richness, across 37 weeks of sample collection in the 13 study dolphins. Fig. S8. Shows the alpha diversity parameter, Shannon-Wiener diversity, across 37 weeks of sample collection in the 13 study dolphins. Fig. S9. Shows the alpha diversity parameter, Chao1, across 37 weeks of sample collection in the 13 study dolphins. Fig. S10. Shows the alpha diversity parameter, ACE, across 37 weeks of sample collection in the 13 study dolphins. Fig. S11. nMDS plot based on Bray-Curtis dissimilarity matrix of 81 dolphin blow and 28 pool water samples. A clear distinction between the microbial community composition in dolphin blow and pool water is evident. Fig. S12. nMDS plot based on Bray-Curtis dissimilarity matrix of 81 dolphin blow samples coloured according to their ID (individual dolphins). Although not clearly evident in this plot, the mvabund-based analysis showed a significant impact of the factor ‘dolphin ID’. Fig. S13. nMDS plot based on Bray-Curtis dissimilarity matrix of 81 dolphin blow samples coloured according to the dolphins’ sex. The diagram provides a hint that the mvabund-based analysis showed a significant impact of the factor ‘sex’ on the microbial communities. Fig. S14. nMDS plot based on Bray-Curtis dissimilarity matrix of 81 dolphin blow samples coloured according to the dolphins’ age groups. The diagram provides some evidence that the mvabund-based analysis showed a significant impact of the factor ‘age’ on the microbial communities. The analysis was based on four age levels: 1: 0–10 years, 2: 11–20 years, 3: 21–30 years, 4: 31–40 years. Fig. S15. Frequency histogram showing the presence of 503 intra-core zOTUs across 11 bottlenose dolphins. Although a large number of intra-core zOTUs is present, only a minority is shared by most dolphins. Fig. S16. Frequency histogram showing the presence of 97 inter-core zOTUs across ten dolphins in week 2, 6, 11, 19, 28, 37. More than half of the inter-core zOTUs were only present at one sampling point. Fig. S17. nMDS plot based on Bray-Curtis dissimilarity matrix of 81 dolphin blow samples coloured according to their health status. The mvabund-based analysis did not provide evidence for a general difference between healthy/untreated and sick/treated dolphin. Fig. S18. nMDS plot based on Bray-Curtis dissimilarity matrix of 16 blow samples of dolphins that had received an antimicrobial treatment during the sample collection period. The samples are coloured according to the timing of their collection relative to the timing of treatment (‘Before’: samples collected before treatment started; ‘Directly_after’: samples collected within one week after treatment). The mvabund-based analysis provided evidence for a significant difference between the ‘Before’ and the ‘Directly_after’ samples. Fig. S19. nMDS plot based on Bray-Curtis dissimilarity matrix of 18 blow samples of dolphins that had received an antimicrobial treatment during the sample collection period. The samples are coloured according to the timing of their collection relative to the timing of treatment (‘After’: samples collected at least two weeks after treatment started; ‘Directly_after’: samples collected within one week after treatment). The mvabund-based analysis provided evidence for a significant difference between the ‘After’ and the ‘Directly_after’ samples. Fig. S20. This scatterplot shows the temporal dynamics of the inter-core in the studied dolphins from week 2 to 37. The inter-core was defined as those zOTUs that were present across ten dolphins, randomly selected from our 13 study dolphins, at a specific time point. We picked weeks 2, 6, 11, 19, 28 and 37 as these points in time. Table S1. Shows those 157 zOTUs and their taxonomy that were identified as technical contaminants and subsequently deleted from the dataset of dolphin blow microbiota. Table S2. Alpha diversity parameters of dolphin blow microbiota for each time point over the sampling period of 37 weeks: richness, diversity, Chao1 and ACE species estimators.