NOVEMBER 2019
Sharon Longford, Senior Assistant Director, Science communications, SCELSE
“Microbial interactions, algal chemical defences and disease: Ecology of a temperate marine holobiont”
Sharon has a background in marine microbial ecology. Her research interests have involved
applying eukaryote ecological theory to microbial communities associated with marine
higher organisms. This has included investigating the bacteria associated with temperate
marine sponges (BSc Hons research) and algae (PhD research), both undertaken at the
University of New South Wales, Australia. Prior to her science research, Sharon completed a
BA (Comms) and worked as a professional writer. Over the last decade, she has melded her
professional backgrounds to embark on a career in science writing, and currently heads
science communications at the Singapore Centre for Environmental Life Sciences
Engineering.
Binu Kundukad, Senior Research Fellow, SCELSE
“Mechanistic action of weak acid drugs on biofilms”
Binu Kundukad is currently a Senior Research Fellow at the Singapore Centre of Environmental Life Sciences Engineering with expertise in Biophysics. Prior to this, she was a Research Scientist at the Singapore MIT Alliance for Research and Technology (SMART), where she led the Biofilm Ecomechanics project group and her focus was on developing and using biophysical tools and microfluidic devices to understand the mechanical properties of biofilms and how these properties contribute to the biofilm structure and function as well as understanding the biofilm’s interaction with the environment. Her focus also included the response of biofilms/biofilm matrix to weak acid drugs
Aditya Bandla, Research Fellow, SCELSE
“Hundreds of metagenome-assembled genomes from the phytobiomes of urban-farmed cruciferous vegetables – the story so far”
Aditya’s research integrates advanced imaging (3D-EM, CLSM), electrochemical (microsensors), microfluidic, mass spectroscopy and molecular techniques (metagenomics, FISH) to gain a predictive understanding of the physicochemical factors governing microbial assemblage, function and processes on sediment particles at such scales.
OCTOBER 2019
Adriana Lopes dos Santos, Assistant Professor, Asian School of the Environment, NTU
“Protists, the other microbes: not animals, not plants, not fungus, not bacteria, just protists..”
Adriana is a marine microbial ecologist interested in understanding the structure of marine eukaryotic plankton communities and how environmental factors shape their diversity. Adriana is from Brazil where she graduated at Federal University of Rio de Janeiro. Part of her PhD was conducted at University of Michigan in Dr. James Tiedje’s laboratory. There, she was “converted” to a molecular ecologist and had the opportunity to discover the potential of high throughput sequencing technologies to investigate the microbial diversity in different environments. Her work combines traditional culture isolation and laboratory studies along with cutting-edge DNA sequencing approaches to elucidate the patterns of marine eukaryotic phytoplankton communities across a wide range of environments. After working at Station Biologique de Roscoff in France, she has moved to Singapore to take a position as Assistant Professor at Nanyang Technological University where she pursues understanding the wonders of the plankton world.
Sarah Geiger, PhD Candidate, NUS Department of Medicine
“Understanding clonal bacterial expansions from a population genetics perspective”
Sarah is currently in her third year of her PhD at the National University of Singapore, where she studies how to better understand the application of population genetic statistics for ongoing and unexplained bacterial expansions. This would offer an unbiased methodology for identifying loci under positive selection and provide the opportunity for more targeted investigations for these organisms. Prior to arriving in Singapore, she received her Bachelor of Science in Microbiology at Miami University of Ohio.
Mao Feijian Jason, Research Fellow, NUS Environmental Research Institute
“Rapid monitoring of Algal Bloom Dynamics with Flow Cytometry”
Mao Feijian (Jason) is a research fellow with NUS Environmental Research Institute
(NERI). He received his Bachelor degree in Biotechnology from Shanghai Ocean
University in 2011 and M. Eng Degree in Environmental Engineering from Shanghai
Jiao Tong University in 2014. He obtained his PhD in Environmental Engineering from
NUS in 2018. He is currently working on the rapid detection of phytoplankton with flow cytometry.
