@article {pmid42709883,
year = {2026},
author = {Liu, Y and Yan, S and Zhang, J and Chen, Y and Zhou, Y and Huang, C and Jiang, T and Gao, Y and Zhu, H and Shi, H and Han, C and Li, F and Zhang, J and Zhao, J and Cao, M},
title = {Curvularia lunata drives biodeterioration of PVC secondary cable insulation involving surface colonization, moisture retention and chemical deterioration.},
journal = {PloS one},
volume = {21},
number = {9},
pages = {e0357774},
pmid = {42709883},
issn = {1932-6203},
mesh = {*Ascomycota/metabolism/isolation & purification/genetics ; *Polyvinyl Chloride/chemistry ; Surface Properties ; Biodegradation, Environmental ; Water/chemistry ; },
abstract = {Microbial degradation of cable insulation materials is a critical issue affecting the reliability of power systems. In this study, metagenomic analysis was employed to reveal the microbial community structure on contaminated substation cables, identifying Curvularia lunata as a dominant fungal species in high-voltage environments. Subsequently, a specific strain, Curvularia lunata B3, was isolated and identified for further investigation. To assess its specific impact on insulation performance, artificial inoculation experiments were conducted on secondary cable samples. Multi-dimensional characterization techniques, including SEM, WCA measurements, halogen moisture analysis, FTIR, XPS, and LCR digital bridge testing, were utilized to evaluate material degradation. The results demonstrated that C. lunata colonization caused significant surface erosion, characterized by the formation of holes and furrows. This physical damage was accompanied by a marked decrease in hydrophobicity, with the water contact angle dropping from 88.30 ± 0.79° to 78.27 ± 1.27°, and a gradual increase in water content to approximately 1.2% over 60 days. Chemical analysis revealed that microbial activity induced oxidation and dechlorination of the PVC insulation, evidenced by the reduction of C-Cl bonds and the emergence of oxygen-containing functional groups. These physicochemical alterations significantly compromised the electrical insulation of the cables, as evidenced by a marked decrease in series resistance (Rs) and an increase in series capacitance (Cs). This study elucidates the mechanisms of fungal erosion on cable insulation and provides a scientific basis for developing targeted protective strategies in power systems.},
}

*Ascomycota/metabolism/isolation & purification/genetics
*Polyvinyl Chloride/chemistry
Surface Properties
Biodegradation, Environmental
Water/chemistry

@article {pmid42710124,
year = {2026},
author = {Yin, G and Shen, Z and Zhao, Y and Liu, X and He, X and Shen, W and Liu, Y and Guo, R and Shang, J and Chen, J and Liao, Q},
title = {Identification of functional microorganisms and genes mediating ciprofloxacin degradation in dynamic habitats of algal bloom decomposition.},
journal = {Journal of hazardous materials},
volume = {517},
number = {},
pages = {143501},
doi = {10.1016/j.jhazmat.2026.143501},
pmid = {42710124},
issn = {1873-3336},
abstract = {Decay of algal blooms in eutrophic lakes generates detritus-rich, redox-dynamic microhabitats that modulate the degradation of emerging pollutants as antibiotics. The degradation pathways of antibiotics within algal-detritus accumulation zones and the associated microbial assimilators remain insufficiently understood. In this study, localized algal bloom decay zones were simulated using static lake microcosms, and DNA-stable isotope probing (DNA-SIP) combined with metagenomic analysis were employed to elucidate ciprofloxacin (CIP) degradation pathways and to identify microorganisms potentially involved in CIP assimilation under elevated CIP exposure. Results demonstrate that ecological succession linked to algal decomposition was closely synchronized with CIP degradation, which primarily proceeded via defluorination, decarboxylation, and piperazine ring modification. The bottom detritus layer showed enrichment of aromatic compound-degrading bacteria, including Hydrogenophaga, Reyranella, and Rhodoblastus, in heavy DNA fractions, indicating their potential role in CIP assimilation. This layer also contained functional genes associated with benzoate, halogenated aromatic compounds, and polycyclic aromatic hydrocarbon degradation pathways. In addition, enrichment of the AAC(6')-Ib-cr gene family in the bottom layer coincided with detection of N-acetylated CIP products, suggesting a possible acetylation-mediated inactivation mechanism. Collectively, the study identified candidate microorganisms and genes linked to CIP-derived assimilation and degradation in algal-detritus-rich microhabitats, providing mechanistic insights into antibiotic degradation in polluted algal decay hotspots.},
}

@article {pmid42710127,
year = {2026},
author = {Liu, S and Ji, Y and Hu, X and Qu, S and Peng, X and Yin, Z and Zhou, S and Tsang, YF},
title = {Microalgal-bacterial sludge enhances dimethyl phthalate (DMP) biodegradation beyond adsorption: Metabolic pathways, microbial responses, and adaptive mechanisms.},
journal = {Journal of hazardous materials},
volume = {517},
number = {},
pages = {143497},
doi = {10.1016/j.jhazmat.2026.143497},
pmid = {42710127},
issn = {1873-3336},
abstract = {Phthalate acid esters (PAEs), as typical environmental endocrine disruptors, pose severe threats to ecosystems and human health due to their persistence in aquatic environments, while conventional wastewater treatment processes exhibit low removal efficiency and risk secondary pollution. This study constructed microalgal-bacterial sludge (MABS) to systematically investigate its removal efficiency and the degradation mechanisms of dimethyl phthalate (DMP). The results demonstrate that, compared to conventional activated sludge (AS), DMP MABS exhibited greater tolerance to DMP and higher DMP removal efficiency, reaching 96.9%, with biodegradation rather than adsorption becoming the dominant removal route, improved settling performance (SVI decreased to 51.19 mL/g), increased biomass, and stimulated secretion of extracellular polymeric substances (EPS, up to 40.00 mg/g VSS) to form a protective barrier against toxicity. Microbial analysis revealed that Pseudomonadota dominated the microbial community and was strongly associated with metabolic functions, while MAG-based metagenomic binning identified Burkholderiales as the largest order-level contributor to DMP-related functional genes. Integrating EPS characterization with metagenomic evidence, we further hypothesize an EPS-mediated microalgal-bacterial interaction model in which LB-EPS enriches DMP at the aggregate interface, TB-EPS stabilizes oxic-anoxic microzones, and microalgal-derived oxygen and carbon sources, signaling, chemotaxis, biofilm formation, and vitamin-associated functions collectively support bacterial DMP catabolism. Qualitatively assigned intermediates together with metagenomic annotations proposing a putative DMP biodegradation pathway involve de-esterification to monomethyl phthalate and phthalic acid (lip, gnl, and pgl, etc.), followed by aerobic dioxygenase-catalyzed or anaerobic decarboxylation to protocatechuic acid (pht3, pht4, and pht5, etc.) or benzoic acid (benA-xylX and benB-xylY), ultimately entering the tricarboxylic acid cycle (pcaG, pcaF, ligK, and galD, etc.). This technology integrates high-efficiency degradation, energy conservation, and resource recovery potential, providing theoretical and technical foundations for wastewater treatment plants to address emerging pollutants.},
}

@article {pmid42710166,
year = {2026},
author = {Podosokorskaya, OA and Merkel, AY and Novikov, AA and Klyukina, AA and Elcheninov, AG},
title = {Melioribacter sulfuriphilus sp. nov., facultatively anaerobic thermophilic sulfur- and thiosulfate-respiring bacterium from Karmadon hot springs of North Ossetia (Russian Federation).},
journal = {Systematic and applied microbiology},
volume = {49},
number = {6},
pages = {126768},
doi = {10.1016/j.syapm.2026.126768},
pmid = {42710166},
issn = {1618-0984},
abstract = {Novel facultatively anaerobic moderately thermophilic bacteria, strains OK-6-Me[T] and OK-1-Me, were isolated from the hot springs of Karmadon (North Ossetia, Russian Federation). Gram-stain-negative, motile rods were present singly, in rosettes, and formed biofilms. Both strains grew optimally at 55 °C, pH 7.0 and did not require sodium chloride. They were chemoorganoheterotrophs, growing on mono-, di- and polysaccharides (cellulose, xylan, lichenan, xyloglucan, mannan, locust bean gum, pectin) as well as proteinaceous substrates (gelatin, casein). Growth under anaerobic conditions was observed both in the presence and absence of external electron acceptors (sulfur, thiosulfate, nitrite, arsenate, Fe-citrate, ferrihydrite). Major cellular fatty acids of both strains were iso-C15:0, anteiso-C15:0, and anteiso-C17:0. The size of the genomes were 3.3 and 3.2 Mb for strain OK-6-Me[T] and OK-1-Me, respectively. Genomic DNA G + C content was 37% for both strains. According to the 16S rRNA gene sequence and conserved protein sequences phylogenies, the strains represented a new species of the genus Melioribacter of family Melioribacteraceae within the class Ignavibacteria, for which the name Melioribacter sulfuriphilus sp. nov. is proposed, with type strain OK-6-Me[T] (= B-3972[T] = CGMCC 1.18264 [T] = BIM B-2154[T] = UQM 41932[T]). Analysis of OK-1 and OK-6 metagenomes revealed presence of various genes involved in carbon (CO2 fixation, carbohydrate hydrolysis, hydrocarbons degradation, fermentation), nitrogen (nitrate, nitrite, NO and N2O reduction) and sulfur cycles (sulfate reduction, sulfur or thiosulfate reduction, oxidation of sulfur compounds). MAGs OK-1-035 and OK-6-024 almost identical to genomes of strain OK-1-Me and OK-6-Me[T] presumably are integral part of these complex trophic chains.},
}

@article {pmid42710654,
year = {2026},
author = {Chen, Y and Li, Y and Chen, Y and Gou, C and Li, H and He, X and Zeng, N and Du, E and Chen, X and Gui, F},
title = {Host detoxification and gut microbiota are associated with chlorantraniliprole resistance in Spodoptera frugiperda.},
journal = {Journal of insect physiology},
volume = {},
number = {},
pages = {105062},
doi = {10.1016/j.jinsphys.2026.105062},
pmid = {42710654},
issn = {1879-1611},
abstract = {Spodoptera frugiperda is a major agricultural pest that causes severe damage in China. Chlorantraniliprole (CAP) is the primary insecticide used for control; however, it is yet unknown how much the intrinsic detoxification system and gut microbiota of the host contribute to resistance. In this study, we used a resistant strain (CR) with a 71.85-fold resistance ratio after 10 generations of CAP selection. The molecular and microbial changes associated with CAP resistance in S. frugiperda were systematically analyzed by integrating phenotypic and multi-omics data. Results demonstrated that detoxification enzyme activities were markedly increased in the CR strain. Host-mediated metabolic pathways driven by Cytochrome P450 and glutathione S-transferase were significantly upregulated. Furthermore, transcriptome evidence indicated that CAP-induced calcium dysregulation was mitigated via enhanced calcium sequestration and endoplasmic reticulum chaperone responses, suggesting physiological tolerance of insects to this insecticide.. Continuous CAP stress also significantly reshaped the gut microbial community structure of S. frugiperda, with Enterococcus emerging as the dominant genus. According to metagenomic annotation, the gut microbiome was enriched in candidate genes associated with CAP degradation, including dehalogenases and amidases, that could potentially break the chemical bonds in CAP and thereby contribute to resistance. Enterococcus mundtii was the most prominently contributor in terms of gene abundance. Phylogenetic analysis revealed sequence similarities and conserved domains between candidate microbial degradation genes and host metabolic detoxification genes, suggesting potential functional similarity. The integrative analyses suggested that S. frugiperda resistance may arise from correlated changes in host endogenous metabolism, calcium homeostasis, and gut-microbiota-mediated degradation potential. The gut microbiota may form a coordinated adaptive regulatory system by encoding candidate degrading enzymes and exhibiting correlative coupling with host genes, which requires further functional validation. These findings highlight the potential synergy between host detoxification and gut microbiota as a contributing factor to CAP resistance in S. frugiperda.},
}

@article {pmid42710694,
year = {2026},
author = {Tian, J and Wang, Y and Lu, L and Hu, X and Zhou, Y and Tian, S and Liu, Y and Yang, H and Fang, H and Zhou, Q and Qiu, Z and Zhu, J and Zhang, C and Wang, W},
title = {Gut microbiota correlating with glycerophospholipid metabolism dysregulation is associated with brain functional alterations in adolescent depression.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {107005},
doi = {10.1016/j.bbi.2026.107005},
pmid = {42710694},
issn = {1090-2139},
abstract = {Gut microbiota dysbiosis has been linked to depression; however, evidence regarding this association in adolescents remains scarce, and the underlying molecular and neuropathological mechanisms are poorly understood. We conducted an integrative multi-omics study combining fecal metagenomic sequencing, serum untargeted metabolomics, resting-state fMRI, and spatial brain transcriptomics in 160 adolescents with depression (PT) recruited from multicenter cohort and 90 local healthy controls (HC) during the same period. Multimodal neuroimaging assessed spontaneous activity, functional connectivity, and structure-function coupling. Cross-omics association, mediation analyses, and machine learning were applied to identify mechanistic pathways and robust biomarkers. Adolescents with depression exhibited distinct gut microbial dysbiosis and pronounced disruption of glycerophospholipid metabolism. Multiple phospholipids and their metabolites were significantly altered and closely associated with differential microbial taxa. Neuroimaging revealed abnormal functional reorganization and regional structure-function decoupling, prominently involving the precuneus and precentral gyrus. Transcriptomic mapping demonstrated that brain regions showing the greatest functional alterations were enriched for genes related to phospholipid metabolism. Mediation analyses indicated that gut microbiota may influence depressive symptoms through glycerophospholipid metabolites and precentral gyrus dysfunction. A cross-validated multi-omics biomarker panel showed strong predictive performance for identifying patients with depression. These findings suggested glycerophospholipid metabolism may be as a key molecular interface linking gut microbial dysbiosis to brain network dysfunction in adolescents with depression, providing a multiscale framework for microbiota-informed stratification and prevention.},
}

@article {pmid42711294,
year = {2026},
author = {Peng, Y and Woods, LC and Perlaza-Jimenez, L and Lappan, R and Jespersen, M and Dong, X and Holland, SR and Chown, SL and Leung, PM and Greening, C},
title = {Widespread horizontal transfer and strong selection enhance microbial adaptation in Antarctic soils.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42711294},
issn = {2041-1723},
support = {FT240100502//Department of Education and Training | Australian Research Council (ARC)/ ; SR200100005//Department of Education and Training | Australian Research Council (ARC)/ ; SR200100005//Department of Education and Training | Australian Research Council (ARC)/ ; SR200100005//Department of Education and Training | Australian Research Council (ARC)/ ; DE230100542//Department of Education and Training | Australian Research Council (ARC)/ ; SR200100005//Department of Education and Training | Australian Research Council (ARC)/ ; SR200100005//Department of Education and Training | Australian Research Council (ARC)/ ; SR200100005//Department of Education and Training | Australian Research Council (ARC)/ ; DE250101210//Department of Education and Training | Australian Research Council (ARC)/ ; SR200100005//Department of Education and Training | Australian Research Council (ARC)/ ; MGS and MITS//Monash University (MU)/ ; },
mesh = {Antarctic Regions ; *Gene Transfer, Horizontal ; *Soil Microbiology ; Phylogeny ; *Selection, Genetic ; Hydrogenase/genetics ; *Adaptation, Physiological/genetics ; Metagenome ; Aldehyde Oxidoreductases/genetics ; Bacteria/genetics/classification ; Multienzyme Complexes ; },
abstract = {Terrestrial Antarctica harbors compositionally diverse and functionally distinct microbial life. Yet the eco-evolutionary processes underlying adaptation to Antarctica's polyextreme conditions remain largely unknown. Here, we address how horizontal gene transfer (HGT) and de novo mutations influence microbial adaptation in 16 Antarctic soils using combined short- and long-read datasets. Phylogenetic reconciliation and mobile genetic element analysis of 676 metagenome-assembled genomes show frequent HGT across communities. While transferred genes span diverse functional categories, those involved in energy metabolism are exchanged at higher frequency. Genes for aerotrophy, i.e. the consumption of atmospheric trace gases to provide energy, carbon, and hydration, are among the most frequently disseminated. Approximately a quarter of carbon monoxide dehydrogenases and [NiFe]-hydrogenases are predicted to be horizontally acquired and are often associated with mobile genetic elements. Analysis of polymorphisms suggests widespread purifying selection, particularly for aerotrophy genes, providing further evidence that aerotrophy is critical for microbial survival in Antarctica. Genetic variation in hydrogenases is tightly associated with predicted protein structures, with intense selection acting on critical sites preserving stability and function. Together, these findings show that previously unrecognized eco-evolutionary dynamics shape the composition and function of Antarctic microbial communities, and confirm aerotrophy is a strongly selected and horizontally disseminated trait.},
}

Antarctic Regions
*Gene Transfer, Horizontal
*Soil Microbiology
Phylogeny
*Selection, Genetic
Hydrogenase/genetics
*Adaptation, Physiological/genetics
Metagenome
Aldehyde Oxidoreductases/genetics
Bacteria/genetics/classification
Multienzyme Complexes

@article {pmid42711738,
year = {2026},
author = {Gao, X and Qin, R and He, J},
title = {Analysis of the pulmonary microbiome in ARDS patients using bronchoalveolar lavage fluid metagenomic next-generation sequencing: a retrospective observational study.},
journal = {Journal of intensive care},
volume = {14},
number = {1},
pages = {},
pmid = {42711738},
issn = {2052-0492},
support = {KJQN202300410//Science and technology research project of Chongqing Education Commission/ ; kryc-yq-2127//Kuanren Talents Program of the second affiliated hospital of Chongqing Medical University/ ; },
abstract = {BACKGROUND: Acute respiratory distress syndrome (ARDS) exhibits significant clinical heterogeneity, with inflammatory subphenotypes (hypoinflammatory and hyperinflammatory) representing a key axis for precision medicine. The role of the pulmonary microbiome in these subphenotypes remains poorly understood.

METHODS: This retrospective study enrolled 159 ARDS patients. Using a validated machine-learning classifier, patients were stratified into hypoinflammatory (n=92) and hyperinflammatory (n=67) groups. Bronchoalveolar lavage fluid (BALF) was analyzed by metagenomic next-generation sequencing (mNGS) and conventional microbiological testing (CMT). Clinical characteristics, pathogen profiles, and pulmonary microbiome composition were compared between groups.

RESULTS: Patients in the hyperinflammatory phenotype had more severe disease, with significantly higher in-hospital mortality (65.7% vs. 30.4%, P < 0.001) and 28-day mortality (53.7% vs. 22.8%, P < 0.001). mNGS demonstrated superior diagnostic performance, identifying pathogens in 18.2% of cases that were negative by conventional microbiological testing (CMT), whereas CMT alone detected pathogens in only 2.5% of mNGS-negative cases. mNGS showed significant advantages in viral detection (74.5% vs. 28.2%, P < 0.001) and in the identification of mixed infections (74.5% vs. 41.1%, P < 0.001). Acinetobacter baumannii was the most prevalent species in both phenotypes; however, the hyperinflammatory phenotype was enriched for Klebsiella pneumoniae, Legionella pneumophila, and influenza A (H1N1), whereas Stenotrophomonas maltophilia and herpesviruses were more prevalent in the hypoinflammatory phenotype. Species richness was significantly reduced in the hyperinflammatory phenotype (Chao1, P < 0.001; ACE, P = 0.001). In adjusted analyses, this association remained virtually unchanged after adjustment for ARDS etiological category and pulmonary vs. extrapulmonary ARDS, and remained significant in the fully adjusted model additionally accounting for age, sex, and immunosuppression (Chao1: P = 0.002; ACE: P = 0.003). Evenness indices (Shannon/Simpson) and overall community structure (β-diversity; PERMANOVA, P = 0.156) did not differ between phenotypes, suggesting a selective depletion of rare, low-abundance taxa rather than a global restructuring of the pulmonary microbiota. Linear discriminant analysis effect size (LEfSe) identified differentially abundant taxa of exploratory significance: the hyperinflammatory phenotype was enriched for Bifidobacterium dentium and Gemella sanguinis, whereas the hypoinflammatory phenotype was enriched for commensals such as Streptococcus mitis. Network analysis revealed well-defined positive and negative correlations between pathogens and commensal taxa.

CONCLUSIONS: The hyperinflammatory phenotype of ARDS is characterized by greater clinical severity and a distinct pulmonary microbiome signature. Metagenomic next-generation sequencing (mNGS) substantially outperforms conventional methods for etiological diagnosis. LEfSe analysis identified differentially enriched taxa, with the hyperinflammatory phenotype enriched for microorganisms that typically colonize the oral cavity or gut (e.g., Bifidobacterium dentium), suggesting potential microbial translocation along the oral-lung or gut-lung axis. These findings provide a novel microbiome dimension for the precision subphenotyping of ARDS.},
}

@article {pmid42711823,
year = {2026},
author = {Saragiotto, GK and de Oliveira, LFV and Geciana Tomaz Dos Santos, B and Nunes Sanches, R and Merizzi de Oliveira, M and Campos Freire, F and Dias de Oliveira Carvalho, R and Sivieri, K and Sartoratto, A and Cabral, L and Azevedo, V and Belli, T and Costa Antunes, AE},
title = {Exploratory case comparison of gut microbiome functional potential in ultramarathoners differing in adiposity and finish time.},
journal = {Journal of the International Society of Sports Nutrition},
volume = {23},
number = {1},
pages = {2725874},
doi = {10.1080/15502783.2026.2725874},
pmid = {42711823},
issn = {1550-2783},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Feces/chemistry/microbiology ; *Adiposity/physiology ; *Obesity/microbiology/physiopathology ; *Marathon Running/physiology ; Fatty Acids, Volatile/analysis/metabolism ; Male ; Body Mass Index ; *Physical Endurance/physiology ; *Running/physiology ; },
abstract = {Understanding variations in gut microbial functional potential among endurance athletes may inform future personalized nutritional strategies. This exploratory case-comparison study aimed to investigate predicted microbial functional potential using shotgun metagenomic sequencing and fecal metabolites, in two post hoc-selected runners who represented extreme and contrasting outcomes from the same single-stage 217 km mountain ultramarathon: a normal-BMI fast-finisher and an obese slow-finisher. The main descriptive findings suggest that the normal-BMI fast finisher exhibited smaller observed differences among the analyzed enzyme-coding functions and pathways in the sample collected after race completion, with a predominance of enzyme-coding functions associated with nucleic acid-related processes and protein biosynthesis. In contrast, the obese slow-finisher showed larger observed differences in predicted functional potential between the pre- and post-race samples. Distinct fecal metabolite patterns were also observed, with selective short-chain fatty acid (SCFA) changes in the normal-BMI fast-finisher and reductions across all analyzed SCFAs in the obese slow finisher. Given the limitations of this study, including the confounding effects of adiposity, unmeasured dietary intake, and post hoc selection bias, these descriptive observations provide hypothesis-generating data rather than establishing causal relationships with performance. Taken together, these findings encourage further investigation in larger cohorts.},
}

Humans
*Gastrointestinal Microbiome/physiology
Feces/chemistry/microbiology
*Adiposity/physiology
*Obesity/microbiology/physiopathology
*Marathon Running/physiology
Fatty Acids, Volatile/analysis/metabolism
Male
Body Mass Index
*Physical Endurance/physiology
*Running/physiology

@article {pmid42711910,
year = {2026},
author = {Bai, J and You, Q and Si, G and Hu, D and Sun, A and Su, S and Wang, R and Fan, J and Gao, S and Zhu, T and Song, CL and Zhou, F and Lv, Y},
title = {Gut Microbiota-Derived Indole-3-Propionic Acid Alleviates Diabetic Osteoporosis Through Nrf2-Mediated Ferroptosis Suppression.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e77649},
doi = {10.1002/advs.77649},
pmid = {42711910},
issn = {2198-3844},
support = {12474461//National Natural Science Foundation of China/ ; 82402806//National Natural Science Foundation of China/ ; 81971160//National Natural Science Foundation of China/ ; 7202222//Beijing Municipality Natural Science Foundation/ ; 2022-2-4096//Capital Health Development Research Special Project/ ; },
abstract = {Diabetic osteoporosis combines impaired bone formation with disproportionate skeletal fragility, yet the microbial metabolites linking diabetes-associated dysbiosis to bone dysfunction remain unclear. This study implicates indole-3-propionic acid (IPA), a gut microbiota-derived tryptophan metabolite, in the maintenance of skeletal homeostasis under diabetic conditions. Circulating IPA was lower in diabetic mice and in a small exploratory cohort of patients with diabetic osteoporosis. IPA concentrations were positively associated with bone mass. Metagenomic profiling linked lower IPA to impaired microbial tryptophan metabolism and reduced Clostridium abundance. In diabetic mice, IPA supplementation improved trabecular microarchitecture and bone formation. In bone marrow mesenchymal stem cells subjected to high glucose and palmitate, IPA also restored GPX4 and SLC7A11 expression and was associated with recovery of Nrf2-mediated antioxidant signaling. Pharmacological inhibition of Nrf2 substantially attenuated these anti-ferroptosis and pro-osteogenic effects. Together, these findings support a gut microbiota-IPA-Nrf2-ferroptosis pathway linking altered microbial tryptophan metabolism to impaired osteogenesis. They provide a rationale for evaluating IPA as a potential therapeutic strategy for diabetic osteoporosis.},
}

@article {pmid42711968,
year = {2026},
author = {Liang, G and Wang, C and Liu, R and Ji, Q and Zhang, X and Zhao, L and Liu, X and Zhang, H and Zhuang, G and Zheng, J},
title = {Assembly Dynamics and Functional Divergence of Anaerobic Communities Driven by Iron Oxides.},
journal = {Environmental microbiology},
volume = {28},
number = {9},
pages = {e70412},
doi = {10.1111/1462-2920.70412},
pmid = {42711968},
issn = {1462-2920},
support = {GYY-NYHJ-2023-WT-002//the Weiqiao-UCAS Innovation Research Projects on Carbon Neutrality Technology/ ; },
mesh = {*Ferric Compounds/metabolism/chemistry ; *Microbiota ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Sewage/microbiology ; Anaerobiosis ; Minerals/metabolism ; Ferrosoferric Oxide/metabolism ; Methane/metabolism ; Iron Compounds ; },
abstract = {Iron oxides play an important role in regulating global biogeochemical cycles, yet how their physicochemical properties influence community structure, function, and assembly remains poorly understood. Here, we investigated the effects of four representative iron oxides-ferrihydrite (Fh), goethite (Gt), haematite (Ht), and magnetite (Mt)-serving as terminal electron acceptors on microbial communities enriched from activated sludge. Metagenomic profiling revealed mineral-dependent divergence in community composition and functional potential. The communities developed on amorphous Fh demonstrated low microbial diversity and were heavily dominated by Pseudomonas_A. In contrast, the communities associated with crystalline oxides (Gt and Ht) maintained intermediate diversity. Notably, the Mt. communities exhibited a more polycentric structure, possessing the highest richness and evenness, alongside a significant enrichment of Geobacter. Methane was detected in crystalline-oxide systems but remained below detection in Fh systems. Mineralogical analyses revealed substantial Fe(III) reduction and secondary mineral formation across treatments. Null-model analysis of pairwise turnover supports mineral-associated community turnover while highlighting that the relative contributions of selection versus undominated processes vary among minerals. Overall, these findings demonstrate that iron oxide identity is associated with differences in anaerobic community structure and biogeochemical outcomes.},
}

*Ferric Compounds/metabolism/chemistry
*Microbiota
*Bacteria/classification/genetics/metabolism/isolation & purification
*Sewage/microbiology
Anaerobiosis
Minerals/metabolism
Ferrosoferric Oxide/metabolism
Methane/metabolism
Iron Compounds

@article {pmid42711992,
year = {2026},
author = {Farese, M and Moraitou, M and Jin, C and Forsythe, A and Micarelli, I and van der Valk, T and Manzi, G and Parducci, L and Tafuri, MA and Guschanski, K},
title = {Lifestyle Impacts the Oral Microbiome of Classical and Post-Classical Societies in Italy.},
journal = {American journal of biological anthropology},
volume = {191},
number = {1},
pages = {e70357},
doi = {10.1002/ajpa.70357},
pmid = {42711992},
issn = {2692-7691},
support = {//Bertil Lundman Foundation for Anthropological Studies (Swedish Phytogeographical Society)/ ; DOT1326JZS//Italian Ministry of University and Research (MUR)/ ; },
mesh = {Humans ; *Microbiota/genetics ; Italy ; History, Ancient ; *Life Style/history ; Dental Calculus/microbiology ; DNA, Ancient/analysis ; *Mouth/microbiology ; Roman World/history ; },
abstract = {OBJECTIVES: The fall of the Roman Empire (476 CE) profoundly affected the lives of its peoples due to the political, administrative, and territorial changes that occurred. The majority of written records of the time focus on the social élite, leaving larger parts of the population understudied. Here, we employ a bioarchaeological approach to understand how differences in lifestyle may be reflected in the oral microbiome of people from different social classes living before and after the fall.

