biostudies-literatureRuscheweyh HJBundesministerium für Bildung und ForschungEidgenössische Technische Hochschule ZürichSwiss National Science FoundationSwiss Federal Institute of Technology Zurich212https://www.ebi.ac.uk/biostudies/studies/S-EPMC9721005biostudies-literatureUnknown10(1)<h4>Background</h4>Taxonomic profiling is a fundamental task in microbiome research that aims to detect and quantify the relative abundance of microorganisms in biological samples. Available methods using shotgun metagenomic data generally depend on the deposition of sequenced and taxonomically annotated genomes, usually from cultures of isolated strains, in reference databases (reference genomes). However, the majority of microorganisms have not been cultured yet. Thus, a substantial fraction of microbial community members remains unaccounted for during taxonomic profiling, particularly in samples from underexplored environments. To address this issue, we developed the mOTU profiler, a tool that enables reference genome-independent species-level profiling of metagenomes. As such, it suppoMicrobiomeCultivation-independent genomes greatly expand taxonomic-profiling capabilities of mOTUs across various environments.PMC9721005205321_184955PHRT #2018-521031A537BPaoli LKarcher NRuscheweyh HJWirbel JMende DRZeller GMilanese AKeller MIClayssen QBork PSunagawa SfalseCultivation-independent genomes greatly expand taxonomic-profiling capabilities of mOTUs across various environments.<h4>Background</h4>Taxonomic profiling is a fundamental task in microbiome research that aims to detect and quantify the relative abundance of microorganisms in biological samples. Available methods using shotgun metagenomic data generally depend on the deposition of sequenced and taxonomically annotated genomes, usually from cultures of isolated strains, in reference databases (reference genomes). However, the majority of microorganisms have not been cultured yet. Thus, a substantial fraction of microbial community members remains unaccounted for during taxonomic profiling, particularly in samples from underexplored environments. To address this issue, we developed the mOTU profiler, a tool that enables reference genome-independent species-level profiling of metagenomes. As such, it suppo2022-01-01T00:00:00Z2022 Dec2025-04-05T15:41:30.971Z2025-02-19T04:34:10.515ZS-EPMC97210053646473110.1186/s40168-022-01410-z