ArticlePloS one2011
Accurate genome relative abundance estimation based on shotgun metagenomic reads.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 71 papers.
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Who cites it
71 citing papers in PubMed.
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- Inherent differential microbial assemblages and functions associated with corals exhibiting different thermal phenotypes.Science advances · 2025Article
- Insights into human respiratory microbiome under dysbiosis and its analysis tool.Frontiers in microbiomes · 2025Review
- A quantitative comparison of urine centrifugation and filtration for the isolation and analysis of urinary nucleic acid biomarkers.Scientific reports · 2024Article
- Exploring the Interspecific Interactions and the Metabolome of the Soil Isolate Hylemonella gracilis.mSystems · 2023Article
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- Comparison of Metagenomics and Metatranscriptomics Tools: A Guide to Making the Right Choice.Genes · 2022Article
- A metagenomic DNA sequencing assay that is robust against environmental DNA contamination.Nature communications · 2022Article
- An adaptive direction-assisted test for microbiome compositional data.Bioinformatics (Oxford, England) · 2022Article
- Cell-free DNA profiling informs all major complications of hematopoietic cell transplantation.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Diversity of RNA viruses of three dominant tick species in North China.Frontiers in veterinary science · 2022Article
- Joint Analysis of Microbial and Immune Cell Abundance in Liver Cancer Tissue Using a Gene Expression Profile Deconvolution Algorithm Combined With Foreign Read Remapping.Frontiers in immunology · 2022Article
- Peritoneal Effluent Cell-Free DNA Sequencing in Peritoneal Dialysis Patients With and Without Peritonitis.Kidney medicine · 2022Article
- Measurement Biases Distort Cell-Free DNA Fragmentation Profiles and Define the Sensitivity of Metagenomic Cell-Free DNA Sequencing Assays.Clinical chemistry · 2021Article
- Bacterial community structure alterations within the colorectal cancer gut microbiome.BMC microbiology · 2021Article
- Bacterial associations in the healthy human gut microbiome across populations.Scientific reports · 2021Article
- Article
- Freshwater phytoplankton diversity: models, drivers and implications for ecosystem properties.Hydrobiologia · 2021Review
- Linking Inflammatory Bowel Disease Symptoms to Changes in the Gut Microbiome Structure and Function.Frontiers in microbiology · 2021Article
11 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Accurate estimation of microbial community composition based on metagenomic sequencing data is fundamental for subsequent metagenomics analysis. Prevalent estimation methods are mainly based on directly summarizing alignment results or its variants; often result in biased and/or unstable estimates. We have developed a unified probabilistic framework (named GRAMMy) by explicitly modeling read assignment ambiguities, genome size biases and read distributions along the genomes. Maximum likelihood method is employed to compute Genome Relative Abundance of microbial communities using the Mixture Model theory (GRAMMy). GRAMMy has been demonstrated to give estimates that are accurate and robust across both simulated and real read benchmark datasets. We applied GRAMMy to a collection of 34 metagenomic read sets from four metagenomics projects and identified 99 frequent species (minimally 0.5% abundant in at least 50% of the data-sets) in the human gut samples. Our results show substantial improvements over previous studies, such as adjusting the over-estimated abundance for Bacteroides species for human gut samples, by providing a new reference-based strategy for metagenomic sample comparisons. GRAMMy can be used flexibly with many read assignment tools (mapping, alignment or composition-based) even with low-sensitivity mapping results from huge short-read datasets. It will be increasingly useful as an accurate and robust tool for abundance estimation with the growing size of read sets and the expanding database of reference genomes.
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