Wild dendrobatid frog microbiomes - bacteria
Data files
Dec 12, 2024 version files 13.23 GB
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README.md
2.46 KB
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Skin-16s-1-102_R1_001.fastq
28.89 MB
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Skin-16s-1-102_R2_001.fastq
28.94 MB
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Skin-16s-1-11_R1_001.fastq
22.29 MB
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Skin-16s-1-11_R2_001.fastq
22.32 MB
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Skin-16s-1-118_R1_001.fastq
31.67 MB
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Skin-16s-1-118_R2_001.fastq
31.68 MB
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Skin-16s-1-120_R1_001.fastq
33.86 MB
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Skin-16s-1-120_R2_001.fastq
33.88 MB
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Skin-16s-1-122_R1_001.fastq
29.97 MB
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Skin-16s-1-122_R2_001.fastq
29.99 MB
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Skin-16s-1-123_R1_001.fastq
26.43 MB
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Skin-16s-1-123_R2_001.fastq
26.46 MB
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Skin-16s-1-125_R1_001.fastq
24.01 MB
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Skin-16s-1-125_R2_001.fastq
24.02 MB
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Skin-16s-1-132_R1_001.fastq
31.65 MB
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Skin-16s-1-132_R2_001.fastq
31.66 MB
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Skin-16s-1-133_R1_001.fastq
27.88 MB
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Skin-16s-1-133_R2_001.fastq
27.90 MB
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Skin-16s-1-135_R1_001.fastq
22.82 MB
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Skin-16s-1-135_R2_001.fastq
22.84 MB
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Skin-16s-1-142_R1_001.fastq
26.90 MB
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Skin-16s-1-142_R2_001.fastq
26.93 MB
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Skin-16s-1-143_R1_001.fastq
24.25 MB
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Skin-16s-1-143_R2_001.fastq
24.27 MB
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Skin-16s-1-146_R1_001.fastq
29.97 MB
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Skin-16s-1-146_R2_001.fastq
30.01 MB
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Skin-16s-1-147_R1_001.fastq
34.14 MB
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Skin-16s-1-147_R2_001.fastq
34.18 MB
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Skin-16s-1-149_R1_001.fastq
29.32 MB
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Skin-16s-1-149_R2_001.fastq
29.35 MB
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Skin-16s-1-150_R1_001.fastq
26.07 MB
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Skin-16s-1-150_R2_001.fastq
26.10 MB
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Skin-16s-1-151_R1_001.fastq
27.59 MB
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Skin-16s-1-151_R2_001.fastq
27.62 MB
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Skin-16s-1-154_R1_001.fastq
26.96 MB
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Skin-16s-1-154_R2_001.fastq
27 MB
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Skin-16s-1-156_R1_001.fastq
37.76 MB
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Skin-16s-1-156_R2_001.fastq
37.79 MB
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Skin-16s-1-159_R1_001.fastq
20.01 MB
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Skin-16s-1-159_R2_001.fastq
20.02 MB
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Skin-16s-1-160_R1_001.fastq
26.62 MB
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Skin-16s-1-160_R2_001.fastq
26.63 MB
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Skin-16s-1-163_R1_001.fastq
25.46 MB
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Skin-16s-1-163_R2_001.fastq
25.48 MB
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Skin-16s-1-166_R1_001.fastq
23.23 MB
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Skin-16s-1-166_R2_001.fastq
23.25 MB
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Skin-16s-1-167_R1_001.fastq
23.08 MB
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Skin-16s-1-167_R2_001.fastq
23.10 MB
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Skin-16s-1-168_R1_001.fastq
23.96 MB
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Skin-16s-1-168_R2_001.fastq
23.97 MB
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Skin-16s-1-169_R1_001.fastq
30.38 MB
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Skin-16s-1-169_R2_001.fastq
30.40 MB
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Skin-16s-1-170_R1_001.fastq
20.29 MB
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Skin-16s-1-170_R2_001.fastq
20.30 MB
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Skin-16s-1-171_R1_001.fastq
30.33 MB
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Skin-16s-1-171_R2_001.fastq
30.34 MB
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Skin-16s-1-172_R1_001.fastq
36.14 MB
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Skin-16s-1-172_R2_001.fastq
36.16 MB
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Skin-16s-1-174_R1_001.fastq
20.24 MB
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Skin-16s-1-174_R2_001.fastq
20.25 MB
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Skin-16s-1-175_R1_001.fastq
