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Academic Qualifications

PhD UF (USA), PhD, Msc IARI, BSc PAU India

Metabolites Biology Laboratory

Our research program involves understanding the biological role of small biomolecules. We work in two broad areas involving mall molecules. First, to understand metabolic networks- including their modularity, connectivity, control mechanisms and to discover new products or pathways of applied value. Second, to understand the role of cyclic nucleotide 2^nd messengers that control diverse pathways in model bacterial species Pseudomonas or in environmental bacterial communities.

In the metabolic networks program, we have adopted mostly a data-driven systems approach to understand cellular responses to perturbations caused by diverse intrinsic or extrinsic signals in the biological system(s). We combine both wet and dry laboratory work within our group. Our model organisms are diverse and include bacteria (Bacillus, Pseudomonas), Arabidopsis, rat and human skin cells. We have developed capabilities to comprehensively map out the changes in the metabolic complement or the ‘metabolome’ of cells in response to perturbations such as metabolic mutations, effector molecules, or environmental stresses. This approach has allowed us in various projects to:

• Uncover some broad connections in metabolic networks;
• Describe novel catabolic pathway in bacteria;
• Identify members of novel family of bioactive compounds;
• Propose a ‘rhizosphere engineering’ approach to increase competitiveness of soil microbes;
• Identify intra- and inter-pathway regulatory controls associated with the ‘metabolome’.

In the signalling program, we have recently described the regulatory mechanism for a novel cyclic nucleotide 2^nd messenger in microbes, cyclic diguanylate. The motility regulator MorA is especially conserved in Pseudomonas, modulates the intracellular messenger levels and controls pathways such as motility and biofilm formation. Current efforts in the laboratory are focused on the elucidation of the structure, function and regulatory circuit of the pathways.

In 2008, we have started applying our fundamental studies to addresses the role of plant-microbial interactions in urban freshwater ecology. This work is being carried out under the umbrella of Singapore-Delft Water Alliance (www.sdwa.nus.edu.sg) and funded by the National Research Foundation. We are taking a taking a multidisciplinary approach incorporating hydraulics, genomics, metabolomics, computational and graphical modelling, and high-resolution imaging to study mechanisms that govern biofilm formation and plant metabolic processes in urban freshwater conditions. Both, single-species (Pseudomonas sp.) model and bacterial communities in aquatic environments are being investigated. We focus on biofilm processes such as bacterial signaling that affect bacterial motility, adhesion, biofilm initiation and metabolic networks including roles of metabolites as nutrients and signals in microbial communities.

Since 2009, we have begun complementary studies at a fundamental level to understand the mechanical properties of motility and biofilm formation in bacteria in relation to their control mechanisms. We are especially interested in understanding the coordinated control of multiple appendages of bacteria such as flagella and pili, taking Pseudomonas as our biological model. This work is being carried out at the Research Centre of Excellence in Mechanobiology funded by the National Research Foundation.

Selected Publications

2020

[1] Pavagadhi, S., & Swarup, S. (2020). Metabolomics for evaluating flavor-associated metabolites in plant-based products. Metabolites, 10(5).

[2] Keyu, G., Pavagadhi, S., Yoon Ting, Y., Cheng-Yen C., Swarup, S., & Naqvi, N.I. (2020). Crosskingdom growth benefits of fungus-derived phytohormones in Choy Sum. BioRxiv.

[3] Mishra, S., Yi, Y. P., Shivshankar, U., Moses, D., & Idris, A. (2020). Developing Sustainable Practices to Mitigate Impacts of Climate Change on Natural and Managed Tropical Peatlands. 15^th International Congress of Peat Society, 416.

[4] Jing ling, Z., Xia Song, Wee Kee, T., Yuting, W., Zhengyang, G., Choon Nam, O., Chiang Shiong, L., Swarup, S., & Jun, L. (2020). Modification of Biomass Okara Using Poly (acrylic acid) through Free-radical Graft Polymerization. Journal of Agricultural and Food Chemistry. (accepted).

[5] Rachelle, E.B., Bandla, A., Swarup, S., & Krassimira, H. (2020). Freshwater Sediment Microbial Communities Are Not Resilient to Disturbance from Agricultural Land Runoff. Frontiers in Microbiology. (accepted).

[6] Saxena, G., Eric, D.H., Ezequiel, M. M., Shivshankar, U., Jun Wei, T., Wei Woo, Y., Peter, D.S., Veronica, B.R., Staffan, K., Rohan, B.H.W., Stefan, W., & Swarup, S. (2020). Integrative systems approach reveals dynamics of microbiome-metal-ion axis in mesocosms representing tropical urban freshwater canal ecosystem. BioRxiv.

2019

[7]  Pavagadhi, S., Bandla, A., Miko, P.C.H., Umashankar, S., Yoon Ting, Y., & Swarup, S. (2019). Host developmental stage is associated with shifts in the exosphere microbiome of urban-farmed Asian green leafy vegetables. BioRxiv.

[8] Pinu, F. R., Beale, D. J., Paten, A. M., Kouremenos, K., Swarup, S., Schirra, H. J., & Wishart, D. (2019). Systems biology and multi-omics integration: Viewpoints from the metabolomics research community. Metabolites, 9(4).

[9] Nur, A.A.H., Faridah, A., Maulidiani, M., Intan S.I., Chau Ling, T., Swarup, S., & Shivshankar, U. (2019). NMR metabolomics for evaluating passage number and harvesting effects on mammalian cell metabolome. Analytical Biochemistry, 576, 20-32.

[10] Bandla, A., Saxena, G., Mishra, R., & Swarup, S. (2019). A Framework to Address the Food, Energy and Water Nexus among Indian Megacities and Their Rapidly Expanding Peripheries. Dialogue – Science. Scientists. Society, Indian Academy of Sciences.10.29195/DSSS.02.01.0019.

[11] Pavagadhi, S., & Swarup, S. (2019). Research Article: Advances in Science. A special issue on Agri-food sciences: From the farm to the plate. Advances in Science, 24(1).

[12] Pan, D., Pavagadhi, S., Umashankar, S., Rai, A., Benke, P. I., Rai, M., & Swarup, S. (2019). Resource partitioning strategies during toxin production in Microcystis aeruginosa revealed by integrative omics analysis. Algal Research, 42.

[13] Nur, A.A.H., Faridah, A., Intan S.I., Chau Ling, T., Maulidiani, M., Ahmed, M., Swarup, S., & Umashankar, S. (2019). 1H-NMR-based metabolomics to investigate the effects of Phoenix dactylifera seed extracts in LPS-IFN-γ-induced RAW 264.7 cells. Food Research International, (125).

[14] Abdul-Hamid, N. A., Abas, F., Ismail, I. S., Tham, C. L., Maulidiani, M., Mediani, A., & Zolkeflee,  N. K. Z. (2019). Metabolites and biological activities of Phoenix dactylifera L. pulp and seeds: A comparative MS and NMR based metabolomics approach. Phytochemistry Letters, 31, 20–32.

[15] Jackson, T., Sayantan, S., Shiguo Jia, J.S. R., Shailendra, M., Sudiana, I.M., Swarup, S., Choon Nam, Ong., & Liya, E.Y. (2019). Impacts of peat-forest smoke on urban PM2.5 in the Maritime Continent during 2012–2015: Carbonaceous profiles and indicators. Environmental Pollution, 248, 496-505.

2018

[16] Keogh, D., Lam, L. N., Doyle, L. E., Matysik, A., Pavagadhi, S., Shivshankar, U., & Swarup, S. (2019). Erratum: Correction for Keogh D., Extracellular Electron Transfer Powers Enterococcus faecalis Biofilm Metabolism. MBio, 10(3).

