Abstract:
:Metagenomic sequencing has greatly improved our ability to profile the composition of environmental and host-associated microbial communities. However, the dependency of most methods on reference genomes, which are currently unavailable for a substantial fraction of microbial species, introduces estimation biases. We present an updated and functionally extended tool based on universal (i.e., reference-independent), phylogenetic marker gene (MG)-based operational taxonomic units (mOTUs) enabling the profiling of >7700 microbial species. As more than 30% of them could not previously be quantified at this taxonomic resolution, relative abundance estimates based on mOTUs are more accurate compared to other methods. As a new feature, we show that mOTUs, which are based on essential housekeeping genes, are demonstrably well-suited for quantification of basal transcriptional activity of community members. Furthermore, single nucleotide variation profiles estimated using mOTUs reflect those from whole genomes, which allows for comparing microbial strain populations (e.g., across different human body sites).
journal_name
Nat Communjournal_title
Nature communicationsauthors
Milanese A,Mende DR,Paoli L,Salazar G,Ruscheweyh HJ,Cuenca M,Hingamp P,Alves R,Costea PI,Coelho LP,Schmidt TSB,Almeida A,Mitchell AL,Finn RD,Huerta-Cepas J,Bork P,Zeller G,Sunagawa Sdoi
10.1038/s41467-019-08844-4subject
Has Abstractpub_date
2019-03-04 00:00:00pages
1014issue
1issn
2041-1723pii
10.1038/s41467-019-08844-4journal_volume
10pub_type
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