Microbial Ecology Tools

At the Swarup lab, we combine extensive field observations and controlled lab-based experiments with state-of-the-art omics techniques, to understand how microbiomes assemble and function. We study microbial assemblages on both abiotic and host-associated systems (holobionts).
We collaborate with government agencies and relevant stakeholders to conduct extensive field work, involving sample collection and manipulative experiments, in highly challenging urban and natural environments. An extensive set of physico-chemical variables, characterizing the ecosystems are also simultaneously logged. Manipulative experiments using field samples are conducted at the Van Kleef Centre (VKC) using an array of custom-built flumes. The facility is located just beside the Sungei Pandan river, enabling access to a continuous flow of freshwater to feed the flumes. Lab-based experiments involve both model-based systems and simplified analogs to more complex systems, to understand mechanisms involved in assembly and functional response.
Multi-omics analysis involves a comprehensive characterization of biomolecules, extracted from the samples. We routinely generate massive sequence-based datasets, leveraging the sequencing capacity available at the Singapore Centre for Environmental Life Sciences Engineering (SCELSE). Marker gene analysis and metagenomics are employed to query the taxonomic and functional composition, while metatranscriptomics is used to gain insights into the realized genomic potential. We also leverage high-performance computing facilities, available through the National Supercomputing Centre Singapore (NSCC), to process these datasets, to gain quick biological and ecological insights. We also specialize in advanced mass-spectrometry based liquid chromatography techniques, using state-of-the-art instruments available at the NUS Environmental Research Institute (NERI), to profile the diverse array of small molecules (or metabolites) present both in the intracellular and extracellular space. Advanced liquid-handling robotic systems and a biological foundry, available through the Synthetic biology consortium SynCTI enable high-throughput molecular assays and analysis.
Following are some of the tools that we routinely use for different analysis

Metagenomics/Metatranscriptomics:
1.DIAMOND - Rapid alignment of short DNA/RNA reads against protein/DNA databases
2.Ribotagger - Inferring community membership from metagenomes/metatranscriptomes using 16S fragments
3.Centrifuge/Kraken - Inferring community membership from metagenomes/metatranscriptomes using functional markers
4.MEGAHIT - Assembly of complex microbiomes
5.USEARCH/VSEARCH/QIIME - Marker gene analysis
6.ARB Tools - Design of primers, in situ hybridization probes
7.CIRCOS - Advanced visualization of genomic assemblies
8.R Packages (Bioconductor suite, vegan) - Multivariate statistical analysis

Flow Cytometry and Cell Sorting:
1. FlowJo

Metabolomics:
1. XCMS
2. Metlin