Article

Rothia marina sp. nov., isolated from an intertidal sediment of the South China Sea

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Abstract

A novel non-sporulating, non-motile, catalase-positive, oxidase-negative, facultatively anaerobic, Gram-positive coccus, designated strain JSM 078151(T), was isolated from an intertidal sediment sample collected from Naozhou Island in the South China Sea, China. Growth was found to occur in the presence of 0-15 % (w/v) NaCl (optimum 0.5-3 % (w/v) NaCl), at pH 6.5-10.5 (optimum pH 7.0-8.0) and at 5-35 °C (optimum 25-30 °C). The peptidoglycan type was determined to be A3a, containing lysine, glutamic acid and alanine. The major cellular fatty acid identified was anteiso-C15:0 and the predominant menaquinones are MK-7 and MK-8. The polar lipids were found to consist of diphosphatidylglycerol, phosphatidylglycerol, glycolipid and one unidentified phospholipid. The genomic DNA G+C content of strain JSM 078151(T) was determined to be 55.2 mol%. A phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain JSM 078151(T) should be assigned to the genus Rothia, and was most closely related to Rothia nasimurium CCUG 35957(T) (98.3 % sequence similarity), followed by Rothia amarae J18(T) (97.5 %) and Rothia terrae L-143(T) (97.3 %). A combination of phylogenetic analysis, DNA-DNA relatedness values, phenotypic characteristics and chemotaxonomic data supports the suggestion that strain JSM 078151(T) represents a novel species of the genus Rothia, for which the name Rothia marina sp. nov. is proposed. The type strain is JSM 078151(T) (= DSM 21080(T) = KCTC 19432(T)).

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... Rothia bacteria are all Gram-positive rods and to date 14 species have been identified (https://www.bacterio.net/genus/rothia): Rothia aeria [8], Rothia aerolata [9], Rothia amarae [10], Rothia arfidiae [11], Rothia dentocariosa [12], Rothia endophytica [13], Rothia halotolerans [14], Rothia koreensis [14], Rothia kristinae [14], Rothia marina [15], Rothia mucilaginosa [16], Rothia nasimurium [16], Rothia nasisuis [17] and Rothia terrae [18]. Furthermore, unclassified and uncultured Rothia genomes have been reconstructed from metagenomic data [19]. ...
Article
Rothia species are understudied members of the phylum Actinobacteria and prevalent colonizers of the human and animal upper respiratory tract and oral cavity. The oral cavity, including the palatine tonsils, is colonized by a complex microbial community, which compete for resources, actively suppress competitors and influence host physiology. We analysed genomic data from 43 new porcine Rothia isolates, together with 112 publicly available draft genome sequences of Rothia isolates from humans, animals and the environment. In all Rothia genomes, we identified biosynthetic gene clusters predicted to produce antibiotic non-ribosomal peptides, iron scavenging siderophores and other secondary metabolites that modulate microbe–microbe and potentially microbe–host interactions. In vitro overlay inhibition assays corroborated the hypothesis that specific strains produce natural antibiotics. Rothia genomes encode a large number of carbohydrate-active enzymes (CAZy), with varying CAZy activities among the species found in different hosts, host niches and environments. These findings reveal competition mechanisms and metabolic specializations linked to ecological adaptation of Rothia species in different hosts.
... In such cases, the polyphasic approach of microbial taxonomical characterization is employed for a more reliable and accurate approach for the novel identification of a species. To date, 14 Rothia species have been described; amongst which "Rothia arfidiae" (Ko et al. 2009), "Rothia marina" (Liu et al. 2013) and "Rothia nasisuis" (Schlattmann et al. 2018) are listed as 'invalidly published' species (Parte et al., 2020). The members of the genus Rothia have been mostly isolated from human skin and tooth, plant rhizosphere, saline soil, air, waste and estuarine water and domesticated animals (Pandhi and Hammond 1975;Fotos et al. 1982;Bednář and Mára 1991;Collins et al., 2000;Chou et al. 2008;Fan et al. 2004;Li et al. 2004;Tang et al., 2009;Park et al. 2010;Xiong et al., 2013;Kämpfer et al., 2016;Ananieva et al. 2018;Nouioui et al. 2018). ...
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A novel, mustard yellow-pigmented aerobic bacterial strain designated AR01T was isolated from hypocotyl tissue of a sandalwood seedling from Bangalore, India. The 16S rRNA gene of strain AR01T had the highest 98.97% sequence similarity with Rothia halotolerans YIM 90716T (KCTC 19172) followed by Rothia kristinae PM 129T (NBRC 15354T) (97.31%) and Rothia koreensis P31T (JCM 15915) (97.11%), respectively. The strain AR01T was coccoid-shaped, non-motile, non-spore forming, oxidase negative and catalase positive. The strain AR01T has a genome size of 3.31 Mb containing 2993 protein-coding genes including 48 tRNA and 10 rRNAs spread across 84 contigs. The genomic DNA G + C content was 71.77 mol%. The calculated dDDH was 31.10% and the OrthoANI value was 85.27% when compared with its closest related type strain Rothia halotolerans YIM 90716T. The predominant cellular fatty acids were C16:0 iso, C15:0 anteiso and C17:0 anteiso. The strain AR01T contains major polar lipids including diphosphatidylglycerol and phosphatidylglycerol. The distinct physiological, biochemical characteristics and genotypic relatedness indicated that AR01T represents a novel species of the genus Rothia, for which the name Rothia santali sp. nov. (Type strain AR01T = MCC 4800T = JCM 35593T) is proposed.
... In such cases, polyphasic approach of microbial taxonomical characterisation is employed for a more reliable and accurate approach for the novel identi cation of a species. To date, 15 Rothia species have been described; among which "Rothia ar diae" (Ko et al. 2009), "Rothia marina" (Liu et al. 2013) and "Rothia nasisuis" (Schlattmann et al. 2018) are listed as 'invalidly published' species (Parte et al., 2020). Members of the genus Rothia have been mostly isolated from human skin and tooth, plant rhizosphere, saline soil, air, waste and estuarine water, Nouioui et al. 2018). ...
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A novel, ‘mustard yellow’ pigmented aerobic bacterial strain designated AR01T was isolated from hypocotyl tissue of a sandalwood seedling from Bangalore, India. The 16S rRNA gene of strain AR01T had the highest 98.97% sequence similarity with Rothia halotolerans YIM 90716T (KCTC 19172) followed by Rothia kristinae PM 129T (NBRC 15354T) (97.31%) and Rothia koreensis P31T (JCM 15915) (97.11%), respectively. The strain AR01T was coccoid-shaped, non-motile, non-spore-forming, oxidase-negative, and catalase-positive. The strain AR01T has a genome size of 3.31 Mb containing 2993 protein-coding genes including 48 tRNA and 10 rRNAs spread across 84 contigs. The genomic DNA G + C content was 71.77 mol%. The calculated dDDH was 31.10%, and the OrthoANI value was 85.27% compared to its closest related type strain Rothia halotolerans YIM 90716T. The predominant cellular fatty acids were C16:0 iso (30.04%), C15:0 anteiso (37.42%), and C17:0 anteiso (21.78%). The strain AR01T contains major polar lipids including diphosphatidylglycerol and phosphatidylglycerol. Based on the distinct physiological, biochemical characteristics and genotypic relatedness indicated that AR01T represents a novel species of the genus Rothia, for which the name Rothia santali sp. nov. (Type strain AR01T = MCC 4800T = JCM 35593T) is proposed. The GenBank/EMBL/DDBJ accession number for the reference 16S rRNA gene sequences of the strain AR01T is OM838448. The accession number of the whole-genome of AR01T is JANAFB000000000
... are ubiquitous Gram-positive, rod-shaped bacteria belonging to the Micrococcaceae family. They can be found in the air, soil, water, or in some healthy mammals [1][2][3][4][5][6]. They colonize the oropharynx and respiratory airways of humans and less often the duodenum [7][8][9][10][11]. ...
