GERMS platform for Microbial Genomics


  • Dr. Paola Flórez DE SESSIONS
  • GERMS wants to be your genomics partner for the investigation of microbial diseases in Singapore.

GERMS is a GIS platform that provides comprehensive genomics solutions for studying the role of microbes in human health and diseases. The GERMS platform integrates GIS’ extensive experimental and analytical expertise in the study of viruses, bacteria, fungi, parasites and microbiomes. The platform supports large cohort studies involving genome sequencing, transcriptomics, functional genomics, metagenomics as well as custom applications. We partner with research and clinical groups around the world to study health and infection in single patients to whole hospitals, communities and beyond. Some recent examples of GERMS-enabled projects include:

MRSA surveillance in a hospital
with Tan Tock Seng Hospital (TTSH), Singapore

Whole-genome phylogeny depicting the relationship between MRSA isolates (colored by ST type)
Methicillin-resistant Staphylococcus aureus (MRSA) infections pose a major threat in hospital environments, especially for patients with weakened immune systems, severe wounds and implants. TTSH and the GERMS platform are using whole-genome sequencing to study transmission patterns and monitor the evolution of the resistant, MRSA strains now circulating in Singapore.

Dengue transmission dynamics and vaccine targets
with Oxford University Clinical Research Unit (OUCRU), Vietnam

Hotspots and coldspots of evolution in the dengue genome during transmission from humans to mosquitoes
The incidence of dengue virus (DENV) infections has grown dramatically over the years with more than 390 million infections per year worldwide. Dengue viruses are extremely diverse and viral infections in a host produce a dynamic population of closely-related sequences that could confer an adaptive advantage. In collaboration with OUCRU we are using viral diversity analysis to track viral dynamics during transmission from infected patients to Aedes aegypti mosquitoes, identifying highly conserved regions in the genome that could serve as vaccine targets.

Sim et al. PLoS Neglected Tropical Diseases, 2015

Fungal life on human skin
with Proctor & Gamble (P&G), Singapore/USA and Institute of Medical Biology (IMB) A*STAR, Singapore

A novel gene family in Malassezia that is specifically up-regulated in nutrient deficient conditions
Fungi on human skin (primarily from the genus Malassezia) are known to cause a range of skin diseases from dandruff to seborrhoeic dermatitis (also known as cradle cap). P&G and IMB are collaborating with GERMS to apply comparative genomics and transcriptomics to identify novel gene families that could explain Malassezia’s ability to survive on lipids from skin, and could serve as therapeutic targets.

Wu et al. PLoS Genet., 2015

Microbiome development in early childhood
with Danone Nutricia Research, Holland/Singapore

This representative Sankey plot is an example of the taxonomical flow of information for our 16S output, sample origin was human stool.
We are becoming increasingly aware of the importance of early childhood nutrition on the effects on health and disease later in life. We are collaborating with Danone Nutricia Research to investigate the effect of a nutritional supplement on young children in this region, to further our understanding of bacteria in the gut and how these bacteria influence health.

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