Asian Skin Microbiome

Metabolomics and Lipidomics: Metabolomics and lipidomics are key to understanding microbiome function as skin metabolites and lipid composition are defined by the skin microbiome. We are establishing capabilities to integrate skin metabolomes and lipidomes, with skin microbiome data to better understand how each impact and interact with one another.

Metatranscriptomics: We are developing robust, reproducible, and validated metatranscriptomic technologies from skin samples. This, in turn, will provide invaluable insight into the various functions of the skin microbiome.

Fungal strain-level analysis: Skin mycobiome analysis is limited by the resolution of marker gene-based approaches and a lack of eukaryotic reference genomes. We have expanded our unique reference datasets and are exploring long-read sequencing technologies for better resolution and cost-effectiveness.

Selected Theme Publications

1. Bertrand, D., Shaw, J., Kalathiyappan, M., Ng, A.H.Q., Kumar, M.S., Li, C., Dvornicic, M., Soldo, J.P., Koh, J.Y., Tong, C., Ng, O.T., Barkham, T., Young, B., Marimuthu, K., Chng, K.R., Sikic, M., Nagarajan, N., 2019. Hybrid metagenomic assembly enables high-resolution analysis of resistance determinants and mobile elements in human microbiomes. Nat Biotechnol 37, 937–944. doi: org/10.1038/s41587-019-0191-2

2. Li, C., Chng, K.R., Kwah, J.S., Av-Shalom, T.V., Tucker-Kellogg, L., Nagarajan, N., 2019. An expectation-maximization algorithm enables accurate ecological modeling using longitudinal microbiome sequencing data. Microbiome 7, 118. doi: org/10.1186/s40168-019-0729-z

Defining skin microbiome function: We have collected skin physiology, health state, consumer-relevant skin health data, metabolite, lipid, and microbiome samples from multiple body sites. We are using this metagenomics, metabolomics, and lipidomic data to generate functional information. To enable further functionalization, we have collected and are investigating a series of locally isolated microbial strains to define Singapore's microbial strain diversity.

Investigating Natural Life Changes: Puberty and menopause are critical biological phases where hormonal changes impact skin physiology and disease predisposition. We collect data from subjects in these vital phases of life and sample individuals poised for these hormonal skin and microbial changes. We hypothesize that the microbial community will change due to sebaceous gland activity and hormonal changes, which we will capture through lipidomic and blood hormone analyses.

Probing with interventions: We are -studying the skin fungal community's targeted removal using Pyrithione Zinc (ZPT), a common anti-fungal ingredient in many consumer care products. These studies shed light on how the fungal community contributes to skin cytokine signalling and "talks" with the immune system.

Selected Theme Publications

1. Leong, C., Wang, J., Toi, M.J., Lam, Y.I., Goh, J.P., Lee, S.M., Dawson, T.L., 2021. Effect of zinc pyrithione shampoo treatment on skin commensal Malassezia. Medical Mycology 59, 210–213. doi: org/10.1093/mmy/myaa068

2. Ambaw, Y.A., Pagac, M.P., Irudayaswamy, A.S., Raida, M., Bendt, A.K., Torta, F.T., Wenk, M.R., Dawson, T.L., 2021. Host/Malassezia Interaction: A Quantitative, Non-Invasive Method Profiling Oxylipin Production Associates Human Skin Eicosanoids with Malassezia. Metabolites 11, 700. doi: org/10.3390/metabo11100700

Culture conditions and microbial metabolism: We are developing polymicrobial cultures to model the skin microbiome reproducibly. Conditions are systematically varied to study their impact on the in vitro community.  Microbial cultures are used in combination with our reconstructed human skin model to mimic body’s microenvironments. This allows us to investigate clinical and consumer-relevant states such as malodour, dry/oily, or inflamed skin.

In vitro models using skin tissue-like materials: As an intermediate between pure microbial cultures and living co-cultures, we are developing models based on minimal nutrients to more naturally mimic skin surface and support microbial cultures. The simplicity of such models provides a useful intermediate for screening microbiome responses.

Living skin co-culture models: We use reconstructed skin models with specific alterations to mimic target skin conditions cultured with microbes or basic microbial communities to study host-microbe interactions. These living skin models provide a means for analytical investigations into host-microbe interactions.

Selected Theme Publications

1. Tay, A.S.L., Li, C., Nandi, T., Chng, K.R., Andiappan, A.K., Mettu, V.S., de Cevins, C., Ravikrishnan, A., Dutertre, Wong, X.F.C.C., Ng, A.H.Q., Matta, S.A., Ginhoux, F., Rötzschke, O., Chew, F.T., Tang, M.B.Y., Yew, Y.W., Nagarajan, N., Common, J.E.A., 2021. Atopic dermatitis microbiomes stratify into ecologic dermotypes enabling microbial virulence and disease severity. Journal of Allergy and Clinical Immunology 147, 1329–1340. doi: org/10.1016/j.jaci.2020.09.031

2. Vijaya Chandra, S.H., Srinivas, R., Dawson, T.L., Common, J.E., 2021. Cutaneous Malassezia: Commensal, Pathogen, or Protector? Front. Cell. Infect. Microbiol. 10, 614446.
doi: org/10.3389/fcimb.2020.614446