@article {pmid42554585,
year = {2026},
author = {Yang, Y and Olah, P and Salava, A and Barker, J and Lauerma, A and Andersson, B and Fyhrquist, N and Homey, B and Alenius, H},
title = {Multi-omics analyses reveal host-microbe interactions in atopic dermatitis and psoriasis.},
journal = {Journal of the European Academy of Dermatology and Venereology : JEADV},
volume = {},
number = {},
pages = {},
doi = {10.1111/jdv.70654},
pmid = {42554585},
issn = {1468-3083},
support = {261366//FP7 Health/ ; 821511//Innovative Medicines Initiative 2 Joint Undertaking/ ; },
abstract = {BACKGROUND: Atopic dermatitis (AD) and psoriasis (PSO) are chronic inflammatory skin diseases that impose substantial physical and psychological burdens. Although fungal-bacterial balance is important for skin immune homeostasis, the role of the skin mycobiome and its interaction with bacterial communities and host immunity in these diseases remains poorly understood.

OBJECTIVES: To characterize alterations in the skin mycobiome and its interactions with bacterial communities and host immune responses in AD and PSO.

METHODS: Adult patients with chronic AD, plaque-type PSO and healthy volunteers were included in this study. Skin microbiota samples and biopsies were collected from lesional and non-lesional skin areas, including the posterior thigh for AD and the lower back for PSO. Whole-metagenome shotgun sequencing was used to profile microbial communities. SparCC was used to construct fungal-bacterial co-occurrence networks, and integration of host transcriptomic and microbial features was performed using O2PLS.

RESULTS: Both AD and PSO showed disease-associated restructuring of Malassezia species and reduced fungal-bacterial ecological connectivity in lesional skin. In AD, Malassezia arunalokei was inversely associated with Staphylococcus aureus and linked to antimicrobial peptide-centred host gene modules enriched for IL-17 signalling. Its abundance decreased with increasing disease severity and inversely correlated with inflammatory immune cell signatures. In PSO, altered Malassezia composition was associated with IL-17-driven transcriptional programmes and lipid metabolic pathways, suggesting interactions between fungal imbalance and inflammatory-metabolic processes.

CONCLUSIONS: Our findings expand current models of skin dysbiosis beyond bacteria and suggest that disrupted fungal-bacterial interactions are linked to immune activation in AD and PSO and, in AD, to disease severity. Although further validation is required, skin microbiome features may provide clinically relevant information for disease monitoring, patient stratification and future microbiome-informed therapeutic strategies. Our study lays the groundwork for microbiome modulation as a potential therapeutic strategy for AD and PSO.},
}

@article {pmid42554630,
year = {2026},
author = {Tandon, A and Bais, AK and Shrinet, J and Tripathi, V and Gupta, D},
title = {Effect of alcohol and smoking on methamphetamine users' oral microbiome and metabolome.},
journal = {The American journal of drug and alcohol abuse},
volume = {},
number = {},
pages = {1-13},
doi = {10.1080/00952990.2026.2697752},
pmid = {42554630},
issn = {1097-9891},
abstract = {Background: The oral microbiome comprises the microbial communities inhabiting the oral cavity, whereas the oral metabolome reflects the small molecules generated by host and microbial metabolic activity. These systems may provide insight into substance-related physiological disruption, including altered inflammation, immune signaling, and host - microbial interactions. Although the individual effects of methamphetamine, alcohol, and smoking have been explored, their combined impact on these systems remains largely unexplored.Objectives: To investigate the metabolic and microbiome alterations associated with chronic methamphetamine use in individuals with alcohol and tobacco use.Methods: High-throughput metabolomic and microbiome datasets from methamphetamine users (Males:168, Females: 50), stratified by self-reported tobacco smoking and alcohol use, were analyzed using integrative bioinformatics approaches, including multivariate and pathway enrichment analyses, to identify dysregulated metabolic pathways and microbial alterations across defined subgroups.Results: The study revealed significant upregulation in metabolites like prostaglandin E2 (log-2-fold-change: 2.63, Cohen's D: |~0.881|, p-val: 7.1 × 10[-10]) and glutamylisoleucine (log-2-fold-change: 1.42, Cohen's D: |~0.88|, p-val: 2.5 × 10[-2]). Microbes such as Bacteroides (log-2-fold-change: -4.91, Cohen's D: |~1.95|, p-val: 1.3 × 10[-4]) and Brachymonas (log-2-fold-change: -2.47, Cohen's D: |~1.09|, p-val: 5.8 × 10[-3]) were significantly downregulated. This suggests that long-term concurrent methamphetamine use, alcohol consumption, and smoking are associated with alterations in microbial and metabolic pathways related to oxidative stress, glutathione metabolism, and neuroactive signaling.Conclusions: The oral microbiome and metabolomic profiles may serve as accessible indicators of substance-related biological disruption. They may also help identify clinically relevant targets for monitoring risk, guiding personalized interventions, and developing informed strategies to support recovery.},
}

@article {pmid42555106,
year = {2026},
author = {Luo, Z and Liu, Y and Wu, H and Xiao, Y and Li, Y and Liu, M and Li, C and Zhu, D and Jin, LN and Dong, T and Yan, W},
title = {Zoo gut plastispheres enable pathogen escape and adaptation.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag207},
pmid = {42555106},
issn = {1751-7370},
abstract = {In zoos, intensive human contact and artificial feeding may create pathways for microplastic (MP) ingestion and gut colonization. We hypothesized that ingested MPs form intestinal plastispheres with elevated pathogenic potential and enhanced environmental persistence. To test this, we surveyed feces from 15 zoo-dwelling species and coupled particle characterization, feces-derived intestinal simulations, metagenomic sequencing, and a subsequent water-exposure experiment. Zoo feces contained more abundant MPs than reported for wild counterparts, with fragments predominating and polyethylene terephthalate (PET)/polystyrene (PS) dominating polymer profiles. MP burdens tracked human-animal interaction patterns, with human-fed species (e.g., Tiger, Elephant) carrying the highest loads (88-212 items/g). MPs supported dense biofilms whose composition diverged from bulk gut communities, exhibiting greater compositional variability and substrate-specific assembly. Metagenomic analyses revealed coordinated enrichment of potentially pathogenic taxa, virulence factor genes (VFGs), and antibiotic resistance genes (ARGs), with ARG profiles dominated by efflux- and inactivation-related mechanisms and tightly associated with mobile genetic elements. Elevated Type II/III/IV/VI secretion systems and effector delivery-related VFGs occurred within extracellular polymeric substance-rich biofilms, suggesting enhanced potential for ARG retention and horizontal gene transfer. During the 35-day aquatic exposure, MP-associated communities persisted longer than non-plastic particle-associated communities and free gut microbiota, suggesting that plastic-specific properties promote microbial persistence. PET/PS plastispheres showed the slowest declines in bacterial activity and favored the persistence of Enterococcus, Enterobacter, and Clostridium. Overall, intestinal MPs in zoo animals may select, enrich, and export high-risk microbiomes, highlighting the need for MP mitigation and evidence-based management of zoos and adjacent ecosystems.},
}

@article {pmid42555404,
year = {2026},
author = {Hosen, MA and Rahman, T and Rahatuzzaman, and Kabir, RB and Ahsan, CR and Rahman, M and Yasmin, M and Jubair, M},
title = {Uncovering the Hidden Diversity and Antimicrobial Resistance of Uropathogens in a Tertiary-Care Hospital in Bangladesh.},
journal = {International journal of microbiology},
volume = {2026},
number = {},
pages = {8327078},
pmid = {42555404},
issn = {1687-918X},
abstract = {Urinary tract infections (UTIs) are among the most common bacterial infections worldwide; however, their diagnosis in low- and middle-income countries often relies on conventional culture and biochemical methods with limited sensitivity. This study evaluated the limitations of routine diagnostic approaches and explored the microbial diversity and antimicrobial resistance (AMR) profiles of uropathogens in a tertiary-care hospital in Bangladesh using integrated culture-based and molecular methods. Among 30 patient urine samples collected in 2025, 10 were selected for detailed analysis due to funding and resource limitations; therefore, the findings should be interpreted as exploratory and may be subject to selection bias. Of these 10 samples, routine hospital diagnostics identified only eight isolates, whereas extended biochemical analysis detected 29 isolates, indicating substantial underestimation of microbial diversity in standard practice. Antibiotic susceptibility testing revealed a high prevalence of multidrug resistance, with 83% and 80% of isolates resistant to ampicillin and clindamycin, respectively. In contrast, nitrofurantoin and fosfomycin retained effectiveness against most isolates, supporting their continued clinical utility. 16S rRNA gene sequencing further revealed complex and heterogeneous microbial communities, with several samples dominated by Escherichia-Shigella, whereas others exhibited polymicrobial profiles including commensal and opportunistic genera. Despite taxonomic variability, microbial diversity did not differ significantly between inpatient and outpatient groups. Functional pathway prediction demonstrated a largely conserved metabolic profile across samples, including pathways associated with virulence, iron acquisition, and AMR. Overall, this study demonstrates that conventional diagnostic methods substantially underestimate uropathogen diversity and may contribute to misdiagnosis and inappropriate antibiotic use. Integrating molecular approaches into routine clinical workflows could improve pathogen detection, enhance AMR surveillance, and support more effective management of UTIs in Bangladesh and similar resource-limited settings.},
}

@article {pmid42555569,
year = {2026},
author = {Vitry, G and Angdisen, J and Arriaga, P and Irgen-Gioro, S and Sawant, MA and Vuong, DC and Ilhardt, P and Fehr, J and Cwikla, B and Ponnaiya, B and Inman, JL and Mao, JH and Snijders, AM and Hamid, S and Caballero-Lima, D and Garty, G and Apfeldorf, K and Laiakis, EC},
title = {Monitoring radiation exposure through skin swab multi-omic profiling.},
journal = {PloS one},
volume = {21},
number = {8},
pages = {e0354734},
pmid = {42555569},
issn = {1932-6203},
mesh = {Humans ; *Skin/radiation effects/metabolism/microbiology ; Animals ; Multiomics ; Mice ; Metabolomics/methods ; *Radiation Exposure/analysis ; Metabolome/radiation effects ; Lipidomics ; Skin Microbiome ; },
abstract = {Exposure to ionizing radiation poses major health risks across medical, occupational, and spaceflight settings, driving the need for rapid, non-invasive biodosimetry tools. As the body's most accessible organ and the most frequent site of radiation injury, the skin represents a promising interface for monitoring exposure. Using colonized human skin equivalents (coHSE; 0 Gy n = 8, 1 Gy n = 6, 4 Gy n = 6) and mice (n = 6/group) models, we performed multi-omic profiling, integrating metabolomics, lipidomics, and metagenomics, on skin swab samples collected after exposure to 0, 1, or 4 Gy of x-rays. We identified two distinct metabolite panels: one discriminating irradiated from non-irradiated skin, and another distinguishing dose-specific response. These panels included conserved radiation-responsive metabolites (e.g., uric acid, xanthine, taurine) and skin-specific markers associated with barrier integrity (e.g., proline, arginine). Diacylglycerol network enrichment and shifts in radioprotective microbial taxa, including Lachnospiraceae and Lactobacillales, further supported a repair-driven molecular response. These data support the feasibility of skin swab signatures for non-invasive exposure classification, providing a molecular and microbial framework for skin based monitoring measure development and motivating validation in human cohorts for real-world biodosimetry.},
}

Humans
*Skin/radiation effects/metabolism/microbiology
Animals
Multiomics
Mice
Metabolomics/methods
*Radiation Exposure/analysis
Metabolome/radiation effects
Lipidomics
Skin Microbiome

@article {pmid42556262,
year = {2026},
author = {Dai, W and Yang, F and Chen, W and Liu, C and Henawy, AR and Liu, X and Huang, F and Cai, M and Zheng, L and Yu, Z and Gong, Y and van Huis, A and Zhang, J and Cheng, W},
title = {Paenibacillus polymyxa drives root fatty acyl metabolites-rhizosphere Pseudomonas abundance interaction to suppress root-knot nematode disease in tomato.},
journal = {Microbiological research},
volume = {312},
number = {},
pages = {128662},
doi = {10.1016/j.micres.2026.128662},
pmid = {42556262},
issn = {1618-0623},
abstract = {Root-knot nematodes (RKNs) pose a severe threat to global agricultural production, highlighting the urgent need for effective biocontrol agents. However, the mechanisms by which biocontrol agents suppress RKNs in complex soil environments remain poorly understood, which hinders the development and practical application of these agents. In the present study, the application of Paenibacillus polymyxa KM2501-1 significantly reduced RKN disease, with a control efficacy of 69.89%. Metabolomics analysis revealed that the biocontrol agent P. polymyxa altered the composition of tomato root exudates, leading to the identification of a key fatty acyl metabolite 8-methylnon-6-enoic acid. Specifically, P. polymyxa increased the abundance of 8-methylnon-6-enoic acid, which exhibited repellent activity against RKNs in vitro and suppressed RKN infection in situ. Metagenomic analysis further demonstrated that P. polymyxa reshaped the tomato rhizosphere microbial community and promoted the enrichment of Pseudomonas putida, particularly its representative strains PR035 and PR036. Both strains exhibited significant biocontrol efficacy against Meloidogyne incognita. A significant positive correlation was observed between the levels of key metabolite 8-methylnon-6-enoic acid and the abundance of P. putida, and their combined application exhibited effective control against M. incognita. Overall, this study demonstrates that the suppression of RKNs by P. polymyxa is associated with triggering the exudation of fatty acyl metabolites from tomato roots and enriching rhizosphere Pseudomonas populations. These findings provide valuable insights into the interplay between root metabolites and the rhizosphere microbiome in mediating synergistic plant disease control, offering a theoretical basis for the development of next-generation microbial nematicides.},
}

@article {pmid42556698,
year = {2026},
author = {Li, E and Xie, X and Zhang, Y and Yan, L and Wang, Y},
title = {Sediment heterogeneity drives divergent arsenic transformation pathways through organic matter-microbial coupling in aquifers.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {408},
number = {},
pages = {128911},
doi = {10.1016/j.envpol.2026.128911},
pmid = {42556698},
issn = {1873-6424},
abstract = {Arsenic (As) speciation in groundwater is controlled not only by aqueous redox chemistry but also by sedimentary matrices that preserve organic matter, structure metabolism, and regulate Fe-S-As coupling. However, how sedimentary organic matter (SOM) and microbial functional differentiation jointly direct arsenic toward thioarsenate formation and methylation remains insufficiently constrained. This study combined sedimentological characterization, X-ray diffraction mineralogical analysis, Fe/As sequential extraction, excitation-emission matrix fluorescence spectroscopy, FT-ICR-MS molecular characterization of SOM, and metagenomic sequencing across three hydrogeochemical zones. Sediments shifted from coarse-grained alluvial deposits in the low-As recharge zone (ALZ) to fine-grained, organic-rich lacustrine sediments in the thioarsenate-enriched zone (HGD) and the methylation zone (SHX), with clay enrichment in HGD and carbonate enrichment in SHX. Along this gradient, ALZ showed open recharge conditions with labile SOM and dynamic redox environments, whereas As in HGD and SHX shifted from surface-bound forms to poorly crystalline and crystalline Fe-associated fractions, alongside SOM evolution toward humified, aromatic, highly unsaturated, and sulfur-containing molecules. The HGD exhibited enrichment of polyphenols and CHOS/CHONS compounds, providing substrates and redox-active ligands for Fe-S-As coupling. Metagenomics revealed zone-specific functional differentiation. The ALZ was dominated by Proteobacteria supporting heterotrophic metabolism, sulfur oxidation, and arsenic resistance. The HGD showed enhanced sat-aprAB-dsrAB pathways and weakened soxABCDXYZ-mediated sulfur oxidation, favoring reduced sulfur accumulation, Fe-As mineral sulfidation, and thioarsenate formation. The SHX displayed enrichment of arsC and arsenic resistance/efflux genes, supporting As(V) reduction and methylated As transformation. These results demonstrate that sediment heterogeneity governs As speciation and migration through coupled SOM evolution and microbial functional reorganization.},
}

@article {pmid42557068,
year = {2026},
author = {, and , },
title = {[Chinese expert consensus on the diagnosis and treatment of pneumoconiosis complicated with tuberculosis].},
journal = {Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and respiratory diseases},
volume = {49},
number = {8},
pages = {821-833},
doi = {10.3760/cma.j.cn112147-20260512-00273},
pmid = {42557068},
issn = {1001-0939},
support = {NHC202309//Open Project of NHC Key Laboratory of Pneumoconiosis/ ; 2022YFC2302900//National Key Research and Development Program/ ; },
mesh = {Humans ; *Pneumoconiosis/diagnosis/complications/therapy ; *Tuberculosis, Pulmonary/diagnosis/complications/therapy ; China ; },
abstract = {Pneumoconiosis complicated with pulmonary tuberculosis is characterized by high prevalence and disability rates, as well as difficulty in early diagnosis, constituting a serious public health problem. The Chinese Society of Tuberculosis (Chinese Medical Association) and the Society of Labor Hygiene and Occupational Diseases (Chinese Preventive Medicine Association) organized multidisciplinary experts in respiratory diseases, occupational diseases, tuberculosis and other related fields to formulate the Chinese expert consensus on the diagnosis and treatment of pneumoconiosis complicated with tuberculosis. This consensus aims to enhance professional practitioners' understanding of the disease, improve the capacity for early clinical diagnosis, and further advance the prevention and treatment of pneumoconiosis complicated with pulmonary tuberculosis in China. It summarizes 12 key clinical issues and proposes 13 targeted recommendations to address difficulties and misconceptions in clinical practice. This consensus was registered on the International Practice Guidelines Registry Platform (PREPARE-2024CN271). It aims to enhance the standardized diagnosis and treatment of pneumoconiosis complicated by pulmonary tuberculosis, improve patient outcomes, and provide practical guidance for the prevention and control of occupational and infectious diseases in China. The main recommendations are as follows.Recommendation 1: Clinicians and pathologists are advised to pay attention to the mixed pathological features of pneumoconiosis complicated with pulmonary tuberculosis. For patients with pneumoconiosis presenting atypical imaging manifestations or poor response to conventional treatment, pathological specimens should be actively obtained to confirm the diagnosis. Combined use of acid-fast staining, Mycobacterium tuberculosis culture or molecular pathological detection is recommended to increase the detection rate (2C).Recommendation 2: When performing chest CT examinations and dynamic follow-up for pneumoconiosis patients, clinicians and radiologists should focus on multifocal and polymorphic lesions, as well as short-term imaging changes suggestive of active tuberculosis (2C).Recommendation 3: For patients with suspected pulmonary tuberculosis complicated with pneumoconiosis: (1) Be aware that sputum bacteriological tests may yield false-negative results due to dust interference. Repeated sampling or combined detection methods are recommended, including bacteriological and molecular tests on bronchoalveolar lavage fluid (BALF) obtained via bronchoscopy. Results of immunological assays such as the interferon-γ release assay (IGRA) and tuberculin skin test (TST)shall also be combined for comprehensive judgment. (2) In cases with atypical imaging findings and clinical symptoms, bronchoscopy-guided pathological sampling (e.g., EBUS-GS [endobronchial ultrasound with guide sheath], ENB [electromagnetic navigation bronchoscopy]) is prioritized. When microbiological evidence is insufficient, percutaneous lung biopsy or pleural biopsy (for patients with pleural effusion) is suggested to clarify the diagnosis (2B).Recommendation 4: The diagnosis of pneumoconiosis complicated with pulmonary tuberculosis shall follow the integrated diagnostic principle. Provided that patients meet the national diagnostic criteria for pneumoconiosis and pulmonary tuberculosis respectively, a comprehensive assessment shall be conducted combining occupational exposure history, dynamic imaging changes and laboratory results. Patients shall be stratified for managementaccording to the activity of tuberculosis (2C).Recommendation 5: For differential diagnosis between pneumoconiosis complicated with pulmonary tuberculosis and non-tuberculous mycobacterial (NTM) lung disease: (1) NTM lung disease commonly involves the apical and anterior segments of the upper lobes, the right middle lobe and the lingular segment of the left upper lobe. Typical imaging manifestations include a combination of centrilobular nodules and bronchiectasis. (2) Multiple thin-walled cavities are frequently seen in silicosis complicated with NTM lung disease. (3) Pathologically, NTM lesions are dominated by epithelioid granulomas with inconspicuous caseous necrosis. (4) Definitive diagnosis relies on mycobacterial culture and species identification, complying with combined clinical, imaging and microbiological criteria (2C).Recommendation 6: For patients with pneumoconiosis complicated with pulmonary tuberculosis who present progressively enlarged cavities or newly developed cavities accompanied by aggravated symptoms after anti-tuberculosis treatment, radiologists shall evaluate imaging signs of pulmonary aspergillosis, such as the early halo sign and the late air crescent sign within cavities (2C).Recommendation 7: For patients with suspected pneumoconiosis complicated with pulmonary aspergillosis: (1) Bronchoscopy is performed to collect BALF or tissue specimens for fungal culture and pathological examination (gold standard). (2) Conduct BALF galactomannan (GM) test, metagenomic next-generation sequencing (mNGS) or other DNA detection assays. (3) Detect serum specific antibodies against Aspergillus fumigatus (e.g., IgE-m3, IgM) (1A).Recommendation 8: For patients with pneumoconiosis complicated with drug-susceptible pulmonary tuberculosis: (1) Adopt the standard first-line four-drug anti-tuberculosis regimen. (2) Ensure a sufficient treatment course (generally ≥6-8 months). (3) Extend the treatment course to≥9-12 months for patients with severe lesions or concomitant tracheal, pleural or extrapulmonary tuberculosis, so as to improve clinical outcomes and reduce recurrence (2A).Recommendation 9: For patients receiving concurrent treatment for pneumoconiosis (including tetrandrine, nintedanib, pirfenidone, glucocorticoids, bronchodilators, etc.) and rifampicin-containing anti-tuberculosis regimens: (1) Be aware that rifampicin, a potent hepatic enzyme inducer, may accelerate the metabolism of concomitant drugs such as glucocorticoids and nintedanib and reduce their efficacy. (2) Adjust the dose of affected drugs accordingly when rifampicin is initiated or discontinued (1B).Recommendation 10: Extracorporeal membrane oxygenation (ECMO) may be used as a bridge to lung transplantation only for end-stage pneumoconiosis patients complicated with pulmonary tuberculosis awaiting transplantation (2D).Recommendation 11: For end-stage patients with pneumoconiosis complicated with pulmonary tuberculosis who have received adequate and standard anti-tuberculosis therapy, the feasibility of lung transplantation shall be evaluated. Pre-transplant precautions: (1) Ensure complete control of active tuberculosis. (2) Optimize the anti-tuberculosis regimen (e.g., replace rifampicin with rifabutin) to maintain the effective concentration of immunosuppressants (2D).Recommendation 12: For patients with severe, end-stage pneumoconiosis complicated with pulmonary tuberculosis who no longer benefit from active treatment, palliative care and hospice care shall be initiated. Clinicians and medical teams shall communicate fully with patients and their families about the condition, prognosis, treatment options and medical burden. The core goals are to relieve symptoms, alleviate suffering and improve quality of life (2D).Recommendation 13: For patients with pneumoconiosis complicated with tuberculosis who meet the indications for surgical or interventional therapy, a multidisciplinary team shall conduct joint decision-making and implement treatment in a timely manner after full assessment of pulmonary function, nutritional status and surgical risks. Surgical treatment is mainly indicated for patients with drug-resistant tuberculosis with localized lesions, persistent cavitary lesions with ongoing mycobacterial excretion, destroyed lung, massive hemoptysis unresponsive to medical treatment, tuberculous empyema and other critical conditions. Interventional therapy can be applied for emergency treatment of massive hemoptysis, as well as palliative treatment for pulmonary artery stenosis secondary to tuberculosis or pneumoconiosis (2C).},
}

Humans
*Pneumoconiosis/diagnosis/complications/therapy
*Tuberculosis, Pulmonary/diagnosis/complications/therapy
China

@article {pmid42557256,
year = {2026},
author = {Gicquel, M and Planillo, A and Heitlinger, E and Forslund-Startceva, SK and Kramer-Schadt, S and Ferreira, SCM and Jarquín-Díaz, VH},
title = {Farming practices exert selection pressures on the resistome of natural populations of house mice.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42557256},
issn = {2041-1723},
support = {FO1279/6-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; HE7320/5-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; KR4266/4-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; F01KI1909A//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; 01KI2404B//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; },
mesh = {Animals ; Mice/microbiology ; *Selection, Genetic ; Anti-Bacterial Agents/pharmacology ; Metagenome ; *Gastrointestinal Microbiome/genetics ; Livestock/microbiology ; Genes, Bacterial ; *Agriculture ; Germany ; Swine ; },
abstract = {The factors maintaining antimicrobial resistance genes (ARGs) in non-domesticated animal microbiomes remain unclear for species inhabiting human-dominated or less human-impacted landscapes. We analysed 875 gut metagenomes from natural populations of house mice (Mus musculus) on German farms between 2016 and 2022 to identify environmental and host determinants of ARG occurrence. Using joint species distribution models, we quantified the influence of landscape, climate and mouse associated characteristics on the occurrence of individual ARGs and on trait dependence among genes. Environmental variables and livestock farming intensity explained 27% of ARG variation, whereas host characteristics accounted for 8%. Analysis of ARG traits revealed that agricultural land use and exposure to livestock increased the occurrence of potentially mobile ARGs. Pig density was strongly associated with an integron-encoded sulfonamide resistance gene (sul1) and genes conferring tetracycline (tet) and beta-lactam resistance (cblA-1) (posterior probability 0.75). Consistently, mouse resistomes have a distinctive resistome, but share more than 50% of ARGs with livestock manure, including widespread genes and those promoted in livestock. Here, we show that landscape conditions, particularly farming intensity, shape the distribution of specific ARGs and potentially mobile ARGs in house mice microbiomes.},
}

Animals
Mice/microbiology
*Selection, Genetic
Anti-Bacterial Agents/pharmacology
Metagenome
*Gastrointestinal Microbiome/genetics
Livestock/microbiology
Genes, Bacterial
*Agriculture
Germany
Swine

@article {pmid42557544,
year = {2026},
author = {Martínez-Cuesta, R and Craighero, A and Walch, S and Helmreich, B and Schloter, M and Schulz, S},
title = {Urban green roofs host intrinsic resistomes shaped by management but not dominated by pathogenic resistance.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {42557544},
issn = {1471-2180},
mesh = {Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics/drug effects/classification/isolation & purification ; Cities ; *Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; Metagenomics/methods ; Plasmids/genetics ; Biodiversity ; },
abstract = {BACKGROUND: Urban green roofs are increasingly introduced to enhance urban biodiversity and ecosystem services, yet their role in shaping antimicrobial resistance in cities remains unclear. Using long-read metagenomic sequencing, we characterized antimicrobial resistance genes (ARGs) across an experimental extensive green roof system with plots under four different management regimes specifically designed to test the influence of vegetation and organic amendments, as green waste, which although widely used to improve substrate quality, has been flagged as a potential ARG source.

RESULTS: We detected 62 ARGs across the four management regimes, which were dominated by target-modification and mixed mechanisms conferring resistance to naturally occurring antibiotics such as bacitracin (bacA) and rifamycin (arr, rox, rph), rather than efflux-based multidrug resistance, which is typically co-selected by anthropogenic pollutants. The ARGs were mainly chromosomally encoded, with only two ARGs located on plasmids, and associated with non-pathogenic environmental taxa. The management regime had a significant effect on ARG richness, ARG composition and plasmid abundance, but not on average genome size-normalized ARG abundance. We also detected aph3-II and tlmA as enriched in the unamended samples, which were carried by oligotrophic bacteria, pointing towards microbial competition in a nutrient-limited environment.

