A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

Nature Biotechnology, Год журнала: 2018, Номер 36(10), С. 996 - 1004

Опубликована: Авг. 27, 2018

Язык: Английский

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A communal catalogue reveals Earth’s multiscale microbial diversity

Nature, Год журнала: 2017, Номер 551(7681), С. 457 - 463

Опубликована: Окт. 31, 2017

Abstract Our growing awareness of the microbial world’s importance and diversity contrasts starkly with our limited understanding its fundamental structure. Despite recent advances in DNA sequencing, a lack standardized protocols common analytical frameworks impedes comparisons among studies, hindering development global inferences about life on Earth. Here we present meta-analysis community samples collected by hundreds researchers for Earth Microbiome Project. Coordinated new methods, particularly use exact sequences instead clustered operational taxonomic units, enable bacterial archaeal ribosomal RNA gene to be followed across multiple studies allow us explore patterns at an unprecedented scale. The result is both reference database giving context sequence data framework incorporating from future fostering increasingly complete characterization Earth’s diversity.

Язык: Английский

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Stochastic Community Assembly: Does It Matter in Microbial Ecology?

Microbiology and Molecular Biology Reviews, Год журнала: 2017, Номер 81(4)

Опубликована: Окт. 12, 2017

Understanding the mechanisms controlling community diversity, functions, succession, and biogeography is a central, but poorly understood, topic in ecology, particularly microbial ecology. Although stochastic processes are believed to play nonnegligible roles shaping structure, their importance relative deterministic hotly debated. The of ecological stochasticity structure far less appreciated. Some main reasons for such heavy debates difficulty defining diverse methods used delineating stochasticity. Here, we provide critical review synthesis data from most recent studies on assembly We then describe both components embedded various processes, including selection, dispersal, diversification, drift. also different approaches inferring observational diversity patterns highlight experimental communities. In addition, research challenges, gaps, future directions research.

Язык: Английский

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Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

Nature Microbiology, Год журнала: 2017, Номер 2(11), С. 1533 - 1542

Опубликована: Сен. 11, 2017

Abstract Challenges in cultivating microorganisms have limited the phylogenetic diversity of currently available microbial genomes. This is being addressed by advances sequencing throughput and computational techniques that allow for cultivation-independent recovery genomes from metagenomes. Here, we report reconstruction 7,903 bacterial archaeal >1,500 public All are estimated to be ≥50% complete nearly half ≥90% with ≤5% contamination. These increase genome trees >30% provide first representatives 17 three candidate phyla. We also recovered 245 Patescibacteria superphylum (also known as Candidate Phyla Radiation) find relative this group varies substantially different protein marker sets. The scale quality data set demonstrate recovering metagenomes provides an expedient path forward exploring dark matter.

Язык: Английский

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Shotgun metagenomics, from sampling to analysis

Nature Biotechnology, Год журнала: 2017, Номер 35(9), С. 833 - 844

Опубликована: Сен. 1, 2017

Язык: Английский

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Best practices for analysing microbiomes

Nature Reviews Microbiology, Год журнала: 2018, Номер 16(7), С. 410 - 422

Опубликована: Май 23, 2018

Язык: Английский

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Function and functional redundancy in microbial systems

Nature Ecology & Evolution, Год журнала: 2018, Номер 2(6), С. 936 - 943

Опубликована: Апрель 12, 2018

Язык: Английский

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A complete domain-to-species taxonomy for Bacteria and Archaea

Nature Biotechnology, Год журнала: 2020, Номер 38(9), С. 1079 - 1086

Опубликована: Апрель 27, 2020

Язык: Английский

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Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system

Nature Communications, Год журнала: 2016, Номер 7(1)

Опубликована: Окт. 24, 2016

Abstract The subterranean world hosts up to one-fifth of all biomass, including microbial communities that drive transformations central Earth’s biogeochemical cycles. However, little is known about how complex in such environments are structured, and inter-organism interactions shape ecosystem function. Here we apply terabase-scale cultivation-independent metagenomics aquifer sediments groundwater, reconstruct 2,540 draft-quality, near-complete complete strain-resolved genomes represent the majority bacterial phyla as well 47 newly discovered phylum-level lineages. Metabolic analyses spanning this vast phylogenetic diversity representing 36% organisms detected system used document distribution pathways coexisting organisms. Consistent with prior findings indicating metabolic handoffs simple consortia, find few within community can conduct multiple sequential redox transformations. As environmental conditions change, different assemblages selected for, altering linkages among major

Язык: Английский

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Scaling laws predict global microbial diversity

Proceedings of the National Academy of Sciences, Год журнала: 2016, Номер 113(21), С. 5970 - 5975

Опубликована: Май 2, 2016

Significance Ecological scaling laws are intensively studied for their predictive power and universal nature but often fail to unify biodiversity across domains of life. Using a global-scale compilation microbial macrobial data, we uncover relationships commonness rarity that scale with abundance at similar rates microorganisms macroscopic plants animals. We then show unified law predicts the dominant species 30 orders magnitude all on Earth. this combined lognormal model biodiversity, predict Earth is home as many 1 trillion (10 12 ) species.

Язык: Английский

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