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SEMINAR:Predictive Genomics-based Metabolic Profiling of Human Gut...

Speaker: Dmitry Rodionov, Sanford Burnham Prebys Medical Discovery Institute, USA

Title: Predictive Genomics-based Metabolic Profiling of Human Gut Microbiota

Date/Time: 22 May 2023 / 10:40 – 11:30

Place: FENS G029 (Physical Only)

Abstract: Prediction of metabolic potential of the human gut microbiome (HGM) is important for understanding of the influence of diet and HGM-generated metabolites on human health. We used the concept of metabolic phenotypes of reference HGM genomes to develop the phenotype profiler method for functional prediction of metagenomics datasets. Our approach is based on a detailed reconstruction of metabolic pathways that determine major phenotypes of HGM bacteria including capabilities to synthesize essential vitamins and amino acids, degrade polysaccharides (dietary fiber) and further utilize the released mono- and oligo-saccharides, and finally to produce short-chain fatty acids (SCFAs). The major SCFAs, namely, acetate, butyrate, and propionate, are synthesized by the gut microbes and are essential for host physiology. Using the SEED genomic platform, we established genomic signatures for these metabolic pathways and classified all studied HGM species (>800 species represented by >2,800 genomes) according to their simplified binary phenotypes (>100 metabolic phenotypes). The obtained Binary Phenotype Matrix (BPM) allowed us to calculate Community Phenotype Index (CPI) as community-wide fractional representation of binary metabolic phenotypes projected over taxonomic abundance profiles of the analyzed metagenomic samples. The predictive metabolic phenotype profiling was further applied to characterize the 16S rRNA amplicon-based and WGS metagenomic-based taxonomic profiles of fecal microbiomes from several major studies with available metadata on age, diet, etc. As results, we report altered metabolic capabilities of gut microbiomes from certain population cohorts and link them to changes in abundances of specific microbial taxa that possess these metabolic phenotypes.

Bio:Dmitry Rodionov holds a Master of Science (MS) in Biophysics from Moscow Engineer Physics University, and a PhD in Molecular Biology from Genetics Research Centre in Moscow, Russia. He has in-depth knowledge of bioinformatics and has made significant computational contributions to the field of microbial genomics and systems biology. Dmitry Rodionov has been involved in the development and application of bioinformatics approaches to the reconstruction of metabolic pathways and regulatory networks in microbial genomes. He pioneered the use of comparative genomics workflows and databases for transcriptional regulatory network inference and metabolic pathway reconstruction. His research focuses on several aspects, such as identifying binding sites for transcription factors, studying the evolution of metabolic pathways in archaea, and reconstructing riboswitch-mediated regulatory networks in bacterial genomes. Dmitry Rodionov has also been a leader in capturing knowledge of microbial metabolic pathways and applying it to uncharacterized bacterial species. In addition, he has developed bioinformatics pipelines for annotation of microbial genomes and metagenomically assembled genomes. With his expertise and experience, Dmitry Rodionov is well equipped to make significant contributions to research projects in comparative genomics, metabolic reconstruction, functional gene annotation, transcriptional networks, and metagenomics.