@article {pmid41865966,
year = {2026},
author = {Zhou, L and Zhu, S and Wu, J and Wang, W and Zhao, Z and Hao, X and Wang, J and Yu, W and Li, Y and Liang, J},
title = {Co-inoculation of arbuscular mycorrhizal fungi and rhizobia reshapes microbial ecology and nutrient metabolism to rehabilitate iron ore tailings.},
journal = {Environmental research},
volume = {},
number = {},
pages = {124325},
doi = {10.1016/j.envres.2026.124325},
pmid = {41865966},
issn = {1096-0953},
abstract = {Arbuscular mycorrhizal fungi (AMF) and rhizobia play crucial roles in soil-plant systems for ecological restoration. However, their specific remediation characteristics and synergistic effects on tailings remain poorly understood. In this study, we investigated the remediation characteristics of tailings inoculated with AMF and rhizobia, focusing specifically on synergy mechanism for iron tailings improvement under the co-inoculation. The results demonstrated that microbial inoculation significantly enhanced overall remediation performance. The co-inoculation led to a 6.25-fold increase in alfalfa biomass, substantial improvements in nutrient availability (N/C/P), and enhanced soil structure through aggregate formation. Concurrently, the cadmium bioavailability was effectively reduced by 35.56%. Functional metabolic analysis revealed that the upregulation of phosphate-related genes (phoB, phoR) enhanced microbial phosphate solubilization and plant phosphate uptake efficiency. Furthermore, the primary pathways for nitrogen uptake shifted from reliance on biological nitrogen fixation to prioritizing internal nitrogen cycling, while activation of the GABA shunt reduced dependence on the TCA cycle. Notably, the restructured microbial community preferentially stimulated organic carbon-nitrogen (C/N) metabolism, and these metabolic shifts were key to enhanced plant nutrients acquisition efficiency. These findings indicate that AMF and rhizobia could stimulate microbial community restructuring and drive the remodeling of nutrient metabolism in tailings, representing a pivotal process in promoting soil formation from tailings.},
}

@article {pmid41866421,
year = {2026},
author = {Mathur, S and Prasad, M and Kumar, S and Chaurasia, A and Ranjan, R},
title = {A metagenomic survey of the rhizosphere bacterial community of P. longum from the herbal garden, Dayalbagh Educational Institute (D.E.I), Agra, India.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {4},
pages = {},
pmid = {41866421},
issn = {1573-0972},
}

@article {pmid41866581,
year = {2026},
author = {Halo, BA and Aljabri, YAS and Glick, BR and Yaish, MW},
title = {Metagenomic and functional insights into root endophytic bacteria associated with drought stress in cowpea.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-45459-4},
pmid = {41866581},
issn = {2045-2322},
support = {IG/SCI/BIOL/24/03//Sultan Qaboos University, College of Science, Oman/ ; },
}

@article {pmid41867450,
year = {2026},
author = {Jia, C and Liu, X and Liu, W and Yao, X and Chen, X and Zhao, J and Wang, P and Ge, W and Han, Y},
title = {Multi-Omics Reveal the Potential Associations of Streptococcus, 13'-Hydroxy-Alpha-Tocopherol and Glutathione Metabolism in Children with Chronic Rhinosinusitis with Nasal Polyps.},
journal = {Journal of inflammation research},
volume = {19},
number = {},
pages = {567582},
pmid = {41867450},
issn = {1178-7031},
abstract = {BACKGROUND: Chronic rhinosinusitis with nasal polyps (CRSwNP) in children is a clinically significant inflammatory disorder characterized by persistent symptoms and complex underlying mechanisms. This study used multi-omics approaches to investigate potential microbial and metabolic associations in pediatric CRSwNP.

METHODS: Nasal secretions from 20 children with CRSwNP and 19 healthy controls were analyzed using metagenomics, untargeted metabolomics, and proteomics.

RESULTS: CRSwNP patients showed higher microbial diversity and altered microbial communities, with increased Streptococcus abundance. Metabolomic sequencing revealed that 13'-Hydroxy-alpha-tocopherol was significantly upregulated in the CRSwNP group and exhibited a positive correlation with the abundance of Streptococcus. Proteomic sequencing revealed that proteins involved in glutathione metabolism were significantly downregulated in the CRSwNP group, with GCLM and GGCT showing a significant negative correlation with 13'-Hydroxy-alpha-tocopherol.

CONCLUSION: These associative findings suggest potential links among Streptococcus, 13'-Hydroxy-α-tocopherol, and glutathione metabolism, indicating that oxidative stress-related imbalance may contribute to pediatric CRSwNP. These results provide preliminary evidence that 13'-Hydroxy-α-tocopherol may serve as a potential biomarker for pediatric CRSwNP.},
}

@article {pmid41867493,
year = {2025},
author = {Alali, M and Imani, M},
title = {Bayesian Topology Inference of Regulatory Networks under Partial Observability.},
journal = {Results in control and optimization},
volume = {19},
number = {},
pages = {},
pmid = {41867493},
issn = {2666-7207},
abstract = {Biological systems, such as microbial communities in metagenomics and gene regulatory networks (GRNs) in genomics, are composed of a vast number of interacting components observed through inherently noisy data. These systems play a critical role in understanding fundamental biological processes, including gene regulation, microbial interactions, and cellular dynamics. For example, microbial communities involve complex interactions between microbes, bacteria, genes, and small molecules observed through omics data, while GRNs consist of numerous interacting genes observed via various gene-expression technologies. However, reconstructing the topology of such networks poses significant challenges due to their large scale, high dimensionality, and the presence of noise. Existing inference techniques often struggle with scalability, interpretability, and overfitting, making them unsuitable for analyzing large and complex biological systems. To overcome these challenges, this paper proposes a Bayesian topology optimization framework for efficient and scalable inference of regulatory networks modeled as partially-observed Boolean dynamical systems (POBDS). The method combines the Boolean Kalman Filter (BKF) as an optimal estimator for POBDS, with Bayesian optimization, which employs Gaussian Process regression and a topology-inspired kernel function to model the log-likelihood function. Numerical experiments demonstrate the superior performance of our framework. In the p53-MDM2 network, our method accurately infers topology with 8 and 16 unknown regulations, achieving higher log-likelihood with 100 and 200 evaluations, respectively. For the mammalian cell cycle network with 10 unknown regulations, proposed method identifies the correct topology among 59,049 possibilities with lower error and faster convergence.},
}

@article {pmid41867523,
year = {2026},
author = {Kanno, N and Ohtani, T and Oda, N and Kato, S and Ohkuma, M and Shigeto, S},
title = {Domain-Level Classification of Archaea and Bacteria Using AI-Assisted Single-Cell Raman Spectroscopy.},
journal = {ACS omega},
volume = {11},
number = {10},
pages = {16913-16921},
pmid = {41867523},
issn = {2470-1343},
abstract = {Archaea and Bacteria are two fundamentally distinct domains of life that share prokaryotic traits, yet differ markedly in molecular and cellular architecture. While many archaeal species identified thus far have been found in extreme environments, recent metagenomic studies have revealed their widespread presence in moderate habitats, including soils, oceans, and even the human microbiome. However, archaea remain less well characterized than bacteria, largely due to the technical challenges associated with culturing and identifying these microorganisms. In this study, we present a culture-independent method for discriminating archaea from bacteria at the single-cell level using Raman spectroscopy combined with machine learning. We constructed a Raman spectral data set comprising 22 prokaryotic species (11 archaea and 11 bacteria) and developed a domain-level Archaea-Bacteria (AB) classifier using the LightGBM tree-based machine learning algorithm. Our AB classification model achieved an average classification accuracy of 89.1% and a sensitivity of 98.1% on eight representative species (including two independent held-out test species) with minimal data size and preprocessing. We also compared its performance to convolutional neural networks with transfer learning, a widely used deep learning approach. Our method provides a robust analytical framework for archaeal detection and represents a valuable addition to the microbiological toolkit, particularly for studying unculturable or low-abundance archaeal populations in complex microbial communities.},
}

@article {pmid41867691,
year = {2026},
author = {Jiang, D and Wang, Y and Ling, Y and Eremin, SA and Mukhametova, LI and Du, J and Hu, H},
title = {Impacts of high-temperature and humidity transportation on rice quality: an integrated analysis of microbial community succession and flavor compound alterations.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1792369},
pmid = {41867691},
issn = {2296-861X},
abstract = {This study investigated the dynamic changes in rice quality, microbial communities, and volatile compound profiles during simulated summer transportation (35 °C, 70% RH, 15 days). Indica rice samples were systematically collected every 3 days and analyzed using HS-SPME-GC-MS/MS, HS-GC-IMS, and metagenomic sequencing. Prolonged transportation significantly altered the physicochemical properties of the rice. Moisture content plateaued on day 12, while germination rates declined significantly starting from day 6. Furthermore, fatty acid values increased continuously due to accelerated lipid hydrolysis and oxidation. Visible mold growth became evident on day 12, marking a critical tipping point for quality deterioration. The odor activity value (OAV) and relative odor activity value (ROAV) analyses revealed that the decline in unsaturated fatty aldehydes such as (E)-2-nonenal and the significant accumulation of alcohols, ketones, and short-chain esters, including 1-octen-3-ol and ethyl acetate, drove the transition from a "fresh and fatty" aroma to one characterized by moldy, fermented, and pungent notes. Metagenomic analysis demonstrated a profound ecosystem shift from bacterial dominance (Proteobacteria, Actinobacteria) to fungal dominance. Notably, Lichtheimia surged from <0.01% to 23.95%, becoming the dominant genus, while Aspergillus increased from 0.03% to 4.57%. Correlation analysis indicated that while Pseudomonas was associated with elevated fatty acid levels, the flavor shift was primarily linked to microbial succession. These findings provide insights into the synergistic mechanisms of rice spoilage and suggest that specific volatile markers could serve as early warning indicators for quality control in real-world grain logistics.},
}

@article {pmid41867766,
year = {2026},
author = {Schmitt, MS and Lee, KK and Bunbury, F and Landsittel, JA and Vitelli, V and Kuehn, S},
title = {Learning functional groups in complex microbiomes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.03.709366},
pmid = {41867766},
issn = {2692-8205},
abstract = {From soil to the gut, communities composed of thousands of microbes perform functions such as carbon sequestration and immune system regulation. Here, we introduce a data-driven approach that explains how community function can be traced to just a few groups of microbes or genes. In gut communities, our neural-network based clustering algorithm correctly recovers known functional groups. In the ocean metagenome, it distills ~500 gene modules down to three sparse groups highlighting survival strategies at different depths. In soils, it distills ~ 4400 bacterial species into two groups that enter a mathematical model of nitrate metabolism. By combining interpretable ML with strain isolation and sequencing experiments, we connect the metabolic specialization of each group to community-wide responses to perturbations. This integrated approach yields simple structure-function maps of microbiomes, allowing the discovery of molecular mechanisms underlying human and environmental health. More broadly, we illustrate how to do function-informed dimensionality reduction in biology.},
}

@article {pmid41867767,
year = {2026},
author = {Nguyen, MH and Schatz, MC},
title = {Perseus: Lineage-Aware Refinement of Kraken2 Taxonomic Classification for Long Read Metagenomes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.06.710148},
pmid = {41867767},
issn = {2692-8205},
abstract = {MOTIVATION: Long-read metagenomic sequencing improves assembly contiguity and enables genome-resolved analysis of complex microbial communities, but accurate taxonomic classification of long reads and assembled contigs remains challenging. Highly scalable k-mer-based classifiers such as Kraken2 frequently over-assign fine-rank taxonomic labels when applied to long-read data, producing high false positive classification rates driven by sparse or localized k-mer matches, particularly in microbiomes with extensive taxonomic novelty.

RESULTS: We present Perseus , a lineage-aware confidence estimation framework for taxonomic classification that models the spatial distribution and hierarchical consistency of k-mer evidence along sequences. This formulation reframes taxonomic classification as a hierarchical confidence estimation problem rather than a single-rank prediction task. Perseus refines k-mer-level taxonomic signals from Kraken2 using a multi-headed convolutional neural network that estimates calibrated confidence scores for taxonomic correctness at each canonical rank. Using these estimates, Perseus confirms assignments, backs off to higher taxonomic ranks, or abstains when evidence is insufficient, prioritizing correctness and lineage consistency over overly specific assignments. Across simulations of taxonomic novelty and real-world metagenomic datasets, Perseus consistently and substantially reduces the false assignment rate while improving precision and lineage-consistent accuracy. These improvements are most pronounced for long reads and assembled contigs, where spatial context enables reliable discrimination between consistent taxonomic signal and spurious matches.

Perseus integrates with existing Kraken2 workflows and is available at https://github.com/matnguyen/perseus .

CONTACT: mnguye99@jh.edu , mschatz@cs.jhu.edu.

SUPPLEMENTARY INFORMATION: Supplementary data are available online.},
}

@article {pmid41868021,
year = {2026},
author = {Zhan, M and Tu, S and Yang, S and Yin, Y and Wang, Z and Zhang, F and Zhang, Y and Wang, Q and Zhao, C and Wang, X and Wang, H and Chen, H},
title = {Clinical Utility of Metagenomic Next-Generation Sequencing in Diagnosing Central Nervous System Infections in Hematopoietic Stem Cell Transplant Recipients: A Retrospective and Prospective Cohort Study.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {554425},
pmid = {41868021},
issn = {1178-6973},
abstract = {BACKGROUND: Diagnosing central nervous system infections (CNSI) in hematopoietic stem cell transplant (HSCT) recipients remains challenging due to nonspecific presentations and low sensitivity of conventional microbiological methods.

METHODS: This study evaluated the clinical utility of cerebrospinal fluid (CSF) metagenomic next-generation sequencing (mNGS) in 127 HSCT recipients (87 retrospective, 40 prospective) from Peking University People's Hospital. Pathogens detected by mNGS and conventional methods were validated via Sanger sequencing.

RESULTS: mNGS identified 20 pathogen-positive samples (19 confirmed by sequencing), while conventional methods detected none. mNGS demonstrated 82.6% sensitivity and 99.0% specificity for CNSI diagnosis, with sensitivity rising to 100.0% when combined with conventional approaches. Notably, mNGS excelled in detecting viral pathogens, particularly in allogeneic HSCT recipients.

CONCLUSION: Our findings advocate for the integration of mNGS into the diagnostic algorithm for CNSI, especially in immunocompromised hosts. This approach enables earlier and more precise pathogen identification, which has the potential to streamline antimicrobial therapy and improve clinical management. To maximize its benefit and ensure reliable interpretation, mNGS results should be correlated with comprehensive clinical and paraclinical data. Further prospective studies are warranted to validate its impact on therapeutic decision-making and patient prognosis.},
}

@article {pmid41868024,
year = {2026},
author = {Wang, QL and Teng, SN and Zhang, XJ and Guo, YX and Kong, Y and Tian, XH and Zhang, Y},
title = {Fatal Primary Amoebic Meningoencephalitis in Coastal Areas of North China in an Immunocompetent Patient: A Case Report and Literature Review.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {559408},
pmid = {41868024},
issn = {1178-6973},
abstract = {PURPOSE: Primary amoebic meningoencephalitis (PAM) is a rapidly fatal infection caused by Naegleria fowleri (N. fowleri) with a mortality rate exceeding 95%. This study presented the clinical course, diagnosis, treatment, and outcome of a confirmed PAM case in an adult female. Additionally, we analyzed the epidemiology of PAM in China and review the therapeutic regimens of surviving cases worldwide, aiming to enhance disease awareness and improve clinical outcomes.

CASE PRESENTATION: The patient was a 50-year-old immunocompetent woman with a history of hot spring bathing before symptom onset, which was not initially disclosed. Moreover, her early infectious symptoms, particularly fever following a tick bite in an orchard, directed clinical suspicion toward tick-borne disease. Four days later, she was hospitalized with generalized convulsions and coma. Clinical examination suggested a bacterial intracranial infection, and treatment with meropenem and vancomycin was initiated. However, her condition deteriorated rapidly. The presence of N. fowleri was identified by cerebrospinal fluid (CSF) metagenomic next-generation sequencing (mNGS) and smear. The etiology was clarified only after retrospective confirmation of hot spring contact, which was later confirmed by blood mNGS. Despite intensive therapy with amphotericin B (AmB), the patient unfortunately died. To provide insights into PAM management in China, we also conducted a systematic analysis of 15 domestic cases and 18 global survivors.

CONCLUSION: PAM is characterized by rapid progression, underscoring the importance of early diagnosis. In cases of rapidly advancing meningoencephalitis, clinicians should maintain a high index of suspicion for rare pathogens such as N. fowleri, with thorough and repeated assessment of recent environmental exposures such as hot spring immersion or freshwater swimming. Early application of mNGS is essential for timely pathogen identification. While AmB remains the first-line therapy, its dosing and duration should be tailored to individual patient factors, and combination therapy should be considered to enhance efficacy. Overall, improved clinical vigilance, advanced pathogen diagnostics, and standardized anti-amoebic therapy form the cornerstone of enhancing outcomes in PAM. As the first documented PAM case in Shandong Province, China, this report highlights the need for heightened awareness in coastal regions while contributing valuable epidemiological insights into this devastating disease.},
}

@article {pmid41868028,
year = {2026},
author = {Wang, Z and Ma, R and Ding, Z and Ma, L and Liu, X and Wang, Y},
title = {Brucellosis Complicated by Thyroid Abscess and Life-Threatening Hemophagocytic Syndrome: A Case Report.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {583365},
pmid = {41868028},
issn = {1178-6973},
abstract = {INTRODUCTION: Brucella infections can affect various systems in the body, such as the osteoarticular and genitourinary systems; however, cases involving the thyroid gland are rare. This case report describes the clinical management of a thyroid abscess associated with brucellosis in a farmer.

CASE PRESENTATION: A 67-year-old male farmer presented to Shanxi Bethune Hospital on 17 March 2024 with a chief complaint of "intermittent fever with fatigue for over 3 months and neck swelling and pain for 2 months". Upon admission, his serum Brucella tube agglutination test titre was 1:200, Rose Bengal plate agglutination test was positive, and blood culture was negative for Brucella. Neck computed tomography revealed a low-density nodular shadow in the right thyroid lobe measuring approximately 4.79×4.45 cm. Coffee-coloured pus was aspirated during thyroid puncture. Pathogenic metagenomic next-generation sequencing and pus culture confirmed Brucella infection as the cause of the thyroid abscess. During treatment, the patient developed hemophagocytic syndrome. The patient's condition was controlled with aggressive anti-infective therapy and glucocorticoid treatment. However, because of symptom recurrence, the patient ultimately underwent surgical intervention, comprising partial thyroidectomy, abscess incision and drainage, and thyroid injection, following which he recovered fully.

CONCLUSION: This article reports an extremely rare case of brucellosis leading to a thyroid abscess. Physicians should consider the possibility of brucellosis when encountering patients with thyroid abscesses and be vigilant of other potential complications.},
}

@article {pmid41868358,
year = {2026},
author = {Ribeiro-Junior, MR and Cardwell, KF and Nascimento, D and Espindola, AS and Ramachandran, A and Gupta, SK and Tyungu, D},
title = {Rapid detection of human and animal respiratory viruses using Microbe Finder (MiFi[®]).},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1743643},
pmid = {41868358},
issn = {1664-302X},
abstract = {Rapid and accurate detection of respiratory pathogens is essential for timely diagnosis, effective treatment, and outbreak monitoring in both human and veterinary medicine. We evaluated the Microbe Finder (MiFi[®]) software for detection of nine RNA viruses of human and veterinary clinical importance. Species specific signature sequences in the different pathogen genomes were identified, and specific electronic probe sets were curated using the MiFi[®] software. Analytical specificity and sensitivity were evaluated through simulated metagenomes and public sequence databases, respectively. Host-specific internal control probes were designed to ensure diagnostic reliability and quality control. Diagnostic performance was assessed using Oxford Nanopore sequence data from clinical nasal swab samples. In silico validation showed 100% specificity across 83 datasets and limits of detection as low as 0.0010% of total reads (10 reads per 10[6]) for some targets. Internal controls generated stable background signals without interfering with pathogen detection. In vivo testing of 44 clinical samples matched PCR performance for Human respiratory syncytial virus (HRSV), Influenza B virus (IBV), Influenza A virus (IAV), Bovine respiratory syncytial virus (BRSV), and Canine distemper virus (CDV). These findings demonstrate that the MiFi[®] software enables rapid, multiplex, and strain-specific detection of respiratory viruses in metagenomic sequence data without the need for advanced bioinformatics expertise. The approach supports scalable use in clinical laboratories, veterinary diagnostics for surveillance and triage, offering a valuable tool for improving respiratory pathogen detection across diverse settings.},
}

@article {pmid41869352,
year = {2026},
author = {Zhou, YM and Cui, XQ and Zhao, P and Peng, ZG and Guo, N and Sun, HB and Liu, SL},
title = {The species, distribution, resistance of donor-derived pathogens and their impact on solid organ transplant recipients.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1777244},
pmid = {41869352},
issn = {1664-3224},
mesh = {Humans ; Middle Aged ; Male ; Female ; Retrospective Studies ; *Tissue Donors ; Adult ; *Transplant Recipients ; *Liver Transplantation/adverse effects ; *Kidney Transplantation/adverse effects ; Aged ; *Organ Transplantation/adverse effects ; Drug Resistance, Multiple, Bacterial ; Incidence ; Bacteria/isolation & purification/drug effects ; },
abstract = {BACKGROUND: Donor-derived infections (DDIs) have become a significant cause of infection in organ transplant recipients. Elaborating on the species, distribution, and resistance of donor-derived pathogens (DDPs) holds important implications.

METHODS: A retrospective cohort study included 302 deceased donors and their corresponding 464 kidney transplant recipients and 175 liver transplant recipients. We detected DDPs in preservation fluid (PF) using both conventional culture and mNGS, and subsequently analyzed the incidence of DDIs after transplantation.

RESULTS: 89.4% (270/302) of donors had positive cultures. Predominant multidrug-resistant organism included HLAR-Enterococcus, CRAB, CRKP, CRPA, MRS and ESBL-Escherichia coli. Compared with conventional culture, mNGS exhibited superior sensitivity for detecting bacteria and fungus in PF, with shorter turnaround time (p < 0.001). The incidences of DDIs in kidney and liver transplant recipients were 16.6% (77/464) and 19.4% (34/175) respectively. The recipients with DDIs were associated with elevated serum creatinine or total bilirubin levels, increased infection events, higher risks of graft loss, elevated mortality, and longer length of hospital stay (p < 0.05).

