- Volume 58, Issue 12, 2008

Four bacterial strains, designated ST18T, HM244, HM250 and DI49, were isolated from the fresh faeces of four thoroughbred horses in Japan. Cells were Gram-positive, strictly anaerobic, catalase-negative, non-spore-forming, non-motile rods that occurred in chains. They were placed in the same subcluster based on 16S rRNA gene sequence analysis, phenotypic characteristics and levels of DNA–DNA relatedness. Their DNA G+C content ranged from 36 to 38 mol%. Lactobacillus catenaformis, Lactobacillus vitulinus and Catenibacterium mitsuokai belong to cluster XVII of the Clostridium subphylum. Strain ST18T was most closely related to L. catenaformis ATCC 25536T in the phylogenetic tree, but these strains shared only 89.9 % (1336/1486 bp) 16S rRNA gene sequence similarity. L. catenaformis, L. vitulinus and C. mitsuokai are homofermentative bacteria, whereas ST18T produced CO2 from glucose. Whereas the cell-wall peptidoglycan type of L. catenaformis and L. vitulinus was l-Lys–l-Ala3, that of C. mitsuokai and the subgroup represented by ST18T was A1γ (l-Ala–d-Glu–meso-diaminopimelic acid). On the basis of 16S rRNA gene sequence divergence of more than 10 % from L. catenaformis as well as phenotypic characteristics, strains ST18T, HM244, HM250 and DI49 are considered to represent a novel species of a new genus belonging to the Clostridium subphylum cluster XVII, for which the name Sharpea azabuensis gen. nov., sp. nov. is proposed. The type strain of Sharpea azabuensis is ST18T (=JCM 14210T =DSM 18934T).

A Lactobacillus strain, designated 203T, previously isolated from Bobal grape must was characterized phylogenetically, genotypically and phenotypically in order to establish whether it represents a novel species. On the basis of the 16S rRNA gene sequence, strain 203T was shown to belong to the genus Lactobacillus, falling within the Lactobacillus alimentarius–Lactobacillus farciminis group and being closely related to the type strains of L. alimentarius, Lactobacillus kimchii and Lactobacillus paralimentarius. DNA–DNA hybridization results confirmed the separate status of strain 203T at the species level. To establish the similarities and differences between 203T and the three aforementioned closest species, the following methods were used: amplified rDNA restriction analysis, analysis of the 16S–23S rDNA intergenic spacer region, random amplification of polymorphic DNA (RAPD) profiling, ribotyping, carbohydrate fermentation and physiological tests. Strain 203T could be differentiated genetically using RAPD analysis and ribotyping. Phenotypically, it can be distinguished from its closest relatives by its ability to grow at pH 3.3, by gas production from gluconate and by certain carbohydrate fermentations. On the basis of these data, strain 203T represents a novel species of the genus Lactobacillus, for which the name Lactobacillus bobalius sp. nov. is proposed. The type strain is 203T (=CECT 7310T =DSM 19674T).

Two anaerobic, non-spore-forming, bacteria (YIT 11850T and YIT 11860T) that stained Gram-negative, were isolated from human faeces. Cells of strain YIT 11850T were coccobacilli, asaccharolytic and largely unreactive, with only traces of lactate and propionate as metabolic end products; however, strain YIT 11850T was able to decarboxylate succinate to propionate. The DNA G+C content of strain YIT 11850T was 51.9 mol%. Following 16S rRNA gene sequence analysis, this strain was found to be most closely related to Dialister propionicifaciens, with 95.1 % sequence similarity between the two taxa. Biochemical data supported the affiliation of strain YIT 11850T to the genus Dialister. Strain YIT 11850T therefore represents a novel species for which the name Dialister succinatiphilus sp. nov. is proposed; the type strain is YIT 11850T (=DSM 21274T=JCM 15077T). Cells of the other isolate, strain YIT 11860T, were non-motile, rod-shaped, positive for aesculin hydrolysis, negative for indole production, produced succinic and acetic acids as end products of glucose metabolism and possessed a DNA G+C content of 45.5 mol%. On the basis of 16S rRNA gene sequence similarity values, this strain was shown to belong to the family ‘Porphyromonadaceae’ related to Barnesiella viscericola (96.0 %); similarity values with species within the family ‘Porphyromonadaceae’ with validly published names were less than 86 %. Biochemical data supported the affiliation of strain YIT 11860T to the genus Barnesiella. Strain YIT 11860T therefore represents a novel species for which the name Barnesiella intestinihominis sp. nov. is proposed; the type strain is YIT 11860T (=DSM 21032T=JCM 15079T).