CONCLUSIONS: Overall, our findings indicate that green roof management supports a substrate resistome driven by ecological constraints rather than clinical threats. However, further research is required to evaluate potential risks and support the safe integration of green roofs within a One Health framework.},
}

Anti-Bacterial Agents/pharmacology
*Bacteria/genetics/drug effects/classification/isolation & purification
Cities
*Drug Resistance, Bacterial/genetics
Genes, Bacterial
Metagenomics/methods
Plasmids/genetics
Biodiversity

@article {pmid42557545,
year = {2026},
author = {Rodríguez Del Río, Á and Cui, Y and Mansour, I and Rillig, MC},
title = {Genomic characteristics and geographical distribution of uncultivated soil prokaryotes.},
journal = {BMC genomics},
volume = {27},
number = {1},
pages = {},
pmid = {42557545},
issn = {1471-2164},
mesh = {*Soil Microbiology ; Metagenomics ; Metagenome ; *Bacteria/genetics/classification ; *Genome, Bacterial ; *Genomics ; Phylogeography ; Phylogeny ; *Prokaryotic Cells ; *Archaea/genetics/classification ; },
abstract = {Most soil prokaryotic species remain uncultivated, limiting our understanding of the terrestrial microbiome. Metagenomic sequencing, and particularly the study of metagenome-assembled genomes (MAGs), represents an unprecedented opportunity to characterize the genomic features and biogeography of uncultivated prokaryotic taxa at the large scale. Here, we analyze 40,039 genomic bins from cultivated and uncultivated soil taxa within the SMAG catalog, and examine the occurrence of uncultivated prokaryotes in 9,012 metagenomic samples from the Sandpiper resource. Compared to genera with cultivated representatives, uncultivated soil prokaryotes show smaller genomes, lower G + C content, tendency to acidophilic, non-alkaline, thermophilic and host-associated lifestyles, and slower growth rates, with the latter having the highest predictive power for cultivation status. Uncultivated soil microbes also show unique gene repertoires, characterized by a depletion of biosynthetic and motility genes. We also show that completely uncultivated genera are more abundant in tropical and arctic soils, indicating substantial hidden diversity in these regions. Our work emphasizes that current cultivation efforts systematically fail to capture a particular fraction of soil prokaryotic diversity, and provides guidelines for future cultivation strategies.},
}

*Soil Microbiology
Metagenomics
Metagenome
*Bacteria/genetics/classification
*Genome, Bacterial
*Genomics
Phylogeography
Phylogeny
*Prokaryotic Cells
*Archaea/genetics/classification

@article {pmid42557906,
year = {2026},
author = {Teklay, YT},
title = {Integrative Bioinformatics Approaches in Environmental Biotechnology: A Review.},
journal = {TheScientificWorldJournal},
volume = {2026},
number = {1},
pages = {e3495506},
pmid = {42557906},
issn = {1537-744X},
mesh = {*Computational Biology/methods ; *Biotechnology/methods ; Multiomics ; Genomics ; Biodegradation, Environmental ; },
abstract = {Environmental biotechnology increasingly relies on bioinformatics to address global challenges in pollution control or degradation, biodiversity conservation, and sustainable resource management. By integrating genomics, computational tools, and artificial intelligence, bioinformatics enables the analysis of complex biological datasets, such as metagenomes and environmental DNA (deoxyribonucleic acid), to uncover microbial diversity, pollutant degradation pathways, and ecological resilience. High-throughput sequencing technologies and multiomics integration provide novel insights into microbial communities and their functional roles in bioremediation and ecosystem monitoring. Predictive modeling further enhances our ability to simulate microbial behavior in contaminated environments and assess the long-term impacts of biotechnological interventions. Despite increased progress, challenges remain in managing large-scale data, fostering interdisciplinary collaboration, and developing user-friendly bioinformatics platforms. Future directions emphasize the application of machine learning, sustainable resource management, and collaborative frameworks to bridge bioinformatics and environmental sciences. Unlike traditional descriptive reviews, this work provides a critical evaluation of the functional gaps between genomic potential and in situ microbial activity. It offers a novel synthesis of how multiomics integration and predictive modeling can move beyond species cataloging toward a more robust, evidence-based framework for environmental sustainability.},
}

*Computational Biology/methods
*Biotechnology/methods
Multiomics
Genomics
Biodegradation, Environmental

@article {pmid42558149,
year = {2026},
author = {Ding, R and Qi, F and Dai, Q and Li, K and Zhang, Y},
title = {Multi-omics analysis identifies a hepatocyte-associated signature in alcohol-related liver injury.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1844110},
pmid = {42558149},
issn = {1664-3224},
mesh = {Animals ; *Hepatocytes/metabolism ; Multiomics ; Humans ; *Liver Diseases, Alcoholic/metabolism/genetics/etiology ; Mice ; Male ; Ethanol/adverse effects ; Metabolomics/methods ; Transcriptome ; Feces/chemistry/microbiology ; Gene Expression Profiling ; Gastrointestinal Microbiome ; Disease Models, Animal ; Liver/metabolism ; Metabolome ; Mice, Inbred C57BL ; Metagenomics ; },
abstract = {Alcohol-related liver disease (ALD) is a major cause of liver-related morbidity and mortality worldwide, yet the associations linking alcohol-induced gut microbial alterations to metabolic remodeling and hepatocyte dysfunction remain incompletely understood. Here, we applied an integrative multi-omics strategy combining untargeted fecal metabolomics, shotgun metagenomics, mouse liver bulk RNA sequencing, and reanalysis of publicly available human hepatic single-cell and bulk transcriptomic datasets to characterize alcohol exposure-associated gut-liver immunometabolic features. In a mouse model of acute ethanol-induced liver injury, fecal metabolomic and metagenomic profiling revealed marked alterations in microbial functional potential and fecal metabolic composition, identifying six convergent metabolic pathways across fecal multi-omics layers, including nucleotide metabolism, the pentose phosphate pathway, histidine metabolism, glycerophospholipid metabolism, glycine/serine/threonine metabolism, and the phosphotransferase system. Reanalysis of human ALD single-cell transcriptomes showed hepatocyte-enriched activity patterns for several corresponding pathways, suggesting potential pathway-level associations between fecal metabolic alterations and hepatic transcriptional responses. Integrative transcriptomic analysis further identified a ten-gene hepatocyte-associated signature, comprising LRG1, ORM1, ORM2, TAT, HP, FGB, FGG, ITIH3, NNMT, and AGT, which was associated with pathway activity and showed consistent upregulation across acute ethanol-induced liver injury and human ALD/AH transcriptomic datasets. In an external human cohort, this signature stratified patients into exploratory molecular subgroups with distinct metabolic pathway activities and clinical outcome distributions. Collectively, these findings provide a hypothesis-generating multi-omics framework for investigating alcohol-related liver injury and support further validation in chronic ethanol exposure models and functional studies.},
}

Animals
*Hepatocytes/metabolism
Multiomics
Humans
*Liver Diseases, Alcoholic/metabolism/genetics/etiology
Mice
Male
Ethanol/adverse effects
Metabolomics/methods
Transcriptome
Feces/chemistry/microbiology
Gene Expression Profiling
Gastrointestinal Microbiome
Disease Models, Animal
Liver/metabolism
Metabolome
Mice, Inbred C57BL
Metagenomics

@article {pmid42558191,
year = {2026},
author = {Wu, D and Wang, X and Li, T and Wang, X},
title = {Persistent CD4[+] lymphopenia is associated with recurrent Nocardia farcinica infection and acquired resistance in an AIDS patient: a case report with immunological warning.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1894622},
pmid = {42558191},
issn = {1664-3224},
mesh = {Humans ; Male ; *Nocardia Infections/immunology/drug therapy/diagnosis/microbiology ; Adult ; *Nocardia/drug effects/immunology ; Recurrence ; Anti-Bacterial Agents/therapeutic use ; *Acquired Immunodeficiency Syndrome/immunology/complications/drug therapy ; CD4 Lymphocyte Count ; *Drug Resistance, Bacterial ; *AIDS-Related Opportunistic Infections/immunology/drug therapy/microbiology ; *CD4-Positive T-Lymphocytes/immunology ; Trimethoprim, Sulfamethoxazole Drug Combination/therapeutic use ; },
abstract = {After severe depletion of CD4 T cells in AIDS patients, they are not only prone to a first-time Nocardia infection, but also, even if cured, unable to form protective immune memory, leaving them susceptible to reinfection with the same pathogen. More seriously, in the absence of immune surveillance, irregular drug use can accelerate the selection of drug-resistant strains. A 32-year-old man with AIDS and persistent CD4+ count below 100 cells/μL for over three years (nadir 2 cells/μL) developed right lower lobe pneumonia caused by Nocardia farcinica four years before the current admission, which was cured with a TMP-SMX-containing regimen. The isolate was sensitive to trimethoprim-sulfamethoxazole (TMP-SMX), and the lesion nearly resolved after treatment. He was prescribed long-term TMP-SMX prophylaxis at discharge but stopped taking it on his own. One year before the current admission, he received sulfadiazine plus pyrimethamine for clinically diagnosed cerebral toxoplasmosis, but his adherence was poor and irregular. On current admission (day 1), he was readmitted with high fever and sepsis. Chest CT showed multiple cavities in the left lower lobe. Blood cultures flagged positive at 25 hours and were identified as Nocardia farcinica. The microbiologist reviewed his old records, found the previous nocardial history, and recommended bronchoalveolar lavage (BAL). BAL metagenomic next-generation sequencing again identified Nocardia farcinica, but susceptibility testing now showed resistance to TMP-SMX (MIC ≥8/152). He improved after switching to imipenem plus amikacin. He received intravenous imipenem plus amikacin for 14 days, followed by oral linezolid for 6 weeks. At the last follow-up (approximately one year after discharge), his CD4[+] had risen to only 11 cells/μL, and he had no further nocardial infection. This case shows that when CD4[+] stays below 100 for a long time, even a first nocardial infection can be cured but may leave insufficient immune memory, rendering the patient susceptible to subsequent infection. The distinction between true reinfection and late relapse could not be definitively established in the absence of strain-level homology data. Irregular, sub-therapeutic sulfonamide exposure, combined with a non-functional immune system, can select for resistant strains.},
}

Humans
Male
*Nocardia Infections/immunology/drug therapy/diagnosis/microbiology
Adult
*Nocardia/drug effects/immunology
Recurrence
Anti-Bacterial Agents/therapeutic use
*Acquired Immunodeficiency Syndrome/immunology/complications/drug therapy
CD4 Lymphocyte Count
*Drug Resistance, Bacterial
*AIDS-Related Opportunistic Infections/immunology/drug therapy/microbiology
*CD4-Positive T-Lymphocytes/immunology
Trimethoprim, Sulfamethoxazole Drug Combination/therapeutic use

@article {pmid42558207,
year = {2026},
author = {Yang, Y and Ren, L and Zhang, Y and Wang, X and Shang, J and Zhang, L},
title = {Microbiota in cholestatic diseases: crosstalk among bile composition, the biliary microbiome, and host immunity.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1884030},
pmid = {42558207},
issn = {1664-3224},
mesh = {Humans ; Animals ; *Microbiota/immunology ; Bile Acids and Salts/metabolism ; *Cholestasis/microbiology/immunology/metabolism ; *Bile/metabolism/immunology/microbiology ; *Gastrointestinal Microbiome/immunology ; },
abstract = {Cholestatic liver diseases are a heterogeneous group of hepatobiliary disorders caused by impaired bile formation, secretion, or excretion, leading to hepatocyte injury, biliary inflammation, fibrosis, and eventually cirrhosis. Traditional studies have largely focused on isolated mechanisms, including bile acid toxicity, immune dysregulation, and genetic susceptibility. However, recent advances in metagenomics, metabolomics, and immunology have highlighted the critical role of the gut and biliary microbiota in disease pathogenesis. This review proposes the core concept of a "tripartite interplay among bile composition, biliary microbiome, and host immunity," integrating the dynamic crosstalk among these three axes in cholestatic liver diseases. Bile composition shapes microbial communities and modulates immune responses through receptors such as FXR and TGR5. In turn, the biliary microbiome regulates bile acid metabolism and immune activity through microbial metabolites. Meanwhile, the host immune system senses microbial signals via pattern-recognition receptors, triggering inflammatory pathways and influencing microbial colonization and metabolism. These reciprocal interactions form complex feedback loops that drive disease progression from early inflammation to chronic fibrosis and cirrhosis. Based on this framework, emerging diagnostic approaches combine microbial signatures, bile acid profiles, and immune markers into multidimensional biomarker systems. Therapeutically, integrated strategies targeting the microbiome, bile acid metabolism, and immune pathways may offer synergistic benefits. Despite challenges including sampling difficulty, interindividual variability, and limitations of current models, future technologies such as single-cell sequencing, spatial transcriptomics, and multi-omics integration may enable precision diagnosis and targeted therapy.},
}

Humans
Animals
*Microbiota/immunology
Bile Acids and Salts/metabolism
*Cholestasis/microbiology/immunology/metabolism
*Bile/metabolism/immunology/microbiology
*Gastrointestinal Microbiome/immunology

@article {pmid42558343,
year = {2026},
author = {Liu, L and Lin, J and Sang, K and Lai, J and Huang, N and Zhong, P and Liu, Y and Chen, S},
title = {Bile acid signaling at the gut-vascular interface: a novel modulator of hantavirus endothelial barrier dysfunction.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1883162},
pmid = {42558343},
issn = {2235-2988},
mesh = {Animals ; Humans ; *Orthohantavirus/pathogenicity/physiology ; *Bile Acids and Salts/metabolism ; *Signal Transduction ; Receptor, Farnesoid X-Activated ; Rats ; *Endothelial Cells/virology/metabolism ; Gastrointestinal Microbiome ; *Hantavirus Infections/virology/metabolism ; Receptors, G-Protein-Coupled/metabolism ; Receptors, Cytoplasmic and Nuclear/metabolism ; NF-kappa B/metabolism ; Lung/virology/microbiology ; Vascular Cell Adhesion Molecule-1/metabolism/genetics ; },
abstract = {Hantavirus infection triggers life-threatening hemorrhagic fever with renal syndrome (HFRS) and hantavirus cardiopulmonary syndrome (HCPS), driven by severe endothelial barrier breakdown and systemic capillary leakage. Clinical severity varies widely with undefined host regulators, and no targeted endothelial-protective treatments exist. Recent data link hantaviruses to gut microbiome remodeling, while bile acid (BA) receptors FXR and TGR5 potently inhibit NF-κB-mediated endothelial inflammation. We synthesize four core lines of evidence. First, metagenomic reports confirm hantavirus reshapes gut/lung microbiota in rodent reservoirs. Second, we re-analyzed three public GEO datasets via standardized RNA-seq/microarray pipelines: (i) GSE245916: SEOV-infected human/rat lung ECs show conserved VCAM1/ICAM1 upregulation (human VCAM1 log2FC=+1.17, P = 0.023; rat Icam1 log2FC=+0.32, padj=0.016) with unaltered FXR; (ii) GSE7271: SEOV-infected rat lung displays sustained Nfkb1 suppression (all timepoints, P<0.05) and day-15 Slc10a2 downregulation (P = 0.028); (iii) GSE270172: PUUV 3D vessel chips feature robust IL6 elevation (log2FC=+1.22, P = 3.1×10[-8]) and disrupted BA transporters (ABCC3 log2FC=-1.44, P = 7.4×10[-][12]). TGR5 (GPBAR1) was undetectable in endothelial cells across all datasets. Third, FXR/TGR5 agonists repress NF-κB inflammation and mitigate lung vascular injury. Fourth, HTNV upregulates CH25H to block HMGCR-dependent cholesterol synthesis, depleting BA precursor substrates. We propose a unified pathogenic model: hantavirus-triggered gut dysbiosis plus virus-impaired cholesterol metabolism deplete circulating FXR/TGR5 agonistic BAs, relieving constitutive inhibition of endothelial NF-κB and monocyte NLRP3 inflammasomes to exacerbate capillary leakage. We define tiered testable predictions covering clinical multi-omics cohorts, in vitro receptor modulation assays and in vivo pharmacological interventions. This gut microbiota-BA-FXR/TGR5 axis represents a repurposable therapeutic target for hantavirus diseases, though direct causal evidence connecting BA signaling to viral vascular damage remains absent; our framework offers a rigorous testable roadmap for subsequent validation.},
}

Animals
Humans
*Orthohantavirus/pathogenicity/physiology
*Bile Acids and Salts/metabolism
*Signal Transduction
Receptor, Farnesoid X-Activated
Rats
*Endothelial Cells/virology/metabolism
Gastrointestinal Microbiome
*Hantavirus Infections/virology/metabolism
Receptors, G-Protein-Coupled/metabolism
Receptors, Cytoplasmic and Nuclear/metabolism
NF-kappa B/metabolism
Lung/virology/microbiology
Vascular Cell Adhesion Molecule-1/metabolism/genetics

@article {pmid42559032,
year = {2026},
author = {Sun, Y and Li, X and Zheng, X and Sun, X and Liu, J and Zhang, S and Zhang, G and He, W and Huo, W and Zuo, J},
title = {Habitat environment is associated with the microbiota of the human terminal airway.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1887778},
pmid = {42559032},
issn = {1664-302X},
abstract = {While environmental exposures are closely associated with the human microbiome, the microbial landscape of the terminal airways remains largely uncharacterized due to the ethical challenges of tissue sampling. To address this gap, we analyzed surgically resected idiopathic lung bullae (localized developmental anomalies surrounded by otherwise normal tissue) to establish a baseline microbiome atlas. We performed ultra-deep metagenomic sequencing on terminal airway tissues from 60 subjects residing in two climatically distinct Chinese cities: Zhuhai (a subtropical coastal region) and Yinchuan (an arid, high-altitude industrial area on the Qinghai-Tibet Plateau). Our analysis revealed that the high-altitude Yinchuan cohort exhibited significantly higher microbial loads and alpha diversity compared to the coastal Zhuhai cohort. Functionally, the Yinchuan microbiome was enriched in taxa associated with fatty acid beta-oxidation, alongside a markedly higher burden of virulence factors and antibiotic resistance genes. These compositional and functional differences may be associated with regional variation in climate, altitude, and local antibiotic usage patterns, whereas the Zhuhai cohort exhibited greater fungal diversity. Ultimately, this study provides the tissue-resolved microbial atlas of the human terminal respiratory tract and reveals substantial differences in microbial composition and function across distinct habitat environments. Furthermore, these findings suggest a potential association between environmental conditions and variation in resident microbiota, providing a basis for future investigations into how environmental change may influence respiratory microecology and human health.},
}

@article {pmid42559092,
year = {2026},
author = {Wang, H and Han, X and Zeng, H and Liu, B and Chen, C and Wu, G},
title = {Lumbar postoperative Aspergillus flavus infection after lumbar spondylolisthesis fusion: a case report and literature review.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1879141},
pmid = {42559092},
issn = {2296-858X},
abstract = {Surgical site infection following lumbar internal fixation and fusion is predominantly bacterial. Aflatoxin-associated discitis is extremely rare in immunocompetent patients and often results in delayed diagnosis and inadequate empirical antimicrobial treatment. This report presents a 74-year-old immunocompetent male patient who underwent elective posterior lumbar interbody fusion for grade II degenerative lumbar spondylolisthesis and developed intractable low back pain 3 months postoperatively. Despite multiple courses of broad-spectrum antibiotic therapy administered at two external hospitals, his symptoms did not resolve. Conventional bacterial, mycobacterial, and fungal cultures, as well as histopathological examination of percutaneous biopsy and intraoperative specimens, yielded negative microbial results. Metagenomic next-generation sequencing (mNGS) specifically identified Aspergillus flavus in all tissue samples, confirming the etiological diagnosis of fungal discitis. The patient received staged combined antifungal and surgical management. Intravenous voriconazole was used for induction therapy, followed by radical debridement of infected spinal tissue, internal fixation revision, and bone graft reconstruction. Oral voriconazole was prescribed for 3 months of postoperative maintenance therapy. A 12-month follow-up showed marked pain relief, and serial imaging and laboratory tests confirmed complete eradication of the infection with no recurrence. This case is systematically compared with previously reported Aspergillus spinal infections in immunocompetent hosts. mNGS serves as a valuable adjunctive diagnostic tool for clinically suspected atypical infections when conventional examinations are negative. Although limited by a single-case, single-center design without statistical generalizability, this report expands clinical recognition of post-fusion fungal discitis in immunocompetent patients and provides practical evidence for precise diagnosis and individualized management of refractory spinal surgical site infections.},
}

@article {pmid42559169,
year = {2026},
author = {Wang, B and Zhao, M and Chen, Q and Zhang, F and Fan, M and Lian, X},
title = {Severe fever with thrombocytopenia syndrome complicated by invasive pulmonary aspergillosis and septic shock: a case report highlighting the role of mNGS.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1888410},
pmid = {42559169},
issn = {2296-858X},
abstract = {BACKGROUND: Severe fever with thrombocytopenia syndrome (SFTS) is an emerging tick-borne viral hemorrhagic fever associated with high mortality, and no specific antiviral therapy is currently available. Patients with SFTS often develop immune dysfunction, rendering them susceptible to secondary opportunistic infections, particularly invasive pulmonary aspergillosis (IPA). Early diagnosis of this co-infection is critical but remains challenging due to nonspecific clinical manifestations and radiological findings.

CASE PRESENTATION: A 61-year-old male farmer from a hilly region presented in July 2024 with fever, dyspnea, and altered consciousness. On admission, he exhibited septic shock and multiple-organ dysfunction, including severe thrombocytopenia, leukopenia, liver injury, and acute kidney injury. Metagenomic next-generation sequencing (mNGS) of blood and bronchoalveolar lavage fluid rapidly identified SFTS virus, Aspergillus fumigatus, Aspergillus flavus, and multiple Gram-negative bacteria. Chest imaging revealed bilateral nodules distributed along the bronchovascular bundles, suggestive of angioinvasive IPA. Treatment consisted of imipenem/cilastatin, isavuconazonium sulfate, continuous renal replacement therapy, and mechanical ventilation. The patient gradually improved and was discharged after 30 days, with complete clinical recovery documented at the 3-month and 9-month follow-up visits.

CONCLUSION: This case highlights the diagnostic value of mNGS in critically ill patients with SFTS and suspected co-infections, as it enables early pathogen identification and targeted therapy. Clinicians in endemic areas should maintain a high index of suspicion for SFTS and IPA in patients presenting with unexplained fever, thrombocytopenia, and organ dysfunction. However, the favorable outcome cannot be attributed solely to mNGS, as multiple supportive interventions were administered concurrently; the clinical improvement likely reflects a synergistic effect of timely targeted therapy and comprehensive intensive care.},
}

@article {pmid42559206,
year = {2026},
author = {Viver, T and Gago, JF and Bustos-Caparros, E and Aldeguer-Riquelme, B and Rodriguez Rojas, LM and Ramírez, AS and Albuquerque, L and Amiour, S and Oren, A and Mutlu, MB and Venter, SN and Baxter, BK and Llames, ME and González, B and Rodríguez-Valdecantos, G and Banciu, HL and Stott, MB and Santos, F and Hedlund, BP and Antón, J and Amann, R and Konstantinidis, KT and Rossello-Mora, R},
title = {Metagenomics reveal unrestricted dispersal of extreme halophiles and higher connectivity among coastal vs. inland solar salterns and hypersaline lakes.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag165},
pmid = {42559206},
issn = {2730-6151},
abstract = {Hypersaline environments constitute ideal systems for studying evolutionary processes and microbial diversification due to their relatively low (and thus tractable) diversity and geographically isolated nature. Based on metagenomic sequencing of samples from 25 hypersaline sites in 11 countries taken within a single year, we explored the relationships between environmental factors, geographic distance, and microbial community structure and diversification. Our results revealed that microbial communities of coastal sites were more similar to each other than those of the inland sites, reflecting higher connectivity due to ocean currents and nearly unrestricted dispersal. Conversely, inland hypersaline environments showed less connectivity and higher genetic and taxonomic dissimilarities that did not correlate with the distance between the sampled sites. The latter results reflect reduced species migration characterizing inland sites as well as site-specific environmental factors selecting for divergent taxa. The 484 MAGs recovered, representing 284 distinct species, revealed a striking global ubiquity, with 62.5% of the species showing cosmopolitanism, defined as being present at both coastal and inland sites. Most cosmopolitan species showed allopatric differentiation, reflected by an increased frequency of non-synonymous substitutions between MAGs of the same species recovered from more distant sites. However, a few cases of truly cosmopolitan genomovars (average nucleotide identity, or ANI > 99.8%), were also observed. Our results suggest that extreme halophiles have nearly unrestricted global dispersal among ocean-connected sites, and to a lesser extent, among geographically isolated inland sites, although cases of allopatric diversification were also observed.},
}

@article {pmid42559331,
year = {2026},
author = {Hajjaji, O and Al-Soudy, AS and Daoud, R and Benhida, R and Mokhtar, MM},
title = {Calibrating tetranucleotide-frequency distances for metagenomic binning with right-skewed distribution models.},
journal = {Bioinformatics advances},
volume = {6},
number = {1},
pages = {vbag207},
pmid = {42559331},
issn = {2635-0041},
abstract = {SUMMARY: Metagenomic binning is a pivotal step in reconstructing metagenome-assembled genomes (MAGs) from complex microbial communities, and it critically depends on reliable measures of similarity between contigs. In many workflows, tetranucleotide-frequency (TNF) distances are translated into probabilistic evidence of a shared genome of origin. Despite their central role, these distances are often modeled with convenient but poorly matched assumptions, even though they are intrinsically non-negative and frequently exhibit pronounced right-skewness-features that can distort tail behavior and weaken downstream thresholding decisions. In this work, we introduce a likelihood-based framework for characterizing intra- and inter-genomic TNF distance distributions with flexible right-skewed parametric models and for converting fitted distributions into calibrated distance-to-probability scores within a MaxBin-style scheme. Our approach provides a principled statistical basis for distributional assessment, probability calibration, and transparent operating-point selection, with the goal of improving robustness and interpretability in TNF-driven binning.

