Research Activities

Bioinformatics and Metagenomics

High-throughput sequencing provides a powerful way to study the ‘unexplored’ and uncultured diversity of microbial communities. My research involves the development of new computational algorithms and pipelines 1) for the processing of sequencing data from new sequencing strategy, including PacBio long read sequencing (Song et al., 2019) and the recently released Nanopore’s adaptive sampling technology; 2) to improve the quality of metagenome-assembled genomes (Song and Thomas, 2017; 3) to link MAGs with their often-missing 16S rRNA gene sequences that are commonly used in phylogenetic analysis and environmental surveys (Song et al., 2022).

Evolution and metabolic interaction of bacteria-sponge symbiosis

Complex multicellular organisms often host complex communities of microbial symbionts, which are essential for their health and function. Marine sponges are the oldest extant metazoan that sister to all other animals, making them unique models for the study of animal-microbe interactions that could be core features of all extant forms of symbioses. Importantly, many sponges harbour dense and diverse microorganisms that often form stable and specific associations (Zhang, Song et al., 2019), making them emerging models in the study of metazoan-microbe symbiosis that could reveal a wide spectrum of symbiotic strategies (Zhang, Song et al., 2022). In addition, knowledge of sponge symbiosis will help to better understand the symbiosis of all animals that have critical ecosystem roles in all marine benthic habitats, including coral, mussels and the deep-sea tubeworms.

Horizontal gene transfer (HGT) and microbial evolution/adaptation

HGT is considered an important driver of microbial evolution and niche adaptation. My research involves the identification of HGTs (Song et al., 2019, Microbiome) in microorganisms from the natural environments, as well as assessment of the role of HGT in the adaptation of microorganisms to different hosts, including marine sponges (Robbins, Song et al., 2021), macroalgae and human. For example, we found that HGTs in the macroalgal biofilms were frequently involved in genes for nutrient transport and degradation, as well as stress responses, which are considered beneficial for bacteria living in this host-associated niche (Song et al., 2021).