Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy

By Christian M. K. Sieber, Alexander J. Probst, A. Sharrar, Brian C. Thomas, M. Hess, Susannah Tringe, Jillian F. Banfield. Nature Microbiology, 2017

1,452 citations recorded by the source corpus.

Microbial communities are critical to ecosystem function. A key objective of metagenomic studies is to analyse organism-specific metabolic pathways and reconstruct community interaction networks. This requires accurate assignment of assembled genome fragments to genomes. Existing binning methods often fail to reconstruct a reasonable number of genomes and report many bins of low quality and completeness. Furthermore, the performance of existing algorithms varies between samples and biotopes. Here, we present a dereplication, aggregation and scoring strategy, DAS Tool, that combines the strengths of a flexible set of established binning algorithms. DAS Tool applied to a constructed community generated more accurate bins than any automated method. Indeed, when applied to environmental and host-associated samples of different complexity, DAS Tool recovered substantially more near-complete genomes, including previously unreported lineages, than any single binning method alone. The ability to reconstruct many near-complete genomes from metagenomics data will greatly advance genome-centric analyses of ecosystems. Here the authors present a tool that enables a flexible set of existing binning algorithms to be combined, resulting in improved binning accuracy and the recovery of more near-complete genomes from metagenomes compared to standalone methods.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/c37cc9c75cead9f24bbf6197ff4c9b12c4107b51

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Ecology

1. Fernando Puente-Sánchez
2. Tong Chen
3. Meiping Lu
4. G. Uritskiy
5. Xubo Qian
6. Yuan Qin
7. Yang Bai
8. Yong-xin Liu

In Molecular Biology

1. Fernando Puente-Sánchez
2. Tong Chen
3. Meiping Lu
4. G. Uritskiy
5. Xubo Qian
6. Yuan Qin
7. Yang Bai
8. Yong-xin Liu

Citations in the corpus

• MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis (2018, methodology): “DAS_Tool consistently produced high-completion bins; however, these bins had relatively high contamination, which is a result of the aggregation approach that DAS_Tool takes.”
• SqueezeMeta, A Highly Portable, Fully Automatic Metagenomic Analysis Pipeline (2018, methodology): “Additionally, SqueezeMeta includes DAS Tool (Sieber et al., 2018) to merge the multiple binning results in just one set.”
• A practical guide to amplicon and metagenomic analysis of microbiome data (2020, methodology): “We recommend using a binning pipe-line such as MetaWRAP (Uritskiy et al., 2018) or DAStool (Sieber et al., 2018), which integrate several binning software packages to obtain re fi ned binning results and more complete genomes with less contamination.”