MATERIAL AND METHODS: We analyzed shotgun sequencing data from dental calculus, the preserved oral microbiome, of 67 individuals belonging to different social classes from two Classical cemeteries (I-III century CE, Lucus Feroniae and Isola Sacra) and one post-Classical cemetery (IV-VIII century CE, Selvicciola), all located in proximity to the city of Rome, Italy.

RESULTS: We detect significant differences in the taxonomic and functional composition of the oral microbiome between the three sites, with the rural town of Lucus Feroniae standing out compared to its two counterparts. Reliable identification of dietary items was not possible.

DISCUSSION: The distinct oral microbiome of Lucus Feroniae could reflect differences in general health and subsistence practices, in line with previously published isotopic and morphological data. Its rural position may have mitigated the cyclical food crises that affected the contemporary Isola Sacra and the later community of Selvicciola, buffering it against the nutritional stress observed in these two locations. This finding supports the temporal stability of the dental calculus microbiome while highlighting the impact of lifestyle on the oral microbial communities.},
}

Humans
*Microbiota/genetics
Italy
History, Ancient
*Life Style/history
Dental Calculus/microbiology
DNA, Ancient/analysis
*Mouth/microbiology
Roman World/history

@article {pmid42712102,
year = {2026},
author = {Pellegrini, C and Ravaioli, F and De Fanti, S and Siliquini, A and Sala, C and Rochat, M and Pollarini, V and Polischi, B and Pasti, A and Grasso, M and Rambaldi, M and Cardoni, F and Grotteschi, N and Caraci, F and Cortelli, P and Provini, F and Lodi, R and Morandi, L and Parchi, P and Pirazzoli, GL and Sambati, L and Tonon, C and Bacalini, MG},
title = {Alterations of gut microbiota in Down syndrome and their association with Alzheimer's disease.},
journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association},
volume = {22},
number = {9},
pages = {e71815},
doi = {10.1002/alz.71815},
pmid = {42712102},
issn = {1552-5279},
support = {PNC0000002//Italian Complementary National Plan PNC-1.1 "Research initiatives for innovative technologies and pathways in the health and welfare sector" D.D. 931 of 06/06/2022, "DARE-DigitAl lifelong pRvEntion" initiative/ ; B53C22006330001//Italian Complementary National Plan PNC-1.1 "Research initiatives for innovative technologies and pathways in the health and welfare sector" D.D. 931 of 06/06/2022, "DARE-DigitAl lifelong pRvEntion" initiative/ ; GR-2019-12369983-Theory-enhancing//Italian Ministry of Health/ ; //Italian Ministry of Health - "Ricerca Corrente" funding/ ; },
mesh = {Humans ; *Down Syndrome/microbiology/blood/complications ; *Alzheimer Disease/blood/microbiology ; Female ; Male ; *Gastrointestinal Microbiome/physiology ; Middle Aged ; Aged ; Adult ; Biomarkers/blood ; Aged, 80 and over ; tau Proteins/blood ; Feces/microbiology ; Young Adult ; RNA, Ribosomal, 16S/genetics ; Neurofilament Proteins/blood ; Glial Fibrillary Acidic Protein/blood ; },
abstract = {INTRODUCTION: Adults with Down syndrome (DS) have a higher risk of Alzheimer's disease (AD). As gut microbiota (GM) alterations have been reported in AD, we investigated their association with cognitive decline and plasma AD biomarkers in DS.

METHODS: Fecal and plasma samples were collected from 58 adults with DS (21-75 years) and 30 euploid controls (CTRL; 25-83 years). GM was profiled using 16S rRNA sequencing, filtering low prevalent taxa. Major neurocognitive disorder (NcD) was diagnosed with Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition (DSM-5) criteria. Plasma levels of phosphorylated tau 181 (p-tau181), neurofilament light chain (NfL), and glial fibrillary acidic protein (GFAP) were measured using Simoa.

RESULTS: DS showed no changes in overall microbial diversity compared to CTRL, but genera including UBA1819 and Intestinibacter were altered. Specific genera showed changes in DS with NcD, like Alistipes (increased) and Roseburia (decreased), with the latter negatively associated with plasma AD biomarkers.

DISCUSSION: Adults with DS display AD-associated changes in GM partially resembling those reported previously in euploid AD patients.},
}

Humans
*Down Syndrome/microbiology/blood/complications
*Alzheimer Disease/blood/microbiology
Female
Male
*Gastrointestinal Microbiome/physiology
Middle Aged
Aged
Adult
Biomarkers/blood
Aged, 80 and over
tau Proteins/blood
Feces/microbiology
Young Adult
RNA, Ribosomal, 16S/genetics
Neurofilament Proteins/blood
Glial Fibrillary Acidic Protein/blood

@article {pmid42712403,
year = {2026},
author = {Kariithi, HM and Carabetta, VJ and Leyson, CL and Goraichuk, IV},
title = {Editorial: Sequencing technologies in advancing veterinary and zoonotic infection research.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1950388},
pmid = {42712403},
issn = {2235-2988},
}

@article {pmid42712443,
year = {2026},
author = {Weng, X and Zhang, H and Liu, P and Gao, W and Li, H},
title = {A case report of a patient with chronic granulomatous disease complicated by invasive aspergillosis and disseminated Burkholderia multivorans infection.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1915139},
pmid = {42712443},
issn = {2296-858X},
abstract = {BACKGROUND: Chronic granulomatous disease (CGD) is a rare inborn error of immunity characterized by defective phagocyte oxidative burst, leading to recurrent, life-threatening infections with catalase-positive bacteria and fungi. Co-infections with Aspergillus and Burkholderia species in CGD are exceedingly rare and often fatal due to synergistic pathogenic mechanisms and limited therapeutic options.

CASE PRESENTATION: We report a fatal case of X-linked CGD in a 14-year-old male with a history of recurrent infections, who presented with severe pneumonia, respiratory failure, and profound growth retardation. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) identified Aspergillus flavus complex, Burkholderia multivorans, and subsequent cultures confirmed disseminated B. multivorans infection and invasive aspergillosis. Whole-exome sequencing revealed a novel missense mutation, c.1514T>A (p.Leu505Gln), in the CYBB gene, predicted to result in loss of NADPH oxidase function, which is consistent with the severe infectious phenotype observed. Despite aggressive antimicrobial therapy and intensive supportive care, the patient developed refractory septic shock and multiorgan failure, and died on day 14 of hospitalization.

CONCLUSIONS: This case underscores the lethal potential of concurrent Aspergillus and Burkholderia infections in X-linked CGD and highlights the critical importance of early diagnosis, which can be achieved through functional assays such as the DHR test or NBT test, followed by genetic confirmation when available. The novel CYBB mutation expands the known genotype-phenotype spectrum of severe X-CGD. Prompt recognition of primary immunodeficiencies in children with recurrent infections caused by typical pathogens is essential to enable timely prophylaxis and curative interventions such as hematopoietic stem cell transplantation before irreversible infectious complications occur.},
}

@article {pmid42712642,
year = {2026},
author = {Li, T and Zhou, X and Xiong, F and Zhao, T and Jiang, N and Cai, Y and Hu, Y and Lu, C and Xuan, Y and Gai, X},
title = {Metagenomic profiling of tobacco root endophytes reveals a disease-suppressive Enterobacter strain against Fusarium solani.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1924993},
pmid = {42712642},
issn = {1664-302X},
abstract = {BACKGROUND: Tobacco root rot, caused by Fusarium species, is a persistent soil-borne disease that threatens tobacco production. To identify endophytic contributors to disease suppression, this study compared the root endophytic microbiomes of healthy and diseased tobacco plants using metagenomic sequencing and isolated functional bacteria from healthy roots.

RESULTS: Metagenomic analysis of 30 root samples (223 Gb) generated 2.9 million non-redundant genes and identified 1,953 core genera. Healthy plants contained distinct endophytic microbial communities enriched in bacterial taxa and pathways associated with secondary metabolite biosynthesis, siderophore production, chemotaxis, biofilm formation, and carbohydrate metabolism. This microbiome-guided approach identified TM-1, an endophytic Enterobacter strain that significantly inhibited Fusarium solani by 62.29% in a dual-culture assay. Transcriptome profiling revealed that TM-1 treatment broadly altered F. solani gene expression, with prominent effects on ribosome function, amino acid biosynthesis, carbon metabolism, and glycolysis. TM-1 disrupted sugar transporter-related gene expression, and deletion of five representative genes significantly restricted fungal mycelial growth, with the strongest inhibition (66.47%) observed for the hexose transporter homolog MRS44_010803.

CONCLUSION: These results indicate that healthy tobacco roots harbor disease-suppressive endophytic microorganisms and suggest that TM-1 may suppress F. solani by interfering with sugar transport and carbon acquisition. These findings provide a potential biocontrol resource for the sustainable management of tobacco root rot.},
}

@article {pmid42712652,
year = {2026},
author = {Yasir, M and Klena, JD and Abd El Ghany, M},
title = {Editorial: Infectious disease control in the microbial functional genomics era.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1934262},
doi = {10.3389/fmicb.2026.1934262},
pmid = {42712652},
issn = {1664-302X},
}

@article {pmid42712876,
year = {2026},
author = {Tsuda, Y and Tanizawa, Y and Vu, TMH and Nishimura, Y and Shintani, M and Abe, H and Hasebe, F and Kasuga, I and Nagao, M and Suzuki, M},
title = {VicMAG, an open-source tool for visualizing circular metagenome-assembled genomes highlighting bacterial virulence and antimicrobial resistance.},
journal = {NAR genomics and bioinformatics},
volume = {8},
number = {3},
pages = {lqag109},
pmid = {42712876},
issn = {2631-9268},
mesh = {*Metagenome ; *Drug Resistance, Bacterial/genetics ; *Genome, Bacterial ; Virulence/genetics ; *Bacteria/genetics/pathogenicity ; *Software ; *Metagenomics/methods ; Virulence Factors/genetics ; Interspersed Repetitive Sequences ; },
abstract = {Bacterial pathogens spread in clinical and environmental settings, and mobile genetic elements (MGEs), such as plasmids and phages, mediate the transfer of virulence factor genes (VFGs) and antimicrobial resistance genes (ARGs) among bacterial communities. Metagenomic analysis of environmental and wastewater samples using highly accurate long-read sequencing technologies, such as Pacific Biosciences (PacBio) HiFi sequencing, provides valuable insights into monitoring the regional spread of VFGs and ARGs, including dissemination mediated by MGEs. No visualization tool is currently available for the comprehensive display of numerous resulting circular metagenome-assembled genomes (cMAGs) with functional gene annotations. Here, we developed visualization of circular metagenome-assembled genome (VicMAG), a visualization tool for highly complex cMAGs derived from long-read metagenome assemblies annotated using updated databases of VFGs, ARGs, and MGEs. Using 353 cMAGs from PacBio HiFi sequencing of a wastewater sample, we demonstrated the utility of VicMAG for metagenome visualization. VicMAG provides comprehensive, size-aware visualization of cMAGs representing bacterial chromosomes and plasmids, annotated with VFGs, ARGs, and phages. By simultaneously visualizing all cMAGs in a framework, VicMAG facilitates a holistic understanding of the distribution and genomic context of VFGs and ARGs across complex microbial communities. This tool supports integrated surveillance of bacteria associated with virulence and antimicrobial resistance across clinical, environmental, and One Health contexts.},
}

*Metagenome
*Drug Resistance, Bacterial/genetics
*Genome, Bacterial
Virulence/genetics
*Bacteria/genetics/pathogenicity
*Software
*Metagenomics/methods
Virulence Factors/genetics
Interspersed Repetitive Sequences

@article {pmid42712939,
year = {2026},
author = {Tiwari, SK and Telatin, A and Singh, D},
title = {Identifying fundamental gaps in functional metagenomics: a step towards unlocking microbiome research potential.},
journal = {NAR genomics and bioinformatics},
volume = {8},
number = {3},
pages = {lqag110},
pmid = {42712939},
issn = {2631-9268},
mesh = {Humans ; *Metagenomics/methods ; *Metagenome ; *Microbiota/genetics ; *Gastrointestinal Microbiome/genetics ; Molecular Sequence Annotation ; },
abstract = {Incomplete functional annotation limits biological interpretation in microbiome studies and their translational potential. Poor annotation arises from multiple causes, with incomplete gene-protein-reaction mapping being one tractable yet under-examined contributor. We address this gap by developing a comprehensive hierarchical framework that systematically integrates gene families in UniRef, proteins in UniProt, and metabolic reactions in MetaCyc and BioCyc through UniProtKB accession, EC number, and Pfam-domain matching. Applied to a human gut metagenome dataset via HUMAnN3, our MetaCyc-based mapping recovers up to 2.3-fold more unique reaction identifiers than the default pipeline and increases reaction prevalence across samples from ≈32% to 52% core reactions, addressing the data sparsity that limits statistical and machine-learning applications in microbiome research. Biological plausibility for the tested functions was supported by positive and negative controls: gut-microbial hormone-metabolism reactions previously linked to this dataset were recovered, while vertebrate-specific hormone-metabolism reactions remained correctly undetected. These gains derive from systematic database integration alone, without predictive algorithms, indicating that a tractable, mapping-related component of functional dark matter and data sparsity in microbiome studies is directly addressable. Because Pfam- and BioCyc-derived mappings trade specificity for coverage, confidence in any individual reaction assignment depends on the supporting evidence tier and source database.},
}

Humans
*Metagenomics/methods
*Metagenome
*Microbiota/genetics
*Gastrointestinal Microbiome/genetics
Molecular Sequence Annotation

@article {pmid42713785,
year = {2026},
author = {Thakur, R and Dhar, H and Kiran, S and Gulati, A},
title = {Metagenomic Insights Into Microbial Diversity of Tea Rhizosphere of the Kangra Valley.},
journal = {MicrobiologyOpen},
volume = {15},
number = {5},
pages = {e70416},
doi = {10.1002/mbo3.70416},
pmid = {42713785},
issn = {2045-8827},
mesh = {*Rhizosphere ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Archaea/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; *Fungi/classification/genetics/isolation & purification ; *Tea/microbiology ; Metagenomics ; Sequence Analysis, DNA ; Biodiversity ; Phylogeny ; DNA, Bacterial/genetics/chemistry ; China ; DNA, Fungal/genetics/chemistry ; DNA, Ribosomal/genetics/chemistry ; DNA, Ribosomal Spacer/genetics/chemistry ; },
abstract = {This study provides the first metagenomic assessment of microbial diversity from the tea rhizosphere of the Kangra valley. Tea rhizosphere soil samples were collected from 4 locations (Dharamshala, Baijnath, Palampur, and Joginder Nagar) of the Kangra valley. DNA extracts of rhizosphere samples were analysed for bacterial and Archaeal diversity using amplicon sequencing (V3-V4) region of the 16S rRNA gene and Fungal diversity using ITS1 and ITS2 regions. Baijnath and Palampur samples showed the highest bacterial richness, while Dharamshala and Palampur had the highest fungal richness. Proteobacteria was a dominant phylum in all the rhizosphere samples, followed by Firmicutes, Actinobacteria, Acidobacteria, and Bacteroidetes. A total of 11 fungal phyla were identified among all the locations, with abundance of Ascomycota and Basidiomycota. For the Archaea domain, uncultured archaeon and Aeropyrum camini were the most common found among all the locations. A small fraction (< 0.5%) of Bacillus and Pseudomonas species were observed among all the locations. Alpha and beta diversity indices displayed notable differences within and between microbial diversities. Soil factors were variably associated with microbial diversity, with nitrogen positively aligned with fungal diversity, while EC and K were associated with Archaeal diversity. Soil pH and OM% showed moderate associations with bacterial diversity. These findings provided valuable and comprehensive insights into tea rhizosphere microbial ecology and could be used to better understand microbial functions and their role in plant health.},
}

*Rhizosphere
*Soil Microbiology
*Bacteria/classification/genetics/isolation & purification
*Archaea/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
*Fungi/classification/genetics/isolation & purification
*Tea/microbiology
Metagenomics
Sequence Analysis, DNA
Biodiversity
Phylogeny
DNA, Bacterial/genetics/chemistry
China
DNA, Fungal/genetics/chemistry
DNA, Ribosomal/genetics/chemistry
DNA, Ribosomal Spacer/genetics/chemistry

@article {pmid42713903,
year = {2026},
author = {van Genderen, PJJ and van Sprang, ENM},
title = {Artificial Intelligence and Complementary Digital Health Technologies Across the Travel Medicine Continuum: A Narrative Review.},
journal = {Journal of travel medicine},
volume = {},
number = {},
pages = {},
doi = {10.1093/jtm/taag082},
pmid = {42713903},
issn = {1708-8305},
abstract = {BACKGROUND: Artificial intelligence (AI) and complementary digital health technologies are increasingly being applied to improve prevention, diagnosis and surveillance in travel medicine. This narrative review evaluates current applications of these technologies across the pre-travel, peri-travel and post-travel phases of the travel continuum.

METHODS: A narrative literature review was conducted using a clinically oriented three-phase framework encompassing pre-travel preparation, peri-travel monitoring and post-travel diagnosis and surveillance. Machine learning, clinical decision-support systems, large language models, wearable technologies, telemedicine, outbreak surveillance, precision diagnostics and interoperable digital health infrastructure were reviewed.

RESULTS: Machine learning improved individualized risk prediction before travel and supported diagnostic decision-making after travel, while clinical decision-support systems enabled more personalized preventive and therapeutic recommendations. During travel, AI-assisted border screening detected SARS-CoV-2 outbreaks up to nine days earlier than conventional surveillance, and wearable Internet of Things (IoT) technologies enabled continuous physiological monitoring in travelers and mass gatherings. The MALrisk model predicted imported malaria with an area under the receiver operating characteristic curve of 0.98, achieving 100% sensitivity and 72% specificity. In hospitalized returned travelers, ChatGPT-4o identified the correct diagnosis in 68% of patients and included the correct diagnosis among its three leading differential diagnoses in 78%, while metagenomic next-generation sequencing increased the diagnostic yield by 24.2% beyond routine investigations.

CONCLUSIONS: AI and complementary digital health technologies have the potential to improve travel healthcare throughout the travel continuum. The principal challenge is no longer the development of individual AI applications, but determining how complementary technologies can be effectively integrated into routine travel medicine. Current evidence remains largely retrospective, highlighting the need for prospective multicenter implementation studies evaluating clinically meaningful outcomes.},
}

@article {pmid42714164,
year = {2026},
author = {Lyashenko, E and Torregrosa, T and Ysasi, AB and Wu, J and Bu, J and Hennessy, M and Na, Y and Ryan, MJ and Takar, M and Manek, R and Hull, JA and Pfister, EL and Mueller, C and Choudhury, SR},
title = {MADCAP: isolation of novel nAb-naïve AAV capsids from metagenomic data.},
journal = {Journal of virology},
volume = {},
number = {},
pages = {e0063026},
doi = {10.1128/jvi.00630-26},
pmid = {42714164},
issn = {1098-5514},
abstract = {UNLABELLED: Gene therapy using adeno-associated virus (AAV) vectors offers promising treatment for genetic disorders, but significant limitations restrict clinical application. Current AAV serotypes exhibit strong liver tropism and require high doses for extra-hepatic targeting, and pre-existing antibodies (NAbs) exclude up to 50% of potential patients. Evolutionarily distant isolates can evade neutralization but typically transduce human tissues poorly and require extensive engineering. We developed MADCAP (Metagenomic AAV Discovery and Capsid Annotation Pipeline) to systematically mine metagenomic data for functional, clinically relevant AAV capsids. We hypothesized that these sources might contain capsids that do not circulate widely in humans, can transduce human cells, and avoid neutralization. We screened 4.2 million metagenomic samples and identified 139 novel AAV capsid isolates which were tested for viral capsid assembly, viability, neutralization evasion, and tissue transduction in non-human primates. While natural serotypes (AAV1, AAV2, AAV9) were neutralized at low dilutions of pooled human immunoglobulin (IVIG), 68% of tested MADCAP capsids exhibited minimal to undetectable neutralization even at supra-physiological IVIG concentrations. Systemically delivered MADCAP capsids effectively transduced multiple clinically relevant tissues in non-human primates. Two capsids, MC46 and MC55, demonstrated improved CNS tropism compared to AAV9 while maintaining comparable production yields. In passive transfer studies, MC46 retained full transduction efficiency in the presence of human antibodies, while AAV9 transduction was completely lost. This work establishes metagenomic mining as a powerful tool for accelerating AAV capsid discovery, identifying isolates with favorable tissue tropisms and resistance to broadly neutralizing antibodies.

IMPORTANCE: This work provides proof of concept that potentially clinically relevant AAVs can be isolated from metagenomic data. Our findings lay the groundwork for accelerated discovery of AAV capsids which could potentially increase the accessibility and effectiveness of AAV gene therapy.},
}

@article {pmid42714244,
year = {2026},
author = {Russell, JA and Keenum, I and Jarvis, K and Sanderson, H and Sussman, MD and Khanipov, K and Lacirignola, J and Xiao, A and Phillips, JM and Johns, M and Ganesan, B and Parsons, C and Davis, B and Sozhamannan, S},
title = {STRATUM-Structured Framework for Reporting, Assessment, and Translational Utility of Metagenomics.},
journal = {Journal of AOAC International},
volume = {},
number = {},
pages = {},
doi = {10.1093/jaoacint/qsag085},
pmid = {42714244},
issn = {1944-7922},
abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) enables broad, untargeted detection of pathogens and microbial signals across complex sample types. However, the diversity of operational contexts, from regulatory enforcement to exploratory discovery, challenges the defining of analytical or interpretive standards appropriate across all applications. Variability in laboratory practices, bioinformatic methods, and reporting conventions continues to limit consistency and decision-maker confidence in mNGS results.

OBJECTIVES: We introduce STRATUM (Structured Framework for Reporting, Assessment, and Translational Utility of Metagenomics), a use-case-stratified framework that aligns quality assurance, metadata reporting, and interpretive standards with the consequence and intended use of metagenomic sequencing outputs.

METHODS: STRATUM is organized around five representative biosurveillance use cases spanning public health, food safety, environmental monitoring, synthetic biology detection, and national security. A three-tier interpretive model calibrates analytical rigor, validation expectations, and reporting requirements to decision consequence; from high-consequence regulatory and clinical determinations (Tier 1), through operational surveillance (Tier 2), to exploratory and hypothesis-generating contexts (Tier 3).

RESULTS: The framework provides graduated guidance across key domains including sample preparation, sequencing design, controls and contamination governance, reference database curation, bioinformatics reproducibility, and multi-factor signal validation. Cross-cutting principles include explicit documentation of evidentiary bases, transparency in database and pipeline provenance, and defined escalation pathways when results transition between interpretive tiers.

CONCLUSION: Realizing the operational potential of mNGS requires evidentiary standards responsive to decision context rather than fixed across applications. STRATUM offers a consequence-tiered model for quality and reporting in applied metagenomics, supporting reproducible, transparent, and defensible sequencing-based surveillance across public health and biodefense domains.},
}

@article {pmid42714425,
year = {2026},
author = {Yang, H and Feng, L and Jiang, Z and Weng, J and Qiu, J and Deng, R and Wu, X and Zeng, K},
title = {Gut Microbiota and Aldosterone Regulate Natriuretic Peptide B Expression to Drive Mitophagy and Metabolic Reprogramming in Sepsis-Like Model of Myocardial Injury.},
journal = {Journal of the American Heart Association},
volume = {},
number = {},
pages = {e046120},
doi = {10.1161/JAHA.125.046120},
pmid = {42714425},
issn = {2047-9980},
abstract = {BACKGROUND: Myocardial injury is a major contributor to mortality in sepsis, yet the mechanisms underlying gut-heart communication in sepsis-induced myocardial injury remain insufficiently defined. Natriuretic peptide B (NPPB) is a cardiac stress-responsive gene, but its involvement in mitochondrial homeostasis and metabolic regulation is unclear. This study investigated how gut microbiota and aldosterone influence myocardial mitophagy and metabolic reprogramming through NPPB in sepsis-induced myocardial injury.

METHODS: A sepsis-like myocardial injury model was induced in mice by intraperitoneal lipopolysaccharide (LPS). Fecal microbiota transplantation from septic mice into pseudo-germ-free recipients assessed microbial contributions. Metagenomic, metabolomic, and transcriptomic analyses identified disrupted metabolites and cardiac gene signatures. Heart-specific NPPB-knockout mice were used to determine its in vivo role. Mitochondrial function and metabolic alterations were evaluated by energy metabolism assays. In vitro, aldosterone-treated AC16 cardiomyocytes were used to examine NPPB-mediated mitophagy and metabolic changes. Molecular docking, dynamics simulation, and machine-learning screening identified Lestaurtinib, whose therapeutic effects were validated pharmacologically.

RESULTS: Sepsis caused pronounced microbial dysbiosis and elevated aldosterone levels. Multi-omics analysis identified NPPB as a central regulator of mitophagy and metabolic remodeling. NPPB deficiency mitigated mitochondrial impairment and metabolic disturbances in vivo. Aldosterone upregulated NPPB in cardiomyocytes, promoting mitophagy and metabolic reprogramming. Lestaurtinib, identified as a candidate targeting the aldosterone-NPPB axis, improved cardiac structure and function while partially restoring microbial and metabolic homeostasis.

CONCLUSIONS: This study uncovers a novel gut microbiota-aldosterone-NPPB axis driving LPS-induced myocardial injury through dysregulated mitophagy and metabolism and highlights Lestaurtinib as a potential therapeutic strategy for sepsis-induced myocardial injury.},
}

@article {pmid42714846,
year = {2026},
author = {Cui, Y and Zhang, B and Jiang, X and Rehemujiang, H and Xu, G and Li, Y and Wang, B},
title = {Perilla seed oil reshapes the rumen microbiome and increases fermentation end-products in vitro.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxag233},
pmid = {42714846},
issn = {1365-2672},
abstract = {AIMS: The effect of Perilla frutescens seed oil (PSO) on an in vitro rumen microbial ecosystem was evaluated by integrating fermentation measurements, microbiome profiling, metagenomics, and untargeted metabolomics.

METHODS AND RESULTS: Rumen inoculum was incubated for 24 h with a control TMR substrate (CK), TMR supplemented with 23.7 mg of Perilla seeds per bottle (PS), or TMR supplemented with 8.5 μL of Perilla seed oil per bottle (PSO), with the PS and PSO treatments providing equivalent amounts of seed oil. Fermentation kinetics and volatile fatty acids were measured, and microbial and metabolic responses were characterized using 16S rRNA gene sequencing, metagenomics, KEGG and CAZy annotation, untargeted metabolomics and MetOrigin2 source tracing. PSO increased maximum gas production and total volatile fatty acid concentrations while maintaining pH within the physiological range. Community diversity was unchanged, but PSO altered microbial composition, including increases in Firmicutes, Verrucomicrobia, Vagococcus, Clostridium and Lactobacillus and decreases in Shigella sonnei and Methanosarcina sp. Ant1. PSO also altered microbial functional profiles and increased several lipid- and vitamin-associated metabolites, including linoleic acid, 13-HODE, 9-oxoODE, pantothenic acid and thiamine, while reducing lactate.

CONCLUSIONS: PSO changed rumen microbial community structure and functional potential in parallel with increased fermentation end-products and extensive metabolic shifts. These in vitro findings identify microbial and metabolic responses that warrant validation in vivo.},
}

@article {pmid42715267,
year = {2026},
author = {Lu, N and Guo, J and Liu, C and Wang, J and Wang, D and Li, X and Yuan, Y},
title = {Clinical Utility of Targeted Third-Generation Sequencing for Pathogen Detection in Community-Acquired Pneumonia: A Real-World Comparative Study of China.},
journal = {Journal of infection in developing countries},
volume = {20},
number = {8},
pages = {1122-1132},
doi = {10.3855/jidc.22870},
pmid = {42715267},
issn = {1972-2680},
mesh = {Humans ; *Community-Acquired Pneumonia/microbiology/diagnosis ; Retrospective Studies ; Female ; China ; *High-Throughput Nucleotide Sequencing/methods ; Sensitivity and Specificity ; Male ; Middle Aged ; Aged ; *Molecular Diagnostic Techniques/methods ; Bacteria/isolation & purification/genetics ; Adult ; Drug Resistance, Bacterial ; *Pneumonia, Bacterial/diagnosis/microbiology ; Community-Acquired Infections/microbiology/diagnosis ; Aged, 80 and over ; Coinfection/diagnosis/microbiology ; },
abstract = {OBJECTIVE: To evaluate the diagnostic performance and clinical utility of targeted third-generation sequencing (tTGS) for pathogen detection in community-acquired pneumonia (CAP), compared with targeted next-generation sequencing (tNGS) and conventional culture.

