metabarcodingtextbook1.bib

@article{Bellemain2010,
  title = {{{ITS}} as an Environmental {{DNA}} Barcode for Fungi: An in Silico Approach Reveals Potential {{PCR}} Biases},
  shorttitle = {{{ITS}} as an Environmental {{DNA}} Barcode for Fungi},
  author = {Bellemain, Eva and Carlsen, Tor and Brochmann, Christian and Coissac, Eric and Taberlet, Pierre and Kauserud, H{\aa}vard},
  year = {2010},
  month = jul,
  volume = {10},
  pages = {189},
  issn = {1471-2180},
  doi = {10.1186/1471-2180-10-189},
  abstract = {During the last 15 years the internal transcribed spacer (ITS) of nuclear DNA has been used as a target for analyzing fungal diversity in environmental samples, and has recently been selected as the standard marker for fungal DNA barcoding. In this study we explored the potential amplification biases that various commonly utilized ITS primers might introduce during amplification of different parts of the ITS region in samples containing mixed templates ('environmental barcoding'). We performed in silico PCR analyses with commonly used primer combinations using various ITS datasets obtained from public databases as templates.},
  file = {C\:\\Users\\shimotsuki\\Dropbox\\PDF\\Primer design\\Bellemain et al_BMC Microbiology_2010_ITS as an environmental DNA barcode for fungi.pdf;C\:\\Users\\shimotsuki\\Zotero\\storage\\3QZ95YNW\\1471-2180-10-189.html},
  journal = {BMC Microbiology}
}

@article{DeWit2012,
  title = {The Simple Fool's Guide to Population Genomics via {{RNA}}-{{Seq}}: An Introduction to High-Throughput Sequencing Data Analysis},
  shorttitle = {The Simple Fool's Guide to Population Genomics via {{RNA}}-{{Seq}}},
  author = {De Wit, Pierre and Pespeni, Melissa H. and Ladner, Jason T. and Barshis, Daniel J. and Seneca, Fran{\c c}ois and Jaris, Hannah and Therkildsen, Nina Overgaard and Morikawa, Megan and Palumbi, Stephen R.},
  year = {2012},
  volume = {12},
  pages = {1058--1067},
  issn = {1755-0998},
  doi = {10.1111/1755-0998.12003},
  abstract = {High-throughput sequencing technologies are currently revolutionizing the field of biology and medicine, yet bioinformatic challenges in analysing very large data sets have slowed the adoption of these technologies by the community of population biologists. We introduce the `Simple Fool's Guide to Population Genomics via RNA-seq' (SFG), a document intended to serve as an easy-to-follow protocol, walking a user through one example of high-throughput sequencing data analysis of nonmodel organisms. It is by no means an exhaustive protocol, but rather serves as an introduction to the bioinformatic methods used in population genomics, enabling a user to gain familiarity with basic analysis steps. The SFG consists of two parts. This document summarizes the steps needed and lays out the basic themes for each and a simple approach to follow. The second document is the full SFG, publicly available at http://sfg.stanford.edu, that includes detailed protocols for data processing and analysis, along with a repository of custom-made scripts and sample files. Steps included in the SFG range from tissue collection to de novo assembly, blast annotation, alignment, gene expression, functional enrichment, SNP detection, principal components and FST outlier analyses. Although the technical aspects of population genomics are changing very quickly, our hope is that this document will help population biologists with little to no background in high-throughput sequencing and bioinformatics to more quickly adopt these new techniques.},
  copyright = {\textcopyright{} 2012 Blackwell Publishing Ltd},
  file = {C\:\\Users\\shimotsuki\\Dropbox\\PDF\\Protocols\\Wit et al_Molecular Ecology Resources_2012_The simple fool's guide to population genomics via RNA-Seq.pdf;C\:\\Users\\shimotsuki\\Zotero\\storage\\P2TITMMA\\1755-0998.html},
  journal = {Molecular Ecology Resources},
  keywords = {bioinformatics,de novo assembly,gene expression,population genomics,RNA-Seq,SNP detection},
  language = {en},
  number = {6}
}

