@article {pmid41648007,
year = {2025},
author = {Schnabel, E and Vuillemin, A and Esser, S and Griesdorn, L and Soares, AR and Mørkved, PT and Jørgensen, SL and Probst, AJ and Kallmeyer, J and , },
title = {Geochemical variability and microbial metabolic functions in oligotrophic sediments exposed to minor seepage.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1720187},
pmid = {41648007},
issn = {1664-302X},
abstract = {Low primary productivity in Barents Sea surface waters and limited nutrient flux to the seafloor favor nitrification and nitrogen fixation in deep waters, resulting in a dearth of organic substrates in local sediments. The addition of labile hydrocarbons naturally occurring through seepage from subsurface reservoirs could promote microbial activity in organic-lean sediments, notably by denitrifying and sulfate-reducing microbes. Using gravity cores from an area with numerous hydrocarbon reservoirs, we document pore water geochemistry, dissolved gas concentrations, and total cell counts supplemented with taxonomic and functional marker gene analyses from metagenomes and metagenome-assembled genomes. We assess the contribution of the subsurface biosphere in producing geochemical gradients in oligotrophic sediments facing different exposure to minor seepage. In pristine seabed, i.e., not affected by hydrocarbon seepage, nitrate and ammonium profiles were consistent with denitrification down to 1 m below seafloor. By contrast, minor hydrocarbon seepage caused very different pore water profiles, which were indicative of more reducing geochemical conditions in the sediment and more advanced consumption of electron acceptors in pore water. Delivery of favorable organic substrates to anaerobic microbes through seepage was reflected in slightly higher cell densities, CH4 and CO2 concentrations, but appeared to have little impact on community diversity. This could be explained by metabolic versatility across functional guilds, with limited differentiation of sedimentary niches, favoring polyvalent fermenters at the expense of canonical denitrifiers and sulfate reducers. These versatile fermenters exhibited diverse predicted capabilities for nitrate and sulfate reduction combined with hydrocarbon degradation, (homo)acetogenesis, and nitrogen fixation. Our results further indicate that specific clades of homoacetogens (Lokiarchaeia, Bathyarchaeia, and Dehalococcoidia) could support cross-feeding interactions when fueled by simple hydrocarbons through seepage, particularly those associated with dissimilatory sulfur metabolism and fermentation of intermediate metabolites. In the absence of hydrocarbon-derived electron donors, the same clades appear capable of energy-conserving (homo)acetogenic fermentation on organic residues. Thus, we conclude that slow-growing (homo)acetogens that are ubiquitous in the marine subseafloor actively contribute to balancing biogeochemical cycles in oligotrophic sediments impacted by minor hydrocarbon seepage.},
}

@article {pmid41648005,
year = {2025},
author = {Liu, JJ and Yang, H and Xiao, ZY and Xie, JH and Su, L and Li, YT and Zheng, XY and Hu, WH and Fu, SJ and Li, CL and Huang, L and Yu, SY and Yu, Z and Yang, S and Yang, J},
title = {Gut microbiota and metabolic dysregulation in polycystic ovary syndrome: effects of acupuncture as an adjunct to in vitro fertilization on gut dysbiosis, metabolism, and oocyte quality.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1730714},
pmid = {41648005},
issn = {1664-302X},
abstract = {INTRODUCTION: Polycystic ovary syndrome (PCOS) is marked by disruptions in metabolic and reproductive endocrine functions. This study synthesizes systemic metabolic profiles, alterations in gut microbiota, and follicular fluid metabolism to elucidate the reproductive and endocrine metabolic changes associated with PCOS. Furthermore, it aims to elucidate the potential mechanisms through which acupuncture may exert therapeutic effects.

METHODS: In this open-label randomized controlled trial conducted in China (November 2021-January 2023), 60 women with PCOS scheduled for In Vitro Fertilization (IVF) were randomized to receive acupuncture combined with IVF treatment or IVF treatment alone, with 30 healthy women serving as controls. Gut microbiota was sequenced and analyzed by 16S rRNA and metagenomics; follicular fluid metabolites were determined by untargeted metabolomics.

RESULTS: Compared with healthy controls, PCOS exhibited gut microbiota dysbiosis and metabolic disorders. The specific gut microbiota in PCOS dominated by s_Lachnospiraceae, s_Blautia_sp. and g_Escherichia-Shigella, which correlated with body mass index (BMI), waist circumference, waist-to-hip ratio, and hormone levels. Acupuncture combined with IVF significantly regulated glucose and lipid metabolism, reduced g_Escherichia-Shigell abundance, and showed potential advantages in enhancing oocyte quality and embryonic developmental potential (p = 0.011). Analysis of the correlation between differential metabolites and oocyte and embryo quality demonstrated that methionine sulfoxide and boldione may be key metabolites to affect follicle quality.

CONCLUSION: PCOS is associated with systemic multi-pathway metabolic dysregulation and gut microbiota dysbiosis. It described the potential therapeutic benefits of acupuncture combined with IVF for PCOS, laying a foundation for further understanding the disease and the mechanisms of acupuncture for PCOS metabolic disorders, and providing directions for future research.},
}

@article {pmid41648004,
year = {2025},
author = {Goncalves, AR and Ranganathan, H and Valdes, C and Zhu, H and Zhang, B and Kok, CR and Martí, JM and Mulakken, NJ and Thissen, JB and Jaing, C and Be, NA},
title = {Beyond microbial abundance: metadata integration enhances disease prediction in human microbiome studies.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1695501},
pmid = {41648004},
issn = {1664-302X},
abstract = {Multiple studies have highlighted the interaction of the human microbiome with physiological systems such as the gut, immune, liver, and skin, via key axes. Advances in sequencing technologies and high-performance computing have enabled the analysis of large-scale metagenomic data, facilitating the use of machine learning to predict disease likelihood from microbiome profiles. However, challenges such as compositionality, high dimensionality, sparsity, and limited sample sizes have hindered the development of actionable models. One strategy to improve these models is by incorporating key metadata from both the human host and sample collection/processing protocols. This remains challenging due to sparsity and inconsistency in metadata annotation and availability. In this paper, we introduce a machine learning-based pipeline for predicting human disease states by integrating host and protocol metadata with microbiome abundance profiles from 68 different studies, processed through a consistent pipeline. Our findings indicate that metadata can enhance machine learning predictions, particularly at higher taxonomic ranks like Kingdom and Phylum, though this effect diminishes at lower ranks. Our study leverages a large collection of microbiome datasets comprising 11,208 samples, therefore enhancing the robustness and statistical confidence of our findings. This work is a critical step toward utilizing microbiome and metadata for predicting diseases such as gastrointestinal infections, diabetes, cancer, and neurological disorders.},
}

@article {pmid41648002,
year = {2025},
author = {Zhang, H and Chen, K and Chen, R and Jia, E},
title = {Feeding patterns reprogram a gut microbial virulence-iron-quorum sensing functional axis linked to atherosclerotic risk.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1751844},
pmid = {41648002},
issn = {1664-302X},
abstract = {The feeding rhythm is a major temporal regulator of metabolic physiology, yet its impact on microbiome-derived functional traits relevant to cardiometabolic disease remains insufficiently understood. Our previous work demonstrated that ad libitum, daytime-restricted, and nighttime-restricted feeding produce markedly different atherosclerotic outcomes in Apoe[-]/[-] mice, indicating that the feeding rhythm acts as a modifiable determinant of atherogenic susceptibility. Here, we used shotgun metagenomics to profile risk-associated microbial functional modules-including Type III and Type VI secretion systems (T3SS/T6SS), siderophore-based iron acquisition pathways, quorum-sensing (QS) regulators, and antimicrobial resistance determinants-across feeding regimens. The feeding rhythm induced pronounced functional segregation independent of α-diversity, which was consistent with selective functional reprogramming rather than taxonomic restructuring. Daytime feeding, which is misaligned with the murine active phase, is associated with coordinated enrichment of the T3SS/T6SS, iron uptake, and QS pathways, forming a tightly interconnected "virulence-iron-QS-ARG" functional consortium. In contrast, circadian-aligned nighttime feeding resulted in attenuated virulence orientation and enhanced metabolic-cooperative signatures. Network inference further revealed strong coactivation of virulence secretion, iron mobilization, and QS modules under circadian misalignment. These findings show that the feeding rhythm modulates atherogenic susceptibility not only through host metabolism but also by remodeling gut microbial functional capacities, highlighting microbial functional ecology as an integral component of diet-host interactions.},
}

@article {pmid41647993,
year = {2025},
author = {Jayakrishnan, T and Sangwan, N and Nair, KG and Kamath, SD and Patel, MH and Joyce, D and Walsh, M and Simon, R and Vadehra, D and Iyer, RV and Fountzilas, C and Khorana, AA},
title = {Tumor microbiome differences in early-onset versus average-onset pancreatic adenocarcinoma.},
journal = {ESMO gastrointestinal oncology},
volume = {9},
number = {},
pages = {100194},
pmid = {41647993},
issn = {2949-8198},
abstract = {BACKGROUND: Compelling evidence supports the biomarker potential of microbiome in pancreatic adenocarcinoma. Given the knowledge gap on the characteristics and significance of microbiome in early-onset pancreatic ductal adenocarcinoma (eoPDAC, age <50 years), we aimed to evaluate microbiome profiles in resected specimens from individuals with eoPDAC and average-onset PDAC (aoPDAC, age >50 years).

MATERIALS AND METHODS: We carried out shotgun metagenomic sequencing in resected specimens from individuals with eoPDAC (n = 24) and aoPDAC (n = 20). Statistical tests included Wilcoxon test, permutational analysis of variance, multiomic classifier modeling, differential abundance analysis, and linear regression. All P values were adjusted for multiple testing and P < 0.05 was considered statistically significant.

RESULTS: We successfully sequenced several bacteria and fungi in the tumor specimens from 44 individuals with resected PDAC (24 eoPDAC and 20 aoPDAC). The alpha diversity of the bacterial microbiome was higher in eoPDAC tumor tissue compared with aoPDAC (P = 0.04). In contrast, the fungal mycobiome's alpha diversity was higher for aoPDAC tumor tissue (P = 0.02). Key organisms with differential abundance between tumor tissue from individuals with eoPDAC and aoPDAC included Bacillus, Candida, Collimonas, Cupriavidus, Enterobacter, Escherichia, Klebsiella, Malasseiza, Mucilaginibacter, Neisseria, and Sphingomonas. Higher bacterial diversity in tumor tissue was associated with better overall survival for individuals with eoPDAC (R = 0.26, P = 0.02).

CONCLUSIONS: Shotgun metagenomic sequencing identified bacterial microbiome and fungal mycobiome in tumors from individuals with eoPDAC and aoPDAC. We observed significant differences in alpha and beta diversity and relative abundances of organisms suggesting distinct microbiome signatures. Microbiome associations with survival were observed in eoPDAC indicating unique potential as prognostic biomarker.},
}

@article {pmid41647522,
year = {2026},
author = {Liu, J and Chen, Y and Sheng, X and Gao, Y},
title = {Case Report: Nocardia farcinica infectious arthritis and myositis in an immunocompromised host: diagnostic and management challenges.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1762442},
pmid = {41647522},
issn = {2296-858X},
abstract = {BACKGROUND: Nocardia farcinica is a rare opportunistic pathogen predominantly affecting immunocompromised hosts. Infectious arthritis, cutaneous and deep soft tissue infections caused by this organism often present with nonspecific clinical manifestations. Additionally, due to its slow-growing and oligotrophic nature, both cultivation and identification pose considerable challenges, thereby complicating clinical diagnosis and management.

CASE PRESENTATION: This case report described an elderly female patient presenting with right shoulder redness, swelling, and pain. Her history included diabetes, local corticosteroid injections, and newly identified humoral immunodeficiency (hypogammaglobulinemia with low B-cell count). Imaging revealed infectious arthritis of the right shoulder, accompanied by infectious myositis and an intermuscular abscess in the right upper arm. Nocardia farcinica was confirmed by metagenomic next-generation sequencing (mNGS) and culture of aspirated fluid. Initial therapy with trimethoprim-sulfamethoxazole (TMP-SMX) and ceftriaxone was limited by renal impairment and gastrointestinal intolerance, and susceptibility testing indicated TMP-SMX resistance. Treatment was switched to linezolid. Due to inadequate clinical response, multiple surgical debridements were performed. Subsequently, therapy was changed to oral minocycline because of linezolid-induced bone marrow suppression and intolerance. At discharge, the maintenance regimen consisted of moxifloxacin combined with minocycline.

CONCLUSION: This case highlights the importance of considering low-virulence pathogens such as Nocardia in immunocompromised patients with atypical infections that respond poorly to initial empiric therapy. Pathogen identification, aided by tools like mNGS for rapid detection, is essential. When classic regimens are limited by adverse effects, susceptibility-guided alternative therapies can be effective. For localized infections refractory to medical management, multidisciplinary surgical intervention remains a critical component of care.},
}

@article {pmid41646408,
year = {2026},
author = {Bosquet, JG and Osazuwa-Peters, O and Wagner, VM and Polio, A and Hoyd, R and Tarhini, AA and Cosgrove, CM and Huang, MS and Corr, BR and Leiser, AL and Salhia, B and Darcy, K and Dood, RL and Dockery, LE and Cavnar, MJ and Landrum, L and Chambers, L and Tan, AC and Jin, N and Rounbehler, RJ and Churchman, ML and Spakowicz, D},
title = {Intrinsic tumor factors and extrinsic environmental and social exposures contribute to endometrial cancer recurrence patterns.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-8682460/v1},
pmid = {41646408},
issn = {2693-5015},
abstract = {Purpose In a previous study, we trained, validated and tested models of endometrial cancer (EC) recurrence integrating clinical, genomic and pathological data from the Oncology Research Information Exchange Network (ORIEN). Preliminary studies also have demonstrated that bacterial communities may influence the risk of EC recurrence by altering the local environment within the upper female genital tract. The objective of this study was to evaluate whether extrinsic and environmental factors, including tumor-associated bacterial communities, tumor immune contexture and air pollution alongside clinical, pathologic and genomic features are associated with EC recurrence across clinically relevant risk groups. Patients and Methods: We performed a retrospective, multi-institution, case-control study with data from the ORIEN network EC dataset. Data was stratified into low-risk, FIGO grade 1 and 2, stage I (N = 329), high-risk, or FIGO grade 3 or stages II-IV (N = 324), and non-endometrioid histology (N = 239) groups. RNA and DNA were extracted from tumor specimens and processed to obtain the necessary genomic/metagenomic data. Genus level microbiome data were extracted and curated) from RNA sequencing using Kraken2 , Bracken and exotic software packages. Risk of EC recurrence was evaluated by integrating microbiome and environmental data alongside existing clinical, pathological and genomic data using topic modelling with latent dirichlet allocation (LDA). Prediction models of EC recurrence were created using machine and deep learning analytics (ML and DL) with MATLAB apps and TensorFlow . Finally, performance of both topic and prediction models were externally validated in an independent EC dataset from TCGA. Results The resulting models, analyzed with topic modelling, demonstrated the complexity of factors involved in recurrence of disease for EC. The components of the resulting topic models, and specifically the microbiome, changed when environmental factors, like air pollutants, were introduced in the model. In the low-risk EC group, microbes that were quite abundant in models before introducing environmental factors, were scarcely seen afterwards, like genera Thermothielavioides , Theileria , Rhizoctonia . Bacillus was the genus with higher per-topic probability within all risk groups, especially for low-risk EC (28%). Ozone (O 3) was a resulting component of all risk groups' models. BMI was the sole informative clinical variable after data integration, and only present in the low-risk group. Resulting models from the high-risk and non-endometrioid groups included differential gene expressions: MMP13, S100A7, SMOC1, ACACA and ADD2, DLX5, SLCO2B1, NWD1 respectively. CNVs also were present in both low-risk and non-endometrioid groups, but their per-topic probabilities were low. The same was true for the immune contexture data. The components of the resulting topic models were used to train, validate and test prediction models of EC recurrence by risk groups. Performances of these models were excellent (@ 0.9). Despite some missing microbiome data in TCGA from resulting topic models, prediction models trained in the ORIEN set, had similar performances in TCGA testing set, with overlapping AUC 95% CIs. Conclusion Both extrinsic factors (tumor-associated bacterial communities, tumor immune contexture and air pollution) and intrinsic factors predict EC recurrence. The complexity of tumor and host factors influencing cancer relapses underscore the need for more individualized prediction models of disease outcomes.},
}

@article {pmid41645540,
year = {2026},
author = {Cuong, TM and Dan, NH and Hang, TTT and Le Luu, T and Scheynen, J and Dries, J},
title = {Enhanced the Treatment of Seafood Processing Wastewater Using the Anaerobic-Anoxic-Oxic (AAO) Process With Granular Sludge.},
journal = {Water environment research : a research publication of the Water Environment Federation},
volume = {98},
number = {2},
pages = {e70293},
doi = {10.1002/wer.70293},
pmid = {41645540},
issn = {1554-7531},
support = {FWO.105-2022.03//Vietnam National Foundation for Science and Technology Development (NAFOSTED)/ ; },
mesh = {*Sewage/microbiology ; Anaerobiosis ; *Waste Disposal, Fluid/methods ; *Wastewater ; Bioreactors/microbiology ; *Seafood ; Phosphorus ; Bacteria/classification/genetics ; Nitrogen ; Aerobiosis ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Seafood processing wastewater contains high concentrations of organics and nutrients that need to have an effective solution. This study aims to explore the use of granular sludge in seafood wastewater treatment using anaerobic-anoxic-aerobic (AAO) process. The results showed that the granular sludges were successfully cultivated from the traditional activated sludge sources. The bioreactor demonstrated robust treatment performance, achieving a high chemical oxygen demand (COD) removal efficiency exceeding 93%, total nitrogen (TN) removal ranging from 56.6% to 68.6%, and ammonium removal (NH4 [+]-N) of 80% to 88.57%. However, total phosphorus (TP) removal efficiency was relatively moderate at 47.36% ± 10.33%. Metagenomic analysis (16S rRNA) revealed a diverse and evenly distributed microbial community within the granular sludge. In anaerobic granular sludge, the dominant phylum was Bacillota (45.3%), followed by Thermodesulfobacteriota (18.2%) and Synergistota (11.24%), with minor contributions from Campylobacterota (7.58%), Chloroflexota (3.98%), and Bacteroidota (3.6%), alongside other less abundant phyla (10.1%). Anoxic granular sludge exhibited a shift, with Pseudomonadota (32.87%) and Thermodesulfobacteriota (25.08%) dominating, while Bacillota (11.95%), Bacteroidota (7.9%), and Chloroflexota (4.1%) contributed less, and other phyla comprised 18.21%. For aerobic granular sludge, Pseudomonadota represented the most prevalent phylum (42.21%), followed by Thermodesulfobacteriota (14.94%) and Bacillota (14.87%), with lower abundances of Bacteroidota (7.74%) and Chloroflexota (4.91%), while other phyla accounted for 15.42%.},
}

*Sewage/microbiology
Anaerobiosis
*Waste Disposal, Fluid/methods
*Wastewater
Bioreactors/microbiology
*Seafood
Phosphorus
Bacteria/classification/genetics
Nitrogen
Aerobiosis
RNA, Ribosomal, 16S/genetics

@article {pmid41645099,
year = {2026},
author = {Qiu, Y and Mo, F and Chen, Y and Lai, Y and Zhang, K and Huang, Z},
title = {Intersite differences in gut microbiome are associated with habitat quality in a limestone forest-dwelling langur.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-04800-7},
pmid = {41645099},
issn = {1471-2180},
support = {2023GXNSFBA026045//Natural Science Foundation of Guangxi Zhuang Autonomous Region/ ; no.32170488//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Studying the compositional structure and function of the gut microbiome is essential for evaluating adaptability of wildlife to their environment. Given the high plasticity of the gut microbiome in primates, studying conspecific populations under different habitat quality can provide valuable insights for the conservation and management. To investigate intersite differences in composition and function of the gut microbiome of endangered François' langurs (Trachypithecus francoisi), we employed 16S rRNA and metagenomic sequencing.

