Stephan C. Schuster
(Dr. rer. nat., Dr. habil.)
Currently a Research Director and Deputy Director at the Singapore Centre for Environmental Life Sciences Engineering (SCELSE) and a professor of Environmental Genomics at Nanyang Technological University, Singapore. As well, he is a founder of the GenomeAsia100K consortium, and acts as its scientific director.
Since the mid 1990’s, Schuster, together with collaborators at various academic and commercial international institutions, has demonstrated the transformative impact of genomics on the Life Sciences, in particular through next-generation sequencing technology (1,2,3).
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Nanyang Technological University
- Singapore Centre for Environmental Life Sciences Engineering
- GenomeAsia100K (NPO for human population sequencing)
Penn State University
- Center for Comparative Genomics and Bioinformatics
- Center for Infectious Disease Dynamics
Max-Planck-Institute for Developmental Biology
Max-Planck-Institute for Biochemistry
California Institute of Technology
Visiting positions (previous and present):
- Conjoint Professor, University New South Wales, Faculty of Medicine, Sydney, NSW, Australia
- Academic Guest, Institute of Evolutionary Medicine, University of Zurich, Switzerland
Schuster held group leader positions at the Max-Planck-Institute for Biochemistry (1994-2000) and the Max-Planck-Institute for Developmental Biology (2000-2004). In 2004, he accepted a Professorship of Molecular Microbial Ecology at Penn State University, in the Department of Biochemistry, Microbiology and Molecular Biology (BMMB). While at Penn State University (2005-2014), he was a member of the Center for Comparative Genomics and Bioinformatics, and the Center for Infectious Disease Dynamics.
In 2011, he became a founding member and Research Director at the Singapore Centre for Environmental Life Sciences Engineering (SCELSE, a MOE and NRF-funded Research Centre of Excellence, while holding a professorship in Environmental Genomics, in the School of Biological Sciences (SBS, at the Nanyang Technological University, Singapore (NTU. Schuster serves currently as a Deputy Director of SCELSE. In 2018 he was awarded the President’s Chair in Genomics at the Nanyang Technological University, Singapore.
In 2016, Schuster and Mahesh Pratapneni, with support from the Nanyang Technological University, EmergeVentures, Medgenome, and Macrogene, founded the GenomeAsia100K initiative, which sequences human genomes from Asian human populations.
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The impact of Schuster's work is noted via contributions in the fields of microbiology and genomics. He is included as one of the top 2% of most influential sceintists in 2019, according to an annually compiled list published by Stanford University.
Schuster is also recognized as a pioneer of the next-generation sequencing (NGS) era, after having published a landmark study in ScienceExpress on 20th December 2005 on “Metagenomics and Paleogenomics of mammoth remains,” which was re-published in Science magazine in spring 2006 (4). This study followed the company 454 Life Sciences’ demonstration of emulsion PCR / pyrosequencing technology in September of the same year (5) and as such represents the first example of addressing a biological problem with NGS technology. Applying the emerging NGS technology to ancient DNA research, together with the use of novel DNA reservoirs (hair) (6), eventually led to the field of paleo-population genomics. This enabled the comparison of 18 complete mammoth mitochondrial genomes (mt genome) to those of a single Indian and single African Elephant mt genome sequence (7). The largely expanded sample number of specimens from an extinct species allowed studying mammoth populations across a time frame of 50,000 years (7). Using the same approach, the first sequences of an extinct marsupial were generated, thereby demonstrating that now extinct species display a reduced genetic diversity before their demise (Tasmanian Tiger, (Thylacinus cynocephalus); Tasmanian devil, (Sarcophilus harrisii)) (8). The genomics analysis of museum specimens was a further adopted to avian species, such as the Moa (9), thereby opening new possibilities for the use of vast collections in national archives for paleo-population genomics studies. The emerging field was coined by Schuster as “Museomics”, referring to museum genomics (10,11,12).
The efforts of Schuster and his main collaborator, Webb Miller, eventually led to the first genome of an extinct species, the mammoth genome, published in Nature magazine in 2008 (13). The research triggered a large media echo globally (14), as news media began speculating about the imminent resurrection of a woolly mammoth (15). This undertaking has not been accomplished to date, despite various attempts to clone genetic material from permafrost frozen tissues or to edit genomes from Indian elephants (16).
In 2009, Schuster and Miller’s work sequencing the woolly mammoth genome was recognized in Time Magazine’s "Time100" awards (17,18).