@article{Filges2019,
  title = {Impact of {{Polymerase Fidelity}} on {{Background Error Rates}} in {{Next}}-{{Generation Sequencing}} with {{Unique Molecular Identifiers}}/{{Barcodes}}},
  author = {Filges, Stefan and Yamada, Emiko and St{\aa}hlberg, Anders and Godfrey, Tony E.},
  year = {2019},
  month = mar,
  volume = {9},
  pages = {1--7},
  issn = {2045-2322},
  doi = {10.1038/s41598-019-39762-6},
  abstract = {Liquid biopsy and detection of tumor-associated mutations in cell-free circulating DNA often requires the ability to identify single nucleotide variants at allele frequencies below 0.1\%. Standard sequencing protocols cannot achieve this level of sensitivity due to background noise from DNA damage and polymerase induced errors. Addition of unique molecular identifiers allows identification and removal of errors responsible for this background noise. Theoretically, high fidelity enzymes will also reduce error rates in barcoded NGS but this has not been thoroughly explored. We evaluated the impact of polymerase fidelity on the magnitude of error reduction at different steps of barcoded NGS library construction. We find that barcoding itself displays largest impact on error reduction, even with low fidelity polymerases. Use of high fidelity polymerases in the barcoding step of library construction further suppresses error in barcoded NGS, and allows detection of variant alleles below 0.1\% allele frequency. However, the improvement in error correction is modest and is not directly proportional to polymerase fidelity. Depending on the specific application, other polymerase characteristics such as multiplexing capacity, PCR efficiency, buffer requirements and ability to amplify targets with high GC content may outweigh the relatively small additional decrease in error afforded by ultra-high fidelity polymerases.},
  copyright = {2019 The Author(s)},
  file = {C\:\\Users\\shimotsuki\\Dropbox\\PDF\\MetabarcodingTextbook1\\Filges et al_Sci Rep_2019_Impact of Polymerase Fidelity on Background Error Rates in Next-Generation.pdf},
  journal = {Scientific Reports},
  language = {en},
  number = {1}
}

@article{Golebiewski2020,
  title = {Generating Amplicon Reads for Microbial Community Assessment with Next-Generation Sequencing},
  author = {Go{\l}{\k{e}}biewski, M. and Tretyn, A.},
  year = {2020},
  volume = {128},
  pages = {330--354},
  issn = {1365-2672},
  doi = {10.1111/jam.14380},
  abstract = {Marker gene amplicon sequencing is often preferred over whole genome sequencing for microbial community characterization, due to its lower cost while still enabling assessment of uncultivable organisms. This technique involves many experimental steps, each of which can be a source of errors and bias. We present an up-to-date overview of the whole experimental pipeline, from sampling to sequencing reads, and give information allowing for informed choices at each step of both planning and execution of a microbial community assessment study. When applicable, we also suggest ways of avoiding inherent pitfalls in amplicon sequencing.},
  copyright = {\textcopyright{} 2019 The Society for Applied Microbiology},
  file = {C\:\\Users\\shimotsuki\\Dropbox\\PDF\\MetabarcodingTextbook1\\Golebiewski_Tretyn_Journal of Applied Microbiology_2020_Generating amplicon reads for microbial community assessment with.pdf},
  journal = {Journal of Applied Microbiology},
  keywords = {16S rRNA gene,error and bias sources,experimental workflow,marker gene amplicons,microbial community assessment,next-generation sequencing},
  language = {en},
  number = {2}
}

@article{Hallmaier-Wacker2018,
  title = {The Impact of Storage Buffer, {{DNA}} Extraction Method, and Polymerase on Microbial Analysis},
  author = {{Hallmaier-Wacker}, Luisa K. and Lueert, Simone and Roos, Christian and Knauf, Sascha},
  year = {2018},
  month = apr,
  volume = {8},
  pages = {1--9},
  issn = {2045-2322},
  doi = {10.1038/s41598-018-24573-y},
  abstract = {Next-generation sequencing approaches used to characterize microbial communities are subject to technical caveats that can lead to major distortion of acquired data. Determining the optimal sample handling protocol is essential to minimize the bias for different sample types. Using a mock community composed of 22 bacterial strains of even concentration, we studied a combination of handling conditions to determine the optimal conditions for swab material. Examining a combination of effects simulates the reality of handling environmental samples and may thus provide a better foundation for the standardization of protocols. We found that the choice of storage buffer and extraction kit affects the detected bacterial composition, while different 16S rRNA amplification methods only had a minor effect. All bacterial genera present in the mock community were identified with minimal levels of contamination independent of the choice of sample processing. Despite this, the observed bacterial profile for all tested conditions were significantly different from the expected abundance. This highlights the need for proper validation and standardization for each sample type using a mock community and blank control samples, to assess the bias in the protocol and reduce variation across the datasets.},
  copyright = {2018 The Author(s)},
  file = {C\:\\Users\\shimotsuki\\Dropbox\\PDF\\MetabarcodingTextbook1\\Hallmaier-Wacker et al_Sci Rep_2018_The impact of storage buffer, DNA extraction method, and polymerase on.pdf},
  journal = {Scientific Reports},
  language = {en},
  number = {1}
}

