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 …

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

RM Bowers, NC Kyrpides, R Stepanauskas… - Nature …, 2017 - nature.com
We present two standards developed by the Genomic Standards Consortium (GSC) for
reporting bacterial and archaeal genome sequences. Both are extensions of the Minimum …

metaFlye: scalable long-read metagenome assembly using repeat graphs

M Kolmogorov, DM Bickhart, B Behsaz, A Gurevich… - Nature …, 2020 - nature.com
Long-read sequencing technologies have substantially improved the assemblies of many
isolate bacterial genomes as compared to fragmented short-read assemblies. However …

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

DH Parks, C Rinke, M Chuvochina, PA Chaumeil… - Nature …, 2017 - nature.com
Challenges in cultivating microorganisms have limited the phylogenetic diversity of currently
available microbial genomes. This is being addressed by advances in sequencing …

Advances in metagenomics and its application in environmental microorganisms

L Zhang, FX Chen, Z Zeng, M Xu, F Sun… - Frontiers in …, 2021 - frontiersin.org
Metagenomics is a new approach to study microorganisms obtained from a specific
environment by functional gene screening or sequencing analysis. Metagenomics studies …

A centimeter-long bacterium with DNA contained in metabolically active, membrane-bound organelles

JM Volland, S Gonzalez-Rizzo, O Gros, T Tyml… - Science, 2022 - science.org
Cells of most bacterial species are around 2 micrometers in length, with some of the largest
specimens reaching 750 micrometers. Using fluorescence, x-ray, and electron microscopy in …

Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection

R Seshadri, SC Leahy, GT Attwood, KH Teh… - Nature …, 2018 - nature.com
Productivity of ruminant livestock depends on the rumen microbiota, which ferment
indigestible plant polysaccharides into nutrients used for growth. Understanding the …

Viruses interact with hosts that span distantly related microbial domains in dense hydrothermal mats

Y Hwang, S Roux, C Coclet, SJE Krause… - Nature Microbiology, 2023 - nature.com
Many microbes in nature reside in dense, metabolically interdependent communities. We
investigated the nature and extent of microbe-virus interactions in relation to microbial …

IMG/M: integrated genome and metagenome comparative data analysis system

IMA Chen, VM Markowitz, K Chu… - Nucleic acids …, 2016 - academic.oup.com
Abstract The Integrated Microbial Genomes with Microbiome Samples (IMG/M: https://img.
jgi. doe. gov/m/) system contains annotated DNA and RNA sequence data of (i) archaeal …

HydDB: a web tool for hydrogenase classification and analysis

D Søndergaard, CNS Pedersen, C Greening - Scientific reports, 2016 - nature.com
H2 metabolism is proposed to be the most ancient and diverse mechanism of energy-
conservation. The metalloenzymes mediating this metabolism, hydrogenases, are encoded …