Mostly Microbes and Infection - by David Ojcius

  ABSTRACT Deoxyribonucleic acid (DNA) is naturally contained within the mitochondria and nucleus of cells. DNA localized outside of these areas is generally considered to constitute damage-associated molecular patterns (DAMP) that trigger innate immune responses. The variety of these immune-stimulatory nucleic acids, coupled with the variety of proteins known to interact with DNA DAMPS and to act as sensors or regulators, is an important layer of regulation that defines the nature and breadth of inflammatory responses within a given cell or tissue. In this review, we describe the various DNA substrates that co-exist in cells, how they are sensed, and what regulates their cytoplasmic availability and recognition. We subsequently discuss how this complexity may dictate tissue-specific immune response and suggest that a more integrated view of the interconnection between pathways is necessary in order to define molecular targets for treatment intervention in inflammatory pathologies....

  Highlights • Climate change and environmental stressors are major drivers affecting global food security and agricultural sustainability. • Microbial communities play a central role in nutrient cycling, plant health, and ecosystem resilience. • Climate variability alters microbial diversity, functions, and plant–microbe interactions. • Beneficial microorganisms enhance crop tolerance to abiotic and biotic stresses. • Microbiome-based strategies offer sustainable alternatives to chemical inputs in agriculture. • Advances in microbial genomics enable the exploration and application of microbial diversity. • Biological control agents represent eco-friendly solutions for plant disease management. • Integrating microbial taxonomy, ecology, and biotechnology is key to climate-resilient food systems.

  Highlights • H1/H3 cross-reactive head antibodies were isolated after seasonal flu vaccination • These cross-subtype antibodies target a conserved HA epitope involving residue 145 • Antibodies targeting this epitope were enriched in people born in the 1990s • H1N1s recently acquired a substitution that abrogated binding of these antibodies

  Highlight • This review examines the evolutionary origin, regulation, and functional diversification of IFN stimulated genes in vertebrates. Evolutionary pathways of IGS, with gene gain and loss, and their connection with redundancy and robustness are discussed.

  Highlights • VMT restores skin  N -bc2S1P linked to early neurodevelopment in cesarean-born neonates • N -bc2S1P engages β-arrestin1-biased S1PR2 signaling in forebrain excitatory neurons • β-arrestin1-biased S1PR2 signaling recruits AP-1/CBP to increase Notch H3K27ac • Engineered  S. epidermidis  sustains  N -bc2S1P and extends rescue of CS-associated deficits

  Highlights • A probiotic-integrated semi-closed RAS protocol significantly improved growth (+0.08%/day) and survival (+6.9%) in Cynoglossus semilaevis. • Probiotic treatment reshaped the gut microbiota from Vibrio dominance to a Photobacterium-enriched community and altered quorum sensing pathways. • Metagenomics revealed enhanced CAZyme activity and nutrient metabolism potential in the probiotic group. • Multi-tissue transcriptomics demonstrated coordinated immune activation (NF-κB, IgA network) and JAK–STAT-mediated metabolic reprogramming. • Functional validation of ccl19 confirmed enhanced resistance against Vibrio harveyi, supporting an immune–metabolic crosstalk model.

  Highlights • CCBs bind the inner pore of the HCMV US21 viroporin and abolish pUS21-mediated ER Ca 2+  leakage. • CCBs inhibit HCMV replication. • CCBs prevent the cytobiological consequences of pUS21 expression. • CCBs treatment restores ER Ca 2+  levels to those of control cells. • CCBs do not affect basal intracellular Ca 2+  homeostasis.

  Highlights • Translation measurements reveal how microbes allocate resources in communities • Functional profiles predict microbial competition and niche allocation • Predictions enable rational design of prebiotic and probiotic interventions • Interventions enable targeted modulation of complex microbiomes  in vitro  and  in vivo

  Highlights • Bacterial CD-NTase synthesizes 2'3'-cGAMP with mammalian cGAS-like enzymatic properties • 2'3'-cGAMP drives stepwise monomer-to-filament assembly of 3TM-SAVED family effectors • Filament assembly reconfigures TM helices and amphipathic hairpins to shear membranes • Vertical membrane shearing defines a distinct mode of membrane disruption

  Highlights • Borrelia spirochetes have a unique mechanism to evade host immune system. • Borrelia persica has one chromosome, 12 linear and one circular plasmids. • Telomeric hairpin motifs were detected in the chromosome and linear plasmids. • Plasmid profiles remained stable after one year of continuous in vitro culture. • A Vlp common variable region kept the same external position across structures.