@article{Hosomichi2013,
  title = {Phase-Defined Complete Sequencing of the {{HLA}} Genes by next-Generation Sequencing},
  author = {Hosomichi, Kazuyoshi and Jinam, Timothy A. and Mitsunaga, Shigeki and Nakaoka, Hirofumi and Inoue, Ituro},
  year = {2013},
  month = may,
  volume = {14},
  pages = {355},
  issn = {1471-2164},
  doi = {10.1186/1471-2164-14-355},
  abstract = {The human leukocyte antigen (HLA) region, the 3.8-Mb segment of the human genome at 6p21, has been associated with more than 100 different diseases, mostly autoimmune diseases. Due to the complex nature of HLA genes, there are difficulties in elucidating complete HLA gene sequences especially HLA gene haplotype structures by the conventional sequencing method. We propose a novel, accurate, and cost-effective method for generating phase-defined complete sequencing of HLA genes by using indexed multiplex next generation sequencing.},
  file = {C\:\\Users\\shimotsuki\\Dropbox\\PDF\\Protocols\\Hosomichi et al_BMC Genomics_2013_Phase-defined complete sequencing of the HLA genes by next-generation sequencing.pdf;C\:\\Users\\shimotsuki\\Zotero\\storage\\WBV655BG\\1471-2164-14-355.html},
  journal = {BMC Genomics},
  number = {1}
}

@article{Hosomichi2014,
  title = {A {{Bead}}-Based {{Normalization}} for {{Uniform Sequencing}} Depth ({{BeNUS}}) Protocol for Multi-Samples Sequencing Exemplified by {{HLA}}-{{B}}},
  author = {Hosomichi, Kazuyoshi and Mitsunaga, Shigeki and Nagasaki, Hideki and Inoue, Ituro},
  year = {2014},
  month = aug,
  volume = {15},
  pages = {645},
  issn = {1471-2164},
  doi = {10.1186/1471-2164-15-645},
  abstract = {Human leukocyte antigen (HLA) is a group of genes that are extremely polymorphic among individuals and populations and have been associated with more than 100 different diseases and adverse drug effects. HLA typing is accordingly an important tool in clinical application, medical research, and population genetics. We have previously developed a phase-defined HLA gene sequencing method using MiSeq sequencing.},
  file = {C\:\\Users\\shimotsuki\\Dropbox\\PDF\\Protocols\\Hosomichi et al_BMC Genomics_2014_A Bead-based Normalization for Uniform Sequencing depth (BeNUS) protocol for.pdf;C\:\\Users\\shimotsuki\\Zotero\\storage\\52UQIE7T\\1471-2164-15-645.html},
  journal = {BMC Genomics},
  number = {1}
}

@article{Ivanova2006,
  title = {An Inexpensive, Automation-Friendly Protocol for Recovering High-Quality {{DNA}}},
  author = {Ivanova, Natalia V. and Dewaard, Jeremy R. and Hebert, Paul D. N.},
  year = {2006},
  volume = {6},
  pages = {998--1002},
  issn = {1471-8286},
  doi = {10.1111/j.1471-8286.2006.01428.x},
  abstract = {Although commercial kits are available for automated DNA extraction, `artisanal' protocols are not. In this study, we present a silica-based method that is sensitive, inexpensive and compliant with automation. The effectiveness of this protocol has now been tested on more than 5000 animal specimens with highly positive results.},
  file = {C\:\\Users\\shimotsuki\\Dropbox\\PDF\\Protocols\\Ivanova et al_Molecular Ecology Notes_2006_An inexpensive, automation-friendly protocol for recovering high-quality DNA.pdf;C\:\\Users\\shimotsuki\\Zotero\\storage\\BXRLBQ3F\\j.1471-8286.2006.01428.html},
  journal = {Molecular Ecology Notes},
  keywords = {DNA barcoding,DNA extraction,liquid handling,robotics},
  language = {en},
  number = {4}
}

