ArticleMicrobiome2022
MetaPop: a pipeline for macro- and microdiversity analyses and visualization of microbial and viral metagenome-derived populations.
Article in Microbiome, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed, 61 citations in OpenAlex.
- Article
- Viral modulation of sulfur-oxidizing bacteria drives organic carbon sink formation during primary succession in deglaciating ecosystems.Nature communications · 2026Article
- Salinity-driven adaptations and evolution of DNA viruses in estuarine-coastal ecosystems.mSystems · 2026Article
- Vicennial metagenomic time series unveils evolutionary dynamics of giant viruses in a freshwater ecosystem.Nature communications · 2026Article
- The Human Virome in Infectious Diseases: Insights from Chronic and Acute Infections Across Body Sites-A Narrative Review.Microorganisms · 2026Review
- Patterns and drivers of macro- and micro-diversity of mudflat intertidal archaeomes along the Chinese coasts.mSystems · 2026Article
- Unveiling the biodiversity of large DNA viruses in intertidal mudflats via metagenomics.Nature communications · 2026Article
- Host factors dictate gut microbiome alterations in chronic kidney disease more strongly than kidney function.Nature microbiology · 2026Article
- Diversity and ecological roles of hidden viral players in groundwater microbiomes.Nature communications · 2026Article
- PopMAG: a Nextflow pipeline for population genetics analysis based on metagenome-assembled genomes.Bioinformatics advances · 2026Article
- Computational Microbial and Viral Ecology Analysis.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Population ecology and biogeochemical implications of ssDNA and dsDNA viruses along a permafrost thaw gradient.Nature communications · 2025Article
- Multi-Habitat Landscape Promotes Microbial Diversity: Insights from the Traditional Agricultural Heritage and the Global Trend.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Biogeography and host interactions of CPR and DPANN viruses in acid mine drainage sediments.Nature communications · 2025Article
- Salinity-driven shifts in estuarine viral community composition and diversity near the Shenzhen coast.Applied and environmental microbiology · 2025Article
- Context matters: assessing the impacts of genomic background and ecology on microbial biosynthetic gene cluster evolution.mSystems · 2025Review
- zol and fai: large-scale targeted detection and evolutionary investigation of gene clusters.Nucleic acids research · 2025Article
- Uneven sequencing (coverage) depth can bias microbial intraspecies diversity estimates and how to account for it.ISME communications · 2025Article
- Unravelling viral ecology and evolution over 20 years in a freshwater lake.Nature microbiology · 2025Article
- Navigating Host Immunity and Concurrent Ozone Stress: Strain-Resolved Metagenomics Reveals Maintenance of Intraspecific Diversity and Genetic Variation inEvolutionary applications · 2025Article
Corrections and comments
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Authors and funding
7 authors at 4 institutions in 3 countries.
Funding
Abstract
backgroundMicrobes and their viruses are hidden engines driving Earth's ecosystems from the oceans and soils to humans and bioreactors. Though gene marker approaches can now be complemented by genome-resolved studies of inter-(macrodiversity) and intra-(microdiversity) population variation, analytical tools to do so remain scattered or under-developed.
resultsHere, we introduce MetaPop, an open-source bioinformatic pipeline that provides a single interface to analyze and visualize microbial and viral community metagenomes at both the macro- and microdiversity levels. Macrodiversity estimates include population abundances and α- and β-diversity. Microdiversity calculations include identification of single nucleotide polymorphisms, novel codon-constrained linkage of SNPs, nucleotide diversity (π and θ), and selective pressures (pN/pS and Tajima's D) within and fixation indices (F
conclusionsThese findings suggest that standardized population and genetic variation analyses will be invaluable for maximizing biological inference, and MetaPop provides a convenient tool package to explore the dual impact of macro- and microdiversity across microbial communities. Video abstract.
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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.