Siu-Kin Ng - Metagenomics analysis on historical samples
Microbiome composition and function are profoundly shaped by environmental factors, with major shifts driven by intensified anthropogenic pressures over the past centuries. This timeframe extends beyond the scope of conventional experimental or longitudinal studies commonly used to investigate microbiome dynamics. Historical specimens preserved in museums and herbaria represent an invaluable yet underutilized resources for exploring host-microbiome interactions across broad temporal and spatial scales. Conventionally, the removal of host DNA removal has been considered essential for accurate taxonomic assignment of metagenomic reads. However, this step is often impractical for historical samples as reference genomes for many host species are unavailable. Here, we demonstrate that host DNA content does not significantly affect metagenomics analyses in either contemporary or historical samples. Additionally, DNA molecules in historical samples are highly fragmented and vary widely in length, making conventional metagenomics analytic workflows suboptimal. We systematically evaluated the accuracy of metagenomic assignments in historical samples through k-mer analyses. Based on these findings, we propose a simple two-step approach in which reads are classified using two annotation databases constructed with k=24 and k=31. Simulation analyses show that this approach outperforms conventional pipeline by effectively recovering microbial signals from a broad range of fragment lengths, including those as short as 24 bp. In this talk, I will present our study that could provide a solid foundation for incorporating natural history collections into host-associated microbiome research for gaining valuable insights into the long-term effects of anthropogenic change on microbial communities.
About the Speaker
Dr Siu-Kin Ng is currently a postdoctoral researcher in Dr Rafal Gutaker’s team (the Royal Botanic Garden, Kew), where he investigates the dynamics of host-associated microbiomes in contemporary and historical rice samples. Before joining the team, he earned his PhD in genomics from the Hong Kong University of Science and Technology (HKUST) and subsequently completed a postdoctoral fellowship on gut microbiome at the Nanyang Technological University (NTU).