All codes related to the article are available through a public GitHub repository at https://github.com/omar-hajjaji/Calibrating-TNF-Distances-for-Metagenomic-Binning-with-Right-Skewed-Distribution-Models.},
}

@article {pmid42560056,
year = {2026},
author = {Bernate, E and Shi, Y and Franck, E and Crofts, TS},
title = {A functionally selected Acinetobacter sp. phosphoethanolamine transferase gene from the goose fecal microbiome confers colistin resistance in E. coli.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0246825},
doi = {10.1128/aem.02468-25},
pmid = {42560056},
issn = {1098-5336},
abstract = {Polymyxins are last-resort antibiotics for infections caused by multidrug-resistant gram-negative bacteria such as Enterobacteriaceae, Pseudomonas aeruginosa, and Acinetobacter baumannii. This makes the rise of bacteria exhibiting polymyxin E (colistin) resistance, largely through modification of lipid A moieties, concerning and suggests that it is important to document the potential sources of the corresponding resistance genes. This study searched for potential emerging colistin resistance genes from the environment by investigating a previously performed functional metagenomic selection for colistin resistance of a goose fecal microbiome. We found that the selection captured Acinetobacter sp. DNA fragments that all contained eptA genes. We confirmed their ability to confer significant colistin resistance in Escherichia coli via modification of lipid A in the outer membrane. Furthermore, we found evidence for mobilization of closely related eptA genes in Acinetobacter genomes, marking them as potential mcr genes or their precursors. This study highlights the potential for functional metagenomic selections for colistin resistance to capture genes from unexpected environmental sources such as the goose fecal microbiome.IMPORTANCEColistin is an important antibiotic of last resort, and increasing resistance to this drug via mobile phosphoethanolamine transferase genes, such as mcr-1, threatens its clinical utility. Given the discovery of mcr-1 in pigs, the ability of animals to act as vectors in the spread of colistin resistance is alarming. We show here that functionally selected Acinetobacter phosphoethanolamine transferase genes from the goose microbiome have the ability to confer clinical levels of colistin resistance when transferred into E. coli. While the genes are annotated as eptA homologs, closer study of these genes suggests that they may be mobilized within the Acinetobacter genus, suggesting that they may be mcr genes of concern instead.},
}

@article {pmid42560070,
year = {2026},
author = {Lambisia, AW and Nyawa, OK and Maina, G and Katama, EN and Mutunga, M and Agoti, CN},
title = {Near-complete genomes from six human coronavirus HKU1-positive samples recovered by metagenomics in coastal Kenya, 2024-2025.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0064226},
doi = {10.1128/mra.00642-26},
pmid = {42560070},
issn = {2576-098X},
abstract = {Human coronavirus HKU1 is globally endemic but genomically understudied. We present six near-complete HKU1 genomes from samples collected in coastal Kenya (2024-2025) that fell into genotypes A (n = 3) and B (n = 3). The data expand the global HKU1 genomic database and will support molecular assay development and phylogeography studies.},
}

@article {pmid42560299,
year = {2026},
author = {Liang, F and Li, J and Yue, Y and Pan, J and Liu, C and Cheng, D and Zhang, N and Li, K and Chu, F and Wu, H},
title = {Distinct Gut Microbiome and Metabolome Profiles Associate with Differential Responses to Immunotherapy in Colorectal Cancer.},
journal = {Polish journal of microbiology},
volume = {75},
number = {2},
pages = {168-194},
pmid = {42560299},
issn = {2544-4646},
mesh = {Humans ; *Colorectal Neoplasms/therapy/microbiology/metabolism ; *Metabolome ; *Immunotherapy ; *Gastrointestinal Microbiome ; Female ; Feces/microbiology ; Male ; Middle Aged ; Aged ; Metabolomics ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {The composition of the intestinal microbiome has been identified as a key factor influencing the efficacy of immune checkpoint inhibitors. This study aimed to systematically evaluate the potential associations among gut microbiota, metabolic profiles, and clinical outcomes in patients with MSI-H advanced colorectal cancer (CRC) treated with immunotherapy. Twenty advanced CRC patients receiving immunotherapy were enrolled and categorized into clinical benefit response (CBR) and non-benefit (NCB) groups based on treatment efficacy. Fecal samples were analyzed using metagenomic sequencing and untargeted metabolomics. The results revealed significant enrichments of s_Clostridium unclassified and metabolites such as guanosine, 3-carboxy-4-methyl-5-propyl-2-furanpropionic acid, and quercetin 3-(6"-malonyl-glucoside) in the CBR group, suggesting their potential positive predictive value for immunotherapy response. Conversely, the NCB group showed significant enrichments of s_Roseburia hominis, s_Marseilla massiliensis, and metabolites including pyrophosphate, riboflavin, and PC(22:5(4Z,7Z,10Z,13Z,16Z)/14:0), indicating a possible association with treatment resistance. By integrating fecal metagenomics and metabolomics, this study reveals distinctive "flora-metabolite" interactions linked to therapeutic response in advanced CRC patients undergoing immunotherapy. Specific microbial and metabolic profiles were positively or negatively correlated with immunotherapy outcomes, highlighting their potential not only as predictive biomarkers but also as a theoretical foundation for developing individualized immunotherapy strategies based on microecological modulation.},
}

Humans
*Colorectal Neoplasms/therapy/microbiology/metabolism
*Metabolome
*Immunotherapy
*Gastrointestinal Microbiome
Female
Feces/microbiology
Male
Middle Aged
Aged
Metabolomics
Bacteria/classification/genetics/isolation & purification

@article {pmid42560300,
year = {2026},
author = {He, X and Ma, S and Zhou, Y and Wei, J and Zhuo, Z and Ma, L},
title = {In Vitro Antibacterial Activity of Sulbactam-Durlobactam and Eravacycline Against Carbapenem-Resistant Acinetobacter baumannii in China and Analysis of Sulbactam-Durlobactam Resistance Mechanisms.},
journal = {Polish journal of microbiology},
volume = {75},
number = {2},
pages = {210-219},
pmid = {42560300},
issn = {2544-4646},
mesh = {*Acinetobacter baumannii/drug effects/genetics ; *Sulbactam/pharmacology ; *Anti-Bacterial Agents/pharmacology ; *Carbapenems/pharmacology ; China ; Microbial Sensitivity Tests ; *Tetracyclines/pharmacology ; *Azabicyclo Compounds/pharmacology ; Humans ; Acinetobacter Infections/microbiology ; *Drug Resistance, Multiple, Bacterial ; Drug Resistance, Bacterial ; },
abstract = {The management of carbapenem-resistant Acinetobacter baumannii (CRAB) infections remains a formidable clinical challenge. This study evaluated the in vitro antimicrobial activities of sulbactam-durlobactam (SUL-DUR) and eravacycline (ERV) against CRAB isolates and elucidated the genomic landscapes of resistance and virulence determinants in SUL-DUR-resistant strains to inform therapeutic decision-making. A total of 233 clinical CRAB isolates were collected and screened for susceptibility to SUL-DUR and ERV using the Kirby-Bauer (K-B) disk diffusion assay. Isolates exhibiting resistance to SUL-DUR were further characterized via metagenomic next-generation sequencing (mNGS) to identify key resistance and virulence factors. SUL-DUR and ERV demonstrated robust in vitro activity, with susceptibility rates of 92.3% and 91.4%, respectively. Notably, no isolates exhibited concurrent non-susceptibility to both agents. Genomic analysis of 14 SUL-DUR-resistant strains revealed a complex and heterogeneous distribution of genetic determinants. The presence of bla NDM-1 was identified as a critical driver of SUL-DUR resistance. Additionally, reduced susceptibility was potentially associated with specific mutations in bla OXA-23, bla OXA-66, and bla TEM-1, while hyperactive efflux systems and altered membrane permeability further synergized to enhance the resistance phenotype. Despite the extensive-drug-resistant (XDR) nature of current CRAB isolates, they maintain high sensitivity to SUL-DUR and ERV. Our findings underscore that SUL-DUR and ERV represent highly promising therapeutic options with significant development potential and broad clinical application prospects for the management of CRAB-related infections.},
}

*Acinetobacter baumannii/drug effects/genetics
*Sulbactam/pharmacology
*Anti-Bacterial Agents/pharmacology
*Carbapenems/pharmacology
China
Microbial Sensitivity Tests
*Tetracyclines/pharmacology
*Azabicyclo Compounds/pharmacology
Humans
Acinetobacter Infections/microbiology
*Drug Resistance, Multiple, Bacterial
Drug Resistance, Bacterial

@article {pmid42560417,
year = {2026},
author = {Gautham, M and Koteswari, P},
title = {Granulomatous amoebic encephalitis: pathogenesis, diagnostic advances, therapeutic challenges, and emerging treatment strategies.},
journal = {Medical microbiology and immunology},
volume = {215},
number = {1},
pages = {},
pmid = {42560417},
issn = {1432-1831},
mesh = {Humans ; *Acanthamoeba/pathogenicity ; *Amebiasis/diagnosis/therapy/drug therapy ; *Balamuthia mandrillaris/pathogenicity ; Blood-Brain Barrier ; *Infectious Encephalitis/diagnosis/therapy ; Animals ; *Central Nervous System Protozoal Infections/diagnosis/therapy ; Antiprotozoal Agents/therapeutic use ; },
abstract = {Granulomatous amoebic encephalitis (GAE) is a rare but highly fatal central nervous system infection caused primarily by Acanthamoeba spp. and Balamuthia mandrillaris. Delayed diagnosis and the absence of standardized treatment protocols contribute to mortality exceeding 90%. This review summarizes current knowledge regarding GAE pathogenesis, diagnosis, therapeutic challenges, and emerging treatment strategies. The pathogenesis involves amoebic adhesion, secretion of proteases and phospholipases, host inflammatory responses, and blood-brain barrier disruption. Recent advances in molecular diagnostics improve early pathogen detection, while drug repurposing, nanotechnology-based delivery systems, and cyst-targeted approaches represent promising therapeutic strategies. Nevertheless, treatment remains challenging because of poor blood-brain barrier penetration, cyst-associated resistance, and limited clinical evidence. Continued integration of molecular diagnostics, mechanistic studies, translational research, and multicentre clinical investigations is essential for improving outcomes in this devastating disease.},
}

Humans
*Acanthamoeba/pathogenicity
*Amebiasis/diagnosis/therapy/drug therapy
*Balamuthia mandrillaris/pathogenicity
Blood-Brain Barrier
*Infectious Encephalitis/diagnosis/therapy
Animals
*Central Nervous System Protozoal Infections/diagnosis/therapy
Antiprotozoal Agents/therapeutic use

@article {pmid42560632,
year = {2026},
author = {Peng, M and Xu, Y and Cao, X and Xue, Y and Pang, J and Zhou, S and Xu, P and Yang, Y and Zhang, X and Qian, J and Wang, Y and Lu, X and Wan, Y and Sun, Y and Hua, X and Xu, Y and Chen, B and Ouyang, J},
title = {Clinical Research on Microecological Landscape for Infection Risk Stratification in Newly Diagnosed Patients with Hematological Conditions.},
journal = {Infectious diseases and therapy},
volume = {},
number = {},
pages = {},
pmid = {42560632},
issn = {2193-8229},
support = {BE2023656//Jiangsu Provincial Key Research and Development Program/ ; QNX25036//Nanjing Municipal Health Science and Technology Development Special Fund/ ; 2021-LCYJ-MS-19//Clinical Trials from the Affiliated Drum Tower Hospital/ ; 2022-LCYJ-PY-46//Center for Clinical Trials, Japan Medical Association/ ; },
abstract = {INTRODUCTION: Infection is a common and potentially fatal complication during the treatment of hematological diseases, particularly in the context of chemotherapy-induced immunosuppression. The nonselective use of antibiotic prophylaxis in patients with neutropenia in China has persistently accelerated antimicrobial resistance. Early identification of patients at high risk for infection before clinical symptom onset could enable targeted preventive strategies; however, reliable and biologically informed screening approaches remain limited.

METHODS: We developed a prediction model for infection risk stratification in newly diagnosed patients with hematological conditions. Plasma metagenomic next-generation sequencing was performed in a prospective cohort of 230 patients. Among them, 116 patients provided prechemotherapy, non-neutropenic plasma samples (cohort A), and 114 patients provided postchemotherapy, neutropenic samples (cohort B). Microbial community profiles were analyzed, and machine learning approaches were applied to construct classifiers for neutropenia status and subsequent infection risk.

RESULTS: Plasma metagenomic profiling revealed a complex microecological landscape in patients with hematological conditions and identified distinct microbial features associated with neutropenia. A trained random forest classifier successfully distinguished patients without neutropenia from patients with neutropenia, achieving an area under the receiver operating characteristic curve of 0.8324. Importantly, a microorganism-based random forest model was established to predict patients at high risk of infection, yielding an area under the curve of 0.942. Nested cross-validation demonstrated high classification accuracy, correctly identifying 99.1% of patients who subsequently developed infections and 72.7% of patients who remained infection-free. Furthermore, integration of microbial features with clinical metrics improved predictive performance, resulting in an area under the curve of 0.953.

CONCLUSIONS: This microorganism-based prediction model provides an effective tool for infection risk stratification in patients with hematological conditions. By enabling early identification of high-risk individuals, the model has potential clinical utility for guiding precise preventive interventions and optimizing infection management strategies, which can significantly reduce the use of prophylactic antibiotics, thereby mitigating the development of resistance.

REGISTRATION NUMBER: ChiCTR2100042992.},
}

@article {pmid42561044,
year = {2026},
author = {Du, P and Zhou, M and Wang, L and Zhang, X},
title = {Pharmacist-Led Management of Elizabethkingia Keratitis: Precision Therapy Guided by Culture and mNGS to Improve Clinical Outcomes and Efficiency.},
journal = {Cornea},
volume = {},
number = {},
pages = {},
pmid = {42561044},
issn = {1536-4798},
abstract = {PURPOSE: This study evaluated the clinical efficacy of a pharmacist-led antimicrobial stewardship program augmented by metagenomic next-generation sequencing (mNGS) for managing rare, multidrug-resistant Elizabethkingia keratitis.

METHODS: We conducted a retrospective case series of 5 male patients (mean age 56.4 years) diagnosed with Elizabethkingia keratitis (3 E. meningoseptica, 2 Elizabethkingia anophelis) between 2020 and 2025. Initial microbiological identification relied on corneal scraping culture and MALDI-TOF MS, while mNGS was strategically used in 1 complex case to identify potential copathogens. Clinical pharmacists provided interventions including minimum inhibitory concentration-guided therapy and the extemporaneous preparation of fortified antibiotic eye drops, such as 2% amikacin and 10% piperacillin/tazobactam. We assessed clinical outcomes, visual acuity (LogMAR), and the length of hospital stay.

RESULTS: Although conventional culture confirmed Elizabethkingia species in all cases, mNGS offered critical genomic insights in 1 complex case by detecting culture-negative co-pathogens Nocardia pneumoniae and Fusarium proliferatum, which directly guided the addition of targeted antifungal and antibacterial therapy. All Elizabethkingia isolates demonstrated extensive resistance to carbapenems and cephalosporins. After pharmacist-led interventions, mean visual acuity improved significantly from 1.56 ± 0.77 to 0.90 ± 0.25 LogMAR. Furthermore, the length of hospital stay decreased markedly from 40 days in the index case to an average of 10.7 ± 4.9 days in the final 3 cases as diagnostic and therapeutic protocols were refined.

CONCLUSIONS: Integrating clinical pharmacists within a multidisciplinary team, supported by mNGS for comprehensive polymicrobial detection, enables precision pharmacotherapy for multidrug-resistant Elizabethkingia keratitis. This approach promotes successful ocular salvage and visual recovery while substantially improving clinical efficiency through shortened hospitalization.},
}

@article {pmid42561698,
year = {2026},
author = {Cai, Y and Zhai, J and Lin, M and Huang, W and Zhang, R and Zheng, CW and Luo, YH and Rittmann, BE},
title = {Biodegradation of potassium amyl xanthate from mining flotation wastewater with minimal CS2 emission.},
journal = {Journal of hazardous materials},
volume = {515},
number = {},
pages = {143195},
doi = {10.1016/j.jhazmat.2026.143195},
pmid = {42561698},
issn = {1873-3336},
abstract = {The mining industry produces significant volumes of flotation wastewater that contains xanthates, such as potassium amyl xanthate (PAX, C6H11OS2K), that pose toxicity risks to ecosystems and humans. In this study, an oxygen-based membrane biofilm reactor (O2-MBfR) was applied to biodegrade high concentrations (75∼200 mg/L) of PAX; the MBfR achieved > 99% removal of PAX with minimal carbon disulfide (CS2) emission at a PAX surface loading rate of 770 mg/m2-d. The microbial community adapted to changing PAX loading and O2 pressure, and it consistently gave efficient removals of PAX and soluble COD, as well as negligible CS2 emission. Metagenomic sequencing revealed that Mesorhizobium, Zoogloea, Sediminibacterium, Afipia, and Devosia were important genera that contributed in different ways to oxidation of PAX, PAX metabolites, and CS2. PAX degradation began with cleavage of C-O or C-S bonds, which was followed by oxidation of sulfur-containing intermediates. Also, the efficient biodegradation of xanthates offers a potential strategy to avoid flotation tailings caused by flotation wastewater reuse.},
}

@article {pmid42561992,
year = {2026},
author = {Mourik, K and Sidorov, I and Meijers, E and van den Brink, S and Bos, S and Aarts, L and Veetil, NK and Boers, SA and Eggink, D and Meijer, A and de Vries, JJC},
title = {Probe-based metagenomic sentinel surveillance of viral respiratory infections in primary care: a prospective, national, pilot study.},
journal = {The Lancet. Microbe},
volume = {},
number = {},
pages = {101473},
doi = {10.1016/j.lanmic.2026.101473},
pmid = {42561992},
issn = {2666-5247},
abstract = {BACKGROUND: With the introduction of metagenomics in clinical diagnostics unfolding and the expanding role of pathogen genomics in national surveillance, conditions are favourable for the further maturation of these approaches in public health surveillance. In this study, we aimed to pilot the use of probe-based metagenomics for nationwide sentinel surveillance through general practitioner (GP) networks and for the genomic characterisation of both anticipated and emerging respiratory viruses in primary care.

METHODS: This prospective, pilot study included patients with acute respiratory illness attending GP practices participating in nationwide sentinel virological surveillance in the Netherlands, from Jan 10, 2025, to April 25, 2025. On predefined selection days, 90-100 combined nasopharyngeal and oropharyngeal swab specimens were analysed through parallel metagenomic testing using probes targeting 15 488 strains of human and animal viruses. Results were compared with a standard two-tiered surveillance strategy comprising PCR targeting 17 viruses, followed by amplicon-based nanopore whole-genome sequencing of influenza viruses, SARS-CoV-2, and respiratory syncytial virus (RSV). The primary outcome was detection and in-depth genomic characterisation of viruses within and beyond the scope of standard screening. Sensitivity, specificity, positive and negative predictive values, and genome coverage were analysed.

FINDINGS: 93 patients were included, with a median age of 51 years (IQR 33-67); 55 (59%) were women and 38 (41%) were men. Overall, 74 (80%) specimens tested positive through standard PCR-based screening. Metagenomic surveillance detected viruses in 88 (95%) specimens, including DNA viruses known to establish latent infections. For viruses targeted by routine PCR, metagenomics showed a pooled sensitivity of 93·8% (95% CI 88·1-98·7), specificity of 99·8% (95% CI 99·5-100·0), positive predictive value of 96·2% (95% CI 91·8-100·0), and negative predictive value of 99·7% (95% CI 91·8-100·0), with a median genome coverage of 99·4% (IQR 96·9-99·9%). Metagenomic data enabled simultaneous full genomic characterisation of circulating viruses targeted by current amplicon-based surveillance, including influenza viruses (success rate 30 [86%] of 35 detections) and RSV (six [86%] of seven), and of viruses that were post hoc characterised by whole-genome sequencing in response to epidemiological findings during the study period (human metapneumoviruses [hMPV], five [50·0%] of ten), and non-targeted viruses such as adenoviruses. The data facilitated characterisation of a reassortant A(H3N2) influenza virus, potential vaccine escape mutants, markers of susceptibility to influenza antiviral drugs and RSV monoclonal antibodies, and a human A(H1N2)v influenza virus infection.

INTERPRETATION: The technically robust and comprehensive performance across heterogeneous circulating viruses shown here supports evaluation in larger prospective studies in high-prevalence settings, where implementation might be most cost-efficient. Further optimisation of probe-based enrichment strategies could reduce turnaround time and facilitate integration into routine public health surveillance.

FUNDING: The Netherlands Organisation for Health Research and Development (ZonMw), and the Ministry of Health, Welfare and Sport (VWS).},
}

@article {pmid42562314,
year = {2026},
author = {Qian, Z and Qian, W and Si-Wei, W and Pei, Z and Yi, L and Shan-Ling, X and Chen, C},
title = {Metagenomic Next-Generation Sequencing (mNGS) for Detecting Pathogens and Antimicrobial Resistance Genes (ARGs), and Guiding Antimicrobial Therapy in Cancer Patients from Southwest China.},
journal = {Journal of global antimicrobial resistance},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jgar.2026.07.026},
pmid = {42562314},
issn = {2213-7173},
abstract = {BACKGROUND: Cancer patients often face etiological diagnosis challenges due to repeated hospitalizations, antibiotic exposure, and conventional microbiology tests (CMTs) limitations (low positivity, long turnaround). Metagenomic next-generation sequencing (mNGS) enables rapid and accurate pathogen detection, however, its clinical utility in cancer patients requires further investigation.

METHODS: Two years of mNGS results and clinical data of cancer patients in Sichuan Cancer Hospital were collected. The pathogens and antimicrobial resistance genes (ARGs) were analyzed. The diagnostic performance was evaluated via sensitivity, specificity, accuracy, positive and negative predictive value. The clinical significance in guiding antimicrobial therapy was assessed by comparing outcomes between mNGS-guided and empirical therapy groups. Multivariable logistic regression analysis was performed to explore risk factors for multidrug-resistant organisms (MDROs) and opportunistic pathogens infections in cancer population.

RESULTS: The study included 340 mNGS results from 267 cancer patients. Streptococcus pneumoniae, Pseudomonas aeruginosa, Candida albicans and Epstein-Barr virus were the most common Gram-positive and Gram-negative bacteria, fungus and virus, respectively. The main ARGs were ESBLs and aminoglycoside resistance genes. mNGS showed high pathogen diagnostic sensitivity (97.50%) and moderate ARGs diagnostic sensitivity (64.29%). The mNGS-guided group had lower mortality (29.5% vs. 34.1%, p=0.65) and shorter duration of mechanical ventilation (39.34 ± 81.15 vs. 42.30 ±102.39 hours, p= 0.88). Age (p=0.028) and prior 90-day antibiotic use (p=0.047) independently predicted MDROs infections; immunodeficiency predicted Pneumocystis jirovecii (p=0.005) and Aspergillus spp. (p=0.010) infections.

CONCLUSION: mNGS was reliable for pathogen diagnosis in cancer patients. However, its clinical significance on guiding antimicrobial therapy requires more prospective multicenter studies to confirm.},
}

@article {pmid42562454,
year = {2026},
author = {Zheng, X and Sun, P and He, C and Liu, M and Qiu, J and Ding, Z and Zhang, Y and Zhou, S and Zhou, J and Sun, J and Feng, W and Zhang, L and Cheng, N and Xu, Q and Li, X and Yang, L and Liang, A},
title = {Royal jelly enhances ovarian function by modulating taurocholic acid metabolism and attenuating oxidative stress in D-galactose-induced POI mice.},
journal = {Food research international (Ottawa, Ont.)},
volume = {241},
number = {},
pages = {119500},
doi = {10.1016/j.foodres.2026.119500},
pmid = {42562454},
issn = {1873-7145},
mesh = {Animals ; Female ; *Oxidative Stress/drug effects ; Royal Jelly ; Galactose ; Mice ; *Fatty Acids/pharmacology ; *Ovary/drug effects/metabolism ; *Taurocholic Acid/metabolism ; Disease Models, Animal ; *Primary Ovarian Insufficiency/chemically induced/drug therapy/metabolism ; Gastrointestinal Microbiome/drug effects ; Mice, Inbred C57BL ; Estradiol/blood ; },
abstract = {Premature ovarian insufficiency (POI) is a complex endocrine and metabolic disorder frequently associated with oxidative stress. Royal jelly (RJ) is a well-recognized natural functional food with multiple health benefits; however, its potential effects on POI remain unexplored. This study aimed to investigate the therapeutic potential and underlying mechanisms of RJ in a D-galactose (D-gal)-induced POI mouse model. The results showed that RJ increased serum estradiol (E2) levels, enhanced ovarian reserve and oocyte maturation, reduced ovarian oxidative stress, and ultimately improved the fertility of D-gal-treated mice. Integrated metagenomic and metabolomic analyses revealed that RJ alleviated D-gal-induced gut microbiota dysbiosis, notably increasing the abundance of Muribaculaceae bacterium, and restored levels of taurocholic acid (TCA), which positively correlated with both Muribaculaceae bacterium abundance and serum E2 levels. Importantly, TCA supplementation alone recapitulated the protective effects of RJ by reversing D-gal-induced reductions in E2 and anti-Müllerian hormone (AMH) levels, restoring follicle numbers, and alleviating oxidative stress. Mechanistically, TCA activated the nuclear factor erythroid 2-related factor 2 (NRF2) antioxidant pathway in ovarian tissue, while simultaneously enhancing intestinal β-glucuronidase activity to modulate systemic E2 metabolism. In conclusion, RJ alleviates D-gal-induced POI in mice by modulating the gut microbiota-bile acid-ovarian axis, providing novel insights into its potential application for POI prevention and treatment.},
}

Animals
Female
*Oxidative Stress/drug effects
Royal Jelly
Galactose
Mice
*Fatty Acids/pharmacology
*Ovary/drug effects/metabolism
*Taurocholic Acid/metabolism
Disease Models, Animal
*Primary Ovarian Insufficiency/chemically induced/drug therapy/metabolism
Gastrointestinal Microbiome/drug effects
Mice, Inbred C57BL
Estradiol/blood

@article {pmid42562478,
year = {2026},
author = {Zhang, HY and Huang, TC and Chai, LJ and Shi, W and He, YX and Lu, ZM and Zhang, XJ and Wang, ST and Shen, CH and Shi, JS and Xu, ZH},
title = {Integrating ecological networks and metagenomics to decipher core microbial drivers of organic acid metabolism during heaped fermentation of sauce-flavor Baijiu.},
journal = {Food research international (Ottawa, Ont.)},
volume = {241},
number = {},
pages = {119702},
doi = {10.1016/j.foodres.2026.119702},
pmid = {42562478},
issn = {1873-7145},
mesh = {*Fermentation ; *Metagenomics/methods ; *Food Microbiology ; *Bacteria/metabolism/genetics/classification ; Volatile Organic Compounds/metabolism/analysis ; Acetic Acid/metabolism/analysis ; Caproates/analysis ; Taste ; Lactic Acid/metabolism/analysis ; *Fermented Foods/microbiology ; *Microbiota ; Pentanoic Acids ; Hemiterpenes ; },
abstract = {Organic acids play crucial roles in both flavor quality and microbial succession of sauce-flavor Baijiu; however, the core microbial drivers responsible for their metabolism remain poorly understood. This study systematically investigated the microbial drivers of organic acid metabolism across six sequential rounds (R1-R6) of heaped fermentation. A total of 24 organic acids were identified, including nine non-volatile organic acids (NVOAs) and 15 volatile organic acids (VOAs). HPLC analysis revealed that the total content of acetic acid and nine NVOAs increased significantly across rounds, rising from 29.35 g/kg in R1 to 66.40 g/kg in R6. Lactic acid was the most abundant NVOA, while acetic acid, isovaleric acid, and hexanoic acid were the primary volatile contributors. Co-occurrence network analysis identified 488 consistently correlated bacterial pairs that clustered into two distinct guilds. Guild 2, mainly comprising Virgibacillus, Kroppenstedtia, Oceanobacillus, and Bacillus, exhibited high abundance (47%-78%) across all rounds and was defined as the core bacterial guild. Spearman correlation analysis revealed that guild 2 was positively correlated with NVOAs (69.41%) but negatively correlated with VOAs (63.02%). Metagenomic analysis reconstructed seven key pathways involved in organic acid biosynthesis. Kroppenstedtia, Lentibacillus, Desmospora, and Oceanobacillus were identified the taxa harboring the genetic potential most frequently detected across multiple pathways, with Kroppenstedtia and Lentibacillus exhibiting the highest gene abundances. These findings provide a theoretical foundation for targeted regulation of organic acid content in sauce-flavor Baijiu production.},
}

*Fermentation
*Metagenomics/methods
*Food Microbiology
*Bacteria/metabolism/genetics/classification
Volatile Organic Compounds/metabolism/analysis
Acetic Acid/metabolism/analysis
Caproates/analysis
Taste
Lactic Acid/metabolism/analysis
*Fermented Foods/microbiology
*Microbiota
Pentanoic Acids
Hemiterpenes

@article {pmid42562481,
year = {2026},
author = {Tan, G and Qi, S and Hu, M and Wang, D and Lin, K and Wang, Y and Chen, S and Zhang, Q and Zhao, L},
title = {Understanding phage dynamics and their potential roles during soy sauce fermentation using metagenome-assembled genomes.},
journal = {Food research international (Ottawa, Ont.)},
volume = {241},
number = {},
pages = {119707},
doi = {10.1016/j.foodres.2026.119707},
pmid = {42562481},
issn = {1873-7145},
mesh = {*Fermentation ; *Bacteriophages/genetics/classification/physiology ; *Soy Foods/microbiology/virology ; *Metagenome ; Genome, Viral ; *Food Microbiology ; Metagenomics ; },
abstract = {The composition and functional roles of phages in fermented foods have been gaining increasing attention. However, their ecological functions and underlying mechanisms in high-salt soy sauce fermentation remain largely unexplored. In this study, we investigated phage communities, their potential functions, phage-host interactions, and host defense mechanisms in two different soy sauce fermentation processes (Cantonese-type process, CP; Japanese-type process, JP) using shotgun metagenomics. A total of 823 phage species (viral operational taxonomic units, vOTUs) were identified, with the majority exhibiting a temperate lifestyle (89.19%). The most abundant family was Straboviridae (CP, 9.95%-11.39%; JP, 12.04%-13.73%), followed by Salasmaviridae (CP, 6.92%-7.94%; JP, 5.70%-7.02%). Although the phage composition differed between the two processes, the number of vOTUs was positively correlated with prokaryotic species richness, total acidity, and amino acid nitrogen content, and negatively correlated with pH. A comparative genomic analysis revealed that 91 phages were associated with 26 bacterial genomes (metagenome-assembled genomes, MAGs), with Lactococcus petauri (MAG16) and Halomonas elongata (MAG51) hosting the most phage species. An analysis of host defense mechanisms showed that all 45 bacterial MAGs harbored CRISPR-Cas type I systems, and 95.6% encoded restriction-modification systems. Functional annotation using the KEGG and CAZymes databases indicated that the phages predominantly encoded genes related to cell growth, replication, and metabolism of amino acids, carbohydrates, and nucleotides, with more genes enriched in the JP than in the CP. Additionally, auxiliary metabolic genes (e.g., pfkA, ldh, adhP, ilvE, and arcA) were identified in 29 phages. These genes are potentially involved in metabolic pathways that may be linked to flavor compound production. Together, these findings provide novel insights into the ecological and potential functional roles of phages during soy sauce fermentation.},
}

*Fermentation
*Bacteriophages/genetics/classification/physiology
*Soy Foods/microbiology/virology
*Metagenome
Genome, Viral
*Food Microbiology
Metagenomics