During a study on lactic acid bacteria (and their species diversity) in spontaneous heap fermentations of Ghanaian cocoa beans, two strains, designated 215T and 194B, were isolated. A phylogenetic analysis based on 16S rRNA gene sequences demonstrated that these strains represented a distinct lineage close to the genus Weissella and showing only 92.1 % 16S rRNA gene sequence similarity with respect to their closest neighbour, Weissella soli LMG 20113T. Whole-cell protein electrophoresis, fluorescent amplified fragment length polymorphism fingerprinting of whole genomes and physiological and biochemical tests confirmed the unique taxonomic position of the two novel isolates. On the basis of the results of the morphological and biochemical tests and 16S rRNA gene sequence analysis, strains 215T and 194B represent the most peripheral lineage of the genus Weissella, for which we propose the name Weissella ghanensis sp. nov. The type strain is 215T (=LMG 24286T=DSM 19935T).

A bacterium, designated strain lac18T, was isolated in pure culture from the mucosal jejunum of a healthy pig, using a medium selective for anaerobic lactic acid bacteria and containing porcine gastric mucin as the main carbon and nitrogen source. Cells of this strain were coccus-shaped, arranged singly or in pairs and were Gram-stain-negative, oxidase-negative, non-spore-forming, anaerobic and microaerotolerant. An analysis based on 16S rRNA gene sequences indicated that strain lac18T should be assigned to the genus Veillonella, class Clostridia, phylum Firmicutes. 16S rRNA and dnaK gene sequence-based phylogenetic analyses both indicated that the most closely related species were Veillonella ratti ATCC 17746T (similarities of 96.6 and 84.5 %, respectively) and Veillonella criceti ATCC 17747T (similarities of 96.6 and 83.4 %, respectively). The results of DNA–DNA hybridizations between strain lac18T and these Veillonella species and the type species of the genus, Veillonella parvula DSM 2008T, confirmed the genotypic distinctness of the novel isolate. Data from phenotypic studies also served to differentiate strain lac18T from related strains. Therefore strain lac18T represents a novel species of the genus Veillonella, for which the name Veillonella magna sp. nov. is proposed. The type strain is lac18T (=CCUG 55454T=CIP 109767T=DSM 19857T=JCM 15053T).

Five isolates that produced large amounts of butyrate were obtained in the course of a study on the butyrate-producing microbiota from the caecal content of a 4-week-old broiler chicken. The five isolates were virtually indistinguishable in biochemical and genetic terms, suggesting that they were derived from a single bacterial clone colonizing this habitat. A phylogenetic analysis based on 16S rRNA gene sequences demonstrated that the five isolates represented a unique lineage within the Clostridium leptum subgroup of the clostridia, with Eubacterium desmolans as the closest phylogenetic neighbour (about 93 % similarity). These data indicate that the five novel isolates represent a single novel species within a novel genus, for which we propose the name Butyricicoccus pullicaecorum gen. nov., sp. nov. The type strain of Butyricicoccus pullicaecorum is 25-3T (=LMG 24109T =CCUG 55265T). The DNA G+C content of strain 25-3T was 54.5 mol% .

