Reused data
To examine the effect of read length on diversity estimates, publicly available data from three experimental datasets were selected. These targeted the soil, water, and animal microbiomes before and 4 days after a single, strong disturbance. Each dataset had at least 5 replicates per time point, had sampled the system before, one day after, and 4 days after disturbance, and had sequenced the resulting DNA by targeting the 515-806 region using an Illumina MiSeq. This 16S rRNA region was selected due to its popularity (Jurburg et al., 2020), standardization (Thompson et al., 2017), and sensitivity (Zhang et al., 2023).
Soil microbiome data was obtained from a microcosm experiment (Jurburg et al., 2017), in which soils were exposed to microwave radiation, and destructively sampled over time. DNA was extracted using the MoBio PowerSoil DNA Extraction Kit (MoBio Laboratories, Carlsbad, CA, U.S.A.), and the resulting data are publicly available in NCBI’s SRA under accession number PRJNA329541. Five replicate samples per time point for the treatment exposed to a single microwave disturbance, with samples taken before, one day after, and 4 days after the disturbance were selected. Where more replicates were available, the five largest files for each dataset x time combination were selected.
Aquatic microbiome data was obtained from a marine microcosm experiment exposing aquatic microbiota to cadmium and phenanthrene (Qian, Ding, Guo, Zhang, & Wang, 2017). Sampling was repeated within each microcosm over time. Water was filtered and DNA was extracted using the MoBio PowerSoil DNA Extraction Kit (MoBio Laboratories, Carlsbad, CA, U.S.A.), and the resulting data are publicly available in NCBI’s SRA under accession number PRJDB4992. Samples simultaneously exposed to phenanthrene and cadmium, taken before, one day after, and 4 days after disturbance were selected, and all five replicates per time point were included.
Finally, animal microbiome data was obtained from an animal experiment in which experimental pigs were exposed to antibiotic treatments and their fecal microbiome was monitored daily (Jurburg, Cornelissen, de Boer, Smits, & Rebel, 2019). Fecal samples were snap-frozen, and DNA was extracted using the AGOWA mag Mini DNA Isolation Kit (AGOWA, Berlin, Germany), and the resulting data are publicly available in NCBI’s SRA under accession number PRJNA528235. Animals exposed to clindamycin, and sampled before, one day after, and 4 days after disturbance were selected, and all five replicates per time point were included.