@article{Majaneva2018,
  title = {Environmental {{DNA}} Filtration Techniques Affect Recovered Biodiversity},
  author = {Majaneva, Markus and Diserud, Ola H. and Eagle, Shannon H. C. and Bostr{\"o}m, Erik and Hajibabaei, Mehrdad and Ekrem, Torbj{\o}rn},
  year = {2018},
  month = mar,
  volume = {8},
  pages = {4682},
  issn = {2045-2322},
  doi = {10.1038/s41598-018-23052-8},
  abstract = {Freshwater metazoan biodiversity assessment using environmental DNA (eDNA) captured on filters offers new opportunities for water quality management. Filtering of water in the field is a logistical advantage compared to transport of water to the nearest lab, and thus, appropriate filter preservation becomes crucial for maximum DNA recovery. Here, the effect of four different filter preservation strategies, two filter types, and pre-filtration were evaluated by measuring metazoan diversity and community composition, using eDNA collected from a river and a lake ecosystem. The filters were preserved cold on ice, in ethanol, in lysis buffer and dry in silica gel. Our results show that filters preserved either dry or in lysis buffer give the most consistent community composition. In addition, mixed cellulose ester filters yield more consistent community composition than polyethersulfone filters, while the effect of pre-filtration remained ambiguous. Our study facilitates development of guidelines for aquatic community-level eDNA biomonitoring, and we advocate filtering in the field, using mixed cellulose ester filters and preserving the filters either dry or in lysis buffer.},
  copyright = {2018 The Author(s)},
  file = {C\:\\Users\\shimotsuki\\Dropbox\\PDF\\Protocols\\Majaneva et al_Scientific Reports_2018_Environmental DNA filtration techniques affect recovered biodiversity.pdf;C\:\\Users\\shimotsuki\\Zotero\\storage\\PZWQFYCM\\s41598-018-23052-8.html},
  journal = {Scientific Reports},
  language = {En},
  number = {1}
}

@article{Miya2015,
  title = {{{MiFish}}, a Set of Universal {{PCR}} Primers for Metabarcoding Environmental {{DNA}} from Fishes: Detection of More than 230 Subtropical Marine Species},
  shorttitle = {{{MiFish}}, a Set of Universal {{PCR}} Primers for Metabarcoding Environmental {{DNA}} from Fishes},
  author = {Miya, M. and Sato, Y. and Fukunaga, T. and Sado, T. and Poulsen, J. Y. and Sato, K. and Minamoto, T. and Yamamoto, S. and Yamanaka, H. and Araki, H. and Kondoh, M. and Iwasaki, W.},
  year = {2015},
  month = jul,
  volume = {2},
  pages = {150088},
  issn = {2054-5703},
  doi = {10.1098/rsos.150088},
  abstract = {We developed a set of universal PCR primers (MiFish-U/E) for metabarcoding environmental DNA (eDNA) from fishes. Primers were designed using aligned whole mitochondrial genome (mitogenome) sequences from 880 species, supplemented by partial mitogenome sequences from 160 elasmobranchs (sharks and rays). The primers target a hypervariable region of the 12S rRNA gene (163\textendash{}185 bp), which contains sufficient information to identify fishes to taxonomic family, genus and species except for some closely related congeners. To test versatility of the primers across a diverse range of fishes, we sampled eDNA from four tanks in the Okinawa Churaumi Aquarium with known species compositions, prepared dual-indexed libraries and performed paired-end sequencing of the region using high-throughput next-generation sequencing technologies. Out of the 180 marine fish species contained in the four tanks with reference sequences in a custom database, we detected 168 species (93.3\%) distributed across 59 families and 123 genera. These fishes are not only taxonomically diverse, ranging from sharks and rays to higher teleosts, but are also greatly varied in their ecology, including both pelagic and benthic species living in shallow coastal to deep waters. We also sampled natural seawaters around coral reefs near the aquarium and detected 93 fish species using this approach. Of the 93 species, 64 were not detected in the four aquarium tanks, rendering the total number of species detected to 232 (from 70 families and 152 genera). The metabarcoding approach presented here is non-invasive, more efficient, more cost-effective and more sensitive than the traditional survey methods. It has the potential to serve as an alternative (or complementary) tool for biodiversity monitoring that revolutionizes natural resource management and ecological studies of fish communities on larger spatial and temporal scales.},
  copyright = {. \textcopyright{} 2015 The Authors. Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited.},
  file = {C\:\\Users\\shimotsuki\\Dropbox\\PDF\\2017Kiban\\Miya et al_Royal Society Open Science_2015_MiFish, a set of universal PCR primers for metabarcoding environmental DNA from.pdf;C\:\\Users\\shimotsuki\\Zotero\\storage\\ECXJ7KRH\\150088.html},
  journal = {Royal Society Open Science},
  language = {en},
  number = {7}
}

