Relevant bibliographies by topics / 16S rRNA gene sequencing

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  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers

Academic literature on the topic '16S rRNA gene sequencing'

Author: Grafiati
Published: 4 June 2021
Last updated: 13 February 2022

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Journal articles on the topic "16S rRNA gene sequencing"

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Il Jun, Kang, Jangsup Moon, Taek Soo Kim, Chang Kyung Kang, Song Mi Moon, Kyoung-Ho Song, Pyoeng Gyun Choe, et al. "238. Direct identification of Bacterial Species with MinION Nanopore Sequencer In Clinical Specimens Suspected of Polybacterial Infection." Open Forum Infectious Diseases 6, Supplement_2 (October 2019): S136. http://dx.doi.org/10.1093/ofid/ofz360.313.

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Abstract Background Conventional culture tests usually identify only a few bacterial species, which can grow well in the culture system, in the cases of polybacterial infection. 16S rRNA gene nanopore sequencing enables semi-quantitative identification of bacterial genetic materials. We aimed to evaluate usefulness of 16s rRNA gene nanopore sequencing in the cases suspected of polybacterial infection. Methods The research was conducted in a single university hospital for one year. Conventional bacterial culture identification and nanopore sequencing of 16s rRNA gene were carried out simultaneously for cases where polybacterial infection is strongly suspected. Blood agar plate was used for conventional culture, and Microscan (Beckman Coulter, United States) and Vitek 2 (Biomerieux, FR) automated systems were used for identification. For nanopore sequencing, 16S rRNA gene PCR was performed from the clinical specimens, and sequencing libraries were generated from the PCR products using the rapid barcoding sequencing kit (Oxford nanopore technologies, UK). MinION sequencing was performed for 1–3 hours and the generated reads were analyzed using the EPI2ME 16S BLAST workflow. Results Specimens were obtained from 15 patients; 6 liver abscess, 2 psoas abscess, 2 thigh abcess, 1 paraspinal abscess, 1 mycotic aneurysm, 1 necrotizing fasciitis, 1 fingertip gangrene and 1 abscess in coccyx area. 16s rRNA gene nanopore sequencing showed monobacterial organism in 8 (53.3%) specimens and polybacterial organisms in 7 (46.6%) specimens. In three (37.5%) cases of 8 cases with monobacterial infections identified by 16s rRNA gene sequencing, no organism was grown in conventional culture, possibly due to previous antibiotic administration. Notably, among 8 cases with polybacterial infection by 16s rRNA gene nanopore sequencing test, traditional culture test showed polybacterial infection in only two (25%) cases and single bacterial organism was identified in the other 6 (75%) cases. Conclusion Nanopore sequencing of 16s rRNA gene using the MinION sequencer may be useful for identification of causing microorganism and differentiation between monobacterial and polybacterial infection when polybacterial infection is suspected. Disclosures All authors: No reported disclosures.
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Yoshimura, Kazuaki, Nobuo Morotomi, Kazumasa Fukuda, Masahiro Nakano, Masamichi Kashimura, Toru Hachisuga, and Hatsumi Taniguchi. "Intravaginal microbial flora by the 16S rRNA gene sequencing." American Journal of Obstetrics and Gynecology 205, no. 3 (September 2011): 235.e1–235.e9. http://dx.doi.org/10.1016/j.ajog.2011.04.018.

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Cloud, Joann L., Jay J. Meyer, June I. Pounder, Kenneth C. Jost, Amy Sweeney, Karen C. Carroll, and Gail L. Woods. "Mycobacterium arupense sp. nov., a non-chromogenic bacterium isolated from clinical specimens." International Journal of Systematic and Evolutionary Microbiology 56, no. 6 (June 1, 2006): 1413–18. http://dx.doi.org/10.1099/ijs.0.64194-0.

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Several Mycobacterium-like organisms related to the Mycobacterium terrae complex have been isolated from clinical samples. In the clinical microbiology laboratory, partial 16S rRNA gene sequencing (approximately the first 500 bp) rather than full 16S rRNA gene sequencing is often used to identify Mycobacterium species. Partial 16S rRNA gene sequence analysis revealed 100 % similarity between 65 clinical isolates and Mycobacterium sp. MCRO 6 (GenBank accession no. X93032). Even after sequencing the nearly full-length 16S rRNA gene, closest similarity was only 99.6 % to Mycobacterium nonchromogenicum ATCC 19530T. Sequencing of the nearly full-length 16S rRNA gene, the 16S–23S internal transcribed spacer region and the hsp65 gene did not reveal genotypic identity with the type strains of M. nonchromogenicum, M. terrae or Mycobacterium triviale. Although sequence analysis suggested that these clinical isolates represented a novel species, mycolic acid analysis by HPLC failed to distinguish them from M. nonchromogenicum. Therefore, phenotypic analysis including growth characterization, antibiotic susceptibility testing and biochemical testing was performed. These strains from clinical samples should be recognized as representing a novel species of the genus Mycobacterium, for which the name Mycobacterium arupense sp. nov. is proposed. The type strain is AR30097T (=ATCC BAA-1242T=DSM 44942T).
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Schloss, Patrick D., Matthew L. Jenior, Charles C. Koumpouras, Sarah L. Westcott, and Sarah K. Highlander. "Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system." PeerJ 4 (March 28, 2016): e1869. http://dx.doi.org/10.7717/peerj.1869.

