New insights into the phylogeny of the Acantharea based on SSU rRNA gene sequencing

2000 ◽  
Vol 36 (1) ◽  
pp. 34-39 ◽  
Author(s):  
Linda A. Amaral Zettler ◽  
David A. Caron
Keyword(s):  
Gene Sequencing ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Ssu Rrna Gene ◽  
Rrna Gene Sequencing

scholarly journals Genotype characterisation of Giardia duodenalis isolates from domestic and farm animals by SSU-rRNA gene sequencing

2004 ◽  
Vol 122 (3) ◽  
pp. 193-199 ◽  
Author(s):  
Federica Berrilli ◽  
David Di Cave ◽  
Claudio De Liberato ◽  
Alessia Franco ◽  
Paola Scaramozzino ◽  
...  
Keyword(s):  
Giardia Duodenalis ◽  
Gene Sequencing ◽  
Farm Animals ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Ssu Rrna Gene ◽  
Rrna Gene Sequencing

scholarly journals Full-Length SSU rRNA Gene Sequencing Allows Species-Level Detection of Bacteria, Archaea, and Yeasts Present in Milk

2021 ◽  
Vol 9 (6) ◽  
pp. 1251
Author(s):  
Isabel Abellan-Schneyder ◽  
Annemarie Siebert ◽  
Katharina Hofmann ◽  
Mareike Wenning ◽  
Klaus Neuhaus
Keyword(s):  
Gene Sequencing ◽  
Raw Milk ◽  
Amplicon Sequencing ◽  
Species Level ◽  
Full Length ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Ssu Rrna Gene ◽  
Milk Samples ◽  
Rrna Gene Sequencing

Full-length SSU rRNA gene sequencing allows species-level identification of the microorganisms present in milk samples. Here, we used bulk-tank raw milk samples of two German dairies and detected, using this method, a great diversity of bacteria, archaea, and yeasts within the samples. Moreover, the species-level classification was improved in comparison to short amplicon sequencing. Therefore, we anticipate that this approach might be useful for the detection of possible mastitis-causing species, as well as for the control of spoilage-associated microorganisms. In a proof of concept, we showed that we were able to identify several putative mastitis-causing or mastitis-associated species such as Streptococcusuberis, Streptococcusagalactiae, Streptococcusdysgalactiae, Escherichiacoli and Staphylococcusaureus, as well as several Candida species. Overall, the presented full-length approach for the sequencing of SSU rRNA is easy to conduct, able to be standardized, and allows the screening of microorganisms in labs with Illumina sequencing machines.

scholarly journals Prevalence and molecular characterization of Cryptosporidium spp. in Père David’s deer (Elaphurus davidianus) in Jiangsu, China

2020 ◽  
Vol 29 (2) ◽  
Author(s):  
Si-Yang Huang ◽  
Yi-Min Fan ◽  
Yi Yang ◽  
Yi-Jun Ren ◽  
Jing-Zhi Gong ◽  
...  
Keyword(s):  
Molecular Characterization ◽  
Small Subunit ◽  
Basic Knowledge ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Ssu Rrna Gene ◽  
Cryptosporidium Spp ◽  
Père David’S Deer ◽  
Rrna Gene Sequencing

Abstract Cryptosporidium is a zoonotic parasite that causes diarrhea in a broad range of animals, including deer. Little is known about the prevalence and genotype of Cryptosporidium spp. in Père David’s deer. In this study, 137 fecal samples from Père David’s deer were collected between July 2017 and August 2018 in the Dafeng Reserve and analyzed for Cryptosporidium spp. by nested-PCR based on the small subunit ribosomal RNA (SSU rRNA) gene, followed by sequence analyses to determine the species. The 60 kDa glycoprotein (gp60) gene was used to characterize Cryptosporidium spp. Among 137 samples, 2 (1.46%) were positive for Cryptosporidium spp. according to SSU rRNA gene sequencing results. Both samples belonged to the Cryptosporidium deer genotype, with two nucleotide deletions and one nucleotide substitution. The prevalence data and molecular characterization of this study provide basic knowledge for controlling and preventing Cryptosporidium infections in Père David’s deer in this area.

