Identification and phylogenetic study of bioluminescent bacteria from squid (Loligo duvaucelii) based on 16S rRNA gene

The species Amycolatopsis fastidiosa (ex Celmer et al. 1977) Henssen et al. 1987 was proposed, based on morphological and chemotaxonomic observations, for a strain originally described as ‘Pseudonocardia fastidiosa’ Celmer et al. 1977 in a US patent. In the course of a phylogenetic study of the taxa with validly published names within the suborder Pseudonocardineae based on 16S rRNA gene sequences, it became apparent that this species was misplaced in the genus Amycolatopsis. After careful evaluation of the phylogeny, morphology, chemotaxonomy and physiology of the type strain, it was concluded that this strain represents a species of the genus Actinokineospora that is unable to produce motile spores. The description of the genus Actinokineospora is therefore emended to accommodate species that do not produce motile spores, and it is proposed that Amycolatopsis fastidiosa be transferred to the genus Actinokineospora as Actinokineospora fastidiosa comb. nov. The type strain is NRRL B-16697T =ATCC 31181T =DSM 43855T =JCM 3276T =NBRC 14105T =VKM Ac-1419T.

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Oxynema aestuarii sp. nov. (Microcoleaceae) isolated from an Indian mangrove forest

Phytotaxa ◽

10.11646/phytotaxa.374.1.2 ◽

2018 ◽

Vol 374 (1) ◽

pp. 24 ◽

Cited By ~ 2

Author(s):

SANDEEP CHAKRABORTY ◽

VEERABADHRAN MARUTHANAYAGAM ◽

ANUSHREE ACHARI ◽

RIDDHI MAHANSARIA ◽

ARNAB PRAMANIK ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Sequence Similarity ◽

Hypersaline Environment ◽

Phylogenetic Study ◽

Rrna Gene ◽

Growth Responses ◽

Nucleotide Substitutions ◽

Intertidal Environment ◽

Group I

Taxonomic characterization by a polyphasic approach was carried out on two cyanobacteria, AP17 and AP24 isolated from soil biofilms of two separate islands, Lothian and Sagar respectively, of the Indian Sundarbans. The strains were studied morphologically by light microscopy, scanning and transmission electron microscopy. Growth responses to various salinities were recorded. Molecular data included sequencing and phylogenetic study of the 16S rRNA gene as well as analysis of the 14 regions of the 16S-23S ITS regions. Morphologically the strains were found to be non-heterocytous, having attenuated trichomes with a narrow, bent terminal cell without any crosswalls. Strains under investigation shared 99–100% 16S rRNA gene sequence similarity with Oxynema thaianum CCALA960, the type species of the novel Oxynema genus, recently separated from the Phormidium-Group I genus. However, cross walls in the apical portion of AP17 and AP24 were totally absent while the same was present in CCALA960. Additionally, optimal growth of AP17 and AP24 was recorded in 5–8% salinity and salinity above 14% inhibited growth of both strains, which were isolated from an intertidal environment; whereas O. thaianum CCALA960 which was found in a hypersaline environment could grow at 40% salinity. Insertion of 9 nucleotides in the D2 with spacer region, insertion of 2 nucleotides in the pre Box B spacer region, deletion of 2 nucleotides in the post Box B spacer region, deletion of 8 nucleotides in the D4 region, deletion of 8 nucleotides in V3 region and insertion of 2 nucleotides in the D5 region of the ITS sequences of AP17 and AP24 were observed in comparison to the analogous regions of CCALA960. Structural details of Box B helices of AP17 and AP24 revealed that although their lengths were identical with the reference, their sequences were completely different from CCALA960. Four nucleotide substitutions were observed in different positions in the Box B helix of O. thaianum CCALA960. Secondary structures of the V3 regions of AP17 and AP24 (containing 51 nucleotides) showed a small terminal bulge and a bigger bilateral bulge while the analogous structure of O. thaianum CCALA 960 (comprising of 59 nucleotides) showed one additional bilateral bulge in comparison to AP17 and AP24. Therefore, based on morphological, ecological and molecular differences in comparison to O. thaianum CCALA960, isolates AP17 and AP24 should be considered as a second novel species in the Oxynema genus, for which the name Oxynema aestuarii sp. nov. is proposed.

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Proposals of Curvibacter gracilis gen. nov., sp. nov. and Herbaspirillum putei sp. nov. for bacterial strains isolated from well water and reclassification of [Pseudomonas] huttiensis, [Pseudomonas] lanceolata, [Aquaspirillum] delicatum and [Aquaspirillum] autotrophicum as Herbaspirillum huttiense comb. nov., Curvibacter lanceolatus comb. nov., Curvibacter delicatus comb. nov. and Herbaspirillum autotrophicum comb. nov.