METHODOLOGY: We conducted a real-world, retrospective study including 356 CAP patients who were tested in parallel with culture, tNGS, and tTGS. Diagnostic sensitivity, pathogen spectrum, mixed-infection detection, and antimicrobial resistance (AMR) gene profiling were compared across methods. Clinical relevance was assessed by analyzing treatment adjustments informed by sequencing results.

RESULTS: tTGS demonstrated the highest overall sensitivity (99.16%), surpassing tNGS (96.35%, p < 0.05) and culture (50.27%, p < 0.01). Across all samples, tTGS identified 135 microbial species - substantially more than tNGS (84 species) and culture (27 species) - including fastidious, rare, and slow-growing pathogens. tTGS also showed an improved ability to detect mixed infections (86.24% vs. 87.64% with tNGS; culture detected none). AMR gene detection was significantly higher with tTGS than with tNGS (58.99% vs. 48.88%, p = 0.008), and long-read sequencing enabled the identification of composite resistance patterns that tNGS missed. Among patients without underlying diseases, sequencing-guided therapeutic adjustment occurred in 67.87% of cases, with nearly 80% of AMR-positive patients demonstrating clinical improvement following regimen optimization.

CONCLUSIONS: tTGS provides markedly enhanced pathogen detection, greater sensitivity, and more comprehensive AMR profiling than both tNGS and culture. Its strong performance in identifying mixed infections and actionable determinants of resistance supports its incorporation into clinical diagnostic workflows for CAP. Further large-scale, prospective studies are warranted to validate its clinical impact and optimize its integration into routine practice.},
}

Humans
*Community-Acquired Pneumonia/microbiology/diagnosis
Retrospective Studies
Female
China
*High-Throughput Nucleotide Sequencing/methods
Sensitivity and Specificity
Male
Middle Aged
Aged
*Molecular Diagnostic Techniques/methods
Bacteria/isolation & purification/genetics
Adult
Drug Resistance, Bacterial
*Pneumonia, Bacterial/diagnosis/microbiology
Community-Acquired Infections/microbiology/diagnosis
Aged, 80 and over
Coinfection/diagnosis/microbiology

@article {pmid42715940,
year = {2026},
author = {Jin, CH and Liu, SR and Song, WT and Yuan, SK and Zhang, YZ and Wang, P and Sun, XT and Liu, XQ and Fang, GY},
title = {Metagenomic Insights into Microbial Assembly and Key Metabolic Genes Driving Flavor Formation in Spontaneously Fermented Zhejiang Rosy Vinegar.},
journal = {Journal of agricultural and food chemistry},
volume = {74},
number = {35},
pages = {27821-27839},
doi = {10.1021/acs.jafc.6c10005},
pmid = {42715940},
issn = {1520-5118},
support = {32401323//National Natural Science Foundation of China/ ; 2024LFR050//Zhejiang A and F University/ ; 2026R412A027//Xinmiao Talent Program/ ; NA//Zhejiang Provincial College Students' Science & Technology Activity Plan/ ; },
mesh = {*Acetic Acid/metabolism/chemistry ; Fermentation ; Acetobacter/genetics/metabolism ; *Bacteria/genetics/metabolism/classification/isolation & purification ; *Flavoring Agents/metabolism/chemistry ; *Fungi/genetics/metabolism/classification/isolation & purification ; Saccharomyces cerevisiae/metabolism/genetics ; Metagenomics ; Microbiota ; Bacterial Proteins/genetics/metabolism ; },
abstract = {The spontaneous fermentation of Zhejiang rosy vinegar (ZRV) is driven by environmental microbiota, but the processes underlying its flavor formation remain poorly understood. Using metagenomic sequencing, we investigated microbial community assembly, environmental drivers, and metabolic networks during industrial-scale ZRV fermentation. Acetic acid dominated the final organic acids. Community assembly shifted toward deterministic selection with rising acidity, with a slight rebound of stochastic processes in the late stage (R2 values of 0.442 and 0.346 for bacteria and fungi, respectively). Mantel tests confirmed that environmental factors significantly regulated microbial assembly. Co-occurrence networks grew more complex, with positive interactions accounting for 85.24% (bacteria) and 90.10% (fungi) in the late stage. Key genes (ldh, gapA, pgk) from Acetobacter pasteurianus and Lactobacillus acetotolerans dominated late-stage fermentation, while genes (adhP, SDH) from Aspergillus oryzae and Saccharomyces cerevisiae supported early- and mid-stage fermentation. These findings elucidate microbiota-driven metabolic pathways in ZRV, supporting the fermentation window optimization and industrial vinegar quality standardization.},
}

*Acetic Acid/metabolism/chemistry
Fermentation
Acetobacter/genetics/metabolism
*Bacteria/genetics/metabolism/classification/isolation & purification
*Flavoring Agents/metabolism/chemistry
*Fungi/genetics/metabolism/classification/isolation & purification
Saccharomyces cerevisiae/metabolism/genetics
Metagenomics
Microbiota
Bacterial Proteins/genetics/metabolism

@article {pmid42716140,
year = {2026},
author = {Bilinsky, L and Shamay, T and Reshef, L and Rabinowitz, K and Vider, ED and Ben-Shachar, A and Friedenberg, A and Pauker, MH and Barkan, R and Yanai, H and White, I and Wasserberg, N and Fischman, M and Godny, L and Ollech, J and Gophna, U and Dotan, I},
title = {Short-Term Success, Long-Term Failure: Strain Turnover and Virulence Re-Emergence May Drive Relapse in Pouchitis.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2026.08.031},
pmid = {42716140},
issn = {1528-0012},
abstract = {BACKGROUND & AIMS: Pouchitis, de-novo small intestinal inflammation is the most common complication developing in patients with ulcerative colitis after total large bowel resection and ileal pouch-anal anastomosis (IPAA) reconstruction. While the first line treatment is antibiotics, the microbial properties underlying flare, remission, and relapse remain vague. We aimed to investigate how antibiotic treatment drives microbial shifts that underlie remission and contribute to relapse.

METHODS: Patients after IPAA were prospectively recruited during clinical flare (active pouchitis defined by the pouchitis disease activity index) and received a two-week course of metronidazole with either ciprofloxacin or doxycycline. Longitudinal follow up was conducted during a year. Clinical data were recorded, and fecal samples were obtained during consequent flares, recovery, and relapses. Microbial gene repertoire, strains, and resistance to antibiotics were determined. Metagenomic sequencing was integrated with whole-genome sequencing of Escherichia coli isolates, providing strain-specific virulence and antibiotic resistance profiles.

RESULTS: Patients (n=21) recruited provided 130 samples over one-year follow-up. Both antibiotic regimens induced rapid but transient clinical improvement, reflected by a decrease in fecal calprotectin (728 to 265 μg/g, p<.05), and a marked reduction in bacterial exotoxin genes (p<.05), yet both parameters rebounded by 6 weeks post-treatment. Antibiotic resistance gene abundance significantly increased during treatment (p<.05), without expansion of resistance gene diversity, indicating that pre-existing resistant strains increased.

CONCLUSIONS: Antibiotic-induced remission in pouchitis likely results from a temporary suppression of exotoxin-producing bacteria, enabling resistant, low-virulence strains to transiently dominate; The fact that harmful strains quickly rebound after treatment cessation highlights the need for targeted approaches to achieve sustained microbial control.},
}

@article {pmid42555549,
year = {2026},
author = {Eiamthong, B and Srimora, T and Amornloetwattana, R and Uttamapinant, C},
title = {Enhancing the Versatility of Polyethylene Terephthalate (PET) Through Strategic Biomolecular Functionalization.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {65},
number = {37},
pages = {e26115},
pmid = {42555549},
issn = {1521-3773},
support = {//VISTEC/ ; B38G690002//National Science Research and Innovation Fund (NRSF)/ ; },
mesh = {*Polyethylene Terephthalates/chemistry/metabolism ; Biocatalysis ; Surface Properties ; *Proteins/chemistry/metabolism ; },
abstract = {As biocatalytic strategies for PET recycling reach maturation, insights gained from PET hydrolase research can be leveraged to inform the design of proteins and surface-functionalization strategies that promote stable association of functional proteins with PET surfaces, enabling the development of functional protein-plastic hybrid materials. Herein, we examine recent developments in biofunctionalization strategies of PET and related materials, with a focus on chemical biology approaches that offer more precise control of the orientation of proteins on PET and related materials. Biophysical insights from protein-polymer interface chemistry studies can inform protein selection, design, and engineering approaches to minimize denaturation and maximize function of proteins upon attachment to surfaces. Finally, we highlight applications of protein-functionalized PET and related synthetic polymers, including for biomedical applications and scalable biocatalysis, showcasing the potential of integrating biological activity into durable synthetic polymers.},
}

*Polyethylene Terephthalates/chemistry/metabolism
Biocatalysis
Surface Properties
*Proteins/chemistry/metabolism

@article {pmid42705727,
year = {2026},
author = {Xu, S and Li, J and Wang, F and Bian, H and Yan, W and Wang, H and Jiang, C and Sun, J and Wang, Z and Li, X},
title = {Depth-dependent microbial succession and interspecies hydrogen transfer drive pit mud maturation in Chinese strong-flavor baijiu fermentation.},
journal = {Food research international (Ottawa, Ont.)},
volume = {243},
number = {Pt 2},
pages = {120362},
doi = {10.1016/j.foodres.2026.120362},
pmid = {42705727},
issn = {1873-7145},
mesh = {*Hydrogen/metabolism ; *Fermentation ; Bacteria/metabolism/classification/genetics ; Archaea/metabolism/genetics/classification ; *Wine/microbiology/analysis ; *Food Microbiology ; *Microbiota ; Metagenomics ; China ; *Alcoholic Beverages/microbiology ; },
abstract = {Microbial communities in fermentation pit mud play a key role in determining the quality of Chinese strong-flavor baijiu (CSFB). However, the ecological processes underlying pit mud maturation across spatial and temporal scales remain unclear. In this study, amplicon sequencing and metagenomic analyses were employed to investigate the taxonomic succession, community assembly, and metabolic functions of bacterial and archaeal communities during the transition from fresh pit mud (FPM) to new pit mud (NPM) and old pit mud (OPM). A pronounced depth-dependent succession pattern was observed, with 4 cm representing a critical ecological boundary separating distinct community structures and maturation trajectories. During surface-layer maturation, community assembly shifted from stochastic to deterministic processes, accompanied by homogeneous selection and increasing network complexity. In contrast, stochastic processes remained dominant throughout deep-layer maturation. Metagenomic analyses revealed a functional transition from lactate and acetate production, primarily associated with Lactobacillus in FPM and NPM, to butyrate and caproate production associated with Clostridium and Caproiciproducens in OPM. This functional transition was accompanied by enhanced amino acid metabolism, which was associated with the enrichment of Proteiniphilum and Aminobacterium. Notably, methanogen-mediated interspecies hydrogen transfer (IHT) emerged as a key ecological feature during pit mud maturation. In OPM, IHT networks primarily involving Methanobacterium and Methanosarcina linked methanogenesis with reverse β-oxidation through diverse hydrogen-transfer pathways, reinforcing metabolic interactions underlying caproate production. These findings provide new insights into the ecological mechanisms underlying pit mud maturation and offer a theoretical basis for the directed cultivation of high-quality pit mud in CSFB production.},
}

*Hydrogen/metabolism
*Fermentation
Bacteria/metabolism/classification/genetics
Archaea/metabolism/genetics/classification
*Wine/microbiology/analysis
*Food Microbiology
*Microbiota
Metagenomics
China
*Alcoholic Beverages/microbiology

@article {pmid42705729,
year = {2026},
author = {Li, Y and Li, J and Deng, J and Xia, P and Zhou, G and Zhu, Z and Ding, Y and Yang, J and Zhang, F},
title = {Phocaeicola vulgatus alleviates obesity through cross-species arginine production and hepatic retinoic acid signaling.},
journal = {Food research international (Ottawa, Ont.)},
volume = {243},
number = {Pt 2},
pages = {120365},
doi = {10.1016/j.foodres.2026.120365},
pmid = {42705729},
issn = {1873-7145},
mesh = {*Arginine/biosynthesis/metabolism ; Animals ; *Obesity/therapy/microbiology/metabolism ; *Liver/metabolism ; Signal Transduction ; *Tretinoin/metabolism ; Rats ; Humans ; Fecal Microbiota Transplantation ; Male ; Gastrointestinal Microbiome ; Diet, High-Fat ; },
abstract = {Fecal microbiota transplantation (FMT) shows inconsistent clinical efficacy in treating obesity, and the specific microbial determinants dictating its success remain poorly characterized. Our previous clinical FMT trial identified Phocaeicola vulgatus as a key microbe contributing to the therapeutic efficacy of obesity treatment. Here, to investigate its role in obesity, we established an independent clinical cohort comprising obese and lean individuals, revealing that the P. vulgatus-centered network and ornithine synthesis are impaired in the obese group. We then confirmed causality by utilizing a humanized rat model carrying microbiota from a P. vulgatus-deficient obese patient, demonstrating that P. vulgatus supplementation significantly mitigates HFD-induced obesity, including reductions in body weight and serum total cholesterol levels, as well as the alleviation of hepatic steatosis. To further explore the functional mechanisms of P. vulgatus, integrated metagenomic and metabolomic analyses revealed a potential functional association between P. vulgatus and Phascolarctobacterium faecium that is associated with enhanced intestinal arginine biosynthesis and systemic availability. Furthermore, hepatic transcriptomics linked these elevated circulating arginine levels to the upregulation of retinoic acid (RA) signaling. Taken together, our findings outline a potential microbial-host network wherein P. vulgatus mitigates obesity via the arginine-RA axis, providing a valuable scientific basis for exploring this strain as a probiotic candidate for metabolic health.},
}

*Arginine/biosynthesis/metabolism
Animals
*Obesity/therapy/microbiology/metabolism
*Liver/metabolism
Signal Transduction
*Tretinoin/metabolism
Rats
Humans
Fecal Microbiota Transplantation
Male
Gastrointestinal Microbiome
Diet, High-Fat

@article {pmid42705740,
year = {2026},
author = {Zhan, F and Yu, R and Zheng, W and Benjakul, S and Pan, D and Zhang, B},
title = {Intestinal content accelerates muscle protein degradation in red shrimp (Solenocera crassicornis) during refrigeration: Insights from metagenomics and metabolomics.},
journal = {Food research international (Ottawa, Ont.)},
volume = {243},
number = {Pt 2},
pages = {120377},
doi = {10.1016/j.foodres.2026.120377},
pmid = {42705740},
issn = {1873-7145},
mesh = {Animals ; *Refrigeration ; *Muscle Proteins/metabolism ; Proteolysis ; *Metagenomics/methods ; *Metabolomics/methods ; *Intestines/microbiology ; *Shellfish/microbiology/analysis ; Food Storage ; },
abstract = {This study systematically explored the effects of intestinal components on muscle quality deterioration and protein degradation of red shrimp during refrigerated storage. The results demonstrated that refrigeration induced continuous quality degradation and muscle protein breakdown in red shrimp, whereas eliminating intestinal tissues effectively retarded muscle spoilage and protein degradation, and optimized muscle texture. The intestinal microorganisms could secrete extracellular proteases to promote muscle protein degradation were primarily Vibrio, Bacillus, Pseudomonas, Photobacterium, and Shewanella. These microorganisms promote protein degradation by secreting zinc proteases, serine proteases, and aspartyl proteases. This study elucidates the molecular mechanisms of intestinal microbial metabolism influences the muscle protein degradation of red shrimp during refrigeration. The findings provide a theoretical foundation for precise regulation of intestinal-targeted microorganisms, thereby maintaining optimal quality of shrimps during refrigeration.},
}

Animals
*Refrigeration
*Muscle Proteins/metabolism
Proteolysis
*Metagenomics/methods
*Metabolomics/methods
*Intestines/microbiology
*Shellfish/microbiology/analysis
Food Storage

@article {pmid42705742,
year = {2026},
author = {Han, G and Li, K and Wang, J and Xu, P and Liu, T and Xu, X and Zhao, Y},
title = {Mechanistic insights into flavor deterioration in bitter sturgeon caviar: Evidence from lipidomics and metagenomics.},
journal = {Food research international (Ottawa, Ont.)},
volume = {243},
number = {Pt 2},
pages = {120381},
doi = {10.1016/j.foodres.2026.120381},
pmid = {42705742},
issn = {1873-7145},
mesh = {Animals ; *Metagenomics ; *Fishes ; *Lipidomics ; *Taste ; Volatile Organic Compounds/analysis ; Odorants/analysis ; Microbiota ; Bacteria ; *Seafood/analysis/microbiology ; Humans ; },
abstract = {This study systematically compared the flavor and multi-omics differences between normal caviar and bitter caviar based on quantitative descriptive analysis (QDA), volatile compounds (VOCs) analysis, untargeted lipidomics, and metagenomics. The results showed that bitter caviar was characterized not only by increased bitterness, but also by decreased positive sensory attributes, including buttery, nutty, and marine fresh. VOCs analysis indicated that the volatile profile of bitter caviar was reorganized. Compounds such as 3-hydroxy-2-butanone, 1-octen-3-ol, and (E, Z)-2,6-nonadienal showed higher relative odor activity values (rOAVs); however, these changes did not improve its overall sensory experience. Untargeted lipidomics identified 492 differential lipids. These changes were mainly characterized by decreased PC and increased DG and LPC in bitter caviar. KEGG pathways analysis showed that these differential lipids were mainly associated with glycerophospholipid metabolism, choline metabolism in cancer, and retrograde endocannabinoid signaling. Metagenomic analysis showed that bacteria dominated the microbial community of caviar. Among them, Bacillus and Micromonospora showed relatively high abundance in the caviar microbiota. They were also closely associated with lipid metabolic changes involving PC, DG, and LPC, suggesting their potential as candidate targets for future microbiota-directed regulation of caviar quality. These findings provide new insights into the mechanisms underlying sensory deterioration and flavor formation in bitter caviar, and offer a theoretical basis for improving caviar quality in industrial production.},
}

Animals
*Metagenomics
*Fishes
*Lipidomics
*Taste
Volatile Organic Compounds/analysis
Odorants/analysis
Microbiota
Bacteria
*Seafood/analysis/microbiology
Humans

@article {pmid42705761,
year = {2026},
author = {Shi, H and Shen, Y and Ye, Q and Yu, H and Tian, M and Wang, H and Wei, Y and Yan, S and Chen, Y and Zhang, J and Li, S and Yang, Y and Zhao, J},
title = {Spatially resolved multi-omics analysis of indigenous Bacillus-fortified high-temperature Daqu.},
journal = {Food research international (Ottawa, Ont.)},
volume = {243},
number = {Pt 2},
pages = {120404},
doi = {10.1016/j.foodres.2026.120404},
pmid = {42705761},
issn = {1873-7145},
mesh = {*Bacillus/metabolism/genetics ; Multiomics ; *Hot Temperature ; *Food, Fortified/microbiology ; Metabolomics ; Metagenomics ; *Food Microbiology ; },
abstract = {Layer-dependent patterns associated with indigenous Bacillus fortification on high-temperature Daqu remain unclear. Here, six indigenous functional Bacillus strains were combined to fortify Daqu at three inoculation levels (QH4, QH5, QH6), with non-fortified as the control (CK). Upper, middle, and lower shelf-layer samples were profiled by physicochemical measurements, volatilomics, organic acid analysis, untargeted metabolomics, 16S/ITS amplicon sequencing, and metagenomics. PERMANOVA showed significant effects of treatment, spatial layer, and their interaction on physicochemical, volatile, bacterial, and fungal profiles (P = 0.001). Among the three inoculation levels, QH5 showed the most balanced performance: QH5_M exhibited the highest observed mean peak temperature (63.3 °C; +4.5 °C relative to CK_M), and its group-mean temperature remained ≥ 60 °C for seven consecutive days. Multi-omics analyses indicated coordinated, non-linear, and layer-dependent differences associated with indigenous Bacillus fortification, with QH5_M showing the most pronounced combined thermal, pyrazine, substrate, microbial, and predicted functional profile. These findings indicate that moderate indigenous Bacillus fortification was associated with distinct layer-dependent thermal and flavor profiles and coordinated microbial, metabolic, and predicted functional differences.},
}

*Bacillus/metabolism/genetics
Multiomics
*Hot Temperature
*Food, Fortified/microbiology
Metabolomics
Metagenomics
*Food Microbiology

@article {pmid42705847,
year = {2026},
author = {de Paula, BB and Miagostovich, MP and Mannarino, CF and Ribeiro, AVC and Lanzarini, NM and de Oliveira, CS and Novo, SPC},
title = {Metagenomics Reveals Microbial Community Shifts Associated With Contrasting Anthropogenic Impacts in Freshwater Sources of A Coastal Protected Area in Southeastern Brazil.},
journal = {Water environment research : a research publication of the Water Environment Federation},
volume = {98},
number = {9},
pages = {e70567},
doi = {10.1002/wer.70567},
pmid = {42705847},
issn = {1554-7531},
support = {25388.010001/2018-23//Brazilian National Health Foundation (FUNASA)/ ; 0406080/2021//Conselho de Desenvolvimento Científico e Tecnológico/ ; 305737/2023-6//Conselho de Desenvolvimento Científico e Tecnológico/ ; PROEP/IOC441653/2024-3//Conselho de Desenvolvimento Científico e Tecnológico/ ; E26/202.266/2024//Fundação de Amparo à Pesquisa do Rio de Janeiro/ ; },
mesh = {Brazil ; *Fresh Water/microbiology ; *Metagenomics ; *Bacteria/genetics/classification ; *Water Microbiology ; *Anthropogenic Effects ; Environmental Monitoring ; },
abstract = {This study aimed to characterize freshwater microbial communities, environmental drivers, and anthropogenic impact patterns across three sites on Marambaia Island (southeastern Brazil) using metagenomics. Samples collected from freshwater sources used for human consumption were processed through concentration, nucleic acid extraction, and sequencing on the Illumina NextSeq 2000 platform. A total of 67.2 million reads were assembled into 89,230 bacterial contigs, mostly attributed to Gammaproteobacteria, Alphaproteobacteria, and Betaproteobacteria. Sites under lower anthropogenic influence exhibited higher microbial diversity, whereas impacted sites showed enrichment of opportunistic and fecal-associated genera. A heterogeneous anthropogenic impact profile was observed across sites, corroborated by the proposed Anthropogenic Impact Index (AII). Fourteen antimicrobial resistance genes conferring resistance to beta-lactams, quinolones, sulfonamides, tetracyclines, and macrolides were detected predominantly in sewage-impacted areas, indicating potential diffuse contamination. Redundancy analysis revealed that environmental variables explained 88.1% of microbial community variation, with conductivity, salinity, and turbidity as key drivers. These findings demonstrate the applicability of metagenomics as a powerful tool for assessing microbial diversity, ecological dynamics, and contamination risks in vulnerable freshwater systems.},
}

Brazil
*Fresh Water/microbiology
*Metagenomics
*Bacteria/genetics/classification
*Water Microbiology
*Anthropogenic Effects
Environmental Monitoring

@article {pmid42706263,
year = {2026},
author = {He, W and Bobanga, T and Piantadosi, A and Popkin-Hall, ZR and Vulu, F and Collins, MH and Kashamuka, MM and Tshefu, AK and Juliano, JJ and Parr, JB},
title = {Evidence of dengue transmission and a diverse Aedes mosquito virome on the Congo's Angola border.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42706263},
issn = {2041-1723},
support = {INV-050353//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; K24AI134990//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; Yang Biomedical Scholar award//UNC | University of North Carolina at Chapel Hill (UNC-Chapel Hill)/ ; },
mesh = {Animals ; *Aedes/virology ; *Dengue Virus/genetics/isolation & purification ; Humans ; Angola/epidemiology ; *Dengue/transmission/epidemiology/virology ; *Virome/genetics ; *Mosquito Vectors/virology ; Democratic Republic of the Congo/epidemiology ; Female ; Congo ; },
abstract = {Aedes mosquitoes are widely distributed across the Democratic Republic of Congo (DRC), and are major vectors of dengue (DENV), Zika, chikungunya (CHIKV), and yellow fever (YFV) viruses. While the high burden of malaria in the DRC receives considerable attention, arboviruses remain understudied. In the setting of recent CHIKV and YFV outbreaks in southwestern DRC, we collect Aedes mosquitoes in three areas of Kimpese, DRC, near the Angola border, to investigate their virome. Metagenomic and targeted sequencing of eight randomly selected field mosquito pools, comprising 155 mosquitoes from three collection sites, confirm high-confidence DENV reads and human blood meals in six (75%) and eight (100%) pools, respectively. We find diverse mosquito viromes including other known and putative human and animal viruses. Our findings provide strong evidence of endemic DENV transmission along the DRC-Angola border and illustrate the potential of wild-caught mosquitoes for xenosurveillance of emerging pathogens.},
}

Animals
*Aedes/virology
*Dengue Virus/genetics/isolation & purification
Humans
Angola/epidemiology
*Dengue/transmission/epidemiology/virology
*Virome/genetics
*Mosquito Vectors/virology
Democratic Republic of the Congo/epidemiology
Female
Congo

@article {pmid42706541,
year = {2026},
author = {Jundzill, M and Hölzer, M and Mangul, S and Marquet, M and Ehricht, R and Lohde, M and Spott, R and Makarewicz, O and Pletz, MW and Brandt, C},
title = {Large-scale benchmarking of prokaryotic annotation tools across thousands of species.},
journal = {Genome biology},
volume = {27},
number = {1},
pages = {},
pmid = {42706541},
issn = {1474-760X},
support = {FKZ:13N15720//Innovative molecular and biochemical assays for rapid diagnostics, drug development and new therapy concepts (LPI-BT5)/ ; [Projekt-Nr.: 512648189]//German Research Foundation and the Open Access Publication Fund of the Thueringer Universitaets und Landesbibliothek Jena/ ; 760073/23.05.2023, code 285/30.11.2022, within Pillar III, Component C9, Investment 81//Ministry of Research, Innovation and Digitization under Romania's National Recovery and Resilience Plan - Funded by EU - NextGenerationEU program, project "Artificial intelligence-powered personalized health and genomics libraries for the analysis of long-term effects in COVID-19 patients (AI-PHGL-COVID)/ ; Förderkennzeichen: MSP24//University Hospital Jena Young Researchers funding program IZKF/ ; },
mesh = {*Molecular Sequence Annotation/methods ; *Genome, Bacterial ; *Genome, Archaeal ; Benchmarking ; *Software ; Archaea/genetics ; Computational Biology/methods ; Metagenome ; Gene Ontology ; },
abstract = {BACKGROUND: Genome annotation is an important step in deriving functional meaning from prokaryotic sequencing data, yet systematic evaluations guiding tool selection are lacking. We present the first large-scale investigation of four prominent open-source annotation tools (Prokka, Bakta, EggNOG-mapper, and PGAP) across 156,033 diverse genomes. This includes Escherichia coli strains for baseline performance, thousands of archaea and bacteria genomes, as well as frameshifted and metagenome-assembled genomes.

RESULTS: Bakta excels in annotating high-quality bacterial genomes, while PGAP was better for archaeal genomes and challenging bacterial assemblies, including metagenome-assembled, fragmented, or contaminated samples. For Gene Ontology annotation, PGAP consistently provides broader term coverage, whereas EggNOG-mapper offers more terms per feature.

CONCLUSIONS: Our findings highlight tool-specific strengths crucial for selecting optimal solutions based on genome quality, taxonomy, and origin (e.g. MAGs). This study provides an evidence-based guide for users and informs future tool development.},
}

*Molecular Sequence Annotation/methods
*Genome, Bacterial
*Genome, Archaeal
Benchmarking
*Software
Archaea/genetics
Computational Biology/methods
Metagenome
Gene Ontology

@article {pmid42706609,
year = {2026},
author = {Sun, YZ and Su, JW and Elsheikha, HM and Lou, WB and Song, YH and Li, JM and Liu, F and Cai, R and Leng, X and Gong, QL and Zhang, XX},
title = {Farming reshapes the gut resistome, virulome, and mobilome of Cervidae.},
journal = {Virulence},
volume = {17},
number = {1},
pages = {2728506},
doi = {10.1080/21505594.2026.2728506},
pmid = {42706609},
issn = {2150-5608},
mesh = {Animals ; Gene Transfer, Horizontal ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; *Deer/microbiology/virology ; Metagenome ; Interspersed Repetitive Sequences ; Virulence Factors/genetics ; Plasmids/genetics ; Bacteriophages/genetics ; Virome ; Bacteria/genetics/drug effects/classification ; Agriculture ; },
abstract = {The rapid expansion of cervid farming raises concerns about antimicrobial resistance (AMR) dissemination, yet its impact on the Cervidae gut microbiome remains poorly characterized. We integrated 89 newly sequenced fecal metagenomes with 599 publicly available datasets, comprising 285 metagenomes from farmed cervids and 370 from wild cervids, to construct a catalog of 15,494 non-redundant metagenome-assembled genomes (MAGs) representing 2,401 species. Our analysis demonstrates that farming profoundly reshapes the gut microbiome's functional composition. Specifically, farmed cervids exhibited significantly higher relative abundance, diversity, and heterogeneity of antimicrobial resistance genes (ARGs) compared to wild counterparts. We observed a robust synergistic relationship between ARGs, virulence factor genes, and mobile genetic element (MGE)-associated genes, identifying 70 ARG-MGE combinations as evidence of potential horizontal gene transfer. Plasmid profiling further suggested that a subset of ARGs may be associated with conjugative plasmids, with plasmid-associated ARGs being significantly more abundant in farmed than in wild cervids. Virome analyses indicated that bacteriophages, particularly Siphoviridae, may serve as mobile reservoirs for ARGs. Notably, Cervidae shared 268 ARG types with humans, including 23 high-risk genes associated with resistance to clinically important antibiotics (e.g. tetX1, vanRD, and bla-CTX-M-178), with Escherichia coli as a key cross-host carrier. These findings highlight that human-impacted cervid gut microbiomes are significant environmental reservoirs of clinically relevant AMR, underscoring the necessity for enhanced antibiotic stewardship and resistance surveillance in managed wildlife within a One Health framework.},
}

Animals
Gene Transfer, Horizontal
*Gastrointestinal Microbiome/genetics
Feces/microbiology
*Deer/microbiology/virology
Metagenome
Interspersed Repetitive Sequences
Virulence Factors/genetics
Plasmids/genetics
Bacteriophages/genetics
Virome
Bacteria/genetics/drug effects/classification
Agriculture

@article {pmid42706715,
year = {2026},
author = {Sahil, R and Jain, M},
title = {Benchmarking of Reference-Based Tools for Strain-Level Resolution of Plant Microbiome.},
journal = {Molecular ecology resources},
volume = {26},
number = {7},
pages = {e70197},
doi = {10.1111/1755-0998.70197},
pmid = {42706715},
issn = {1755-0998},
support = {BT/PR40261/BTIS/137/55/2023//Department of Biotechnology, Ministry of Science and Technology, India/ ; },
mesh = {*Microbiota ; *Metagenomics/methods/standards ; *Plants/microbiology ; Benchmarking ; *Computational Biology/methods ; Metagenome ; },
abstract = {Strain-level identification of each microbe is crucial for understanding its role in the host. Most of the existing tools have primarily been evaluated on human metagenomic datasets, whereas the plant microbiome exhibits greater diversity and complexity and thus poses a challenge in the strain-level resolution of individual microbes. In this study, we conducted a comprehensive benchmarking of available reference-based tools for strain-level resolution of the plant microbiome. We evaluated seven tools on various performance parameters, like computational requirements, F1-score and relative abundances using synthetic datasets comprising microbes known to have strong associations with plants as well as real plant microbiome datasets. Our results demonstrated a better performance of StrainScan on the synthetic data, achieving higher F1-score and more accurate relative abundance estimates as compared to other tools, but its performance declined gradually with increasing strain diversity. However, StrainGE and StrainScan exhibited competitive performance on real plant metagenome data. Overall, though StrainGE exhibited better performance, it was more computationally expensive. However, StrainScan performed better in detecting low-abundance strains. Our findings suggest the comparative suitability of the available tools for the strain-level analysis of plant metagenome data and highlight the need for the development of more efficient and accurate taxonomic classifiers capable of handling the complex plant metagenome data while maintaining computational efficiency.},
}

*Microbiota
*Metagenomics/methods/standards
*Plants/microbiology
Benchmarking
*Computational Biology/methods
Metagenome

@article {pmid42707077,
year = {2026},
author = {Mello-Grand, M and Gregnanin, I and Peraldo-Neia, C and Ostano, P and Guana, F and Testino, N and Malfitana, V and Marchi, G and Zaramella, S and Robertson, E and Chiorino, G},
title = {Application of PathoChip to urine-derived nucleic acids for broad microbial profiling in men with suspected prostate cancer: setup of a methodological workflow and pilot feasibility study.},
journal = {The journal of liquid biopsy},
volume = {13},
number = {},
pages = {100490},
pmid = {42707077},
issn = {2950-1954},
abstract = {BACKGROUND: Urine-based liquid biopsy is an attractive non-invasive source of prostate cancer (PCa) biomarkers, but urinary microbiome studies have mainly relied on 16S rRNA sequencing or shotgun metagenomics. This pilot study optimized and evaluated a practical workflow using PathoChip - a broad-spectrum microarray designed to detect bacterial, viral, fungal, and parasitic signatures - for microbial profiling of urine sediments from men with suspected PCa, an application not previously established.

METHODS: First-morning urine was collected without prostatic massage from 35 men scheduled for biopsy; 19 were diagnosed with PCa and 16 were biopsy-negative. Different urine volumes and extraction strategies were evaluated to optimize DNA/RNA recovery. A setup phase compared 25 ng versus 50 ng of urine DNA and RNA input. DNA/RNA isolated from human B cells was used as reference control. An analysis pipeline was developed to detect outlier probes and create a presence/absence matrix. Reproducibility was assessed via library yield, Pearson correlation, blank-control subtraction, outlier probe detection. Prevalence comparisons were performed between clinical groups.

RESULTS: An 8 mL starting volume was chosen as consistently available from self-collected urine. Sequential DNA/RNA extraction using the AllPrep DNA/RNA Micro Kit from sediment provided the best balance between nucleic-acid recovery, purity, and clinical compatibility. Reducing the input from 50 ng to 25 ng preserved highly concordant hybridization profiles, with matched samples clustering together with strong correlations. Exploratory analysis revealed PCa- and grade-associated patterns involving Actinomycetaceae, Aerococcaceae, and Streptococcaceae, with Streptococcaceae enriched in PCa of higher grades (ISUP GG ≥ 2). Other signatures, including Mobiluncus, Prevotella, Rhodotorula, Hymenolepis, and JC polyomavirus, were broadly detected but not PCa-discriminating.

CONCLUSIONS: PathoChip can be adapted to urine sediments, generating reproducible microbial profiles from limited DNA/RNA input without prostatic massage. This platform provides a quick and accessible approach to broad screening, extending beyond 16S rRNA sequencing by enabling simultaneous multi-kingdom detection. The observed PCa- and grade-associated patterns are hypothesis-generating and require validation in larger independent cohorts.},
}

@article {pmid42707087,
year = {2026},
author = {Xia, Y and Fu, L and Cao, X and Zheng, X and Nie, B},
title = {Acute Coxiella burnetii infection presenting as sepsis with multisystem involvement in an immunosuppressed patient: a case report.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1899347},
pmid = {42707087},
issn = {2296-858X},
abstract = {Q fever, caused by Coxiella burnetii, rarely presents as severe disseminated disease, and timely diagnosis can be difficult because clinical manifestations are nonspecific and routine microbiological tests are often unrevealing. We report a 68-year-old man with rheumatoid arthritis receiving long-term immunosuppressive therapy who presented with persistent unexplained fever, pancytopenia, hepatic dysfunction, polyserosal effusions, and sepsis with multisystem involvement, without a clear epidemiological exposure history. Blood cultures and routine respiratory pathogen testing were negative. Peripheral-blood metagenomic next-generation sequencing (mNGS) detected C. burnetii nucleic acid sequences, and subsequent antibody testing and targeted qPCR supported the diagnosis of acute Q fever with disseminated manifestations. Doxycycline-based targeted therapy was followed by defervescence and marked clinical and laboratory improvement. This case suggests that, in selected immunocompromised patients with severe infection and persistently negative conventional investigations, mNGS may serve as an adjunctive tool to facilitate timely pathogen identification and guide targeted antimicrobial therapy.},
}

@article {pmid42707228,
year = {2026},
author = {Liang, H and Qin, H and Chen, J and Qin, C and Li, X and Wang, Q and Luo, G and Chen, Y},
title = {Integrating metagenomic next-generation sequencing into a multimodal diagnostic framework for spinal infection: enhancing etiological identification and clinical prediction.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1904634},
pmid = {42707228},
issn = {2235-2988},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; Female ; *Metagenomics/methods ; Retrospective Studies ; Male ; Middle Aged ; Sensitivity and Specificity ; Bacteria/genetics/classification/isolation & purification ; Aged ; *Spinal Diseases/diagnosis/microbiology ; },
abstract = {BACKGROUND: Spinal infection (SI) remains diagnostically challenging because of heterogeneous etiologies, nonspecific clinical manifestations, and the limited sensitivity of conventional microbiological approaches, particularly following empirical antimicrobial exposure. Although metagenomic next-generation sequencing (mNGS) enables unbiased pathogen detection, its incremental clinical value beyond pathogen identification and its role within integrated diagnostic strategies remain incompletely established.

METHODS: We retrospectively analyzed 208 consecutive patients with suspected SI between August 2022 and August 2025. Final diagnoses were established using a multidisciplinary-adjudicated composite reference standard incorporating clinical, radiological, microbiological, and histopathological evidence. The diagnostic performance of mNGS was compared with conventional culture and histopathology. Furthermore, multimodal predictive models integrating clinical variables and microbiological information were developed using L1-regularized logistic regression.

RESULTS: In the comparative cohort, mNGS achieved a significantly higher diagnostic yield than culture (66.5% vs. 27.41%, P < 0.001). Among confirmed SI cases, mNGS demonstrated higher sensitivity than conventional culture (91.67% vs. 40.15%, P < 0.001). mNGS identified a substantially broader pathogen spectrum, ranging from fastidious organisms such as Mycobacterium tuberculosis and Brucella to rare pathogens including Talaromyces marneffei and Coxiella burnetii, and maintained robust sensitivity (98.2%) despite prior antibiotic exposure. While an integrated clinical model achieved an AUC of 0.916, mNGS as a standalone modality provided superior discriminative power (AUC = 0.889) compared to histopathology (AUC = 0.836), the Conventional Biomarker Model (AUC = 0.742), and culture (AUC = 0.693).

CONCLUSIONS: mNGS is a high-yield diagnostic tool for spinal infection, particularly in culture-negative and antibiotic-pretreated scenarios. Integrating mNGS into a multimodal clinical framework facilitates etiological clarity and precision antimicrobial therapy.},
}

Humans
*High-Throughput Nucleotide Sequencing/methods
Female
*Metagenomics/methods
Retrospective Studies
Male
Middle Aged
Sensitivity and Specificity
Bacteria/genetics/classification/isolation & purification
Aged
*Spinal Diseases/diagnosis/microbiology

@article {pmid42707924,
year = {2026},
author = {Wang, J and Wang, Y and Wang, R},
title = {Prognosis of Patients Infected With Talaromyces marneffei Across Various Risk Factors.},
journal = {Journal of general and family medicine},
volume = {27},
number = {5},
pages = {e70171},
pmid = {42707924},
issn = {2189-7948},
abstract = {BACKGROUND: Talaromyces marneffei (TM) is an opportunistic infectious fungus, and more patients in HIV-negative populations are infected with TM.

METHODS: We reviewed the adult patients with TM infections (TMIs) between November 1, 2020 and April 30, 2025. This single-center retrospective study was conducted at a tertiary care hospital located in an urban area, eastern China. Patients with TMI were divided into the following four groups: the HIV group, the non-HIV with solid organ transplant (SOT) group, the non-HIV with stem cell transplantation (SCT) group, and the non-HIV with other factors group.

RESULTS: There were a total of 218 cases of talaromycosis: 165 in the HIV group, 16 in the non-HIV with SOT group, 4 in the non-HIV with SCT group, and 33 in the non-HIV with other factors group. The number (proportion) of patients diagnosed through metagenomic next-generation sequencing (mNGS) in the four groups was as follows: 51 (30.9%), 11 (68.8%), 2 (50.0%), and 25 (75.8%), respectively. The number (proportion) of patients who tested positive in both culture and mNGS was as follows: 19 (11.5%), 1 (6.3%), 0 (0.0%), and 1 (3.0%), respectively. Kaplan-Meier estimates indicated that the patients in the non-HIV with SCT group had the worst prognosis and those in the non-HIV with other factors group had poorer prognosis than the patients in the HIV group.

CONCLUSIONS: TMI in patients who are HIV-negative without SOT may have poorer prognosis. If talaromycosis is suspected, mNGS can be an important supplementary tool for confirming TMI.},
}

@article {pmid42707963,
year = {2026},
author = {Babu, P and Prakash, V and Subhash, S and Vanuopadath, M and Haripriyan, J and Rajan, K and Geetha, AA and P, S and Kumar, GB and Nair, BG and Madhavan, A},
title = {Gut-microbiota-mediated host immune modulation: mechanisms, pathological dysbiosis, and therapeutic frontiers.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1905445},
pmid = {42707963},
issn = {2235-2988},
mesh = {Humans ; *Dysbiosis/immunology/therapy/microbiology ; Animals ; *Gastrointestinal Microbiome/immunology ; Host-Pathogen Interactions/immunology ; *Immunomodulation ; },
abstract = {The mammalian immune system has evolved in constant dialogue with its diverse microbiota, forming an ecological and molecular partnership that is fundamental to health. This review examines how microbial communities shape immunity across developmental and functional axes, the immunological consequences of dysbiosis during infection and inflammatory disease, and emerging microbiota-targeted interventions. The host-microbiota-pathogen triad offers a framework to understand how commensals and pathogens compete for ecological niches and immune recognition, and how disturbances in this balance can cascade into chronic inflammation or infection. Microbial metabolites such as short-chain fatty acids, secondary bile acids, and tryptophan derivatives act as key bioactive intermediaries translating microbial activity into host immune architecture, influencing epigenetic programming, cellular differentiation, and mucosal barrier function. These interactions orchestrate tolerance toward commensals while maintaining effector readiness against pathogens, particularly through regulatory T cell (Treg)-Th17 balance, B cell education, and Immunoglobulin A (IgA) responses. When perturbed, as in infections caused by Clostridioides difficile, Klebsiella pneumoniae, Salmonella enterica, or Listeria monocytogenes, the ensuing dysbiosis reinforces immune dysfunction in a self-perpetuating cycle. Therapeutic frontiers now extend beyond conventional antimicrobial strategies to include live biotherapeutics, bacteriophage therapy, fecal microbiota transplantation, and metabolite-based (postbiotic) interventions. Future efforts must reconcile inter-individual microbiome variability with precision medicine, integrating metagenomic and metabolomic profiling to design safe, effective, and personalized microbiota-centered therapeutics.},
}

Humans
*Dysbiosis/immunology/therapy/microbiology
Animals
*Gastrointestinal Microbiome/immunology
Host-Pathogen Interactions/immunology
*Immunomodulation

@article {pmid42707980,
year = {2026},
author = {Li, ZL and Qu, RN and Liu, SX and Wang, W},
title = {Research progress and clinical translation prospects of the urinary tract microbiome in prostate cancer.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1911969},
pmid = {42707980},
issn = {1664-3224},
mesh = {Humans ; Male ; *Prostatic Neoplasms/microbiology/immunology ; *Microbiota ; *Urinary Tract/microbiology ; Translational Research, Biomedical ; Tumor Microenvironment ; Animals ; },
abstract = {Prostate cancer (PCa) is one of the most common malignancies in men worldwide, and its development is influenced by multiple factors, including genetic susceptibility, hormonal dysregulation, chronic inflammation, immune dysregulation, and remodeling of the tumor microenvironment. In recent years, the urinary tract microbiome has emerged as an important component of the tumor ecosystem and has attracted increasing attention in PCa research. Accumulating evidence indicates that patients with PCa exhibit characteristic microbial alterations in urine, expressed prostatic secretions, semen, and prostate tissue, and that certain taxa are associated with tumor grade, stage, and recurrence risk. These microbes may participate in tumor initiation and progression through a variety of mechanisms, such as inducing chronic inflammation, activating signaling pathways including TLR/NF-κB and STAT3, modulating the Treg/Th17 balance, influencing macrophage polarization, and interfering with androgen metabolism. Meanwhile, advances in 16S rRNA sequencing, metagenomics, metatranscriptomics, and multi-omics integration have provided powerful tools for characterizing host-microbe interactions and their functional relevance. In addition, microbiome-based biomarkers derived from non-invasive samples such as urine, together with artificial intelligence and causal inference approaches applied to multi-cohort data, may offer promising opportunities for early screening, risk stratification, treatment monitoring, and personalized intervention in PCa. However, current evidence remains largely associative, and the causal relationship between microbial changes and PCa has not yet been fully established. Major challenges, including contamination in low-biomass samples and inter-cohort heterogeneity, continue to hinder clinical translation. Future research should focus on longitudinal cohort studies, multicenter validation, standardized sampling workflows, and mechanistic experiments to clarify key microbial signatures and their biological functions, thereby accelerating the clinical application of the urinary tract microbiome in precision diagnosis and treatment of PCa.},
}

Humans
Male
*Prostatic Neoplasms/microbiology/immunology
*Microbiota
*Urinary Tract/microbiology
Translational Research, Biomedical
Tumor Microenvironment
Animals

@article {pmid42708205,
year = {2026},
author = {Cruz, K and Chaudry, TE and McTigue, SM and Huang, H and Bauer, JA and Kim, M},
title = {Opportunistic premise plumbing pathogens (OPPPs) in the built environment: transmission, resistance, and strategies for detection and mitigation.},
journal = {Reviews on environmental health},
volume = {},
number = {},
pages = {},
pmid = {42708205},
issn = {2191-0308},
abstract = {Healthcare associated infections (HAIs) lead to tens of thousands of deaths annually, with 21.6 % being caused by water, according to Collier S, Deng L, Adam E, Benedict K, Beshearse E, Blackstock A, et al. Estimate of burden and direct healthcare cost of infectious waterborne disease in the United States. Emerging Infect Disease J 2021;27:140. This is partially due to Opportunistic Premise Plumbing Pathogens (OPPPs); which may exhibit resistance to disinfection and thrive in pipe biofilms. Evidence found in literature indicates the rate of infections caused by OPPPs are going to increase with time, highlighting the need for better understanding of their detection and mitigation. The aim of this review is to provide insight on the latest status of OPPP research and highlight areas that need further investigation. It also emphasizes the importance of proactive surveillance, extensive water management protocols, and advanced detection technologies in reducing waterborne healthcare-associated infections. Ultimately, it was found there is still extensive research needed to fully mitigate and prevent pathogenic outbreaks.},
}

@article {pmid42708583,
year = {2026},
author = {Yu, H-L and Elsheikha, HM and Wang, H-P and Gao, Y-Q and Liu, R and Ma, H and Jiang, J and Li, Y and Zhang, X-X},
title = {Genome-resolved analysis reveals disruption of gut microbial vitamin B and K2 biosynthesis during Toxoplasma gondii infection in mice.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0156426},
doi = {10.1128/spectrum.01564-26},
pmid = {42708583},
issn = {2165-0497},
abstract = {UNLABELLED: Toxoplasma gondii infection remodels the gut microbiome, yet its impact on microbial vitamin biosynthetic potential and host redox metabolism remains unclear. Here, we integrated mouse gut metagenomes with publicly available metagenome-assembled genomes (MAGs) to construct a genome-resolved atlas of B-vitamin and vitamin K2 biosynthesis. From 45,697 MAGs, we curated 4,771 representative genomes, of which 2,682 met high-quality criteria (completeness ≥90%, contamination <5%). Functional annotation identified 229,717 vitamin-related genes corresponding to 177 Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologs across de novo pathways for eight B vitamins, thiamine (B1), riboflavin (B2), niacin (B3), pantothenate (B5), pyridoxine (B6), biotin (B7), folate (B9), cobalamin (B12), and vitamin K2. Among the high-quality genomes, 1,665 encoded complete de novo pathways for at least one vitamin, highlighting functional specialization and community-level complementarity. Transcripts per million-normalized metagenomic read counts revealed significant differences in KEGG ortholog abundances across six of the nine vitamin pathways. Reanalysis of metagenomic data from infected mice (acute, chronic, and control; n = 10 per group) revealed a stage-dependent reduction in α-diversity of vitamin biosynthesis pathways during acute infection, and a clear β-diversity separation from chronic and control groups. Core niacin biosynthesis genes (nadB, nadA, nadC) displayed phylum-specific redistribution, indicating selective remodeling of microbial NAD[+] precursor production under infection-induced metabolic stress. These results suggest that T. gondii infection disrupts cooperative vitamin biosynthetic networks while specifically modulating niacin pathways linked to host NAD[+] metabolism.

IMPORTANCE: Gut microbes can synthesize essential vitamins, but how infection alters this function is poorly understood. By integrating mouse gut metagenomes with genome-resolved microbial data, we show that Toxoplasma gondii infection reshapes the vitamin biosynthetic potential of the gut microbiome in a stage-dependent manner. Acute infection reduces the diversity of vitamin biosynthesis pathways and shifts the taxonomic distribution of key niacin biosynthesis genes involved in microbial NAD[+] precursor production. These findings identify vitamin metabolism, especially niacin-related pathways, as a sensitive functional axis of microbiome remodeling during infection. Our work links microbial taxonomic changes to functional metabolic consequences and suggests that microbiome-mediated regulation of NAD[+]-related metabolism may contribute to host redox adaptation during T. gondii infection.},
}

@article {pmid42708586,
year = {2026},
author = {Solanki, R and Wiszniak, E and Yi, L and Cabria, G and Strous, M and Davila Aleman, FD},
title = {Genome mining of alkaliphilic cyanobacterial consortia: identification of biosynthetic gene clusters in Sodalinema and associated heterotrophs.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0078026},
doi = {10.1128/aem.00780-26},
pmid = {42708586},
issn = {1098-5336},
abstract = {Alkaline soda lakes are high-pH environments that host specialized microbial communities with potential for biotechnology and natural product discovery. We characterized three Sodalinema-dominated cyanobacterial consortia enriched from Canadian soda lakes over 510 days. Using hybrid metagenomic sequencing and metatranscriptomics across pH, alkalinity, and temperature gradients, we reconstructed high-quality metagenome-assembled genomes and assessed functional activity. All consortia converged toward cyanobacteria dominance and exhibited temperature optima between 21°C and 30°C. Phylogenetic analysis placed Sodalinema genomes within a distinct clade affiliated with Candidatus Sodalinema alkaliphilum. Genomic analysis indicated complete biosynthetic pathways for vitamin B5, vitamin B7, and the molybdenum cofactor, but incomplete pathways for vitamins B1, B9, and B12, consistent with patterns observed in Sodalinema yuhuli. Metatranscriptomic profiles showed increased expression of genes involved in phycocyanin and carotenoid biosynthesis at pH 10.2 relative to pH 8.5. Biosynthetic gene cluster analysis revealed that most secondary metabolic potential resided in heterotrophic community members. Roseinatronobacter encoded pathways for N-acyl homoserine lactones, osmoprotectants, betalactones, and prodigiosin, while Alkalimonas, Wenzhouxiangella, and members of the Kiloniellales encoded clusters for lanthipeptides, cyclodipeptides, hydrogen cyanide, and pyrroloquinoline quinone. These findings indicate functional partitioning within the consortia and highlight the contribution of heterotrophs to secondary metabolism.IMPORTANCEAlkaline soda lakes contain microbial communities adapted to high pH that remain underexplored for biotechnology. This study focuses on Sodalinema, a filamentous cyanobacterium that dominates enriched consortia from Canadian soda lakes, and its associated heterotrophic partners. We show that while Sodalinema drives primary productivity, heterotrophic bacteria encode most of the pathways for antimicrobial and signaling compounds. These interactions may support community stability and defense against competing microorganisms. By linking genomic potential with gene expression, this work identifies alkaline cyanobacterial consortia as a source of bioactive compounds and provides a framework for exploring extremophilic microbial communities for natural product discovery.},
}

@article {pmid42708591,
year = {2026},
author = {Jaffe, AL and Zulli, A and Duong, D and Shelden, B and Goldman, M and Richardson, M and Wolfe, MK and Boehm, AB},
title = {Divergent avian strains drive an off-season influenza A peak in municipal wastewater.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0202726},
doi = {10.1128/spectrum.02027-26},
pmid = {42708591},
issn = {2165-0497},
abstract = {Wastewater sequencing is an increasingly valuable tool in tracking the spread of infectious disease agents across space and time in areas of dense human settlement. Among pathogens that can be readily detected by this approach is influenza A, which follows predictable patterns of prevalence through the winter months in North America. Here, we leverage routine surveillance of a municipal wastewater treatment plant in Northern California to describe an atypical, off-season spike in influenza A concentrations that rivals that of the winter respiratory virus season. Drawing upon metagenomic data generated through hybrid-capture sequencing, we assemble and subsequently characterize fragments of divergent influenza genomes that appear to derive predominantly from the avian H16 clade. These strains exhibit close evolutionary relationships to influenza isolated from migratory shorebirds, hinting at potential host species and mechanisms of geographic spread. Analysis of read abundances suggests that these avian strains dominate the pool of influenza circulating during the summer months, when typical human-infecting strains are essentially absent. Together, our results expand the value of wastewater sequencing to encompass sensitive tracking of outbreaks within animals in interface regions where human settlement abuts wildlands, increasing overall pandemic preparedness.IMPORTANCEResearchers now commonly search municipal wastewater for viral genetic material, which can indicate trends in the diversity and abundance of strains circulating in communities. Here, we show that under certain conditions, municipal wastewater can also capture the signatures of viruses circulating among animal populations, such as birds. Specifically, we draw on a targeted form of nucleic acid sequencing to discover a strain of influenza that is fairly genetically distinct from known relatives and may be circulating among shorebirds in Northern California. These findings both broaden the possible use cases of wastewater sequencing and provide new insights into avian viruses, some of which can jump host species to make other animals or people sick.},
}

@article {pmid42708949,
year = {2026},
author = {Jiang, Y and Chen, L and Dong, H and Li, Q and Zhao, W and Zhu, F and Jiang, J and Zhang, Y and Huang, S and Xue, S},
title = {Ecological Restoration of the Soil-Like Function in the Bauxite Residue: Natural Microbiomes Mediated Molecular Transformation of Dissolved Organic Matter.},
journal = {Environmental science & technology},
volume = {60},
number = {35},
pages = {24764-24775},
doi = {10.1021/acs.est.5c18355},
pmid = {42708949},
issn = {1520-5851},
support = {42030711//National Natural Science Foundation of China (NSFC)/ ; 42477437//National Natural Science Foundation of China (NSFC)/ ; 42671661//National Natural Science Foundation of China (NSFC)/ ; },
mesh = {*Soil/chemistry ; *Microbiota ; *Dissolved Organic Matter ; Soil Microbiology ; Aluminum Oxide ; Carbon ; },
abstract = {Soilization of bauxite residues offers a scalable route for long-term carbon management and ecological restoration. However, the microbial processes that transform exogenous organic inputs into stable soil-like carbon pools remain poorly resolved. Here, we combined cross-ecosystem meta-analysis, machine-learning prediction, native synthetic community (SynCom) construction, 13C-labeled straw microcosms, field validation, Fourier transform ion cyclotron resonance mass spectrometry, and genome-resolved metagenomics to unravel microbiome-mediated carbon transformation at the dissolved organic matter (DOM) molecular scale. Our meta-analysis revealed that alkaline industrial wastes retained soil-like DOM signatures but were enriched in microbial humic- and protein-like components, indicating active yet incomplete carbon processing. Guided by these patterns, native SynCom inoculation increased 13C incorporation into total organic carbon (TOC) and dissolved organic carbon (DOC), enlarged biodegradable and adsorbable DOC fractions, and shifted DOM from recalcitrant aromatic pools toward oxygenated carbohydrate-, tannin-, and phenolic-like molecular classes. Genome-resolved analyses linked this transformation to complementary polymer degradation and nutrient-cycling functions across fungal and bacterial guilds, including enriched carbohydrate-active enzymes in straw-carbon-utilizing metagenome-assembled genomes. Null model and thermodynamic analyses further showed that microbial communities were constrained by homogeneous selection, whereas DOM molecules were diversified through variable selection and redox-dependent transformation. Field-scale validation confirmed that SynCom promoted TOC and DOC accumulation and humic-like, high-density DOM fractions under alkaline conditions. Together, these findings establish a mechanistic framework in which functional microbiomes couple plant carbon depolymerization, DOM molecular diversification, and mineral-interactive carbon stabilization, providing a microbiome-guided strategy for carbon sequestration and soilization in the bauxite residue.},
}