@article{Miya2016,
  title = {Use of a {{Filter Cartridge}} for {{Filtration}} of {{Water Samples}} and {{Extraction}} of {{Environmental DNA}}},
  author = {Miya, Masaki and Minamoto, Toshifumi and Yamanaka, Hiroki and Oka, Shin-ichiro and Sato, Keiichi and Yamamoto, Satoshi and Sado, Tetsuya and Doi, Hideyuki},
  year = {2016},
  month = nov,
  pages = {e54741},
  issn = {1940-087X},
  doi = {10.3791/54741},
  abstract = {Recent studies demonstrated the use of environmental DNA (eDNA) from fishes to be appropriate as a non-invasive monitoring tool. Most of these studies employed disk fiber filters to collect eDNA from water samples, although a number of microbial studies in aquatic environments have employed filter cartridges, because the cartridge has the advantage of accommodating large water volumes and of overall ease of use. Here we provide a protocol for filtration of water samples using the filter cartridge and extraction of eDNA from the filter without having to cut open the housing. The main portions of this protocol consists of 1) filtration of water samples (water volumes {$\leq$}4 L or {$>$}4 L); (2) extraction of DNA on the filter using a roller shaker placed in a preheated incubator; and (3) purification of DNA using a commercial kit. With the use of this and previously-used protocols, we perform metabarcoding analysis of eDNA taken from a huge aquarium tank (7,500 m3) with known species composition, and show the number of detected species per library from the two protocols as the representative results. This protocol has been developed for metabarcoding eDNA from fishes, but is also applicable to eDNA from other organisms.},
  file = {C\:\\Users\\shimotsuki\\Dropbox\\PDF\\Protocols\\Miya et al_JoVE (Journal of Visualized Experiments)_2016_Use of a Filter Cartridge for Filtration of Water Samples and Extraction of.pdf;C\:\\Users\\shimotsuki\\Zotero\\storage\\IC7CFNCC\\use-filter-cartridge-for-filtration-water-samples-extraction.html},
  journal = {JoVE (Journal of Visualized Experiments)},
  number = {117}
}

@article{Potapov2017,
  title = {Examining {{Sources}} of {{Error}} in {{PCR}} by {{Single}}-{{Molecule Sequencing}}},
  author = {Potapov, Vladimir and Ong, Jennifer L.},
  year = {2017},
  month = jan,
  volume = {12},
  pages = {e0169774},
  issn = {1932-6203},
  doi = {10.1371/journal.pone.0169774},
  abstract = {Next-generation sequencing technology has enabled the detection of rare genetic or somatic mutations and contributed to our understanding of disease progression and evolution. However, many next-generation sequencing technologies first rely on DNA amplification, via the Polymerase Chain Reaction (PCR), as part of sample preparation workflows. Mistakes made during PCR appear in sequencing data and contribute to false mutations that can ultimately confound genetic analysis. In this report, a single-molecule sequencing assay was used to comprehensively catalog the different types of errors introduced during PCR, including polymerase misincorporation, structure-induced template-switching, PCR-mediated recombination and DNA damage. In addition to well-characterized polymerase base substitution errors, other sources of error were found to be equally prevalent. PCR-mediated recombination by Taq polymerase was observed at the single-molecule level, and surprisingly found to occur as frequently as polymerase base substitution errors, suggesting it may be an underappreciated source of error for multiplex amplification reactions. Inverted repeat structural elements in lacZ caused polymerase template-switching between the top and bottom strands during replication and the frequency of these events were measured for different polymerases. For very accurate polymerases, DNA damage introduced during temperature cycling, and not polymerase base substitution errors, appeared to be the major contributor toward mutations occurring in amplification products. In total, we analyzed PCR products at the single-molecule level and present here a more complete picture of the types of mistakes that occur during DNA amplification.},
  file = {C\:\\Users\\shimotsuki\\Dropbox\\PDF\\MetabarcodingTextbook1\\Potapov_Ong_PLOS ONE_2017_Examining Sources of Error in PCR by Single-Molecule Sequencing.pdf;C\:\\Users\\shimotsuki\\Zotero\\storage\\83TP3Y3N\\article.html},
  journal = {PLOS ONE},
  keywords = {DNA damage,DNA polymerase,DNA replication,DNA sequencing,Next-generation sequencing,Polymerase chain reaction,Polymerases,Substitution mutation},
  language = {en},
  number = {1}
}

@article{Rohland2012,
  title = {Cost-Effective, High-Throughput {{DNA}} Sequencing Libraries for Multiplexed Target Capture},
  author = {Rohland, Nadin and Reich, David},
  year = {2012},
  month = jan,
  volume = {22},
  pages = {939--946},
  issn = {1088-9051, 1549-5469},
  doi = {10.1101/gr.128124.111},
  abstract = {Improvements in technology have reduced the cost of DNA sequencing to the point that the limiting factor for many experiments is the time and reagent cost of sample preparation. We present an approach in which 192 sequencing libraries can be produced in a single day of technician time at a cost of about \$15 per sample. These libraries are effective not only for low-pass whole-genome sequencing, but also for simultaneously enriching them in pools of approximately 100 individually barcoded samples for a subset of the genome without substantial loss in efficiency of target capture. We illustrate the power and effectiveness of this approach on about 2000 samples from a prostate cancer study.},
  file = {C\:\\Users\\shimotsuki\\Dropbox\\PDF\\Protocols\\Rohland_Reich_Genome Res._2012_Cost-effective, high-throughput DNA sequencing libraries for multiplexed target.pdf;C\:\\Users\\shimotsuki\\Zotero\\storage\\XWWJLN2P\\939.html},
  journal = {Genome Research},
  language = {en},
  number = {5},
  pmid = {22267522}
}

