Microbiome, 2020 Background High-throughput sequencing of bacterial 16S rRNA gene (16S-seq) is a useful and common method for studying bacterial community structures. However, contamination of the 16S rRNA genes from the mitochondrion and plastid hinders the sensitive ...
Luyang Song, Kabin Xie
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Primer selection impacts specific population abundances but not community dynamics in a monthly time-series 16S rRNA gene amplicon analysis of coastal marine bacterioplankton. [PDF]
, 2018 Primers targeting the 16S small subunit ribosomal RNA marker gene, used to characterize bacterial and archaeal communities, have recently been re-evaluated for marine planktonic habitats.
Carlson, Craig A +3 more
core +1 more source
Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons.
Genome Research, 2011 Bacterial diversity among environmental samples is commonly assessed with PCR-amplified 16S rRNA gene (16S) sequences. Perceived diversity, however, can be influenced by sample preparation, primer selection, and formation of chimeric 16S amplification ...
B. Haas +14 more
semanticscholar +1 more source
Reconciliation between operational taxonomic units and species boundaries [PDF]
, 2017 The development of high-throughput sequencing technologies has revolutionised the field of microbial ecology via 16S rRNA gene amplicon sequencing approaches.
Boon, Nico +7 more
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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
Increased variability of microbial communities in restored salt marshes nearly 30 years after tidal flow restoration [PDF]
, 2012 We analyzed microbial diversity and community composition from four salt marsh sites that were impounded for 40–50 years and subsequently restored and four unimpounded sites in southeastern Connecticut over one growing season.
Bernhard, Anne E +2 more
core +3 more sources
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
Nitrogen removal in a two-chambered microbial fuel cell: Establishment of a nitrifying-denitrifying microbial community on an intermittent aerated cathode [PDF]
, 2016 A microbial fuel cell (MFC) was used to study nitrogen dynamics and its feasibility for high strength wastewater treatment. Intermittent aeration was applied on the cathode chamber accomplishing the establishment of a simultaneous nitrifying-denitrifying
Bonmatí Blasi, August +3 more
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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
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Anoxic nitrification in marine sediments [PDF]
, 2004 Nitrate peaks are found in pore-water profiles in marine sediments at depths considerably below the conventional zone of oxic nitrification. These have been interpreted to represent nonsteady- state effects produced by the activity of nitrifying ...
Anschutz, P. +8 more
core +1 more source