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Over the past 10 years, microbial ecologists have largely abandoned sequencing 16S rRNA genes by the Sanger sequencing method and have instead adopted highly parallelized sequencing platforms. These new platforms, such as 454 and Illumina’s MiSeq, have allowed researchers to obtain millions of high quality but short sequences. The result of the added sequencing depth has been significant improvements in experimental design. The tradeoff has been the decline in the number of full-length reference sequences that are deposited into databases. To overcome this problem, we tested the ability of the PacBio Single Molecule, Real-Time (SMRT) DNA sequencing platform to generate sequence reads from the 16S rRNA gene. We generated sequencing data from the V4, V3–V5, V1–V3, V1–V5, V1–V6, and V1–V9 variable regions from within the 16S rRNA gene using DNA from a synthetic mock community and natural samples collected from human feces, mouse feces, and soil. The mock community allowed us to assess the actual sequencing error rate and how that error rate changed when different curation methods were applied. We developed a simple method based on sequence characteristics and quality scores to reduce the observed error rate for the V1–V9 region from 0.69 to 0.027%. This error rate is comparable to what has been observed for the shorter reads generated by 454 and Illumina’s MiSeq sequencing platforms. Although the per base sequencing cost is still significantly more than that of MiSeq, the prospect of supplementing reference databases with full-length sequences from organisms below the limit of detection from the Sanger approach is exciting.
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Fujimoto, Naoshi, Keigo Mizuno, Tomoki Yokoyama, Akihiro Ohnishi, Masaharu Suzuki, Satoru Watanabe, Kenji Komatsu, et al. "Community analysis of picocyanobacteria in an oligotrophic lake by cloning 16S rRNA gene and 16S rRNA gene amplicon sequencing." Journal of General and Applied Microbiology 61, no. 5 (2015): 171–76. http://dx.doi.org/10.2323/jgam.61.171.

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Callahan, Benjamin J., Joan Wong, Cheryl Heiner, Steve Oh, Casey M. Theriot, Ajay S. Gulati, Sarah K. McGill, and Michael K. Dougherty. "High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution." Nucleic Acids Research 47, no. 18 (July 3, 2019): e103-e103. http://dx.doi.org/10.1093/nar/gkz569.

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AbstractTargeted PCR amplification and high-throughput sequencing (amplicon sequencing) of 16S rRNA gene fragments is widely used to profile microbial communities. New long-read sequencing technologies can sequence the entire 16S rRNA gene, but higher error rates have limited their attractiveness when accuracy is important. Here we present a high-throughput amplicon sequencing methodology based on PacBio circular consensus sequencing and the DADA2 sample inference method that measures the full-length 16S rRNA gene with single-nucleotide resolution and a near-zero error rate. In two artificial communities of known composition, our method recovered the full complement of full-length 16S sequence variants from expected community members without residual errors. The measured abundances of intra-genomic sequence variants were in the integral ratios expected from the genuine allelic variants within a genome. The full-length 16S gene sequences recovered by our approach allowed Escherichia coli strains to be correctly classified to the O157:H7 and K12 sub-species clades. In human fecal samples, our method showed strong technical replication and was able to recover the full complement of 16S rRNA alleles in several E. coli strains. There are likely many applications beyond microbial profiling for which high-throughput amplicon sequencing of complete genes with single-nucleotide resolution will be of use.
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Reischl, U., K. Feldmann, L. Naumann, B. J. M. Gaugler, B. Ninet, B. Hirschel, and S. Emler. "16S rRNA Sequence Diversity in Mycobacterium celatum Strains Caused by Presence of Two Different Copies of 16S rRNA Gene." Journal of Clinical Microbiology 36, no. 6 (1998): 1761–64. http://dx.doi.org/10.1128/jcm.36.6.1761-1764.1998.

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Direct sequencing of the 16S rRNA gene (16S rDNA) ofMycobacterium celatum isolates showed ambiguities, suggesting heterogeneity. Cloned 16S rDNA yielded two copies of the gene, which differed by insertion of a thymine at position 214 and by additional mismatches. Restriction fragment length polymorphism analysis confirmed the presence of two copies of 16S rDNA within the bacterial chromosome.
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Kennedy, Katherine, Michael W. Hall, Michael D. J. Lynch, Gabriel Moreno-Hagelsieb, and Josh D. Neufeld. "Evaluating Bias of Illumina-Based Bacterial 16S rRNA Gene Profiles." Applied and Environmental Microbiology 80, no. 18 (July 7, 2014): 5717–22. http://dx.doi.org/10.1128/aem.01451-14.

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ABSTRACTMassively parallel sequencing of 16S rRNA genes enables the comparison of terrestrial, aquatic, and host-associated microbial communities with sufficient sequencing depth for robust assessments of both alpha and beta diversity. Establishing standardized protocols for the analysis of microbial communities is dependent on increasing the reproducibility of PCR-based molecular surveys by minimizing sources of methodological bias. In this study, we tested the effects of template concentration, pooling of PCR amplicons, and sample preparation/interlane sequencing on the reproducibility associated with paired-end Illumina sequencing of bacterial 16S rRNA genes. Using DNA extracts from soil and fecal samples as templates, we sequenced pooled amplicons and individual reactions for both high (5- to 10-ng) and low (0.1-ng) template concentrations. In addition, all experimental manipulations were repeated on two separate days and sequenced on two different Illumina MiSeq lanes. Although within-sample sequence profiles were highly consistent, template concentration had a significant impact on sample profile variability for most samples. Pooling of multiple PCR amplicons, sample preparation, and interlane variability did not influence sample sequence data significantly. This systematic analysis underlines the importance of optimizing template concentration in order to minimize variability in microbial-community surveys and indicates that the practice of pooling multiple PCR amplicons prior to sequencing contributes proportionally less to reducing bias in 16S rRNA gene surveys with next-generation sequencing.
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Szymczak, Aleksander, Stanisław Ferenc, Joanna Majewska, Paulina Miernikiewicz, Jan Gnus, Wojciech Witkiewicz, and Krystyna Dąbrowska. "Application of 16S rRNA gene sequencing in Helicobacter pylori detection." PeerJ 8 (May 13, 2020): e9099. http://dx.doi.org/10.7717/peerj.9099.