CONCLUSIONS: Multidrug-resistant organism are prevalent in deceased donors, with PF contamination primarily originating from donors. Integration of mNGS into donor screening protocols enables timely antimicrobial intervention, potentially improving transplant outcomes.},
}

Humans
Middle Aged
Male
Female
Retrospective Studies
*Tissue Donors
Adult
*Transplant Recipients
*Liver Transplantation/adverse effects
*Kidney Transplantation/adverse effects
Aged
*Organ Transplantation/adverse effects
Drug Resistance, Multiple, Bacterial
Incidence
Bacteria/isolation & purification/drug effects

@article {pmid41869502,
year = {2026},
author = {Wang, D and Xu, X and Liu, L and Wang, C and Deng, Y and Polz, MF and Zhang, T},
title = {Hi-C sequencing deciphers phage and plasmid host networks in wastewater biofilms.},
journal = {Environmental science and ecotechnology},
volume = {30},
number = {},
pages = {100683},
pmid = {41869502},
issn = {2666-4984},
abstract = {Mobile genetic elements (MGEs) such as bacteriophages and plasmids profoundly shape microbial community structure and drive horizontal gene transfer across ecosystems. Wastewater treatment systems, with their high cell densities, steep physicochemical gradients and close cell-to-cell contact, act as hotspots for MGE proliferation and exchange, yet the in situ assembly dynamics and host interaction networks of these elements have remained largely unresolved because conventional methods fail to establish direct MGE-host linkages in complex matrices. Here we show that an integrated framework combining metagenomics, metatranscriptomics, metaviromics, and Hi-C proximity ligation sequencing enables the efficient elucidation of DNA phage and plasmid assembly dynamics alongside their host interaction networks in biofilms. We reconstructed 17,672 viral operational taxonomic units and 11,454 high-confidence non-redundant plasmids, and established 529 phage-host and 5739 plasmid-host associations that link up to 52 % of phages to 56 % of prokaryotes and 70 % of plasmids to 91 % of prokaryotes, respectively. Hi-C substantially expanded and refined these networks, revealing taxon-specific and multi-host patterns. Host community composition and biofilm architecture emerge as primary drivers of MGE occurrence and abundance along the reactor flow path. Expression of auxiliary metabolic genes, antibiotic resistance genes and virulence factors carried by these MGEs demonstrates their active roles in modulating biogeochemical cycles and maintaining ecosystem stability. These findings establish a scalable, cultivation-independent framework for deciphering MGE-host networks in complex microbial ecosystems, and underscore the power of Hi-C sequencing to transform our mechanistic understanding of gene flow, resistome dissemination, and ecological resilience in engineered and natural microbiomes.},
}

@article {pmid41869518,
year = {2026},
author = {Liu, J and Wu, R},
title = {Intraoperative sampling for postoperative metagenomic next-generation sequencing to guide biofilm-targeted therapy for Cutibacterium acnes infective endocarditis complicated by ruptured sinus of Valsalva aneurysm: a case report.},
journal = {Frontiers in cardiovascular medicine},
volume = {13},
number = {},
pages = {1707117},
pmid = {41869518},
issn = {2297-055X},
abstract = {BACKGROUND: Cutibacterium acnes is an easily overlooked pathogen in infective endocarditis (IE) due to its slow growth, propensity for biofilm formation, and high rate of culture-negative results. When complicated by structural heart disease such as a ruptured sinus of Valsalva aneurysm (RSVA), its indolent course can lead to severe hemodynamic compromise.

CASE SUMMARY: A 35-year-old male with a known ventricular septal defect (VSD) and unruptured aortic sinus aneurysm presented with persistent fever and progressive heart failure (NYHA class IV). Echocardiography revealed a ruptured right coronary sinus of Valsalva aneurysm (RCSVA) into the right ventricular outflow tract (RVOT) with a large vegetation. Blood cultures were negative. After 6 days of ineffective empirical antibiotic therapy, emergency surgery was performed to resect the aneurysm and vegetation and repair the cardiac structures. Intraoperatively, a vegetation sample was collected for metagenomic next-generation sequencing (mNGS). Postoperatively, mNGS identified Cutibacterium acnes with high sequence reads (1,284) and coverage (47.62%), enabling a definitive diagnosis. Pathology confirmed microcolonies and necrotic inflammation. The antibiotic regimen was switched to a regimen with potential activity against biofilms with oral doxycycline and intravenous clindamycin for 6 weeks. The patient's inflammatory markers normalized, and cardiac function recovered to NYHA class I, with no recurrence at 12-month follow-up.

CONCLUSION: This case highlights the diagnostic synergy of intraoperative histopathology and mNGS for pathogen identification, underscores the rationale for biofilm-conscious adjuvant therapy, and reaffirms the crucial role of early surgical debridement and repair in achieving cure.},
}

@article {pmid41869816,
year = {2026},
author = {Tumeo, A and Miliotis, G and O'Connor, A and Vijayakumar, V and Sengupta, P and McDonagh, F and Kovarova, A and Clarke, C and Hooban, B and Kumar Singh, N and Rosado, AS and Raman, K and Venkateswaran, K},
title = {Plasmidome, resistome, and virulence-associated gene characterization of Acinetobacter johnsonii in NASA cleanrooms and a clinical setting.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0250325},
doi = {10.1128/spectrum.02503-25},
pmid = {41869816},
issn = {2165-0497},
abstract = {Evidence suggests the persistence of non-spore-forming Acinetobacter johnsonii in high-stakes controlled and nutrient-limited environments. Here, we investigated the mechanisms underlying this adaptability through a comprehensive genomic analysis of 22 isolates of A. johnsonii from NASA's Payload Hazardous Servicing Facility (PHSF) and one carbapenem-resistant strain (E154408A) from patient colonization in Ireland. Core-genome phylogeny revealed clustering of PHSF-originating isolates in a monophyletic clade divergent from the main species lineage. Species-wide virulence-associated genes and metabolic reconstruction indicated the exclusive presence in PHSF-originating isolates of two complete efflux pumps and a conserved allantoin racemase, suggesting adaptability for multiple environmental stresses. The ubiquity of blaOXA in genomes analyzed (n = 112) and the phenotypically validated multidrug-resistant profile of the E154408A strain highlight A. johnsonii's potential as an antimicrobial resistance (AMR) reservoir. Plasmidome analysis suggested gain/loss events across the monophyletic population and potential AMR acquisition pathways. Genome-to-metagenome mapping identified genomic signatures of A. johnsonii in PHSF >10 years post-initial isolation.IMPORTANCEAcinetobacter johnsonii is increasingly recognized as an emerging human pathogen, with growing evidence of its ability to persist in controlled, high-stakes environments, posing risks as both a persistent environmental contaminant and an antimicrobial resistance (AMR) reservoir. Yet, gaps remain in our understanding of its AMR profile and the mechanisms that enable its enhanced environmental adaptability. This knowledge is necessary in contexts where biological cleanliness is a priority, such as clinical settings and spacecraft assembly facilities' cleanrooms, where contamination of hardware with terrestrial microorganisms is concerning. In this study, we aim to address some of the key knowledge gaps by providing genomic insights into a rare multidrug-resistant clinical isolate and 22 NASA cleanroom isolates that persisted for over a decade in extremely clean conditions. Our findings will help assess the contamination risk of A. johnsonii in high-stakes environments and ultimately strengthen our ability to manage this microbial contaminant across terrestrial and extraterrestrial settings.Cleanroom-derived A. johnsonii genomes show traits consistent with increased adaptability.Genomic signatures of A. johnsonii persisted in the cleanrooms for over 10 years.blaOXA is ubiquitously found in all 112 A. johnsonii genomes analyzed.Isolate E154408A is the first reported patient colonization case by carbapenem-resistant A. johnsonii in Europe.},
}

@article {pmid41869825,
year = {2026},
author = {Mehta, A and Stebliankin, V and Mathee, K and Narasimhan, G},
title = {MEditome: Computational Detection of RNA Edit Sites Using de Novo Assembly in Microbiomes.},
journal = {Journal of computational biology : a journal of computational molecular cell biology},
volume = {},
number = {},
pages = {15578666261428562},
doi = {10.1177/15578666261428562},
pmid = {41869825},
issn = {1557-8666},
abstract = {RNA editing is a post-transcriptional modification that alters single-nucleotide sites within RNA strands, thus diversifying transcriptomes and proteomes and modulating gene expression. While better characterized in eukaryotes and in a few microbes, the study of RNA editing in entire microbiomes remains unexplored. Recent studies have demonstrated that A-to-I RNA editing contributes to bacterial adaptation and pathogenicity. Previously, we developed MetaEdit, a reference-based computational pipeline to detect RNA edit sites in microbiomes. While MetaEdit successfully identified RNA edit sites in Escherichia coli within the context of the human gut microbiome, including previously reported loci, it relied primarily on aligning reads to reference genomes of target bacteria. This dependence on reference genomes introduced potential biases, as editing can only be identified in reference genomes, while editing in novel microbial strains missing from the reference databases could be overlooked. Even for reference genomes, the search for edit sites is inefficient since it would have to be conducted one reference genome at a time.Here, we introduce MEditome, employing de novo assembly to overcome these limitations. This crucial change enables the detection of RNA edit sites across all microbial organisms in the microbiome, including novel bacterial strains for which comprehensive reference genomes are unavailable. Using sequencing data from the Integrative Human Microbiome Project, MEditome identified 2,295 unique RNA editing sites across diverse bacterial taxa. Several of these overlaps with previously identified edits in E. coli detected by MetaEdit in hok/gef gene family and arginine-associated genes, providing in silico validation of accuracy. We observed taxon-specific editing patterns and gene-level differential editing associated with inflammatory bowel disease, highlighting RNA editing as a potential regulatory mechanism influencing microbial adaptation and host-microbe interactions.},
}

@article {pmid41869887,
year = {2026},
author = {Wang, Z and Guo, S and Li, J and Huang, Q and Ning, J and Xia, B and Lv, X and Liu, X and Gao, Z and Li, J and Liu, L and Song, M and Wang, J},
title = {Identifying Cytokine Motif-Containing, Immunomodulatory Bacterial Proteins in Human Gut Microbiome.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e20332},
doi = {10.1002/advs.202520332},
pmid = {41869887},
issn = {2198-3844},
support = {2025YFA1309200//National Key Research and Development Program of China/ ; 2023KF-05//Open funding project of State Key Laboratory of Pharmaceutical preparation/ ; },
abstract = {Accumulating evidence emphasizes the importance of microbiota-immune interactions in health and disease development, and identified bacteria-derived small-molecule metabolites as well as macromolecules such as peptides and proteins as promising therapeutic approaches. Here, we identify cytokine motif-containing, immunomodulatory bacterial proteins (CMCPs) as a special category of bacterial proteins in both bacterial genomes and gut metagenomes using Hidden Markov Models (HMMs). We further find eight colorectal cancer‑associated CMCPs differentially enriched in patients or healthy controls. Engineered E. coli Nissle 1917 (EcN) expressing selected CMCPs administered to Apc[min/+] mice selectively colonize intestinal tumors, deliver functional CMCPs in situ, and elicit significant antitumor immune responses while reducing tumor burden. In vitro, purified CMCPs modulate mouse splenic T cells, bone marrow‑derived macrophages and dendritic cells. Our findings indicate that bacterially encoded CMCPs can directly modulate tumor immunity and serve as microbiota‑derived proteins as candidate immunomodulators, which can further be applied in microbiome-mediated immune therapies for CRC.},
}

@article {pmid41870053,
year = {2026},
author = {Pasaribu, B and Vincent Mishael Dilens, C and Wahyudin Lewaru, M and Ayuningrum, D and Patria, MP and Juliandri Prihadi, D and Purba, NP and Untung Kurnia Agung, M and Maqbul, I and Sulistiowati, S},
title = {Shotgun metagenomic dataset of seawater bacterial communities from Pari Islands, Indonesia.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0147625},
doi = {10.1128/mra.01476-25},
pmid = {41870053},
issn = {2576-098X},
abstract = {Pari Island is located in Seribu Islands, Indonesia, and is well-known for its marine biodiversity. Shotgun metagenomic sequencing was performed using the DNaseq-G400 platform, and bioinformatics approaches were applied to analyze the sequence data.},
}

@article {pmid41870088,
year = {2026},
author = {Park, J-Y and Yoon, CK and Lee, J-J and Shin, YJ and Kim, B-S},
title = {Potential role of the ocular surface microbiome in dry eye: microbial interactions and symptom alleviation.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0010426},
doi = {10.1128/msystems.00104-26},
pmid = {41870088},
issn = {2379-5077},
abstract = {Dry eye is a prevalent ocular disorder characterized by tear film instability, inflammation, and ocular discomfort. Although the ocular surface (OS) microbiome contributes to immune regulation and pathogen defense, its role in dry eye pathophysiology remains unclear. Therefore, the present study aimed to characterize alterations in the OS microbiome of patients with dry eye undergoing cyclosporin A or NewHyalUni treatment and to identify their potential roles related to clinical improvement. Patients with dry eye were treated with either cyclosporin A and NewHyalUni drop combination or NewHyalUni alone. OS samples were collected before and after treatment, and the microbiome was analyzed by whole metagenome sequencing. Potential contaminants were removed before downstream analysis to account for the low-biomass nature of OS samples. Clinical evaluations included symptom scores and the assessment of meibomian gland dysfunction (MGD). No significant differences in the overall microbial composition were observed between the treatment groups. Nevertheless, both groups demonstrated symptomatic improvement. OS microbiome alterations were strongly correlated with improvements in MGD scores. Moreover, microbial interactions were found to shift following treatment. Key species (Staphylococcus epidermidis, Staphylococcus pseudintermedius, Streptomyces lividans, and Edwardsiella tarda) were identified as potential mediators of MGD score improvement by modulating microbiome functions and suppressing inflammation-associated species. Although distinct treatment regimens did not lead to divergent microbiome profiles, symptomatic improvement was associated with alterations in a specific microbiome. These findings highlight the OS microbiome's potential role in dry eye and support the development of microbiome-based therapeutic strategies.IMPORTANCEDry eye is a common ocular disorder with complex pathophysiology that extends beyond tear deficiency and inflammation. Despite growing evidence of host-microbiome interactions at mucosal surfaces, the contribution of the ocular surface (OS) microbiome to dry eye remains poorly understood. Our findings in this study reveal that shifts in specific taxa and ecological interactions correlate with improvements in meibomian gland function and dry eye symptoms, even in the absence of major changes in overall microbiota. By identifying microbial signatures potentially linked to clinical improvement, we provide systems-level insight into the role of low-biomass microbiomes in ocular health. This work expands the current understanding of microbiome-host dynamics in non-gut environments and supports future development of microbiome-informed therapeutic strategies.CLINICAL TRIALSThis study is registered with ClinicalTrials.gov as NCT06936462.},
}

@article {pmid41870133,
year = {2026},
author = {Ni, B and Chen, XP and Lin, D and Yao, Z and Xia, J and Zhang, TL and Zheng, J and Cai, TG and Wang, X and Vollertsen, J and Zhu, D and Zhu, DZ},
title = {Potential Viral Regulation of Sulfur Cycling in Urban Sewer Sediments.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c15040},
pmid = {41870133},
issn = {1520-5851},
abstract = {Sewer sediments are microbial hotspots for sulfur cycling and sulfide generation, which is the leading cause of sewer corrosion and poses significant economic losses and public safety concerns. However, viruses in sewer sediments remain inadequately explored regarding their characteristics, interactions with their hosts, and ecological regulatory potential for sulfur cycling. In this study, we explored viral characteristics and virus-host interactions in sewer sediments from three distinct types of urban functional areas through metagenomics and viromics. Compared with single-function (commercial and residential) areas, sewer sediments in multifunctional areas contain higher nutrients and nutrient-induced acidification, which can promote host density and drive a shift from lytic to lysogenic infection. This shift may potentially enhance sulfide formation through the insertion of more auxiliary metabolic genes related to sulfate reduction into host genomes. Conversely, a higher viral lytic tendency in single-function area can lyse sulfate-reducing microorganisms, thereby mitigating sulfide formation. Phage transplantation experiments and the high prevalence of key viral hosts across global sewers (76 cities across six countries) demonstrated the high potential of viruses in alleviating sewer corrosion. Our findings reveal the dual role of viruses as metabolic "tuners" in sewer sulfur dynamics, suggesting that comprehensive urban sewer management requires consideration of exploiting viral lysis.},
}

@article {pmid41870192,
year = {2026},
author = {Ranga, A and Malhotra, AG and Singh, J and Pandey, KM},
title = {Genomic Sequencing from Sanger to Next-Generation Sequencing: Historical Context, Comparative Advances, and Prospects for Next-Generation Phenomics.},
journal = {Omics : a journal of integrative biology},
volume = {},
number = {},
pages = {15578100261433762},
doi = {10.1177/15578100261433762},
pmid = {41870192},
issn = {1557-8100},
abstract = {DNA sequencing has revolutionized biological and biomedical research, offering profound insights into genome organization, function, and variability. From the pioneering Sanger capillary electrophoresis method to the advent of next-generation sequencing, the field has evolved toward unprecedented speed, scalability, and cost decreases over the years. These advancements have enabled diverse applications across genomics, transcriptomics, metagenomics, epigenomics, and precision medicine, powering global initiatives such as the Human Genome Project, the Human Microbiome Project, and the 1000 Genomes Project. Bioinformatics has also advanced in data processing, variant detection, and functional annotation, helping transform raw sequencing data into biologically meaningful insights and knowledge. Although highly advanced, sequencing technologies still encounter challenges, including accuracy trade-offs and the need for efficient management of rapidly increasing volumes of data. Leveraging the genomic revolution, this review explores the shifts toward next-generation phenomics (NGP), an archetype that uses artificial intelligence that integrates multi-omics data with digital phenotyping, the Internet of Things, and real-time analytics. The goal of NGP is to integrate genotypic and phenotypic data to support predictive modeling of health, disease, and environmental interactions. By tracing history, advances in sequencing technologies, and future perspectives on NGP, this article offers a comprehensive overview for researchers and clinicians, highlighting how the integration of omics and digital data will drive the generation of personalized and systems-level biology.},
}

@article {pmid41870201,
year = {2026},
author = {Li, N-P and Gupta, S and Kollipara, SK and Hung, T-H and Rao, GP and Kuo, C-H},
title = {Draft genome sequence of "Candidatus Phytoplasma australasiaticum" strain TBB-AP associated with tomato big bud disease in India.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0003326},
doi = {10.1128/mra.00033-26},
pmid = {41870201},
issn = {2576-098X},
abstract = {We report the draft metagenome-assembled genome (MAG) of "Candidatus Phytoplasma australasiaticum" strain TBB-AP, obtained from a symptomatic tomato plant collected in Andhra Pradesh, India. This assembly provides a genomic resource for functional and evolutionary studies of phytoplasmas associated with tomato big bud disease.},
}

@article {pmid41870280,
year = {2026},
author = {Werbowy, O and Håkansson, M and Dorawa, S and Stefańska-Kaźmierczak, A and Svensson, LA and Al-Karadaghi, S and Jurczak-Kurek, A and Kwiatkowska-Semrau, K and Plotka, M and Fridjonsson, OH and Hreggvidsson, GO and Aevarsson, A and Dąbrowski, S and Kaczorowska, AK and Kaczorowski, T},
title = {Structural and functional characterization of a hyperthermostable single-stranded DNA-binding protein from a hot spring metagenome.},
journal = {Protein science : a publication of the Protein Society},
volume = {35},
number = {4},
pages = {e70538},
doi = {10.1002/pro.70538},
pmid = {41870280},
issn = {1469-896X},
support = {UMO-2019/34/H/NZ2/00584//National Science Centre (Poland)/ ; 685778//European Union Horizon 2020/ ; },
mesh = {*Hot Springs/microbiology ; *DNA-Binding Proteins/chemistry/genetics/metabolism ; *Metagenome ; Crystallography, X-Ray ; *DNA, Single-Stranded/metabolism/chemistry ; Models, Molecular ; Escherichia coli/genetics/metabolism ; *Bacterial Proteins/chemistry/genetics/metabolism ; Amino Acid Sequence ; Protein Multimerization ; },
abstract = {We present the structural and functional characterization of a single-stranded DNA-binding protein (SSB-M5) identified from a hot spring metagenome in Vatnajökull National Park, Iceland. This small protein (136 aa; 15,695 Da) shares 100% amino acid sequence identity with two previously uncharacterized SSBs from hyperthermophilic Fervidobacterium species. Functional complementation assay demonstrated that SSB-M5 can substitute for Escherichia coli SSB in an ssb[-] mutant strain, confirming its biological activity. A recombinant C-terminally His-tagged SSB-M5 was overproduced, purified to homogeneity, and subjected to structural, biochemical, and biophysical analysis. The crystal structure revealed that SSB-M5 forms a dimer through a crystallographic twofold axis, with each monomer contributing to a large antiparallel β-sheet. The flat surfaces of the β-sheets from the two dimers are packed together via a second crystallographic twofold axis, forming a tetramer that serves as the functional unit of the SSB-M5. Electrophoretic mobility shift assays showed that SSB-M5, after heat treatment up to 100°C, forms stable DNA-protein complexes with the (dT)40 oligo. Quantitative analyses revealed that SSB-M5 binds (dT)70 oligonucleotide with very high affinity (KD = 72 ± 6 pM). Hill analysis indicated cooperative binding, yielding an EC50 of 141 pM and a Hill coefficient of 2. Moreover, inclusion of SSB-M5 in PCR reactions significantly enhanced amplification by eliminating non-specific products. Together, these findings identify SSB-M5 as a hyperthermostable, high-affinity single-stranded DNA-binding protein with potential applications in molecular biology and biotechnology.},
}

*Hot Springs/microbiology
*DNA-Binding Proteins/chemistry/genetics/metabolism
*Metagenome
Crystallography, X-Ray
*DNA, Single-Stranded/metabolism/chemistry
Models, Molecular
Escherichia coli/genetics/metabolism
*Bacterial Proteins/chemistry/genetics/metabolism
Amino Acid Sequence
Protein Multimerization

@article {pmid41871361,
year = {2026},
author = {Lipovac, J and Šikić, M and Vicedomini, R and Križanović, K},
title = {MADRe: Strain-level Metagenomic Classification Through Assembly-Driven Database Reduction.},
journal = {GigaScience},
volume = {},
number = {},
pages = {},
doi = {10.1093/gigascience/giag030},
pmid = {41871361},
issn = {2047-217X},
abstract = {Strain-level metagenomic classification is essential for understanding microbial diversity and functional potential, yet remains challenging, particularly when sample composition is unknown and reference databases are large and redundant. Here we present MADRe, a modular and scalable pipeline for long-read strain-level metagenomic classification based on Metagenome Assembly-Driven Database Reduction. Beyond system-level integration, MADRe introduces statistical strategies that leverage assembly-derived genomic context to guide database reduction and probabilistic read reassignment. Specifically, it combines long-read metagenome assembly, contig-to-reference reassignment using an expectation-maximization framework for reference reduction, and probabilistic read mapping reassignment on a reduced database to achieve sensitive and precise strain-level classification. We extensively evaluated MADRe on simulated datasets, mock communities, and a real anaerobic digester sludge metagenome. Across diverse similarity and coverage conditions, MADRe consistently improves precision by reducing false-positive strain detections. MADRe's design allows users to apply either the database reduction or read classification step individually. Using only the read classification step shows results on par with other tested tools. MADRe is open source and publicly available at https://github.com/lbcb-sci/MADRe.},
}

@article {pmid41871943,
year = {2026},
author = {Awoniyi, M and El Hag, M and Hernandez, J and Yang, Q and Evans, N and Nemet, I and Ngo, B and Coskuner, D and Zhou, J and Farmer, M and Su, L and Zhou, H and Roach, J and Stappenbeck, T and Sartor, RB},
title = {Dysbiotic microbiota trigger colitis-associated colorectal cancer and imprint a distinctive bile acid profile in a PSC-IBD model.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-336675},
pmid = {41871943},
issn = {1468-3288},
abstract = {BACKGROUND: Primary sclerosing cholangitis-associated UC (PSC-UC) carries excess colorectal neoplasia despite often mild-appearing endoscopy, implicating persistent microscopic inflammation and microbiota-bile acid (BA) dysfunction.

OBJECTIVE: To test whether PSC-UC neoplasia is driven by transferable microbiota-mediated inflammation linked to secondary BA loss.

