The Gut Health Gurus Podcast Prof Philip Hugenholtz on Metagenomic Stool Analysis for Optimal Gut Health
Nov 14, 2019
56:05
We have a groundbreaking discussion with Prof Philip Hugenholtz co-founder of Microba, a company specialising in Metagenomic Stool Testing using DNA based sequencing to analyse the microbiome. We cover the history and application of DNA based sequencing to classify and identify micro-organisms, using the technology to improve health outcomes on a personalised level, the future prospects for precision medicine, IBD, what a healthy microbiome looks like and much more. Bio: Professor Hugenholtz is a microbiologist who has made contributions in the field of culture-independent analysis of microorganisms. He discovered and characterised numerous previously unrecognised major bacterial and archaeal lineages each with greater evolutionary divergence than animals and plants combined. He has participated in the development and application of metagenomics, the genome-based characterisation of microbiomes, which has revolutionised our understanding of microbial ecology and evolution. He has made several discoveries in environmental and clinical microbiology sometimes overturning decades of misdirected culture-based studies. Topics discussed:
- Phil’s Origin story
- Microbial Classification and Morphology
- The Development of DNA based sequencing technology
- Carl Woese- 16s rRNA - ribosomal RNA sequencing
- Did we evolve from ancient Archaea?
- Norm Pace- Application of 16s rRNA sequencing in Ecology
- Culture indépendant analytical techniques
- Craig Venter- Metagenomic Sequencing
- Blueprints for identifying bacteria
- Development of Sequencing Technology
- Discovery of Microbes
- Growing Microbes on plates
- What is the Greengenes reference database
- 16s rRNA genes identification vs Whole Genome shotgun sequencing (Metagenomics)
- Metagenomics, Big Data and health patterns
- The limitation of 16s rRNA technology- conserved genes
- Whole Genome Sequencing Resolution
- ITS gene and Fungal Classification
- Virus and Parasite Classification
- The Metagenomic workflow
- GTDB Database for Whole-genome sequencing
- Predicting IBD, IBS, Crohns
- Predicting response to drug response- Depression, Cancer
- The Gut Microbiome as an early warning system
- The future of Microbiome
- What does a healthy cohort’s gut microbiome look like?
- Discovery of new species
- Faecalibacterium prausnitzii
- Anti Inflammatory genes and properties
- The uniqueness of the gut microbiome
- Characterising IBD
- The impact of the immune system
- Opportunistic Pathogens- Clostridium difficile, Bilophila wadsworthia, Desulfovibrio, Helicobacter pylori
- Gut Metabolite production by microbes- e.g GABA (a neurotransmitter linked to depression) via KEGG
- The future of Gut Microbiome Testing
- Metabolomics
- Artificial Intelligence and Machine Learning Algorithms for health predictions
- Diet as a key driver of the microbiome
- Personalised Diet based on a microbiome profile
- Prebiotics and Probiotics and Precise Medicine
- Fibre and Butyrate Balance
- Phil’s top gut health tip
- Microbiome changes and improved mental health via diet and exercise