My research focusses on two areas:

(1) host-microbe interactions in various non-model organisms

(2) climate change microbiology with a focus on aquatic systems

In the first, I am in interested in the role of microorganisms in habitat acclimation and nutrition in the sponge meta-organism, the genetic mechanisms of adaptation facilitating invertebrate colonization at the marine/land boundary, and the role and evolutionary history of the enteric microbiome in herbivorous surgeonfish and how they impact reef biogeochemical processes.

In the second area of my research, I am interested in the eco-evolutionary responses of aquatic microorganisms to environmental change, and in particular the link between ecosystem service provision and microbial biodiversity in the context of climate change. In both research areas, I extensively use large-scale metagenomes and other omics data coupled with cutting-age computational biology approaches, including machine learning techniques, to gain insights into future biodiversity trends and to elucidate functional responses of keystone species in an ecosystem constrained by global climate change.

Education

2024 Diploma in Data Science (Machine Learning), University of Sorbonne, France

2005–2008 PhD (Microbial Ecology), MPI for Terrestrial Microbiology, Germany

2002–2004 MSc. (Microbiology), Jomo Kenyatta University of Agriculture and Technology, Kenya

1997–2002 Bachelor of Education, Kenyatta University, Kenya

Academic Positions

2018–2023 Junior Group Leader, Leibniz Institute DSMZ, Braunschweig, Germany

2016 –2018 Senior bioinformatics research scientist, KAUST, Saudi Arabia

2010–2016 Research Scientist, Red Sea Research Center, KAUST, Saudi Arabia

2008–2010 Postdoc, MPI for Terrestrial Microbiology, Marburg, Germany

• ISME12 travel grant from the International Max Planck Research School (Germany)
• Doctoral fellowship from the German Academic Exchange Service (DAAD)
• Internship fellowship from the International Max Planck Research School, Germany

• (2021–2024) - 246,995 € research grant, the German Research Foundation (DFG) as Co-Principal investigator
• (2020–2024) - 253,000 € research grant, the German Research Foundation (DFG) as Principal investigator

Managing Board Member for Peer Community in Microbiology (PCI Microbiology)

Associate Editor for Marine Biology and Frontiers Microbiology

[* corresponding author; ^† co-first authors]

[1]. Ngugi DK*, Salcher MM, Andrei A-S, Ghai R, Klotz F, Chiriac M-C, Ionescu D, Buesing P, Grossart H-P, Xing P, Priscu JC, Alymkulov S, and Pester M. (2023). Postglacial adaptations enabled colonization and quasi-clonal dispersal of ammonia-oxidizing archaea in modern European large lakes. Science Advances, 9:adc9392.

[2]. Ngugi DK*, Silvia GA, Sánchez P, Gasol JM, Agusti S, Karl DM, and Duarte CM. (2023). Abiotic selection of microbial genome size in the global ocean. Nature Communication, 14: 1384.

[3]. Fusi M^†, Ngugi DK^†, Marasco R, Booth JM, Cardinale M, Sacchi L, Clamenti E, Garuglieri E, Foderlianakis S, Michoud G, and Daffonchio D. (2023). Gill bacterial symbionts are homogenously selected in bimodal mangrove crabs to sustain host-terrestrialisation process. Microbiome, 11:1–21.

[4]. Diao M. Dyksma S, Koeksoy E, Ngugi DK, Anantharaman K, Loy A, and Pester M. (2023). Global diversity and inferred ecophysiology of microorganisms with the potential for dissimilatory sulfate/sulfite reduction. FEMS Microbiology Reviews, 47:fuad058.

[5]. Pogoreutz C, Oakley CA, Raedecker N, Cárdenas A, Perna G, Peng L, Davy SK, Ngugi DK, and Voolstra CR. (2022). Coral holobiont cues prime Endozoicomonas to a symbiotic lifestyle. The ISME Journal, 16:1883–1895.

[6]. Klotz F, Kitzinger K, Ngugi DK, Buesing P, Littmann S, Kuypers MMM, Schink B., and Pester M. (2022). Quantification of archaea-driven freshwater nitrification from single cell to ecosystem levels. The ISME Journal, 16:1647–1656.

[7]. Michoud G^†, Ngugi DK^†, Barozzi A, Merlino G, Calleja ML, Delgardo-Huertas A, Moran XAG, and Daffonchio D. (2021). Fine-scale metabolic discontinuity in a stratified prokaryote microbiome of a Red Sea deep halocline. The ISME Journal, 15:2351–2365.

[8]. Duarte CM^†*, Ngugi DK^†*, Alam I^†, Pearman J, Kamau A, Eguiluz VM, Gojobori T, Acinas S, Gasol JM, Bajic VB, and Irigoien X. (2020). Sequencing effort dictates gene discovery in marine microbial metagenomes. Environmental Microbiology, 22:4589–4603.

[9]. Ngugi DK*, Ziegler M, Duarte CM, and Voolstra CR. (2020). Genomic blueprint of glycine betaine metabolism in coral metaorganisms and their contribution to reef nitrogen budgets. iScience, 23:101120.

[10]. Ngugi DK^†*, Miyake S^†, Cahill MJ, Vinu M, Hackmann TJ, Blom J, Tietbohl M., Berumen M., and Stingl U. (2017). Genomic diversification of giant enteric symbionts reflects host dietary lifestyle. PNAS, 114:E7592–E7601.

Prof. Dr. Michael Pester, Leibniz Institute DSMZ (German Collection of Microorganisms and Cell Cultures), Braunschweig, Germany

Prof. Dr. Hans-Peter Grossart, Leibniz Institute for Freshwater Ecology and Inland Fisheries, Berlin, Germany

Dr.  Michaela M. Salcher, Institute of Hydrobiology, Biology Center CAS, Czechia

Dr. Adrian Stefan-Andrea, Limnological Station, University of Zurich, Switzerland

Prof. Dr. Andreas Brune, MPI for Terrestrial Microbiology, Marburg, Germany

Prof. Carlos M. Duarte, King Abdullah University of Science & Technology, Saudi Arabia

Dr. Silvia G. Acinas, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Spain

Prof. Dr. Christian Voolstra, University of Konstanz, Germany

Prof. Dr. Sarahi L. Garcia, University of Oldenburg, Oldenburg, Germany