Fig. 5

Detection of differentially abundant taxa in low-/high-level-methane-emitting sheep rumen microbiomes. a A comparison between metagenomic profilers shows that mOTUs3 detected 131 differentially abundant species (q value <0.05 and an absolute generalized fold change > 1; indicated by dotted lines) between low- and high-level methane-emitting sheep, while MetaPhlAn3 and Bracken detected nine and two species, respectively. Most of the species detected by mOTUs were represented by ext-mOTUs only, demonstrating the added value of reference genome-independent profiling enabled by mOTUs3. b Archaeal mOTUs present in the sheep rumen microbiome (highlighted in gray) were phylogenetically contextualized with Methanobrevibacter spp. and Methanosphaera spp. represented by ref-mOTUs. All differentially abundant ext-mOTUs (middle panel) correspond to distinct yet undescribed Methanobrevibacter spp. as supported by all MG sequence identities (“MG identity [%]”, right panel) to the closest known reference genome being below the species-level cutoff of 96.5% (dotted vertical line)