Neighbour-group-based phenotype predictions
This approach identifies reference bacteria that are closely related to the MAGs in this study and uses these high-quality reference genomes for phenotype predictions that are robust to variation in MAG quality. Examination of groups of closely related reference organisms suggested that close phylogenetic neighbour genomes tend to either possess or lack an entire pathway variant, whereas more distant neighbours (such as other neighbour groups) often carry more divergent pathway variants that specify the same phenotype. We used this observation to develop heuristics that minimize false-negative phenotype assignments emerging from the other two prediction strategies. We compiled a set of neighbour groups comprising MAGs and closely related reference genomes (Mash/MinHash