The smallest known heliozoans are the Erebor lineage (nom. clad. n.) inside Microheliella maris (Eukaryota, Diaphoretickes), with the amendation of M. maris diagnosis and description of Berkeleyaesol magnus gen. nov., comb. nov. (Eukaryota, incertae sedis)

2021 ◽  
Vol 71 (4) ◽  
Author(s):  
Yegor Shishkin ◽  
Daria Drachko ◽  
Vasily V. Zlatogursky
Keyword(s):  
New Genus ◽  
Gene Sequencing ◽  
Sister Group ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Morphometric Data ◽  
Free Living ◽  
Incertae Sedis ◽  
Rrna Gene Sequencing ◽  
Cell Body Size

A new strain of planktonic heliozoans (ZI172) belonging to the genus Microheliella (the sister group of Cryptista in Diaphoretickes), closely related to the only one known strain of Microheliella maris (CCAP 1945/1), was studied with light microscopy and SSU rRNA gene sequencing. Morphometric data obtained from 127 cells and based on 254 measurements showed that this strain represents the smallest heliozoan (1.66–3.42 µm, av. 2.56 µm) in diameter known to date and one of the smallest free-living eukaryotes. We also did morphometry for strain CCAP 1945/1. Its cell body size is 3.20–6.47 µm (av. 4.15 µm; n=141; m=282). The secondary structures of hairpin 15 of the SSU rRNA molecules were reconstructed for ZI172 and CCAP 1945/1 and they were compared The possible biochemical explanation for the smaller size of the ZI172 strain, which is smaller than the CCAP 1945/1 strain, is discussed, including all published electron micrographs of CCAP 1945/1. The necessary taxonomic work is also carried out. The diagnosis of Microheliella maris is amended and the new infraspecific clade Erebor is described to include ZI172. The measurements and systematics of the enigmatic heliozoan ‘Raphidiophrys’ magna O’Donoghue 1922 (non 1921; the biggest known heliozoan) are also discussed and it is transferred to the new genus Berkeleyaesol.

Clypifer cribrifer gen. nov., sp. nov. (Clypiferidae fam. nov., Pterocystida, Centroplasthelida), with notes on evolution of centrohelid siliceous coverings

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
Yegor Shishkin ◽  
Daria Drachko ◽  
Vasily V. Zlatogursky
Keyword(s):  
New Genus ◽  
Light And Electron Microscopy ◽  
Gene Sequencing ◽  
Gulf Of Aqaba ◽  
Cell Diameter ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
New Family ◽  
Molecular Phylogenetic ◽  
Rrna Gene Sequencing

A new family, genus and species of centrohelid heliozoans, Clypifer cribrifer gen. nov., sp. nov. (Clypiferidae fam. nov.), from the Gulf of Aqaba (Israel) was studied with light and electron microscopy and SSU rRNA gene sequencing. Clypifer cribrifer has only one type of scales, partially running up the sides of the axopodia. Plate scales [0.8–2.3 (av. 1.5)×0.6–1.8 (av. 1.2) μm] are flat, elliptical or circular, fenestrated with holes of irregular shape and have a marginal rim and a very short axial rib. The cell diameter is 3.9–9.6 (av. 6.0) μm. Molecular phylogenetic analysis robustly places C. cribrifer in the C4 clade for which the new family Clypiferidae is proposed here. This position is confirmed with the short sequences in the panacanthocystid increased regions. The morphology of the new genus has similarities to the genus Raphidocystis. The probability that another Clypifer species was described under a different name in the centrohelid literature is discussed. Clypiferidae represent the second lineage of Pterocystida, which are characterized by the presence of only tangentially oriented plate scales of one type. Possible ways of evolution of the centrohelid siliceous coverings are also discussed.

scholarly journals Morphological redescriptions and neotypification of two poorly known tintinnine ciliates (Alveolata, Ciliophora, Tintinnina), with a phylogenetic investigation based on SSU rRNA gene sequences

2020 ◽  
Vol 70 (4) ◽  
pp. 2515-2530 ◽  
Author(s):  
Rui Wang ◽  
Wen Song ◽  
Yang Bai ◽  
Alan Warren ◽  
Lifang Li ◽  
...  
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Morphological Data ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Gene Sequences ◽  
Ssu Rrna Gene ◽  
Unbiased Test ◽  
Rrna Gene Sequencing ◽  
Ssu Rrna Gene Sequence

Two poorly known tintinnine ciliates collected from the coastal waters of PR China, viz., Codonellopsis mobilis Wang, 1936 and Tintinnopsis chinglanensis Nie & Ch’eng, 1947, were redescribed and neotypified using live observation, protargol staining and SSU rRNA gene sequencing. Ciliature information and SSU rRNA gene sequence data of both species were revealed for the first time and improved diagnoses were given based on the original descriptions and data from the present study. Further phylogenetic analyses inferred from SSU rRNA gene sequences and morphological data suggested that the genus Tintinnopsis is polyphyletic and that the genus Codonellopsis is non-monophyletic. The approximately unbiased test, however, does not reject the possibility that Codonellopsis is monophyletic.

