Mostly Microbes and Infection - by David Ojcius

Summary Antibiotics are among medicine’s greatest successes, but resistance evolution threatens their continued efficacy. Decades of research have deepened our understanding of the mechanisms and evolutionary dynamics of antimicrobial resistance. More recently, advances in machine learning (ML) and artificial intelligence (AI) show promise in predicting antimicrobial resistance in pathogens based on rapid whole-genome sequencing and other accessible data. In this perspective, we highlight advances in understanding the mechanisms and spread of antimicrobial resistance. We discuss how this knowledge, coupled with ML- and AI-based approaches, can inform the prediction of resistance and a precision-medicine strategy that targets pathogenic bacteria specifically, thereby limiting resistance evolution and collateral damage to the microbiome. These accurate predictions of bacterial vulnerabilities will enable the adaptation of classical antimicrobial treatments with adjuvants, as well as the ...

Highlights • Halococci differ from other haloarchaea by their thick cell wall structure. • Currently no viruses are known to infect Halococci. • Seven novel Halococcus strains were characterized and the genomes sequenced. • The novel Halococcus strains contain predicted anti-viral defence mechanisms. • Detected proviruses indicate that Halococci are infected by viruses in nature.

Highlights • Lysine phenylacetylation (Kpaa) is a diet- and gut microbiota-derived PTM • Kpaa is enriched in mitochondria and regulated by SIRT3 • High Kpaa impairs mitochondrial function and correlates with MASH • K481 phenylacetylation of HSP60 leads to the mitochondrial unfolded protein response

Highlights • Gut microbiome CRC signature is universal across age groups and sequencing approaches • Tumor-enriched microbes are concordant with fecal CRC signatures • Increasing dietary fiber intake reduces the microbiome CRC signature score • Fusobacterium subspecies show biogeographic variation in CRC enrichment

Highlights • Climate stressors restructure soil microhabitats, reassembling microbial guilds that regulate C–N–P cycling and resilience. • Cross-domain feedbacks link pore architecture and soil chemistry to microbiome functions and emergent soil health outcomes. • Rhizosphere mechanisms (exudates, siderophores, ACC deaminase, ISR, AMF/N-fixing symbioses) provide actionable leverage points under stress. • Integrative indicators connect physical, chemical, and biological metrics to soil multifunctionality for monitoring under climate extremes. • Emerging tools (meta-omics, 3D imaging, spectroscopy, isotopic tracing, in situ sensors) enable mechanistic diagnosis and decision support.

Highlights • CBASS antagonizes phage replication while preserving cell viability in P. aeruginosa • 3′,3′-cGAMP-activated CapV targets diverse phages and overcomes CBASS inhibitors • CBASS-sensitive phages transcribe and replicate their genome • CBASS activity limits packaged phage DNA, reducing virion production