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Abstract:

is composed of three main genera, , , and , and is represented currently by 43 described or proposed species. Unlike spp., that are associated with warm-blooded avian and mammalian hosts, members of the and genera are non-host-associated, free-living, environmental organisms. spp. can grow aerobically, unlike , which are restricted to microaerobic and/or anaerobic environments. The organisms whose genomes have been or are being sequenced are (i) host-associated or free-living; (ii) nonpathogenic, human commensals, or human pathogens (oral or gastrointestinal); or (iii) food or environmental isolates. Analysis of these genomes alongside comparative genomics will provide clues pertaining to the genetic nature of pathogenicity, host association, environmental adaptation, and evolution. The chapter addresses the topics related to the and genomes. The coding sequences (CDSs) with assigned function are fairly consistent across the sequenced genomes, with an assigned function/total CDSs average of 45%. It is possible that many species are composed of multiple host-associated phylogenetic clusters. Comparative genomics of the and genomes has not identified any pathogenicity islands containing toxin-encoding genes or other virulence determinants. and species provide fertile ground for comparative genomics. Therefore, comparative genomics of and should provide insights into pathogenicity, host adaptation and specificity, evolution, and environmental adaptation and survival. The degree of variation within and is an important consideration.

Citation: Miller W, Parker C. 2011. and , p 49-65. In Fratamico P, Liu Y, Kathariou S (ed), Genomes of Foodborne and Waterborne Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555816902.ch4

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Figures

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Figure 1

Condensed phylogenetic tree, based on sequence similarity of the 16S rDNA sequences. 16S sequences representing known, characterized taxa are labeled. Species for which genomic sequencing projects have been completed or are currently in progress are underlined. Bootstrap values ( 75%) are shown.

Citation: Miller W, Parker C. 2011. and , p 49-65. In Fratamico P, Liu Y, Kathariou S (ed), Genomes of Foodborne and Waterborne Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555816902.ch4
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Figure 2

Whole genome comparisons of genes and proteins. (A) Average amino-acid identities of the proteomes. Values represent average amino-acid identities between the core protein sets = 764 proteins) of any two given proteomes. (B) Common and unique genes within selected genomes. The Venn diagram illustrates the number of shared or unique genes within the five completed genomes. subsp subsp. strains 11168, 1221, 81116, and 81-176 are members of the MLST clonal complexes, ST-21, ST-354, ST-283, and ST-42, respectively.

Citation: Miller W, Parker C. 2011. and , p 49-65. In Fratamico P, Liu Y, Kathariou S (ed), Genomes of Foodborne and Waterborne Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555816902.ch4
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Figure 3

Chromosomal locations of the plasticity regions and CJIEs. (A) Location of the plasticity regions of strain RM1221. Numbers in bold represent the RM1221 plasticity regions: regions 1 to 16 are equivalent to the strain NCTC 11168 regions from Taboada et al. and regions 17 and 18 are from Parker et al. ( ). (B) Location of the CJIEs of strain RM1221. CMLP (CJIE1): Mu-like phage; CJIE: integrated element.

Citation: Miller W, Parker C. 2011. and , p 49-65. In Fratamico P, Liu Y, Kathariou S (ed), Genomes of Foodborne and Waterborne Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555816902.ch4
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Figure 4

Flagellar clustering in strain RM4018 and phylogenetic analysis of flagellins. (A) Location of the flagellar genes of strain RM1221 and strain RM4018. The diagram is reprinted from reference . strain RM4018 flagellar gene clusters are indicated by an asterisk (*). (B) Phylogenetic relationship of epsilonproteobacterial flagellins. The scale bar represents substitutions per site. subsp. subsp. subsp. and FlaA sequences in normal font were obtained from GenBank; flagellin sequences in bold are from completed or draft genomes. Bootstrap values ( 75%) are shown; phylogenetic tree is rooted to K-12.

Citation: Miller W, Parker C. 2011. and , p 49-65. In Fratamico P, Liu Y, Kathariou S (ed), Genomes of Foodborne and Waterborne Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555816902.ch4
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Tables

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Table 1

General features of the sequenced genomes

Citation: Miller W, Parker C. 2011. and , p 49-65. In Fratamico P, Liu Y, Kathariou S (ed), Genomes of Foodborne and Waterborne Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555816902.ch4

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