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At least 19 recordsLinked to original sources
PubMed2003

Development and validation of a nested-PCR-denaturing gradient gel electrophoresis method for taxonomic characterization of bifidobacterial communities.

The taxonomic characterization of a bacterial community is difficult to combine with the monitoring of its temporal changes. None of the currently available identification techniques are able to visualize a "complete" community, whereas techniques designed for analyzing bacterial ecosystems generally display limited or labor-intensive identification potential. This paper describes the optimization and validation of a nested-PCR-denaturing gradient gel electrophoresis (DGGE) approach for the species-specific analysis of bifidobacterial communities from any ecosystem. The method comprises a Bifidobacterium-specific PCR step, followed by purification of the amplicons that serve as template DNA in a second PCR step that amplifies the V3 and V6-V8 regions of the 16S rRNA gene. A mix of both amplicons is analyzed on a DGGE gel, after which the band positions are compared with a previously constructed database of reference strains. The method was validated through the analysis of four artificial mixtures, mimicking the possible bifidobacterial microbiota of the human and chicken intestine, a rumen, and the environment, and of two fecal samples. Except for the species Bifidobacterium coryneforme and B. indicum, all currently known bifidobacteria originating from various ecosystems can be identified in a highly reproducible manner. Because no further cloning and sequencing of the DGGE bands is necessary, this nested-PCR-DGGE technique can be completed within a 24-h span, allowing the species-specific monitoring of temporal changes in the bifidobacterial community.

Animals↗
PubMed1999

Taxonomic characterization of denitrifying bacteria that degrade aromatic compounds and description of Azoarcus toluvorans sp. nov. and Azoarcus toluclasticus sp. nov.

A taxonomic characterization of twenty-one strains capable of degrading aromatic compounds under denitrifying conditions, isolated from ten different geographical locations, was performed on the basis of general morphological and physiological characteristics, cellular fatty acids, DNA base composition, small ribosomal (16S) subunit DNA sequences, whole-cell protein patterns and genomic DNA fragmentation analysis, in addition to DNA similarity estimations using hybridization methods. The collection of strains was subdivided into a number of different groups. A first group, consisting of four strains, could be assigned to the previously described species Azoarcus tolulyticus. A second group (five strains) had DNA which reannealed highly to that of strains of the first group, and it is considered to represent a genomovar of A. tolulyticus. The third and fourth groups, composed of a total of five strains, represent a new species of Azoarcus, Azoarcus toluclasticus (group 3) and a genomovar of this species (group 4), respectively. Finally, the fifth group, with two strains, corresponds to another new species of the genus Azoarcus, Azoarcus toluvorans. In addition to these five groups, the collection includes five individual strains perhaps representing as many different new species. The above classification is partially consistent with the results of approaches other than DNA-DNA hybridization (electrophoretic patterns of whole-cell proteins and of the fragments obtained after digestion of total DNA with infrequently cutting restriction enzymes). On the other hand, no correlation of these groupings was found in terms of the cellular fatty acid composition. It is also unfortunate that no simple sets of easily determinable phenotypic properties could be defined as being characteristic of each of the groups.

Aerobiosis↗
PubMed2002

Taxonomic characterization of Haloferax sp. (" H. alicantei") strain Aa 2.2: description of Haloferax lucentensis sp. nov.

An extremely halophilic archaeon, previously named as Haloferax sp. strain Aa 2.2 or "Haloferax alicantei" that has been extensively used for genetic studies with halobacteria, was taxonomically characterized by using phenotypic tests (including morphological, physiological, biochemical and nutritional features), DNA-DNA hybridization and 16S rRNA sequence phylogenetic analysis. This organism was isolated in 1986 by Torreblanca et al. from a pond of a Spanish saltern located in Alicante. The cells were pleomorphic, Gram negative and grew optimally at 25% NaCl. The polar lipid composition was similar to that of species of the genus Haloferax. The DNA G+C content of this strain was 64.5 mol%. Phylogenetic analysis based on 16S rRNA sequence comparison confirmed that this archaeon is a member of the genus Haloferax and was most closely related to Haloferax volcanii. DNA-DNA hybridization between strain Aa 2.2 and the type strain of all named species of the genus Haloferax revealed low levels of relatedness (25-2%), supporting the placement of this organism in a new species. On the basis of the phenotypic characteristics, molecular data and phylogenetic analysis we propose to name strain Aa 2.2 as a new species, Haloferax lucentensis sp. nov. The type strain is Aa 2.2 (=JCM 9276=NCIMB 13854=CIP 107410=DSM 14919=CECT 5871=CCM 7023).

