ena-STUDY-UNIVERSITY OF CALGARY-09-03-2017-03:27:42:004-104
Quantification of mock microbial communities with metagenomes, 16S rRNA gene amplicons and metaproteomics
In this study we compared methods for quantifying taxonomic composition of microbial communities. The compared methods included metagenomics, 16S rRNA amplicon sequencing and metaproteomics. This ENA study contains the metagenomic and the 16S rRNA amplicon data. The metaproteomic data is available from ProteomeXchange via the PRIDE repository(PXD006118). For the comparison of the methods we analyzed three types of mock communities with all three methods. The communities contain between 28 to 32 species and strains of bacteria, archaea, eukaryotes and bacteriophage. For each community type 4 biological replicate communities were generated. All four replicates were analyzed by 16S rRNA sequencing. Three replicates of each community type were analyzed with metagenomics. The "C" type communities have same cell/phage particle number for all community members (C1 to C4). The "P" type communities have the same protein content for all community members (P1 to P4). The "U" (uneven) type communities cover a large range of protein amounts and cell numbers (U1 to U4). The 16S rRNA libraries were sequenced twice in independent runs. The prefixes "rep1_" and "rep2_" indicate the two individual runs. The 16S rRNA read files without prefix are rep1 and rep2 merged.
In this study we compared methods for quantifying taxonomic composition of microbial communities. The compared methods included metagenomics, 16S rRNA amplicon sequencing and metaproteomics. This ENA study contains the metagenomic and the 16S rRNA amplicon data. The metaproteomic data is available from ProteomeXchange via the PRIDE repository(PXD006118). For the comparison of the methods we analyzed three types of mock communities with all three methods. The communities contain between 28 to 32 species and strains of bacteria, archaea, eukaryotes and bacteriophage. For each community type 4 biological replicate communities were generated. All four replicates were analyzed by 16S rRNA sequencing. Three replicates of each community type were analyzed with metagenomics. The "C" type communities have same cell/phage particle number for all community members (C1 to C4). The "P" type communities have the same protein content for all community members (P1 to P4). The "U" (uneven) type communities cover a large range of protein amounts and cell numbers (U1 to U4). The 16S rRNA libraries were sequenced twice in independent runs. The prefixes "rep1_" and "rep2_" indicate the two individual runs. The 16S rRNA read files without prefix are rep1 and rep2 merged.