SEPTEMBER 2019
Diane McDougald, Associate Professor, The ithree Institute, University of Technology Sydney
“Protozoans in expelled food vacuoles are an unrecognised vector for transmission of cholera”
Associate Professor Diane McDougald leads the Pathogen Evolution group located at The ithree Institute (Infection, Immunology and Innovation), University of Technology Sydney. She is also a Visiting Senior Researcher at the Singapore Centre on Environmental Life Sciences Engineering at Nanyang Technological University, Singapore. A/Prof McDougald has made significant contributions to the fields of Vibrio biology, bacterial adaptation to stress and mechanisms of molecular control of these responses, cell-to-cell communication, biofilm formation and interactions of bacteria with higher eukaryotes. The Pathogen Evolution group’s major research interests are the mechanisms of survival and persistence of pathogens in the environment, and what impact these mechanisms have on virulence and pathogenicity in the host. The team investigates the evolutionary drivers and consequences of bacterial adaptation to stresses, including interactions with higher organisms. Broadly, the team studies the interactions of prokaryotes and eukaryotes using a number of model systems to investigate the impact of predation by protozoa on microbial communities and how evolution of grazing defences drives the evolution of pathogenicity in the environment. Predation is an important selection pressure that pathogens face in the environment, and as a result, pathogens may evolve phenotypes that not only increase their fitness in the environment, but may also increase their fitness in the human host. This research platform will allow us to test key aspects of the Coincidental Selection Hypothesis, which states that the virulence of many opportunistic human pathogens may be an accidental by-product of selection for adaptations not related to human disease.Predicting the emergence of new pathogens is difficult but important for developing public policy. Building predictive tools relies on high quality knowledge input to which knowledge of the evolutionary drivers and consequences of bacterial adaptation to stresses can make important contributions.
Yolanda Plowman, PhD Candidate, University of Sydney
“AMF community assembly on wheat plants driven by crop rotation and P fertiliser”
Yolanda oversees the operations of JAMS and organises Sydney JAMS events. She’s
currently in the third year of her PhD at the University of Sydney, investigating the
relationship between arbuscular mycorrhizal fungi (AMF) and environmental variables,
such as agricultural soil treatments, to elucidate functional differences between AMF
species. This research has promising applications for the sustainable intensification of
agriculture, and Yolanda is working toward a career in food security research and
development. Prior to this Yolanda completed her Bachelor of Environmental Systems (Hon I) at the
University of Sydney, and Bachelor of Biological Science at the Queensland University of
Technology. She currently teaches various microbiology and food security units of study at
the University of Sydney.
Shree Harsha, Senior research fellow, Skin research institute of Singapore
“In vitro models for skin microbiome research”
Shree Harsha has a PhD in Cell Biology from Friedrich-Alexander University, Erlangen, Germany. His research interests have been in the areas of infectious disease and antibacterial drug discovery (Tuberculosis and anti-TB drugs), Cancer biology and Genetic engineering. He is currently a Senior Research Fellow at Skin Research Institute of Singapore where he is involved in studying the skin microbiome. With particular emphasis on investigating host-pathogen interactions, he is working on developing and validating in vitro models of skin microbiome which have potential for multiple applications in the field for skin research.
AUGUST 2019
Kimberly Kline, Associate Professor, SCELSE, School of Biological Sciences, NTU
“Dr. Jekyll and Mr. Hide: The multiple personalities of Enterococcus faecalis”
Kimberly Kline received an MPH in Biostatistics and Epidemiology and PhD in Microbiology and Immunology from Northwestern University. Kimberly went on as a postdoctoral fellow at Washington University in St. Louis and at the Karolinska Institute in Stockholm Sweden. In 2011, Kimberly joined Nanyang Technological University in Singapore as a Nanyang Assistant Professor. Kimberly has received multiple awards for her contributions to the field of microbiology, including a NIH K99 Career Development Award in 2011, the Singapore National Research Foundation Fellowship in 2011, the ICAAC Young Investigator Award from the American Society of Microbiology in 2014, and the Nanyang Education Award in 2017. The goal of Kimberly’s research is to understand the molecular mechanisms by which Enterococcus faecalis interacts with other bacterial species and the host in the context of these polymicrobial, biofilm-associated infections.