Bacterial Typing Techniques↗
PubMed2026

Polyphasic taxonomic characterization of Brachybacterium netajii sp. nov., a metabolically versatile bacterium isolated from the river Ganges, India.

A comprehensive polyphasic taxonomic strategy was applied to the systematic characterization of strain DNPG3T, which was isolated from the river Ganges, Hooghly, West Bengal, India. The Gram-positive, halotolerant, heavy-metal-tolerant strain exhibited the ability to degrade p-nitrophenol (PNP). Cellular fatty acid analysis revealed that the predominant components were anteiso-C15:0 (24.61%), C11:0 (21.06%), iso-C16:0 (11.89%), C16:0 (11.58%), and anteiso-C17:0 (11.24%). Notably, the presence of C11:0, C10:0 2-OH as major fatty acids differentiate strain DNPG3T from its closely related members of the genus Brachybacterium. The predominant respiratory quinone was identified as menaquinone-7 (MK-7). Analysis of 16S rRNA gene sequence indicated that B. zhongshanense strain JBT was the closest relative of DNPG3T, sharing 97.08% sequence similarity. Genome-based ANI value calculated using the EzBioCloud server revealed that B. zhongshanense JCM 15471T was the closest genomic relative (85.49%). These values were further substantiated by digital DNA-DNA hybridization (dDDH) estimates calculated using the GGDC server. Taxonomic assignment using the GTDB database further indicated that strain DNPG3T constitutes a previously unrecognized species within the genus Brachybacterium. Genome analysis of strain DNPG3T identified eleven genomic islands, along with a rich repertoire of 194 carbohydrate-active enzyme (CAZyme) families, comprising 95 glycoside hydrolases and 53 glycosyltransferases. In addition, five biosynthetic gene clusters were detected. Collectively, these genomic features indicate the involvement of horizontal gene transfer events and highlighted the pronounced metabolic versatility of the strain, underscoring its potential for industrial enzyme production and secondary metabolite biosynthesis. Pan-genome analysis further indicates that the Brachybacterium pan-genome is open, reflecting substantial genetic diversity and ongoing gene acquisition within the genus. Comprehensive biochemical, physiological, chemotaxonomic, and phylogenetic analyses supported the assignment of strain DNPG3T to the genus Brachybacterium while clearly distinguishing it from all currently described species within the genus. Accordingly, strain DNPG3T was proposed to represent a novel species, for which the name Brachybacterium netajii sp. nov. is suggested. The type strain was DNPG3T (= MTCC13125T).

India↗
PubMed2005

[Taxonomic characterization and antibiotic resistance of pathogens of perinatal infectious inflammatory pathology in infants in Orenburg].

The materials on regional features of the nosologic structure, taxonomic spectrum and antibiotic resistance of the pathogens of perinatal infectious inflammatory pathology (IIP) in infants in Orenburg are presented. From 2002 to 2005 the average level of IIP of 19.0 cases per 1000 living new borns and the dominance of skin inflammatory diseases (vesiculopustulosis in particular) in the nosologic structure among the other forms of IIP (including conjunctivitis and pneumonia) were observed. The prevalence of the gram positive cocci with the leadership of coagulase negative staphylococci among the skin and eye forms of IIP was shown. Their portion reached 62.8%. The portion of the other microorganisms was much lover. Gramnegative bacteria (Neisseria spp., E. coli, K. ozaenae) were isolated from 6.1, 4.3 and 0.6% of the cases. The Candida isolates were detected in 1% of the cases. The regional antibiotic resistance register for the pathogens of IIP was developed. Its use is obligatory in prescribing drugs for empirical therapy of such pathology and prevention of its complications.