The concept of analyzing extinct and extant genomes using NGS technologies were further explored by Schuster, Hayes, Miller and collaborators through a project that sequenced two Tasmanian Devil genomes (Cedric and Spirit) together with several museum specimens (19). This enabled the genotyping of the Tasmanian Devil population, thereby revealing the remaining population structure (20). The work eventually led to the concept of informed breeding for species conservation (21). Further work with collaborator Lindqvist included the sequencing of the first published polar bear genomes and unravelling the species’ recent population history (22,23).
In 2010, Schuster, Miller, Hayes and a global team of collaborators extended their genome analysis efforts to humans. In a study, they described the sequencing and comparison of genomes from Khoisan ethnicities, southern African hunter-gatherers in Namibia, as well as the genome of Archbishop Tutu, a representative of south African Xhosa and Motswana ethnicities (24). At the time of publication, only 8 human genomes had previously been published. Later population genetics analysis (2014) showed that the hunter-gatherer populations of Namibia, Botswana and South Africa represent the oldest living human ethnic groups, as well as being the largest population in terms of
effective population size throughout modern-human history (25).
Unravelling today’s remaining human genetic diversity is currently pursued by Schuster within the GenomeAsia100K project, which aims at mapping the entire Asian genetic diversity by sequencing 100,000 Asian human genomes. A special focus of the project is given on the remaining hunter-gatherer populations of Asia (26).
Before entering the NGS era, Schuster sequenced bacterial genomes, with Wolinella succinogenes being of note as the first genome of a bovine rumen bacterium (2003) (27), and Bdellovibrio bacteriovorus, representing the first bacterial predator genome (2004) (28). The novel understanding the organisms’ molecular tool kit, termed predatosome, a collection of proteases and lyases, renewed interests in this class of predatory bacteria as living antibiotics.
Parallel to his work on microbial genomes, Schuster and his team also contributed large-scale sequencing data of BAC clones to the zebrafish genome project led by the Sanger Center (29). At the beginning of his career, Schuster’s scientific interest was centered around bacterial motility and signal transduction (30,31).
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Current & Future Work
Based on his previous work in ancient DNA, Schuster advanced the fields of environmental genomics by developing ultra-low biomass protocols for NGS sequencing (32). By establishing robust and automatable protocols, he and his research team were able to conduct large environmental surveys on the microbiome of house and blowflies (33).
Within a 5-year MOE funded project, Schuster’s group developed an approach to sequence DNA from air with high temporal and taxonomic resolution. This led to the discovery of the diel cycle of airborne microorganisms, which revealed that tropical and temperate air is more similar in its microbial composition between days than between day and night times (34, Drautz). The translational outcome of this research included respiratory health studies of various clinical cohorts (35).
Work during Covid-19 pandemic
The methodological developments for studying the air microbiome presented an ideal starting point for environmental surveys during the Covid-19 pandemic, as it allowed Schuster’s team to deploy large numbers of air samplers in the Singapore built environment, while demonstrating that SARS-Cov-2 is detectable in air samples (36,37). The developed air surveillance technologies were instantly deployed in medical settings, leading to studies aimed at the protection of medical personnel (37,38,39).
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SCELSE Environmental Air Surveillance Unit
Indoor SARS-Cov2 environmental surveillance sampling
NTU Balcony Group Photo
The team standing with a full fleet of SASS air samplers after publication of "Microbial communities in the tropical air ecosystem follow a precise diel cycle" manuscript (34)
Outdoor Environmental Surveillance
Large cross-team sampling effort across a spacious park during Covid-19 safe re-opening
SCELSE-NTU Air Microbiome Team Photo
Gathering for a team photo after a shared holiday get-together
Awards & Honourable Mention
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- President’s Chair in Genomics - 2019, Nanyang Technological University, Singapore
- Raine Visiting Professorship – 2014, Awarded by The Raine Medical Research Foundation, University of Western Australia
- iDEA Challenge 2011 - Illumina's Data Excellence Award Conference, Overall Winner (academic), together with Fangqing Zhao and Ji Qi
- Science Magazine, Insights2010, (Breakthrough of the decade, ancient DNA 1 of 10 areas mentioned)
- Science Magazine, Breakthrough of the year 2010, top 10
- Time Magazine World's top 100 most influential people, 2009 (with Webb Miller)
- Time Magazine Top 10 Scientific Discoveries 2008
- Science Magazine, Breakthrough of the year 2008, top 10
- Science Magazine, Breakthrough of the year 2006, runner up
- Visiting Scholar, Department of Biology, Saint Joseph's University, November 2006
- Otto Hahn Medal, Max-Planck-Society, 1992
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Next-generation sequencing transforms today’s biology (2008)
Nature Methods 5(1):16-18. doi: 10.1038/nmeth1156. [Epub 2007 December 19].
