ArticleNature biotechnology2015
ConStrains identifies microbial strains in metagenomic datasets.
Article in Nature biotechnology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 150 papers, 1 of them a synthesis that pooled it.
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Who cites it
150 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Mother-to-infant vertical transmission in early life: a systematic review and proportional meta-analysis of Bifidobacterium strain transmissibility.NPJ biofilms and microbiomes · 2025Pooled it
- A bacterial pangenome association study identifies a role for polyamine metabolism and alkaline tolerance in middle ear infections.PLoS pathogens · 2026Article
- Strain Diversity in the Human Microbiome: Personal Variation, Pathobionts, Therapeutics, and Methodological Challenges.Microorganisms · 2026Review
- An ANIr-based methodology to determine if two sequence-discrete populations are identical and identify cosmopolitan prokaryotic populations.ISME communications · 2026Article
- Long-read metagenomics for strain tracking after faecal microbiota transplant.Nature microbiology · 2025Article
- Assessing live microbial therapeutic transmission.Gut microbes · 2025Review
- 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
- Challenges and Opportunities in Analyzing Cancer-Associated Microbiomes.Cancer research · 2025Review
- Intraspecies associations from strain-rich metagenome samples.Cell reports · 2025Article
- Long read metagenomics-based precise tracking of bacterial strains and genomic changes after fecal microbiota transplantation.bioRxiv : the preprint server for biology · 2025Article
- Longitudinal profiling of low-abundance strains in microbiomes with ChronoStrain.Nature microbiology · 2025Article
- Human Gut Microbiome Researches Over the Last Decade: Current Challenges and Future Directions.Phenomics (Cham, Switzerland) · 2025Article
- Methods for Chromosome-Scale Haplotype Reconstruction.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Enhanced metagenomic strategies for elucidating the complexities of gut microbiota: a review.Frontiers in microbiology · 2025Review
- An integrated strain-level analytic pipeline utilizing longitudinal metagenomic data.Microbiology spectrum · 2024Article
- Inferring the composition of a mixed culture of natural microbial isolates by deep sequencing.bioRxiv : the preprint server for biology · 2024Article
- Floria: fast and accurate strain haplotyping in metagenomes.Bioinformatics (Oxford, England) · 2024Article
- Birthmode and environment-dependent microbiota transmission dynamics are complemented by breastfeeding during the first year.Cell host & microbe · 2024Article
- Decoding populations in the ocean microbiome.Microbiome · 2024Article
90 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors.
Funding
Abstract
An important fraction of microbial diversity is harbored in strain individuality, so identification of conspecific bacterial strains is imperative for improved understanding of microbial community functions. Limitations in bioinformatics and sequencing technologies have to date precluded strain identification owing to difficulties in phasing short reads to faithfully recover the original strain-level genotypes, which have highly similar sequences. We present ConStrains, an open-source algorithm that identifies conspecific strains from metagenomic sequence data and reconstructs the phylogeny of these strains in microbial communities. The algorithm uses single-nucleotide polymorphism (SNP) patterns in a set of universal genes to infer within-species structures that represent strains. Applying ConStrains to simulated and host-derived datasets provides insights into microbial community dynamics.
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