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were found to be underrepresented or even missing in taxonomic profiles when using unsuitable primer combinations, outdated reference databases, or inadequate pipeline settings.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 +7 more
doaj +4 more sources
Species identification and profiling of complex microbial communities using shotgun Illumina sequencing of 16S rRNA amplicon sequences. [PDF]
PLoS ONE, 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
Swee Hoe Ong +7 more
doaj +18 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 +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 +14 more
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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 +6 more
doaj +4 more sources
Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system [PDF]
PeerJ, 2016 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.
Patrick D. Schloss +4 more
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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 +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 +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 +7 more
doaj +3 more sources
Diagnostic Yield and Impact on Antimicrobial Management of 16S rRNA Testing of Clinical Specimens
Microbiology Spectrum, 2022 16S rRNA gene sequencing is increasingly used in clinical practice for bacterial identification of clinical specimens. However, studies on its applicability to direct clinical specimens are limited. Here, we studied the diagnostic yield and impact of 16S
Pruke Eamsakulrat +2 more
doaj +1 more source