title: Comparative Genome Analysis of Fusobacterium nucleatum.
abstract: Fusobacterium nucleatum is considered to be a key oral bacterium in recruiting periodontal pathogens into subgingival dental plaque. Currently F. nucleatum can be subdivided into five subspecies. Our previous genome analysis of F. nucleatum W1481 (referred to hereafter as W1481), isolated from an 8-mm periodontal pocket in a patient with chronic periodontitis, suggested the possibility of a new subspecies. To further investigate the biology and relationships of this possible subspecies with other known subspecies, we performed comparative analysis between W1481 and 35 genome sequences represented by the five known Fusobacterium subspecies. Our analyses suggest that W1481 is most likely a new F. nucleatum subspecies, supported by evidence from phylogenetic analyses and maximal unique match indices (MUMi). Interestingly, we found a horizontally transferred W1481-specific genomic island harboring the tripartite ATP-independent (TRAP)-like transporter genes, suggesting this bacterium might have a high-affinity transport system for the C4-dicarboxylates malate, succinate, and fumarate. Moreover, we found virulence genes in the W1481 genome that may provide a strong defense mechanism which might enable it to colonize and survive within the host by evading immune surveillance. This comparative study provides better understanding of F. nucleatum and the basis for future functional work on this important pathogen.
authors.affiliation: Genome Informatics Research Laboratory, Centre for Research in Biotechnology for Agriculture (CEBAR), High Impact Research Building, University of Malaya, Kuala Lumpur, Malaysia Department of Oral and Craniofacial Sciences, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia.
authors.forename: Mia Yang
authors.initials: MY
authors.lastname: Ang
authors.affiliation: Genome Informatics Research Laboratory, Centre for Research in Biotechnology for Agriculture (CEBAR), High Impact Research Building, University of Malaya, Kuala Lumpur, Malaysia.
authors.forename: Avirup
authors.initials: A
authors.lastname: Dutta
authors.affiliation: Genome Informatics Research Laboratory, Centre for Research in Biotechnology for Agriculture (CEBAR), High Impact Research Building, University of Malaya, Kuala Lumpur, Malaysia Department of Oral and Craniofacial Sciences, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia.
authors.forename: Wei Yee
authors.initials: WY
authors.lastname: Wee
authors.affiliation: School of Oral & Dental Sciences, University of Bristol, Bristol, United Kingdom.
authors.forename: David
authors.initials: D
authors.lastname: Dymock
authors.affiliation: Department of Oral and Craniofacial Sciences, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia Oral Cancer Research and Coordinating Centre (OCRCC), Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia.
authors.forename: Ian C
authors.initials: IC
authors.lastname: Paterson
authors.affiliation: Genome Informatics Research Laboratory, Centre for Research in Biotechnology for Agriculture (CEBAR), High Impact Research Building, University of Malaya, Kuala Lumpur, Malaysia Department of Oral and Craniofacial Sciences, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia Genome Solutions Sdn Bhd, Suite 8, Innovation Incubator UM, Level 5, Research Management & Innovation Complex, University of Malaya, Kuala Lumpur, Malaysia l.choo@genomesolutions.com.my.
authors.forename: Siew Woh
authors.initials: SW
authors.lastname: Choo
mesh_terms: D016967:Fusobacterium nucleatum / Q000145:classification / Q000235:genetics*; D022761:Gene Transfer, Horizontal; D016680:Genome, Bacterial; D044404:Genomic Islands; D010802:Phylogeny
keywords:  Fusobacterium nucleatum; F. nucleatum W1481; comparative genomics