Aarthi Ravikrishnan, Postdoctoral Fellow, GIS, (A*STAR)
“A graph-theoretic approach to unravel microbial interactions in the gut microbiome”
Aarthi has a PhD in Computational Systems Biology from the Indian Institute of Technology Madras. Her research is interdisciplinary and involves an interesting combination of computer science and biology. Notably, she develops algorithms and computational tools to understand the metabolism in microbial communities and carries out experiments with the predictions obtained. Currently, she is a Postdoctoral fellow at Genome Institute of Singapore, where she works on investigating the skin microbiome through computational and experimental approaches.
Samuel Ruli, Global Product Manager, QIAGEN RNAseq Technology and Applications
“QIAseq FastSelect 5S/16S/23S: Novel method to efficiently remove rRNA without hybridization-capture or enzymatic removal”
JULY 2019
Eric Alm – Professor, Biological Engineering, Civil & Environmental Engineering, Massachusetts Institute of Technology
Eric is co-director for the Center for Microbiome Informatics & Therapeutics at MIT and the director of OpenBiome. Eric earned his Bachelors from the University of Illinois (Champaign-Urbana), his Masters from the University of California (Riverside), and his PhD from the University of Washington (Seattle). He held a postdoctoral appointment at the University of California (Berkeley) and Lawrence Berkeley National Lab prior to joining the faculty at MIT. His research group is an interdisciplinary team of computer scientists, computational biologists, molecular biologists, and microbial ecologists. Research in his group includes both computational/theoretical and experimental approaches to understanding and engineering the human microbiome. Some areas of special interest include: Developing therapeutics based on synthetic microbial communities, Personalised medicine, Monitoring human activities through Smart Sewers, Smart Toilets that track human health, and Discovering low-cost non-invasive biomarkers.
Ryan B. De Sotto – PhD Candidate, Civil & Environmental Engineering, National University of Singapore
“Antibiotics + Nutrient Removal = ? (Effects of antimicrobials on nutrient-removing communities and their functional genes)”
Ryan is currently finishing his PhD in Environmental Engineering under the Civil and Environmental Engineering Department of the National University of Singapore. His PhD work centers on the influence of operational, chemical, and biological disturbances on the nutrient removal of two distinct modified Ludzack-Ettinger (MLE) membrane bioreactors (MBRs) using conventional and advanced molecular methods. During his Master of Engineering in Korea University, South Korea, Ryan used zebrafish as his model organism to study the effects of environmentally relevant concentrations of select antibiotics on its development, behavior, and metabolism. Meanwhile, his undergraduate degree in Microbiology was conferred by the University of Santo Tomas, Philippines, where he isolated indigenous fungal species that are able to withstand and degrade high concentrations of hexavalent Chromium from heavy-metal polluted sites. In his free time, Ryan volunteers for Action for AIDS, cooks, plays boardgames, travels, and makes friends with people from different walks of life.
Qingkun Wang – PhD Candidate, Civil & Environmental Engineering, National University of Singapore
“The Nitrogen loss mechanism associated with Sulfur Cycling in Tropical Wetland Ecosystems”
Qingkun is currently a PhD candidate in the Department of Civil & Environmental Engineering, National University of Singapore (NUS). His research mainly focuses on Fixed Nitrogen Removal from Wastewater via Novel Pathways and Associated Microorganisms Characterization. He obtained his bachelor degree in Engineering at Sun Yat-sen University, China in 2015.
JUNE 2019
Aaron E. Darling – Professor, The ithree Institute, University of Technology Sydney
“High resolution metagenomic analysis via metagenomic Hi-C”
Aaron is a distinguished academic known for the development of cutting edge computational and molecular techniques for the study of microbial genomes.
He is a Professor of Computational Genomics and Bioinformatics at the ithree institute, University of Technology Sydney, where he leads a team of computational scientists and molecular biologists. His research is widely cited and creates real-world impact; his software packages for genome assembly and comparison (A5-miseq, Mauve) are used by thousands of academic researchers as well as a range of private industries, public health (Centers for Disease Control), government and environmental organisations. His academic publications have been highly cited, with over 20000 citations to date and an H-index of 38. Aaron currently holds the title of President of the Australian Bioinformatics and Computational Biology Society (ABACBS). He is on the editorial board of PLOS Computational Biology and formerly on the editorial board of BMC Bioinformatics.