  Highlights • Neurospora crassa  has lower sugar metabolic gene redundancy than  Aspergillus niger • The mating type of  N. crassa  affects growth of sugar metabolic deletion strains • We present a strongly improved sugar metabolic model for  N. crassa

  Highlights • HapX is essential for iron-limited growth in  Talaromyces marneffei . • Deletion of hapX impairs siderophore biosynthesis and disrupts iron-responsive gene regulation. • Loss of HapX reduces conidiation, conidial germination, and stress tolerance (cell wall, membrane, and nitrosative stress). • The Δ hapX  mutant shows increased susceptibility to amphotericin B. • HapX is required for intracellular survival and full virulence in infection models. .

Fecal microbiota transplantation (FMT) is an effective therapy for recurrent   Clostridioides difficile   infection and is increasingly being explored for other microbiota-associated diseases. However, general research has largely focused on bacterial engraftment, overlooking the contribution of the gut virome. In this perspective, we highlight phage-mediated horizontal gene transfer (HGT) as a potentially influential process occurring following FMT. Donor-derived phages may potentially influence community structure, engraft in resident bacteria, and modulate microbial functions or host physiology. In addition, temperate phages are well-equipped to mobilize bacterial genes, such as metabolic functions, stress-response traits, and antibiotic resistance determinants, raising the possibility that gene flow could well contribute to FMT outcomes. We propose a conceptual model in which phages act as bidirectional mediators of adaptation, not only accompanying bacterial communities b...

  Article highlights • Screening of 578  Mucorales  isolates from clinical and fermented food indicated that endosymbiotic bacteria occur exclusively in  Rhizopus  species. • 16S rDNA sequencing and FISH analyses confirmed  Mycetohabitans  as the predominant bacterial symbiont detected in pathogenic  Rhizopus  strains. • A  Rhizopus homothallicus  isolate was found to harbor  Mycetohabitans  sp. showing 98.37% 16S rRNA similarity to  M. rhizoxinica , suggesting a potential novel species-level lineage. • Ecological and geographic data compilation illustrated that  Mucorales  - bacteria associations span multiple environments and continents.

Highlights • Long-term organic-free enrichment with hydrothermal sulfide/iron-rich sediment successfully constructed diverse sulfur-oxidizing communities. • 36 potential sulfur-oxidizing bacteria (including 10 novel species) were isolated from the mineral-enriched community. • Sulfitobacter  sp. L-8 and  Roseovarius  sp. B-10 achieved 68%–93% thiosulfate consumption and mediated diverse and significant mineral transformation. • This study connects microbial sulfur-oxidizing metabolisms with sulfide weathering, expanding insights into microbial roles in sulfide mineral weathering and utilization. • SOB act as key drivers of sulfide transformation, biogeochemical cycling and energy dynamics in deep-sea hydrothermal vents ecosystems.

  Highlights • High rhizosphere microbial diversity improves soybean performance under drought • Diversity-triggered 2-naphthoic acid accumulates under drought stress • Sinorhizobium  CS204 senses 2-naphthoic acid via chemoreceptors and ABC transporters • S .CS204-metabolite synergy boosts nitrogen cycling and plant drought tolerance

  Highlights • Microbiota-driven inflammation and lipid uptake drive intestinal ILC3 lipotoxicity • Inflammatory signaling suppresses fatty acid oxidation in ILC3s but not Th17 cells • ILC3-specific immunometabolic vulnerability is conserved in intestine of mice and human • HFD-mediated intestinal ILC3 depletion is reversible upon dietary normalization

  Highlights • A global atlas and biogeography of human bacterial pathogens in soils are reported • Dominant human bacterial pathogens are more abundant in wet ecosystems worldwide • Soil biodiversity is negatively associated with the prevalence of human pathogens • Many dominant pathogens are likely to increase their proportion in future climates

  Highlights • Bacteria were more abundant in coco coir, particularly in stationary clinostats • Pseudomonadota  and  Actinomycetota  phyla were abundant under simulated gravity • Biomarkers were highest in horizontal clinostats' coco coir under simulated gravity • The GT2 and GT4 classes of glycosyl transferases were abundant in coco-coir samples • The top four antibiotic resistance genes were  adeF, vanY, vanT , and  qacG

  Highlights • Unexplored source of microorganisms with antibacterial activity; • New species of  Bacillus  sp. with activity against multidrug-resistant  K. pneumoniae ; • Potential chemical and molecular novelty of antibacterial compounds based on genome mining.