14.66 MB
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Skin-16s-1-175_R2_001.fastq
14.66 MB
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Skin-16s-1-176_R1_001.fastq
31.77 MB
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Skin-16s-1-176_R2_001.fastq
31.79 MB
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Skin-16s-1-185_R1_001.fastq
12.88 MB
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Skin-16s-1-185_R2_001.fastq
12.89 MB
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Skin-16s-1-186_R1_001.fastq
27.20 MB
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Skin-16s-1-186_R2_001.fastq
27.22 MB
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Skin-16s-1-187_R1_001.fastq
30.93 MB
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Skin-16s-1-187_R2_001.fastq
30.94 MB
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Skin-16s-1-189_R1_001.fastq
26.88 MB
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Skin-16s-1-189_R2_001.fastq
26.90 MB
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Skin-16s-1-191_R1_001.fastq
28.36 MB
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Skin-16s-1-191_R2_001.fastq
28.38 MB
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Skin-16s-1-197_R1_001.fastq
24.41 MB
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Skin-16s-1-197_R2_001.fastq
24.43 MB
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Skin-16s-1-2_R1_001.fastq
37.44 MB
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Skin-16s-1-2_R2_001.fastq
37.47 MB
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Skin-16s-1-201_R1_001.fastq
33.17 MB
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Skin-16s-1-201_R2_001.fastq
33.20 MB
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Skin-16s-1-205_R1_001.fastq
12.25 MB
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Skin-16s-1-205_R2_001.fastq
12.26 MB
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Skin-16s-1-206_R1_001.fastq
23.78 MB
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Skin-16s-1-206_R2_001.fastq
23.80 MB
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Skin-16s-1-209_R1_001.fastq
23.34 MB
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Skin-16s-1-209_R2_001.fastq
23.37 MB
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Skin-16s-1-210_R1_001.fastq
33.33 MB
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Skin-16s-1-210_R2_001.fastq
33.34 MB
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Skin-16s-1-211_R1_001.fastq
31.91 MB
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Skin-16s-1-211_R2_001.fastq
31.94 MB
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Skin-16s-1-217_R1_001.fastq
25.07 MB
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Skin-16s-1-217_R2_001.fastq
25.08 MB
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Skin-16s-1-218_R1_001.fastq
24.52 MB
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Skin-16s-1-218_R2_001.fastq
24.52 MB
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Skin-16s-1-219_R1_001.fastq
28.27 MB
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Skin-16s-1-219_R2_001.fastq
28.28 MB
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Skin-16s-1-224_R1_001.fastq
31.59 MB
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Skin-16s-1-224_R2_001.fastq
31.62 MB
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Skin-16s-1-225_R1_001.fastq
29.79 MB
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Skin-16s-1-225_R2_001.fastq
29.82 MB
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Skin-16s-1-229_R1_001.fastq
25.24 MB
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Skin-16s-1-229_R2_001.fastq
25.25 MB
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Skin-16s-1-23_R1_001.fastq
34.21 MB
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Skin-16s-1-23_R2_001.fastq
34.25 MB
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Skin-16s-1-230_R1_001.fastq
17.93 MB
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Skin-16s-1-230_R2_001.fastq
17.93 MB
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Skin-16s-1-231_R1_001.fastq
14.64 MB
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Skin-16s-1-231_R2_001.fastq
14.64 MB
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Skin-16s-1-233_R1_001.fastq
22.88 MB
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Skin-16s-1-233_R2_001.fastq
22.90 MB
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Skin-16s-1-235_R1_001.fastq
12.53 MB
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Skin-16s-1-235_R2_001.fastq
12.53 MB
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Skin-16s-1-239_R1_001.fastq
29.22 MB
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Skin-16s-1-239_R2_001.fastq
29.25 MB
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Skin-16s-1-240_R1_001.fastq
22.62 MB
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Skin-16s-1-240_R2_001.fastq
22.62 MB
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Skin-16s-1-242-A_R1_001.fastq
19.79 MB
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Skin-16s-1-242-A_R2_001.fastq
19.80 MB
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Skin-16s-1-242-B_R1_001.fastq
7.69 MB
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Skin-16s-1-242-B_R2_001.fastq
7.68 MB
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Skin-16s-1-27_R1_001.fastq
16.81 MB
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Skin-16s-1-27_R2_001.fastq
16.82 MB
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Skin-16s-1-28_R1_001.fastq
