ArticleNature biotechnology2022
Fast and accurate metagenotyping of the human gut microbiome with GT-Pro.
Article in Nature biotechnology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers, 2 of them syntheses that pooled it.
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Who cites it
29 citing papers in PubMed, 2 syntheses or guidelines pooled it, 49 citations in OpenAlex.
- A human gut metagenome-assembled genome catalogue spanning 41 countries supports genome-scale metabolic models.Nature microbiology · 2026Pooled it
- Maast: genotyping thousands of microbial strains efficiently.Genome biology · 2023Pooled it
- Vaginal microbiota impacts of a Lactobacillus crispatus live biotherapeutic and predictors of colonization in randomized controlled trial.Cell host & microbe · 2026Trial
- Genomic Map of Escherichia coli and Single Nucleotide Polymorphism Markers in Colorectal Cancer.Microbial biotechnology · 2026Article
- Linkage of nucleotide and functional diversity varies across gut bacteria.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Functional divergence of the gut microbiome associated with lifestyle and helminth infection in Indigenous Peninsular Malaysian.Research square · 2026Article
- Exploring differences in the human gut microbiome between Han Chinese and non-Chinese populations.Genome biology · 2026Article
- Microbiota effects and predictors ofmedRxiv : the preprint server for health sciences · 2025Article
- StrainFacts accurately quantifies both endogenous and live biotherapeutic product strain abundances in simulated and clinical vaginal microbiota samples.bioRxiv : the preprint server for biology · 2025Article
- The soil-plant-human gut microbiome axis into perspective.Nature communications · 2025Review
- Accurate estimation of intraspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGC.Genome research · 2025Article
- A comprehensive multi-omics analysis uncovers the associations between gut microbiota and pancreatic cancer.Frontiers in microbiology · 2025Article
- Multi-cohort metagenomics reveals strain functional heterogeneity and demonstrates fecal microbial load correction improves colorectal cancer diagnostic models.Frontiers in microbiology · 2025Article
- Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn's disease.Cell host & microbe · 2024Article
- An integrated strain-level analytic pipeline utilizing longitudinal metagenomic data.Microbiology spectrum · 2024Article
- Enhancing insights into diseases through horizontal gene transfer event detection from gut microbiome.Nucleic acids research · 2024Article
- Genome-resolved metagenomics: a game changer for microbiome medicine.Experimental & molecular medicine · 2024Review
- Substantial viral diversity in bats and rodents from East Africa: insights into evolution, recombination, and cocirculation.Microbiome · 2024Article
- Benchmarking spatial clustering methods with spatially resolved transcriptomics data.Nature methods · 2024Article
- Dynamics of bacterial recombination in the human gut microbiome.PLoS biology · 2024Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Single nucleotide polymorphisms (SNPs) in metagenomics are used to quantify population structure, track strains and identify genetic determinants of microbial phenotypes. However, existing alignment-based approaches for metagenomic SNP detection require high-performance computing and enough read coverage to distinguish SNPs from sequencing errors. To address these issues, we developed the GenoTyper for Prokaryotes (GT-Pro), a suite of methods to catalog SNPs from genomes and use unique k-mers to rapidly genotype these SNPs from metagenomes. Compared to methods that use read alignment, GT-Pro is more accurate and two orders of magnitude faster. Using high-quality genomes, we constructed a catalog of 104 million SNPs in 909 human gut species and used unique k-mers targeting this catalog to characterize the global population structure of gut microbes from 7,459 samples. GT-Pro enables fast and memory-efficient metagenotyping of millions of SNPs on a personal computer.
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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.