Daniel R. Mende

Research Statement

AI generated · Oct 29, 2026

Daniel R. Mende's indexed work centers on accurate, universal delineation of prokaryotic species, a methodological thread that runs from his first-author framework for species-level taxonomy through to the proGenomes resources for consistent functional and taxonomic annotation of prokaryotic genomes, which he led across successive releases and later oversaw as senior author. A related line examines how environmental gradients structure microbial communities, including environmental drivers of a genomic transition zone in the ocean's interior and persistent core populations shaping the water column microbiome of the North Pacific Subtropical Gyre. Earlier first-author work on assessing metagenomic assembly with simulated sequencing data established benchmarking practices that recur throughout this body of research. Beyond these, Mende contributed as a middle author to large consortia, including the human gut microbial gene catalogue and the global ocean microbiome structure and function survey, and to eggNOG orthology resources alongside Damian Szklarczyk. His most recent senior-author work extends into host-associated ecology, addressing priority effects and milk glycan metabolism in infant gut Bifidobacterium dynamics. No software, datasets, grants, or patents are indexed beyond these publications. Taken together, the arc runs from taxonomic and assembly methodology toward large-scale, consistently annotated genomic resources and their application to environmental and host-associated microbiomes.

Most Cited Works

A human gut microbial gene catalogue established by metagenomic sequencing

Junjie Qin, Ruiqiang Li, Jeroen Raes, Manimozhiyan Arumugam, Kristoffer Solvsten Burgdorf, Chaysavanh Manichanh, Trine Nielsen, Nicolas Pons, Florence Levenez, Takuji Yamada, Daniel R Mende, Junhua Li, Junming Xu, Shaochuan Li, Dongfang Li, Jianjun Cao, Bo Wang, Huiqing Liang, Huisong Zheng, Yinlong Xie, Julien Tap, Patricia Lepage, Marcelo Bertalan, Jean-Michel Batto, Torben Hansen, Denis Le Paslier, Allan Linneberg, H Bjørn Nielsen, Eric Pelletier, Pierre Renault, Thomas Sicheritz-Ponten, Keith Turner, Hongmei Zhu,

Research Areas

Microbial Community Ecology and PhysioloGenomics and Phylogenetic StudiesGut microbiota and healthEnvironmental DNA in Biodiversity StudieMarine and coastal ecosystems

Affiliations & Education

Education

2009–2013
European Molecular Biology Laboratory(DE)
PhD · SCB
2004–2008
Goethe-Universitat Frankfurt am Main(DE)
Diplom-Bioinformatik · Computer Science / Biology

Employment

2025–present· now
Keio University(JP)

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Sources

Research Statement

Most Cited Works

A human gut microbial gene catalogue established by metagenomic sequencing

Research Areas

Affiliations & Education

Education

Employment

Enterotypes of the human gut microbiome

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

Structure and function of the global ocean microbiome

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences