ArticleCell systems2023
Pitfalls of genotyping microbial communities with rapidly growing genome collections.
Article in Cell systems, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers, 1 of them a synthesis that pooled it.
What it found
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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.
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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.
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Who cites it
19 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Maast: genotyping thousands of microbial strains efficiently.Genome biology · 2023Pooled it
- Ocular community state types reveal distinct microbial compositions among microbiomes with implications for trachoma control.bioRxiv : the preprint server for biology · 2026Article
- Quantitative detection of gut microbial eukaryotes with EukDetect2 reveals global distribution of commensal protists and association with distinct microbial community structure.bioRxiv : the preprint server for biology · 2026Article
- Multikingdom microbiome-based machine learning enables multiple sclerosis diagnosis.NPJ biofilms and microbiomes · 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
- PopMAG: a Nextflow pipeline for population genetics analysis based on metagenome-assembled genomes.Bioinformatics advances · 2026Article
- A comparison of methods for the optimal recovery of the human fecal virome.ISME communications · 2026Article
- Taxonomy-free fecal microbiome profiles enable robust prediction of immunotherapy response and toxicity in melanoma.bioRxiv : the preprint server for biology · 2025Article
- Bacterial Systematic Genetics and Integrated Multi-Omics: Beyond Static Genomics Toward Predictive Models.International journal of molecular sciences · 2025Review
- Small amounts of misassembly can have disproportionate effects on pangenome-based metagenomic analyses.mSphere · 2025Article
- Accurate estimation of intraspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGC.Genome research · 2025Article
- Improved detection of microbiome-disease associations via population structure-aware generalized linear mixed effects models (microSLAM).PLoS computational biology · 2025Article
- Comprehensive profiling of genomic invertons in defined gut microbial community reveals associations with intestinal colonization and surface adhesion.Microbiome · 2025Article
- New Drinking Water Genome Catalog Identifies a Globally Distributed Bacterial Genus Adapted to Disinfected Drinking Water Systems.Environmental science & technology · 2024Article
- PUPpy: a primer design pipeline for substrain-level microbial detection and absolute quantification.mSphere · 2024Article
- Multi-omic analysis tools for microbial metabolites prediction.Briefings in bioinformatics · 2024Review
- INSaFLU-TELEVIR: an open web-based bioinformatics suite for viral metagenomic detection and routine genomic surveillance.Genome medicine · 2024Article
- Identifying species-specific k-mers for fast and accurate metagenotyping with Maast and GT-Pro.STAR protocols · 2023Article
- Genotyping Microbial Communities with MIDAS2: From Metagenomic Reads to Allele Tables.Current protocols · 2022Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Detecting genetic variants in metagenomic data is a priority for understanding the evolution, ecology, and functional characteristics of microbial communities. Many tools that perform this metagenotyping rely on aligning reads of unknown origin to a database of sequences from many species before calling variants. In this synthesis, we investigate how databases of increasingly diverse and closely related species have pushed the limits of current alignment algorithms, thereby degrading the performance of metagenotyping tools. We identify multi-mapping reads as a prevalent source of errors and illustrate a trade-off between retaining correct alignments versus limiting incorrect alignments, many of which map reads to the wrong species. Then we evaluate several actionable mitigation strategies and review emerging methods showing promise to further improve metagenotyping in response to the rapid growth in genome collections. Our results have implications beyond metagenotyping to the many tools in microbial genomics that depend upon accurate read mapping.
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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.