title: Phylogeny of Helicobacter isolates from bird and swine feces and description of Helicobacter pametensis sp. nov.
abstract: Previously, nine fecal isolates from wild birds and a domestic swine were identified as helicobacters by phenotypic characterization and reaction with a helicobacter genus-specific DNA probe. These isolates fell into three biotypes by analysis of phenotypic traits. To further characterize these isolates, full 16S rRNA sequences were determined for strains representing each biotype, and sequence comparison indicated that the strains represented three novel, phylogenetically defined Helicobacter species. Three 16S rRNA-based DNA probes were designed and used to identify the remaining strains. Probe reactivity divided the strains into the same three groups identified phenotypically. Six of the isolates represented a new species of the genus Helicobacter for which we propose the name Helicobacter pametensis sp. nov. The following phenotypic features distinguished H. pametensis from other Helicobacter and Campylobacter species: positive tests for oxidase, catalase, alkaline phosphatase, nitrate reduction, growth at 42 degrees C, and growth in the presence of 1% glycine; negative tests for urease, gamma glutamyl transpeptidase, indoxyl acetate hydrolysis, and hippurate hydrolysis; and susceptibility to nalidixic acid and cephalothin. H. pametensis cells were motile and possessed one subterminal sheathed flagellum at each end. The two additional Helicobacter species were similar to H. pametensis except that they were urease positive, hydrolyzed indoxyl acetate, and were resistant to cephalothin. Because these two additional species are phenotypically similar and are represented by only two isolates for one species and one isolate for the other, they are not formally named but are referred to as Helicobacter sp. "Bird-B" and Helicobacter sp. "Bird-C."(ABSTRACT TRUNCATED AT 250 WORDS)
authors.affiliation: Department of Molecular Genetics, Forsyth Dental Center, Boston, Massachusetts 02115.
authors.forename: F E
authors.initials: FE
authors.lastname: Dewhirst
authors.forename: C
authors.initials: C
authors.lastname: Seymour
authors.forename: G J
authors.initials: GJ
authors.lastname: Fraser
authors.forename: B J
authors.initials: BJ
authors.lastname: Paster
authors.forename: J G
authors.initials: JG
authors.lastname: Fox
mesh_terms: D000818:Animals; D001483:Base Sequence; D001717:Birds / Q000382:microbiology*; D015342:DNA Probes / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics; D004275:DNA, Ribosomal / Q000235:genetics; D005243:Feces / Q000382:microbiology; D016998:Helicobacter / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D008854:Microscopy, Electron; D008969:Molecular Sequence Data; D010802:Phylogeny; D012329:RNA, Bacterial / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D013045:Species Specificity; D013552:Swine / Q000382:microbiology*
chemical_list: D015342:DNA Probes; D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S