Article
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... The genus of Rothia is a gram positive bacterium and it comprises of ten species, Rothia dentocariosa [9], [10], Rothia mucilaginosa [11], Rothia nasimurium [11], Rothia amarae [12], Rothia aeria [13], Rothia terrae [14], Rothia arfidiae [15], Rothia endophytica [16], Rothia marina [17], and Rothia aerolata [18]. R. aeria and R. amarae were isolated from air samples and sludge of a foul water sewer, respectively and R. nasimurium was found from the nose of a healthy mouse. ...
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... Rothia species are not generally recognised as marine bacteria, although a few examples are available. Rothia terrae was isolated from sediment in the Baltic Sea (Shubenkova et al. 2010), and Rothia marina from sediment in the South China Sea was described by Liu et al. (2013), but no information could be found on the R. amarae of marine origin. Tsukamurella (Actinobacteria) are mostly known as human pathogens, but strains have been isolated from a marine sponge (Olson et al. 2007), deep sea sediments (Pathom-aree et al. 2006) and intertidal biofilms (Lee et al. 2003). ...
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A new method called the neighbor-joining method is proposed for reconstructing phylogenetic trees from evolutionary distance data. The principle of this method is to find pairs of operational taxonomic units (OTUs [= neighbors]) that minimize the total branch length at each stage of clustering of OTUs starting with a starlike tree. The branch lengths as well as the topology of a parsimonious tree can quickly be obtained by using this method. Using computer simulation, we studied the efficiency of this method in obtaining the correct unrooted tree in comparison with that of five other tree-making methods: the unweighted pair group method of analysis, Farris's method, Sattath and Tversky's method, Li's method, and Tateno et al.'s modified Farris method. The new, neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods.
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Four Gram-positive bacteria, strains A1-17BT, A1-22T, A1-3T and A1-8, isolated from the air in the Russian space laboratory Mir, were subjected to a polyphasic taxonomic study. Phylogenetic analysis of the bacteria based on their 16S rDNA sequence showed that they belong to the genera Rothia (A1-17BT), Rhodococcus (A1-22T) and Arthrobacter (A1-3T and A1-8). Morphological, physiological, chemotaxonomic and genomic characteristics supported the assignments of these strains to these genera, but they could not be classified as any existing species within each respective genus. 16S rDNA similarity values between strain A1-17BT and its neighbours, Rothia dentocariosa genomovar II, Rothia dentocariosa, Rothia mucilaginosa and Rothia nasimurium, were respectively 99·8, 98·0, 96·4 and 95·4 %. Polyphasic taxonomic evidence indicated that strain A1-17BT should be categorized together with the unofficially named Rothia dentocariosa genomovar II, but clearly differentiated them from the established species of the genus Rothia. Strain A1-22T formed a coherent cluster with Rhodococcus erythropolis, Rhodococcus globerulus, Rhodococcus marinonascens and Rhodococcus percolatus in 16S rDNA sequence analysis, but DNA–DNA relatedness values were only 45·5, 35·3, 18·9 and 21·9 %. Strains A1-3T and A1-8 shared 99·9 % 16S rDNA sequence similarity, and strain A1-3T showed the highest level of 16S rDNA similarity, 96·6 %, to Arthrobacter polychromogenes. Contrasting biochemical characteristics were also identified. Finally, as a result of the polyphasic taxonomic study, three of the strains are proposed as type strains of novel species: Rothia aeria sp. nov. (A1-17BT=GTC 867T=JCM 11412T=DSM 14556T), Rhodococcus baikonurensis sp. nov. (A1-22T=GTC 1041T=JCM 11411T=DSM 44587T) and Arthrobacter russicus sp. nov. (A1-3T=GTC 863T=JCM 11414T=DSM 14555T).
Article
Rothia gen. nov. (Actinomycetaceae) is proposed as the name of a monotypic genus with the species Rothia dentocariosus comb. nov. (basionym Actinomyces dentocariosus Onisi 1949), synonyms Nocardia dentocariosus (Onisi) Roth 1957; Nocardia salivae Davis and Freer 1960, No strain of Onisi's original isolates is extant. ATCC 17931 is described and proposed as the neotype strain of Rothia dentocariosus (Onisi) Georg and Brown 1967.
