ArticleEnvironmental microbiology2013
Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities.
Article in Environmental microbiology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 100 papers, 1 of them a synthesis that pooled it.
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Who cites it
100 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- Comparison of the rhizospheric soil bacteriomes of Oryza sativa and Solanum melongena crop cultivars reveals key genes and pathways involved in biosynthesis of ectoine, lysine, and catechol meta-cleavage.Functional & integrative genomics · 2025Article
- Metagenomic analysis reveals methanogenic and other archaeal genes in the digestive tract of invasive Japanese beetle larvae and associated soil.Frontiers in microbiology · 2025Article
- kMetaShot: a fast and reliable taxonomy classifier for metagenome-assembled genomes.Briefings in bioinformatics · 2024Article
- Graph-based self-supervised learning for repeat detection in metagenomic assembly.Genome research · 2024Article
- YACHT: an ANI-based statistical test to detect microbial presence/absence in a metagenomic sample.Bioinformatics (Oxford, England) · 2024Article
- YACHT: an ANI-based statistical test to detect microbial presence/absence in a metagenomic sample.bioRxiv : the preprint server for biology · 2023Article
- Predicting environmental stressor levels with machine learning: a comparison between amplicon sequencing, metagenomics, and total RNA sequencing based on taxonomically assigned data.Frontiers in microbiology · 2023Article
- Benchmarking second and third-generation sequencing platforms for microbial metagenomics.Scientific data · 2022Article
- Constructing metagenome-assembled genomes for almost all components in a real bacterial consortium for binning benchmarking.BMC genomics · 2022Article
- Potential Use of Microbial Community Genomes in Various Dimensions of Agriculture Productivity and Its Management: A Review.Frontiers in microbiology · 2022Review
- KOMB: K-core based de novo characterization of copy number variation in microbiomes.Computational and structural biotechnology journal · 2022Article
- Transformation of Silver Nanoparticles (AgNPs) during Lime Treatment of Wastewater Sludge and Their Impact on Soil Bacteria.Nanomaterials (Basel, Switzerland) · 2021Article
- METAMVGL: a multi-view graph-based metagenomic contig binning algorithm by integrating assembly and paired-end graphs.BMC bioinformatics · 2021Article
- Kssd: sequence dimensionality reduction by k-mer substring space sampling enables real-time large-scale datasets analysis.Genome biology · 2021Article
- Functional plasticity in oyster gut microbiomes along a eutrophication gradient in an urbanized estuary.Animal microbiome · 2021Article
- Localized effect of treated wastewater effluent on the resistome of an urban watershed.GigaScience · 2020Article
- Metabolomics as an Emerging Tool in the Search for Astrobiologically Relevant Biomarkers.Astrobiology · 2020Review
- ADEPT: a domain independent sequence alignment strategy for gpu architectures.BMC bioinformatics · 2020Article
40 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors.
Funding
Abstract
Next-generation sequencing has dramatically changed the landscape of microbial ecology, large-scale and in-depth diversity studies being now widely accessible. However, determining the accuracy of taxonomic and quantitative inferences and comparing results obtained with different approaches are complicated by incongruence of experimental and computational data types and also by lack of knowledge of the true ecological diversity. Here we used highly diverse bacterial and archaeal synthetic communities assembled from pure genomic DNAs to compare inferences from metagenomic and SSU rRNA amplicon sequencing. Both Illumina and 454 metagenomic data outperformed amplicon sequencing in quantifying the community composition, but the outcome was dependent on analysis parameters and platform. New approaches in processing and classifying amplicons can reconstruct the taxonomic composition of the community with high reproducibility within primer sets, but all tested primers sets lead to significant taxon-specific biases. Controlled synthetic communities assembled to broadly mimic the phylogenetic richness in target environments can provide important validation for fine-tuning experimental and computational parameters used to characterize natural communities.
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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.