*Soil/chemistry
*Microbiota
*Dissolved Organic Matter
Soil Microbiology
Aluminum Oxide
Carbon

@article {pmid42708950,
year = {2026},
author = {Zhang, X and Yuan, J and Wang, L and Chen, J and Zhang, L and Ding, T and Zheng, G and Li, J and Zeng, EY},
title = {Soil Type Governs the Degradation Dynamics and Microbial Assimilation of Biodegradable Plastic Polybutylene Adipate Terephthalate.},
journal = {Environmental science & technology},
volume = {60},
number = {35},
pages = {24909-24920},
doi = {10.1021/acs.est.6c11170},
pmid = {42708950},
issn = {1520-5851},
support = {22576140//National Natural Science Foundation of China/ ; 42377025//National Natural Science Foundation of China/ ; x2hjD6242050//South China University of Technology/ ; },
mesh = {Biodegradation, Environmental ; *Polyesters ; *Soil/chemistry ; Soil Microbiology ; Biodegradable Plastics ; Soil Pollutants ; },
abstract = {Biodegradable plastics like polybutylene adipate terephthalate (PBAT) are increasingly marketed as alternatives to conventional plastics, yet how soil properties regulate degradation kinetics, how intact films and microplastic fragments differentially affect microbial communities, and which metabolic pathways and functional genes govern mineralization remain unclear. The present study investigated PBAT degradation mechanisms in 10 distinct agricultural soils by integrating metagenomics, microbial community analysis, and strain isolation. The results revealed that the environmental fate of PBAT is critically modulated by soil properties. Neutral-alkaline powdery loam soils exhibited the highest degradation efficiency. Soil physicochemical properties indirectly modulate PBAT weight loss by altering the gene abundance of hydrolases and aromatic-degrading enzymes, with soil nitrogen content serving as a key regulatory factor. Metagenomic correlation analysis suggests that PBAT degradation is associated with specific microbial consortia, including Hydrogenophaga and Ascomycota fungi. Microplastic particles of PBAT induced greater disturbances than intact films, as evidenced by significant reductions in microbial diversity, altered community structure, and shifts in functional gene composition. A complete degradation pathway, including initial polymer cleavage followed by terephthalic acid assimilation via the β-ketoadipate pathway, was elucidated. These results provide mechanistic insights into soil-specific PBAT degradation and facilitate risk assessment and sustainable management of biodegradable plastics.},
}

Biodegradation, Environmental
*Polyesters
*Soil/chemistry
Soil Microbiology
Biodegradable Plastics
Soil Pollutants

@article {pmid42708953,
year = {2026},
author = {Francescato, L and Ghiotto, G and Valerin, MC and De Bernardini, N and Fraulini, S and Sandon, A and Treu, L and Lavagnolo, MC and Campanaro, S},
title = {Adaptive Evolution Reveals Metabolic Plasticity and Functional Redundancy in an Anaerobic Microbiome under Extreme Ammonia Stress.},
journal = {Environmental science & technology},
volume = {60},
number = {35},
pages = {24776-24791},
doi = {10.1021/acs.est.6c05759},
pmid = {42708953},
issn = {1520-5851},
mesh = {*Ammonia ; *Microbiota ; Anaerobiosis ; Methane/metabolism ; },
abstract = {Ammonia toxicity represents a primary biochemical bottleneck governing microbial community structure and performance during the anaerobic digestion of the organic fraction of municipal solid waste. However, the mechanistic basis of microbial adaptation to chronic ammonia levels remains poorly characterized. In this study, a long-term sequential enrichment strategy under progressively increasing ammonia concentrations (350-1500 mgN L-1), integrated with genome-centric metagenomics and metatranscriptomics, was employed to resolve the response of an organic waste-degrading microbiome over a 240 day period. Increasing ammonia pressure induced a progressive decline in methanogenesis and accumulation of volatile fatty acids, particularly acetate. Despite these inhibitory pressures, methane production was only halved relative to the initial baseline reflecting a resilient methanogenic community. This stability was driven by a restructuring of the microbiome, where functional redundancy across divergent taxa preserved core metabolic functions. Key adaptive responses included the reconfiguration of carbon fixation pathways, specifically via a variant of the Wood-Ljungdahl pathway coupled with the glycine cleavage system acting as an alternative acetate oxidation route, as well as sustained osmoprotectant biosynthesis. Cellular homeostasis was preserved through H+ replenishment via multiple energy-converting complexes and K+ influx to maintain cation-proton balance. Collectively, these findings demonstrate that metabolic plasticity and the preservation of core metabolic functions are the primary determinants of ammonia resilience, sustaining methane production under inhibitory conditions.},
}

*Ammonia
*Microbiota
Anaerobiosis
Methane/metabolism

@article {pmid42708973,
year = {2026},
author = {Zhu, X and Zhang, W and Ye, T and Zhang, H and Tan, J and Sun, Y},
title = {Malassezia May Contribute to Basal Cell Carcinoma Development via Inflammatory and Oxidative Stress Pathways.},
journal = {MicrobiologyOpen},
volume = {15},
number = {5},
pages = {e70401},
doi = {10.1002/mbo3.70401},
pmid = {42708973},
issn = {2045-8827},
support = {2023YZ06//Yangtze University Science and Technology Aid to Tibet Medical Talent Training Program Project/ ; 2024BCB043//Key Research and Development Program of Hubei Province/ ; 2024AFC034//Natural Science Foundation of Hubei Province/ ; 2025HD18//Jingzhou Science and Technology Plan Project/ ; },
mesh = {Humans ; *Malassezia/isolation & purification/genetics/pathogenicity ; *Oxidative Stress ; *Basal Cell Carcinoma/microbiology/pathology ; *Skin Neoplasms/microbiology/pathology ; Cell Proliferation ; Superoxide Dismutase 2 ; Keratinocytes/microbiology ; Superoxide Dismutase/genetics ; Cell Line, Tumor ; *Inflammation ; Tumor Necrosis Factor-alpha/genetics ; Superoxide Dismutase-1/genetics ; Gene Expression Profiling ; Interleukin-1beta/genetics ; },
abstract = {Basal cell carcinoma (BCC) is the most common malignant skin tumor. Skin-resident lipophilic Malassezia yeasts are associated with various cutaneous disorders, while their correlative patterns and potential biological effects in BCC tissues remain insufficiently defined. We used RT-qPCR screening of archived FFPE BCC specimens and metagenomic sequencing of three paired fresh tumor and peritumoral tissues to characterize tissue-associated Malassezia colonization. M. globosa was the most abundant species in FFPE samples and was also detectable in fresh tissues. In vitro functional assays (CCK-8, EdU) in HaCaT keratinocytes and A-431 epidermoid carcinoma cells showed that 12 h stimulation with optimal concentrations of M. globosa (1.2 × 10[7] CFU/mL) and M. yamatoensis (1.6 × 10[7] CFU/mL) significantly promoted epithelial cell proliferation. Transcriptome sequencing and subsequent RT-qPCR validation further showed that both strains significantly upregulate pro-inflammatory genes (IL-1β, IL-6, TNF-α) and oxidative stress-related genes (SOD1, SOD2) in these cell lines. Collectively, our findings describe a correlative association between Malassezia colonization and BCC lesions and offer preliminary in vitro mechanistic clues.},
}

Humans
*Malassezia/isolation & purification/genetics/pathogenicity
*Oxidative Stress
*Basal Cell Carcinoma/microbiology/pathology
*Skin Neoplasms/microbiology/pathology
Cell Proliferation
Superoxide Dismutase 2
Keratinocytes/microbiology
Superoxide Dismutase/genetics
Cell Line, Tumor
*Inflammation
Tumor Necrosis Factor-alpha/genetics
Superoxide Dismutase-1/genetics
Gene Expression Profiling
Interleukin-1beta/genetics

@article {pmid42709036,
year = {2026},
author = {Pilgrim, J and Rzeszutek, A and Cunningham-Oakes, E and Bonner, S and Roberts, L and Darby, AC and Radford, AD},
title = {Expanded detection of canine enteric viruses in UK dogs with diarrhoea.},
journal = {Microbial genomics},
volume = {12},
number = {9},
pages = {},
doi = {10.1099/mgen.0.001799},
pmid = {42709036},
issn = {2057-5858},
mesh = {Animals ; Dogs ; *Diarrhea/veterinary/virology ; *Dog Diseases/virology/epidemiology ; United Kingdom ; Metagenomics/methods ; Feces/virology ; Phylogeny ; *Viruses/genetics/isolation & purification/classification ; },
abstract = {Canine enteric viruses are an important cause of gastrointestinal disease in pet dogs worldwide. Routine diagnosis often relies on pathogen-specific PCR assays, which may fail to detect some viruses, particularly neglected pathogens or genetically divergent variants of established threats. This limits both clinical characterization of affected patients and broader understanding of disease ecology. To address these limitations, we applied metagenomics and a viral discovery bioinformatics pipeline to faecal samples from diarrhoeic dogs in the UK that had been submitted routinely for PCR-based diagnostic testing. Across 80 dogs, we identified 12 viruses known to infect canids, 9 of which have not previously been reported in UK dogs. Among these, several taxa with prior associations to gastrointestinal disease were identified, including canine sapovirus and canine minute virus. By contrast, for other viruses newly detected in the UK, including bufavirus and rotavirus C, clinical relevance in dogs remains unclear. Notably, an identified protoparvovirus fell within the same species as human-canine-associated parvovirus 1, a recently described lineage detected in both canine and human oropharyngeal samples. We also identified a canine parvovirus 2 strain that clustered with a predominantly wildlife-associated lineage, consistent with occasional exposure at the domestic-wildlife interface rather than established circulation in dogs. These two detections illustrate how genome-level surveillance can help prioritize viruses for targeted investigation of host range and transmission context. Overall, these data broaden the catalogue of viruses associated with diarrhoeic dogs in the UK and support periodic review of diagnostic targets informed by viral metagenomic surveillance, while highlighting the need for controlled studies to assess causality and clinical relevance.},
}

Animals
Dogs
*Diarrhea/veterinary/virology
*Dog Diseases/virology/epidemiology
United Kingdom
Metagenomics/methods
Feces/virology
Phylogeny
*Viruses/genetics/isolation & purification/classification

@article {pmid42709542,
year = {2026},
author = {Pinedo-Bardales, M and Erreygers, I and Allonsius, CN and Hiel, M and Eilers, T and Van Rillaer, T and Gehrmann, T and Ahannach, S and Dillen, J and De Boeck, I and Verhoeven, V and Van Puyvelde, S and Segata, N and Wittouck, S and Lebeer, S},
title = {Species and strain sharing in the vaginal microbiome of mothers and their adult daughters.},
journal = {Cell reports},
volume = {45},
number = {9},
pages = {117942},
doi = {10.1016/j.celrep.2026.117942},
pmid = {42709542},
issn = {2211-1247},
abstract = {The vaginal microbiome is key for women's health. However, its establishment, interindividual variation and dynamics remain poorly understood. Here, we investigate bacterial relatedness at species and strain level in adult mother-daughter pairs from the large-scale citizen-science program Isala. Using metagenomic sequencing with quality control including 16S rRNA profile comparison, along with targeted culturing, we assess intergenerational microbiome sharing. At species level, daughters' vaginal microbiomes are significantly more similar to their mothers' than to those of unrelated mothers, with a strong mother-daughter correlation in Lactobacillus crispatus dominance. Strain-level analyses of metagenomes and isolate genomes reveal intraspecies diversity in L. crispatus, with up to two strains observed within the same host, and support intergenerational vaginal bacteria sharing. SNV counts in shared L. crispatus strains show no correlation with daughters' ages. Together, these findings suggest that maternal transmission, host factors, and (shared) environment collectively shape the vaginal microbiome, providing fundamental ecological insights into vaginal microbiome dynamics and perspectives toward lactobacilli-based applications.},
}

@article {pmid42709766,
year = {2026},
author = {Frybortova, V and Satka, S and Jourova, L and Anzenbacher, P and Zapletalova, I and Kraus, M and Kostovcikova, K and Kverka, M and Anzenbacherova, E},
title = {Ketogenic diet-induced changes in hepatic drug metabolism with potential implications for ozanimod pharmacokinetics in mice.},
journal = {PloS one},
volume = {21},
number = {9},
pages = {e0357797},
doi = {10.1371/journal.pone.0357797},
pmid = {42709766},
issn = {1932-6203},
mesh = {Animals ; Female ; *Liver/metabolism/drug effects ; Mice, Inbred C57BL ; Mice ; *Diet, Ketogenic ; *Indans/pharmacokinetics ; *Oxadiazoles/pharmacokinetics ; Cytochrome P-450 Enzyme System/metabolism/genetics ; },
abstract = {Ketogenic diet (KD) is increasingly considered as an adjunctive therapeutic approach across a range of diseases, but its effects on the pharmacokinetics of concomitantly administered drugs remain unclear. Such interactions may be particularly relevant in multiple sclerosis, where KD is being explored as a complementary strategy alongside disease-modifying therapies, such as ozanimod. We therefore investigated whether KD affects ozanimod metabolism and pharmacokinetics and explored potential factors that may contribute to such effects. Specific pathogen-free female C57BL/6 mice were fed either a control diet containing 10% of calories from fat or a ketogenic diet containing 90% of calories from fat for 4 weeks. Metabolic, inflammatory, and hormonal parameters were determined in plasma. Gut microbiota composition was analyzed by whole-metagenome shotgun sequencing. In parallel, hepatic cytochrome P450 (CYP) enzymes were evaluated by mRNA expression and activity together with ozanimod pharmacokinetics. KD induced the expected metabolic adaptation to ketosis and led to a significant increase in plasma cholesterol accompanied by changes in gut microbiota composition. Other metabolic and inflammatory parameters showed only modest changes. In addition, KD altered the expression and activity of hepatic CYP enzymes, including enzymes involved in ozanimod metabolism: CYP1A activity and mRNA expression were significantly increased in KD-fed mice, whereas lower CYP2C activity was observed in pooled samples and CYP3A activity showed a non-significant trend toward lower values. Ozanimod exposure tended to be higher in KD-fed mice, resulting in an approximately 17% increase in area under the concentration-time curve, although this effect did not reach statistical significance. In conclusion, our findings demonstrate that KD altered the expression and activity of hepatic CYP enzymes and revealed a non-significant trend toward increased ozanimod exposure. These observations highlight the potential importance of considering dietary interventions as a factor contributing to variability in drug response.},
}

Animals
Female
*Liver/metabolism/drug effects
Mice, Inbred C57BL
Mice
*Diet, Ketogenic
*Indans/pharmacokinetics
*Oxadiazoles/pharmacokinetics
Cytochrome P-450 Enzyme System/metabolism/genetics

@article {pmid42700609,
year = {2026},
author = {Li, J and Zuo, X and Qiu, L and Meng, F},
title = {Metabolic niche differentiation and napA evolution stabilize partial denitrification in wastewater ecosystems.},
journal = {Water research},
volume = {308},
number = {Pt A},
pages = {126810},
doi = {10.1016/j.watres.2026.126810},
pmid = {42700609},
issn = {1879-2448},
abstract = {Although partial denitrification (PD) is increasingly applied as a nitrite-supplying strategy for anammox-based nitrogen removal, the ecological distribution, metabolic specialization, and genomic determinants of stable nitrite accumulation remain poorly understood at the ecosystem scale. Here, we reconstructed 516 high-quality metagenome-assembled genomes (MAGs) using high-depth metagenomic sequencing of 107 wastewater treatment plants and classified denitrifiers according to their nitrite production or consumption capacities. Of these genomes, 23% (120 MAGs) were classified as partial denitrifiers, 41% (211 MAGs) as complete denitrifiers, and 36% (185 MAGs) as nitrite-reducing denitrifiers, revealing pronounced functional partitioning rather than dominance by complete denitrification pathways. Comparative genomics showed that partial denitrifiers possess metabolic architectures favoring rapid carbon oxidation and NADH generation while exhibiting constrained NADPH production and biosynthetic investment, thereby promoting nitrate-to-nitrite conversion but limiting subsequent nitrite reduction. Nitrite accumulation does not result from incomplete denitrification pathways but from metabolic niche differentiation. These metabolic trade-offs were further associated with the evolutionary divergence of the periplasmic nitrate reductase gene, napA, which displayed distinct sequence characteristics and genomic contexts between partial and complete denitrifiers. Integration of carbohydrate-active enzyme repertoires further revealed metabolic complementarity between partial denitrifiers and anammox bacteria, supporting efficient carbon handoff without direct substrate competition. From an engineering perspective, operating conditions that impose moderate electron limitation, such as low or fluctuating C/N ratios and intermittent carbon feeding, may selectively enrich partial denitrifiers and enhance a stable nitrite supply for PD-anammox systems. Together, these findings identify PD as a predictable ecological state shaped by genome-encoded metabolic specialization and provide a mechanistic basis for designing robust, low-carbon nitrogen-removal processes.},
}

@article {pmid42700718,
year = {2026},
author = {Maglione, A and Rosso, R and Tortarolo, D and Pantini, F and Pernice, S and Contaldo, SG and Lanzillo, R and Spiezia, AL and Cordioli, C and Virgilio, E and Masuzzo, F and Matta, M and Malucchi, S and Cavalla, P and Cocolin, L and Sirovich, R and Beccuti, M and Ferrocino, I and Cordero, F and Clerico, M and Rolla, S},
title = {Gut microbiome profiling at multiple sclerosis onset as a potential early prognostic marker of disease course: evidence from an observational cohort study.},
journal = {EBioMedicine},
volume = {132},
number = {},
pages = {106470},
doi = {10.1016/j.ebiom.2026.106470},
pmid = {42700718},
issn = {2352-3964},
abstract = {BACKGROUND: Alterations in gut microbiome composition have been associated with multiple sclerosis (MS), but their impact on disease severity and early progression remains poorly understood. In this study we investigated whether gut microbiome profiling at diagnosis could identify microbial signatures associated with clinical and radiological features of early MS and provide prognostic information.

METHODS: We analysed the gut microbiome of 53 treatment-naïve patients with MS (pwMS) and 55 healthy donors (HD) using shotgun metagenomic sequencing, combined with clinical features collected over 1 year from diagnosis. To clarify whether gut microbiome composition at MS onset could have prognostic relevance, pwMS were stratified according to lesion burden, lesion localisation, and magnetic resonance imaging (MRI) activity.

FINDINGS: Overall beta diversity in Bacteria, Archaea, and Eukarya differed significantly between pwMS and HD (p-value <0.001, <0.02, <0.03, respectively). Within the MS group, glucocorticoid treatment at disease onset was the clinical factor most strongly associated with gut microbiota diversity. Stratification according to lesion burden, lesion localisation, and MRI activity identified two clinically distinct MS subgroups with different baseline clinical characteristics at onset (p-value <0.03) and different risk of early disease progression. The cluster associated with an unfavourable prognosis showed greater progression within 12 months and was enriched for motor symptoms and spinal cord lesions at diagnosis.

INTERPRETATION: Our findings suggest that gut microbiome alterations are detectable at the earliest stages of MS and are associated with clinical and radiological features linked to short-term disease evolution. Gut microbial profiling may therefore represent a promising early prognostic biomarker and may help to identify candidate targets for early intervention and therapeutic development in MS, although further validation in larger longitudinal cohorts is needed.

FUNDING: This study was supported by grants from the Italian Multiple Sclerosis Foundation, the Cassa di Risparmio di Torino Foundation, and the Italian Ministry of University and Research.},
}

@article {pmid42700855,
year = {2026},
author = {Ning, X and Zhou, L and Zeng, Y and Wang, S and Lv, M and Wang, J and Li, T and Wang, X},
title = {Cable bacteria accelerate nitrogen removal in freshwater sediments by mitigating diffusion limitation via long-distance electron transport.},
journal = {Environmental research},
volume = {308},
number = {Pt 1},
pages = {125593},
doi = {10.1016/j.envres.2026.125593},
pmid = {42700855},
issn = {1096-0953},
abstract = {The sustainable remediation of nitrogen polluted aquatic sediments is often constrained by the spatial separation of electron donors and acceptors, which limits intrinsic microbial nitrogen removal. The long-distance electron transport capacity of cable bacteria offers a natural strategy to overcome this limitation but the kinetic mechanisms remains poorly understood. Herein cable bacteria were enriched from ammonia impacted freshwater sediments and their role in enhancing nitrogen removal was systematically investigated. Biogeochemical analysis showed that cable bacteria reduced ammonium by 93% and increased sulfate accumulation 2.07 times relative to controls. Critically, DGT induced fluxes in sediments and soils (DIFS) modeling at depths of 4 mm and 20 mm revealed that cable bacteria maintained uniformly low nitrate and ammonium diffusion fluxes, whereas in the control nitrate fluxes were 4.5-fold higher and ammonium fluxes were 8.9- to 53-fold higher. This kinetic evidence indicates that cable bacteria accelerate nitrogen removal by enhancing the coupling between nitrification and denitrification, thereby mitigating the classical diffusion limitation that restricts these processes in surface sediments. Metagenomic analysis showed that cable bacteria orchestrated a community shift increasing Nitrospira abundance from 0.4% to 20% and enriching genes for respiratory nitrate reduction (narG) and assimilatory sulfate reduction (cysH, sir), establishing a self-sustaining syntrophic network that coordinated nitrogen and sulfur fluxes. These findings establish cable bacteria as a promising bioremediation tool for cleaner nitrogen management in contaminated aquatic systems.},
}

@article {pmid42700902,
year = {2026},
author = {Li, Z and Li, M and He, X and Zhang, H and Feng, C and Ding, M and Huang, G and Liu, J},
title = {Forty-three years of partial organic substitution shapes microbial assembly and multifaceted network stability in a paddy soil.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135760},
doi = {10.1016/j.biortech.2026.135760},
pmid = {42700902},
issn = {1873-2976},
abstract = {Partial substitution of chemical fertilizers with organic amendments is a promising strategy to sustain soil productivity while reducing chemical inputs. However, the ecological mechanisms by which organic substitution and inorganic reduction reshape soil microbial community assembly, life‑history strategies, and nutrient cycling potential remain poorly understood. A 43-year field experiment with different proportions of organic fertilizer substituting for inorganic nitrogen was conducted. Microbial community structure, assembly processes, keystone taxa, and functional genes involved in nitrogen (N) and sulfur (S) cycles were investigated with high-throughput amplicon and metagenomic sequencing. Our results showed that organic substitution significantly reshapes microbial community composition, increasing community evenness while maintaining species richness. It significantly reduced the proportion of transient and persistent microorganisms while increasing intermittent taxa. Organic substitution significantly reduced (p < 0.05) the contribution of stochastic processes in soil microbes in comparison to those treated only with chemical fertilizers. This shift was accompanied by the enrichment of specific functional phyla such as Actinomycetota (class Thermoleophilia), Myxococcota, and Gemmatimonadota, which served as keystone species in co‑occurrence networks. Functionally, organic substitution significantly upregulated genes involved in organic nitrogen mineralization (glnAB&ureABC&gdhA&GLUL) and anaerobic ammonium oxidation (anammox), while downregulating nitrification, dissimilatory nitrate reduction to ammonium (DNRA), and assimilatory nitrate reduction. Likewise, organic substitution reduced organic sulfur mineralization and hydrogen sulfide production (sreAB) but enhanced assimilatory sulfate reduction. The findings of this study provide new insights into the ecological mechanisms through which organic substitution regulates soil microbiomes and nutrient cycling.},
}

@article {pmid42702111,
year = {2026},
author = {Zhang, M and Wang, Z and Xia, J and Zhen, Y and Jiang, F and Zhang, L},
title = {Magnetite facilitates phage-bacteria interactions and phage-associated metabolic coordination for medium-chain fatty acid biosynthesis under ammonia stress.},
journal = {Water research},
volume = {308},
number = {Pt A},
pages = {126856},
doi = {10.1016/j.watres.2026.126856},
pmid = {42702111},
issn = {1879-2448},
abstract = {Medium-chain fatty acid (MCFA) production from waste activated sludge (WAS) is considered to rely on the syntrophic interactions among distinct functional microorganisms. Whether phages represent an overlooked ecological component involved in MCFA biosynthesis remains unclear. MCFA production is often inhibited by high total ammonia nitrogen (TAN). Conductive materials have been proposed as effective strategies to enhance or recover MCFA production under TAN stress. Therefore, the inhibition-recovery system could provide a useful framework for investigating whether viral ecological responses are associated with MCFA-related metabolic processes. In this study, magnetite (Fe3O4) was selected as the recovery strategy of MCFA production under TAN stress. Results showed that a total of 3915 vOTUs and 118 metagenome-assembled genomes were recovered from the anaerobic bioreactors subjected to three conditions: Control (without TAN stress), TAN stress, and TAN stress with Fe3O4 presence. Under high TAN environment (∼5 g/L), MCFA production reduced by 49% (1.3 g COD/L) in comparison to that without high TAN stress. The ecological coupling between temperate phages and MCFA-related bacterial hosts was weakened, accompanied by substantial decreases in the abundance and transcriptional abundance of phage-associated auxiliary metabolic genes (AMGs) related to MCFA synthesis (e.g., fatty acid biosynthesis, acyl-chain metabolism). In the presence of Fe3O4 (i.e., 10 g/L), MCFA production was four and two times higher than those with and without high TAN stress. In addition to enhanced phage-bacteria ecological coupling and increased the abundance and transcription of AMGs related to MCFA formation, Fe3O4 increased the abundance and expressions of electron-transfer-related AMGs (e.g., cbb3-type cytochrome c oxidase, type IV pilus assembly genes) and QS-related LuxR-family and HTH-type regulators, indicating that such indirect pathway could be largely overlooked during MCFA synthesis. This is also the first-time reporting that phages could represent an ecological layer responsive to iron oxide. Analyses of publicly available metagenomes collected from MCFA-oriented anaerobic systems further confirmed that phages could be broadly associated with the metabolic processes involved in MCFA biosynthesis. Taken together, this study reveals that phages could serve as an overlooked ecological layer associated with MCFA metabolism and provide a viral-ecology perspective for understanding TAN inhibition and iron oxide-mediated recovery during WAS-to-MCFA bioconversion.},
}

@article {pmid42702160,
year = {2026},
author = {Liu, W and Shen, J and Chen, Q and Liu, Z and Han, J and Ni, L},
title = {Metagenomic and physicochemical insights into ultrasound-assisted fermentation: Reprogramming Komagataeibacter intermedius metabolic efficiency for astringency control.},
journal = {Ultrasonics sonochemistry},
volume = {133},
number = {},
pages = {108041},
doi = {10.1016/j.ultsonch.2026.108041},
pmid = {42702160},
issn = {1873-2828},
abstract = {Oral astringency remains a major challenge limiting consumer acceptance of functional fermented beverages. Conventional mitigation strategies often reduce astringency at the expense of bioactive polyphenols, highlighting the need for non-destructive quality improvement approaches. In this study, low-power ultrasound-assisted fermentation (20 kHz, 240 W, 16.68 min/day) was applied to Kombucha, and the underlying mechanisms of astringency alleviation were investigated through integrated physicochemical characterization, metagenomic analysis, and temporal data modeling. Ultrasound significantly reduced sensory astringency and saliva-protein precipitation (OD650, p < 0.05) by Day 7 while preserving monomeric catechins, thereby maintaining antioxidant potential. Small-angle X-ray scattering (SAXS) and spectroscopic analyses revealed that ultrasound promoted the accumulation of water-soluble polysaccharides (1.69 mg/mL on Day 7, p < 0.01), which acted as macromolecular steric barriers and modified the aggregation behavior of polyphenol-salivary protein complexes. Consequently, the radius of gyration (Rg) increased to 608.67 nm, suppressing the formation of large aggregates associated with astringency perception. Furthermore, temporal machine-learning and time-lagged correlation analyses indicated that the reduction in astringency was associated not with increased abundance of Komagataeibacter intermedius, but with upregulated specific metabolic activity during the early fermentation stage. This early-stage metabolic adaptation was strongly associated with subsequent polysaccharide accumulation and sensory improvement. The findings suggest that low-power ultrasound can modulate microbial metabolic activity without altering microbial community structure, thereby influencing polysaccharide biosynthesis and colloidal interactions during fermentation. These results provide new insights into the biological and physicochemical mechanisms underlying ultrasound-assisted fermentation.},
}

