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Exploring the Effects of Spaceflight on Mouse Physiology using the Open Access NASA GeneLab Platform

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Published on: January 13, 2019

Metagenomic ventures into outer sequence space.

¹Theoretical Biology and Bioinformatics; Utrecht University ; Utrecht, The Netherlands ; Centre for Molecular and Biomolecular Informatics; Radboud Institute for Molecular Life Sciences, Radboud University Medical Centre ; Nijmegen, The Netherlands ; Department of Marine Biology, Institute of Biology; Federal University of Rio de Janeiro ; Rio de Janeiro, Brazil.

|October 14, 2015

Summary

This summary is machine-generated.

Unexplored microbial DNA sequences, or "biological dark matter," are often missed in research. Optimally mining metagenomic data is key to discovering new genomes and understanding biosphere diversity.

Keywords:

biological dark matter crAssphage human gut human virome metagenome assembly metagenomics unknowns

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Area of Science:

Environmental DNA sequencing
Metagenomics
Microbial genomics

Background:

Environmental sequencing yields many unannotated DNA/RNA reads, termed "unknowns."
These unknowns represent vast unexplored microbial sequence space, or "biological dark matter."
Current research practices may overlook abundant, widespread genomes due to incomplete data mining.

Purpose of the Study:

To highlight the significance of "unknowns" in metagenomic datasets.
To emphasize the potential for discovering novel microbial life and viruses.
To address the question of the total size of biological sequence space.

Main Methods:

Analysis of metagenomic datasets.
Focus on de novo assembly of shotgun metagenomes.
Comparison of annotated and unannotated sequencing reads.

Main Results:

Unknown sequences may be enriched in bacteriophages, the most abundant biosphere component.
Incomplete mining of metagenomic data can lead to overlooking significant microbial genomes.
The de novo assembly of shotgun metagenomes is crucial for exploring sequence space.

Conclusions:

Optimally mining metagenomic data is essential for a comprehensive understanding of the biosphere.
Further research into "unknowns" is necessary to fully characterize microbial diversity.
De novo assembly is a powerful tool for quantifying biological sequence space.