ArticleFrontiers in bioinformatics2022
Scalable Microbial Strain Inference in Metagenomic Data Using StrainFacts.
Article in Frontiers in bioinformatics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 20 citations in OpenAlex.
- Vaginal microbiota impacts of a Lactobacillus crispatus live biotherapeutic and predictors of colonization in randomized controlled trial.Cell host & microbe · 2026Trial
- MetaStrainer: accurate reconstruction of bacterial strain genotypes from short-read metagenomic samples.Bioinformatics (Oxford, England) · 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
- Article
- kSanity: A k-mer based application for precision bacterial strain detection and quantification.bioRxiv : the preprint server for biology · 2025Article
- 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
- Microbiome Single Cell Atlases Generated with a Commercial Instrument.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Rapidly evolving orphan immunity genes protect human gut bacteria from intoxication by the type VI secretion system.bioRxiv : the preprint server for biology · 2025Article
- Accurate estimation of intraspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGC.Genome research · 2025Article
- Longitudinal profiling of low-abundance strains in microbiomes with ChronoStrain.Nature microbiology · 2025Article
- stana: an R package for metagenotyping analysis and interactive application based on clinical data.NAR genomics and bioinformatics · 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
- Sustained mucosal colonization and fecal metabolic dysfunction by Bacteroides associates with fecal microbial transplant failure in ulcerative colitis patients.Scientific reports · 2024Article
- Inferring the composition of a mixed culture of natural microbial isolates by deep sequencing.bioRxiv : the preprint server for biology · 2024Article
- A metagenomic approach to demystify the anaerobic digestion black box and achieve higher biogas yield: a review.Frontiers in microbiology · 2024Review
- Genotyping Microbial Communities with MIDAS2: From Metagenomic Reads to Allele Tables.Current protocols · 2022Article
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
While genome databases are nearing a complete catalog of species commonly inhabiting the human gut, their representation of intraspecific diversity is lacking for all but the most abundant and frequently studied taxa. Statistical deconvolution of allele frequencies from shotgun metagenomic data into strain genotypes and relative abundances is a promising approach, but existing methods are limited by computational scalability. Here we introduce StrainFacts, a method for strain deconvolution that enables inference across tens of thousands of metagenomes. We harness a "fuzzy" genotype approximation that makes the underlying graphical model fully differentiable, unlike existing methods. This allows parameter estimates to be optimized with gradient-based methods, speeding up model fitting by two orders of magnitude. A GPU implementation provides additional scalability. Extensive simulations show that StrainFacts can perform strain inference on thousands of metagenomes and has comparable accuracy to more computationally intensive tools. We further validate our strain inferences using single-cell genomic sequencing from a human stool sample. Applying StrainFacts to a collection of more than 10,000 publicly available human stool metagenomes, we quantify patterns of strain diversity, biogeography, and linkage-disequilibrium that agree with and expand on what is known based on existing reference genomes. StrainFacts paves the way for large-scale biogeography and population genetic studies of microbiomes using metagenomic data.
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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.