Sequences of non-mammalian origin, Tulane/F953 derived sequences and a number of 'redundant' sequences of human origin were excluded in this analysis.
To ascertain whether databases containing DNA sequences, genome assemblies and trace archive reads were contaminated with human sequences, we performed an in depth search for sequences of human origin in non-human species.
Removal of sequences of human origin was performed following a MegaBLAST search against the human genome database from the NCBI released 16/08/2011.
It is noteworthy that these sequences are of human origin and appear to have adopted G2 like forms of R1 (Fig 1B, 1C, Fig 2 R1 tree).
Because our starting nucleic acid material is RNA from human epithelial cells, the majority of the sequencing reads are of human origin (>95%% mapping to human genome; ~75 % mapping to human transcriptome).
The genome sequences of bifidobacteria of human origin display a remarkable enrichment in genes involved in breakdown, uptake, and utilisation of a wide variety of complex polysaccharides of dietary and host origin [ 13, 85– 92].
Strikingly, more than half of the miss-assigned sequences (n = 11) are of human origin.
A relatively high percentage of the sequences in cluster 3c is of human origin (43%).
In cluster 3f, only 1 (5%) of 21 sequences identified during 2004 2006 was of human origin.
The first step of metagenomic data analysis requires the execution of certain pre-filtering steps, including the removal of redundant, low-quality sequences and sequences of probable eukaryotic origin (especially in metagenomes of human origin).
To date, five complete genome sequences and 10 draft genome sequences of S. agalactiae have been made publicly available, including nine isolates of human origin, four of fish origin and two of bovine origin.