[17] Mishra, R., Chitre, M., & Swarup, S. (2018). Online informative path planning using sparse Gaussian processes. In OCEANS – MTS/IEEE Kobe Techno-Oceans, OCEANS – Kobe.

[18] Mishra, R., Chitre, M., & Swarup, S. (2018). Informed Sampling and Adaptive Monitoring using Sparse Gaussian Processes. In AUV – IEEE/OES Autonomous Underwater Vehicle Workshop, Proceedings.

[19] Liu, Y., Zhang, H., Umashankar, S., Liang, X., Lee, H. W., Swarup, S., & Ong, C.N. (2018). Characterization of plant volatiles reveals distinct metabolic profiles and pathways among 12 brassicaceae vegetables. Metabolites, 8(4).

[20] Birrer, S.C., Dafforn, K.A., Sun, M.Y., Williams, R.B.H., Potts, J., Scanes, P., Swarup, S., & Johnston, E.L. (2019). Using meta-omics of contaminated sediments to monitor changes in pathways relevant to climate regulation. Environmental Microbiology, 21(1), 389–401.

[21] Balan, P., Chong, Y. S., Umashankar, S., Swarup, S., Loke, W. M., Lopez, V., & Seneviratne, C. J. (2018). Keystone species in pregnancy gingivitis: A snapshot of oral microbiome during pregnancy and postpartum period. Frontiers in Microbiology, 9.

[22] Balan, P., Chong, Y. S., Umashankar, S., Swarup, S., Loke, W. M., Lopez, V., & Seneviratne, C. J. (2018). Keystone species in pregnancy gingivitis: A snapshot of oral microbiome during pregnancy and postpartum period. Frontiers in Microbiology, 9.

[23] Vello, V., Umashankar, S., Phang, S.M., Chu, W.L., Lim, P.E., Nazia, A.M., Liew, K., Swarup, S., & Chew, F.T. (2018). Metabolomic profiles of tropical Chlorella and Parachlorella species in response to physiological changes during exponential and stationary growth phase. Algal Research, 35, 61–75.

[24] Saxena, G., Mitra, S., Marzinelli, E. M., Xie, C., Wei, T.J., Steinberg, P.D., Williams, R.B.H., Kjelleberg, S., Lauro, F. M., & Swarup, S. (2018). Metagenomics reveals the influence of land use and rain on the benthic microbial communities in a tropical urban waterway. MSystems, 3(3).

[25] Keogh, D., Lam, L.N., Doyle, L.E., Matysik, A., Pavagadhi, S., Umashankar, S., Dale, J.L., Song, Y., Boothroyd, C.B., Dunny, G.M., Swarup, S., Williams, R.B.H., & Kline, K.A. (2018). Extracellular electron transfer powers Enterococcus faecalis biofilm metabolism. MBio, 9(2).

2017

[26] Chua, S. L., Ding, Y., Liu, Y., Cai, Z., Zhou, J., Swarup, S., Daniela, I.M., Stephan, C.S., Staffan, K., Michael, G., & Yang, L. (2017). Erratum: Correction to Reactive oxygen species drive evolution of pro-biofilm variants in pathogens by modulating cyclic-di-GMP levels. Open Biology, 7(9).

[27] Suriyanarayanan, T., Seneviratne, C.J., W.L. Ng, Pavagadhi, S., & Swarup, S. (2017). Metabolomics of Microbial Biofilms: Current Status and Future Directions. Microbial Biofilms, 7(30).

[28] Teh, B.T., Lim, K., Yong, C.H., Ng, C.C.Y., Rao, S.R., Rajasegaran, V., Lim, W.K., Ong, C.K., Chan, K., Cheng, V.K.Y., Soh P. S., Swarup S., Rozen S.G., Nagarajan, N., & Tan, P. (2017). The draft genome of tropical fruit durian (Durio zibethinus). Nature Genetics, 49(11).

