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Table 1 Comparison of rRNA abundance in control vs. ribodepleted samples

From: SAMSA: a comprehensive metatranscriptome analysis pipeline

Phylum 4012, P4 4012, P1 4015, P4 4015, P1 % depleted
Gemmatimonadetes 3 1 28 5 74.40
Spirochaetes 3 4 14 55 163.10
Nitrospirae 4 1 22 0 87.50
Fusobacteria 5 5 24 9 31.25
Fibrobacteres 6 0 21 0 100.00
Synergistetes 6 5 14 2 51.19
Thermi 6 1 11 1 87.12
Chlorobi 6 1 34 0 91.67
Chloroflexi 7 6 29 2 53.69
Caldiserica 8 0 64 0 100.00
Caldithrix 11 0 70 2 98.57
Tenericutes 67 6 411 28 92.12
Chlamydiae 74 1 410 15 97.50
Acidobacteria 94 5 453 7 96.57
Euryarchaeota 175 15 942 693 58.93
Parvarchaeota 241 8 1298 22 97.49
Cyanobacteria 262 210 974 59 56.89
Planctomycetes 303 7 2019 23 98.28
Crenarchaeota 514 183 2474 106 80.06
Lentisphaerae 1045 19 6324 151 97.90
Verrucomicrobia 1107 29 6679 117 97.81
Actinobacteria 2739 5432 8394 5326 30.89
Proteobacteria 43585 3780 61436 2612 93.54
Bacteroidetes 486595 218584 1163164 98778 73.29
Firmicutes 939246 127130 2178859 38923 92.34
TOTALS 1476112 355433 3434266 146948 75.98
  1. Two pilot metatranscriptomes were sequenced twice; the P1 protocol involved a ribodepletion step, while the P4 protocol did not. Comparisons of the organism annotations reveal that ribodepletion led to a decrease in 16S rRNA reads for most, but not all, bacterial phyla