Bacteria↗
PubMed2004

Taxonomic characterization of nine strains isolated from clinical and environmental specimens, and proposal of Corynebacterium tuberculostearicum sp. nov.

Nine unidentified Gram-positive, lipophilic corynebacteria were isolated from clinical and food samples and subjected to a polyphasic taxonomic analysis. The bacteria were distinguished from Corynebacterium species with validly published names by biochemical tests, fatty acid content and whole-cell protein analysis. Comparative 16S rRNA gene sequence analysis demonstrated unambiguously that the nine strains were related phylogenetically to the species 'Corynebacterium tuberculostearicum' and represented a distinct subline within the genus Corynebacterium. On the basis of both phenotypic and phylogenetic evidence, the formal description of Corynebacterium tuberculostearicum sp. nov. is proposed. The type strain of C. tuberculostearicum is Medalle XT (=LDC-20T=CIP 107291T=CCUG 45418T=ATCC 35529T).

Bacterial Proteins↗
PubMed1996

Taxonomic characterization of closely related Streptomyces spp. based on the amino acid sequence analysis of protease inhibitor proteins.

Amino acid sequences of protease inhibitors (Streptomyces subtilisin inhibitor-like proteins) widely distributed in Streptomyces were compared to clarify the taxonomic status of three strains of Streptomyces spp., S. coelicolor A3(2), S. lividans 66 and S. coelicolor Müller, which are closely related by conventional taxonomical procedures. The sequence comparison indicated that S. coelicolor A3(2) is distinct from the type strain S. coelicolor Müller, but belongs to the same taxon as S. lividans 66.

Amino Acid Sequence↗
PubMed2002

Taxonomic characterization of Mogibacterium diversum sp. nov. and Mogibacterium neglectum sp. nov., isolated from human oral cavities.

Novel isolates, strains HM-7, HM-6, HH-31, P9a-hT and UJB13-d, which were isolated from tongue plaque and necrotic dental pulp, were studied taxonomically and phylogenetically. These organisms were anaerobic, non-spore-forming, gram-positive, rod-shaped bacteria that were inert in most of the conventional biochemical tests and phenotypically resemble Mogibacterium species or asaccharolytic Eubacterium species. The G+C contents of the DNAs from the novel isolates ranged from 41 to 42 mol %. DNA-DNA hybridization studies demonstrated that these strains might be assigned to the genus Mogibacterium but not to the previously described species. It was also apparent that strain HM-7 belonged to the same species as strains HM-6 and HH-31, and that strains P9a-hT and UJB13-d belonged to a second species. The levels of DNA-DNA relatedness to asaccharolytic Eubacterium species, including Eubacterium brachy, Eubacterium nodatum, Eubacterium saphenum and the more recently proposed Eubacterium minutum and Eubacterium exiguum (reclassified as Slackia exigua), are less than 2%. The results of 16S rDNA sequence comparisons revealed that these organisms represent novel lineages distinct from all previously described species of gram-positive, rod-shaped bacteria. On the basis of phenotypic characteristics, DNA-DNA hybridization data and phylogenetic analysis with 16S rRNA gene sequence data, new species are proposed, namely Mogibacterium diversum (for strains HM-7, HM-6 and HH-31) and Mogibacterium neglectum (for strains P9a-hT and UJB13-d). HM-7T (= ATCC 700923T = JCM 11205T) is the type strain of the former and P9a-hT (= ATCC 700924T = JCM 11204T) is the type strain for the latter.

Anaerobiosis↗
PubMed2001

Taxonomic characterization of new alkaliphilic and alkalitolerant methanotrophs from soda lakes of the Southeastern Transbaikal region and description of Methylomicrobium buryatense sp.nov.