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.02975-0 ◽

2004 ◽

Vol 54 (6) ◽

pp. 2223-2230 ◽

Cited By ~ 105

Author(s):

Linxian Ding ◽

Akira Yokota

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Type Strain ◽

Phylogenetic Study ◽

Well Water ◽

Rrna Gene ◽

Bacterial Strains ◽

Gram Negative ◽

Morphological Studies ◽

The 16S Rrna Gene

Two strains of curved bacteria, 7-1T and 7-2T, isolated from well water, were phylogenetically examined to determine their taxonomic position. Strain 7-1T is a Gram-negative, slightly curved rod. Analysis of the 16S rRNA gene sequence showed that strain 7-1T formed a cluster with [Aquaspirillum] delicatum and [Pseudomonas] lanceolata. It has some similar characteristics to [A.] delicatum and [P.] lanceolata, but has sufficient distance to separate it from other genera. DNA–DNA hybridization analysis, as well as chemotaxonomic and morphological studies, demonstrated that strain 7-1T, [A.] delicatum and [P.] lanceolata belong to a new genus, Curvibacter gen. nov. Strain 7-1T (=IAM 15033T=ATCC BAA-807T) is classified as the type strain of Curvibacter gracilis gen. nov., sp. nov., and [A.] delicatum and [P.] lanceolata are classified as Curvibacter delicatus comb. nov. and Curvibacter lanceolatus comb. nov., respectively. Strain 7-2T is a Gram-negative spirillum. Phylogenetic study based on the 16S rRNA gene sequences showed that it formed a cluster with the members of the genus Herbaspirillum, [Pseudomonas] huttiensis and [Aquaspirillum] autotrophicum. The classification is therefore proposed of strain 7-2T (=IAM 15032T=ATCC BAA-806T) as the type strain of Herbaspirillum putei sp. nov., and [P.] huttiensis and [A.] autotrophicum are transferred to the genus Herbaspirillum as Herbaspirillum huttiense comb. nov. and Herbaspirillum autotrophicum comb. nov., respectively.

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Hexachlorocyclohexane-degrading bacterial strains Sphingomonas paucimobilis B90A, UT26 and Sp+, having similar lin genes, represent three distinct species, Sphingobium indicum sp. nov., Sphingobium japonicum sp. nov. and Sphingobium francense sp. nov., and reclassification of [Sphingomonas] chungbukensis as Sphingobium chungbukense comb. nov.

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.63201-0 ◽

2005 ◽

Vol 55 (5) ◽

pp. 1965-1972 ◽

Cited By ~ 92

Author(s):

Rinku Pal ◽

Shashi Bala ◽

Mandeep Dadhwal ◽

Mukesh Kumar ◽

Gauri Dhingra ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Phylogenetic Study ◽

Rrna Gene ◽

Sphingomonas Paucimobilis ◽

Gene Sequences ◽

16S Rrna Gene Sequences ◽

Dna Relatedness ◽

Sphingobium Chlorophenolicum ◽

Sphingomonas Xenophaga

Three strains of Sphingomonas paucimobilis, B90A, UT26 and Sp+, isolated from different geographical locations, were found to degrade hexachlorocyclohexane. Phylogenetic analysis based on 16S rRNA gene sequences indicated that these strains do not fall in a clade that includes the type strain, Sphingomonas paucimobilis ATCC 29837T, but form a coherent cluster with [Sphingomonas] chungbukensis IMSNU 11152T followed by Sphingobium chlorophenolicum ATCC 33790T. The three strains showed low DNA–DNA relatedness values with Sphingomonas paucimobilis ATCC 29837T (8–25 %), [Sphingomonas] chungbukensis IMSNU 11152T (10–17 %), Sphingobium chlorophenolicum ATCC 33790T (23–54 %) and Sphingomonas xenophaga DSM 6383T (10–28 %), indicating that they do not belong to any of these species. Although the three strains were found to be closely related to each other based on 16S rRNA gene sequence similarity (99·1–99·4 %), DNA–DNA relatedness (19–59 %) and pulsed-field gel electrophoresis (PFGE) patterns indicated that they possibly represent three novel species of the genus Sphingobium. The three strains could also be readily distinguished by biochemical tests. The three strains showed similar polar lipid profiles and contained sphingoglycolipids. The strains differed from each other in fatty acid composition but contained the predominant fatty acids characteristic of other Sphingobium species. A phylogenetic study based on 16S rRNA gene sequences showed that [Sphingomonas] chungbukensis IMSNU 11152T formed a cluster with members of the genus Sphingobium. Based on these results, it is proposed that strains B90A, UT26 and Sp+, previously known as Sphingomonas paucimobilis, are the type strains of Sphingobium indicum sp. nov. (=MTCC 6364T=CCM 7286T), Sphingobium japonicum sp. nov. (=MTCC 6362T=CCM 7287T) and Sphingobium francense sp. nov. (=MTCC 6363T=CCM 7288T), respectively. It is also proposed that [Sphingomonas] chungbukensis be transferred to Sphingobium chungbukense comb. nov.

