ArticleNucleic acids research2012
Unsupervised discovery of microbial population structure within metagenomes using nucleotide base composition.
Article in Nucleic acids research, 2012. 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.
- A review of neural networks for metagenomic binning.Briefings in bioinformatics · 2025Review
- Solving genomic puzzles: computational methods for metagenomic binning.Briefings in bioinformatics · 2024Review
- Genome-resolved metagenomics: a game changer for microbiome medicine.Experimental & molecular medicine · 2024Review
- Strategies to access biosynthetic novelty in bacterial genomes for drug discovery.Nature reviews. Drug discovery · 2022Review
- MetaCRS: unsupervised clustering of contigs with the recursive strategy of reducing metagenomic dataset's complexity.BMC bioinformatics · 2022Article
- Improved metagenome binning and assembly using deep variational autoencoders.Nature biotechnology · 2021Article
- Discovering multiple types of DNA methylation from bacteria and microbiome using nanopore sequencing.Nature methods · 2021Article
- Article
- PlasFlow: predicting plasmid sequences in metagenomic data using genome signatures.Nucleic acids research · 2018Article
- Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation.Nature biotechnology · 2018Article
- Comprehensive Insights Into Composition, Metabolic Potentials, and Interactions Among Archaeal, Bacterial, and Viral Assemblages in Meromictic Lake Shunet in Siberia.Frontiers in microbiology · 2018Article
- Identification of a novel interspecific hybrid yeast from a metagenomic spontaneously inoculated beer sample using Hi-C.Yeast (Chichester, England) · 2018Article
- CoMet: a workflow using contig coverage and composition for binning a metagenomic sample with high precision.BMC bioinformatics · 2017Article
- Interpreting Microbial Biosynthesis in the Genomic Age: Biological and Practical Considerations.Marine drugs · 2017Review
- High-resolution characterization of the human microbiome.Translational research : the journal of laboratory and clinical medicine · 2017Review
- Bioinformatics strategies for taxonomy independent binning and visualization of sequences in shotgun metagenomics.Computational and structural biotechnology journal · 2017Review
- Droplet barcoding for massively parallel single-molecule deep sequencing.Nature communications · 2016Article
- Review
- Molecular Ecology of Hypersaline Microbial Mats: Current Insights and New Directions.Microorganisms · 2016Review
- Metagenome Analysis Exploiting High-Throughput Chromosome Conformation Capture (3C) Data.Trends in genetics : TIG · 2015Review
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
An approach to infer the unknown microbial population structure within a metagenome is to cluster nucleotide sequences based on common patterns in base composition, otherwise referred to as binning. When functional roles are assigned to the identified populations, a deeper understanding of microbial communities can be attained, more so than gene-centric approaches that explore overall functionality. In this study, we propose an unsupervised, model-based binning method with two clustering tiers, which uses a novel transformation of the oligonucleotide frequency-derived error gradient and GC content to generate coarse groups at the first tier of clustering; and tetranucleotide frequency to refine these groups at the secondary clustering tier. The proposed method has a demonstrated improvement over PhyloPythia, S-GSOM, TACOA and TaxSOM on all three benchmarks that were used for evaluation in this study. The proposed method is then applied to a pyrosequenced metagenomic library of mud volcano sediment sampled in southwestern Taiwan, with the inferred population structure validated against complementary sequencing of 16S ribosomal RNA marker genes. Finally, the proposed method was further validated against four publicly available metagenomes, including a highly complex Antarctic whale-fall bone sample, which was previously assumed to be too complex for binning prior to functional analysis.
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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.