Five strains of obligate methanotrophic bacteria (4G, 5G, 6G, 7G and 5B) isolated from bottom sediments of Southeastern Transbaikal soda lakes (pH 9.5-10.5) are taxonomically described. These bacteria are aerobic, Gram-negative monotrichous rods having tightly packed cup-shaped structures on the outer cell wall surface (S-layers) and Type I intracytoplasmic membranes. All the isolates possess particulate methane monooxygenase (pMMO) and one strain (5G) also contains soluble methane monooxygenase (sMMO). They assimilate methane and methanol via the ribulose monophosphate pathway (RuMP). The isolates are alkalitolerant or facultatively alkaliphilic, able to grow at pH 10.5-11.0 and optimally at pH 8.5-9.5. These organisms are obligately dependent on the presence of sodium ions in the growth medium and tolerate up to 0.9-1.4 M NaCl or 1 M NaHCO3. Although being mesophilic, all the isolates are resistant to heating (80 degrees C, 20 min), freezing and drying. Their cellular fatty acids profiles primarily consist of C(16:1). The major phospholipids are phosphatidylethanolamine and phosphatidylglycerol. The main quinone is Q-8. The DNA G+C content ranges from 49.2-51.5 mol %. Comparative 16S rDNA sequencing showed that the newly isolated methanotrophs are related to membres of the Methylomicrobium genus. However, they differ from the known members of this genus by DNA-DNA relatedness. Based on pheno- and genotypic characteristics, we propose a new species of the genus Methylomicrobium Methylomicrobium buryatense sp. nov.

DNA, Ribosomal↗
PubMed2001

Taxonomic characterization of Ketogulonigenium vulgare gen. nov., sp. nov. and Ketogulonigenium robustum sp. nov., which oxidize L-sorbose to 2-keto-L-gulonic acid.

Four bacterial strains that oxidize L-sorbose to 2-keto-L-gulonic acid, a key intermediate in the synthesis of vitamin C, were isolated from soils of geographically distinct locations. All were Gram-negative, facultatively anaerobic, chemoheterotrophic rods. Comparative analysis revealed nearly identical 16S rDNA sequences amongst them (99.7-100% identical) and identified them as members of the alpha-subclass of the Proteobacteria. Phylogenetic analysis identified the closest taxonomically defined genus as Roseobacter (92.1-92.8% identical). On the basis of phylogenetic, phenotypic and genotypic analyses, a new genus is proposed, Ketogulonigenium gen. nov. Based upon these analyses, we also propose the reclassification of strain DSM 4025TP, originally identified as Gluconobacter oxydans, to the genus Ketogulonigenium. Two species are proposed: the type species Ketogulonigenium vulgare gen. nov., sp. nov., consisting of strains 62A-12APP, 266-13BPP and the type strain K. vulgare DSM 4025TP, and Ketogulonigenium robustum gen. nov., sp. nov., consisting of the type strain K. robustum X6LTP (= NRRL B-21627 = KCTC 0858BP). The species affiliation of the fifth strain (291-19PP) remains unresolved.

Base Sequence↗
PubMed1978

Further taxonomic characterization of the genus Bdellovibrio.

Cultures of Bdellovibrio isolated from different geographic locations have been studied in terms of deoxyribonucleic acid analysis (% G + C, genome size, and DNA hybridization), cytochrome spectrum, and host range. Isolates of the genus exhibit a broad range of % G + C ranging from 37 to 51% and the genome sizes extend from 1300 x 10(6) to 1700 x 10(6) daltons. DNA hybridization continues to reveal a high level of genetic heterogeneity. Bdellovibrio 3294 exhibits 32% relative reassociation to Bdellovibrio W, 37% to Bdellovibrio stolpii Uki2, and an undetectible level to Bdellovibrio starrii A3.12 Bdellovibrio W is 23% related to B. starri A3.12 and 28.5% to B. stolpii Uki2. For the first time differential absorption techniques have revealed peaks of cytochrome b. The analysis of the cytochrome spectrum seems to be limited as a taxonomic tool since most of the recent isolates studied share a common cytochrome spectrum. Host-range studies have been found to be dependent on the experimental conditions, and with the exception of one isolate (B. starrii A3.12) the taxonomic significance of such techniques must be taken with caution.

Bdellovibrio↗
PubMed2006

Taxonomic characterization of two marine peritrichous ciliates, Epicarchesium corlissi n. sp. and Pseudovorticella jiangi n. sp. (Ciliophora: Peritrichia), from northern China.