RESULTS: The results showed that higher gut microbiota diversity of François' langurs was associated with higher habitat quality, possibly driven by the dietary diversity. In contrast, François' langurs inhabiting lower-quality habitats had a higher relative abundance of Bacillota and more enriched functional genes related to amino acid metabolism and metabolic pathways than those in higher-quality habitats, which support enhanced fiber degradation to meet energy demands. Additionally, the proportion of tetracycline-related ARGs (tetA(58)) was more abundant in lower-quality habitats, likely due to villagers applying livestock and poultry manure.

CONCLUSION: Our study concludes that intersite differences in gut microbiome are associated with habitat quality in the François' langurs, underscoring its role in habitat adaptation and necessity for physiological indicators to elucidate the mechanisms by which wildlife responds to human disturbance and ecological variability. In addition, we recommend prioritizing the restoration of native vegetation diversity in the langurs' habitats, which leverages their gut microbiota's adaptive potential to provide a suitable fundamental environment for the langurs' long-term survival.},
}

@article {pmid41645073,
year = {2026},
author = {Xu, C and Zhang, L and Liu, T and Zhu, G and Wei, H and Zheng, Y and Shi, J and Qiu, L and Xiao, Z and Zhu, X and Wang, J and Guo, J and Fan, Y and Song, Y and Jiang, E and Feng, S},
title = {Respiratory and blood samples metagenomic sequencing in diagnosing pulmonary infections in hematologic patients.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-026-12734-8},
pmid = {41645073},
issn = {1471-2334},
support = {2021-I2M-1-039//Chinese Academy of Medical Sciences Innovation Fund for Medical Sciences/ ; 2021-I2M-1-017//Chinese Academy of Medical Sciences Innovation Fund for Medical Sciences/ ; 2023ZD0510400//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; 3332024210//Fundamental Research Funds for the Central Universities, Peking Union Medical College/ ; 82470208//National Natural Sciences Foundation of China/ ; },
}

@article {pmid41645054,
year = {2026},
author = {Zhang, XX and Zhang, H and Zhao, JX and Yu, HL and Wang, CR and Shang, KM and Wei, YJ and Qin, Y and Li, JM and Zhao, ZY and Xia, CY and Chen, BN and Elsheikha, HM and Ma, H},
title = {Gut microbiota response to Enterocytozoon bieneusi infection in wild rodents: enhanced vitamin B and K2 biosynthesis pathways.},
journal = {BMC genomics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12864-026-12575-4},
pmid = {41645054},
issn = {1471-2164},
support = {Grant No. 32170538//the National Natural Science Foundation of China/ ; 2022YFF0710503//the National Key R&D Program of China/ ; 32500449//the National Natural Science Foundation of China-Youth Science Fund/ ; ZD2022C006//the Natural Science Foundation of Heilongjiang Province/ ; Grant No. 667/2424025//the Horizontal Project of Qingdao Agricultural University/ ; },
abstract = {Enterocytozoon bieneusi (E. bieneusi) is a pathogenic microsporidian that affects immunocompromised individuals, including those with HIV, and represents a major cause of diarrhea. It can severely impact human health, causing gastrointestinal disease, nutritional deficits, and life-threatening complications. However, the microbial mechanisms by which E. bieneusi affects host nutrition are not well understood. Wild rodents have long been considered valuable models for studying human diseases due to similarities in gut microbiota dynamics and immune responses, making them particularly relevant for investigating parasitic infections. Here, we assembled a comprehensive catalog of 9,929 non-redundant microbial genomes from wild rodent gut metagenomes and evaluated their potential for B vitamins and vitamin K2 biosynthesis using comparative functional genomics. We identified 2,307 genomes encoding complete pathways for de novo biosynthesis of at least one essential vitamin, though no single genome encoded all pathways, indicating a distributed metabolic capacity within the microbial community. Infection with E. bieneusi significantly altered the microbial composition and the potential for vitamin biosynthesis, with a notable expansion of Methanobacteriota and reprogramming of pyridoxine (vitamin B6) biosynthesis pathways. These changes reveal a functional shift in microbial metabolism in response to parasitic pressure. By elucidating the microbial basis of vitamin biosynthesis in wild rodents and the impact of E. bieneusi infection on microbial functions, this study provides new insights into the role of gut microbiota in maintaining host health and supporting nutrient provision under parasitic stress. Moreover, the findings will provide valuable insights into the prevention and control of E. bieneusi infection in a variety of host, including humans.},
}

@article {pmid41644796,
year = {2026},
author = {Krukowski, H and Valkenburg, S and Vich Vila, A and Maciel, LF and Vázquez-Castellanos, JF and Gryp, T and Joossens, M and Van Biesen, W and Verbeke, F and Derrien, M and Huys, GRB and Glorieux, G and Raes, J},
title = {Host factors dictate gut microbiome alterations in chronic kidney disease more strongly than kidney function.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41644796},
issn = {2058-5276},
support = {860329//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 860329//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 860329//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 860329//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 860329//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 101149152//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; G017815N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; G017815N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; G017815N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; },
abstract = {Despite recent progress, microbial associations reported in chronic kidney disease (CKD) remain inconsistent. Here we combined quantitative faecal metagenomics (n = 130) and cross-study biomarker comparisons (ntotal = 4,420) to study microbiome associations with estimated glomerular filtration rate (eGFR; kidney function) and 4-year CKD progression. Intestinal transit time (ITT) and medications significantly explained microbiome variation, surpassing eGFR-related effects. Lower eGFR was associated with increased p-cresol and indole biosynthetic potential and reduced plant-to-animal CAZyme ratios. This was consistent with community-wide saccharolytic-to-proteolytic microbiome transitions linked to dietary guidelines and slowed-down ITT. Peritoneal dialysis patients showed distinct microbiome dysbiosis accompanied by increased intestinal inflammation. Only Escherichia coli, an unnamed Alistipes species and Bifidobacterium adolescentis were covariate-independent markers for eGFR, but neither these nor previous microbial markers convincingly replicated across 11 studies. No predictors for CKD progression were found. Nevertheless, our study adds insight into plausible ITT and nutrition-related effects, highlighting their potential in CKD interventions.},
}

@article {pmid41644585,
year = {2026},
author = {Zhou, Y and Liu, K and Gong, P and Wu, J and Ren, Z and Jin, E},
title = {Integrated metagenomic and 16S rRNA analysis reveals temporal associations between resistance genes and microbial communities during dairy manure composting.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-37092-y},
pmid = {41644585},
issn = {2045-2322},
abstract = {Dairy manure composting is widely applied to stabilize organic waste and reduce environmental pollution, yet the behavior of resistance determinants during this process remains insufficiently resolved. In this study, shotgun metagenomic sequencing was used to characterize temporal changes in antibiotic resistance genes (ARGs), metal resistance genes (MRGs), biocide resistance genes (BRGs), mobile genetic elements (MGEs), and microbial community composition during dairy manure composting. Rather than inferring direct mechanistic causation, our analyses focused on identifying statistically supported trends, associations, and co-occurrence patterns across composting stages. We observed a rapid decline in the relative abundance of ARGs compared with MRGs and BRGs during the thermophilic phase, coinciding with increasing temperature, while specific genes such as sul2 persisted throughout the process. Shifts in microbial community composition, particularly changes in the relative dominance of Actinobacteria and Proteobacteria, were significantly associated with variations in resistome profiles. Correlation and network analyses further revealed strong associations among ARGs, MRGs, BRGs, and MGEs, suggesting potential co-selection and horizontal gene transfer linkages without implying direct causal mechanisms. In addition, several opportunistic bacterial genera showed positive associations with aminoglycoside- and macrolide-lincosamide-streptogramin-type ARGs, indicating possible dissemination risks following compost application. Overall, this study provides an integrated, association-based overview of resistome and microbial community dynamics during dairy manure composting and highlights the importance of considering multiple resistance determinants when evaluating composting as a manure management strategy.},
}

@article {pmid41644553,
year = {2026},
author = {Wen, R and Xin, Y and Bao, S and Zhang, X and Wang, Q and Dang, Z and Zhou, Z and Wu, J and Song, D and Fu, L and Li, W and Niu, J and Wen, Y and Zhou, X and Han, M and Zhao, J},
title = {The gut microbiota mediates depression-like behaviors in mice with chronic Echinococcus multilocularis infection.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00929-5},
pmid = {41644553},
issn = {2055-5008},
support = {NO. 32160181//National Natural Science Foundation of China/ ; 2022AAC02076//Ningxia Natural Science Found Project/ ; 2024BEG02028//Key research and development projects of the Ningxia Hui Autonomous Region/ ; },
abstract = {Alveolar echinococcosis (AE), a chronic parasitic disease caused by Echinococcus multilocularis (E. multilocularis), remains poorly characterized with respect to central nervous system (CNS) involvement, and its long-term effects on mental health have not been systematically investigated. In this study, we established a BALB/c mouse model of chronic E. multilocularis infection and applied an integrative framework combining behavioral assessments, histomorphological analyses (hematoxylin-eosin staining, Nissl staining, and transmission electron microscopy), cytometric bead array (CBA), and multi-omics approaches (16S rRNA sequencing, metagenomics, and untargeted metabolomics) to investigate infection-induced neuroimmune-gut microbiota interactions. Chronically infected mice exhibited pronounced depression-like behavioral phenotypes, accompanied by hippocampal neuronal nuclear membrane atrophy and disrupted microglial homeostasis. Both peripheral and central inflammatory profiling revealed elevated levels of pro-inflammatory mediators, particularly IL-6 and MCP-1, suggesting coordinated systemic immune activation and neuroimmune alterations. Notably, fecal microbiota transplantation (FMT) from infected donors was sufficient to induce depression-like behaviors in recipient mice, supporting a contributory role of infection-associated gut microbiota alterations in behavioral abnormalities. Integrated multi-omics analyses further revealed a marked reduction in Lactobacillus abundance in infected mice, which was positively correlated with decreased levels of key metabolites within the tryptophan/5-hydroxytryptamine (5-HT) metabolic pathway. Collectively, these findings suggest that chronic E. multilocularis infection may be associated with depression-like behaviors through gut microbiota dysbiosis and related metabolic perturbations. This study provides initial insights into the potential mechanisms underlying neuropsychiatric complications in AE and proposes a conceptual framework for future investigations into early intervention and microbiota-targeted therapeutic strategies.},
}

@article {pmid41644450,
year = {2026},
author = {Yan, D and Huang, W and Li, KS},
title = {[Advances in clinical diagnosis and treatment of pythium keratitis].},
journal = {[Zhonghua yan ke za zhi] Chinese journal of ophthalmology},
volume = {62},
number = {2},
pages = {156-160},
doi = {10.3760/cma.j.cn112142-20250820-00351},
pmid = {41644450},
issn = {0412-4081},
support = {2025JJ90271//Enterprise Joint Fund Project/ ; },
mesh = {Humans ; *Pythium ; *Keratitis/diagnosis/therapy/microbiology ; *Pythiosis/diagnosis/therapy ; },
abstract = {Pythium insidiosum is an aquatic algal oomycete that can induce Pythium insidiosum keratitis (PIK). PIK typically presents as acute, highly invasive corneal ulcers, rapidly progressing to corneal dissolution and perforation, and in severe cases, may lead to blindness. Due to its clinical presentation resembling fungal infections, it is often misdiagnosed as fungal keratitis. Epidemiological studies indicate that PIK is predominantly found in tropical and subtropical regions, with a higher incidence during the monsoon season. It is often associated with exposure to contaminated water sources or minor trauma caused by plants. Diagnostic methods include staining of corneal scrapings, PCR, metagenomic next-generation sequencing, and confocal microscopy. Since PIK shows a poor response to conventional antifungal treatments, antibiotics are the preferred treatments, with a combination of linezolid and azithromycin often used as the first-line therapy. Severe cases may require penetrating keratoplasty. In China, reports of PIK cases are relatively rare. This review summarizes the epidemiology, etiology, clinical manifestations, diagnosis, and treatment of PIK, aiming to provide a reference for its clinical management.},
}

Humans
*Pythium
*Keratitis/diagnosis/therapy/microbiology
*Pythiosis/diagnosis/therapy

@article {pmid41644290,
year = {2026},
author = {Yang, F and Xiang, B and Xia, D and Wu, Y and Chang, X and Sun, P and Zhang, M and Zhang, Y},
title = {Lipidomic and Metagenomic Profiling of Chinese Female Emerging Adults With Oily Scalp.},
journal = {Journal of cosmetic dermatology},
volume = {25},
number = {2},
pages = {e70714},
doi = {10.1111/jocd.70714},
pmid = {41644290},
issn = {1473-2165},
support = {//Proya Cosmetics Co. Ltd/ ; },
mesh = {Humans ; Female ; *Sebum/metabolism ; *Lipidomics/methods ; *Scalp/microbiology/metabolism ; Young Adult ; Adult ; *Dermatitis, Seborrheic/microbiology ; Metagenomics ; Microbiota ; *Scalp Dermatoses/microbiology ; China ; Dandruff/microbiology ; Lipids/analysis ; Paper ; East Asian People ; },
abstract = {BACKGROUND: Excessive sebum secretion leads to oily scalps, which can disturb microbial homeostasis and cause various scalp issues, such as sensitive scalp, dandruff, and seborrheic dermatitis.

AIMS: This study aimed to investigate the characteristics of scalp lipids and microbiota in a group of females with excessive sebum secretion using omics technology, and to identify important relationships between feature lipids and dominant functional microbes on oily scalp.

METHODS: Through comparison of three lipidomic sampling methods, we first selected absorbent paper (AP) as a cost-effective and practical method for untargeted lipidomic profiling. Using this method, we then collected scalp surface lipids from 85 Chinese female emerging adults with varying degrees of excessive sebum and performed internal standard quantified lipidomic profiling using UPLC-QE Plus-MS equipped with LipidSearch software version 5.1. Simultaneously, we collected and analyzed scalp microorganisms using PE150 pair-end metagenomic sequencing on the Illumina NovaSeq platform followed by taxonomic and functional annotation with bioinformatic tools and databases. Afterwards, multivariate statistical analysis and bioinformatics were used to identify feature lipids related to high sebum levels, discern the roles of dominant microbes involved in lipid metabolism, and explore potential correlations between feature lipids and dominant functional microbes of oily scalp.

RESULTS: After comparison of three lipidomic sampling materials, absorbent paper (AP) was selected to collect scalp surface lipids from 85 volunteers. A total of 13 lipid classes were annotated and the most abundant in ESI (+) mode was triacylglycerol (TG, 99.18%) whereas in ESI (-) mode were fatty acid (FA, 56.94%) and O-acyl-(gamma-hydroxy) FA (OAHFA, 34.15%). We identified 27 TGs and 3 FAs as the major lipid molecules contributing to high sebum levels. Seventy percent of these TGs were unsaturated (33% monounsaturated, 26% diunsaturated, 11% triunsaturated), and 30% were saturated. Meanwhile, we found that although the dominant microorganisms, Cutibacterium, Lawsonella, Malassezia, and Staphylococcus were all involved in lipid metabolism on the scalp, only some of them were related to the degree of sebum level and also displayed species-specific preferences for lipids. Among them, Lawsonella clevelandensis and Malassezia globosa were weakly negatively associated with both unsaturated and saturated TGs, while Malassezia restricta and Cutibacterium granulosum were only weakly negatively correlated with saturated TGs, and Cutibacterium namnetense was weakly positively correlated with FA (26:0).

