🦠Malte Rühlemann
(he/him)
Postdoctoral Researcher and Project PI
Professional Summary
I am a molecular biologist by training and a bioinformatician by practice. My research focuses on how gut microbial communities evolve, adapt to host environments, and contribute to chronic inflammatory disease. I combine large-scale human metagenomics, microbial genomics, host genetics, and ecological modeling to study host–microbiome systems across human populations and disease contexts.
Education
Dr. rer. nat. Biology
2014
2020
Kiel University, Germany
M.Sc. Medical Life Sciences
2012
2014
Kiel University, Germany
B.Sc. Life Science
2008
2011
University of Hannover, Germany
Interests
Human microbiome
Metagenomics
Host-microbiome interactions
Inflammatory bowel disease
Microbial ecology
Bioinformatics
Large-scale microbiome meta-analysis
📚 My Research
I am a molecular biologist by training and a bioinformatician by practice. My research focuses on how gut microbial communities evolve, adapt to host environments, and contribute to chronic inflammatory disease.
I combine large-scale human metagenomics, microbial genomics, host genetics, and ecological modeling to study host–microbiome systems across human populations and disease contexts. Current work includes international IBD meta-analysis in the EU-funded miGut-Health project, analysis of global human-associated microbiomes through the Global Microbiome Conservancy, and an independent DFG CRC1182 project on the functional consequences of the Prevotella-to-Bacteroides enterotype shift.
Methodologically, I work at the interface of microbiome bioinformatics, microbial genomics, pangenome analysis, functional annotation, statistical genetics, and computational ecology.
Recent Publications
(2026).
P1320 Longitudinal metagenomic profiling reveals early microbial changes during infliximab response in IBD..
Journal of Crohn’s and Colitis.
(2025).
Bacterial metabolite patterns of infants receiving multi-strain probiotics and risk of late-onset sepsis.
Cell Reports.
Featured Publications
Convergent genomic responses of human gut bacteria to variations in industrialization
To what extent gut bacteria respond to the distinct ecological pressures imposed by human lifestyle remains unclear. Here, we investigate how genomic adaptation in gut bacteria …
malte-ruehlemann
Functional host-specific adaptation of the intestinal microbiome in hominids
m.-c.-ruhlemann
Key Publications
(2025).
Industrialization drives convergent microbial and physiological shifts in the human metaorganism.
openRxiv.
(2025).
Convergent genomic responses of human gut bacteria to variations in industrialization.
bioRxiv.
(2024).
Functional host-specific adaptation of the intestinal microbiome in hominids.
Nature Communications.
(2022).
MAGScoT: a fast, lightweight and accurate bin-refinement tool.
Bioinformatics.
(2021).
Ecology impacts the decrease of Spirochaetes and Prevotella in the fecal gut microbiota of urban humans.
BMC Microbiology.
(2021).
Primate phageomes are structured by superhost phylogeny and environment.
Proceedings of the National Academy of Sciences.
(2021).
Genome-wide association study in 8,956 German individuals identifies influence of ABO histo-blood groups on gut microbiome.
Nature Genetics.
(2021).
Large-scale association analyses identify host factors influencing human gut microbiome composition.
Nature Genetics.
(2020).
Genomewide Association Study of Severe Covid-19 with Respiratory Failure.
New England Journal of Medicine.
(2020).
Genome-wide associations of human gut microbiome variation and implications for causal inference analyses.
Nature Microbiology.
(2019).
Comparative analysis of amplicon and metagenomic sequencing methods reveals key features in the evolution of animal metaorganisms.
Microbiome.
(2019).
Obese Individuals with and without Type 2 Diabetes Show Different Gut Microbial Functional Capacity and Composition.
Cell Host & Microbe.
(2018).
Epidermal lipid composition, barrier integrity, and eczematous inflammation are associated with skin microbiome configuration.
Journal of Allergy and Clinical Immunology.
(2018).
Sucrase-isomaltase 15Phe IBS risk variant in relation to dietary carbohydrates and faecal microbiota composition.
Gut.
(2017).
Application of the distance-based F test in an mGWAS investigating ?? diversity of intestinal microbiota identifies variants in SLC9A8 (NHE8) and 3 other loci.
Gut Microbes.
(2017).
Application of the distance-based F test in an mGWAS investigating beta diversity of intestinal microbiota identifies variants in SLC9A8 (NHE8) and three other loci..
Gut microbes.