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Microbial abundance, activity and population genomic profiling with mOTUs2

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Item Type:Article
Title:Microbial abundance, activity and population genomic profiling with mOTUs2
Creators Name:Milanese, A. and Mende, D.R. and Paoli, L. and Salazar, G. and Ruscheweyh, H.J. and Cuenca, M. and Hingamp, P. and Alves, R. and Costea, P.I. and Coelho, L.P. and Schmidt, T.S.B. and Almeida, A. and Mitchell, A.L. and Finn, R.D. and Huerta-Cepas, J. and Bork, P. and Zeller, G. and Sunagawa, S.
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).
Keywords:Algorithms, Cluster Analysis, Computational Biology, DNA Sequence Analysis, Essential Genes, Gene Expression Profiling, Genetic Markers, Genome, Host Microbial Interactions, Metagenomics, Microbiota, Molecular Sequence Annotation, Phylogeny, Sequence Alignment
Source:Nature Communications
ISSN:2041-1723
Publisher:Nature Publishing Group (U.K.)
Volume:10
Number:1
Page Range:1014
Date:4 March 2019
Official Publication:https://doi.org/10.1038/s41467-019-08844-4
PubMed:View item in PubMed

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