Pathogenicity—the ability to cause infectious disease—is widespread among bacteria and eukaryotes but conspicuously absent from archaea, the third domain of life. To understand why archaea are non-pat...

Pseudomonas aeruginosa is a common culprit in hospital-acquired bacterial infections and is growing more resistant to antibiotics. New findings from Aaron Smith, professor of chemistry and…

Fever is a common adverse reaction to vaccination, contributing to vaccine hesitancy and reduced uptake. To understand variation in fever risk, we longitudinally profiled fecal microbiota, oral temper...

Run MHC binding, presentation, immunogenicity and antigen-processing predictors through one predict() call

Heritable microbes profoundly influence insect biology, yet the traits they confer often evolve rapidly and differ among closely related symbiont s...

Published in Microbial genomics

Published in PloS one

NSF Postdoctoral Research Fellowships in Biology

This Community Page presents the 100 Diatom Genomes Project, which aims to sequence the genomes and transcriptomes of 100 diatom species across major lineages, life forms and ecological strategies. Th...

Microbiome - Symbiotic microorganisms can profoundly impact insect biology, including their life history traits, population dynamics, and evolutionary trajectories. However, microbiota remain...

Authigenic minerals reflect specific respiration and fermentation pathways leading to diagenetic redistribution of iron and carbon isotopes during burial, according to an in-depth characterization of ...

DIAMOND DeepClust provides an ultra-fast clustering method for organizing the protein universe of life at low sequence identity, enabling large-scale dimensionality reduction and improving downstream ...

Results from a panel of assays that analyse different aspects of DNA sequence specificity reveal more than 100 new motifs to aid the characterization of putative human transcription factors.

Formation and burial of pyrite (iron sulfide) in marine sediments exert a fundamental control on atmospheric oxygenation and seawater buffering ove...

All living organisms are constrained by environmental boundaries that govern where growth is possible, such as minimum and maximum temperatures or pH. An organism’s maximum specific growth rate places...

Prokaryotic taxonomy now relies on both marker-gene and genome-wide sequence comparisons, but these methods differ in taxonomic range, scalability, and sensitivity to genome quality. Here, we benchmar...

The in vitro experiments that used the artificial genetic codes tested here did not provide support for the error minimization theory.

Tillering plasticity is a key adaptive trait in sorghum influencing resource use efficiency via a plant’s ability to adjust branching to neighbour density. Neighbour detection through red:far-red (R:F...

A platform for targeted annotation of (meta)genomic and (meta)transcriptomic datasets using HMM sets. - Arkadiy-Garber/MagicLamp

Genome and metagenome annotation tools designed for large databases are ill-suited to the discovery of specialized, ecologically relevant microbial functions. MagicLamp (<https://github.com/Arkadiy-Ga...

Members of Geobacter sulfurreducens are electroactive bacteria that transfer electrons to extracellular solid electron acceptors using extracellular electron...

Abstract. Prokaryotic genomes are usually densely packed with intact and functional genes. However, in certain contexts, such as after recent ecological sh

Abstract. Mealybugs are insects that maintain intracellular bacterial symbionts to supplement their nutrient-poor plant sap diets. Some mealybugs have a si

Published in Genome biology and evolution

The Candidate Phyla Radiation (CPR) consists of microorganisms with highly reduced genomes and limited metabolic capabilities, including the inability to synthesize nucleotides and amino acids. Previo...

Download release 20.0 of the NCBI protein profile Hidden Markov models (HMMs) used by the Prokaryotic Genome Annotation Pipeline (PGAP). You can search this collection against your favorite prokaryoti...

Published in bioRxiv : the preprint server for biology

Oxygen is one of the most important environmental variables affecting microbial activity and composition, but is often difficult to measure in situ. We developed a tool, OxyMetaG, that leverages differences in bacterial gene content across known aerobic and anaerobic taxa to predict the oxygen level of a given sample directly from shotgun metagenomic reads. OxyMetaG works on samples with low sequencing depth and avoids computationally expensive genome assembly, which often captures only a fraction of the microbial community in a given environment. With OxyMetaG, bacteria can be used as bioindicators of oxygen availability over broader time scales than just a single measurement and provide crucial environmental context in cases where oxygen has not been or cannot be measured. OxyMetaG is publicly available and can be used to answer a wide variety of ecological questions in both environmental and host-associated systems.