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Synthetic spike-in standards for high-throughput 16S rRNA gene amplicon sequencing
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Modern Applied Statistics with S
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ggplot2: Elegant Graphics for Data Analysis
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Introduction and Motivation
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Compositional data analysis of the microbiome: fundamentals, tools, and challenges
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Multicenter quality assessment of 16S ribosomal DNA-sequencing for microbiome analyses reveals high inter-center variability
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A method for simultaneous measurement of soil bacterial abundances and community composition via 16S rRNA gene sequencing
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Reproducibility and quantitation of amplicon sequencing-based detection
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Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms
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Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution
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Minimum entropy decomposition: Unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences
inferredcites →https://doi.org/10.1038/ismej.2016.117openalex-snapshot
Absolute quantification of microbial taxon abundances
inferredcites →https://doi.org/10.1038/nbt.3601openalex-snapshot
Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies
inferredcites →https://doi.org/10.1038/ncomms6125openalex-snapshot
Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures
inferredcites →https://doi.org/10.1038/nmeth.1184openalex-snapshot
Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex
inferredcites →https://doi.org/10.1038/nmeth.2276openalex-snapshot
Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing
inferredcites →https://doi.org/10.1038/nmeth.2604openalex-snapshot
UPARSE: highly accurate OTU sequences from microbial amplicon reads
inferredcites →https://doi.org/10.1038/nmeth.3869openalex-snapshot
DADA2: High-resolution sample inference from Illumina amplicon data
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QIIME allows analysis of high-throughput community sequencing data
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An assessment of US microbiome research
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Single-cell identification in microbial communities by improved fluorescence in situ hybridization techniques
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Sample storage conditions significantly influence faecal microbiome profiles
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Search and clustering orders of magnitude faster than BLAST
inferredcites →https://doi.org/10.1093/bioinformatics/btr381openalex-snapshot
UCHIME improves sensitivity and speed of chimera detection
inferredcites →https://doi.org/10.1093/bioinformatics/btu170openalex-snapshot
Trimmomatic: a flexible trimmer for Illumina sequence data
inferredcites →https://doi.org/10.1093/nar/gkg595openalex-snapshot
Mfold web server for nucleic acid folding and hybridization prediction
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Sequence-specific error profile of Illumina sequencers
inferredcites →https://doi.org/10.1093/nar/gku1341openalex-snapshot
Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform
inferredcites →https://doi.org/10.1093/nar/gkv1113openalex-snapshot
A novel conceptual approach to read-filtering in high-throughput amplicon sequencing studies
inferredcites →https://doi.org/10.1101/gr.121095.111openalex-snapshot
Synthetic spike-in standards for RNA-seq experiments
inferredcites →https://doi.org/10.1111/1462-2920.12610openalex-snapshot
Limits to robustness and reproducibility in the demarcation of operational taxonomic units
inferredcites →https://doi.org/10.1111/1462-2920.13139openalex-snapshot
Diversity analysis of sulfite‐ and sulfate‐reducing microorganisms by multiplex dsrA and dsrB amplicon sequencing using new primers and mock community‐optimized bioinformatics
inferredcites →https://doi.org/10.1128/aem.01043-13openalex-snapshot
Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform
inferredcites →https://doi.org/10.1128/aem.01541-09openalex-snapshot
Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
inferredcites →https://doi.org/10.1128/aem.02206-14openalex-snapshot
Performance Comparison of Illumina and Ion Torrent Next-Generation Sequencing Platforms for 16S rRNA-Based Bacterial Community Profiling
inferredcites →https://doi.org/10.1186/1471-2164-13-455openalex-snapshot
A mechanistic basis for amplification differences between samples and between genome regions
inferredcites →https://doi.org/10.1186/1471-2164-15-110openalex-snapshot
SASI-Seq: sample assurance Spike-Ins, and highly differentiating 384 barcoding for Illumina sequencing
inferredcites →https://doi.org/10.1186/1471-2180-10-255openalex-snapshot
Effects of polymerase, template dilution and cycle number on PCR based 16 S rRNA diversity analysis using the deep sequencing method
inferredcites →https://doi.org/10.1186/s12866-015-0351-6openalex-snapshot
The truth about metagenomics: quantifying and counteracting bias in 16S rRNA studies
inferredcites →https://doi.org/10.1186/s12866-016-0738-zopenalex-snapshot
16S rRNA gene sequencing of mock microbial populations- impact of DNA extraction method, primer choice and sequencing platform
inferredcites →https://doi.org/10.1186/s13059-015-0841-8openalex-snapshot
The microbiome quality control project: baseline study design and future directions
inferredcites →https://doi.org/10.1186/s40168-016-0175-0openalex-snapshot
Adjusting microbiome profiles for differences in microbial load by spike-in bacteria
inferredcites →https://doi.org/10.1371/journal.pone.0043093openalex-snapshot
PCR Biases Distort Bacterial and Archaeal Community Structure in Pyrosequencing Datasets
inferredcites →https://doi.org/10.1371/journal.pone.0121659openalex-snapshot
RNA Preservation Agents and Nucleic Acid Extraction Method Bias Perceived Bacterial Community Composition
inferredcites →https://doi.org/10.1371/journal.pone.0148028openalex-snapshot
Comparing Apples and Oranges?: Next Generation Sequencing and Its Impact on Microbiome Analysis
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Cutadapt removes adapter sequences from high-throughput sequencing reads
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vegan: Community Ecology Package
inferredcites →https://doi.org/10.32614/r.manualsopenalex-snapshot
R: A Language and Environment for Statistical Computing
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Incoming claims: where this work appears in other papers’ reference lists and arguments.
