Generation of Multimillion-Sequence 16S rRNA Gene Libraries from Complex Microbial Communities by Assembling Paired-End Illumina Reads

By Andrea K. Bartram, M. Lynch, J. Stearns, Gabriel Moreno-Hagelsieb, Josh D. Neufeld. Applied and Environmental Microbiology, 2011

754 citations recorded by the source corpus.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/11829e868afba3c6cc0ce24b88b81faa2dae463c

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Citations in the corpus

PANDAseq: paired-end assembler for illumina sequences (2012, methodology): “Next-generation sequencing platforms, such as Illumina, are now adapted for the generation of multi-million-member sequence libraries for sample comparisons [1-4].”
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).”
Methods for Analyzing Diversity of Microbial Communities in Natural Environments (2013, background): “…and Illumina-based sequencing, the possibility of discovering new groups of microorganism in complex environmental systems without cultivated strains has been accrued and these real-time sequencing techniques are shedding light into the complexities of microbial populations (Bartram et al., 2011).”
Culture-independent molecular tools for soil and rhizosphere microbiology (2013, background): “demonstrated a low cost access to DNA from organisms with low relative abundances [169].”
Mesocosm Experiments as a Tool for Ecological Climate-Change Research (2013, background): “…would a more useful measure of functional diversity, and recent advances in microbial molecular ecology, such as the in situ application of metagenomics and metatranscriptomics in mesocosm experiments, could provide key new insights here (Bartram et al., 2011; He et al., 2010; Purdy et al., 2010).”
What drives study‐dependent differences in distance–decay relationships of microbial communities? (2021, methodology): “…methods [e.g., denaturing gradient gel electrophoresis (DGGE), terminal restriction fragment length polymorphism (TRFLP) or phospholipid fatty acid (PLFA) analysis] are limited in their ability to detect rare taxa (Bartram et al., 2011) and often miss them completely (Low- Décarie et al., 2016).”
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.”
Computational meta'omics for microbial community studies (2013, methodology): “The Illumina platform is currently preferred for meta’omic sequencing, and is also supplanting the Roche 454 platform widely used in microbial community analysis for rRNA gene surveys (Bartram et al , 2011; Caporaso et al , 2012).”