In addition to his academic work, Aaron is the co-founder and CSO of Sydney-based startup Longas Technologies Pty Ltd. Longas has developed the Morphoseq virtual long read technology. Morphoseq enables short read sequencers to generate high accuracy 8-10kbp reads at low cost.
Aaron holds a PhD in Computational Biology from the University of Wisconsin, Madison, USA.
Maria Yung – Manager, Tropical Science Marine Institute (TMSI)
“Microbe-sediment interactions in the coastal marine environment”
Maria has a PhD from the University of New South Wales (2010) studying the phylogenetic and functional diversity of the microbes within marine sponges. She moved to Singapore for her postdoc in NUS and NTU working on microbiomes in various environmental settings using -omics approaches. She is currently a manager at the St John’s Island National Marine Laboratory, the off-shore marine station in Singapore.
Thomas Jeffries – Lecturer in Microbiology, Western Sydney University
“Microbial ecology of warming global drylands”
Thomas Jeffries is a Lecturer in Microbiology at Western Sydney University, Australia, with an expertise in microbial ecology. His research focuses on using ecogenomic tools to understand microbial biogeography in habitats ranging from the ocean, the desert and the human body. He has authored over 40 publications and is the co-chair and incoming director of JAMS in Australia.
MAY 2019
Swaine Chen – Associate Professor, Infectious Diseases Group, GIS (A*STAR)
“Culturing millions of fish doesn’t provide food for just people – follow up studies from the 2015 raw fish-associated Group B Streptococcus outbreak in Singapore”
Dr. Swaine Chen is an Associate Professor of Medicine at the National University of Singapore and a Group Leader in Infectious Diseases at the Genome Institute of Singapore. He has a broad background in medicine, biology, and chemistry. In his lab, he studies not only why some bacteria cause infections, but also tries to develop new methods so that we can diseases more quickly in the future. Another major aspect of his work is using DNA sequencing to detect and understand outbreaks of infectious diseases, especially those that are unexpected, like the Group B Streptococcus outbreak associated with yu sheng fish in 2015 in Singapore.
Henry Wang – Senior Market Development Manager, QIAGEN bioinformatics
“The challenge of metagenomics data analysis and rapid solution for biologists”
Henry graduated with a Masters in Marine Resources from National Sun Yat-Sen University with a research interest in Microbiology and Molecular Biology. He is currently holds the position of Senior Market Development Manager at QIAGEN Asia-Pacific.
Xiaoqiong Gu – Research Fellow, Singapore-MIT Alliance for Research and Technology (SMART)
“A 24-hour non-targeted viral sequencing analysis of residential sewage reveals short term changes in virome patterns”
Xiaoqiong obtained her PhD in Civil and Environmental Engineering from the National University of Singapore in 2018, where she studied spatial and temporal variations of viromes in the urban water cycle (i.e., surface water and sewage water), and public health associated viral pathogens and indicators. She is fascinated by virus-host interactions and viral community analysis. As a Research Fellow at Singapore-MIT Alliance for Research and Technology (SMART), her focus is on data-mining of untargeted time-series and space-scale sewage metagenomes, and time-series changes in human gut RNA viromes.
APRIL 2019
Rohan Williams – Head of Integrative Analysis Unit, SCELSE, NUS
“MAGs from MinION: recent progress on recovering metagenome-assembledgenomes using Nanopore sequencing”
Rohan Williams is Head of the Integrative Analysis Unit at the Singapore Centre for Environmental Life Sciences Engineering (SCELSE), an autonomous research centre in microbial ecology and biofilm biology co-hosted by the National University of Singapore and Nanyang Technological University. Following undergraduate studies in Physics,
Williams obtained a PhD in Medicine from the University of New South Wales (Sydney, Australia) in 2003. From 2004-2007 he was an NHMRC Peter Doherty Fellow at UNSW and then a Group Leader at the Australian National University in Canberra (2007-2011) prior to taking up his present appointment. His interests and expertise lie in statistical
bioinformatics, design, analysis and interpretation of experiments using genomic technologies, systems microbiology and the analysis of complex microbial communities using multi-omics approaches.