@misc{Speicher2017,
  title = {Storing Oligos: 7 Things You Should Know},
  author = {Speicher, Nolan},
  year = {2017},
  month = jun,
  url = {https://sg.idtdna.com/pages/education/decoded/article/storing-oligos-7-things-you-should-know},
  urldate = {2019-07-07},
  file = {C\:\\Users\\shimotsuki\\Zotero\\storage\\JKTI5WI3\\storing-oligos-7-things-you-should-know.html}
}

@article{Stevens2013,
  title = {Slowing {{PCR}} Ramp Speed Reduces Chimera Formation from Environmental Samples},
  author = {Stevens, Julia L. and Jackson, Ronneshia L. and Olson, Julie B.},
  year = {2013},
  month = jun,
  volume = {93},
  pages = {203--205},
  issn = {0167-7012},
  doi = {10.1016/j.mimet.2013.03.013},
  abstract = {Chimeric sequences falsely increase the apparent diversity within samples. To examine chimera formation in PCR products from environmental DNA, clone libraries were prepared using different ramp speeds to reach the designated temperatures for each step of the PCR program. Slowing the thermocycler ramp speed to 1\textdegree{}Cs-1 reduced chimera formation.},
  file = {C\:\\Users\\shimotsuki\\Dropbox\\PDF\\Protocols\\Stevens et al_Journal of Microbiological Methods_2013_Slowing PCR ramp speed reduces chimera formation from environmental samples.pdf;C\:\\Users\\shimotsuki\\Zotero\\storage\\GQL46GJI\\S0167701213001073.html},
  journal = {Journal of Microbiological Methods},
  keywords = {Chimera detection,Chimera formation,Environmental samples,PCR temperatures},
  number = {3}
}

@article{Sze2019,
  title = {The {{Impact}} of {{DNA Polymerase}} and {{Number}} of {{Rounds}} of {{Amplification}} in {{PCR}} on {{16S rRNA Gene Sequence Data}}},
  author = {Sze, Marc A. and Schloss, Patrick D.},
  year = {2019},
  month = jun,
  volume = {4},
  pages = {e00163-19},
  issn = {2379-5042},
  doi = {10.1128/mSphere.00163-19},
  abstract = {PCR amplification of 16S rRNA genes is a critical yet underappreciated step in the generation of sequence data to describe the taxonomic composition of microbial communities. Numerous factors in the design of PCR can impact the sequencing error rate, the abundance of chimeric sequences, and the degree to which the fragments in the product represent their abundance in the original sample (i.e., bias). We compared the performance of high fidelity polymerases and various numbers of rounds of amplification when amplifying a mock community and human stool samples. Although it was impossible to derive specific recommendations, we did observe general trends. Namely, using a polymerase with the highest possible fidelity and minimizing the number of rounds of PCR reduced the sequencing error rate, fraction of chimeric sequences, and bias. Evidence of bias at the sequence level was subtle and could not be ascribed to the fragments' fraction of bases that were guanines or cytosines. When analyzing mock community data, the amount that the community deviated from the expected composition increased with the number of rounds of PCR. This bias was inconsistent for human stool samples. Overall, the results underscore the difficulty of comparing sequence data that are generated by different PCR protocols. However, the results indicate that the variation in human stool samples is generally larger than that introduced by the choice of polymerase or number of rounds of PCR.
IMPORTANCE A steep decline in sequencing costs drove an explosion in studies characterizing microbial communities from diverse environments. Although a significant amount of effort has gone into understanding the error profiles of DNA sequencers, little has been done to understand the downstream effects of the PCR amplification protocol. We quantified the effects of the choice of polymerase and number of PCR cycles on the quality of downstream data. We found that these choices can have a profound impact on the way that a microbial community is represented in the sequence data. The effects are relatively small compared to the variation in human stool samples; however, care should be taken to use polymerases with the highest possible fidelity and to minimize the number of rounds of PCR. These results also underscore that it is not possible to directly compare sequence data generated under different PCR conditions.},
  copyright = {Copyright \textcopyright{} 2019 Sze and Schloss.. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.},
  file = {C\:\\Users\\shimotsuki\\Dropbox\\PDF\\MetabarcodingTextbook1\\Sze_Schloss_mSphere_2019_The Impact of DNA Polymerase and Number of Rounds of Amplification in PCR on.pdf;C\:\\Users\\shimotsuki\\Zotero\\storage\\DM3NDBK9\\e00163-19.html},
  journal = {mSphere},
  language = {en},
  number = {3},
  pmid = {31118299}
}

