Prokaryotic pan-genome analysis is crucial for understanding microbial diversity, however current analytical methods often struggle to balance accuracy and computational efficiency. Here the authors p...

Understanding bumble bee gut health is imperative as these vital pollinators are subjected to pathogenic infections and thermal stress from climate change. The gut microbiome serves as an indicator fo...

Abstract. The genus Enterococcus comprises a diverse group of species, many of which are commensal members of the gut microbiota of humans and animals. The

Arabidopsis thaliana was always an unlikely candidate for the limelight. But 25 years ago, the diminutive thale cress launched the botanical world into the molecular era.

Author summary Escherichia coli demonstrates a remarkable ability to adapt to diverse environments. This adaptability is in part connected to its ability to recombine incoming DNA in its chromosome, a...

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More evidence highlighting the benefit, and limitations, of covid-19 vaccines

Human reads are a key contaminant in microbial metagenomics and enrichment-based studies, requiring removal for computational efficiency, biological a…

AbstractMotivation. Accurate genome size estimation is an important component of genomic analyses such as assembly and coverage calculation, though existin

Genetic association tests prioritize candidate genes based on different criteria.

The exploration of life in extreme environments gained prominence with Thomas Brock’s “Life at High Temperatures” (1), and his subsequent isolation of Thermus aquaticus with Hudson Freeze in 1969 (2) ...

Exclusive: The inside story of why Moderna now faces a crisis unlike any in its 15-year-history.

An exploration of previously undescribed variants from the long tail of the CRISPR–Cas distribution.

Transposable elements (TEs) are repetitive DNA sequences that can alter their position and abundance within genomes. While TEs are known to have various impacts on genome structure and function, our u...

Bacterial genome evolution is characterized by gains, losses, and rearrangements of functional genetic segments. The extent to which large-scale genomic alterations influence genotype-phenotype relationships has not been investigated in a high-throughput manner. In the symbiotic soil bacterium Sinorhizobium meliloti, the genome is composed of a chromosome and two large extrachromosomal replicons (pSymA and pSymB, which together constitute 45% of the genome). Massively parallel transposon insertion sequencing (Tn-seq) was employed to evaluate the contributions of chromosomal genes to growth fitness in both the presence and absence of these extrachromosomal replicons. Ten percent of chromosomal genes from diverse functional categories are shown to genetically interact with pSymA and pSymB. These results demonstrate the pervasive robustness provided by the extrachromosomal replicons, which is further supported by constraint-based metabolic modeling. A comprehensive picture of core S. meliloti metabolism was generated through a Tn-seq-guided in silico metabolic network reconstruction, producing a core network encompassing 726 genes. This integrated approach facilitated functional assignments for previously uncharacterized genes, while also revealing that Tn-seq alone missed over a quarter of wild-type metabolism. This work highlights the many functional dependencies and epistatic relationships that may arise between bacterial replicons and across a genome, while also demonstrating how Tn-seq and metabolic modeling can be used together to yield insights not obtainable by either method alone.

A comprehensive analysis of English health records finds higher risk of rare heart complications in children and adolescents who caught COVID-19 compared to those who received an mRNA-based COVID vacc...

Bacteria employ a range of competition systems that deliver toxins to inhibit competing strains. This study shows that these systems are particularly important for the ecology of virulent and antibiot...