A Gram-positive, halophilic bacterium was isolated from a sediment sample from Ai-Ding salt lake in China. The isolate, designated strain 17-5T, grew at salinities of 8–33 % (w/v) NaCl (optimally at 12 %, w/v). The genomic DNA G+C content of strain 17-5T was 48.1 mol%. The predominant isoprenoid quinone was MK-7(H2) and the cell-wall peptidoglycan contained meso-diaminopimelic acid. The major polar lipids were diphosphatidylglycerol and an unidentified glycolipid. The major cellular fatty acids were anteiso-C15 : 0, anteiso-C17 : 0, iso-C16 : 0 and C16 : 0. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 17-5T was a member of the genus Bacillus, being most closely related to Bacillus qingdaonensis JCM 14087T (96.0 % sequence similarity) and Bacillus salarius DSM 16461T (95.6 %). The levels of 16S rRNA gene sequence similarity with respect to other Bacillus species were less than 91.7 %. Comparative analysis of the 16S rRNA gene sequence data, chemotaxonomy and phenotypic features of the novel isolate and related species of Bacillus indicated that strain 17-5T represents a novel species within the genus Bacillus, for which the name Bacillus aidingensis sp. nov. is proposed. The type strain is 17-5T (=CGMCC 1.3227T=DSM 18341T).

A Gram-positive bacterium, designated strain CW 7T, was isolated from forest soil in Anhui Province, south-east China. Cells were strictly aerobic, motile with peritrichous flagella and rod-shaped. The strain grew optimally at 30–37 °C and pH 7.0–8.0. The major fatty acids of strain CW 7T were anteiso-C15 : 0, iso-C15 : 0 and anteiso-C17 : 0. The predominant menaquinone was MK-7. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The G+C content of the genomic DNA was 42.3 mol%. Phylogenetic analysis indicated that strain CW 7T belonged to a monophyletic cluster within the genus Bacillus and showed 16S rRNA gene sequence similarities of less than 96.5 % to recognized species of the genus Bacillus. The results of the polyphasic taxonomic study, including phenotypic, chemotaxonomic and phylogenetic analyses, showed that strain CW 7T represents a novel species of the genus Bacillus, for which the name Bacillus pallidus sp. nov. is proposed. The type strain is CW 7T (=KCTC 13200T=CCTCC AB 207188T=LMG 24451T).

A novel mesophilic and acidophilic Gram-positive bacterium, designated strain TC-34T, was isolated from solfataric soil. Strain TC-34T grew aerobically at 17–40 °C and pH 2.0–6.0, and optimally at 28 °C and pH 3.0. Analysis based on 16S rRNA gene sequences showed that strain TC-34T was phylogenetically related to members of the genus Alicyclobacillus, with the highest similarity (94.8 %) to Alicyclobacillus pomorum. Strain TC-34T showed a range of phenotypic characteristics that differentiated it from recognized Alicyclobacillus species, including growth temperature, assimilation of carbon sources and production of acids from a range of compounds. Strain TC-34T was able to oxidize ferrous iron and its growth was correlated with the oxidation of Fe2+ in culture medium. ω-Alicyclic fatty acids were not detected. On the basis of these results, it was concluded that strain TC-34T represents a novel species of the genus Alicyclobacillus, for which the name Alicyclobacillus ferrooxydans (type strain TC-34T=JCM 15090T=CGMCC 1.6357T) is proposed.

A Gram-positive, small coccus-shaped lactic acid bacterium, strain LMG 23999T, was isolated from Argentinean wheat flour. 16S rRNA gene sequence analysis revealed that the phylogenetic position of the novel strain was within the genus Pediococcus, with Pediococcus stilesii, Pediococcus pentosaceus and Pediococcus acidilactici as its closest relatives (97.7, 97.3 and 96.9 % gene sequence similarity, respectively). Fluorescent amplified fragment length polymorphism fingerprinting of whole genomes and whole-cell protein electrophoresis confirmed the unique taxonomic status of the novel strain. DNA–DNA hybridizations, DNA G+C content determination, comparative sequence analysis of the pheS, rpoA and atpA genes and physiological and biochemical characterization demonstrated that strain LMG 23999T (=CCUG 54535T=CRL 776T) represents a novel species for which the name Pediococcus argentinicus sp. nov. is proposed. Multi-locus sequence analysis based on pheS, rpoA and atpA genes was found to be a suitable method for the identification of species of the genus Pediococcus.

