Microbial diversity in extreme environments

WS Shu, LN Huang - Nature Reviews Microbiology, 2022 - nature.com
A wide array of microorganisms, including many novel, phylogenetically deeply rooted taxa,
survive and thrive in extreme environments. These unique and reduced-complexity …

Metabolic exchanges are ubiquitous in natural microbial communities

C Kost, KR Patil, J Friedman, SL Garcia… - Nature Microbiology, 2023 - nature.com
Microbial communities drive global biogeochemical cycles and shape the health of plants
and animals—including humans. Their structure and function are determined by ecological …

CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning

A Chklovski, DH Parks, BJ Woodcroft, GW Tyson - Nature Methods, 2023 - nature.com
Advances in sequencing technologies and bioinformatics tools have dramatically increased
the recovery rate of microbial genomes from metagenomic data. Assessing the quality of …

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 …

Microbiome definition re-visited: old concepts and new challenges

G Berg, D Rybakova, D Fischer, T Cernava… - Microbiome, 2020 - Springer
The field of microbiome research has evolved rapidly over the past few decades and has
become a topic of great scientific and public interest. As a result of this rapid growth in …

A unified catalog of 204,938 reference genomes from the human gut microbiome

A Almeida, S Nayfach, M Boland, F Strozzi… - Nature …, 2021 - nature.com
Comprehensive, high-quality reference genomes are required for functional characterization
and taxonomic assignment of the human gut microbiota. We present the Unified Human …

DRAM for distilling microbial metabolism to automate the curation of microbiome function

M Shaffer, MA Borton, BB McGivern… - Nucleic acids …, 2020 - academic.oup.com
Microbial and viral communities transform the chemistry of Earth's ecosystems, yet the
specific reactions catalyzed by these biological engines are hard to decode due to the …

Proposal to reclassify the proteobacterial classes Deltaproteobacteria and Oligoflexia, and the phylum Thermodesulfobacteria into four phyla reflecting major …

DW Waite, M Chuvochina, C Pelikan… - … of Systematic and …, 2020 - microbiologyresearch.org
The class Deltaproteobacteria comprises an ecologically and metabolically diverse group of
bacteria best known for dissimilatory sulphate reduction and predatory behaviour. Although …

MiDAS 4: A global catalogue of full-length 16S rRNA gene sequences and taxonomy for studies of bacterial communities in wastewater treatment plants

MKD Dueholm, M Nierychlo, KS Andersen… - Nature …, 2022 - nature.com
Microbial communities are responsible for biological wastewater treatment, but our
knowledge of their diversity and function is still poor. Here, we sequence more than 5 million …

Metal contamination and bioremediation of agricultural soils for food safety and sustainability

D Hou, D O'Connor, AD Igalavithana… - Nature Reviews Earth & …, 2020 - nature.com
Agricultural soil is a non-renewable natural resource that requires careful stewardship in
order to achieve the United Nations' Sustainable Development Goals. However, industrial …