DESIGN: Surveillance colonoscopies (2012-2022) from PSC-UC (n=251) and UC-only (n=8839) were compared for segmental endoscopic/histological activity and dysplasia. We generated multidrug resistance protein 2 (MDR2)[-/-] × interleukin (IL)-10[-/-] double-knockout (DKO) mice and used germ-free (GF) derivation, faecal microbiota transplantation (FMT), antibiotic conditioning and cohousing with shotgun metagenomics and liquid chromatography-tandem mass spectrometry BA profiling.

RESULTS: PSC-UC showed greater inflammatory activity and a right-shifted dysplasia burden versus UC-only. Under specific-pathogen-free conditions, DKO mice developed early right-predominant colitis and multifocal dysplasia progressing with age. DKO communities were depleted of 7α-dehydroxylation capacity with near absence of deoxycholic and lithocholic acids and no enrichment of canonical bacterial genotoxins. GF DKO mice were protected, whereas live DKO donor FMT reinstated severe colitis and dysplasia; sterile-filtered stool supernatant was inactive. IL-10[-/-] donor FMT or cohousing attenuated colitis and increased recipient secondary BA, whereas wild-type/MDR2[-/-] donor transfers were non-colitogenic. In GF DKO mice, direct deoxycholic acid repletion caused hepatotoxicity.

CONCLUSION: PSC-UC neoplasia associates with transmissible microbiota-dependent inflammation and secondary BA deficiency. Controlled restoration of BA-transforming microbial functions, rather than indiscriminate secondary BA replacement, is a rational translational direction.},
}

@article {pmid41680704,
year = {2026},
author = {Huang, Y and Huang, X and Wei, X and Yang, X and Su, T and Duan, Q and Wan, J and Sun, Y and Xu, Y},
title = {Characterization of multiple herpes viremia via next-generation sequencing in patients with lower respiratory tract infections: a retrospective cohort study.},
journal = {BMC infectious diseases},
volume = {26},
number = {1},
pages = {},
pmid = {41680704},
issn = {1471-2334},
support = {H-2024060//the Yunnan health training project of high level talents/ ; XDYC-QNRC-2024-448//the Yunnan revitalization talent support program/ ; 202302AA310044-01//Key Projects of Yunnan Province Science and Technology Department/ ; },
abstract = {BACKGROUND: Lower respiratory tract infections (LRTIs) are a leading cause of the substantial morbidity and mortality associated with severe pneumonia. Herpesviruses (HHVs) frequently reactivate during critical illness, but their bronchoalveolar lavage fluid (BALF) coinfection patterns and clinical correlates remain incompletely defined.

METHODS: A retrospective cohort study was conducted among hospitalized adults with suspected LRTIs who underwent BALF next-generation sequencing (NGS) at the Yunnan First People’s Hospital between November 2024 and May 2025. Two analytical workflows were evaluated, namely metagenomic DNA sequencing (mNGS-DNA) and a targeted NGS (tNGS) panel, including 289 and 675 patients, respectively. Participants were subsequently classified into a herpesvirus-detected (HD) group and a non-herpesvirus-detected group (non-HD).

RESULTS: In mNGS-DNA, detection frequencies were EBV 17.30%, CMV 14.88%, HHV-7 9.00%, HSV-1 8.30%, HHV-6 4.15%, and VZV 0.34%, single- and multi-virus positivity were 22.84% and 11.76%. In tNGS, the corresponding values were 17.93%, 12.00%, 7.11%, 10.07%, 2.96%, and 0.30%, single- and multi-virus positivity were 24.44% and 15.11%. HD patients were older and more likely to have severe pneumonia in both cohorts (P < 0.0001). Bacteria were the predominant pathogens in the patients with suspected LRTIs, followed by viruses and fungi. In matched BALF subsets, sequencing outperformed culture for bacterial detection (mNGS-DNA 37.90% vs. 20.56%; tNGS 87.45% vs. 13.45%; all P < 0.001), underscoring the complementary yield over conventional culture methods. HHVs exhibited the highest co-infection rates with pathogens such as Stenotrophomonas maltophilia, Klebsiella pneumoniae, and Candida albicans.

CONCLUSIONS: In BALF from hospitalized LRTI patients, EBV and CMV predominate among herpesviruses, with HHV-7 a frequent coinfection partner. These findings underscore the need for prospective studies to define the prognostic impact of HHV coinfections.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12879-026-12866-x.},
}

@article {pmid41860726,
year = {2026},
author = {Stevens, KA and de Souza, JO and Li, H and Ouro-Djobo, A and Alabi, OJ and Al Rwahnih, M},
title = {Agave associated crinivirus A: a novel monopartite crinivirus homolog isolated from agave.},
journal = {Archives of virology},
volume = {171},
number = {4},
pages = {},
pmid = {41860726},
issn = {1432-8798},
abstract = {UNLABELLED: We describe the complete genome of the first monopartite and putative member of the genus Crinivirus which we propose naming agave associated crinivirus A (AaCA). AaCA was identified by high-throughput sequencing in an Agave tequilana leaf sample during a routine metagenomic screening of Agave plants from California. The 16,161 bp genome contains the protein hallmarks of the family Closteroviridae, the HSP70h and the three coat protein homologs (CPh, CP, CPm), along with the open reading frames (ORFs) unique to criniviruses. Two ORFs downstream of the CPm are unique to AaCA. The monopartite nature of the genome was verified by PCR and Sanger sequencing. Phylogenetic analysis of the HSP70h gene clusters AaCA basally with existing criniviruses.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00705-026-06580-x.},
}

@article {pmid41862850,
year = {2026},
author = {Li, Z and Wu, C and Huang, D and Liang, Y and Zhai, Y and Mai, C and Han, Y and Tang, LA and Wang, W and Ning, C and Tan, W},
title = {Metagenomics reveals pathogenic diversity and temporal dynamics in severe pneumonia among patients in adult intensive care unit.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-026-13107-x},
pmid = {41862850},
issn = {1471-2334},
support = {2021YFC2300101//the National Key Research and Development Program of China/ ; },
}

@article {pmid41863347,
year = {2026},
author = {Lutfi, A and Holstein, T and Andreotti, S and Muth, T},
title = {MegaPX: fast and space-efficient peptide assignment method using IBF-based multi-indexing.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btag134},
pmid = {41863347},
issn = {1367-4811},
abstract = {MOTIVATION: A central problem for metaproteomic analysis is the often-unknown taxonomic composition of the analyzed microbiomes. Using a database search, the standard approach requires prior knowledge of which proteins and taxa to include in the protein reference database or to use tailored metagenome-derived databases, which are expensive and error-prone in their generation. A possible strategy to circumvent this database search issue is de novo sequencing, where peptide sequences are directly identified from mass spectra. However, these sequences must still be mapped back to potentially extensive databases. Here, alignment-based approaches enable robust and precise results, with the potential drawback of high memory usage and long run times.

RESULTS: We present MegaPX, a software for rapidly classifying de novo peptide sequences against large protein databases. MegaPX implemented as a C ++-based tool, uses an alignment-free, k-mer approach as a taxonomic classification method with the possibility of generating mutated reference databases for error-tolerant searching. It uses various algorithms, including interleaved Bloom filters, to efficiently compute approximate membership queries, ensuring fast processing times while querying and indexing large databases in a multi-indexing fashion. We demonstrate the potential of MegaPX by analyzing different samples, including metaproteomics, against extensive reference databases, highlighting its use as a fast screening tool.},
}

@article {pmid41863618,
year = {2026},
author = {Majumder, D and Dash, S and Bhattacharya, D and Gill, HS and Raja, V and Dewi, JR and Roy, A and Rajeev, M and Pandit, S and Sharma, S and Dwivedi, SP and Nag, M and Lahiri, D},
title = {Genetically engineered lipases: advances in expression and upscaling for industrial applications.},
journal = {Archives of microbiology},
volume = {208},
number = {6},
pages = {},
pmid = {41863618},
issn = {1432-072X},
}

@article {pmid41863619,
year = {2026},
author = {Jonathan, AR and Balasubramanian, VK and Ho, ST and Chen, YP and Khunnamwong, P and Chou, JY},
title = {Next-generation strategies for PLA degradation: microbial consortia, metagenomics, enzyme engineering and AI-guided approaches.},
journal = {Archives of microbiology},
volume = {208},
number = {6},
pages = {},
pmid = {41863619},
issn = {1432-072X},
support = {MOST 111-2621-B-018-001 to Jui-Yu Chou//Ministry of Science and Technology, Taiwan/ ; },
mesh = {*Metagenomics/methods ; *Microbial Consortia ; Biodegradation, Environmental ; *Polyesters/metabolism ; Artificial Intelligence ; Fungi/metabolism/genetics ; Bacteria/metabolism/genetics ; },
abstract = {Polylactic acid (PLA) is one of the most widely used biodegradable bioplastics; however, its slow degradation under natural conditions limits its environmental sustainability. This review summarizes recent advances in microbial and biotechnological strategies that enhance PLA biodegradation across diverse ecosystems. Emerging approaches include screening insect gut microbiota, isolating fungal species with strong adsorption or enzymatic capacities, and exploring soil, compost, and aquatic microbiomes using metagenomics and environmental DNA (eDNA) tools. Microbial consortia, thermophilic degraders, and co-culture systems are highlighted as effective solutions to overcome the intrinsic crystallinity and hydrolysis-dependent breakdown of PLA. Beyond natural systems, this review emphasizes the increasing role of synthetic biology, directed evolution, and artificial intelligence (AI) in engineering high-performance PLA-degrading enzymes. AI-driven structural prediction and machine-learning platforms offer new possibilities for designing robust depolymerases with improved specificity, thermostability, and catalytic efficiency. Collectively, these multidisciplinary strategies provide a roadmap for accelerating PLA degradation in industrial composting, wastewater treatment, and bioremediation. Future integration of ecological screening with computational enzyme engineering is expected to advance scalable and sustainable PLA waste management.},
}

*Metagenomics/methods
*Microbial Consortia
Biodegradation, Environmental
*Polyesters/metabolism
Artificial Intelligence
Fungi/metabolism/genetics
Bacteria/metabolism/genetics

@article {pmid41863708,
year = {2026},
author = {Mishra, AK and Verma, S and Mishra, A and Khan, G and Singh, H},
title = {Unlocking the role of microbiome through gut-skin axis to alleviate aging: current perspectives and future scope.},
journal = {GeroScience},
volume = {},
number = {},
pages = {},
pmid = {41863708},
issn = {2509-2723},
abstract = {The microbiota of intestinal origin has a significant impact on the aging process, affecting skin health and overall cell longevity. Aging is marked by physiological alterations, such as enhanced oxidative stress, which is intensified by external factors like UV radiation and environmental pollution. The gut microbiota profoundly influences immune functions and results in reduced inflammation, which contributes to the anti-aging process. The present review is an attempt to showcase the current studies on the gut-skin axis, investigating the impact of gut-derived metabolites, particularly short-chain fatty acids, postbiotics, synbiotics, and psychobiotics, on the function of skin barriers and the aging process. Dietary supplements, including prebiotics along with probiotics, have demonstrated significant potential in altering gut microbiota composition and, in turn, improving skin health. Future studies must focus on investigating the connection between gut microbiota and cellular senescence, the effectiveness of microbiota-targeted therapeutics, and the incorporation of targeted therapy to delay the aging process. Comprehending these processes may facilitate the development of novel ways to enhance healthy aging and alleviate age-related diseases through the gut-skin axis via microbiome regulation.},
}

@article {pmid41863933,
year = {2026},
author = {Dong, X and Zhu, L and He, Y and Li, C and Wu, R and Li, D},
title = {Microbial degradation of plastics in the environment: Mechanisms, enzymatic pathways, and constraints from laboratory studies to environmental reality.},
journal = {Journal of environmental management},
volume = {404},
number = {},
pages = {129422},
doi = {10.1016/j.jenvman.2026.129422},
pmid = {41863933},
issn = {1095-8630},
abstract = {Microplastic (MP) pollution has become a persistent environmental challenge, raising increasing concern due to its global distribution and potential risks to human health. Biological degradation, including microbial and insect mediated processes, represents a promising and environmentally sustainable strategy for mitigating plastic and MP pollution; however, its effectiveness remains highly variable and strongly context dependent. This review systematically summarizes recent advances in microbial degradation of plastic, as well as emerging research on insect mediated plastic biodegradation, focusing on degrading microorganisms, key enzymes, metagenomic discovery, and enzyme engineering strategies. A wide range of bacterial and fungal taxa capable of degrading major plastic polymers, including polyethylene (PE), polypropylene (PP), polyethylene terephthalate (PET), polystyrene (PS), polyvinyl chloride (PVC), polyurethane (PU), and polylactic acid (PLA), has been reported. In addition, several insect species capable of ingesting and transforming plastics have been identified as model systems for studying plastic degradation, where mechanical fragmentation, host digestive processes, and gut microbial metabolism jointly contribute to polymer transformation. Among these, PET degrading enzymes, particularly PETase, are the most extensively characterized, benefiting from detailed structural insights and intensive protein engineering efforts that have markedly enhanced catalytic efficiency and thermostability. In contrast, enzymatic mechanisms involved in the biodegradation of polyolefins such as PE and PP remain poorly understood, representing a major knowledge gap. Recent metagenomic approaches have substantially expanded the repertoire of candidate plastic degrading enzymes by accessing uncultured MP associated microbial communities and insect gut microbiomes. Nevertheless, functional validation and evaluation under environmentally relevant conditions remain critical bottlenecks. Moreover, most reported degradation efficiencies are derived from optimized laboratory settings and may substantially overestimate microbial performance under natural environmental constraints, including low temperature, high salinity, nutrient limitation, and mixed polymer substrates. Overall, this review highlights the gap between laboratory based biodegradation studies and real world applications and emphasizes the need for integrated strategies to advance scalable plastic and MP remediation solutions.},
}

@article {pmid41863937,
year = {2026},
author = {Liu, X and Liu, X and Zhu, D and Wang, J and Wang, Z and Liu, W and Zhou, X and Zhou, H and Wu, L},
title = {Harvesting reshapes greenhouse gas exchange in reservoir drawdown soils via soil state control and context-dependent microbial functions.},
journal = {Journal of environmental management},
volume = {404},
number = {},
pages = {129375},
doi = {10.1016/j.jenvman.2026.129375},
pmid = {41863937},
issn = {1095-8630},
abstract = {Reservoir drawdown zones, the seasonally exposed and re-flooded margins of reservoirs, are extensive pulsed wetlands that can act as hotspots of greenhouse gas (GHG) exchange. Vegetation harvesting is common in these zones, yet its net climate effect across CO2, CH4, and N2O, and the controls behind it, remain unclear. We compared harvested and unharvested plots across longitudinal river reaches and elevation bands in the drawdown zone of the Three Gorges Reservoir (China). We measured soil-atmosphere fluxes of CO2, CH4, and N2O, together with soil physicochemical properties and metagenome-derived functional markers. Harvesting increased CO2 flux and decreased CH4 flux, while N2O showed no detectable net treatment effect. Across analyses, soil hydrothermal and nutrient conditions were the dominant predictors of flux variation; microbial functional signals added information mainly through soil-dependent interactions. In CO2-equivalent terms, lower CH4 emissions only partly compensated for higher CO2, leaving a net positive effect under both 20- and 100-year horizons. These results underscore that harvest impacts in drawdown soils should be assessed as multi-gas trade-offs and interpreted through soil moisture-redox dynamics.},
}

@article {pmid41863981,
year = {2026},
author = {Fu, Z and Fu, J and Wang, Y and Zhan, K and Liang, Y and Ao, N and Shen, Q and Liu, C},
title = {Effects of tea polyphenols on intestinal barrier, antioxidant capacity, and cecal microbiota in lion-head geese.},
journal = {Poultry science},
volume = {105},
number = {6},
pages = {106706},
doi = {10.1016/j.psj.2026.106706},
pmid = {41863981},
issn = {1525-3171},
abstract = {Tea polyphenols are natural bioactive compounds associated with enhanced antioxidant capacity and improved gut health in poultry. This study evaluated the effects of dietary supplementation with tea polyphenols on intestinal morphology, barrier integrity, antioxidant status, and cecal microbiota in lion-head geese. A total of 240 one-day-old male lion-head geese were randomly allocated to 2 treatments: a basal diet (control) or the same diet supplemented with 1,000 mg/kg tea polyphenols (catechin purity, 50.4%) for 18 wk (6 replicates/treatment; 20 birds/replicate). Compared with the control, dietary supplementation with tea polyphenols significantly increased villus height and villus-to-crypt ratio (V/C) in the jejunum and ileum (P < 0.05) and reduced serum lipopolysaccharide (LPS) concentration (P < 0.05), whereas serum diamine oxidase (DAO) activity did not differ (P > 0.05). In the jejunum, mRNA expression of ZO-1, Claudin-5, and Occludin was significantly upregulated (P < 0.05); in the ileum, mRNA expression of ZO-1, Claudin-5, Occludin, and E-cadherin was significantly upregulated (P < 0.05). Tea polyphenols increased jejunal total antioxidant capacity (T-AOC) and upregulated GPX1, GPX2, HO-1, and Nrf2 mRNA expression (P < 0.05). In the ileum, tea polyphenols significantly increased glutathione peroxidase (GSH-Px) and total superoxide dismutase (T-SOD) activities, decreased malondialdehyde (MDA) content, and upregulated SOD1, GPX1, GPX2, HO-1, and Nrf2 mRNA expression (P < 0.05). Metagenomic sequencing showed lower relative abundances of Firmicutes and Verrucomicrobia at the phylum level (P < 0.05). At the genus level, tea polyphenols increased Prevotella and Subdoligranulum and decreased Oscillibacter and Desulfovibrio (P < 0.05). Functional annotation (KEGG, eggNOG, and CAZy) indicated enrichment of carbohydrate transport and metabolism, glycosyltransferases (GT), and polysaccharide lyases (PL) in the tea polyphenol group. Spearman correlation analysis indicated positive associations of Prevotella with KEGG thermogenesis and the two-component system, and of Desulfovibrio with biotin metabolism (P < 0.05). Overall, tea polyphenols promoted intestinal development, enhanced barrier- and antioxidant-related responses, and altered the composition and functional potential of the cecal microbiota, supporting improved gut health in lion-head geese.},
}

@article {pmid41864025,
year = {2026},
author = {Yu, H and Zhang, X and Liang, Y and Mu, Q and Shi, X and Deng, Z and Chen, J and Cao, J and Deng, Y and Han, Z and Chen, H and Zhang, C},
title = {Deciphering the environmental fate of halogenated organic compounds in cold seep sediments: Insights from non-targeted analysis and metagenomics across vertical redox gradients.},
journal = {Journal of hazardous materials},
volume = {507},
number = {},
pages = {141804},
doi = {10.1016/j.jhazmat.2026.141804},
pmid = {41864025},
issn = {1873-3336},
abstract = {Halogenated organic compounds (HOCs) are pervasive in marine environments, yet their molecular diversity, vertical distribution, and fate in deep-sea ecosystems remain largely uncharted. Here, we integrated non-targeted analysis, geochemical profiling, and metagenomics to systematically analyze a 500-cm sediment core from the Haima deep-sea cold seep, deciphering these key aspects and their controlling factors. Non-targeted analysis identified 669 HOCs (at molecular formula level), predominantly of marine origin with saturated structures. The highest HOC diversity was found in the oxic/suboxic (OS) zone, where 73.4% of the frequently detected HOCs reached their peak abundance. Concurrently, a marked decrease in organochlorines was observed at the OS-suboxic/anoxic (SA) interface, followed by level stabilization below this transition, suggesting regulation by abrupt redox shifts. Correlation analyses revealed co-regulation of HOC distribution by geochemical (e.g., depth, pH, and SO4[2-]) and microbial (e.g., reductive and hydrolytic dehalogenases) factors. Metagenomics combined with redundancy analysis further demonstrated significant interactions between HOCs and dehalogenating microbial community along the vertical profile. In summary, this study provided an integrated perspective on the biogeochemical cycling of HOCs in the deep-sea cold seep, linking their removal at redox boundaries, long-term burial, and spatial organization to underlying microbial and geochemical drivers.},
}

@article {pmid41864266,
year = {2026},
author = {Wang, X and Wang, Y and Yan, G and Chu, N and Huang, H and Nie, W},
title = {The Clinical Diagnostic Value of Metagenomic Next-Generation Sequencing for Patients with Suspected Nontuberculous Mycobacterial Osteoarticular Infection: A National Multicenter Clinical Cohort.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {108578},
doi = {10.1016/j.ijid.2026.108578},
pmid = {41864266},
issn = {1878-3511},
abstract = {OBJECTIVE: This study aimed to determine the accuracy of metagenomic next-generation sequencing (mNGS) in diagnosing non-tuberculous mycobacteria (NTM) osteoarticular infection (OAI) and compare it with mycobacteria growth indicator tube (MGIT) culture.

METHODS: This study was conducted on 193 patients with suspected NTM OAI treated from January 2019 to July 2022 at the Beijing Chest Hospital, Capital Medical University, Yantai Qishan Hospital or The Fourth People's Hospital of Nanning who had mNGS assay and MGIT culture results. Clinical comprehensive diagnosis was taken as the "gold standard". We investigated the diagnostic sensitivity, specificity, predictive value, and likelihood ratio of these tests.

RESULTS: Of the 193 patients, 26 (13.47%) were diagnosed with NTM OAI, and 167 (86.53%) had non-NTM OAI. Compared to the MGIT culture results, mNGS showed higher sensitivity (100.0% vs. 7.7%), specificity (99.4% vs. 80.2%), positive predictive value (96.3% vs. 5.7%), negative predictive value (100.0% vs. 84.8%), positive likelihood ratio (167.000 vs. 0.389) and negative likelihood ratio (0.000 vs. 1.150). The area under the curve of the mNGS assay was 0.997 (95% confidence interval, 0.990-1.000).