A novel anaerobic, extremely thermophilic, facultatively chemolithoautotrophic bacterium designated strain SRT was isolated from a terrestrial hot spring in Kamchatka (Russia). The cells of the novel strain were spore-forming rods with a Gram-positive type of cell wall. The novel isolate grew at 60–82 °C (optimum 75 °C) and pH 6.0–7.5 (optimum 6.8). Molecular hydrogen and formate were used as electron donors. Thiosulfate, sulfate or elemental sulfur served as electron acceptors yielding hydrogen sulfide. No growth was observed on either substrate in the presence of nitrate as the electron acceptor. The G+C content of the DNA was 56.2 mol%. Phylogenetic analyses of the 16S rRNA gene showed that strain SRT was most closely related to Ammonifex degensii (96.4 % gene sequence similarity). However, the novel isolate possessed phenotypic characteristics that differed significantly from those of A. degensii, the only other recognized species of the genus Ammonifex. It is concluded that strain SRT (=DSM 19636T=VKM B-2461T) represents the type strain of a novel species of the genus Ammonifex, for which the name Ammonifex thiophilus sp. nov. is proposed. An emendation of the genus Ammonifex is proposed based on the phenotypic characteristics of the novel species.

Strains TRF-1T and TC-9 were isolated from transfer spikes of two separate bottles containing 0.9 % NaCl (physiological saline) solution used repeatedly to wash wounds in hospital wards, months apart. Phylogenetic analysis of 16S rRNA gene sequences revealed that strains TRF-1T and TC-9 formed a distinct branch within the family Bacillaceae most closely related to the members of the genus Jeotgalicoccus. The two strains, with identical 16S rRNA gene sequences, showed sequence similarities of 89.8–93.9 % with species of Jeotgalicoccus, 91.1–91.8 % with species of Salinicoccus and 89.1–89.7 % with species of Staphylococcus. Strains TRF-1T and TC-9 are Gram-positive, non-spore-forming and non-motile cocci, with an optimum growth temperature of about 37 °C. Strain TRF-1T grew optimally in medium containing 3 % (w/v) NaCl (maximum about 14 % NaCl), while strain TC-9 grew optimally in medium with 1 % (w/v) NaCl. Both strains produce a brown pigment when grown in the presence of NaCl. The cell-wall peptidoglycan is of the A3α type with a cross-linkage containing the peptide l-Lys–Gly4–l-Ser–Gly. The major respiratory quinones are menaquinone 7 (MK-7) and menaquinone 8 (MK-8), the major fatty acids are straight-chain C14 : 0 and C16 : 0 (more than 85 % of the total) and the major polar lipid is an unknown aminophospholipid. The DNA G+C content is 33.5 mol%. On the basis of the phylogenetic analysis and physiological and biochemical characteristics, we are of the opinion that strains TRF-1T and TC-9 represent a novel species of a new genus, for which we propose the name Nosocomiicoccus ampullae gen. nov., sp. nov. The type strain of Nosocomiicoccus ampullae is strain TRF-1T (=LMG 24060T =CIP 109506T).