@article {pmid42562486,
year = {2026},
author = {Sehar, H and Chen, Z and Zhang, J and Wu, K and Li, BS and Yan, H},
title = {Microbial composition, dynamics, and functional roles in jinhua ham fermentation: integrating starter cultures and multi-omics for quality and safety.},
journal = {Food research international (Ottawa, Ont.)},
volume = {241},
number = {},
pages = {119711},
doi = {10.1016/j.foodres.2026.119711},
pmid = {42562486},
issn = {1873-7145},
mesh = {*Fermentation ; *Meat Products/microbiology/analysis ; Multiomics ; *Food Microbiology ; Animals ; Bacteria/metabolism/classification ; *Microbiota ; Food Safety ; Swine ; Fungi/metabolism ; },
abstract = {Jinhua ham, a traditional Chinese dry-cured meat product with nearly a millennium of production history, derives its characteristic colour, layered aroma, and umami-rich taste from the coordinated biochemical activity of a dynamic microbial ecosystem across an eight-to-ten-month fermentation timeline. This review provides a critical synthesis of research between 2018 and 2025 on microbial composition, community dynamics, functional roles, safety risks, starter culture applications, and multi-omics characterisation of Jinhua ham fermentation, unified by precision fermentation as an organising framework. High-throughput sequencing has established that halotolerant bacterial genera, Staphylococcus, Psychrobacter, Halomonas, and Lactobacillus, and fungal communities comprising Aspergillus, Debaryomyces, Meyerozyma, and Penicillium undergo deterministic, physicochemically driven succession, with their enzymatic activities governing proteolysis, lipolysis, volatile compound formation, colour stabilisation, and the accumulation of biogenic amines, mycotoxins, and antimicrobial resistance genes (ARGs). Autochthonous starter cultures, including Staphylococcus xylosus, Lactiplantibacillus plantarum, and Penicillium aethiopicum, improve process controllability, safety, and sensory consistency, yet their mechanistic basis and validation remain incompletely established. Genomic and metabolomic approaches have generated datasets, but integrated metagenomics-metabolomics coupling, capable of linking microbial gene networks to flavour compound production, and metatranscriptomic characterisation of gene expression remain the unmet methodological needs. Five research directions are proposed: achieving species-level microbial resolution through long-read sequencing and longitudinal sampling; validating flavour-forming pathways through isotopic tracing and controlled inoculation; standardising analytical protocols for cross-study comparability; conducting starter culture and ARG safety validation; and developing low-salt fermentation strategies. Together, these directions define the research investment required to advance Jinhua ham production from empirical tradition to precision-engineered consistency.},
}

*Fermentation
*Meat Products/microbiology/analysis
Multiomics
*Food Microbiology
Animals
Bacteria/metabolism/classification
*Microbiota
Food Safety
Swine
Fungi/metabolism

@article {pmid42562511,
year = {2026},
author = {Lee, JW and Kim, YM and Kim, YJ and Jeong, KC and Kim, SA},
title = {Wastewater irrigation reshapes the microbiome and resistome of radish sprouts: Insights from 16S rRNA and shotgun metagenomic sequencing.},
journal = {Food research international (Ottawa, Ont.)},
volume = {241},
number = {},
pages = {119739},
doi = {10.1016/j.foodres.2026.119739},
pmid = {42562511},
issn = {1873-7145},
mesh = {*Raphanus/microbiology/growth & development ; *Wastewater/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Agricultural Irrigation/methods ; Animals ; Metagenomics/methods ; Shotgun Sequencing ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Swine ; },
abstract = {Water scarcity is increasing the reliance on treated wastewater in fresh produce production, yet its effects on the microbial and hygienic quality of fresh produce remain unclear. This study evaluated the influence of wastewater irrigation on the microbiome and antibiotic resistance gene (ARG) profiles of radish sprouts grown under commercially relevant conditions. Using culture-dependent methods and integrated sequencing (16S rRNA and shotgun metagenomics), we tracked microbial and resistome dynamics across the sprout production process under three irrigation regimes: swine wastewater, treated wastewater, and sterile distilled water. Wastewater irrigation markedly increased microbial loads, with aerobic plate counts exceeding 8.0 log CFU/g in final radish sprouts. Both wastewater treatments were dominated by Pseudomonas and Acinetobacter. Resistome profiling showed persistent multidrug, bacitracin, and polymyxin resistance genes in wastewater-irrigated sprouts, while sulfonamide resistance genes occurred exclusively under wastewater irrigation, suggesting wastewater-associated environmental transmission. Higher ARG subtype richness in wastewater treatments suggested that conventional wastewater treatment processes do not completely eliminate diverse ARGs. ARG-host linkage analysis suggested an elevated potential for horizontal gene transfer within edible plant tissues. Overall, wastewater irrigation altered the microbiological quality of radish sprouts and facilitated ARG persistence, underscoring the need for improved post-treatment and preventive water management to safeguard fresh produce safety.},
}

*Raphanus/microbiology/growth & development
*Wastewater/microbiology
*RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
*Agricultural Irrigation/methods
Animals
Metagenomics/methods
Shotgun Sequencing
Bacteria/genetics
Drug Resistance, Microbial/genetics
Swine

@article {pmid42551498,
year = {2026},
author = {Da Costa, A and Groussin, P and Barengo, A and Yvorel, C and Mohammed, R and Romeyer, C and Boukhris, M and Benali, K},
title = {Cardiac Implantable Electronic Device Infections: Emerging Paradigms in Precision Prevention and Personalized Management.},
journal = {Trends in cardiovascular medicine},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tcm.2026.08.002},
pmid = {42551498},
issn = {1873-2615},
abstract = {Cardiac implantable electronic device (CIED) infections remain a major source of morbidity, mortality, and healthcare expenditure despite continuing advances in device technology. Increasing procedural complexity, repeat interventions, and an aging population with multiple comorbidities have shifted the focus from treatment alone toward comprehensive infection prevention. Biofilm formation is now recognized as the central pathogenic mechanism underlying CIED infection, explaining both the limited efficacy of antimicrobial therapy in the presence of retained hardware and the need for complete system extraction in established infection. This narrative review summarizes contemporary evidence supporting a multimodal approach to CIED infection prevention and personalized management. Prevention extends beyond perioperative antibiotic prophylaxis and skin antisepsis to encompass structured patient optimization, procedural contamination control, hematoma prevention, targeted Staphylococcus aureus decolonization, antibacterial envelopes, taurolidine-based pocket antisepsis, emerging antibiofilm technologies, and novel device platforms such as leadless pacemakers and extravascular implantable cardioverter-defibrillators. Risk stratification using PADIT, BLISTER, and complementary prediction models enables individualized allocation of preventive interventions according to estimated infection risk rather than uniform prophylaxis. Advances in diagnosis now combine multimodality imaging with biofilm-oriented microbiology, including device sonication, molecular diagnostics, and metagenomic sequencing, supporting pathogen-directed antimicrobial therapy and individualized clinical decision-making. Contemporary management likewise requires multidisciplinary expertise integrating extraction-risk assessment, complete hardware removal when indicated, optimized antimicrobial stewardship, and carefully planned reimplantation strategies. Rather than using the term precision medicine in its traditional genomic sense, this review emphasizes precision prevention and personalized management, whereby preventive and therapeutic interventions are tailored to each patient's quantified infection risk by integrating procedural, microbiological, host-related, and biofilm-associated determinants. Future improvements in clinical outcomes will depend on implementing integrated, risk-guided prevention strategies supported by multidisciplinary expert teams and emerging diagnostic and preventive technologies.},
}

@article {pmid42551604,
year = {2026},
author = {Liu, J and Ni, Y and Chen, M and Zhang, Y and Zhang, H and Kong, Q},
title = {Iron-carbon enhanced constructed wetland microbial fuel cells for sulfamethoxazole wastewater treatment: Performance evaluation and mechanistic insights.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135565},
doi = {10.1016/j.biortech.2026.135565},
pmid = {42551604},
issn = {1873-2976},
abstract = {Sulfamethoxazole (SMX) is frequently found in aquatic environments, causing ecological toxicity and accelerating the spread of antibiotic resistance genes (ARGs). The conventional constructed wetlands (CWs) face challenges in removing antibiotics and recovering energy. Constructed wetland-microbial fuel cells (CW-MFCs) are a combination of constructed wetlands and bio-electrochemical technology, enhancing pollutant removal and bioelectricity production. In this study, an iron-carbon particle-enhanced CW-MFC (FCCW) was constructed for SMX removal. The decontamination performance, electrochemical properties, metagenomic profiles, ARG distribution, and transformation products of SMX were analyzed. The results showed that the FCCW displayed superiority in power generation performance with an average voltage of 286.16 mV, a peak power density of 5.40 mW·m[-2], a peak current density of 32.48 mW·m[2], and a low internal resistance of 382.10 Ω. The FCCW achieved the highest removal rates of TN (51.66±1.63%), NH4[+]-N (65.49±1.96%), TP (96.69±2.46%), COD (80.90±2.98%), and SMX (96.49±2.77%). Metagenomic analysis revealed that Proteobacteria and Actinobacteria dominated in the three systems and the iron-carbon particles increased the relative abundance of genes associated with energy metabolism and pollutant transformation. Additionally, the FCCW showed a more diffuse distribution of ARGs and no localized accumulation. The analysis of transformation intermediates showed that the FCCW may rely on a glutathione (GSH)-related conjugation pathway associated with lower accumulation of certain toxic intermediates. Overall, the enhanced performance of the FCCW was attributed to improved redox conditions, more efficient electron transfer, and changes in microbial functional composition. Therefore, the FCCW system offers a promising approach for in-situ electricity generation and stable pollutant treatment performance.},
}

@article {pmid42551623,
year = {2026},
author = {Shahid, M and Raj, A and Shafi, Z and Ali, S},
title = {Nanopesticides-rhizo-microbiome interactions: Biochemical mechanisms, ecotoxicological effects and implications for pesticide fate and transformation.},
journal = {Comparative biochemistry and physiology. Toxicology & pharmacology : CBP},
volume = {},
number = {},
pages = {110651},
doi = {10.1016/j.cbpc.2026.110651},
pmid = {42551623},
issn = {1532-0456},
abstract = {Nano-enabled pesticides (NanoPs) formulations have emerged as promising alternative to conventional pesticides by improving ingredient stability, delivery, and controlled release. However, their unique physicochemical properties also influence interactions with soil microorganisms, raising concerns regarding ecological safety and long-term impacts on soil ecosystem functions. This review has critically synthesized the current knowledge about NanoPs-microbiome interactions with a focus on biochemical mechanisms underlying microbial responses and implications for pesticide fate and transformation. We review how the properties of NPs (e.g., particle size, surface charge, coatings, dissolution, and eco-corona formation) influence mobility, bioavailability, and microbial exposure. Mechanistic evidence of oxidative stress, membrane damage, enzyme inhibition, metal-ion-mediated toxicity and quorum sensing interference is critically synthesized to elucidate biochemical basis of NanoPs-induced microbial responses. Recent advances in high throughput sequencing and multi-omics technologies are also used to assess changes in microbial diversity, community composition, functional redundancy, microbial interaction networks and ecosystem resilience. The review further compares conventional and nano-formulated pesticides, highlighting differences in microbial toxicity, degradation kinetics, transformation pathways, and metabolite profiles. Current challenges associated with environmental fate assessment, standardized ecotoxicological testing, and microbiome-informed risk evaluation are critically discussed. Emerging opportunities for integrating metagenomics, artificial intelligence, and predictive modelling into environmental risk assessment are also highlighted. Finally, we propose a future research framework centered on microbiome-informed safe-by-design NanoPs, standardized testing protocols, and long-term field validation to support development of environmentally responsible nano-enabled crop protection technologies while preserving soil biodiversity and ecosystem functions.},
}

@article {pmid42551913,
year = {2026},
author = {Liao, T and Ding, SC and Yu, J and Gu, W},
title = {Enriching Microbial Cell-Free DNA in Clinical Metagenomics Using Epigenetic Filters.},
journal = {Clinical chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1093/clinchem/hvag089},
pmid = {42551913},
issn = {1530-8561},
support = {CA230156//NIH K08/ ; //Burroughs-Wellcome CAMS Award/ ; },
abstract = {INTRODUCTION: Noninvasive cell-free DNA (cfDNA) metagenomic sequencing enables hypothesis-free detection of microbial pathogens in patients with suspected infections. However, its clinical sensitivity is often limited by the overwhelming background of host-derived cfDNA, which can obscure low-abundance microbial signals. We developed an epigenetically guided enrichment strategy, termed Epigenetically filtered Metagenomic Sequencing (EpiMeta-seq), to selectively enrich microbial cfDNA based on fundamental differences in DNA methylation between microbial and human genomes.

METHODS: EpiMeta-seq uses the methylation-sensitive restriction enzyme HpaII to selectively digest unmethylated CCGG sites, which are prevalent in microbial genomes but largely methylated in human DNA. Only fragments cleaved once at unmethylated sites are incorporated into sequencing libraries, thereby enriching microbial cfDNA prior to sequencing. We assessed plasma samples from patients with microbiologically confirmed infections. Metagenomics informatics involved alignment, removal of host DNA, and taxonomic classification of sequencing reads to a curated reference database.

RESULTS: In spike-in experiments at a 1:1000 dilution, EpiMeta-seq achieved a mean enrichment of 24.5-fold for fungal species and 11.4-fold for bacterial species compared with unenriched whole-genome sequencing. In 23 clinical plasma samples representing 12 pathogens, EpiMeta-seq produced an average 10.0-fold increase in microbial reads per million. Viral DNA showed the highest enrichment (mean 11.5-fold), while bacterial enrichment varied across species (1.2- to 30.8-fold).

CONCLUSIONS: By leveraging genome-wide methylation differences between host and microbial DNA, EpiMeta-seq is a proof-of-concept, orthogonal enrichment strategy for improving microbial cfDNA signal-to-background ratio across diverse pathogen types in metagenomic sequencing.},
}

@article {pmid42552309,
year = {2026},
author = {Lal, A and Riopelle, JC and Villarin, K and Mathur, M and Enriquez, L and Xiao, R and Phemister-Jimenez, N and Gilbert, K and Cole, SD and Tilyou, M and Kennedy, KP and Vaca, E and Castillo, W and Weisberg, M and Mattei, LM and Beiting, DP},
title = {Human wastewater contamination drives the emergence of multidrug-resistant bacteria in the Galápagos marine ecosystem.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42552309},
issn = {2041-1723},
support = {STS-1557138//National Science Foundation (NSF)/ ; },
mesh = {*Wastewater/microbiology ; *Drug Resistance, Multiple, Bacterial/genetics ; Humans ; Ecuador ; Ecosystem ; Anti-Bacterial Agents/pharmacology ; Escherichia coli/genetics/drug effects/isolation & purification ; *Bacteria/genetics/drug effects/isolation & purification ; Seawater/microbiology ; Plasmids/genetics ; Sewage/microbiology ; Metagenomics ; Enterobacteriaceae/genetics/isolation & purification/drug effects ; },
abstract = {Antimicrobial resistance poses a global threat to public health. Mobile microbiological laboratories can enable environmental monitoring of antimicrobial resistance, particularly in geographically remote and resource-limited locations, such as the Galápagos archipelago. Here, we report the development of a mobile laboratory for antimicrobial resistance surveillance of marine sites surrounding San Cristóbal, the archipelago's second most populated island, which has experienced rapid urbanization and intense international tourism pressure. On-site metagenomic sequencing of wastewater-contaminated marine sites reveals a stark shift in microbial genera and a higher count of antimicrobial resistance genes compared to uncontaminated marine sites, mirroring metagenomic results of local untreated sewage. Over 40% of lactose-fermenting Enterobacteriaceae isolates collected directly from sewage or marine environments near sites of wastewater outfall exhibit multidrug resistance. Long-read sequencing and de novo assembly of bacterial genomes and plasmids from multidrug-resistant Escherichia coli reveal frequent and rapid reassortment of antimicrobial resistance genes on plasmids, generating a diverse and functional resistome on the island. This study not only provides a framework for conducting antimicrobial resistance research in low-resource settings but also underscores the impact of wastewater contamination on the environmental antimicrobial resistance landscape and highlights potential threats to human and animal health.},
}

*Wastewater/microbiology
*Drug Resistance, Multiple, Bacterial/genetics
Humans
Ecuador
Ecosystem
Anti-Bacterial Agents/pharmacology
Escherichia coli/genetics/drug effects/isolation & purification
*Bacteria/genetics/drug effects/isolation & purification
Seawater/microbiology
Plasmids/genetics
Sewage/microbiology
Metagenomics
Enterobacteriaceae/genetics/isolation & purification/drug effects

@article {pmid42552346,
year = {2026},
author = {Wu, YL and Fairweather, JH and Campbell, M and Hergt, J and Yusiharni, E and Smirk, M and Dodd, A and Sun, X and Clode, P and Hubbard, A and Allentoft, ME and McDonald, J},
title = {Biological contributions to manganese oxides in rock varnish at Murujuga (Western Australia).},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42552346},
issn = {2045-2322},
support = {LP190100724//Australian Research Council/ ; },
mesh = {*Oxides/chemistry/metabolism/analysis ; *Manganese Compounds/chemistry/metabolism/analysis ; Western Australia ; X-Ray Diffraction ; *Paint/analysis ; Metagenome ; Manganese ; },
abstract = {Rock varnish is a ubiquitous Mn-rich coating on exposed rock surfaces in arid environments, yet the mechanisms underlying its formation remain debated. Here, we investigate rock varnish from Murujuga, Western Australia, to assess the role of microbial processes in manganese (Mn) accumulation. Bulk compositional and mineralogical analyses confirm high concentrations of Mn, Fe, Al, and Si; however, the Mn matrix is predominantly composed of amorphous to poorly crystalline phases that fall below the indexing or detection thresholds of X-ray diffraction (XRD) and electron backscatter diffraction (EBSD). Nanoscale characterization reveals a Mn-rich matrix encasing discrete Fe and Al-Si grains, featuring nanometre scale laminations and particle size distribution characteristic of biogenic Mn oxides. High-quality metagenome-assembled genomes (MAGs) reveal a pronounced dominance of Chroococcidiopsidaceae and Rubrobacter_F, pioneer taxa known to accumulate intracellular Mn for defence mechanisms. Furthermore, targeted functional annotation using Hidden Markov Models (HMMs) confirms a widespread, community-level genomic potential for biologically influenced Mn accumulation and utilization. Because this biomineralisation is an ongoing process governed by local environmental stressors, these rock coatings have high potential as long-term paleoenvironmental and climate proxies. This is the first microbiomic characterisation of the rock varnish from the Murujuga Cultural Landscape, and an important step in unlocking the potential of this deposit as a chronological marker for this region's petroglyphs.},
}

*Oxides/chemistry/metabolism/analysis
*Manganese Compounds/chemistry/metabolism/analysis
Western Australia
X-Ray Diffraction
*Paint/analysis
Metagenome
Manganese

@article {pmid42553031,
year = {2026},
author = {Wang, Y and Lei, J and Cui, S and Zhou, P and Wu, Y},
title = {Beyond detection: quantitative interpretation of Aspergillus-positive bronchoalveolar lavage fluid metagenomic next-generation sequencing for diagnostic stratification and prediction of respiratory deterioration.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1897649},
pmid = {42553031},
issn = {2235-2988},
mesh = {Humans ; *Aspergillus/genetics/isolation & purification ; *Bronchoalveolar Lavage Fluid/microbiology ; Retrospective Studies ; *Invasive Pulmonary Aspergillosis/diagnosis/microbiology/drug therapy ; Female ; *High-Throughput Nucleotide Sequencing ; *Metagenomics/methods ; Male ; Middle Aged ; Aged ; Prognosis ; ROC Curve ; Antifungal Agents/therapeutic use ; },
abstract = {BACKGROUND: The increasing use of bronchoalveolar lavage fluid (BALF) metagenomic next-generation sequencing (mNGS) has substantially improved the detection of Aspergillus species in patients with suspected pulmonary infections. However, positive mNGS results frequently present a clinical dilemma because Aspergillus may represent invasive pulmonary aspergillosis (IPA), airway colonization, or transient fungal detection. The clinical value of quantitative fungal burden assessment remains insufficiently defined, particularly regarding risk stratification among untreated patients.

METHODS: We conducted a retrospective real-world cohort study including 114 hospitalized patients with BALF mNGS-positive Aspergillus detected between April 2024 and November 2025. Patients were classified according to clinical IPA diagnosis, antifungal treatment status, and occurrence of respiratory deterioration during a 3-month follow-up period. Quantitative fungal burden was expressed as reads per ten million (RPTM). Receiver operating characteristic (ROC) analysis, logistic regression, integrated discrimination improvement (IDI), and category-free net reclassification improvement (NRI) were used to evaluate diagnostic and prognostic performance.

RESULTS: Among 114 patients, 31 met clinical diagnostic criteria for IPA and 83 were classified as non-IPA. Aspergillus burden was significantly higher in IPA patients than in non-IPA patients (logarithmic scale median RPTM 2.46 vs. 0.30, P < 0.001). ROC analysis identified an exploratory cohort-derived diagnostic threshold of 75 RPTM for IPA discrimination (AUC = 0.853, 95% CI 0.745-0.960). Among 77 patients who did not receive antifungal therapy, 31 experienced respiratory deterioration during follow-up. Higher RPTM values were independently associated with deterioration (adjusted OR = 5.27, 95% CI 1.78-17.06, P = 0.001). An exploratory RPTM threshold of 2.5 showed modest discriminatory ability for subsequent respiratory deterioration, with an AUC of 0.682. Incorporation of quantitative fungal burden significantly improved discrimination and reclassification performance beyond conventional clinical variables. In contrast, baseline RPTM showed no significant association with respiratory deterioration among patients receiving antifungal therapy.

CONCLUSIONS: Quantitative interpretation of Aspergillus-positive BALF mNGS results may provide additional information beyond simple pathogen detection. Two exploratory cohort-derived thresholds were identified: a higher threshold associated with clinical IPA adjudication and a lower threshold associated with subsequent respiratory deterioration among untreated patients. These findings are hypothesis-generating and require external validation before clinical application. RPTM should be interpreted as an adjunctive marker within the overall clinical context rather than as a standalone diagnostic or prognostic threshold.},
}

Humans
*Aspergillus/genetics/isolation & purification
*Bronchoalveolar Lavage Fluid/microbiology
Retrospective Studies
*Invasive Pulmonary Aspergillosis/diagnosis/microbiology/drug therapy
Female
*High-Throughput Nucleotide Sequencing
*Metagenomics/methods
Male
Middle Aged
Aged
Prognosis
ROC Curve
Antifungal Agents/therapeutic use

@article {pmid42553092,
year = {2026},
author = {Guo, N and Chen, S and Guo, L and Qiu, X and Li, Z},
title = {Metagenomic next-generation sequencing: new horizons in microbiology.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1824160},
pmid = {42553092},
issn = {2235-2988},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Animals ; COVID-19/diagnosis ; Computational Biology/methods ; Pandemics ; SARS-CoV-2/genetics ; Public Health ; One Health ; },
abstract = {The COVID-19 pandemic has exposed vulnerabilities in global health systems while accelerating the adoption of metagenomic next-generation sequencing (mNGS) as a transformative tool for culture-independent, unbiased microbial detection. In clinical diagnostics, mNGS enables simultaneous detection of diverse pathogens without prior hypothesis, though its yield depends heavily on specimen type and clinical context. In public health, mNGS has demonstrated remarkable utility in outbreak tracing, novel pathogen discovery, antimicrobial resistance (AMR) surveillance, and One Health initiatives. However, massive data volumes pose persistent challenges in bioinformatics, standardization, and computational demands. Future integration of artificial intelligence, automated platforms, and multi-omics approaches will enhance the conversion of raw data into actionable insights. Collectively, mNGS is poised to drive a paradigm shift from reactive responses to proactive, system-level microbial surveillance across human, animal, and environmental health.},
}

Humans
*High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
Animals
COVID-19/diagnosis
Computational Biology/methods
Pandemics
SARS-CoV-2/genetics
Public Health
One Health

@article {pmid42553304,
year = {2026},
author = {Geng, Q and Wang, Y and Fan, Y and Liu, N and Zhao, X},
title = {First reported survival of anthrax meningoencephalitis in a low-incidence region: successful management with mNGS-guided combination therapy.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1792720},
pmid = {42553304},
issn = {2235-2988},
mesh = {Humans ; Male ; *Meningoencephalitis/drug therapy/microbiology/diagnosis ; *Anti-Bacterial Agents/therapeutic use ; Middle Aged ; *Anthrax/drug therapy/diagnosis/microbiology ; Drug Therapy, Combination/methods ; *Bacillus anthracis/genetics/isolation & purification/drug effects ; Ciprofloxacin/therapeutic use ; High-Throughput Nucleotide Sequencing ; Amikacin/therapeutic use ; Treatment Outcome ; Animals ; Penicillin G/therapeutic use ; Linezolid/therapeutic use ; Levofloxacin/therapeutic use ; Cerebrospinal Fluid/microbiology ; },
abstract = {We report a rare survival case of anthrax meningoencephalitis in a 56-year-old male from a low-incidence region. The patient presented with nasal discharge, fever, headache, and rapid onset of coma following the slaughter of a diseased cow. Physical examination revealed a characteristic ulcerative eschar on the right index finger, while laboratory investigations showed significant leukocytosis and hemorrhagic cerebrospinal fluid (CSF) characterized by elevated protein and decreased glucose levels. Although initial microscopy misidentified the pathogen as Bacillus cereus, metagenomic next-generation sequencing (mNGS) of the CSF confirmed Bacillus anthracis within 48 hours. This rapid molecular diagnosis enabled a timely switch to a CDC-recommended combination regimen, initially with quadruple therapy (penicillin G, ciprofloxacin, amikacin, and linezolid) followed by optimization to triple therapy (penicillin G, levofloxacin, and linezolid) during the ICU stay, ultimately leading to the patient's full neurological recovery. This case underscores that the synergistic use of rapid mNGS-based diagnosis and appropriate combination therapy is critical for achieving survival in anthrax meningoencephalitis.},
}

Humans
Male
*Meningoencephalitis/drug therapy/microbiology/diagnosis
*Anti-Bacterial Agents/therapeutic use
Middle Aged
*Anthrax/drug therapy/diagnosis/microbiology
Drug Therapy, Combination/methods
*Bacillus anthracis/genetics/isolation & purification/drug effects
Ciprofloxacin/therapeutic use
High-Throughput Nucleotide Sequencing
Amikacin/therapeutic use
Treatment Outcome
Animals
Penicillin G/therapeutic use
Linezolid/therapeutic use
Levofloxacin/therapeutic use
Cerebrospinal Fluid/microbiology

@article {pmid42553918,
year = {2026},
author = {Chen, H and Zhang, B and Zhu, B and Zhou, P and Xu, C and Li, Q and Chen, W},
title = {Comparison of the effects of stent-based diversion technique versus prophylactic double-lumen ileostomy on intestinal flora in postoperative patients with rectal cancer.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1791364},
pmid = {42553918},
issn = {1664-302X},
abstract = {BACKGROUND: The stent-based diversion technique (SDT), as a novel surgical approach for reducing anastomotic leakage (AL) following low anterior resection (LAR), achieving effective intestinal diversion while avoiding ileostomy and subsequent stoma reversal surgery. Although multicenter randomized controlled trials have demonstrated the safety of SDT, the alterations in postoperative intestinal microbiota following SDT remain inadequately characterized.

METHODS: This study enrolled 40 patients with mid-low rectal cancer (21 SDT, 19 PDI). Rectal swab samples were collected preoperatively and at 3 weeks and 3 months postoperatively (n = 120) for metagenomic sequencing. α- and β-diversity analyses were performed to compare microbial community characteristics. LEfSe was used for differential analysis of species and KEGG functional pathways. Postoperative clinical outcomes including AL and anastomotic stricture (AS) were assessed.

RESULTS: The SDT group showed a significantly lower incidence of AS compared with the PDI group (4.76% vs. 31.58%, p < 0.05). Preoperative α- and β-diversity were comparable between groups. Postoperatively, the SDT group exhibited higher microbial richness at both 3 weeks and 3 months (both p < 0.05). In the PDI group, the α-diversity showed a continuous decline from 3 weeks to 3 months postoperatively compared with the preoperative baseline (p < 0.05). However, the SDT group demonstrated no significant decrease in α-diversity at 3 weeks (p > 0.05), but did at 3 months (p < 0.05). Significant intergroup β-diversity divergence emerged from 3 weeks onward (both p < 0.05). The SDT group showed significant structural changes from 3 weeks to 3 months (p < 0.05), whereas the PDI group remained stable. At 3 weeks, opportunistic pathogens (e.g., Parvimonas micra) were enriched in the PDI group, while the SDT group enriched beneficial taxa (e.g., Akkermansia). By 3 months, the PDI group exhibited enrichment of oral/genitourinary-derived bacteria (Prevotellaceae, Porphyromonas, Fusobacterium), whereas the SDT group showed higher abundance of beneficial Bacteroidota (e.g., Phocaeicola vulgatus). Functionally, the SDT group enriched amino acid and carbohydrate metabolism pathways, while the PDI group enriched translation and energy metabolism pathways.

