Results 1 to 10 of about 505,000 (387)

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were found to be underrepresented or even missing in taxonomic profiles when using unsuitable primer combinations, outdated reference databases, or inadequate pipeline settings.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   +5 more sources

Phylogenies of the 16S rRNA gene and its hypervariable regions lack concordance with core genome phylogenies

Microbiome, 2022
Background The 16S rRNA gene is used extensively in bacterial phylogenetics, in species delineation, and now widely in microbiome studies. However, the gene suffers from intragenomic heterogeneity, and reports of recombination and an unreliable ...
Hayley B. Hassler, Brett Probert, Carson Moore, Elizabeth Lawson, Richard W. Jackson, Brook T. Russell, Vincent P. Richards   +6 more
doaj   +2 more sources

Defining reference sequences for Nocardia species by similarity and clustering analyses of 16S rRNA gene sequence data. [PDF]

PLoS ONE, 2011
BACKGROUND: The intra- and inter-species genetic diversity of bacteria and the absence of 'reference', or the most representative, sequences of individual species present a significant challenge for sequence-based identification.
Manal Helal, Fanrong Kong, Sharon C A Chen, Michael Bain, Richard Christen, Vitali Sintchenko   +5 more
doaj   +3 more sources

Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets

Microbiome, 2020
Background The low cost of 16S rRNA gene sequencing facilitates population-scale molecular epidemiological studies. Existing computational algorithms can resolve 16S rRNA gene sequences into high-resolution amplicon sequence variants (ASVs), which ...
Isabel F. Escapa, Yanmei Huang, Tsute Chen, Maoxuan Lin, Alexis Kokaras, Floyd E. Dewhirst, Katherine P. Lemon   +6 more
doaj   +2 more sources

The Variability of the 16S rRNA Gene in Bacterial Genomes and Its Consequences for Bacterial Community Analyses

PLoS ONE, 2013
16S ribosomal RNA currently represents the most important target of study in bacterial ecology. Its use for the description of bacterial diversity is, however, limited by the presence of variable copy numbers in bacterial genomes and sequence variation ...
Tomáš Větrovský, Petr Baldrián
openalex   +3 more sources

Do we need a standardized 16S rRNA gene amplicon sequencing analysis protocol for poultry microbiota research? [PDF]

Poultry Science
Bacteria are the major component of poultry gastrointestinal tract (GIT) microbiota and play an important role in host health, nutrition, physiology regulation, intestinal development, and growth.
Joshua M. Lyte, Mitiku M. Seyoum, Diana Ayala, Jannigje G. Kers, Valentina Caputi, Timothy Johnson, Li Zhang, Joshua Rehberger, Guolong Zhang, Sami Dridi, Brett Hale, Jean E. De Oliveira, Daniel Grum, Alexandra H. Smith, Michael Kogut, Steven C. Ricke, Anne Ballou, Bill Potter, Monika Proszkowiec-Weglarz   +18 more
doaj   +2 more sources

A comparison of 16S rRNA-gene and 16S rRNA-transcript derived microbial communities in bulk and rhizosphere soils [PDF]

Frontiers in Microbiology
Root exudates in a plant’s rhizosphere alters microbial community membership and activity, which can in turn alter a plant’s health and fitness. In this study we characterized bacterial community composition, using 16S rRNA-gene (DNA) sequencing to ...
Alessandra Ceretto, Alessandra Ceretto, Cynthia Weinig, Cynthia Weinig, Cynthia Weinig   +4 more
doaj   +2 more sources

Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences

Nature Reviews Microbiology, 2014
Pablo Yarza, Pelİn Yilmaz, Elmar Pruesse   +2 more
exaly   +2 more sources

Impact of 16S rRNA Gene Sequence Analysis for Identification of Bacteria on Clinical Microbiology and Infectious Diseases [PDF]

Clinical Microbiology Reviews, 2004
Jill E. Clarridge
openalex   +2 more sources

Species Identification and Profiling of Complex Microbial Communities Using Shotgun Illumina Sequencing of 16S rRNA Amplicon Sequences [PDF]

, 2013
The high throughput and cost-effectiveness afforded by short-read sequencing technologies, in principle, enable researchers to perform 16S rRNA profiling of complex microbial communities at unprecedented depth and resolution. Existing Illumina sequencing
Hibberd, Martin Lloyd, Ho, Eliza Xin Pei, Kukkillaya, Vinutha Uppoor, Lay, Christophe, Low, Louie, Nagarajan, Niranjan, Ong, Swee Hoe, Wilm, Andreas   +7 more
core   +13 more sources