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16S rRNA gene

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Identification of bacteroides spp. from ducks using 16s RRNA gene PCR assay: Prelude to its application in microbial source tracking

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Chimera sequences in the partial 16S rRNA gene sequences of Bacteroides were checked using Decipher version 2.11.03 (Wright et al., 2012) and rectified.. Using MEGA X (Version 10.0.4), a phylogenetic tree was constructed using the Neighbor-Joining (NJ) method. Isolation and molecular identification of Bacteroides spp..

Exploring protocol bias in airway microbiome studies: One versus two PCR steps and 16S rRNA gene region V3 V4 versus V4

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We also included a mock community sample, obtained through BEI Resources NIAID, NIH as part of the Human Microbiome Project: Genomic DNA from Microbial Mock Community B (Staggered, Low Concentration), v5.2L, for 16S rRNA Gene Sequencing, HM783D.. We processed the same DNA extracts through three dif- ferent library preparation setups for MiSeq sequencing of the bacterial 16S rRNA marker gene: Setup 1 (2-step PCR.

Optimisation of 16S rRNA gut microbiota profiling of extremely low birth weight infants

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Samples names are coded highlighting the 16S rRNA gene library they belong.

Identification and optimization of protease production by bacillus sp. B9 isolated from waste water

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PCR product electrophoresis of 16S rRNA gene. amplification of Bacillus sp. B9: PCR product of Bacillus sp. Results comparing 16S rRNA gene sequence of Bacillus sp. Phylogenetic tree of Bacillus sp. B9 based on 16S rRNA gene sequences (the numbers at the branches are bootstrap confidence percentages from 1000 bootstrapped. Clear zone surrounding colony of Bacillus sp. B9 showing protease activity on LB agar stained with HgCl 2 10%.

Long-read metagenomics retrieves complete single-contig bacterial genomes from canine feces

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Y-axis scale is 500 for better visualization of the insertions and deletions. the HQ MAGs to link them to 16S rRNA gene-based microbiome studies (Fig. 4, and Additional File 6) –most of the microbiome studies use this genetic marker. Table 3 Prevalence of the bacterial species identified in public microbiome surveys. 4 Similarity of 16S rRNA gene from Sutterella HQ MAGs to public datasets. a Phylogenetic 16S rRNA gene tree of Sutterella HQ MAGs.

Horizontal acquisition of hydrogen conversion ability and other habitat adaptations in the Hydrogenovibrio strains SP-41 and XCL-2

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The relatedness of SP-41 and XCL-2 was already sug- gested by a previous partial sequencing of the 16S rRNA gene of SP-41 (Genbank KJ573628), in which only 3 dif- ferences were found compared to the 16S rRNA gene of XCL-2 (which itself has 3 identical 16S copies) [9]. The 16S rRNA gene sequences obtained from the genome sequencing of SP-41 confirm one of the 3 differences, located in the V7 hypervariable region, present in all three 16S rRNA gene copies of SP-41 (Additional file 5).

Polyphasic taxonomy analyse of comamonas testosteronі resistant то hexachlorobenzene

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Figure 1 The affinitying the 16S rRNA gene nucleotide sequences of isolates # 46 and # 47 and the 16S rRNA gene nucleotide sequences of typical members from the families Comamonadaceae, Burkholdereaceae and Pseudomonadaceae stored in the GenBank rRNA database (dendogram was constructed by software Mega 5.0.).

Using quantitative real-time polymerase chain reaction (qRT-PCR) for detection microcystin producing cyanobacteria

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Table 2: The efficiencies and other standard curve parameters were obtained by real-time qPCR analysis for (a) the cyanobacterial 16S rRNA and (b) the Microcystis 16S rRNA specific primer sets. Microcystis 16S rRNA. The Microcystis 16S rRNA gene was dominant, accounting for of the to- tal cyanobacteria abundance.

Comparative genomic analysis of Flavobacteriaceae: Insights into carbohydrate metabolism, gliding motility and secondary metabolite biosynthesis

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Isolation of the bacterial strains and their characterization by 16S rRNA gene analysis was done by DV and JG. AG wrote the first draft and all authors contributed to the preparation of the final manuscript.. The raw sequencing data of the genomes and the partial 16S rRNA gene sequences [146] of the strains isolated in this study were deposited in the European Nucleotide Archive (ENA) under accession number PRJEB35092 [147].

Whole genome sequencing and function prediction of 133 gut anaerobes isolated from chicken caecum in pure cultures

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coverage predicted more 10 copies of 16S rRNA genes).

