Evolutionary relationships of Fusobacterium nucleatum based on phylogenetic analysis and comparative genomics

Institute : University of Miguel Hernández, Alicante, SPAIN
Programming Language : PERL
Operating System : Linux Fedora Core 2
Software Tools : CVS, gnuplot
Bioinformatics Tools : BLAST, Clustalw, PHYLIP, Reputer
Team Size : 5
Duration : Jan. 2004 - Jul. 2004


The phylogenetic position and evolutionary relationships of Fusobacteria remain uncertain. Especially intriguing is their relatedness to low G+C Gram positive bacteria (Firmicutes) by ribosomal molecular phylogenies, but their possession of a typical gram negative outer membrane. Taking advantage of the recent completion of Fusobacterium nucleatum genome sequence we have examined the evolutionary relationships of Fusobacterium genes by phylogenetic analysis and comparative genomics tools. The results indicate that Fusobacterium has a core genome of very different nature to other bacterial lineages, and branches out at the base of Firmicutes. However, depending on the method used, 35-56% of Fusobacterium genes appear to have a xenologous origin from bacteroidetes, proteobacteria, spirochaetes and the Firmicutes themselves. Many instances of similarity to other inhabitants of the dental plaque that have been sequenced were found, suggesting that the close physical contact found there might facilitate horizontal gene transfer. A high number of hypothetical ORFs with unusual codon usage and short lengths were found and hypothesized to be remnants of transferred genes that were discarded. Some proteins and operons are also hypothesized to be of mixed ancestry. A large portion of the Gram-negative cell wall-related genes seems to have been transferred from proteobacteria.


Mira A., Pushker R., Legault B. A., Moreira D. and Rodríguez-Valera F. (2004) Evolutionary relationships of Fusobacterium nucleatum based on phylogenetic analysis and comparative genomics. BMC Evolutionary Biology, 4:50.


© 2004 Mira et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

The electronic version of this article is the complete one and can be found online at: