ArticleNucleic acids research2013
Composition-based classification of short metagenomic sequences elucidates the landscapes of taxonomic and functional enrichment of microorganisms.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed, 65 citations in OpenAlex.
- Connect the dots: sketching out microbiome interactions through networking approaches.Microbiome research reports · 2023Review
- Metagenomic shifts in mucus, tissue and skeleton of the coral Balanophyllia europaea living along a natural COISME communications · 2022Article
- Music of metagenomics-a review of its applications, analysis pipeline, and associated tools.Functional & integrative genomics · 2022Review
- CVTree: A Parallel Alignment-free Phylogeny and Taxonomy Tool Based on Composition Vectors of Genomes.Genomics, proteomics & bioinformatics · 2021Article
- Whole genome strategies and bioremediation insight into dehalogenase-producing bacteria.Molecular biology reports · 2021Review
- Low-Abundant Microorganisms: The Human Microbiome's Dark Matter, a Scoping Review.Frontiers in cellular and infection microbiology · 2021Article
- Alterations of gut microbiome accelerate multiple myeloma progression by increasing the relative abundances of nitrogen-recycling bacteria.Microbiome · 2020Article
- Shotgun Metagenomics of Gut Microbiota in Humans with up to Extreme Longevity and the Increasing Role of Xenobiotic Degradation.mSystems · 2020Article
- gcMeta: a Global Catalogue of Metagenomics platform to support the archiving, standardization and analysis of microbiome data.Nucleic acids research · 2019Article
- MetaBinG2: a fast and accurate metagenomic sequence classification system for samples with many unknown organisms.Biology direct · 2018Article
- Single-cell metagenomics: challenges and applications.Protein & cell · 2018Review
- A clinician's guide to microbiome analysis.Nature reviews. Gastroenterology & hepatology · 2017Review
- A Study of the Microbial Spatial Heterogeneity of Bahamian Thrombolites Using Molecular, Biochemical, and Stable Isotope Analyses.Astrobiology · 2017Article
- Gut microbiota and hematopoietic stem cell transplantation: where do we stand?Bone marrow transplantation · 2017Review
- Elucidating and Regulating the Acetoin Production Role of Microbial Functional Groups in Multispecies Acetic Acid Fermentation.Applied and environmental microbiology · 2016Article
- Characterization of the stromatolite microbiome from Little Darby Island, The Bahamas using predictive and whole shotgun metagenomic analysis.Environmental microbiology · 2016Article
- Characterization of Microbial Mat Microbiomes in the Modern Thrombolite Ecosystem of Lake Clifton, Western Australia Using Shotgun Metagenomics.Frontiers in microbiology · 2016Article
- Evaluation of shotgun metagenomics sequence classification methods using in silico and in vitro simulated communities.BMC bioinformatics · 2015Article
- Marine Metagenome as A Resource for Novel Enzymes.Genomics, proteomics & bioinformatics · 2015Review
- Metagenomic surveys of gut microbiota.Genomics, proteomics & bioinformatics · 2015Review
Corrections and comments
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Authors and funding
7 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Compared with traditional algorithms for long metagenomic sequence classification, characterizing microorganisms' taxonomic and functional abundance based on tens of millions of very short reads are much more challenging. We describe an efficient composition and phylogeny-based algorithm [Metagenome Composition Vector (MetaCV)] to classify very short metagenomic reads (75-100 bp) into specific taxonomic and functional groups. We applied MetaCV to the Meta-HIT data (371-Gb 75-bp reads of 109 human gut metagenomes), and this single-read-based, instead of assembly-based, classification has a high resolution to characterize the composition and structure of human gut microbiota, especially for low abundance species. Most strikingly, it only took MetaCV 10 days to do all the computation work on a server with five 24-core nodes. To our knowledge, MetaCV, benefited from the strategy of composition comparison, is the first algorithm that can classify millions of very short reads within affordable time.
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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.