28.64 MB
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Skin-16s-1-28_R2_001.fastq
28.67 MB
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Skin-16s-1-29_R1_001.fastq
28.30 MB
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Skin-16s-1-29_R2_001.fastq
28.32 MB
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Skin-16s-1-30_R1_001.fastq
34.32 MB
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Skin-16s-1-30_R2_001.fastq
34.35 MB
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Skin-16s-1-32_R1_001.fastq
23.10 MB
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Skin-16s-1-32_R2_001.fastq
23.11 MB
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Skin-16s-1-36_R1_001.fastq
26.84 MB
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Skin-16s-1-36_R2_001.fastq
26.87 MB
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Skin-16s-1-38_R1_001.fastq
32.74 MB
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Skin-16s-1-38_R2_001.fastq
32.77 MB
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Skin-16s-1-39_R1_001.fastq
31.07 MB
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Skin-16s-1-39_R2_001.fastq
31.09 MB
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Skin-16s-1-43_R1_001.fastq
29.20 MB
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Skin-16s-1-43_R2_001.fastq
29.22 MB
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Skin-16s-1-45_R1_001.fastq
32.32 MB
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Skin-16s-1-45_R2_001.fastq
32.36 MB
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Skin-16s-1-47_R1_001.fastq
18.83 MB
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Skin-16s-1-47_R2_001.fastq
18.85 MB
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Skin-16s-1-49_R1_001.fastq
31.36 MB
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Skin-16s-1-49_R2_001.fastq
31.38 MB
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Skin-16s-1-50_R1_001.fastq
27.95 MB
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Skin-16s-1-50_R2_001.fastq
27.97 MB
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Skin-16s-1-52_R1_001.fastq
24.24 MB
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Skin-16s-1-52_R2_001.fastq
24.26 MB
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Skin-16s-1-57_R1_001.fastq
23.05 MB
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Skin-16s-1-57_R2_001.fastq
23.08 MB
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Skin-16s-1-6_R1_001.fastq
22.25 MB
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Skin-16s-1-6_R2_001.fastq
22.26 MB
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Skin-16s-1-60_R1_001.fastq
27.08 MB
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Skin-16s-1-60_R2_001.fastq
27.07 MB
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Skin-16s-1-69_R1_001.fastq
32.40 MB
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Skin-16s-1-69_R2_001.fastq
32.41 MB
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Skin-16s-1-70_R1_001.fastq
20.51 MB
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Skin-16s-1-70_R2_001.fastq
20.51 MB
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Skin-16s-1-74_R1_001.fastq
31.17 MB
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Skin-16s-1-74_R2_001.fastq
31.17 MB
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Skin-16s-1-75_R1_001.fastq
25.26 MB
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Skin-16s-1-75_R2_001.fastq
25.27 MB
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Skin-16s-1-76_R1_001.fastq
22.51 MB
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Skin-16s-1-76_R2_001.fastq
22.52 MB
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Skin-16s-1-82_R1_001.fastq
28.92 MB
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Skin-16s-1-82_R2_001.fastq
28.93 MB
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Skin-16s-1-83_R1_001.fastq
12.53 MB
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Skin-16s-1-83_R2_001.fastq
12.54 MB
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Skin-16s-1-85_R1_001.fastq
31.88 MB
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Skin-16s-1-85_R2_001.fastq
31.90 MB
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Skin-16s-1-86_R1_001.fastq
32.62 MB
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Skin-16s-1-86_R2_001.fastq
32.65 MB
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Skin-16s-1-88_R1_001.fastq
28.15 MB
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Skin-16s-1-88_R2_001.fastq
28.17 MB
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Skin-16s-1-9_R1_001.fastq
33.01 MB
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Skin-16s-1-9_R2_001.fastq
33.05 MB
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Skin-16s-1-92_R1_001.fastq
31.33 MB
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Skin-16s-1-92_R2_001.fastq
31.34 MB
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Skin-16s-1-97_R1_001.fastq
32.15 MB
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Skin-16s-1-97_R2_001.fastq
32.18 MB
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Skin-16s-1-98-A_R1_001.fastq
33.06 MB
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Skin-16s-1-98-A_R2_001.fastq
33.08 MB
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Skin-16s-1-98-B_R1_001.fastq
34.10 MB
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Skin-16s-1-98-B_R2_001.fastq
34.13 MB
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Skin-16s-1-PCR-1-Control-A_R1_001.fastq
430.64 KB
