Estimated bacterial genome proportions. For the two simulated metagenomes (100 and 1,000 bacterial genomes, respectively), colored de Bruijn graphs were utilized to estimate the nucleotide proportion of each bacterial genome in its containing metagenome. Genome proportions in metagenomes followed a power law. Black lines show the expected nucleotide proportion for bacterial genomes while blue points represent proportions measured by colored de Bruijn graphs. (A) For the 100-genome metagenome, only two bacterial genomes were not correctly measured (2.0%), namely Methanococcus maripaludis X1 and Serratia AS9. Methanococcus maripaludis X1 was not detected because it was duplicated in the dataset as Methanococcus maripaludis XI, thus providing zero uniquely colored k-mers. Serratia AS9 was not detected because it shares almost all its k-mers with Serratia AS12. (B) For the 1,000-genome metagenome, 4 bacterial genomes were overestimated (0.4%) while 20 were underestimated (2.0%). These errors were due to highly similar bacterial genomes, hence they did not provide uniquely colored k-mers. This problem can be alleviated either by using a curated set of reference genomes or by using a taxonomy. The remaining 976 bacterial genomes had a measured proportion near the expected value.
Boisvert et al. Genome Biology 2012 13:R122 doi:10.1186/gb-2012-13-12-r122