The Singapore Centre for Environmental Life Sciences Engineering (SCELSE) is an interdisciplinary Research Centre of Excellence (RCE), funded by National Research Foundation (NRF), Singapore Ministry of Education (MOE), Nanyang Technological University (NTU), National University of Singapore (NUS), and hosted by NTU in partnership with NUS.
SCELSE’s main premises are on the beautiful green campus of NTU, in a dedicated building connected to the School of Biological Sciences. The centre also enjoys significant shared laboratory and office space at NUS. SCELSE’s operation benefits from its exceptionally state-of-the-art research laboratories and modern facilities for advanced imaging, automated high-throughput sequencing, bioreactor experimentation, and with instrumentation at both NTU and NUS.
Prof Alain Filloux
Centre Director, SCELSE
Professor, School of Biological Sciences, NTU
Professor, Lee Kong Chian School of Medicine
The importance of microbes
Microbes, and particularly bacteria, represent more than three quarters of total living organisms on earth. They are found in all habitats, from deep oceanic subsurfaces to surface ground soil and water, atmosphere, phyllosphere, animals and humans. It is astonishing to realise that more than 50% of our cells are bacteria or that there are more bacterial species than stars in the galaxy. The biological activity of these microbes is fundamental for the evolution, sustainability and equilibrium of all ecosystems. There is not a single field in biology and life sciences that would not justify the importance of microbes.
The SCELSE acronym does not flag the term “Microbiology”, but instead has adopted the broader “Life Sciences” and “Engineering” terms. This best reflects SCELSE’s mission and multidisciplinary engagement, which is not restricted to narrow domains. Instead, SCELSE aims at producing basic and mechanistic knowledge on how microorganisms live, cooperate or compete in any given ecosystem where they establish polymicrobial communities, and which are coined “biofilms” and “microbiomes”. The dynamic and evolution of these consortia match changes in the environment or human health. Using emerging technologies in engineering will then help translate our knowledge and understanding of these phenomena, to harness and control microbial biofilm communities and microbiomes. In all, our mission is:
“To discover, control and direct the behaviour of microbial biofilm communities and microbiomes for sustainable environmental, engineering, public health and medical applications.”
Human activity has driven the drastic transformation of planet earth that is transpiring. Fast growing urbanisation, chemical pollution, greenhouse gas and climate change, massive usage of antimicrobials, to cite a few, have changed the environment and the organisms living within. All these changes have compromised previously unlimited access to essential resources including clean water and air or safe food, and also triggered the emergence of infectious diseases, to an extent that the sustainability of a life-supporting environment is now threatened. What has been done cannot be undone. Yet harnessing and engineering the biological activities of microbial communities is one of the key solutions to regain control on the trajectory of these changes. SCELSE is designed to meet these challenges since microbes turn the wheels of all biogeochemical cycles in both natural and engineered systems.
SCELSE research – Biofilms and Microbiomes
SCELSE is organised into research clusters that span its remit and visibility from basic research, integrated modern ‘omics approaches, engineering and translation, to environment and public health.
Biofilms and microbiomes form the focus of our research. It is now a universally accepted concept that in natural ecosystems microbes exist in complex multi-species communities, which reached an equilibrium to live together, benefit from each other, as well as being optimally adapted to their environment. The composition and biodiversity of these populations is dynamic and reflects environmental changes and further adaptation. Their organisation and structure is sophisticated and reflects billion years of co-evolution.
The molecular basis underpinning the organisation and evolution of microbial consortia is essential to understand community dynamics and interactions with their environment. These key biological questions and mechanisms are dissected through the basic expertise and exploratory power available to SCELSE researchers. They are then analysed in a broader context and in full-scale environmental, medical and engineered systems. This natural progression of our research is essential since in these settings the activity of microorganisms far surpasses the combined activities of individual member species.