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Helicobacter pylori is one of the major stomach microbiome components, promoting development of inflammation and gastric cancer in humans. H. pylori has a unique ability to transform into a coccoidal form which is difficult to detect by many diagnostic methods, such as urease activity detection, and even histopathological examination. Here we present a comparison of three methods for H. pylori identification: histological assessment (with eosin, hematoxylin, and Giemsa staining), polymerase chain reaction (PCR) detection of urease (ureA specific primers), and detection by 16S rRNA gene sequencing. The study employed biopsies from the antral part of the stomach (N = 40). All samples were assessed histologically which revealed H. pylori in eight patients. Bacterial DNA isolated from the bioptates was used as a template for PCR reaction and 16S rRNA gene sequencing that revealed H. pylori in 13 and in 20 patients, respectively. Thus, 16S rRNA gene sequencing was the most sensitive method for detection of H. pylori in stomach biopsy samples.
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Angell, Inga Leena, Morten Nilsen, Karin C. Lødrup Carlsen, Kai-Håkon Carlsen, Gunilla Hedlin, Christine M. Jonassen, Benjamin Marsland, et al. "De novo species identification using 16S rRNA gene nanopore sequencing." PeerJ 8 (October 21, 2020): e10029. http://dx.doi.org/10.7717/peerj.10029.

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Nanopore sequencing is rapidly becoming more popular for use in various microbiota-based applications. Major limitations of current approaches are that they do not enable de novo species identification and that they cannot be used to verify species assignments. This severely limits applicability of the nanopore sequencing technology in taxonomic applications. Here, we demonstrate the possibility of de novo species identification and verification using hexamer frequencies in combination with k-means clustering for nanopore sequencing data. The approach was tested on the human infant gut microbiota of 3-month-old infants. Using the hexamer k-means approach we identified two new low abundant species associated with vaginal delivery. In addition, we confirmed both the vaginal delivery association for two previously identified species and the overall high levels of bifidobacteria. Taxonomic assignments were further verified by mock community analyses. Therefore, we believe our de novo species identification approach will have widespread application in analyzing microbial communities in the future.
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Dissertations / Theses on the topic "16S rRNA gene sequencing"

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Kam, Sin-yee. "Application of 16S rRNA gene sequencing in laboratory diagnosis of mycobacteria other than tuberculosis." Click to view the E-thesis via HKUTO, 2003. http://sunzi.lib.hku.hk/hkuto/record/B31971052.

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金倩儀 and Sin-yee Kam. "Application of 16S rRNA gene sequencing in laboratory diagnosis of mycobacteria other than tuberculosis." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2003. http://hub.hku.hk/bib/B31971052.

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Ng, Ho-yin Ricky, and 吳浩然. "Identification of anaerobic, non-sporulating, Gram-positive bacilli from blood cultures by 16S rRNA gene sequencing." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2010. http://hub.hku.hk/bib/B44670424.

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Calus, Szymon Tomasz. "Evaluation of nanopore-based sequencing technology for gene marker based analysis of complex microbial communities : method development for accurate 16S rRNA gene amplicon sequencing." Thesis, University of Glasgow, 2018. http://theses.gla.ac.uk/41086/.

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Nucleic acid sequencing can provide a detailed overview of microbial communities in comparison with standard plate-culture methods. Expansion of high-throughput sequencing (HTS) technologies and reduction in analysis costs has allowed for detailed exploration of various habitats with use of amplicon, metagenomics, and metatranscriptomics approaches. However, due to a capital cost of HTS platforms and requirements for batch analysis, genomics-based studies are still not being used as a standard method for the comprehensive examination of environmental or clinical samples for microbial characterization. This research project investigated the potential of a novel nanopore-based sequencing platform from Oxford Nanopore Technologies (ONT) for rapid and accurate analysis of various environmentally complex samples. ONT is an emerging company that developed the first-ever portable nanopore-based sequencing platform called MinIONTM. Portability and miniaturised size of the device gives an immense opportunity for de-centralised, in-field, and real-time analysis of environmental and clinical samples. Nonetheless, benchmarking of this new technology against the current gold-standard platform (i.e., Illumina sequencers) is necessary to evaluate nanopore data and understand its benefits and limitations. The focus of this study is on the evaluation of nanopore sequencing data: read quality, sequencing errors, alignment quality but also bacterial community structure. For this reason, mock bacterial community samples were generated, sequenced and analysed with use of multiple bioinformatics approaches. Furthermore, this study developed sophisticated library preparation and data analyses methods to enable high-accuracy analysis of amplicon libraries from complex microbial communities for sequencing on the nanopore platform. Besides, the best performing library preparation and data analyses methods were used for analysis of environmental samples and compared to high-quality Illumina metagenomics data. This work opens a new possibility for accurate, in-field amplicon analysis of complex samples with the use of MinIONTM and for the development of autonomous biosensing technology for culture-free detection of pathogenic and non-pathogenic microorganisms in water, soil, food, drinks or blood.
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Varna, Klaidas. "Pienarūgščių bakterijų paieška ir jų identifikavimas migruojančių didžiųjų ančių (Anas platyrhynchos) žarnyne naudojant dalinių 16S rRNR geno sekų analizę ir kultivavimu paremtus metodus." Master's thesis, Lithuanian Academic Libraries Network (LABT), 2009. http://vddb.library.lt/obj/LT-eLABa-0001:E.02~2007~D_20090908_194033-88862.

