Experimental factors affecting PCR-based estimates of microbial species richness and evenness

By A. Engelbrektson, Victor Kunin, K. Wrighton, Natasha Zvenigorodsky, F. Chen, Howard Ochman, Philip Hugenholtz. The ISME Journal, 2010

618 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/46df8937fb44797ee83df3a826f631cce63e1ab8

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Citations in the corpus

• EMIRGE: reconstruction of full-length ribosomal genes from microbial community short read sequencing data (2011, background): “As it is described here, EMIRGE does not suffer from potential primer bias introduced by so-called ‘universal’ primers [16], allowing for discovery of novel species that may not have canonical primer binding sites [18].”
• Spatial patterns of bacterial richness and evenness in the NW Mediterranean Sea explored by pyrosequencing of the 16S rRNA (2010, background): “…to marine samples a handful of times (Sogin et al. 2006, Huber et al. 2007, Galand et al. 2009, Gilbert et al. 2009, Kirchman et al. 2010), to the microbiota of humans (Claesson et al. 2009), termites (Engelbrektson et al. 2010), soils (Youssef & Elshahed 2009), and lakes (Xing et al. 2009).”
• Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions (2010, neutral): “Although it was recently shown that amplicon length somewhat affected phylotype richness when comparing pyrosequencing reads of the V1–V2 and V8 regions of microbiota from the termite hindgut, the choice of region had a much larger impact on diversity values such as community richness and evenness (”
• Quantification of ammonia oxidation rates and ammonia‐oxidizing archaea and bacteria at high resolution in the Gulf of California and eastern tropical North Pacific Ocean (2012, methodology): “We used the Bacteria-specific primers 27F (59-GAGTTTGATCNTGGCTCAG-39) and 519R (59-GWNTTACNGCGGCKGCTG-39) (Engelbrektson et al. 2010) mod-”
• New primers to amplify the fungal ITS2 region--evaluation by 454-sequencing of artificial and natural communities. (2012, background): “Unexpectedly large effects of mismatches far from the 3′ end have previously been observed during amplification of SSU markers from bacterial communities (Engelbrektson et al., 2010).”
• Influence of corn, switchgrass, and prairie cropping systems on soil microbial communities in the upper Midwest of the United States (2016, methodology): “Sequencing tags were analyzed using the software tool PYROTAGGER (Kunin & Hugenholtz, 2010) using a 180 bp sequence length threshold as described in Engelbrektson et al. (2010).”
• A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: application for characterizing coral reef fish gut contents (2013, background): “, < 400 bp) to maximize richness estimates [15,16] and increase the probability of recovering DNA templates that are more degraded (sheared), such as samples preserved for extended periods of time [17] or prey items in the gut and faecal contents of predators [18,19].”
• The gut microbiota of insects - diversity in structure and function. (2013, background): “These factors can have major effects on community profiles detected in samples (Engelbrektson et al., 2010).”
• Ecology and exploration of the rare biosphere (2015, background): “PCR introduces amplification biases 121 , which obscure the representation of microorganisms in the environment 122 , 123 .”
• A preliminary survey of lichen associated eukaryotes using pyrosequencing (2011, background): “2010), which may be attributable to overestimation by our pyrosequencing approach (Engelbrektson et al .”