ArticleMicrobiome2014
CopyRighter: a rapid tool for improving the accuracy of microbial community profiles through lineage-specific gene copy number correction.
Article in Microbiome, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 128 papers, 1 of them a synthesis that pooled it.
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Who cites it
128 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Prenatal Maternal Stress and Infant Gut Microbiome in Human and Animal Studies: A Comprehensive Systematic Review.Developmental psychobiology · 2026Pooled it
- Synergistic Benefits of Butyric Acid and Resistant Potato Starch on Growth and Gut Health in Weaned Pigs.Journal of animal physiology and animal nutrition · 2026Article
- Seasonal dynamics of the gut microbiota inFrontiers in insect science · 2026Article
- Organic acid-preserved grain improves growth and gut health in weanling pigs fed zinc oxide free diets.Scientific reports · 2025Article
- DNA reference reagents isolate biases in microbiome profiling: a global multi-lab study.mSystems · 2025Article
- Cervicovaginal microbial features predictInfection and immunity · 2025Article
- Mock Plant Communities and a Large Mammal Case Study Reveal ITS2 Primer Bias Against Graminoids.Ecology and evolution · 2025Article
- Effect of Maternal Probiotic and Piglet Dietary Tryptophan Level on Performance and Piglet Intestinal Health Parameters Pre-Weaning.Microorganisms · 2025Article
- A curated bacterial and archaeal 16S rRNA Gene Oral Sequences dataset.Scientific data · 2025Article
- Effects of Butyric Acid Supplementation on the Gut Microbiome and Growth Performance of Weanling Pigs Fed a Low-Crude Protein, Propionic Acid-Preserved Grain Diet.Microorganisms · 2025Article
- Effects of organic acid-preserved cereal grains in sow diets during late gestation and lactation on the performance and faecal microbiota of sows and their offspring.Journal of animal science and biotechnology · 2025Article
- Impact of Reduced Dietary Crude Protein and Propionic Acid Preservation on Intestinal Health and Growth Performance in Post-Weaned Pigs.Animals : an open access journal from MDPI · 2025Article
- Absolute abundance calculation enhances the significance of microbiome data in antibiotic treatment studies.Frontiers in microbiology · 2025Article
- Does Antibiotic Use Contribute to Biofilm Resistance in Sink Drains? A Case Study from Four German Hospital Wards.Antibiotics (Basel, Switzerland) · 2024Article
- Article
- Deep longitudinal lower respiratory tract microbiome profiling reveals genome-resolved functional and evolutionary dynamics in critical illness.Nature communications · 2024Article
- Characterization of the microbiome of Aedes albopictus populations in different habitats from Spain and São Tomé.Scientific reports · 2024Article
- Long journey of 16S rRNA-amplicon sequencing toward cell-based functional bacterial microbiota characterization.iMetaOmics · 2024Review
- The bacterial microbiome and resistome of house dust mites in Irish homes.Scientific reports · 2024Article
- No Evidence of Gut Microbiota Alteration in Psoriasis Patients Switching to Brodalumab after Loss of TNFα Inhibition Effect.International journal of molecular sciences · 2024Article
68 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundCulture-independent molecular surveys targeting conserved marker genes, most notably 16S rRNA, to assess microbial diversity remain semi-quantitative due to variations in the number of gene copies between species.
resultsBased on 2,900 sequenced reference genomes, we show that 16S rRNA gene copy number (GCN) is strongly linked to microbial phylogenetic taxonomy, potentially under-representing Archaea in amplicon microbial profiles. Using this relationship, we inferred the GCN of all bacterial and archaeal lineages in the Greengenes database within a phylogenetic framework. We created CopyRighter, new software which uses these estimates to correct 16S rRNA amplicon microbial profiles and associated quantitative (q)PCR total abundance. CopyRighter parses microbial profiles and, because GCN estimates are pre-computed for all taxa in the reference taxonomy, rapidly corrects GCN bias. Software validation with in silico and in vitro mock communities indicated that GCN correction results in more accurate estimates of microbial relative abundance and improves the agreement between metagenomic and amplicon profiles. Analyses of human-associated and anaerobic digester microbiomes illustrate that correction makes tangible changes to estimates of qPCR total abundance, α and β diversity, and can significantly change biological interpretation. For example, human gut microbiomes from twins were reclassified into three rather than two enterotypes after GCN correction.
conclusionsThe CopyRighter bioinformatic tools permits rapid correction of GCN in microbial surveys, resulting in improved estimates of microbial abundance, α and β diversity.
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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.