ArticleNucleic acids research2013
High-resolution microbial community reconstruction by integrating short reads from multiple 16S rRNA regions.
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 18 papers.
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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.
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Who cites it
18 citing papers in PubMed.
- Using short-read 16S rRNA sequencing of multiple variable regions to generate high-quality results to a species level.Frontiers in bioinformatics · 2025Article
- Benchmarking 16S rRNA Gene-Based Approaches to Bacterial Taxonomy Assignment Based on Amplicon Sequencing With Illumina and Oxford Nanopore.International journal of microbiology · 2025Article
- Utilisation ofFrontiers in microbiology · 2024Article
- Cellulase-lactic acid bacteria synergy action regulates silage fermentation of woody plant.Biotechnology for biofuels and bioproducts · 2023Article
- Use of compressed sensing to expedite high-throughput diagnostic testing for COVID-19 and beyond.PLoS computational biology · 2022Article
- Effects of different harvest frequencies on microbial community and metabolomic properties of annual ryegrass silage.Frontiers in microbiology · 2022Article
- Dynamics of Fermentation Parameters and Bacterial Community in High-Moisture Alfalfa Silage with or without Lactic Acid Bacteria.Microorganisms · 2021Article
- Impacts of Low Temperature and Ensiling Period on the Bacterial Community of Oat Silage by SMRT.Microorganisms · 2021Article
- Effects of N Fertilization During Cultivation andFrontiers in microbiology · 2021Article
- Characterization of ecto- and endoparasite communities of wild Mediterranean teleosts by a metabarcoding approach.PloS one · 2019Article
- Optimized detection of bacteria in bloodstream infections.PloS one · 2019Article
- Combining 16S rRNA gene variable regions enables high-resolution microbial community profiling.Microbiome · 2018Article
- Bacterial microbiota of Kazakhstan cheese revealed by single molecule real time (SMRT) sequencing and its comparison with Belgian, Kalmykian and Italian artisanal cheeses.BMC microbiology · 2017Article
- A Novel Lactobacilli-Based Teat Disinfectant for Improving Bacterial Communities in the Milks of Cow Teats with Subclinical Mastitis.Frontiers in microbiology · 2017Article
- RNA Interference Directed against the Transglutaminase Gene Triggers Dysbiosis of Gut Microbiota in Drosophila.The Journal of biological chemistry · 2016Article
- Bacterial Landscape of Bloodstream Infections in Neutropenic Patients via High Throughput Sequencing.PloS one · 2015Article
- Delayed development induced by toxicity to the host can be inherited by a bacterial-dependent, transgenerational effect.Frontiers in genetics · 2014Article
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Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
The emergence of massively parallel sequencing technology has revolutionized microbial profiling, allowing the unprecedented comparison of microbial diversity across time and space in a wide range of host-associated and environmental ecosystems. Although the high-throughput nature of such methods enables the detection of low-frequency bacteria, these advances come at the cost of sequencing read length, limiting the phylogenetic resolution possible by current methods. Here, we present a generic approach for integrating short reads from large genomic regions, thus enabling phylogenetic resolution far exceeding current methods. The approach is based on a mapping to a statistical model that is later solved as a constrained optimization problem. We demonstrate the utility of this method by analyzing human saliva and Drosophila samples, using Illumina single-end sequencing of a 750 bp amplicon of the 16S rRNA gene. Phylogenetic resolution is significantly extended while reducing the number of falsely detected bacteria, as compared with standard single-region Roche 454 Pyrosequencing. Our approach can be seamlessly applied to simultaneous sequencing of multiple genes providing a higher resolution view of the composition and activity of complex microbial communities.
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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.