Mardis, Elaine R. "The impact of next-generation sequencing technology on genetics." Trends in genetics 24, no. 3 (2008): 133-141. doi:10.1016/j.tig.2007.12.007.
Shendure, Jay, and Hanlee Ji. "Next-generation DNA sequencing." Nature biotechnology 26, no. 10 (2008): 1135-1145.
Metagenomics to paleogenomics: Large scale sequencing of mammoth DNA (2006, 2005)
H.N. Poinar, C. Schwarz, J. Qi, B. Shapiro, R.D.E. MacPhee, B. Buigues, A. Tikhonov, D.H. Huson, L.P. Tomsho, A. Auch., M. Rampp, W. Miller, S.C. Schuster.
Science 311:392-94; Science Express Reports 2005 Dec 20. doi: 10.1126/science.1123360.
Egholm, M., M. Margulies, W. E. Altman, S. Attiya, J. S. Bader, L. A. Bemben, J. Berka et al. "Genome sequencing in open microfabricated high density picoliter reactors." Nature 437 (2005): 376-380. DOI: 10.1038/nature03959.
Whole-genome shotgun sequencing of mitochondria from ancient hair shafts (2007)
M.T.P. Gilbert, L.P. Tomsho, S. Rendulic, M. Packard, D.I. Drautz, A. Sher, A. Tikhonov, T. Kuznetsova, P. Kosintsev, P.F. Campos, L. Dálen, T. Higham, M.J. Collins, A.S. Wilson, B. Buiges, P.G.P. Ericson, M. Germonpré, A. Götherström, P. Iacumin, V. Nikolaev, M. Nowak-Kemp, E. Willerslev, A. Lesk, J.R. Knight, G.P. Irzyk, C.S. Perbost, K.M. Fredrikson, T.T. Harkins, S. Sheridan, W. Miller, S.C. Schuster.
Science 317(5846):1927-30. doi: 10.1126/science.1146971.
Intraspecific Phylogenetic Analysis of Siberian Woolly Mammoths Using Complete Mitochondrial Genomes (2008)
M.T.P. Gilbert, J. Qi, C.H. Hsu, A.M. Lesk, L.P. Tomsho, S. Rendulic, M. Packard, D.I. Drautz, A. Ratan, P.F. Campos, A. Sher, A. Tikhonov, E. Willerslev, B. Buigues, L. Dalén, P.G.P. Ericson, M. Germonpré, A. Götherström, P. Iacumin, P. Kosintsev, T. Kuznetsova, V. Nikolaev, M. Nowak-Kemp, F. Shidlovskiy, J.R. Knight, G.P. Irzyk, C.S. Perbost, K.M. Fredrikson, T.T. Harkins, S. Sheridan, W. Miller, S.C. Schuster.
Proceedings of the National Academy of Sciences of the United States of America,
105(24):8327-32. doi: 10.1073/pnas.080231505. [Epub 2008 May 9]
Miller, W., Drautz, D. I., Janecka, J. E., Lesk, A. M., Ratan, A., Tomsho, L. P., ... & Schuster, S. C. (2009). The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus).
Genome research, 19(2), 213-220. doi: 10.1101/gr.082628.108.
Allentoft, Morten E., Stephan C. Schuster, Richard N. Holdaway, Marie L. Hale, Emma McLay, Charlotte Oskam, M. Thomas P. Gilbert, Peter Spencer, Eske Willerslev, and Michael Bunce. "Identification of microsatellites from an extinct moa species using high-throughput (454) sequence data." Biotechniques 46, no. 3 (2009): 195-200. doi: 10.2144/000113086.
Sequencing the Nuclear Genome of the Extinct Woolly Mammoth (2008)
W. Miller, D. Drautz, A. Ratan, B. Pusey, J. Qi, A.M. Lesk, L. Tomsho, M. Packard, F. Zhao, A. Sher, A. Tikhonov, B. Raney, N. Patterson, K. Lindblad-Toh, E.S. Lander, J.R. Knight, G.P. Irzyk, K.M. Fredrikson, T.T. Harkins, S. Sheridan, T. Pringle, S.C. Schuster.