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Pienarūgščių bakterijų paieška ir jų identifikavimas migruojančių didžiųjų ančių (Anas platyrhynchos) žarnyne naudojant dalinių 16S rRNR geno sekų analizę ir kultivavimu paremtus metodus Klaidas VARNA Vilniaus Universiteto Ekologijos Institutas, Hidrobiontų Ekologijos ir Fiziologijos Laboratorija bei Populiacinės Genetikos Laboratorija, Akademijos-2, Vilnius-21, 08412, Lietuva. Šiame tyrime pavasarinių ir rudeninių didžiųjų ančių (Anas platyrhynchos) migrantų iš Nemuno deltos virškinamojo trakto pieno rūgšties bakterijų įvairovė buvo ištirta naudojant molekulinius metodus (polimerazės grandininės reakcijos amplifikacija ir dalinių 16S rRNR geno sekų sekvenavimas) ir kultivavimu paremtus metodus. Migruojančių didžiųjų ančių (Anas platyrhynchos) pieno rūgšties bakterijų paieška buvo atlikta pirmą kartą. Rudeniniai didžiųjų ančių migrantai plonojo žarnyno sienelėse (1.2×107 iki 2.1×107 k.f.v./g) ir jų turinyje (nuo 3.4×107 iki 1.1×108 k.f.v./g) turi didesnį pieno rūgšties bakterijų skaičių nei pavasariniai migrantai (atitinkamai nuo 3.2×106 iki 4.8×106 k.f.v./g ir nuo 1.0×107 iki 2.2×107 k.f.v./g). Tiek rudeninių tiek ir pavasarinių didžiųjų ančių migrantų plonojo žarnyno sienelėse ir jų turinyje dominavo kokinės pieno rūgšties bakterijų formos (atitinkamai 65% ir 83.5% bei 81.4% ir 91.6%), o lazdelių buvo mažiau (atitinkamai 35% ir 16.5% bei 18.6% ir 8.4%). Manoma, kad minėtus skirtumus įtakoja keli veiksniai: ilgai trunkanti migracija, perėjimo periodas, skirtingas maistas ir... [toliau žr. visą tekstą]
Identification of lactic acid bacteria in the migrant mallard ducks Anas platyrhynchos intestinal tract by partial 16S rRNA gene sequence analysis and using culture-based techniques Klaidas VARNA Institute of Ecology of Vilnius University, Laboratory of Hydrobionts Ecology and Physiology, Laboratory of Population Genetics, Akademijos-2, Vilnius-21, 08412, Lithuania. In this study the lactic acid bacteria diversity of the intestinal tract content of the vernal and autumnal migrant mallard ducks (Anas platyrhynchos) from Nemuno delta has been investigated by molecular methods: polymerase chain reaction amplification and sequencing of partial 16S rRNA genes and using culture-based techniques. The investigation of the lactic acid bacteria of the migrant mallard ducks has been performed the first time. Autumnal migrant mallard ducks in the small intestine walls (from 1.2×107 until 2.1×107 c.f.u./g) and in their content (from 3.4×107 until 1.1×108 c.f.u./g have the greatest number of the lactic acid bacteria then vernal migrants (respectively from 3.2×106 until 4.8×106 c.f.u./g and from 1.0×107 until 2.2×107 c.f.u./g). In the small intestine walls and in their content of the autumnal and vernal migrant mallard ducks, dominated cocci-shaped lactic acid bacteria (respectively 65% and 83.5%, 81.4% and 91.6%), whereas rod-shaped was under (respectively 35% and 16.5%, 18.6% and 8.4%). Supposedly, that these defferences determine some factors: a long migration, period of incubate... [to full text]
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Yeung, Shiu-yan, and 楊兆恩. "Update and evaluation of 16SpathDB, an automated comprehensive database for identification of medically important bacteria by 16S rRNA gene sequencing." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2013. http://hdl.handle.net/10722/193552.

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Identification of pathogens is one of the important duties of clinical microbiology laboratory. Traditionally, phenotypic tests are used to identify the bacteria. However, due to some limitations of the phenotypic tests, the bacteria may not be identified sometimes and cannot be identified promptly. 16S rRNA gene sequencing is a rapid and accurate method to achieve this target. It is especially useful for identify rare or slow growing bacteria. However, the interpretation of the 16S rRNA gene sequencing result is one of the challenging duties to laboratory technicians and microbiologists. Apart from the well known 16S rRNA gene databases such as Genbank, The Ribosomal Database Project (RDP-II), MicroSeq databases, Ribosomal Differentiation of medical Microorganism database (RIDOM), SmartGene IDNS, 16SpathDB is an automated and comprehensive database for interpret the 16S rRNA gene result. The 16SpathDB first version was established in 2011. In this study, 16SpathDB was updated based on the all clinical important bacteria present in the 10th edition of the Manual of Clinical Microbiology (MCM)(Versalovic. et al., 2011) into this new version of database, 16SpathDB 2.0. The database was evaluated by using 689 16S rRNA gene sequences from 689 complete genomes of medically important bacteria. Among the 689 16S rRNA gene sequences, none was wrongly identified by 16SpathDB 2.0, with 247 (35.8%) 16S rRNA gene sequences reported in only one single bacterial species with more than 98% nucleotide identity with the query sequence (category 1), 440 (63.9%) reported as more than one bacterial species having more than 98% nucleotide identity with the query sequence (category 2), 2 (0.3%) reported to the genus level (category 3), and none reported as “no species in 16SpathDB 2.0 found to be sharing high nucleotide identity to your query sequence” (category 4). 16SpathDB 2.0 is an updated, automated, user-friendly, efficient and accurate database for 16S rRNA gene sequence interpretation in clinical microbiology laboratories.
published_or_final_version
Microbiology
Master
Master of Medical Sciences
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Fisher, Marc Lewis. "Comparison of Subterranean Termite (Rhinotermitidae: Reticulitermes) Gut Bacterial Diversity Within and Between Colonies and to Other Termite Species Using Molecular Techniques (ARDRA and 16S rRNA Gene Sequencing)." Diss., Virginia Tech, 2006. http://hdl.handle.net/10919/27379.

