I am a trained molecular biologist turned to data analyst.

Since 2023 I am a PostDoc in the newly established Groussin Poyet Lab - Host microbiome systems in health & disease @ IKMB, Kiel, the founders of the Global Microbiome Conservancy.

I finished my PhD in the lab of Andre Franke at the Institue of Clinical Molecular Biology (IKMB) in 2020 and stayed as PostDoc until end of 2022, with a brief 6-months guest stay at the lab of Jeroen Raes @ VIB / KU Leuven.

In addition, I am a guest scientist at the Insitute for Medical Microbiology and Hospital Epidemiology in the group of Marius Vital @ Hannover Medical School.

Reasearch Interest

I am a PostDoc and elected junior representative in the steering commitee of the DFG-funded Collaborative Research Centre 1182 - Origin and Function of Metagenomes.

My projects focus on the factors that shape the human intestinal microbiota, i.e. chronic disease, genetics, evolution and environmental factors. To achieve this, I am analyzing data generated by 16S rRNA gene amplicon sequencing and shotgun metagenomics, using existing methods and my own tools and pipelines.

I have given courses and workshops on different aspects of microbiome analysis 1, 2, 3.

Selected Publications

• Comparative metagenomics reveals host-specific functional adaptation of intestinal microbiota across hominids - Rühlemann et al., BioRXiv (2023). Preprint

• Host genetic factors related to innate immunity, environmental sensing and cellular functions are associated with human skin microbiota - Moitinho-Silva, …, Rühlemann, Nature Communications (2022). Full Text (Senior Author)

• MAGScoT: a fast, lightweight and accurate bin-refinement tool - Rühlemann et al., Bioinformatics (2022). Full Text

• Genome-wide association study in 8,956 German individuals identifies influence of ABO histo-blood groups on gut microbiome - Rühlemann et al., Nature Genetics (2021). Full Text

• Primate phageomes are structured by superhost phylogeny and environment - Gogarten, Rühlemann et al., PNAS (2021). Full Text

• Genomewide association study of severe Covid-19 with respiratory failure - The Severe Covid-19 GWAS Group, New England Journal of Medicine (2020). Full Text (Contributor to the Severe Covid-19 GWAS Group)

• Consistent Alterations in Faecal Microbiomes of Patients With Primary Sclerosing Cholangitis Independent of Associated Colitis - Rühlemann et al., AP&T (2019). Full Text

• Gut mycobiome of primary sclerosing cholangitis patients is characterised by an increase of Trichocladium griseum and Candida species - Rühlemann et al., Gut (2019). Full Text

• Comparative analysis of amplicon and metagenomic sequencing methods reveals key features in the evolution of animal metaorganisms - Rausch*, Rühlemann * et al., Microbiome (2019). Open Access

• Obese Individuals with and without Type 2 Diabetes Show Different Gut Microbial Functional Capacity and Composition - Thingholm, Rühlemann et al., Cell Host & Microbe (2019). Full Text

For a full and up-to-date list of publications go to PubMed, Google Scholar or visit my ResearchGate profile.

Grants, Awards, Invitations

• 2022 - Speaker @ Darwin Day Youtube (German)

• 2021 - DFG Sequencing Cost Grant: Identification of microbiome-host genetics associations using full-length 16S rRNA gene sequencing

• 2021 - SymbNET Kick-Off Meeting Youtube

• 2020 - KLS PostDoc Award (6,000 €).

• 2020 - CRC1182 Young Investigator Award (15,000 €).

• 2017 - ZMB Young Scientist Grant for PhD Students (10,000 €).

• 2017 - Selected abstract for a talk at the Life Science Nord student conference, Kiel.

Collaborations

• Part of the International MiBioGen Consortium, investigating microbiome-host genetics associations: 1 2

• Epidemiology of highly pathogenic microorganisms - The Leendertz Lab @ RKI 1 2

• DFG Clinical Research Unit 306: Primary Sclerosing Cholangitis @ UKE Hamburg 1

• Genomics and Metagenomics in Inflammatory Disorders @ Oslo University Hospital 1 2

• University Medicine Greifswald 1 2

• Group ‘Evolutionary Genomics’ @ MPI Plön 1 2

• Raes Lab @ VIB / KU Leuven. 1