Article
Because a natural entity 'species' cannot be recognized as a group of strains that is genetically well separated from its phylogenetic neighbors, a pragmatic approach was taken to define a species by a polyphasic approach (L. G. Wayne, D. J. Brenner, R. R. Colwell, P. A. D. Grimont, O. Kandler, M. I. Krichevsky, L. H. Moore, W. E. C. Moore, R. G. E. Murray, E. Stackebrandt, M. P. Starr, and H. G. Truper, Int. J. Syst. Bacteriol. 37:463-464, 1987), in which a DNA reassociation value of about 70% plays a dominant role. With the establishment of rapid sequence analysis of 16S rRNA and the recognition of its potential to determine the phylogenetic position of any prokaryotic organism, the role of 16S rRNA similarities in the present species definition in bacteriology needs to be clarified. Comparative studies clearly reveal the limitations of the sequence analysis of this conserved gene and gene product in the determination of relationships at the strain level for which DNA-DNA reassociation experiments still constitute the superior method. Since today the primary structure of 16S rRNA is easier to determine than hybridization between DNA strands, the strength of the sequence analysis is to recognize the level at which DNA pairing studies need to be performed, which certainly applies to similarities of 97% and higher.
Article
Fitch, W. M. (Dept. of Physiological Chemistry, Univ. of Wisconsin, Madison, Wisconsin, 53706), 1971. Toward defining the course of evolution: minimum change for a specific tree topology. Syst. Zool., 20:406-416.A method is presented that is asserted to provide all hypothetical ancestral character states that are consistent with describing the descent of the present-day character states in a minimum number of changes of state using a predetermined phylogenetic relationship among the taxa represented. The character states used as examples are the four messenger RNA nucleotides encoding the amino acid sequences of proteins, but the method is general.
Article
The name Stomatococcus mucilaginosus gen.nov., sp.nov., ep.rev., is pro- posed for a group of organisms previously called 'Micrococcus mucilaginosus ," a name which is not on the Approved Lists of Bacterial Names. Stomatococcus mucilaginosus consists of gram-positive, encapsulated, nonmotile, non-spore- forming spheres. The distinctive biochemical characters of this organism are as follows: catalase test weakly positive or negative; acid, but not gas, is produced from glucose, trehalose, and glycerol; no acid is produced from mannitol, lactose, or xylose; hydrolyzes gelatin and esculin; produces acetoin; and reduces nitrate to nitrite. This organism is negative in tests for coagulase, deoxyribonuclease, phosphatase, and arginine dihydrolase; it does not grow on nutrient agar supple- mented with 5% NaCl. The guanine-plus-cytosine content of its deoxyribonucleic acid varies between 56 and 60 mol%. The genus is placed in the family Micrococcaceae since the strains possess most of the characteristics of this family. Four striking differences between S. mucilaginosus and species of the genus Micrococcus are found in the following: encapsulation of cells, catalase reaction, ability to grow on nutrient agar supplemented with 5% NaCl, and guanine-plus-cytosine content of the deoxyribonucleic acid. Strain CCM 2417 (= ATCC 25296 = NCTC 10663) is the type strain of this new species. S. mucilaginosus is the type species of the genus Stomatococcus.
Article
Fifty strains of Rothia dentocariosa Georg and Brown were characterized morphologically, biochemically, and serologically. All strains had characteristics agreeing with previous morphological descriptions of this organism, although there was greater biochemical and serological strain variation than previously reported. Four biotypes were established on the basis of variability in reduction of nitrite, production of urease, hydrolysis of esculin, and formation of acid from lactose, mannitol, mannose, raffinose, rhamnose, salicin, and trehalose. Three serotypes and a group of fluorescent antibody-negative strains were identified on the basis of the fluorescent antibody technique. A relationship between the four biotypes and the three serotypes was established.