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Termites are known to harbor within their gut a diverse assemblage of symbiotic microorganisms. Little work has been done, however, to describe the diversity and function of the bacteria in the economically important eastern subterranean termite, Reticulitermes flavipes. The first object of this study was to characterize the bacterial diversity in the gut of R. flavipes using amplified rDNA restriction analysis (ARDRA) and 16S rRNA gene sequencing. It was determined that ARDRA was an effective technique for characterizing the diversity of the termite gut microbiota. Of the 512 clones analyzed in the ARDRA study, 261 different ARDRA profiles were found. Forty-two 16S rRNA gene sequences were also analyzed, resulting in 33 different ribotypes. Representatives from six major bacterial phyla, Proteobacteria, Spirochaetes, Bacteroidetes, Firmicutes, Actinobacteria, and the newly proposed â Endomicrobia,â were discovered. Further analysis indicated that the gut of R. flavipes may harbor as many as 1,318 ribotypes per termite. The second objective was to determine if the gut bacterial diversity could be manipulated by changing the termiteâ s food source. Using ARDRA analysis, I found no evidence that changing the food source affected the termite gut bacterial diversity. In addition, changing the food source did not induce aggression in nestmates fed on different food sources. The third objective was to search for patterns of coevolution between termites and their gut symbiotic bacteria. Using rRNA gene sequences from this study and sequences from public databases (1,450 sequences total), a neighbor-joining tree demonstrated strong evidence for coevolution of termites and their symbiotic bacteria, especially in the phyla Bacteroidetes, Actinobacteria, Spirochaetes, and â Endomicrobia.â Many monophyletic clusters were entirely composed of phylotypes specific to Isoptera.
Ph. D.
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Valešová, Nikola. "Bioinformatický nástroj pro klasifikaci bakterií do taxonomických kategorií na základě sekvence genu 16S rRNA." Master's thesis, Vysoké učení technické v Brně. Fakulta informačních technologií, 2019. http://www.nusl.cz/ntk/nusl-403138.

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Tato práce se zabývá problematikou automatizované klasifikace a rozpoznávání bakterií po získání jejich DNA procesem sekvenování. V rámci této práce je navržena a popsána nová metoda klasifikace založená na základě segmentu 16S rRNA. Představený princip je vytvořen podle stromové struktury taxonomických kategorií a používá známé algoritmy strojového učení pro klasifikaci bakterií do jedné ze tříd na nižší taxonomické úrovni. Součástí práce je dále implementace popsaného algoritmu a vyhodnocení jeho přesnosti predikce. Přesnost klasifikace různých typů klasifikátorů a jejich nastavení je prozkoumána a je určeno nastavení, které dosahuje nejlepších výsledků. Přesnost implementovaného algoritmu je také porovnána s několika existujícími metodami. Během validace dosáhla implementovaná aplikace KTC více než 45% přesnosti při predikci rodu na datových sadách BLAST 16S i BLAST V4. Na závěr je zmíněno i několik možností vylepšení a rozšíření stávající implementace algoritmu.
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Yamaguti, Mauricio. "Isolamento de micoplasma de suínos com problemas respiratórios e tipificação dos isolados pela PFGE e seqüenciamento do gene 16S rRNA." Universidade de São Paulo, 2009. http://www.teses.usp.br/teses/disponiveis/42/42132/tde-29102009-091226/.

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As doenças respiratórias são responsáveis, na suinocultura, por grandes perdas econômicas e entre os agentes destacam-se os micoplasmas. Foram coletadas 126 amostras de muco nasal/tonsilar, e fragmentos de 78 pulmões, 2 de traquéia e 2 de tonsila. No isolamento foi utilizado o meio FRIIS modificado, na identificação, a Multiplex-PCR e na tipificação, a PFGE e sequenciamento do gene 16S rRNA. Foram obtidos 59 isolados identificados como M. hyopneumoniae (1,70%), M. flocculare (3,40%) e M. hyorhinis (94,90%). A PFGE dos isolados de M. hyorhinis, resultou em 10 e 9 perfis com a enzima AvaI e XhoI, respectivamente. O sequenciamento do gene 16S rRNA dos isolados M. hyorhinis apresentaram baixo polimorfismo quando comparados entre si e com a cepa de referência. A sequência do gene 16S rRNA do isolado de M. hyopneumoniae, quando comparada a seqüência da cepa J e os isolados 7448 e 232, resultaram em polimorfismo. O M. hyopneumoniae continua sendo o mais difícil de isolar. Os dendrogramas obtidos da PFGE resultaram em grande heterogeneidade entre os isolados de M. hyorhinis. O seqüenciamento do gene 16S rRNA permitiu o estudo de variabilidade interespecífica e intraespecífica dos isolados de micoplasmas.
Economic losses in swine production are common due the respiratory diseases in these animals. M. hyopneumoniae and M. hyorhinis are the most frequent microbial agents. The aim of this study was recover this isolates in FRIIS medium, indentify them by Multiplex PCR and detect their genotypic variations by PFGE and sequencing the 16s rRNA gene. One hundred twenty six swabs from tonsil and nasal mucus of swine with respiratory disturbances were analyzed. It was included 78 lungs, two trachea and two tonsils. It was obtained 59 isolates; 1.70% of M. hyopneumoniae, 3.40% of M. flocculare and 94.90% of M. hyorhinis. The PFGE of M. hyorhinis, allowed obtain 10 profiles with enzyme AvaI and nine profiles with XhoI. A low polymorphism of gene 16sRNS was detected in M. hyorhinis isolates when compared with the type strain at the GenBank. The M. hyopneumoniae isolates resulted in polymorphisms when comparated with strain J, 7448 and 232. M. hyopneumoniae is still the most difficult to isolate. M. hyorhinis isolates of different herds showed a large heterogenicity with enzymes AvaI e XhoI. The sequencing of gene 16S rRNA allowed analyse the interespecífic and intraespecífic variations of mycoplasmas isolated.
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Sjöholm, Billie, and Babak Bahrami. "Prevalence and Identification of Lactobacillus Species Isolated from Infected Root Canals by MALDI-TOF Mass Spectrometry, 16S rRNA Gene Sequencing and API 50 CHL." Thesis, Umeå universitet, Tandläkarutbildning, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-97871.

