Reference Genome Analysis
A set of analyses were run on 178 annotated microbial reference genomes, as described in A catalog of reference genomes from the human microbiome. Here we present figures & downloadable datasets resulting from these analyses. Where possible, analyses will be rerun periodically as additional reference genomes are submitted to NCBI with annotation, and updated datasets will be added.
Phylogenetic Analysis of 16S rDNA sequence of HMP Reference Genomes
Bacterial HMP Reference Genomes currently represent more than 10 phyla, 18 classes, and 24 orders. The trees shown here have been used by the HMP Consortium to identify regions of the tree of life underrepresented by HMP Reference Genomes, in order to drive selection of isolates to target for sequencing.
Phylogenetic trees were created using 16S rDNA sequences available from the greengenes Download directory.These files were last updated on March 20, 2010. HMP Collaborators: click here to submit your HMP Reference Genome 16S sequence to greengenes.
HMP_strains_16S_aligned.fasta.gz
contains NAST aligned 16S sequences from all HMP Reference Genomes from which 16S has been sequenced and deposited either to NCBI or directly to greengenes.
Human_assoc_strains_16S_aligned.fasta.gz
contains NAST aligned 16S sequences from cultured organisms with sequenced 16S rDNA in greengenes known to be associated with human hosts.
The 'All HMP Reference Genomes' tree was created using ~1800 16S rDNA sequences representing unique species. Bacterial HMP Reference Genomes are highlighted in blue, overlaid upon represented phyla color coded as indicated on each tree. These datasets have been further broken down by individual body site. Alignment files are available below.
Alignment Files: