A genomic catalog of Earth's microbiomes

S Nayfach, S Roux, R Seshadri, D Udwary… - Nature …, 2021‏ - nature.com
The reconstruction of bacterial and archaeal genomes from shotgun metagenomes has
enabled insights into the ecology and evolution of environmental and host-associated …

The Fe(II)-oxidizing Zetaproteobacteria: historical, ecological and genomic perspectives

SM McAllister, RM Moore, A Gartman… - FEMS microbiology …, 2019‏ - academic.oup.com
The Zetaproteobacteria are a class of bacteria typically associated with marine Fe (II)-
oxidizing environments. First discovered in the hydrothermal vents at Loihi Seamount …

Genome-centric view of carbon processing in thawing permafrost

BJ Woodcroft, CM Singleton, JA Boyd, PN Evans… - Nature, 2018‏ - nature.com
As global temperatures rise, large amounts of carbon sequestered in permafrost are
becoming available for microbial degradation. Accurate prediction of carbon gas emissions …

Biosynthetic potential of uncultured Antarctic soil bacteria revealed through long-read metagenomic sequencing

V Waschulin, C Borsetto, R James… - The ISME …, 2022‏ - academic.oup.com
The growing problem of antibiotic resistance has led to the exploration of uncultured
bacteria as potential sources of new antimicrobials. PCR amplicon analyses and short-read …

Genomic exploration of coral-associated bacteria: identifying probiotic candidates to increase coral bleaching resilience in Galaxea fascicularis

T Doering, K Tandon, SH Topa, SJ Pidot, LL Blackall… - Microbiome, 2023‏ - Springer
Background Reef-building corals are acutely threatened by ocean warming, calling for
active interventions to reduce coral bleaching and mortality. Corals associate with a wide …

gcType: a high-quality type strain genome database for microbial phylogenetic and functional research

W Shi, Q Sun, G Fan, S Hideaki, O Moriya… - Nucleic Acids …, 2021‏ - academic.oup.com
Taxonomic and functional research of microorganisms has increasingly relied upon genome-
based data and methods. As the depository of the Global Catalogue of Microorganisms …

Metagenome-assembled genomes provide new insight into the microbial diversity of two thermal pools in Kamchatka, Russia

LGE Wilkins, CL Ettinger, G Jospin, JA Eisen - Scientific reports, 2019‏ - nature.com
Culture-independent methods have contributed substantially to our understanding of global
microbial diversity. Recently developed algorithms to construct whole genomes from …

[HTML][HTML] The importance of designating type material for uncultured taxa

M Chuvochina, C Rinke, DH Parks, MS Rappé… - Systematic and applied …, 2019‏ - Elsevier
Naming of uncultured Bacteria and Archaea is often inconsistent with the International Code
of Nomenclature of Prokaryotes. The recent practice of proposing names for higher taxa …

[HTML][HTML] Effect of long-term farming practices on agricultural soil microbiome members represented by metagenomically assembled genomes (MAGs) and their …

J Nelkner, C Henke, TW Lin, W Pätzold, J Hassa… - Genes, 2019‏ - mdpi.com
To follow the hypothesis that agricultural management practices affect structure and function
of the soil microbiome regarding soil health and plant-beneficial traits, high-throughput (HT) …

Neutral theory, microbial practice: challenges in bacterial population genetics

EPC Rocha - Molecular biology and evolution, 2018‏ - academic.oup.com
I detail four major open problems in microbial population genetics with direct implications to
the study of molecular evolution: the lack of neutral polymorphism, the modeling of …