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Chapter 4 : Campylobacter and Arcobacter
Category: Applied and Industrial Microbiology; Food Microbiology
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Campylobacteraceae is composed of three main genera, Campylobacter, Sulfurospirillum, and Arcobacter, and is represented currently by 43 described or proposed species. Unlike Campylobacter spp., that are associated with warm-blooded avian and mammalian hosts, members of the Sulfurospirillum and Arcobacter genera are non-host-associated, free-living, environmental organisms. Arcobacter spp. can grow aerobically, unlike campylobacters, 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 Campylobacter and Arcobacter genomes. The coding sequences (CDSs) with assigned function are fairly consistent across the sequenced Campylobacteraceae genomes, with an assigned function/total CDSs average of 45%. It is possible that many Campylobacter species are composed of multiple host-associated phylogenetic clusters. Comparative genomics of the Campylobacter and Arcobacter genomes has not identified any pathogenicity islands containing toxin-encoding genes or other virulence determinants. Campylobacter and Arcobacter species provide fertile ground for comparative genomics. Therefore, comparative genomics of Campylobacter and Arcobacter should provide insights into pathogenicity, host adaptation and specificity, evolution, and environmental adaptation and survival. The degree of variation within Campylobacter and Arcobacter is an important consideration.
Condensed phylogenetic tree, based on sequence similarity of the Campylobacteraceae 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.
Whole genome comparisons of C. jejuni genes and Campylobacter proteins. (A) Average amino-acid identities of the Campylobacter proteomes. Values represent average amino-acid identities between the core protein sets (N = 764 proteins) of any two given Campylobacter proteomes. (B) Common and unique genes within selected C. jejuni genomes. The Venn diagram illustrates the number of shared or unique genes within the five completed C. jejuni genomes. Cj, C. jejuni subsp jejuni; Cjd, C. jejuni subsp. doylei. Cj strains 11168, 1221, 81116, and 81-176 are members of the MLST clonal complexes, ST-21, ST-354, ST-283, and ST-42, respectively.
Chromosomal locations of the plasticity regions and CJIEs. (A) Location of the plasticity regions of C. jejuni 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. ( 68 ) and regions 17 and 18 are from Parker et al. ( 51 ). (B) Location of the CJIEs of C. jejuni strain RM1221. CMLP (CJIE1): Campylobacter Mu-like phage; CJIE: Campylobacter jejuni integrated element.
Flagellar clustering in A. butzleri strain RM4018 and phylogenetic analysis of Campylobacteraceae flagellins. (A) Location of the flagellar genes of C. jejuni strain RM1221 and A. butzleri strain RM4018. The diagram is reprinted from reference 40 . A. butzleri strain RM4018 flagellar gene clusters are indicated by an asterisk (*). (B) Phylogenetic relationship of epsilonproteobacterial flagellins. The scale bar represents substitutions per site. Cjj, Campylobacter jejuni subsp. jejuni; Cjd, C. jejuni subsp. doylei; Cc, C. coli; Cu, C. upsaliensis; Cl, C. lari; Cff, C. fetus subsp. fetus; Ccur, C. curvus; Ccon, C. concisus; Ab, A. butzleri; Ac, A. cryaerophilus; As, A. skirrowii; Ah, A. halophilus; Acib, A. cibarius; Ws, W. succinogenes; Sd, S. deni-trificans; Hh, H. hepaticus; Hac, H. acinonychis; Hp, H. pylori; Nit, Nitratiruptor sp.; Ec, Escherichia coli. Campylobacter and Arcobacter 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 E. coli K-12.
General features of the sequenced Campylobacteraceae genomes a