Pauliina Rajala – Research Fellow, SCELSE, NTU
“Microbially-influenced corrosion in the deep sea”
Dr. Pauliina Rajala is a Research Fellow in the Singapore Centre for Environmental Life Sciences Engineering, working with microbially-influenced corrosion in deep marine environments. Prior to joining the SCELSE, she was a Research Scientist and Project Manager at VTT Technical Research Centre of Finland Ltd. In her previous role, she investigated the microbially induced corrosion of steels and copper in deep groundwater environments related to the repository concepts of the hazardous wastes. In addition to her corrosion research, she has been working with the marine biofouling issues and terrestrial deep biosphere microbial community’s response to changing environmental conditions. The overall objectives of her research are to elucidate both the biodiversity and metabolic functions of microbial communities (bacteria, archaea and fungi) attached to metallic surfaces, as well as, annotate the capability of these microbes to induce corrosion of metallic materials, combining electrochemical and molecular biological methods.
You Fang – Research Fellow, Civil & Environmental Engineering, NUS
“Isolation and characterization of a cyanophage infecting Microcystis aeruginosa from a Singaporean reservoir”
You Fang received her PhD in Chemical & Biomolecular Engineering from National University of Singapore, where she worked on developing biosensors for understanding the toxicity of nanomaterials. She is now a Research Fellow at the Department of Civil and Environmental Engineering (NUS), and her research focuses on algal bloom and its biosolution.
FEBRUARY 2019
Tom L Dawson – Senior Principal Investigator (A*STAR)
“The Skin Microbiome: Friend, Foe, or Frenemy”
In 2015 Tom joined A*STAR to develop hair and skin health programs. He leads the A*STAR cutaneous microbiome program, which was recently awarded significant funding (the “Asian Skin Microbiome Program” or ASMP). The ASMP will define the healthy skin microbiome and its role in skin homeostasis. Tom remains committed to leveraging microbiology to improve skin health and retains his emphasis on Malassezia, including leading the global consortium on Malassezia phylogeny, physiology, and pathogenesis (the “Malassezia Research Consortium”). He also leads a translational program fusing hair shaft biogenesis, biochemical synthesis, and physical measurement to create better hair treatments.
Tom is the President of the Singapore Society for Skin Research, Vice Chair of Mycology and Eukaryotic Microbiology, IUMS, Academic Editor of PLoS 1, and Chair of the A*STAR SRIS Human Biomedical Research Act committee. He is also the CEO of a private consulting firm, Beauty Care Strategics, consulting with multiple consumer care companies, both multi-national and local.
Ezequiel Santillan – Research Fellow, SCELSE, NTU
“Relationship between diversity, disturbance and performance in complex biofilms”
Ezequiel holds a Ph.D. (2018) and a M.Sc. (2015) in Civil & Environmental Engineering from the University of California, Davis, as well as a B.Sc. in Chemical Engineering (2008) from the National University of Salta, Argentina. Specializing in wastewater treatment, his research focuses on understanding the effect of perturbations on function and structure of microbial communities in activated sludge from a multidisciplinary perspective that includes engineering, molecular biology, ecology and statistics. Eze believes that ecological theory provides fundamental guidance towards this quest, and sludge bioreactors are model systems for microbial ecology. His research has so far explored concepts like the intermediate disturbance hypothesis, mechanisms of community assembly, trait-based life-history strategies, resistance and resilience of nitrifiers and nitrification under sustained perturbations, and different mechanisms of community assembly and diversity for taxa and genes. The ultimate goal is to find ways to drive microbial communities using perturbations towards achieving desired functions, like degradation of pollutants or the production of certain compounds.
Boonfei Tan – Research Scientist, Kemin Animal & Nutrition, Asia Pacific
“Probiotics as an alternative to antibiotic growth promoters in the livestock industry”
Boonfei has a PhD from the University of Alberta (2014) where he worked on investigating microbial biodegradation/bioremediation of pollutants in oil sands tailings pond. He moved to Singapore for his Postdoctoral research at Singapore-MIT Alliance for Research & Technology Centre (SMART) and subsequently joined Kemin Industries where he leads a research team in R&D of animal health and nutritional products for gut health and feed hygiene platforms.