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Skin-16s-1-PCR-1-Control-A_R2_001.fastq
430.63 KB
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Skin-16s-1-PCR-1-Control-B_R1_001.fastq
4.63 MB
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Skin-16s-1-PCR-1-Control-B_R2_001.fastq
4.63 MB
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Skin-16s-2-101_R1_001.fastq
25.88 MB
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Skin-16s-2-101_R2_001.fastq
25.91 MB
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Skin-16s-2-104_R1_001.fastq
24.81 MB
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Skin-16s-2-104_R2_001.fastq
24.84 MB
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Skin-16s-2-107_R1_001.fastq
39.68 MB
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Skin-16s-2-107_R2_001.fastq
39.73 MB
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Skin-16s-2-108_R1_001.fastq
16.15 MB
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Skin-16s-2-108_R2_001.fastq
16.17 MB
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Skin-16s-2-110_R1_001.fastq
33.20 MB
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Skin-16s-2-110_R2_001.fastq
33.22 MB
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Skin-16s-2-111_R1_001.fastq
32.56 MB
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Skin-16s-2-111_R2_001.fastq
32.58 MB
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Skin-16s-2-115_R1_001.fastq
32.05 MB
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Skin-16s-2-115_R2_001.fastq
32.06 MB
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Skin-16s-2-116_R1_001.fastq
25.13 MB
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Skin-16s-2-116_R2_001.fastq
25.14 MB
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Skin-16s-2-117_R1_001.fastq
14.41 MB
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Skin-16s-2-117_R2_001.fastq
14.43 MB
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Skin-16s-2-119_R1_001.fastq
26.11 MB
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Skin-16s-2-119_R2_001.fastq
26.11 MB
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Skin-16s-2-12_R1_001.fastq
35.05 MB
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Skin-16s-2-12_R2_001.fastq
35.08 MB
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Skin-16s-2-127_R1_001.fastq
24.37 MB
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Skin-16s-2-127_R2_001.fastq
24.38 MB
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Skin-16s-2-128_R1_001.fastq
29.69 MB
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Skin-16s-2-128_R2_001.fastq
29.71 MB
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Skin-16s-2-130_R1_001.fastq
12.18 MB
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Skin-16s-2-130_R2_001.fastq
12.18 MB
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Skin-16s-2-131_R1_001.fastq
15.72 MB
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Skin-16s-2-131_R2_001.fastq
15.73 MB
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Skin-16s-2-137_R1_001.fastq
23.38 MB
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Skin-16s-2-137_R2_001.fastq
23.38 MB
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Skin-16s-2-138_R1_001.fastq
28.19 MB
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Skin-16s-2-138_R2_001.fastq
28.20 MB
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Skin-16s-2-14_R1_001.fastq
30.01 MB
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Skin-16s-2-14_R2_001.fastq
30.04 MB
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Skin-16s-2-140_R1_001.fastq
28.82 MB
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Skin-16s-2-140_R2_001.fastq
28.84 MB
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Skin-16s-2-141_R1_001.fastq
26.51 MB
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Skin-16s-2-141_R2_001.fastq
26.55 MB
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Skin-16s-2-145_R1_001.fastq
27.14 MB
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Skin-16s-2-145_R2_001.fastq
27.17 MB
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Skin-16s-2-148_R1_001.fastq
37.59 MB
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Skin-16s-2-148_R2_001.fastq
37.64 MB
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Skin-16s-2-15_R1_001.fastq
21.07 MB
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Skin-16s-2-15_R2_001.fastq
21.10 MB
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Skin-16s-2-152_R1_001.fastq
21.79 MB
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Skin-16s-2-152_R2_001.fastq
21.83 MB
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Skin-16s-2-153_R1_001.fastq
11.58 MB
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Skin-16s-2-153_R2_001.fastq
11.59 MB
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Skin-16s-2-155_R1_001.fastq
11.88 MB
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Skin-16s-2-155_R2_001.fastq
11.89 MB
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Skin-16s-2-157_R1_001.fastq
30.74 MB
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Skin-16s-2-157_R2_001.fastq
30.76 MB
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Skin-16s-2-162_R1_001.fastq
25.18 MB
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Skin-16s-2-162_R2_001.fastq
25.20 MB
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Skin-16s-2-164_R1_001.fastq
23.52 MB
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Skin-16s-2-164_R2_001.fastq
23.54 MB
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Skin-16s-2-173_R1_001.fastq
24.46 MB