CONCLUSIONS: This study describes relevant lipid molecules contributing to higher sebum production, and reveals that L. clevelandensis, M. restricta, M. globosa, C. namnetense, and C. granulosum on the scalp are closely correlated with these lipids, showing species-specific preference. These findings provide new insights into the interaction between key surface lipids and dominant functional microorganisms on oily scalps.},
}

Humans
Female
*Sebum/metabolism
*Lipidomics/methods
*Scalp/microbiology/metabolism
Young Adult
Adult
*Dermatitis, Seborrheic/microbiology
Metagenomics
Microbiota
*Scalp Dermatoses/microbiology
China
Dandruff/microbiology
Lipids/analysis
Paper
East Asian People

@article {pmid41644119,
year = {2026},
author = {Hung, JY and Cooke, I and Sato, Y and Miller, DJ and Bourne, DG},
title = {Microbial Metabolism and Disease Virulence Changes Across Day and Night in Coral Black Band Disease Lesions.},
journal = {Environmental microbiology},
volume = {28},
number = {2},
pages = {e70219},
doi = {10.1111/1462-2920.70219},
pmid = {41644119},
issn = {1462-2920},
support = {//Earthwatch Institute/ ; //James Cook University/ ; //Mitsubishi Corporation/ ; //JCU CTBMB grant/ ; //JCU OIRS Morris Family Trust grant/ ; },
mesh = {*Anthozoa/microbiology ; Animals ; Virulence ; *Bacteria/metabolism/genetics/pathogenicity ; *Cyanobacteria/metabolism/genetics ; Photosynthesis ; Metagenome ; Microbiota ; Light ; },
abstract = {Coral black band disease (BBD) is characterised as a cyanobacteria-dominated microbial mat that rapidly kills underlying coral tissue. Solar radiation promotes lesion progression by fuelling the cyanobacterial photosynthesis, while sulphate-reducing bacteria and sulphide-oxidising bacteria are implicated in sulphide dynamics within the mat. How the metabolism of the key microbial communities in the mat varies under light and dark conditions and impacts lesion virulence is poorly characterised, however. To compare microbial gene expression under different light regimes, we recovered 28 near-complete BBD-derived metagenome-assembled genomes (MAGs) using Oxford Nanopore Technologies long-read sequencing and profiled Illumina metatranscriptomic reads from BBD lesions collected at day and night by mapping to these MAGs. Genes from the cyanobacterium Roseofilum reptotaenium dominated the differentially expressed genes, with photosynthesis highly represented during the daytime. Relative expression of sulphur and nitrogen metabolism, cofactor biosynthesis, chemotaxis and motility increased among the non-cyanobacterial members at night. Enhanced sulphur reduction by Campylobacteriales and Desulfovibrionaceae at night likely supports a sulphide-rich and low oxygen micro-environment in the lesion, while increased chemotaxis and motility by Campylobacteriales and other heterotrophic bacteria drive lesion progression towards healthy coral tissue. This study provides insights into how diurnal light dynamics drive microbial metabolic pathways changes, thereby promoting BBD virulence.},
}

*Anthozoa/microbiology
Animals
Virulence
*Bacteria/metabolism/genetics/pathogenicity
*Cyanobacteria/metabolism/genetics
Photosynthesis
Metagenome
Microbiota
Light

@article {pmid41642221,
year = {2026},
author = {Pavan, RR and Sullivan, MB and Tisza, MJ},
title = {CRESSENT: a bioinformatics toolkit to explore and improve ssDNA virus annotation.},
journal = {Microbial genomics},
volume = {12},
number = {2},
pages = {},
doi = {10.1099/mgen.0.001632},
pmid = {41642221},
issn = {2057-5858},
mesh = {*Computational Biology/methods ; Genome, Viral ; *DNA Viruses/genetics/classification ; *DNA, Single-Stranded/genetics ; Phylogeny ; Metagenomics/methods ; *Molecular Sequence Annotation/methods ; *Software ; },
abstract = {ssDNA viruses are important components of diverse ecosystems; however, it remains challenging to systematically identify and classify them. This is partly due to their broad host range and resulting genomic diversity, structure and rapid evolutionary rates. In addition, distinguishing genuine ssDNA genomes from contaminating sequences in metagenomic datasets (e.g. from commercial kits) has been an unresolved issue for years. Here, we present CRESSENT (CRESS-DNA Extended aNnotation Toolkit), a comprehensive and modular bioinformatic pipeline focused on ssDNA virus 'genome-to-analysis' and annotation. The pipeline integrates multiple functionalities organized into several modules: sequence dereplication, decontamination, phylogenetic analysis, motif discovery, stem-loop structure prediction and recombination detection. Each module can be used independently or in combination with others, allowing researchers to customize their analysis workflow. With this tool, researchers can comprehensively and systematically include ssDNA viruses in their viromics workflows and facilitate comparative genomic studies, which are often limited to dsDNA viruses, therefore leaving behind a crucial component of the microbiome community under study. Benchmarking analyses demonstrated that CRESSENT efficiently processes ssDNA virus datasets of varying scales, completing small family-level analyses within minutes and moderate comparative genomics studies within hours using standard computing resources. Its modular, parallelized design ensures scalability and low memory usage, making it accessible to research groups with diverse computational capacities.},
}

*Computational Biology/methods
Genome, Viral
*DNA Viruses/genetics/classification
*DNA, Single-Stranded/genetics
Phylogeny
Metagenomics/methods
*Molecular Sequence Annotation/methods
*Software

@article {pmid41642002,
year = {2026},
author = {Williams, A and Maros, A and France, MT and Ravel, J and Holm, JB},
title = {Not all vaginal microbiomes are equal: functional context shapes immune landscapes.},
journal = {mBio},
volume = {},
number = {},
pages = {e0364525},
doi = {10.1128/mbio.03645-25},
pmid = {41642002},
issn = {2150-7511},
abstract = {Taxonomic classification alone fails to capture the ecological and functional diversity of vaginal microbiomes, particularly those dominated by Gardnerella species. Using the expanded VIRGO2 gene catalog, we developed the vaginal inference of subspecies and typing algorithm (VISTA), a novel ortholog-based framework that defined metagenomic subspecies and 25 metagenomic community state types (mgCSTs), including six distinct Gardnerella-dominated profiles. The mgCSTs exhibit marked differences in species composition, functional gene content, transcriptional activity, and host immune responses. These findings reveal that Gardnerella predominance does not uniformly equate to dysbiosis and underscore the importance of functional context in shaping host-microbiome interactions. VISTA provides scalable classifiers and an interactive application to support mechanistic studies of vaginal microbiome function and its implications for reproductive health.IMPORTANCEThe vaginal microbiome plays a central role in reproductive and gynecologic health, yet its functional diversity and ecological organization remain poorly understood. Traditional 16S rRNA approaches provide only a partial view of this complexity, overlooking the strain-level variation that often determines microbial behavior and host outcomes. By applying metagenomic sequencing and scalable computational modeling, we developed the vaginal inference of subspecies and typing algorithm, a framework that defines gene-based subspecies and community state types across diverse populations. These classifications reveal new insights into the genomic and ecological foundations of vaginal community structure and offer a standardized resource for comparative and translational microbiome research. This work establishes the foundation for functionally informed diagnostics and precision interventions targeting women's reproductive health.},
}

@article {pmid41641352,
year = {2025},
author = {Cao, XG and Zhu, XF and Ni, JX and Meng, HD and Huang, CJ},
title = {Optimizing metagenomic next-generation sequencing in CNS infections: a diagnostic model based on CSF parameters.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1681643},
pmid = {41641352},
issn = {2235-2988},
mesh = {Humans ; Female ; Male ; Retrospective Studies ; Middle Aged ; *Central Nervous System Infections/diagnosis/cerebrospinal fluid/microbiology ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Adult ; Aged ; ROC Curve ; *Cerebrospinal Fluid/cytology/chemistry ; Logistic Models ; Young Adult ; },
abstract = {OBJECTIVE: This study aimed to assess the association between routine cerebrospinal fluid (CSF) biochemical parameters and metagenomic next-generation sequencing (mNGS) results, and to develop a predictive model to optimize mNGS testing strategies in patients with suspected central nervous system (CNS) infections.

METHODS: We retrospectively enrolled 110 patients with suspected CNS infections between December 2019 and January 2024. All underwent both CSF analysis and mNGS testing. Patients were divided into mNGS-positive (n = 62) and negative (n = 48) groups. Logistic regression identified independent predictors, and a nomogram was constructed based on CSF cell count and protein concentration. Model performance was assessed via receiver operating characteristic (ROC) curves, calibration plots, and decision curve analysis (DCA). Internal validation included 10-fold cross-validation and 1000-sample bootstrap. An external validation was performed using a cohort of 40 patients enrolled from another hospital campus (May-October 2024). The derivation cohort was retrospectively collected, whereas the external validation cohort was prospectively enrolled.

RESULTS: mNGS positivity rate was 56.36%, significantly higher than CSF culture (6.36%), with an overall diagnostic concordance of 79.09%. Compared to the mNGS-negative group, positive patients had significantly higher CSF cell counts, protein levels, turbidity, ICU admission (ICUA), antimicrobial regimen adjustment (AAR), and mortality, while glucose was significantly lower (P < 0.05). Logistic regression confirmed CSF cell count binary variables (BV) and protein-BV as independent predictors (P < 0.05). The areas under curve (AUCs) for the cell-count, protein-only, and combined models were 0.827, 0.813, and 0.782, respectively. Internal validation showed stable results: 10-fold CV AUC = 0.773 ± 0.184 (95% CI: 0.641-0.904), bootstrap AUC = 0.770 ± 0.064 (95% CI: 0.766-0.774). External validation yielded an AUC of 0.763 (95% CI: 0.554-0.918), with sensitivity and specificity of 77.8% and 67.7%. Calibration and DCA demonstrated good agreement and clinical utility.

CONCLUSION: CSF cell count and protein are reliable predictors of mNGS positivity. The model for practice showed consistent diagnostic performance and may aid in guiding precision mNGS testing, particularly in resource-constrained settings.},
}

Humans
Female
Male
Retrospective Studies
Middle Aged
*Central Nervous System Infections/diagnosis/cerebrospinal fluid/microbiology
*High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
Adult
Aged
ROC Curve
*Cerebrospinal Fluid/cytology/chemistry
Logistic Models
Young Adult

@article {pmid41641055,
year = {2025},
author = {Lai, SY and Chang, L and Duan, JX and Che, GL and Yang, QX and Teng, J and Jian, H and Liu, XJ and Liu, F},
title = {Clinical and epidemiological characteristics of cat scratch disease in children from southwestern China: a retrospective analysis of mNGS-confirmed cases.},
journal = {Frontiers in public health},
volume = {13},
number = {},
pages = {1743423},
pmid = {41641055},
issn = {2296-2565},
mesh = {Humans ; *Cat-Scratch Disease/epidemiology/diagnosis/drug therapy ; Child ; Male ; Retrospective Studies ; Female ; China/epidemiology ; Adolescent ; *Bartonella henselae/isolation & purification/genetics ; Anti-Bacterial Agents/therapeutic use ; Cats ; Animals ; },
abstract = {BACKGROUND AND AIM: Cat scratch disease (CSD) is a zoonotic infection predominantly caused by Bartonella henselae, typically featured by regional lymphadenopathy and febrile illness. Although these classic features characterize most cases, the clinical spectrum extends to severe systemic manifestations including meningitis and neuroretinitis, leading to poor prognosis. Given this potential for diverse clinical presentations, prompt microbiological confirmation becomes essential for accurate diagnosis and appropriate management of CSD. The present study aimed to provide a comprehensive analysis of epidemiological patterns, clinical characteristics, diagnostic findings, and therapeutic outcomes in pediatric CSD cases, with the ultimate goal of optimizing early detection and enhancing the clinical understanding of this disease.

METHODS: This single-center retrospective study analyzed 20 pediatric cases diagnosed with CSD at West China Second University Hospital in southwestern China between September 2021 and July 2025. All diagnoses were established based on comprehensive clinical evaluation including medical history, characteristic symptoms, and imaging findings. Definitive B. henselae identification was achieved through metagenomic next-generation sequencing (mNGS). These diagnostic characteristics were systematically evaluated and discussed in detail.

RESULTS: Among the 20 patients with CSD included in the study, 18 (90.00%) reported a history of cat contact. Ten patients were male (50.00%). School-aged children (6-14 years) accounted for the majority of patients. Eleven cases (55.00%) occurred in autumn. Fever and lymphadenopathy were the primary reasons for hospitalization. B. henselae was detected in all cases using mNGS. Nine patients were diagnosed with atypical CSD, seven of whom were female. Atypical CSD was associated with higher body temperature and longer hospitalization stay. Antimicrobial agents, including azithromycin, doxycycline, and rifampin, achieved satisfactory therapeutic outcomes.

CONCLUSION: This study elucidates the epidemiological, clinical, and laboratory characteristics of CSD in children. mNGS may serve as a powerful tool to facilitate the diagnosis of CSD, including its atypical manifestations.},
}

Humans
*Cat-Scratch Disease/epidemiology/diagnosis/drug therapy
Child
Male
Retrospective Studies
Female
China/epidemiology
Adolescent
*Bartonella henselae/isolation & purification/genetics
Anti-Bacterial Agents/therapeutic use
Cats
Animals

@article {pmid41640977,
year = {2026},
author = {Xia, L and Xu, J and Chen, Z and Shen, Y and Zou, Y},
title = {Disseminated tuberculosis secondary to polymicrobial co-infection following long-term immunotherapy for sarcomatoid mesothelioma: A case report.},
journal = {Respiratory medicine case reports},
volume = {59},
number = {},
pages = {102367},
pmid = {41640977},
issn = {2213-0071},
abstract = {Malignant pleural mesothelioma (MPM), particularly its sarcomatoid subtype, is a highly aggressive sarcoma of the pleural lining with a dismal prognosis. Prolonged use of immune checkpoint inhibitors (ICIs), while improving survival in selected patients, can induce profound immunosuppression, increasing susceptibility to life-threatening opportunistic infections. This report describes a 77-year-old male with sarcomatoid MPM who developed fatal disseminated tuberculosis (TB), accompanied by concurrent Aspergillus and herpesvirus infections during extended immunotherapy. The case underscores the critical role of metagenomic next-generation sequencing (mNGS) in enabling rapid diagnosis of atypical TB reactivation in an immunocompromised host, even when conventional cultures are negative. mNGS identified co-infections with Aspergillus flavus and herpesviruses (HHV-5, HHV-4, HHV-1), demonstrating its superiority in polymicrobial infection detection.},
}

@article {pmid41640872,
year = {2026},
author = {Chen, YX and Sun, NQ and Mo, SJ},
title = {Rhapontin activating nuclear factor erythroid 2-related factor 2 to ameliorate Parkinson's disease-associated gastrointestinal dysfunction.},
journal = {World journal of gastroenterology},
volume = {32},
number = {4},
pages = {114468},
pmid = {41640872},
issn = {2219-2840},
mesh = {*NF-E2-Related Factor 2/metabolism ; Gastrointestinal Microbiome/drug effects ; Animals ; Humans ; *Parkinson Disease/complications ; *Gastrointestinal Diseases/etiology/therapy/microbiology ; Mice ; Disease Models, Animal ; Kelch-Like ECH-Associated Protein 1/metabolism ; Signal Transduction/drug effects ; Fecal Microbiota Transplantation ; Brain-Gut Axis/drug effects ; 1-Methyl-4-phenyl-1,2,3,6-tetrahydropyridine ; },
abstract = {This commentary provides a critical evaluation of the study by Wang et al, which focuses on rhapontin activating colonic nuclear factor erythroid 2-related factor 2 (NRF2) to explore its therapeutic potential for Parkinson's disease (PD)-associated gastrointestinal dysfunction. The commentary acknowledges the academic value of the study: It has not only validated intestinal NRF2 as a therapeutic target for PD but also provided experimental support for the "enteric pathology hypothesis". However, several key gaps remain unresolved in the study. At the gut microbiota level, the exploration of the causal relationship of the microbiota is insufficient, with no validation conducted via methods such as fecal microbiota transplantation; additionally, it fails to systematically integrate the gut-brain axis with PD and does not assess the impact of rhapontin on the composition or function of the gut microbiota. At the pathway mechanism level, it lacks an analysis of the crosstalk between NRF2 and other rhapontin-targeted pathways, including nuclear factor kappa-B, mitogen-activated protein kinase, adenosine monophosphate-activated protein kinase, and sirtuin 1. At the experimental method level, the behavioral testing methods for PD mouse models and the limitations of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine-induced mouse models need attention. Additionally, certain flaws exist in some experimental result figures. Furthermore, this commentary puts forward improvement suggestions for the study. Future research should prioritize multi-omics analysis, encompassing combined metabolomics and metagenomics detection, while conducting mechanistic validation of NRF2-interacting molecules (KEAP1 and p62). In addition, it is necessary to improve refined behavioral tests, focusing on incorporating cognitive function and anxiety-related assessment items.},
}

*NF-E2-Related Factor 2/metabolism
Gastrointestinal Microbiome/drug effects
Animals
Humans
*Parkinson Disease/complications
*Gastrointestinal Diseases/etiology/therapy/microbiology
Mice
Disease Models, Animal
Kelch-Like ECH-Associated Protein 1/metabolism
Signal Transduction/drug effects
Fecal Microbiota Transplantation
Brain-Gut Axis/drug effects
1-Methyl-4-phenyl-1,2,3,6-tetrahydropyridine

@article {pmid41640705,
year = {2026},
author = {Wang, HJ and Zhang, YN and An, L},
title = {Clinical and radiographic feature of pulmonary nocardiosis: A study of 102 cases.},
journal = {World journal of radiology},
volume = {18},
number = {1},
pages = {114552},
pmid = {41640705},
issn = {1949-8470},
abstract = {BACKGROUND: Nocardia pneumonia is an infection that occurs in patients with underlying diseases. Previously, due to limited detection methods, its detection rate and typing posed significant challenges. However, with advancements in detection techniques, the detection rate has significantly increased, and different Nocardia species exhibit distinct imaging characteristics.

AIM: To retrospectively analyze the etiological and imaging features of pulmonary Nocardia pneumonia and to examine the differences in chest imaging manifestations among different Nocardia species.

METHODS: The medical records of 102 patients with pulmonary nocardiosis who were admitted to Beijing Chaoyang Hospital from January 2017 to December 2024 were collected. Data including name, gender, underlying comorbidities, etiological characteristics, diagnostic methods, chest computed tomography features, and therapeutic agents were recorded.

RESULTS: Among the 102 patients, 55 were male and 47 were female, with a median age of 61 years. Bronchiectasis was the most common comorbidity, observed in 54 patients (52.9%). Sixty percent were diagnosed using metagenomic next-generation sequencing. Nocardia gelsenkin was the most prevalent Nocardia specie, while Aspergillus and Pseudomonas aeruginosa were identified as the predominant co-pathogens in these pulmonary nocardiosis cases. Pneumonia caused by Nocardia wallacei primarily presented with bronchopneumonia as the main imaging feature, while other Nocardia species more commonly manifested as consolidation, often accompanied by nodules, cavities, and pleural effusion. The imaging features in immunosuppressed patients were more diverse, with frequent coexistence of multiple patterns.

CONCLUSION: Nocardia pneumonia commonly coexists with bronchiectasis. While metagenomic next-generation sequencing has greatly enhanced its detection rate, Nocardia wallacei pneumonia is distinguished on chest computed tomography by its primary presentation of bronchopneumonia, unlike other types.},
}

@article {pmid41640408,
year = {2025},
author = {Sun, G and Zou, Q and Wang, B},
title = {The interplay of carbon and nitrogen cycling driven by watershed microorganisms.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1696238},
pmid = {41640408},
issn = {1664-302X},
abstract = {Microorganisms play central roles in regulating carbon and nitrogen cycling across watersheds, driving processes such as organic matter decomposition, primary production, nitrification, and denitrification. Rapid advances in high-throughput sequencing and environmental monitoring have enabled unprecedented insights into the taxonomic diversity and functional capacities of microbial communities under global change. In this review, we synthesize findings from studies published in recent years to evaluate how hydrological connectivity, redox gradients, temperature shifts, and nutrient loading shape microbial metabolism across rivers, lakes, wetlands, and coastal interfaces. We further summarize emerging evidence on how antibiotic resistance genes (ARGs) propagate through these ecosystems and influence microbial functions. The integration of multi-omics technologies including metagenomics, metatranscriptomics, combined with ecological and biogeochemical modeling provides new opportunities to quantify microbe-mediated carbon sequestration and nitrogen transformation. Finally, we discuss current knowledge gaps, including the limited understanding of ARG-driven community restructuring and the insufficient mechanistic resolution of microbe-environment interactions under future climate scenarios. This review highlights the need for cross-scale, data-integrated frameworks to better predict how microbial processes regulate watershed-level biogeochemical cycles in a rapidly changing world.},
}

@article {pmid41640402,
year = {2025},
author = {Williams, AD and Hooton, SPT and King, E and Avery, LM and Hough, RL and Hobman, JL and Stekel, DJ and Neal, AL and West, HM},
title = {Temporal signals in dairy cattle slurry and fertilized field soil resistomes and bacterial communities.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1666851},
pmid = {41640402},
issn = {1664-302X},
abstract = {INTRODUCTION: Dairy cattle waste is a globally significant source of organic fertilizer which contains a cocktail of microbes and antibiotic resistance genes (ARGs). These ARGs may present a risk to human and animal health, yet there is still limited farm-system-level understanding of how long-term and multiple slurry applications alter field soil resistomes and total microbial communities.

METHODS: Using metagenomics, we assessed both immediate and longer-term changes in grassland field soil resistomes and bacterial communities over a year of routine cattle slurry application.

RESULTS: Our findings suggest that soil microbial communities are resilient to bacteria and ARGs introduced via slurry, even after repeated applications. Most slurry-borne ARGs were not enriched in field soil, however, those common in soil, such as rifamycin resistance genes, were consistently elevated relative to field soil with no history of slurry application. We observed transient increases in slurry-associated macrolide-lincosamide-streptogramin ARGs, however, their persistence appeared to be influenced by timing of slurry application. Similar transient effects were shown by the recovery of a high quality, slurry-associated Proteiniphilum spp. metagenome assembled genome (MAG).

DISCUSSION: We show that MAGs represent a powerful tool for examining the transfer of slurry-borne microorganisms, as they can be more characteristic of these environments than typical sentinel organisms which are easily cultivated. Our findings indicate that while the soil bacterial community shows considerable resilience to slurry-borne bacteria and ARGs, this may be diminished by temporal factors that remain largely unexplored and poorly understood. This is important because resilience inferred from short-term observations may not fully capture delayed or transient responses, potentially leading to underestimation of the persistence of slurry-borne bacteria and ARGs.},
}

@article {pmid41640388,
year = {2026},
author = {Li, S and Li, W and Zhang, X and Zhou, H and Zhan, J},
title = {Harnessing Population Genomics, Gut Microbiota, and Environmental DNA Surveillance for the Conservation of Chinese Spotted Seals in a Changing World.},
journal = {Ecology and evolution},
volume = {16},
number = {2},
pages = {e72952},
pmid = {41640388},
issn = {2045-7758},
abstract = {The triple planetary crisis-encompassing climate change, biodiversity loss, and pollution-poses escalating threats to Earth's systems, particularly impacting marine mammals. The spotted seal (Phoca largha Pallas 1811), currently recognized as the only pinniped species known to breed in China, holds the status of a National Grade I protected species in China. To elucidate the genetic diversity of Chinese spotted seal populations and provide scientific foundations for their conservation and management, this review systematically summarized the fundamental biological characteristics and documented migration routes of spotted seal populations in China, with particular emphasis on reviewing molecular-level research advancements regarding population genetic structure. Early studies primarily employed molecular markers such as microsatellite DNA and mitochondrial DNA (mtDNA), revealing relatively low genetic diversity levels within Chinese spotted seal populations. In recent years, rapid developments in omics technologies have enabled comprehensive investigations into both genomic compositions, as well as gut microbial community diversity and functional profiles of this species. Furthermore, this review critically examined current research limitations and challenges while proposing the potential advantages and developmental trends of environmental DNA (eDNA) technology in future population studies. These technological and strategic advancements are anticipated to significantly enhance survey efficiency and conservation effectiveness for Chinese spotted seal populations.},
}

@article {pmid41639832,
year = {2026},
author = {Ma, R and Sun, J and Zhu, J and Wu, Y and Shi, Y and Yang, Y and Wang, S and Han, X and Li, S and Gao, L and Zhao, X and Hua, R and Wang, Y},
title = {Metagenomic next-generation sequencing for efficient detection of human parvovirus B19 in amniotic fluid: a case study of diagnosis and prenatal management of fetal infection.},
journal = {BMC pregnancy and childbirth},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12884-026-08743-9},
pmid = {41639832},
issn = {1471-2393},
support = {HHJH2412//Medical Science and Technology Talent Promotion Project of The International Peace Maternity and Child Health Hospital/ ; 2023YFC2705901//National Science and Technology Major Project/ ; 22Y11902300//Science and Technology Commission of Shanghai Municipality/ ; 202440131//Shanghai Municipal Health Commission/ ; YG2023ZD26//Shanghai Jiao Tong University/ ; },
}

@article {pmid41639568,
year = {2026},
author = {Zeng, Y and Qi, H and Guo, W and Tan, X and Huang, B and Hu, R and Ouyang, X},
title = {Multi-omics insights into Shenling Baizhu Powder's amelioration of murine asthma through gut microbiota and Glutamine-GLS1 pathway.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-38440-8},
pmid = {41639568},
issn = {2045-2322},
support = {2023BSQD002//Doctoral Scientific Initiate Project of Shunde Women and Children's Hospital of Guangdong Medical University (Maternity & Child Healthcare Hospital of Shunde Foshan)/ ; 20241090//The Project of Administration of Traditional Chinese Medicine of Guangdong Province/ ; 2023A04J0550//Guangzhou Municipal Science and Technology Project/ ; 20250403//Medical Research Project of Foshan Municipal Health Bureau/ ; },
abstract = {Shenling Baizhu Powder (SLBZP) is a prominent formulation widely used in the treatment of pulmonary diseases. However, studies examining the mechanisms of SLBZP for treating asthma are limited. This study aimed to clarify the efficacy and possible mechanisms of SLBZP in the context of asthma from the perspective of gut microbiota-metabolism-immune crosstalk. Key parameters including airway hyperresponsiveness, lung pathological features and the expression of inflammatory mediators from Th2 and Th17 cells were employed to validate the anti-inflammatory properties of SLBZP. The anti-asthma mechanism of SLBZP was investigated using metagenomic sequencing, metabolomics, flow cytometry, RT-qPCR, immunohistochemistry (IHC) and immunofluorescence (IF). SLBZP demonstrated significant capacity to mitigate histopathological alterations associated with ovalbumin-induced asthma and suppress the secretion of inflammatory mediators (IL-4, IL-5, IL-13 and IL-17A) in BALF. Metagenomic results demonstrated that the protective effects of SLBZP were primarily associated with Ligilactobacillus, Eubacterium and Clostridium. Additionally, metabolomics results identified that three vital metabolic pathways were substantially regulated by SLBZP in asthmatic mice, especially D-glutamine and -glutamate metabolism. Furthermore, IHC and IF results showed that SLBZP significantly inhibited the expression of GLS1 and GOT1, which inhibited the conversion of L-glutamine to α-ketoglutarate and regulated the imbalance of Th1/Th2 and Treg/Th17. RT-qPCR results showed that SLBZP promoted the expressions of T-bet, IFN-γ, IL-10 and Foxp3 mRNA, and inhibited the expression of GATA3, IL-4, IL-5, IL-13, IL-17A and RORγt mRNA. The findings from flow cytometry provided additional evidence. Thus, this modulated the imbalance of Th1/Th2 and Treg/Th17 and exerted the immunomodulatory properties of SLBZP. SLBZP exerted protective effects against OVA-induced asthma and modified the structure and functional characteristics of the gut microbiota, and serum metabolite profiles in asthmatic mice. The anti-asthma mechanism of SLBZP may be associated with the modulation of the gut microbiota and Glutamine-GLS1 pathway.},
}

@article {pmid41639269,
year = {2026},
author = {Piera Líndez, P and Danielsen, LS and Kovačić, I and Pielies Avellí, M and Nesme, J and Jensen, LJ and Andersen, JN and Sørensen, SJ and Rasmussen, S},
title = {Accurate plasmid reconstruction from metagenomics data using assembly-alignment graphs and contrastive learning.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {41639269},
issn = {1546-1696},
support = {NNF20OC0062223//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF14CC0001//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF23SA0084103//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF20OC0062223//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF23SA0084103//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF20OC0062223//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF14CC0001//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF20OC0062223//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF20OC0062223//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF23SA0084103//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF20OC0062223//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; },
abstract = {Plasmids are extrachromosomal DNA molecules that enable horizontal gene transfer in bacteria, often conferring advantages such as antibiotic resistance. Despite their importance, plasmids are underrepresented in genomic databases because of challenges in assembling them, caused by mosaicism and microdiversity. Current plasmid assemblers rely on detecting circular paths in single-sample assembly graphs but face limitations because of graph fragmentation, entanglement and low coverage. We introduce PlasMAAG (plasmid and organism metagenomic binning using assembly-alignment graphs), a method to recover plasmids and cellular genomes from metagenomic samples. PlasMAAG complements assembly graph signals across samples by generating an 'assembly-alignment graph', which is used alongside common binning features for improved plasmid reconstruction. On synthetic benchmark datasets, PlasMAAG reconstructed 50-121% more near-complete plasmids than competing methods and improved the Matthews correlation coefficient of geNomad contig classification by 28-106%. On hospital sewage samples, PlasMAAG outperformed competing methods, reconstructing 33% more plasmid sequences. PlasMAAG enables the study of organism-plasmid associations and intraplasmid diversity across samples.},
}

@article {pmid41639055,
year = {2026},
author = {Lai, D and Mosier, D and Palmer, M and Mayali, X and Johnston, J and Saldivar, W and Covington, JK and Jiao, JY and Murali, R and Seymour, CO and Liu, L and Hua, ZS and Li, WJ and Weber, PK and Pett-Ridge, J and Colman, DR and Boyd, ES and Nunoura, T and Dodsworth, JA and Hedlund, BP},
title = {Branched-chain amino acid specialization drove diversification within Calditenuaceae (Caldarchaeia) and enables their cultivation.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-68859-6},
pmid = {41639055},
issn = {2041-1723},
support = {1557042//National Science Foundation (NSF)/ ; 2038420//National Science Foundation (NSF)/ ; 80NNSC17KO548//National Aeronautics and Space Administration (NASA)/ ; 80NSSC25M0046//National Aeronautics and Space Administration (NASA)/ ; 80NSSC19M0150//National Aeronautics and Space Administration (NASA)/ ; 92251302//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32370011//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Many thermophiles that are abundant in high-temperature geothermal systems have never been cultivated and are poorly understood, including deeply branching members of the archaeal phylum Thermoproteota. Here, we describe the genome-guided cultivation of one such organism, Calditenuis ramacidaminiphagus, and show that it has evolved a heterotrophic metabolism focused on branched-chain amino acids (BCAAs). Initially, fluorescence in situ hybridization and nanoscale secondary ion mass spectrometry (FISH-nanoSIMS) showed that Cal. ramacidaminiphagus assimilated amino acids rapidly in casamino acid-amended enrichment cultures. Metagenome and metaproteome analyses showed a high abundance and expression of BCAA transporter genes, suggesting a BCAA-focused metabolism. This inference was supported by the subsequent enrichment of Cal. ramacidaminiphagus in BCAA-fed cultures, reaching 2.66×10[6] cells/mL and 48.7% of the community, whereas it was outcompeted when polar amino acids were included. Metabolic reconstruction and metaproteomics suggest that BCAAs are channeled into the mevalonate pathway for lipid biosynthesis and fuel ATP production through the TCA cycle coupled with aerobic respiration and through production of branched-chain organic acids by overflow metabolism. Ancestral state reconstructions and phylogenetic analyses of 62 Caldarchaeales genomes revealed multiple horizontal transfers of BCAA transporters to the ancestor of the genus Calditenuis. Our study highlights the crucial role of BCAAs in the early evolution and niche of this genus, and suggests a high degree of resource partitioning even within low-diversity thermophilic communities.},
}

@article {pmid41638592,
year = {2026},
author = {Xiao, Y and Cheng, Z and Cai, J and Guo, Z and Chen, J and Su, Y and Cao, F and Chen, D},
title = {Metagenomic and metatranscriptomic analysis of sulfur-driven autotrophic denitrification coupled with carbon assimilation: roles of sulfur-to-nitrogen ratio and hydraulic retention time.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134153},
doi = {10.1016/j.biortech.2026.134153},
pmid = {41638592},
issn = {1873-2976},
abstract = {The sulfur autotrophic denitrification (SAD) process is a promising technology for nitrogen-containing wastewater treatment, with research predominantly focused on nitrate and sulfide transformations, while the potential for inorganic carbon assimilation remains underexplored. In this study, a long-term stable SAD system was maintained in an airlift bioreactor by adding an inorganic carbon source to evaluate the effects of sulfur-to-nitrogen (S/N) ratio and hydraulic retention time (HRT) on operational performance. Under optimal operating conditions (S/N = 3:2; HRT = 8h), the system sustained high performance, achieving 99.56 ± 1.47% nitrate removal, 60.28 ± 4.19% elemental sulfur yield, and 46.48 ± 4.07% inorganic carbon assimilation efficiency. Biomass sulfur acted as a sink for extracellular free organic carbon (EFOC), thereby alleviating its accumulation-induced negative feedback on carbon assimilation. Microbial community analysis revealed a substantial enrichment of the autotrophic sulfur-oxidizing bacterium Sulfurovum, showing a marked 9.46-fold increase in relative abundance compared with the original sludge. At S/N = 3:2, metagenomic and metatranscriptomic analyses detected a 6.39-fold increase in the transcription of CBB cycle genes (rbcL/rbcS), driving a clear shift in metabolic flux toward carbon assimilation. Shortening the HRT (4 h) preferentially activated the denitrification pathway, which was evidenced by an 84.65% rise in nosZ expression (from 2,623.29 to 4,844.01 TPM), thereby bolstering N2O reduction. Our findings offered critical insights for designing engineering solutions that enable concurrent efficient denitrification, sulfur recovery, and reduced carbon emissions.},
}

@article {pmid41638346,
year = {2026},
author = {Behrens, LMP and Fernandes, GDS and Gonçalves, GF and Nunes, FVM and Weimer, RD and Moreira, JCF and Dorn, M},
title = {Limitations and opportunities in multi-omics integration for neurodevelopmental, neurodegenerative and psychiatric disorders: A systematic review.},
journal = {Neuroscience},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.neuroscience.2026.01.019},
pmid = {41638346},
issn = {1873-7544},
abstract = {Recent advances in high-throughput technologies have led to an increased generation of biological data across genomics, transcriptomics, proteomics, epigenomics, and metabolomics. However, a major challenge remains: effectively integrating these multi-omics datasets to allow a more holistic understanding of the complex, interconnected mechanisms underlying human diseases. Neurodevelopmental, neurodegenerative, and psychiatric disorders are particularly multifactorial and heterogeneous, making them candidates for multi-omics approaches. In this context, this systematic review assesses the current state of multi-omics integration in neurological research. Records retrieved from five major databases were processed, and 156 studies were included for further analysis. The most frequently studied conditions were Alzheimer's Disease, Depressive Disorder and Parkinson's Disease, with epigenomics-transcriptomics and metagenomics-metabolomics emerging as the most common omics pairings. The field remains dominated by studies integrating pairs of omics layers. Only a limited number of computational tools are currently being applied to the integration of more than two omics layers, highlighting a gap in comprehensive multi-omics modeling. Despite progress, key challenges persist, including data accessibility and the need for standardized frameworks to allow cross-study comparisons. Moreover, most computational findings lack experimental validation in wet-laboratory settings. Future research should address these challenges, develop scalable algorithms for integrating multi-omics data, and leverage large, open-access datasets. Integrating computational predictions with experimental validation could help researchers prioritize high-confidence biomarkers relevant to clinical applications. Collaborative efforts among bioinformaticians, clinicians, and experimentalists will be essential to translating these advances into clinically actionable solutions.},
}

@article {pmid41638332,
year = {2026},
author = {Wu, B and Zhang, N and Yang, G and Yu, N and Xie, Z and Xia, J and Luo, W and Liu, X and Wang, D and Zhang, Y and Tang, L},
title = {Unraveling the microbial and functional mechanisms driving rapid algal-bacterial granular sludge formation in mariculture wastewater.},
journal = {Environmental research},
volume = {},
number = {},
pages = {123941},
doi = {10.1016/j.envres.2026.123941},
pmid = {41638332},
issn = {1096-0953},
abstract = {Algal-bacterial granular sludge (ABGS) has unique advantages and broad application prospects in the treatment of mariculture wastewater. However, the rapid granulation process and performance evolution of ABGS under high salt stress have not been clearly defined. Compared with AGS, the influence of algal intervention on the structural integrity and metabolic activity of particles under the same salinity gradient is also unknown. Therefore, in this study, a parallel ABGS and AGS system was established. The results showed that intertwined algal filaments provided a structural skeleton for particle formation and led to complete granulation of ABGS within 20 days. Compared with conventional AGS, ABGS formed under high-salinity conditions exhibited a larger average particle size (1.07 mm), higher biomass (7.59 g/L) and higher extracellular polymeric substance (EPS) secretion (258.56 mg/g VSS). Additionally, chemical oxygen demand (COD) and total inorganic nitrogen (TIN) removal efficiencies exceeded 99% and 66%, respectively. Metagenomic analysis revealed that Thauera, Fragilaria and Nitzschia were dominant taxa associated with granule formation and stabilization. ABGS also showed an elevated abundance of functional genes associated with nitrogen metabolism (nxrA, nasA, and nasD) and polysaccharide metabolism (glmM, glmU, and pmm-pgm), which were in accordance with the enhanced nitrogen removal and granulation capability. Increased abundance of tricarboxylic acid cycle genes further indicated the superior granulation performance of ABGS. Overall, this study clarifies the morphological evolution and microbial functional mechanisms underlying rapid ABGS formation in mariculture wastewater, offering valuable insights for engineering optimisation and application of this technology in saline wastewater treatment.},
}

@article {pmid41638014,
year = {2026},
author = {Song, Y and Song, X and Liu, X and Jiang, L and Chai, L},
title = {Metagenomics and targeted metabolomics uncover concomitant gut microbiota dysbiosis and bile acid metabolism alteration in norfloxacin-exposed Bufo gargarizans tadpoles.},
journal = {Aquatic toxicology (Amsterdam, Netherlands)},
volume = {292},
number = {},
pages = {107742},
doi = {10.1016/j.aquatox.2026.107742},
pmid = {41638014},
issn = {1879-1514},
abstract = {Norfloxacin (NOR) is a fluoroquinolone antibiotic widely detected in aquatic environments, yet little is known about its toxic effects on amphibians. Bile acids (BAs) are crucial metabolites derived from gut microbiota-host co-metabolism and play vital roles in maintaining host health. BA composition is regulated by the gut microbiota through specific enzymes: bile salt hydrolases (BSHs) deconjugate primary BAs; bile acid-inducible enzymes (BAIs) and hydroxysteroid dehydrogenases (HSDHs) then convert them into secondary BAs. This study investigated the effects of NOR on Bufo gargarizans tadpoles using a combination of intestinal-targeted BA metabolomics, metagenomics, and histopathological analysis. Tadpoles were exposed to 10 and 100 μg/L NOR from Gs26 to Gs36, with 4 independent biological replicates per group. Our results showed that NOR exposure significantly increased the relative abundance of gut microbiota encoding BAIs, HSDHs, and/or BSHs, which was accompanied by a decrease in the ratios of primary/secondary BAs and conjugated/deconjugated BAs. Meanwhile, NOR treatment elevated antibiotic resistance gene abundance and induced intestinal histopathological alterations in tadpoles, characterized by reduced epithelial cell height and hypertrophy of smooth muscle cells (SMCs). In summary, environmentally relevant concentrations (10 and 100 μg/L) of NOR affected the intestinal microbiota, thereby disrupting BAs biotrasformation, ultimately potentially compromising intestinal health in tadpoles. This highlighted the potential ecological risks posed by NOR pollution in aquatic ecosystems.},
}