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Lactobacillus, a part of the commensal oral microflora, is frequently found in infected root canals but is not considered to be an endodontic pathogen. Lactobacilli have proven to be difficult to identify on species level with biochemical and gene sequencing methods. MALDI-TOF is a new identification method and to our knowledge it has not been used on lactobacilli from infected root canals. The aims of this study were to evaluate the prevalence of lactobacilli in infected root canals and to examine if MALDI-TOF is a suitable method for identifying lactobacilli species. In the retrospective study, we evaluated 449 microbial samples obtained from 361 patients. In the prospective study, 100 consecutive microbial samples were collected from 93 patients with infected root canals. Twelve clinical isolates from eight patients were obtained and six selected reference strains were included in the study. MALDI-TOF, 16S rRNA gene sequencing and API 50 CHL identification methods were used to identify lactobacilli isolates and reference strains on species level. In conclusion, the prevalence of lactobacilli in infected root canals was 22% in our material. Molars were the most frequent tooth group infected with lactobacilli. For identification of the reference strains, MALDI-TOF performed slightly better than the other methods. The identification of clinical isolates was inconclusive. MALDI-TOF is an inexpensive, simple and rapid method for identification of lactobacilli and performs well in comparison with conventional methods. However, all of the three identification methods used in this study have limitations when differentiating between closely related lactobacilli species.
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Books on the topic "16S rRNA gene sequencing"

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Kirchman, David L. Community structure of microbes in natural environments. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198789406.003.0004.

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Community structure refers to the taxonomic types of microbes and their relative abundance in an environment. This chapter focuses on bacteria with a few words about fungi; protists and viruses are discussed in Chapters 9 and 10. Traditional methods for identifying microbes rely on biochemical testing of phenotype observable in the laboratory. Even for cultivated microbes and larger organisms, the traditional, phenotype approach has been replaced by comparing sequences of specific genes, those for 16S rRNA (archaea and bacteria) or 18S rRNA (microbial eukaryotes). Cultivation-independent approaches based on 16S rRNA gene sequencing have revealed that natural microbial communities have a few abundant types and many rare ones. These organisms differ substantially from those that can be grown in the laboratory using cultivation-dependent approaches. The abundant types of microbes found in soils, freshwater lakes, and oceans all differ. Once thought to be confined to extreme habitats, Archaea are now known to occur everywhere, but are particularly abundant in the deep ocean, where they make up as much as 50% of the total microbial abundance. Dispersal of bacteria and other small microbes is thought to be easy, leading to the Bass Becking hypothesis that “everything is everywhere, but the environment selects.” Among several factors known to affect community structure, salinity and temperature are very important, as is pH especially in soils. In addition to bottom-up factors, both top-down factors, grazing and viral lysis, also shape community structure. According to the Kill the Winner hypothesis, viruses select for fast-growing types, allowing slower growing defensive specialists to survive. Cultivation-independent approaches indicate that fungi are more diverse than previously appreciated, but they are less diverse than bacteria, especially in aquatic habitats. The community structure of fungi is affected by many of the same factors shaping bacterial community structure, but the dispersal of fungi is more limited than that of bacteria. The chapter ends with a discussion about the relationship between community structure and biogeochemical processes. The value of community structure information varies with the process and the degree of metabolic redundancy among the community members for the process.
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Kirchman, David L. Predation and protists. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198789406.003.0009.

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Protists are involved in many ecological roles in natural environments, including primary production, herbivory and carnivory, and parasitism. Microbial ecologists have been interested in these single-cell eukaryotes since Antonie van Leeuwenhoek saw them in his stool and scum from his teeth. This chapter focuses on the role of protozoa (purely heterotrophic protists) and other protists in grazing on other microbes. Heterotrophic nanoflagellates, 3–5 microns long, are the most important grazers of bacteria and small phytoplankton in aquatic environments. In soils, flagellates are also important, followed by naked amoebae, testate amoebae, and ciliates. Many of these protists feed on their prey by phagocytosis, in which the prey particle is engulfed into a food vacuole into which digestive enzymes are released. This mechanism of grazing explains many factors affecting grazing rates, such as prey numbers, size, and composition. Ingestion rates increase with prey numbers before reaching a maximum, similar to the Michaelis–Menten equation describing uptake as a function of substrate concentration. Protists generally eat prey that are about ten-fold smaller than they are. In addition to flagellates, ciliates and dinoflagellates are often important predators in the microbial world and are critical links between microbial food chains and larger organisms Many protists are capable of photosynthesis. In some cases, the predator benefits from photosynthesis carried out by engulfed, but undigested photosynthetic prey or its chloroplasts. Although much can be learnt from the morphology of large protists, small protists (<10 μ‎m) often cannot be distinguished by morphology, and as seen several times in this book, many of the most abundant and presumably important protists are difficult to cultivate, necessitating the use of cultivation-independent methods analogous to those developed for prokaryotes. Instead of the 16S rRNA gene used for bacteria and archaea, the 18S rRNA gene is key for protists. Studies of this gene have uncovered high diversity in natural protist communities and, along with sequences of other genes, have upended models of eukaryote evolution. These studies indicate that the eukaryotic Tree of Life consists almost entirely of protists, with higher plants, fungi, and animals as mere branches.
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Kirchman, David L. Genomes and meta-omics for microbes. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198789406.003.0005.