Article
The recently-developed statistical method known as the "bootstrap" can be used to place confidence intervals on phylogenies. It involves resampling points from one's own data, with replacement, to create a series of bootstrap samples of the same size as the original data. Each of these is analyzed, and the variation among the resulting estimates taken to indicate the size of the error involved in making estimates from the original data, In the case of phylogenies, it is argued that the proper method of resampling is to keep all of the original species while sampling characters with replacement, under the assumption that the characters have been independently drawn by the systematist and have evolved independently. Majority-rule consensus trees can be used to construct a phylogeny showing all of the inferred monophyletic groups that occurred in a majority of the bootstrap samples. If a group shows up 95% of the time or more, the evidence for it is taken to be statistically significant. Existing computer programs can be used to analyze different bootstrap samples by using weights on the characters, the weight of a character being how many times it was drawn in bootstrap sampling. When all characters are perfectly compatible, as envisioned by Hennig, bootstrap sampling becomes unnecessary; the bootstrap method would show significant evidence for a group if it is defined by three or more characters.
Article
Publisher Summary This chapter discusses the analysis of the chemical composition and primary structure of the murein. Murein (peptidoglycan, mucopeptide) is the main cell wall polymer of eubacteria and is common to both Gram-negative and Gram-positive bacteria. There are only a few prokaryotic organisms, such as mycoplasmas and archaebacteria, which lack murein. The glycan moiety is rather uniform and shows only a few variations such as O-acetylation or O-phosphorylation or the exceptional absence of peptide substituents. The peptide moiety of the murein shows, in contrast to the glycan part, a considerable variation. Extensive investigation of the chemical structure of murein has demonstrated the existence of almost 100 different variations of the peptide moiety. Depending on the mode of cross-linking two main groups of murein, named A and B, have been distinguished. The different structure of cell walls of Gram-positive and Gram-negative bacteria necessitates discrete methods for preparing cell walls. The cell walls of Gram-positive bacteria reveal in profile one thick and more or less homogeneous layer, whereas Gram-negative bacteria have thinner, but distinctly layered cell walls with an outer membrane resembling the cytoplasmic membrane in profile.
Article
Publisher Summary This chapter discusses analysis of isoprenoid quinones. The respiratory quinones represent an important group of isoprenoid lipids that occur in the cytoplasmic membrane of most prokaryotes. Two major structural groups of bacterial isoprenoid quinones can be recognized: the naphthoquinones and benzoquinones. Naphthoquinones can be divided further into two major types: phylloquinones and menaquinones. In choosing the methods to be employed for the extraction and purification of menaquinones, ubiquinones, and related quinones one must take into account the susceptibility of these compounds to degradation. Isoprenoid quinones are quite rapidly photo-oxidized in the presence of oxygen and strong light. They are also particularly susceptible to alkaline conditions (the last limitation rules out alkaline saponification). Thus, it is preferable to conduct extraction and subsequent purification procedures fairly rapidly, avoiding extremes of pH and strong light. The composition of natural mixtures of bacterial quinones can be investigated using partition chromatography. Separation of compounds by partition chromatography is generally on the basis of relative solubilities, which in the case of homologous series such as ubiquinones and menaquinones is determined by the length and degree of hydrogenation of the multiprenyl side chain.
Article
A rapid method for distinction between gram-negative and grampositive bacteria by means of a 3% solution of potassium hydroxide is tested on 71 gram-positive and 55 gram-negative bacterial strains. The method proved reliable with one exception only, a Bacillus macerans strain. That strain was definately gram-negative on staining. Other Bacillus strains were proved gram-positive by the test, even those being gram-negative on staining.