@article {pmid41637515,
year = {2026},
author = {Liu, X and Cheng, X and Zhang, Y and Zhao, R and Wang, W and Li, Y and Chen, ZQ and Qiu, X and Tuovinen, OH and Bull, ID and Evershed, RP and Wang, H},
title = {High-efficiency methane consumption by atmospheric methanotrophs in subsurface karst caves: The irrefutable methane sink.},
journal = {Science advances},
volume = {12},
number = {6},
pages = {eady5942},
pmid = {41637515},
issn = {2375-2548},
mesh = {*Methane/metabolism ; *Caves/microbiology ; Oxidation-Reduction ; *Atmosphere/chemistry ; Soil Microbiology ; Phylogeny ; },
abstract = {Subsurface karst systems represent substantial but underexplored methane sinks, yet the identities and activities of cave-dwelling methanotrophs remain poorly characterized. We detected increased methane oxidation rates from 2.9 ± 0.1 to 90.7 ± 4.5 ng·g[-1]·hour[-1] while supplied with 2 to 500 parts per million (ppm) CH4 to cave sediments. Atmospheric methanotroph Upland Soil Clusters γ (USCγ), responsible for this oxidation, was further assigned to three genera within the family Candidatus (Ca.) Methyloligotrophaceae, including two previously unrecognized genera. Nano-scale secondary ion mass spectrometry (NanoSIMS) imaging and the produced [13]C-PLFAs (phospholipid fatty acids) and [13]CO2 in [13]CH4-fed microcosm confirmed methane as both carbon and energy sources. These methanotrophs exhibited low half-saturation constant (Km; 138.8 ± 15.8 ppm), high carbon assimilation efficiency (>50%), and metabolic versatility, as revealed by metagenomics and metatranscriptomics analyses. By extrapolating global distribution of Ca. Methyloligotrophaceae and comparing methane oxidation rates between caves and soil ecosystems, we conservatively estimate that subsurface karst in southwest China sequester ~0.56 Tg CH4 annually. These findings highlight the ecological importance of karst ecosystems as a previously overlooked methane sink.},
}

*Methane/metabolism
*Caves/microbiology
Oxidation-Reduction
*Atmosphere/chemistry
Soil Microbiology
Phylogeny

@article {pmid41637508,
year = {2026},
author = {Kaur, G and Crawford, SE and Javornik Cregeen, S and Surathu, A and Ayyar, BV and Apostol, CV and Phuc, HN and Ettayebi, K and Boussattach, A and Zeng, XL and Blutt, SE and Doddapaneni, H and Muzny, DM and Coarfa, C and Anish, R and Prasad, BVV and Atmar, RL and Ramani, S and Estes, MK},
title = {Overcoming host restrictions to enable continuous passaging of GII.3 human norovirus in human intestinal enteroids.},
journal = {Science advances},
volume = {12},
number = {6},
pages = {eaeb0455},
pmid = {41637508},
issn = {2375-2548},
mesh = {Humans ; *Norovirus/physiology/genetics ; Virus Replication/drug effects ; *Caliciviridae Infections/virology ; *Intestines/virology ; *Host-Pathogen Interactions ; *Organoids/virology ; Chemokines/metabolism/genetics ; Gastroenteritis/virology ; },
abstract = {The establishment of human intestinal enteroids (HIEs) as a model for human norovirus (HuNoV) replication has been transformative for studying this leading cause of gastroenteritis. However, indefinite passaging of HuNoVs in HIEs remained a challenge, necessitating the use of patient stool samples as viral inocula. Using RNA-seq, we identified CXCL10, CXCL11, and CCL5 as up-regulated chemokines, suggesting their potential as host restriction factors. TAK-779, a CXCR3/CCR5/CCR2 antagonist, enhanced GII.3 HuNoV replication and viral spread in a dose- and time-dependent manner, enabling successful passaging of GII.3 HuNoV in two different HIE lines and generation of viral stocks. Sequencing passaged virus revealed one consensus change in the major capsid protein and several dynamic adaptations, suggesting emergence of variants. TAK-779 also enhanced replication of GI.1 and GII.17 strains, but not GII.4, suggesting strain-specific host interactions. This breakthrough in passaging provides insight into HuNoV-host interactions, establishes a scalable in vitro system for virus propagation, and opens avenues for structural, biochemical, and therapeutic studies.},
}

Humans
*Norovirus/physiology/genetics
Virus Replication/drug effects
*Caliciviridae Infections/virology
*Intestines/virology
*Host-Pathogen Interactions
*Organoids/virology
Chemokines/metabolism/genetics
Gastroenteritis/virology

@article {pmid41637142,
year = {2026},
author = {Dos Santos, SJ and Gloor, GB},
title = {Incorporating Scale Uncertainty into Differential Expression Analyses Using ALDEx2.},
journal = {Current protocols},
volume = {6},
number = {2},
pages = {e70307},
pmid = {41637142},
issn = {2691-1299},
mesh = {Uncertainty ; *Gene Expression Profiling/methods ; *Software ; *Transcriptome ; Humans ; Principal Component Analysis ; *Metagenomics/methods ; Sequence Analysis, RNA/methods ; RNA-Seq/methods ; },
abstract = {Differential abundance or expression analyses are routinely performed on metagenomic, metatranscriptomic, and amplicon sequencing data. In such datasets, analysts usually have no information regarding the true scale (i.e., size) of the microbial community or sample under study, with inter-sample differences in sequencing depth instead being driven by technical variation rather than biological factors. Recent work has demonstrated that normalizations used in all analysis tools make incorrect assumptions about the biological scale of the system in question, leading to unacceptably high false-discovery rates in the output. To mitigate this, analysts can acknowledge and account for the uncertainty of the overall system scale during normalization by building scale models of the data-a feature that has been integrated into the ALDEx2 R package. Here, we provide reproducible examples that demonstrate how to incorporate scale models into differential expression analyses of RNA-seq data using bulk transcriptome and metatranscriptomic datasets, as well as the consequences of not doing so. We also show how to use the output of ALDEx2 to create high-level exploratory visualizations of their data through principal component analysis. © 2026 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Using a simple scale model for differential expression analysis to avoid dual-cutoff P value/significance thresholds Basic Protocol 2: Implementing a full informed scale model to correct scale-related data asymmetry in differential expression analyses Basic Protocol 3: Visualizing ALDEx2 outputs using a compositional approach: Principal component analysis.},
}

Uncertainty
*Gene Expression Profiling/methods
*Software
*Transcriptome
Humans
Principal Component Analysis
*Metagenomics/methods
Sequence Analysis, RNA/methods
RNA-Seq/methods

@article {pmid41636536,
year = {2026},
author = {Della-Negra, O and Servien, R and Milferstedt, K and Hamelin, J and Klopp, C and Hoede, C},
title = {Metagenome-assembled genomes from oxygenic photogranules obtained from photobioreactors treating synthetic wastewater.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0131025},
doi = {10.1128/mra.01310-25},
pmid = {41636536},
issn = {2576-098X},
abstract = {Twenty-five high-quality metagenome-assembled genomes (MAGs) were recovered from photogranules to treat synthetic wastewater. They were dominated by Leptolyngbya boryana. Cyanobacterial MAGs encoded photosynthesis and nitrogen fixation pathways, supporting internal oxygen and nitrogen cycling. Most heterotrophic MAGs contributed to nitrogen removal, highlighting the metabolic complementarity within photogranules studied for wastewater treatment.},
}

@article {pmid41636510,
year = {2026},
author = {Anne Hallowell, H and Malogan, J and Suez, J},
title = {Tools and approaches to study the human gut virome: from the bench to bioinformatics.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0100225},
doi = {10.1128/msystems.01002-25},
pmid = {41636510},
issn = {2379-5077},
abstract = {The human gastrointestinal tract is home to a diverse community of microorganisms from all domains of life, collectively referred to as the gut microbiome. While gut bacteria have been studied extensively in relation to human host health and physiology, other constituents remain underexplored. This includes the gut virome, the collection of bacteriophages, eukaryotic viruses, and other mobile genetic elements present in the intestine. Like gut bacteria, the gut virome has been causatively linked to human health and disease. However, the gut virome is substantially more difficult to characterize, given its high diversity and complexity, as well as multiple challenges related to in vitro cultivation and in silico detection and annotation. In this mini-review, we describe various methodologies for examining the gut virome using both culture-dependent and culture-independent tools. We highlight in vitro and in vivo approaches to cultivate viruses and characterize viral-bacterial host dynamics, as well as high-throughput screens to interrogate these relationships. We also outline a general workflow for identifying and characterizing uncultivated viral genomes from fecal metagenomes, along with several key considerations throughout the process. More broadly, we aim to highlight the opportunities to synergize and streamline wet- and dry-lab techniques to robustly and comprehensively interrogate the human gut virome.},
}

@article {pmid41636495,
year = {2026},
author = {Kopp, OS and Morandi, SC and Kreuzer, M and Uldry, A-C and Eldridge, N and Zinkernagel, MS and Zysset-Burri, DC},
title = {Impact of contact lenses on the ocular surface microbiome, tear proteome, and dry eye disease.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0226425},
doi = {10.1128/spectrum.02264-25},
pmid = {41636495},
issn = {2165-0497},
abstract = {Although contact lens wear is widespread and known to affect the ocular surface, its impact on the ocular surface microbiome (OSM) remains poorly understood, with existing studies reporting conflicting findings. Additionally, the relationship between contact lens wear, tear proteome, and dry eye disease (DED) is unclear. In this study, we aimed to characterize the OSM (via whole-metagenome shotgun sequencing) and the tear proteome of 25 contact lens wearers and 23 age- and sex-matched controls. The dominant phyla were Actinobacteria, Proteobacteria, and Firmicutes, with Cutibacterium acnes being the most abundant species. No significant differences in microbial composition, diversity, or tear proteome were observed between contact lens wearers and controls. DED parameters (tear breakup time, Schirmer's test, tear osmolarity, and Ocular Surface Disease Index [OSDI]) also showed no significant differences, although contact lens wearers reported a trend toward higher subjective symptoms (OSDI). Sex-stratified analysis revealed a marginal difference in microbial beta diversity between male contact lens wearers and male controls, along with increased tear production in male contact lens wearers. Female contact lens wearers reported a higher OSDI compared to female controls. These findings suggest that contact lens wear does not significantly alter the OSM or tear proteome in healthy individuals, although sex-specific responses may warrant further investigation.IMPORTANCEContact lenses are worn by millions of people, yet the scientific literature contains conflicting reports about their impact on the microbial communities that are naturally present on the eye surface. This study addresses these knowledge gaps by examining both the eye microbiome and tear proteins using advanced sequencing and linking them to dry eye symptoms. Understanding the relationship between contact lens wear, natural eye bacteria, and tear composition is essential for resolving contradictory findings in the field. Additionally, identifying potential sex-specific differences in how individuals respond to contact lens wear could lead to more personalized approaches to contact lens management.},
}

@article {pmid41636304,
year = {2026},
author = {Brown, LP and Marizzi, A and Borrego, CM and Gionchetta, G and Zhengzheng, Z and Carneiro, RB and Gago-Ferrero, P and Matamoros, V and Subirats, J},
title = {Metagenomic Assessment of Full-Scale Wastewater Treatment Plants Identifies Sentinel Antibiotic Resistance Gene Families for Monitoring Reclaimed Wastewater and Treated Sludge.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c13541},
pmid = {41636304},
issn = {1520-5851},
abstract = {The new European (EU) regulation on water reuse explicitly incorporates antimicrobial resistance (AMR) into routine monitoring and risk management, creating an urgent need to define target antibiotic resistance genes (ARGs) for reclaimed irrigation water and agricultural sludge. However, existing global data largely focus on secondary effluents, providing little actionable evidence for reuse-oriented systems. Here, we present the first integrated framework combining targeted antibiotic residue analysis with shotgun metagenomics of the resistome, mobilome, and microbiome across full-scale reuse-oriented wastewater treatment plants (WWTPs) in Southern Europe to identify sentinel antibiotic resistance families for monitoring. Reclaimed effluents exhibited lower AMR exposure levels than those typically reported for secondary effluents (<0.5 ARGs/cell), while mobile genetic element (MGE) abundances were comparable to secondary effluents (1-2 MGEs/cell). Effluent communities differed by WWTP configuration: membrane bioreactor combined with ultrafiltration favored nutrient-removal/oxidative-stress taxa and reduced transferable MGEs, whereas plants relying on physical separation (sand filtration or reverse osmosis) retained fecal-associated taxa and MGEs. Specific clinically relevant ARGs persisted after treatments, including aadA and aph(3'')-Ibs (resistance to aminoglycosides), ermB and mphA (resistance to macrolides), and blaOXA-129 (resistance to beta-lactams), which we identify as sentinel markers for monitoring reclaimed water and sludge. We advance a generalizable two-step framework, metagenomic discovery to identify sentinel markers, followed by targeted assays for streamlined surveillance, that provides the first operational blueprint for integrating AMR into water reuse management under the EU regulation.},
}

@article {pmid41635749,
year = {2025},
author = {de Oliveira Guimarães, L and de Almeida, AR and Ramos, EDSF and Telles-de-Deus, J and Helfstein, VC and Morais, VDS and Dos Santos, JM and Pandey, RP and de Camargo-Neves, VLF and da Costa, AC and Kirchgatter, K and Leal, É},
title = {Evolutionary features of new picorna-like viruses in Culex (Melanoconion) mosquitoes.},
journal = {Current research in parasitology & vector-borne diseases},
volume = {8},
number = {},
pages = {100333},
pmid = {41635749},
issn = {2667-114X},
abstract = {In this study, we investigated unclassified picorna-like viruses in Culex (Melanoconion) mosquitoes from São Paulo, Brazil, an area of high mosquito biodiversity and arbovirus activity. Two mosquito pools were processed using next-generation sequencing (NGS), and datasets were analyzed via de novo assembly to reconstruct viral genomes and assess evolutionary relationships. We identified two highly similar viral genomes, named Culex (Melanoconion) picorna-like virus, CmV_B38 and CmV_B39, exhibiting 99.93% nucleotide identity, both of which encode a three-domain replication block characteristic of viruses within the order Picornavirales. Phylogenetic reconstruction based on the RNA-dependent RNA polymerase (RdRp) gene revealed that these viruses form a distinct, previously undescribed clade, most closely related to Yongsan picorna-like virus 4 and several other unclassified viruses that have been reported predominantly in Asian regions. These findings may indicate possible geographical connectivity or convergence in viral evolution across distinct ecosystems. Notably, the results highlight the underexplored diversity of insect-specific viruses, particularly those associated with mosquito vectors. Furthermore, the data are consistent with the hypothesis that ecological factors and host specificity could influence the evolutionary dynamics of these viral lineages. The study not only enhances our understanding of the mosquito-associated virome but also emphasizes the critical need for ongoing viral surveillance, especially in biodiverse regions. Such efforts are essential for elucidating the evolutionary dynamics of RNA viruses and for anticipating the emergence of novel viral pathogens that may pose future risks to public health or agriculture.},
}

@article {pmid41635321,
year = {2026},
author = {Ozturk, SZ and Aydin, B and Cifcibasi, E},
title = {Antibiotic Resistance Genes in the Subgingival Microbiome in Periodontitis: A Scoping Review of Prevalence, Mobility, and Future Directions.},
journal = {Cureus},
volume = {18},
number = {1},
pages = {e100685},
pmid = {41635321},
issn = {2168-8184},
abstract = {The objective of the study is to evaluate the prevalence, diversity, and mobility of antibiotic-resistant species and resistance genes within the subgingival microbiome of patients with periodontitis. A systematic scoping review was conducted in accordance with PRISMA-ScR (Preferred Reporting Items for Systematic Reviews and Meta-Analyses Extension for Scoping Reviews) guidelines. Five electronic databases were searched for studies published between January 2020 and December 2025 that used molecular techniques (shotgun metagenomics, PCR/qPCR, 16S + PCR) to detect antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in the subgingival plaque of patients with clinically diagnosed periodontitis. Only peer-reviewed articles presenting original data were included; reviews, animal studies, and investigations lacking clear methodological details were excluded. Data extraction included study design, sample size, identified ARGs, associated MGEs, and clinical context. Nine eligible studies involving over 900 subgingival samples were identified. A core resistome was consistently identified across all cohorts, predominantly comprising tetracycline genes (tetM, tetQ, tet32) and macrolide-lincosamide determinants (ermB, ermF, msrD), as well as β-lactamase genes such as cfxA. Sites affected by periodontitis showed higher abundance of these ARGs than healthy controls. Mobile elements, especially Tn916-family conjugative transposons, were often associated with macrolide resistance genes, suggesting potential for horizontal transfer. Methodological differences prevented meta-analysis, and no study compared results based on the 2017 stage/grade classification of periodontitis. The subgingival resistome in periodontitis features a consistent set of tetracycline, macrolide, and β-lactam resistance genes that are increased in disease and frequently associated with mobile transposons. Currently, the evidence remains primarily descriptive; future research should include standardized antibiotic washout periods, longitudinal follow-up, stage/grade stratification, and integrated multi-omics approaches to evaluate functional activity and guide personalized antimicrobial therapies.},
}

@article {pmid41635301,
year = {2025},
author = {Jin, X and Ren, L and Ren, X and Wang, J},
title = {Integrative single-cell and metagenomic analysis dissects SARS-CoV-2 shedding modes in human respiratory tract.},
journal = {Biosafety and health},
volume = {7},
number = {1},
pages = {5-16},
pmid = {41635301},
issn = {2590-0536},
abstract = {It is crucial to understand how severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sheds in human respiratory tract, but this question remains elusive due to technical limitations. In this study, we integrated published human metagenomic data of SARS-CoV-2 and developed a novel algorithm named RedeCoronaVS to systematically dissect SARS-CoV-2 shedding modes with single-cell data as reference. Our study demonstrated that SARS-CoV-2 particles were the dominant mode of viral shedding in the very early infection phase (≤24 h after hospitalization). Within the first week after hospitalization, SARS-CoV-2 replicas within host cells dominated viral shedding alongside viral particles. One week later, viral fragments became the dominant mode in patients with mild or moderate symptoms, while viral replicas still dominated in some patients with severe symptoms. In addition to epithelial cells, SARS-CoV-2 replicas in neutrophils, macrophages, and plasma cells also played significant roles and were associated with sampling time and disease severity.},
}

