Sebastian Theobald
Technical University of Denmark
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Featured researches published by Sebastian Theobald.
Proceedings of the National Academy of Sciences of the United States of America | 2018
Inge Kjærbølling; Tammi Camilla Vesth; Jens Christian Frisvad; Jane L. Nybo; Sebastian Theobald; Alan Kuo; Paul Bowyer; Yudai Matsuda; Stephen J. Mondo; Ellen Kirstine Lyhne; Martin Engelhard Kogle; Alicia Clum; Anna Lipzen; Asaf Salamov; Chew Yee Ngan; Chris Daum; Jennifer Chiniquy; Kerrie Barry; Kurt LaButti; Sajeet Haridas; Blake A. Simmons; Jon K. Magnuson; Uffe Hasbro Mortensen; Thomas Ostenfeld Larsen; Igor V. Grigoriev; Scott E. Baker; Mikael Rørdam Andersen
Significance The genus of Aspergillus holds fungi relevant to plant and human pathology, food biotechnology, enzyme production, model organisms, and a selection of extremophiles. Here we present six whole-genome sequences that represent unexplored branches of the Aspergillus genus. The comparison of these genomes with previous genomes, coupled with extensive chemical analysis, has allowed us to identify genes for toxins, antibiotics, and anticancer compounds, as well as show that Aspergillus novofumigatus is potentially as pathogenic as Aspergillus fumigatus, and has an even more diverse set of secreted bioactive compounds. The findings are of interest to industrial biotechnology and basic research, as well as medical and clinical research. The fungal genus of Aspergillus is highly interesting, containing everything from industrial cell factories, model organisms, and human pathogens. In particular, this group has a prolific production of bioactive secondary metabolites (SMs). In this work, four diverse Aspergillus species (A. campestris, A. novofumigatus, A. ochraceoroseus, and A. steynii) have been whole-genome PacBio sequenced to provide genetic references in three Aspergillus sections. A. taichungensis and A. candidus also were sequenced for SM elucidation. Thirteen Aspergillus genomes were analyzed with comparative genomics to determine phylogeny and genetic diversity, showing that each presented genome contains 15–27% genes not found in other sequenced Aspergilli. In particular, A. novofumigatus was compared with the pathogenic species A. fumigatus. This suggests that A. novofumigatus can produce most of the same allergens, virulence, and pathogenicity factors as A. fumigatus, suggesting that A. novofumigatus could be as pathogenic as A. fumigatus. Furthermore, SMs were linked to gene clusters based on biological and chemical knowledge and analysis, genome sequences, and predictive algorithms. We thus identify putative SM clusters for aflatoxin, chlorflavonin, and ochrindol in A. ochraceoroseus, A. campestris, and A. steynii, respectively, and novofumigatonin, ent-cycloechinulin, and epi-aszonalenins in A. novofumigatus. Our study delivers six fungal genomes, showing the large diversity found in the Aspergillus genus; highlights the potential for discovery of beneficial or harmful SMs; and supports reports of A. novofumigatus pathogenicity. It also shows how biological, biochemical, and genomic information can be combined to identify genes involved in the biosynthesis of specific SMs.