The extremely diverse genus Lactobacillus is the largest among the lactic acid bacteria, with over 145 recognized species. In this work, which to our knowledge is the largest comparative phylogenomics study of a single genus to date, 12 genomes of Lactobacillus strains were subjected to an array of whole-genome and single-marker phylogenetic approaches, to investigate the case for extracting subgeneric groups and to determine whether a single congruent phylogeny could be identified. We conclude that GroEL is a more robust single-gene phylogenetic marker for the genus Lactobacillus than the 16S rRNA gene, when no whole-genome information is available. Significant incongruence was found, both within a set of trees based on 141 core proteins and within those phylogenies based on numbers of orthologues, concatenated RNA polymerase subunits and single gene/protein markers. This is possibly due to different evolutionary rates, hidden paralogies or horizontal gene transfer. Such phylogenetic ambiguities are efficiently visualized with cluster-networks. Although the genus contains some highly unstable taxa, four subgeneric groups were distinguished. Qualitative and quantitative gene analysis of these groups resulted in three findings: there is a relatively small number of group-specific proteins, the majority of which are poorly characterized; major groupings are functionally better distinguishable by absent genes rather than gained/retained genes; and, finally, a gene cluster possibly involved in purine metabolism is uniquely present in four lactobacilli associated with meat. In conclusion, because of either significantly different branching patterns or the availability of too few members, three of the four identified groups could not serve as the basis for identifying candidate novel genera within the current genus. We therefore suggest targeted sequencing of key taxonomic species identified here, which are likely to add sufficient depth for a future reclassification, followed by phylogenomic analysis involving the core proteins identified here. This will ideally be combined with phenotypic data using a polyphasic approach.

The Prodiscocephalus-like ciliates, or discocephalines, are cephalized organisms that are traditionally considered to be hypotrichs (sensu lato) but whose precise systematic position has long been uncertain. The main reasons for this are that these organisms exhibit several intermediate morphological and morphogenetic features and that hitherto none has been investigated using molecular methods. In the present study, the cortical development of Prodiscocephalus borrori was observed during binary division and this can be summarized as follows: (i) in the parental adoral zone of membranelles, only the posterior end is renewed by dedifferentiation of the old structures; (ii) the oral primordium in the opisthe occurs de novo on the cell surface as seen in other typical stichotrichs; (iii) in both dividers, the undulating membranes anlage does not split longitudinally in the usual way but, instead, divides transversely to form the paroral and endoral membranes; (iv) usually seven frontoventral transverse cirral anlagen are formed in the primary mode which then divide into two sets, one each for the proter and opisthe; (v) both left and right marginal rows divide into two parts, thus giving rise to a post-lateral marginal segment at the posterior end of each; (vi) invariably five caudal cirri are formed at the posterior end of the three rightmost dorsal kinety anlagen. Thus, it was found that, like other related discocephalines, P. borrori exhibits more similarities to stichotrichs than to euplotids. Based on a combination of morphological and morphogenetic data, a phylogenetic tree was constructed which suggests that the discocephalines group within the stichotrichs and separate from the euplotids. In addition, the complete small-subunit rRNA gene (SSU rDNA) of P. borrori was sequenced and analysed. In the resulting SSU rDNA tree, the discocephalines represent an intermediate group between the euplotids and the Stichotrichia–Oligotrichia–Choreotrichia assemblage, albeit with low bootstrap support. From these data, we conclude that the discocephalines might be a divergent, or possibly an ancestral, group within the Stichotrichia. Furthermore, our findings further support the suggestion that these organisms should be considered as a distinct order, i.e. Discocephalida Wicklow, 1982, in the subclass Stichotrichia Small & Lynn, 1985 .

It is proposed that the type strain of Melittangium lichenicola (Thaxter 1892) McCurdy 1971 is ATCC 25946 (=DSM 14877), which was originally designated as a reference strain by McCurdy, and not ATCC 25944T, as given in the Approved Lists. Swarm appearance, myxospore morphology and 16S rRNA gene sequence data suggest that ATCC 25946 is a representative of the species Melittangium lichenicola, while strain ATCC 25944 is clearly a member of the Myxococcus–Corallococcus clade. A Request for an Opinion to this effect is made to the Judicial Commission of the International Committee on Systematics of Prokaryotes.