CONCLUSION: We found that SDT better preserves postoperative gut microbiota diversity, promotes the restoration of beneficial bacteria, and influences microbial functional pathways, thereby establishing a more favorable microbiome environment for patients.},
}

@article {pmid42554318,
year = {2026},
author = {Lin, H and Wu, W and Fang, H and Chen, Y and Wu, H and Lai, X and Li, L},
title = {Integrated Metabolomic and Metagenomic Profiling Reveals Distinct Microbial-Metabolic Signatures in the Adenoma-Carcinoma Sequence of Colorectal Cancer.},
journal = {Biomedical chromatography : BMC},
volume = {40},
number = {9},
pages = {e70588},
doi = {10.1002/bmc.70588},
pmid = {42554318},
issn = {1099-0801},
support = {3502Z202374067//Natural Science Foundation of Xiamen, China/ ; },
mesh = {Humans ; *Colorectal Neoplasms/metabolism/microbiology ; *Metabolomics/methods ; *Adenoma/metabolism/microbiology ; *Metabolome/physiology ; Feces/microbiology ; *Metagenomics/methods ; Male ; Female ; Multiomics ; Middle Aged ; *Gastrointestinal Microbiome/physiology/genetics ; Biomarkers, Tumor/metabolism/analysis ; Aged ; },
abstract = {Colorectal cancer (CRC) arises via the stepwise adenoma-carcinoma sequence (ACS). Gut microbial dysbiosis and host metabolic reprogramming jointly correlate with CRC onset and advancement, yet their stage-specific crosstalk across ACS remains largely unclear. Limited multi-omics research on microbial-metabolic interactions throughout ACS hinders the development of early diagnostic biomarkers and preventive strategies. Here, we combined untargeted mucosal metabolomics and fecal shotgun metagenomic sequencing in 36 participants, covering healthy controls, ACS, and CRC patients. We systematically analyzed microbial composition, functions, differential metabolites, and enriched pathways and integrated multi-omics data to screen stage-specific signatures. Distinct gut microbial profiles and progressive functional shifts toward pathogenicity and abnormal carbohydrate metabolism were observed along ACS. Mucosal metabolism was continuously disrupted, with prominent alterations in taurine-hypotaurine, sphingolipid, and bile acid pathways. Core differential metabolites showed excellent diagnostic performance. Microbe-metabolite interactions were progressively enhanced to form a concerted pro-tumor axis. This study characterizes unique ACS-stage microbial-metabolic features. Dysregulated metabolic pathways and key microbe-metabolite crosstalk are closely associated with CRC progression, offering novel non-invasive biomarkers and premalignant intervention targets.},
}

Humans
*Colorectal Neoplasms/metabolism/microbiology
*Metabolomics/methods
*Adenoma/metabolism/microbiology
*Metabolome/physiology
Feces/microbiology
*Metagenomics/methods
Male
Female
Multiomics
Middle Aged
*Gastrointestinal Microbiome/physiology/genetics
Biomarkers, Tumor/metabolism/analysis
Aged

@article {pmid42554471,
year = {2026},
author = {Olivo, D and Collins, D and de Koch, M and Revekant, C and Kraberger, S and Varsani, A},
title = {Metagenome-assembled genomes of papillomaviruses from mallard and northern pintail cloacal swabs.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0072626},
doi = {10.1128/mra.00726-26},
pmid = {42554471},
issn = {2576-098X},
abstract = {There is little known about papillomavirus diversity in waterfowl. From cloacal swabs of one mallard and three northern pintails sampled in New Mexico (USA), we identified four papillomavirus genomes. These papillomaviruses share >92.7% genome-wide nucleotide pairwise identity with Anas platyrhynchos papillomavirus 3 (AplaPV3) identified from a mallard in Missouri (USA).},
}

@article {pmid42546224,
year = {2026},
author = {Pavlovic, NR and Malings, CA and Huang, M and He, Y and Diez, S and Bratburd, J and Mahmoud, H and Schnell, J and Hang, Y and Anderson, L and Grodzinsky, G and deSouza, P and Mead, MI and Rao, Y and Velho, R and Davignon, D and Munde, S and Sayeed, A and Aekakkararungroj, A and Joshi, A and Olayinka, O and Rondouba, HD and Pant, P},
title = {Satellite-derived air quality data can effectively support health needs when use cases, Earth observing capabilities, and capacities align.},
journal = {Journal of the Air & Waste Management Association (1995)},
volume = {},
number = {},
pages = {1-27},
doi = {10.1080/10962247.2026.2698602},
pmid = {42546224},
issn = {2162-2906},
abstract = {Advances in Earth observation (EO) remote sensing technologies have delivered a range of aerosol and trace gas pollution data with ever-improving spatial and temporal resolution, significantly benefitting assessments of global air quality (AQ). Furthermore, the application of data synthesis techniques incorporating satellite EO with other information sources has improved the availability of satellite-derived estimates of pollutant exposure at local to global scales. These data have been applied to address a diversity of use cases in AQ monitoring and public health, from long-term trend tracking, exposure assessment, and epidemiological analysis to short-term emissions identification and early warning. Successful application of satellite EO to address AQ and AQ-related health problems requires an alignment between (1) the technical capabilities of satellite data to provide relevant information, (2) a defined case for using this information to address a particular need, and (3) the human capacity, computational resources, operational plans, and policy and governance frameworks to implement a solution and take action, and to sustain the solution for as long as the need remains. Only when there is substantial alignment across all these factors can satellite EO information be effectively translated into public health benefits. This paper surveys applications of satellite EO to AQ assessment and AQ-related health management globally, synthesizing key commonalities into recommendations for how satellite EO can effectively support health needs. We also identify gaps in current satellite EO capabilities, use-case applications, and feasibility factors where future research and investment could reduce barriers to increased application of satellite EO to address pressing public health concerns related to AQ worldwide.Implications: This paper summarizes insights collected through the Group on Earth Observations (GEO) Health Community of Practice Air Quality and Respiratory Health Work Group on the current state and gaps in the use of satellite EO to support air quality and related health decision-making globally. We synthesize these insights into general recommendations for how satellite EO capabilities, use cases, and feasibility considerations can be aligned towards effective use of satellite EO data for air quality and related health effects. We also identify barriers and gaps in current capabilities, uses, and capacities, making recommendations for how these might be addressed.},
}

@article {pmid42546623,
year = {2026},
author = {Chen, J and Zhang, X and Liu, N and Chen, X and Wang, Y and Lin, Q and Bao, Y},
title = {Multi-omics analysis provides mechanistic insights into tanninase-assisted flavor evolution in Phyllanthus emblica L. wine.},
journal = {Food chemistry},
volume = {525},
number = {Pt 3},
pages = {150651},
doi = {10.1016/j.foodchem.2026.150651},
pmid = {42546623},
issn = {1873-7072},
abstract = {Winemaking from Phyllanthus emblica L. is limited by astringency and tannin-associated instability. This study evaluated tanninase pretreatment followed by Saccharomyces cerevisiae fermentation for improving tannin-rich P. emblica L. wine. Metagenomics, LC-MS, and HS-SPME-GC-MS were used to characterize microbial succession and metabolite profiles. A total of 231 non-volatile metabolite features and 183 volatile flavor compounds were putatively annotated. Tanninase pretreatment reduced tannin content from 0.23% to 0.15% before inoculation and was associated with increased ellagic acid, suggesting partial hydrolysis of hydrolysable tannins. The NF group showed higher S. cerevisiae abundance, reaching 77.64%, and altered phenolic, organic acid, fatty acid, amino acid-related, and aroma-related metabolite profiles. Microbial-metabolite analysis suggested that aromatic amino acid metabolism may contribute to floral and fruity ester formation through the Ehrlich pathway. Sensory evaluation showed reduced bitterness/astringency, clearer appearance, and improved overall quality in NF wine.},
}

@article {pmid42546643,
year = {2026},
author = {Liu, S and Li, Y and Du, C and Zhu, X and Wang, S and Zeng, X and Jia, Y},
title = {Metal(loid) contamination shifts microbial carbon and nitrogen cycling potential in paddy soils.},
journal = {Journal of hazardous materials},
volume = {515},
number = {},
pages = {143137},
doi = {10.1016/j.jhazmat.2026.143137},
pmid = {42546643},
issn = {1873-3336},
abstract = {Trace metal(loid) contamination in paddy soils derived from either geogenic sources or mining activities is widely occurring in mid-south to south China and south to south east Asia. Due to their toxicities, these trace metal(loid)s may influence microbial community assembly and carbon/nitrogen (C/N) cycling. However, how metal(loid) contamination reshapes community composition, functional potential, and genomic traits of key functional microorganisms remains unclear. Here, we collected paddy soil samples from mid-south to south China and classified them into low- and high-contamination groups based on the Nemerow index. The associations among contamination level, microbial community composition, C/N-cycling potential, and genomic traits of key functional microorganisms were examined by combining soil physicochemical characterization, 16S rRNA gene amplicon sequencing, metagenomics, and metagenome-assembled genome (MAG) reconstruction. Bacterial and archaeal richness did not differ significantly between contamination levels, whereas community composition varied markedly. Methane oxidation genes were enriched in high-contamination soils, whereas methanogenesis genes were more abundant in low-contamination soils. Denitrification- and dissimilatory nitrate reduction to ammonium (DNRA)-related genes increased under heavy contamination, whereas several nitrogen fixation genes declined. Environmental association analyses identified As, Cd, Pb, Cr, and Zn as key variables associated with C/N cycling genes. Several MAGs carried both elemental cycling genes and metal(loid)-response or transformation genes, suggesting potential multifunctionality in contaminated paddy soils. Overall, metal(loid) contamination, together with associated edaphic variation, reorganized microbial communities and redistributed C/N cycling potential. This work provides a genomic basis for identifying microorganisms that could serve as bioindicators or functional targets in contaminated paddy soils.},
}

@article {pmid42546794,
year = {2026},
author = {Li, S and Chen, T and Liu, J and Lu, K and Chen, X and Lin, L and Lin, Y},
title = {Enriched microplastic-associated biofilms exacerbate gut microbial dysbiosis and metabolic disruption in mice.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {128873},
doi = {10.1016/j.envpol.2026.128873},
pmid = {42546794},
issn = {1873-6424},
abstract = {Microplastics (MPs) and opportunistic pathogens are recognized as emerging environmental hazards, yet the health risks associated with mammalian exposure to biofilms enriched on MP surfaces remain poorly characterized. This study evaluated the characteristics of microbial biofilms enriched on MPs from aquatic and sediment matrices over 12 weeks and assessed their potential health impacts using a murine mammalian model. Metagenomic profiling showed that the enriched biofilms exhibited alterations in community composition, accompanied by an overrepresentation of genes associated with antibiotic resistance, iron acquisition, and virulence traits. In the murine model, dietary exposure to the MP-associated biofilms coincided with changes in host intestinal inflammatory markers and a distinct shift in the gut microbiota profile. Metabolomic analysis further revealed synchronous alterations in extracellular and fecal metabolite profiles, including profiles linked to secondary bile acid pathways, alongside a downregulation of intestinal barrier tight junction markers. These parallel taxonomic and metabolic shifts indicate that environmental biofilms enriched on microplastics can provoke complex physiological responses in a mammalian host. This study provides a valuable framework for assessing the potential mammalian health risks posed by plastisphere-associated microbial complexes.},
}

@article {pmid42548291,
year = {2026},
author = {Nicolas, P and Beigneux, Y and Guennoc, AM and Destras, G and Mossad, M and Bal, A and Talagrand-Reboul, E and Rodriguez, C and Cappy, P and Gubavu, C and Marignier, R and Vukusic, S and Jarraud, S and Maillart, E and Josset, L and Pourcher, V},
title = {Borrelia miyamotoi meningoradiculitis complicating ocrelizumab treatment for multiple sclerosis: A report of three cases.},
journal = {Multiple sclerosis (Houndmills, Basingstoke, England)},
volume = {},
number = {},
pages = {13524585261473068},
doi = {10.1177/13524585261473068},
pmid = {42548291},
issn = {1477-0970},
abstract = {Ocrelizumab is an anti-CD20 monoclonal antibody that is highly effective in multiple sclerosis (MS) but is associated with an increased risk of opportunistic infections that may be difficult to diagnose. We report three MS patients treated with ocrelizumab who developed severe meningoradiculitis. Routine investigations failed to identify any pathogen, whereas metatranscriptomic analysis of cerebrospinal fluid (CSF) detected Borrelia miyamotoi RNA. All patients improved after appropriate antibiotic therapy. B. miyamotoi should be considered in anti-CD20-treated MS patients presenting with meningoradiculitis, and CSF metatranscriptomics should be used to investigate undiagnosed central or peripheral nervous system infections, particularly in immunocompromised individuals. Ocrelizumab is a highly effective treatment widely used in MS but has been associated with an increased risk of infection. We report three cases of B. miyamotoi infections in patients receiving ocrelizumab in which routine laboratory tests failed to detect the pathogen.},
}

@article {pmid42548466,
year = {2026},
author = {Yang, L and Tao, Y and He, Y and Liu, S and Gan, L and Dai, A and Ni, Q and Wang, Y and Li, F and Liu, Q and Hu, Y and Wang, Y and Lu, W},
title = {Metagenomic and metabolomic profiling in primary aldosteronism with coexisting obstructive sleep apnea.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1858100},
pmid = {42548466},
issn = {1664-2392},
mesh = {Humans ; *Sleep Apnea, Obstructive/metabolism/complications/microbiology/genetics ; Female ; *Hyperaldosteronism/metabolism/complications/genetics/microbiology ; Male ; *Metagenomics/methods ; *Metabolomics/methods ; Prospective Studies ; Middle Aged ; *Gastrointestinal Microbiome/genetics ; *Metabolome ; Adult ; Feces/microbiology ; Polysomnography ; },
abstract = {BACKGROUND: Primary aldosteronism (PA) frequently coexists with obstructive sleep apnea (OSA), and this comorbidity is associated with increased cardiometabolic risk. Although both PA and OSA have been individually linked to gut microbiome alterations, it remains unclear which layer of gut microbiome-associated variation best reflects clinical heterogeneity in PA with coexisting OSA.

METHODS: In this prospective observational study, we performed shotgun metagenomic sequencing and untargeted fecal metabolomic profiling in 29 adults with clinically confirmed PA, who were stratified according to OSA severity (G1-G4) based on overnight polysomnography. Microbial gene richness, taxonomic composition, functional potential based on KEGG annotation, and antibiotic resistance gene profiles were analyzed using standardized bioinformatic workflows. Metabolomic variation was assessed using multivariate analysis, pathway enrichment, and additional exploratory analyses incorporating apnea-hypopnea index (AHI) as a continuous variable. Multiple-testing correction was applied to metabolite-level comparisons.

RESULTS: Global gut microbial gene richness, alpha diversity, beta diversity, and broad functional profiles did not show strong group-level separation across OSA severity strata. Additional analyses using AHI as a continuous variable similarly showed no significant association between AHI and overall gene richness or alpha diversity indices. Nevertheless, selective genera showed exploratory associations with AHI, suggesting that localized taxonomic signals may occur despite relative stability of global community structure. Antibiotic resistance gene profiles showed marked inter-individual variability without clear group-level separation, although ARO richness showed an exploratory inverse association with AHI. In contrast, fecal metabolomic profiling revealed nominal phenotype-associated differences, including trehalose-related metabolites and FAHFA species that showed inverse exploratory associations with AHI. However, no individual metabolite remained significant after global Benjamini-Hochberg false discovery rate correction.

CONCLUSIONS: In PA with coexisting OSA, gut microbiome-associated heterogeneity appears to be more readily reflected by selected taxonomic and metabolic signals than by global microbial diversity or broad functional potential. However, given the small sample size, limited control of clinical and lifestyle confounders, and lack of metabolite-level significance after global FDR correction, these findings should be interpreted as exploratory and hypothesis-generating. Larger controlled cohorts incorporating PA subtype, medication exposure, dietary assessment, and longitudinal validation are needed.},
}

Humans
*Sleep Apnea, Obstructive/metabolism/complications/microbiology/genetics
Female
*Hyperaldosteronism/metabolism/complications/genetics/microbiology
Male
*Metagenomics/methods
*Metabolomics/methods
Prospective Studies
Middle Aged
*Gastrointestinal Microbiome/genetics
*Metabolome
Adult
Feces/microbiology
Polysomnography

@article {pmid42548546,
year = {2026},
author = {Cao, L and Zhao, Y and Wang, R and Liu, Y and Luo, L and Yan, H and Li, N},
title = {The value of mNGS in the diagnosis of central nervous system infections in immunodeficient hosts with decompensated cirrhosis complicated by Listeria encephalitis: Case Report.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1857949},
pmid = {42548546},
issn = {2296-858X},
abstract = {INTRODUCTION: The incidence of central nervous system (CNS) infections caused by Listeria monocytogenes is rising, yet it remains rarely reported and frequently misdiagnosed in patients with decompensated cirrhosis. This report evaluates the diagnostic utility of metagenomic next-generation sequencing (mNGS) in this specific population.

CASE PRESENTATION: A 62-year-old male with a 7-year history of cirrhosis presented with fever, headache, and loss of consciousness. At admission, the patient was in a decompensated state with a Child-Pugh score of 9 (Grade B) and a Model for End-Stage Liver Disease (MELD) score of 12, characterized by hypoalbuminemia and mild ascites.

DIAGNOSIS AND INTERVENTION: To avoid delayed treatment, broad-spectrum antibiotics were used before the results of blood and cerebrospinal fluid cultures were available. Preliminary cerebrospinal fluid (CSF) analysis showed an atypical inflammatory response in the context of cirrhosis-associated immune dysfunction. Although conventional CSF cultures remained negative, mNGS detected Listeria monocytogenes sequences within 16 h. Early mNGS-guided targeted therapy, followed by multidisciplinary management under real-world drug availability constraints, was associated with significant clinical improvement and successful discharge.

CONCLUSION: Cirrhosis-associated immune dysfunction (CAID) and hypersplenism can mask typical CSF diagnostic markers. mNGS provides a rapid, unbiased diagnostic paradigm that is crucial for shortening diagnostic duration and guiding precision therapy in immunocompromised hosts.},
}

@article {pmid42548723,
year = {2026},
author = {Zhang, L and Huang, D and Song, J and Zhao, T and Yang, F and Li, C and Zheng, F},
title = {Case Report: Intestinal mycobacterium abscessus infection in a child.},
journal = {Frontiers in pediatrics},
volume = {14},
number = {},
pages = {1815227},
pmid = {42548723},
issn = {2296-2360},
abstract = {The diagnosis and treatment of Mycobacterium abscessus infections present significant challenges, especially in the rare cases of extrapulmonary involvement in pediatric patients. These cases are characterized by diagnostic difficulties, limited therapeutic options, scarce clinical experience, and a lack of evidence-based treatment guidelines. This article reports on a 6-year-old child who experienced fever and abdominal pain. Metagenomic next-generation sequencing (mNGS) facilitated the rapid and accurate identification of Mycobacterium abscessus as the causative pathogen. Under a standardized full-course protocol, an individualized therapy regimen (that includes Imipenem, Azithromycin, and Linezolid) led to favorable clinical outcomes. Through the analysis of this successfully treated case, we aim to derive clinical insights and identify potential limitations, with the goal of exploring effective diagnostic and therapeutic approaches for pediatric patients with non-tuberculous mycobacterial (NTM) infections in the future.},
}

@article {pmid42548731,
year = {2026},
author = {Xu, X and Yu, T and Wu, H and Guo, Y and Li, M and Han, Y and Zhao, L and Yu, X},
title = {The composition alteration of gut microbiota in lung cancer: a systematic review and meta-analysis.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1873706},
pmid = {42548731},
issn = {1664-302X},
abstract = {BACKGROUND: The association between the gut microbiota and lung cancer remains understudied. In this study, we conducted a comprehensive systematic review and meta-analysis to quantitatively synthesize evidence from multiple cohorts to identify robust and consistent alterations in gut microbial diversity and taxonomy associated with lung cancer.

METHODS: A systematic literature search was performed across PubMed, Cochrane Library, Embase, and Web of Science databases up to June 5, 2025. The analysis summarized key microbiota characteristics from the selected studies, including alpha diversity, beta diversity, and relative taxonomic abundance. This meta-analysis was conducted in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) 2020 guidelines.

RESULTS: Our systematic search identified 12,810 articles, out of which 27 studies comprising 2,263 individuals, involving 1,234 lung cancer patients and 1,029 non-cancer controls, were included for qualitative synthesis. Meta-analysis revealed a significant reduction in microbial alpha diversity of 25 studies in lung cancer patients. Significant decreases were indicated in the ACE index (SMD = -0.64, 95% CI: -1.14 to -0.13), Chao1 index (SMD = -0.31, 95% CI: -0.60 to -0.02), and Shannon index (SMD = -0.25, 95% CI: -0.57 to 0.08). Chinese cohorts showed significantly lower Chao1and Shannon by subgroup analysis. Twenty-seven studies assessed beta diversity, in which 20 studies (74.0%) reported a significant difference in overall microbial community structure between lung cancer patients and non-cancer controls. Quantitative meta-analysis by forest plot revealed, compared to non-cancer controls, lung cancer patients exhibited decreased relative abundances of phylum Firmicutes (SMD = -0.47, 95% CI: -0.91 to -0.02), and increased abundances of phylum Bacteroidetes (SMD = 0.53, 95% CI: 0.24 to 0.82). Furthermore, we observed a marked depletion of beneficial short-chain fatty acid producers of genus Lachnospira (SMD = -1.01, 95% CI: -1.29 to -0.73).

CONCLUSION: This meta-analysis demonstrates that lung cancer is consistently associated with gut microbiota dysbiosis characterized by reduced microbial diversity and reproducible taxonomic alterations. Clinically, these findings suggest that gut microbiota may serve as non-invasive biomarkers for lung cancer detection and patient stratification, and may also help predict immunotherapy response and inform future microbiota-targeted therapeutic strategies.

https://www.crd.york.ac.uk/PROSPERO/view/CRD42024537463, CRD42024537463.},
}

@article {pmid42549413,
year = {2026},
author = {Feng, S and Si, X and Lu, C and Gao, Z and Wang, J and Yang, Q and Lu, S and Su, T and Yang, J and He, X and Wu, L},
title = {Washed microbiota transplantation improves clinical symptoms, gut microbiota, and metabolic profiles in autism spectrum disorder in a twin cohort.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1885281},
pmid = {42549413},
issn = {1664-302X},
abstract = {OBJECTIVE: Autism spectrum disorder (ASD) is a heterogeneous neurodevelopmental condition characterized by impaired social communication, repetitive behaviors, and restricted interests. Dysregulation of the microbiota-gut-brain axis is closely associated with the pathogenesis of ASD. Washed microbiota transplantation (WMT) has emerged as a promising intervention for ASD, but existing cohort studies lack genetically identical controls, making it difficult to distinguish intervention-related changes from genetic and environmental confounding factors. This twin-paired controlled study adopted a study design that minimizes the influence of genetics and shared environment, to explore the associations of WMT with clinical symptoms, gut microbiota, and metabolic profiles in children with ASD.

METHODS: Three pairs of age- and environment-matched twins (one ASD-affected, one typically developing sibling) were enrolled. WMT was administered to the ASD participant in each pair. Fecal samples were collected at baseline and post-intervention. Gut microbiota and metabolic profiles were analyzed using metagenomic sequencing and targeted metabolomics, respectively. Clinical outcomes were evaluated using the Childhood Autism Rating Scale (CARS), Autism Behavior Checklist (ABC), Sleep Disturbance Scale for Children (SDSC), and Bristol Stool Form Scale (BSFS). Relevant observations were carried out to explore potential changing trends.

RESULTS: After WMT, CARS, ABC, SDSC, and BSFS exhibited small numerical directional shifts toward healthier values, but none reached statistical significance. Gut microbial structure and function presented a shifting trend toward the profile of their typically developing twin siblings. Abnormal lipid and energy metabolism indicators showed partial ameliorative trends, and the number of differential metabolites between ASD patients and healthy siblings was markedly reduced. Tyrosine and phenylalanine metabolic pathways, together with Segatella, Negativibacillus, and Sangeribacter, may be associated with incomplete phenotypic changes in this cohort.

LIMITATIONS: Although the twin-pair design has high internal validity and can provide strong causal inference evidence for the effect of microbiota transplantation in treating ASD, this study has limitations such as a small sample size, a single-center non-randomized observational design. All findings in this pilot study are merely descriptive trends, and the relevant mechanism analysis only provides correlational clues. A single session of microbiota transplantation failed to fully adjust aromatic amino acid metabolism in ASD children. No definitive causal relationship can be concluded based on the findings of this small-sample pilot study.

CONCLUSION: Under tightly controlled genetic and environmental conditions, gut microbial dysbiosis presents correlational characteristics with ASD-related phenotypes. WMT was associated with consistent remodeling of gut microbial ecology and partial resolution of metabolic dysregulation in ASD children, with multi-omic signatures converging toward healthy twins. Clinical rating scales only displayed non-significant minor numerical shifts, which cannot be interpreted as evidence of clinical symptom improvement. These initial findings provide exploratory mechanistic clues and phenotypic data supporting WMT as a targeted microbiome intervention approach for ASD, and await further validation through large-scale randomized controlled trials.

CLINICAL TRIAL REGISTRATION: Identifier ChiCTR2400091105.},
}

@article {pmid42549419,
year = {2026},
author = {Li, X and Jiang, J and Li, X and Jian, G and Li, F},
title = {Effects of diarrhea and antibiotic-induced microbial elimination on dynamic changes in fecal microbial communities and antibiotic resistance of Hu sheep lambs (Ovis aries).},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e21574},
pmid = {42549419},
issn = {2167-8359},
mesh = {Animals ; *Diarrhea/microbiology/veterinary/drug therapy ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Sheep/microbiology ; *Feces/microbiology ; *Sheep Diseases/microbiology/drug therapy ; *Gastrointestinal Microbiome/drug effects/genetics ; Bacteria/drug effects/genetics ; *Drug Resistance, Bacterial/genetics ; Metagenome ; *Drug Resistance, Microbial/genetics ; },
abstract = {BACKGROUND: As a highly reproductive meat sheep breed in China, Hu sheep is an important economic group in ruminant animal breeding. However, research on its intestinal microbiomes under the background of diarrhea and antibiotic treatment remains relatively limited.

METHODS: This study investigated the intestinal microbiota of Hu sheep lambs in the preliminary stage of diarrhea (group DM), the late recovery stage of diarrhea (group DL), and the healthy stage (group H). Diseased individuals (groups DM and DL) were treated with a combination of Shuanghuanglian, Cefazolin, Lincomycin, and Dexamethasone (0.2 mL dosage). To characterize the intestinal microbiota, fecal samples were collected from all groups, and metagenomic sequencing was performed. Using metagenomic binning tools and co-assembly methods, we reconstructed 482 high-quality non-redundant metagenome assembled genomes (MAGs).

RESULTS: Among these MAGs, 70% belong to the phyla Bacillota, Bacteroidota, and Pseudomonadota, highly consistent with the typical structure of intestinal microbiota in ruminants. Functional annotation revealed that the genes encoding carbohydrate-active enzymes (CAZymes) are more abundant in Bacillota and Bacteroidota, which supports the degradation and energy metabolism functions of Hu sheep on fibrous feed. During the preliminary stage of diarrhea, the virulence genes carried by symbiotic bacteria such as Lachnospiraceae, Acutalibacteraceae and Bacteroidaceae were enriched. Although diarrhea symptoms alleviated during the late recovery stage of diarrhea, the combined use of multiple antibiotics led to the continuous enrichment of antibiotic resistance genes (ARGs) related to lincosamides and cephalosporins. The average abundance of cephalosporin-related ARGs in group DL was significantly higher than that in group DM and H, indicating a risk of residual ARGs. Microbial diversity analysis showed that there was no significant overall difference in MAGs between group DM and H, but both groups showed significant differences compared to group DL, suggesting that antibiotic driven clearance of sensitive bacteria is the core driving force. Moreover, our study shows that the abundance of the zoonotic pathogens Barnesiella and Campylobacter significantly increased in the diarrhea group (p <  0.05), and they carry 567 and 382 virulence genes, respectively. Their pathogenicity is regulated by the dynamic changes in the host intestinal microbiota.

