Research Overview

We utilize genomic, metagenomic, and bioinformatic tools to investigate microbial genome evolution and diversity.

We are interested in studying microorganisms because: 1) they are the most genetically and ecologically diverse organisms on Earth, 2) they are the most important components of our biotic environment and influence almost every aspect of human life, and 3) they have abundant genomic information available for examining the genetic basis of diversification. The recent research projects in our lab encompass the following three areas:

Genome evolution in host-dependent bacteria

In microbial evolution, the development of a host-dependent lifestyle (such as symbiosis or parasitism) has profound effects in shaping the genomes of host-associated microorganisms. Using selected groups within the class Mollicutes, including phytoplasmas (a group of important plant pathogens; see Chen et al. 2012, PLOS ONE; Chung et al. 2013, PLOS ONE) and spiroplasmas (mostly insect symbionts; see Lo et al. 2013, BMC Genomics; Ku et al. 2013, Genome Biol Evol; Lo et al. 2013, Genome Biol Evol; Chang et al. 2014, Genome Biol Evol; Lo et al. 2015, Genome Biol Evol) as our main study system, we apply whole-genome sequencing to conduct comparative analysis. Our main goal in this area is to understand the genetic mechanisms and evolutionary processes involved in the adaptation to host-dependent lifestyles in these bacteria.

Biodiversity and functions of microbial communities

Naturally occurring microbial communities harbor extensive levels of biological diversity and control many important functions of the ecosystem. Traditionally, the characterization of these complex communities has been hindered by the technical limitation that most microorganisms cannot be cultured in laboratory. Due to the rapid advancements of metagenomic tools in recent years, now we can use culture-independent methods (e.g., sequencing of the microbial DNA recovered from environmental samples; see Ochman et al. 2010, PLOS Biol; Shelomi et al. 2013, BMC Res Notes; Liu et al. 2015, J Biotechnol) to study the species composition and gene functions of complex microbial communities. Through collaborations, our current interest in this area is to investigate the microbial communities in soil, animal guts, and industrial environments.

Global patterns of genome evolution in bacteria

To gain insight into the major determinants of genome complexity across diverse groups of bacteria, we take advantage of the complete genome sequences available from public databases to perform large-scale comparative analysis. Our research projects in this area are mainly focused on characterizing the evolution of non-coding regions and the evolution of overall genome size.

Our previous work demonstrated that an elevated level of genetic drift is the main determinant of genome reduction in bacteria, which is commonly observed among pathogens and endosymbionts (Kuo et al. 2009, Genome Res). Intriguingly, this trend is opposite to that observed in eukaryotes and is attributable to the differences in mutational input between the two major domains of life. Compared to eukaryotes, neutral mutations in most prokaryotes are strongly biased towards deletions and the extent of this deletional bias is a good predictor of gene density (Kuo & Ochman 2009, Genome Biol Evol). Furthermore, we documented a wide range of substitution rates across bacterial taxa (Kuo & Ochman 2009, Biol Direct) and found signature of positive selection for the removal of pseudogenes in Salmonella (Kuo & Ochman 2010, PLOS Genet).