Fig. 6
From: Simulating metagenomic stable isotope probing datasets with MetaSIPSim
Examples of MAG quality improvements achieved with metagenomic-SIP relative to conventional shotgun metagenomics for three target genomes of low abundance in the community. These examples are taken from the 50% G + C skewed (medGC) reference set sequenced at 5,000,000 reads. Genomes presented here are Clostridium stercorarium, Prevotella denticola, and Altererythrobacter ishigakiensis. a Percentage of each genome recovered in reads across 6 simulation trials in which community composition and 13C-labelling were varied randomly (T1 – T5); ‘con’ indicates the 12C-control, ‘L’ indicates a trail in which the organism was 13C-labeled. b Percentage of each genome recovered in contigs from the co-assembly of all 6 trials. c The NGA50 of the contigs from the co-assembly mapped to each genome. d The percentage of each genome recovered in a MAG bin. e The percentage each MAG bin that is contamination from other genomes. Note that we have no NGA50 for the shotgun metagenomics assembly of P. denticola as less than 50% of this genome was recovered from the co-assembly. Similarly, we recovered no bin mapping to P. denticola from the shotgun metagenome