ArticleApplied and environmental microbiology2016
Microbial Community Analysis with Ribosomal Gene Fragments from Shotgun Metagenomes.
Article in Applied and environmental microbiology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- Consistent microbial insights across sequencing methods in soil studies: the role of reference taxonomies.mSystems · 2025Article
- Propane Monooxygenases in Soil Associated Metagenomes Align Most Closely to those in the Genera Kribbella, Amycolatopsis, Bradyrhizobium, Paraburkholderia and Burkholderia.Current microbiology · 2024Article
- Article
- Metagenomics reveals novel microbial signatures of farm exposures in house dust.medRxiv : the preprint server for health sciences · 2023Article
- Metagenomics reveals novel microbial signatures of farm exposures in house dust.Frontiers in microbiology · 2023Article
- Responses of soil micro-eukaryotic communities to decadal drainage in a Siberian wet tussock tundra.Frontiers in microbiology · 2023Article
- Microbial metabolic responses and COJournal of microbiology (Seoul, Korea) · 2022Article
- RiboTaxa: combined approaches for rRNA genes taxonomic resolution down to the species level from metagenomics data revealing novelties.NAR genomics and bioinformatics · 2022Article
- NetCom: A Network-Based Tool for Predicting Metabolic Activities of Microbial Communities Based on Interpretation of Metagenomics Data.Microorganisms · 2021Article
- Phagotrophic Protists and Their Associates: Evidence for Preferential Grazing in an Abiotically Driven Soil Ecosystem.Microorganisms · 2021Article
- Metagenomic analysis reveals the shared and distinct features of the soil resistome across tundra, temperate prairie, and tropical ecosystems.Microbiome · 2021Article
- CaptureSeq: Hybridization-Based Enrichment ofMicroorganisms · 2021Article
- phyloFlash: Rapid Small-Subunit rRNA Profiling and Targeted Assembly from Metagenomes.mSystems · 2020Article
- From Seabed to Bedside: A Review on Promising Marine Anticancer Compounds.Biomolecules · 2020Review
- Design of targeted primers based on 16S rRNA sequences in meta-transcriptomic datasets and identification of a novel taxonomic group in the Asgard archaea.BMC microbiology · 2020Article
- Community members in activated sludge as determined by molecular probe technology.Water research · 2020Article
- Article
- High-throughput DNA sequencing technologies for water and wastewater analysis.Science progress · 2019Review
- Review, Evaluation, and Directions for Gene-Targeted Assembly for Ecological Analyses of Metagenomes.Frontiers in genetics · 2019Article
- Dynamics of microbial populations mediating biogeochemical cycling in a freshwater lake.Microbiome · 2018Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Shotgun metagenomic sequencing does not depend on gene-targeted primers or PCR amplification; thus, it is not affected by primer bias or chimeras. However, searching rRNA genes from large shotgun Illumina data sets is computationally expensive, and no approach exists for unsupervised community analysis of small-subunit (SSU) rRNA gene fragments retrieved from shotgun data. We present a pipeline, SSUsearch, to achieve the faster identification of short-subunit rRNA gene fragments and enabled unsupervised community analysis with shotgun data. It also includes classification and copy number correction, and the output can be used by traditional amplicon analysis platforms. Shotgun metagenome data using this pipeline yielded higher diversity estimates than amplicon data but retained the grouping of samples in ordination analyses. We applied this pipeline to soil samples with paired shotgun and amplicon data and confirmed bias against Verrucomicrobia in a commonly used V6-V8 primer set, as well as discovering likely bias against Actinobacteria and for Verrucomicrobia in a commonly used V4 primer set. This pipeline can utilize all variable regions in SSU rRNA and also can be applied to large-subunit (LSU) rRNA genes for confirmation of community structure. The pipeline can scale to handle large amounts of soil metagenomic data (5 Gb memory and 5 central processing unit hours to process 38 Gb [1 lane] of trimmed Illumina HiSeq2500 data) and is freely available at https://github.com/dib-lab/SSUsearch under a BSD license.
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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.