New Screening Software Shows that Most Recent Large 16S rRNA Gene Clone Libraries Contain Chimeras

By K. Ashelford, N. Chuzhanova, J. Fry, Antonia J. Jones, A. Weightman. Applied and Environmental Microbiology, 2006

721 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/1cc130b505085112f38dde31c850ecf97fc5c9ec

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Citations in the corpus

Drivers of bacterial β-diversity depend on spatial scale (2011, methodology): “Next, we passed the GreenGenes aligned sequence batches through three detection programs: Bellerophon (40), available through the GreenGenes server, Mallard (41), and Chimera_Check v2.”
Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi (2015, neutral): “For nSSU sequences, the proportion of chimeric sequences can be extensive (Ashelford et al. 2005; Ashelford et al. 2006; Fonseca et al. 2012; Haas et al. 2011; Wang and Wang 1997) leading to ‘false diversity estimates and false novel taxa.”
Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. (2011, background): “Individual sequence libraries vary greatly in sequence quality and contain few to more than 45% chimeric sequences (Ashelford et al. 2005; Ashelford et al. 2006 ;Huber et al. 2004; Quince et al. 2009).”
Microbial community profiling for human microbiome projects: Tools, techniques, and challenges. (2009, background): “Chimeras can be detected in small 16S rRNA data sets using several techniques (Huber et al. 2004; Ashelford et al. 2006), although no solution yet exists for the large data sets produced by pyrosequencing.”
Prokaryotic Populations and Activities in an Interbedded Coal Deposit, Including a Previously Deeply Buried Section (1.6–2.3 km) Above ∼ 150 Ma Basement Rock (2009, methodology): “Clone libraries were constructed, screened and analysed (Webster et al. 2006) and chimeras were removed when detected (Ashelford et al. 2006).”
Comparison of free-living, suspended particle, and aggregate-associated bacterial and archaeal communities in the Laptev Sea (2009, methodology): “Sequences were checked for chimeras using the Bellepheron tool supplied as part of the Greengenes database (http:// greengenes.lbl.gov; DeSantis et al. 2006) and crosschecked using the Mallard program (www.bioinformatics-toolkit.org/Mallard/index.html; Ashelford et al. 2006).”
The Ribosomal Database Project: improved alignments and new tools for rRNA analysis (2008, background): “Infernal also correctly aligns some known problem sequences that have been reported with the RNAcad-based RDP 9 alignment of a small number of short partial sequences (6).”
High-throughput clone library analysis of the mucosa-associated microbiota reveals dysbiosis and differences between inflamed and non-inflamed regions of the intestine in inflammatory bowel disease (2011, methodology): “Sequences were tested for chimeras with Mallard [79], Bellerophon at Greengenes [77] and Pintail [80] and any that appeared to be chimeric were removed.”
Towards the human intestinal microbiota phylogenetic core. (2009, methodology): “Chimera check was performed using MALLARD software (Ashelford et al., 2006).”
Salmonella enterica Serovar Typhimurium Exploits Inflammation to Compete with the Intestinal Microbiota (2007, methodology): “Contigs were built from each three-primer set of sequences using the GAP4 software package [51] and converted to ‘‘sense’’ orientation using OrientationChecker software [52].”
A Guide to the Natural History of Freshwater Lake Bacteria (2011, methodology): “Sequences that were thought to be chimeras (checked with the software program Mallard [10]) or those that contained many ( 10) ambiguous bases were removed from the database.”
Diversity of rock varnish bacterial communities from Black Canyon, New Mexico (2010, positive): “…was submitted to the CHIMERA_ CHECK program of the Ribosomal Database Project (RDP) [Maidak et al., 2001] (http://rdp.cme.msu.edu/) or to the Mallard program (http://www.bioinformatics‐toolkit. org/Mallard/index.html [Ashelford et al., 2006]) to detect the presence of possible chimeric artifacts.”
The Pervasive Effects of an Antibiotic on the Human Gut Microbiota, as Revealed by Deep 16S rRNA Sequencing (2008, methodology): “Of 203 V3 RefDB sequences matching V3_Clostridiales_refOTU_2, 29 were excluded from the analysis as suspected chimeras due to one or more of the following: failure to align with the RDP automated aligner, being marked as ‘‘suspect: in the RDP database, or being flagged by Mallard [92] as a likely ch”
A microbiotic survey of lichen-associated bacteria reveals a new lineage from the Rhizobiales (2009, methodology): “Cloned 16S rRNA gene sequences derived from amplicon pools produced using primer combination 533F/1185aR were aligned to one another in a separate file as previously described and checked for chimeras using Mallard (Ashelford et al., 2006).”