Nature Biotechnology - A comprehensive microbial resource reconciles genomic and 16S rRNA data in a single tree.

Biologists with bioinformatic skills will be better prepared for the job market, but relatively few biology programs require bioinformatics courses. Inclusio...

Abstract. The Interactive Tree Of Life (https://itol.embl.de) is an online tool for the management, display, annotation and manipulation of phylogenetic an

Microbes are constantly confronted with changes and challenges in their environment. A proper response to these environmental cues is needed for optimal cell...

DNA extraction and preservation bias is a ubiquitous issue in molecular microbial ecology that needs to be considered in every study. We compared the effect of several DNA preservation and extracti...

Nature Reviews Microbiology - In this Review, Lyons, Tino and colleagues explore the evolution of microbial life on Earth and examine the diversity of early microbial metabolic pathways, their...

Background The drive to understand how microbial communities interact with their environments has inspired innovations across many fields. The data generated from sequence-based analyses of microbial...

Abstract. PHASTEST (PHAge Search Tool with Enhanced Sequence Translation) is the successor to the PHAST and PHASTER prophage finding web servers. PHASTEST

Nature Microbiology - The authors review archaeal morphology, surface features, internal organization and cell division, discussing the state of the art and future research directions.

Horizontal gene transfer (HGT) drives microbial adaptation but is often under the control of mobile genetic elements (MGEs) whose interests are not necessarily aligned with those of their hosts. In...

A perfect bacterial genome assembly is one where the assembled sequence is an exact match for the organism’s genome—each replicon sequence is complete and contains no errors. While this has been...

A proposed metagenomic diversity index provides simple and easily intrepretable information to link microbial functional potential and ecosystem processes.

Nature Microbiology - Here the authors use 71 E. coli strains to generate a fosmid library that is experimentally tested for anti-phage activity and find dozens of new candidate defence systems,...

The human microbiome has become an area of intense research due to its potential impact on human health. However, the analysis and interpretation of this dat...

Whole-genome shotgun (WGS) metagenomic sequencing of microbial communities allows us to discover the functions, physiologies, and evolutionary histories of microbial prokaryote and eukaryote members...

Nature Ecology & Evolution - Using deep learning to identify the assembly rules of microbial communities from different habitats, the authors develop a framework to quantify and predict the...

Microbial ecologists are increasingly turning to machine learning (ML) models to better identify and predict meaningful biological patterns and relationships in molecular microbial community data...

Scientific Data - The OceanDNA MAG catalog contains over 50,000 prokaryotic genomes originated from various marine environments

Nature Communications - Here, the authors construct 102 complete metagenome-assembled genomes (cMAGs) from Pacific Biosciences (PacBio) high-accuracy long-read (HiFi) metagenomic sequencing,...

Nature Ecology & Evolution - Landscapes of microbial community function inferred statistically from a broad range of datasets can predict community function on the basis on presence and absence...

This mini-review explores the behaviour of conjugative plasmids in various environments, discusses recent methodologies for tracking mobile genetic elements (MGE) dynamics, and underscores the...

The complexity of microbial communities suggests prevalent interactions involving more than just pairs of species. These so-called higher-order interactions may reveal new molecules that enable...

Assessing the quality of metagenome-derived genome bins using machine learning - chklovski/CheckM2

Abstract. The Reference Sequence (RefSeq) project at the National Center for Biotechnology Information (NCBI) contains over 315 000 bacterial and archaeal

Nature - In situ experiments have demonstrated chemotaxis of marine bacteria and archaea towards specific phytoplankton-derived dissolved organic matter, which leads to microscale partitioning of...

Nature Communications - Here, Leviatan et al. produce 241,118 genome assemblies to produce a new human gut microbiome reference set of 3,594 species genomes, of which 310 represent previously...

The bacterial sequence data publicly available at the global DNA archives is a vast source of information on the evolution of bacteria and their mobile elements. However, most of it is either...

