Investigation of bacterial and fungal communities in indoor and outdoor air of elementary school classrooms by 16S rRNA gene and ITS region sequencing

The 16S rRNA gene sequences for 34 strains, including 11 isolates, were determined to classify scab-causing Streptomyces spp. and relatives isolated from potato scab lesions collected in Jeju, Korea. The 16S–23S rDNA internally transcribed spacer (ITS) sequences were determined to investigate whether the 16S–23S ITS region is useful for analysing intra- and interspecific relationships in these bacteria. On the basis of phylogenetic analysis of 16S rRNA gene sequences, most of the isolates were classified as Streptomyces scabiei and Streptomyces acidiscabies. Isolate KJO61 was placed in an ambiguous taxonomic position between Streptomyces reticuliscabiei and Streptomyces turgidiscabies. 16S–23S ITS region sequence analysis showed that tRNA genes were not found in this region of Streptomyces spp. The 16S–23S ITS regions of Streptomyces spp. exhibited various lengths and highly variable sequence similarities (35–100 %) within strains as well as intra- and interspecies. It was revealed that Streptomyces europaeiscabiei could be clearly differentiated from Streptomyces scabiei. However, it was clarified that ITS regions are not useful in phylogenetic analysis of Streptomyces spp.

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Aetokthonos hydrillicola gen. et sp. nov.: Epiphytic cyanobacteria on invasive aquatic plants implicated in Avian Vacuolar Myelinopathy

Phytotaxa ◽

10.11646/phytotaxa.181.5.1 ◽

2014 ◽

Vol 181 (5) ◽

pp. 243 ◽

Cited By ~ 24

Author(s):

Susan Bennett Wilde ◽

Jeffrey R. Johansen ◽

Henry Dayton Wilde ◽

Peng Jiang ◽

Bradley Bartelme ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Aquatic Vegetation ◽

Its Region ◽

Bald Eagle ◽

Rrna Gene ◽

Scanning Electron Micrographs ◽

Invasive Aquatic Plants ◽

Avian Vacuolar Myelinopathy ◽

True Branching

Research into the taxonomy of a novel cyanobacterial epiphyte in locations where birds, most notably Bald eagle and American coots, are dying from a neurologic disease (Avian Vacuolar Myelinopathy—AVM) has been ongoing since 2001. Field investigations revealed that all sites where birds were dying had extensive invasive aquatic vegetation with dense colonies of an unknown cyanobacterial species growing on the underside of leaves. Morphological evaluation indicated that this was a true-branching, heterocystous taxon falling within the former order Stigonematales. However, 16S rRNA gene sequence demonstrated that it did not match closely with any described genus or species. More recent sequence analysis of the 16S rRNA gene and associated ITS region from additional true branching species resulted in a unique phylogenetic placement distant from the other clades of true-branching cyanobacteria. Light, epifluorescent, and transmission and scanning electron micrographs confirm the novel characteristics of this species, which is true-branching form with uniseriate basal filaments. It is encased within a firm sheath and has heterocytes both within the filaments and at the tips of the branches. The species is in a new genus of uncertain family assignment, and is herein named Aetokthonos hydrillicola gen. et sp. nov.

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Phylogenetic placement of Dapisostemon gen. nov. and Streptostemon, two tropical heterocytous genera (Cyanobacteria)

Phytotaxa ◽

10.11646/phytotaxa.245.2.4 ◽

2016 ◽

Vol 245 (2) ◽

pp. 129 ◽

Cited By ~ 25

Author(s):

GUILHERME SCOTTA HENTSCHKE ◽

JEFFREY R. JOHANSEN ◽

NICOLE PIETRASIAK ◽

MARLI DE FATIMA FIORE ◽

JANAINA RIGONATO ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Gene Sequence ◽

