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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.

From: i-rDNA: alignment-free algorithm for rapid in silico detection of ribosomal gene fragments from metagenomic sequence data sets

(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  
  1. * 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.
  2. # 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.