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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