[29] Seneviratne, C. J., Suriyanarayanan, T., Swarup, S., Chia, K. H. B., Nagarajan, N., & Zhang, C. (2017). Transcriptomics Analysis Reveals Putative Genes Involved in Biofilm Formation and Biofilm-associated Drug Resistance of Enterococcus faecalis. Journal of Endodontics, 43(6), 949–955.

[30] Ling, H., Foo, J.L., Saxena, G., Swarup, S., & Chang, M.W. (2017). Drug Targeting of the Human Microbiome. Systems Biology, 7.

2016

[31] Rai, A., Umashankar, S., Rai, M., Kiat, L. B., Bing, J. A. S., & Swarup, S. (2016). Coordinate regulation of metabolite glycosylation and stress hormone biosynthesis by TT8 in Arabidopsis. Plant Physiology, 171(4), 2499–2515.

[32] Chua, S. L., Ding, Y., Liu, Y., Cai, Z., Zhou, J., Swarup, S., Drautz-Moses, D.I., Schuster, S.C., Kjelleberg, S., Givskov, M., & Yang, L. (2016). Reactive oxygen species drive evolution of pro-biofilm variants in pathogens by modulating cyclic-di-GMP levels. Open Biology, 6(11).

[33] Suriyanarayanan, T., Periasamy, S., Lin, M.H., Ishihama, Y., & Swarup, S. (2016). Flagellin FliC phosphorylation affects type 2 protease secretion and biofilm dispersal in Pseudomonas aeruginosa PAO1. PLoS ONE, 11(10).

[34] Fazi, S., Bandla, A., Pizzetti, I., & Swarup, S. (2016). Microbial biofilms as one of the key elements in modulating ecohydrological processes in both natural and urban water corridors. Ecohydrology and Hydrobiology, 16(1), 33–38.

2015

[35] Ravichandran, A., Ramachandran, M., Suriyanarayanan, T., Wong, C. C., & Swarup, S. (2015). Global regulator MorA affects virulence-associated protease secretion in Pseudomonas aeruginosa PAO1. PLoS ONE, 10(4).

[36] Mynampati, K. C., Lee, Y. J., Wijdeveld, A., Reuben, S., Samavedham, L., Kjelleberg, S., & Swarup, S. (2015). RhizoFlowCell system reveals early effects of micropollutants on aquatic plant rhizosphere. Environmental Pollution, 207, 205–210.

[37] Patkar, R. N., Benke, P. I., Qu, Z., Chen, Y. Y. C., Yang, F., Swarup, S., & Naqvi, N. I. (2015). A fungal monooxygenase-derived jasmonate attenuates host innate immunity. Nature Chemical Biology, 11(9), 733–740.

[38] Saxena, G., Marzinelli, E. M., Naing, N. N., He, Z., Liang, Y., Tom, L., Ping, H., Josh, U.M., Reuben, S., Mynampati, K.C., Mishra, S., Umashankar, S., Mitra, S., Andersen, G., Kjelleberg, S.,  & Swarup, S. (2015). Ecogenomics reveals metals and land-use pressures on microbial communities in the waterways of a megacity. Environmental Science and Technology, 49(3), 1462–1471.

[39] Benke, P. I., Vinay Kumar, M. C. S., Pan, D., & Swarup, S. (2015). A mass spectrometry-based unique fragment approach for the identification of microcystins. Analyst, 140(4), 1198–1206.

2014

[40] Mishra, S., Lee, W. A., Hooijer, A., Reuben, S., Sudiana, I. M., Idris, A., & Swarup, S. (2014). Microbial and metabolic profiling reveal strong influence of water table and land-use patterns on classification of degraded tropical peatlands. Biogeosciences, 11(7), 1727–1741.

[41] Reuben, S., Banas, K., Banas, A., & Swarup, S. (2014). Combination of synchrotron radiation-based Fourier transforms infrared microspectroscopy and confocal laser scanning microscopy to understand spatial heterogeneity in aquatic multispecies biofilms. Water Research, 64, 123–133.