CONCLUSIONS: The mNGS assay had greater diagnostic accuracy than the MGIT culture in patients with suspected NTM OAI.},
}

@article {pmid41864408,
year = {2026},
author = {Wang, Z and Chen, Z and Zhu, L and Liu, Y and Wen, Q},
title = {Substrate type determines the interplay between metabolic efficiency and microbial stress response in mixed culture PHA production under high salinity.},
journal = {Environmental research},
volume = {},
number = {},
pages = {124330},
doi = {10.1016/j.envres.2026.124330},
pmid = {41864408},
issn = {1096-0953},
abstract = {Polyhydroxyalkanoates (PHAs) from mixed cultures offer a sustainable alternative to plastics, and high salinity presents a promising selective pressure for PHA producers. However, the osmotic stress imposed by high salinity perturbs carbon and energy metabolism, yet how different volatile fatty acid (VFA) substrates influence PHA synthesis efficiency under sustained saline conditions remains poorly understood, particularly regarding carbon flux partitioning and energy trade-offs. This study investigated the effects of single VFA (acetate, propionate, butyrate, and valerate) on the enrichment, PHA accumulation, and metabolic flux of PHA-producing mixed cultures under 1.8% salinity. Butyrate and valerate-fed systems achieved superior PHA accumulation (0.636 ± 0.015 and 0.698 ± 0.005 g PHA/g VSS, respectively) compared to acetate (0.541 ± 0.006 g PHA/g VSS) and propionate (0.382 ± 0.021 g PHA/g VSS). This was due to more direct precursor supply and lower energy demands. Carbon flux analysis confirmed butyrate and valerate directed over 85% of utilized carbon to PHA, whereas propionate diverted more to cell maintenance. Metagenomics revealed that Paracoccus was a versatile salt-tolerant PHA producer across all substrates. Cultures fed with butyrate and valerate also exhibited enhanced respiratory chain activity and higher ATP/NAD(P)H, enabling better salt stress while maximizing PHA synthesis. These findings highlight the critical interplay between VFA type, salt stress, and metabolic trade-offs, providing crucial insights for optimizing high-salinity waste to PHA bioprocesses.},
}

@article {pmid41864933,
year = {2026},
author = {Dai, QB and Lai, LM and Zhu, Q and Yuan, L},
title = {Clinical efficacy of plasma cell-free dna metagenomic next-generation sequencing in diagnosing bloodstream infections.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-026-13134-8},
pmid = {41864933},
issn = {1471-2334},
support = {20242BAB20430//the Natural Science Foundation of Jiangxi Province/ ; 202510284//the Science and Technology Plan of Jiangxi Provincial Health Commissio/ ; },
}

@article {pmid41865546,
year = {2026},
author = {Fan, X and Wang, Y and Liang, W and Ma, X and Zhang, W and Yu, C},
title = {Organic fertilizers reduce N2O and NH3 emissions by regulation soil nitrogen pool and microbiome.},
journal = {Journal of environmental management},
volume = {404},
number = {},
pages = {129432},
doi = {10.1016/j.jenvman.2026.129432},
pmid = {41865546},
issn = {1095-8630},
abstract = {Organic fertilizers are generally considered beneficial towards maintaining long term soil health, yet they could elevate N2O and NH3 emissions which raise concerns regarding air pollution and climate change. In this study, four types of organic fertilizers (raw sheep manure, RSM; composted sheep-manure organic fertilizer, OF; biochar-amended organic fertilizer, CharOF; sterilized OF, SOF) were applied onto three kinds of soils in microcosm cultivation to explore their effects on N2O and NH3 emissions and the underlining mechanisms. The results showed that traditional organic fertilizers (RSM and OF) significantly increased N2O and NH3 emissions from the soils, whereas CharOF reduced by as much as 23.0% in N2O and 18.4% in NH3 from that of RSM/OF peaks. Both OF and SOF significantly increased soil total nitrogen (TN) and organic nitrogen (Org-N), while CharOF significantly improved soil NO3[-]-N, NH4[+]-N and microbial biomass nitrogen (MBN). Metagenomic sequencing showed that RSM and OF significantly increased denitrification genes norB and narI, dissimilatory nitrate reduction genes nasA, napA and nirB, and mineralization gene ureC, while CharOF slightly suppressed denitrification genes nirS and narI, dissimilatory nitrate reduction genes nasA/B, napA, nirB and NR, and mineralization gene ureC. RDA analysis revealed that NO3[-]-N, NH4[+]-N, MBN and pH were the environmental factors affecting NC relevant genes and gas emissions. PLS-PM model revealed that soil nitrogen pool correlated stronger to the NH3 and N2O emissions than that of nitrogen cycle (NC) relevant genes. This study provides a theoretical foundation for the promotion of low-pollution fertilization practices in green agriculture, and contributes to the advancement of agricultural sustainability. Additionally, it offers fresh perspectives on organic fertilizer production and its role in enhancing socio-economic systems for public benefits.},
}

@article {pmid41865575,
year = {2026},
author = {Xie, H and Zhou, J and Shi, Y},
title = {Bioaugmentation of weathered petroleum-contaminated soil with a yeast-based consortium: Degradation performance and mechanism insights.},
journal = {Journal of hazardous materials},
volume = {507},
number = {},
pages = {141830},
doi = {10.1016/j.jhazmat.2026.141830},
pmid = {41865575},
issn = {1873-3336},
abstract = {Bioremediation of total petroleum hydrocarbons (TPHs) in weathered soil is often constrained by the inefficiency of indigenous microbial synergistic networks. The mechanisms governing these network responses remain poorly understood, frequently overlooking the system-level functional dynamics. This 7-week study contrasted biostimulation (NZ) with yeast-based bioaugmentation (NS), linking microbial succession and functional network reconstruction to TPHs degradation. The NS group showed a clear advantage in TPHs removal (83.1%) and, crucially, in degrading the heavy C22-C40 fraction (76.3%). The NZ community, despite possessing degradation genes, was trapped in a "functional lock", lacking a cohesive synergistic network. The TPHs and heavy C22-C40 fraction removal efficiencies of the NZ community are only 75.3% and 39.3%, respectively. In contrast, the introduced Saccharomyces cerevisiae in the NS group acted as a pioneer species. It initiated a system-wide reconstruction by (1) altering the soil microenvironment through intense metabolic stress responses (e.g., upregulation of protein quality control systems and high-affinity MFS transporters) and (2) activating a novel, synergistic indigenous consortium, including Altererythrobacter and Cellulosimicrobium. It is indicated that effective bioaugmentation is not the mere addition of strains but a deliberate ecological network reconstruction. The pioneer species alleviates the functional stagnation of the native community, driving the emergence of a novel, highly effective synergistic degradation system. This provides a key theoretical basis for developing bioremediation technologies centered on ecological network regulation.},
}

@article {pmid41865593,
year = {2026},
author = {Asokan, S and Banerjee, N and Saleem, M and Atiyah, HM and Pandey, RK and Abbas, RK and Yousif, SIA and Radhamanalan, G and Parashar, A and Gowtham, B and Balaji, VK and Jacob, T and Vijayan, S and Rajeswary, D and Atiyah, MM},
title = {Healthcare associated infections (HAI): Insights into epidemiology, microbiology, and diagnostics.},
journal = {Diagnostic microbiology and infectious disease},
volume = {115},
number = {3},
pages = {117376},
doi = {10.1016/j.diagmicrobio.2026.117376},
pmid = {41865593},
issn = {1879-0070},
abstract = {Healthcare associated infections remain a major global health concern because they increase illness, mortality, hospital stay, and healthcare costs. This review provides an updated synthesis of recent evidence on the epidemiology, microbiology, diagnostics, and prevention of healthcare associated infections. These infections arise from patient susceptibility, invasive procedures, antibiotic overuse, contaminated equipment, and poor infection control practices. Device associated infections such as catheter associated urinary tract infection, central line associated bloodstream infection, ventilator associated pneumonia, and surgical site infection are common and often involve multidrug resistant pathogens. Biofilm formation on devices and hospital surfaces creates persistent reservoirs that promote resistance spread. Advances in automated culture systems, rapid molecular assays, metagenomics, and whole genome sequencing improve detection and surveillance. This article integrates evidence from 2020 to 2025 to provide a multidisciplinary framework for understanding and controlling HAIs.},
}

@article {pmid41865818,
year = {2026},
author = {Wang, J and Sun, Y and Zhang, Y and Guo, Y and Liu, J and Wang, X and Yang, Y and Shi, L},
title = {Mechanisms underlying differences in nitrogen removal characteristics of anammox granular sludge immobilization filler with varying particle sizes: Performance, structure, and nitrogen removal pathways.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134471},
doi = {10.1016/j.biortech.2026.134471},
pmid = {41865818},
issn = {1873-2976},
abstract = {The anaerobic ammonium oxidation (anammox) process serves as a green, low-carbon, and sustainable wastewater nitrogen removal technology. However, anammox processes based on granular sludge systems face structural instability issues, resulting in the loss of anammox bacteria (AnAOB). In this study, an immobilized filler system for AnAOB based on hydrogel encapsulation was constructed using anammox granular sludge (AnGS) of varying particle sizes (G1: < 0.10 cm, G2: 0.10-0.20 cm, G3: 0.20-0.32 cm, and G4: > 0.32 cm). The differences in nitrogen removal characteristics, microstructures, and pathways of these AnGS immobilized fillers were thoroughly investigated. The large particles (G3 and G4) immobilized fillers showed the best nitrogen removal performance, with total nitrogen removal rates reaching 0.591 kgN·m[-3]·d[-1] and 0.615 kgN·m[-3]·d[-1], respectively. The G2 immobilized filler was more conducive to the self-growth and enrichment of AnAOB, and the absolute abundance and relative abundance of Candidatus Brocadia increased by 23-fold and 9.20-fold, respectively. Conversely, the G1 immobilized filler displayed the poorest nitrogen removal rate due to insufficient microbial growth. The G1-G3 immobilized fillers possessed uniform and dense small pores, whereas the G4 filler featured uniform large pores. Metagenomic analysis confirmed that the abundance of denitrification-related genes in G3 and G4 immobilized fillers was highest, indicating that anammox and denitrification synergistically achieve nitrogen removal, whereas G2 immobilized fillers mainly relied on anammox. This study provides a crucial theoretical basis and technical guidance for optimizing the application of anammox immobilized filler systems.},
}

@article {pmid41865820,
year = {2026},
author = {Luo, Z and Li, W and Zhang, N and Lei, M and Chen, B and Li, Y and Liu, Q and Zhang, M and Lv, S and Cheng, F and Li, J},
title = {A novel continuous-flow three-stage tandem system based on partial nitrification/Anammox granular sludge and partial denitrification-Anammox biofilm (PN/A-PD-A) for advanced nitrogen removal from mature landfill leachate.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134474},
doi = {10.1016/j.biortech.2026.134474},
pmid = {41865820},
issn = {1873-2976},
abstract = {A novel continuous-flow system coupling partial nitrification/Anammox (PN/A), partial denitrification (PD), and Anammox (Amx) biofilm reactors was developed (PN/A-PD-A) to treat mature landfill leachate (MLL). To maximize synergy, the NH4[+]-N removal in the PN/A reactor was regulated based on the NO2[-]-N accumulation ratio (NAR) in the PD stage, ensuring optimal substrate stoichiometry for the final Amx polishing step. Over 174 days of operation, the system achieved a superior total nitrogen removal efficiency (TNRE) of 98.30 ± 0.14% (effluent TN: 21.80 ± 1.71 mg/L). The PN/A granular sludge, enriched with Candidatus_Kuenenia (5.87%) and Nitrosomonas (9.73%), demonstrated high adaptability to MLL characteristics and contributed to 83.51% of the TN removal. In the PD stage, the dominant genus Thauera (43.91%) facilitated efficient NAR (82.86 ± 1.61%) at a limited COD/NO3[-]-N ratio of 2.32 ± 0.02. The Anammox biofilm (Candidatus_Kuenenia, 27.80%) in the Amx reactor contributed to 13.10% of TN removal, ensuring to meet the MLL discharge standard. Kinetic and metagenomic analyses confirmed that distinct shifts from complete to partial nitrification (and denitrification) in enzymes activity and gene abundance under chronic MLL stress underpinned the robust NO2[-]-N accumulation in both PN/A and PD reactors. Notably, compared to conventional nitrification-denitrification process, the PN/A-PD-A system significantly reduced oxygen demand (60.18%), exogenous organic carbon consumption (91.61%), sludge yield (83.72%), and CO2 emission (94.66%), demonstrating a sustainable pathway for low-carbon nitrogen removal from high-strength wastewater.},
}

@article {pmid41865821,
year = {2026},
author = {Wang, X and Liang, BJ and Wu, DN and Zhang, XM and Zhao, HP and Lai, CY},
title = {Efficient anaerobic metformin biodegradation driven by a Cross-Feeding Consortium: Novel Pathways, Enzymes, and toxicity dynamics.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134473},
doi = {10.1016/j.biortech.2026.134473},
pmid = {41865821},
issn = {1873-2976},
abstract = {Metformin is one of the most widely prescribed antidiabetic drugs worldwide and is now ubiquitously detected in aquatic environments, yet its anaerobic biodegradation remains largely unexplored and mechanistically unresolved. Here, an anaerobic membrane bioreactor (AnMBR) was operated and near-complete metformin removal (∼98%) at influent concentrations up to 5.3 mg/L was achieved, corresponding to a maximum degradation rate of 7.2 mg/L/d, approximately sixfold higher than previously reported anaerobic systems degrading metformin. High-resolution mass spectrometry identified three concurrent anaerobic metformin transformation pathways. Notably, a previously unreported biological C-N bond cleavage route yielding dimethylguanidine was discovered, expanding the known anaerobic metabolic repertoire of metformin. In silico toxicity prediction revealed a non-monotonic toxicity trajectory during metformin transformation, with transiently elevated toxicity at intermediates (particularly 2,4-AMT) followed by an overall attenuation at the terminal product guanidine. Metagenomic and metatranscriptomic analyses uncovered a cooperative, cross-feeding microbial network dominated by Ignavibacterium album and Denitrolinea symbiosum, and identified HypAB (metformin-to-guanylurea), YafV and AmiA/B/C/E (guanylurea-to-guanidine), and, critically, SpeB as the key enzyme initiating the newly proposed C-N bond cleavage pathway. Molecular dynamics simulations further suggested stable binding of metformin to SpeB with strong affinity, providing mechanistic support for SpeB-mediated initiation of the novel pathway. Overall, this study establishes the first mechanistic framework for anaerobic metformin biodegradation, reveals an unprecedented C-N scission pathway, and demonstrates that high-rate, low-carbon pharmaceutical removal can be achieved through intrinsic microbial metabolism, offering new conceptual and practical foundations for energy-efficient treatment of emerging pharmaceutical contaminants.},
}

@article {pmid41865866,
year = {2026},
author = {Wang, Y and Wang, D and Wang, H},
title = {Comparative analysis of the gut microbiome and bile acid profiles in sympatric Rana chensinensis and Fejervarya multistriata tadpoles.},
journal = {Comparative biochemistry and physiology. Part A, Molecular & integrative physiology},
volume = {},
number = {},
pages = {111996},
doi = {10.1016/j.cbpa.2026.111996},
pmid = {41865866},
issn = {1531-4332},
abstract = {Environmental temperature is an essential exogenous factor influencing the gut microbiota of amphibians, which exerts profound physiological impacts on the host by modifying bile acids (BAs). Even sympatric amphibians often have considerably different optimal breeding temperatures. However, the effect of different developmental temperatures on gut microbiota and BA profiles in sympatric amphibians remains unclear. To address this deficiency, morphological, histological, metagenomics and metabolomics information were compared between Rana chensinensis (R. chensinensis) and Fejervarya multistriata (F. multistriata) tadpoles. Morphological and histological results showed that body mass index (BMI), intestinal mass to body mass ratio (IM/BM), and enterocyte height (EH) were higher in F. multistriata, whereas body mass (BM), total length (TL), and intestine mass (IM) were higher in R. chensinensis. Metagenomics analysis revealed the relative abundance of microorganisms (Bacteroides, Clostridium, and Enterococcus) producing bile salt hydrolase (BSH) is higher in F. multistriata, whereas the relative abundance of microorganisms (Dorea spp, Extibacter muris, Clostridium leptum, and Proteocatella sphenisci) possessing the BAI operon is higher in R. chensinensis. Comparative metabolomic analysis identified that F. multistriata has a higher ratio of unconjugated to conjugated BAs (CA/TCA, CDCA/TCDCA, and DCA/TDCA), which may suppress the abundance of pathogen (e.g., Clostridioides difficile). Additionally, the lower TDCA content in F. multistriata may be potentially linked to its stronger absorptive capacity. In contrast, R. chensinensis exhibits a higher ratio of DCA to CA, which probabaly enhance their cold tolerance. Overall, this study elucidated the potential impacts of developmental temperature-driven differences in gut microbiota and BAs on sympatric amphibians' physiological metabolism.},
}

@article {pmid41784805,
year = {2026},
author = {Shen, J and Gao, J and Gao, L and Yan, D and Wang, Y and Meng, J and Li, H and Chen, D and Wu, J},
title = {Melatonin ameliorates autistic-like behaviors by restoring gut microbiota-derived tryptophan metabolites.},
journal = {Cellular and molecular life sciences : CMLS},
volume = {83},
number = {1},
pages = {},
pmid = {41784805},
issn = {1420-9071},
support = {2023-MS-310, 2019-BS-098//Natural Science Foundation of Liaoning Province/ ; LJKQZ2021149//Scientific Research Fund of Liaoning Provincial Education Department/ ; },
abstract = {UNLABELLED: Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by social deficits and repetitive stereotyped behavior. Disrupted microbiota‒gut‒brain axis (MGBA) signaling contributes to the pathology of ASD and cognitive disability. Melatonin (MT), a naturally occurring compound, has shown potential in ameliorating core symptoms of ASD and mitigating gut microbiota dysbiosis, yet the underlying mechanism is poorly understood. This study aimed to investigate whether exogenous melatonin improves behavioral deficits in valproic acid (VPA)-exposed male offspring rats, and the modulation of gut microbiota-derived tryptophan metabolites. In prenatal VPA-induced model rats, microbial diversity and construction was analyzed through metagenomic sequencing, targeted-metabolomics and transcriptomics were conducted to explore related metabolic pathways and molecular profiles. We identified 7 gut bacterial genus causally associated to ASD: Faecali-bacterium, Lachnospiraceae, Ruminococcaceae, Butyricimonas, and Bacteroides exhibited protection, whereas Erysipelotrichaceae and Clostridia enhanced risk. The exacerbation of Erysipelotrichaceae and Clostridia by VPA versus restoration of Faecalibacterium, Butyricimonas, Bacteroides and Bifidobacterium by melatonin, which are known to participate in tryptophan metabolism. Correspondingly, systemic metabolomics pointed to melatonin’s restoration of tryptophan metabolic disorders (IDO1-kynurenine, TPH1/2-serotonin-melatonin, and Indole-3-propionic acid (IPA)) induced by VPA, paralleled the rectification of microglial reactivity, synaptic proteins, dendritic morphology, and hippocampal neurogenesis. These molecular profiles were further integrated by transcriptomics, highlighted tryptophan-derived neurotransmitters and neuroactive ligand-receptor interaction, contributing to enhanced social and cognitive behaviors under melatonin intervention. Based on multi-omic analysis, our findings underscore key bacteria and metabolites contributing to neurological and immune dysfunction in VPA-exposed rats, providing novel targets for possible therapeutics of melatonin.

GRAPHICAL ABSTRACT: [Image: see text]

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00018-026-06163-8.},
}

@article {pmid41862052,
year = {2026},
author = {Rajalakshmi, SG and Ramesh Babu, K and Viswanathan, P},
title = {Investigating gut microbiome dysbiosis in adults with chronic kidney disease: Diabetes-induced alterations via metagenomics and qPCR.},
journal = {Life sciences},
volume = {},
number = {},
pages = {124336},
doi = {10.1016/j.lfs.2026.124336},
pmid = {41862052},
issn = {1879-0631},
abstract = {BACKGROUND: Type 2 diabetes (T2D) is a major contributor to diabetic nephropathy, the leading cause of chronic kidney disease (CKD). This study investigated gut microbial dysbiosis and composition shift among healthy individuals and diabetic patients with or without CKD using a 16S rRNA metagenomic approach, validated by qRT-PCR and clinical data integration to identify the significant key genera associated with disease progression.

METHODS: Stool samples from 22 individuals were analysed using 16S rRNA amplicon sequencing to assess gut microbiota composition. Differential abundance analysis, LEfSe, and network-based methods were employed to identify key taxa. Significant features were validated by qRT-PCR. Integrated approaches, including Pearson correlation, WGCNA, random forest, and propensity score matching, were used to associate microbial features with clinical markers. Functional enrichment of microbial pathways was predicted using PICRUSt2.

KEY FINDINGS: A total of 1409 amplicon sequence variants (ASVs) were identified. Bray-Curtis dissimilarity showed significant microbial diversity differences between disease and healthy subjects (p < 0.031). Key taxa associated with eGFR and serum creatinine (sCr) included Bacteroidetes uniformis (LFC +9), Ruminococcus (LFC +8.1), and Dialister succinatiphilus (LFC +6.7), linked to disease progression and metabolic regulation. In contrast, protective taxa such as Bifidobacterium adolescentis (LFC -9.5), Faecalibacterium prausnitzii (LFC -6.39), Collinsella, and Megasphaera elsdenii were reduced. Integration of Pearson correlation, WGCNA, propensity score matching, and random forest classification revealed microbial features associated with clinical covariates.

SIGNIFICANCE: Our findings show the gut microbiome shifts begin in diabetics without CKD conditions but become more pronounced in diabetics with CKD, with a lower ratio of beneficial bacteria, reflecting a gradual microbial imbalance along disease progression.},
}

@article {pmid41856866,
year = {2026},
author = {Jelen, BI and Baker, BJ},
title = {Mapping environmental microbiomes across an entire country.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2026.02.013},
pmid = {41856866},
issn = {1878-4380},
abstract = {Microbial diversity underpins ecosystem function and resilience, yet large-scale spatial baselines remain rare. Singleton et al. present a Danish atlas of environmental microbiomes, revealing nationwide patterns of diversity. By emphasizing gamma diversity, they show how nitrifying communities differ in scale and composition between natural and disturbed habitats.},
}

@article {pmid41857415,
year = {2026},
author = {},
title = {Metagenomic surveillance of zoonotic yellow fever and spillover dynamics at a forest-urban interface.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41857415},
issn = {2058-5276},
}

@article {pmid41857851,
year = {2026},
author = {Yu, X and Wen, Z and Zhou, W and Zheng, Y and Chen, J and Xiao, WJ and Lin, S and Liang, H and Duan, X and Wang, W and Wu, H and Chen, X},
title = {Respiratory syndromic disease study in Shanghai community population.},
journal = {BMJ open},
volume = {16},
number = {3},
pages = {e103001},
doi = {10.1136/bmjopen-2025-103001},
pmid = {41857851},
issn = {2044-6055},
mesh = {Humans ; China/epidemiology ; Male ; Female ; *Respiratory Tract Infections/epidemiology/microbiology ; Adult ; Prospective Studies ; Middle Aged ; Adolescent ; Aged ; Child ; Young Adult ; Child, Preschool ; Incidence ; Coinfection/epidemiology ; Urban Population ; Seasons ; },
abstract = {PURPOSE: This prospective community-based cohort study (Acute Respiratory Infection Epidemiological Characteristics Assessment Study (ARI-ECAS)) aims to systematically monitor acute respiratory infection (ARI) incidence, characterise multiple pathogen coinfection patterns and explore microbial landscape dynamics in Shanghai's general population. By integrating syndromic surveillance, molecular diagnostics and metagenomic sequencing, the study seeks to enhance understanding of ARI epidemiology, seasonal variation and host-pathogen interactions to inform predictive modelling and optimise public health interventions in high-density urban environments.

PARTICIPANTS: The study enrolled 15 199 permanent residents from all 16 districts of Shanghai, with baseline oropharyngeal swab samples across five representative districts (Xuhui, Jing'an, Jiading, Songjiang and Fengxian). Inclusion criteria required residency ≥6 months and consent for weekly follow-ups. Exclusion criteria addressed mobility limitations (planned relocation >6 months) and recent ARI history. Participants provided demographic, behavioural and clinical data via the Shanghai Health Cloud platform, with baseline and symptomatic-phase biological samples collected for analysis.

FINDINGS TO DATE: During the initial 8-month surveillance period (May 2024-January 2025), the ARI-ECAS cohort demonstrated critical insights into the epidemiology of acute respiratory infections in Shanghai's urban communities. Among 15 199 participants, 10.96% reported symptomatic episodes, of whom 21.43% experienced recurrent infections. Pathogen detection using targeted next-generation sequencing (tNGS) identified microbial aetiologies in 53.52% of symptomatic cases, revealing a high prevalence of coinfections: 27.96% involved dual pathogens, while 33.01% showed polymicrobial interactions (≥3 pathogens). Notably, 85.09% of symptomatic episodes were self-managed, underscoring a low healthcare-seeking rate (14.91%) consistent with patterns observed in urban China during postpandemic transitions.

FUTURE PLANS: The current phase of data collection will conclude in June 2025; however, syndromic surveillance and tNGS protocols will be sustained to capture multiyear seasonal transmission patterns. To enhance comparative rigour, future protocols will aim to collect samples from participants during asymptomatic periods in the subsequent year to serve as seasonal baseline controls. Building on this foundation, the study will integrate contact behaviour and mobility surveys to quantify parameters critical for understanding pathogen transmission dynamics (eg, household contacts and public transportation usage). Furthermore, pathogen detection and metagenomic data will be combined with transcriptomic and metabolomic profiling in selected cases to model multipathogen interaction networks and delineate host immune response pathways, thereby advancing mechanistic insights into polymicrobial cocirculation.},
}

Humans
China/epidemiology
Male
Female
*Respiratory Tract Infections/epidemiology/microbiology
Adult
Prospective Studies
Middle Aged
Adolescent
Aged
Child
Young Adult
Child, Preschool
Incidence
Coinfection/epidemiology
Urban Population
Seasons

@article {pmid41857857,
year = {2026},
author = {Ngoumou, GB and Ngandeu Schepanski, S and Blakeslee, SB and Diedering, A and Twal, E and Raue, SL and Schroeder, M and Wicaksono, WA and Stritter, W and Berg, G and Seifert, G},
title = {Effects of fermented versus unfermented red cabbage on symptoms, immune response, inflammatory markers and the gut microbiome in young adults with allergic rhinoconjunctivitis: a randomised controlled trial protocol.},
journal = {BMJ open},
volume = {16},
number = {3},
pages = {e115290},
doi = {10.1136/bmjopen-2025-115290},
pmid = {41857857},
issn = {2044-6055},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; Adult ; Young Adult ; *Brassica ; Quality of Life ; *Fermented Foods ; Adolescent ; Randomized Controlled Trials as Topic ; *Conjunctivitis, Allergic/immunology/diet therapy ; *Rhinitis, Allergic/immunology/diet therapy ; Female ; Male ; Biomarkers ; },
abstract = {INTRODUCTION: Allergic rhinoconjunctivitis (ARC) is a highly prevalent immune-mediated condition associated with substantial symptom burden, impaired quality of life and increased healthcare use. Emerging evidence highlights the role of the gut microbiome in immune regulation and allergic disease. Fermented foods may contain live microbes (when unpasteurised or uncooked) and bioactive postbiotic metabolites that can modulate immune responses. Despite growing interest in dietary strategies targeting the microbiome, no randomised controlled trial has compared fermented versus unfermented red cabbage for ARC.

METHODS AND ANALYSES: This single-centre, randomised, controlled trial with a sensory-matched, unfermented cabbage comparator investigates the effects of daily consumption of fermented red cabbage for 8 weeks compared with an unfermented red cabbage control in young adults (18-35 years) with ARC. A total of 158 participants will be randomly assigned (1:1). The primary outcome is change in Total Nose and Eye Symptom Score from baseline to week 8. Secondary outcomes include daily symptoms and medication use captured via mobile ecological momentary assessments, quality of life, psychological well-being, gastrointestinal symptoms, systemic inflammatory markers, total IgE, immune cell profile and metagenomic characterisation of stool samples. A nested qualitative component explores participants' experiences and acceptability of the intervention. Analyses will include mixed-effects models, time-series analyses incorporating daily pollen counts and comprehensive microbiome statistics. Safety outcomes and adverse events will also be assessed.

ETHICS AND DISSEMINATION: This study was approved by the Ethics Committee of Charité-Universitätsmedizin Berlin (EA4/043/25) and is conducted in accordance with the Declaration of Helsinki and Good Clinical Practice. Results will be disseminated through peer-reviewed publications, conference presentations and a lay summary provided to participants. Anonymised datasets and analysis scripts will be made available in public repositories, and metagenomic sequencing data will be deposited in an international sequence archive to ensure transparency and reproducibility.

TRIAL REGISTRATION NUMBER: DRKS00036475.},
}

Humans
*Gastrointestinal Microbiome/immunology
Adult
Young Adult
*Brassica
Quality of Life
*Fermented Foods
Adolescent
Randomized Controlled Trials as Topic
*Conjunctivitis, Allergic/immunology/diet therapy
*Rhinitis, Allergic/immunology/diet therapy
Female
Male
Biomarkers

@article {pmid41858204,
year = {2026},
author = {Chen, X and Ji, M and Yan, D and Liu, Y and Chen, Y and Dong, R and Shen, L and Takeuchi, N and Kong, W},
title = {Metabolic capacities and potential microbial interactions in red and green snow of the Antarctic Peninsula.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.71089},
pmid = {41858204},
issn = {1469-8137},
support = {32161123004//National Natural Science Foundation of China/ ; 42171138//National Natural Science Foundation of China/ ; 72574092//National Natural Science Foundation of China/ ; },
abstract = {Colored (red and green) snow is widespread in Antarctica due to climate warming. This phenomenon reduces snow albedo, accelerates snowmelt, alters microbial functions, and impacts regional geochemical cycles. Diverse microorganisms are associated with this phenomenon, yet their functions remain poorly understood. We employed metagenomic sequencing to reveal the metabolic interactions and functional specialization within microbial communities of colored snow, focusing on carbon, nitrogen, phosphorus, and sulfur metabolism. While broad metabolic profiles were similar between red and green snow, targeted analysis of specific pathways revealed significant enrichment of denitrification and organic-phosphorus mineralization genes in green snow and labile carbon degradation genes in red snow. Betaproteobacteria were dominant drivers of nitrogen, sulfur, and phosphorus transformation, while diverse eukaryotic algae and bacteria were responsible for carbon fixation. Additionally, we recovered 2257 bacteriophages, 529 algal viruses, and 2302 secondary metabolite gene clusters. Specifically, viruses encoded 126 auxiliary metabolic genes that may influence the elemental cycling of hosts, while secondary metabolites, such as pyoverdine, may assist algal iron acquisition. Our findings offer new insights into the metabolic potentials and interactions of microbial communities in Antarctic colored snow, highlighting their potential relevance to snow biogeochemical processes.},
}

@article {pmid41858247,
year = {2026},
author = {Groninga, J and Wittig, L and Bouderka, F and Bornemann, TLV and Lipp, JS and Schubotz, F and Keden, S and Probst, AJ and Hinrichs, KU},
title = {Novel Extended Tetraether Lipids Found in a High-CO2 Geyser.},
journal = {Environmental microbiology},
volume = {28},
number = {3},
pages = {e70286},
doi = {10.1111/1462-2920.70286},
pmid = {41858247},
issn = {1462-2920},
support = {101118631/ERC_/European Research Council/International ; },
mesh = {*Carbon Dioxide/metabolism/analysis ; *Archaea/genetics/metabolism/chemistry ; Germany ; *Groundwater/microbiology ; *Lipids/chemistry ; *Ethers/chemistry ; Metagenome ; *Glyceryl Ethers/chemistry ; },
abstract = {The growing research into the archaeal lipidome has uncovered a remarkable structural diversity in isoprenoidal glycerol dialkyl glycerol tetraethers (iGDGTs) and revealed complex membrane adaptations, especially in extreme environments. We performed a comprehensive analysis of the lipidome from the subsurface aquifer of the CO2-rich, cold-water Geyser Andernach (Germany), using ultra-high-resolution mass spectrometry. We detected iGDGT-0, presumably derived from the dominant community member Candidatus Altiarchaeum, providing supporting evidence for its ability to synthesise tetraethers, as previously predicted from metagenomic data. Beyond the typical iGDGT-0 and acyclic glycerol trialkyl glycerol tetraether (iGTGT-0), we discovered novel structural derivatives, here referred to as extended iGDGTs and iGTGTs, characterised by the asymmetrical addition of up to two isoprenoid units to only one of their hydrocarbon side chains, analogous to those found in extended archaeols. The apparent absence of GDGT ring synthase A and B genes in the corresponding metagenome-assembled genome raises the possibility that the producing archaea may utilise extended iGDGTs as a membrane adaptation to cope with the nutrient-depleted conditions of the geyser environment, highlighting the adaptive flexibility of archaea to extreme physicochemical conditions.},
}

*Carbon Dioxide/metabolism/analysis
*Archaea/genetics/metabolism/chemistry
Germany
*Groundwater/microbiology
*Lipids/chemistry
*Ethers/chemistry
Metagenome
*Glyceryl Ethers/chemistry

@article {pmid41858251,
year = {2026},
author = {Morissette, O and Côté, G and Couillard, MA and Pouliot, R and Bernatchez, L},
title = {Trait-Based Biomonitoring Using eDNA Metabarcoding to Assess Anthropogenic Disturbances on Freshwater Fish Communities.},
journal = {Molecular ecology resources},
volume = {26},
number = {3},
pages = {e70131},
doi = {10.1111/1755-0998.70131},
pmid = {41858251},
issn = {1755-0998},
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Fishes/classification/genetics ; *DNA, Environmental/genetics ; Quebec ; Ecosystem ; Fresh Water ; Rivers ; *Biological Monitoring/methods ; Biodiversity ; *Environmental Monitoring/methods ; *Metagenomics/methods ; *Biota ; },
abstract = {Various anthropogenic disturbances affect the succession of aquatic habitats along dendritic river networks. Bioindicator taxa, such as fish, can be used to assess the effects of these disturbances on habitat quality. Environmental DNA (eDNA) metabarcoding offers a novel approach to complement traditional sampling and analysis of bioindicator taxa. Here, we apply a trait-based biomonitoring framework, focusing on fish tolerance to pollution, to assess habitat quality and fragmentation within two watersheds in southern Québec (Canada). We sampled 193 sites within the dendritic networks of the Châteauguay and St. François watersheds and estimated fish community tolerance indices on the basis of 12S metabarcoding. We found a significant correlation between the fish community tolerance index and environmental factors such as subwatershed land use, precipitation and elevation. We also found that river fragmentation caused by dams affected fish assemblages and native fish movement but also prevented the spread of the non-native common carp. Finally, we applied random-forest modelling to predict the tolerance of fish communities to disturbances in unsampled areas, providing a broader understanding of habitat quality within catchments. Our research highlights how eDNA metabarcoding for large-scale biomonitoring and river fragmentation studies provides a cost-effective and non-invasive method for assessing fish biodiversity and riverine ecosystem health.},
}

Animals
*DNA Barcoding, Taxonomic/methods
*Fishes/classification/genetics
*DNA, Environmental/genetics
Quebec
Ecosystem
Fresh Water
Rivers
*Biological Monitoring/methods
Biodiversity
*Environmental Monitoring/methods
*Metagenomics/methods
*Biota

@article {pmid41858257,
year = {2026},
author = {Geerts, MM and Curto, M and Alverson, AJ and Stone, J and Gante, HF},
title = {Disentangled Assembly Graphs Reveal Hidden Eukaryotic Diversity in eDNA Metagenomic Data.},
journal = {Molecular ecology resources},
volume = {26},
number = {3},
pages = {e70128},
doi = {10.1111/1755-0998.70128},
pmid = {41858257},
issn = {1755-0998},
support = {STG/21/044//KU Leuven Research Fund/ ; 11Q4724N//Fonds Wetenschappelijk Onderzoek/ ; UIDP/50027/2020//InBIO Programático FUI 2020-2023/ ; DEB-2331644//Division of Environmental Biology/ ; },
mesh = {*Metagenomics/methods ; *Diatoms/genetics/classification ; Phylogeny ; *Computational Biology/methods ; *DNA, Environmental/genetics ; *Eukaryota/genetics/classification ; Metagenome ; *Biodiversity ; Czech Republic ; Fresh Water/microbiology ; },
abstract = {Genome assembly graphs contain valuable yet frequently overlooked information that can enhance assembly completeness by revealing contig connectivity. Here, we demonstrate how leveraging these information-rich structures enables the discovery of hidden microeukaryotic diversity in environmental DNA shotgun metagenomic datasets. While GetOrganelle has previously been used for organellar genome assembly from isolated tissues, we present its first application to water eDNA metagenomic data, using diatoms as an example. We tested the efficiency of this organellar genome assembly tool on three freshwater eDNA metagenomic datasets with varying diatom abundances, finding that GetOrganelle alone yields fragmented scaffolds due to mixed-species complexity. By implementing manual disentanglement of assembly graphs, we successfully recovered complete organellar genomes from these assemblies. From high-abundance bloom samples, we recovered complete plastomes of Stephanodiscus hantzschii with 99.9% pairwise identity across distant geographical locations (USA and Czech Republic). From a lower abundance non-bloom sample, we reconstructed a potentially novel Cyclotella plastome with only 94.0% identity to its closest available reference, Cyclotella atomus. Our assembly quality assessment confirmed effective manual disentanglement even at low diatom abundances. By integrating sequence similarity, gene order conservation and phylogenetic analysis, we achieved robust species-level resolution and resolved previous taxonomic uncertainties. Our findings demonstrate that mining eDNA metagenomic data with GetOrganelle reveals previously hidden microeukaryotic diversity and provides higher taxonomic resolution than traditional binning methods. This approach proves especially valuable for microeukaryotes, where reference organellar genomes remain underrepresented in existing databases.},
}

*Metagenomics/methods
*Diatoms/genetics/classification
Phylogeny
*Computational Biology/methods
*DNA, Environmental/genetics
*Eukaryota/genetics/classification
Metagenome
*Biodiversity
Czech Republic
Fresh Water/microbiology

@article {pmid41858380,
year = {2026},
author = {Beran, P and Rost, M and Beranová, K and Kváč, M and Stehlíková, D and Udoh, OE and Jozová, E and Čurn, V},
title = {genCRC32: collision-free CRC32-based hashing of DNA sequences.},
journal = {Bioinformatics advances},
volume = {6},
number = {1},
pages = {vbaf315},
pmid = {41858380},
issn = {2635-0041},
abstract = {MOTIVATION: Efficient and collision-free hashing of DNA sequences is essential for accuracy and performance in bioinformatics applications such as genome assembly, sequence alignment, and metagenomic classification. Traditional hashing methods often result in collisions, impacting the precision and/or performance of downstream analyses. Thus, it is highly advantageous to have hashing functions that guarantee collision-free mappings for DNA sequences, particularly for k-mers up to length 16, where practical limits for 32-bit hashing are reached. In this study, we evaluate genCRC32 as a hashing primitive, reporting collision behavior, bucket balance, sensitivity to single-base changes, and speed to inform its potential use in downstream tools. Evaluation within specific software tools is outside the scope of this paper and is planned as future work.

RESULTS: We present genCRC32, an innovative hashing method that integrates a straightforward preprocessing step (gen32) with CRC32 hashing, specifically identifying eight CRC32 polynomials that ensure collision-free hashing for all DNA k-mers up to 16 nucleotides in length. Through extensive empirical evaluations, genCRC32 demonstrated zero collisions for these k-mers, achieving a one-to-one mapping without auxiliary data structures. Benchmark tests confirmed minimal computational overhead introduced by preprocessing, maintaining hashing performance comparable to established methods such as MurmurHash3 and xxHash32.

The source code for genCRC32 is publicly available at: https://github.com/berybox/genCRC32. The implementation is provided in Go (version 1.24) and leverages only standard libraries, ensuring portability and ease of integration into existing bioinformatics workflows.},
}

@article {pmid41858392,
year = {2026},
author = {Tu, W and Zeng, P and Wu, Z and Li, Z and Yu, T and Zhang, W and Chen, R and Liang, L},
title = {A case report of brain abscess caused by Nocardia cyriacigeorgica identified by metagenomic next-generation sequencing.},
journal = {World journal of emergency medicine},
volume = {17},
number = {2},
pages = {199-201},
pmid = {41858392},
issn = {1920-8642},
}

@article {pmid41858535,
year = {2026},
author = {Zhang, L and Chen, S and Li, H and Li, L and Liu, H},
title = {Molecular epidemiology and genomic analysis of bulbul coronavirus in Guangdong, China.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1659863},
pmid = {41858535},
issn = {2297-1769},
abstract = {INTRODUCTION: Bulbul coronavirus (BuCoV), a delta coronavirus recently identified in passerine birds, remains poorly characterized regarding its ecology and evolutionary dynamics. This study aimed to determine the prevalence of BuCoV in wild avifauna, clarify its evolutionary relationship with other delta coronaviruses, and identify genetic signatures potentially relevant to host adaptation and cross-species transmission in southern China.

METHODS: From 2023 to 2024, we conducted molecular surveillance across 12 regions in Guangdong Province, China. A total of 2,145 avian fecal samples were collected and screened for BuCoV using real-time quantitative PCR. The complete genomes of representative strains were obtained using next-generation sequencing. Subsequent analyses included phylogenetic reconstruction using maximum likelihood methods, recombination detection using RDP4 and SimPlot, and comparative amino acid analysis.

RESULTS: BuCoV was detected exclusively in Shenzhen (3/168, 1.78%), with all positive samples originating from bulbuls (Pycnonotus spp.). The Shenzhen strain GD2411 exhibited the highest nucleotide identity with BuCoV strains HKU11-796 (97.26%) and HKU11-934 (96.79%), but far lower similarity (78.9%-82.4%) to other delta coronaviruses. Phylogenetic analysis placed GD2411 in a monophyletic clade with HKU11 strains. Recombination analyses revealed mosaic structures within the spike (S) gene, involving multiple coronavirus lineages. Thirty-one amino acid substitutions were detected in the S protein, together with mutations in RdRp, 3CLpro, and nucleocapsid.

DISCUSSION: These findings suggest that BuCoV GD2411 emerged through inter-lineage recombination and is undergoing adaptive evolution, particularly in the spike protein. The detection of BuCoV exclusively in Shenzhen, a critical node in the East Asian-Australasian Flyway, suggests that migratory birds may facilitate viral dissemination. The identified mutations may affect viral replication, host adaptation, or immune evasion. These findings provide essential baseline genomic and epidemiological data critical for understanding BuCoV diversity and assessing potential zoonotic risks in southern China.},
}

@article {pmid41858674,
year = {2026},
author = {Zholdasbek, A and Tekebayeva, Z and Kulzhanova, K and Abzhalelov, A and Bekshin, Z and Yevneyeva, D and Saylau, M and Li, X and Tan, Z and Wang, Z and Temirkhanov, A and Nurbekova, Z},
title = {Microbiome and plant relationship: a symbiosis against phytopathogens.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1722279},
pmid = {41858674},
issn = {1664-462X},
abstract = {Phytopathogens are among the major biotic stressors limiting global crop productivity. Conventional control methods, including chemical pesticides and fungicides, have contributed to pathogen resistance, environmental pollution, and soil degradation, highlighting the need for sustainable alternatives. This review highlights innovative, eco-friendly strategies that exploit plant-microbe interactions to enhance plant health and resilience across diverse agroecosystems. Rhizosphere-, phyllosphere-, and endosphere-associated microbial assemblages contribute to plant immune enhancement through induced systemic resistance, competitive nutrient exclusion, antimicrobial metabolite production, and mycoparasitism. The review emphasizes the functional roles of beneficial microbial communities and the emerging applications of synthetic consortia and bio-organic fertilizers to improving disease suppression, nutrient use efficiency, and soil fertility. In addition, recent progress in omics-based tools and microbial formulation technologies is discussed as a key driver for translating laboratory findings into practical field applications. However, large-scale implementation remains challenged by high research costs, limited metagenomic infrastructure, and the lack of standardized microbial formulations across environments. Strengthening institutional capacity, integrating omics-based tools, and improving technology transfer will be essential to unlock the full potential of microbiome-based pathogen control. Overall, this review highlights microbiome-based interventions as a sustainable alternative to chemical-intensive plant protection strategies under changing environmental conditions.},
}

@article {pmid41859061,
year = {2026},
author = {Wang, Z and Yang, R and Xiao, Y and Huang, B and Yang, Z and Yang, L},
title = {Primary Cutaneous Aspergillosis Due to Aspergillus flavus in an Immunocompetent Patient.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {565781},
pmid = {41859061},
issn = {1178-6973},
abstract = {Invasive aspergillosis is a life-threatening infection caused by Aspergillus species, affecting the lungs, central nervous system, nasal and orbital regions, and skin. Primary cutaneous aspergillosis (PCA) occurs through direct skin inoculation via trauma, burns, or surgical wounds, with Aspergillus fumigatus, Aspergillus flavus, and Aspergillus niger as common causative species, and is rare in immunocompetent individuals. We report a case of PCA in a 56-year-old immunocompetent patient with facial and right ankle ulcers, persisting for two years. The patient had no history of diabetes, corticosteroid use, or immunodeficiency. Fungal culture and metagenomic next-generation sequencing (mNGS) confirmed A. flavus infection. Voriconazole therapy, surgical debridement, and specialized wound care led to the gradual healing of the ulcers. This case highlights the importance of early diagnosis and intervention to prevent infection spread and progression to systemic aspergillosis or septic shock.},
}

@article {pmid41859064,
year = {2026},
author = {Gu, P and An, X and Wei, Y and Xu, W and Han, Y and Gao, Q and Liu, S and Bi, Y},
title = {Elusive Diagnosis of Recurrent Subcutaneous Emphysema: Nocardia farcinica Infection in an Immunocompetent Female Patient.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {556094},
pmid = {41859064},
issn = {1178-6973},
abstract = {This case report describes an immunocompetent female with recurrent subcutaneous emphysema and refractory soft tissue infections involving multiple non-contiguous sites-bilateral breasts, chest wall, and upper limb-over seven years, consistent with disseminated nocardiosis. Initial presentations mimicked bacterial mastitis, with localized swelling, erythema, crepitus, and elevated inflammatory markers. Despite repeated incision and drainage procedures, antibiotic therapies, and bilateral mastectomies, symptoms recurred persistently. Conventional microbial cultures repeatedly failed to identify a pathogen, while metagenomic next-generation sequencing (mNGS) of a late-stage chest wall lesion ultimately revealed Nocardia farcinica, an opportunistic actinomycete with a known propensity for systemic dissemination even in immunocompetent hosts. The patient's atypical clinical course-marked by multifocal gas-forming soft tissue necrosis, chronic recurrence, and resistance to empiric treatments-underscores the diagnostic challenges posed by fastidious pathogens like Nocardia. Key lessons include the utility of mNGS in identifying culture-elusive organisms, the importance of considering nocardiosis in refractory subcutaneous infections regardless of immune status, and the necessity of prolonged, targeted antimicrobial regimens (eg, sulfonamides) combined with surgical intervention. This case highlights evolving paradigms in managing complex disseminated infections through advanced genomic diagnostics and multidisciplinary approaches.},
}

@article {pmid41859067,
year = {2026},
author = {Jiang, X and Wu, L and Duan, S and Bian, J and Lv, T and Zheng, L and Zhao, Y and Shen, P and He, J and Chen, Y},
title = {Long-Term Antibiotic-Driven Gut Microbiota Disruption Promotes Toxigenic Clostridioides difficile Proliferation: A Four-Year Retrospective Study of a Single ICU Patient.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {562973},
pmid = {41859067},
issn = {1178-6973},
abstract = {OBJECTIVE: This four-year longitudinal study of a single critically ill patient leverages deep temporal profiling to unravel the dynamic interplay between antibiotic pressure, gut microbiota, and Clostridioides difficile (C. difficile) colonization, providing temporal insights unattainable through cross-sectional designs.

METHODS: We performed a retrospective analysis of one critically ill patient (2015-2019). Sixty-four fecal samples were subjected to toxigenic C. difficile culture and metagenomic sequencing. To isolate short-term effects, we implemented a 7-day retrospective window, categorizing each sample based on antibiotic exposure in the preceding week: no antibiotics, monotherapy, or polypharmacy.

RESULTS: Antibiotic exposure significantly reduced microbial diversity and promoted dysbiosis. Crucially, we identified a transitional C. difficile colonization state (Tcd±) that potentially determines progression to toxigenic (Tcd+) or non-toxigenic (Tcd-) outcomes. Analysis using the 7-day window revealed that intensive antibiotic pressure was strongly associated with successional progression towards toxigenic dominance. Conversely, brief antibiotic-free intervals were linked to partial restoration of microbial network complexity and a competitive landscape favoring non-toxigenic strains.

CONCLUSION: This deep temporal profiling of a single case provides novel, hypothesis-generating insights. The identification of a transitional colonization state and the association between short-term antibiotic pressure and colonization outcomes define critical dynamics for future validation. These findings highlight the potential of longitudinal data to inform precise antibiotic stewardship strategies in high-risk, critically ill populations.},
}

@article {pmid41859237,
year = {2026},
author = {Xiao, Y and Zhao, R and Zhao, W and Wang, P and Xiao, X and Peng, X and Jing, H},
title = {Genomics-based insights into the expanded diversity and adaptation strategies of hadal trench anammox bacteria.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag011},
pmid = {41859237},
issn = {2730-6151},
abstract = {Anaerobic ammonium oxidation (anammox) bacteria are an important functional guild in the nitrogen cycle and contribute up to 50% of nitrogen loss in the global ocean. Hadal trenches have been recognized as a hotspot of marine biogeochemical cycles; however, the metabolic traits, ecological adaptations, and potential origins of anammox bacteria in this critical habitat remain largely unexplored. Here, we reconstructed eight anammox metagenome-assembled genomes from sediments of four hadal trenches (Diamantina, Kermadec, Mariana, and Yap), which represent four out of the five distinct anammox bacterial families (i.e. Candidatus Scalinduaceae, Ca. Anammoxibacteraceae, Ca. Subterrananammoxibiaceae, and Ca. Bathyanammoxibiaceae). The dominant trench anammox bacteria, affiliated with Ca. Scalindua, were similar to those found in shallow coastal sediments and oxygen-deficient seawaters. Beyond the core anammox metabolism, the hadal Ca. Scalindua genomes contain genes encoding cyanase and urease, indicating that they can utilize cyanate and urea besides ammonium to thrive in the hadal trenches. Compared to trench-derived Ca. Subterrananammoxibiaceae and Ca. Bathyanammoxibiaceae, ABC-type Fe[3+] transporter and sulfate transporter CysZ could help trench-derived Ca. Anammoxibacteraceae genomes to uptake Fe[3+] and synthesize sulfur-containing amino acids. Molecular clock analysis suggests that the ancestors of the hadal anammox bacterial lineages appeared on Earth 1.46-0.07 billion years ago, significantly earlier than the geological formation of the trenches. The first hadal anammox bacteria were likely derived from shallower sediments and were transported into the trenches via sediment wasting. Overall, our study reveals a remarkable diversity of hadal anammox bacteria and their origin as well as survival strategies in hadal sediments.},
}

@article {pmid41859321,
year = {2026},
author = {Salama, RA and Abdel Kader, RG and Wadid, NA},
title = {Artificial intelligence in combating challenges in antimicrobial resistance: a narrative review.},
journal = {Infection prevention in practice},
volume = {8},
number = {2},
pages = {100522},
pmid = {41859321},
issn = {2590-0889},
abstract = {Antimicrobial resistance (AMR) is a major global health challenge that threatens the effective prevention and treatment of infections. It arises from increasing resistance rates, limited diagnostic capacity, inappropriate antimicrobial use, and a declining pipeline of new antibiotics. These challenges highlight the need for innovative approaches to complement existing AMR control strategies. Artificial intelligence (AI) has emerged as a valuable tool to address the complexity and scale of AMR. This narrative review examines how AI can be more effectively integrated into key components of AMR management. By analysing large clinical and laboratory datasets, AI-based surveillance and predictive models enable near real-time monitoring of resistance patterns and early outbreak detection. AI-powered diagnostic tools, including image analysis and genomic methods, improve rapid pathogen identification and prediction of antimicrobial susceptibility. In clinical practice, AI-driven decision support systems strengthen antimicrobial stewardship by optimizing prescribing and monitoring antibiotic use. In addition, deep learning approaches accelerate antimicrobial drug discovery and repurposing, reducing development timelines. AI also enhances the detection and surveillance of resistance genes through genomic and metagenomic analyses across human, animal, and environmental settings. Despite its potential, AI applications in AMR face challenges related to data quality, bias, interoperability, privacy, and clinician adoption. Therefore, AI should be seen as a tool that supports, rather than replaces, existing AMR strategies. When regulated well and integrated within One Health frameworks, AI can strengthen surveillance, improve treatment decisions, and support evidence-based interventions to curb AMR.},
}

@article {pmid41859442,
year = {2026},
author = {Wang, Y and Zhang, L and Huang, W and Wang, N and Sun, M and Wu, L and Wang, W and Shi, C},
title = {Metagenomic analysis of the community structure and functional potential of Tamarix rhizosphere microbiomes along a soil salinity gradient.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1756020},
pmid = {41859442},
issn = {1664-302X},
abstract = {INTRODUCTION: Soil salinization strongly shapes rhizosphere microbial communities and their functional potential in arid ecosystems. Tamarix is a key halophytic shrub in desert saline-alkali environments, yet how its rhizosphere microbiomes respond to natural salinity gradients remains insufficiently understood. Here, we compared community structure, functional potential, and potential salt-adaptation strategies across a soil salinity gradient.

METHODS: Rhizosphere soils of Tamarix were collected from four sites (S1-S4) in Xinjiang, China spanning increasing salinity. Soil physicochemical properties were measured, followed by shotgun metagenomic sequencing. Taxonomic profiles and functional annotations were generated from metagenomic data and compared among salinity groups.

RESULTS: Salinity was associated with clear shifts in community composition. Bacteria dominated at low-to-moderate salinity, whereas archaeal relative abundance increased at higher salinity, with Euryarchaeota becoming dominant in the high-salinity group. Functional profiling indicated that core metabolic pathways remained prevalent along the gradient, suggesting relative stability in overall metabolic capacity. However, higher salinity was accompanied by enrichment of functions linked to genetic information processing (e.g., translation and replication/repair) and ion transport, while lipid metabolism, cell motility, and signal transduction were reduced.

DISCUSSION: Together, these results support a salinity-driven transition in microbial functional strategy from "growth expansion" toward "homeostasis maintenance." Under high salinity, microbes appear to allocate more resources to maintaining cellular integrity and coping with stress, consistent with the observed enrichment of genetic information processing and repair-related functions. Mechanistically, the increased representation of Na[+]/H[+] antiporter systems and V/A-type ATPases in the very high salinity group suggests that energy-dependent ion homeostasis is a prominent adaptation, helping regulate intracellular ion balance and mitigate salt toxicity. In contrast, pathways for compatible solute synthesis (e.g., betaine and ectoine biosynthesis) were relatively reduced, indicating that osmoprotection may rely less on de novo solute production and more on ion regulation and maintenance processes along this gradient. Overall, the metagenomic evidence clarifies how Tamarix rhizosphere microbiomes restructure taxonomically and functionally with increasing salinity and highlights key candidate mechanisms underpinning salt-stress adaptation. These insights provide a microbial basis for understanding plant-microbe interactions in desert saline-alkali soils and may inform ecological restoration and management in salinized regions.},
}

@article {pmid41859445,
year = {2026},
author = {Huang, Y and Liang, Q and Shen, Y and Chen, J and Xu, W},
title = {Oral microbiome dysbiosis in autism spectrum disorder: the oral-gut-brain axis and future perspectives: a narrative review.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1783810},
pmid = {41859445},
issn = {1664-302X},
abstract = {Autism spectrum disorder (ASD) is a complex neurodevelopmental condition with a steadily increasing global prevalence, yet its etiology remains largely unclear. Emerging evidence suggests that oral microbiome dysbiosis may contribute to the pathogenesis of ASD, potentially through the oral-gut-brain axis, although the exact role and causality remain to be fully established. In this narrative review, we synthesize recent clinical and metagenomic evidence on oral microbiome alterations in ASD and critically evaluate the potential pathways through which these microbial imbalances may impact neurodevelopmental outcomes. We summarize the key host-microbe interactions, including inflammatory signaling, epithelial barrier disruption, and immune-neural crosstalk, while emphasizing that direct causal evidence is still limited. Dysbiosis in individuals with ASD is characterized by altered microbial communities, including increased Streptococcus and decreased Prevotella, which correlate with clinical symptom severity. Moreover, metagenomic profiling has indicated the presence of potential biomarkers in the oral microbiome, which may serve as promising noninvasive diagnostic tools for ASD. While the clinical applications of oral microbiome diagnostics are still in the early stages, we explore the challenges and opportunities for developing these biomarkers for risk stratification. Finally, we outline future research directions that could enhance the understanding of the oral microbiome's role in ASD and facilitate the development of personalized intervention strategies.},
}

@article {pmid41859451,
year = {2026},
author = {Cristofolini, M and Ronsivalle, M and Pramazzoni, M and Zaccarini, G and Pizzamiglio, V and Solieri, L},
title = {Role of microbial interactions in the impaired cultivability of thermophilic lactic acid bacteria in natural whey starter for Parmigiano Reggiano PDO cheese production.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1755652},
pmid = {41859451},
issn = {1664-302X},
abstract = {Natural whey starter (NWS) cultures play a pivotal role in the production of Parmigiano Reggiano (PR) Protected Designation of Origin (PDO) cheese; however, their microbial ecology and functional dynamics remain only partially understood. In particular, Lactobacillus delbrueckii subsp. lactis, a dominant species in type-D NWS communities, exhibits impaired cultivability that limits its isolation and characterization. Consequently, most studies have focused on strain variability within Lactobacillus helveticus, which is predominant in type-H NWS communities. In this study, we evaluated the effects of 14 different medium supplementations on the recovery and maintenance of L. delbrueckii subsp. lactis isolates from two PR NWS samples representatives of type-D and type-H communities. Although most supplementations increased lactobacilli plate counts compared with the control MRS medium, they failed to sustain cell viability during the purification for culture collection establishment. Moreover, these media altered species ratios in favor of L. helveticus, even when L. delbrueckii dominated the community according to metagenomic profiling (type-D NWS). Supplementation of MRS medium with cysteine and formic acid enabled the recovery of viable L. delbrueckii subsp. lactis isolates, accounting for 35% of the strains obtained from type-D NWS. Cross-feeding experiments further revealed that co-culturing L. delbrueckii with the formate-producing Streptococcus thermophilus significantly enhanced milk acidification compared with monocultures, indicating a beneficial metabolic interaction. In contrast, no such improvement was observed in the presence of L. helveticus, likely due to negative interactions with L. delbrueckii subsp. lactis. Accordingly, the impaired cultivability of L. delbrueckii subsp. lactis could thus be partially alleviated either in co-culture with S. thermophilus or under axenic conditions mimicking natural metabolite exchange between these species.},
}

@article {pmid41860433,
year = {2026},
author = {Boers, D and Chapleur, O and Andersson, AF and Schnürer, A},
title = {Comparing the performance of functional versus taxonomic metagenomics for detecting ammonia disturbances in the biogas system.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiag029},
pmid = {41860433},
issn = {1574-6941},
abstract = {Biogas is a renewable energy source with great potential, but its production is frequently hindered by process disturbances, of which a high ammonia concentration is one common cause. It is desirable that such disturbances are found as early as possible; metagenomics data has the potential to improve this detection. This study compares functional and taxonomic aspects of metagenomics data, hypothesising that functional data will perform better for detecting ammonia disturbances. The hypothesis was tested by metagenomic sequencing of samples from three independent studies, which followed lab-scale reactors during ammonia disturbances. The resulting sequences were used to predict genes, which were functionally and taxonomically annotated. The read counts of these features were fitted to disturbance states and ammonia concentrations of reactor samples using regularised regression, which allowed filtering out irrelevant features even with limited sample sizes. Within studies, taxonomic data had similar or better performance in detecting ammonia disturbances and in fitting ammonia concentrations. When applying trained models to other studies however, while performance was generally poor, functional models more often performed better compared to taxonomic models than the other way around. All in all, our hypothesis that functional metagenomics would outperform taxonomic metagenomics only found limited support.},
}

@article {pmid41860453,
year = {2026},
author = {Shen, S and Zhao, S and He, Z and An, X and Dong, J and Wang, L and Ji, W and Li, A},
title = {The Efflux-Two-Component System (TCS)-Virulence Axis Drives Resistance-Virulence Convergence in Aquatic "Superhost Precursors" under Pollution Stress.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c09604},
pmid = {41860453},
issn = {1520-5851},
abstract = {The coexpression of antibiotic resistance and virulence traits in aquatic bacteria represents an emerging ecological and public health threat, yet the mechanisms underlying their coordinated regulation under complex environmental pressures remain unclear. In this work, we integrated metagenomic, proteomic, and metabolomic data sets from surface water samples across the Yangtze River Basin in Jiangsu Province to elucidate the drivers of resistance-virulence convergence under multipollutant stress. Among 392 multidrug-resistant (MDR; resistant to ≥3 antibiotic classes) isolates, approximately 5% were identified as "culturable superhost precursors" exhibiting pandrug-resistant (PDR; resistant to ≥10 antibiotic classes) phenotypes. Multiomics analyses indicated frequent colocalization and synchronous activation of antibiotic resistance genes (ARGs) and virulence factors (VFs) in these environmental reservoirs. Functional assays under subinhibitory antibiotic exposure demonstrated enhanced cytotoxicity and efflux activity, accompanied by the upregulation of tolC and two-component regulators evgA/evgS. Together, these results characterize a putative redox-coupled efflux-two-component system (TCS)-virulence functional axis that synchronizes adaptive gene expression under pollution stress. Crucially, our findings challenge traditional antimicrobial resistance (AMR) surveillance approaches, which rely primarily on static gene abundance metrics, by demonstrating that the dynamic regulatory activation of this axis provides a more sensitive indicator of environmental health risks. Furthermore, tolC and evgA were identified as potential transcript-level biomarkers, providing a proof of concept for environmental antimicrobial resistance early warning tools within the One Health framework.},
}

@article {pmid41860568,
year = {2026},
author = {Zhang, Y and Wu, Y and Li, X and Ren, T and Zhang, H and Chen, J},
title = {Klebsiella Enrichment Is Associated with Disease Severity in Ulcerative Colitis.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxag079},
pmid = {41860568},
issn = {1365-2672},
abstract = {BACKGROUND AND OBJECTIVE: Ulcerative colitis (UC), a chronic inflammatory bowel disease. This study uniquely undertook a parallel, severity-stratified comparison of both fecal and mucosal microbiota and metabolites in UC patients. Our objective was to identify niche-specific (fecal vs. mucosal) and severity-associated microbial and metabolic signatures, clarifying its potential clinical utility.

METHODS: A prospective cohort study (ChiCTR2300071816) enrolled 83 UC patients (≥18 years) from First Affiliated Hospital of Nanjing Medical University and Northern Jiangsu People's Hospital (Jan 2022-Dec 2024) and 30 healthy controls. Clinical data, stool, and rectal mucosal samples were collected. Metagenomic sequencing and metabolomics were performed. Disease severity was stratified by modified Mayo score to analyze microbiota diversity, differential genera, metabolites, and enriched metabolic pathways.

RESULTS: Fecal microbiota α-diversity was significantly lower in UC vs. controls (Shannon index 4.15 vs. 5.44, p=0.005); mucosal diversity showed no difference (p=0.63). Beta diversity did not differ. Severe UC exhibited a non-significant decrease in α-diversity (fecal: 3.99 vs. 4.37, p=0.14; mucosal: 3.40 vs. 3.72, p=0.92), significantly higher fecal/mucosal Klebsiella abundance, and lower Erysipelatoclostridium and Blautia abundance vs. mild-to-moderate UC. Metabolomics identified 363 fecal differential metabolites (e.g., allopurinol, histidine), enriching tyrosine and alanine/aspartate/glutamate metabolism pathways. Mucosal analysis revealed 127 differential metabolites (e.g., quinic acid, sphingosine), implicating sphingolipid metabolism and lysine synthesis.

CONCLUSION: UC demonstrates gut dysbiosis and metabolic disruption correlating with severity. Elevated Klebsiella abundance suggests a pathogenic role in progression. Distinct fecal and mucosal metabolic pathway alterations provide novel insights for disease classification and therapeutic targeting.},
}

@article {pmid41860897,
year = {2026},
author = {Olaleye, M and O'Ferrall, AM and Goodman, RN and Kabila, DW and Peters, M and Falq, G and Samuel, J and Doyle, D and Gomez, D and Oloruntuyi, G and Isah, S and Adetunji, AS and Farley, E and Evans, NJ and Sherlock, M and Roberts, AP and Amirtharajah, M and Ainsworth, S},
title = {Shotgun metagenomic analysis of the oral microbiomes of children with noma.},
journal = {PLoS neglected tropical diseases},
volume = {20},
number = {3},
pages = {e0014118},
doi = {10.1371/journal.pntd.0014118},
pmid = {41860897},
issn = {1935-2735},
abstract = {Noma is a rapidly progressive orofacial gangrene that predominantly affects children living in extreme poverty. Despite its documentation since antiquity and its designation as a World Health Organisation Neglected Tropical Disease in 2023, the microbiological cause of noma remains poorly understood, with no specific organisms confidently identified as definitive aetiological agents. Here, we present the first deep shotgun metagenomic profiling of oral saliva microbiomes from 19 Nigerian children with acute noma. Our analyses of this preliminary study reveal marked microbial dysbiosis in noma microbiomes, with machine learning and multivariate statistical analyses indicating significant enrichment of Treponema, Porphyromonas, and Bacteroides, alongside depletion of Streptococcus and Rothia, as key microbial signatures of noma disease. From the dataset we recovered 40 high-quality Treponema metagenome assembled genomes (MAGs) spanning 19 species, 14 of which were novel. Notably, a novel species designated Treponema sp. A was detected in 15 of the 19 noma participants and was entirely absent from an internationally representative set of healthy saliva metagenomes. Re-analysis of previously published 16S rRNA datasets from children with noma in Niger also revealed Treponema sp. A to be highly prevalent in noma cases but extremely rare in controls. While these findings highlight Treponema, particularly Treponema sp. A, as an organism of interest and a potential contributor to noma pathogenesis, further comprehensive studies will be required to confirm this association and to clarify whether it reflects a causal role and/or is a genuine marker of noma dysbiosis. Additionally, analysis of antimicrobial resistance determinants detected in noma metagenomes revealed concerning levels of resistance to antibiotics commonly used in noma treatment, particularly β-lactams and metronidazole, especially among Prevotella spp. These findings provide the first high-resolution microbial framework for noma and offer a foundation for future research into its pathogenesis and the development of novel diagnostics, therapeutics, and preventive strategies in endemic settings.},
}

@article {pmid41861238,
year = {2026},
author = {Yao, ML and Dai, Y and Zhang, W},
title = {Natural Products from the Oral Microbiome.},
journal = {Annual review of biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-biochem-051024-050248},
pmid = {41861238},
issn = {1545-4509},
abstract = {The human oral microbiome is a densely populated and chemically dynamic ecosystem where interspecies competition and cooperation shape community structure and influence host health. Metagenomic analyses reveal the immense biosynthetic potential of oral microbes to encode biosynthetic gene clusters (BGCs) and produce natural products. These metabolites are increasingly recognized as key mediators of microbial interactions, with many oral BGCs linked to health and disease. This review focuses on natural products in the oral microbiome derived from nonribosomal peptide synthetases and polyketide synthases, which are notable for their large size, modular machinery, and ecological relevance. We review the biosynthetic origins and bioactivities of these specialized metabolites in oral bacteria and discuss their biosynthetic regulation within the broader microbial community. Continued investment in whole-genome sequencing, integrative omics, and natural product discovery pipelines is essential for elucidating the microbial biochemical drivers of disease and advancing strategies to promote oral health.},
}

@article {pmid41861543,
year = {2026},
author = {Mohapatra, RK and Choi, Y},
title = {Exploring multi-omics approaches in anammox-based wastewater treatment processes: A review of recent applications and technological advances.},
journal = {Journal of environmental management},
volume = {404},
number = {},
pages = {129342},
doi = {10.1016/j.jenvman.2026.129342},
pmid = {41861543},
issn = {1095-8630},
abstract = {Anaerobic ammonium oxidation (anammox) has arisen as a sustainable and energy-efficient approach for nitrogen removal in wastewater treatment. Recently, the utilization of multi-omics approaches, mainly metagenomics, metatranscriptomics, metaproteomics, and metabolomics has risen to reveal the complexity and functionality of anammox-based systems. These integrated approaches offer a comprehensive investigation of microbial community structure, gene expression, protein function, and metabolite dynamics across diverse operating contexts. Progress in high-throughput sequencing, mass spectrometry, and bioinformatics has facilitated the discovery of novel anammox bacteria, functional genes, and metabolic pathways, resulting in vital processes such as nitrogen cycling, microbial interactions, and system resilience. Metagenomics has shown the taxonomic and functional diversity within anammox consortia, whereas metatranscriptomics and metaproteomics have elucidated active metabolic pathways and functional responses to environmental alterations. Metabolomics has furnished direct evidence of metabolic states and biomarkers for enhancing reactor health and efficacy. Researchers have begun to elucidate the intricate physiological and biochemical mechanisms that govern the stability, recovery, and effectiveness of the anammox process through the integration of multi-omics datasets. This review explores recent technological breakthroughs and cutting-edge applications of multi-omics methods in anammox-based wastewater treatment. The article summarizes the principal research findings presented by numerous researchers, providing significant insights for the strategic design and management of robust and efficient water treatment systems aimed at future environmental sustainability.},
}

@article {pmid41861844,
year = {2026},
author = {Tam, KK and Suster, CJE and Fong, W and Golubchik, T and Sivalingam, V and Jeoffreys, N and Tay, E and Ko, D and Wehrhahn, MC and Ginn, AN and Robson, J and Gardner, I and Papanicolas, LE and Kennedy, K and Graham, M and Tran, T and Speers, D and Cooley, L and Baird, RW and Meumann, EM and Harbidge, J and Campbell, S and Basile, K and Chen, SC and Sintchenko, V and Kok, J and Rockett, RJ},
title = {Genomic Surveillance Reveals Emergence and Spread of Macrolide-Resistant Mycoplasma pneumoniae in Australia During the 2023-2024 Epidemic.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiag163},
pmid = {41861844},
issn = {1537-6613},
abstract = {BACKGROUND: The resurgence of Mycoplasma pneumoniae (MP), first reported in China in 2023 was attributed to waning post-pandemic immunity with notable increases in macrolide-resistant MP (MRMP) (>80%). In Australia, infections peaked in early 2024, particularly among children under 15. While MRMP remains low in Europe, North America, and Australia (<5%), limited routine testing and surveillance restricts understanding of resistance dynamics. As macrolides are first-line therapy in many health settings, MRMP surveillance is essential for guiding empirical treatment and stewardship.

METHODS: We applied a novel capture-based targeted metagenomic sequencing (tNGS) to PCR-positive MP specimens (n=356) from across Australia. This approach enabled whole-genome recovery and MRMP detection directly from clinical specimens, without culture. MRMP detections were benchmarked against RT-PCR and clinical data were analysed to assess associations between resistance and healthcare utilisation.

RESULTS: This is the first genomics-informed national study of MP in Australia. We recovered 124 high-quality genomes, revealing a genetically diverse population with co-circulation of P1 Type 1 (69%) and Type 2 (31%). MRMP was identified in 13% of genomes, all belonging to clades prior to 2024 had only been reported in Asia (ST3 and ST14). MRMP cases were geographically widespread, suggesting importation and local transmission. Unlike reports from China, macrolide-susceptible clades (ST3, ST7, ST17 and ST20) predominated (87%) and were associated to significant lower healthcare utilisation compared to MRMP cases.

CONCLUSION: Our findings demonstrate the utility of tNGS for genomic epidemiology and highlight the need for MRMP surveillance. Although macrolides remain effective in Australia, emerging MRMP strains require close monitoring to inform treatment guidelines and antimicrobial stewardship.},
}

@article {pmid41861946,
year = {2026},
author = {Wang, ST and Li, L and Yang, Q and Zhang, GF},
title = {Artificial reef age reshapes benthic microbial communities and modulates the genetic potential for nitrogen and sulfur cycling.},
journal = {Environmental research},
volume = {},
number = {},
pages = {124314},
doi = {10.1016/j.envres.2026.124314},
pmid = {41861946},
issn = {1096-0953},
abstract = {Artificial reefs (ARs) are widely used to restore coastal ecosystems; however, the impact of reef age on microbial communities and their biogeochemical functions remains unknown. This study integrated metagenomic sequencing with physicochemical analysis to examine successional changes in benthic nitrogen and sulfur cycling along a chronosequence spanning from non-artificial reefs (0 years) to 14-year-old ARs in the coastal waters of the Bohai Sea, China. Our analysis revealed a systematic, time-dependent reorganization of the benthic microbiome, characterized by significant enrichment of ammonia-oxidizing archaea (Nitrososphaerota) and bacteria (Nitrospirota) in reefs older than 6 years. Conversely, taxa involved in coupled nitrate reduction and sulfur oxidation (Sulfurovum) declined significantly. Functionally, this led to a shift in genetic potential: the abundance of nitrification genes (amoB and amoC) increased, while genes associated with dissimilatory nitrate reduction (nirB and nrfA), denitrification (nosZ and napB), thiosulfate reduction (phsC and ttrB), and sulfur oxidation (sqr and sox) decreased. Genome-resolved analysis further demonstrated that these functional shifts were driven by the proliferation of nitrifiers and concurrent decline of versatile bacterial lineages. Importantly, this genomic shift was corroborated by geochemical observations of decreased ammonium and increased nitrate concentrations in both bottom seawater and sediments of ARs compared to non-artificial reefs. These results indicate that reef age reshapes benthic microbial communities and functions, favoring aerobic nitrification over anaerobic or microaerophilic nitrate reduction and sulfur metabolism. This study provides a scientific basis for AR adaptive management, underscoring the necessity of integrating microbial functional metrics into the long-term impact assessment of marine infrastructures.},
}

@article {pmid41861947,
year = {2026},
author = {Guo, J and Liang, X and Lei, W and Zhang, Z and Shen, Y and Han, S and Wang, H and Qian, Y and Nie, B and Wang, L and He, S},
title = {Contrasting microbial sources of soil N2O emissions revealed by metagenomics in natural and agricultural soils along the Yellow River.},
journal = {Environmental research},
volume = {},
number = {},
pages = {124311},
doi = {10.1016/j.envres.2026.124311},
pmid = {41861947},
issn = {1096-0953},
abstract = {Soil nitrous oxide (N2O) emission is a potent greenhouse gas source, yet the dominant production pathway (nitrification vs. denitrification) and its microbial mechanisms in regions like the Yellow River Basin remain unclear, particularly under different land uses. In this study, we integrated qPCR quantification, metagenomic sequencing and binning, as well as microbial network analysis to investigate the dominant microbial processes and regulatory mechanisms underlying potential soil N2O production. Results showed that denitrification dominated regional potential N2O production (N2ODen, 56.71±102.94 nmol/(kg·h)), significantly exceeding nitrification (N2ONif, 4.34±4.27 nmol/(kg·h)). On average, both N2ODen (115.34±143.60 nmol/(kg·h)) and N2ONif (5.29±4.42 nmol/(kg·h)) in natural soils were higher than in cultivated soils (28.56±62.52 and 3.88±4.22 nmol/(kg·h), respectively). Mechanistically, natural soils were enriched with ammonia-oxidizing archaea (AOA) and incomplete denitrifiers (e.g., Acidobacteriota), which, along with a higher norB/nosZ and more stable co-occurrence network, favored N2O accumulation. In cultivated soils, microbial community stability was reduced; however, they were enriched with strong N2O reducers (e.g., Pseudomonadota, Gemmatimonadota), resulting in lower potential N2O production. Altitude, total nitrogen, and pH collectively influenced the potential N2O emission patterns by regulating functional genes and microbial metabolism. This study provides a scientific basis for regional greenhouse gas mitigation from a microbial ecology perspective.},
}

@article {pmid41418935,
year = {2026},
author = {Chen, S and Li, W and Fan, L and Xu, C and Liu, S and Li, H and Liu, P and Zhu, W and Wu, X and Qin, P and Li, J and Ma, X and Wei, Y},
title = {Metatranscriptomics profiling reveals rodent- and shrew-borne viral diversity and evolutionary relationships in Guangzhou, China.},
journal = {Virologica Sinica},
volume = {41},
number = {1},
pages = {35-47},
doi = {10.1016/j.virs.2025.12.009},
pmid = {41418935},
issn = {1995-820X},
mesh = {Animals ; China/epidemiology ; *Shrews/virology ; *Rodentia/virology ; *Viruses/genetics/classification/isolation & purification ; Phylogeny ; *Virome ; Rats ; Genetic Variation ; Evolution, Molecular ; Metagenomics ; Gene Expression Profiling ; },
abstract = {Emerging zoonotic infectious diseases, predominantly caused by viruses, pose increasing public health threats globally. Rodents and shrews are natural hosts for a variety of zoonotic viruses. Guangzhou is one of China's most densely populated cities and experiences frequent international and domestic population movements, making it a hotspot for infectious diseases. This study reports the metatranscriptomics virome of 208 rodents and shrews collected between June 2023 and December 2024 from four main urban areas (Tianhe, Baiyun, Liwan, Yuexiu) and five non-main urban areas (Zengcheng, Huadu, Conghua, Panyu, Nansha) in Guangzhou. Individual libraries were constructed from mixed tissue samples (liver, spleen, lung, and kidney) of each animal. Metatranscriptomics sequencing revealed diverse viral communities, identifying 24 viral strains across eight mammalian-associated viral families. Notably, we identified 17 known viruses and seven potentially novel viruses, including Seoul virus (5.2% prevalence in Rattus norvegicus from Panyu), Wenzhou mammarenavirus (13.2% in Rattus norvegicus from Conghua and Huadu), Jeilongvirus (29.4% in Rattus andamanensis from Panyu), and a divergent lineage of arteriviruses that may represent a new genus (maximum positivity rates of 2.9% in Rattus norvegicus and 5.7% in Rattus tanezumi). Phylogenetic analysis elucidated evolutionary relationships within key families such as Hantaviridae, Arenaviridae, Flaviviridae, and Parvoviridae, revealing distinct viral carriage patterns in Guangzhou City that are shaped by host species and geographical location. This is the first macro-level study of rodent and shrew viromes in Guangzhou and provides a scientific basis for strengthening surveillance of mammalian-associated viruses and preventing emerging zoonotic infectious diseases in the region.},
}

Animals
China/epidemiology
*Shrews/virology
*Rodentia/virology
*Viruses/genetics/classification/isolation & purification
Phylogeny
*Virome
Rats
Genetic Variation
Evolution, Molecular
Metagenomics
Gene Expression Profiling

@article {pmid41850962,
year = {2026},
author = {Zhao, Y and Zheng, J and Liu, Q},
title = {The diversity of emerging tick-borne viruses globally.},
journal = {Trends in parasitology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.pt.2026.03.001},
pmid = {41850962},
issn = {1471-5007},
abstract = {Zhang et al. provide the first global synthesis of 230 emerging tick-borne viruses, introducing a genomic model that predicts zoonotic risk. Their approach identifies 25 very-high-risk viruses and clinically validates three novel human pathogens, shifting the paradigm from reactive discovery to proactive risk assessment for global health security.},
}

@article {pmid41851124,
year = {2026},
author = {Luzmore, A and Grauer, J and Barber, D and Lau, P and Jorgensen, G and Jain, S and Perron, GG},
title = {Seasonal frost improves probiotic and nutrient availability in fermented vegetables.},
journal = {NPJ science of food},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41538-026-00776-w},
pmid = {41851124},
issn = {2396-8370},
abstract = {Climate-driven shifts in seasonal frost patterns raise important questions about their impact on food quality and resilience. Here, we show that a single 12-h frost event at harvest can enhance both the microbial and nutritional properties of fermented cabbage and carrots, two cold-tolerant crops widely grown in the U.S. Northeast. Using microbial amplicon and metagenomic sequencing, we found that frost exposure led to subtle but consistent changes in microbial composition, including greater abundance of cold-adapted taxa such as Leuconostoc and Debaryomyces. These changes corresponded to increased abundance of genes involved in vitamin biosynthesis, particularly menaquinone (K2), cobalamin (B12), and threonine pathways. Nutritional assays confirmed higher concentrations of vitamins A and E in frost-conditioned carrot ferments and increased vitamin K1 in cabbage. Our findings suggest that exposure to seasonal frost can enhance the health-promoting and sensory qualities of fermented vegetables, offering a novel strategy for value-added, climate-resilient food production in temperate regions.},
}

@article {pmid41851530,
year = {2026},
author = {Cohen, Y and Jansen, T and Onwuka, S and Elinav, E},
title = {Advances and opportunities in measuring dietary intake: from omics to AI.},
journal = {Nature metabolism},
volume = {},
number = {},
pages = {},
pmid = {41851530},
issn = {2522-5812},
abstract = {Accurate measurement of dietary intake remains a cornerstone challenge in optimizing the efficacy of nutritional interventions in human disease. Traditional self-reporting methods, although scalable and widely used, are prone to major bias and measurement error, thereby limiting their precision and clinical utility. In this Review, we highlight recent advances in technology-assisted food intake measurement, including image-based logging, wearable sensors and artificial intelligence (AI)-based dietary estimation, which may reduce reliance on recall and improve intake estimation. We review the emergence of non-invasive biological methodologies, such as metagenome-informed metaproteomics, in accurately enabling objective measurement of food intake and nutrient digestion and absorption in molecular resolution. We explore the possible interactions and effects of the gut microbiome in modulating such person-specific digestive and absorptive patterns and discuss challenges and prospects in the convergence of omics-based, measurement-based and AI-based dietary assessment tools into precision nutrition, in fulfilling its immense potential towards optimization of patient care.},
}

@article {pmid41851880,
year = {2026},
author = {Sharma, AA and Martinou, AF and Cadar, D and Omirou, M and Neira, M and Christophides, GK},
title = {Integrated vector and arbovirus surveillance in Cyprus: first reports of Usutu virus and Culex pipiens bioform diversity highlight potential for zoonotic arbovirus transmission.},
journal = {Parasites & vectors},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13071-026-07350-z},
pmid = {41851880},
issn = {1756-3305},
support = {856612//Horizon 2020/ ; },
abstract = {BACKGROUND: Anthropogenic pressures, including urbanisation, globalisation and climate change, have facilitated an increased risk for emergence or re-emergence of mosquito-borne diseases into regions such as the Eastern Mediterranean and Middle East. Cyprus is a major stop-over site for migratory birds and has previously experienced outbreaks of West Nile virus (WNV). The island has native mosquito vector populations; however, it has also seen the recent establishment of invasive Aedes albopictus and Ae. aegypti mosquitoes. Given the dynamic climatic conditions and the shifting ecological and epidemiological landscapes in the region, the need for routine vector and pathogen surveillance has never been more critical.

METHODS: Herein, we present the results from localised adult mosquito surveillance that were conducted in two cities of Cyprus between 2019 and 2022. Mosquito taxa were identified through morphological analysis, and molecular techniques were used to further characterise the Culex pipiens bioforms. Engorged mosquito midguts were analysed to determine host blood meals. Metagenomic next-generation sequencing was employed to screen mosquito pools for arboviruses.

RESULTS: Our results provide the first report of Usutu virus in Cx. pipiens mosquitoes in Cyprus. Blood meal analysis identified multiple vertebrate hosts, including Cetti's warbler, a bird species previously reported to be seropositive for WNV on the island. Additionally, we report the presence of both Cx. pipiens pipiens and Cx. pipiens molestus, an ornithophilic and a mammophilic bioform, respectively, as well as their hybrids.

CONCLUSIONS: Our findings highlight the urgent need for enhanced mosquito surveillance strategies where mosquito populations will be regularly screened for pathogens to mitigate emerging risks of arbovirus transmission in Cyprus.},
}

@article {pmid41851941,
year = {2026},
author = {Shrestha, E and Katuwal, N and Sitaula, RK and Gurung, H and Shrestha, A and Karki, P and Shrestha, R},
title = {Identification of the Causative Pathogen in the 2023 Conjunctivitis Outbreak of Nepal Using Unbiased Metagenomic Next Generation Sequencing.},
journal = {Journal of Nepal Health Research Council},
volume = {23},
number = {3},
pages = {527-532},
doi = {10.33314/jnhrc.v23i03.4749},
pmid = {41851941},
issn = {1999-6217},
mesh = {Humans ; Nepal/epidemiology ; *Disease Outbreaks ; Female ; *High-Throughput Nucleotide Sequencing ; Male ; Child ; *Metagenomics/methods ; *Conjunctivitis/epidemiology/virology ; Adult ; Child, Preschool ; *Enterovirus C, Human/isolation & purification/genetics ; Adolescent ; Young Adult ; Middle Aged ; Infant ; },
abstract = {BACKGROUND: In mid-2023, Nepal experienced a significant outbreak of conjunctivitis, affecting over 60% of outpatients in eye hospitals and prompting school closures. The outbreak, peaking in August, predominantly impacted children and individuals with compromised immunity. Clinical manifestations included sudden-onset redness, foreign body sensation, watery discharge, and occasional lid swelling. Most cases exhibited acute haemorrhagic conjunctivitis, with management involving ocular lubricants, personal hygiene, and topical antibiotics. This case series from Himalaya Eye Hospital in Pokhara details the genomic epidemiology and clinical characteristics of conjunctivitis cases during the outbreak.

METHODS: To understand the causative agents, conjunctival swabs from patients were subjected to unbiased metagenomic next-generation sequencing (mNGS) in Illumina iSeq100 at Dhulikhel Hospital Kathmandu University Hospital Results: This case series revealed the presence of Enterovirus C (coxsackievirus strain A24) as the major pathogen responsible for the outbreak.

CONCLUSIONS: This case series contributes valuable insights into the genomic diversity of conjunctivitis-associated viruses, highlighting the potential of mNGS in enhancing diagnostic capabilities and guiding public health responses.},
}

Humans
Nepal/epidemiology
*Disease Outbreaks
Female
*High-Throughput Nucleotide Sequencing
Male
Child
*Metagenomics/methods
*Conjunctivitis/epidemiology/virology
Adult
Child, Preschool
*Enterovirus C, Human/isolation & purification/genetics
Adolescent
Young Adult
Middle Aged
Infant

@article {pmid41852102,
year = {2026},
author = {Qu, X and Liao, Y and Muthuri, CW and Winowiecki, LA and Zi, H and Zhang, Y and Li, X},
title = {Soil Functionality Undermined by Symbiotic Fungal Decline Following Forest Conversion.},
journal = {Environmental microbiology},
volume = {28},
number = {3},
pages = {e70268},
doi = {10.1111/1462-2920.70268},
pmid = {41852102},
issn = {1462-2920},
support = {W2412011//National Natural Science Foundation of China/ ; 32430069//National Natural Science Foundation of China/ ; jxsq2023102214//Double Thousand Plan of Jiangxi Province/ ; },
mesh = {*Soil Microbiology ; *Forests ; *Symbiosis ; *Soil/chemistry ; *Fungi/genetics/classification/physiology ; China ; Phosphorus/metabolism ; Carbon/metabolism ; Nitrogen/metabolism ; Biodiversity ; Bacteria/genetics/classification ; Ecosystem ; },
abstract = {The conversion of native forests to other terrestrial ecosystems represents a profound form of land-use change, threatening aboveground biodiversity and biomass. However, its impact on soil ecological functions remains uncertain, particularly the regulatory role of soil microbial communities. To address this, we evaluated soil functionality related to carbon, nitrogen and phosphorus cycling by measuring nine enzyme activities in soils from native forests, plantations and croplands in subtropical China. Our results demonstrated a significant decline in soil functionality following the conversion of native forests, with the most pronounced reductions observed in croplands. This decline in soil functionality was strongly associated with a decrease in fungal richness but was independent of bacterial alpha-diversity. Specifically, the reduction in the abundance of symbiotic fungi, including key taxa such as Lactifluus and Tomentella, was identified as a primary driver of the functional impairment. Metagenomic analyses further confirmed that the loss of microbial functional genes was linked to the observed decline in soil functionality. Our findings underscore the critical role of key fungal taxa in maintaining soil processes and highlight the importance of their conservation and restoration to ensure ecosystem functionality in managed landscapes.},
}

*Soil Microbiology
*Forests
*Symbiosis
*Soil/chemistry
*Fungi/genetics/classification/physiology
China
Phosphorus/metabolism
Carbon/metabolism
Nitrogen/metabolism
Biodiversity
Bacteria/genetics/classification
Ecosystem

@article {pmid41852114,
year = {2026},
author = {Kaneko, Y and Hino, T and Taminishi, S and Matoba, Y and Motooka, D and Hoshino, A and Matoba, S},
title = {Inhibition of N-Terminal Acetyltransferase C Mitigates Endoplasmic Reticulum Stress-Mediated Muscle Atrophy in Cancer Cachexia.},
journal = {Journal of cachexia, sarcopenia and muscle},
volume = {17},
number = {2},
pages = {e70249},
doi = {10.1002/jcsm.70249},
pmid = {41852114},
issn = {2190-6009},
support = {22H03071//JSPS Grant-in-Aid Scientific Research/ ; 25K02651//JSPS Grant-in-Aid Scientific Research/ ; //Nakatomi Foundation/ ; },
mesh = {Animals ; *Cachexia/etiology/pathology ; *Endoplasmic Reticulum Stress ; *Muscular Atrophy/etiology/pathology/metabolism ; Mice ; Male ; *Neoplasms/complications ; Humans ; Unfolded Protein Response ; },
abstract = {BACKGROUND: Cancer cachexia is a complex syndrome marked by weight loss and muscle wasting, significantly impacting patient quality of life and survival. Mechanistically, it is characterized by suppressed protein synthesis and enhanced muscle catabolism, with the role of endoplasmic reticulum (ER) stress and unfolded protein response (UPR) becoming increasingly evident. This study aimed to explore ER stress-tolerant factors in muscle wasting and evaluate their potential to prevent muscle loss in cancer cachexia.

METHODS: A genome-wide CRISPR screening was conducted in the context of ER stress-mediated growth inhibition of C2C12 myoblasts. The candidate genes resistant to ER stress were further evaluated in C2C12 myotubes treated with conditioned medium of Lewis lung adenocarcinoma (LLC) cells. Twelve-week-old male mice were administered LLC cells and shRNA against Naa35 via adeno-associated virus. Four weeks later, tibialis anterior (TA) muscles were analysed for muscle mass, grip strength and molecular changes with quantitative polymerase chain reaction, western blotting and histological analysis.

RESULTS: CRISPR screening identified Naa35, Naa38 and Naa30, all three components of N-terminal acetyltransferase C, as key molecules for resistance to ER stress. The atrophic muscles of mice bearing LLC demonstrated an elevation of UPR, as well as 1.64-fold upregulation of Naa35 protein (p = 0.0072). Among the three branches of the UPR, an ATF6 inhibitor, AEBSF, abolished upregulation of Naa35, Naa38 and Naa30, and an ATF6 activator, AA147, induced Naa35 expression in a dose-dependent manner (p < 0.001). In cells treated with LLC conditioned medium, Naa35 knockdown reduced the amount of cathepsin K (CTSK) protein, which subsequently resulted in the CTSK-mediated proteolysis of insulin receptor substrate 1. In LLC-bearing mice, Naa35 knockdown led to a 65.4% reduction in CTSK protein expression (p < 0.001) and preservation of the phosphorylation levels of protein kinase B (p < 0.0324) and anabolic-related S6 kinase (p < 0.0375). Concurrently, the expression of catabolism-related genes was repressed (MuRF1, p < 0.0015; MAFbx1, p < 0.0265). These alterations were associated with the restoration of TA muscle mass (2.52 ± 0.19 vs. 3.72 ± 0.45 mg/g, p = 0.0004), fibre area (1741 ± 992 vs. 2099 ± 1264 mm[2], p < 0.0001), grip strength in all four limbs (0.0328 ± 0.0076 vs. 0.0506 ± 0.0130 N/g, p = 0.0295) and wire mesh hanging time (496 ± 331 vs. 1038 ± 370 s, p = 0.0406).

CONCLUSIONS: Inhibition of N-terminal acetyltransferase C prevents ER stress-induced muscle wasting via the downregulation of CTSK and subsequent activation of the anabolic pathway. This suggests that N-terminal acetyltransferase C is a potential therapeutic target for combating muscle wasting in cancer cachexia.},
}

Animals
*Cachexia/etiology/pathology
*Endoplasmic Reticulum Stress
*Muscular Atrophy/etiology/pathology/metabolism
Mice
Male
*Neoplasms/complications
Humans
Unfolded Protein Response

@article {pmid41852383,
year = {2025},
author = {Urrutia-Angulo, L and Lavín, JL and Oporto, B and Aduriz, G and Hurtado, A and Ocejo, M},
title = {Resistome and microbiome profiling of bovine milk following antimicrobial dry cow therapy: insights from short- and long-read metagenomic sequencing.},
journal = {Frontiers in microbiomes},
volume = {4},
number = {},
pages = {1672438},
pmid = {41852383},
issn = {2813-4338},
abstract = {Selective antimicrobial dry cow therapy (DCT) is implemented as part of mastitis control programs, particularly in dairy cows with recent clinical episodes or elevated somatic cell counts. In this study, we investigated the effects of the use of antimicrobials at drying-off on the milk microbiota and resistome by comparing treated (T, n=18) and untreated (NT, n=13) cows. Milk samples from all animals were analyzed using short-read Illumina shotgun sequencing and a subset of 10 samples were also subjected to long-read Oxford Nanopore Technologies (ONT) sequencing. No significant differences in microbial composition or diversity were observed between treated and untreated groups with either technique, indicating that antimicrobial DCT may not induce long-term shifts in the milk microbiota. However, cows receiving antibiotic treatment showed a higher diversity and abundance of genetic determinants of resistance (GDRs) in their milk resistome. Findings from the two sequencing platforms revealed limited concordance in antimicrobial resistance gene content, highlighting that sequencing platform and bioinformatic pipeline choices substantially influence resistome profiling outcomes. Furthermore, the high proportion of host DNA limited sequencing depth and sensitivity, underscoring the need for improved host DNA depletion or targeted enrichment strategies. This study provides insights into the biological and methodological challenges of milk resistome characterization, particularly in low-biomass, host-DNA-rich samples and demonstrates the lack of standardized analytical approaches in resistome studies. Overall, our findings support the prudent use of antibiotics and highlight the need for further longitudinal studies to clarify the temporal dynamics of antimicrobial DCT effects on the milk resistome and microbiota.},
}

@article {pmid41852393,
year = {2025},
author = {Wadop, YN and Muhammad, J and Bernal, R and Satizabal, CL and Beiser, A and Vasan, RS and Xavier, R and Kautz, T and Seshadri, S and Himali, JJ and Fongang, B},
title = {Adherence to Life's Essential 8 enhances gut microbiota diversity and cognitive performance.},
journal = {Frontiers in microbiomes},
volume = {4},
number = {},
pages = {1592023},
pmid = {41852393},
issn = {2813-4338},
abstract = {INTRODUCTION: Emerging evidence suggests a complex interplay among cardiovascular health, gut microbiome composition, and cognitive function. Life's Essential 8 (LE8), developed by the American Heart Association, includes vital metrics of cardiovascular health, such as diet, physical activity, nicotine exposure, sleep health, body mass index (BMI), blood glucose, blood lipids, and blood pressure.