@article {pmid42702602,
year = {2026},
author = {Li, Y and Chen, T and Li, P and Zhang, G and Tian, Y and Wang, J and Ni, J},
title = {Elevation-structured viral ecological strategies along glacier-fed rivers on the Qinghai-Tibet Plateau.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42702602},
issn = {2041-1723},
support = {U2240205//National Natural Science Foundation of China (National Science Foundation of China)/ ; 51721006//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Ice Cover/virology ; Tibet ; *Rivers/virology ; Altitude ; Ecosystem ; *Viruses/genetics/classification/isolation & purification ; Metagenome ; *Virome/genetics ; Genome, Viral ; },
abstract = {The Qinghai-Tibet Plateau, a climate-vulnerable source of Asia's major rivers, harbors underexplored viral communities critical to ecosystem functions. By integrating 597 metagenomes from the Yangtze, Yellow, Lancang, and Yarlung Tsangpo rivers with 85 public available glacial metagenomes (Tibetan Glacier Genome and Gene catalog), we built the Glacier-to-River Virome Catalogue, encompassing 36,358 vOTUs and 897,250 viral protein clusters, to decode viral adaptation and ecological influence across elevation gradients. Our results reveal that high-altitude conditions favor viruses with elevated Guanine-Cytosine content, larger genomes and more cold-adaptation genes. A central finding is a systematic viral lifestyle shift from temperate in glaciated regions to lytic viruses downstream, accompanied with decline of pathogens carrying antibiotic resistance genes along the glacier-to-river gradients. Further, viral auxiliary metabolic genes transition from glacier nutrient scavenging (e.g., nitrogen and sulfur transporters) to downstream mineralization processes (e.g., denitrification) in plains highlights their role in biogeochemical cycling. These findings position viruses as pivotal regulators of microbial community structural and functional dynamics to glacier-to-river gradient change and biogeochemistry in the Qinghai-Tibet Plateau, providing critical insights into climate response in vulnerable Asian water towers.},
}

*Ice Cover/virology
Tibet
*Rivers/virology
Altitude
Ecosystem
*Viruses/genetics/classification/isolation & purification
Metagenome
*Virome/genetics
Genome, Viral

@article {pmid42702845,
year = {2026},
author = {Xue, Z and Xu, H and Zhu, L and Zhao, D},
title = {Prevotella melaninogenica Alleviate Mycoplasma pneumoniae Infection Through the Butyrate Based on Multi-Omic Analysis and Experimental Validation.},
journal = {Chemical biology & drug design},
volume = {108},
number = {3},
pages = {e70397},
doi = {10.1111/cbdd.70397},
pmid = {42702845},
issn = {1747-0285},
mesh = {Animals ; Humans ; Multiomics ; *Prevotella melaninogenica/metabolism/physiology ; *Pneumonia, Mycoplasma/microbiology/metabolism/drug therapy ; *Mycoplasma pneumoniae ; Mice ; *Butyrates/metabolism ; Male ; Female ; RNA, Ribosomal, 16S/genetics ; Bronchoalveolar Lavage Fluid/microbiology ; Child ; Child, Preschool ; Disease Models, Animal ; Microbiota ; },
abstract = {Mycoplasma pneumoniae (MP) is one of the main pathogens causing atypical pneumonia in children. The susceptible population is mainly children and adolescents over 5 years old, and the infection rate has increased in recent years. At present, there is limited research on the pulmonary microbiota of patients with Mycoplasma pneumoniae pneumonia, and the characteristics of their microbiota are not yet clear. We included MPP children in stages and established two independent cohorts. Cohort I (n = 175) performed 16S rRNA sequencing on bronchoalveolar lavage fluid (BALF) to explore microbial genus level characteristics, while Cohort II (n = 41) performed metagenomic and transcriptome sequencing to explore microbial species level characteristics and predict inter group differential metabolic pathways. Finally, a murine model infected with MP was established to validate the effects of Prevotella melaninogenica and its metabolite butyrate. Based on Multi-Omic Analysis, we discovered that P. melaninogenica was the most discriminative species enriched in the critically ill group. Functional profiling demonstrated that butanoate metabolism pathways were significantly enriched in the severe group and positively correlated with P. melaninogenica abundance. Transcriptomic analysis revealed that P. melaninogenica-associated host genes were significantly enriched in immune regulation pathways. Animal experiments confirmed that both P. melaninogenica and butyrate pretreatment significantly attenuated MP-induced pulmonary inflammation, pathogen load, and immune cell infiltration. Respiratory microbiota dysbiosis may be associated with MPP severity. Prevotella melaninogenica, a potential protective commensal enriched in severe group MPP patients, may alleviate airway inflammation through its metabolite butyrate.},
}

Animals
Humans
Multiomics
*Prevotella melaninogenica/metabolism/physiology
*Pneumonia, Mycoplasma/microbiology/metabolism/drug therapy
*Mycoplasma pneumoniae
Mice
*Butyrates/metabolism
Male
Female
RNA, Ribosomal, 16S/genetics
Bronchoalveolar Lavage Fluid/microbiology
Child
Child, Preschool
Disease Models, Animal
Microbiota

@article {pmid42703041,
year = {2026},
author = {Zhang, Y and Zhu, D and Gao, F and Chen, Z and Hu, H and Yuan, C},
title = {Soil Acidification Enriches Antibiotic Resistome.},
journal = {Global change biology},
volume = {32},
number = {9},
pages = {e71087},
doi = {10.1111/gcb.71087},
pmid = {42703041},
issn = {1365-2486},
support = {42577555//National Natural Science Foundation of China/ ; 2026A1515010684//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 77000-31610011//Fundamental Research Funds for the Central Universities/ ; GZC20233289//Postdoctoral Fellowship Program of CPSF/ ; },
mesh = {Hydrogen-Ion Concentration ; *Soil Microbiology ; *Soil/chemistry ; *Bacteria/genetics/drug effects ; *Drug Resistance, Microbial/genetics ; *Genes, Bacterial ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Soil acidification represents a critical global change issue. Its impacts on antibiotic resistance genes (ARGs), however, remain poorly understood. Here we first analyzed a published global dataset comprising 1012 sampling sites and found a significant negative correlation between soil pH and the total richness and relative abundance of ARGs. To validate the observed pattern, we subjected three soils (with initial pH 7.8-7.9) each to 4 acidification levels (pH 7, 6, 5, and 4) for 30 days and subsequent recovery for another 30 days in microcosms. Shotgun metagenomic sequencing revealed that acidification (pH 6, 5, and 4) significantly increased the total richness and relative abundance of ARGs, as well as the relative abundances of 175 ARG subtypes, across all three soils. These 175 acidification-enriched ARGs together accounted for more than 70% of all the ARGs under severely acidified conditions (pH 5 and 4). Moreover, 93% of the bacteria carrying acidification-enriched ARGs also carried various virulence factor genes homologs associated with pathogenicity in reference databases, resulting in increased risk score. The total relative abundance of the acidification-enriched ARGs was primarily associated with changes in bacterial community traits (community composition, acidification-enriched metabolic functions, and genome size), followed by the increase in availability of toxic metals. When soil recovered from severe acidification (pH 5 and 4), the total relative abundance of the acidification-enriched ARGs significantly declined, demonstrating that the effect of soil acidification is partially reversible. This study reveals an underrecognized risk of ARGs caused by soil acidification, highlighting that the prevention and mitigation of soil acidification are crucial for combating antibiotic resistance.},
}

Hydrogen-Ion Concentration
*Soil Microbiology
*Soil/chemistry
*Bacteria/genetics/drug effects
*Drug Resistance, Microbial/genetics
*Genes, Bacterial
*Drug Resistance, Bacterial/genetics
Anti-Bacterial Agents/pharmacology

@article {pmid42703182,
year = {2026},
author = {Mansour, MA and Wahid, M and El Molla, MAS and Helmy, MH and Adel, TM and Mostafa, HN},
title = {Central Nervous System Aspergillosis: Advances in Diagnosis, Therapeutics, and Multidisciplinary Management (2026 Update).},
journal = {Mycoses},
volume = {69},
number = {9},
pages = {e70214},
doi = {10.1111/myc.70214},
pmid = {42703182},
issn = {1439-0507},
mesh = {Humans ; *Antifungal Agents/therapeutic use/pharmacokinetics ; *Neuroaspergillosis/diagnosis/drug therapy ; Voriconazole/therapeutic use ; *Central Nervous System Fungal Infections/diagnosis/drug therapy ; },
abstract = {BACKGROUND: Central nervous system (CNS) aspergillosis is a life-threatening infection with mortality rates exceeding 50%, especially in immunocompromised patients. Significant challenges persist due to limited antifungal drug penetration into the CNS, emerging resistance, and diagnostic delays, despite advancements in therapy and diagnostics.

OBJECTIVE: This comprehensive review aims to synthesize pivotal advances in the management of CNS aspergillosis from 2020 to 2026 and to provide a multidisciplinary framework for addressing these ongoing challenges.

METHODS: We conducted a comprehensive evaluation of the latest clinical data, pharmacokinetic studies, and expert recommendations from the specified period. The review critically appraises evidence on pharmacological therapies, diagnostic technologies, and adjunctive treatment strategies.

FINDINGS: Key findings include: Pharmacotherapy: Voriconazole remains the cornerstone of therapy due to its superior CNS penetration (CSF:Plasma ratio ~50%). The roles of alternatives like isavuconazole, salvage combination regimens, and novel agents (e.g., olorofim, fosmanogepix) are evolving.

DIAGNOSTICS: Cutting-edge tools such as AI-assisted imaging, metagenomic next-generation sequencing (mNGS), and MR spectroscopy for trehalose detection show significant potential for enabling earlier and more accurate diagnosis. Adjunctive Strategies: Neurosurgical intervention, immunomodulation, and therapeutic drug monitoring (TDM) are critical for optimizing outcomes. Emerging strategies like nanoparticle-based drug delivery and host-directed therapies (e.g., PD-1/PD-L1 blockade) offer promising avenues to overcome the blood-brain barrier.

CONCLUSION: This review integrates the latest evidence to provide a timely and actionable resource for clinicians. It bridges gaps in existing guidelines by offering a multidisciplinary approach that addresses the complex management of CNS aspergillosis, with particular relevance for high-risk populations such as COVID-19 and immunocompromised patients.},
}

Humans
*Antifungal Agents/therapeutic use/pharmacokinetics
*Neuroaspergillosis/diagnosis/drug therapy
Voriconazole/therapeutic use
*Central Nervous System Fungal Infections/diagnosis/drug therapy

@article {pmid42703537,
year = {2026},
author = {Wu, J and Luo, X and Fu, S and Zhou, S and He, J and Zhang, D and Zheng, W},
title = {Fatal Pharyngeal Cellulitis Caused by Rhizopus microsporus in a Patient with Acute Myeloid Leukemia.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {608970},
pmid = {42703537},
issn = {1178-6973},
abstract = {INTRODUCTION: Patients with immunodeficiency are highly susceptible to life-threatening fungal infections. Pharyngeal cellulitis caused by Rhizopus microsporus are exceptionally rare.

CASE PRESENTATION: We reported a case of relapsed acute myeloid leukemia (AML) complicated by post-chemotherapy Rhizopus microsporus pharyngeal cellulitis. This cellulitis resulted in severe tissue necrosis, pharyngeal obstruction, and sub-sequent suffocation. Emergency bedside tracheotomy was administered after acute respiratory distress. The metagenomic next-generation sequencing (mNGS) identified Rhizopus microsporus, Klebsiella pneumoniae, Candida albicans, and SARS-CoV-2. Despite surgical intervention and combination antimicrobial therapy (amphotericin B, posaconazole, daptomycin, ceftriaxone, and molnupiravir), the patient stabilized for 2 months before culminating in fatal carotid artery rupture.

CONCLUSION: Rhizopus microsporus-related pharyngeal cellulitis is rare yet highly aggressive, demanding timely diagnosis and close monitoring. This case highlights the critical role of rapid mNGS in diagnosing polymicrobial infections, underscores the necessity of combining aggressive surgical debridement with antifungal/antimicrobial regimens, and stresses rigorous surveillance to prevent life-threatening vascular complications.},
}

@article {pmid42703994,
year = {2026},
author = {Kar, P and Halder, J and Rout, SR and Dash, P and Das, C and Ghosh, G and Rath, G and Kar, B},
title = {Marine-derived Bioactive Compounds: A Promising Frontier against Multidrug-resistant Microbial Infections.},
journal = {Mini reviews in medicinal chemistry},
volume = {26},
number = {12},
pages = {841-858},
pmid = {42703994},
issn = {1875-5607},
mesh = {Humans ; *Biological Products/chemistry/pharmacology/isolation & purification ; *Anti-Bacterial Agents/pharmacology/chemistry/isolation & purification ; Animals ; *Aquatic Organisms/chemistry/metabolism ; *Drug Resistance, Multiple, Bacterial/drug effects ; Bacteria/drug effects ; *Bacterial Infections/drug therapy ; Microbial Sensitivity Tests ; },
abstract = {The global escalation of Multidrug-Resistant (MDR) bacterial infections poses a serious and growing threat to public health, contributing to increased morbidity, mortality, and substantial economic burden worldwide. The widespread and often indiscriminate use of antibiotics in clinical and agricultural settings has accelerated the emergence of resistance, significantly diminishing the efficacy of conventional antimicrobial therapies. This pressing challenge necessitates the exploration of alternative sources for novel antibiotics. Marine ecosystems-renowned for their immense biodiversity and ecological complexity-have gained attention as a rich and largely untapped reservoir of bioactive natural products with potent antimicrobial activity. Marine organisms, such as sponges, tunicates, algae, and bacteria and fungi derived from marine sources, produce structurally diverse and pharmacologically active metabolites, including peptides, polyketides, alkaloids, terpenoids, sterols, lactones, and halogenated compounds. Many of these marine-derived molecules possess unique chemical scaffolds and novel mechanisms of action, offering the potential to circumvent existing resistance pathways. Some compounds have shown promising activity against MDR pathogens, including Staphylococcus aureus, Pseudomonas aeruginosa, and Acinetobacter baumannii. However, challenges such as low natural abundance, difficulty in cultivation, and structural complexity have limited their clinical translation. Recent advancements in marine biotechnology, genomics, metagenomics, and synthetic biology have opened new avenues for the discovery, biosynthesis, and structural optimization of these compounds. These innovative approaches not only facilitate sustainable production but also enhance the pharmacological properties.},
}

Humans
*Biological Products/chemistry/pharmacology/isolation & purification
*Anti-Bacterial Agents/pharmacology/chemistry/isolation & purification
Animals
*Aquatic Organisms/chemistry/metabolism
*Drug Resistance, Multiple, Bacterial/drug effects
Bacteria/drug effects
*Bacterial Infections/drug therapy
Microbial Sensitivity Tests

@article {pmid42704537,
year = {2026},
author = {de Freitas Germano, J and Leite, G and Pimentel, M},
title = {Do Multi-Omics Approaches Improve the Diagnosis of Microbial Overgrowth Syndromes?.},
journal = {Current gastroenterology reports},
volume = {28},
number = {1},
pages = {},
pmid = {42704537},
issn = {1534-312X},
mesh = {Humans ; Multiomics ; *Intestine, Small/microbiology ; Proteomics/methods ; *Blind Loop Syndrome/diagnosis/microbiology ; Breath Tests/methods ; Gastrointestinal Microbiome ; Metagenomics/methods ; Syndrome ; },
abstract = {PURPOSE OF REVIEW: This review investigates how advances in breath testing (BT), small bowel (SB) culture, metagenomics, metatranscriptomics, transcriptomics and proteomics are reshaping the definition and diagnosis of small intestinal bacterial overgrowth (SIBO). It also discusses whether SIBO should be redefined as part of a larger group of microbial overgrowth syndromes.

RECENT FINDINGS: Recent studies identify distinct hydrogen-, methane-, and hydrogen sulfide-associated overgrowth phenotypes, termed SIBO, intestinal methanogen overgrowth (IMO), and intestinal sulfide overproduction (ISO). SB sampling shows that these conditions involve different microbial patterns and functional activity, symptoms, and host responses. Quantitative shotgun metagenomics provides greater taxonomic and functional resolution than culture, while metatranscriptomics reveals active microbial pathways. On top of that, host transcriptomics and proteomics contribute to the better understanding of the predominant microbial effects in host cellular mechanisms in each of the distinct small bowel overgrowth types. SIBO has been increasingly identified as a disorder of microbial ecology and function rather than bacterial quantity alone. Integrating BT with SB sampling and multi-omics approaches may improve classification, clarify symptom mechanisms, and support a more individualized treatment, although standardized methods and further clinical validation remain necessary.},
}

Humans
Multiomics
*Intestine, Small/microbiology
Proteomics/methods
*Blind Loop Syndrome/diagnosis/microbiology
Breath Tests/methods
Gastrointestinal Microbiome
Metagenomics/methods
Syndrome

@article {pmid42704656,
year = {2026},
author = {Bates, KA and Rivera, VB and Glicklich, D and Diflo, T and Chaturvedi, V and Nog, R},
title = {Urinary microbiome in renal transplant patients with BK polyomavirus reactivation.},
journal = {Journal of medical microbiology},
volume = {75},
number = {9},
pages = {},
doi = {10.1099/jmm.0.002196},
pmid = {42704656},
issn = {1473-5644},
mesh = {Humans ; *BK Virus/physiology/genetics ; *Kidney Transplantation/adverse effects ; *Polyomavirus Infections/urine/microbiology/virology ; *Microbiota ; Male ; Female ; Middle Aged ; Adult ; *Virus Activation ; Bacteria/classification/genetics/isolation & purification ; *Tumor Virus Infections/urine/microbiology/virology ; Aged ; DNA, Viral/blood ; *Urine/microbiology ; },
abstract = {Introduction. BK polyomavirus (BKPyV) reactivation is a significant health risk among renal transplant recipients that can lead to nephropathy and allograft loss.Hypothesis/Gap statement. While the microbiota is increasingly recognized as an important determinant of viral infection and pathogenesis, as well as itself undergoing compositional changes in response to infection, the urinary microbiome has yet to be investigated in the context of BK polyomavirus reactivation.Aim. This study aimed to investigate associations between the urinary microbiome and BKPyV-DNAemia in renal transplant patients.Methodology. Shotgun metagenomics of the urinary microbiome was conducted for 22 renal transplant recipients, 11 of whom had BKPyV-DNAemia. Sequence data were analysed using two complementary approaches to identify common microbiome associations with BKPyV-DNAemia: (1) Kaiju - a DNA-to-Protein method that captures bacteria, archaea, fungi, microeukaryotes and DNA viruses and (2) MetaPhlAn4 - a DNA-to-Marker method using a reference database of specific marker genes of prokaryotes.Results. We found increased observed diversity of bacterial taxa in control patients compared to those with BKPyV-DNAemia for data analysed with MetaPhlAn4 (P=0.037) but not Kaiju (P>0.05), which followed a similar trend. Significant differences in microbial beta diversity between the control and BKPyV-DNAemia patient group were identified for the Kaiju dataset (P=0.027) but not for MetaPhlAn4 (P>0.05), with viral reads likely driving these differences in the Kaiju dataset. Both Kaiju and MetaPhlAn4 identified Proteobacteria, Firmicutes and Actinobacteria as bacterial phyla with greatest relative abundance across samples. Screening bacterial species data generated from Kaiju and MetaPhlAn4 against a database of 243 human pathogens identified 8 pathogenic species recovered from both datasets that were present in the urinary microbiome of renal transplant patients.Conclusion. The observed evidence for differences in microbiome diversity and composition associated with BKPyV-DNAemia may play an important role in its pathology and guide the development of diagnostic biomarkers. Our findings warrant further investigation across larger patient cohorts that are more evenly balanced for gender.},
}

Humans
*BK Virus/physiology/genetics
*Kidney Transplantation/adverse effects
*Polyomavirus Infections/urine/microbiology/virology
*Microbiota
Male
Female
Middle Aged
Adult
*Virus Activation
Bacteria/classification/genetics/isolation & purification
*Tumor Virus Infections/urine/microbiology/virology
Aged
DNA, Viral/blood
*Urine/microbiology

@article {pmid42704958,
year = {2026},
author = {Miller, AK and Heremia, L and Waller, SJ and Blanchard, SL and Taylor, JT and Treece, JM and Wille, M and Gemmell, NJ and Winter, D and Dowle, EJ and Geoghegan, JL},
title = {Evaluating sampling strategies for the detection of avian influenza viruses in the environment.},
journal = {Virology},
volume = {625},
number = {},
pages = {111069},
doi = {10.1016/j.virol.2026.111069},
pmid = {42704958},
issn = {1096-0341},
abstract = {Highly pathogenic avian influenza (HPAI) viruses pose an increasing threat to wildlife, livestock and human health, underscoring the need for scalable and early-warning surveillance systems. Environmental RNA (eRNA) monitoring offers a non-invasive, cost-effective alternative to traditional host-based sampling by detecting viral genetic material shed into the environment. Despite its utility, the relative performance of different environmental sampling approaches for avian influenza virus (AIV) detection remains poorly resolved. Here, we conducted a longitudinal study with monthly sampling over approximately one year across two urban waterfowl ponds in Aotearoa New Zealand to evaluate four eRNA sampling strategies - fresh faeces, sediment, active-filtered water and passive-filtered water - for their ability to detect AIV. Using a combination of metagenomic sequencing and RT-qPCR, we show that all sample types can detect AIV, although detections were highly inconsistent across sampling methods, locations and time points. While metagenomic sequencing provided valuable genomic data, including subtype identification and phylogenetic context, RT-qPCR exhibited greater sensitivity, with active-filtered water yielding the highest detection rates, and is currently the more cost-effective approach for large-scale surveillance. Notably, AIV detections were asynchronous among sample types and frequently lacked temporal concordance, suggesting that environmental heterogeneity, RNA persistence, and methodological detection limits strongly influence surveillance outcomes. Despite these inconsistencies, phylogenetic analyses revealed that detected viruses belong to established Australasian lineages, highlighting the ability of environmental surveillance to capture ecologically relevant viral diversity. Our findings demonstrate that while eRNA-based surveillance holds substantial promise as a complementary tool for AIV monitoring, its effectiveness is highly dependent on the environmental sampling strategies and laboratory detection methods used.},
}

@article {pmid42704972,
year = {2026},
author = {Li, J and Shen, F and Chen, Z},
title = {Arbuscular mycorrhizal fungi stabilize ammonium-rich nitrogen removal in constructed wetlands through plant-mediated microbial functional shifts.},
journal = {Water research},
volume = {308},
number = {Pt A},
pages = {126836},
doi = {10.1016/j.watres.2026.126836},
pmid = {42704972},
issn = {1879-2448},
abstract = {Arbuscular mycorrhizal fungi (AMF) are increasingly proposed as a low-energy means of intensifying constructed wetlands (CWs), but whether their benefits depend on influent nitrogen speciation has not been tested. We compared inoculated and uninoculated CWs across three influent N forms at equal N loading. CWs planted with Iris pseudacorus were inoculated with Rhizophagus irregularis (AMF+) or left uninoculated (AMF-) and fed NO3[-]-only (N1), NH4[+]-only (N2), or mixed NO3[-]/NH4[+] (N3) influents at equal total N. Compared with AMF-, AMF+ systems showed higher plant height and chlorophyll content, 30-70% higher SOD/POD activities, and 30-50% lower MDA content and O2·[-] production, especially under N2 and N3. Under N2, AMF prevented TN-removal collapse (83% vs. 26%) and lowered effluent NH4[+]-N (∼3 vs. ∼9 mg N L[-1]). Under N3, AMF maintained ∼88% TN removal (vs. 72%). Selective NH4[+]-N accumulation with negligible effluent NO2[-]-N and NO3[-]-N indicated reduced ammonia-oxidation capacity as the primary N2 bottleneck. Only N2 showed significant AMF-associated community separation (ANOSIM R = 0.77, p = 0.03), accompanied by higher ammonia and nitrite-oxidation potentials (log2FC = 2.20 and 3.99) and increased metagenomic abundances of amoABC, hao, and nxrB. PLS-PM accounted for 68% of the variation in N-removal performance and identified N-cycling functional potential as its strongest positive correlate (β = 0.81), while significant colonization-plant and plant-microbiome paths highlighted host physiological maintenance within the proposed association framework. Overall, AMF benefits were more closely aligned with N-form-specific bottlenecks than with colonization intensity, supporting context-dependent application to stabilize N removal in low-energy CWs treating ammonium-rich or compositionally variable wastewater.},
}

@article {pmid42705201,
year = {2026},
author = {Zhao, X and Meng, T and Zhang, Z and Hu, L and Xiang, X},
title = {Vegetable trimming pellets in laying hen diets drive cecal remodeling and dose-dependent plasma-egg metabolomic dissociation.},
journal = {Poultry science},
volume = {105},
number = {11},
pages = {107637},
doi = {10.1016/j.psj.2026.107637},
pmid = {42705201},
issn = {1525-3171},
abstract = {Vegetable trimming pellets (TVP) provide a potential route for recovering plant biomass as poultry feed, but their dose-dependent effects across production and biological compartments remain unclear. We evaluated diets containing 0% (A), 3% (B), 6% (C), or 9% (D) TVP (80% lettuce and 20% cabbage trimmings) in 240 17-wk-old Hy-Line Grey hens (6 pens of 10 hens per diet) for 12 wk. Diets had similar calculated crude protein, while calculated metabolizable energy decreased from 2.854 to 2.659 Mcal/kg. We assessed production, egg quality, serum, intestine, cecal microbiota and metagenome, and plasma and egg metabolomes. Full-period feed conversion ratio increased from 2.74 in A to 2.88 in D (P = 0.026), and average daily feed intake differed (P = 0.001), while egg production, egg weight, and egg mass remained similar (P > 0.05). At wk 12, shell breaking strength was lower in D than in A to C (3.55 vs. 3.92 to 4.02 kgf/cm[2]; P = 0.030), and yolk color differed among diets (P = 0.007). Serum hormones, several biochemical indices, catalase, and malondialdehyde differed at wk 12 (P < 0.05; marker-specific n = 3 to 6). Cecal community composition differed (permutational multivariate analysis of variance: R[2] = 0.571, P = 0.0006; dispersion P = 0.229), while Shannon diversity remained similar (P = 0.582). Five A-vs.-D metagenomic pathways met a false discovery rate (FDR) < 0.05. In D vs. A, exploratory screening identified 254 annotated plasma and 338 annotated egg candidates, of which 62 and 80, respectively, also met FDR < 0.05; exact annotation matching identified one shared candidate. Graded TVP inclusion maintained major egg-output traits while producing dose-related shifts in feed use, cecal microbial features, and compartment-specific molecular profiles. At the higher inclusion levels, less favorable feed conversion and the lower late-period shell strength at 9% were the principal practical responses.},
}

@article {pmid42705234,
year = {2026},
author = {MacKenzie, C and Seo, H and Schlechte, J and Herik, A and Bains, I and Yu, IL and McCoy, KD and Thornton, CS and McDonald, B},
title = {ON-Time enables rapid microbiome sequencing and analysis for precision medicine.},
journal = {Cell reports methods},
volume = {},
number = {},
pages = {101593},
doi = {10.1016/j.crmeth.2026.101593},
pmid = {42705234},
issn = {2667-2375},
abstract = {Clinical application of microbiome-guided therapies in the intensive care unit (ICU) requires a method to rapidly analyze patient microbiomes to guide urgent treatment decisions. Conventional microbiome sequencing and analysis methods require long turnaround times, methodological complexity, and high costs that are barriers to clinical application. Here, we describe a method for rapid (<5 h turnaround from sample to results) and accurate metagenomic sequencing and taxonomic analysis of microbiomes in individual patient fecal samples, called ON-Time. ON-Time uses a simplified and rapid wet-lab workflow coupled with point-and-click data analysis. Accuracy and precision of ON-Time data were validated using defined mock microbial communities and head-to-head comparison with conventional shotgun metagenomics of ICU patient samples. Key limitations include stochastic identification of functional genes such as antimicrobial resistance and virulence factors. Taken together, ON-Time offers a rapid, accurate, and cost-effective method to analyze individual patient samples for clinically actionable microbiome features to guide personalized therapeutics.},
}

