Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

By J. Gregory Caporaso, C. Lauber, William Walters, Donna berg-Lyons, Catherine A. Lozupone, Peter J. Turnbaugh, Noah Fierer, Rob Knight. Proceedings of the National Academy of Sciences of the United States of America, 2010

8,898 citations recorded by the source corpus.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/4dc5a37d61e7dbd4d3d55f8679209e022ea09473

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Citations in the corpus

The effect of captivity on the cutaneous bacterial community of the critically endangered Panamanian golden frog (Atelopus zeteki) (2014, methodology): “Sequence data were assembled with Fastq-join (https://www. code.google.com/p/ea-utils/wiki/FastqJoin) with default parameters and processed with the Quantitative Insights Into Microbial Ecology pipeline (QIIME v. 1.7.0; Caporaso et al., 2010a).”
Examining the global distribution of dominant archaeal populations in soil (2011, methodology): “Sequence processing, assigning taxonomic identity, abundance and phylogeny Before analyses, raw sequence data generated from the 454-sequencing runs were processed using QIIME (Caporaso et al., 2010).”
PEAR: a fast and accurate Illumina Paired-End reAd mergeR (2013, positive): “…from whole-genome sequencing (Liu et al. , 2012; Wang et al. , 2010) to profiling microbial communities by sequencing the hypervariable regions of the 16S ribosomal RNA (rRNA) gene (Bartram et al. , 2011; Caporaso et al. , 2011; Degnan and Ochman, 2012; Rodrigue et al. , 2010; Zhou et al. , 2011).”
Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms (2012, background): “Interest in amplicon sequencing on Illumina is growing (Bartram et al., 2011; Caporaso et al., 2011; Zhou et al., 2011), largely due to lower cost per sequence than other platforms, enabling highthroughput microbial ecology at the greatest coverage yet possible.”
Removing Noise From Pyrosequenced Amplicons (2011, background): “These principles will be equally applicable to other pyrosequencing platforms, for example the Illumina HiSeq 2000 which is capable of generating orders of magnitude more reads per run [27,28].”
Long-term and legacy effects of manure application on soil microbial community composition (2018, methodology): “Briefly, for the first PCR reaction, the V4 hypervariable region of the prokaryotic (bacterial and archaeal) 16S rRNA gene was amplified using the primer set 515F ( G TG CCAGCMGCCGCGG TAA ) a n d 8 0 6 R (GGACTACHVGGGTWTCTAAT) (Caporaso et al. 2011), and the internal transcribed spacer region 1 (ITS”
Soil microbiomes with distinct assemblies through vertical soil profiles drive the cycling of multiple nutrients in reforested ecosystems (2018, methodology): “The acquired sequences were filtered for quality according to previous work [74], and any chimeric sequences were removed with the USEARCH tool based on the UCHIME algorithm [75].”
Plant diversity represents the prevalent determinant of soil fungal community structure across temperate grasslands in northern China (2017, background): “The OTUs containing less than five reads were eliminated to reduce the risk of artificially inflating richness due to sequencing errors (Caporaso et al., 2011).”
EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data (2011, methodology): “Like other methods that use next generation sequencing technologies [3-5], the method also removes potential cloning bias introduced with Sanger sequencing.”