Analysis of 16S rRNA metagenomic experiments

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.

Ezgi was born in Istanbul, Turkey. She studied Molecular Biology and Genetics at the Middle East Technical University, Ankara and received her B.Sc. in 2014. She continued her education at the faculty of Biology in the same university where she obtained her M.Sc. diploma in 2015.

Ezgi followed her interest for evolutionary biology and continued her studies at the Max Planck Institute for Evolutionary Biology in Germany, working within the Environmental Genomics group as PhD student.  She obtained her PhD degree in 2020.

Ezgi is currently working as a PostDoc in Hildebrand group. Her main interests are metagenomics data analysis and vertical transmission of microbial communities.

Joachim Fritscher studied Bioinformatics in his BSc and MSc. He got into metagenomics at the end of his MSc and wrote his thesis about a k-mer based taxonomic classifier for metagenomic reads using a protein reference.

Now Joachim is trying to use the k-mer based approach as well as other methods to improve the resolution of taxonomic classification and SNP calling to strain level. He's also striving to learn and apply new methods on biological data and making them performant with C++.