@article {pmid42705487,
year = {2026},
author = {Huang, J and Li, L and Ye, W and Han, L and Liu, Y and Zhan, B and Xu, Y and Peng, X},
title = {Ethanol pretreatment drives microbial community adaptation to overcome acidification in high-solid anaerobic digestion of food waste under rapid organic loading shock.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135803},
doi = {10.1016/j.biortech.2026.135803},
pmid = {42705487},
issn = {1873-2976},
abstract = {This study investigated how ethanol pretreatment (EP) enhances the resilience of high-solid anaerobic digestion against rapid organic loading shocks. Semi-continuous reactors fed with either untreated or EP-treated food waste were compared, and the underlying mechanisms were elucidated by integrating thermodynamic calculations with metagenomic analyses. At an organic loading rate of 6.0 g VS/(Lˑd), the control group (untreated) collapsed due to the accumulation of propionate and other longer-chain volatile fatty acids (VFAs), resulting in a methane yield decrease exceeding 70%. In contrast, the EP group maintained stability, exhibiting a methane yield decrease of less than 5%, with VFAs dominated by readily degradable acetate. Thermodynamic analysis confirmed that EP significantly lowered the energy barriers for VFA degradation. Metagenomic analysis revealed that both propionate/butyrate activation pathways (with lower energy cost or independence from acetyl-CoA) and syntrophic acetate oxidation were activated in the EP group, thereby avoiding the VFA metabolic stress observed in the control group. Furthermore, higher abundances of conductive type IV pili genes, Complex II, and archaeal V/A-type ATPase were detected in the EP group, suggesting the establishment of direct interspecies electron transfer and enhanced electron flux and energy capture efficiency. Moreover, under high loading conditions, only a few high-abundance metagenome-assembled genomes (MAGs) were detected in the control group, while multiple MAGs carrying identical VFA-degrading enzyme systems were identified in the EP group. The functionally redundant microbiota, unobstructed VFA metabolic pathways, and efficient electron transfer and energy supply collectively sustained the stability of the EP group under loading shocks.},
}

@article {pmid42705715,
year = {2026},
author = {Li, G and Shen, L and Nie, L and Tang, P and Shan, Q and Qin, L and Fan, S and Guo, X},
title = {Integrated electronic nose, GC-MS, and metagenomic analyses reveal volatile flavor and microbial community differences in heap-fermented grains of Jiangxiangxing Baijiu across different fermentation degrees.},
journal = {Food research international (Ottawa, Ont.)},
volume = {243},
number = {Pt 2},
pages = {120307},
doi = {10.1016/j.foodres.2026.120307},
pmid = {42705715},
issn = {1873-7145},
mesh = {*Fermentation ; *Volatile Organic Compounds/analysis ; *Gas Chromatography-Mass Spectrometry/methods ; *Electronic Nose ; *Metagenomics/methods ; *Microbiota ; *Food Microbiology/methods ; Taste ; Odorants/analysis ; *Edible Grain/microbiology/chemistry ; *Fermented Foods/microbiology/analysis ; Bacteria/classification/metabolism/genetics ; },
abstract = {The fermentation degree of heap-fermented grains in Jiangxiangxing Baijiu production is a critical factor influencing base Baijiu quality. However, conventional assessment methods largely rely on empirical experience and therefore suffer from limited objectivity and accuracy. In this study, integrated volatile profiling and metagenomic approaches were employed to investigate volatile characteristics and microbial functional potential differentiation in fermented grains with different fermentation degrees (under-fermented, normally fermented, and over-fermented). Significant differences in physicochemical properties were observed among fermentation degrees, particularly in acidity and reducing sugar content. Electronic nose analysis revealed distinct sensor response patterns among different fermentation degrees, indicating differences in overall volatile odor fingerprint patterns. A total of 81 volatile compounds were identified by HS-SPME-GC-MS, with aldehydes, ketones, and pyrazines showing pronounced variations among fermentation degrees, and acetaldehyde exhibiting strong discriminatory potential. LEfSe analysis identified 18 microbial taxa as potential biomarkers associated with different fermentation degrees, including Pichia kudriavzevii, Lentibacillus daiqui, and Acetobacter pasteurianus. Correlation analysis revealed significant positive associations between acetaldehyde levels and Acetobacter abundance. Furthermore, KEGG, CAZy, and eggNOG analyses revealed differentiated functional potentials among fermentation degrees, providing insights into the potential metabolic basis associated with flavor differentiation. Overall, these findings highlight that fermentation degree differentiation is closely associated with coordinated changes in physicochemical conditions, microbial communities, and functional potentials, providing ecological insights into flavor differentiation and theoretical support for objective fermentation degree evaluation and quality control of Jiangxiangxing Baijiu production.},
}

*Fermentation
*Volatile Organic Compounds/analysis
*Gas Chromatography-Mass Spectrometry/methods
*Electronic Nose
*Metagenomics/methods
*Microbiota
*Food Microbiology/methods
Taste
Odorants/analysis
*Edible Grain/microbiology/chemistry
*Fermented Foods/microbiology/analysis
Bacteria/classification/metabolism/genetics

@article {pmid42705723,
year = {2026},
author = {Tong, W and Wang, H and Yang, Y and Xu, J and Huang, Z and Huang, D and Luo, H and Zhao, L and Zhang, S},
title = {Enzyme-driven synthesis and metabolic mechanism of ferulic acid in strong-flavor Daqu: pathway elucidation and microbial drivers.},
journal = {Food research international (Ottawa, Ont.)},
volume = {243},
number = {Pt 2},
pages = {120354},
doi = {10.1016/j.foodres.2026.120354},
pmid = {42705723},
issn = {1873-7145},
mesh = {*Coumaric Acids/metabolism/analysis ; Fermentation ; Carboxylic Ester Hydrolases/metabolism ; *Alcoholic Beverages/microbiology/analysis ; *Flavoring Agents/metabolism ; Carboxy-Lyases/metabolism ; Bacteria/metabolism ; Metabolic Networks and Pathways ; Microbiota ; },
abstract = {Ferulic acid (FA) is a bioactive phenolic compound in strong-flavor Baijiu with important health functions. Its microbial synthesis and metabolic mechanisms in strong-flavor Daqu remain unclear, limiting the understanding of its production. This study explored FA synthesis and metabolic dynamics during Daqu fermentation from D0-D90 using physicochemical detection, feruloyl esterases (FAEs) activity assay, and metagenomic sequencing. Results indicated that FA content fluctuated dynamically throughout fermentation, reaching a final level of 4.39 ± 0.17 mg/kg, and FAEs activity was significantly positively correlated with FA content. Genera significantly associated with FA dynamics were identified. High-abundance genera including Lichtheimia, Saccharopolyspora, Aspergillus, Byssochlamys and Rasamsonia exhibited significantly positive correlations with FA accumulation at respective fermentation stages. This phenomenon may be attributed to their capacity to secrete FAEs, thereby promoting the release of FA. The dynamic change of free FA content was also associated with the expression of ferulic acid decarboxylase, a key enzyme potentially involved in free FA degradation. A comprehensive FA metabolic network in Daqu was constructed, including the cell wall release pathway and the shikimate biosynthesis pathway. A metabolic association model was established based on the phasic succession of fungal and bacterial communities and their coupling with FA metabolic enzyme systems, which suggested a potential division of labor. Fungi are likely to participate in free FA release through secretion of FAEs and auxiliary degrading enzymes, while bacteria may mainly participate in the metabolic turnover and consumption of free FA. This study expands the current understanding of phenolic acid metabolism in strong-flavor Daqu, and provides a theoretical basis for interpreting FA metabolic characteristics during Daqu fermentation.},
}

*Coumaric Acids/metabolism/analysis
Fermentation
Carboxylic Ester Hydrolases/metabolism
*Alcoholic Beverages/microbiology/analysis
*Flavoring Agents/metabolism
Carboxy-Lyases/metabolism
Bacteria/metabolism
Metabolic Networks and Pathways
Microbiota

@article {pmid42705725,
year = {2026},
author = {Xiao, L and Wan, Y and Jiang, M and Liu, Z and Chen, G and Ke, S and Jiang, J and Guo, S and Yu, P and Wu, H and Wang, A and Ning, M and Zhou, Z},
title = {Effects of extraction methodologies on structural characterization and gut microbiota fermentation properties of Apocynum venetum polysaccharides.},
journal = {Food research international (Ottawa, Ont.)},
volume = {243},
number = {Pt 2},
pages = {120357},
doi = {10.1016/j.foodres.2026.120357},
pmid = {42705725},
issn = {1873-7145},
mesh = {*Fermentation ; *Polysaccharides/chemistry/isolation & purification/metabolism/pharmacology ; *Gastrointestinal Microbiome/physiology ; *Apocynum/chemistry ; Prebiotics ; Bacillus/metabolism ; *Plant Extracts/chemistry ; Hydrogen-Ion Concentration ; },
abstract = {Apocynum venetum L. polysaccharides are classified into neutral-to-acidic heteropolysaccharides rich in glucuronic acid, exhibiting antioxidant, immunomodulatory, and potential prebiotic activities. Different extraction methods have a significant impact on the structural characterization and biological activity of polysaccharides. This study aims to compare the structural characteristics and in vitro prebiotic activity of the Apocynum venetum L. polysaccharides BAC and CEL-U obtained via Bacillus velezensis fermentation and the combined ultrasonic-cellulase method, respectively. The results showed that BAC and CEL-U were acidic heteropolysaccharides composed of rhamnose, arabinose, galactose, glucose and galacturonic acid, and they all showed linear branching structure. Compared with CEL-U, BAC had lower molecular weight (17.51 kDa), higher uronic acid content (27.27%) and typical triple helix structure. In vitro fermentation showed that BAC can produce more propionic acid and butyric acid, maintain a lower pH, promote the proliferation of beneficial bacteria (Segatella and Prevotella), and inhibit potentially harmful bacteria. Metagenome analysis further revealed that BAC played a prebiotic role by activating specific glycosidase-mediated degradation pathways and enriching functional pathways related to carbohydrate metabolism. These findings clarify the structure-activity relationship of Apocynum venetum polysaccharide and provide a theoretical basis for its targeted application in the field of intestinal health.},
}

*Fermentation
*Polysaccharides/chemistry/isolation & purification/metabolism/pharmacology
*Gastrointestinal Microbiome/physiology
*Apocynum/chemistry
Prebiotics
Bacillus/metabolism
*Plant Extracts/chemistry
Hydrogen-Ion Concentration

@article {pmid42700597,
year = {2026},
author = {Pan, M and Shen, L and Feng, J and Li, Z and Wu, L and Wu, R and Du, S and Liu, H},
title = {Metagenomic analysis of florfenicol and microplastics effects on microbial function and antibiotic resistome in rice seedling rhizosphere soil.},
journal = {Journal of hazardous materials},
volume = {517},
number = {},
pages = {143454},
doi = {10.1016/j.jhazmat.2026.143454},
pmid = {42700597},
issn = {1873-3336},
abstract = {Antibiotics enrich antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) in farmland, but the contribution of microplastics (MPs) to this process remains unclear. Here, through metagenome analysis, we revealed the add-on effects of PE and PLA on ARGs and VFGs enrichment in rice seedling rhizosphere soil under florfenicol (FF) stress. Compared with controls, root iron plaque content decreased by 35%, 66% and 69% under FF, FF + PE and FF + PLA treatments, disrupting microbial iron balance and activating ABC transporter pathways. Loss of beneficial/core microbes weakened community resistance; bacteria were more sensitive to stress than fungi. Among 945 ARGs and 391 VFs detected, antibiotic efflux abundance rose by 184% under FF, while mobile genetic elements (MGEs) increased from 0.5% to 38.1%, facilitating horizontal ARG transfer. In addition to horizontal gene transfer (HGT) mediated by mobile genetic elements (MGEs), our finding suggests a potential mechanism by which virulence factors (VFs) may promote ARG enrichment through the accumulation of tissue-damaging free radicals. Only one ARG-carrying human pathogen existed in controls, whereas six multi-drug-resistant pathogens emerged under combined pollution. This study provides new insights into the environmental risks of the add-on effects of MPs under antibiotics stress and contributing to the "One Health" goal.},
}

@article {pmid42700605,
year = {2026},
author = {Su, R and Zhao, D and Zhang, X and Wu, QL and Zeng, J},
title = {Trade-off mechanisms between N2O emissions and nitrogen multifunctionality in a lake littoral mesocosm wetland under seasonal water-level fluctuations: insights from metagenomics and machine learning.},
journal = {Water research},
volume = {308},
number = {Pt A},
pages = {126777},
doi = {10.1016/j.watres.2026.126777},
pmid = {42700605},
issn = {1879-2448},
abstract = {Freshwater littoral wetlands are hydrologically dynamic interfaces that regulate nitrogen (N) metabolism (e.g., removal, retention, and N2O emission); however, the effect of seasonal water-level fluctuations on N2O emissions and nitrogen multifunctionality (NMF) remains poorly quantified. This hydrological variability challenges accurate estimates of greenhouse gas (GHG) emissions and complicates ecosystem management strategies that aim to balance climate mitigation with ecosystem functions and sustainability. Here, using a water-level controlled mesocosm at Poyang Lake Wetland Research Station, China, we combine static-chamber measurements, [15]N isotope pairing, metagenomic binning, and an interpretable causal machine learning framework to elucidate the microbial mechanisms and environmental thresholds governing the trade-off between limiting N2O emissions and maintaining NMF. N2O flux (-27.678 to 86.791 μg m[-][2] h[-][1]) was observed at the source-sink transition with rising water levels, whereas NMF was higher in both the continuously dry (0.379) and wet (0.158) zones than in zones subject to water-level fluctuations. A functional quadrant plot revealed the asynchronous relationship between N2O emissions and NMF maintenance. Metagenomic binning demonstrated that distinct dominant microbial taxa mediated N2O and NMF and their trade- off via cooperative and competitive interactions. Moreover, key thresholds, including soil organic matter contents and abundances of hao, hzsABC, nosZII, nirKS, and nasAB genes, drive the system toward a low-emissions and high-function state. This study clarifies the trade-off mechanisms between N2O emissions and NMF maintenance, and provides an ecological basis for reconciling climate mitigation with ecosystem functions in aquatic ecosystems.},
}

@article {pmid42697040,
year = {2026},
author = {Frangieh, MR and Saad, M and Fattouh, N and Sawan, S},
title = {Antibiotics and nanoparticles in Parkinson's disease: From gut microbiota dysbiosis to neuroprotection and targeted nanotherapies.},
journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie},
volume = {203},
number = {},
pages = {119903},
doi = {10.1016/j.biopha.2026.119903},
pmid = {42697040},
issn = {1950-6007},
abstract = {Parkinson's disease (PD) is increasingly linked to gut-brain axis dysfunction. While broad-spectrum antibiotics may contribute to gut dysbiosis, which has been associated with an increased abundance of curli-producing Enterobacteriaceae and processes implicated in α-synuclein aggregation, certain antibiotic classes, particularly tetracyclines and β-lactams, have demonstrated neuroprotective properties in pre-clinical models of PD. This creates a therapeutic paradox: antibiotics may exert either beneficial or detrimental effects depending on many factors including host microbiome composition. Importantly, much of the current evidence remains observational or pre-clinical, and a direct causal relationship between antibiotic exposure and PD has not yet been established. This review synthesizes current epidemiological, mechanistic, and pre-clinical evidence regarding this paradox and explores the emerging role of nanotechnology in resolving it. Preclinical studies suggest that nanoparticle-based drug delivery systems may enhance BBB penetration and enable more targeted drug release. Such approaches have been proposed as a means to reduce systemic exposure and potentially limit microbiota disruption, although these benefits have not yet been demonstrated in clinical PD populations. We further discuss the translational hurdles, including nanotoxicity and regulatory requirements, and propose a roadmap for future research that integrates metagenomics with precision nanomedicine. Collectively, these findings provide a framework for future investigation of targeted therapeutic strategies for PD. However, substantial mechanistic, clinical, and translational validation is required before their therapeutic potential can be established.},
}

@article {pmid42697290,
year = {2026},
author = {Ansari, SK and Shah, NH and Elboughdiri, N and Chaudhary, AA and Ali, MAM and Wani, AK},
title = {Extremozymes for food fermentation: Integrating AI, metagenomics, and protein engineering.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {154351},
doi = {10.1016/j.ijbiomac.2026.154351},
pmid = {42697290},
issn = {1879-0003},
abstract = {Climate change-induced fluctuations in temperature, pH, salinity, and water activity are increasingly compromising microbial metabolism and fermentation efficiency, exposing the limitations of conventional mesophilic enzymes in maintaining process stability and product consistency. Extremozymes, derived from extremophilic microorganisms, exhibit exceptional structural stability and catalytic activity under harsh physicochemical conditions, making them promising biocatalysts for climate-resilient food fermentation. Although considerable progress has been achieved in extremozyme discovery and engineering, challenges remain in bridging computational prediction with experimental validation, functional characterization, large-scale production, and industrial deployment. This review critically examines the diversity, biochemical properties, and functional roles of extremozymes in food fermentation while evaluating the influence of climate-induced process stresses on microbial performance, enzyme functionality, and fermentation outcomes. It further synthesizes recent advances in Artificial Intelligence (AI)-assisted metagenomics, machine learning, transformer-based protein modelling, generative protein design, multi-omics (MO) integration, and high-throughput screening platforms, including microfluidics, droplet-based systems, and cell-free expression technologies, that are accelerating enzyme discovery, engineering, and validation. Particular emphasis is placed on the integration of computational and experimental workflows to improve the accuracy, scalability, and industrial translation of next-generation extremozymes. Unlike previous reviews that primarily describe individual enzyme classes or AI methodologies, this review provides a comprehensive and critical framework linking climate-driven fermentation challenges with emerging computational and biotechnological solutions. It identifies current knowledge gaps, technological bottlenecks, and future research priorities for developing robust, programmable, and energy-efficient fermentation systems capable of sustaining product quality, process reliability, and sustainable food production under increasingly variable environmental conditions.},
}

@article {pmid42697635,
year = {2026},
author = {Shan, M and Wang, J and Chen, W and Zheng, C and Zhang, L and Yu, Y and Han, L and Fang, H},
title = {Hexaconazole enantiomers drive the dissemination and risks of antibiotic resistance genes in the soil-earthworm system.},
journal = {Pesticide biochemistry and physiology},
volume = {223},
number = {},
pages = {107319},
doi = {10.1016/j.pestbp.2026.107319},
pmid = {42697635},
issn = {1095-9939},
mesh = {Animals ; *Triazoles/chemistry/pharmacology/toxicity ; *Oligochaeta/drug effects/microbiology/genetics ; Soil Microbiology ; Stereoisomerism ; *Soil Pollutants/chemistry ; *Drug Resistance, Microbial/genetics ; *Fungicides, Industrial/chemistry/pharmacology ; Soil/chemistry ; *Genes, Bacterial ; },
abstract = {Chiral fungicides constitute a substantial proportion of commonly used pesticides; however, the spread of antibiotic resistance genes (ARGs) in agricultural settings under repeated exposure to different enantiomers is still unclear. Here, the prevalence and potential risks of ARGs were investigated in the soil-earthworm ecosystem when exposed to hexaconazole (HEX) enantiomers. Metagenomic analysis indicated that R-HEX and S-HEX facilitated the dissemination of ARGs in soil without earthworms, but this effect diminished with successive exposures. Notably, S-HEX exhibited a greater effect on ARG profiles compared to R-HEX. Furthermore, HEX enantiomers, particularly S-HEX, increased the mobility potential of ARGs and enhanced host pathogenicity, thereby contributing to elevated ecological risks. Specifically, exposure to the HEX enantiomer led to an enrichment of dominant pathogenic ARG hosts, such as Enterobacteriaceae. Importantly, earthworms alleviated the enantiomer-driven dissemination of ARGs and weakened their association with mobile genetic elements (MGEs). Overall, this study offers novel perspectives on the enantiomer-driven propagation of ARGs induced by the chiral pesticide hexaconazole in soil and highlights the role of earthworms in mitigating ARG contamination. These findings contribute significantly to the risk assessment and remediation strategies for chiral pesticides.},
}

Animals
*Triazoles/chemistry/pharmacology/toxicity
*Oligochaeta/drug effects/microbiology/genetics
Soil Microbiology
Stereoisomerism
*Soil Pollutants/chemistry
*Drug Resistance, Microbial/genetics
*Fungicides, Industrial/chemistry/pharmacology
Soil/chemistry
*Genes, Bacterial

@article {pmid42697647,
year = {2026},
author = {Huang, C and Dai, X and Chen, Y and Ge, H and Zhang, L and Yu, Y and Fang, H},
title = {Chitosan mitigates the dissemination of antibiotic resistance genes caused by metalaxyl in the soil-earthworm system.},
journal = {Pesticide biochemistry and physiology},
volume = {223},
number = {},
pages = {107278},
doi = {10.1016/j.pestbp.2026.107278},
pmid = {42697647},
issn = {1095-9939},
mesh = {Animals ; *Chitosan/pharmacology ; *Oligochaeta/drug effects ; Soil Microbiology ; *Alanine/analogs & derivatives/toxicity/pharmacology ; *Fungicides, Industrial/toxicity/pharmacology ; *Drug Resistance, Microbial/genetics ; *Soil Pollutants/toxicity ; Soil/chemistry ; Bacteria/genetics/drug effects ; Gene Transfer, Horizontal/drug effects ; },
abstract = {The widespread use of agricultural fungicides can lead to residual contamination and accelerate the emergence and spread of antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARBs) in soil ecosystems. Developing green remediation strategies that simultaneously reduce fungicide residues and mitigate antibiotic resistance risks is therefore beneficial for soil pollutant control. Here, we investigated the effects of chitosan (CHI) on the dissipation of metalaxyl (MET) enantiomers and their influence on the soil-earthworm resistome and microbiome through pot experiments and metagenomics analysis. The results showed that CHI significantly accelerated MET dissipation in soil and reduced its bioaccumulation in earthworms. MET enantiomers, particularly S-MET, promoted the dissemination of ARGs, including high-risk ARGs, in the soil-earthworm system, whereas CHI suppressed these effects, likely by limiting the potential for mobile genetic element (MGE)-mediated horizontal gene transfer (HGT). Compared with the corresponding treatments without CHI amendment, CHI amendment reduced the total relative abundance of ARGs by 16.8%-24.7% in soil and by 34.1%-58.3% in earthworm guts. Furthermore, CHI reshaped microbial community structure in both soil and earthworm gut samples by driving ecological niche differentiation of Actinomycetota and Pseudomonadota and reduced ARG host abundance. These findings offer practical insights for controlling contamination by fungicides and ARGs in agricultural soils.},
}

Animals
*Chitosan/pharmacology
*Oligochaeta/drug effects
Soil Microbiology
*Alanine/analogs & derivatives/toxicity/pharmacology
*Fungicides, Industrial/toxicity/pharmacology
*Drug Resistance, Microbial/genetics
*Soil Pollutants/toxicity
Soil/chemistry
Bacteria/genetics/drug effects
Gene Transfer, Horizontal/drug effects

@article {pmid42697668,
year = {2026},
author = {Zhu, S and Liu, X and Yang, X and Wu, W and Ahmed, T and Jiang, H and Ding, T},
title = {Amplicon and metagenomic sequencing reveal thifluzamide drive rhizosphere microbial structural shifts and functional adaption.},
journal = {Pesticide biochemistry and physiology},
volume = {223},
number = {},
pages = {107299},
doi = {10.1016/j.pestbp.2026.107299},
pmid = {42697668},
issn = {1095-9939},
mesh = {*Rhizosphere ; Fungi/drug effects/genetics ; Oryza/microbiology ; Bacteria/drug effects/genetics ; Metagenomics ; *Fungicides, Industrial/pharmacology ; Soil Microbiology ; *Microbiota/drug effects ; Metagenome ; },
abstract = {Thifluzamide (TF) is a widely used phenyl urea fungicide in rice production; however, its impacts on the structural composition and functional dynamics of the rhizosphere microbiome remain poorly understood. Here, we systematically investigated the effects of TF on the structure, interactions, and functional potential of the rice (Oryza sativa L.) rhizosphere microbiome using integrated amplicon sequencing and metagenomic approaches. TF application significantly altered both bacterial and fungal community composition, bacterial diversity was markedly reduced, whereas fungal diversity increased. With bacterial diversity markedly reduced while fungal diversity increased. Beta-diversity analyses revealed strong treatment-driven community separation, indicating pronounced TF-induced microbial restructuring. Co-occurrence network analysis demonstrated reduced complexity and connectivity in bacterial networks but increased negative co-occurrence patterns within fungal communities, suggesting contrasting stability responses between microbial kingdoms. Metagenomic profiling further revealed substantial functional shifts, including the differential enrichment of KEGG and COG pathways associated with xenobiotic metabolism. Notably, while total ARG abundance remained stable, TF exposure altered the resistome profile by selectively enriching specific classes of antibiotic resistance genes (ARGs), biocide resistance genes (BRGs), and mobile genetic elements (MGEs). Strong positive correlations between MGEs and ARGs highlighted an elevated potential for horizontal gene transfer. Metagenome-assembled genome (MAG) analysis identified specific TF-enriched bacterial taxa, including Methylophilus, Sulfurospirillum, and Azospirillum, which harbored genes involved in pesticide degradation and xenobiotic transformation. Collectively, these findings demonstrate that TF profoundly reshapes the rice rhizosphere microbiome by altering microbial diversity, interaction networks, resistance gene profiles, and functional capacities. This study provides genomic insights into fungicide-microbiome interactions, underscoring the potential ecological implications associated with TF application, while identifying candidate microbial taxa that may contribute to pesticide degradation and rhizosphere microecology resilience.},
}

*Rhizosphere
Fungi/drug effects/genetics
Oryza/microbiology
Bacteria/drug effects/genetics
Metagenomics
*Fungicides, Industrial/pharmacology
Soil Microbiology
*Microbiota/drug effects
Metagenome

@article {pmid42697801,
year = {2026},
author = {Htut, M and Lee, K and Nathwani, N and Rosenzweig, M and Janakiram, M and Goldsmith, S and Sanchez, JF and Scott, M and Keats, J and Krishnan, A and Rosen, ST and Wang, SS},
title = {Gut Microbiome Composition Is Associated With Response to CD38 Antibody (Daratumumab) Treatment Among Relapsed Multiple Myeloma Patients.},
journal = {Clinical lymphoma, myeloma & leukemia},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.clml.2026.08.004},
pmid = {42697801},
issn = {2152-2669},
abstract = {INTRODUCTION: Growing data support interactions between host-gut microbes and treatment responses in multiple myeloma (MM), where a higher abundance of Eubacterium hallii in stool samples has been found among MM patients with negative minimal residual disease after induction therapy. Here, we evaluated changes in the gut microbiome associated with daratumumab (dara) based therapy in 40 MM patients, before and after therapy.

PATIENTS AND METHODS: Patients with relapsed MM and prior autologous transplantation who had received 1 to 4 prior lines of therapy were eligible. Two stool samples were collected, one within 1 week prior to dara (predara) and one immediately after 4 doses of dara (postdara). Metagenomics sequencing was conducted. Microbiome taxonomic analyses were performed using MetaPhlAn4, and microbial functional pathway analyses were conducted using HUMAnN3.6. QIIME2 was used for compositional and statistical analyses.

RESULTS: Of 40 participants enrolled, there were 5 nonresponders; 35 patients achieved partial response (PR) or better (responders). Among responders, 10 patients achieved complete remission (CR), and 25 patients achieved either very good partial response (VGPR) or PR. There were no statistically significant differences between overall pre and postdara gut microbiomes. Differential abundance analysis (ANCOM-BC) showed statistically significant (q ≤ 0.05) overgrowth of Alistipes finegoldii and Acidaminococcus intestini species in responders and Ruminococcus torques, Sellimonas intestinalis and Clostridium symbiosum in nonresponders. Compared to non-CR, CR samples showed enrichment of Faecalibacterium prausnitzii; non-CR samples were enriched in Segatella copri and Faecalimonas umbilicata.

