Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis
Nature Communications, 2019 The 16S rRNA gene has been a mainstay of sequence-based bacterial analysis for decades. However, high-throughput sequencing of the full gene has only recently become a realistic prospect.
Jethro S. Johnson +11 more
semanticscholar +1 more source
Comparing bioinformatic pipelines for microbial 16S rRNA amplicon sequencing
PLoS ONE, 2020 Microbial amplicon sequencing studies are an important tool in biological and biomedical research. Widespread 16S rRNA gene microbial surveys have shed light on the structure of many ecosystems inhabited by bacteria, including the human body.
A. Prodan +5 more
semanticscholar +1 more source
Crinoid phylogeny: a preliminary analysis (Echinodermata: Crinoidea) [PDF]
, 2004 We describe the first molecular and morphological analysis of extant crinoid high-level inter-relationships. Nuclear and mitochondrial gene sequences and a cladistically coded matrix of 30 morphological characters are presented, and analysed by ...
Ameziane, N. +3 more
core +2 more sources
Conservative fragments in bacterial 16S rRNA genes and primer design for 16S ribosomal DNA amplicons in metagenomic studies. [PDF]
PLoS ONE, 2009 Bacterial 16S ribosomal DNA (rDNA) amplicons have been widely used in the classification of uncultured bacteria inhabiting environmental niches. Primers targeting conservative regions of the rDNAs are used to generate amplicons of variant regions that ...
Yong Wang, Pei-Yuan Qian
doaj +1 more source
Comparison of five assays for DNA extraction from bacterial cells in human faecal samples [PDF]
, 2020 Aim To determine the most effective DNA extraction method for bacteria in faecal samples. Materials and Results This study assessed five commercial methods, that is, NucliSens easyMag, QIAamp DNA Stool Mini kit, PureLink Microbiome DNA purification kit ...
Glorieux, Griet +3 more
core +1 more source
Mitochondrial DNA. Part B. Resources, 2018 Microhyla ornata, a species originally described from the southwest coast of India in 1841, was long reported to be wide-ranging throughout South, Southeast, and East Asia. Although the name M.
Sonali Garg +3 more
doaj +1 more source
OTU analysis using metagenomic shotgun sequencing data. [PDF]
PLoS ONE, 2012 Because of technological limitations, the primer and amplification biases in targeted sequencing of 16S rRNA genes have veiled the true microbial diversity underlying environmental samples. However, the protocol of metagenomic shotgun sequencing provides
Xiaolin Hao, Ting Chen
doaj +1 more source
Microbial Composition and Diversity of High-demand Street-vended Foods in Ecuador
Journal of Food ProtectionDeveloping countries such as Ecuador carry a heavy food safety burden but reports on the microbiological quality of their foods are scarce. In this investigation, the microbial diversity of 10 high-risk and mass-consumption street-vended foods including ...
Byron Díaz Cárdenas +6 more
doaj +1 more source
DNA sequence evidence for speciation, paraphyly and a Mesozoic dispersal of cancellothyridid articulate brachiopods [PDF]
, 2002 Because the classification of extant and fossil articulate brachiopods is based largely upon shell characters observable in fossils, it identifies morphotaxa whose biological status can, in practice, best be inferred from estimates of genetic divergence.
Cohen, B.L., Luter, C.
core +1 more source
16S classifier: a tool for fast and accurate taxonomic classification of 16S rRNA hypervariable regions in metagenomic datasets. [PDF]
PLoS ONE, 2015 The diversity of microbial species in a metagenomic study is commonly assessed using 16S rRNA gene sequencing. With the rapid developments in genome sequencing technologies, the focus has shifted towards the sequencing of hypervariable regions of 16S ...
Nikhil Chaudhary +4 more
doaj +1 more source