• Research

Falk Hildebrand

Group Leader

Falk Hildebrand


Contact details:

  • +44 1603 255 359



Falk Hildebrand is a bioinformatician with a passion for microbial ecosystems, bacterial evolution and developing computational systems to tackle these subjects in a combined perspective. Falk joined Earlham Institute in early 2019, where his new Hildebrand Group (also at Quadram Institute) will be developing metagenomic tools for tracking bacterial strains at high resolutions, to predict their genomic capabilities and explore their associations to diseases.

During his early career, Falk was working at the University of Constance (Germany) and the University of Sussex (UK) on bacterial evolution and tracking outbreaks of pathogens through following changes in their genomes. Moving from a genome centric view to a metagenomic view of whole microbial ecosystems, he worked during his PhD at the University of Brussels (Belgium) on bacterial associations to complex diseases such as IBD, obesity and Diabetes. For this, Falk developed bioinformatic pipelines to process 16S data (LotuS) as well as the statistical tools.

During his postdoc at EMBL Heidelberg (Germany), Falk continued his research on association to the human microbiome of complex diseases such as Diabetes and Parkinson’s disease, among others. His interests soon developed to track strains in the metagenomic datasets, as well as de novo assembling genomes from metagenomes. These techniques are mostly applied to the gut microbiome of mammals. Another interest of his is environmental metagenomics. For example, in 2018 he proved that in soils more fungi are usually connected to more antibiotic resistance in bacteria, and this is true on a local but also global scale.

Developing specialised algorithms that help answer complex questions on large biological datasets is the key ingredient for Falk’s scientific work.


Antibiotics-induced monodominance of a novel gut bacterial order

Hildebrand F, Moitinho-Silva L, et al. (2018) BMJ Journals - Gut (January 2019)

Towards the structure and function of the global topsoil microbiome

Bahram M, Hildebrand F, Forslund K, et al. (2018) Nature 560 (233-237)

Enterotypes in the landscape of gut microbial community composition

Costea P, Hildebrand F, Arumugam M, Baeckhed F et al. (2018) Nature Microbiology 3(1): 8-16

Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota

Forslund K, Hildebrand F, Nielsen T et al. (2015) Nature 528(7581): 262-266

Inflammation-associated enterotypes, host genotype, cage and inter-individual effects drive gut microbiota variation in common laboratory mice

Hildebrand F, Nguyen TLA, Brinkman B et al. (2013) Genome Biology 14(1):R4

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