Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2022:2522:487-527.
doi: 10.1007/978-1-0716-2445-6_33.

Reconstruction of Archaeal Genomes from Short-Read Metagenomes

Till L V Bornemann  1 , Panagiotis S Adam  2 , Alexander J Probst  3   4
Affiliations

Reconstruction of Archaeal Genomes from Short-Read Metagenomes

Till L V Bornemann et al. Methods Mol Biol. 2022.

Abstract

As the majority of biological diversity remains unexplored and uncultured, investigating it requires culture-independent approaches. Archaea in particular suffer from a multitude of issues that make their culturing problematic, from them being frequently members of the rare biosphere, to low growth rates, to them thriving under very specific and often extreme environmental and community conditions that are difficult to replicate. OMICs techniques are state of the art approaches that allow direct high-throughput investigations of environmental samples at all levels from nucleic acids to proteins, lipids, and secondary metabolites. Metagenomics, as the foundation for other OMICs techniques, facilitates the identification and functional characterization of the microbial community members and can be combined with other methods to provide insights into the microbial activities, both on the RNA and protein levels. In this chapter, we provide a step-by-step workflow for the recovery of archaeal genomes from metagenomes, starting from raw short-read sequences. This workflow can be applied to recover bacterial genomes as well.

Keywords: Genome curation; Genome-resolved metagenomics; Prokaryotes; Rare biosphere; Short-read sequencing.

PubMed Disclaimer

References

    1. Tyson GW, Chapman J, Hugenholtz P et al (2004) Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428:37–43. https://doi.org/10.1038/nature02340 - DOI - PubMed
    1. Venter JC, Remington K, Heidelberg JF et al (2004) Environmental genome shotgun sequencing of the Sargasso Sea. Science 304:66–74. https://doi.org/10.1126/science.1093857 - DOI - PubMed
    1. Eloe-Fadrosh EA, Ivanova NN, Woyke T, Kyrpides NC (2016) Metagenomics uncovers gaps in amplicon-based detection of microbial diversity. Nat Microbiol 1:1–4. https://doi.org/10.1038/nmicrobiol.2015.32 - DOI
    1. Brown CT, Hug LA, Thomas BC et al (2015) Unusual biology across a group comprising more than 15% of domain Bacteria. Nature 523:208. https://doi.org/10.1038/nature14486 - DOI - PubMed
    1. Huber H, Hohn MJ, Rachel R et al (2002) A new phylum of Archaea represented by a nanosized hyperthermophilic symbiont. Nature 417:63–67. https://doi.org/10.1038/417063a - DOI - PubMed

LinkOut - more resources