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Genes 2019, 10(3), 220; https://doi.org/10.3390/genes10030220

Applying Genome-Resolved Metagenomics to Deconvolute the Halophilic Microbiome

Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
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Received: 15 February 2019 / Revised: 8 March 2019 / Accepted: 11 March 2019 / Published: 14 March 2019
(This article belongs to the Special Issue Genetics of Halophilic Microorganisms)
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Abstract

In the past decades, the study of microbial life through shotgun metagenomic sequencing has rapidly expanded our understanding of environmental, synthetic, and clinical microbial communities. Here, we review how shotgun metagenomics has affected the field of halophilic microbial ecology, including functional potential reconstruction, virus–host interactions, pathway selection, strain dispersal, and novel genome discoveries. However, there still remain pitfalls and limitations from conventional metagenomic analysis being applied to halophilic microbial communities. Deconvolution of halophilic metagenomes has been difficult due to the high G + C content of these microbiomes and their high intraspecific diversity, which has made both metagenomic assembly and binning a challenge. Halophiles are also underrepresented in public genome databases, which in turn slows progress. With this in mind, this review proposes experimental and analytical strategies to overcome the challenges specific to the halophilic microbiome, from experimental designs to data acquisition and the computational analysis of metagenomic sequences. Finally, we speculate about the potential applications of other next-generation sequencing technologies in halophilic communities. RNA sequencing, long-read technologies, and chromosome conformation assays, not initially intended for microbiomes, are becoming available in the study of microbial communities. Together with recent analytical advancements, these new methods and technologies have the potential to rapidly advance the field of halophile research.
Keywords: Extremophiles; halophilic microorganisms; hypersaline habitats; metagenomics; microbiome; shotgun sequencing; genome assembly and binning; functional annotation Extremophiles; halophilic microorganisms; hypersaline habitats; metagenomics; microbiome; shotgun sequencing; genome assembly and binning; functional annotation
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited (CC BY 4.0).
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Uritskiy, G.; DiRuggiero, J. Applying Genome-Resolved Metagenomics to Deconvolute the Halophilic Microbiome. Genes 2019, 10, 220.

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