EESS talk on "Mining the biosynthetic potential of the global ocean microbiome: from unsuspected taxa to enzymatic novelties"
Event details
| Date | 16.11.2021 |
| Hour | 12:15 › 13:15 |
| Speaker | Dr Shinichi Sunagawa, Professor, Institute of Microbiology, ETH Zurich |
| Location | Online |
| Category | Conferences - Seminars |
| Event Language | English |
Abstract:
Natural microbial communities are phylogenetically and metabolically diverse. This diversity encompasses, in addition to underexplored lineages a rich discovery potential for enzymes and biochemical compounds including ecologically and/or biotechnologically relevant ones. However, exploring microbial diversity in the environment to identify genomic pathways producing such compounds and assigning them to their hosts remains challenging. For example, the biosynthetic potential of microbes in the open ocean remains, despite their known taxonomic diversity, largely unexplored. We reconstructed >25,000 draft genomes, including from >2,500 uncharacterized species, from globally distributed ocean microbial communities, and combined them with ~10,000 genomes from cultivated and single cells. Mining this integrative data resource revealed ~40,000 putative biosynthetic gene clusters (BGCs), many from unknown phylogenetic groups. Among these, we discovered a BGC-rich lineage (Candidatus Eudoremicrobiaceae) that belongs to an uncultivated bacterial phylum and represents the most biosynthetically diverse microbes detected in the open oceans. By integrating metatranscriptomic data, we shed light on their ecology and hypothesize a niche-partitioning role for BGC products in environmental populations. Furthermore, we experimentally characterized cases of unusual enzymology and bioactive compound structure within selected biosynthetic pathways. Together, this work illustrates how microbiomics-driven strategies enable prospecting for yet unknown enzymes and natural products in underexplored microbial groups and environments.
Short biography:
Shinichi Sunagawa studied Biochemistry and Marine Ecology in Germany, and obtained his PhD in 2010 at the University of California, Merced, USA. Afer returning to Germany, he joined the European Molecular Biology Laboratory in Heidelberg as a postdoctoral fellow, and continued to work on ocean and human gut microbial communities as a research- and staff scientist. In 2016, he established the Microbiome Research Laboratory at the Institute of Microbiology at ETH Zürich, which combines bioinformatic and experimental approaches to integrate quantitative ‘meta-omics’ readouts with contextual information to study and the role of environmental microorganisms and mechanisms of host-microbial homeostasis. The group develops data resources and tools that have enabled the scientific community to (a) profile species-, gene- and single nucleotide variant-resolved compositions of microbial community genomes, (b) integrate metagenomics and metatranscriptomics data sets, and more recently, (c) predict inducible prophages. Currently, the group focuses on i) studying human gut microbial features in the context of acute myeloid leukemia and inborn metabolic diseases, ii) reconstructing microbial genomes from metagenomic data from diverse environments, and iii) exploring the global ocean microbiome for its phylogenomic diversity and biosynthetic potential.
Natural microbial communities are phylogenetically and metabolically diverse. This diversity encompasses, in addition to underexplored lineages a rich discovery potential for enzymes and biochemical compounds including ecologically and/or biotechnologically relevant ones. However, exploring microbial diversity in the environment to identify genomic pathways producing such compounds and assigning them to their hosts remains challenging. For example, the biosynthetic potential of microbes in the open ocean remains, despite their known taxonomic diversity, largely unexplored. We reconstructed >25,000 draft genomes, including from >2,500 uncharacterized species, from globally distributed ocean microbial communities, and combined them with ~10,000 genomes from cultivated and single cells. Mining this integrative data resource revealed ~40,000 putative biosynthetic gene clusters (BGCs), many from unknown phylogenetic groups. Among these, we discovered a BGC-rich lineage (Candidatus Eudoremicrobiaceae) that belongs to an uncultivated bacterial phylum and represents the most biosynthetically diverse microbes detected in the open oceans. By integrating metatranscriptomic data, we shed light on their ecology and hypothesize a niche-partitioning role for BGC products in environmental populations. Furthermore, we experimentally characterized cases of unusual enzymology and bioactive compound structure within selected biosynthetic pathways. Together, this work illustrates how microbiomics-driven strategies enable prospecting for yet unknown enzymes and natural products in underexplored microbial groups and environments.
Short biography:
Shinichi Sunagawa studied Biochemistry and Marine Ecology in Germany, and obtained his PhD in 2010 at the University of California, Merced, USA. Afer returning to Germany, he joined the European Molecular Biology Laboratory in Heidelberg as a postdoctoral fellow, and continued to work on ocean and human gut microbial communities as a research- and staff scientist. In 2016, he established the Microbiome Research Laboratory at the Institute of Microbiology at ETH Zürich, which combines bioinformatic and experimental approaches to integrate quantitative ‘meta-omics’ readouts with contextual information to study and the role of environmental microorganisms and mechanisms of host-microbial homeostasis. The group develops data resources and tools that have enabled the scientific community to (a) profile species-, gene- and single nucleotide variant-resolved compositions of microbial community genomes, (b) integrate metagenomics and metatranscriptomics data sets, and more recently, (c) predict inducible prophages. Currently, the group focuses on i) studying human gut microbial features in the context of acute myeloid leukemia and inborn metabolic diseases, ii) reconstructing microbial genomes from metagenomic data from diverse environments, and iii) exploring the global ocean microbiome for its phylogenomic diversity and biosynthetic potential.
Practical information
- General public
- Free
- This event is internal
Organizer
- EESS - IIE
Contact
- Prof. Tom Battin, SBER