Moore, Edward R. B.

The naming of prokaryotes is governed by the International Code of Nomenclature of Prokaryotes (ICNP) and partially by the International Code of Nomenclature for Algae, Fungi and Plants (ICN). Such codes must be able to determine names of taxa in a universal and unambiguous manner, thus serving as a common language across different fields and activities. This unity is undermined when a new code of nomenclature emerges that overlaps in scope with an established, time-tested code and uses the same format of names but assigns different nomenclatural status values to the names. The resulting nomenclatural confusion is not beneficial to the wider scientific community. Such ambiguity is expected to result from the establishment of the ‘Code of Nomenclature of Prokaryotes Described from DNA Sequence Data’ (‘SeqCode’), which is in general and specific conflict with the ICNP and the ICN. Shortcomings in the interpretation of the ICNP may have exacerbated the incompatibility between the codes. It is reiterated as to why proposals to accept sequences as nomenclatural types of species and subspecies with validly published names, now implemented in the SeqCode, have not been implemented by the International Committee on Systematics of Prokaryotes (ICSP), which oversees the ICNP. The absence of certain regulations from the ICNP for the naming of as yet uncultivated prokaryotes is an acceptable scientific argument, although it does not justify the establishment of a separate code. Moreover, the proposals rejected by the ICSP are unnecessary to adequately regulate the naming of uncultivated prokaryotes. To provide a better service to the wider scientific community, an alternative proposal to emend the ICNP is presented, which would result in Candidatus names being regulated analogously to validly published names. This proposal is fully consistent with previous ICSP decisions, preserves the essential unity of nomenclature and avoids the expected nomenclatural confusion.

The phenotypic and genotypic characteristics of four Bordetella hinzii-like strains from human respiratory specimens and representing nrdA gene sequence based genogroups 3, 14 and 15 were examined. In a 16S rRNA gene sequence based phylogenetic tree, the four strains consistently formed a single coherent lineage but their assignment to the genus Bordetella was equivocal. The respiratory quinone, polar lipid and fatty acid profiles generally conformed to those of species of the genus Bordetella and were characterized by the presence of ubiquinone 8, of phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and several aminolipids, and of high percentages of C16 : 0, cyclo-C17 : 0 and summed feature 2, as major chemotaxonomic marker molecules, respectively. The DNA G+C content was about 66 mol%, which corresponded with that of the high-percentage DNA G+C content genera of the family Alcaligenaceae including the genus Bordetella. DNA–DNA hybridization experiments revealed the presence of three distinct genomospecies and thus confirmed phenotypic differences as revealed by means of extensive biochemical characterization. We therefore propose to formally classify Bordetella genogroups 3, 14 and 15 as Bordetella bronchialis sp. nov. (type strain LMG 28640T = AU3182T = CCUG 56828T), Bordetella sputigena sp. nov. (type strain LMG 28641T = CCUG 56478T) and Bordetella flabilis sp. nov. (type strain LMG 28642T = AU10664T = CCUG 56827T). In addition, we propose to reclassify Achromobacter sediminum into the novel genus Verticia, as Verticia sediminum, gen. nov., comb. nov., on the basis of its unique phylogenetic position, its marine origin and its distinctive phenotypic, fatty acid and polar lipid profile.

ABSTRACT “ Candidatus Neoehrlichia mikurensis” is the tick-borne agent of neoehrlichiosis, an infectious disease that primarily affects immunocompromised patients. So far, the genetic variability of “ Ca . Neoehrlichia” has been studied only by comparing 16S rRNA genes and groEL operon sequences. We describe the development and use of a multilocus sequence analysis (MLSA) protocol to characterize the genetic diversity of clinical “ Ca . Neoehrlichia” strains in Europe and their relatedness to other species within the Anaplasmataceae family. Six genes were selected: ftsZ , clpB , gatB , lipA , groEL , and 16S rRNA. Each MLSA locus was amplified by real-time PCR, and the PCR products were sequenced. Phylogenetic trees of MLSA locus relatedness were constructed from aligned sequences. Blood samples from 12 patients with confirmed “ Ca . Neoehrlichia” infection from Sweden ( n = 9), the Czech Republic ( n = 2), and Germany ( n = 1) were analyzed with the MLSA protocol. Three of the Swedish strains exhibited identical lipA sequences, while the lipA sequences of the strains from the other nine patients were identical to each other. One of the Czech strains had one differing nucleotide in the clpB sequence from the sequences of the other 11 strains. All 12 strains had identical sequences for the genes 16S rRNA, ftsZ , gatB , and groEL . According to the MLSA, among the Anaplasmataceae , “ Ca . Neoehrlichia” is most closely related to Ehrlichia ruminantium , less so to Anaplasma phagocytophilum , and least to Wolbachia endosymbionts. To conclude, three sequence types of infectious “ Ca . Neoehrlichia” were identified: one in the west of Sweden, one in the Czech Republic, and one spread throughout Europe.

A novel bacterial strain designated HA-01T was isolated from a freshwater terrestrial hot spring located at Hot Springs National Park, Arkansas, USA. Cells were Gram-negative-staining, rod-shaped, aerobic, chemo-organotrophic, oxidase- and catalase-positive, non-spore-forming and motile by means of a single polar flagellum. Growth occurred at 37–60 °C, with an optimum between 45 and 50 °C, and at pH 6.5–8.5, with an optimum between pH 6.5 and 7.0. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the closest relatives of strain HA-01T were Solimonas aquatica NAA-16T (93.8 %), Solimonas flava CW-KD 4T (94.1 %), Solimonas soli DCY12T (93.1 %), Solimonas variicoloris MN28T (94.0 %), Nevskia ramosa Soe1T (91.2 %) and Hydrocarboniphaga effusa AP103T (91.1 %). Major fatty acids consisted of C16 : 0, iso-C16 : 0, C16 : 1ω5c and summed feature 8 (C18 : 1ω9c, C18 : 1ω7c and C18 : 1ω6c). Polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine, and the major isoprenoid quinone was Q-8. The DNA G+C content was 64.4 mol%. Based on phylogenetic, phenotypic and chemotaxonomic evidence, it is proposed that strain HA-01T represents a novel species in a new genus for which the name Fontimonas thermophila gen. nov., sp. nov. is proposed. The type strain of the type species is HA-01T ( = DSM 23609T = CCUG 59713T). A new family, Solimonadaceae fam. nov., is also proposed to replace Sinobacteriaceae Zhou et al. 2008.