Bacterial Diversity Studies Using the 16S rRNA Gene Provide a Powerful Research-Based Curriculum for Molecular Biology Laboratory

ABSTRACT Hydrothermal vent activity is often associated with submarine volcanism. Here, we investigated the presence of microorganisms related to hydrothermal activity in the Orca seamount. Data profiling of the 16S rRNA gene amplicon sequences revealed a diversity pattern dominated mainly by the phyla Proteobacteria, Acidobacteria, Planctomycetes, and Bacteroidetes.

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Bacterial diversity in the saliva of patients with different oral hygiene indexes

Brazilian Dental Journal ◽

10.1590/s0103-64402012000400017 ◽

2012 ◽

Vol 23 (4) ◽

pp. 409-416 ◽

Cited By ~ 5

Author(s):

Juliana Vianna Pereira ◽

Luciana Leomil ◽

Fabíola Rodrigues-Albuquerque ◽

José Odair Pereira ◽

Spartaco Astolfi-Filho

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Bacterial Diversity ◽

Oral Hygiene ◽

Dental Plaque ◽

High Index ◽

Rrna Gene ◽

Operational Taxonomic Units ◽

Gene Libraries ◽

The 16S Rrna Gene

The objective of the present study was to evaluate the bacterial diversity in the saliva of patients with different oral hygiene indexes using of two 16S rRNA gene libraries. Each library was composed of samples from patients with different averages of the differentiated Silness-Löe biofilm index: the first library (A) with an index between 1.0 and 3.0 (considered a high index) and the second library (B) between 0 and 0.5 (considered a low index). Saliva DNA was extracted and the 16S rRNA gene was amplified and cloned. The obtained sequences were compared with those stored at NCBI and RDP GenBank. The saliva of patients with high index presented five known genera - Streptococcus, Granulicatella, Gemella, Veillonella and Peptostreptococcus - and 33.3% of nonculturable bacteria grouped into 23 operational taxonomic units (OTUs). The saliva of patients with low index differed significantly from the first library (p=0.000) and was composed of 42 OTUs distributed into 11 known genera - Streptococcus, Granulicatella, Gemella, Veillonella, Oribacterium, Haemophilus, Escherichia, Neisseria, Prevotella, Capnocytophaga, Actinomyces - including 24.87% of nonculturable bacteria. It was possible to conclude that there is greater bacterial diversity in the saliva of patients with low dental plaque in relation to patients with high dental plaque.

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16S rRNA Gene Primer Validation for Bacterial Diversity Analysis of Vegetable Products

Journal of Food Protection ◽

10.4315/0362-028x.jfp-17-346 ◽

2018 ◽

Vol 81 (5) ◽

pp. 848-859

Author(s):

MIYO NAKANO

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Bacterial Diversity ◽

High Throughput Sequencing ◽

Animal Feed ◽

Rrna Gene ◽

Universal Primer ◽

Food Matrices ◽

Taxonomic Groups ◽

The 16S Rrna Gene

ABSTRACT High-throughput sequencing of the 16S rRNA gene enhances understanding of microbial diversity from complex environmental samples. The 16S rRNA gene is currently the most important target in bacterial evolution and ecology studies, particularly for determination of phylogenetic relationships among taxa, exploration of bacterial diversity in a given environment, and quantification of the relative abundance of taxa at various levels. However, some parts of the conserved region of the bacterial 16S rRNA gene are similar to the conserved regions of plant chloroplasts and eukaryotic mitochondria. Therefore, if DNA contains a large amount of nontarget DNA, this nontarget DNA can be coamplified and consequently produce useless sequence reads. We experimentally assessed the primer pair 335f/769r and the widely used bacterial primer pair SD (S-D-Bact-0341-b-S-17/S-D-Bact-0785-a-A-21). The primer pair 335f/769r was examined for its ability to amplify bacterial DNA in plant and animal feed samples by using the single-strand confirmation polymorphism method. In our present study, these primer pairs were validated for microbial community structure analysis with complex food matrices by using next-generation sequencing. The sequencing results revealed that the primer pair 335f/769r successfully resulted in fewer chloroplast and mitochondrial sequence reads than generated by the universal primer pair SD and therefore is comparatively suitable for metagenomic analyses of complex food matrices, particularly those that are rich in plant DNA. Additionally, some taxonomic groups were missed entirely when only the SD primer pair was used.

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Bacterial diversity and community structure in the East China Sea by 454 sequencing of the 16S rRNA gene

Chinese Journal of Oceanology and Limnology ◽

10.1007/s00343-014-3215-2 ◽

2014 ◽

Vol 32 (3) ◽

pp. 527-541 ◽

Cited By ~ 11

Author(s):

Yi Dong ◽

Yuan Zhao ◽

Wenyan Zhang ◽

Yan Li ◽

Feng Zhou ◽

...

