bacteria (other)

bofasa improves orthology inference for bacterial genomes by addressing limitations of eukaryotic methods, achieving higher accuracy and better core genome recovery.

MicroDUET is a genomic foundation model that provides fast, accurate representations for pathogen surveillance by distinguishing phylogeny and function.

The paper examines thermal adaptation in bacterial chaperone mRNAs, finding no strong structural differences but a significant shortening of the groL coding sequence in thermophiles.

This study identifies CsrA as a global regulator of carbon preference and gut colonization in Acinetobacter baumannii, revealing its role in repressing arginine/ornithine catabolism and enhancing competitive fitness.

The paper introduces a SURFAR platform to identify and characterize new P. aeruginosa phages by targeting specific receptors, isolating two novel phages with distinct host ranges.

This study identifies TilR, a MarR-family regulator in Klebsiella oxytoca, as a repressor of tilimycin biosynthesis and links it to metabolic and virulence-related gene expression.

CauloBrowser 2.0 updates the systems-biology database for Caulobacter crescentus with AI-powered tools for querying and visualizing experimental data.

This study uses genomic analysis to reclassify the Streptococcus anginosus group into four taxa, revealing diversity and lineage-associated traits linked to invasive disease.

MicrobeRT is a framework of fine-tuned language models for metagenomic analysis, achieving strong performance in taxonomic classification, antibiotic resistance detection, and pathogenicity assessment.

This study evaluates Sourmash's ability to profile microbial strains from long-read metagenomes, showing accurate gene content recovery and abundance estimation.

This study identifies anti-phage defense systems in VREfm genomes and finds limited associations between specific systems and phage resistance, with one candidate gene reducing susceptibility.

This study quantifies transcriptional dysregulation in antibiotic tolerance using single-cell RNA-seq and introduces GMP-Cor to analyze gene-gene correlations in disrupted growth-arrest states.

This study shows that proteolytic feedback regulates quorum sensing in Pseudomonas aeruginosa by controlling RhlR stability, affecting virulence and biofilm formation.

The paper identifies a bacterial pathway, Cerberus, that uses DNA damage sensing to regulate defense operon expression through anti-sigma factor cleavage.

This study identifies regulatory interactions between sRNAs and transcription factors in S. aureus, showing their roles in stress responses and virulence.

This paper reports the complete genome sequence and metabolic features of a new extremophile isolate, Vreelandella zhaodongensis BS253, from a hypersaline lake, highlighting its potential for biotechnological applications in carbon capture and sustainable processes.

The paper compares Profftella genomes across Diaphorina species, finding conserved gene organization but lineage-specific variation in diaphorin biosynthetic genes, particularly in ACP domain amplification.

The paper investigates how a bacterial chaperone-usher pathway enables interkingdom protection of a fungus from antimicrobial compounds.

ARG-PASS v2.0 identifies previously unrecognized antibiotic resistance genes in environmental samples and links them to human gut microbiomes through dietary exposure.

GBactPro improves cross-species bacterial promoter prediction using element-resolved promoter definitions, achieving high AUROC across multiple species and outperforming existing predictors.

This study links genomic diversity to phenotypic virulence in Pseudomonas aeruginosa by analyzing multiple strains and their functional behaviors.

This paper optimizes the ORBIT protocol for efficient gene deletion in Mycobacterium abscessus, enabling precise genetic manipulation for studying its physiology and pathogenesis.

The paper identifies sRNA candidates in B. burgdorferi and maps their regulatory interactions across growth phases, revealing a dynamic RNA-RNA interactome.

The paper develops a genomic ratio to quantify resource-acquisition strategies in bacteria, finding uptake-optimised bacteria dominate early decomposition and depolymerisation-optimised bacteria dominate later stages.

The paper isolates and cultures bacteria from four Mediterranean corals, identifying 84 pure isolates, including novel species, to better understand their roles in the coral holobiont.

This study shows that bacterial fermentation, not respiration, dominates in upland soils during hypoxia, challenging the assumption that respiration is the primary metabolic strategy.

The paper analyzes early genetic contexts of blaNDM-1 in Acinetobacter and Enterobacterales isolates to understand its spread and resistance mechanisms.

Agent K automates the mapping of bacterial genomes to biosynthetic pathways and metabolite discovery using an agent-orchestrated framework with a large-language model.

The paper identifies diverse phage-encoded proteins associated with bacterial cell envelope functions in huge phages, revealing potential roles in host interactions.

The paper develops a maximum-likelihood framework to estimate gene prevalence from incomplete genomes and applies it to Prochlorococcus, revealing a pangenome dominated by rare genes.