Daniel R. Mende

Keio University — Japan

Environmental Science · Physical Sciences

43h-index38.9kcitations133works7.52yr avg
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Research Topics

Microbial Community Ecology and Physiology(45), Genomics and Phylogenetic Studies(43), Gut microbiota and health(26), Bacteriophages and microbial interactions(12), Marine and coastal ecosystems(9)

Publications131 total

proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes
Nucleic Acids Research·2025· 1 citedOpen Access
Microbiota-derived indole metabolites inhibit rotavirus infection <i>in vitro</i> and <i>in vivo</i> and in human infants
2025
Hidden but discoverable diversity in the global microbiome
2025· 4 citedOpen Access
Unique ecology of co-occurring functionally and phylogenetically undescribed species in the infant oral microbiome
2025Open Access
Dietary patterns in Tanzania’s transitioning rural and urban areas
Journal of Health Population and Nutrition·2025· 6 citedOpen Access
Identification of specific microbiota members that induce beige fat biogenesis in response to dietary cues
2024Open Access
The mOTUs online database provides web-accessible genomic context to taxonomic profiling of microbial communities
Nucleic Acids Research·2024· 27 citedOpen Access
Systematic review of associations between gut microbiome composition and stunting in under-five children
npj Biofilms and Microbiomes·2024· 24 citedOpen Access
FAIR compliant database development for human microbiome data samples
Frontiers in Cellular and Infection Microbiology·2024· 7 citedOpen Access
Disentangling top-down drivers of mortality underlying diel population dynamics of Prochlorococcus in the North Pacific Subtropical Gyre
Nature Communications·2024· 13 citedOpen Access
Extra-intestinal pathogenic lineages of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli are associated with prolonged ESBL gene carriage
Access Microbiology·2024· 7 citedOpen Access
mOTUs3 - genome metadata
Zenodo (CERN European Organization for Nuclear Research)·2023Open Access
mOTUs3 - genome metadata
Zenodo (CERN European Organization for Nuclear Research)·2023Open Access
Extraintestinal pathogenic lineages of extended-spectrum β-lactamase (ESBL)-producing E. coli are associated with prolonged ESBL gene carriage
2023Open Access
PA-836 Antimicrobial resistance patterns and molecular characterisation of shigella isolates from under-five children in Zambia
2023· 1 citedOpen Access
SPIRE: a Searchable, Planetary-scale mIcrobiome REsource
Nucleic Acids Research·2023· 77 citedOpen Access
Impact of antibiotics on gut microbiome composition and resistome in the first years of life in low- to middle-income countries: A systematic review
PLoS Medicine·2023· 47 citedOpen Access
Extraintestinal pathogenic lineages of extended-spectrum β-lactamase (ESBL)-producing E. coli are associated with prolonged ESBL gene carriage
2023Open Access
mOTUs database
2023Open Access
Reviewer response for version 1
2023Open Access
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Frequent Co-authors

Peer Bork(29), Shinichi Sunagawa(22), Edward F. DeLong(13), Georg Zeller(12), Manimozhiyan Arumugam(10), Jaime Huerta‐Cepas(9), Luís Pedro Coelho(9), Thomas Schmidt(8), Julien Tap(7), Ivica Letunić(7), Alessio Milanese(7), Hans‐Joachim Ruscheweyh(7), Jeroen Raes(6), Damian Szklarczyk(6), Sofia K. Forslund(6), Jens Roat Kultima(6), Lucas Paoli(6), John M. Eppley(6), Takuji Yamada(5), Henrik Bjørn Nielsen(5)