DISCUSSION/CONCLUSION: Our results suggest differences in species between clinical responders and nonresponders, but larger prospective studies are needed to confirm these results.},
}

@article {pmid42698579,
year = {2026},
author = {Murugesan, M and Thankappan, S and Mageshwaran, V and Ramasamy, R and Singaram, A},
title = {Decoding the functional diversity of plant growth-promoting bacterial communities in the soils of Western Ghats, Tamil Nadu, India.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1865342},
doi = {10.3389/fmicb.2026.1865342},
pmid = {42698579},
issn = {1664-302X},
abstract = {Western ghats in India, one of the world's biodiversity hot spots is the reservoirs of microbial resources having agricultural and industrial significance. However, the diversity of plant growth-promoting microbial communities associated with the plants and soil in the Western Ghats is untapped vault. The current emphasis on natural farming is more depending on the indigenous microbial communities and their metabolic functions towards sustainable one -health. With this background, the present study examines the bacterial diversity of soils from the Western Ghats of Nilgiris, Coimbatore and Dindigul regions. Among the 10 soil samples collected (S1 to S10), three soil samples (S2, S4 and S6) representing respective three regions were subjected for metagenomic studies based on their distinct soil chemical and biological properties. The computational analysis of the metagenome revealed the core genus Bradhyrhizobium in all soil samples, while Trebonia, Arthrobacter, Streptomyces, and Pseudomonas are the next most abundant genera, which varied substantially. The results collectively demonstrate that soil sample from Dindigul harbours the richest and most diverse microbial community among the three regions. In culturable studies, a total of 101 bacterial isolates were obtained from 10 soil samples (S1 to S10). Among them four Gram-negative bacterial isolates showed potential plant growth-promoting attributes, such as Ammonia, Indole Acetic Acid, Hydrogen cyanide and siderophore production, phosphorus, potassium, and zinc solubilization. The 16S rDNA analysis revealed that the bacterial isolates were Pseudomonas glycinae S6B1, Pseudomonas tolaasii S2B3, Pseudomonas azotoformans S9H10, and Pseudomonas poae S10B2. The isolate, S10B2, exhibited the maximum inhibition, with 81.25%, 70.1%, and 35% against plant pathogenic fungi, Rhizoctonia solani, Sclerotium rolfsii, and Fusarium oxysporum, respectively, indicating strong biocontrol potential. The effect of bacterial inoculants on chick pea (Cicer arietinum var. JG 62), showed that P. glycinae S6B1 significantly promoted plant growth such as root length, shoot length, and fresh/dry biomass. These findings unlock the core microbiome of soils of Western Ghats, which can be utilized to develop a synthetic microbial consortium to boost agricultural productivity.},
}

@article {pmid42698876,
year = {2026},
author = {Wang, X and Gao, R and Shen, W and Wu, X},
title = {Clinical characteristics of Tropheryma whipplei pneumonia: A retrospective analysis based on five cases.},
journal = {IDCases},
volume = {45},
number = {},
pages = {e02730},
doi = {10.1016/j.idcr.2026.e02730},
pmid = {42698876},
issn = {2214-2509},
abstract = {OBJECTIVE: Acute pulmonary infection caused by Tropheryma whipplei (TW) is rare. This article summarizes the medical records of TW pneumonia patients to provide clinical insights into diagnosis and treatment.

METHODS: A retrospective analysis was conducted on five patients diagnosed with TW pneumonia from 2021 to 2023 in Changzhou No. 2 People's Hospital. The study focused on clinical symptoms, imaging characteristics, diagnostic methods, and treatment approaches.

RESULTS: Patients aged 35-65 years had underlying diseases and presented with fever, cough, expectoration, and chest tightness. Laboratory tests showed white blood cells, procalcitonin, C-reactive protein, and erythrocyte sedimentation rate increased, and the patients had anemia and hypoalbuminemia. Chest CT showed nodular lesions, cavities and patchy shadows. TW was detected in bronchoalveolar lavage fluid (BALF) by metagenomic next-generation sequencing (mNGS). Four patients received ceftriaxone combined with doxycycline or compound sulfamethoxazole tablets, while one treated empirically with cefotetan. All patients showed significant improvement.

CONCLUSION: TW pneumonia often occurs in patients with underlying diseases, and immunocompromised patients have more severe lung damage. Most chest CT shows nodular lesions with atypical distribution and shape. Early diagnosis requires relies on mNGS, and treatment mainly bases on the third-generation cephalosporin combined with tetracycline or sulfonamides. Sequential therapy with sulfamethoxazole and clarithromycin is effective, and close follow-up needs to determine the total course of treatment.},
}

@article {pmid42698879,
year = {2026},
author = {Cioletti, G and Kenney, S and Hovingh, E and Springer, H and Haley, BJ and Ganda, E},
title = {Nasopharyngeal microbiome and resistome profiles in dairy calves fed milk replacer with low-level β-lactams.},
journal = {JDS communications},
volume = {7},
number = {5},
pages = {670-677},
doi = {10.3168/jdsc.2025-0994},
pmid = {42698879},
issn = {2666-9102},
abstract = {Feeding waste milk (WM) to preweaning dairy calves is a common management practice that offers economic benefits but may influence the microbiome and antimicrobial resistance (AMR) due to the presence of antibiotic residues. The objective of this study was to describe longitudinal patterns in the nasopharyngeal microbiome and AMR gene profiles of dairy calves fed either nonsupplemented milk replacer or milk replacer supplemented with low-level β-lactam antibiotics to simulate WM exposure during the preweaning period. Using shotgun metagenomic sequencing, we profiled the nasopharyngeal microbiome and resistome of 11 Holstein bull calves fed milk replacer with (MR+A; n = 6) or without (MR; n = 5) low levels of β-lactam antibiotics. Antibiotic concentrations were selected to reflect residue levels reported in WM. Deep nasopharyngeal swabs were collected every 2 wk from 1 to 15 wk of age; samples from wk 3 and 15 were excluded due to elevated contaminant burden, resulting in 6 retained time points. No significant differences in microbial α-diversity, β-diversity, or community structure were detected by dietary treatment or sampling age. Tetracycline, macrolide-lincosamide-streptogramin, aminoglycoside, metal, acid, and biocide resistance classes were among the most prominent, with descriptive differences in z-score patterns between groups but no significant differences detected. Larger-scale studies are needed to evaluate the long-term effects of WM feeding on respiratory health and AMR dynamics in dairy calves.},
}

@article {pmid42699185,
year = {2026},
author = {McGregor, K and Okaeme, N and Khorasaniha, R and Veniamin, S and Jovel, J and Miller, R and Mahmood, R and Graham, M and Bonner, C and Bernstein, CN and Arnold, DL and Bar-Or, A and Marrie, RA and O'Mahony, J and Yeh, EA and Zhao, Y and Banwell, B and Waubant, E and Knox, N and Van Domselaar, G and Zhu, F and Mirza, AI and Tremlett, H and Armstrong, H},
title = {Proportionality-based association metrics in count compositional data.},
journal = {NAR genomics and bioinformatics},
volume = {8},
number = {3},
pages = {lqag102},
doi = {10.1093/nargab/lqag102},
pmid = {42699185},
issn = {2631-9268},
mesh = {Animals ; Mice ; Single-Cell Analysis ; Metagenomics/methods ; Sequence Analysis, RNA ; Algorithms ; },
abstract = {Compositional data comprise vectors that describe the constituent parts of a whole. Data arising from various -omics platforms such as 16S and RNA sequencing are compositional in nature. In this kind of data, correlations between features on raw counts have no meaningful interpretation. Metrics of proportionality were formulated to address this problem. However, an inherent bias arises when these metrics are calculated empirically on count-based measures due to variability in read depths. We quantify the bias introduced by empirically calculating proportionality-based association metrics in count data. Additionally, we propose a means of estimating these metrics within a logit-normal multinomial model in pursuit of more accurate estimates. The model-based estimates are shown to outperform empirical estimates in simulated data and are applied to a mouse embryonic stem cell single-cell sequencing dataset, as well as a pediatric-onset multiple sclerosis metagenomic dataset.},
}

Animals
Mice
Single-Cell Analysis
Metagenomics/methods
Sequence Analysis, RNA
Algorithms

@article {pmid42699249,
year = {2026},
author = {Xue, Z and Li, H and Wang, X and Cai, Y and Huang, Z and Li, W and Su, Y and Wu, Z and Fang, X and Zhang, W},
title = {Diagnostic and Therapeutic Impact of Metagenomic Next-Generation Sequencing in Tuberculous Osteoarticular Infections with Negative or Confounding Conventional Cultures.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {620236},
doi = {10.2147/IDR.S620236},
pmid = {42699249},
issn = {1178-6973},
abstract = {PURPOSE: Diagnosing tuberculous osteoarticular infections (TB-OAI) remains challenging due to frequent false-negative or confounding conventional culture results. This study evaluated the diagnostic and therapeutic utility of metagenomic next-generation sequencing (mNGS) for occult TB-OAI in patients presenting with negative or misleading culture outcomes.

PATIENTS AND METHODS: We retrospectively analyzed 13 patients with confirmed TB-OAI, encompassing periprosthetic, fracture-related, and native joint infections. Patients were stratified by conventional culture results into strictly culture-negative (n=8) and culture-confounded (n=5; yielding non-mycobacterial organisms) groups. A composite reference standard of mNGS positivity combined with histopathological or clinical validation established the definitive diagnosis. We assessed diagnostic yield, therapeutic modifications, and clinical outcomes.

RESULTS: Conventional culture failed to identify Mycobacterium tuberculosis in all 13 cases (0% sensitivity) and yielded misleading non-mycobacterial flora in 5 cases (38.5%). Conversely, mNGS successfully identified the pathogen in 100% (13/13) of patients, corroborated by histopathology in all cases. Consequently, mNGS results changed clinical management from empirical antibiotics to targeted anti-tuberculosis therapy in all cases (100%). Postoperative erythrocyte sedimentation rate (ESR) and C-reactive protein (CRP) levels decreased significantly (P < 0.05). Over a mean follow-up of 17.5 ± 3.0 months, 12 patients achieved durable infection eradication. One patient experienced early recurrence requiring a two-stage revision, ultimately achieving successful infection control.

CONCLUSION: mNGS serves as a promising diagnostic rescue tool for occult TB-OAI when conventional cultures are negative or misleading. While limited by sample size, these preliminary findings suggest mNGS effectively guides the transition from empirical to targeted anti-tuberculosis therapy and limits diagnostic delays.},
}

@article {pmid42699313,
year = {2026},
author = {Prachansuwan, A and Sukkha, P and Thiyajai, P and Chamtim, P and Kitdumrongthum, S and Sridonpai, P and Dee-Uam, A and Tongdonpo, K and Trachootham, D and Srichamnong, W and Thaipisuttikul, I and Raethong, N},
title = {Gut microbiome and metabolic responses to cricket powder supplementation in Thai subjects with high or borderline-high LDL cholesterol: an exploratory, randomized, crossover controlled trial.},
journal = {Current research in food science},
volume = {13},
number = {},
pages = {101536},
doi = {10.1016/j.crfs.2026.101536},
pmid = {42699313},
issn = {2665-9271},
abstract = {Edible insects are emerging as sustainable functional foods, yet human evidence for microbiome-mediated effects remains limited, particularly in Asian populations. Therefore, this study investigated whether cricket powder supplementation modulates gut microbiome composition and metabolic outputs in Thai subjects with high or borderline-high LDL cholesterol. In a randomized, crossover controlled trial, 17 subjects received cricket powder or control products for 21 days, separated by a 4-week washout. Gut microbiome composition was profiled using full-length 16S rRNA gene sequencing, and fecal short-chain fatty acids (SCFAs) were quantified by gas chromatography-mass spectrometry. Blood lipids and gastrointestinal tolerance were also assessed. As a result, cricket powder did not alter overall microbial diversity or community structure but induced targeted species-level shifts, including enrichment of Blautia faecis and Mediterraneibacter glycyrrhizinilyticus. Despite these compositional changes, fecal SCFAs remained unchanged. Notably, branched-chain SCFAs were not increased, indicating no shift toward proteolytic fermentation and preservation of microbial metabolic balance. Gastrointestinal tolerance was maintained without adverse effects. Blood lipid parameters were unchanged, with a modest trend toward increased high-density lipoprotein cholesterol (HDL-C). Collectively, cricket powder induces selective microbiome remodeling without disrupting metabolic homeostasis, supporting its potential as a sustainable, microbiome-targeted functional food.},
}

@article {pmid42699484,
year = {2026},
author = {Chen, J and Zhou, Q and Zhang, Y and Chen, J and Zheng, X and Ye, F},
title = {What constitutes a true polymicrobial periprosthetic joint infection? From multiple detections to organism-level causality.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1936444},
doi = {10.3389/fmicb.2026.1936444},
pmid = {42699484},
issn = {1664-302X},
abstract = {Polymicrobial periprosthetic joint infection (PJI) is often defined by recovery of two or more microorganisms from the same clinical episode, but this numerical definition is biologically incomplete. A second organism may represent a true co-pathogen, colonization, contamination, reagent background, nonviable DNA after antimicrobial exposure, or an analytically plausible signal of uncertain clinical importance. Established PJI definitions determine whether infection is present but do not provide a validated organism-level rule for assigning causality to every detection. We therefore propose a sequential approach: first establish PJI using accepted episode-level criteria, then adjudicate each detected microorganism separately before classifying the episode as polymicrobial. This Mini Review examines evidence relevant to organism-level causal attribution, including sampling integrity, reproducibility across independent deep specimens, anatomical coherence, orthogonal confirmation, quantitative and temporal signal, organism biology, and clinical concordance. We also consider how tissue culture, synovial fluid culture, sonication, blood culture, PCR, and metagenomic sequencing generate different interpretive challenges, particularly after antimicrobial exposure. Finally, we propose a pragmatic four-category vocabulary-strongly supported participant, probable participant, uncertain detection, and likely contaminant-to make organism-level causal confidence explicit in multidisciplinary interpretation and research reporting. This framework is intended as an interpretive aid rather than a validated diagnostic score. Whether it improves inter-rater consistency, antimicrobial precision, or organism-specific outcomes requires prospective validation.},
}

@article {pmid42699605,
year = {2026},
author = {Yue, Y and Wei, W and Wu, C and Suo, N and Zhang, Z and Liu, W and Su, Q and Wang, M and Zhang, Y and Xie, B},
title = {Four-domain gut metagenomics reveals archaeal-centered cross-kingdom remodeling across coronary artery disease and acute myocardial infarction.},
journal = {iScience},
volume = {29},
number = {9},
pages = {117227},
doi = {10.1016/j.isci.2026.117227},
pmid = {42699605},
issn = {2589-0042},
abstract = {Cardiovascular microbiome research has focused mainly on bacterial taxa and pathways. We profiled stool archaea, bacteria, fungi, and viruses in patients with acute myocardial infarction (AMI) and healthy controls. Paired plasma metabolomics was examined in a subset. An independent angiography-defined cohort included angiographically normal controls, severe coronary artery disease (CAD), and AMI. No archaeal genus remained differentially abundant after multiple-testing correction. In the discovery cohort, archaeal-bacterial correlations were predominantly positive in healthy controls and negative in AMI, while archaeal-fungal rewiring was prominent. The extension cohort identified sign-flip archaeal-virome edges between severe CAD and AMI, while severe CAD showed the lowest archaeal-bacterial connectivity. Plasma metabolomics captured a broad AMI-associated systemic shift. These findings show that gut archaeal signals are expressed through multi-kingdom ecological organization across coronary disease states.},
}

@article {pmid42700527,
year = {2026},
author = {Yin, Z and Ping, H and Li, C},
title = {Antimony species-dependent enrichment and transcriptional activity of antibiotic and metal resistance genes in the gut microbiome of male mice.},
journal = {Journal of environmental management},
volume = {417},
number = {},
pages = {130867},
doi = {10.1016/j.jenvman.2026.130867},
pmid = {42700527},
issn = {1095-8630},
abstract = {The gut microbiome is a reservoir for antibiotic resistance genes (ARGs) and is sensitive to environmental pollutants. ARGs in environmental and host-associated microbiomes can be enriched by metal(loid)s through co-selection with metal resistance genes (MRGs). However, as a ubiquitous toxic metalloid, antimony (Sb) induced alterations of ARGs in the gut microbiome and the underlying mechanisms remain unclear. Here, by integrating genome-resolved metagenomics and metatranscriptomics, we characterized the genomic potential and transcriptional activity of ARGs and MRGs in the gut microbiome of mice exposed to Sb(III)- and Sb(V)-contaminated drinking water. We found that both Sb(III) and Sb(V) significantly increased ARGs abundance, whereas only Sb(III) enhanced ARGs transcription (288.40 ± 41.67 TPM, P < 0.05). Co-selection of ARGs and MRGs was observed through metagenome-assembled genomes (MAGs) analysis, and key taxa driving this process were identified (e.g., Eubacterium_J and Lachnospiraceae_COE1). Sb(III), but not Sb(V), induced co-regulation of macrolide-lincosamide-streptogramin resistance genes and arsRABC operon. A potentially higher risk of ARG dissemination under Sb(III) stress was suggested by the increased abundance and transcription of mobile genetic elements (MGEs). This study advances our understanding of the interactions between Sb and ARGs in the gut microbiome and highlights the potential chemical species-dependent enrichment and transcriptional activation of ARGs.},
}

@article {pmid42692700,
year = {2026},
author = {Li, Z and Guo, Y and Zhang, X and Xie, N and Zhang, F and Zhen, Z},
title = {Integrated microbiome and metabolome analysis reveals microbial and metabolic dynamics associated with goose foie gras spoilage during refrigerated storage.},
journal = {Food research international (Ottawa, Ont.)},
volume = {243},
number = {Pt 1},
pages = {120303},
doi = {10.1016/j.foodres.2026.120303},
pmid = {42692700},
issn = {1873-7145},
mesh = {Animals ; *Metabolome ; *Food Storage/methods ; *Refrigeration ; *Microbiota ; *Geese/microbiology ; Thiobarbituric Acid Reactive Substances/analysis ; *Food Microbiology ; Metabolomics ; RNA, Ribosomal, 16S/genetics ; Colony Count, Microbial ; Bacteria ; Chromatography, High Pressure Liquid ; },
abstract = {Goose foie gras spoils rapidly under refrigeration, yet its microbial and metabolite dynamics during storage are poorly described. Samples from a single Landes production batch were stored at 4 °C in air-sealed polyethylene pouches and analysed on days 0, 2, 4, 6, 8, 10 and 12. Three biological replicates per time point were processed for total viable count (TVC), total volatile basic nitrogen (TVB-N), thiobarbituric acid reactive substances (TBARS), 16S ribosomal RNA (rRNA) amplicon sequencing, and ultra-high-performance liquid chromatography-mass spectrometry (UHPLC-MS)-based untargeted metabolomics. TVC increased from 3.85 to 6.16 log CFU/g, TVB-N from 8.99 to 27.77 mg/100 g and TBARS from 0.18 to 0.72 mg MDA/kg between day 0 and day 12, with the steepest changes appearing after day 6. The maximum TVC reached 6.16 log CFU g[-1] on day 12, below the 7 log CFU g[-1] level cited for some meat products; no sensory evaluation was performed. The late storage period is therefore described as a phase of concurrent rises in TVC, TVB-N and TBARS rather than as a confirmed spoilage endpoint. The 14 most abundant genera were retained for multivariate analysis. Seven genera, including Brochothrix, Pseudomonas, Lactobacillus and Lactococcus, met the operational definition of candidate spoilage-associated taxa. Forty candidate metabolites were screened by random forest. Five (tyramine, 4-hydroxyphenylacetaldehyde, adenosine monophosphate, oxidized glutathione and γ-glutamylcysteine) were prioritized on the joint basis of random forest importance, Benjamini-Hochberg-adjusted Kruskal-Wallis p < 0.05, ROC AUC ≥ 0.85 and KEGG pathway interpretability. Microbe-metabolite co-variation was quantified through Benjamini-Hochberg-adjusted Spearman correlation, yielding 108 microbe-metabolite pairs at BH-adjusted P < 0.05 (|ρ| ≥ 0.6), and canonical correlation analysis explained 73.39% of the joint cross-covariance in the first two variates. This study establishes a quantitative microbial-metabolic deterioration signature for refrigerated goose foie gras under air-sealed storage, provides a set of biomarker candidates with defined ROC performance, and identifies shifts in specific tyrosine, glutathione, purine and phospholipid pathways. The concordance between microbial succession and these pathway changes is hypothesis-generating and requires metagenomic confirmation, and these findings are presented as preliminary biochemical anchors for future targeted validation and preservation research.},
}

Animals
*Metabolome
*Food Storage/methods
*Refrigeration
*Microbiota
*Geese/microbiology
Thiobarbituric Acid Reactive Substances/analysis
*Food Microbiology
Metabolomics
RNA, Ribosomal, 16S/genetics
Colony Count, Microbial
Bacteria
Chromatography, High Pressure Liquid

@article {pmid42692847,
year = {2026},
author = {Budinská, E},
title = {Microbiome in early cancer detection - biomarker potential and limitations.},
journal = {Klinicka onkologie : casopis Ceske a Slovenske onkologicke spolecnosti},
volume = {39},
number = {Supplementum 1},
pages = {63-66},
doi = {10.48095/ccko2026S63},
pmid = {42692847},
issn = {1802-5307},
mesh = {Humans ; *Early Detection of Cancer/methods ; *Neoplasms/diagnosis/microbiology ; *Microbiota ; *Biomarkers, Tumor ; },
abstract = {BACKGROUND: Microbiome analysis in cancer research has experienced a surge in interest comparable to the introduction of microarrays for tumor gene expression profiling 25 years ago. Associative studies investigating the composition of the microbiome in stool, tumor tissue swabs and tumor biopsies of oncology patients have been conducted across most cancer types, and their number continues to grow. Screening approaches based on non-invasive or minimally invasive sampling, including the analysis of stool, saliva, urine, and buccal and rectal swabs, are from a clinical perspective among the most promising, owing in part to simpler logistics and the possibility of repeated sampling. These types of specimens are commonly used in microbiome studies, making the microbiome an attractive target for both screening and diagnostic applications.

AIM: This review aims to summarize current knowledge regarding the potential of the microbiome in the early detection of cancer, emphasizing its clinical applicability and limitations in the context of population-based prevention.},
}

Humans
*Early Detection of Cancer/methods
*Neoplasms/diagnosis/microbiology
*Microbiota
*Biomarkers, Tumor

@article {pmid42692903,
year = {2026},
author = {Hejndorf, S and Gulay, A and Zheng, C and Nielsen, RV and Rasmussen, SB and Grønlykke, L and Nørgaard, JC and Rasmussen, KK and Rafiq, S and Català-Moll, F and Ravn, HB and Lundgren, J and Murray, DD and Ilett, E},
title = {The Relationship Between the Preoperative Gut Microbiome and Systemic Inflammatory Response Syndrome After Cardiac Surgery: A Prospective Cohort Study.},
journal = {Journal of cardiothoracic and vascular anesthesia},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.jvca.2026.08.119},
pmid = {42692903},
issn = {1532-8422},
abstract = {OBJECTIVES: To determine whether preoperative intestinal microbiome characteristics are associated with the development of systemic inflammatory response syndrome (SIRS) after cardiac surgery.

DESIGN: Single-center prospective observational cohort study.

SETTING: Tertiary university hospital.

PARTICIPANTS: A total of 196 adults undergoing elective cardiac surgery with extracorporeal circulation between 2018 and 2019.

INTERVENTIONS: No microbiome-targeted intervention was performed.

MEASUREMENTS AND MAIN RESULTS: Shotgun metagenomic sequencing was used to assess microbial diversity (inverse Simpson index, gene richness, dominance), taxonomic composition, and functional potential. The primary outcome was development of SIRS within 24 hours postoperatively. Associations were evaluated using Wilcoxon rank-sum tests, χ[2] tests, and logistic regression adjusted for age and sex. Forty-four patients (22%) developed SIRS. Microbiome diversity did not differ significantly between patients with and without SIRS (median inverse Simpson index 20.4 v 19.3, p = 0.12; gene richness, p = 0.30; dominance, p = 0.61). In adjusted analyses, diversity was not associated with SIRS risk (odds ratio, 1.04; 95% confidence interval, 0.99-1.07). Descriptive analyses of taxonomic composition and functional potential similarly revealed no significant differences between SIRS and non-SIRS groups.

CONCLUSIONS: In this cohort of elective cardiac surgery patients, preoperative gut microbiome diversity, composition, and functional potential were not associated with the development of postoperative SIRS. These findings do not support a strong causal or predictive role of the presurgical gut microbiome in postoperative inflammatory responses after cardiac surgery.},
}

@article {pmid42692915,
year = {2026},
author = {Pushpakumara, BLDU and Coffey, MJ and Hudson, J and Halim, J and Chuang, S and Prentice, B and Jaffe, A and Edwards, R and Day, AS and Oliver, M and Ranganathan, S and Wainwright, C and Selvadurai, H and van Dorst, J and Ooi, CY},
title = {The cystic fibrosis gut microbial dysbiosis index (CF-GMDI): a quantitative measure of gut microbial imbalance in children with cystic fibrosis.},
journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jcf.2026.08.007},
pmid = {42692915},
issn = {1873-5010},
abstract = {BACKGROUND: Gut dysbiosis is a hallmark of cystic fibrosis (CF), typically characterised using non-specific diversity metrics and study-specific taxonomic lists, limiting comparability across studies. We aimed to develop a metagenomic, species-level CF Gut Microbial Dysbiosis Index (CF-GMDI) to standardise measurement of gut microbial imbalance in children with CF (cwCF) METHODS: CF-GMDI was derived using stool metagenomic data from the PEARL-CF study (70 cwCF; 67 healthy controls (HC); 0-6 years). Differentially abundant taxa were identified between cwCF and HC using MaAsLin2. The index was calculated as the log10 ratio of the summed relative abundances of taxa enriched in CF vs HC to those depleted in CF vs HC. Reproducibility was assessed in the independent EARTH cohort (56 cwCF; 56 HC; 0-18 years). Responsiveness to therapy was evaluated using publicly available metagenomic data from an Elexacaftor/Tezacaftor/Ivacaftor (ETI) study (39 cwCF; 6-18 years).

RESULTS: CF-GMDI was significantly higher in cwCF than HC (p < 0.001), inversely correlated with species richness (ρ = -0.74, p < 0.001), and higher in pancreatic-insufficient vs pancreatic-sufficient cwCF in the PEARL-CF cohort (p = 0.01). Key ecological and clinical associations were replicated in the EARTH cohort. In the ETI study, CF-GMDI decreased significantly at 6 and 12 months post-treatment, whereas alpha diversity remained unchanged.

CONCLUSIONS: CF-GMDI is a CF-associated metric that captures clinically relevant gut microbiome restructuring not detected by standard diversity measures in cwCF (0-18 years). It differentiates disease and pancreatic status and tracks therapeutic modulation, supporting its use as a novel endpoint in CF intervention studies.},
}

@article {pmid42693003,
year = {2026},
author = {Quesada-Ocampo, LM and Miles, T and Prieto-Torres, M and Chilvers, MI and Crandall, SG and Gent, D and Gold, KM and Heger, L and Kudenov, M and Naegele, RP and Xiang, L},
title = {Invisible Threats, Relentless Hunters: Biosurveillance of Airborne Plant Pathogens.},
journal = {Annual review of phytopathology},
volume = {64},
number = {1},
pages = {493-519},
doi = {10.1146/annurev-phyto-011325-093123},
pmid = {42693003},
issn = {1545-2107},
mesh = {*Air Microbiology ; *Plant Diseases/microbiology/prevention & control ; *Biosurveillance/methods ; Metagenomics ; *Plants/microbiology ; },
abstract = {Airborne dispersal enables plant pathogens to travel across fields, regions, and continents, fueling rapid epidemics and emerging disease threats. Biosurveillance, the systematic monitoring of airborne inoculum, offers the opportunity to detect pathogens before symptoms appear and informs timely, risk-based management. Recent advances in air sampling, molecular diagnostics, metagenomics, and imaging technologies have expanded the scale and resolution of pathogen monitoring, from single-species qPCR assays to community-level aerobiome surveys. Integration of biosurveillance data with decision-support systems, remote sensing, and artificial intelligence is transforming early-warning capabilities and providing novel insights into pathogen ecology, evolution, and fungicide resistance. Yet major challenges remain, including assay standardization, data interpretation, and translation into actionable tools for growers. This review synthesizes current approaches, highlights case studies in which biosurveillance has advanced disease management, and outlines future directions toward coordinated surveillance networks and precision agriculture applications.},
}

*Air Microbiology
*Plant Diseases/microbiology/prevention & control
*Biosurveillance/methods
Metagenomics
*Plants/microbiology