Article
A novel non-sporulating, non-motile, catalase- and oxidase-positive, strictly aerobic, Gram-positive-staining coccus, strain JSM 077023(T), was isolated from an intertidal sediment sample collected from Naozhou Island in the South China Sea, China. Growth occurred in the presence of 0.5-25 % (w/v) NaCl [optimum, 2-5 % (w/v) NaCl] and at pH 5.5-10.5 (optimum, pH 7.0-8.0) and at 4-45 °C (optimum, 30-35 °C). The major amino acid constituents of the cell wall were alanine, glycine and lysine. The major cellular fatty acids were anteiso-C₁₅:₀ and iso-C₁₅:₀. The strain contained MK-7 and MK-6 as the predominant respiratory quinones and diphosphatidylglycerol, phosphatidylglycerol and an unidentified phospholipid as the polar lipids. The genomic DNA G+C content of strain JSM 077023(T) was 41.3 mol%. A phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strain JSM 077023(T) should be assigned to the genus Jeotgalicoccus and was most closely related to the type strains of Jeotgalicoccus halotolerans (sequence similarity 99.0 %) and Jeotgalicoccus aerolatus (99.0 %), followed by Jeotgalicoccus coquinae (98.6 %) and Jeotgalicoccus psychrophilus (97.4 %). 16S rRNA gene sequence similarities of less than 97 % were observed with other species of the genus Jeotgalicoccus. Levels of DNA-DNA relatedness between strain JSM 077023(T) and the type strains of J. halotolerans, J. aerolatus, J. coquinae and J. psychrophilus ranged from 36.8 to 22.7 %. The combination of phylogenetic analysis, DNA-DNA relatedness values, phenotypic characteristics and chemotaxonomic data supported the suggestion that strain JSM 077023(T) represents a novel species of the genus Jeotgalicoccus, for which the name Jeotgalicoccus nanhaiensis sp. nov. is proposed. The type strain is JSM 077023(T) ( = DSM 23006(T) = KCTC 13714(T)). An emended description of the genus Jeotgalicoccus is also presented.
Article
A Gram-positive, non-motile, white-pigmented, short rod actinobacterium, designated YIM 90734T, was isolated from a saline soil sample collected from Ganjiahu Suosuo Forest National Nature Reserve in Xinjiang province, north-west China, and its taxonomic position was investigated by using a polyphasic approach. Strain YIM 90734T grew optimally at 28-37 degrees C and pH 6.0-8.0 and in 5% (w/v) NaCl. The peptidoglycan type was A4alpha, L-Lys-L-Ala-L-Glu and tyvelose and mannose were the major cell-wall sugars. The predominant menaquinones were MK-10 and MK-9. Major cellular fatty acids (>10% of total) were anteiso-C15:0 and anteiso-C17:0. The polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, one unknown phospholipid and two unknown glycolipids. The DNA G+C content was 70.3 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM 90734T belonged to the genus Zhihengliuella. The 16S rRNA gene sequence similarity between strain YIM 90734T and the type strain of the only recognized Zhihengliuella species, Zhihengliuella halotolerans, was 97.7%. However, the level of DNA-DNA relatedness of the two strains was 41.4%. The DNA-DNA relatedness data and differential phenotypic properties, together with the phylogenetic distinctiveness, demonstrated that strain YIM 90734T could be differentiated from Z. halotolerans. On the basis of the data presented, strain YIM 90734T is considered to represent a novel species of the genus Zhihengliuella, for which the name Zhihengliuella alba sp. nov. is proposed. The type strain is YIM 90734T (=KCTC 19375T=DSM 21143T). The description of the genus Zhihengliuella has also been emended.
Article
A novel Gram-negative, facultatively anaerobic, non-sporulating, non-motile, catalase- and oxidase-positive, rod-shaped bacterium (strain JSM 061001(T)) was isolated from a tidal flat in the South China Sea, China. Growth occurred with 0-5 % (w/v) NaCl [optimum, 0.5-1 % (w/v) NaCl], at pH 5.0-10.0 (optimum, pH 7.0) and at 4-35 degrees C (optimum, 25-30 degrees C). The major cellular fatty acids were C(16 : 0), cyclo C(17 : 0), C(18 : 1)omega7c and C(16 : 1). Strain JSM 061001(T) contained ubiquinone Q-8 as the predominant respiratory quinone, and phosphatidylglycerol, phosphatidylethanolamine and an unidentified phospholipid as the polar lipids. The genomic DNA G+C content was 65.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain JSM 061001(T) belongs to the family Alcaligenaceae and was related most closely to the type strains of the two recognized species of the genus Pigmentiphaga. The three strains formed a robust cluster in the neighbour-joining, maximum-parsimony and maximum-likelihood phylogenetic trees. Levels of DNA-DNA relatedness between strain JSM 061001(T) and the type strains of Pigmentiphaga daeguensis and Pigmentiphaga kullae were 15.8 and 10.5 %, respectively. The combination of phylogenetic analysis, DNA-DNA hybridization data, phenotypic characteristics and chemotaxonomic differences supported the view that strain JSM 061001(T) represents a novel species of the genus Pigmentiphaga, for which the name Pigmentiphaga litoralis sp. nov. is proposed. The type strain is JSM 061001(T) (=CCTCC AA207034(T)=KCTC 22165(T)).
