Microbiology Research News and Articles - by David Ojcius

This study examines how different sequencing methods influence microbial community analysis in the rhizosphere and phyllosphere of Cinnamomum migao. Variations in annotation resolution, microbial domain, and quantification significantly altered network parameters and keystone taxa identification, highlighting the need for careful interpretation of microbial interactions.

Rhizopus arrhizus emerges as a key fungal driver of metabolic steatotic liver cancer. Its conditioned medium boosts proliferation of human tumor cells, while kynurenic acid produced by the fungus promotes tumor growth in mice. Kynurenic acid binds IQGAP1 and activates MAPK signaling, revealing a pathogenic host–fungus interaction that may be therapeutically targeted to suppress disease progression.

Plasma gelsolin reduces acute inflammation and fungal burden in a 24‑hour mouse model of candidemia. Treatment lowers inflammatory gene expression, decreases renal and pulmonary injury, and improves fungal clearance. In human monocytes, plasma gelsolin boosts fungal uptake, enhances intracellular killing, and modulates reactive radical production without direct candidacidal activity.

Cryo‑electron tomography of native and antibiotic‑perturbed Mycoplasma pneumoniae cells yields 140 in‑cell maps capturing translation initiation, elongation, and recycling. The study visualizes transcription‑translation assemblies, proposes a threading‑based reinitiation mechanism, and provides structural evidence for a supercomplex coordinating transcription, translation, and membrane attachment

Cryo‑electron tomography of Mycoplasma pneumoniae reveals a surface complex combining the conserved Sec‑translocon with a dome‑like assembly formed by three previously uncharacterized Mdps. Integrative proteomics and structural modeling show Mdps resemble PrsA‑like foldases, with Mdp444 retaining catalytic activity. The study provides sub‑nanometer maps of SecA‑mediated translocation coordinated with extracellular protein folding.

Migratory locust eggs emit the microbial volatile 2,4,6‑trimethylpyridine, attracting conspecific females through LmOR34 and LmOR36 to synchronize oviposition. The compound is produced by Enterobacter roggenkampii via lysine degradation, and its loss disrupts attraction. Beyond coordination, 2,4,6‑trimethylpyridine repels soil predators, revealing a dual reproductive and defensive signaling system.

Clostridium immunis protects mice from obesity by secreting a phosphocholine‑modified exopolysaccharide that lowers IL‑22 in the intestine and visceral fat, boosting metabolic activity in adipose tissue. Mutant studies show phosphocholine is essential. Humans with obesity show reduced phosphocholine‑gene abundance, highlighting a translatable strategy to reduce visceral fat.

Analysis of 507 gastric biopsies from 193 children revealed diverse microbial signatures, with HHV6/HHV7 frequently detected and EBV present in a consistent subset. H. pylori showed the strongest link to moderate‑to‑severe inflammation, while EBV also correlated with inflammation, including in H. pylori‑negative patients, highlighting complex pediatric gastric microbial interactions.

The Mononuclear Phagocyte System spans the body and supports homeostasis through highly adaptable interactions beyond immunity. This article introduces a special issue reviewing key phagocyte populations across major organ systems, highlighting their physiologic roles comparable to neuro‑endocrine networks and offering guidance for further study.

First‑line fecal microbiota transplantation yields rapid improvement in most patients with immune checkpoint inhibitor–mediated colitis. In this cohort, 76.9% responded within a median 1.5 days, with increased microbial diversity and reduced immune‑cell activation after treatment. Multi‑omics profiling highlights potential mechanisms underlying FMT response.

Programmed ribosomal frameshifting acts as a regulatory stress signal that activates GCN2 and shuts down host translation. A minimal SARS‑CoV‑2 frameshift element triggers this response independently of ZAKα and is required for viral propagation. DRG1 and IGF2BP3 mediate GCN2 activation, and the mechanism extends to HIV‑1 and West Nile virus.

