ArticleBioinformatics (Oxford, England)2023
ggpicrust2: an R package for PICRUSt2 predicted functional profile analysis and visualization.
Article in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 158 papers, 3 of them syntheses that pooled it.
What it found
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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.
The trial behind it
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
158 citing papers in PubMed, 3 syntheses or guidelines pooled it.
- Worldwide research trends on theFrontiers in immunology · 2026Pooled it
- Meta-Analysis of 16S rRNA Sequencing Reveals Altered Fecal but Not Vaginal Microbial Composition and Function in Women with Endometriosis.Medicina (Kaunas, Lithuania) · 2025Pooled it
- Pooled it
- Trial
- Effects of Soluble Corn Fiber Consumption on Executive Functions and Gut Microbiota in Middle to Older Age Adults: A Randomized Controlled Crossover Trial.The Journal of nutrition · 2026Trial
- Cholesterol-lowering effects of oats induced by microbially produced phenolic metabolites in metabolic syndrome: a randomized controlled trial.Nature communications · 2026Trial
- Trial
- The role of gut microbiota in chronic intestinal pseudo-obstruction: exploring fecal microbiota transplantation as a treatment option.Gut microbes · 2026Article
- IgA deficiency reveals a microbiota-dependent pathway to gluten sensitivity.Gut microbes · 2026Article
- Dynamic flexibility of the murine gut microbiota during morphine disturbance enables escape from the stable dysbiosis that is associated with addiction-like behavior.Gut microbes · 2026Article
- Distinct Microbiota and Functional Pathway Profiles Define Success and Failure in Regenerative Endodontic Treatment.International endodontic journal · 2026Observational
- Age-adjusted machine learning identifies facial skin microbes associated with skin quality among Korean women.mSystems · 2026Article
- Microbial and Metabolic Flexibility in Response to Habitat Disturbance in an Ecologically Specialist Primate.Molecular ecology · 2026Article
- Article
- Insights into the food safety implications of a commercialApplied and environmental microbiology · 2026Article
- Gut Microbiota Signatures and Ecological Network Alterations Associated with Hemodialysis.Microorganisms · 2026Article
- Maternal gut and vaginal microbiota, alcohol use during pregnancy, and infant fetal alcohol spectrum disorder diagnosis in a South African cohort.medRxiv : the preprint server for health sciences · 2026Article
- Assessing the female urogenital-rectal axis microbiome: focus on endometriosis and recurrent implantation failure.Reproductive biology and endocrinology : RB&E · 2026Article
- Tracking Microbiome Composition and Stability Across Indian Social Honeybees Foraging in a Homogeneous Mustard Crop Landscape.Microbial ecology · 2026Article
- Resistant Starch Supplementation Modulates Gut Microbiota, Short-Chain Fatty Acids, and Markers of Gut Barrier Integrity in Estrogen-Deficient Mice.Current developments in nutrition · 2026Article
98 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
summaryMicrobiome research is now moving beyond the compositional analysis of microbial taxa in a sample. Increasing evidence from large human microbiome studies suggests that functional consequences of changes in the intestinal microbiome may provide more power for studying their impact on inflammation and immune responses. Although 16S rRNA analysis is one of the most popular and a cost-effective method to profile the microbial compositions, marker-gene sequencing cannot provide direct information about the functional genes that are present in the genomes of community members. Bioinformatic tools have been developed to predict microbiome function with 16S rRNA gene data. Among them, PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) has become one of the most popular functional profile prediction tools, which generates community-wide pathway abundances. However, no state-of-art inference tools are available to test the differences in pathway abundances between comparison groups. We have developed ggpicrust2, an R package, for analyzing functional profiles derived from 16S rRNA sequencing. This powerful tool enables researchers to conduct extensive differential abundance analyses and generate visually appealing visualizations that effectively highlight functional signals. With ggpicrust2, users can obtain publishable results and gain deeper insights into the functional composition of their microbial communities. AVAILABILITY AND IMPLEMENTATION: The package is open-source under the MIT and file license and is available at CRAN and https://github.com/cafferychen777/ggpicrust2. Its shiny web is available at https://a95dps-caffery-chen.shinyapps.io/ggpicrust2_shiny/.
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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.