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Phylogenetic and morphological evaluation of the genera Anabaena, Aphanizomenon, Trichormus and Nostoc (Nostocales, Cyanobacteria)

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.63276-0 ◽

2005 ◽

Vol 55 (1) ◽

pp. 11-26 ◽

Cited By ~ 226

Author(s):

Pirjo Rajaniemi ◽

Pavel Hrouzek ◽

Klára Kaštovská ◽

Raphaël Willame ◽

Anne Rantala ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Sequence Data ◽

Morphological Changes ◽

Phylogenetic Analyses ◽

Phylogenetic Study ◽

Rrna Gene ◽

Monophyletic Cluster ◽

Morphological Studies

The heterocytous cyanobacteria form a monophyletic group according to 16S rRNA gene sequence data. Within this group, phylogenetic and morphological studies have shown that genera such as Anabaena and Aphanizomenon are intermixed. Moreover, the phylogeny of the genus Trichormus, which was recently separated from Anabaena, has not been investigated. The aim was to study the taxonomy of the genera Anabaena, Aphanizomenon, Nostoc and Trichormus belonging to the family Nostocaceae (subsection IV.I) by morphological and phylogenetic analyses of 16S rRNA gene, rpoB and rbcLX sequences. New strains were isolated to avoid identification problems caused by morphological changes of strains during cultivation. Morphological and phylogenetic data showed that benthic and planktic Anabaena strains were intermixed. In addition, the present study confirmed that Anabaena and Aphanizomenon strains were not monophyletic, as previously demonstrated. The evolutionary distances between the strains indicated that the planktic Anabaena and Aphanizomenon strains as well as five benthic Anabaena strains in cluster 1 could be assigned to a single genus. On the basis of the 16S rRNA, rpoB and rbcLX gene sequences, the Anabaena/Aphanizomenon strains (cluster 1) were divided into nine supported subclusters which could also be separated morphologically, and which therefore might represent different species. Trichormus strains were morphologically and phylogenetically heterogeneous and did not form a monophyletic cluster. These Trichormus strains, which were representatives of three distinct species, might actually belong to three genera according to the evolutionary distances. Nostoc strains were also heterogeneous and seemed to form a monophyletic cluster, which may contain more than one genus. It was found that certain morphological features were stable and could be used to separate different phylogenetic clusters. For example, the width and the length of akinetes were useful features for classification of the Anabaena/Aphanizomenon strains in cluster 1. This morphological and phylogenetic study with fresh isolates showed that the current classification of these anabaenoid genera needs to be revised.

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Multilocus sequence phylogenetic study of the genus Haemophilus with description of Haemophilus pittmaniae sp. nov.

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.63325-0 ◽

2005 ◽

Vol 55 (1) ◽

pp. 449-456 ◽

Cited By ~ 45

Author(s):

Niels Nørskov-Lauritsen ◽

Brita Bruun ◽

Mogens Kilian

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Dna Hybridization ◽

Gene Sequence ◽

16S Rrna Gene Sequence ◽

Phylogenetic Study ◽

Rrna Gene ◽

Rrna Gene Sequence ◽

Hybridization Data ◽

Gene Similarity

The phylogeny of human isolates of Haemophilus species was estimated based on partial sequences of four separate housekeeping genes. The clustering of each set of sequences was in accordance with speciation of the strains with few exceptions: of 108 gene fragments examined, only three appeared to have been subject to recombination events across the species barrier. Housekeeping gene similarity supported previous DNA–DNA hybridization data for the genus rather than the phylogeny inferred from 16S rRNA gene sequence comparison. The similarity of sequences of Haemophilus parainfluenzae with those of Haemophilus influenzae suggested preservation of the former species in the genus Haemophilus. Three strains representing a novel taxon were unique with respect to the four investigated gene loci. 16S rRNA gene sequence analysis suggested that this taxon belonged to the Parainfluenzae cluster. DNA–DNA hybridization data supported this generic placement. Nine strains of the novel taxon were available for analysis. They were distinct from representatives of all current species of the genus Haemophilus by conventional phenotypic characterization. Genotypic and phenotypic data show that the strains merit recognition as a novel species of Haemophilus. The name Haemophilus pittmaniae sp. nov. is proposed, with HK 85T (=CCUG 48703T=NCTC 13334T) as the type strain.