Unexpected genomic, biosynthetic and species diversity of Streptomyces bacteria from bats in Arizona and New Mexico, USA

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We initially used sequence variation in the 16S rRNA locus to delineate species boundaries. 1a), with each cluster representing a distinct species based on the 97% sequence similarity threshold in the 16S rRNA gene (Fig.

KIEM NGHIEM

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Mặc dù 16S rRNA gene từ vi khuẩn khác nhau sẽ có một vài nucleotide khác nhau nằm rải rác trong các trình tự, những nucleotide ở đầu hoặc cuối của gen là như nhau với sinh vật sinh vật. http://www.microbeworld.org/careers/tools-of-the-trade/genetic-tools-and- techniques/16s-rrna Phương pháp PCR: 1. Trang 1 Trang 1 GIỚI THIỆU: Các gen rRNA là bảo tồn nhất (ít nhất là biến) DNA trong tất cả các tế bào. Một số phần của rDNA chuỗi từ sinh vật có quan hệ xa gần tương tự.

Comparative genomic analysis reveals the evolution and environmental adaptation strategies of vibrios

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Strikingly, vibrios contain a much higher number of 16S rRNA gene copies (7–15) than most of the other marine bacteria (3 on average) used for comparison in our study (Fig. In addition, the genome size of the large dataset ranges from 2.9 to 6.7 Mb, and the G + C content ranges from 38.0% to. a Comparison of the genome sizes. b Comparison of the copy numbers of 16S rRNA gene. c Comparison of the percentage of HGT genes. d Comparison of the number of chitinase coding genes.

Comparison of DNA standards for real-time-pcr based quantification of lactobacillus acidophilus in dairy products

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The plasmid encoding part of the L. acidophilus 16S rRNA gene was constructed through the amplification of a 227- bp fragment within the conserved region of the 16S rRNA gene using the specific primer pairs including Acidfor (5′-. (Tabasco et al. The primer sequences and PCR conditions with the genomic DNA of the bacteria as the template were similar to the previous study published by these authors..

Phân lập và định danh chủng xạ khuẩn có khả năng đối kháng với vi khuẩn Xanthomonas oryzae pv. oryzae gây bệnh bạc lá lúa

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The identification of the actinomycete strain 43 was based on the similarity of the 16S rRNA gene fragment with actinomycete strains published in the gene bank. The primers 27F and 1492R were used to amplify 16S rRNA gene fragment of strain 43. We compared the obtained sequence with other sequences in the gene bank by blast tool and built phylogentic trees for strain 43 (Figure 6)..

Đặc điểm phân loại chủng xạ khuẩn HT17.8 có khả năng kháng nấm gây bệnh trên chè tại Thái Nguyên

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On the basis of morphological, culture, biochemical and physiological characteristics and the sequence analysis of 16S rRNA gene, the strain HT17.8 was identified as Streptomyces sp. HT17.8 were determined on A - 4H medium.. Key words: antibiotic, antifungal, antibiotic activity, actinomycetes, 16S rRNA gene

Comparative genomics of cocci-shaped Sporosarcina strains with diverse spatial isolation

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Phylogenetic relatedness based on the 16S rRNA gene indicates that these cocci-shaped Sporosarcina strains in- cluding S. newyorkensis, but it also confirmed the diver- sity of the cocci-shaped Sporosarcina strains predicted from previous studies, as it divided the 28 sequenced strains, DSM 2281, and four additional S. Additionally, using the single 16S rRNA gene did not provide the resolution needed to decipher the phylogenetic relationships of the cocci- shaped Sporosarcina strains.

Robust Sub-nanomolar Library Preparation for High Throughput Next Generation Sequencing

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Results: Extensive studies were conducted to validate a robust sub-nanomolar (initial library of 100 pM) protocol using PhiX DNA (as a control), genomic DNA (Bordetella bronchiseptica and microbial mock community B for 16S rRNA gene sequencing), messenger RNA, microRNA, and other small noncoding RNA samples.

The microbiota structure in the cecum of laying hens contributes to dissimilar H2S production

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The primer sequences of the aprA gene and 16S rRNA gene. The relative abundance of the. CH, SX, WC and XL involved in acquisition of funding, experimental design and review of the manuscript. The funders had no role in the design, analysis, or interpretation of these experiments.. The 16S rRNA datasets generated and analysed during the current study are available in the European Nucleotide Archive database under the accession number PRJEB30541..

Effect of biofilm forming plant growth promoting rhizobacteria on salinity tolerance in barley

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The identification of the isolate was eventually confirmed through sequencing of 16S rRNA gene. The 16S rRNA gene sequences of the selected isolate showed 97.4% similarity to Bacillus amyloliq- uefaciens. These results of characterization and identification were in accordance with those of Sushil et al. Cv.×PGPR . Cv.×Salt . Cv.