GORG‑Dark, a dataset of 9,698 single‑cell genomes from deep‑ocean prokaryoplankton, reveals extensive vertical stratification, unexpected particle‑attached Pelagibacterales, and high Patescibacteria and Nanoarchaeota abundance in marginal seas. Coding analyses uncover chemolithoautotrophy, novel proteorhodopsins, and secondary metabolisms across aphotic lineages.

Incretin therapies now improve multiple obesity‑related diseases, with expanding organ‑specific indications. This review explains their mechanisms, evaluates evidence across conditions, and provides a practical framework for using incretin agents beyond endocrinology—covering drug selection, sequencing, monitoring, safety, long‑term management, and access‑limited prescribing.

Predicted bacteriocin genes reveal potential but not function. This review defines four forms of bacteriocin silence—transcriptional, conditional, phenotypic, and ecological—and outlines a function‑first roadmap using condition‑resolved omics, cue‑dissection, structured assays, and defined consortia to link gene catalogs to real ecological impact.

Researchers identify PfSR1‑MT as a melatonin‑responsive GPCR‑like receptor in Plasmodium falciparum . PfSR1‑MT binds melatonin with high affinity, triggers ECD movement and Ca²⁺ signaling, and is selectively activated by ARL34, which inhibits parasite growth and gametocyte development, highlighting a promising antimalarial target.

SCFA‑producing gut bacteria are depleted in Alzheimer’s disease, weakening microbiota‑gut‑brain axis control of neuroinflammation. SCFAs shape microglial and astrocytic states, suppress NLRP3 activation, and influence amyloid, tau, and synaptic integrity. The review evaluates dietary, probiotic, postbiotic, and FMT strategies and outlines biomarker‑guided, personalized therapeutic approaches.

GLP‑1 analogs rely on structural features that enhance stability, receptor affinity, and half‑life. N‑terminal protection, C‑terminal and backbone stabilization, and lipidation drive potency and duration, while structural variation shapes signaling bias. Multi‑receptor agonists and computational design now guide next‑generation incretin therapies.

A cross‑sectional study of SARS‑CoV‑2 patients reveals reduced gut microbial diversity, lower vitamin D, increased Enterococcus faecalis, and loss of key commensals. Functional assays show Bacteroides uniformis can modulate inflammatory responses without altering viral entry. Findings highlight gut microbes’ potential to influence COVID‑19 outcomes and future preparedness.

Rice uses the circadian regulator Nhd1 to time root exudation and coordinate rhizosphere microbial nitrogen cycling. Day‑peaking quercetin 3‑gentiobioside and baseline baimaside activate microbial N‑cycling genes, boosting ammonium availability when plant demand is highest. Engineering microbes to match this rhythm increased grain yield and NUE in field trials.

Corynebacterium glucuronolyticum‑like bacteria are enriched in calcium oxalate stone patients and promote crystal nucleation and aggregation by degrading the anti‑crystallization metabolite hippuric acid and forming biofilms. Their multidrug resistance limits antibiotic efficacy, while hippuric acid supplementation or cranberry diets reduce crystallization in models.

KRAS‑mutant colorectal tumors reshape their microbiome, enriching Bacteroides acidifaciens, which predicts poor prognosis. Using KRAS‑mutant cells and mice, the bacterium drives malignancy via SusF‑mediated stabilization of ARHGEF2, boosting KRAS–RAF–MEK–ERK signaling. Loss of SusF or ARHGEF2 blocks these effects, revealing therapeutic targets for KRAS‑driven colorectal cancer.

Deep learning reveals and redesigns the multifunctional targeting landscape of the T7 phage receptor‑binding protein. Comparing four model architectures, the study engineers phages optimized for 26 tasks, showing that complex specificities can be tuned with few mutations. Multiobjective models uncover principles of phage biology and offer a general strategy for optimizing multifunctional proteins.

Cyclic exposure to the biocide DEAPA selects Salmonella Typhimurium variants with sharply increased tolerance to disinfection, heat, and gentamicin. Adaptive evolution produced multidrug‑tolerant strains carrying mutations across metabolic, signaling, transport, and motility genes, revealing broad cellular rewiring and highlighting risks for food‑processing sanitation.