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Genetic characterization and phylogenetic study of Indonesian cuscuses from Maluku and Papua Island based on 16S rRNA gene

Veterinary World ◽

10.14202/vetworld.2020.2319-2325 ◽

2020 ◽

Vol 13 (11) ◽

pp. 2319-2325

Author(s):

Rini Widayanti ◽

Richo Apriladi Bagas Pradana ◽

Rony Marsyal Kunda ◽

Suhendra Pakpahan

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Genetic Characterization ◽

16S Rrna Gene Sequencing ◽

Phylogenetic Study ◽

Rrna Gene ◽

Close Relationship ◽

Rrna Gene Sequencing ◽

Ethics Guidelines

Background and Aim: Indonesian cuscuses are now becoming scarce because of the reduction of habitat and poaching. Further, molecular characterization of Indonesian cuscuses is still very lacking. This study aimed to determine genetic markers and phylogenetic relationships of Indonesian cuscuses based on 16S rRNA gene sequences. Materials and Methods: This study used 21 cuscuses caught from two provinces and 16 islands: 13 from Maluku and eight from Papua. Cuscus samples were taken by biopsy following ethics guidelines for animals. The genome isolation was done using gSYNC DNA Mini Kit (Geneaid Biotech Ltd., Taiwan). The 16S rRNA gene was amplified by primers (16SKUSAF and 16SKUSAR), and the polymerase chain reaction product obtained was 1875 base pair (bp). The analysis of genetic characterization and the phylogenetic relationship was performed using MEGA version X software (https://www. megasoftware.net/). Results: 16S rRNA gene sequencing attained 1598 bp for all samples. Based on the 16S rRNA nucleotide sequences, cuscuses from Papua and Maluku belong to the genus Phalanger and Spilocuscus. Phalanger spp. and Spilocuscus spp. from Papua can be distinguished from Phalanger and Spilocuscus from Maluku, except Spilocuscus from Ternate has a very close relationship with cuscus from Sentani, Papua. Conclusion: Indonesian cuscuses were derived into two clades based on 16S rRNA gene sequence, one group to genus Phalanger and another group to Spilocuscus.

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Molecular Phylogenetic study of Acila divaricata vigila based on the Partial Sequence of 16S rRNA Gene

The Korean Journal of Malacology ◽

10.9710/kjm.2011.27.4.395 ◽

2011 ◽

Vol 27 (4) ◽

pp. 395-400

Author(s):

Bong-Seok Kim ◽

Se-Won Kang ◽

Ji-Eun Jeong ◽

Jung-Yeon Park ◽

Jung-Ha Kang ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Partial Sequence ◽

Phylogenetic Study ◽

Rrna Gene ◽

Molecular Phylogenetic Study ◽

Molecular Phylogenetic

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Phylogenetic analysis of vibrios and related species by means of atpA gene sequences

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.65223-0 ◽

2007 ◽

Vol 57 (11) ◽

pp. 2480-2484 ◽

Cited By ~ 39

Author(s):

Cristiane C. Thompson ◽

Fabiano L. Thompson ◽

Ana Carolina P. Vicente ◽

Jean Swings

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Gene Sequence ◽

16S Rrna Gene Sequence ◽

Phylogenetic Study ◽

Species Differentiation ◽

Rrna Gene ◽

Rrna Gene Sequence ◽

Gene Sequences ◽

Suitable Alternative

We investigated the use of atpA gene sequences as alternative phylogenetic and identification markers for vibrios. A fragment of 1322 bp (corresponding to approximately 88 % of the coding region) was analysed in 151 strains of vibrios. The relationships observed were in agreement with the phylogeny inferred from 16S rRNA gene sequence analysis. For instance, the Vibrio cholerae, Vibrio halioticoli, Vibrio harveyi and Vibrio splendidus species groups appeared in the atpA gene phylogenetic analyses, suggesting that these groups may be considered as separate genera within the current Vibrio genus. Overall, atpA gene sequences appeared to be more discriminatory for species differentiation than 16S rRNA gene sequences. 16S rRNA gene sequence similarities above 97 % corresponded to atpA gene sequences similarities above 80 %. The intraspecies variation in the atpA gene sequence was about 99 % sequence similarity. The results showed clearly that atpA gene sequences are a suitable alternative for the identification and phylogenetic study of vibrios.

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