Taxonomic classification of living organisms and understanding their ancestry is the basis of all biology. Microorganisms such as bacteria represent the most diverse branch of life, and are found in every environment on earth capable of supporting life. We now understand that bacteria are involved in almost every aspect of our daily life, yet we have a poor understanding of how these organisms are related to each other and the full extent of their genetic capabilities. Confusing this issue further is the fact that bacteria are capable of swapping their genes between each other in a process called Lateral Gene Transfer (LGT).

Rather than receiving DNA solely from their ‘parents’ (as humans do) bacteria can augment their genome with genetic material from distantly related species that live alongside them, or even absorb DNA from the environment and utilise it. This has led to the observation that rather than a ‘tree’ of life, with genes passed down through generations, bacteria are more of a web, with genes passed down, but also sideways and back up to the previous generation.

At ACE we are interested with teasing apart these effects in order to create the most comprehensive understanding of the evolution of microorganisms to date. By making use of over 100,000 bacterial genomes this project aims to study bacterial descent through two lenses.

1. Objective classification of prokaryotes

Taxonomy is an organizing principle of biology and is ideally based on evolutionary relationships among organisms. We have proposed a standardized taxonomic classification of bacterial and archaeal genomes by placing them into domain-specific, concatenated protein reference trees. Taxa are required to be monophyletic with respect to these trees and normalized using an approximation to time of divergence. This taxonomy is available at

2. Lateral gene transfer and the network of life

While bacteria have been shown to pass genes between different species, or to incorporate genetic elements from non-bacterial sources, the degree to which this happens throughout the entire bacterial domain is unclear. By studying the evolution of genes independently of the strict inheritance model traditionally used, we hope to ascertain the degree to which LGT occurs in bacteria and understand the relative importance of LGT in driving bacterial colonisation and survival in environments from the frozen arctic to geothermal sites.

While neither of these models will perfectly explain the manner in which bacteria evolve, by analysing bacteria using both approaches side by side we can draw powerful inferences about the relative contributions of these two mechanisms on the ecology of microorganisms and to better understand the processes that have driven their expansion across the globe.

Principal investigator: Prof. Phil Hugenholtz
Consultant: Dr. Donovan Parks
Software Developer: Mr. Pierre Chaumeil
ARC Future Fellow: Dr. Christian Rinke
Senior Research Assistant: Dr. Maria Chuvochina


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University of Queensland
Brisbane, Australia

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