Research Features

For the characterization and description of bacterial taxa, unique phenotypic or physiological traits in conjunction with phylogenetic support, are required to differentiate closely related bacteria. However, the use of biochemical tests have been increasingly shown to provide unreliable results that are often not reproducible. In addition, databases for characters are often incomplete as a limited number of tests are often performed.

With the advances in genome sequencing, approaches for functional genomics have become increasingly popular. This allows for metabolic pathways to be predicted from genome sequences where all necessary genetic information for functioning systems are present. These approaches thus provide the opportunity to infer the metabolic capacity of organisms and provide the basis for many comparative genomics studies.

Dr Marike Palmer, who recently completed her PhD, employed this approach in an article, where biological processes were inferred that could be associated with the divergence of closely related bacterial species. In the article the shared gene sets of two bacterial genera, Pantoea and Tatumella, and the respective lineages within Pantoea were functionally annotated to aid in identifying taxon specifying characteristics. Overall, Pantoea was found to utilize a wider variety of energy sources in the form of carbohydrates, fatty acids and nucleotides and were able to recycle nutrients more efficiently. This may contribute to increased fitness under nutrient limiting conditions and play a role in the opportunistic nature of members of Pantoea.

This paper has already gained some traction in the scientific community after it was mentioned on the blog Microbiome Digest. It has also been retweeted a number of times and even gained some interest amongst the members of the public.


Palmer M, Steenkamp ET, Coetzee MPA, Blom J, Venter SN. (2018) Genome-based characterization of biological processes that differentiate closely related bacteria. Frontiers in Microbiology 9:113. 10.3389/fmicb.2018.00113 PDF