Article
A new method called the neighbor-joining method is proposed for reconstructing phylogenetic trees from evolutionary distance data. The principle of this method is to find pairs of operational taxonomic units (OTUs [= neighbors]) that minimize the total branch length at each stage of clustering of OTUs starting with a starlike tree. The branch lengths as well as the topology of a parsimonious tree can quickly be obtained by using this method. Using computer simulation, we studied the efficiency of this method in obtaining the correct unrooted tree in comparison with that of five other tree-making methods: the unweighted pair group method of analysis, Farris's method, Sattath and Tversky's method, Li's method, and Tateno et al.'s modified Farris method. The new, neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods.
Article
A new method is proposed to measure relatedness amongst bacteria, based on renaturation rate determinations of DNA types and their mixture. The equations, relating the degree of binding with renaturation rates, are calculated for several cases. The optimal conditions for measurements are given. The method was checked in several ways. The advantages are summarized.
Article
Calculating the rate of evolution in terms of nucleotide substitutions seems to give a value so high that many of the mutations involved must be neutral ones.
Article
The application of maximum likelihood techniques to the estimation of evolutionary trees from nucleic acid sequence data is discussed. A computationally feasible method for finding such maximum likelihood estimates is developed, and a computer program is available. This method has advantages over the traditional parsimony algorithms, which can give misleading results if rates of evolution differ in different lineages. It also allows the testing of hypotheses about the constancy of evolutionary rates by likelihood ratio tests, and gives rough indication of the error of ;the estimate of the tree.
Article
Some simple formulae were obtained which enable us to estimate evolutionary distances in terms of the number of nucleotide substitutions (and, also, the evolutionary rates when the divergence times are known). In comparing a pair of nucleotide sequences, we distinguish two types of differences; if homologous sites are occupied by different nucleotide bases but both are purines or both pyrimidines, the difference is called type I (or "transition" type), while, if one of the two is a purine and the other is a pyrimidine, the difference is called type II (or "transversion" type). Letting P and Q be respectively the fractions of nucleotide sites showing type I and type II differences between two sequences compared, then the evolutionary distance per site is K = -(1/2) ln [(1-2P-Q) square root of 1-2Q]. The evolutionary rate per year is then given by k = K/(2T), where T is the time since the divergence of the two sequences. If only the third codon positions are compared, the synonymous component of the evolutionary base substitutions per site is estimated by K'S = -(1/2) ln (1-2P-Q). Also, formulae for standard errors were obtained. Some examples were worked out using reported globin sequences to show that synonymous substitutions occur at much higher rates than amino acid-altering substitutions in evolution.
Article
An unknown, Gram-positive, ovoid-shaped bacterium isolated from the nose of a mouse was subjected to a polyphasic taxonomic analysis. Comparative 16S rRNA gene sequencing demonstrated that the unknown organism was a member of the family Micrococcaceae and possessed a specific phylogenetic association with Rothia dentocariosa and Stomatococcus mucilaginosus. Phenotypically, the bacterium closely resembled R. dentocariosa and S. mucilaginosus but could be distinguished from these species by biochemical tests and electrophoretic analysis of whole-cell proteins. Based on both phylogenetic and phenotypic evidence, it is proposed that the unknown bacterium be classified in the genus Rothia, as Rothia nasimurium sp. nov. In addition, it is proposed that S. mucilaginosus be reclassified in the genus Rothia, as Rothia mucilaginosa comb. nov.