ArticlePLoS computational biology2021
RESCRIPt: Reproducible sequence taxonomy reference database management.
Article in PLoS computational biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 545 papers, 3 of them syntheses that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
545 citing papers in PubMed, 3 syntheses or guidelines pooled it.
- Exploring the chicken respiratory microbiome: a comprehensive meta-analysis of factors shaping chicken respiratory microbiota.Scientific reports · 2026Pooled it
- Comparison of Gut Microbiological Profiles of Inbred and Outbred Healthy Mice.MicrobiologyOpen · 2025Pooled it
- Meta-analysis of sources and transmission pathways of Apis mellifera (Hymenoptera: Apidae) microbiota based on 16S sequencing data.Journal of insect science (Online) · 2025Pooled it
- Fecal microbiota transplantation for the decolonization of mucosal adherent-invasive Escherichia coli in Crohn's disease: an open-label pilot study.Nature communications · 2026Trial
- Individual variability in hydrogen-producing microbes influences the response to hydrogen supplementation on sleep quality: a randomized, double-blind, placebo-controlled, parallel study.Scientific reports · 2026Trial
- The Effects of a Powdered Meal Replacement on Inflammation, Gut Microbiota, and Metabolism in People With Excess Body Weight-A Randomized Controlled Trial.The Journal of nutrition · 2026Trial
- Maternal stress is associated with oral microbiota diversity patterns in pregnant women in Quito, Ecuador.Comprehensive psychoneuroendocrinology · 2026Article
- Gut microbiota are linked to gastrointestinal symptoms and behavioral changes but not inflammation in autism spectrum disorder: a cross-sectional analysis.Pediatric research · 2026Article
- Early-life microbial contact with adult hens modulates cecal microbiota and mitigates host responses to lipopolysaccharide-induced stress in broilers.Journal of animal science and biotechnology · 2026Article
- Comparative metataxonomic analysis of total, viable, and active rumen microbial communities under methane-mitigated conditions.Environmental microbiome · 2026Article
- Soil microbial growth rate, trophic strategy, and the oligotroph-copiotroph continuum.Applied and environmental microbiology · 2026Article
- Disentangling the gut microbiome and inflammation in inflammatory bowel diseases: longitudinal observations from the IBSEN III study.Inflammatory bowel diseases · 2026Article
- Soil Microbial Assembly Mirrors a Savanna Mosaic Amid Plant Invasion and Soil Disturbance.Ecology and evolution · 2026Article
- Effect of Protein Supplementation on the Gut Microbiome of Omnivorous and Herbivorous Goliath Beetles.Insects · 2026Article
- Supporting crop yields under climate change by engineering innate soil microbiomes.Applied and environmental microbiology · 2026Article
- Diurnal dynamics of maize gene expression is associated with phyllosphere microbiome composition.International microbiology : the official journal of the Spanish Society for Microbiology · 2026Article
- Low Prevalence and Abundance ofMicroorganisms · 2026Article
- Comparative pathogenicity of Ma5 vaccine and a field isolate of the avian infectious bronchitis virus in SPF chickens.Poultry science · 2026Article
- Structure, Diversity, and Metabolic Potential of Bacterioplankton in an Urban River at a Long Low-Level Water Period.Water environment research : a research publication of the Water Environment Federation · 2026Article
- Nanopore sequencing reveals coordinated host and microbiome responses across barley genotypes.BMC biology · 2026Article
485 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Nucleotide sequence and taxonomy reference databases are critical resources for widespread applications including marker-gene and metagenome sequencing for microbiome analysis, diet metabarcoding, and environmental DNA (eDNA) surveys. Reproducibly generating, managing, using, and evaluating nucleotide sequence and taxonomy reference databases creates a significant bottleneck for researchers aiming to generate custom sequence databases. Furthermore, database composition drastically influences results, and lack of standardization limits cross-study comparisons. To address these challenges, we developed RESCRIPt, a Python 3 software package and QIIME 2 plugin for reproducible generation and management of reference sequence taxonomy databases, including dedicated functions that streamline creating databases from popular sources, and functions for evaluating, comparing, and interactively exploring qualitative and quantitative characteristics across reference databases. To highlight the breadth and capabilities of RESCRIPt, we provide several examples for working with popular databases for microbiome profiling (SILVA, Greengenes, NCBI-RefSeq, GTDB), eDNA and diet metabarcoding surveys (BOLD, GenBank), as well as for genome comparison. We show that bigger is not always better, and reference databases with standardized taxonomies and those that focus on type strains have quantitative advantages, though may not be appropriate for all use cases. Most databases appear to benefit from some curation (quality filtering), though sequence clustering appears detrimental to database quality. Finally, we demonstrate the breadth and extensibility of RESCRIPt for reproducible workflows with a comparison of global hepatitis genomes. RESCRIPt provides tools to democratize the process of reference database acquisition and management, enabling researchers to reproducibly and transparently create reference materials for diverse research applications. RESCRIPt is released under a permissive BSD-3 license at https://github.com/bokulich-lab/RESCRIPt.
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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.