ArticleNature communications2020
A quantitative sequencing framework for absolute abundance measurements of mucosal and lumenal microbial communities.
Article in Nature communications, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 113 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
113 citing papers in PubMed, 175 citations in OpenAlex.
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- Not every gene is special: Modelling scale controls the false discovery rate when analysing high-throughput sequencing data.PLoS computational biology · 2026Article
- The calf holobiont under challenge: longitudinal microbiota-pathogen dynamics and respiratory health.Veterinary research · 2026Article
- Robust and Interpretable Metagenomic Modeling Through Structure-Aware Multi-View Learning and Attribution-Guided Biological Insight.Research square · 2026Article
- Oral hydrogel systems in lower gastrointestinal disorders: From disease-based therapy to microbiota-guided design.Materials today. Bio · 2026Review
- Comparing DNA metabarcoding with light microscopy to identify eukaryotic phytoplankton in the Baltic Sea, Kattegat and Skagerrak.Scientific reports · 2026Article
- The elephant (bird) in the room: unknown mechanisms and unresolved impacts of low DNA yields in avian microbiome research.Animal microbiome · 2026Article
- Life-Stage-Dependent Variation in Gastrointestinal Microbial Communities of Drosophila melanogaster.Microbial ecology · 2026Article
- Scale reliant mixed effects models enhance microbiome data analysis.Microbiome · 2026Article
- Article
- Quantitative metagenomics using a portable protocol.Applied and environmental microbiology · 2026Article
- Predator-mediated local convergence fosters global microbial community divergence.Nature communications · 2026Article
- MaAsLin 3: refining and extending generalized multivariable linear models for meta-omic association discovery.Nature methods · 2026Article
- Advancing Plant Microbiome Research Through Host DNA Depletion Techniques.Plant biotechnology journal · 2026Review
- Human DNA levels in feces reflect gut inflammation and associate with presence of gut species in IBD patients across the age spectrum.Microbiome · 2026Article
- Population-Level Amplicon and Metagenomic Analyses Uncover Distinct Effects of Landscape-Level Pesticides on the Maternal Gut Microbiome.Environment & health (Washington, D.C.) · 2026Article
- Incorporating Scale Uncertainty into Differential Expression Analyses Using ALDEx2.Current protocols · 2026Article
- Microbiome assembly statistics toward ecosystem-scale insights, forecasting, and management.The ISME journal · 2026Review
- Comparison of ESKAPE Pathogen Levels in Wastewater and Receiving Water Bodies Using Agar-Based Enumeration and Real-Time PCR.Current microbiology · 2026Article
53 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
A fundamental goal in microbiome studies is determining which microbes affect host physiology. Standard methods for determining changes in microbial taxa measure relative, rather than absolute abundances. Moreover, studies often analyze only stool, despite microbial diversity differing substantially among gastrointestinal (GI) locations. Here, we develop a quantitative framework to measure absolute abundances of individual bacterial taxa by combining the precision of digital PCR with the high-throughput nature of 16S rRNA gene amplicon sequencing. In a murine ketogenic-diet study, we compare microbial loads in lumenal and mucosal samples along the GI tract. Quantitative measurements of absolute (but not relative) abundances reveal decreases in total microbial loads on the ketogenic diet and enable us to determine the differential effects of diet on each taxon in stool and small-intestine mucosa samples. This rigorous quantitative microbial analysis framework, appropriate for diverse GI locations enables mapping microbial biogeography of the mammalian GI tract and more accurate analyses of changes in microbial taxa in microbiome studies.
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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.