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

2014 ◽  
Vol 32 (3) ◽  
pp. 527-541 ◽  
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

scholarly journals Saccharomonospora marina sp. nov., isolated from an ocean sediment of the East China Sea

2010 ◽  
Vol 60 (8) ◽  
pp. 1854-1857 ◽  
Author(s):  
Zui Liu ◽  
Yan Li ◽  
Liu-Qiang Zheng ◽  
Yao-Jian Huang ◽  
Wen-Jun Li
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
East China Sea ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
East China ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
The East China Sea ◽  
Ocean Sediment

A novel, aerobic, Gram-positive actinomycete strain, designated XMU15T, was isolated from an ocean sediment collected from Zhaoan Bay in the East China Sea and was subjected to a polyphasic approach to determine its taxonomic position. The isolate grew optimally at 28 °C and at pH 7.0 in the presence of 3 % (w/v) NaCl on ISP medium 2. Gelatin liquefaction, milk coagulation and nitrate reduction were positive. Cellulose and starch hydrolysis, hydrogen sulfide and melanin production, and catalase, urease and oxidase activities were negative. The predominant menaquinone of the isolate was MK-9 (H4), and meso-diaminopimelic acid was the diagnostic amino acid in the cell wall. The phospholipids of the isolate comprised diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, and a minor amount of phosphatidylethanolamine. The major fatty acids of the strain were iso-C16 : 0 (26.36 %), C17 : 1 ω6c (16.80 %), C15 : 0 (16.2 %), C16 : 0 (8.90 %), C17 : 1 ω8c (7.69 %) and iso-C16 : 1 H (5.95 %). The DNA G+C content of the genomic DNA was 68.1 mol%. A phylogenetic tree based on 16S rRNA gene sequences showed that the isolate fell within the evolutionary radiation encompassed by the genus Saccharomonospora and showed the highest 16S rRNA gene sequence similarity (96.7 %) to Saccharomonospora xinjiangensis DSM 44391T. Based on the results of 16S rRNA gene sequence analysis and phenotypic and genotypic characterization, strain XMU15T (=KCTC 19701T =CCTCC AA 209048T) represents a novel species of the genus Saccharomonospora, for which the name Saccharomonospora marina sp. nov. is proposed.

scholarly journals Bacterial Diversity Profiling around the Orca Seamount in the Bransfield Strait, Antarctica, Based on 16S rRNA Gene Amplicon Sequences

2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Wilbert Serrano ◽  
Raul M. Olaechea ◽  
Luis Cerpa ◽  
Jose Herrera ◽  
Aldo Indacochea
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Diversity ◽  
Hydrothermal Vent ◽  
Hydrothermal Activity ◽  
Rrna Gene ◽  
Diversity Pattern ◽  
Submarine Volcanism ◽  
Data Profiling ◽  
The 16S Rrna Gene

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.

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

2012 ◽  
Vol 23 (4) ◽  
pp. 409-416 ◽  
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.

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

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.

Bacterial diversity and community structure of Western Indian Himalayan red kidney bean (Phaseolus vulgaris) rhizosphere as revealed by 16S rRNA gene sequences

Biologia ◽  
2015 ◽  
Vol 70 (3) ◽  
Author(s):  
Deep Chandra Suyal ◽  
Amit Yadav ◽  
Yogesh Shouche ◽  
Reeta Goel
Keyword(s):  
Community Structure ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Bacterial Diversity ◽  
Kidney Bean ◽  
Pcr Analysis ◽  
Rrna Gene ◽  
Rhizospheric Soil ◽  
Functional Studies ◽  
Red Kidney Bean

AbstractAgriculture is an important livelihood activity in the Himalayan regions. Our previous studies revealed the presence of diverse diazotrophic assemblage in indigenous red kidney bean (RKB) rhizospheric soil from two different locations of Western Indian Himalaya, namely S1 (Chhiplakot, 30.70◦ N/80.30° E) and S2 (Munsyari, 30.60◦ N/80.20° E), selected on the basis of real-time PCR analysis. In this study, two 16S rRNA gene clone libraries (SB1 and SB2, respectively) were constructed using the same rhizospheric soil samples for assessing the total bacterial diversity and their community structure. A total of 760 clones were obtained, with ∼54-59% of these sequences belonging to the phylum Proteobacteria. While sequences belonging to Bacteroidetes, Chloroflexi, Acidobactria, Planctomycetes, Firmicutes, Nitrospira, Gemmatimonadetes, Cyanobacteria, Verrucomicrobia, OD1, OP11 and Actinobacteria were encountered in both the soils, sequences belonging to bacteria from the classes Chlorobi and BRC1 were only detected in the S1 soil. Both the libraries showed similar bacterial community compositions, with Pseudomonas (∼33-34%) as predominant genus. Phylogenetic analysis revealed that all the clone sequences were clustered in different bacterial groups as per their resemblance with their respective phylogenetic neighbours. Major clusters were formed by Gammapreoteobacteria followed by Bacteroidetes and Alphaproteobacteria. A good fraction of the clone sequences has no resemblance with existing groups, thereby suggesting the need of culture-dependent studies from Himalayan regions. To the best of our knowledge, this study is the first major metagenomic effort on Himalayan RKBs rhizobacteria revealing fundamental information that needs to be explored for functional studies.

scholarly journals Characterization of ruminal bacteria in grazing Nellore steers

2019 ◽  
Vol 32 (4) ◽  
pp. 248-260 ◽  
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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