@article {pmid41634852,
year = {2026},
author = {Yan, A and Li, X and Cheng, J and Cheng, Y and Gebeyew, K and Tan, Z and Kang, J and He, Z},
title = {The developmental trajectory and maturation of the Hulunbuir sheep (Ovis aries) microbiome.},
journal = {Animal microbiome},
volume = {8},
number = {1},
pages = {10},
pmid = {41634852},
issn = {2524-4671},
support = {32350410422//National Natural Science Foundation of China/ ; 2022JJ10054//Natural Science Foundation of Hunan Province of China/ ; 32350410422//the National Natural Science Foundation of China/ ; 32302783//Natural Science Foundation of China/ ; },
abstract = {The rumen microbiota plays a pivotal role in the growth performance of host animals, primarily due to its ability to ferment ingested feed. Hulunbuir sheep exhibited a slow growth rate compared to other local breeds. A deeper comprehension of the development of the rumen bacteria community in Hulunbuir sheep can offer insights into the factors contributing to their slow growth rate. This study utilized metagenomic analysis of rumen content samples from Hulunbuir sheep to investigate the patterns of microbial growth and their relationship with the ADG. The results of the PCoA and enterotype analyses demonstrated that the ruminal bacterial community developed distinct characteristics following weaning. The dominant bacterial phyla in the rumen of Hulunbuir sheep, Bacteroidetes and Firmicutes, exhibited a significant age-related change. At the genus level, while the abundance of dominant bacterial genera changed with the growth of Hulunbuir sheep, Prevotella consistently maintained a high abundance across all age time points. We then examined the effects of age on microbial function by analyzing carbohydrate-metabolizing enzymes and protein-metabolizing peptidases. The abundance of carbohydrate-metabolizing enzymes decreased with growth, while peptidases showed opposite dynamics. Under the current feeding conditions correlation analysis showed that the abundances of Firm-04, CAG-83, and GCA-900,199,385 were negatively correlated with ADG (R<-0.4, p < 0.05), while the abundance of Ga6A1 was positively correlated with ADG (R > 0.5, p < 0.05). In addition, we found 67 MAGs related to ADG, which are capable of secreting carbohydrates-metabolizing enzymes and peptidase. This study uncovers the temporal dynamics of rumen microbiota development during the early to late fattening phase and identifies microbes associated with ADG, which could inform strategies to improve growth and production efficiency.},
}

@article {pmid41634818,
year = {2026},
author = {Schuster, L and Greening, C and Malerba, ME and Trevathan-Tackett, S and Athukorala, N and Ricci, F},
title = {Cattle manure suppresses methane consumption and enhances denitrification-associated nitrous oxide production in farm dams.},
journal = {Microbiome},
volume = {14},
number = {},
pages = {},
pmid = {41634818},
issn = {2049-2618},
support = {APP1178715//National Health and Medical Research Council/ ; FT240100502//Australian Research Council/ ; DE220100752//Australian Research Council/ ; DE210101029//Australian Research Council/ ; ECPF24-4273843556//Faculty of Medicine, Nursing and Health Sciences, Monash University/ ; },
abstract = {BACKGROUND: Farm dams (or agricultural ponds) are often heavily polluted freshwater systems because of nutrient-rich manure entering the water through direct deposition and runoff. Accordingly, these systems have among the highest greenhouse gas emissions per area, accounting for 41% of global freshwater methane emissions. Sustainable management actions, such as limiting livestock access through fencing, can significantly reduce nutrient concentrations and greenhouse gas emissions. However, the microbes, processes, and factors controlling greenhouse gas cycling in these systems have not been described. Here, we systematically compared the composition, functions, and activities of the microbes in paired fenced and unfenced cattle farm dams in southeastern Australia.

RESULTS: We found that in situ methane (CH4) and nitrous oxide (N2O) emissions were strongly reduced in fenced dams. Even though methanogen abundance was higher in fenced dams, fencing increased levels of aerobic methanotrophs, including two previously uncharacterised, metabolically flexible species profiled via metagenome-assembled genomes (MAGs). In contrast, we provide gene- and genome-centric evidence that N2O emissions are likely higher in unfenced dams due to increased production (via denitrification) rather than decreased consumption. Manure likely increases CH4 and N2O emissions primarily by driving nutrient-induced eutrophication and hypoxia that, respectively, stimulate denitrifiers and inhibit methanotrophs. However, we also provide evidence that manure-associated methanogens and bacteria occur in farm dams, where they potentially enhance emissions.

CONCLUSIONS: Our findings highlight how anthropogenic activities such as livestock farming can impact microbial communities and biogeochemical cycling, thereby increasing greenhouse gas emissions from freshwater systems, and how simple management actions like fencing can mitigate such emissions. Video Abstract.},
}

@article {pmid41634815,
year = {2026},
author = {Hao, X and Wang, X and Wang, X and Wang, C and Li, C and Lu, Y and Cheng, Q and Chen, Z and Zhu, L and Li, C and Shen, X},
title = {Synthetic community derived from the root core microbes of a desert shrub Caragana korshinskii enhances wheat drought tolerance.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02350-8},
pmid = {41634815},
issn = {2049-2618},
abstract = {BACKGROUND: Drought, intensified by climate change, poses a mounting threat to global food security by severely constraining crop productivity. While microbial inoculants offer promise for drought tolerance, their poor adaptability remains insufficient for extremely water-deficient environments. Desert plants host unique drought-adapted microbiomes that remain largely unexplored for agricultural applications.

RESULTS: Here, we investigated the microbial community of the desert shrub Caragana korshinskii and identified a core set of drought-responsive strains. A synthetic microbial community (SynCom) derived from these strains significantly improved wheat growth under drought stress. Metagenomic analyses revealed that microbial functions related to biofilm formation, quorum sensing, and carbon metabolism were enriched, with Pseudomonas identified as a key functional taxon. Guided by inter-strain interactions in biofilm assembly, we streamlined the consortium into a five-member synthetic community, where quorum-sensing signals promoted community-wide biofilm formation. Community biofilm production improved strain colonization and conferred greater drought tolerance compared to monocultures. In plants, mechanistic investigations indicated that the simplified SynCom inoculation universally upregulated MAPK and jasmonic acid signaling pathways. Furthermore, carbohydrate metabolic pathways such as starch and sucrose metabolism were specifically activated, suggesting a multi-level mechanism underlying SynCom-mediated drought tolerance.

CONCLUSIONS: These findings demonstrate that SynCom constructed on the endophytic flora of desert plants can significantly enhance crop drought tolerance. Our work highlights the pivotal role of community biofilm synthesis in facilitating root colonization and activating a multidimensional drought tolerance network in plants. This study not only gives an ecological perspective on desert microbiome adaptations but also offers a strategic framework for developing effective microbial inoculants for arid-region agriculture. Video Abstract.},
}

@article {pmid41634410,
year = {2026},
author = {Chen, YJ and Ho, HJ and Tseng, CH and Chen, YF and Shieh, JJ and Wu, CY},
title = {Akkermansia Muciniphila Ameliorates Imiquimod-Induced Skin Thickening, Colitis, and Gut Microbiota Alterations: A Metagenome Association Study.},
journal = {Inflammation},
volume = {},
number = {},
pages = {},
doi = {10.1007/s10753-025-02436-9},
pmid = {41634410},
issn = {1573-2576},
support = {NSTC 108-2314-B-075A-008//National Science Technology Council/ ; 110-2314-B-075A-008//National Science Technology Council, Taiwan/ ; TCVGH- 1136801B//Taichung Veterans General Hospital/ ; },
}

@article {pmid41491012,
year = {2026},
author = {Li, L and Khan, M and Haak, L and Verma, SC and Pagilla, K},
title = {High prevalence of tomato brown rugose fruit virus in domestic wastewater as a potential viral indicator for treatment systems.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {4698},
pmid = {41491012},
issn = {2045-2322},
abstract = {UNLABELLED: Waterborne pathogenic viruses present a critical public health challenge, particularly in potable water reuse systems where stringent safety standards must be met. Achieving the necessary Log Reduction Values (LRVs) for viruses in water treatment remains difficult due to their low prevalence and high detection limits. This study investigated tomato brown rugose fruit virus (ToBRFV) as a novel viral indicator to assess advanced treatment efficacy of advanced treatment systems in achieving target Log10 Reduction Values (LRVs) for pathogenic viruses. Over 13 months, wastewater samples from the Reno-Sparks Metropolitan Region (Nevada, USA) were analyzed using metagenomics and RT-qPCR to compare ToBRFV, pepper mild mottle virus (PMMoV), and MS2 bacteriophage. Results demonstrated that ToBRFV was consistently detected at high concentrations across all samples, exhibiting minimal seasonal variability. In contrast, PMMoV showed moderate fluctuations, while MS2 was detected at lower levels. The robustness and stability of ToBRFV suggest it could serve as a reliable indicator for verifying LRVs in potable reuse systems, complementing existing methods. Additionally, its plant-based origin reduces human health risks during handling. These findings support ToBRFV’s potential to enhance treatment monitoring and public health safeguards. Further research should validate its applicability across diverse geographic and climatic conditions, as well as its correlation with enteric virus removal, to optimize water reuse frameworks.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-025-34782-x.},
}

@article {pmid41634308,
year = {2026},
author = {Campos-Madueno, EI and Aldeia, C and Endimiani, A},
title = {Gut microbiota and resistome profiles of Swiss expatriates in Africa revealed by Nanopore metagenomics.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-38302-3},
pmid = {41634308},
issn = {2045-2322},
support = {192514//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; },
abstract = {The gut microbiota and resistome may change upon exposure to environments with high prevalence of multidrug-resistant pathogens, potentially impacting health and contributing to the spread of antimicrobial resistance genes (ARGs). In this context, expatriates may acquire endemic microbial communities and ARGs while living abroad. In this work, we investigated the microbiota and resistome of Swiss expatriates living in African countries using Nanopore shotgun metagenomics (SMS).Stool samples from expatriates residing in African and European countries (n = 33 and n = 39, respectively) were sequenced using Nanopore V14 chemistry. Taxonomic and resistome profiling was performed with Kraken2 and ResFinder, respectively. Diversity metrics (e.g., Shannon, Simpson) assessed microbial composition. ARG and bacteria associations were determined using GTDB-Tk on metagenome-assembled genomes (MAGs). Plasmid-borne ARGs were characterized with PlasmidFinder.Our results indicated that microbiota composition did not differ between expatriates in African and European countries. However, resistome analysis revealed a higher prevalence of tetracycline (tet) and folate pathway antagonist (dfr, sul) ARGs in those residing in Africa, suggesting adaptation to the local microbial environment or antibiotic policy. Unique plasmid families were also identified in Gram-negative (IncF) and -positive (repUS43) bacteria across African and European cohorts, indicating the potential for ARG dissemination via mobile genetic elements. Overall, Nanopore-based SMS may provide an alternative approach to monitor microbiota and resistome dynamics, and thus assisting early epidemiological surveys.},
}

@article {pmid41633490,
year = {2026},
author = {Kelly, MS and Huang, CY and Kim, M and Haghnazari, D and Baig, A and Sun, Y and Lenneman, BR and Tisza, MJ and Cunningham, A and Gold, D and Phipatanakul, W and Lai, PS},
title = {Nasal microbiome and phageome profiles are associated with prospective respiratory viral infection risk in school-aged children.},
journal = {The Journal of allergy and clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaci.2026.01.017},
pmid = {41633490},
issn = {1097-6825},
abstract = {BACKGROUND: Respiratory viral infections are common and can trigger asthma exacerbations in children. The roles of the nasal microbiome and phageome (viruses that infect microbes) are not well understood.

OBJECTIVE: To characterize the epidemiology of respiratory viral infections and the interplay between the nasal microbiome, phageome, and viral infections in school-aged children with asthma.

METHODS: We performed metagenomic sequencing and RT-qPCR detection of respiratory viruses on 375 nasal samples from 227 school-age children with asthma collected routinely three times over one year. Surveys on parent-reported cold and asthma symptoms were administered routinely every two months. We evaluated multi-kingdom changes to the nasal microbiome during infection. A sPLS-DA model identified microbial signatures associated with prospective viral infection risk.

RESULTS: Respiratory viruses were identified in 124 (33%) samples, with rhinovirus most prevalent. Cold and asthma symptoms within the prior 14 days had a sensitivity of 79% and 59%, respectively, for RT-qPCR-confirmed infection. Respiratory viral infection increased asthma symptoms and was accompanied by loss of nasal bacterial diversity and a reproducible bloom of pathobionts with no change in the mycobiome or phageome. A baseline bacteriome-dominated profile was protective (adjusted OR 0.41 [95% CI, 0.25 - 0.67]; P < 0.001), whereas phageome profiles increased risk (adjusted OR 3.74 [1.85 - 7.55]; P < 0.001) of viral infection. Specific phages inversely correlated with Staphylococcus epidermidis abundance, the most protective commensal against infection risk.

CONCLUSION: The nasal microbiome and phageome exert opposing influences on respiratory viral infection risk, highlighting their potential roles in modulating susceptibility to viral infections.},
}

@article {pmid41633147,
year = {2026},
author = {Klaes, S and Gerundt, K and Deobald, D and Henneberger, L and Escher, B and Adrian, L and Cooper, M},
title = {Sequential exposure to anoxic/oxic conditions leads to biotransformation and reduced sitagliptin toxicity in urban hyporheic zones.},
journal = {Journal of hazardous materials},
volume = {504},
number = {},
pages = {141299},
doi = {10.1016/j.jhazmat.2026.141299},
pmid = {41633147},
issn = {1873-3336},
abstract = {Pharmaceuticals are increasingly recognized as contaminants of concern in aquatic environments. Sitagliptin, an antidiabetic drug that carries a C-CF3 group, which is a precursor of the persistent trifluoroacetic acid, is excreted largely unmetabolized and inefficiently removed in wastewater treatment plants, leading to its widespread detection in surface waters. The hyporheic zone, a region between surface water and groundwater, serves as a natural bioreactor with high microbial activity and diverse redox conditions, offering the potential for sitagliptin attenuation. This study explored the biotransformation of sitagliptin in hyporheic sediments under varying redox conditions through batch experiments and field observations. We showed that batch experiments can complement field observations to capture both mechanistic insights and their environmental relevance. Batch experiments revealed amide hydrolysis and N-acetylation of sitagliptin under anoxic conditions, with subsequent deamination and oxidation of transformation products under oxic conditions. Metagenome-resolved metaproteomics suggested Pseudomonas asiatica as a key player in the oxic transformation. Field analysis of pore water samples identified up to 6.47 µg L[-1] sitagliptin and ten transformation products with concentrations of up to 4.82 µg L[-1] . Amide hydrolysis products were the most abundant transformation products and preferentially formed under anoxic conditions. All investigated transformation products exhibited lower cytotoxicity and oxidative stress responses than sitagliptin in in vitro bioassays, highlighting the toxicity reducing potential of the hyporheic zone. By identifying conditions that promote sitagliptin transformation and characterizing its transformation products toxicologically, our work provides parameters for enhanced sitagliptin removal in aquatic environments and improved risk assessment of fluorinated trace organic contaminants.},
}

@article {pmid41633137,
year = {2026},
author = {Zhang, FY and Shu-Kui, D and Wang, LL and Ma, YT and Wu, MZ and Yuan, HM and Yang, JN and Zhang, Y and Zhang, GA and Zhao, J and Liu, C and Guan, DW and Zhao, R},
title = {Metagenomic profiling reveals lung multi-kingdom microbes as forensic markers for aquatic corpses investigation.},
journal = {Forensic science international. Genetics},
volume = {83},
number = {},
pages = {103435},
doi = {10.1016/j.fsigen.2026.103435},
pmid = {41633137},
issn = {1878-0326},
abstract = {The forensic investigation of corpses recovered from aquatic environments presents a major practical challenge. Recent studies have demonstrated that the bacterial community in the lung serves as a valuable indicator for diagnosing drowning, determining the drowning medium and estimating postmortem submersion interval (PMSI). However, the application and significance of lung multi-kingdom microbiome (archaea, eukaryota, and viruses) remains inadequately characterized. Meanwhile, the insufficient sequencing depth of commonly employed techniques, such as amplicon sequencing, restricts our understanding of microbial communities. In this study, we characterized the postmortem lung microbiome of mice submerged in water for up to 10 days using metagenomic sequencing, and subsequently validated the potential microbial biomarkers in both murine and human forensic specimens via qPCR. Integrated analyses were conducted followed by the confirmation of significant lung bacterial communities for drowning diagnosis, inference of drowning site, and estimation of the PMSI. Our findings revealed that bacteria constituted the predominant component of the lung microbiome in submerged murine carcasses, with eukaryota serving as the secondary dominant taxa. Seventeen bacterial and nine eukaryotic features at the species level were identified as potential biomarkers for drowning diagnosis. By detecting the specific molecular markers for Aeromonas species in both murine and human samples, the positive detection of Aeromonas species, particularly Aeromonas hydrophila, provides solid evidence for drowning diagnosis. Additionally, 14 and 17 bacterial species were identified as biomarkers for the inference of drowning site and estimation of PMSI, respectively. Based on the identified potential biomarkers, robust forensic models were constructed using the random forest (RF) algorithm. The accuracy of the bacterial model for drowning diagnosis was 89.29 %, while the accuracy of the eukaryotic model was 87.5 %. For the inference of the drowning site, the bacterial model achieved an accuracy of 100 %. Furthermore, the estimation of the PMSI yielded a mean absolute error of 0.66 ± 0.097 days. Collectively, our findings revealed that the selected 17 bacterial and 9 eukaryotic features in the lungs, particularly Aeromonas hydrophila, are beneficial for drowning diagnosis. Additionally, the other selected bacterial species contribute to the estimation of the drowning site and PMSI, thereby providing more comprehensive and refined information for accurate forensic investigations of corpses recovered from aquatic environments.},
}

@article {pmid41633112,
year = {2026},
author = {Tang, X and Bao, Y and Li, J and Liu, B and Huang, Y and Hou, L and Lee, PKH and Han, P},
title = {Microplastics promote N2O emissions by enhancing nitrification via ammonia-oxidizing bacteria in estuarine and coastal sediments.},
journal = {Water research},
volume = {293},
number = {},
pages = {125458},
doi = {10.1016/j.watres.2026.125458},
pmid = {41633112},
issn = {1879-2448},
abstract = {Estuarine and coastal ecosystems are critical interfaces between land and ocean, serving as sinks for anthropogenic pollutants such as ammonium and microplastics. However, the impact of microplastic pollution on nitrification processes in these environments remains largely unexplored. This study investigates the coastal region of the Yangtze River to examine how different microplastic types (polyethylene terephthalate, polypropylene, and polyethylene) affect nitrous oxide (N2O) emissions and the dynamics of nitrifiers, including ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), complete ammonia-oxidizing (comammox) Nitrospira, and nitrite-oxidizing Nitrospira. Results from incubation experiments show that all microplastic types significantly increase N2O emissions across sediment samples. The reconstructed representative metagenome-assembled genomes revealed that AOA belong to group I.1a, while AOB are classified within the Nitrosomonas genus. Microplastics were found to have a stronger stimulatory effect on AOB, which are linked to higher N2O production, than on AOA, which are associated with low N2O production, thereby enhancing N2O emissions during nitrification. Furthermore, AOB genomes encode a range of putative plastic-degrading enzymes, which may partially explain their enrichment in microplastic-contaminated environments, although other factors such as differential tolerance to ammonium or oxidative stress cannot be ruled out.},
}