Nature Genetics | 2018
Tammi Camilla Vesth; Jane L. Nybo; Sebastian Theobald; Jens Christian Frisvad; Thomas Ostenfeld Larsen; Kristian Fog Nielsen; Jakob Blæsbjerg Hoof; Julian Brandl; Asaf Salamov; Robert Riley; John Gladden; Pallavi Phatale; Morten Thrane Nielsen; Ellen Kirstine Lyhne; Martin Engelhard Kogle; Kimchi Strasser; Erin McDonnell; Kerrie Barry; Alicia Clum; Cindy Chen; Kurt LaButti; Sajeet Haridas; Matt Nolan; Laura Sandor; Alan Kuo; Anna Lipzen; Matthieu Hainaut; Elodie Drula; Adrian Tsang; Jon K. Magnuson
Aspergillus section Nigri comprises filamentous fungi relevant to biomedicine, bioenergy, health, and biotechnology. To learn more about what genetically sets these species apart, as well as about potential applications in biotechnology and biomedicine, we sequenced 23 genomes de novo, forming a full genome compendium for the section (26 species), as well as 6 Aspergillus niger isolates. This allowed us to quantify both inter- and intraspecies genomic variation. We further predicted 17,903 carbohydrate-active enzymes and 2,717 secondary metabolite gene clusters, which we condensed into 455 distinct families corresponding to compound classes, 49% of which are only found in single species. We performed metabolomics and genetic engineering to correlate genotypes to phenotypes, as demonstrated for the metabolite aurasperone, and by heterologous transfer of citrate production to Aspergillus nidulans. Experimental and computational analyses showed that both secondary metabolism and regulation are key factors that are significant in the delineation of Aspergillus species.De novo assembly of 23 Aspergillus section Nigri and 6 Aspergillus niger genome sequences allows for inter- and intraspecies comparisons and prediction of secondary metabolite gene clusters.
29th Fungal Genetics Conference | 2017
Tammi Camilla Vesth; Jane Lind Nybo Rasmussen; Sebastian Theobald; R.P. de Vries; Igor V. Grigoriev; Scott E. Baker; Mikael Rørdam Andersen
29th Fungal Genetics Conference | 2017
Jane Lind Nybo Rasmussen; Tammi Camilla Vesth; Sebastian Theobald; Inge Kjærbølling; Jens Christian Frisvad; Thomas Ostenfeld Larsen; Robert Riley; Asaf Salamov; Igor V. Grigoriev; Scott E. Baker; Mikael Rørdam Andersen
14th International Aspergillus Meeting | 2017
Sebastian Theobald; Tammi Camilla Vesth; Jane Lind Nybo Rasmussen; Inge Kjærbølling; Jens Christian Frisvad; Kristian Fog Nielsen; Thomas Ostenfeld Larsen; Igor V. Grigoriev; Asaf Salamov; Uffe Hasbro Mortensen; Scott E. Baker; Mikael Rørdam Andersen
european conference on computational biology | 2016
Sebastian Theobald; Tammi Camilla Vesth; Jane Lind Nybo Rasmussen; Inge Kjærbølling; Jens Christian Frisvad; Kristian Fog Nielsen; Thomas Ostenfeld Larsen; Igor V. Grigoriev; Asaf Salamov; Uffe Hasbro Mortensen; Scott E. Baker; Mikael Rørdam Andersen
european conference on computational biology | 2016
Inge Kjærbølling; Tammi Camilla Vesth; Jens Christian Frisvad; Jane Lind Nybo Rasmussen; Sebastian Theobald; Thomas Ostenfeld Larsen; Uffe Hasbro Mortensen; Mikael Rørdam Andersen
Archive | 2016
Jane Lind Nybo Rasmussen; Sebastian Theobald; Julian Brandl; Tammi Camilla Vesth; Mikael Rørdam Andersen
F1000Research | 2016
Tammi Camilla Vesth; Jane Lind Nybo Rasmussen; Sebastian Theobald; Inge Kjærbølling; Jens Christian Frisvad; Kristian Fog Nielsen; Ellen Kirstine Lyhne; Martin Engelhard Kogle; Alan Kuo; Robert Riley; R.P. de Vries; Igor V. Grigoriev; Uffe Hasbro Mortensen; Bernard Henrissat; Scott E. Baker; Mikael Rørdam Andersen
Cell Symposia: Technology. Biology. Data Science 2016 | 2016
Jane Lind Nybo Rasmussen; Tammi Camilla Vesth; Sebastian Theobald; Jens Christian Frisvad; Igor V. Grigoriev; Scott E. Baker; Mikael Rørdam Andersen