Insertions or Deletions (Indels) in the rrn 16S-23S rRNA Gene Internal Transcribed Spacer Region (ITS) Compromise the Typing and Identification of Strains within the Acinetobacter calcoaceticus-baumannii (Acb) Complex and Closely Related Members

The 16S–23S rRNA gene internal transcribed spacer (ITS) regions of 11 reference strains of Porphyromonas species, together with Bacteroides distasonis and Tannerella forsythensis, were analysed to examine interspecies relationships. Compared with the phylogenetic tree generated using 16S rRNA gene sequences, the resolution of the ITS sequence-based tree was higher, but species positioning and clustering were similar with both approaches. The recent separation of Porphyromonas gulae and Porphyromonas gingivalis into distinct species was confirmed by the ITS data. In addition, analysis of the ITS sequences of 24 clinical isolates of Porphyromonas asaccharolytica plus the type strain ATCC 25260T divided the sequences into two clusters, of which one was α-fucosidase-positive (like the type strain) while the other was α-fucosidase-negative. The latter resembled the previously studied unusual extra-oral isolates of ‘Porphyromonas endodontalis-like organisms' (PELOs) which could therefore be called ‘Porphyromonas asaccharolytica-like organisms' (PALOs), based on the genetic identification. Moreover, the proposal of α-fucosidase-negative P. asaccharolytica strains as a new species should also be considered.

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Identification of the genusGeobacillususing genus-specific primers, based on the 16Sâ23S rRNA gene internal transcribed spacer

FEMS Microbiology Letters ◽

10.1111/j.1574-6968.2007.00954.x ◽

2007 ◽

Vol 277 (2) ◽

pp. 165-172 ◽

Cited By ~ 19

Author(s):

Nomeda Kuisiene ◽

Juozas Raugalas ◽

Milda Stuknyte ◽

Donaldas Chitavichius

Keyword(s):

Internal Transcribed Spacer ◽

23S Rrna ◽

Rrna Gene ◽

Specific Primers ◽

23S Rrna Gene

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Tuberibacillus calidus gen. nov., sp. nov., isolated from a compost pile and reclassification of Bacillus naganoensis Tomimura et al. 1990 as Pullulanibacillus naganoensis gen. nov., comb. nov. and Bacillus laevolacticus Andersch et al. 1994 as Sporolactobacillus laevolacticus comb. nov.

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.64303-0 ◽

2006 ◽

Vol 56 (11) ◽

pp. 2545-2551 ◽

Cited By ~ 66

Author(s):

Kouta Hatayama ◽

Hirofumi Shoun ◽

Yasuichi Ueda ◽

Akira Nakamura

Keyword(s):

Dna Hybridization ◽

Phylogenetic Analyses ◽

Physiological Characteristics ◽

23S Rrna ◽

Rrna Gene ◽

The Novel ◽

16S Rrna Gene Sequences ◽

Internal Transcribed Spacer Region ◽

Physiological Characterization ◽

23S Rrna Gene

Two thermophilic strains, designated 607T and 606b, were isolated from a compost pile in Japan. The novel strains were Gram-positive, aerobic, spore-forming rods. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strains 607T and 606b were closely related to Bacillus naganoensis (94.0–94.1 % similarity) and separated from clusters of the related genera Bacillus (<91.9 %) and Sporolactobacillus (91.0–92.5 %). In addition, some chemotaxonomic and physiological characteristics of strains 607T and 606b differed from those of B. naganoensis and the two related genera. Several differences in physiological characteristics and 16S–23S rRNA gene internal transcribed spacer region nucleotide sequences were observed between strains 607T and 606b; however, DNA–DNA hybridization indicated that these two strains belonged to the same species. From these results, it is proposed that strains 607T and 606b represent the type species of a new genus, Tuberibacillus calidus gen. nov., sp. nov., with strain 607T (=JCM 13397T=DSM 17572T) as the type strain. In addition, the results of phylogenetic analyses, as well as chemotaxonomic and physiological characterization, indicated that B. naganoensis and Bacillus laevolacticus did not belong to the genus Bacillus. Based on these results, it is proposed that B. naganoensis and B. laevolacticus should be transferred to Pullulanibacillus naganoensis gen. nov., comb. nov. and Sporolactobacillus laevolacticus comb. nov., respectively.

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