@article {pmid41633028,
year = {2026},
author = {Xue, L and Zhao, W and Wang, C and Ma, Y and Tian, J and Yang, L and Ma, L and Jiang, Q and Chen, Y and Tian, X and Ji, X and Zhang, J and Gu, Y},
title = {Integrating multi-omics to characterize the dynamics of rumen microorganisms and metabolites in Angus cattle at different growth stages.},
journal = {Research in veterinary science},
volume = {203},
number = {},
pages = {106092},
doi = {10.1016/j.rvsc.2026.106092},
pmid = {41633028},
issn = {1532-2661},
abstract = {The development of the bovine rumen microbiome is crucial for growth, yet the dynamic interactions between the microbiome and metabolome during key growth stages remain poorly understood. This study aims to integrate metagenomics and metabolomics approaches to decipher the stage-specific patterns of rumen microbial community and metabolite changes in castrated Angus cattle at three critical growth stages (6, 12, and 18 months of age), and to elucidate their associations with host growth performance. We collected rumen fluid samples from 24 Angus steers (8 per age group) reared under standardized conditions and performed metagenomic and non-targeted metabolomic analyses. Integrated analysis revealed distinct rumen ecosystem succession patterns: multiple species represented by Prevotella_sp._ne3005 dominated at 6 months, Fibrobacter_succinogenes showed significantly increased abundance at 12 months, and Methanobrevibacter_millerae exhibited the most pronounced enrichment at 18 months. Concurrently, key metabolites 12,13-Dihydroxyoleic Acid, Delta-12-Pgj2, and Cortisol exhibited a significant positive correlation with age. Further Pearson correlation analysis revealed strong correlations between the 18-month-enriched characteristic microorganism Methanobrevibacter_millerae and key metabolites (12,13-Dihydroxyoleic Acid, Delta-12-Pgj2, and Cortisol) as well as higher body weight. This study delineates a dynamic map of synergistic interactions between the rumen microbiome and metabolome, confirming their close association with host growth performance. This work provides a systematic multi-omics framework for understanding rumen development in ruminants and identifies potential targets for optimizing beef cattle production performance through microbial or metabolic interventions.},
}

@article {pmid41632347,
year = {2026},
author = {Yang, H and Hensley, MK and Nguyen, VD and Al-Yousif, NS and Britton, N and Haidar, G and Yang, L and Shah, F and Bain, W and Wang, X and Qin, S and Ahmed, AA and Blauwkamp, T and Bercovici, S and Kaufman, BA and Redding, KM and Fitch, A and Methé, B and Benos, PV and McVerry, BJ and Morris, A and Kitsios, GD},
title = {Microbial lung-to-blood translocation associates with systemic inflammation in severe pneumonia: evidence from paired plasma and lower respiratory tract metagenomics.},
journal = {Intensive care medicine experimental},
volume = {14},
number = {1},
pages = {10},
pmid = {41632347},
issn = {2197-425X},
support = {R01HL176668/HL/NHLBI NIH HHS/United States ; P01 HL 114453/HL/NHLBI NIH HHS/United States ; },
abstract = {BACKGROUND: Biological heterogeneity in host inflammatory responses to severe pneumonia predicts clinical outcomes and may influence the effectiveness of immunomodulatory therapy. The upstream drivers of this heterogeneity remain poorly defined. We hypothesized that microbial translocation from the lungs to the bloodstream, detectable via multi-compartment metagenomic analysis, contributes to divergent host responses in pneumonia.

METHODS: In this nested case-control study of mechanically ventilated patients with severe pneumonia, we collected paired plasma and endotracheal aspirate samples at baseline. Plasma samples underwent microbial cell-free DNA (mcfDNA) sequencing, and endotracheal aspirates were analyzed by Nanopore metagenomic sequencing. Host-response biomarkers were measured in both plasma and endotracheal aspirate samples. Microbial translocation of pulmonary origin was defined by the genus-level concordance of detectable taxa between matched endotracheal aspirate and plasma samples.

RESULTS: Among 98 patients (76 pneumonia, 22 controls), plasma mcfDNA was markedly higher in microbiologically confirmed pneumonia compared with culture-negative pneumonia (median 4015 vs. 210 molecules/μL, p = 0.0006). Pulmonary microbial translocation was identified in 31 (41%) pneumonia patients and correlated significantly with plasma soluble ST2 levels, independent of clinical severity. Patients classified into the prognostically adverse hyperinflammatory subphenotype exhibited greater translocating microbial DNA levels compared to hypoinflammatory patients (p = 0.04), further linking translocation to host-response heterogeneity.

CONCLUSIONS: Microbial lung-to-blood translocation is a measurable biological process associated with systemic inflammatory heterogeneity in severe pneumonia. This pathway may represent a novel mechanistic target for precision therapeutic strategies aimed at mitigating immune dysregulation.},
}

@article {pmid41632094,
year = {2026},
author = {Gómez-Martínez, D and Ngou, JS and Ugolini, V and Lai, FY and Nilsson, RH and Kristiansson, E and Corcoll, N},
title = {Antibiotic resistance gradient along a large Scandinavian river influenced by wastewater treatment plants.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiag007},
pmid = {41632094},
issn = {1574-6941},
abstract = {Recent studies have identified the environment as a key reservoir from which antibiotic resistance genes (ARGs) can be acquired and transmitted to pathogens. However, our knowledge about the presence of ARGs in high-flow river sediments is still limited. We analyzed the resistome of sediment bacterial communities along the Swedish river Göta Älv and investigated the potential dissemination of ARGs and antimicrobials from effluents of wastewater treatment plants (WWTPs). While we detected nine different antimicrobials in the effluent water from the WWTPs through HPLC-MS, their presence was not observed in river surface water. Analysis by qPCR revealed that the genes sul1 and ermB were the most dominant ARGs among sediment, sludge, and effluent samples. Shotgun metagenomics revealed unique differences between the sludge resistomes of the WWTPs. Moreover, our findings show that ARGs increase downstream of the Göta Älv and their diversity differs from the upstream sites. Efflux pump resistance-related genes were most abundant in sediment samples, and beta-lactams and tetracyclines were the most common antibiotic classes targeted by ARGs. Our study emphasizes the importance of urban river sediments as a reservoir of ARGs, as tracking ARGs in WWTPs and their receiving environments improves our understanding of their spread and characteristics.},
}

@article {pmid41631112,
year = {2026},
author = {Ji, X and Wang, M and Jin, P and Kong, L and Xu, Y and Chen, W and Liu, B and Wang, Q},
title = {Intracranial hepatitis B virus (HBV) infection following intracerebral hemorrhage in a patient with seronegative occult HBV infection.},
journal = {IDCases},
volume = {43},
number = {},
pages = {e02502},
pmid = {41631112},
issn = {2214-2509},
abstract = {Hepatitis B virus (HBV) infection is primarily associated with liver diseases but can also manifest with various extrahepatic complications. While numerous extrahepatic manifestations have been reported in acute or chronic hepatitis B patients, intracranial HBV infection remains clinically rare. A 43-year-old male had a pre-existing diagnosis of serologically negative occult HBV infection (OBI), which was initially diagnosed by detecting HBV DNA in serum while HBsAg, anti-HBs, anti-HBe, and anti-HBc were all negative. Following intracerebral hemorrhage, the patient's consciousness gradually restored through a course of rehabilitation therapy. Subsequently, the patient developed persistent fever and his level of consciousness progressively deteriorated. Serological testing confirmed the presence of HBsAg and HBeAg, the HBV loads in the serum was high, subsequent metagenomic next-generation sequencing (mNGS) of the cerebrospinal fluid (CSF) revealed positivity for HBV. After 8 weeks of treatment with entecavir, the HBV loads in the serum and CSF decreased significantly, the patient's consciousness improved, and the patient's temperature returned to normal. This study first reported a seronegative OBI patient developing intracranial HBV infection following intracerebral hemorrhage and clarified the diagnostic value of mNGS in rare intracranial infections.},
}

@article {pmid41630880,
year = {2026},
author = {Liu, MK and Liu, CY and Tang, YM and Liu, Y and Su, Y and Tian, XH and Feng, J and Ni, XL},
title = {Innovative use of unhulled rice in Baijiu brewing: impact on flavor and microbial composition.},
journal = {Food chemistry: X},
volume = {34},
number = {},
pages = {103569},
pmid = {41630880},
issn = {2590-1575},
abstract = {The quality of light-flavor Baijiu (LFB), a traditional Chinese liquor, is strongly influenced by fermentation raw materials. Traditional Baijiu brewing uses rice husk as an excipient, requiring energy-intensive steaming to remove off-flavors-a process that increases production time and costs. This study introduces an innovative co-fermentation technique using unhulled rice (Jingkangyou/Pinxiangyou varieties) with sorghum, improving LFB quality while reducing expenses. Metagenomic and flavoromic analyses compared three groups: a rice husk control and two experimental groups with varying proportions of unhulled rice. Results showed significant flavor differences, with D-lactic acid, leucinic acid, and putrescine levels correlating significantly positively to unhulled rice content. Experimental groups exhibited altered microbial diversity, flavor profiles, and physicochemical properties compared to the control. Key metabolic pathways, including galactose, phenylalanine, and lysine metabolism, were significantly modified, indicating unhulled rice reshaped biochemical reactions. These findings advance understanding of LFB fermentation dynamics and offer strategies for raw material optimization.},
}

@article {pmid41630783,
year = {2026},
author = {Sachdeva, C and Prasad, SS and Shenoy, KR and Kudva, A and Badareesh, L and Veerabhadrappa, BS and Krishna, SM and Murali, TS},
title = {A longitudinal profiling of microbiome of diabetic foot ulcers shows functional role of microbial communities in wound worsening and chronicity.},
journal = {Current research in microbial sciences},
volume = {10},
number = {},
pages = {100544},
pmid = {41630783},
issn = {2666-5174},
abstract = {Microbial communities in infected diabetic foot ulcers (DFUs) play a critical role in wound morbidity and healing outcomes. While cross-sectional studies that profile the microbial communities using culture-independent approaches are available, we conducted a longitudinal microbiome analysis of 30 diabetic individuals to elucidate the relationship between microbial composition, host factors, and wound healing trajectories. Using a 16S rRNA-based metagenomic approach, we characterized the core microbial communities associated with DFU. Alpha diversity analysis revealed significant differences between DFU microbiome from same individuals across visits, and between DFU and non-DFU cohorts, while no significant differences in beta diversity was observed. Core microbiome analysis identified Pseudomonas to be consistently present across all cohorts, higher abundance of Escherichia and Prevotella in DFU samples across visits while Acinetobacter and Morganella were predominant in non-DFU wounds. Healed DFUs were enriched in Alcaligenes and Corynebacterium while worsened DFUs showed increased abundance of Enterococcus and Serratia. In amputated individuals, Escherichia was found in high abundance, while Staphylococcus was reduced. DFU subjects with high HbA1c levels (7.3-14.9%) had higher abundance of Pseudomonas and Acinetobacter, while Prevotella and Escherichia were abundant in individuals with lower HbA1c (<7.2%). Functional predictive profiling of microbiome communities using MicrobiomeAnalyst showed significant differences between healed and worsened DFUs, especially related to genes with roles in wound healing, drug resistance, biofilm formation, tissue invasion and pathogenicity. Our findings provide insights into the microbial ecology of DFUs, while the longitudinal screening of microbes associated with DFU revealed microbial dynamics and their probable role on wound outcome.},
}

@article {pmid41630746,
year = {2025},
author = {Yang, B and Zhang, Y and Su, S and He, J and Hu, J and Wang, K},
title = {Metagenomic next-generation sequencing identifies tick-carried pathogens on Tarim Red Deer in Southern Xinjiang.},
journal = {Open veterinary journal},
volume = {15},
number = {11},
pages = {6109-6117},
pmid = {41630746},
issn = {2218-6050},
mesh = {Animals ; *Deer/parasitology ; High-Throughput Nucleotide Sequencing/veterinary ; Metagenomics ; China/epidemiology ; *Tick Infestations/veterinary/parasitology/epidemiology ; *Ticks/virology/microbiology ; },
abstract = {BACKGROUND: Ticks are important vectors for a wide range of pathogens, including viruses, bacteria, and protozoa, that impact both humans and animals. Recent advances in metagenomic sequencing have established it as a powerful tool for uncovering the microbial diversity within ticks, enabling the discovery of previously unrecognized pathogens.

AIM: This study aimed to enrich the pathogen database for Tarim red deer in southern Xinjiang and provide experimental data to aid in the diagnosis, prevention, control, and treatment of viral diseases in Tarim red deer.

METHODS: Metagenomic sequencing was employed to analyze the viral species carried by ticks parasitizing the red tarim deer. Additionally, enzyme-linked immunosorbent assay based antibody testing was conducted on 195 red deer samples from four farms M01, M02, M03, and M04 to detect antibodies against the Orf virus.

RESULTS: Next-generation sequencing was used to obtain partial sequences of viruses and bacteria, with further analysis focusing on viruses with higher abundance, such as mule deer pox virus and Orf virus. Serological testing for Orf virus antibodies in 195 red deer samples identified 7 positive cases, resulting in a positivity rate of 3.59% (7/195). Positivity rates were 5.26% (4/76) and 6.12% (3/49) for farms M02 and M04, respectively, whereas no seropositive individuals were identified at farms M01 and M03.

CONCLUSION: This study expands the current knowledge of tick-borne pathogens in southern Xinjiang by identifying diverse viral species associated with tick-infested Tarim red deer. The findings confirm the presence of Orf virus in red deer populations, particularly on farms M02 and M04. These results underscore the importance of ongoing surveillance efforts and offer valuable insights into the diversity and geographical distribution of tick-associated viruses within the arid and semi-arid ecosystems of southern Xinjiang.},
}

Animals
*Deer/parasitology
High-Throughput Nucleotide Sequencing/veterinary
Metagenomics
China/epidemiology
*Tick Infestations/veterinary/parasitology/epidemiology
*Ticks/virology/microbiology

@article {pmid41630294,
year = {2026},
author = {Li, R and Liu, X and Song, G and Zhang, CQ and Shen, LJ and Li, WX and Bai, ZP},
title = {Misdiagnosis of pulmonary paragonimiasis as tuberculosis: A case report.},
journal = {Medicine},
volume = {105},
number = {5},
pages = {e47555},
pmid = {41630294},
issn = {1536-5964},
mesh = {Humans ; *Paragonimiasis/diagnosis/drug therapy ; Female ; Adolescent ; *Tuberculosis, Pulmonary/diagnosis/drug therapy ; *Diagnostic Errors ; Praziquantel/therapeutic use ; Antitubercular Agents/therapeutic use ; Anthelmintics/therapeutic use ; *Lung Diseases, Parasitic/diagnosis/drug therapy ; Animals ; },
abstract = {RATIONALE: Pulmonary paragonimiasis and pulmonary tuberculosis exhibit overlapping clinical and imaging manifestations, resulting in frequent misdiagnosis in endemic areas. This case underscores the value of metagenomic next-generation sequencing (mNGS) in correcting such misdiagnoses and emphasizes the importance of managing drug-drug interactions between antituberculosis agents and praziquantel.

PATIENT CONCERNS: An 18-year-old female from Yunnan, a paragonimiasis-endemic region, presented with recurrent cough, expectoration, and hemoptysis for 4 years. She was initially diagnosed with pulmonary tuberculosis based on a positive tuberculin pure protein derivative test and chest computed tomography findings but failed to respond to antituberculosis therapy.

DIAGNOSES: Pulmonary paragonimiasis (initially misdiagnosed as pulmonary tuberculosis).

INTERVENTIONS: In-hospital tuberculosis-related tests (GeneXpert MTB/RIF, sputum/bronchoalveolar lavage fluid culture, bronchoscopic biopsy) were negative. Bronchoalveolar lavage fluid mNGS identified 87 Paragonimus sequences, and Paragonimus antibody enzyme-linked immunosorbent assay was positive. A history of raw crab ingestion was confirmed. Antituberculosis treatment was discontinued for 4 weeks (due to drug interaction), followed by oral praziquantel (1.2 g, 3 times daily for 3 consecutive days).

OUTCOMES: Hemoptysis resolved within 15 days of treatment initiation, and peripheral blood parameters returned to normal ranges. Chest computed tomography at 2 months posttreatment showed marked reduction in lesion size, and complete resolution of pulmonary cavities was observed at the 6-month follow-up, with no recurrence of symptoms.

LESSONS: For chronic respiratory symptoms unresponsive to antituberculosis treatment in endemic regions, proactive inquiry of raw freshwater crustacean consumption history and combined use of serology/mNGS can improve diagnostic accuracy. A 4-week washout period after rifampicin discontinuation is critical before praziquantel administration.},
}

Humans
*Paragonimiasis/diagnosis/drug therapy
Female
Adolescent
*Tuberculosis, Pulmonary/diagnosis/drug therapy
*Diagnostic Errors
Praziquantel/therapeutic use
Antitubercular Agents/therapeutic use
Anthelmintics/therapeutic use
*Lung Diseases, Parasitic/diagnosis/drug therapy
Animals

@article {pmid41630175,
year = {2026},
author = {Lim, SJ and Breitbart, M},
title = {Genetic Features of the Scuticociliate Pathogen Philaster sp. Isolate FWC2 That Causes Sea Urchin Mass Mortality.},
journal = {The Journal of eukaryotic microbiology},
volume = {73},
number = {2},
pages = {e70065},
pmid = {41630175},
issn = {1550-7408},
support = {//University of South Florida/ ; OCE- 2527605//National Science Foundation/ ; },
mesh = {Animals ; *Sea Urchins/parasitology/microbiology ; Phylogeny ; *Oligohymenophorea/genetics/isolation & purification/classification ; Base Composition ; Genome, Mitochondrial ; Sequence Analysis, DNA ; },
abstract = {A scuticociliate most closely related to Philaster apodigitiformis caused mass mortalities of diadematoid sea urchins and was cultured as Philaster sp. isolate FWC2. We sequenced the metagenomic content of this isolate, which was predicted to represent ≤ 56% of the complete genome. Based on k-mer counts, the haploid genome size was predicted to be 122-136 Mbp. We assembled and annotated a 4,088 bp nuclear ribosomal operon, a 41,396 bp mitochondrial genome with 19.22% G + C content, 24 protein-coding genes, 6 tRNA genes, and 2 rRNA genes, and a protein sequence homologous to β-PKA in Philaster apodigitiformis potentially involved in host infection.},
}

Animals
*Sea Urchins/parasitology/microbiology
Phylogeny
*Oligohymenophorea/genetics/isolation & purification/classification
Base Composition
Genome, Mitochondrial
Sequence Analysis, DNA

@article {pmid41630101,
year = {2026},
author = {Zheng, A and Wang, F and Li, Y and Li, W and Wu, W and Gan, J and Jin, Y},
title = {Concurrent pulmonary candidiasis and tuberculosis in type 2 diabetes mellitus: immune pathogenesis and multidisciplinary management challenges: a case report.},
journal = {Journal of medical case reports},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13256-026-05853-y},
pmid = {41630101},
issn = {1752-1947},
abstract = {BACKGROUND: Type 2 diabetes mellitus predisposes to opportunistic pulmonary infections. We report sequential invasive pulmonary candidiasis followed by tuberculoma in a patient with newly diagnosed type 2 diabetes mellitus and summarize diagnostic pitfalls and management lessons.