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The sequencing of entire genomes of microbes grown in pure cultures is now routine. The sequence data from cultivated microbes have provided insights into these microbes and their uncultivated relatives. Sequencing studies have found that bacterial genomes range from 0.18 Mb (intracellular symbiont) to 13 Mb (a soil bacterium), whereas genomes of eukaryotes are much bigger. Genomes from eukaryotes and prokaryotes are organized quite differently. While bacteria and their small genomes often grow faster than eukaryotes, there is no correlation between genome size and growth rates among the bacteria examined so far. Genomic studies have also highlighted the importance of genes exchanged (“horizontal gene transfer”) between organisms, seemingly unrelated, as defined by rRNA gene sequences. Microbial ecologists use metagenomics to sequence all microbes in a community. This approach has revealed unsuspected physiological processes in microbes, such as the occurrence of a light-driven proton pump, rhodopsin, in bacteria (dubbed proteorhodopsin). Genomes from single cells isolated by flow cytometry have also provided insights about the ecophysiology of both bacteria and protists. Oligotrophic bacteria have streamlined genomes, which are usually small but with a high fraction of genomic material devoted to protein-encoding genes, and few transcriptional control mechanisms. The study of all transcripts from a natural community, metatranscriptomics, has been informative about the response of eukaryotes as well as bacteria to changing environmental conditions.
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Kirchman, David L. Processes in anoxic environments. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198789406.003.0011.

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During organic material degradation in oxic environments, electrons from organic material, the electron donor, are transferred to oxygen, the electron acceptor, during aerobic respiration. Other compounds, such as nitrate, iron, sulfate, and carbon dioxide, take the place of oxygen during anaerobic respiration in anoxic environments. The order in which these compounds are used by bacteria and archaea (only a few eukaryotes are capable of anaerobic respiration) is set by thermodynamics. However, concentrations and chemical state also determine the relative importance of electron acceptors in organic carbon oxidation. Oxygen is most important in the biosphere, while sulfate dominates in marine systems, and carbon dioxide in environments with low sulfate concentrations. Nitrate respiration is important in the nitrogen cycle but not in organic material degradation because of low nitrate concentrations. Organic material is degraded and oxidized by a complex consortium of organisms, the anaerobic food chain, in which the by-products from physiological types of organisms becomes the starting material of another. The consortium consists of biopolymer hydrolysis, fermentation, hydrogen gas production, and the reduction of either sulfate or carbon dioxide. The by-product of sulfate reduction, sulfide and other reduced sulfur compounds, is oxidized back eventually to sulfate by either non-phototrophic, chemolithotrophic organisms or by phototrophic microbes. The by-product of another main form of anaerobic respiration, carbon dioxide reduction, is methane, which is produced only by specific archaea. Methane is degraded aerobically by bacteria and anaerobically by some archaea, sometimes in a consortium with sulfate-reducing bacteria. Cultivation-independent approaches focusing on 16S rRNA genes and a methane-related gene (mcrA) have been instrumental in understanding these consortia because the microbes remain uncultivated to date. The chapter ends with some discussion about the few eukaryotes able to reproduce without oxygen. In addition to their ecological roles, anaerobic protists provide clues about the evolution of primitive eukaryotes.
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Book chapters on the topic "16S rRNA gene sequencing"

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Einarsson, Gisli G., and Sébastien Boutin. "Techniques: culture, identification and 16S rRNA gene sequencing." In The Lung Microbiome, 18–34. Sheffield, United Kingdom: European Respiratory Society, 2019. http://dx.doi.org/10.1183/2312508x.10000819.

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Fantini, Elio, Giulio Gianese, Giovanni Giuliano, and Alessia Fiore. "Bacterial Metabarcoding by 16S rRNA Gene Ion Torrent Amplicon Sequencing." In Methods in Molecular Biology, 77–90. New York, NY: Springer New York, 2015. http://dx.doi.org/10.1007/978-1-4939-1720-4_5.

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James, Greg. "Universal Bacterial Identification by PCR and DNA Sequencing of 16S rRNA Gene." In PCR for Clinical Microbiology, 209–14. Dordrecht: Springer Netherlands, 2010. http://dx.doi.org/10.1007/978-90-481-9039-3_28.

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Formenti, Fabio, Gabriel Rinaldi, Cinzia Cantacessi, and Alba Cortés. "Helminth Microbiota Profiling Using Bacterial 16S rRNA Gene Amplicon Sequencing: From Sampling to Sequence Data Mining." In Methods in Molecular Biology, 263–98. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1681-9_15.

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Hirakata, Y., M. Hatamoto, M. Oshiki, N. Araki, and T. Yamaguchi. "Eukaryotic Community in UASB Reactor Treating Domestic Sewage Based on 18S rRNA Gene Sequencing." In Lecture Notes in Civil Engineering, 218–24. Cham: Springer International Publishing, 2017. http://dx.doi.org/10.1007/978-3-319-58421-8_34.

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Christensen, Henrik, Anna Jasmine Andersson, Steffen Lynge Jørgensen, and Josef Korbinian Vogt. "16S rRNA Amplicon Sequencing for Metagenomics." In Introduction to Bioinformatics in Microbiology, 135–61. Cham: Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-319-99280-8_8.

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Benlloch, Susana, Francisco Rodríguez-Valera, Silvia G. Acinas, and Antonio J. Martínez-Murcia. "Heterotrophic bacteria, activity and bacterial diversity in two coastal lagoons as detected by culture and 16S rRNA genes PCR amplification and partial sequencing." In Coastal Lagoon Eutrophication and ANaerobic Processes (C.L.E.AN.), 3–17. Dordrecht: Springer Netherlands, 1996. http://dx.doi.org/10.1007/978-94-009-1744-6_1.

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Hall, Michael, and Robert G. Beiko. "16S rRNA Gene Analysis with QIIME2." In Methods in Molecular Biology, 113–29. New York, NY: Springer New York, 2018. http://dx.doi.org/10.1007/978-1-4939-8728-3_8.

