International Journal of Systematic and Evolutionary Microbiology

Filamentous bacteria frequently occurring in the pelagic zone of natural freshwater lakes and ponds were previously identified as being related to Haliscomenobacter hydrossis based upon their 16S rRNA gene sequences. These bacteria exhibit a specific morphology characterized by the formation of straight, stick-like filaments of variable length (5 to >100 μm) and quite stable, but narrow, width (0.25 to 0.35 μm). Bacteria with these morphological characteristics form a monophyletic but broad phylogenetic group with a maximal divergence of 16S rRNA gene sequences of 12.0 %. This monophyletic group consists of at least three monophyletic subclusters. H. hydrossis is affiliated to one of these subclusters and represents the sole recognized species affiliated to the broad monophyletic group. ‘Candidatus Haliscomenobacter calcifugiens' and ‘Candidatus Aquirestis calciphila’ are uncultured representatives of the other two subclusters and have 16S rRNA gene sequence dissimilarities of 5.4 % and 8.2 %, respectively, with the type strain of H. hydrossis. ‘Candidatus H. calcifugiens' and ‘Candidatus A. calciphila’ have a 16S rRNA gene sequence dissimilarity of 8.5 %. These large ribosomal divergences justify the classification of these environmentally important bacteria as a novel species and a new genus, respectively. Intensive attempts to cultivate these filamentous bacteria have resulted in the establishment of mixed cultures, however, attempts to establish pure cultures have failed.

Six strains (CB7T, CB18, CB23, CB26, CB28 and CB35T) were isolated from human faeces. Based on phylogenetic analysis, phenotypic characteristics, cellular fatty acid profiles and menaquinone profiles, these strains could be included within the genusPrevotellaand made up two clusters. 16S rRNA gene sequence analysis indicated that five strains were most closely related toPrevotella veroralis, sharing about 92 % sequence similarity; the remaining strain was most closely related toPrevotella shahii, sharing about 90 % sequence similarity. All six strains were obligately anaerobic, non-pigmented, non-spore-forming, non-motile, Gram-negative rods. The cellular fatty acid compositions of the six strains differed significantly from those of otherPrevotellaspecies. Five strains (CB7T, CB18, CB23, CB26 and CB28) contained dimethyl acetals and the major menaquinones of these strains were MK-11, MK-12 and MK-13. The major menaquinones of CB35Twere MK-12 and MK-13. Based on phenotypic and phylogenetic findings, two novel species,Prevotella coprisp. nov. andPrevotella stercoreasp. nov., are proposed, representing the two different strain clusters. The DNA G+C contents of strains CB7Tand CB35Twere 45.3 and 48.2 mol%, respectively. The type strains ofP. copriandP. stercoreaare CB7T(=JCM 13464T=DSM 18205T) and CB35T(=JCM 13469T=DSM 18206T), respectively.

A Gram-negative, chemoheterotrophic, facultatively anaerobic coccus, designated IMCC1545T, was isolated from the digestive tract of a marine clamworm, Periserrula leucophryna, inhabiting a tidal flat of the Yellow Sea. Cells of strain IMCC1545T are non-motile, dividing by binary fission. The predominant fatty acids are anteiso-C15 : 0 and C18 : 0. The respiratory quinone is menaquinone-7 and the DNA G+C content is 52.1 mol%. Phylogenetic analyses based on 16S rRNA gene sequences using three treeing algorithms revealed that the strain formed a novel genus-level lineage within the phylum ‘Verrucomicrobia’. The most closely related named organisms to strain IMCC1545T are ‘Fucophilus fucoidanolyticus’ SI-1234 (86.5 % 16S rRNA gene sequence similarity), Alterococcus agarolyticus ADT3T (81.8 %) and Opitutus terrae PB90-1T (80.3 %), which belong to subdivision 4 of the ‘Verrucomicrobia’. Subdivision 4 of the ‘Verrucomicrobia’ (here named Opitutae classis nov.) was divided into two clades, a clade containing strain IMCC1545T and a clade containing Opitutus terrae. From the taxonomic data obtained in this study, it is proposed that the new marine isolate be placed into a novel genus and species named Puniceicoccus vermicola gen. nov., sp. nov. (the type strain of Puniceicoccus vermicola is IMCC1545T=KCCM 42343T=NBRC 101964T) within Puniceicoccaceae fam. nov and Puniceicoccales ord. nov in the class Opitutae. The family Opitutaceae fam. nov. and order Opitutales ord. nov. are also formally proposed.

Four formate-utilizing methanogens were isolated from ovine (strain KM1H5-1PT) and bovine (strains AK-87, OCP and ZA-10T) rumen contents. Based on 16S rRNA gene sequence analysis, the methanogen strains were found to belong to the orderMethanobacterialesin the genusMethanobrevibacter. Strains ZA-10Tand KM1H5-1PTgained energy for growth by the reduction of CO2to CH4using H2or formate exclusively as electron donors. Increasing formate concentrations to 220 mM in batch cultures increased the growth of strain KM1H5-1PTbut did not affect the growth of strain ZA-10T. Substrate specificity and resistance to cell-wall lysis supported the affiliation of the strains to the genusMethanobrevibacter. Strains ZA-10Tand KM1H5-1PTshowed 16S rRNA gene sequence similarity of 98.0 and 98.6 % to their closest recognized relatives,Methanobrevibacter thaueriCWTandMethanobrevibacter ruminantiumM1T, respectively. DNA–DNA hybridization experiments indicated that the strains were not affiliated at the species level to their closest recognized relatives, with DNA reassociation values of only 28 % between strains ZA-10TandMethanobrevibacter thaueriCWTand <25 % between strains KM1H5-1PTandMethanobrevibacter ruminantiumM1T. Based on the data presented, the new strains are considered to represent two novel species of the genusMethanobrevibacter, for which the namesMethanobrevibacter milleraesp. nov. (type strain ZA-10T=DSM 16643T=OCM 820T) andMethanobrevibacter olleyaesp. nov. (type strain KM1H5-1PT=DSM 16632T=OCM 841T) are proposed.

