Note: Extensive 16S rRNA gene sequence diversity in Campylobacter hyointestinalis strains: Taxonomic and applied implications
Department of Medical Microbiology, University of Aberdeen, Foresterhill, UK.International journal of systematic bacteriology (Impact Factor: 2.27). 08/1999; 49 Pt 3(3):1171-5. DOI: 10.1099/00207713-49-3-1171
Phylogenetic relationships of Campylobacter hyointestinalis subspecies were examined by means of 16S rRNA gene sequencing. Sequence similarities among C. hyointestinalis subsp. lawsonii strains exceeded 99.0%, but values among C. hyointestinalis subsp. hyointestinalis strains ranged from 96.4 to 100%. Sequence similarities between strains representing the two different subspecies ranged from 95.7 to 99.0%. An intervening sequence was identified in certain of the C. hyointestinalis subsp. lawsonii strains. C. hyointestinalis strains occupied two distinct branches in a phylogenetic analysis of the genus Campylobacter, emphasizing the need for multiple strain analysis when using 16S rRNA gene sequence comparisons for taxonomic investigations.
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- "In some species, the sequence variation between strains can be high and extensive, that is not restricted to a specific region of the gene. C. hyointestinalis (Harrington and On, 1999) is known to exhibit high variation levels in their 16S rRNA genes between strains of the same species, with similarities as low as 95–97% (Harrington and On, 1999). Today, many available tools to determine the presence of pathogenic bacteria in any type of samples are mainly based on the detection of functional genes, in particular, virulence genes (Shrestha et al., 2002; Malorny et al., 2003; Toma et al., 2003; Wilson et al., 2003). "
ABSTRACT: Campylobacter is a microaerophilic, spiral shaped, Gram-negative bacterium comprising 16 species. Although many of these species are thermotolerant, i.e. able to grow at 42ÂºC, C. jejuni, C. coli, C lari, and C. upsaliensis are the most prevalent foodborne pathogens. The need for a fast detection of these bacteria in foodstuff has fostered the development of rapid method, most of them based on PCR techniques. Nevertheless, the use of the appropriate targets has limited the development of reliable methods. This difficulty arises, in part, from the fact that target genes used commonly, either virulence genes or ribosomal, contain high variability, even among strains. This has serious implications, for instance, as false negative results. As a consequence, the number of available PCR protocols to detect thermotolerant Campylobacters is very limited. The use of strongly conserved, housekeeping genes as PCR targets has resulted in a good approach to the ideal real-time PCR based method. The difficulty in such a task is actually reflected in the scarce officially certified tools commercially available.
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- "On the other hand 16S rRNA sequences often contain insufficient information to show relationships at lower taxonomic ranks, particularly at the level of species and subspecies (Stackebrandt et al. 2002). In addition, nucleotide variations within multiple rRNA operons in a given genome (Harrington and On 1999; Pei et al. 2010), as well as the possibility of 16S rRNA genes derived from HGT (Ueda et al. 1999; Schouls et al. 2003), may distort relationships between taxa in phylogenetic trees. Since Darwin's era, systematists have been classifying individual species in order to reflect their inferred evolutionary relationships. "
ABSTRACT: As an essential and basic biological discipline, prokaryotic systematics is entering the era of genomics. This paradigmatic shift is significant not only for understanding molecular phylogeny at the whole genome level but also in revealing the genetic or epigenetic basis that accounts for the phenotypic criteria used to classify and identify species. These developments provide an opportunity and a challenge for systematists to reanalyze the molecular mechanisms underlying the taxonomic characteristics of prokaryotes by drawing the knowledge from studies of genomics and/or functional genomics employing platform technologies and related bioinformatics tools. It is expected that taxonomic books, such as Bergey's Manual of Systematic Bacteriology may evolve into a systematics library indexed by phylogenomic information with an comprehensive understanding of prokaryotic speciation and associated increasing knowledge of biological phenomena.
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- "Scale bar used was nucleotide substitutions per position. different IVSs that have been reported since then in the 16S rRNA gene of several Campylobacter species, including C. sputorum and C. hyointestinalis (Etoh et al., 1998; Harrington and On, 1999 "
ABSTRACT: Campylobacters other than Campylobacter jejuni or C. coli were isolated in 35% of 343 farms recently analyzed in northern Spain. This study was aimed at identifying at the species level the 120 isolates collected (21 ovine, 52 beef cattle, 44 dairy cattle, and 3 porcine) by species-specific polymerase chain reaction and 16S rRNA gene sequencing analysis. Thus, five species were identified: Campylobacter hyointestinalis (90 isolates), Campylobacter lanienae (12), Campylobacter fetus subsp. fetus (10), Campylobacter lari (1), and Campylobacter sputorum (1). Ambiguous results were obtained for six isolates. Phylogenetic analyses of the 16S rRNA gene sequence placed three of them (cattle isolates) as an intermediate clade between C. hyointestinalis subsp. hyointestinalis and C. fetus, two ovine isolates formed a new clade clustering with Campylobacter concisus despite sharing higher similarity with Campylobacter mucosalis, and one porcine isolate shared similarly high homology with C. lanienae and C. hyointestinalis subsp. lawsonii. C. hyointestinalis was the predominant species, particularly in cattle, but it was also isolated from sheep and swine. C. lanienae was only found in sheep, C. fetus in cattle and sheep, and C. lari in a single dairy cattle farm. Although previously reported, the isolation of C. lari from cattle is not common, and this is the first report of C. lanienae and C. hyointestinalis in sheep. This study demonstrated the wide distribution in livestock of several emerging zoonotic Campylobacter species and provided valuable information on their host animal reservoirs.