Phylogeny strongly constrains glycoside hydrolase multidomain architecture across bacterial genera, while environmental factors fine‑tune domain organization in cosmopolitan lineages. Analysis of 158k GH proteins using domain‑adjacency networks reveals conserved lineage‑specific patterns and highlights accessory domains as key drivers of microbial functional adaptation.

A single‑patient study shows how repeat‑associated deletion of a blaNDM‑1 resistance module in Klebsiella pneumoniae produced divergent carbapenem phenotypes among otherwise closely related isolates. Stable genomes, a validated 10.5‑kb plasmid deletion, and growth differences highlight how structural plasmid variation can drive clinically relevant heteroresistance.

A study maps age‑related gut microbiome shifts and introduces MicroAge, a microbiome‑based aging clock. It identifies  Bifidobacterium   pseudocatenulatum as a geroprotective species depleted with age. In mice, supplementation restored intestinal balance, reduced systemic inflammaging, improved cognition and motor function, and extended healthspan. Its metabolite  5-aminovaleric acid betaine (5-AVAB)  reproduced many benefits.

Defined human Clostridia consortia 17‑mix and 11‑mix reverse established colitis in multiple murine IBD models. Beyond SCFA and IL‑10 pathways, these live biotherapeutic products suppress resident pathobionts and activate anti‑inflammatory AhR signaling via bacterial tryptophan metabolites, revealing IL‑10‑independent mechanisms of microbiome‑based therapy.

Gut microbiome diversity and composition differed across predefined age groups in a Taiwanese cohort. Several age‑associated genera showed partial agreement across complementary analytic methods. Adult gut microbiome profiles could predict chronological age, though only with modest accuracy, underscoring both biological signal and methodological limits.

Bacterial endosymbionts in Fusarium oxysporum enhance fungal virulence by reshaping the rhizosphere microbiome. Achromobacter spp. endosymbionts reduce disease‑suppressive bacteria, including Streptomyces, through beauvericin production. This tripartite interaction weakens microbiome‑based plant defense and intensifies pathogen impact.

Paired oral–fecal microbiomes from 507 individuals revealed elevated mouth‑to‑gut bacterial transmission in gastrointestinal cancers. A mouth‑to‑feces index captured disease‑specific signatures and powered a classifier that outperformed fecal occult blood testing, enabling sensitive, non‑invasive detection across multiple cohorts.

Gut microbes convert dietary nitrate and non‑heme iron into dinitrosyl iron complexes (DNICs) that circulate systemically and improve host metabolism. DNICs were detected in conventional but not germ‑free mice, and supplementation or synthetic DNICs boosted tissue levels and reduced cardiometabolic dysfunction. DNICs also lowered steatosis and normalized sGC‑mTORC1 signaling.

Structured RNA elements across the norovirus genome were mapped and functionally tested, revealing conserved motifs that regulate replication and translation. Disrupting key structures reduced viral fitness in cells and animals, enabling design of a stable attenuated virus that elicits protective immunity and supports RNA‑guided antiviral strategies.

A comprehensive proteomic analysis of Plasmodium falciparum chromatin identified 214 proteins associated with heterochromatin, euchromatin, and (peri)centromeric regions. Using three proximity-labeling methods, researchers uncovered new epigenetic factors, complexes involved in histone variant exchange and chromatin-RNA interactions, and evidence for a spindle assembly checkpoint previously thought absent.

Nipah virus (NiV) is a highly lethal zoonotic pathogen with significant pandemic potential due to its broad host range, cross-species transmission capacity, and ability to evade immune responses. This review examines NiV structure, pathogenesis, and the latest progress in vaccine development, highlighting promising candidates, key scientific challenges, knowledge gaps, and priorities for future prevention and control efforts.

Plant-microbe interactions are essential for sustainable agriculture, improving crop productivity, soil fertility, and resilience to stress. This review examines the role of plant growth-promoting microbes (PGPM) as biofertilizers and microbial inoculants, their mechanisms of action, factors influencing their effectiveness, and emerging technologies that support environmentally friendly farming and enhanced food security.

