ArticleMicrobial genomics2024
On the limits of 16S rRNA gene-based metagenome prediction and functional profiling.
Article in Microbial genomics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 120 papers, 1 of them a synthesis that pooled it.
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Who cites it
120 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- Deep-sea Microbial Dataset of the Antarctic Ocean (dsMDAO): A high-resolution deep-sea microbial dataset of the Antarctic Ocean reveals potential for taxonomic and functional diversity.Microbial genomics · 2026Article
- Functional-Taxonomic Scaling Resolves Conflicting Average Genome Size Estimates Across Environmental Gradients.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
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- Metabolite-Resolved Validation of Bacterial Organophosphate Transformation in Soil: A Critical Review of Selected Organophosphate Case Studies.Microorganisms · 2026Review
- TwoInternational journal of molecular sciences · 2026Article
- Microbiota Transfer Supports Contribution, Not Dependence, in the Metabolic Effects of Cyclocarya paliurus Polysaccharides.Journal of gastroenterology and hepatology · 2026Article
- Supernatants of Water Extraction-Ethanol Precipitation from Roots ofPharmaceuticals (Basel, Switzerland) · 2026Article
- The Effects of Vitamin DAnimals : an open access journal from MDPI · 2026Article
- Seasonal Patterns of Soil Bacterial and Fungal Communities Under Practical Organic Fertilizer Regimes in a Tea Plantation.Microorganisms · 2026Article
- Dose-dependent effects of dietary Maotai distillers' grains on growth performance and selected intestinal responses in Pekin ducks.Poultry science · 2026Article
- Metabolomic-Metabolite Profiling: Progressive Insight and Biochemical Pathway in Crude Oil Waste Sludge Co-Composting Bioremediation.Metabolites · 2026Article
- Phosphorus alleviates age-associated osteoporosis in laying hens by reshaping bone metabolism and modulating cecal microbial communities.Poultry science · 2026Article
- Associations of Breed andMicroorganisms · 2026Article
- Roux-en-Y gastric bypass alters microbial circadian rhythms with links to metabolic improvement.American journal of physiology. Gastrointestinal and liver physiology · 2026Article
60 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Molecular profiling techniques such as metagenomics, metatranscriptomics or metabolomics offer important insights into the functional diversity of the microbiome. In contrast, 16S rRNA gene sequencing, a widespread and cost-effective technique to measure microbial diversity, only allows for indirect estimation of microbial function. To mitigate this, tools such as PICRUSt2, Tax4Fun2, PanFP and MetGEM infer functional profiles from 16S rRNA gene sequencing data using different algorithms. Prior studies have cast doubts on the quality of these predictions, motivating us to systematically evaluate these tools using matched 16S rRNA gene sequencing, metagenomic datasets, and simulated data. Our contribution is threefold: (i) using simulated data, we investigate if technical biases could explain the discordance between inferred and expected results; (ii) considering human cohorts for type two diabetes, colorectal cancer and obesity, we test if health-related differential abundance measures of functional categories are concordant between 16S rRNA gene-inferred and metagenome-derived profiles and; (iii) since 16S rRNA gene copy number is an important confounder in functional profiles inference, we investigate if a customised copy number normalisation with the rrnDB database could improve the results. Our results show that 16S rRNA gene-based functional inference tools generally do not have the necessary sensitivity to delineate health-related functional changes in the microbiome and should thus be used with care. Furthermore, we outline important differences in the individual tools tested and offer recommendations for tool selection.
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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.