Screening and Molecular Characterization of Cellulase Producing Actinobacteria from Litchi Orchard

2019 ◽  
Vol 13 (1) ◽  
pp. 90-101
Author(s):  
Sanju Kumari ◽  
Utkarshini Sharma ◽  
Rohit Krishna ◽  
Kanak Sinha ◽  
Santosh Kumar
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Molecular Characterization ◽  
Biochemical Characterization ◽  
Evolutionary Relationship ◽  
Gene Sequencing ◽  
Cellulase Activity ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Rrna Gene Sequencing

Background: Cellulolysis is of considerable economic importance in laundry detergents, textile and pulp and paper industries and in fermentation of biomass into biofuels. Objective: The aim was to screen cellulase producing actinobacteria from the fruit orchard because of its requirement in several chemical reactions. Methods: Strains of actinobacteria were isolated on Sabouraud’s agar medium. Similarities in cultural and biochemical characterization by growing the strains on ISP medium and dissimilarities among them perpetuated to recognise nine groups of actinobacteria. Cellulase activity was measured by the diameter of clear zone around colonies on CMC agar and the amount of reducing sugar liberated from carboxymethyl cellulose in the supernatant of the CMC broth. Further, 16S rRNA gene sequencing and molecular characterization were placed before NCBI for obtaining recognition with accession numbers. Results: Prominent clear zones on spraying Congo Red were found around the cultures of strains of three groups SK703, SK706, SK708 on CMC agar plates. The enzyme assay for carboxymethylcellulase displayed extra cellulase activity in broth: 0.14, 0.82 and 0.66 µmol mL-1 min-1, respectively at optimum conditions of 35°C, pH 7.3 and 96 h of incubation. However, the specific cellulase activities per 1 mg of protein did not differ that way. It was 1.55, 1.71 and 1.83 μmol mL-1 min-1. The growing mycelia possessed short compact chains of 10-20 conidia on aerial branches. These morphological and biochemical characteristics, followed by their verification by Bergey’s Manual, categorically allowed the strains to be placed under actinobacteria. Further, 16S rRNA gene sequencing, molecular characterization and their evolutionary relationship through phylogenetics also confirmed the putative cellulase producing isolates of SK706 and SK708 subgroups to be the strains of Streptomyces. These strains on getting NCBI recognition were christened as Streptomyces glaucescens strain SK91L (KF527284) and Streptomyces rochei strain SK78L (KF515951), respectively. Conclusion: Conclusive evidence on the basis of different parameters established the presence of cellulase producing actinobacteria in the litchi orchard which can convert cellulose into fermentable sugar.

scholarly journals Much ado about nothing? Off-target amplification can lead to false-positive bacterial brain microbiome detection in healthy and Parkinson’s disease individuals

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Janis R. Bedarf ◽  
Naiara Beraza ◽  
Hassan Khazneh ◽  
Ezgi Özkurt ◽  
David Baker ◽  
...  
Keyword(s):  
Parkinson’S Disease ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
False Positive ◽  
Gene Sequencing ◽  
Bacterial Biomass ◽  
16S Rrna Gene Sequencing ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Rrna Gene Sequencing

Abstract Background Recent studies suggested the existence of (poly-)microbial infections in human brains. These have been described either as putative pathogens linked to the neuro-inflammatory changes seen in Parkinson’s disease (PD) and Alzheimer’s disease (AD) or as a “brain microbiome” in the context of healthy patients’ brain samples. Methods Using 16S rRNA gene sequencing, we tested the hypothesis that there is a bacterial brain microbiome. We evaluated brain samples from healthy human subjects and individuals suffering from PD (olfactory bulb and pre-frontal cortex), as well as murine brains. In line with state-of-the-art recommendations, we included several negative and positive controls in our analysis and estimated total bacterial biomass by 16S rRNA gene qPCR. Results Amplicon sequencing did detect bacterial signals in both human and murine samples, but estimated bacterial biomass was extremely low in all samples. Stringent reanalyses implied bacterial signals being explained by a combination of exogenous DNA contamination (54.8%) and false positive amplification of host DNA (34.2%, off-target amplicons). Several seemingly brain-enriched microbes in our dataset turned out to be false-positive signals upon closer examination. We identified off-target amplification as a major confounding factor in low-bacterial/high-host-DNA scenarios. These amplified human or mouse DNA sequences were clustered and falsely assigned to bacterial taxa in the majority of tested amplicon sequencing pipelines. Off-target amplicons seemed to be related to the tissue’s sterility and could also be found in independent brain 16S rRNA gene sequences. Conclusions Taxonomic signals obtained from (extremely) low biomass samples by 16S rRNA gene sequencing must be scrutinized closely to exclude the possibility of off-target amplifications, amplicons that can only appear enriched in biological samples, but are sometimes assigned to bacterial taxa. Sequences must be explicitly matched against any possible background genomes present in large quantities (i.e., the host genome). Using close scrutiny in our approach, we find no evidence supporting the hypothetical presence of either a brain microbiome or a bacterial infection in PD brains.

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