The purpose of this announcement is to effect the valid publication of the following new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof, or an electronic copy of the published paper, to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries (i.e. documents certifying deposition and availability of type strains). It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below, and these authors' names will be included in the author index of the present issue and in the volume author index. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in bacteriological nomenclature. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.

An intracellular bacterium with the unique ability to enter mitochondria exists in the European vector of Lyme disease, the hard tick Ixodes ricinus. Previous phylogenetic analyses based on 16S rRNA gene sequences suggested that the bacterium formed a divergent lineage within the Rickettsiales (Alphaproteobacteria). Here, we present additional phylogenetic evidence, based on the gyrB gene sequence, that confirms the phylogenetic position of the bacterium. Based on these data, as well as electron microscopy (EM), in situ hybridization and other observations, we propose the name ‘Candidatus Midichloria mitochondrii’ for this bacterium. The symbiont appears to be ubiquitous in females of I. ricinus across the tick's distribution, while lower prevalence is observed in males (44 %). Based on EM and in situ hybridization studies, the presence of ‘Candidatus M. mitochondrii’ in females appears to be restricted to ovarian cells. The bacterium was found to be localized both in the cytoplasm and in the intermembrane space of the mitochondria of ovarian cells. ‘Candidatus M. mitochondrii’ is the first bacterium to be identified that resides within animal mitochondria.

Two Gram-positive bacilli, designated as strains SMC 4352-1T and SMC 4352-2T, were isolated sequentially from the blood of a newborn child with sepsis. They could not be identified by using conventional clinical microbiological methods. 16S rRNA gene sequencing and phylogenetic analysis revealed that both strains belonged to the genus Bacillus but clearly diverged from known Bacillus species. Strain SMC 4352-1T and strain SMC 4352-2T were found to be closely related to Bacillus firmus NCIMB 9366T (98.2 % sequence similarity) and Bacillus cibi JG-30T (97.1 % sequence similarity), respectively. They also displayed low DNA–DNA reassociation values (less than 40 %) with respect to the most closely related Bacillus species. On the basis of their polyphasic characteristics, strain SMC 4352-1T and strain SMC 4352-2T represent two novel species of the genus Bacillus, for which the names Bacillus infantis sp. nov. (type strain SMC 4352-1T=KCCM 90025T=JCM 13438T) and Bacillus idriensis sp. nov. (type strain SMC 4352-2T=KCCM 90024T=JCM 13437T) are proposed.

The taxonomic position of a group of mesophilic actinomycetes isolated from arid Australian soils was determined using a polyphasic approach. The organisms shared chemical and morphological markers typical of members of the genusAmycolatopsis. They had identical 16S rRNA gene sequences and formed a distinct phyletic line in theAmycolatopsis mediterraneiclade, being most closely related toA. mediterranei. In addition, they shared a range of phenotypic properties that distinguished them from representatives of all of the species classified in this clade. The combined genotypic and phenotypic data indicate that the strains merit species status within the genusAmycolatopsis. The name proposed for the novel species isAmycolatopsis australiensissp. nov.; the type strain is GY048T(=DSM 44671T=NCIMB 14142T).

Despite differences in their morphologies, comparative analyses of 16S rRNA gene sequences revealed high levels of similarity (>94 %) between strains of the filamentous bacterium ‘CandidatusNostocoida limicola’ and the cocciTetrasphaera australiensisandTetrasphaera japonicaand the rodTetrasphaera elongata, all isolated from activated sludge. These sequence data and their chemotaxonomic characters, including cell wall, menaquinone and lipid compositions and fingerprints of their 16S–23S rRNA intergenic regions, support the proposition that these isolates should be combined into a single genus containing six species, in the familyIntrasporangiaceaein theActinobacteria. This suggestion receives additional support from DNA–DNA hybridization data and when partial sequences of therpoC1gene are compared between these strains. Even though few phenotypic characterization data were obtained for these slowly growing isolates, it is proposed, on the basis of the extensive chemotaxonomic and molecular evidence presented here, that ‘CandidatusN. limicola’ strains Ben 17, Ben 18, Ben 67, Ben 68 and Ben 74 all be placed into the speciesTetrasphaera jenkinsiisp. nov. (type strain Ben 74T=DSM 17519T=NCIMB 14128T), ‘CandidatusN. limicola’ strain Ben 70 intoTetrasphaera vanveeniisp. nov. (type strain Ben 70T=DSM 17518T=NCIMB 14127T) and ‘CandidatusN. limicola’ strains Ver 1 and Ver 2 intoTetrasphaera veronensissp. nov. (type strain Ver 1T=DSM 17520T=NCIMB 14129T).