Moving towards complex systems requires capacity and interdisciplinarity. SCELSE has established these partnerships to investigate microbial communities in marine, wastewater, air or human contexts. Synergy and complementarity between microorganisms in a complex environment will drive drastic changes in gene expression and metabolic activity at the individual species level and this can only be captured using the most advanced molecular and analytical tools in genomics, proteomics and metabolomics. The acquisition of ‘big data’ and their repository in multi-layered databases is currently exploited at SCELSE through advanced bio-informatics and bio-computational tools. The latter are instrumental to our research, by enabling biological meaning to be derived from large-scale data sets, and the subsequent development of novel concepts that emerge from systematic analysis. SCELSE might seek to expand this analytical power by exploiting machine learning and artificial intelligence to assess ground-breaking theories. Overall, we strive to predict the evolution of microbial consortia in the face of environmental stresses, and engineer the composition of microbial communities to the benefit of natural and engineered environments, or the human host.
Biofilms are the common mode of life for microorganisms
Microorganisms most commonly reside in dynamically structured communities of multiple species embedded in an extracellular polymeric matrix, collectively known as a biofilm. The matrix provides microbial inhabitants with shelter from external stressors such as predators, host immune systems and antibiotics, as well as protection from desiccation. The proximity of cells within the matrix facilitates intercellular chemical communication/signalling, as well as horizontal gene transfer, which can readily disseminate resistance genes between cells.
The distinction between biofilms and microbiomes can be tenuous but one can say that the former provides a close look at the structure and organisation of microbial consortia, whereas the latter focusses almost entirely on the composition of the community. SCELSE has contributed to major advances in biofilm research. The field has moved from description of single-species mushroom-shaped bacterial towers surrounded by fluid-filled channels that transfer nutrients, to an impressively detailed vision of molecular mechanisms at play in often highly complex and diverse microbial communities. This includes the structural and functional description of matrix components or surface adhesins, as well as regulatory networks coordinating the movement of bacterial cells towards a surface and a switch in lifestyle, which require the universal c-di-GMP second messenger or the density-dependent quorum sensing system. SCELSE has also been a major player in microbiome analysis including the microbiomes in air or water environments as well as co-infections in wounds, and host-associated microbiomes for plants, invertebrates and mammals.
SCELSE is well embedded across Singapore’s R&D landscape
To take full advantage of the state-of-the-art technologies available at SCELSE and create an effective platform with notable added value, the centre has established a collaborative atmosphere of R&D partnerships, and is continuously expanding its research interactions. SCELSE is integrated across numerous schools and departments at its host universities and has extensive reach among Singapore’s research organisations; clinics and hospitals; national agencies; and industry.
In recent years, the translational potential for biofilm and microbiome research in Singapore has been bolstered with the creation of the Singapore National Biofilm Consortium (SNBC), which fosters significant interactions and close collaborations among academic research institutions, government agencies and industry. SCELSE is the research lead and administrative co-host for SNBC, which leverages the centre’s multidisciplinary expertise to effectively deliver scientific and applied outcomes. SCELSE provides exquisite examples of key basic research developments for very specific applications. It is noteworthy that since microbial interactions with the environment are governed by surface chemistry, SCELSE’s approach also accommodates the merging of nano-technological tools.
SCELSE – beyond a decade of research excellence
SCELSE reached its 10 year milestone in 2021. As a new director I feel privileged and excited to open a new chapter and be at the helm of a centre that over the years has developed the multidisciplinary expertise needed to control and harness biofilm processes to our advantage. A continuum between environment and human health is evident, through the air we breathe, the food we eat and the water we drink, all of which impact our microbiome, as will antibiotic or immunosuppressive treatments. It is SCELSE’s place to be positioned in this continuum and further our understanding on how these communities move from one ecosystem to another. With this goal SCELSE needs to maintain its core expertise and facilities while attracting new talent and scientific excellence to respond effectively to emerging challenges in biofilm and microbiome research.
Prof Alain Filloux
Centre Director, SCELSE
Professor, School of Biological Sciences, NTU
Professor, Lee Kong Chian School of Medicine, NTU