The future is now: single-cell genomics of bacteria and archaea.
Paul C. Blainey,Paul C. Blainey +1 more
TLDR
Over the next decade, increasingly powerful tools for single-cell genome sequencing and analysis will play key roles in accessing the genomes of uncultivated organisms, determining the basis of microbial community functions, and fundamental aspects of microbial population biology.Abstract:
Interest in the expanding catalog of uncultivated microorganisms, increasing recognition of heterogeneity among seemingly similar cells, and technological advances in whole-genome amplification and single-cell manipulation are driving considerable progress in single-cell genomics. Here, the spectrum of applications for single-cell genomics, key advances in the development of the field, and emerging methodology for single-cell genome sequencing are reviewed by example with attention to the diversity of approaches and their unique characteristics. Experimental strategies transcending specific methodologies are identified and organized as a road map for future studies in single-cell genomics of environmental microorganisms. Over the next decade, increasingly powerful tools for single-cell genome sequencing and analysis will play key roles in accessing the genomes of uncultivated organisms, determining the basis of microbial community functions, and fundamental aspects of microbial population biology.read more
Citations
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Journal ArticleDOI
Decoupling function and taxonomy in the global ocean microbiome
TL;DR: It is found that environmental conditions strongly influence the distribution of functional groups in marine microbial communities by shaping metabolic niches, but only weakly influence taxonomic composition within individual functional groups.
Journal ArticleDOI
Ten years of next-generation sequencing technology.
TL;DR: An overview of the evolution of NGS is provided and the most significant improvements in sequencing technologies and library preparation protocols are discussed and the current landscape of N GS applications is explored to provide a perspective for future developments.
Journal ArticleDOI
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
Robert M. Bowers,Nikos C. Kyrpides,Ramunas Stepanauskas,Miranda Harmon-Smith,Devin F. R. Doud,T. B. K. Reddy,Frederik Schulz,Jessica K. Jarett,Adam R. Rivers,Adam R. Rivers,Emiley A. Eloe-Fadrosh,Susannah G. Tringe,Susannah G. Tringe,Natalia Ivanova,Alex Copeland,Alicia Clum,Eric D. Becraft,Rex R. Malmstrom,Bruce W. Birren,Mircea Podar,Peer Bork,George M. Weinstock,George M. Garrity,Jeremy A. Dodsworth,Shibu Yooseph,Granger G. Sutton,Frank Oliver Gloeckner,Jack A. Gilbert,William C. Nelson,Steven J. Hallam,Sean P. Jungbluth,Sean P. Jungbluth,Thijs J. G. Ettema,Scott Tighe,Konstantinos T. Konstantinidis,Wen Tso Liu,Brett J. Baker,Thomas Rattei,Jonathan A. Eisen,Brian P. Hedlund,Katherine D. McMahon,Noah Fierer,Rob Knight,Robert D. Finn,Guy Cochrane,Ilene Karsch-Mizrachi,Gene W. Tyson,Christian Rinke,Alla Lapidus,Folker Meyer,Pelin Yilmaz,Donovan H. Parks,A. M. Eren,Lynn M. Schriml,Jillian F. Banfield,Philip Hugenholtz,Tanja Woyke +56 more
TL;DR: Two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences are presented, including the Minimum Information about a Single Amplified Genome (MISAG) and the Minimum information about a Metagenome-Assembled Genomes (MIMAG), including estimates of genome completeness and contamination.
Journal ArticleDOI
Single-cell sequencing-based technologies will revolutionize whole-organism science
TL;DR: The unabated progress in next-generation sequencing technologies is fostering a wave of new genomics, epigenomics, transcriptomics and proteomics technologies, enabling high-throughput, multi-dimensional analyses of individual cells that will produce detailed knowledge of the cell lineage trees of higher organisms, including humans.
Journal ArticleDOI
Single-cell genome sequencing: current state of the science
TL;DR: An overview of the current state of the field of single-cell genome sequencing is provided, focusing on the technical challenges of making measurements that start from a single molecule of DNA, and how some of these recent methodological advancements have enabled the discovery of unexpected new biology.
References
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