Mostly Microbes and Infection - by David Ojcius

Highlights • Pristine river ecosystem hosts ESBL ARGs, like bla TEM and bla CTX-M . • The Yamuna River hosts multidrug, fluoroquinolone, fosfomycin, and β-lactam resistance genes. • Predominance of biofilm-forming bacteria and their co-occurrence with the ARGs.

Highlights • Qdr3 coordinates cellular homeostasis in C. auris. • qdr3 deletion remodels mitochondrial function. • Loss of Qdr3 alters biofilm architecture and extracellular matrix production. • qdr3 deletion enhances virulence. • Qdr3 links membrane transport, mitochondrial function, and virulence.

Highlights • C. albicans Th17 cells are restricted to a few proteins contained in fungal EVs • The oral mucosa is a major reservoir of Th17 cells, dominated by C. albicans reactivity • C. albicans -reactive Th17 cells are shared between oral and gut tissues • Homeostatic C. albicans Th17 cells adapt pathogenic traits in Crohn’s disease

Highlights • Single-cell Raman spectroscopy coupled with D 2 O labeling was first applied to Vibrio splendidus persisters. • V. splendidus persisters are metabolically active rather than fully dormant. • Persisters show remodeled cellular components with decreased nucleic acids and increased lipids and polysaccharides. • Vitamin C inhibits persisters by suppressing the stringent response, providing a green anti-persister approach. Abstract Persister cells, a multidrug-tolerant bacterial subpopulation, pose challenges to disease control, with research hindered by technical limitations. In this study, single-cell Raman spectroscopy (SCRS) combined with heavy water (D 2 O) labeling was employed to explore the metabolic activity and compositional changes of Vibrio splendidus persisters. Raman analysis revealed distinct biochemical profiles between persisters and normal cells: persisters reduced nucleic acid-related band intensity but increased lipid and polysaccharide-related bands. Usi...

Highlights • Sublethal oxytetracycline and CuCl 2 elevated per-cell 18S rDNA/rRNA copy numbers, disrupting allometric scaling with cell volume in two ciliated protists. • Oxytetracycline selectively increased rRNA: rDNA ratios, revealing stressor-specific ribosomal regulation. • Both stressors induced persistent intragenomic polymorphisms of 18S rRNA gene. • Pollutant-induced ASV inflation may bias microbial diversity estimates.

Highlights • Bedtime probiotic intake retains 100,000x more bacteria than daytime intake. • Oral-origin L. reuteri strain colonizes better than the non-oral isolate. • Probiotic persistence varies widely interindividually, some individuals retain strains 7+ days. • Supragingival plaque shows highest proportional probiotic abundance by site. • Higher probiotic levels correlate with greater pocket depth reduction in periodontitis.

Highlights • The global regulator ppGpp plays a central role in controlling AIEC virulence. • Loss of ppGpp impairs virulence across in vitro and in vivo infection models. • Two candidate biomarkers with discriminatory potential for AIEC identification were defined.

People who live together share more oral and gut microbes with each other than with other people in their communities, according to a study published June 15, 2026, in the Cell Press journal Cell Press Blue . This was true regardless of the cohabitants’ relationships—siblings, parents, and offspring all shared similar numbers of microbial strains, and romantic partners shared even more oral (but not gut) microbes with each other, likely due to kissing. The research, covered in NPR, Gizmodo , and IFLScience , also found a link between more transmissible microbes and health, particularly type 2 diabetes. The findings could help design more targeted therapies for improving people’s microbiomes.   

Abstract Pit mud (PM) microbiota play a vital role in Baijiu flavor formation, yet its ecological and functional succession during maturation remains incompletely elucidated. Here, physicochemical profiling, amplicon sequencing, and metagenomics were integrated to investigate 5-, 15-, and 30-year PM of Sichuan Tang Dynasty Laojiao cellars. Bacteria dominated the community (82.59%), followed by Archaea (16.99%), with Lactobacillus acetotolerans, Ruminococcaceae CPB6, and Methanobacterium paludis as major species. Discrepancies between sequencing methods were reflected in fungal taxa which had low-abundance. The 15-year PM exhibited distinct community and functional features, indicating a critical transitional stage. Functional analysis revealed that fermentation-relevant functions were mainly contributed by 7 key genera and 5 species. Physicochemical properties changed with pit age, characterized by increased moisture as well as decreased acidity and humic substance levels. Moisture,...

Highlights • Microbial pantothenic acid (PA) supply is reduced in individuals with MetS • panC enables B. fragilis to supply PA to the colonic microenvironment • B. fragilis PA biosynthesis preserves the gut barrier and alleviates MetS • Microbial PA sustains KLF4 via the PANK2/3-CoA axis to support differentiation

Highlight • Bacterial isolates showed positive or negative effects on barley growth. • GR effects were neutralized by GP and NA isolates in SynCom. • GP isolates suppressed GR via contact-dependent T6SS activity. • Cytokinin produced by GP/NA; Variovorax degraded IAA. • Root microbiome shaped by fertilization and season, not inoculation.

Highlights • Deficiency of MrMFS1 was confirmed to underlie to the accelerated growth. • No morphological or physiological alterations were observed upon deletion of MrMFS1 . • The deletion mutant exhibits enhanced stress tolerance and insecticidal activity. • MrMFS1 mediates the proton-coupled efflux of acetic acid.

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

Highlights • Isolated TPD-causing V. parahaemolyticus strain P40.49 from infected shrimp. • Experimental infection confirmed the pathogenicity of the TPD-causing strain P40.49. • Whole genome sequencing confirmed the presence of ∼69 kbp TPD-associated plasmid. • The shrimp stomach and intestine tissues are ideal for early TPD detection (6 hpi). • Four unique TPD-associated genes may serve as additional markers for TPD detection.

Highlights • W. chondrophila encodes two Ndk paralogs, unlike most Chlamydiota. • ndk genes are early expressed and protein levels peak during bacterial replication. • WcNdk1 is inclusion-bound, while WcNdk2 localizes to host cell compartments. • AZT inhibits bacterial growth and protects host cells from infection-induced death. • AZT sensitivity is linked to ndk2 presence, implicating WcNdk2 as functional target.