@article{Takada-Hoshino2004,
  title = {An {{Improved DNA Extraction Method Using Skim Milk}} from {{Soils That Strongly Adsorb DNA}}},
  author = {{Takada-Hoshino}, Yuko and Matsumoto, Naoyuki},
  year = {2004},
  volume = {19},
  pages = {13--19},
  doi = {10.1264/jsme2.19.13},
  abstract = {DNA extraction has been difficult from some types of soil. Seven soil samples from agricultural fields and a forest, which were mainly volcanic ash soils, were used. Soil DNA could be extracted from only two of them using a commercially available kit exploiting bead-beating. When skim milk was added to the extraction buffer at 40 mg g-1 soil, DNA could be detected by electrophoresis from all the samples, indicating that the DNA from lysed cells was adsorbed by soil colloids. The addition of skim milk did not affect PCR-DGGE profiles. The improved method is applicable to the analysis of molecular communities in soils which strongly adsorb DNA.},
  file = {C\:\\Users\\shimotsuki\\Dropbox\\PDF\\Protocols\\Takada-Hoshino_Matsumoto_Microbes and Environments_2004_An Improved DNA Extraction Method Using Skim Milk from Soils That Strongly.pdf;C\:\\Users\\shimotsuki\\Zotero\\storage\\DCVXRR88\\_article.html},
  journal = {Microbes and Environments},
  keywords = {Andisol,DNA extraction from soil,skim milk},
  number = {1}
}

@article{Ushio2019,
  title = {Use of a Filter Cartridge Combined with Intra-Cartridge Bead-Beating Improves Detection of Microbial {{DNA}} from Water Samples},
  author = {Ushio, Masayuki},
  year = {2019},
  volume = {0},
  issn = {2041-210X},
  doi = {10.1111/2041-210X.13204},
  abstract = {Microbial communities play an important role in driving the dynamics of aquatic ecosystems. As difficulties in DNA sequencing faced by microbial ecologists are continuously being reduced, sample collection methods and DNA extraction protocols are becoming more critical to the outcome of any sequencing study. In the present study, I added a manual, intra-cartridge, bead-beating step in the protocol using a DNeasy\textregistered{} Blood \& Tissue kit for DNA extraction from a filter cartridge without breaking the cartridge unit (``Beads'' method) and compared its performance with those of two other protocols (``NoBeads'' method, which was similar to the Beads method but without the bead-beating step and ``PowerSoil'' method, which followed the manual of the DNeasy\textregistered{} PowerSoil kit after breaking apart the filter cartridge). Water samples were collected from lake, river, pond and coastal ecosystems in Japan and DNA was extracted using the three protocols. Then, the V4 region of prokaryotic 16S rRNA genes was amplified. In the library preparation process, internal standard DNAs were included to estimate the number of DNA copies. The DNA library was sequenced using Illumina MiSeq and sequences were analysed using the amplicon sequence variant (ASV) approach. I found that, (a) the total prokaryotic DNA yields were highest with the Beads method, (b) the number of ASVs (a proxy for species richness) was also highest with the Beads method, (c) overall community compositions were significantly different among the three methods and (d) the number of method-specific ASVs was highest with the Beads method. These results were generally robust across samples from all aquatic ecosystems examined. In conclusion, the inclusion of a bead-beating step performed inside the filter cartridge increased the DNA yield as well as the number of prokaryotic ASVs detected compared with the other two methods. Performing the bead-beating step inside the filter cartridge causes no dramatic increase in either handling time or processing cost and it can reduce the potential contamination risk from the ambient air and/or other samples. Therefore, this method has the potential to become one of the major choices when one aims to extract aquatic microbial DNAs.},
  copyright = {\textcopyright{} 2019 The Authors. Methods in Ecology and Evolution \textcopyright{} 2019 British Ecological Society},
  file = {C\:\\Users\\shimotsuki\\Dropbox\\PDF\\Protocols\\Ushio_Methods in Ecology and Evolution_Use of a filter cartridge combined with intra-cartridge bead-beating improves.pdf;C\:\\Users\\shimotsuki\\Zotero\\storage\\68W6H2QZ\\2041-210X.html},
  journal = {Methods in Ecology and Evolution},
  keywords = {aquatic ecosystem,bead-beating,DNA extraction,filter cartridge,Illumina MiSeq,microbial DNA,Sterivex},
  language = {en},
  number = {0}
}