Keyword(s):

Community Structure ◽

16S Rrna ◽

16S Rrna Gene ◽

Bacterial Diversity ◽

East China Sea ◽

454 Sequencing ◽

East China ◽

Rrna Gene ◽

The East China Sea ◽

The 16S Rrna Gene

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Characterization of ruminal bacteria in grazing Nellore steers

Revista Colombiana de Ciencias Pecuarias ◽

10.17533/udea.rccp.v32n4a01 ◽

2019 ◽

Vol 32 (4) ◽

pp. 248-260 ◽

Cited By ~ 1

Author(s):

Raphael Barbetta-de-Jesus ◽

Yury T Granja-Salcedo ◽

Juliana D Messana ◽

Luciano Takeshi-Kishi ◽

Eliana Gertrudes Macedo-Lemos ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Bacterial Diversity ◽

Molecular Techniques ◽

Rumen Content ◽

Rrna Gene ◽

Tropical Pastures ◽

Rumen Microorganisms ◽

Culture Techniques ◽

The 16S Rrna Gene

Background: Rumen microorganisms have developed a series of complex interactions, representing one of the best examples of symbiosis between microorganisms in nature. Conventional taxonomic methods based on culture techniques are being replaced by molecular techniques that are faster and more accurate. Objective: To characterize rumen bacterial diversity of Nellore steers grazing on tropical pastures by sequencing the 16S rRNA gene using Illumina sequenctng. Methods: Three rumen-cannulated Nellore steers were used. The liquid and solid fractions of the rumen contents were processed to extract metagenomic DNA, and the VI and V2 hypervariable regions of the 16S rRNA gene were sequenced using Illumina sequencing. Results: A total of 11,407,000 reads of adequate quality were generated, and 812 operational taxonomic units (OTUs) were found at the species level. Twenty-seven phyla were identified, and the predominant phyla were Firmicutes (23%), Bacteroidetes (14%), Proteobacteria (10%), Spirochaetes (9%), Fibrobacteres (7%), Tenericutes (5%), and Actinobacteria (2%), which represented 70% of the total phyla identified in the rumen content. Conclusion: Rumen environment in grazing Nellore steers showed high bacterial diversity, with Firmicutes, Bacteroidetes, Proteobacteria, Spirochaetes, and Fibrobacteres as the predominant phyla.

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Bacterial Diversity Studies Using the 16S rRNA Gene Provide a Powerful Research-Based Curriculum for Molecular Biology Laboratory

Microbiology Education ◽

10.1128/me.3.1.18-25.2002 ◽

2002 ◽

Vol 3 (1) ◽

pp. 18-25

Author(s):

SARAH M. BOOMER ◽

DANIEL P. LODGE ◽

BRYAN E. DUTTON

Keyword(s):

Molecular Biology ◽

16S Rrna ◽

Student Performance ◽

Hot Spring ◽

16S Rrna Genes ◽

Rrna Genes ◽

Rrna Gene ◽

Computer Based ◽

Diversity Studies ◽

Biology Laboratory

We have developed a ten-week curriculum for molecular biology that uses 16S ribosomal RNA genes to characterize and compare novel bacteria from hot spring communities in Yellowstone National Park. The 16S rRNA approach bypasses selective culture-based methods. Our molecular biology course offered the opportunity for students to learn broadly applicable methods while contributing to a long-term research project. Specifically, students isolated and characterized clones that contained novel 16S rRNA inserts using restriction enzyme, DNA sequencing, and computer-based phylogenetic methods. In both classes, students retrieved novel bacterial 16S rRNA genes, several of which were most similar to Green Nonsulfur bacterial isolates. During class, we evaluated student performance and mastery of skills and concepts using quizzes, formal lab notebooks, and a broad project assignment. For this report, we also assessed student performance alongside data quality and discussed the significance, our goal being to improve both research and teaching methods.

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Phyllobacterium loti sp. nov. isolated from nodules of Lotus corniculatus

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.052993-0 ◽

2014 ◽

Vol 64 (Pt_3) ◽

pp. 781-786 ◽

Cited By ~ 33

Author(s):

Maximo Sánchez ◽

Martha-Helena Ramírez-Bahena ◽

Alvaro Peix ◽

María J. Lorite ◽

Juan Sanjuán ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Sequence Similarity ◽

Carbon Sources ◽

Lotus Corniculatus ◽

Culture Conditions ◽

Rrna Gene ◽

Content Type ◽

Link Type ◽

The 16S Rrna Gene

Strain S658T was isolated from a Lotus corniculatus nodule in a soil sample obtained in Uruguay. Phylogenetic analysis of the 16S rRNA gene and atpD gene showed that this strain clustered within the genus Phyllobacterium . The closest related species was, in both cases, Phyllobacterium trifolii PETP02T with 99.8 % sequence similarity in the 16S rRNA gene and 96.1 % in the atpD gene. The 16S rRNA gene contains an insert at the beginning of the sequence that has no similarities with other inserts present in the same gene in described rhizobial species. Ubiquinone Q-10 was the only quinone detected. Strain S658T differed from its closest relatives through its growth in diverse culture conditions and in the assimilation of several carbon sources. It was not able to reproduce nodules in Lotus corniculatus. The results of DNA–DNA hybridization, phenotypic tests and fatty acid analyses confirmed that this strain should be classified as a representative of a novel species of the genus Phyllobacterium , for which the name Phyllobacterium loti sp. nov. is proposed. The type strain is S658T( = LMG 27289T = CECT 8230T).

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