Subtractive assembly for comparative metagenomics, and its application to type 2 diabetes metagenomes

Table 1 Species composition of the artificial metagenomic samples in simulation 1

	Group 1					Group 2				Group 3
	S1	S2	S3	S4	S5	S1	S2	S3	S4	S1	S2	S3
Ferroplasma acidarmanus fer1	1^a	16	1	1	1	1	12	1	1	1	10	1
Lactobacillus gasseri ATCC 33323	2	2	16	2	2	2	2	12	2	2	2	10
Pediococcus pentosaceus ATCC 25745	4	4	4	16	4	4	4	4	12	4	4	4
Prochlorococcus marinus NATL2A	8	8	8	8	16	8	8	8	8	8	8	8
Streptococcus thermophilus LMD-9	16	1	2	4	8	12	1	2	4	10	1	2
RA ratio (S ₁ /S _i, i ! = 1)^b		16^c	8	4	2		12	6	3		10	5

^aRelative abundance (RA) of the F. acidarmanus species in sample S1
^bRelative abundance of the S. thermophilus genome in S1 relative to S2, S3 and so on. Pairs of datasets (S1 in each group, and another one in the same group) were subjected to subtractive assembly
^cThe relative abundance of the S. thermophilus genome in S1 versus S2

ISSN: 1474-760X