Abstract. The eggNOG (evolutionary gene genealogy Non-supervised Orthologous Groups) database is a bioinformatics resource providing orthology data and com

Competition is prevalent and could be harnessed as an alternative to antibiotics

Nature Microbiology - Carbon catabolism of heterotrophic bacteria can be described using a simple general principle, which is their preference for either glycolytic (sugars) or gluconeogenic (amino...

Eukaryotic genome sequencing and de novo assembly, once the exclusive domain of well-funded international consortia, have become increasingly affordable, thus fitting the budgets of individual...

Aerobic respiration evolved by bricolage, with modules cobbled together as microbial biochemistry coevolved with Earth’s geochemistry. The mitochondrial electron transport chain represents a patchw...

Background Cumulative sequencing efforts have yielded enough genomes to construct pangenomes for dozens of bacterial species and elucidate intraspecies gene conservation. Given the diversity of...

Molecular profiling techniques such as metagenomics, metatranscriptomics or metabolomics offer important insights into the functional diversity of the microbiome. In contrast, 16S rRNA gene sequenc...

ISME Communications - Impact of microbial genome completeness on metagenomic functional inference

Nature Reviews Microbiology - In this Review, Vardi and colleagues examine the different microbial interactions that modulate algal blooms in the ocean, discuss the role of microbial chemicals in...

Nature Ecology & Evolution - A longitudinal analysis of microbial community assembly dynamics reveals that communities cultured in metabolically complex media are more different from each other...

Humans and many other hosts establish a diverse community of beneficial microbes anew each generation, but what determines the success of the assembly process remains poorly understood. This study...

Nature Communications - Here, Qi et al. assembled ~3000 archaeal genomes from hot springs, capturing temporal dynamics and environmental diversity, and systematically explored functional niches and...

Background The 16S rRNA gene is used extensively in bacterial phylogenetics, in species delineation, and now widely in microbiome studies. However, the gene suffers from intragenomic heterogeneity,...

Background The rapid growth of high-throughput sequencing-based microbiome profiling has yielded tremendous insights into human health and physiology. Data generated from high-throughput sequencing...

Abstract. We present MediaDive (https://mediadive.dsmz.de), a comprehensive and expert-curated cultivation media database, which comprises recipes, instruc

Nature Microbiology - Microbiology must be represented at climate change talks

Nature Ecology & Evolution - An unsupervised, annotation-free method is developed that can identify microbial functional groups on the basis of variation in microbiome data and environmental...

The ISME Journal - Microbial volatiles mediate bacterial evolutionary dynamics

Author summary The metabolic activity of microbes is essential to sustaining life on Earth, biotechnological processes, and host fitness. As a result, the metabolic traits of microbes have been a...

Antimicrobial resistance genes (ARG) are commonly found on acquired mobile genetic elements (MGEs) such as plasmids or transposons. Understanding the spread of resistance genes associated with mobile...

Nature Communications - The timing of cellular evolution is poorly constrained. Here, the authors used improved molecular dating approaches to study the evolution of the ATP synthase in light of a...

Nature Reviews Microbiology - The order and timing of the arrival (priority effects) of members of a microbiome can influence microbiome composition and function. In this Review, Debray and...

Journal of Microbiology - Pure cultivation of microbes is still limited by the challenges of microbial uncultivability, with most microbial strains unable to be cultivated under standard laboratory...

AbstractMotivation. In metagenomics, the study of environmentally associated microbial communities from their sampled DNA, one of the most fundamental comp

Nature - Ancient microbiomes from palaeofaeces are more similar to non-industrialized than industrialized human gut microbiomes regardless of geography, but 39% of their de novo reconstructed...

An R package designed for reading geographical data, manipulating and visualizing geographical boundary data, downloading spatial datasets, calculating mic

Nature Protocols - In this Protocol Extension, the authors extend their original Protocol used to generate a genome-scale metabolic model for a single strain to enable multi-strain models to be...