@article{Wang2012,
  title = {A Novel Method for {{RNA}} Extraction from {{Andosols}} Using Casein and Its Application to {{amoA}} Gene Expression Study in Soil},
  author = {Wang, Yong and Nagaoka, Kazunari and Hayatsu, Masahito and Sakai, Yoriko and Tago, Kanako and Asakawa, Susumu and Fujii, Takeshi},
  year = {2012},
  month = nov,
  volume = {96},
  pages = {793--802},
  issn = {1432-0614},
  doi = {10.1007/s00253-012-4342-3},
  abstract = {The lack of a universal method to extract RNA from soil hinders the progress of studies related to nitrification in soil, which is an important step in the nitrogen cycle. It is particularly difficult to extract RNA from certain types of soils such as Andosols (volcanic ash soils), which is the dominant agricultural soil in Japan, because of RNA adsorption by soil. To obtain RNA from these challenging soils to study the bacteria involved in nitrification, we developed a soil RNA extraction method for gene expression analysis. Autoclaved casein was added to an RNA extraction buffer to recover RNA from soil, and high-quality RNA was successfully extracted from eight types of agricultural soils that were significantly different in their physicochemical characteristics. To detect bacterial ammonia monooxygenase subunit A gene (amoA) transcripts, bacterial genomic DNA and messenger RNA were co-extracted from two different types of Andosols during incubation with ammonium sulfate. Polymerase chain reaction\textendash{}denaturing gradient gel electrophoresis and reverse transcription polymerase chain reaction\textendash{}denaturing gradient gel electrophoresis analyses of amoA in soil microcosms revealed that only few amoA, which had the highest similarities to those in Nitrosospira multiformis, were expressed in these soils after treatment with ammonium sulfate, although multiple amoA genes were present in the soil microcosms examined.},
  file = {C\:\\Users\\shimotsuki\\Dropbox\\PDF\\Protocols\\Wang et al_Appl Microbiol Biotechnol_2012_A novel method for RNA extraction from Andosols using casein and its.pdf},
  journal = {Applied Microbiology and Biotechnology},
  keywords = {amoA,Andosol,Autoclaved casein,RNA extraction,Soil},
  language = {en},
  number = {3}
}

@article{Yamanaka2017,
  title = {A Simple Method for Preserving Environmental {{DNA}} in Water Samples at Ambient Temperature by Addition of Cationic Surfactant},
  author = {Yamanaka, Hiroki and Minamoto, Toshifumi and Matsuura, Junichi and Sakurai, Sho and Tsuji, Satsuki and Motozawa, Hiromu and Hongo, Masamichi and Sogo, Yuki and Kakimi, Naoki and Teramura, Iori and Sugita, Masaki and Baba, Miki and Kondo, Akihiro},
  year = {2017},
  month = apr,
  volume = {18},
  pages = {233--241},
  issn = {1439-863X},
  doi = {10.1007/s10201-016-0508-5},
  abstract = {Environmental DNA (eDNA) analysis is a powerful tool within ecology for the study of the distribution or abundance of aquatic species, although the simplification of water sampling is required for enabling light and fast field sampling to expand further application of eDNA analysis. Here, certain candidate chemicals belonging to the group of cationic surfactants were examined for their effectiveness as preservatives for eDNA water samples by simply adding the chemicals to water samples to suppress the degradation of eDNA. The quaternary ammonium compound benzalkonium chloride (BAC) at a final concentration of 0.01\% was effective to retain 92\% of eDNA derived from the bluegill sunfish Lepomis macrochirus in an 8-h incubation test at ambient temperature, which assumed a transportation of water samples in 1-day field sampling during the daytime. Meanwhile, eDNA in water samples without BAC retained only 14\% of the initial eDNA. Moreover, an additional long-term incubation test (up to 10 days) revealed BAC-treated samples retained \textasciitilde{}70 and 50\% of bluegill DNA compared to the initial amount after 1- and 10-day incubation at ambient temperature, respectively. Meanwhile, eDNA in na{\"i}ve samples reduced to 20\% after 1-day incubation and reached undetectable levels after 10 days. Up to now, many eDNA studies have adopted on-site filtration followed by filter fixation, which requires many pieces of equipment. Addition of BAC can protect eDNA in water samples with less effort and equipment resulting in an increase of measurement accuracy of the eDNA quantity and detection probability of rare species by preventing the disappearance of rare sequences in water samples.},
  file = {C\:\\Users\\shimotsuki\\Dropbox\\PDF\\MetabarcodingTextbook1\\Yamanaka et al_Limnology_2017_A simple method for preserving environmental DNA in water samples at ambient.pdf},
  journal = {Limnology},
  keywords = {Degradation,eDNA,Less equipment requirements,Macroorganism,Preservatives},
  language = {en},
  number = {2}
}