Such methods may also result in false positives, in part because of the similarity of some microbial sequences with the sequence of the host cell.
Therefore, this alignment-free clustering method was successfully applied to the phylogenetic classification of genome sequence fragments [ 15] and to the analysis of a large number of microbial sequences obtained by metagenome studies of environmental and clinical samples [ 16].
The alignment-free clustering methods, BLSOM and SOM, have been successfully applied to phylogenetic classification of a large number of microbial sequences obtained by metagenome studies of environmental and clinical samples.
Our investigation confirmed the presence of microbial sequences in 31 (24%) of 131 CSF samples; 25 were identified by MassTag PCR.
As expected, although a minority of microbial sequences is present, >85% of the sequences generated from the termite gut tissue are homologous to known genes previously sequenced from insects or from other invertebrates.
For example, in three separate studies 3 Gb of microbial sequences were generated from fecal samples of only 33 individuals from the USA or Japan [ 2, 29, 37].
The profile of microbial sequences detected is almost certainly influenced by the composition of the wider microbiome, particularly in the gut.
These results perhaps provide a line of preliminary evidence for the presence of microbial sequences in these lepidopteran genomes, possibly by horizontal transfer.
Recognition of these microbial sequences is mediated by a member of the TLR family, namely TLR9.
We therefore filtered the assembled contigs based on G+C content, coverage, and sequence homology, in order to minimize the mis-annotation of microbial sequences as V. destructor, as well as to identify novel microbes of interest.