CONCLUSIONS: This study not only expands the genomic database of ruminant intestinal microorganisms but also provides a key theoretical basis for formulating intestinal microecological regulation strategies and optimizing diarrhea treatment regimens for Hu sheep.},
}

Animals
*Diarrhea/microbiology/veterinary/drug therapy
*Anti-Bacterial Agents/pharmacology/therapeutic use
Sheep/microbiology
*Feces/microbiology
*Sheep Diseases/microbiology/drug therapy
*Gastrointestinal Microbiome/drug effects/genetics
Bacteria/drug effects/genetics
*Drug Resistance, Bacterial/genetics
Metagenome
*Drug Resistance, Microbial/genetics

@article {pmid42549425,
year = {2026},
author = {Maynez-Perez, AO and Cahyo, HN and Niu, P and Aho, VTE and Pope, PB and Schwarm, A},
title = {Intricate microbiome differences observed in lactating cows across methane intensity phenotypes.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag155},
pmid = {42549425},
issn = {2730-6151},
abstract = {Methane emissions from ruminants can be expressed through several metrics as total production, yield, or intensity, each reflecting distinct aspects of energy utilisation. Among these, methane intensity defined as grams of methane emitted per kilograms of energy-corrected milk, directly links emissions to productive efficiency; however, the microbial mechanisms underlying variation in this trait remain unclear. Here, we applied genome-resolved metagenomics and metatranscriptomics to characterise rumen microbial identity, functional potential, and transcriptional activity in lactating cows differing in methane intensity while sharing breed and diet. Microbial community composition and diversity were comparable across phenotypes. However, rumen microbial gene expression revealed marked functional divergence. The rumen content of low-methane-intensity cows showed enriched transcription of fructan-degrading carbohydrate-active enzymes and butyrate-forming pathways, primarily encoded by RUG440 (Atopobiaceae) metagenome-assembled genomes. These functions suggest a fructan-butyrate metabolic axis supported by potential cross-feeding between primary degraders and butyrate producers. Conversely, the high-methane intensity rumen exhibited greater transcription of pectin-degrading carbohydrate-active enzymes, mainly carried by Prevotella metagenome-assembled genomes, suggesting methyl-ester hydrolysis and methanol release. Despite higher methanogenesis transcript levels in high-methane intensity cows, total methane production did not differ between groups. Together, these findings reveal two contrasting functional configurations of the rumen microbiome in Norwegian Red dairy cattle: a fructan-butyrate-oriented metabolism in low-methane-intensity cows and a pectin-methanol-oriented metabolism in high-methane-intensity counterparts. This study provides genome-resolved, multi-omic evidence that microbial carbohydrate specialization and fermentation routing contribute to methane intensity phenotypes in dairy cows, offering mechanistic insights for improving ruminant climate efficiency.},
}

@article {pmid42549478,
year = {2026},
author = {Armstrong, E and Pinto, R and Kulikova, M and Yee, NR and Rishu, A and Muscedere, J and Sibley, S and Maslove, DM and Boyd, JG and Evans, GA and Detsky, M and Marshall, JC and Taggart, LR and Friedrich, JO and Tsang, JLY and Duan, E and Ali, KF and McCullagh, D and Findlater, A and Daley, P and Ramendra, R and Lother, S and Lamontagne, F and Fowler, R and Daneman, N and Coburn, B},
title = {Association of anti-anaerobic antibiotics with mortality and the gut microbiome: a sub-study of the BALANCE randomized clinical trial.},
journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America},
volume = {},
number = {},
pages = {},
doi = {10.1093/cid/ciag460},
pmid = {42549478},
issn = {1537-6591},
abstract = {BACKGROUND: Patients with suspected bloodstream infection often receive broad-spectrum antibiotics with anaerobic activity in the absence of clinical indication for anaerobic coverage. Anti-anaerobic antibiotics have been linked to adverse clinical outcomes in other populations, potentially by depleting intestinal anaerobes.

METHODS: We conducted a planned sub-study of the multisite BALANCE randomized controlled trial of antibiotic duration for bloodstream infection to assess the impact of anti-anaerobic antibiotics (receipt from three days pre-index culture to seven days post-index) on mortality and gut microbiome composition with metagenomic sequencing in patients without clinical indication for anaerobic coverage who survived to seven days post-index culture. The primary exposure was receipt of anti-anaerobic antibiotics from three days prior to the index culture to seven days post-index culture.

RESULTS: Among the 2851 eligible patients included in our primary analysis, 2106 (74%) received anti-anaerobic antibiotics and 745 (26%) did not. After balancing measured potential confounders through inverse probability of treatment weighting, anti-anaerobic antibiotics were associated with higher 90-day mortality (OR = 1.41, 95% CI 1.03 to 1.92, p = 0.03) and depletion of gut anaerobe relative abundance (fixed effect estimate = -16.59, 95% CI -30.67 to -2.52, p = 0.02). Increased duration of anti-anaerobic antibiotics was associated with greater mortality risk and additional gut anaerobe depletion.

CONCLUSIONS: Anti-anaerobic antibiotics are associated with increased mortality and gut microbiome disruption in patients with bloodstream infection. Minimizing exposure to anti-anaerobic antibiotics for bloodstream infection should be further explored in clinical trials as a potential treatment strategy to improve patient outcomes.},
}

@article {pmid42549897,
year = {2026},
author = {Schultz, J and Altalhi, S and Camargo, AP and Kyrpides, NC and Rosado, AS},
title = {Catalog of metagenome-assembled genomes of prokaryotic communities from the Red Sea hydrothermal vents.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0048226},
doi = {10.1128/mra.00482-26},
pmid = {42549897},
issn = {2576-098X},
abstract = {This study presents medium- and high-quality prokaryotic metagenome-assembled genomes (MAGs) from microbial mats and sediments at Hatiba Mons, a Red Sea hydrothermal system. We recovered 1,217 bacterial and archaeal MAGs across 75 phyla, dominated by Planctomycetota and Thermoproteota. Approximately 70% of these genomes likely represent previously uncharacterized taxa.},
}

@article {pmid42549916,
year = {2026},
author = {Liu, X and Fan, X and Wu, W and Ni, W and Hu, Y and Yang, Q and Wei, J and Yan, F and Chen, X and Yang, J and Hu, B and Yu, X and Li, W},
title = {Comparative evaluation of probe-capture and conventional metagenomic sequencing across multiple clinical sample types, with analysis of paired bronchoalveolar lavage fluid and blood samples.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0405725},
doi = {10.1128/spectrum.04057-25},
pmid = {42549916},
issn = {2165-0497},
abstract = {Conventional metagenomic next-generation sequencing (mNGS) suffers from host nucleic acid interference and poor performance in low-biomass samples. Probe-capture metagenomic sequencing (PC-mNGS), which enriches microbial targets via hybridization probes, shows superior sensitivity but lacks systematic multi-sample evaluations. This study compared PC-mNGS and mNGS across diverse clinical specimens (bronchoalveolar lavage fluid [BALF], blood, cerebrospinal fluid [CSF]) and assessed the clinical utility of pathogen co-detection in paired BALF-blood samples from sepsis patients. A total of 282 samples (81 BALF, 141 blood, 25 CSF, 35 others) sequenced by both PC-mNGS and mNGS were analyzed. Additionally, 621 paired BALF-blood samples from sepsis patients with pulmonary infections were evaluated. PC-mNGS achieved higher pathogen detection rates (66.67% vs 57.10%, P = 0.000198) than mNGS, particularly in blood (66.67% vs 47.52%, P = 2.5 × 10[-5]). PC-mNGS detected more bacteria (19 species exclusive) and fungi (11 species exclusive) than mNGS. Viruses showed comparable detection. BALF and CSF exhibited high overall agreement (OPA: 96.30% and 88%, respectively), while blood had lower concordance (NPA: 54.05%, OPA: 70.92%). A total of 60.55% of BALF-positive samples (PC-mNGS) had co-detected pathogens in blood. Gram-negative bacteria (e.g., Klebsiella pneumoniae) and fungi (e.g., Candida albicans) showed higher blood co-detection rates than viruses. In this study, PC-mNGS detected more pathogens and showed a higher positivity rate than mNGS in blood samples. BALF sequencing data, particularly bacterial reads per million (RPM), may predict bloodstream co-detection, aiding in sepsis management. However, clinical validation and integration with traditional diagnostics are needed to confirm utility. This study highlights PC-mNGS as a promising tool for complex infections but underscores the need for rigorous multi-context validation.IMPORTANCEAccurate and rapid identification of pathogens is critical for effective treatment of severe infectious diseases, such as sepsis. This study demonstrates that probe-capture metagenomic sequencing (PC-mNGS) detected more pathogens in blood samples compared to conventional metagenomic sequencing, especially for bacterial and fungal infections. By analyzing paired lung and blood samples, we show that high pathogen levels in lung fluid may predict bloodstream infection, offering a potential early warning for clinicians. These findings support the use of PC-mNGS as a more sensitive diagnostic tool, which could lead to faster, more targeted therapies and better outcomes for patients with complex infections.},
}

@article {pmid42550599,
year = {2026},
author = {Miozzi, L and Rotunno, S and Frascati, F and Marra, M and Nugnes, F and Bernardo, U and Marian, D and Bertacca, S and Ballardini, M and Accotto, GP and Vaira, AM and Noris, E},
title = {Vector-enabled metagenomics reveals the first detection of the geminivirus beet curly top Iran virus in Europe.},
journal = {The Journal of general virology},
volume = {107},
number = {8},
pages = {},
doi = {10.1099/jgv.0.002271},
pmid = {42550599},
issn = {1465-2099},
mesh = {*Geminiviridae/genetics/isolation & purification/classification ; *Metagenomics/methods ; Animals ; *Plant Diseases/virology ; *Insect Vectors/virology ; Europe ; Citrullus/virology ; Cucurbita/virology ; *Hemiptera/virology ; DNA, Viral/genetics ; Phylogeny ; Genome, Viral ; },
abstract = {Geminiviruses are among the most threatening emerging insect-borne viruses and are responsible for serious outbreaks worldwide. Climate change (i.e. higher temperatures) could further exacerbate their impact on crops, highlighting the need for new diagnostic approaches to manage potentially dangerous situations. vector-enabled metagenomics (VEM) exploits the natural ability of highly mobile insects to accumulate viruses acquired from plants over time and space within an ecosystem; this approach is effective for monitoring the presence of new invasive or indigenous viruses in large areas. Geminiviruses have circular ssDNA genomes that can be readily targeted by rolling circle amplification (RCA). The combination of RCA and VEM largely increases the chances of detecting geminiviruses. This approach enabled us to identify the becurtovirus beet curly top Iran virus (BCTIV, Becurtovirus betae) in insects collected in Europe. BCTIV is a major pathogen of sugar beet but can also infect plants of other families; it is transmitted by cicadellids and has so far been detected only in Iran and Anatolia (Turkey). We also show that two cucurbit species, watermelon (Citrullus lanatus) and zucchini (Cucurbita pepo) are both natural and experimental hosts for BCTIV.},
}

*Geminiviridae/genetics/isolation & purification/classification
*Metagenomics/methods
Animals
*Plant Diseases/virology
*Insect Vectors/virology
Europe
Citrullus/virology
Cucurbita/virology
*Hemiptera/virology
DNA, Viral/genetics
Phylogeny
Genome, Viral

@article {pmid42551151,
year = {2026},
author = {Deng, WQ and Lu, ZM and Li, XB and Fan, ZY and Li, T and Zhang, XJ and Chai, LJ and Xu, HY and Zhang, QS and Shi, JS and Chen, G and Xu, ZH},
title = {Decoding the thermocyclic solar-driven fermentation: Multi-omics insights into microbial and metabolic dynamics of traditional Chishui river basin soy sauce.},
journal = {Food chemistry},
volume = {525},
number = {Pt 4},
pages = {150595},
doi = {10.1016/j.foodchem.2026.150595},
pmid = {42551151},
issn = {1873-7072},
abstract = {Traditional Chishui River Basin soy sauce is produced through prolonged solar-cycle fermentation under diurnal temperature fluctuations and moisture absorption. Here, we employed integrated metagenomic and metabolomic analyses to investigate microbial and metabolic dynamics throughout fermentation. Results revealed a three-phase microbial succession: initial fungal-hydrolytic phase dominated by Aspergillus oryzae (82.28%), marked by proteolysis and amino acid accumulation; transitional phase enriched with Weissella (23.45%) and Zygosaccharomyces rouxii (5.85%), producing organic acids, esters, and maillard intermediates; maturation phase dominated by Bacillus (86.48%), associated with sharp increases in umami-enhancing peptides, pyrazines (e.g., tetramethylpyrazine), and phenolic compounds (e.g., 4-ethylguaiacol). Extended sun exposure selects for Bacillus dominance, allows sufficient time for slow chemical reactions, and enriches the volatile profile with stable pyrazines and phenolic compounds. These findings validate the flavor and mechanisms of traditional Chishui River Basin soy sauce and offer strategies for fermentation optimization via environmental and microbial regulation while maintaining product authenticity.},
}

@article {pmid42551230,
year = {2026},
author = {Zhuang, T and Wang, X and Zheng, W and Lu, W and Hao, L and Wang, X and Huang, C and Wang, R and Hu, Y and Wang, Z and Chen, K and Li, T and Yang, Q and Yang, L and Ding, L},
title = {Enrichment of Akkermansia muciniphila by red ginseng promotes GDF15 secretion and suppresses obesity in mice.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {160},
number = {},
pages = {158600},
doi = {10.1016/j.phymed.2026.158600},
pmid = {42551230},
issn = {1618-095X},
abstract = {BACKGROUND: Obesity is a growing global health burden with rising incidence. Red ginseng (RGS), a traditional processed ginseng product, shows potential for improving metabolic parameters, though its anti-obesity mechanism remains incompletely understood.

PURPOSE: This study investigated the therapeutic effects of short-term RGS administration on obesity and sought to elucidate the underlying mechanism.

METHODS: A high-fat diet (HFD)-induced obese mouse model was used to assess short-term RGS effects. Antibiotic treatment and fecal microbiota transplantation were performed to evaluate gut microbiota involvement. 16S rRNA sequencing and metagenomic analysis identified key bacterial species, and mass spectrometry-based proteomics identified A. muciniphila-derived proteins. The growth differentiation factor 15 (GDF15)-GFRAL axis was interrogated using Gfral[‒/‒] mice.

RESULTS: Short-term RGS treatment suppressed appetite, reduced body weight, and elevated circulating GDF15 in diet-induced obese (DIO) mice. RGS enriched A. muciniphila, and its depletion abrogated RGS-mediated weight loss and appetite suppression. The A. muciniphila-derived protein Amuc_1631 was identified as a key effector promoting GDF15 secretion. Mechanistically, RGS upregulated colonic Gdf15 transcription via the PERK-eIF2α-ATF4-CHOP axis and activated the brainstem GDF15-GFRAL pathway. The RGS 50% ethanol eluate (RGS/50) fraction was identified as the potential active component responsible for A. muciniphila enrichment and GDF15 elevation.

CONCLUSIONS: This study identifies a gut microbiota-dependent mechanism underlying the anti-obesity effects of RGS, centered on A. muciniphila enrichment and its derived protein Amuc_1631, which promotes GDF15 secretion to suppress food intake via the GDF15-GFRAL axis.},
}

@article {pmid42551280,
year = {2026},
author = {Filker, S and Katzenmeier, S and Breiner, HW and Brandt, MI and Hestetun, JT and Dahlgren, TG and Kupczok, A and Stoeck, T},
title = {Response of marine benthic viral communities to anthropogenic disturbances.},
journal = {The Science of the total environment},
volume = {1049},
number = {},
pages = {182106},
doi = {10.1016/j.scitotenv.2026.182106},
pmid = {42551280},
issn = {1879-1026},
abstract = {Viruses are key regulators of microbial mortality, gene flow, and metabolic functioning in marine sediments, yet their responses to different forms of anthropogenic disturbance remain poorly understood. Here, we present the first comparative viral metagenomic analysis of benthic viral communities across two major but contrasting disturbance regimes: organic enrichment beneath salmon aquaculture farms and crude-oil contamination near offshore oil installations. Using 123 sediment metagenomes from Scotland and Norway, we assessed how virus diversity, taxonomic composition, and community structure vary between high- and low-impact sites within each disturbance type and across regions. Virus alpha-diversity increased consistently under high-impact conditions in all environments, suggesting enhanced microbial turnover or productivity in disturbed sediments. Viral taxonomic profiles revealed strong habitat specificity. Beta-diversity analyses showed that viral community composition differed clearly between disturbance regimes, although these patterns were expressed within the context of region-specific environmental settings and sedimentary processes that also influence benthic microbial dynamics. Only a very small core set of vOTUs occurred in all samples with peak abundances throughout all low-impact categories suggesting strong environmental filtering. Together, these findings reveal that benthic viral communities are highly sensitive to environmental perturbation and reflect the contrasting microbial and geochemical processes associated with organic enrichment and hydrocarbon contamination. Our results advance the understanding of viral ecology in industrially impacted marine sediments and highlight the potential of virus-based indicators in next-generation biomonitoring tools that capture the full complexity of benthic microbial dynamics in anthropogenically impacted coastal and offshore ecosystems.},
}

@article {pmid42551374,
year = {2026},
author = {Wu, Y and Liu, K and Ding, Y and Yan, Q and Guo, F and Zhang, H and Wu, X},
title = {Glycitein-mediated rhizosphere signaling recruitment and CobB deacetylation synergistically enhance fomesafen bioremediation by Klebsiella variicola W28.},
journal = {Journal of hazardous materials},
volume = {515},
number = {},
pages = {143171},
doi = {10.1016/j.jhazmat.2026.143171},
pmid = {42551374},
issn = {1873-3336},
abstract = {Fomesafen, a persistent diphenyl ether herbicide, causes carry-over phytotoxicity and threatens agricultural soil ecosystems. Here, the previously isolated fomesafen-degrading strain Klebsiella variicola W28 was used to elucidate a cross-kingdom rhizosphere signaling mechanism linking soybean root exudates to bacterial colonization and fomesafen degradation. Untargeted metabolomics showed that fomesafen stress selectively enriched glycitein in soybean root exudates. Glycitein enhanced W28 chemotaxis, motility, biofilm formation, and root-surface colonization, while metagenomic and random forest analyses revealed the assembly of a cooperative rhizosphere consortium enriched in Azotobacter, Klebsiella, cobB, and pcaG/H. Mechanistically, glycitein activated purine metabolism and the NAD[+] salvage pathway, thereby supporting the NAD[+]-dependent deacetylase CobB. GST pull-down, BiFC, and LCA confirmed direct CobB-LysR-pca interaction. EMSA showed that LysR-pca repressed the pcaGH promoter, whereas CobB-mediated deacetylation weakened DNA binding and relieved transcriptional repression. Molecular docking and product profiling demonstrated that heterologously expressed PcaGH directly transformed fomesafen, producing benzoic acid. Pot experiments confirmed that glycitein enhanced W28-mediated fomesafen degradation in soil. These findings define a root exudate-NAD[+] homeostasis-lysine deacetylation-pcaGH activation circuit, reveal how plant signals coordinate rhizosphere recruitment with intracellular catabolic activation, and provide a mechanistic basis for precision in situ bioremediation of diphenyl ether-contaminated soils.},
}

@article {pmid42551380,
year = {2026},
author = {Zhang, H and Chen, C and Wei, G and Zhang, B and Yang, X and Zhang, Y and Wu, H and Qiu, G and Zhu, S and Wei, C},
title = {Process architecture governs nitrate fate by controlling dissimilatory nitrate reduction to ammonium (DNRA)-denitrification competition in industrial wastewater systems.},
journal = {Water research},
volume = {306},
number = {},
pages = {126590},
doi = {10.1016/j.watres.2026.126590},
pmid = {42551380},
issn = {1879-2448},
abstract = {Dissimilatory nitrate reduction to ammonium (DNRA) is increasingly recognized as an alternative nitrate reduction pathway, yet its quantitative importance and regulatory mechanisms in engineered wastewater treatment systems remain poorly resolved. Here, DNRA and denitrification were systematically quantified across four full-scale coking wastewater treatment plants operated under contrasting recirculation and non-recirculation modes. Long-term performance monitoring combined with [15]N stable isotope tracing showed that DNRA accounted for 8.0-29.5% of total nitrate reduction, with substantially higher contributions under recirculation-based operation. Although denitrification remained the dominant pathway for nitrate removal, enhanced DNRA promoted ammonium accumulation and significantly impaired total nitrogen removal efficiency. Process configuration was associated with contrasting nitrate-reduction outcomes by reshaping local substrate stoichiometry and toxicity exposure: high COD/NO3[-] ratios and persistent nitrogenous toxicants in recirculation systems were associated with greater DNRA contribution, whereas spatially decoupled non-recirculation configurations maintained more balanced conditions that favored denitrification and supported anaerobic ammonium oxidation. Integrated analyses of microbial community assembly, ecological networks, and metagenome-resolved functions revealed that non-recirculation systems maintained higher microbial diversity, functional redundancy, and network robustness, while recirculation systems exhibited undominated assembly and enrichment of DNRA-associated taxa and genes. Collectively, these results demonstrate that nitrate reduction pathways are not solely determined by microbial functional potential, but instead emerge from the coupled interactions among process configuration, material composition, and microbial functionality. This study highlights that controlling the fate of nitrogen in engineered wastewater systems relies heavily on designing environmental conditions that selectively favor the utilization of existing metabolic potential.},
}

@article {pmid42542144,
year = {2026},
author = {Li, X and Wang, B and Zeng, W and Zhang, L and Peng, Y},
title = {Robust nitrogen removal through simultaneous denitrification and anammox driven by alkaline sludge fermentation liquid at varying nitrification levels.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135552},
doi = {10.1016/j.biortech.2026.135552},
pmid = {42542144},
issn = {1873-2976},
abstract = {Operational instability of partial nitrification (PN) remains a major barrier to mainstream energy-efficient wastewater treatment. Here, a stable simultaneous denitrification-anammox system driven by alkaline sludge fermentation liquor (ASFL) under varying nitrification levels (PN, complete nitrification, and their coexistence) has been presented. Through a 240-day continuous operation treating municipal wastewater, this system achieved high nitrogen removal efficiency, ranging from 96.9 ± 2.0% under PN to 95.7 ± 2.4% under coexistence of PN and complete nitrification. Isotope tracing and microbial analyses indicated that ASFL-supported heterotrophic denitrification was the dominant nitrogen removal pathway, whereas anammox activity remained detectable but contributed only to a limited extent under the investigated conditions. Metagenomic analysis revealed functional shifts in nitrogen metabolism while the core carbon metabolic potential remained largely conserved. Combined with an optimized iron-assisted strategy for effluent polishing, this ASFL-driven simultaneous denitrification-anammox framework provides a sustainable, circular pathway for energy-efficient nitrogen removal, addressing the inherent vulnerability of mainstream PN applications.},
}

@article {pmid42542146,
year = {2026},
author = {McKnight, MM and Lakshminarasimman, N and Parker, W and Neufeld, JD},
title = {Microbiology of a membrane aerated biofilm reactor upgrade in a municipal wastewater treatment facility.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135550},
doi = {10.1016/j.biortech.2026.135550},
pmid = {42542146},
issn = {1873-2976},
abstract = {Novel wastewater treatment biotechnologies, including membrane aerated biofilm reactors (MABR), aim to reduce energy consumption, and improve nitrogen removal and nitrification in cold weather conditions. A municipal wastewater treatment plant (WWTP) in southern Ontario was upgraded with a large-scale MABR system in 2022, which was installed upstream of the existing conventional activated sludge (CAS) system. Here we evaluated how the MABR upgrade impacted mixed liquor and MABR biofilm microbial communities spatially and temporally, which previously has not been done in large-scale hybrid MABR-CAS systems. Microbial communities were characterized using 16S rRNA gene amplicon sequencing, with selected MABR biofilm samples analyzed with metagenomics to evaluate the functional potential of the biofilm for nitrification and denitrification. The CAS mixed liquor before the upgrade included ammonia-oxidizing bacteria (AOB; Nitrosomonas) and nitrite-oxidizing bacteria (NOB; Nitrotoga), which exhibited seasonal abundance and activity patterns. Following the upgrade, seeding from the MABR biofilm increased diversity of the mixed liquor, including nitrifiers. Along with AOB, Nitrospira NOB and comammox Nitrospira were present in the MABR biofilm, representing upwards of 10 % of microbial community profiles. Metagenomic sequencing showed that biofilm microbial communities were equipped to perform nitrification and denitrification in the system. Overall, characterization of microbial communities in the WWTP showed that the MABR installation increased microbial diversity, concomitant with increased representation of nitrifier groups and coinciding with reductions in plant effluent nitrogen concentrations.},
}

@article {pmid42542148,
year = {2026},
author = {Zhong, Y and Su, Q and Pan, X and Zou, X and Zhang, J and He, J and Ng, HY},
title = {Long-term stability of anaerobic digestion of thermally hydrolyzed waste activated sludge driven by N-doped Biochar-Supported Magnetite: Metagenomic insights into direct interspecies electron transfer.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135546},
doi = {10.1016/j.biortech.2026.135546},
pmid = {42542148},
issn = {1873-2976},
abstract = {Fluctuations in organic loading often destabilize anaerobic digestion (AD) performance, thereby limiting methane (CH4) production. This study evaluated effects of hybrid conductive material, N-doped biochar-supported magnetite (Fe3O4@N-BC), on long-term stability of AD of thermally hydrolyzed waste activated sludge in up-flow anaerobic sludge blanket (UASB) reactors under decreasing hydraulic retention times (18-6 days). Fe3O4@N-BC-amended reactor maintained superior and stable performance, achieving 22-122% higher CH4 yields than the Control reactor over the 150-day operational period. Enhanced stability was associated with improved hydrolysis and the establishment of direct interspecies electron transfer (DIET) between Clostridium and Methanosarcina. Electron transfer was facilitated through multiple pathways, including conductive materials, e-pili, and extracellular polymeric substances. The CH4/CO2 ratio is proposed as a rapid and practical indicator of DIET under comparable conditions. The results provide metagenomic insights into the mechanism of Fe3O4@N-BC-mediated DIET during AD and highlight its potential application in reactors under dynamic operational conditions.},
}

@article {pmid42543104,
year = {2026},
author = {Fan, J and Cao, S and Du, R and Peng, Y},
title = {Synergistic operational optimizations and microbial responses stabilize filamentous-dominated continuous-flow partial denitrification-anammox at low-temperature.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135549},
doi = {10.1016/j.biortech.2026.135549},
pmid = {42543104},
issn = {1873-2976},
abstract = {The operational stability of continuous-flow partial denitrification-anammox (PD/A) systems is frequently constrained by insufficient nitrite supply and temperature sensitivity of anammox bacteria, particularly under low-temperature stress. In such conditions, filamentous bacteria often proliferate excessively, and their overgrowth has long been associated with reactor instability and performance deterioration. Here, we demonstrate stable nitrogen removal in a filamentous-dominated continuous-flow PD/A reactor at an average temperature of 16.7 °C through operational optimizations and microbial responses. The reactor achieved 89.8 % total nitrogen removal, with ammonium and nitrate removal efficiencies of 97.2 % and 91.5 %, respectively, with anammox contributing up to 98.3 % of nitrogen removal. Metagenomic analyses revealed that the filamentous genus Sphaerotilus dominated the microbial community (29.3-41.5 %) but sustained the genomic potential for nitrite availability to support anammox. Genome-centric reconstruction confirmed that a Sphaerotilus-affiliated MAG5 possessed adaptive features under low temperature. Additional heterotrophs, including Leptothrix, Rubrivivax, and Thauera, harbored genomic potential for auxiliary nitrate-to-nitrite conversion. Crucially, the synergy between this genomic potential for nitrite provision and engineered biomass retention (specifically mesh filtration and regular sludge return) facilitated the enrichment of Ca. Brocadia, increasing its relative abundance from 2.4 % to 5.4 %. Concurrently, Ca. Brocadia reinforced low-temperature adaptability by expanding the genetic potential of energy-generating carbon metabolic pathways and increasing its contribution to the cold shock protein gene cspA from 6.6 % to 21.0 %. Collectively, this study reveals that integrating strategic biomass retention with microbial responses provides a viable pathway to sustain stable nitrogen removal in filamentous-dominated continuous-flow PD/A systems.},
}

@article {pmid42543651,
year = {2026},
author = {Nannya, Y},
title = {[Hematopoietic cell transplantation in the era of genome analysis].},
journal = {[Rinsho ketsueki] The Japanese journal of clinical hematology},
volume = {67},
number = {7},
pages = {794-801},
doi = {10.11406/rinketsu.67.794},
pmid = {42543651},
issn = {0485-1439},
mesh = {Humans ; *Hematopoietic Stem Cell Transplantation/methods ; Myelodysplastic Syndromes/genetics/therapy ; *Genomics ; Neoplasm, Residual ; Polymorphism, Single Nucleotide ; *Hematologic Neoplasms/genetics/therapy ; Leukemia, Myeloid, Acute/genetics/therapy ; Graft vs Host Disease ; },
abstract = {Genomic information for hematologic malignancies is now routinely available in clinical practice, supporting the adaptation of hematopoietic cell transplantation, selection of conditioning intensity, and implementation of post-transplant maintenance therapy through refinement of disease risk assessment and minimal residual disease (MRD) measurement. This review presents the current evidence on the effective utilization of genomic information for acute myeloid leukemia (AML), myelodysplastic syndromes (MDS), and myeloproliferative neoplasms (MPN). It also presents an up-to-date framework for optimal donor selection based on donor genome information, addressing both donor clonal hematopoiesis of indetermined significance and the risk that related donor candidates may carry the same hereditary predisposition. Finally, it discusses research showing that patient and donor genetic polymorphisms (SNPs) can predict transplant complications such as GVHD, and that reduced gut microbiota diversity, as detected by metagenomic analysis, impacts GVHD severity and survival. These examples illustrate the multifaceted role of genomic information in research efforts to improve hematopoietic cell transplantation outcomes.},
}

