Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation

By J. Beaulaurier, Shijia Zhu, G. Deikus, Ilaria Mogno, Xue-Song Zhang, Austin G. Davis-Richardson, Ronald Canepa, E. Triplett, Jeremiah J. Faith, Robert P. Sebra and 2 more. 2017

136 citations recorded by the source corpus.

Shotgun metagenomics methods enable characterization of microbial communities in human microbiome and environmental samples. Assembly of metagenome sequences does not output whole genomes, so computational binning methods have been developed to cluster sequences into genome 'bins'. These methods exploit sequence composition, species abundance, or chromosome organization but cannot fully distinguish closely related species and strains. We present a binning method that incorporates bacterial DNA methylation signatures, which are detected using single-molecule real-time sequencing. Our method takes advantage of these endogenous epigenetic barcodes to resolve individual reads and assembled contigs into species- and strain-level bins. We validate our method using synthetic and real microbiome sequences. In addition to genome binning, we show that our method links plasmids and other mobile genetic elements to their host species in a real microbiome sample. Incorporation of DNA methylation information into shotgun metagenomics analyses will complement existing methods to enable more accurate sequence binning.

Subfields: Molecular Biology

How researchers see this paper

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

In Molecular Biology

1. Pavlin Gregor Policar
2. Martin Stražar
3. Blaz Zupan
4. C. Hill
5. A. Shkoporov
6. Dmitry Kobak
7. Philipp Berens

Citations in the corpus

• openTSNE: a modular Python library for t-SNE dimensionality reduction and embedding (2019, background): “…as single-cell transcriptomics (Macosko et al. 2015; Cao et al. 2019; Tasic et al. 2018), human genetics (Hirata et al. 2019), metagenomic assembly (Beaulaurier et al. 2018), spatial organization of microbial communities (Sheth, Li, Jiang, Sims, Leong, and Wang 2019), and metabolomics (Tkachev et…”
• Bacteriophages of the Human Gut: The "Known Unknown" of the Microbiome. (2019, background): “…participate in host metabolic processes (Everard and Cani, 2013), stimulate normal development of immunity and brain functions in early ontogenesis (Dinan and Cryan, 2017), provide a barrier against incoming pathogens, and balance local immune responses throughout life (Belkaid and Hand, 2014).”