ReviewPLoS computational biology2010
A primer on metagenomics.
Review in PLoS computational biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 226 papers.
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.
The trial behind it
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
226 citing papers in PubMed.
- Microbial Community and Enzymes for Biodeterioration of PVC Plastic Buried in Soil and Compost Environment.Current microbiology · 2026Article
- Is the endophyte-based plant protection against aphids mediated by changes in the insect microbiome?Insect science · 2026Article
- Effects of aquaculture practices onApplied and environmental microbiology · 2026Article
- Metalog: curated and harmonised contextual data for global metagenomics samples.Nucleic acids research · 2026Article
- Maize stover mulching combined with an optimized fertilization strategy reshapes rhizosphere microbial communities and functions in greenhouse potato.Frontiers in microbiology · 2026Article
- Diagnostic value of metagenomic next-generation sequencing in patients with febrile lung cancer with negative conventional microbiological tests and without neutropenia.Frontiers in cellular and infection microbiology · 2026Article
- Review
- Globally aggregated biodiversity data impact predictive and descriptive research.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- CarpeDeam: a de novo metagenome assembler for heavily damaged ancient datasets.Genome biology · 2025Article
- Modulation of the rhizosphere microbiome structure and optimization of beneficial functions in winter wheat induced by Bacillus subtilis: a metagenomic and phenotypic study.FEMS microbiology ecology · 2025Article
- Mechanistic Elucidation ofJournal of agricultural and food chemistry · 2025Article
- I-SVVS: integrative stochastic variational variable selection to explore joint patterns of multi-omics microbiome data.Briefings in bioinformatics · 2025Article
- Decoding the Tumor-Associated Microbiota: From Origins to Nanomedicine Applications in Cancer Therapy.Biology · 2025Review
- An interdisciplinary perspective of the built-environment microbiome.FEMS microbiology ecology · 2025Review
- Application of the metagenomic next-generation sequencing technology to identify the causes of pleural effusion.Frontiers in medicine · 2025Article
- Whole-genome Metagenomic Sequencing Reveals Gut Microbiota Composition and Function Associated with Differential Growth Performance in Two Chicken Breeds.The journal of poultry science · 2025Article
- Microbiome data: tell me which metrics and I will tell you which communities.ISME communications · 2025Article
- Graph-based self-supervised learning for repeat detection in metagenomic assembly.Genome research · 2024Article
- Benchmarking bacterial taxonomic classification using nanopore metagenomics data of several mock communities.Scientific data · 2024Article
- AFITbin: a metagenomic contig binning method using aggregate l-mer frequency based on initial and terminal nucleotides.BMC bioinformatics · 2024Article
166 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Metagenomics is a discipline that enables the genomic study of uncultured microorganisms. Faster, cheaper sequencing technologies and the ability to sequence uncultured microbes sampled directly from their habitats are expanding and transforming our view of the microbial world. Distilling meaningful information from the millions of new genomic sequences presents a serious challenge to bioinformaticians. In cultured microbes, the genomic data come from a single clone, making sequence assembly and annotation tractable. In metagenomics, the data come from heterogeneous microbial communities, sometimes containing more than 10,000 species, with the sequence data being noisy and partial. From sampling, to assembly, to gene calling and function prediction, bioinformatics faces new demands in interpreting voluminous, noisy, and often partial sequence data. Although metagenomics is a relative newcomer to science, the past few years have seen an explosion in computational methods applied to metagenomic-based research. It is therefore not within the scope of this article to provide an exhaustive review. Rather, we provide here a concise yet comprehensive introduction to the current computational requirements presented by metagenomics, and review the recent progress made. We also note whether there is software that implements any of the methods presented here, and briefly review its utility. Nevertheless, it would be useful if readers of this article would avail themselves of the comment section provided by this journal, and relate their own experiences. Finally, the last section of this article provides a few representative studies illustrating different facets of recent scientific discoveries made using metagenomics.
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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.