Results 11 to 20 of about 245,723 (333)

Primer, Pipelines, Parameters: Issues in 16S rRNA Gene Sequencing [PDF]

mSphere, 2021
In 16S rRNA gene sequencing, certain bacterial genera were found to be underrepresented or even missing in taxonomic profiles when using unsuitable primer combinations, outdated reference databases, or inadequate pipeline settings.
Isabel Abellan-Schneyder, Monica S. Matchado, Sandra Reitmeier, Alina Sommer, Zeno Sewald, Jan Baumbach, Markus List, Klaus Neuhaus   +7 more
doaj   +4 more sources

metaSPARSim: a 16S rRNA gene sequencing count data simulator [PDF]

BMC Bioinformatics, 2019
Background In the last few years, 16S rRNA gene sequencing (16S rDNA-seq) has seen a surprisingly rapid increase in election rate as a methodology to perform microbial community studies.
Ilaria Patuzzi, Giacomo Baruzzo, Carmen Losasso, Antonia Ricci, Barbara Di Camillo   +4 more
doaj   +3 more sources

De novo species identification using 16S rRNA gene nanopore sequencing [PDF]

PeerJ, 2020
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 ...
Inga Leena Angell, Morten Nilsen, Karin C. Lødrup Carlsen, Kai-Håkon Carlsen, Gunilla Hedlin, Christine M. Jonassen, Benjamin Marsland, Björn Nordlund, Eva Maria Rehbinder, Carina Saunders, Håvard Ove Skjerven, Anne Cathrine Staff, Cilla Söderhäll, Riyas Vettukattil, Knut Rudi   +14 more
doaj   +8 more sources

Application of 16S rRNA gene sequencing in Helicobacter pylori detection [PDF]

PeerJ, 2020
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 ...
Aleksander Szymczak, Stanisław Ferenc, Joanna Majewska, Paulina Miernikiewicz, Jan Gnus, Wojciech Witkiewicz, Krystyna Dąbrowska   +6 more
doaj   +4 more sources

Phylogenetic inference of Coxiella burnetii by 16S rRNA gene sequencing. [PDF]

PLoS ONE, 2017
Coxiella burnetii is a human pathogen that causes the serious zoonotic disease Q fever. It is ubiquitous in the environment and due to its wide host range, long-range dispersal potential and classification as a bioterrorism agent, this microorganism is ...
Heather P McLaughlin, Blake Cherney, Janetta R Hakovirta, Rachael A Priestley, Andrew Conley, Andrew Carter, David Hodge, Segaran P Pillai, Linda M Weigel, Gilbert J Kersh, David Sue   +10 more
doaj   +4 more sources

MinION™ Nanopore Sequencing of Skin Microbiome 16S and 16S-23S rRNA Gene Amplicons [PDF]

Frontiers in Cellular and Infection Microbiology, 2022
Human skin microbiome dysbiosis can have clinical consequences. Characterizing taxonomic composition of bacterial communities associated with skin disorders is important for dermatological advancement in both diagnosis and novel treatments.
Miquel Rozas, Miquel Rozas, François Brillet, Chris Callewaert, Bernhard Paetzold   +4 more
doaj   +4 more sources

Controlling for Contaminants in Low-Biomass 16S rRNA Gene Sequencing Experiments

mSystems, 2019
Microbial communities are commonly studied using culture-independent methods, such as 16S rRNA gene sequencing. However, one challenge in accurately characterizing microbial communities is exogenous bacterial DNA contamination, particularly in low ...
Lisa Karstens, Mark Asquith, Sean Davin, Damien Fair, W. Thomas Gregory, Alan J. Wolfe, Jonathan Braun, Shannon McWeeney   +7 more
doaj   +3 more sources

Catheter-Related Microbacterium Bacteremia Identified by 16S rRNA Gene Sequencing [PDF]

Journal of Clinical Microbiology, 2002
ABSTRACT We describe the application of 16S rRNA gene sequencing in defining two cases of catheter-related Microbacterium bacteremia. In the first case, a gram-positive bacillus was isolated from both the blood culture and central catheter tip of a 39-year-old woman with chronic myeloid leukemia.
Susanna K. P. Lau, Patrick C. Y. Woo, Gibson K. S. Woo, Kwok‐Yung Yuen   +3 more
openalex   +5 more sources

Virtual metagenome reconstruction from 16S rRNA gene sequences [PDF]

Nature Communications, 2012
Microbial ecologists have investigated roles of species richness and diversity in a wide variety of ecosystems. Recently, metagenomics have been developed to measure functions in ecosystems, but this approach is cost-intensive. Here we describe a novel method for the rapid and efficient reconstruction of a virtual metagenome in environmental microbial ...
Shujiro, Okuda, Yuki, Tsuchiya, Chiho, Kiriyama, Masumi, Itoh, Hisao, Morisaki   +4 more
openaire   +2 more sources

Benchmarking of 16S rRNA gene databases using known strain sequences [PDF]

Bioinformation, 2021
16S rRNA gene analysis is the most convenient and robust method for microbiome studies. Inaccurate taxonomic assignment of bacterial strains could have deleterious effects as all downstream analyses rely heavily on the accurate assessment of microbial taxonomy.
Dixit, Kunal, Davray, Dimple, Chaudhari, Diptaraj, Kadam, Pratik, Kshirsagar, Rudresh, Shouche, Yogesh, Dhotre, Dhiraj, Saroj, Sunil D   +7 more
openaire   +2 more sources