CSP New Investigator Call | Joint Genome Institute

The CSP New Investigator Call is for investigators and research initiatives new to the JGI. Projects must be independent of ongoing JGI proposals, and lead PIs cannot have been lead PI on any previous...

jointgeno.me

Fungicide Drives <fi>De Novo</fi> Evolution of Multidrug Resistance in the Plant Growth Promoting Rhizobacterium, <fi>Pseudomonas fluorescens</fi>

Soil microbial communities underpin key ecosystem processes, including plant health, nutrient cycling and primary productivity. In agricultural soils, beneficial soil bacteria are often exposed to mu...

onlinelibrary.wiley.com

Effector loss and gain drives host range at a fitness cost

Author summary Pathogenic microorganisms emerge and adapt to new niches posing problems for host health, such as when disease outbreaks occur. Microorganisms may quickly adapt by modifying their genom...

journals.plos.org

TriMic: a Triticum aestivum microbial culture collection and synthetic community for dissecting wheat-microbe interactions

Understanding the molecular mechanisms underlying plant–microbe interactions is essential for developing innovative microbe-based agrotechnologies. However, deciphering these mechanisms within the com...

biorxiv.org

Comparison of spectral imaging modalities for identification and classification of air-liquid interface biofilms

Biofilms formed at air-liquid interfaces represent a significant challenge for the food industry due to their resistance to cleaning and the difficult…

sciencedirect.com

Imaging Staphylococcus aureus biofilms in vivo reveals neutrophil exclusion by PNAG exopolysaccharide | mBio

The biofilm-associated exopolysaccharide PNAG is frequently expressed in Staphylococcus aureus clinical isolates but is often reduced during laboratory passage, with expression highly dependent on gro...

journals.asm.org

Virulent strains of Pseudomonas aeruginosa are more disruptive during invasion of a microbial model community

Abstract. Pseudomonas aeruginosa, a major opportunistic pathogen involved in cystic fibrosis and many nosocomial infections, exhibits strong competitive ab

academic.oup.com

Mathstory – Mathstory competition

mathstory.org

biorxiv.org

The Master Regulator <fc>Spo0A</fc> Integrates <fc>DNA</fc> Sequence and Shape to Regulate the Sporulation Kinase Gene <fi>kinA</fi> in <fi>Bacillus subtilis</fi>

During starvation, progressive Spo0A~P accumulation is decoded by three Spo0A~P-binding sites and intrinsic DNA bending within the kinA promoter. Together, these features fine-tune kinA transcription...

onlinelibrary.wiley.com

A novel stress response pathway mediates biofilm architecture in Pseudomonas aeruginosa

Author summary Biofilm formation by the opportunistic pathogen Pseudomonas aeruginosa represents a major clinical challenge, with biofilms typically associated with chronic infection, increased antibi...

journals.plos.org

sciencedirect.com

metaSMASH: Scalable Biosynthetic Gene Cluster Detection for Large Metagenomic Assemblies

antiSMASH is widely used for biosynthetic gene cluster (BGC) detection and annotation, but its standard workflow is poorly suited to large metagenomic assemblies, where massive contig counts create severe runtime bottlenecks and complicate downstream result exploration. We present metaSMASH, a re-engineered fork of antiSMASH for metagenome-scale BGC analysis. metaSMASH preserves the original antiSMASH detection and annotation logic while introducing streaming, memory-bounded execution, record-level parallelisation, optional output filtering, and an interactive dashboard for large result sets. Across 25 benchmark metagenome datasets, metaSMASH reproduced identical BGC detection results while dramatically reducing computational cost. Relative to the default antiSMASH configuration, metaSMASH was a geometric-mean 38x faster. It also outperformed an ad hoc chunked antiSMASH workflow: in the default configuration it achieved a geometric-mean 2.9x speed-up and 1.7x lower peak memory, and with extended-analysis modules enabled it was 2.7x faster and used 3.1x less memory while completing all datasets, whereas the ad hoc workflow ran out of memory on the two largest assemblies. By substantially reducing the computational burden of large-scale metagenome analysis without sacrificing result equivalence, metaSMASH makes routine mining of assembled metagenomes more practical and provides a scalable foundation for natural product discovery from complex microbial communities. ### Competing Interest Statement The authors have declared no competing interest. German Center for Infection Research, TTU Novel Antibiotics 09.716 Volkswagen Foundation, 0072511-00

biorxiv.org

Postdoc Microbial Biochemistry: Biosynthetic Enzyme Discovery in Cable Bacteria

Elucidating the biosynthesis of a unique nickel-containing conductive structure for long-range electron transport in cable bacteria

kuleuven.be

Emerging tools and best practices for studying gut microbial community metabolism - Nature Metabolism

In this Perspective, Noecker and Turnbaugh provide a detailed guide for studying microbial community metabolism and discuss the best practices in the field.

nature.com