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Skin-16s-2-173_R2_001.fastq
24.47 MB
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Skin-16s-2-178_R1_001.fastq
18.70 MB
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Skin-16s-2-178_R2_001.fastq
18.73 MB
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Skin-16s-2-179_R1_001.fastq
13.10 MB
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Skin-16s-2-179_R2_001.fastq
13.10 MB
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Skin-16s-2-18_R1_001.fastq
35.45 MB
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Skin-16s-2-18_R2_001.fastq
35.48 MB
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Skin-16s-2-181_R1_001.fastq
25.01 MB
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Skin-16s-2-181_R2_001.fastq
25.02 MB
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Skin-16s-2-182_R1_001.fastq
24.83 MB
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Skin-16s-2-182_R2_001.fastq
24.84 MB
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Skin-16s-2-188_R1_001.fastq
20.62 MB
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Skin-16s-2-188_R2_001.fastq
20.64 MB
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Skin-16s-2-194_R1_001.fastq
6.09 MB
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Skin-16s-2-194_R2_001.fastq
6.10 MB
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Skin-16s-2-196_R1_001.fastq
28.07 MB
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Skin-16s-2-196_R2_001.fastq
28.10 MB
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Skin-16s-2-198_R1_001.fastq
23.54 MB
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Skin-16s-2-198_R2_001.fastq
23.56 MB
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Skin-16s-2-199_R1_001.fastq
32.77 MB
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Skin-16s-2-199_R2_001.fastq
32.82 MB
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Skin-16s-2-200_R1_001.fastq
24.39 MB
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Skin-16s-2-200_R2_001.fastq
24.41 MB
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Skin-16s-2-203_R1_001.fastq
31.82 MB
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Skin-16s-2-203_R2_001.fastq
31.83 MB
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Skin-16s-2-204_R1_001.fastq
32.89 MB
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Skin-16s-2-204_R2_001.fastq
32.89 MB
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Skin-16s-2-207_R1_001.fastq
27.93 MB
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Skin-16s-2-207_R2_001.fastq
27.94 MB
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Skin-16s-2-21_R1_001.fastq
167.11 KB
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Skin-16s-2-21_R2_001.fastq
167.18 KB
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Skin-16s-2-212_R1_001.fastq
31.21 MB
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Skin-16s-2-212_R2_001.fastq
31.26 MB
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Skin-16s-2-214_R1_001.fastq
34.77 MB
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Skin-16s-2-214_R2_001.fastq
34.78 MB
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Skin-16s-2-215_R1_001.fastq
31.82 MB
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Skin-16s-2-215_R2_001.fastq
31.85 MB
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Skin-16s-2-216_R1_001.fastq
14.90 MB
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Skin-16s-2-216_R2_001.fastq
14.91 MB
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Skin-16s-2-22_R1_001.fastq
23.56 MB
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Skin-16s-2-22_R2_001.fastq
23.59 MB
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Skin-16s-2-221_R1_001.fastq
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wild_bacteria_metadata.xlsx
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Abstract
Shifts in microbiome community composition can have large effects on host health. It is therefore important to understand how perturbations, like those caused by the introduction of exogenous chemicals, modulate microbiome community composition. In poison frogs within the family Dendrobatidae, the skin microbiome is exposed to the alkaloids that the frogs sequester from their diet and use for defense. Given the demonstrated antimicrobial effects of these poison frog alkaloids, these compounds may be structuring the skin microbial community. To test this, we first characterized microbial communities from chemically defended and closely related non-defended frogs from Ecuador. Then we conducted a laboratory experiment to monitor the effect of the alkaloid decahydroquinoline (DHQ) on the microbiome of a single frog species. In both the field and lab experiments, we found that alkaloid-exposed microbiomes are more species rich and phylogenetically diverse, with an increase in rare taxa. To better understand the strain-specific behavior in response to alkaloids, we cultured microbial strains from poison frog skin and found the majority of strains exhibited either enhanced growth or were not impacted by the addition of DHQ. Additionally, stable isotope tracing coupled to nanoSIMS suggests that some of these strains are able to metabolize DHQ. Taken together, these data suggest that poison frog chemical defenses open new niches for skin-associated microbes with specific adaptations, including the likely metabolism of alkaloids, that enable their survival in this toxic environment. This work helps expand our understanding of how exposure to exogenous compounds like alkaloids can impact host microbiomes.