Nature 456(7220):387-90. doi: 10.1038/nature07446.
Nicholls, Henry. "Darwin 200: Let's make a mammoth." Nature News 456, no. 7220 (2008): 310-314. doi: 10.1038/456310a.
Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil). (2011)
W. Miller, V. M. Hayes, A. Ratan, D. C. Petersen, N. E. Wittekindt, J. Miller, B. Walenz, J. Knight, J. Qi and F. Zhao.
Proceedings of the National Academy of Sciences 108(30):12348-12353. doi: 10.1073/pnas.1102838108.
Miller, Webb, Stephen J. Wright, Yu Zhang, Stephan C. Schuster, and Vanessa M. Hayes. "Optimization methods for selecting founder individuals for captive breeding or reintroduction of endangered species." In Biocomputing 2010, pp. 43-53. 2010. doi: 10.1142/9789814295291_0006.
Complete mitochondrial genome of a Pleistocene jawbone unveils the origin of polar bear. (2010)
C. Lindqvist, S. C. Schuster, Y. Sun, S. L. Talbot, J. Qi, A. Ratan, L. P. Tomsho, L. Kasson, E. Zeyl and J. Aars, W. Miller.
Proceedings of the National Academy of Sciences 107(11):5053-5057. doi: 10.1073/pnas.0914266107
Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change. (2012)
W. Miller, S. C. Schuster, A. J. Welch, A. Ratan, O. C. Bedoya-Reina, F. Zhao, H. L. Kim, R. C. Burhans, D. I. Drautz and N. E. Wittekindt.
Proceedings of the National Academy of Sciences 109(36):E2382-E2390. doi: 10.1073/pnas.1210506109
Complete Khoisan and Bantu genomes from southern Africa. (2010)
Stephan C. Schuster, Webb Miller, Aakrosh Ratan, Lynn P. Tomsho, Belinda Giardine, Lindsay R. Kasson, Robert S. Harris, Desiree C. Petersen, Fangqing Zhao, Ji Qi, Can Alkan, Jeffrey M. Kidd, Yazhou Sun, Daniela I. Drautz, Pascal Bouffard, Donna M. Muzny, Jeffrey G. Reid, Lynne V. Nazareth, Qingyu Wang, Richard Burhans, Cathy Riemer, Nicola E. Wittekindt, Priya Moorjani, Elizabeth A. Tindall, Charles G. Danko, Wee Siang Teo, Anne M. Buboltz, Zhenhai Zhang, Qianyi Ma, Arno Oosthuysen, Abraham W. Steenkamp, Hermann Oostuisen, Philippus Venter, John Gajewski, Yu Zhang, B. Franklin Pugh, Kateryna D. Makova, Anton Nekrutenko, Elaine R. Mardis, Nick Patterson, Tom H. Pringle, Francesca Chiaromonte, James C. Mullikin, Evan E. Eichler, Ross C. Hardison, Richard A. Gibbs, Timothy T. Harkins & Vanessa M. Hayes
Nature 463(7283):943-947. doi: 10.1038/nature08795
Khoisan hunter-gatherers have been the largest population throughout most of modern-human demographic history. (2014)
H. L. Kim, A. Ratan, G. H. Perry, A. Montenegro, W. Miller and S. C. Schuster.
Nature Communications 5(Article number: 5692.10.1038/ncomms6692. doi: 10.1038/ncomms6692.
GenomeAsia 100K Consortium, The GenomeAsia 100K Project enables genetic discoveries across Asia.
Nature 576, 106 (2019). doi: 10.1038/s41586-019-1793-z
Baar, Claudia, Mark Eppinger, Guenter Raddatz, Jörg Simon, Christa Lanz, Oliver Klimmek, Ramkumar Nandakumar et al. "Complete genome sequence and analysis of Wolinella succinogenes." Proceedings of the National Academy of Sciences 100, no. 20 (2003): 11690-11695. doi: 10.1073/pnas.1932838100
A predator unmasked: The life cycle of Bdellovibrio bacteriovorus from a genomic perspective (2004)
S. Rendulic, P. Jagtap, A. Rosinus, M. Eppinger, C. Baar, C. Lanz, H. Keller, C. Lambert, K.J. Evans, R. Till, A. Goesmann, F. Meyer, R.E. Sockett, and S.C. Schuster.