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inferred← citeshttps://doi.org/10.1111/1755-0998.13730openalex-snapshot
Pitfalls in the statistical analysis of microbiome amplicon sequencing data
inferred← citeshttps://doi.org/10.1111/1758-2229.13189openalex-snapshot
A quantitative sequencing method using synthetic internal standards including functional and phylogenetic marker genes
inferred← citeshttps://doi.org/10.1111/2041-210x.14073openalex-snapshot
Optimizing insect metabarcoding using replicated mock communities
inferred← citeshttps://doi.org/10.1111/2041-210x.70351openalex-snapshot
Accuracy of occurrence and abundance estimates from insect metabarcoding
inferred← citeshttps://doi.org/10.1111/gcb.16877openalex-snapshot
Climate change drives loss of bacterial gut mutualists at the expense of host survival in wild meerkats
inferred← citeshttps://doi.org/10.1111/gcb.17395openalex-snapshot
Intrinsic microbial temperature sensitivity and soil organic carbon decomposition in response to climate change
inferred← citeshttps://doi.org/10.1111/mec.70485openalex-snapshot
Mycobiome Simplification in Wheat Is Associated With the Pathogen Parastagonospora nodorum
inferred← citeshttps://doi.org/10.1111/obr.12661openalex-snapshot
Microbiota in obesity: interactions with enteroendocrine, immune and central nervous systems
inferred← citeshttps://doi.org/10.1128/9781555818852.ch1openalex-snapshot
Definitions and Historical Perspectives in Environmental Forensics
inferred← citeshttps://doi.org/10.1128/aem.00456-20openalex-snapshot
Chinese Liquor Fermentation: Identification of Key Flavor-Producing Lactobacillus spp. by Quantitative Profiling with Indigenous Internal Standards
inferred← citeshttps://doi.org/10.1128/aem.02627-17openalex-snapshot
The Madness of Microbiome: Attempting To Find Consensus “Best Practice” for 16S Microbiome Studies
inferred← citeshttps://doi.org/10.1128/mbio.02658-24openalex-snapshot
Blanking on blanks: few insect microbiota studies control for contaminants
inferred← citeshttps://doi.org/10.1128/mbio.03173-20openalex-snapshot
Metagenomic Quantification of Genes with Internal Standards
inferred← citeshttps://doi.org/10.1128/microbiolspec.emf-0015-2018openalex-snapshot
Future Technologies
inferred← citeshttps://doi.org/10.1128/microbiolspec.emf-0016-2018openalex-snapshot
Definitions and Historical Perspectives in Environmental Forensics
inferred← citeshttps://doi.org/10.1128/msphere.00490-25openalex-snapshot
Microbiota diversity of Anopheles gambiae in Bankeng, southern Cameroon, and its association with Plasmodium falciparum infection
inferred← citeshttps://doi.org/10.1128/msystems.00294-21openalex-snapshot
Characterizing Microbiomes via Sequencing of Marker Loci: Techniques To Improve Throughput, Account for Cross-Contamination, and Reduce Cost
inferred← citeshttps://doi.org/10.1128/msystems.00447-22openalex-snapshot
synDNA—a Synthetic DNA Spike-in Method for Absolute Quantification of Shotgun Metagenomic Sequencing
inferred← citeshttps://doi.org/10.1128/msystems.00964-20openalex-snapshot
Gradient Internal Standard Method for Absolute Quantification of Microbial Amplicon Sequencing Data
inferred← citeshttps://doi.org/10.1128/msystems.00984-25openalex-snapshot
Metagenomic estimation of absolute bacterial biomass in the mammalian gut through host-derived read normalization
inferred← citeshttps://doi.org/10.1128/spectrum.01294-23openalex-snapshot
A metagenomics method for the quantitative detection of bacterial pathogens causing hospital-associated and ventilator-associated pneumonia
inferred← citeshttps://doi.org/10.1128/spectrum.01915-21openalex-snapshot
Characterization and Demonstration of Mock Communities as Control Reagents for Accurate Human Microbiome Community Measurements
inferred← citeshttps://doi.org/10.1128/spectrum.02754-25openalex-snapshot
Evaluating preservation effects on honeybee gut microbiota inocula
inferred← citeshttps://doi.org/10.1128/spectrum.02806-24openalex-snapshot
Analytical assessment of metagenomic workflows for pathogen detection with NIST RM 8376 and two sample matrices
inferred← citeshttps://doi.org/10.1186/s12864-023-09429-8openalex-snapshot
