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

BMC Genomics

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.