2013

[42] Reuben, S., Rai, A., Pillai, B. V. S., Rodrigues, A., & Swarup, S. (2013). A bacterial quercetin oxidoreductase quoa-mediated perturbation in the phenylpropanoid metabolic network increases lignification with a concomitant decrease in phenolamides in arabidopsis. Journal of Experimental Botany, 64(16), 5183–5194.

[43] Nagarajan, K., Loh, K.-C., & Swarup, S. (2013). Bioinformatics and molecular biology for the quantification of closely related bacteria. Applied Microbiology and Biotechnology, 97(14), 6489–6502.

[44] Qian, C., Ching Wong, C., Swarup, S., & Chiama, K.-H. (2013). Bacterial tethering analysis reveals a ‘run-reverse-turn’ mechanism for pseudomonas species motility. Applied and Environmental Microbiology, 79(15), 4734–4743.

2012

[45] Reuben, S., Chua, C. L. N., Fam, K. D., Thian, Z. Y. A., Kang, M. K., & Swarup, S. (2012). Bacterial diversity on different surfaces in urban freshwater. Water Science and Technology, 65(10), 1869–1874.

[46] Zhang, W. C., Ng, S.-C., Yang, H., Rai, A., Umashankar, S., Ma, S., Soh, B.S., Sun, L.L., Tai, B.C., Nga, M.E., Bhakoo, K.K., Jayapal, S.R., Nichane, M., Yu, Q., Ahmed, D.A., Tan, C., Sing, W.P., Tam, J., Thirugananam, A., Noghabi, M.S., Pang, Y.H., Ang, H.S., Mitchell, W., Robson, P., Kaldis, P., Soo, R.A., Swarup, S., Lim, E.H., Lim, B. (2012). Glycine decarboxylase activity drives non-small cell lung cancer tumor-initiating cells and tumorigenesis. Cell, 148(1–2), 259–272.

2011

[47] Biswas, A., Rao, R., Umashankar, S., Mynampati, K. C., Reuben, S., Parab, G., & Swarup, S. (2011). datPAV-an online processing, analysis and visualization tool for exploratory investigation of experimental data. Bioinformatics, 27(11), 1585–1586.

 

Book chapter

2020

[1]   Bandla, A., Pavagadhi, S., & Swarup, S. (2020). Harnessing Soil Microbiomes for Creating Healthy and Functional Urban Landscapes. Soil Analysis: Recent Trends and Applications, 325–338.

Conference 2019

[1]   Saxena, G., Pavagadhi, S., & Swarup, S. (2019). Live- Exudation Assisted Phytobiome Culturing System (LEAP-CS) to characterize metabolic, molecular, and physiological phenotypes. miCROPe. 2-5 December, Vienna, Austria.

[2]   Pan, D., Pavagadhi, S., Umashankar, S., Rai, A., Benke, P.I., Rai, M., Saxena, G., Gangu, V., & Swarup, S. (2019). Integrative omics analysis reveals resource partitioning strategies during toxin production in Microcystis aeruginosa. Metabolomics, 23-27 June, Hague.

[3]   Saxena, G., Liang, Y., Pavagadhi, S., Miko, P.C.H., Yoon Ting, Y., & Swarup, S. (2019). A novel plant-microbiome co-culturing system reveals key associations of specific metabolites with plant growth and stress tolerance. Metabolomics, 23-27 June, The Hague (keynote presentation).

[4] Akhtar, H., Lupascu, M., Pavagadhi, S., Miko, P.C.H., N. Bisht, R. S. Sukri, Smith, E. L. Thomas, R.A.C., & Swarup, S. (2019). Effects of post-fire vegetation structure on CH4 emissions from a degraded tropical peatland in Brunei. Geophysical Research Abstracts, 21(1).