METHODS: In this study, we analyzed data from 781 participants in the Framingham Heart Study (FHS) to explore the relationship between LE8 adherence, gut microbiota, and cognitive performance. Multivariable linear regression models and mediation analysis were used to investigate this relationship.

RESULTS: Participants with greater adherence to LE8 demonstrated significantly increased gut microbial diversity (α-diversity: Chao1, p = 0.0014; Shannon, p = 0.0071) and distinct microbial compositions (β-diversity: PERMANOVA p = 1e-4). Higher adherence to LE8 was related to an increased abundance of genera Barnesiella and Ruminococcus, while a reduced abundance of Clostridium was associated with higher LE8 adherence. Greater gut microbial diversity (α-diversity: Chao1, p = 0.0012; Shannon, p = 0.0066), and beneficial genera like Oscillospira correlated with better global cognitive scores (GCS). Taxonomic overlap analyses revealed microbial taxa that simultaneously influence both LE8 adherence and cognitive outcomes. Mediation analyses indicated that specific taxa, including Barnesiella and Lentisphaerae, mediated the link between LE8 adherence and cognitive performance. These taxa may serve as key modulators in the gut-brain axis, connecting cardiovascular and brain health. Conversely, higher Clostridium abundance was associated with poorer cognitive performance.

DISCUSSION: This study highlights the significance of comprehensive cardiovascular health metrics in shaping gut microbiota and enhancing cognitive resilience. Our findings underscore the therapeutic potential of targeting gut microbiota to mitigate cognitive decline, warranting further exploration through longitudinal and metagenomic studies.},
}

@article {pmid41852395,
year = {2025},
author = {Ortega-Reyes, D and Takeuchi, T and Ogata, Y and Iwami, T and Suda, W and Kubota, T and Kubota, N and Kadowaki, T and Tomizuka, K and Ohno, H and Horikoshi, M and Terao, C},
title = {Interplay between host genetics and gut microbiome composition in the Japanese population.},
journal = {Frontiers in microbiomes},
volume = {4},
number = {},
pages = {1635907},
pmid = {41852395},
issn = {2813-4338},
abstract = {BACKGROUND: Host genetics significantly influence the composition of the gut microbiota, but this relationship remains poorly understood, especially in non-European populations. This study aims to investigate the associations between host genetic variation and gut microbiome composition in the Japanese population and to assess methodological factors affecting reproducibility in microbiome research.

METHODS: We performed whole-genome sequencing on 306 Japanese individuals and obtained their gut microbiome profiles using shotgun metagenomic sequencing. Genome-wide association studies (GWAS) were conducted to identify associations between host genetic variants and the relative abundance of microbial taxa and bacterial pathways. Phenome-wide association studies (PheWAS) were performed on predicted high-impact variants. Additionally, we compared methodological approaches to assess their impact on microbiome composition and reproducibility.

RESULTS: We identified significant associations between host genetic variants and the relative abundance of one bacterial family, one genus, one species and eight bacterial pathways (p ≤ 5×10[-8]). However, none of these associations surpassed the stringent significance threshold of p ≤ 2.75×10[-11]. Notably, we were unable to replicate associations reported in prior studies, including those conducted in Japanese populations, even regarding the direction of effects. Our PheWAS analysis uncovered a frameshift variant in the OR6C1 gene (rs5798345-CA) that was significantly associated with an increased abundance of Bacteroides uniformis. Furthermore, comparative analyses highlighted that methodological differences, particularly in sample processing and DNA extraction protocols, substantially influence the observed gut microbiome composition. This variability may be a key factor contributing to the lack of reproducibility across studies.

CONCLUSION: Our findings enhance the understanding of how host genetics shape the gut microbiota in the Japanese population and underscore the importance of methodological standardization in microbiome research. The identified associations between host genetic variants and specific microbial taxa provide insights into the complex interplay between genetics and the gut microbiome. Addressing methodological discrepancies is crucial for improving reproducibility and advancing knowledge of host-microbiome interactions.},
}

@article {pmid41852396,
year = {2025},
author = {Zoruk, P and Morozov, M and Veselovsky, V and Strokach, A and Babenko, V and Klimina, K},
title = {Impact of DNA extraction techniques and sequencing approaches on microbial community profiling accuracy.},
journal = {Frontiers in microbiomes},
volume = {4},
number = {},
pages = {1688681},
pmid = {41852396},
issn = {2813-4338},
abstract = {BACKGROUND: Quality control in metagenomic data analysis is crucial for ensuring the accuracy and reliability of research results. Among the key steps in microbiome research, DNA extraction plays a critical role, as it directly determines DNA yield, integrity, and representation of microbial taxa.

RESULTS: We compared three commercial DNA extraction kits and our protocol specifically developed for the recovery of high molecular weight (HMW) DNA from complex microbial communities, using the ZymoBIOMICS Gut Microbiome Standard. The PureLin[™] Microbiome DNA Purification Kit and our custom protocol provided superior recovery of DNA from Gram-positive bacteria, while the Wizard[®] kit and our protocol yielded HMW DNA suitable for long-read Oxford Nanopore sequencing. Among sequencing approaches, metagenomic sequencing on the Illumina platform provided the most accurate representation of the reference composition. However, all methods showed limited ability to detect taxa below 0.5% of relative abundance. Additionally, taxonomic classification based on 16S rRNA gene amplicon sequencing data misclassified closely related species due to high gene homology, a limitation not observed with metagenomic approaches.

CONCLUSIONS: Our study establishes that a customized DNA extraction protocol is optimal for comprehensive microbiome studies utilizing long-read sequencing technologies. We show that metagenomic sequencing outperforms 16S rRNA gene amplicon sequencing for species-level accuracy, providing a validated benchmark for future gut microbiome research.},
}

@article {pmid41852403,
year = {2025},
author = {Helal, M and Bari, VK},
title = {Insights into human respiratory microbiome under dysbiosis and its analysis tool.},
journal = {Frontiers in microbiomes},
volume = {4},
number = {},
pages = {1549166},
pmid = {41852403},
issn = {2813-4338},
abstract = {The human respiratory tract microbiome is a multi-kingdom microbial ecology that inhabits several habitats along the respiratory tract. The respiratory tract microbiome promotes host health by strengthening the immune system and avoiding pathogen infection. The lung microbiome mostly originates in the upper respiratory tract. The balance between microbial immigration and removal determines the nature of the lung microbiome. Identification and characterization of microbial communities from airways have been made much easier by recent developments in amplicon and shotgun metagenomic sequencing and data analysis techniques. In pulmonary medicine, there is a growing interest in the respiratory microbiome, which has been linked to human health and illness. However, the primary causes of bacterial co-occurrence seem to be interactions with fungi and bacteria as well as host and environmental factors. This study focused on identifying techniques and the current understanding of the relationship between the microbiota and various lung diseases.},
}

@article {pmid41852404,
year = {2025},
author = {Xuan, L and Sun, X and Wang, B and Chen, F and Yi, Y and Mao, H and Wang, Y and Zhao, G and Wang, J and Zhang, Y},
title = {Cold-water immersion alleviates intestinal damage induced by exertional heat stroke via modulation of gut microbiota in rats.},
journal = {Frontiers in microbiomes},
volume = {4},
number = {},
pages = {1531991},
pmid = {41852404},
issn = {2813-4338},
abstract = {OBJECTIVE: The pathogenesis of exertional heatstroke (EHS) involves substantial contributions from gut microbiota and their metabolites. In this study, we assessed whether cold water immersion (CWI) mitigates EHS-induced intestinal damage via alterations in the microbiome.

METHODS: An EHS model was created with 18 Wistar rats divided into three groups, that is, the EHS group comprising rats with exertional heat stroke, the CWI group with rats with heatstroke treated with cold water immersion, and the control (CTRL) group (rats with normothermia control). Pathological changes, core temperature (Tcore), and lactic acid (Lac) and endotoxin lipopolysaccharide (LPS) levels were evaluated. Fecal samples were subjected to metagenomic shotgun sequencing and liquid chromatography-mass spectrometry for microbiota and metabolomic profiling.

RESULTS: Hematoxylin and eosin staining showed that CWI treatment significantly reduced EHS-induced intestinal congestion, edema, and necrosis compared to the EHS group. The EHS group had the highest Tcore, while the CWI group had significantly lower Tcore than the EHS group. The CWI group had significantly reduced LPS and Lac levels, similar to those observed in the CTRL group. Microbiome analysis indicated that EHS disrupted gut bacteria, with an increase in the proportion of pathogens such as Desulfovibrio fairfieldensis, Desulfamplus magnetovallimortis, and Desulfococcus oleovorans (P<0.05). CWI treatment resolved these disturbances and restored the gut microbiota to a level similar to that of the CTRL group. Metagenomic analysis showed that CWI restored gut microbiota diversity (Shannon index, P<0.05), significantly reducing the proportion of pathogenic Desulfovibrio. Metabolomic profiling identified key metabolites, such as inosine, hypoxanthine, guanosine, and taurine (Variable importance in projection>1, P<0.05 with P-values adjusted for multiple comparisons using the Benjamini-Hochberg method, FDR<0.05), differentiating between the CWI and EHS groups.

CONCLUSION: The metabolites inosine, taurine, hypoxanthine, and guanosine correlated with restored gut microbiota, reduced proportion of Desulfovibrio, and attenuated inflammation (lower LPS/Lac), suggesting that their dual role in mitigating intestinal damage. These findings underscore the therapeutic potential of CWI by modulating microbial-derived metabolites, highlighting its impact on the intestinal health of patients with EHS.},
}

@article {pmid41852413,
year = {2025},
author = {Guerrero-Toledo, FM and Espinosa-Solares, T and Hernández-Eugenio, G and Huber, DH},
title = {Community assembly following disturbance in batch anaerobic digesters displays highly reproducible secondary succession and a shifting stochastic-deterministic balance.},
journal = {Frontiers in microbiomes},
volume = {4},
number = {},
pages = {1707779},
pmid = {41852413},
issn = {2813-4338},
abstract = {The great diversity of anaerobic digestion (AD) microbiomes indicates high redundancy and flexibility in the assembly of the community. Moreover, AD microbiomes are frequently subjected to disturbances during start-up and operation that require (re)assembly. We tested the reproducibility of secondary succession and AD community assembly mechanisms using a pre-assembled microbiome that was subjected to intense disturbances. Microbiome diversity and functions were followed in replicate mesophilic batch digesters initiated with multiple stressors, including high feed-to-inoculum ratio and many foreign species. Three 10 L batch digesters were derived from a single long-term CSTR digester pre-adapted to poultry litter feedstock and operated in parallel. Physicochemical parameters (methane, acetate, propionate, butyrate, pH, N-NH3, COD) were measured. Metagenome samples were used to assess diversity and functions. Three performance phases were found along the successional gradient: (1) methane inhibition, (2) high methane production, and (3) low methane plateau. The inventory of species (>1600) remained nearly the same, however the relative abundance of species, families, and functions changed during each successional stage. Syntrophic bacteria peaked in abundance during the mid-succession, high methane stage. Succession of overall KEGG functions was highly similar although species and carbohydrate functions diverged during late succession, suggesting diversity of niche partitioning during degradation of recalcitrant organic matter. We estimated the relative contributions of stochastic and deterministic processes and found a shift in the balance during succession. Early succession was not dominated by either dispersal or selection while late succession was dominated by variable selection. In conclusion, methane production recovered following severe (non-lethal) disturbance in a pre-adapted digester microbiome through a reproducible community assembly pathway that shifted toward deterministic, variable selection over time.},
}

@article {pmid41852418,
year = {2025},
author = {Berdy, BM and Williams, CE and Sizova, M and Jung, D and Tandogan, N and Goluch, ED and Epstein, S},
title = {Diverse cultivation strategies are necessary to capture microbial diversity in High Arctic lake sediment.},
journal = {Frontiers in microbiomes},
volume = {4},
number = {},
pages = {1619859},
pmid = {41852418},
issn = {2813-4338},
abstract = {While metagenomics has revolutionized our understanding of microbial diversity and function, the cultivation of microorganisms remains indispensable for elucidating their physiological characteristics and potential biotechnological applications. Cultivation provides context to the vast metagenomic datasets and helps verify metagenome-based hypotheses on microbial interactions. The majority of microorganisms remain uncultivated, and this is particularly prominent from extreme environments such as the Arctic. Here we aimed to contribute to the growing body of work investigating microbial ecology in extreme environments by assessing the efficacy of a variety of cultivation approaches in lake sediment in the High Arctic. To try and capture the full breadth of organisms present, we used standard, in situ, and anoxic cultivation methods. We cultured a total of 1,109 microorganisms which clustered into 155 OTUs (97% rRNA gene sequence similarity), representing organisms from Proteobacteria, Actinobacteria, Bacteroidota, and Firmicutes. Importantly, no single method of cultivation proved to be sufficient to represent the cultivable organisms within the environment. Rather, each method resulted in many unique OTUs. Therefore, multiple approaches should be used in conjunction to access the bulk of microbial taxa in a given environment.},
}

@article {pmid41852432,
year = {2025},
author = {Mhuireach, GÁ and Collins, S and Dietz, L and Horve, PF and Laguerre, A and Northcutt, D and Stenson, J and Wymelenberg, KVD and Gall, E and Fretz, M},
title = {Effects of wetting events on mass timber surface microbial communities and VOC emissions: implications for building operation and occupant well-being.},
journal = {Frontiers in microbiomes},
volume = {4},
number = {},
pages = {1395519},
pmid = {41852432},
issn = {2813-4338},
abstract = {INTRODUCTION: Humans have used wood as a construction material throughout history. Currently, mass timber products, such as cross-laminated timber (CLT), are becoming more popular as a structural material, since they are renewable and have a lower carbon footprint than concrete or steel. Nonetheless, some building types, such as healthcare, veterinary, and food manufacturing, avoid using structural mass timber due to concerns about microbial growth in the event of wetting. One solution is to use protective coatings on mass timber products to increase moisture resistance, although the coatings themselves may generate concerns about volatile organic compound (VOC) emissions. Natural uncoated wood also produces VOCs, some of which may have intrinsic antimicrobial effects.

METHODS: In this study, we inoculated coated and uncoated cross- laminated timber (CLT) blocks with a mock microbial community and isolated each block within individual sealed microcosms. We characterized VOCs and surface microbial communities from the CLT blocks before, during, and after wetting periods of varying durations. VOC concentration and emission rate were analyzed with chromatography-mass spectrometry (GC-MS), while microbial community abundance, diversity, and composition were analyzed through qPCR and shotgun metagenomics.

RESULTS: VOC emissions were elevated immediately after inoculation, then decreased through the remainder of the experiment, except for a plateau during the wetting period. VOCs from uncoated CLT blocks were primarily terpenes, while coated blocks emitted VOCs associated with coatings, plastics, and industrial solvents, as well as terpenes. One VOC-acetoin (3-hydroxy, 2-butanone)-was present at high levels across all samples immediately after microbial inoculation. Bacteria comprised 99.54% of the identified microbial sequences. The plastic control microcosm (not containing a CLT block) had higher abundance of viable bacteria for the majority of the study, but there was no difference in abundance between coated and uncoated blocks. Prior to wetting periods, microbial composition was driven primarily by sampling day, whereas surface type played a larger role during and after wetting periods.},
}

@article {pmid41852435,
year = {2025},
author = {Trubl, G and Malard, L and Rahlff, J},
title = {Editorial: Ecology, evolution, and biodiversity of microbiomes and viromes from extreme environments.},
journal = {Frontiers in microbiomes},
volume = {4},
number = {},
pages = {1604002},
doi = {10.3389/frmbi.2025.1604002},
pmid = {41852435},
issn = {2813-4338},
}

@article {pmid41852443,
year = {2025},
author = {Palazzi, CM and Ciampaglia, G and Binato, B and Ragazzini, M and Bertuccioli, A and Cavecchia, I and Matera, M and Cazzaniga, M and Zonzini, GB and Zerbinati, N and Tanda, ML and Di Pierro, F},
title = {Position statement of the Microbiota International Clinical Society.},
journal = {Frontiers in microbiomes},
volume = {4},
number = {},
pages = {1657750},
pmid = {41852443},
issn = {2813-4338},
}

@article {pmid41852664,
year = {2026},
author = {Shibata, N and Yoshifuji, A and Oyama, E and Komatsu, M and Azegami, T and Hayashi, K and Ishii, Y and Hasegawa, N and Namkoong, H},
title = {Urinary microbiota and bacterial membrane vesicles in chronic kidney disease: contribution to antimicrobial-resistant urinary tract infections.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1748638},
pmid = {41852664},
issn = {2235-2988},
mesh = {Humans ; Male ; *Urinary Tract Infections/microbiology ; *Renal Insufficiency, Chronic/complications/microbiology ; Middle Aged ; *Microbiota ; *Drug Resistance, Bacterial ; RNA, Ribosomal, 16S/genetics ; Aged ; *Urine/microbiology ; Metagenomics ; *Bacteria/genetics/drug effects/classification/isolation & purification ; Adult ; Microscopy, Electron, Transmission ; Sequence Analysis, DNA ; DNA, Bacterial/genetics/chemistry ; DNA, Ribosomal/chemistry/genetics ; *Extracellular Vesicles/ultrastructure ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Chronic kidney disease (CKD) is associated with an increased risk of severe urinary tract infections (UTIs), particularly those caused by antimicrobial-resistant bacteria. Although urinary microbiota and bacterial membrane vesicles (BMVs) are thought to contribute to UTI pathogenesis, their roles in CKD remain insufficiently understood. In this exploratory study, urine samples were collected from 10 male patients with CKD (eGFR <45 mL/min/1.73 m[2]) and 10 male non-CKD controls (eGFR ≥60 mL/min/1.73 m[2]). Urinary microbiota and BMV fractions were isolated and analyzed to compare microbial composition and antimicrobial resistance gene (ARG) profiles, and to evaluate their potential involvement in UTI development and the emergence of antimicrobial resistance in CKD. Both fractions were subjected to shotgun metagenomic sequencing; metagenomic analysis of BMVs was performed using pooled samples within each group. In addition, BMV fractions were characterized by transmission electron microscopy and 16S rRNA gene PCR. Urinary microbiota α-diversity was significantly lower in patients with CKD than in controls (ACE index, p = 0.04). Vesicle-like structures consistent with BMVs, with diameters of 20-200 nm, were detected in urine samples from both controls and patients with CKD. Principal coordinate analysis demonstrated that BMV fractions clustered within the corresponding urinary microbiota profiles. Furthermore, multiple antimicrobial resistance genes (ARGs), including ftsI and adeF, were identified in both urinary microbiota and BMV fractions. This study provides exploratory evidence of reduced urinary microbiota α-diversity in patients with CKD and the presence of ARGs in both urinary microbiota and BMV fractions from controls and patients with CKD. These findings suggest microbiological factors that may contribute to the high incidence of antimicrobial-resistant UTIs in this population. Future validation in larger cohorts with individual-level BMV profiling will be required to determine whether analyses focusing on urinary microbiota and BMVs can contribute to a better understanding of antimicrobial-resistant UTIs and to improved infection risk assessment in patients with CKD.},
}

Humans
Male
*Urinary Tract Infections/microbiology
*Renal Insufficiency, Chronic/complications/microbiology
Middle Aged
*Microbiota
*Drug Resistance, Bacterial
RNA, Ribosomal, 16S/genetics
Aged
*Urine/microbiology
Metagenomics
*Bacteria/genetics/drug effects/classification/isolation & purification
Adult
Microscopy, Electron, Transmission
Sequence Analysis, DNA
DNA, Bacterial/genetics/chemistry
DNA, Ribosomal/chemistry/genetics
*Extracellular Vesicles/ultrastructure
Anti-Bacterial Agents/pharmacology

@article {pmid41852665,
year = {2026},
author = {Zhang, Y and Wang, H and Yan, R and Wang, K and Man, J and Yang, L},
title = {Research advances on the urinary microbiome in non-infectious urinary tract diseases: from community composition to clinical prospects.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1728182},
pmid = {41852665},
issn = {2235-2988},
mesh = {Humans ; *Microbiota ; Dysbiosis/microbiology ; *Urologic Diseases/microbiology/diagnosis ; *Urinary Tract/microbiology ; *Urine/microbiology ; Prostatic Neoplasms/microbiology ; },
abstract = {INTRODUCTION: With the rapid development of 16S rRNA sequencing and metagenomic technologies, the traditional concept of sterile urine has been completely overturned, and a diverse urinary microbiome has been identified even in healthy individuals. Increasing evidence indicates that dysbiosis of the urinary microbiome is closely associated with the onset and progression of various non-infectious urological diseases.

METHODS: This review systematically summarizes recent advances in the role of the urinary microbiome in non-infectious urological diseases, including bladder cancer, benign prostatic hyperplasia, prostate cancer, nephrolithiasis, interstitial cystitis/bladder pain syndrome, and urinary incontinence, with a focus on microbial dysbiosis, pathogenic mechanisms, and clinical applications.

RESULTS: Studies have shown that alterations in the composition and diversity of the urinary microbiome are closely related to chronic inflammation, immune dysregulation, metabolic disturbances, and changes in the local microenvironment. These alterations may contribute to disease pathogenesis through mechanisms such as persistent low-grade inflammation, abnormal metabolic activity, and biofilm formation. In recent years, non-invasive detection based on urinary microbial profiles has shown promising potential in the early diagnosis of bladder and prostate cancers, with some machine learning models achieving diagnostic accuracies above 80 percent. Furthermore, the urinary microbiome may influence the efficacy of immunotherapy, offering new insights for personalized precision medicine.

CONCLUSIONS: This review summarizes the mechanisms, research status, and clinical prospects of the urinary microbiome in non-infectious urological diseases, emphasizing the importance of methodological standardization and highlighting its potential applications in early screening, diagnostic stratification, and microbiome-targeted interventions.},
}

Humans
*Microbiota
Dysbiosis/microbiology
*Urologic Diseases/microbiology/diagnosis
*Urinary Tract/microbiology
*Urine/microbiology
Prostatic Neoplasms/microbiology