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.