Science 303(5658):689-92. doi: 10.1126/science.1093027.
The zebrafish reference genome sequence and its relationship to the human genome. (2013)
K. Howe, M. D. Clark, C. F. Torroja, J. Torrance, C. Berthelot, M. Muffato, J. E. Collins, S. Humphray, K. McLaren and L. Matthews … (and many authors)
Nature 496(7446):498-503. doi: 10.1038/nature12111.
An archimedian spiral: The basal disk of the Wolinella motor. (1993)
H. Engelhardt, S.C. Schuster *, E. Baeuerlein. (* equal first author)
Science 262(5136):1046-1048. doi: 10.1126/science.8235620.
Assembly and function of a quaternary signal transduction complex monitored by surface plasmon resonance (1993)
S.C. Schuster, R.V. Swanson, L.A. Alex, R.B. Bourret, M.I. Simon.
Nature 365(6444):343-47. doi: 10.1038/365343a0.
Luhung, Irvan, Akira Uchida, Serene BY Lim, Nicolas E. Gaultier, Carmon Kee, Kenny JX Lau, Elena S. Gusareva et al. "Experimental parameters defining ultra-low biomass bioaerosol analysis." NPJ biofilms and microbiomes 7, no. 1 (2021): 1-11. doi: 10.1038/s41522-021-00209-4.
Junqueira, Ana Carolina M., Aakrosh Ratan, Enzo Acerbi, Daniela I. Drautz-Moses, Balakrishnan NV Premkrishnan, Paul I. Costea, Bodo Linz et al. "The microbiomes of blowflies and houseflies as bacterial transmission reservoirs." Scientific reports 7, no. 1 (2017): 1-15. doi: 10.1038/s41598-017-16353-x.
E. S. Gusareva, E. Acerbi, K. J. Lau, I. Luhung, B. N. Premkrishnan, S. Kolundžija, R. W. Purbojati, A. Wong, J. N. Houghton and D. Miller, Microbial communities in the tropical air ecosystem follow a precise diel cycle.
Proceedings of the National Academy of Sciences 116, 23299-23308 (2019). doi: 10.1073/pnas.1908493116.
Tiew, Pei Yee, Fanny Wai San Ko, Sze Lei Pang, Sri Anusha Matta, Yang Yie Sio, Mau Ern Poh, Kenny JX Lau et al. "Environmental fungal sensitisation associates with poorer clinical outcomes in COPD." European Respiratory Journal 56, no. 2 (2020). doi: 10.1183/13993003.00418-2020.
Chia, Po Ying, Kristen Kelli Coleman, Yian Kim Tan, Sean Wei Xiang Ong, Marcus Gum, Sok Kiang Lau, Xiao Fang Lim et al. "Detection of air and surface contamination by SARS-CoV-2 in hospital rooms of infected patients." Nature communications 11, no. 1 (2020): 1-7. doi: 10.1038/s41467-020-16670-2.
Ang, Alicia XY, Irvan Luhung, Bintou A. Ahidjo, Daniela I. Drautz‐Moses, Paul A. Tambyah, Chee Keng Mok, Kenny JX Lau et al. "Airborne SARS‐CoV‐2 surveillance in hospital environment using high‐flowrate air samplers and its comparison to surface sampling." Indoor air (2021). doi: 10.1111/ina.12930.
Daniel, Dan, Marcus Lin, Irvan Luhung, Tony Lui, Anton Sadovoy, Xueqi Koh, Anqi Sng et al. "Effective design of barrier enclosure to contain aerosol emissions from COVID‐19 patients." Indoor air (2021). doi: 10.1111/ina.12828.
Daryl KA Chia, Lim Zhixue, Ang Jiajun, Paul Anantharajah Tambyah, Kelly SH Lau, Joe Ong, Vincent TK Chow, David Michael Allen, Javis Fung, Kenny Lau, Irvan Luhung, Stephan C. Schuster, Lee Chuen Neng, Kim Guowei, Jimmy BY So, Davide Lomanto, Asim Shabbir (2021). A preclinical model assessing the viability of live coronavirus in surgical plume generated during minimally-invasive surgery and potential solutions for safe smoke evacuation.
British Jornal of Surgery in Press
Get In Touch
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Singapore Centre for Environmental Life Sciences Engineering (SCELSE) Nanyang Technological University
60 Nanyang Drive, SBS-01N-27
stephan.c.schuster [at] gmail.com