Other data related to this manuscript can be found in the following locations:
https://doi.org/10.5061/dryad.5qfttdzd5, Wild dendrobatid frog microbiomes - bacteria
https://doi.org/10.5061/dryad.gxd2547t1, Oophaga sylvatica decahydroquinoline quantification
https://doi.org/10.5061/dryad.9ghx3ffqn, Ecuadorian Dendrobatid frog alkaloid profiles
https://doi.org/10.5061/dryad.tdz08kq62, Feeding experiment microbiome - bacteria
https://doi.org/10.5061/dryad.4mw6m90hn, Feeding experiment microbiome - fungi
https://doi.org/10.5061/dryad.2ngf1vhzc, Poison frog microbiome metagenomics data
https://doi.org/10.5061/dryad.9cnp5hqrm, Wild dendrobatid microbiomes – fungi
README: Wild dendrobatid frog microbiomes
https://doi.org/10.5061/dryad.5qfttdzd5
16S amplicon sequencing data from poison frogs collected in Ecuador in 2019.
Other data related to this manuscript can be found in the following locations:
https://doi.org/10.5061/dryad.5qfttdzd5, Wild dendrobatid frog microbiomes - bacteria
https://doi.org/10.5061/dryad.gxd2547t1, Oophaga sylvatica decahydroquinoline quantification
https://doi.org/10.5061/dryad.9ghx3ffqn, Ecuadorian Dendrobatid frog alkaloid profiles
https://doi.org/10.5061/dryad.tdz08kq62, Feeding experiment microbiome - bacteria
https://doi.org/10.5061/dryad.4mw6m90hn, Feeding experiment microbiome - fungi
https://doi.org/10.5061/dryad.2ngf1vhzc, Poison frog microbiome metagenomics data
https://doi.org/10.5061/dryad.9cnp5hqrm, Wild dendrobatid microbiomes – fungi
16S sample metadata
Metadata details can be found in wild_bacteria_metadata.xlsx
- sample.names: Names of samples that correspond to FASTQ files.
- Plate: 96 well plate number for library preps
- sample.number: Sample identifier, used in library preps
- FrogID: Frog identifier, used to link with alkaloid data. Blanks denote frog was not given this type of identifier number.
- Species: Frog species
- Population: Geographic location of frog collection.
- Toxic: Categorized into toxic (contains both high and medium alkaloid quantities) and non-toxic (referred to as low alkaloids in the associated paper)
- Province: Province of frog collection location. Blanks denote information not recorded.
- Sex: Frog sex. Entries with question marks denote uncertainty, generally meaning ovaries or testes were not found but appearance suggests the indicated sex. Blanks denote information not recorded.
- Weight: Frog weight in grams. Blanks correspond to measurements not taken.
- Length: Snout-vent length in millimeters. Blanks correspond to measurements not taken.
Samples with mostly blank rows correspond to samples that, when processed, had illegible identifiers that could not be associated with a frog species or location.