Additional file 3: of Improved taxonomic assignment of human intestinal 16S rRNA sequences by a dedicated reference database

Rarefaction based on known taxa. The figure shows the numbers of taxa calculated from samples of sequence data used for constructing the HITdb. Boxplots showing the numbers of found species (A) and genera (B) at two sample sizes (about 90 % and 80 % of sequences, n = 9 and n = 10, respectively). The horizontal red dashed line shows the number of OTUs in all sequences (100 % of sequences). (PDF 52 kb

Additional file 1: of Improved taxonomic assignment of human intestinal 16S rRNA sequences by a dedicated reference database

Phylogenetic trees. Package containing Newick and figure files of bacterial and archaeal phylogenies in HITdb. (PDF 22521 kb

Metadata

Metadata for the 1172 samples in the HITChip data matrix including age, sex, geographic region, DNA extraction information, projectID, probe-level Shannon diversity, BMI group,subjectID and time point. For units and other details, see the README file

HITChip phylogenetic microarray data matrix

Profiling of 130 genus-like taxa across 1006 western subjects based on the Human Intestinal Tract (HIT)Chip phylogenetic microarray

Additional file 14: of Signatures of ecological processes in microbial community time series

Figure S12. Variability of noise-type classification across rarefactions. The noise types of 100 taxa selected to be top abundant in one rarefaction were computed for repeated rarefactions in the stool data set of individual A [3]. (PDF 5 kb

Additional file 8: of Signatures of ecological processes in microbial community time series

Figure S6. The test for temporal structure with noise types is robust to noise. (a) Noise-type profile in the presence of noise generated with the Poisson distribution for each species and each sample. (b) Noise-type distribution in the presence of noise generated with the multinomial distribution for each sample. Labels for time series are colored according to the level of non-zero intrinsic noise (sigma) for Ricker, according to the death rate if larger than one for Hubbell, according to the interval if larger than one (with interval coloring taking precedence over sigma) and black otherwise. (PDF 8 kb

Additional file 12: of Signatures of ecological processes in microbial community time series

Figure S10. The accuracy of network inference with LIMITS decreases more strongly when applied to the last 100 than to the first 100 time points. (a) LIMITS accuracy, i.e., mean correlation of inferred and known interaction matrix, for the first 100 time points. (b) LIMITS goodness of fit for the first 100 time points. The goodness of fit was computed as the mean correlation between original and predicted time series. (c) LIMITS accuracy for the last 100 time points. Since gLV time series are constant, no network could be inferred for them. (d) LIMITS goodness of fit for the last 100 time points. The correlation between the goodness of fit to the Ricker model and the intrinsic noise strength observed in noise-free time series is lost. The data points are colored according to the connectance in panels (a) and (c), according to interval in panel (b) and according to the intrinsic noise strength sigma in panel (d). (PDF 17 kb

Additional file 9: of Signatures of ecological processes in microbial community time series

Figure S7. Increasing the time series length improves the accuracy of the test for temporal structure. Noise types were computed for time series sub-sets from 1000 to 1010 (a) and 1000 to 1025 (b) for all data sets with more than 1000 time points. Labels for time series are colored according to the level of non-zero intrinsic noise (sigma) for Ricker, according to the death rate if larger than one for Hubbell, according to the interval if larger than one (with interval coloring taking precedence over sigma) and black otherwise. (PDF 8 kb

Additional file 6: of Signatures of ecological processes in microbial community time series

Figure S4. The noise-type classification and the neutrality test are robust for a wide parameter range in the Hubbell model, but noise types are affected by the death rate. (a) The percentage of taxa with black, brown, pink and white noise types is plotted against the death rate. There is a significant negative correlation between the percentage of brown species and the death rate (Spearman’s rho: − 0.85, p value < 0.000001) and a corresponding positive correlation of the percentage of pink species to the death rate (Spearman’s rho: 0.94, p value < 0.000001). (b) The p values of the neutrality test are plotted against the death rate. (c) The percentage of taxa with black, brown, pink, and white noise types is plotted against the number of individuals. (d) The p values of the neutrality test are plotted against the number of individuals. (d) The percentage of taxa with black, brown, pink, and white noise types is plotted against the immigration rate. (e) The p values of the neutrality test are plotted against the immigration rate. Neutrality is rejected for a p value below 0.05. The p value of 0.05 is indicated by a dashed horizontal line. Time series were generated for 100 species and 3000 time points. For the immigration rate, the percentage of noise types of taxa with non-zero abundances was plotted, since for the low immigration rates tested in this simulation, many taxa have abundances of zero. (PDF 40 kb

Additional file 4: of Signatures of ecological processes in microbial community time series

Figure S2. The noise-type classification and the neutrality test for Ricker and gLV are robust to positive edge percentage, but connectance affects noise types in Ricker. (a, c) The percentage of taxa with black, brown, pink and white noise types is plotted against the connectance of the interaction matrix for Ricker and gLV, respectively. The percentage of black taxa in Ricker was positively correlated to connectance (Spearman’s rho: 0.86, p value < 0.00001), whereas the percentage of pink taxa in Ricker was negatively correlated to connectance (Spearman’s rho: − 0.71, p value = 0.00049). (b, d) The percentage of taxa with black, brown, pink, and white noise types is plotted against the positive edge percentage of the interaction matrix for Ricker and gLV, respectively. All neutrality test p values were zero, indicating non-neutral dynamics. Time series were generated for 100 species and 3000 time points. (PDF 16 kb