The Origin and Diversification of Mitochondria

Current Biology, Journal Year: 2017, Volume and Issue: 27(21), P. R1177 - R1192

Published: Nov. 1, 2017

Language: Английский

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A genomic catalog of Earth’s microbiomes

Nature Biotechnology, Journal Year: 2020, Volume and Issue: 39(4), P. 499 - 509

Published: Nov. 9, 2020

Abstract The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has enabled insights into the ecology evolution environmental host-associated microbiomes. Here we applied this approach to >10,000 collected diverse habitats covering all Earth’s continents oceans, including human animal hosts, engineered environments, natural agricultural soils, capture extant microbial, metabolic functional potential. This comprehensive catalog includes 52,515 metagenome-assembled representing 12,556 novel candidate species-level operational taxonomic units spanning 135 phyla. expands known phylogenetic diversity bacteria archaea by 44% is broadly available for streamlined comparative analyses, interactive exploration, modeling bulk download. We demonstrate utility collection understanding secondary-metabolite biosynthetic potential resolving thousands new host linkages uncultivated viruses. resource underscores value genome-centric approaches revealing genomic properties microorganisms that affect ecosystem processes.

Language: Английский

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Major New Microbial Groups Expand Diversity and Alter our Understanding of the Tree of Life

Cell, Journal Year: 2018, Volume and Issue: 172(6), P. 1181 - 1197

Published: March 1, 2018

Language: Английский

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Archaea and the origin of eukaryotes

Nature Reviews Microbiology, Journal Year: 2017, Volume and Issue: 15(12), P. 711 - 723

Published: Nov. 10, 2017

Language: Английский

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An evolving view of methane metabolism in the Archaea

Nature Reviews Microbiology, Journal Year: 2019, Volume and Issue: 17(4), P. 219 - 232

Published: Jan. 21, 2019

Language: Английский

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Phylogenetically Novel Uncultured Microbial Cells Dominate Earth Microbiomes

mSystems, Journal Year: 2018, Volume and Issue: 3(5)

Published: Sept. 24, 2018

To describe a microbe's physiology, including its metabolism, environmental roles, and growth characteristics, it must be grown in laboratory culture. Unfortunately, many phylogenetically novel groups have never been cultured, so their physiologies only inferred from genomics characteristics. Although the diversity, or number of different taxonomic groups, uncultured clades has studied well, global abundances, numbers cells any given environment, not assessed. We quantified degree similarity 16S rRNA gene sequences diverse environments publicly available metagenome metatranscriptome databases, which we show far less culture bias present primer-amplified surveys, to those nearest cultured relatives. Whether normalized scaffold read depths not, highest abundances metagenomic belong seawater, freshwater, terrestrial subsurface, soil, hypersaline environments, marine sediment, hot springs, hydrothermal vents, nonhuman hosts, snow, bioreactors (22% 87% genera classes 0% 64% phyla). The exceptions were human human-associated dominated by (45% 97%). estimate that phyla could comprise 7.3 × 10

Language: Английский

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Coral microbiome dynamics, functions and design in a changing world

Nature Reviews Microbiology, Journal Year: 2019, Volume and Issue: 17(9), P. 557 - 567

Published: July 1, 2019

Language: Английский

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A standardized archaeal taxonomy for the Genome Taxonomy Database

Nature Microbiology, Journal Year: 2021, Volume and Issue: 6(7), P. 946 - 959

Published: June 21, 2021

Language: Английский

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Bathyarchaeota: globally distributed metabolic generalists in anoxic environments

FEMS Microbiology Reviews, Journal Year: 2018, Volume and Issue: 42(5), P. 639 - 655

Published: May 18, 2018

Bathyarchaeota, formerly known as the Miscellaneous Crenarchaeotal Group, is a phylum of global generalists that are widespread in anoxic sediments, which host relatively high abundance archaeal communities. Until now, 25 subgroups have been identified Bathyarchaeota. The distinct bathyarchaeotal diverged to adapt marine and freshwater environments. Based on physiological genomic evidence, acetyl-coenzyme A-centralized heterotrophic pathways energy conservation proposed function Bathyarchaeota; these microbes able anaerobically utilize (i) detrital proteins, (ii) polymeric carbohydrates, (iii) fatty acids/aromatic compounds, (iv) methane (or short chain alkane) methylated and/or (v) potentially other organic matter. Furthermore, members wide metabolic capabilities, including acetogenesis, metabolism, dissimilatory nitrogen sulfur reduction, they also potential interactions with anaerobic methane-oxidizing archaea, acetoclastic methanogens bacteria. These results not only demonstrated multiple important ecological functions this phylum, but paved way for detailed understanding evolution metabolism archaea such. This review summarizes recent findings pertaining ecological, aspects highlighting vital role carbon cycling.

Language: Английский

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Principles for Integrative Structural Biology Studies

Cell, Journal Year: 2019, Volume and Issue: 177(6), P. 1384 - 1403

Published: May 1, 2019

Integrative structure determination is a powerful approach to modeling the structures of biological systems based on data produced by multiple experimental and theoretical methods, with implications for our understanding cellular biology drug discovery. This Primer introduces theory methods integrative approaches, emphasizing kinds that can be effectively included in developing models using nuclear pore complex as an example illustrate practice challenges involved. These guidelines are intended aid researcher applying structural their interest thus take advantage this rapidly evolving field.

Language: Английский

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