Its Region ◽

16S Rrna Gene Sequence ◽

Southeastern Brazil ◽

Natural Material ◽

Rrna Gene ◽

Rrna Gene Sequence ◽

Weak Support

Two species of heterocytous cyanobacteria from the Mata Atlântica of Southeastern Brazil were studied intensively to determine if they were congeneric or belong to different genera. Additionally, their affinity to established genera in the Tolypothricaceae such as Tolypothrix Bornet & Flahault, Hassallia Bornet & Flahault and Spirirestis Flechtner & Johansen was investigated. Dapisostemon apicaliramis gen. et sp. nov. isolated from a wooden bridge in a mangrove swamp was found to be basal to a clade containing Tolypothricaceae, Nostocaceae, and Aphanizomenonaceae (but with weak support) by means of 16S rRNA gene sequence analyses. Moreover, D. apicaliramis had a 16S-23S ITS region similar in length, sequence, and secondary structure to the members of the terrestrial Tolypothricaceae. Streptostemon Sant’Anna et al. was placed in the Microchaetaceae (now the Tolypothricaceae) at the time of its description based on unsequenced natural material, but in this study it was found to be even more phylogenetically distant from that clade than Dapisostemon based on 16S rRNA gene sequence. It is in an unsupported and unresolved basal position in the Nostocales. It also presents a unique 16S-23S ITS region. The higher level evolutionary relationships of both genera are uncertain at this time, but neither genus can remain in the Microchaetaceae or Tolypothricaceae as the Nostocales undergo future revision. We conclude that Dapisostemon is sufficiently unique and separate that it requires a new family, the Dapisostemonaceae. This study further demonstrates that the cyanobacteria of tropical regions often represent novel taxa in unstudied lineages and that the study of tropical cyanobacteria will yield new insights in the biodiversity of this ecologically important group of photosynthetic microorganisms.

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Variations in the 16S–23S rRNA internal transcribed spacer of fibrolytic Butyrivibrio isolates from the reindeer rumen

Canadian Journal of Microbiology ◽

10.1139/w11-038 ◽

2011 ◽

Vol 57 (7) ◽

pp. 617-622 ◽

Cited By ~ 2

Author(s):

Kirsti E. Præsteng ◽

Roderick I. Mackie ◽

Isaac K.O. Cann ◽

Svein D. Mathiesen ◽

Monica A. Sundset

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Rangifer Tarandus ◽

Its Region ◽

16S Rrna Gene Sequencing ◽

23S Rrna ◽

Rrna Gene ◽

Its Sequence ◽

Neighbor Joining ◽

Phylogenetic Neighbor

Strains of Butyrivibrio are principal cellulytic bacteria in the rumen of the High Arctic Svalbard reindeer ( Rangifer tarandus platyrhynchus ). According to phylogenetic analysis based on 16S rRNA gene sequencing, Butyrivibrio can be divided into three subgroups within the Clostridia class of the phylum Firmicutes, but the current phenotypic and genotypic differentiation within the family Lachnospiraceae is insufficient. This current study describes the sequence diversity of the 16S–23S rRNA intergenic transcribed spacer (ITS) region of Butyrivibrio isolates from reindeer. A total of 17 different ITS sequences with sizes between 449 and 784 nt were obtained. Genes encoding tRNAIle and tRNAAla were identified in four of the sequences. Phylogenetic neighbor-joining trees were constructed based on the ITS sequence and compared with a phylogenetic neighbor-joining tree based on 16S rRNA gene sequences previously obtained for the same isolates. These comparisons indicated a better differentiation between strains in the ITS sequence than the 16S rRNA gene based tree. Through this study, a better means for identifying and tracking fibrolytic and potentially probiotic Butyrivibrio strains in reindeer and other ruminants has been provided.

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Diversity of 16S rRNA gene, ITS region and aclB gene of the Aquificales

Extremophiles ◽

10.1007/s00792-006-0009-2 ◽

2006 ◽

Vol 11 (1) ◽

pp. 57-64 ◽

Cited By ~ 30

Author(s):

I. Ferrera ◽

S. Longhorn ◽

A. B. Banta ◽

Y. Liu ◽

D. Preston ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Its Region ◽

Rrna Gene

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CHARACTERIZATION OF THE 16S rRNA GENE AND ASSOCIATED 16S-23S ITS REGION IN MICROCOLEUS (CYANOPHYTA)

