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Chapter 1 : Taxonomy of the Family

Authors: Lies Debruyne1, Dirk Gevers2, Peter Vandamme3
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Affiliations: 1: Laboratory of Microbiology, Ghent University, K.L. Ledeganckstraat 35, B-9000 Gent, Belgium; 2: Bioinformatics and Evolutionary Genomics, Ghent University/VIB, Technologiepark 927, B-9052 Gent, Belgium; 3: Laboratory of Microbiology, Ghent University, K.L. Ledeganckstraat 35, B-9000 Gent, Belgium
Content Type: Monograph
Publication Year: 2008

Category: Bacterial Pathogenesis

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Abstract:

This chapter presents an overview of the biological diversity of species and species and also addresses the taxonomic information that has become available through whole-genome sequence analysis. Classical biochemical tests routinely used for the identification of clinical bacteria often yielded negative or variable results within species. This poor biochemical reactivity and lack of clear-cut differential characters led to the wide application of vernacular names for many groups of Campylobacter-like organisms (CLOs). Some of the CLO groups were later classified as novel species, but several were identified as biochemical variants of well-known species. The first isolated was almost certainly . In 1914, a researcher observed a vibrio, later classified as , in sputum of a patient with bronchitis. Similar bacteria isolated from the bovine vagina and semen were classified as . During a study of the bacterial flora of the cloacae of whooping cranes, 10 atypical isolates were recovered on two separate occasions and were classified as . Strain NP4, isolated from groundwater with high arsenic concentrations, is classified as a species on the basis of 16S rRNA gene sequence analysis, and it differs from the other isolates in its carbon source and electron acceptor usage profiles. Representative strains of species were included in a polyphasic taxonomic study to elucidate their taxonomic status. Strains have been isolated from superficial ulcers and soft tissue infections, urethritis, vaginosis, and periodontal disease.

Citation: Debruyne L, Gevers D, Vandamme P. 2008. Taxonomy of the Family , p 3-25. In Nachamkin I, Szymanski C, Blaser M (ed), , Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815554.ch1

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Taxonomy of the Family Campylobacteraceae
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Citation: Debruyne L, Gevers D, Vandamme P. 2008. Taxonomy of the Family , p 3-25. In Nachamkin I, Szymanski C, Blaser M (ed), , Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815554.ch1
/content/10.1128/9781555815554.ch01.ch01fig01
Figure 1.
Phylogenetic tree of the family and related bacteria, based on percentage of 16S rRNA gene sequence similarity.
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10.1128/9781555815554/f0006-01.gif
Image of Figure 1.
Figure 1.

Phylogenetic tree of the family and related bacteria, based on percentage of 16S rRNA gene sequence similarity.

Citation: Debruyne L, Gevers D, Vandamme P. 2008. Taxonomy of the Family , p 3-25. In Nachamkin I, Szymanski C, Blaser M (ed), , Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815554.ch1
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Figure 2.
Whole-genome-based phylogeny of and related bacteria. Out of 365 core gene families, a concatenation of 60 carefully selected genes was used to estimate the phylogeny of these bacteria by maximum likelihood. Orthologous protein families were determined by OrthoMCL ( ). Protein sequence alignments were generated by Muscle ( ), and poorly conserved regions were trimmed by Gblocks ( ). Phylogenetic trees with 100 bootstrap replicates were obtained by the PhyML algorithm ( ) with a JTT amino acid substitution matrix and a discrete gamma model. All nodes had 100% bootstrap support.
10.1128/9781555815554/f0007-01_thmb.gif
10.1128/9781555815554/f0007-01.gif
Image of Figure 2.
Figure 2.

Whole-genome-based phylogeny of and related bacteria. Out of 365 core gene families, a concatenation of 60 carefully selected genes was used to estimate the phylogeny of these bacteria by maximum likelihood. Orthologous protein families were determined by OrthoMCL ( ). Protein sequence alignments were generated by Muscle ( ), and poorly conserved regions were trimmed by Gblocks ( ). Phylogenetic trees with 100 bootstrap replicates were obtained by the PhyML algorithm ( ) with a JTT amino acid substitution matrix and a discrete gamma model. All nodes had 100% bootstrap support.

Citation: Debruyne L, Gevers D, Vandamme P. 2008. Taxonomy of the Family , p 3-25. In Nachamkin I, Szymanski C, Blaser M (ed), , Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815554.ch1
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Figure 3.
Genetic diversity among genomes of and related bacteria. Every data point represents a whole-genome comparison between two genomes (both intra- and interspecies) and shows the percentage ANI on the axes plotted against the percentage of gene content similarity on the axes. Only comparisons with ANI values above 70% are shown because this is the range in which ANI is considered to be a robust and sensitive method for measuring evolutionary relatedness ( ). ANI values were calculated as described previously ( ), and gene content similarity values were calculated on the basis of reciprocal best BLASTp hits.
10.1128/9781555815554/f0008-01_thmb.gif
10.1128/9781555815554/f0008-01.gif
Image of Figure 3.
Figure 3.

Genetic diversity among genomes of and related bacteria. Every data point represents a whole-genome comparison between two genomes (both intra- and interspecies) and shows the percentage ANI on the axes plotted against the percentage of gene content similarity on the axes. Only comparisons with ANI values above 70% are shown because this is the range in which ANI is considered to be a robust and sensitive method for measuring evolutionary relatedness ( ). ANI values were calculated as described previously ( ), and gene content similarity values were calculated on the basis of reciprocal best BLASTp hits.

Citation: Debruyne L, Gevers D, Vandamme P. 2008. Taxonomy of the Family , p 3-25. In Nachamkin I, Szymanski C, Blaser M (ed), , Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815554.ch1
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Figure 4.
In silico MLSA analysis with variable loci count. For a variable number ( = 1–15) of concatenated loci ( axis) randomly selected from the set of best-performing genes ( Table 1 ), the differences in tree topology and branch lengths with the whole-genome-based phylogeny was determined and expressed as a tree distance value ( axis). For each number of loci, the procedure was repeated 100 times, and the distributions of the distances between the maximum likelihood trees are plotted as box and whisker plots.
10.1128/9781555815554/f0011-01_thmb.gif
10.1128/9781555815554/f0011-01.gif
Image of Figure 4.
Figure 4.

In silico MLSA analysis with variable loci count. For a variable number ( = 1–15) of concatenated loci ( axis) randomly selected from the set of best-performing genes ( Table 1 ), the differences in tree topology and branch lengths with the whole-genome-based phylogeny was determined and expressed as a tree distance value ( axis). For each number of loci, the procedure was repeated 100 times, and the distributions of the distances between the maximum likelihood trees are plotted as box and whisker plots.

Citation: Debruyne L, Gevers D, Vandamme P. 2008. Taxonomy of the Family , p 3-25. In Nachamkin I, Szymanski C, Blaser M (ed), , Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815554.ch1
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Tables

Taxonomy of the Family Campylobacteraceae
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Citation: Debruyne L, Gevers D, Vandamme P. 2008. Taxonomy of the Family , p 3-25. In Nachamkin I, Szymanski C, Blaser M (ed), , Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815554.ch1
/content/10.1128/9781555815554.ch01.ch01tab01
Table 1.
Functional classification of 60 selected phylogenetic markers for the
Generic image for table
Table 1.

Functional classification of 60 selected phylogenetic markers for the

Citation: Debruyne L, Gevers D, Vandamme P. 2008. Taxonomy of the Family , p 3-25. In Nachamkin I, Szymanski C, Blaser M (ed), , Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815554.ch1

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