ArticleNature methods2016
Strain-level microbial epidemiology and population genomics from shotgun metagenomics.
Article in Nature methods, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 219 papers, 2 of them syntheses that pooled it.
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
219 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- [Advances in the Application of Forensic Microbiome Analysis in Tissue Source Inference].Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition · 2025Pooled it
- Meta-Analysis of Altered Gut Microbiota Reveals Microbial and Metabolic Biomarkers for Colorectal Cancer.Microbiology spectrum · 2022Pooled it
- Cotrimoxazole reduces systemic inflammation in HIV infection by altering the gut microbiome and immune activation.Science translational medicine · 2019Trial
- Convergent methodologies in prosthetic joint infection research: integrating transdisciplinary approaches to understand and prevent biofilm-driven failure of orthopaedic prostheses.Journal of medical microbiology · 2026Review
- Quantitative evaluation of microbiome sequencing resolution under varying experimental conditions using defined mock communities.Scientific reports · 2026Article
- Vaginal Microbiota and Ovarian Cancer: A New Frontier in Immunomodulation and Diagnosis.Immunology · 2026Review
- Complex correlations between mitochondrial DNA variants and gut microbiome in major depressive disorder: a genome-wide association analysis.BMC psychiatry · 2026Article
- Shotgun metagenome sequencing and informatics can accurately form a metagenome-assembled genome (MAG) of the bacterial tier 1 select agentMicrobiology spectrum · 2026Article
- Strain Diversity in the Human Microbiome: Personal Variation, Pathobionts, Therapeutics, and Methodological Challenges.Microorganisms · 2026Review
- Gut microbial ethanol metabolism contributes to auto-brewery syndrome in an observational cohort.Nature microbiology · 2026Observational
- Advances in Shotgun Metagenomics for Cheese Microbiology: From Microbial Dynamics to Functional Insights.Foods (Basel, Switzerland) · 2026Review
- Microbial collagenase activity is linked to oral-gut translocation in advanced chronic liver disease.Nature microbiology · 2026Article
- Impacts of COVID-19 pandemic on early life gut microbiome.Gut microbes · 2025Article
- Review
- Strainify: Strain-Level Microbiome Profiling for Low-Coverage Short-Read Metagenomic Datasets.bioRxiv : the preprint server for biology · 2025Article
- Strain-level characterization of bacterial pathogens using metagenomic sequencing for patients with pneumonia.Journal of translational medicine · 2025Article
- Land-use legacies shape soil microbial communities and nutrient cycling functions in rotational shifting cultivation fields of Northern Thailand.Microbial ecology · 2025Article
- Microbiome composition and co-occurrence dynamics in wildMicrobiology spectrum · 2025Article
- Targeted Intervention Strategies for Maternal-Offspring Transmission of Christensenellaceae in Pigs via a Deep Learning Model.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Chinese soy-based microbiome and associated microbial risks: a metagenomic investigation.NPJ biofilms and microbiomes · 2025Article
159 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
10 authors.
Funding
Abstract
Identifying microbial strains and characterizing their functional potential is essential for pathogen discovery, epidemiology and population genomics. We present pangenome-based phylogenomic analysis (PanPhlAn; http://segatalab.cibio.unitn.it/tools/panphlan), a tool that uses metagenomic data to achieve strain-level microbial profiling resolution. PanPhlAn recognized outbreak strains, produced the largest strain-level population genomic study of human-associated bacteria and, in combination with metatranscriptomics, profiled the transcriptional activity of strains in complex communities.
Indexed as
Identifiers
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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.