Journal of Phycology ◽

10.1111/j.1529-8817.2001.jpy37303-12.x ◽

2008 ◽

Vol 37 ◽

pp. 7-8

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Its Region ◽

Rrna Gene ◽

The 16S Rrna Gene

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Massive parallel 16S rRNA gene pyrosequencing reveals highly diverse fecal bacterial and fungal communities in healthy dogs and cats

FEMS Microbiology Ecology ◽

10.1111/j.1574-6941.2011.01058.x ◽

2011 ◽

Vol 76 (2) ◽

pp. 301-310 ◽

Cited By ~ 228

Author(s):

Stefanie Handl ◽

Scot E. Dowd ◽

Jose F. Garcia-Mazcorro ◽

Jörg M. Steiner ◽

Jan S. Suchodolski

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Fungal Communities ◽

Rrna Gene ◽

16S Rrna Gene Pyrosequencing ◽

Healthy Dogs

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“Comparative Analysis of Gut Microbiome in Individuals of the Old Civilization of Caral-Supe Based on Data from 16S rRNA and ITS region”

10.1101/2020.04.24.060582 ◽

2020 ◽

Author(s):

Andrés Vásquez-Domínguez ◽

Luis Jaramillo-Valverde ◽

Kelly S. Levano ◽

Pedro Novoa-Bellota ◽

Marco Machaguay-Romero ◽

...

Keyword(s):

Comparative Analysis ◽

16S Rrna ◽

16S Rrna Gene ◽

High Throughput ◽

High Throughput Sequencing ◽

Its Region ◽

Rrna Gene ◽

Sequencing Data ◽

Ancient Civilization ◽

High Throughput Sequencing Data

ABSTRACTGenetic and microbiome studies of ancient Caral-Supe civilization have not yet been published. For this reason, the objective of this work is to identify the microorganisms and possible diseases that existed in this ancient civilization using coprolites samples. To do this, two coprolites samples were analyzing through high-throughput sequencing data of 16S rRNA gene and an intergenic region (ITS).

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Phylogenetic analysis of the genera Bradyrhizobium, Mesorhizobium, Rhizobium and Sinorhizobium on the basis of 16S rRNA gene and internally transcribed spacer region sequences

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.63097-0 ◽

2005 ◽

Vol 55 (1) ◽

pp. 263-270 ◽

Cited By ~ 72

Author(s):

Soon-Wo Kwon ◽

Jin-Young Park ◽

Jong-Shik Kim ◽

Jun-Won Kang ◽

Yang-Hee Cho ◽

...

Keyword(s):

Phylogenetic Analysis ◽

16S Rrna ◽

16S Rrna Gene ◽

Its Region ◽

Taxonomic Resolution ◽

Rrna Gene ◽

Group I ◽

Internally Transcribed Spacer ◽

Reference Strains ◽

The 16S Rrna Gene

A total of 128 strains was isolated from more than 23 legume hosts in Korea. Phylogenetic relationships between these Korean isolates and reference strains of the genera Bradyrhizobium, Mesorhizobium, Rhizobium and Sinorhizobium were analysed using their 16S rRNA gene and internally transcribed spacer (ITS) region sequences. Among the Bradyrhizobium strains, dendrograms based on both the 16S rRNA gene and ITS region sequences produced two main groups. The ITS tree yielded at least two new clusters that were discernable from the seven previously delineated genospecies. Large discrepancies were revealed between phylogenetic dendrograms based on 16S rRNA gene and ITS region sequences for members of the genus Rhizobium, reflecting their taxonomic heterogeneity. The amalgamation of Rhizobium and former members of Agrobacterium was confirmed using the 16S rRNA tree. Phylogenetic analysis of ITS region sequences showed that the Rhizobium giardinii clade (group II) and the Rhizobium radiobacter/Rhizobium rubi clade (group III) could be tentatively recognized as groups that are separable from the core group (group I), which includes Rhizobium leguminosarum. Dendrograms based on the 16S rRNA gene and ITS region sequences of Mesorhizobium strains were highly conflicting due to the poor taxonomic resolution of the 16S rRNA gene sequences and the low confidence in the ITS dendrogram. Several Korean isolates within the genus Mesorhizobium are thought to represent novel taxa when considering their relatively low ITS region sequence similarities (<80 %) to the reference strains.

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