RESEARCH
We co-exist with complex communities of micro-organisms (the microbiome) which play important roles in maintaining health or exacerbating disease. For example, several gut microbes produce butyrate which promotes gut epithelial health, while other skin microbes can contribute to body odour or skin irritation. Although shotgun sequencing of microbial DNA fragments (metagenomics) is a powerful tool to study the diverse species present in a community, it is a composite snapshot of living, dead, active and inactive organisms. New approaches and technologies can complement metagenomics to study microbiome function in vivo or in situ, thus aiding efforts to leverage these microbes or their products for clinical benefits.
Our research is themed around uncovering native host-microbial interactions using RNA and spatial-omics technologies, with the goal of accelerating microbiome research towards clinical and functional relevance. Data from these techniques can be used to identify expressed host and microbial genes that are signatures of disease, or to chart how microbial species and host cells co-localize in specific tissue microenvironments (spatial distributions as a “smoking gun”). Knowledge of expressed microbial RNAs can be further complemented with functional predictions based on sequence annotations and in silico folding of their encoded peptides/proteins.
Ongoing projects include:
1) Applying RNA technologies to study the activity of the skin microbiome in disease cohorts e.g. eczema or acne with longitudinal sampling (before and after clinical resolution).
2) Optimizing and comparing different spatial-omics technologies to map host and microbial distributions in colorectal cancer tissues.
Selected Publications
- Tham EH, Chia M, Riggioni C, Nagarajan N, Common JEA, Kong HH. The skin microbiome in pediatric atopic dermatitis and food allergy. Allergy. 2024
- Tan CCS, Ko KKK, Chen H, Liu J, Loh M, SG10K Health Consortium, Chia M*, Nagarajan N*. No evidence for a common blood microbiome based on a population study of 9,770 healthy humans. Nat Microbiol. 2023;8(5):973–85.
- Gounot JS*, Chia M*, Bertrand D*, Saw WY, Ravikrishnan A, Low A, et al. Genome-centric analysis of short and long read metagenomes reveals uncharacterized microbiome diversity in Southeast Asians. Nat Commun. 2022;13(1):6044.
- Chia M, Naim ANM, Tay ASL, Lim K, Chew KL, Yow SJ, et al. Shared signatures and divergence in skin microbiomes of children with atopic dermatitis and their caregivers. Journal of Allergy and Clinical Immunology. 2022;150(4):894–908.
- Chia M, Tresenrider A, Chen J, Spedale G, Jorgensen V, Ünal E, et al. Transcription of a 5’extended mRNA isoform directs dynamic chromatin changes and interference of a downstream promoter. Elife. 2017;6:e27420.
- Chia M*, Li C*, Marques S, Pelechano V, Luscombe NM, van Werven FJ. High-resolution analysis of cell-state transitions in yeast suggests widespread transcriptional tuning by alternative starts. Genome Biol. 2021;22:1–37.
* denotes equal contribution