Vibrio-Sequins - dPCR-traceable DNA standards for quantitative genomics of Vibrio spp
inferred← citeshttps://doi.org/10.1186/s12864-026-12986-3openalex-snapshot
Stable nutritional endosymbiosis across cryptic diversity of a leafhopper species complex
inferred← citeshttps://doi.org/10.1186/s12915-024-01914-0openalex-snapshot
Co-habiting ants and silverfish display a converging feeding ecology
inferred← citeshttps://doi.org/10.1186/s40168-018-0470-zopenalex-snapshot
Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin
inferred← citeshttps://doi.org/10.1186/s40168-022-01412-xopenalex-snapshot
An improved workflow for accurate and robust healthcare environmental surveillance using metagenomics
inferred← citeshttps://doi.org/10.1186/s40168-025-02169-9openalex-snapshot
What lurks in the dark? An innovative framework for studying diverse wild insect microbiota
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1011447openalex-snapshot
RSim: A reference-based normalization method via rank similarity
inferred← citeshttps://doi.org/10.1371/journal.pone.0202049openalex-snapshot
Detection of pathogenic bacteria in the blood from sepsis patients using 16S rRNA gene amplicon sequencing analysis
inferred← citeshttps://doi.org/10.1371/journal.pone.0262912openalex-snapshot
Development of an efficient antimicrobial susceptibility testing method with species identification by Nanopore sequencing of 16S rRNA amplicons
inferred← citeshttps://doi.org/10.1371/journal.pone.0300381openalex-snapshot
Early assessment of fungal and oomycete pathogens in greenhouse irrigation water using Oxford nanopore amplicon sequencing
inferred← citeshttps://doi.org/10.1371/journal.pwat.0000094openalex-snapshot
Significant antimicrobial-producing vegetation uniquely shapes the stormwater biofilter microbiome with implications for enhanced faecal pathogen inactivation
inferred← citeshttps://doi.org/10.18174/445530openalex-snapshot
Gastrointestinal function and microbiota development in preterm infants
inferred← citeshttps://doi.org/10.18307/2024.0511openalex-snapshot
Comparative study on the biodiversity of phytoplankton based on environmental DNA technology and morphological identification
inferred← citeshttps://doi.org/10.18307/2025.0407openalex-snapshot
Comparative study on the biodiversity of zooplankton in Lake Fuxian based on environmental DNA technology and morphological identification
inferred← citeshttps://doi.org/10.20517/mrr.2024.94openalex-snapshot
Assessment of absolute abundance in mother-infant gut microbiome using marine-sourced bacterial DNA spike-in and comparison with conventional quantification methods
inferred← citeshttps://doi.org/10.20517/mrr.2025.100openalex-snapshot
Quantification of the absolute abundance of the jejunal mucosa-associated microbiota of pigs using spike-in control
inferred← citeshttps://doi.org/10.21037/atm-20-393openalex-snapshot
Comparative evaluation of peptidome and microbiota in different types of saliva samples
inferred← citeshttps://doi.org/10.21203/rs.3.rs-117421/v1openalex-snapshot
Handling of Spurious Sequences Affects the Outcome of High-Throughput 16S rRNA Gene Amplicon Profiling
inferred← citeshttps://doi.org/10.21203/rs.3.rs-4190256/v1openalex-snapshot
In-depth Proteomic Analysis of Alfalfa Silage Inoculated with Lactiplantibacillus plantarum Reveals Protein Transformation Mechanisms and Optimizes Dietary N Utilization
inferred← citeshttps://doi.org/10.2144/btn-2018-0089openalex-snapshot
Spike-in Genomic DNA for Validating Performance of Metagenomics Workflows
inferred← citeshttps://doi.org/10.2144/btn-2020-0153openalex-snapshot
A Comparison of DNA/RNA Extraction Protocols for High-Throughput Sequencing of Microbial Communities
inferred← citeshttps://doi.org/10.2144/btn-2022-0032openalex-snapshot
A Comparison of Six DNA Extraction Protocols for 16S, ITS and Shotgun Metagenomic Sequencing of Microbial Communities
inferred← citeshttps://doi.org/10.2478/aoas-2025-0119openalex-snapshot
The microbiome's dynamics throughout swarming preparation in honey bees ( Apis mellifera )
inferred← citeshttps://doi.org/10.31274/td-20240329-318openalex-snapshot
