ArticleBioinformatics (Oxford, England)2025
PICRUSt2-SC: an update to the reference database used for functional prediction within PICRUSt2.
Article in Bioinformatics (Oxford, England), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
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- Metabolite-Resolved Validation of Bacterial Organophosphate Transformation in Soil: A Critical Review of Selected Organophosphate Case Studies.Microorganisms · 2026Review
- The Biotechnological Applications of Marine Bacteria.Biology · 2026Review
- TwoInternational journal of molecular sciences · 2026Article
- Vertical Stratification in Composition, Metabolic Potential and Co-Occurrence Networks of Archaeal Communities in Mangrove Sediments, Zhanjiang, China.Ecology and evolution · 2026Article
- Gut Microbiota Signatures and Ecological Network Alterations Associated with Hemodialysis.Microorganisms · 2026Article
- Analysis of biofilms formed by static culture of bacterial communities in the Inba floodway (Lake Inbanuma-Tokyo Bay).World journal of microbiology & biotechnology · 2026Article
- Spatial Partitioning of Microbial Functional Potential Suggests Complex Nitrogen Cycling in a Subterranean Estuary.Environmental microbiology · 2026Article
- Impact ofFoods (Basel, Switzerland) · 2026Article
- Early-Life Iron Exposure Influences Long-Term Gut Microbiota Recovery After Intestinal Dysbiosis.Microorganisms · 2026Article
- Assessing soil microbiome alterations in agricultural land exposed to pesticides through amplicon-based sequencing.Biodegradation · 2026Article
- Antibiotic use in early life impairs MAIT cell-mediated immunity in adulthood.The Journal of experimental medicine · 2026Article
- Fecal microbiome predicts treatment response after the initiation of semaglutide or empagliflozin uptake.Scientific reports · 2026Article
- Nutritional pressure from serum amplifies dysbiotic features in an oral microbiome synthetic community.The ISME journal · 2026Article
- Shao-Ma-Zhi-Jing granules alleviate Tourette Syndrome by modulating the cAMP/PI3K/AKT/NF-κB signaling pathway, T cell differentiation, microglia, and gut microbiota.Frontiers in physiology · 2026Article
- EasyAmplicon 2: Expanding PacBio and Nanopore Long Amplicon Sequencing Analysis Pipeline for Microbiome.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Interpreting UniFrac with absolute abundance: a conceptual and practical guide.ISME communications · 2026Article
- Geographic and species-specific determinants of rhizosphere microbiome assembly inISME communications · 2026Article
- Upwelling periodically disturbs the ecological assembly of microbial communities in Lake Ontario.ISME communications · 2026Article
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2 authors.
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Abstract
summaryPICRUSt2 is a bioinformatic tool that predicts microbial functions in amplicon sequencing data using a database of annotated reference genomes. We have constructed an updated database for PICRUSt2 that has substantially increased the number of bacterial (19,493 to 26,868) and archaeal (406 to 1,002) genomes as well as the number of functional annotations present. The previous PICRUSt2 database relied on many timely and computationally intensive manual processes that made it difficult to update. We constructed a new streamlined process to allow regular upgrades to the PICRUSt2 database on an ongoing basis, and used this process to create a new database, PICRUSt2-SC (Sugar-Coated). Additionally, we have shown that this updated database contains genomes that more closely match study sequences from a range of different environments. The genomes contained in the database therefore better represent these environments and this leads to an improvement in the predicted functional annotations obtained from PICRUSt2. AVAILABILITY AND IMPLEMENTATION: PICRUSt2 source code is freely available at https://github.com/picrust/picrust2 and at https://anaconda.org/bioconda/picrust2. The latest version of PICRUSt2 at the time of writing is also archived: https://doi.org/10.5281/zenodo.15119781. The PICRUSt2-SC database comes pre-installed with PICRUSt2 from version 2.6.0 onwards. Step-by-step instructions for making the updated database are at https://github.com/picrust/picrust2/wiki/Updating-the-PICRUSt2-database. All code used for the analyses and figures in this manuscript is at https://github.com/R-Wright-1/PICRUSt2-SC_application_note and https://doi.org/10.5281/zenodo.15119770.
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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.