Two new marine peritrich ciliates, Epicarchesium corlissi n. sp. and Pseudovorticella jiangi n. sp., were discovered in mariculture waters on the coast of northern China near Qingdao. Their morphology, infraciliature and silverline system were investigated based on both living and silver-impregnated specimens. E. corlissi is characterized as follows: marine Epicarchesium with dichotomously branched stalk; zooids elongate, approximately 60-70 x 25-35 microm in vivo; peristomial collar double-folded; macronucleus J-shaped; single, small contractile vacuole ventrally positioned; more than 60 striations between peristome and aboral trochal band, 13-18 from aboral trochal band to scopula; abstomal end of row 1 of infundibular polykinety 3 terminating at same level as rows 2 and 3 of infundibular polykinety 3; rows 2 and 3 of infundibular polykinety 3 much longer than row 1 and converging adstomally with infundibular polykinety 1. The new species P. jiangi is diagnosed as follows: marine Pseudovorticella; zooid inverted bell-shaped, approximately 80x60 microm in vivo and with a broad, flat, thin peristomial collar that measures approximately 90 microm across; pellicle with transparent cortical vesicles; macronucleus J-shaped; number of silverlines between peristome and aboral trochal band 20-24, from aboral trochal band to scopula 9-11; abstomal end of row 1 of infundibular polykinety 3 diverges from the other two rows of this polykinety and ends alongside row 3 of infundibular polykinety 2.

Animals↗
PubMed2006

Taxonomic characterization of members of the genus Corallococcus: molecular divergence versus phenotypic coherency.

Corallococcus coralloides DSM 2259(T), Corallococcus exiguus DSM 14696(T), Corallococcus macrosporus DSM 14697(T) and more than 35 strains identified as members of Corallococcus on the basis of morphology were subjected to partial sequences analysis of three housekeeping genes (lepA, fusA and rpoB), complementing a recent phylogenetic analysis based on genes coding for 16S rRNA and gyrB. Phylogenetic analysis of each gene, generated by maximum likelihood and two different additive treeing algorithms, resulted in the separate position of C. macrosporus DSM 14697(T) and a few Corallococcus strains that were more closely related to Myxococcus xanthus than to the other members of Corallococcus. The latter strains formed three clearly separate clusters by 16S rRNA gene phylogeny. This relationship, however, was only partially recovered by the other gene trees. Group 1, embracing the type strains of C. coralloides and C. exiguus, only emerged as a coherent cluster in the 16S rRNA gene tree. In all other gene trees this cluster embraced organisms of cluster 3, which either formed coherent subclusters (gyrB, lepA) or which appeared polyphyletic (fusA, rpoB). Group 2 organisms consistently constituted a monophyletic cluster, though their branching within the gene trees differed. A concatenated tree, based on the analysis of about 5400 nucleotides of all five partial genes was most similar to the 16S rRNA gene tree. In order to determine whether the individual clusters that emerged by 16S rRNA gene analysis (>99.1% intracluster similarities) show phenetic properties that would allow their description as new species, a few strains of each group were subjected to the analysis of whole cell fatty acid and physiological properties. Riboprint patterns were generated for some members of group 1. While the DNA-DNA reassociation values and riboprint patterns confirmed the genomic heterogeneity of members of cluster 1, none of the other properties investigated were sufficiently discriminative to allow the formal description of strain clusters as new species.

Bacterial Proteins↗
PubMed2000

Taxonomic characterization of Ochrobactrum sp. isolates from soil samples and wheat roots, and description of Ochrobactrum tritici sp. nov. and Ochrobactrum grignonense sp. nov.

