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Metagenomic species profiling using universal phylogenetic marker genes


To quantify known and unknown microorganisms at species-level resolution using shotgun sequencing data, we developed a method that establishes metagenomic operational taxonomic units (mOTUs) based on single-copy phylogenetic marker genes. Applied to 252 human fecal samples, the method revealed that on average 43% of the species abundance and 58% of the richness cannot be captured by current reference genome–based methods. An implementation of the method is available at

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Figure 1: Phylogenetic marker gene–based mOTUs.
Figure 2: Phylogenetic analysis of mOTU linkage groups.
Figure 3: Performance and application of mOTU linkage groups.

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We thank members of the European Molecular Biology Laboratory Information Technologies core facility and Y. Yuan for managing the high-performance computing resources and the members of the Bork group for fruitful discussions. This work was supported by funding from European Molecular Biology Laboratory, the European Community's Seventh Framework Programme via the MetaHIT (HEALTH-F4-2007-201052) and International Human Microbiome Standards, (HEALTH-F4-2010-261376) grants, The Novo Nordisk Foundation, The Lundbeck Foundation, institutional funding by the Heidelberg Institute for Theoretical Studies and Deutsche Forschungsgemeinschaft grants STA 860/2 and STA 860/3, the Metagenopolis ANR-11-DPBS-0001 grant, and the European Research Council Advanced Grants (MicrobesInside and CancerBiome grant agreement numbers 250172 and 268985 to W.M.d.V. and P.B., respectively).

Author information

Authors and Affiliations



P.B. and S.S. conceived the study, S.S., D.R.M., G.Z., F.I.-C., S.A.B., M.A., J.T. and A.S. designed and performed the analyses, S.S., D.R.M., G.Z., J.R.K., L.P.C. and J.L. developed and implemented the program, O.P., F.G., J.D. and J.W. provided data, S.S., D.R.M., G.Z. and P.B. wrote the manuscript, and M.A., J.T., H.B.N., S.R., O.P., F.G., W.M.d.V., S.D.E. and A.S. gave conceptual advice and revised the manuscript.

Corresponding author

Correspondence to Peer Bork.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–8, and Supplementary Tables 4, 5 and 7 (PDF 2053 kb)

Supplementary Table 1

Prokaryotic reference genomes used in this study. (XLSX 159 kb)

Supplementary Table 2

Summary of benchmark results for speed and accuracy of marker gene identification. (XLSX 13 kb)

Supplementary Table 3

Metagenomic data sets used in this study. (XLSX 21 kb)

Supplementary Table 6

Summary of mOTU linkage groups with taxonomic annotations. (XLSX 67 kb)

Supplementary Software

mOTU profiling tool. (ZIP 86115 kb)

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Sunagawa, S., Mende, D., Zeller, G. et al. Metagenomic species profiling using universal phylogenetic marker genes. Nat Methods 10, 1196–1199 (2013).

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