Experimental and genetic tools for elucidating the contribution of secreted public goods and genetic pathways to rhizosphere competence of Pseudomonas putida
inferred← citeshttps://doi.org/10.3389/fgene.2019.01366openalex-snapshot
NG-Tax 2.0: A Semantic Framework for High-Throughput Amplicon Analysis
inferred← citeshttps://doi.org/10.3389/fmicb.2018.00780openalex-snapshot
Development of a Custom MALDI-TOF MS Database for Species-Level Identification of Bacterial Isolates Collected From Spacecraft and Associated Surfaces
inferred← citeshttps://doi.org/10.3389/fmicb.2018.02160openalex-snapshot
Microbiome Interaction Networks and Community Structure From Laboratory-Reared and Field-Collected Aedes aegypti, Aedes albopictus, and Culex quinquefasciatus Mosquito Vectors
inferred← citeshttps://doi.org/10.3389/fmicb.2020.01403openalex-snapshot
Repeated Inoculation of Young Calves With Rumen Microbiota Does Not Significantly Modulate the Rumen Prokaryotic Microbiota Consistently but Decreases Diarrhea
inferred← citeshttps://doi.org/10.3389/fmicb.2020.575625openalex-snapshot
Plant Genotype Influences Physicochemical Properties of Substrate as Well as Bacterial and Fungal Assemblages in the Rhizosphere of Balsam Poplar
inferred← citeshttps://doi.org/10.3389/fmicb.2020.599614openalex-snapshot
Patterns of Relative and Quantitative Abundances of Marine Bacteria in Surface Waters of the Subtropical Northwest Pacific Ocean Estimated With High-Throughput Quantification Sequencing
inferred← citeshttps://doi.org/10.3389/fmicb.2021.798023openalex-snapshot
Relative and Quantitative Rhizosphere Microbiome Profiling Results in Distinct Abundance Patterns
inferred← citeshttps://doi.org/10.3389/fmicb.2022.1020329openalex-snapshot
Spatiotemporal and ontogenetic variation, microbial selection, and predicted Bd-inhibitory function in the skin-associated microbiome of a Rocky Mountain amphibian
inferred← citeshttps://doi.org/10.3389/fmicb.2023.1329330openalex-snapshot
Application of next-generation sequencing to identify different pathogens
inferred← citeshttps://doi.org/10.3389/fmicb.2024.1433656openalex-snapshot
The impact of gradient variable temperature fermentation on the quality of cigar tobacco leaves
inferred← citeshttps://doi.org/10.3389/fmicb.2025.1481197openalex-snapshot
Absolute abundance calculation enhances the significance of microbiome data in antibiotic treatment studies
inferred← citeshttps://doi.org/10.3389/fmicb.2025.1552305openalex-snapshot
Quantitative microbial taxonomy across particle size, depth, and oxygen concentration
inferred← citeshttps://doi.org/10.3389/fmicb.2025.1684366openalex-snapshot
Advancing time-since-interval estimation for clandestine graves: a forensic ecogenomics perspective into burial and translocation timelines using massively parallel sequencing
inferred← citeshttps://doi.org/10.3389/fmicb.2026.1746815openalex-snapshot
A novel internal reference microorganism-based method reveals wild-enriched Penicillium for enhancing growth and disease resistance in Fritillaria thunbergii
inferred← citeshttps://doi.org/10.3389/fmicb.2026.1752237openalex-snapshot
Insights into community profiles, environmental influence, and assembly mechanisms of oyster-associated bacteriome from Yueqing Bay, China via absolute quantitation by metabarcoding
inferred← citeshttps://doi.org/10.3389/fmicb.2026.1870167openalex-snapshot
Validation of a long-read 16S rRNA-gene sequencing approach for analysis of clinical samples and bacterial identification in a routine clinical laboratory
inferred← citeshttps://doi.org/10.3389/frmbi.2024.1441290openalex-snapshot
Navigating regulatory and analytical challenges in live biotherapeutic product development and manufacturing
inferred← citeshttps://doi.org/10.3390/fermentation8020088openalex-snapshot
A CRISPR-Cas12a-Based Assay for Efficient Quantification of Lactobacillus panis in Chinese Baijiu Brewing Microbiome
inferred← citeshttps://doi.org/10.3390/fermentation8080345openalex-snapshot
A High-Throughput Absolute Abundance Quantification Method for the Characterisation of Daqu Core Fungal Communities
inferred← citeshttps://doi.org/10.3390/microorganisms8010020openalex-snapshot
The Effect of Thermal Stress on the Bacterial Microbiome of Exaiptasia diaphana
