Table 2

Comparison of the taxonomic assignments* of 16S sequences (identified by i-rDNA and the meta-RNA program) in the malnourished child gut metagenome# at the taxonomic levels of (A) Order (B) Class and (C) Phylum.

(A) Order

16S sequences identified by

Percentage of 16S sequences identified by


i-rDNA

meta-RNA

i-rDNA

meta-RNA


Bacteroidales

1456

1469

60.9

59.5

Campylobacterales

247

286

10.3

11.6

Clostridiales

208

208

8.7

8.4

Fusobacteriales

143

182

6.0

7.4

Aeromonadales

143

130

6.0

5.3

Enterobacteriales

78

78

3.3

3.2

Burkholderiales

78

78

3.3

3.2

Mycoplasmatales

13

13

0.5

0.5

Erysipelotrichales

13

13

0.5

0.5

Bifidobacteriales

13

13

0.5

0.5


TOTAL

2392

2470


(B) Class

16S sequences identified by

Percentage of 16S sequences identified by


i-rDNA

meta-RNA

i-rDNA

meta-RNA


Bacteroidia

1456

1469

60.5

59.2

Epsilonproteobacteria

260

286

10.8

11.5

Gammaproteobacteria

221

221

9.2

8.9

Clostridia

208

208

8.6

8.4

Fusobacteria

143

182

5.9

7.3

Betaproteobacteria

78

78

3.2

3.1

Mollicutes

13

13

0.5

0.5

Erysipelotrichi

13

13

0.5

0.5

Actinobacteria

13

13

0.5

0.5


TOTAL

2405

2483


(C) Phylum

16S sequences identified by

Percentage of 16S sequences identified by


i-rDNA

meta-RNA

i-rDNA

meta-RNA


Bacteroidetes

1508

1599

61.1

60.3

Proteobacteria

572

624

23.2

23.5

Firmicutes

221

221

8.9

8.3

Fusobacteria

143

182

5.8

6.9

Tenericutes

13

13

0.5

0.5

Actinobacteria

13

13

0.5

0.5


TOTAL

2470

2652


* The taxonomic affiliations were obtained by providing the sequences as input to the RDP classifier (Wang Q, Garrity GM, Tiedje JM, Cole JR. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol. 2007 73(16):5261-7.

# Gupta SS, Mohammed MH, Ghosh TS, Kanungo S, Nair GB, Mande SS. Metagenome of the gut of a malnourished child. Gut Pathog. 2011 May 20;3:7.

Mohammed et al. BMC Genomics 2011 12(Suppl 3):S12   doi:10.1186/1471-2164-12-S3-S12

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