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Bally, René, Jacqueline Haurat, and Philippe Normand. "Azospirillum Phylogeny Based on rrs (16S rRNA Gene) Sequences." In Azospirillum VI and Related Microorganisms, 129–35. Berlin, Heidelberg: Springer Berlin Heidelberg, 1995. http://dx.doi.org/10.1007/978-3-642-79906-8_12.

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Douglas, Gavin M., André M. Comeau, and Morgan G. I. Langille. "Processing a 16S rRNA Sequencing Dataset with the Microbiome Helper Workflow." In Methods in Molecular Biology, 131–41. New York, NY: Springer New York, 2018. http://dx.doi.org/10.1007/978-1-4939-8728-3_9.

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Conference papers on the topic "16S rRNA gene sequencing"

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Kazarina, Alisa, Ilva Pole, Viktorija Leonova, Viktorija Igumnova, Janis Kimsis, Valentina Capligina, Renate Ranka, Guntis Gerhards, and Elina Petersone-Gordina. "Insights into archaeological human sample microbiome using 16S rRNA gene sequencing." In 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM). IEEE, 2017. http://dx.doi.org/10.1109/bibm.2017.8218018.

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Chawla, Archit, and Anthony Byrne. "16S rRNA gene sequencing improves microbial diagnosis of culture-negative pleural effusions." In ERS International Congress 2019 abstracts. European Respiratory Society, 2019. http://dx.doi.org/10.1183/13993003.congress-2019.oa5140.

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Vasileva, E. N., A. M. Afonin, G. A. Akhtemova, V. A. Zhukov, and I. A. Tikhonovich. "Endophytic bacteria isolated from garden pea (Pisum sativum L.)." In 2nd International Scientific Conference "Plants and Microbes: the Future of Biotechnology". PLAMIC2020 Organizing committee, 2020. http://dx.doi.org/10.28983/plamic2020.265.

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Endophytic bacteria were isolated from surface-sterilized aerial parts of pea. Taxonomic status of isolated strains was determined by sequencing of 16S rRNA gene. Moreover, genomes of growth-promoting endophytes were sequenced.
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Brill, Simon, Phillip James, Leah Cuthbertson, Michael Cox, William Cookson, Jadwiga Wedzicha, and Miriam Moffatt. "Profiling the COPD airway microbiome using quantitative culture and 16S rRNA gene sequencing." In ERS International Congress 2016 abstracts. European Respiratory Society, 2016. http://dx.doi.org/10.1183/13993003.congress-2016.oa1787.

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Shelton, Jenna L., Elliott Barnhart, Leslie F. Ruppert, Aaron Jubb, Madalyn S. Blondes, and Christina DeVera. "REPETITIVE SAMPLING AND CONTROL THRESHOLD IMPROVE 16S RRNA GENE SEQUENCING RESULTS FROM NIOBRARA SHALE PRODUCED WATER." In GSA 2020 Connects Online. Geological Society of America, 2020. http://dx.doi.org/10.1130/abs/2020am-351340.

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Kanellakis, NI, E. Bedawi, JP Corcoran, S. Gerry, R. Hallifax, R. Mercer, V. George, et al. "S13 The microbiology of pleural infection, an approach based on 16s RRNA gene next generation sequencing." In British Thoracic Society Winter Meeting 2019, QEII Centre, Broad Sanctuary, Westminster, London SW1P 3EE, 4 to 6 December 2019, Programme and Abstracts. BMJ Publishing Group Ltd and British Thoracic Society, 2019. http://dx.doi.org/10.1136/thorax-2019-btsabstracts2019.19.

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Bolig, T., R. Chanderraj, J. Erb-Downward, P. Ranjan, T. Spilker, J. Lipuma, and R. P. Dickson. "Strain-Specific Detection of Burkholderia Cepacia Complex in Cystic Fibrosis Sputum: Concordance Between Real-Time Metagenomics and 16s rRNA Gene Sequencing." In American Thoracic Society 2020 International Conference, May 15-20, 2020 - Philadelphia, PA. American Thoracic Society, 2020. http://dx.doi.org/10.1164/ajrccm-conference.2020.201.1_meetingabstracts.a5408.

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Al-Farha, Abd Al-Bar. "Phylogenetic relationship among field isolates of mycoplasmas and acholeplasmas in two South Australian dairy herds based on sequencing of a short 16S rRNA gene fragment." In Proceedings of the 1st International Multi-Disciplinary Conference Theme: Sustainable Development and Smart Planning, IMDC-SDSP 2020, Cyperspace, 28-30 June 2020. EAI, 2020. http://dx.doi.org/10.4108/eai.28-6-2020.2298229.

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Peck, Kayla, Robert Stedtfeld, Jordan RoseFigura, Brett Reed, Drew McUsic, Jon Irish, Brett Etchebarne, Timothy Johnson, Laurie Kurihara, and Vladimir Makarov. "Abstract 1484: Microbial sequencing using a single-pool target enrichment of multiple variable regions of the 16S rRNA gene, the nuclear ribosomal internal transcribed spacer (ITS) region, and antimicrobial resistance genes." In Proceedings: AACR Annual Meeting 2019; March 29-April 3, 2019; Atlanta, GA. American Association for Cancer Research, 2019. http://dx.doi.org/10.1158/1538-7445.am2019-1484.

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Peck, Kayla, Robert Stedtfeld, Jordan RoseFigura, Brett Reed, Drew McUsic, Jon Irish, Brett Etchebarne, Timothy Johnson, Laurie Kurihara, and Vladimir Makarov. "Abstract 1484: Microbial sequencing using a single-pool target enrichment of multiple variable regions of the 16S rRNA gene, the nuclear ribosomal internal transcribed spacer (ITS) region, and antimicrobial resistance genes." In Proceedings: AACR Annual Meeting 2019; March 29-April 3, 2019; Atlanta, GA. American Association for Cancer Research, 2019. http://dx.doi.org/10.1158/1538-7445.sabcs18-1484.

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