Humans
*Hematopoietic Stem Cell Transplantation/methods
Myelodysplastic Syndromes/genetics/therapy
*Genomics
Neoplasm, Residual
Polymorphism, Single Nucleotide
*Hematologic Neoplasms/genetics/therapy
Leukemia, Myeloid, Acute/genetics/therapy
Graft vs Host Disease

@article {pmid42543873,
year = {2026},
author = {Wang, J and Peng, Q},
title = {Innovations, Applications, and Future Trends in Veterinary Diagnostic Technologies.},
journal = {Transboundary and emerging diseases},
volume = {2026},
number = {1},
pages = {e6973879},
doi = {10.1155/tbed/6973879},
pmid = {42543873},
issn = {1865-1682},
support = {32470195//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Veterinary Medicine/trends/methods ; *Animal Diseases/diagnosis ; High-Throughput Nucleotide Sequencing/veterinary ; },
abstract = {Veterinary diagnostics is undergoing a significant transformation driven by technological advancements, extending its scope from the traditional confirmation of specific pathogens to the continuous, dynamic surveillance of animal population's health. This paradigm shift has the potential to enable more timely disease control, precise intervention, and enhanced public health security. Traditional clinical and laboratory diagnostic methods, such as microbial culture, serological assays, and nucleic acid-based polymerase chain reaction, form the cornerstone of the current diagnostic framework and are widely applied based on varying detection needs and practical environments. Nonetheless, the field is experiencing profound innovation. Firstly, novel detection technologies are emerging, such as digital PCR (dPCR), CRISPR-Cas-based molecular diagnostic tools, next-generation sequencing (NGS), and metagenomic sequencing. These technologies have not only achieved breakthroughs in sensitivity and specificity but, more importantly, enable the unbiased discovery of novel pathogens. Secondly, the deep integration of artificial intelligence (AI) and big data is reshaping the diagnostic pipeline. By consolidating and analyzing multimodal information streams from imaging, genomics, wearable devices, and production data, AI algorithms can provide objective, quantitative decision support, facilitating a transition from post-symptomatic diagnosis towards predictive and preventive health management. This scoping review systematically summarizes both mainstream and emerging veterinary diagnostic technologies, elaborates and discusses their advantages and limitations as well as future developmental directions, while highlighting that the combined application of multiple methods represents an optimal diagnostic strategy.},
}

Animals
*Veterinary Medicine/trends/methods
*Animal Diseases/diagnosis
High-Throughput Nucleotide Sequencing/veterinary

@article {pmid42545016,
year = {2026},
author = {Seo, Y and Kim, J and Yeom, M and Park, S-Y and Lee, S and Ahn, S and Hahm, D-H and Kim, K and Kwon, S-K and Park, H-J},
title = {Gut microbiota contributes to the therapeutic effect of acupuncture in atopic dermatitis.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0391225},
doi = {10.1128/spectrum.03912-25},
pmid = {42545016},
issn = {2165-0497},
abstract = {UNLABELLED: The gut microbiome is increasingly recognized as a central regulator of immune homeostasis, metabolic balance, and therapeutic outcomes. Atopic dermatitis (AD), a chronic inflammatory skin disease, is closely linked to gut microbial dysbiosis. Traditionally regarded as a neurostimulatory therapy, acupuncture (Acu) has demonstrated increasing efficacy in alleviating AD symptoms and improving gastrointestinal function. These observations suggest that the therapeutic effects of Acu in AD may be mediated, in part, by modulation of the gut microbiome. In this study, AD patients were stratified into responder (R) and non-responder (NR) groups based on clinical improvement. Gut microbiome profiling revealed that R patients exhibited greater microbial diversity and compositional stability, indicative of a more balanced gut ecosystem. Specific taxa, including Alistipes ihumii and Odoribacter splanchnicus, were enriched in R individuals and may serve as microbial predictors of treatment responsiveness. Importantly, fecal microbiota transplantation (FMT) from R donors restored Acu efficacy in a mouse model of AD, whereas FMT from NR donors did not. These findings support the gut-skin axis and highlight the integral role of the gut microbiome in mediating the therapeutic effects of Acu for AD, suggesting potential for microbiome-based personalized treatment.

IMPORTANCE: Increasing evidence supports the gut microbiome's role in modulating treatment responses in atopic dermatitis (AD), but direct evidence linking acupuncture efficacy with microbiome composition has been lacking. Previous studies did not assess causal relationships via fecal microbiota transplantation (FMT) or functional metagenomics. This study identifies specific gut microbes associated with acupuncture response in AD and confirms their causal role using FMT. It also links functional metabolic pathways to therapeutic efficacy, offering a mechanism-based insight. Our findings support microbiome-informed personalized acupuncture approaches for AD and suggest gut microbiota as a therapeutic modulator in neuroimmune regulation.

CLINICAL TRIALS: This study was registered in the Korean Clinical Trial Registry (CRIS, registration number: KCT0005422).},
}

@article {pmid42545024,
year = {2026},
author = {Carlson-Jones, JAP and Goddard, TR and Papudeshi, B and Mallawaarachchi, V and Whiteson, KL and Warner, MS and Morton, JM and Jersmann, HPA and Edwards, RA},
title = {DNA sequencing for microbial surveillance in cystic fibrosis airways: advances, challenges, and clinical translation.},
journal = {Clinical microbiology reviews},
volume = {},
number = {},
pages = {e0035225},
doi = {10.1128/cmr.00352-25},
pmid = {42545024},
issn = {1098-6618},
abstract = {SUMMARYDNA sequencing has revolutionized microbial surveillance in cystic fibrosis (CF), transforming pathogen identification from culture-dependent to total microbial community identification using molecular-based approaches. Techniques such as 16S rRNA gene sequencing have uncovered the complexity of the CF airway microbiome, while shotgun metagenomics, metatranscriptomics, and viromics now provide strain-level, functional, and viral insights beyond bacterial identification. Despite these advances, key technical and logistical challenges remain, including the processing of high-viscosity sputum samples, overwhelming host DNA contamination, managing large data sets, and the integration of complex bioinformatic outputs into clinical workflows. Emerging innovations such as host DNA depletion protocols, targeted enrichment panels, and adaptive sampling on Oxford Nanopore platforms are helping to overcome these barriers, improving microbial recovery and sequencing efficiency. As cystic fibrosis transmembrane conductance regulator (CFTR) modulator therapies are changing the lives of people with cystic fibrosis (pwCF), sequencing offers an unprecedented opportunity to track potential microbial adaptation in response. This review investigates current advances, limitations, and translational opportunities in DNA sequencing for CF airway microbiome surveillance, highlighting how these technologies can help reshape research and clinical microbiology in the post-modulator era.},
}

@article {pmid42545805,
year = {2026},
author = {},
title = {Correction to: Ghost-rocks' microbiota: metagenomic insights into their influence on the biogeochemistry of karstic cave and groundwater.},
journal = {FEMS microbiology ecology},
volume = {102},
number = {8},
pages = {},
doi = {10.1093/femsec/fiag088},
pmid = {42545805},
issn = {1574-6941},
}

@article {pmid42546031,
year = {2026},
author = {Kawagishi, T and Sakai, Y and Oki, H and Nouda, R and Kanai, Y and Kawahara, K and Nakamura, S and Shimojima, M and Saijo, M and Matsuura, Y and Kobayashi, T},
title = {Nelson Bay Orthoreovirus cell attachment protein σC determines strain-specific differences in infectivity and pathogenesis.},
journal = {PLoS pathogens},
volume = {22},
number = {8},
pages = {e1014409},
doi = {10.1371/journal.ppat.1014409},
pmid = {42546031},
issn = {1553-7374},
mesh = {Animals ; *Orthoreovirus/pathogenicity/genetics/metabolism ; Virulence ; *Reoviridae Infections/virology/metabolism ; Chiroptera/virology ; Mice ; Humans ; *Sigma Factor/metabolism/genetics ; },
abstract = {Nelson Bay orthoreovirus (NBV) was initially discovered in a bat sample but has since been isolated from patients with acute respiratory tract diseases. Accumulating reports of NBV isolation from patients with respiratory tract viral infections suggest that NBV is able to transmit and cause disease in humans. However, the underlying molecular mechanisms remain unclear. We previously established a reverse genetics system for NBV Miyazaki-Bali/2007 (MB) strain isolated from a patient with an acute respiratory tract disease. We found that the fusion-associated small transmembrane protein (FAST)-which is necessary for syncytium formation-and cell attachment protein σC play crucial roles in MB virulence; however, whether these gene products determine the strain-specific difference in NBV virulence remains unclear. Therefore, here, we compared the virulence of the MB strain with that of the NBV strain isolated from a bat sample (NelB strain). We found that the NelB strain did not cause a virulent phenotype in the mouse model. Using reverse genetics, we found that the S1 gene segment correlates with the virulent phenotypes of NBV strains. Moreover, among the three proteins encoded by the S1 gene segment, structural protein σC, but not nonstructural proteins FAST or p17, contributed to the difference in virulence in vivo. Further analysis using a panel of σC mutant viruses showed that the middle body domain in σC was involved in the different virulent phenotypes, rather than the C-terminal head domain, which contains a putative receptor-binding domain. These results provide new insights into the mechanisms underlying NBV transmission and pathogenesis.},
}

Animals
*Orthoreovirus/pathogenicity/genetics/metabolism
Virulence
*Reoviridae Infections/virology/metabolism
Chiroptera/virology
Mice
Humans
*Sigma Factor/metabolism/genetics

@article {pmid42542141,
year = {2026},
author = {Liu, W and Zhang, Y and Yue, C and Wang, J and Li, J and Lu, H and He, S and Peng, Y},
title = {Impacts of carbon source type on metabolic pathways and microbial synergy in the simultaneous anammox and endogenous denitrification process.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135540},
doi = {10.1016/j.biortech.2026.135540},
pmid = {42542141},
issn = {1873-2976},
abstract = {Simultaneous anammox and endogenous denitrification (SAED) process enables efficient nitrogen removal from low carbon-to-nitrogen wastewater, yet how carbon source type influences microbial synergy and system robustness remains unclear. This study evaluated the sludge characteristics, performance, and ecological traits of three SAED systems fed with acetate (HAc), propionate (HPr), and glucose (Glc) over 476 days. Results showed that the Glc-fed system achieved the highest and most stable nitrogen removal performance (95.0 % ± 2.4 %), significantly outperforming the HAc-fed (93.3 % ± 2.7 %) and HPr-fed (87.6 % ± 2.5 %) systems. Glucose promoted the formation of large (∼870 μm), dense granules with a high organic fraction (0.904), effectively mitigating the sludge washout and inorganic mineral precipitation observed in HAc-fed and HPr-fed systems. Microbial ecological network analysis reveals that different types of carbon sources reconfigured heterotrophic communities by mediating distinct microbial interactions. The Glc-fed system exhibited the highest proportion of positive correlations (90.9 %), particularly between Denitratisoma (13.5 %) and Candidatus Brocadia (22.2 %), bolstering system robustness. Furthermore, metagenomic analysis further confirms that nitrate reductase genes (nar/nap at 674.8 RPKM in total) were significantly more enriched than nitrite reductase genes (nir at 210.6 RPKM in total) in the Glc-fed system, facilitating an efficient nitrate-to-nitrite shunt for anammox bacteria while bypassing the competitive pathways (e.g., full denitrification in HAc-fed; DNRA in HPr-fed). Therefore, leveraging glucose-driven metabolic flux optimizes both sludge characteristics and microbial interactions in SAED process, providing a robust treatment for low-carbon wastewater.},
}

@article {pmid42537279,
year = {2026},
author = {Sohrab, A and Stancheva, R and Mansoor, F and Wei, B and Stubler, S and Boyer, GL and Shriver, R and Blaszczak, J and Goel, R},
title = {Cyanobacterium Microcoleus in toxic benthic mats on different streambed substrates: Ecophysiology and important metabolic pathways.},
journal = {Water research},
volume = {306},
number = {},
pages = {126515},
doi = {10.1016/j.watres.2026.126515},
pmid = {42537279},
issn = {1879-2448},
abstract = {Benthic cyanobacteria, notably the genus Microcoleus, are a common contributor to benthic harmful algal blooms globally and can produce neurotoxins. Microcoleus can thrive in nutrient-limited freshwater environments, which present significant environmental and public health challenges. In May 2023, we observed Microcoleus mat growing in a small tributary of the Virgin River in Zion National Park near the Temple of Sinawava and collected benthic mats from three rock and three sandy substrate (strata) sites in the Virgin River. The overall objective of this study was to evaluate the effect of the bottom substrate (sand versus rock) on the ecophysiology of cyanobacteria, primarily Microcoleus, and other coexisting bacteria. Toxin measurements revealed that all the benthic mat samples contained anatoxin-a (ATX377.13±18.05 µg/g of wet mat) and dihydroanatoxin-a (15±0.3 µg/g of wet mat), and anatoxin-A was also present in the water column (0.377 µg/L). Low chlorophyll-a levels and microscopy results indicate that the toxins in the water flowing into the Virgin River presumably originated from benthic sources rather than from planktonic algae. Community analysis showed strong cyanobacterial dominance (>60%) in mats. Biofilms, especially those formed on sand as compared to those formed on rocks, supported greater heterotrophic bacterial diversity. A single dominant toxigenic Microcoleus genotype occurred across both strata (rock and sand) at all sampled sites, and it is closely related to the Microcoleus anatoxicus previously found in the Russian River, CA. Bottom strata type effects were most prominent in phosphorus acquisition: rock-associated heterotrophic communities showed higher expression of phosphonate utilization genes (C-P lyase) and glycerophosphodiester utilization (ugp). Samples from both substrates showed strong expression of pst/pho regulators, indicating organic phosphorus uptake. Active nitrogen fixation genes were also found in some metagenomic-assembled genomes (MAGs), suggesting internal nitrogen cycling in Microcoleus mats. Despite producing dihydroanatoxin-a, Microcoleus MAGs from this study lack the anaK gene, which is hypothesized to convert anatoxin-a to dihydroanatoxin-a. Toxic Microcoleus genomes recovered from Zion National Park encoded a complete thiamine biosynthesis pathway, including thiD. This contrasts with previous studies, which reported thiD loss in toxic Microcoleus. Overall, our results show a stable toxic Microcoleus genotype that dominates across substrates, while substrate-linked community functions between rock and sand habitats vary, especially in phosphorus acquisition.},
}

@article {pmid42537940,
year = {2026},
author = {Jiang, Q and Xu, Y and Xu, P and Kang, Y and Ou, R and Wu, X and Peng, X and Li, L},
title = {Untangling how thermal pretreatment and distiller's grains enhance humification and reduce emissions in food waste residue composting.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135527},
doi = {10.1016/j.biortech.2026.135527},
pmid = {42537940},
issn = {1873-2976},
abstract = {To address the challenges of slow start-up, poor humification efficiency, and elevated gaseous pollutant emissions during food waste residue composting, this study employed a synergistic strategy combining high-temperature pretreatment (HTP) with the addition of distiller's grains (DG). By monitoring the composting process, humification, gas emissions, and conducting metagenomic analysis, the enhancement potential and underlying mechanisms of this strategy were elucidated. The results indicated that, compared to conventional composting, the synergistic enhancement of HTP and DG significantly shortened the maturity period by 35.7 %, increased the humification index by over 55.0 %, and elevated the total nitrogen, total phosphorus, and total potassium contents of the final product by 28.1 %, 14.3 %, and 17.1 %, respectively, while achieving the highest levels of available nutrients and synergistic reductions in greenhouse gas and odor emissions. Mechanistically, HTP rapidly improved the physical structure of the feedstock, establishing a favorable foundation for microbial activity; DG selectively enriched core functional genera, including Pseudomonas and Marinobacter, and upregulated functional genes associated with N2O reduction (nosZ), sulfur oxidation, and lignocellulose degradation, thereby enhancing humus synthesis and pollutant gas mitigation at the metabolic level. This study elucidates the synergistic mechanism of physical pretreatment and bioaugmentation from a microbial functional perspective, providing not only a feasible 'waste-treats-waste' technical pathway for the resource utilization of food waste residue but also a theoretical basis for the targeted design of efficient and low-emission composting processes.},
}

@article {pmid42538237,
year = {2026},
author = {Szentiványi, T and Vásárhelyi, Z and Garamszegi, LZ},
title = {Emerging methods in noninvasive parasite surveillance in wildlife disease ecology.},
journal = {Trends in parasitology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.pt.2026.07.006},
pmid = {42538237},
issn = {1471-5007},
abstract = {Noninvasive approaches are increasingly reshaping parasite and disease surveillance by reducing stress and harm to hosts while expanding opportunities for ecological and epidemiological research. In this opinion article, we discuss these emerging approaches, which rely on molecular, citizen-science, and computational methods, for monitoring parasites, vectors, and hosts. These tools can improve spatial and temporal coverage, support the surveillance of rare or threatened hosts and parasites, and contribute to the understanding of transmission pathways and disease dynamics. However, their reliability depends on careful validation, standardized protocols, and awareness of methodological limitations. While not direct substitutes for invasive methods, these approaches lift a considerable burden from wildlife. Integrating noninvasive approaches thus provides a strong basis for advancing disease ecology, wildlife health monitoring, and biodiversity conservation.},
}

@article {pmid42538347,
year = {2026},
author = {Rath, C and Fursule, A and Wong, F and Rao, S and Patole, S},
title = {Influence of probiotics on faecal antibiotic resistome in neonates: a systematic review.},
journal = {Pediatric research},
volume = {},
number = {},
pages = {},
pmid = {42538347},
issn = {1530-0447},
abstract = {BACKGROUND: Antimicrobial resistance (AMR) and its associated complications represent a major global health threat. Probiotics, among the limited available preventive strategies, may play an important role in reducing the risk of AMR.

METHODS: A systematic review of studies assessing faecal antibiotic resistome in neonates who did versus did not receive probiotic supplementation. Databases were searched in October 2025.

RESULTS: Eighteen studies (n = 3496) were included, comprising eight randomized controlled trials (RCTs) and ten observational studies (non-RCTs). Ten of the eighteen studies (RCTs: 5, non-RCTs: 5) reported significant reduction in the prevalence of faecal antibiotic resistome among probiotic supplemented infants. Five of the eight studies that reported no reduction relied on culture or polymerase-chain reaction-based methods rather than metagenomic analyses. No consistent associations were observed between probiotic dose and strain, or type of milk feeding and resistome colonization. Most included studies were assessed as having a low risk of bias. The certainty of evidence was rated as low to very low.

CONCLUSION: Probiotic supplementation may reduce faecal AMR gene colonization in neonates. Future RCTs should employ standardized study designs and include quantitative assessment of AMR gene abundance, along with clinically relevant outcomes such as sepsis and its associated complications.

IMPACT: The first comprehensive systematic review focused on the effect of probiotics on neonatal fecal resistome and mobile genetic elements, incorporating evidence from 18 studies involving 3496 neonates. Suggests a potential role for targeted probiotic strategies as an intervention for reducing early neonatal antimicrobial resistance colonization, particularly in preterm infants at high risk of multi-drug resistance sepsis. Positions microbiome modulation as a strategy complementary to antibiotic stewardship in tackling global neonatal antimicrobial resistance.},
}

@article {pmid42538924,
year = {2026},
author = {Bechara, NR and Garcia, M and Bland, MJ and Raymann, K},
title = {Parallel and Divergent Evolution in Pseudomonas aeruginosa Under Constant and Fluctuating Predator-Mediated Selection.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.07.22.739916},
pmid = {42538924},
issn = {2692-8205},
abstract = {UNLABELLED: Environmental predation is a major driver of bacterial evolution and may indirectly influence virulence through coincidental selection. However, how sustained versus fluctuating predator pressure shapes long-term evolutionary trajectories remains poorly understood. Here, we used experimental evolution to investigate the genetic and phenotypic responses of Pseudomonas aeruginosa to continuous, absent, or fluctuating exposure to the protozoan predator Tetrahymena thermophila over 180 days. Whole-population and isolate-level shotgun metagenomic sequencing revealed fewer mutations over time but increasing frequencies of surviving mutations, consistent with selection, extensive gene-level parallel evolution, and signatures of both positive and purifying selection. Recurrently mutated genes encompassed diverse functional pathways, reflecting both shared and treatment-specific adaptive responses. Despite this parallelism, historical contingency was evident, with starting conditions influencing subsequent evolutionary trajectories. We also observed the emergence of hypermutator lineages, which are frequently recovered from chronic lung infections, suggesting that repeatedly evolving elevated mutation rates may represent a common adaptive strategy of P. aeruginosa across environmental and host-associated settings. Fluctuating predation repeatedly reshaped the adaptive landscape, leading to greater temporal turnover of mutations and a higher accumulation of mutations that ultimately reached fixation than in constant environments. Phenotypic assays revealed widespread divergence in fitness, motility, biofilm formation, siderophore production, protease activity, hemolysis, and cell size, whereas virulence in an invertebrate host model varied among treatments but did not differ significantly. Together, these findings demonstrate that variation in predator-mediated selection reshapes the dynamics and genetic targets of bacterial adaptation, highlighting the roles of ecological context, historical contingency, and hypermutability in driving the evolutionary trajectories of opportunistic pathogens.

SIGNIFICANCE STATEMENT: Environmental predators are drivers of bacterial evolution, yet their effects on adaptation remain poorly understood. We used experimental evolution to show that constant and fluctuating protozoan predation produce evolutionary trajectories in Pseudomonas aeruginosa, altering tempo, predictability, and targets of adaptation. Adaptation to predator-present or predator-absent environments shaped evolutionary trajectories, demonstrating importance of historical contingency. Fluctuating predation promoted turnover of mutations as populations adapted to selective pressures. We also observed repeated emergence of hypermutator lineages, a hallmark of chronic infections, suggesting that elevated mutation rates represent a favored adaptive strategy across environmental and host-associated settings. These findings provide insight into the environmental origins of genetic changes commonly associated with opportunistic pathogens, while showing that these changes do not necessarily increase virulence.},
}

@article {pmid42539019,
year = {2026},
author = {Paulson, JN and Whalen, AJ and Tindimwebwa, S and Hansen, J and Natukwatsa, D and Steven, K and Ochora, M and Mulondo, R and Kabachelor, EM and Ramelmeier, K and Nsubuga, BK and Omadi, PO and Magombe, J and Cohen, C and Muzahura, N and Onen, J and Ssenyonga, P and Broach, JR and Morton, SU and Osman, M and Joloba, M and Kigozi, E and Katabalwa, A and Apako, J and Amutuhaire, H and Tumuhairwe, JB and Kayemba, A and Namyalo, J and Masengere, H and Nambuya, H and Namutosi, A and Kasuswa, S and Omo, E and Tibenkana, I and Yayi, A and Muvawala, J and Nadiope, W and Muwanguzi, A and Kumbakumba, E and Ericson, JE and Schiff, SJ},
title = {Village-level surveillance of neonatal disease with integrated real-time dashboards and quality-control in Uganda.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.07.21.26358401},
pmid = {42539019},
abstract = {INTRODUCTION: Neonatal mortality remains disproportionately high in sub-Saharan Africa, where an estimated 27 neonatal deaths per 1,000 live births occur annually. Infections, including sepsis and meningitis, account for a substantial proportion of these deaths, while neural tube defects (NTDs) contribute significantly to both neonatal mortality and long-term disability. Existing surveillance systems in the region are predominantly facility-based, missing the substantial proportion of births and deaths that occur in the community. Population-based surveillance platforms that capture community-level data are urgently needed to generate accurate incidence estimates, identify modifiable risk factors, and guide evidence-based interventions.

COHORT DESCRIPTION: The Consortium to Reduce Infant Mortality (CONRIM) is a multi-institutional partnership among Ugandan physicians and scientists, Yale University, Penn State University, Boston Children's Hospital/Harvard Medical School, and Uganda's National Planning Authority. CONRIM conducts prospective, community-based neonatal surveillance within the Busoga Kingdom in eastern Uganda. A network of 813 trained Village Health Team members conducts household-level visits using a structured Open Data Kit (ODK)-based mobile questionnaire to capture every birth, assess for danger signs of possible serious bacterial infection (pSBI), screen for NTDs, and record maternal nutrition and folic acid use, water, sanitation and hygiene (WASH) conditions, and health care utilization.

FINDINGS TO DATE: Since surveillance began in June 2025, the platform has registered approximately 22,200 household submissions and over 5,700 newborn encounters across the Jinja District (population 660,000). Early data have identified higher than expected rates of infants with NTDs including encephalocele and spina bifida; documented folic acid non-use in before and during most pregnancies; characterized WASH conditions in birthplaces; and mapped geospatial hotspots of neonatal infection risk in northeastern rural subcounties. Prospective 28-day follow-up of all live births has demonstrated a neonatal mortality rate of 21.5 per 1000 live births. A real-time data quality monitoring system with 21 automated quality control flags maintains a 99% clean-record rate.

FUTURE PLANS: Ongoing and planned activities include laboratory-based confirmation of neonatal sepsis via blood culture and cerebrospinal fluid analysis with polymerase chain reaction capacity, portable neuroimaging for NTDs, environmental sampling, genomic studies of folate metabolism pathway genes, linkage with facility-based records at Jinja Regional Referral Hospital and Mulago National Referral Hospital, and community-level interventions informed by surveillance findings.

KEY MESSAGES: What is already known on this topic: Neonatal mortality remains disproportionately high in sub-Saharan Africa, with sepsis and neural tube defects (NTDs) among the leading preventable causes. Existing surveillance systems are predominantly facility-based and fail to capture births, deaths, and environmental exposures occurring at the community level. Emerging approaches in digital health, geospatial analytics, and pathogen genomics have demonstrated potential to enhance infectious disease surveillance, but these have rarely been integrated into population-based neonatal monitoring systems in low-resource settings.What this study adds: The Consortium to Reduce Infant Mortality (CONRIM) is a multidisciplinary initiative designed to develop scalable, population-based systems for understanding and reducing neonatal mortality through integrated epidemiologic, environmental, and biologic data. This paper describes one implementation of the CONRIM framework in the Busoga Kingdom of eastern Uganda, where a network of 813 trained Village Health Team members conducts longitudinal, community-based surveillance of births, neonatal outcomes, NTDs, maternal nutrition (including folic acid use), water, sanitation and hygiene (WASH) conditions, and care-seeking behaviour. This implementation integrates: real-time digital data capture with automated quality control,geospatial information systems (GIS) and remote sensing to characterize environmental risk factors,population-level genomic and metagenomic sampling to investigate host and pathogen factors, anda One Health framework linking human, animal, and environmental exposures. Early findings highlight high data completeness, geospatial clustering of neonatal infection risk, low preconception folic acid use, and identification of NTD cases not captured by facility-based systems.How this study might affect research, practice, or policy: This study demonstrates the feasibility of implementing a community-based, real-time neonatal surveillance system within an existing community health worker network in a low-resource setting. By integrating geospatial, genomic, and environmental data within a unified platform, the CONRIM framework enables more precise identification of drivers of neonatal morbidity and mortality.The approach supports targeted public health interventions, including geographically informed infection control strategies, improved referral pathways, and evidence generation for folic acid fortification policies. More broadly, CONRIM provides a scalable infrastructure for future interventional studies and precision public health strategies aimed at reducing neonatal mortality.},
}

@article {pmid42539242,
year = {2026},
author = {De Santiago, A and Bik, H},
title = {MeioBIOME: A snakemake workflow for the parallel analysis of meiofaunal genomes and host-associated bacteria/archaea.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.07.23.740139},
pmid = {42539242},
issn = {2692-8205},
abstract = {Microbes closely interact with every living organism, including meiofauna (i.e., microbial eukaryotes 38 μm - 1 mm in length), and influence the development, life cycle, and evolution of diverse metazoans. Together, meiofauna and their microbiomes, collectively referred to as the holobiont, underpin biogeochemical cycles and drive decomposition of organic matter. However, our understanding of the ecological and evolutionary dynamics of meiofauna microbiomes are limited, typically owed to low-resolution 16S rRNA surveys, which cannot accurately delineate bacterial taxa. Single-specimen holobiont sequencing can help overcome the limitations of metabarcoding approaches by 1) generating metagenome-assembled genomes (MAGs) of the host microbiome and 2) recovering host single-copy genes (SCGs) to phylogenetically confirm the identity of the host organism. However, most bioinformatics pipelines for the assembly of metagenomic datasets have been developed for the assembly of high-complexity microbial communities of bulk sediment or soil samples (and cannot be used for the assembly of host genomes), rely on co-assembly approaches (which collapses strain-level genomic information of bacterial taxa), and focus on binning either prokaryotic or eukaryotic taxa. Therefore, there is a tremendous need for a computational workflow for the dual analysis of host genomes and their microbiomes. Here, we developed MeioBIOME, a modular Snakemake pipeline for the reproducible analysis of holobiont metagenomes obtained from individually sequenced microbial metazoa. We analyze publicly available single-specimen metagenomics datasets to show the utility of MeioBIOME and recover host-associated symbiont MAGs and host SCGs. Additionally, we integrate state-of-the-art binning algorithms which generate more MAGs than the DOE Joint Genome Institute metagenomic pipeline. We anticipate that MeioBIOME will facilitate studies of phylosymbiosis by generating high-quality host genome skims (to build well-supported host phylogenetic trees) and host-associated prokaryotic MAGs obtained from single specimens.},
}

@article {pmid42539626,
year = {2026},
author = {Han, J and Zhao, W and Deng, R and Wang, Y and Gong, W and Wang, Z and Sun, G and Liu, H and Geng, M and Zhang, Y},
title = {Sodium oligomannate reduces cerebral infarction and improves neurological function through microbiota remodeling in MCAO/R rats.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1880590},
doi = {10.3389/fphar.2026.1880590},
pmid = {42539626},
issn = {1663-9812},
abstract = {BACKGROUND: Ischemic stroke is the second leading cause of death worldwide, characterized by high mortality and a narrow therapeutic window for thrombolysis. Gut microbiota dysbiosis and gliosis following ischemic stroke are key drivers of post-stroke neurological impairment. Sodium oligomannate (GV-971) is a low-molecular-weight acidic oligosaccharide that targets the gut-brain axis. It alleviates gliosis and improves cognitive dysfunction by remodeling gut microbiota in Alzheimer's disease. However, it is still unknown whether GV-971 has pharmacological activity against ischemic stroke.

