Mostly Microbes and Infection - by David Ojcius

  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.

  Highlights • Bacterial serine proteases play a crucial role in the interaction between bacteria and their hosts, facilitating bacterial invasion and contributing to pathogenicity. Mycobacterium tuberculosis possesses multiple serine proteases; however, the mechanisms of action of these proteases remain incompletely understood. In this study, we characterized the role of a novel serine protease, Rv1815, by purifying it in Escherichia coli and creating a rv1815 deletion mutant in M. tuberculosis to investigate its function. Our research revealed that Rv1815 is located in the cytoplasm of macrophages, exhibits serine protease activity, and can be secreted extracellularly. Moreover, we found that rv1815 is essential for bacterial virulence, survival, metabolism, and antibiotic resistance, as demonstrated by proteomic analysis. Rv1815 also influences bacterial morphology, enhances bacterial growth in vitro, and promotes intracellular survival of M. tuberculosis in macrophages. Further...

  Highlights • Human cytomegalovirus RNA2.7 sequesters RNA-binding proteins to stabilize host mRNAs • RNA2.7 enforces G1-S arrest specifically in actively cycling cells • An adenosine-rich RNA2.7 region is required for cell-cycle arrest • RNA2.7-driven cell-cycle arrest promotes efficient HCMV replication

  Highlights • XAI–SERS platform enables accurate discrimination of  E. coli  pathotypes and  Shigella. • 1D-CNN model achieved 97.7% accuracy, surpassing traditional classifiers. • SHAP analysis identified key spectral features linked to molecular components. • Provides a precise, interpretable approach for bacterial diagnostics.

  Highlights • One-year multicenter survey of fosfomycin-resistant Enterobacterales in Czech Republic hospitals. • FosA3-producing  Proteus mirabilis  predominates. • FosA3-positive  P. mirabilis  ST185 forms a local clonal cluster while  E. coli  clones are heterogeneous. • Transporter defects (GlpT/UhpT) are widespread; most  fosA  strains carry ESBL genes. • Molecular surveillance is crucial to monitor and contain emerging fosfomycin resistance.

  Highlights • XDR  Klebsiella oxytoca  found in hospital wastewater with 59 resistance genes • Mega plasmid pKO611.1 carries 28 resistance genes, enabling multidrug resistance • Novel  tet (E) variant and AmpC β-lactamase confer tetracycline & β-lactam resistance • Plasmid pKO611.1 transfers efficiently to  Escherichia coli , spreading resistance • Plasmid recombination shows potential as resistance gene reservoir for dissemination

  Highlights • Aridity index, rather than degradation level, is the paramount driver shaping soil bacterial and fungal communities (explaining ∼43% and ∼30% of the variation, respectively). • The ecosystem harbors an exceptionally stable core microbiome, with 18,510 bacterial ASVs shared across aridity gradients. • Dry sub-humid (alternating wet-dry) conditions promote the most complex and stable microbial co-occurrence networks. • Community assembly of both bacteria and fungi is predominantly governed by stochastic processes (ecological drift). • Microbial functional profiling reveals nitrogen cycling as the dominant process, with distinct adaptations along the aridity gradient.

  Highlights • E. coli  isolates from healthy or diseased hosts exhibit distinct metabolic profiles • D-serine utilization is more prevalent in E. coli isolates from Crohn’s patients • The D-serine associated  dsdCXA  cluster enhances E. coli fitness in the gut

A new leadership team is now in place to help guide the future of research at the Arthur A. Dugoni School of Dentistry. Dr. David Ojcius, chair of the Department of Biomedical Sciences, was recently named to a new role as assistant dean for research. He will continue to serve as department chair in addition to his new duties. Ojcius brings a wide range of research, scholarship and leadership skills to this role.

Dean Prof. Dr. Zahid Yousaf of the University of Gujrat (UOG) embarked on a significant visit to the University of the Pacific, California, US, from May 20 to May 25. This visit was planned on the special invitation of Dr Qingwen Dong, Director graduate program and a leading academic from the department of communication. This visit not only facilitated fruitful discussions among academics from both countries but also laid the groundwork for a series of innovative collaborations between the two esteemed institutions. During this visit, Prof. Dr. Zahid Yousaf Engaged in dialogues with key stakeholders including President Christopher Callahan, Vice President Mary Lomax-Ghirarduzzi,  Associate Provost David Ojcius, Dean Lee Skinner, Director of International Scholars and Services, Patrick Wolak, Director Admissions among others. These meetings underscored a shared vision for enhancing academic cooperation and global engagement.

  Highlight • Blood SCFA concentrations are reduced in patients with depression, especially in clinically diagnosed patients. • SCFA supplementation may improve depressive-like behaviors in animal models. • SCFA deficiency may contribute to depression, supporting SCFAs as potential biomarkers and therapeutic targets.