FusoBase: an online Fusobacterium comparative genomic analysis platform

Abstract

Fusobacterium are anaerobic gram-negative bacteria that have been associated with a wide spectrum of human infections and diseases. As the biology of Fusobacterium is still not well understood, comparative genomic analysis on members of this species will provide further insights on their taxonomy, phylogeny, pathogenicity and other information that may contribute to better management of infections and diseases. To facilitate the ongoing genomic research on Fusobacterium, a specialized database with easy-to-use analysis tools is necessary. Here we present FusoBase, an online database providing access to genome-wide annotated sequences of Fusobacterium strains as well as bioinformatics tools, to support the expanding scientific community. Using our custom-developed Pairwise Genome Comparison tool, we demonstrate how differences between two user-defined genomes and how insertion of putative prophages can be identified. In addition, Pathogenomics Profiling Tool is capable of clustering predicted genes across Fusobacterium strains and visualizing the results in the form of a heat map with dendrogram.

Database url: http://fusobacterium.um.edu.my.

Figure 1.

Four Tier Web application architecture of FusoBase.

Figure 2.

Browsing Fusobacterium strains. (A) Front page of FusoBase. (B) Overview of Fusobacterium species. (C) Overview of strains of F. nucleatum species. (D) List of putative ORFs in F. nucleatum ATCC10953. (E) ORF details page of the F. nucleatum ATCC10953.

Figure 3.

Real-time data searching system.

Figure 4.

The influence of different cutoffs of minimum percent identity (%), LT and MT on the final output of PGC.

Figure 5.

Comparison between two genomes using PGC reveals putative prophages. (A) Visualization of two aligned draft genomes, F. necrophorum 1_1_36S and F. necrophorum ATCC51357 revealing three insertions in the F. necrophorum 1_1_36S genome, which are associated with putative prophages as predicted by PHAST. (B) Overview of the CDSs in the putative prophages.

Figure 6.

The heat map generated using PathoProT, showing the cluster of Fusobacterium strains based on their virulence gene profiles. The threshold used in this analysis was 50% sequence identity and 50% sequence completeness.

Figure 7.

Pan- and core-genomes size prediction for Fusobacterium. The blue curve denotes the pan-genome size, while the red curve represents the core-genome size. The dot represents every genome comparison with different combination and the median values have been used to draw the curve.

Figure 8.

Gene distributions for the Fusobacterium genus. The circle in the middle denotes the core gene cluster for the Fusobacterium genus, while the seven segments surrounding the circle represent the number of specific genes for each Fusobacterium species.

Figure 9.

Strain-specific genes for the Fusobacterium genomes. Fusobacterium necrophum 1_1_36S has 1443 strain-specific gene clusters, which is the highest and F. nucleatum F0401 has the lowest, which is 27 gene clusters.