Mucin plays a key role in shaping interactions between enteropathogenic Yersinia enterocolitica and its mucus-adherent phage fMtkYen801. In vitro, mucin exposure increased phage replication by 100-fold, altered post-infection bacterial growth, and reduced biofilm formation. Resistant variants acquired mutations linked to virulence, quorum sensing, and antibiotic resistance, highlighting implications for phage therapy.

A 10-year study of 154 ocular MRSA isolates in Taiwan found major shifts in bacterial clones, with formerly dominant CC59 declining and fluoroquinolone-resistant CC8 increasing. While CC59 remained highly susceptible to fluoroquinolones, CC8 showed marked resistance, raising concerns about standard empirical treatment for eye infections and underscoring the need for ongoing molecular surveillance.

Lors de ma balade au Bois de Vincennes, j’ai vu ces champignons. L' IA pense qu’il s’agit d’un poulet-des-bois (Laetiporus spp.), mais avec seulement 80 % de certitude... donc 80 % de confiance aussi pour sa comestibilité. 🙃🍄

Using chemically induced  Effector-Triggered Immunity ( ETI) and single-cell transcriptomics in Arabidopsis leaves, researchers show that although pathogen effectors are broadly perceived, individual cell types mount distinct immune responses. A shared defense core is complemented by specialized programs shaped by cell identity and chromatin state. Epidermal regulators are crucial for preventing pathogen entry, revealing a layered, spatially organized plant immune system.

Scientists identified TgPRO, the first dedicated regulator of metabolic gene expression in apicomplexan parasites. In Toxoplasma gondii , TgPRO helps parasites adapt to crowding-induced oxidative stress by controlling genes involved in carbon metabolism and iron-sulfur cluster assembly. Loss of TgPRO increased reactive oxygen species and reduced fitness, revealing a convergently evolved metabolic control mechanism.

Researchers found that insoluble dietary fiber slows colorectal cancer progression in mice by altering gut microbiota and reducing production of the tumor-promoting ganglioside GM3. Fiber lowered levels of Paramuribaculum intestinale and a glycosphingolipid-related microbial enzyme, while GM3 was shown to stimulate tumor growth and inhibit cancer cell apoptosis.

Three Chlamydia species infect humans: C. trachomatis , C. pneumoniae and C. psittaci . C. trachomatis is the leading bacterial sexually transmitted infection, often asymptomatic but capable of causing pelvic inflammatory disease, infertility and neonatal infections. It also causes trachoma, a major source of preventable blindness. C. pneumoniae causes respiratory illnesses and may be linked to cardiovascular disease. Chlamydial infections occur worldwide, with trachoma concentrated in poorer regions. Globally, about 89 million new sexually transmitted cases arise annually.    

Many people who walk by Bastille don't realize that there's a pretty little alley a few meters from the crowded cafés.

Clouds are more than water droplets. They host active microbial communities and, potentially, vast numbers of viruses. This article explores evidence that the global cloud virome contains roughly 10²¹ virus particles, examines how virus-bacteria interactions may shape microbial ecology during atmospheric transport, and highlights key research priorities for understanding the ecological role of the cloud virosphere.

Age-linked loss of beneficial Lactobacillus and rise of L. iners impair endometrial receptivity and embryo transfer outcomes. L. gasseri and its exopollysaccharides (EPSs) counteract senescence, enhance implantation in aged mice, and act through Hippo‑YAP signaling, suggesting microbiome‑based strategies to improve fertility in older women.

Background The relationship between gastric microbiota composition, Helicobacter pylori infection, and eradication outcomes remains unclear. This study aims to explore the association of gastric microbiota composition among patients with refractory H. pylori infection with the outcomes of rescue therapy. Material and Methods Patients who failed to respond to second- or third-line eradication therapies were prospectively enrolled. The composition of the gastric microbiota was analyzed using 16S rRNA gene sequencing prior to rescue therapy. The eradication outcomes were confirmed using the [ 13 C]-urea breath test. Results Among 1,590 screened participants, 23 patients with refractory H. pylori infection who underwent rescue therapy based on antimicrobial susceptibility testing were enrolled. The alpha diversity did not differ between success and failure groups; however, the beta diversity analysis revealed a distinct microbial composition. The success group was enriched in Streptococ...

