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Genome sequence and identification of candidate vaccine antigens from the animal pathogen Dichelobacter nodosus

Nature Biotechnology volume 25, pages 569–575 (2007)Cite this article

Abstract

Dichelobacter nodosus causes ovine footrot, a disease that leads to severe economic losses in the wool and meat industries. We sequenced its 1.4-Mb genome, the smallest known genome of an anaerobe. It differs markedly from small genomes of intracellular bacteria, retaining greater biosynthetic capabilities and lacking any evidence of extensive ongoing genome reduction. Comparative genomic microarray studies and bioinformatic analysis suggested that, despite its small size, almost 20% of the genome is derived from lateral gene transfer. Most of these regions seem to be associated with virulence. Metabolic reconstruction indicated unsuspected capabilities, including carbohydrate utilization, electron transfer and several aerobic pathways. Global transcriptional profiling and bioinformatic analysis enabled the prediction of virulence factors and cell surface proteins. Screening of these proteins against ovine antisera identified eight immunogenic proteins that are candidate antigens for a cross-protective vaccine.

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Figure 1: Circular representation of the D. nodosus VCS1703A genome.
Figure 2: Overview of metabolism and transport in D. nodosus.
Figure 3: Immunoblot demonstrating recognition of D. nodosus proteins by pooled sera from experimentally infected sheep.

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Acknowledgements

The research was supported by an Initiative for Future Agriculture and Food Systems Grant No. 2001-52100 11445 from the USDA Cooperative State Research, Education, and Extension Service, and by grants from the Australian Research Council. D.P was the recipient of an Australian Postgraduate Award and a Monash Faculty of Medicine, Nursing, and Health Sciences Postgraduate Excellence Award. We thank I. McPherson for technical assistance, C. Whitchurch for helpful discussions, B. Cheetham for providing unpublished information and helpful discussions, and the TIGR faculty, sequencing facility and informatics group for expert advice and assistance.

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Author notes

  1. Garry S A Myers and Dane Parker: These authors contributed equally to this work.

  2. Department of Veterinary Science, University of Arizona, Tucson, Arizona 85721, USA.

Authors and Affiliations

  1. The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, 20850, Maryland, USA

    Garry S A Myers, Qinghu Ren, Jonathan H Badger, Jeremy D Selengut, Robert T DeBoy, Hervé Tettelin, William C Nelson, Ramana Madupu, Yasmin Mohamoud, Tara Holley, Nadia Fedorova, Hoda Khouri & Ian T Paulsen

  2. Australian Research Council Centre of Excellence in Structural and Functional Microbial Genomics, Monash University, Melbourne, 3800, Victoria, Australia

    Dane Parker, Keith Al-Hasani, Ruth M Kennan, John D Boyce, Victoria P McCarl, Xiaoyan Han, Steven P Bottomley, Richard J Whittington, Ben Adler & Julian I Rood

  3. Department of Microbiology, Monash University, Melbourne, 3800, Victoria, Australia

    Dane Parker, Keith Al-Hasani, Ruth M Kennan, John D Boyce, Xiaoyan Han, Ben Adler & Julian I Rood

  4. Victorian Bioinformatics Consortium, Monash University, Melbourne, 3800, Victoria, Australia

    Dane Parker, Torsten Seemann, Ben Adler & Julian I Rood

  5. Department of Biochemistry and Molecular Biology, Monash University, Melbourne, 3800, Victoria, Australia

    Victoria P McCarl, Steven P Bottomley & J Glenn Songer

  6. Faculty of Veterinary Science, University of Sydney, Sydney, 2570, New South Wales, Australia

    Richard J Whittington

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Correspondence to Ian T Paulsen.

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Supplementary information

Supplementary Fig. 1

Distribution of database hits to γ-proteobacteria, β-proteobacteria and other phylogenetic groups. (PDF 1132 kb)

Supplementary Fig. 2

Bootstrapped maximum parsimony tree of representative sequenced species from the β- and γ-proteobacteria. (PDF 73 kb)

Supplementary Fig. 3

Graphical representation of genes displaying variability using comparative genomic hybridization. (PDF 5083 kb)

Supplementary Fig. 4

Comparative genomic locations of type IV fimbrial biogenesis genes in D. nodosus and P. aeruginosa. (PDF 83 kb)

Supplementary Fig. 5

Graphical representation of the D. nodosus outer membrane protein locus. (PDF 71 kb)

Supplementary Fig. 6

Immunoblots demonstrating recognition of D. nodosus proteins by pooled sera from experimentally infected sheet. (PDF 316 kb)

Supplementary Table 1

Characteristics of strains used in CGH analysis. (PDF 66 kb)

Supplementary Table 2

Comparison of selected metabolic capabilities between organisms with small genome sizes. (PDF 93 kb)

Supplementary Table 3

Differentially expressed genes of D. nodosus when grown on hoof agar. (PDF 155 kb)

Supplementary Table 4

Oligonucleotide primers used for QRT-PCR. (PDF 83 kb)

Supplementary Table 5

Statistical comparison of normal and atypical regions of nucleotide composition within the D. nodosus genome. (PDF 83 kb)

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Myers, G., Parker, D., Al-Hasani, K. et al. Genome sequence and identification of candidate vaccine antigens from the animal pathogen Dichelobacter nodosus. Nat Biotechnol 25, 569–575 (2007). https://doi.org/10.1038/nbt1302

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