METHODS: Here, we explore the efficacy of GV-971 on infarct volume, gliosis, blood-brain barrier integrity, gut microbiota composition, and post-stroke cognitive impairment (PSCI) using a middle cerebral artery occlusion/reperfusion (MCAO/R) model in male Sprague-Dawley rats.

RESULTS: Administer medication before surgery for 4 consecutive days and once after surgery, after stroke 24-hour triphenyltetrazolium chloride (TTC) staining revealed that 0.3 mg/kg GV-971 significantly reduced infarct volume in ischemic brain tissue from 37.81±2.391% to 13.30±4.801% and neurological impairment score of GV-971 treatment significantly decreased from 11.50±0.54 to 7.29±1.47. After stroke 24-hour immunofluorescence analysis of glial activation confirmed that GV-971 significantly reduced central inflammatory responses. Western blot combined with Evans blue staining collectively demonstrated that after stroke 24-hour, GV-971 exerts a significant protective effect on the blood-brain barrier. In the gut, GV-971 reversed microbial dysbiosis, as revealed by shotgun metagenomics, enhanced intestinal barrier integrity, and suppressed colonic inflammation. Antibiotic depletion abolished GV-971's neuroprotective effect, while fecal microbiota transplantation from GV-971-treated donors restored protection, supporting a microbiota-dependent contribution. Furthermore, GV-971-treated rats subjected to MCAO/R exhibited significant improvements in motor and cognitive function. For example, on day 35, Y-maze test results indicated that GV-971 administered either before MCAO/R (pre-treatment) or during the perioperative period (co-treatment) increased spontaneous alternation rate from 60.95±4.91% to 85.60±6.32% and 85.64±5.027%. On day 32, novel object recognition assay results indicated that GV-971 treatment increased new-object exploration from 0.2039±0.03752 to 0.3991±0.1122 (pre-treatment) and 0.5066±0.06982 (co-treatment). On day 42, Barnes maze test results indicated that GV-971 treatment reduced the time required to locate the target hole from 76.45±17.41s to 31.03±20.75 s and 33.37±19.30 s for pre- and co-treatment, respectively.

CONCLUSION: Taken together, GV-971 demonstrated neuroprotective potential in experimental ischemic stroke.},
}

@article {pmid42539687,
year = {2026},
author = {Wang, Z and Yang, H and Liu, J and Li, X},
title = {Diagnostic value of metagenomic next-generation sequencing in deep neck space infections: a retrospective study of 32 patients.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1874210},
doi = {10.3389/fcimb.2026.1874210},
pmid = {42539687},
issn = {2235-2988},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; Retrospective Studies ; *Metagenomics/methods ; *Neck/microbiology ; Female ; Male ; *Bacteria/genetics/classification/isolation & purification ; Middle Aged ; Aged ; *Bacterial Infections/diagnosis/microbiology ; Adult ; Aged, 80 and over ; DNA, Bacterial/genetics ; },
abstract = {INTRODUCTION: Deep neck space infections (DNSI) are rapidly progressive suppurative conditions in which early identification of causative pathogens is critical for clinical decision-making. This study evaluated the diagnostic performance and clinical utility of metagenomic next-generation sequencing (mNGS) in patients with DNSI.

METHODS: In this retrospective observational study, 32 patients with radiologically confirmed DNSI who underwent surgical drainage between October 2023 and August 2025 were included. Intraoperative purulent specimens were analyzed using both conventional bacterial culture and mNGS. A composite clinical reference standard integrating clinical presentation, imaging findings, surgical observations, inflammatory markers, and expert assessment was used to evaluate the clinical relevance of detected microorganisms.

RESULTS: mNGS detected microbial DNA in 84.4% of patients and demonstrated a broader pathogen detection spectrum and shorter reporting time than conventional culture, particularly for anaerobic and fastidious organisms. Frequently detected organisms included Prevotella spp. and Streptococcus constellatus. Interpretation of these findings required careful consideration of anatomical involvement, organism abundance, and prior antimicrobial exposure to distinguish clinically relevant pathogens from colonizing organisms or residual nonviable DNA. Discordant findings between culture and mNGS, including culture-positive/mNGS-negative and dual-negative cases, were observed and likely reflected differences in sampling adequacy, organism viability, sequencing depth, and methodological limitations. Antimicrobial therapy was adjusted in selected patients following mNGS reporting.

DISCUSSION: mNGS may serve as a valuable adjunct to conventional microbiological diagnostics by expanding pathogen detection in selected DNSI cases, particularly when fastidious or anaerobic organisms are involved. However, its results should be interpreted cautiously in the context of clinical and microbiological findings. Prospective controlled studies are needed to further define the clinical role of mNGS in the management of DNSI.},
}

Humans
*High-Throughput Nucleotide Sequencing/methods
Retrospective Studies
*Metagenomics/methods
*Neck/microbiology
Female
Male
*Bacteria/genetics/classification/isolation & purification
Middle Aged
Aged
*Bacterial Infections/diagnosis/microbiology
Adult
Aged, 80 and over
DNA, Bacterial/genetics

@article {pmid42539859,
year = {2026},
author = {Vuth, H and Wang, W and Qin, W and Yang, M and Li, Y and Zhou, Q and Xu, X and Zhang, J and Zhao, H},
title = {Application of metagenomic next-generation sequencing as an adjunct to conventional microbiological testing for the diagnosis of infection in kidney transplant recipients.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1713707},
doi = {10.3389/fcimb.2026.1713707},
pmid = {42539859},
issn = {2235-2988},
mesh = {Humans ; *Kidney Transplantation/adverse effects ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Retrospective Studies ; Female ; Male ; *Transplant Recipients ; Bronchoalveolar Lavage Fluid/microbiology ; Middle Aged ; Adult ; Sputum/microbiology ; Bacteria/genetics/isolation & purification ; *Microbiological Techniques/methods ; Aged ; },
abstract = {BACKGROUND: Kidney transplant recipients are highly susceptible to opportunistic and nosocomial infections that demand rapid and accurate diagnosis due to the broad and complex spectrum of pathogens. Conventional microbiological testing (CMT) is often limited, particularly when patients are already receiving antimicrobial therapy at the time of sampling. This study aimed to evaluate the clinical value of metagenomic next-generation sequencing (mNGS) as a complementary diagnostic approach to CMT, with a focus on concordance and discrepancies between the two methods across peripheral blood, sputum, bronchoalveolar lavage fluid (BALF), and urine samples.

METHODS: We conducted a retrospective study of kidney transplant recipients with suspected infections who underwent simultaneous mNGS and CMT testing between March 2022 and May 2024. The impact of prior antibiotic exposure on diagnostic yield was assessed. Detection of antimicrobial resistance (AMR) genes by mNGS and subsequent modifications in anti-infective management were also analyzed.

RESULTS: A total of 243 samples (57 blood, 96 sputum, 71 BALF, 19 urine) were included. Across all sample types, mNGS demonstrated significantly higher positive rates than CMT (blood: 78.95% vs 21.05%; BALF: 90.14% vs 19.72%; sputum: 92.71% vs 20.83%; urine: 89.47% vs 36.84%; all P<0.001). Prior antibiotic exposure markedly reduced CMT positivity but had minimal impact on mNGS detection. Concordance analysis showed 40.35% of samples were positive by both methods, while 60.1% were negative by CMT but positive by mNGS. In addition to pathogens identified by CMT, mNGS detected a broader range of microorganisms, including viruses (e.g., cytomegalovirus, Epstein-Barr virus, SARS-CoV-2), fungi (Pneumocystis jirovecii), and parasites (Strongyloides stercoralis, Toxoplasma gondii). Overall, mNGS-guided results refined antibiotic treatment strategies in 110 cases (60.11%).

CONCLUSION: mNGS serves as a valuable adjunct to CMT in kidney transplant recipients, providing rapid and comprehensive pathogen identification. However, from a health economics perspective, mNGS should be applied selectively according to clinical needs, rather than as a universal first-line diagnostic method.},
}

Humans
*Kidney Transplantation/adverse effects
*High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
Retrospective Studies
Female
Male
*Transplant Recipients
Bronchoalveolar Lavage Fluid/microbiology
Middle Aged
Adult
Sputum/microbiology
Bacteria/genetics/isolation & purification
*Microbiological Techniques/methods
Aged

@article {pmid42540632,
year = {2026},
author = {Li, Y and He, J and He, X and Peng, Y and Luo, X and Xie, X and Fu, Y and Long, H},
title = {Clinical Characteristics of Patients With AIDS and Talaromyces marneffei Infection of the Central Nervous System: A Retrospective Observation Study.},
journal = {AIDS research and treatment},
volume = {2026},
number = {},
pages = {9954449},
doi = {10.1155/arat/9954449},
pmid = {42540632},
issn = {2090-1240},
abstract = {OBJECTIVE: To analyze the clinical characteristics of patients with acute immunodeficiency syndrome (AIDS) combined with Talaromyces marneffei (TM) infection of the central nervous system (CNS), thereby improving awareness toward early diagnosis and treatment.

METHODS: The clinical data of eight patients with AIDS who were treated for CNS TM infection in the Guiyang Public Health Treatment Center from May 2021 to November 2022 were retrospectively analyzed.

RESULTS: The median age of the patients was 43.50 (range: 35.00-58.00) years, and all eight were male. TM infection was confirmed via metagenomic next-generation sequencing (mNGS) in three cases, positive cerebrospinal fluid (CSF) cultures of TM in four cases, and both in one case. CSF and blood cultures were both positive for one patient, whereas multiple blood cultures were negative for the other seven. The number of nucleated cells and the protein level in the CSF were elevated in five and six patients, respectively, and the CSF levels of glucose and chloride were low in four patients each. Seven patients had intracranial lesions upon head imaging, and all eight were discharged from the hospital with improvement after antifungal treatment. The median CD4+ T-cell count was 58.50/μL (range: 39.00-73.00/μL), indicating severe immunosuppression.

CONCLUSION: The clinical characteristics and CSF-related examinations of patients with AIDS combined with CNS TM infection are not distinct, complicating diagnosis and increasing the likelihood of misdiagnosis. Early diagnosis and systemic antifungal therapy can improve patients' prognosis.},
}

@article {pmid42540776,
year = {2026},
author = {Ren, C and Zhuo, X and Yang, X and Yao, X and Gong, S and Xiong, H and Fang, F and Zhang, W},
title = {Copy number variation analysis of cerebrospinal fluid metagenomic next-generation sequencing data in assisting the diagnosis of pediatric brain tumors.},
journal = {Pediatric investigation},
volume = {},
number = {},
pages = {},
doi = {10.1002/ped4.70076},
pmid = {42540776},
issn = {2574-2272},
}

@article {pmid42541130,
year = {2026},
author = {Verhoeven, JTP and Shapiro, JT and Holm Jensen, R and McCleery, RA and Monadjem, A and Hansen, AJ and Pénzes, JJ and Canuti, M},
title = {Characterizing the parvovirome of Swazi bats: novel species, highly divergent lineages, endogenous viral elements, and taxonomic challenges.},
journal = {Virus evolution},
volume = {12},
number = {1},
pages = {veag042},
doi = {10.1093/ve/veag042},
pmid = {42541130},
issn = {2057-1577},
abstract = {Parvoviridae (small, nonenveloped ssDNA viruses) currently includes 281 species in two vertebrate- and four invertebrate-infecting subfamilies. While parvovirus-derived sequences are frequently identified in viromes, their taxonomy and host affiliation can be challenging due to high host and genetic diversity. We investigated the faecal parvovirome of 46 bats (7 insectivorous and 1 frugivorous species) from Eswatini and identified 28 novel viral species in 29 individuals (63.0%). The majority of these (22/28, 78.6%) belonged to nine genera (including two that are previously undescribed) within the invertebrate-infecting subfamily Densovirinae. A novel virus in the genus Brevipenbrevirus (arthropod-infecting subfamily Penbrevirinae) was found in 19.6% of the animals, including several frugivorous Epomophorus wahlbergi bats. A novel bat protoparvovirus (vertebrate-infecting subfamily Parvovirnae) was found both in the faeces and blood of one Afronycteris nanus bat. A highly divergent virus (Swazi bat-associated megaparvovirus 1, SwaBA-MePV-1) was found in the faeces, but not in the blood, of two insectivorous bats (Mops pumilus and Scotophilus viridis). Compared to other parvoviruses, SwaBA-MePV-1 presented two additional coding cassettes, significantly increasing its genome size. Homology modelling showed capsid protein C-terminal elongation, a previously undescribed strategy of parvoviral particle size expansion. Exploring public repositories identified 10 related uncharacterized viruses with similar genome organization and complete endogenous viral elements (EVEs) in eight beetle species, suggesting a coleopteran host affiliation. The complete genome of another highly divergent virus (SwaBA microparvovirus 1), without any detectable exogenous or endogenous relatives, was found in the faeces, but not in the blood, of one insectivorous Mops condylurus bat. Importantly, when comparing our sequences to references in Genbank, we observed that taxonomic mislabelling in sequence repositories can seriously misguide automatic taxonomy assignments (~75% of sequences initially identified as parvoviruses were discarded as false positives). These errors are amplified as new mislabelled sequences become dominant, highlighting the importance of prioritizing taxonomy validation and correct annotations in repositories. This study demonstrates that faecal samples from insectivorous chiropterans are rich in (novel) parvoviruses from various hosts. The discovery of highly divergent lineages (outside current sub-families) and EVEs helps clarify parvovirus evolutionary history and emphasizes how much of the parvoviral world remains unexplored.},
}

@article {pmid42541871,
year = {2026},
author = {Mo, H and Meng, G and Wei, Y and Liu, J and Chai, B},
title = {Low-dose heavy metals reprogram microbial carbon metabolism and decouple genomic potential from carbon fluxes in riverine wetlands.},
journal = {Journal of environmental management},
volume = {415},
number = {},
pages = {130618},
doi = {10.1016/j.jenvman.2026.130618},
pmid = {42541871},
issn = {1095-8630},
abstract = {River wetland sediments represented an important global carbon sink. Low-dose heavy metal pollution was widespread in aquatic ecosystems, yet its impacts on microbial carbon cycling remained poorly understood. Here, we demonstrated that even when metal concentrations remained within current environmental quality standards, heavy metals could fundamentally reprogram microbial carbon metabolism in riverine wetlands under long-term low-dose heavy metal stress. In the Fen River Basin, microbial communities associated with carbon cycling were significantly restructured: α-diversity (Shannon index) was significantly higher in polluted sites (p < 0.05), and the abundance of core carbon-degradation and carbon-fixation genes (e.g., GAPDH, sucC, accC) was significantly elevated, while methanogenesis genes (e.g., hdrB2) were suppressed, leading to a pronounced functional trade-off. Notably, we inferred a potential decoupling between microbial functional potential and actual ecosystem processes in laboratory microcosms, where CO2 and CH4 emissions were suppressed despite elevated genetic potential, exhibiting a non-monotonic dose-response pattern. Together, these findings revealed a cascading mechanism linking environmental filtering, community restructuring, functional differentiation, and carbon flux regulation, highlighting a stress-induced metabolic state characterized by high maintenance costs and low efficiency. These results challenge current environmental standards and underscore the hidden ecological risks of low-dose pollution to wetland carbon sinks.},
}

@article {pmid42541893,
year = {2026},
author = {Akhtar, MS and Zaman, W},
title = {Portable metagenomics for preventive surveillance and outbreak control in livestock and poultry: Pathogen detection, resistome profiling, and antimicrobial stewardship.},
journal = {Research in veterinary science},
volume = {210},
number = {},
pages = {106352},
doi = {10.1016/j.rvsc.2026.106352},
pmid = {42541893},
issn = {1532-2661},
abstract = {Conventional diagnostics for livestock and poultry outbreaks commonly rely on culture or targeted PCR panels, which may be too slow or too narrow to guide early control decisions. Portable metagenomics, particularly real-time nanopore sequencing, offers a route to broad pathogen detection, antimicrobial-resistance gene profiling, and outbreak investigation within an integrated workflow. This implementation-focused review evaluates how near-point-of-care metagenomics may support preventive veterinary medicine through earlier detection, surveillance, cohorting, biosecurity decisions, and antimicrobial stewardship. We synthesize sample-to-answer workflows for enteric and respiratory disease in food-producing animals, including sampling, nucleic-acid extraction, host depletion or target enrichment, library preparation, sequencing, bioinformatics, quality control, and interpretation. Applications in calf diarrhea, bovine respiratory disease, poultry outbreaks, mastitis, and resistome monitoring are considered alongside the central limitation that detection alone does not establish causation. Pathogen and resistance-gene signals must therefore be interpreted with clinical signs, lesions, epidemiology, controls, and confirmatory testing. We also propose a minimum reporting checklist, intended as a practical framework rather than a validated consensus standard. Portable metagenomics is not a replacement for conventional diagnostics, but appropriately validated workflows can reduce uncertainty during time-sensitive outbreaks and support more judicious antimicrobial use.},
}

@article {pmid42542139,
year = {2026},
author = {Xu, JJ and Xu, ZQ and Yu, J and Wang, MH and Li, WH and Jin, RC},
title = {Biochar-driven regulation of anammox systems under varying nitrogen loads: performance, microbial community and metabolic mechanisms.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135542},
doi = {10.1016/j.biortech.2026.135542},
pmid = {42542139},
issn = {1873-2976},
abstract = {This study examined the effects of wheat straw biochar on the anaerobic ammonium oxidation (anammox) process during stepwise decrease in influent substrate concentrations. Biochar exerted a dual role depending on nitrogen load. During phase I (300 mg·L[-1] NH4[+]-N and NO2[-]-N), the biochar group exhibited 1-4% higher relative abundances of selected anammox related genes, including hzs and hdh, than the control group. At the end of phases III and IV, the electron transport system activity in the biochar-amended reactor was 10% and 46% above the corresponding control values, respectively, whereas improvement in specific anammox activity (SAA) and total nitrogen removal efficiency (TNRE) was observed after stabilization in phase IV. At 50 mg·L[-1] NH4[+]-N and 50 mg·L[-1] NO2[-]-N, the SAA reached 12.5 mg N·(g volatile suspended solids (VSS)·d) [-1], 7% higher than that of the control group, while the TNRE was approximately 6% higher. Metagenomic analysis revealed phase-dependent differences in functional-gene relative abundance. The biochar group showed higher relative abundances of denitrification genes (nirS, norB, and nosZ) and genes related to dissimilatory nitrate reduction to ammonium (DNRA), including nrfA, together with lower relative abundances of nitrification genes (amoA, amoB, and amoC). These differences were consistent with reduced substrate competition and potential coupling between anammox and denitrification. These findings provided a mechanistic basis for applying wheat straw biochar to anammox systems operated under changing nitrogen loading conditions.},
}

@article {pmid42531833,
year = {2026},
author = {Wang, Y and Liu, Z and Hou, Q and Xu, Y and Chen, W and Chen, M and Liu, J and Tang, J and Wang, Y and Zhou, M and Wu, X and Wang, X},
title = {Poricoic acid a ameliorates ulcerative colitis via AMPK/PPARγ pathway-dependent cellular senescence inhibition and concomitant gut microbiota-metabolome modulation.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {160},
number = {},
pages = {158628},
doi = {10.1016/j.phymed.2026.158628},
pmid = {42531833},
issn = {1618-095X},
abstract = {BACKGROUND: Ulcerative colitis (UC) is an intractable inflammatory bowel disorder characterized by persistent intestinal inflammation and impaired gut barrier integrity. Its pathogenesis is multifactorial, involving gut microbiota dysbiosis, metabolic dysfunction, and cellular senescence. Current therapeutic regimens remain limited, underscoring an urgent need for innovative agents that target these interrelated pathological cascades.

PURPOSE: This study aimed to evaluate the pharmacological effects of poricoic acid A (PAA) on DSS-induced senescence in intestinal epithelial cells and in a murine model of ulcerative colitis (UC), as well as the underlying molecular mechanisms.

METHODS: We established a DSS-stimulated senescent intestinal epithelial cell model and a DSS-induced UC mouse model. Multi-omics and bioinformatics strategies, including network pharmacology, transcriptome profiling, gut metagenomics, and intestinal targeted metabolomics, were combined with molecular docking to predict candidate signaling axes. Subsequent pharmacological inhibition and siRNA-mediated silencing assays were performed to validate core pathways functionally.

RESULTS: PAA robustly suppressed DSS-induced senescence and inflammatory responses in intestinal epithelial cells. In vivo assays verified that PAA alleviated UC-related manifestations, including body weight loss, rectal hemorrhage, and colonic histological injury. Joint network pharmacology and transcriptomic screening identified the AMPK/PPARγ as the core pathway mediating PAA's bioactivity. Mechanistic experiments confirmed that PAA directly bound and activated PPAR, further functionally triggering downstream AMPK/SirT1/PGC1α signaling. Blockade of AMPK via pharmaceutical antagonists or siRNA largely abolished PAA's anti-senescence and anti-inflammatory capacities; PPARγ suppression, in turn, secondary deactivated the AMPK and its downstream functional effectors. In mouse models, AMPK inhibition drastically compromised PAA's protective effects against UC. Moreover, PAA treatment of UC is closely associated with remodeling of the gut microbiome-metabolome axis and restoration of intestinal homeostasis.

CONCLUSION: PAA exerts potent anti-senescence, anti-inflammatory, and colon-protective effects in UC via activating the AMPK/PPARγ signaling pathway. Such beneficial activity may be associated with the normalization of gut microbiota-metabolome homeostasis. This work identifies novel molecular targets and a promising lead compound for the intervention of ulcerative colitis.},
}

@article {pmid42531877,
year = {2026},
author = {Zhu, X and Zhang, X and Zhang, X and Al-Dhabi, NA and Tang, W and Wu, P and Wang, A},
title = {Decoding the metabolic synergy and extracellular electron transfer bottleneck in manganese-driven nitrogen removal: Mechanisms underlying the dominance of comammox bacteria.},
journal = {Water research},
volume = {306},
number = {},
pages = {126584},
doi = {10.1016/j.watres.2026.126584},
pmid = {42531877},
issn = {1879-2448},
abstract = {Manganese-redox-driven autotrophic nitrogen removal holds immense potential for low-carbon wastewater treatment, yet practical operations suffer from oxygen intrusion that triggers complete ammonia oxidation (comammox). This study employed a step-wise Mn acclimation strategy (10 to 20 mg/L Mn[2+]) over 180 days to decipher the metabolic synergy among manganese-dependent anaerobic ammonium oxidation (Mnammox), comammox, and manganese-autotrophic denitrification (MnAD) consortia. Results revealed that comammox enrichment elevated ammonia removal to 41.1 % but shifted nitrate removal from 95.5 % to net accumulation (negative values). Metagenomics confirmed that comammox Nitrospira secured niche dominance (abundance surging to 7.7 %) due to high substrate affinity and robust genomic flexibility (encoding 17 manganese oxidases). Furthermore, Nitrospira exhibited dual "deoxygenation" and "ammonia oxidation synergy" functions, alleviating the over-reduction of solid-phase biogenic manganese oxides (BioMnOx). Mineralogical characterization suggested that this mechanism stabilized the Mn[4+] proportion, sustaining the material basis of Mn transformation. However, activity tests demonstrated that the nitrate generation rate of comammox (1.6 mg/L/h) significantly outpaced the reduction rate of MnAD (0.8 mg/L/h). This bottleneck stems from the low inorganic electron donor utilization and solid-liquid interfacial mass transfer resistance, which suppress extracellular electron transfer (EET) efficiency. In conclusion, this study unveils a novel coupled metabolic pathway between comammox and Mn transformation, while clarifying the existence of an EET bottleneck within the system. These findings theoretically highlight the necessity of interfacial regulation strategies (e.g., incorporating conductive media) in future studies, thereby balancing comammox activity and MnAD capacity for optimized nitrogen removal.},
}

@article {pmid42532286,
year = {2026},
author = {Zhang, Y and Hu, L and Ding, X and Liu, L and Xue, L and Miao, L},
title = {Investigating Gut Microbiota and their metabolites as Biomarkers for Tacrolimus Pharmacokinetic Variability.},
journal = {European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences},
volume = {},
number = {},
pages = {107626},
doi = {10.1016/j.ejps.2026.107626},
pmid = {42532286},
issn = {1879-0720},
abstract = {Tacrolimus (TAC), a cornerstone immunosuppressant in transplantation, presents a clinical challenge due to its narrow therapeutic index and substantial interindividual pharmacokinetic (PK) variability. This exploratory study investigated the association between gut microbiota composition, short-chain fatty acid (SCFA) metabolites, and TAC PK variability during the early post-kidney transplantation period. Based on prediction errors derived from a previously established population PK model, 36 transplant recipients were stratified into positive (n=17) and negative (n=19) deviation groups. Metagenomic sequencing and targeted SCFA metabolomic analysis of fecal samples revealed that the negative deviation group exhibited significantly reduced gut microbial diversity and altered community structure. Among 142 differentially abundant taxa, 10 microbial features, including Enterococcaceae - associated taxa, showed discriminative potential between the two PK phenotypes (AUC > 0.7), with three Enterococcus species (E. durans, E. faecium, and E. hirae) showing particularly robust signals (Cohen's d > 1.0 and power > 80%). Functional analysis suggested downregulation of butyrate biosynthesis pathways in the negative deviation group, which was consistent with significantly lower fecal butyrate and total SCFA concentrations. These hypothesis-generating findings suggest that gut microbiota and SCFAs are associated with TAC PK phenotypes, but independent validation in larger cohorts is required before clinical translation.},
}

@article {pmid42532775,
year = {2026},
author = {Nealon, NJ},
title = {Next-Generation Sequencing in Companion Animal Practice for Infectious Disease Diagnostics and Characterizing Normal Microbiomes.},
journal = {The Veterinary clinics of North America. Small animal practice},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cvsm.2026.06.005},
pmid = {42532775},
issn = {1878-1306},
abstract = {The purpose of this article is to review and compare the most common and emergent next-generation sequencing methodologies used in small animal veterinary practice, with a focus on their applications to bacterial diagnostics and assessment of the healthy gut microbiome. These methodologies include whole genome sequencing, amplicon sequencing, shotgun metagenomic sequencing, and transcriptomics. Understanding the benefits and limitations of each methodology will help small animal practitioners to make informed decisions for their patients and maximize the utility of each test as part of a complete patient health assessment.},
}