Metabolomics of single-strain & co-cultures of 7 Fusarium strains causing Fusarium head blight reveals metabolic modifications induced by strain co-occurrence. FHB metabolomics reveals species‑specific biomarkers & interaction‑driven shifts in co‑cultures.

Hadal microbes show distinct in situ activity, using refractory substrates & diverse electron acceptors to drive unique deep‑ocean biogeochemistry.

Microbial communities shift with salinity and K⁺, altering succession & carbon‑use strategies across evaporation stages.

Ecosystem Settings & Urbanization Shape Microbial Communities & Antibiotic Resistance Genes on Coastal microplastics Plastispheres differ by habitat & urbanization, with urban mangroves showing the highest ARG diversity.

Highlights • Genomics-driven discovery of a family of lanthipeptide BGCs with anti-phage function • Anti-phage function is confirmed for 6 lanthipeptides in native or heterologous hosts • Key enzymes and residues are identified for anti-phage function • Lanthivirin expression inhibits phage replication through interaction with proteins

Highlights • SidL is an actin-dependent adenylyltransferase that targets host glycolysis • SidL adenylates 3PG to produce 2-AMP-3PG • Expression of SidL in human cells disrupts glycolysis and blocks mTORC1 signaling • Production of 2-AMP-3PG by SidL occurs early during the Legionella infection cycle

Highlights • An introduced analytical framework quantifies taxon–community associations to identify computationally inferred candidate keystone taxa. • Application to five PVTGs identifies 121 candidate keystone taxa, most of which are population-specific, with a reproducible subset across traditional populations. • Several candidate keystone taxa associated with lower community dispersion also show consistent associations with multiple disease conditions, highlighting priorities for future investigation. • A conserved metabolic core coexists with population-specific functions, while acculturation is associated with reduced microbial diversity and increased disease-associated taxa.

Highlights • This review provides a mechanistic classification of bacterial neurotoxins. • Neurotoxins are discussed as modulators of neural and neuroimmune networks. • Emerging links between bacterial neurotoxins and the gut–brain axis are highlighted. • The role of neurotoxins in neurodegenerative disorders is critically evaluated. • Engineered neurotoxin platforms show promise for targeted neural therapeutics. • Current translational opportunities and limitations in precision neurology are reviewed.

Highlights • Maternal vitamin B12 deficiency aggravates offspring obesity • Vitamin B12 deficiency reduces B. pseudolongum in dams and offspring • Loss of B. pseudolongum during lactation worsens obesity in offspring • Restoring B. pseudolongum or acetate alleviates this obesity via Ffar2-Ehhadh

Highlights • Engineered GSDMs are tailored as VIDAs to sense viral protease • VIDA is inert without infection and has potent antiviral effects in vitro and in vivo • VIDA elicits a “kill-and-alert” antiviral immune response in mice • AI-driven accelerated evolution generates safer and more potent VIDAs

Highlights • Bulk meta-transcriptomics separates recurrent and condition-specific responses. • Heat ramp triggers a broader, more structured program than heat shock. • WGCNA, GO and motif analyses identify recurrent non-specific modules. • Heat ramp-specific signatures link ribosome biogenesis and proteostasis. • Stress-responsive modules show limited overlap with evolutionarily young genes.

Highlights • Seeds can transmit a subset of associated bacteria to the next plant generation. • Seed-associated bacteria can influence germination, nutrient acquisition, and pathogen suppression. • Seed-focused SynComs enable tests of bacterial persistence, seed-to-seedling transfer and effects on crop traits.

Highlights • NiV as a highly pathogenic zoonotic agent, poses a persistent and severe threat to global public health. • This review systematically reviews the viral structure and pathogenic mechanisms of NiV. • This review summarizes the progress and breakthroughs in vaccine development and addresses current research limitations. • The review provides theoretical support for the precise prevention and control of NiV.

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...