ArticleNature communications2018
Synthetic microbe communities provide internal reference standards for metagenome sequencing and analysis.
Article in Nature communications, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers.
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Who cites it
63 citing papers in PubMed.
- Effects of elexacaftor/tezacaftor/ivacaftor on the nasal microbial metagenome in cystic fibrosis.Microbiology spectrum · 2026Article
- Wastewater Metagenomics for Antimicrobial Resistance and Pathogen Surveillance: A Bibliometric Analysis.Microorganisms · 2026Review
- Quantitative metagenomics using a portable protocol.Applied and environmental microbiology · 2026Article
- Advancing Plant Microbiome Research Through Host DNA Depletion Techniques.Plant biotechnology journal · 2026Review
- Design, processing, and modeling for longitudinal multiomics microbiome data.Frontiers in cellular and infection microbiology · 2026Review
- Smoking-induced microbial dysbiosis: a key driver of systemic diseases and emerging therapeutic opportunities.Cell death discovery · 2025Review
- Optimization of Mapping Tools and Investigation of Ribosomal RNA Influence for Data-Driven Gene Expression Analysis in Complex Microbiomes.Microorganisms · 2025Article
- Tracking Different States of Spiked Environmental DNA Using Multiplex Digital PCR Assays.Environmental microbiology · 2025Article
- Evaluating Quantitative Metagenomics for Environmental Monitoring of Antibiotic Resistance and Establishing Detection Limits.Environmental science & technology · 2025Article
- Development of a quantitative metagenomic approach to establish quantitative limits and its application to viruses.Nucleic acids research · 2025Article
- The quest for environmental analytical microbiology: absolute quantitative microbiome using cellular internal standards.Microbiome · 2025Review
- Absolute abundance unveils Basidiobolus as a cross-domain bridge indirectly bolstering gut microbiome homeostasis.The ISME journal · 2025Article
- The role and challenges of intratumoral microbiota in colorectal cancer immunotherapy.Frontiers in pharmacology · 2025Review
- Synthetic spike-in metabarcoding for plant pathogen diagnostics results in precise quantification of copy number within the genusISME communications · 2025Article
- Dental caries shallow-layer microbe harvest and data display method shows taxa pre-harvest spatial positions, absolute and relative abundance and diversity related to lesion pulpal depth.Journal of oral microbiology · 2025Article
- Synthetic DNA spike-in standards for cross-domain absolute quantification of microbiomes by rRNA gene amplicon sequencing.ISME communications · 2025Article
- Unveiling errors in soil microbial community sequencing: a case for reference soils and improved diagnostics for nanopore sequencing.Communications biology · 2024Article
- A universal molecular control for DNA, mRNA and protein expression.Nature communications · 2024Article
- A novel synthetic nucleic acid mixture for quantification of microbes by mNGS.Microbial genomics · 2024Article
- Early assessment of fungal and oomycete pathogens in greenhouse irrigation water using Oxford nanopore amplicon sequencing.PloS one · 2024Article
3 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
13 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The complexity of microbial communities, combined with technical biases in next-generation sequencing, pose a challenge to metagenomic analysis. Here, we develop a set of internal DNA standards, termed "sequins" (sequencing spike-ins), that together constitute a synthetic community of artificial microbial genomes. Sequins are added to environmental DNA samples prior to library preparation, and undergo concurrent sequencing with the accompanying sample. We validate the performance of sequins by comparison to mock microbial communities, and demonstrate their use in the analysis of real metagenome samples. We show how sequins can be used to measure fold change differences in the size and structure of accompanying microbial communities, and perform quantitative normalization between samples. We further illustrate how sequins can be used to benchmark and optimize new methods, including nanopore long-read sequencing technology. We provide metagenome sequins, along with associated data sets, protocols, and an accompanying software toolkit, as reference standards to aid in metagenomic studies.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.