A large collection of bacterial strains, immunotrapped from soil and from the wheat rhizoplane, was subjected to polyphasic taxonomy by examining various pheno- and genotypic parameters. Strains were grouped on (inter) repetitive extragenic palindromic DNA (REP) PCR profiles at the intraspecies level. Pheno- and genotypic characters were assessed for representatives from 13 different REP groups. Strains of nine REP groups constituting two physiological BIOLOG clusters fell in the coherent DNA-DNA reassociation group of Ochrobactrum anthropi. Strains of two REP groups constituting a separate BIOLOG cluster fell in the coherent DNA-DNA reassociation group of Ochrobactrum intermedium. Additional phenotypic characters differentiating O. anthropi and O. intermedium were found. REP group K strains constituted a different BIOLOG cluster, a separate DNA-DNA reassociation group and a distinct phylogenetic lineage in 165 rDNA homology analysis, indicating that REP group K strains represent a new species. Diagnostic phenotypic characters were found. Closest relatives were Ochrobactrum species. The name Ochrobactrum grignonense sp. nov. is proposed (type strain OgA9aT = LMG 18954T = DSM 13338T). REP group J strains again constituted a different BIOLOG cluster, a separate DNA-DNA reassociation group and showed, as a biological particularity, a strict preference for the rhizoplane as habitat. Diagnostic phenotypic characters were found. This indicated that REP group J strains represent a further new species, although phylogenetic analyses using 16S rDNA homology were not able to separate the cluster of REP group J sequences significantly from 16S rDNA sequences of Ochrobactrum anthropi. The name Ochrobactrum tritici sp. nov. is proposed (type strain SCII24T = LMG 18957T = DSM 13340T).

Alphaproteobacteria↗
PubMedDate not supplied

Taxonomic characterization of two marine peritrichous ciliates, Pseudovorticella clampi n. sp. and Zoothamnium pararbuscula n. sp. (Ciliophora: Peritrichia), from North China.

The morphology, infraciliature, and silverline system of two new peritrichous ciliates, Pseudovorticella clampi n. sp. and Zoothamnium pararbuscula n. sp., have been investigated based on both living and silver-impregnated specimens. Partial sequence of 18S-ITS1-5.8S rDNA of Z. pararbuscula is also determined in order to compare it with the closely related congener, Zoothamnium arbuscula. Zoothamnium pararbuscula can be distinguished from its close form Z. arbuscula by the different habitats, the appearance of the main stalk, the position of the contractile vacuole, and the information derived from 18S-ITS1-5.8S rDNA sequence analysis. Pseudovorticella clampi n. sp. is distinguished from its congeners by its body shape and size, pellicle granules, habitat, and number of transverse silverlines.

Animals↗
PubMedDate not supplied

Taxonomic characterization of Vorticella fuscaPrecht, 1935 and Vorticella parapulchella n. sp., two marine peritrichs (Ciliophora, Oligohymenophorea) from China.

Two marine peritrich ciliates, Vorticella fuscaPrecht (1935) and Vorticella parapulchella n. sp. were discovered in the littoral zone of Qingdao, northern China. Their morphology, infraciliature, and silverline system were described using live observation and silver impregnation. The poorly known species V. fusca is redescribed, adding information about the oral infraciliature and pellicular morphology. Vorticella parapulchella n. sp. is superficially similar to Vorticella pulchellaSommer (1951) but is distinguished from it by being markedly smaller and having much more widely spaced pellicular ridges. The infundibular infraciliature of V. parapulchella is extremely unusual in having infundibular polykinety 3 reduced to two rows, one of which has almost disappeared.

Animals↗
PubMed2001

Taxonomic characterization of two rubber degrading bacteria belonging to the species Gordonia polyisoprenivorans and analysis of hyper variable regions of 16S rDNA sequences.

Two cis-1,4-polyisoprene (isoprene rubber) degrading bacteria, strains VH2 and Y2K, were identified as strains of the species Gordonia polyisoprenivorans belonging to the Corynebacterineae, a suborder of the order Actinomycetales. Both showed characteristic growth and degradation of isoprene rubber as described previously for the type strain of G. polyisoprenivorans Kd2 (DSM 44302(T)). For strain VH2 the chemotaxonomic properties were investigated, and DNA-DNA hybridization experiments with the type strain revealed the affiliation to the species G. polyisoprenivorans. The comparison of the 16S rDNA sequences, and especially hyper variable regions of these, led to the classification of strain Y2K to the same species. At present, the species G. polyisoprenivorans comprises three different isolates which share the ability to degrade isoprene rubber potently but which were obtained from different geographic regions.

Actinomycetales↗