inferred← citeshttps://doi.org/10.3390/microorganisms8091277openalex-snapshot
A First Insight into the Structural and Functional Comparison of Environmental Microbiota in Freshwater Turtle Chinemys reevesii at Different Growth Stages under Pond and Greenhouse Cultivation
inferred← citeshttps://doi.org/10.3390/microorganisms9091797openalex-snapshot
Current Applications of Absolute Bacterial Quantification in Microbiome Studies and Decision-Making Regarding Different Biological Questions
inferred← citeshttps://doi.org/10.3390/ph19091372openalex-snapshot
Supernatants of Water Extraction–Ethanol Precipitation from Roots of Rosa davurica Pall. Ameliorate Ulcerative Colitis in Mice: From Gut Microbes to Metabolites
inferred← citeshttps://doi.org/10.3390/w13243551openalex-snapshot
Molecular Methods for Pathogenic Bacteria Detection and Recent Advances in Wastewater Analysis
inferred← citeshttps://doi.org/10.6084/m9.figshare.26726842openalex-snapshot
Additional file 1 of Co-habiting ants and silverfish display a converging feeding ecology
inferred← citeshttps://doi.org/10.6084/m9.figshare.26726845openalex-snapshot
Additional file 6 of Co-habiting ants and silverfish display a converging feeding ecology
inferred← citeshttps://doi.org/10.64898/2026.06.24.734267openalex-snapshot
Insect COI barcoding data as an untapped resource for surveying Wolbachia symbioses
inferred← citeshttps://doi.org/10.65390/fdiv.2026.136017openalex-snapshot
Absolute-quantitative microbiome profiling identifies pathogen-sensitive windows and cross-domain assembly rules in Morchella cultivation soils
inferred← citeshttps://doi.org/10.7287/peerj.4514v0.1/reviews/1openalex-snapshot
Peer Review #1 of "Assessing soil bacterial community and dynamics by integrated high-throughput absolute abundance quantification (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.4514v0.1/reviews/2openalex-snapshot
Peer Review #2 of "Assessing soil bacterial community and dynamics by integrated high-throughput absolute abundance quantification (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.4925v0.1/reviews/1openalex-snapshot
Peer Review #1 of "Non-biological synthetic spike-in controls and the AMPtk software pipeline improve mycobiome data (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.8722v0.1/reviews/1openalex-snapshot
Peer Review #1 of "Probabilistic model based on circular statistics for quantifying coverage depth dynamics originating from DNA replication (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.8722v0.1/reviews/2openalex-snapshot
Peer Review #2 of "Probabilistic model based on circular statistics for quantifying coverage depth dynamics originating from DNA replication (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj.8722v0.2/reviews/1openalex-snapshot
Peer Review #1 of "Probabilistic model based on circular statistics for quantifying coverage depth dynamics originating from DNA replication (v0.2)"
inferred← citeshttps://doi.org/10.7287/peerj.8722v0.2/reviews/2openalex-snapshot
Peer Review #2 of "Probabilistic model based on circular statistics for quantifying coverage depth dynamics originating from DNA replication (v0.2)"
inferred← citeshttps://doi.org/10.7717/peerj.10799openalex-snapshot
The effect of ethanol concentration on the morphological and molecular preservation of insects for biodiversity studies
inferred← citeshttps://doi.org/10.7717/peerj.18025openalex-snapshot
Implementing high-throughput insect barcoding in microbiome studies: impact of non-destructive DNA extraction on microbiome reconstruction
inferred← citeshttps://doi.org/10.7717/peerj.4514openalex-snapshot
Assessing soil bacterial community and dynamics by integrated high-throughput absolute abundance quantification
inferred← citeshttps://doi.org/10.7717/peerj.4925openalex-snapshot
Non-biological synthetic spike-in controls and the AMPtk software pipeline improve mycobiome data
inferred← citeshttps://doi.org/10.7717/peerj.8722openalex-snapshot
Probabilistic model based on circular statistics for quantifying coverage depth dynamics originating from DNA replication
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