Abstract. Both deterministic (e.g. species-environment interactions) and stochastic processes (e.g. random birth and death events) shape communities, but i

Conjugative plasmids are a key reservoir of antimicrobial resistance (AMR) in commensal and pathogenic bacteria within the gut microbiome. Plasmid-dependent phage (PDPs) are a promising therapeutic op...

Sabnis et al. explain why non-conjugative plasmids move at a low rate in nature. While increased mobility can easily evolve by incorporating phage DNA into plasmids, this is disadvantageous because it...

Environmental stress drives biodiversity loss by altering competitive hierarchies and pushing taxa towards extinction. Parasites and their communities are particularly vulnerable to stress due to envi...

Panoptes, an anti-phage defence system against virus-mediated immune suppression, is revealed.

This work presents Spacedust, a tool for de novo identification of conserved gene clusters from metagenomic data.

by Stephen Thomas, Ayatollah S. El-Zayat, James Gurney, Jennifer Rattray, Sam P. Brown Bacterial quorum sensing is often mediated by multiple signaling systems that interact with each other. The quorum-sensing systems of Pseudomonas aeruginosa, for example, are considered hierarchical, with the las system acting as a master regulator. By experimentally controlling the concentration of auto-inducer signals in a signal deficient strain (PAO1ΔlasIΔrhlI), we show that the two primary quorum-sensing systems—las and rhl—act reciprocally rather than hierarchically. Just as the las system’s 3‑oxo‑C12‑HSL can induce increased expression of rhlI, the rhl system’s C4‑HSL increases the expression level of lasI. We develop a mathematical model to quantify relationships both within and between the las and rhl quorum-sensing systems and the downstream genes they influence. The results show that not only do the systems interact in a reciprocal manner, but they do so asymmetrically, cooperatively, and nonlinearly, with the combination of C4‑HSL and 3‑oxo‑C12‑HSL increasing expression level far more than the sum of their individual effects. We next extend our parameterized mathematical model to generate quantitative predictions on how a QS-controlled effector gene (lasB) responds to changes in wildtype bacterial stationary phase density and find close quantitative agreement with an independent dataset. Finally, we use our parameterized model to assess how changes in multi-signal interactions modulate functional responses to variation in social (population density) and physical (mass transfer) environment and demonstrate that a reciprocal architecture is more responsive to density and more robust to mass transfer than a strict hierarchy.

Why are there so few pathogens, and what determines their emergence? This Perspective argues that ecological and evolutionary forces (host availability, geographic exposure and microbial innovation) w...

Microbial communities are shaped by complex forces, including interspecies interactions and the effects of mobile genetic elements such as plasmids. How these forces interact to affect community respo...

Competition assays are a mainstay of modern microbiology, offering a simple and cost-effective means to quantify microbe–microbe interactions in vitro. Here, we demonstrate a key weakness of this meth...

Background Variation within the prokaryotic pangenome is not random, and natural selection that favours particular combinations of genes appears to dominate over random drift. What is less clear is wh...

CRISPR-Cas systems are diverse, with microbes harboring multiple classes and subtypes. Type I DNA-targeting and type III RNA-targeting systems often c…

Multiple bacterial immune systems, including CBASS, Thoeris, and Pycsar, employ signaling molecules that activate the immune response following phage infection. Phages counteract bacterial immune sign...

Bacteriophage (phage) genome annotation is essential for understanding their functional potential and suitability for use as therapeutic agents. Here we introduce Phold, an annotation framework utilis...