CASE PRESENTATION: A 67-year-old Han Chinese man with no previously known diabetes presented with cough and severe hyperglycemia (random glucose 36.3 mmol/L; HbA1c 12.7%). Initial chest computed tomography showed right‑upper‑lobe consolidation. Bronchoalveolar lavage metagenomic next‑generation sequencing detected abundant Candida albicans and sputum Gram stain showed Gram‑negative bacteria predominance; sputum culture yielded no definite pathogen, blood cultures were negative, and human immunodeficiency virus test was negative. After intravenous then oral fluconazole plus intensive insulin therapy, the consolidation regressed. Suspected secondary organizing pneumonia was treated with tapering methylprednisolone. One month later, a new 1.5 cm × 1.3 cm solid nodule appeared in the prior lesion bed. computed tomography‑guided biopsy revealed necrosis, and tissue metagenomic next-generation sequencing confirmed Mycobacterium tuberculosis; standard anti‑tuberculosis therapy was initiated.

CONCLUSION: In patients with diabetes and pulmonary lesions, concomitant or sequential fungal and tuberculous infections should be actively sought with stepwise microbiology (including bronchoalveolar lavage and tissue‑based methods) and early molecular testing (metagenomic next-generation sequencing/Xpert). Steroid exposure for organizing pneumonia may worsen or unmask tuberculosis and must be weighed against infectious risk. Multidisciplinary care (endocrinology-pulmonology-infectious diseases) and rigorous glucose control are essential.},
}

@article {pmid41630069,
year = {2026},
author = {Jia, X and Zhang, Y and Tian, B and Zhang, G and Mao, S and Qian, W and Sun, D and Liu, J},
title = {Integrative analysis of rumen microbiota and host multi-organ interactions underlying feed conversion efficiency in Hu sheep.},
journal = {Journal of animal science and biotechnology},
volume = {17},
number = {1},
pages = {19},
pmid = {41630069},
issn = {1674-9782},
support = {2021YFF1000703//National Key Research and Development Program of China/ ; KJJQ2025020//Fundamental Research Funds for the Central Universities/ ; HS202302//Research Fund of Tarim University/ ; },
abstract = {BACKGROUND: Rumen microbiota drive fermentation and contribute to variation in feed efficiency among ruminants, yet the underlying host-microbe mechanisms remain poorly understood. This study explores how rumen microbes shape feed conversion efficiency (FCR) through integrated interactions with multiple host organs.

RESULTS: We applied a multi-omics strategy-combining rumen metagenomics and host multi-organ transcriptomics-in Hu sheep with divergent FCR. From a uniform cohort of 150 weaned male Hu lambs, 13 low-FCR (LFCR) and 13 high-FCR (HFCR) individuals were selected for integrated analyses. LFCR sheep exhibited greater growth performance and higher ruminal propionate concentrations compared with HFCR animals. The ruminal microbiomes were enriched in Saccharofermentans and Succinivibrionaceae_UBA2804, and showed functional convergence on amino acid biosynthesis, central carbon metabolism, and propionate-oriented fermentation in LFCR sheep. Carbohydrate-active enzyme profiles indicated that LFCR animals favored fiber- and starch-associated modules (GH126, CBM27, EPS-GT), whereas HFCR animals were enriched in host-glycan and uronic acid-degrading families (CE14, GH89, PL15). Hydrogen metabolism highlighted a clear dichotomy: LFCR animals redirected H₂ toward propionate and sulfate reduction, while HFCR animals retained greater butyrate-producing and methanogenic capacity. Transcriptomic profiling across rumen epithelium, liver, and muscle identified tissue-specific regulatory modules. Only the liver showed strong enrichment of carbohydrate metabolism, with a complete glycogen turnover and glucose export system (GYS2, PYGL, PGM2, G6PC1) and pathways linking microbial short-chain fatty acids to gluconeogenesis. In contrast, muscle efficiency modules were dominated by contractile and cytoskeletal genes (e.g., MYL2, TNNC1, TPM3), reflecting optimized energy expenditure rather than substrate metabolism. No efficiency-associated modules were detected in the rumen epithelium, consistent with its role in propionate absorption rather than metabolism.

CONCLUSIONS: The rumen microbiota of LFCR sheep possess highly efficient capacities for volatile fatty acid and amino acid synthesis, thereby enhancing energy utilization at its source. The resulting propionate further promotes hepatic gluconeogenesis, directly supplying energy for muscle cell growth and ultimately improving FCR. Thus, co-metabolism between rumen microbiota and the liver provides energy for muscle cell growth and is a key determinant of improved feed efficiency.},
}

@article {pmid41629888,
year = {2026},
author = {Luo, M and Xiao, X and Wu, Y},
title = {Impact of phototherapy on gut microbiota composition and function in neonates with hyperbilirubinemia: a metagenomic analysis.},
journal = {BMC pediatrics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12887-026-06531-0},
pmid = {41629888},
issn = {1471-2431},
support = {No. YTWS20210102//Science and Technology Funding Program of Yantian District Bureau of Science and Technology/ ; },
}

@article {pmid41629580,
year = {2026},
author = {Khurajog, B and Saenkankam, I and Apiwatsiri, P and Supimon, N and Kamwa, R and Niyomtham, W and Yindee, J and Phupolphan, C and Hampson, DJ and Prapasarakul, N},
title = {Effectiveness of probiotic supplementation on growth performance, gut microbiota, and Salmonella reduction in broiler chicks challenged with Salmonella Typhimurium.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-37506-x},
pmid = {41629580},
issn = {2045-2322},
support = {FOOD66310012//the 2022-Fundamental Fund, Thailand Science Research and Innovation (TSRI), Chulalongkorn University/ ; },
abstract = {Salmonella infection poses a major threat to poultry production, affecting both animal health and food safety. With rising concerns over antimicrobial resistance, probiotics have gained attention as effective non-antibiotic interventions to control enteric pathogens while supporting gut health. This study evaluated the efficacy of a locally isolated probiotic blend comprising Ligilactobacillus salivarius BF12, and Pediococcus acidilactici strains BF9 and BYF20 (ProCU) in comparison with a commercial Clostridium butyricum-based probiotic (TOP GUT) in broiler chicks challenged with Salmonella Typhimurium (ST). A total of 196 chicks were assigned to seven groups receiving different treatments with or without Salmonella challenge. Parameters assessed included growth performance, intestinal histomorphometry, cecal Salmonella load, and microbiota composition and function. Before challenge, ProCU increased fecal lactic acid bacteria (LAB) and enriched amino acid and carbohydrate metabolism pathways. Post-challenge, TOP GUT significantly reduced Salmonella load and maintained growth, while ProCU showed a limited effect on pathogen reduction. Both probiotics improved intestinal morphology, increased Lactobacillus and Akkermansia abundance, and upregulated oxidative stress defense genes. Notably, TOP GUT also enriched Parabacteroides and other Bacteroidetes members and prolonged microbial metabolic activity. These findings emphasize strain-specific probiotic effects and suggest that continuous supplementation, particularly with spore-forming strains, may enhance gut health and reduce the Salmonella burden in poultry.},
}

@article {pmid41629563,
year = {2026},
author = {Suksa, W and Li, WJ and Luo, ZH and Jiao, JY and Ponce, V and Nuñez-Montero, K and Arce-Johnson, P and Sharma, NR and Thamchaipenet, A and Narsing Rao, MP},
title = {Metagenomic analysis revealed the presence of novel Actinomycetota "Candidatus Solincola uaceae" sp. nov., obtained from a hot spring.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-37544-5},
pmid = {41629563},
issn = {2045-2322},
support = {PHD/0136/2561//The Royal Golden Jubilee Ph.D. Program (RGJ Ph.D.), Thailand Research Fund, National Research Council of Thailand (NRCT)/ ; },
abstract = {Metagenomic analysis of the hot spring led to the recovery of a high-quality metagenome-assembled genome (MAG), MPNR_HS_01, affiliated with the phylum Actinomycetota. Taxonomy analysis assigned the MAG to "Candidatus Solincola", clustering closely with "Candidatus Solincola tengchongensis". MPNR_HS_01 was 2.82 Mb in size, assembled into 27 contigs, with a G+C content of 63.4%, 49 tRNAs, 4 rRNAs, 98.7% completeness, and no detectable contamination. Functional annotation revealed the presence of complete glycolysis and nonoxidative pentose phosphate pathways, while the tricarboxylic acid cycle was incomplete. Notably, MPNR_HS_01 encoded Wood-Ljungdahl pathway, suggesting carbon assimilation. Energy conservation was supported by hydrogenases, heterodisulfide reductase, Rnf complex, and V-type ATPase. Stress adaptation traits included genes for heat shock proteins, proline biosynthesis, and ion transporters involved in osmotic homeostasis. Although lacking flagellar machinery, MPNR_HS_01 possessed type IV pili and genes associated with twitching motility. Secondary metabolite analysis identified a betalactone biosynthetic gene cluster. Genome-relatedness analyses showed that MPNR_HS_01 was distinct from "Candidatus Solincola" species, with both average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values falling below the established species threshold (95-96% ANI and 70% for dDDH), supporting its designation as a novel species, for which we propose the name "Candidatus Solincola uaceae" sp. nov.},
}

@article {pmid41629364,
year = {2026},
author = {Spörri, L and Studer, JM and Kreuzer, M and Rotzetter, J and Schärer, D and Largiadèr, CR and Jaggi, D and Zinkernagel, MS and Zysset-Burri, DC},
title = {Linking the microbiome to the complement system in geographic atrophy.},
journal = {NPJ genomic medicine},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41525-026-00550-7},
pmid = {41629364},
issn = {2056-7944},
support = {CF10000044-EPFL SCR0237812//Foundation Bertarelli Catalyst Fund, EPFL (Ecole Polytechnique Fédérale de Lausanne), Lausanne, Switzerland/ ; CF10000044-EPFL SCR0237812//Foundation Bertarelli Catalyst Fund, EPFL (Ecole Polytechnique Fédérale de Lausanne), Lausanne, Switzerland/ ; },
abstract = {Age-related macular degeneration (AMD) is the leading cause of vision loss in the aged population with the late stage geographic atrophy (GA). Risk factors for AMD include age, genetic variants in the complement system, nutritional factors, and alterations in the gut microbiome (GM). To identify taxonomic and functional differences in the microbiome associated to disease pathophysiology and genetic risk factors, this study investigated the GM and the ocular surface microbiome (OSM) of GA patients compared to healthy controls by whole-metagenome shotgun sequencing. 16 AMD-associated SNPs were genotyped from blood samples using TaqMan assays and Sanger sequencing. While GA patients showed differences in the GM, and altered metabolic pathways including inosine 5'-phosphate degradation, NAD salvage, and ketogenesis, no alterations in the OSM were found. Genetic analysis associated SNP rs1061170 in the complement factor H gene with GA. These findings suggest that microbial alterations may contribute to GA through inflammation and oxidative stress.Registry: ClinicalTrials.gov, NCT02438111, Registration date: 28 April 2015, and NCT04658238, Registration date: 01 December 2020.},
}

@article {pmid41629097,
year = {2026},
author = {Lyu, WT and Jia, QQ and Tong, X and Fan, H},
title = {[STAT1 gain-of-function mutation leading to disseminated Talaromyces marneffei infection combined with hemophagocytic syndrome: a case report].},
journal = {Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and respiratory diseases},
volume = {49},
number = {2},
pages = {184-187},
doi = {10.3760/cma.j.cn112147-20250730-00456},
pmid = {41629097},
issn = {1001-0939},
mesh = {Humans ; Male ; Talaromyces ; Adult ; *Lymphohistiocytosis, Hemophagocytic/genetics/complications/microbiology ; *STAT1 Transcription Factor/genetics ; *Gain of Function Mutation ; *Mycoses/genetics/complications/microbiology ; Antifungal Agents/therapeutic use ; Mutation ; },
abstract = {This study reports a 28-year-old HIV-negative male with a STAT1 gain-of-function mutation who presented with a systemically disseminated Talaromyces marneffei (TM) infection, which was complicated by hemophagocytic lymphohistiocytosis (HLH). The patient presented with recurrent fever, weight loss, oral mucosal ulcers, as well as lymphopenia and markedly elevated inflammatory markers during the acute phase of the illness. Imaging revealed scattered ground-glass opacities and nodular shadows in both lungs, as well as localized bronchiectasis, and splenomegaly. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid and bone marrow aspirate specimens revealed TM-specific sequences. Whole-exome sequencing was performed to elucidate the underlying mechanism of recurrent fungal infections. This revealed a de novo heterozygous dominant mutation in the STAT1 gene (c.1151G>A, p.Gly384Asp), localized to the DNA-binding domain at amino acid position 384. This confirmed a STAT1 gain-of-function (STAT1-GOF) variant, which is consistent with the clinical phenotype of impaired antifungal immunity. Over the clinical course, the patient developed HLH. Following a two-week course of intravenous amphotericin B liposome (5 mg/kg per day), followed by oral voriconazole maintenance therapy (200 mg, twice daily), the patient exhibited significant improvements in clinical symptoms and laboratory parameters. Notably, the marked resolution of HLH was closely linked to the successful eradication of the fungal infection. This case highlights three critical clinical implications: (1) Patients with a predisposition to primary immunodeficiency disorders (e.g., STAT1-GOF mutations) should be evaluated for disseminated TM infections, even if they are HIV-negative; (2) mNGS is instrumental in etiological diagnosis and facilitates early intervention for fungal infections; (3) early identification of genetic defects establishes a theoretical basis for precision medicine and guides targeted therapeutic strategies.},
}

Humans
Male
Talaromyces
Adult
*Lymphohistiocytosis, Hemophagocytic/genetics/complications/microbiology
*STAT1 Transcription Factor/genetics
*Gain of Function Mutation
*Mycoses/genetics/complications/microbiology
Antifungal Agents/therapeutic use
Mutation

@article {pmid41628881,
year = {2026},
author = {Sun, G and Guo, S and Yao, Y and Lin, Z and Gao, H and Stauber, RH and Li, BC and Ding, GB},
title = {Facile immobilization of an unstable recombinant α-L-rhamnosidase on magnetite nanoparticles for efficient naringin biotransformation.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {150652},
doi = {10.1016/j.ijbiomac.2026.150652},
pmid = {41628881},
issn = {1879-0003},
abstract = {α-L-Rhamnosidase is a significant biocatalyst that specifically cleaves terminal α-L-rhamnose group from natural flavonoid diglycosides, enabling the biocatalytic production of high-value flavonoid glucosides like prunin from naringin. Compared to its precursor naringin, prunin exhibits superior solubility and bioavailability, making this enzymatic conversion commercially valuable for the food and pharmaceutical industry. However, the industrial application of free α-L-rhamnosidases faces significant challenges, including enzyme instability, difficulty in recovery, and unsatisfactory reusability. To address these issues, this study developed an innovative magnetically recoverable biocatalyst (Fe3O4-Rha) through covalent immobilization of recombinant α-L-rhamnosidase from human fecal metagenome onto Fe3O4 nanoparticles using EDC/NHS chemistry, and the immobilization parameters were systematically optimized. The successful preparation of Fe3O4-Rha was verified by TEM, FTIR, TGA, and SQUID analysis. Fe3O4-Rha retained the catalytic property of free Rha in terms of optimal pH and temperature but exhibited superior tolerance on organic solvent especially ethanol and isopropanol. Moreover, Fe3O4-Rha could effectively biotransform naringin to prunin and maintained 61.34% of initial activity after 5 cycles. In a scaled-up reaction system, Fe3O4-Rha also efficiently converted naringin into prunin and the complete conversion was achieved within 10 h. This work successfully developed a magnetically recoverable immobilized α-L-rhamnosidase system for the efficient and reusable biotransformation of naringin, offering a promising approach for the enzymatic modification of bioactive small molecules using biological macromolecular catalysts.},
}

@article {pmid41628768,
year = {2026},
author = {Frizzera, A and Vázquez, N and Sacristán, H and Tapella, F and Lovrich, G and Khalaf, A and Bojko, J and Cremonte, F},
title = {Patagonian king crabs (Lithodes santolla and Paralomis granulosa) and their diseases: Pathogen survey and taxonomic clarification of Areospora rohanae (Microsporidia).},
journal = {Journal of invertebrate pathology},
volume = {216},
number = {},
pages = {108560},
doi = {10.1016/j.jip.2026.108560},
pmid = {41628768},
issn = {1096-0805},
abstract = {Lithodid crabs constitute a valuable natural resource with commercial interest; however, their health status in South America is scarcely studied. The presence of pathogens may have a negative impact on affected populations, endangering the fishery. This study surveys the symbionts present in populations of the king crab, Lithodes santolla, and the stone/false king crab, Paralomis granulosa, using histology, transmission electronic microscopy, and molecular analyses to characterise various symbionts. The histological and molecular data revealed a wide range of infections in L. santolla, including prokaryotic microorganisms, Areospora rohanae (Microsporidia), apicomplexan gregarines, ciliated protozoans, ectoparasitic crustaceans, and various epibiotic associations. In the case of P. granulosa, apicomplexan gregarines, ciliated protozoans, and various ectoparasites were observed. Molecular analyses confirmed the presence of the microsporidian A. rohanae, occurring at high prevalences (30%) in L. santolla, and some bacterial associations. We use metagenomic tools to extract a partial genome of this parasite to aid in its identification and taxonomic position, which leads us to erect the taxonomic orders Astathelohaniida and Areosporida and further clarify the previously assigned: "Glugeida+". The results of this study represent the first broad survey for symbionts in both king crab species and take us another step forward to a more accurate microsporidian taxonomy.},
}

@article {pmid41628665,
year = {2026},
author = {Hartog, M and Korsten, SGPJ and Popa, CD and Pelle, T and Gavriilidou, A and van den Bemt, BJF and Willemsen, LEM and Koenders, MI and Vermeiden, JPW and Smidt, H and van den Ende, CHM},
title = {Effectiveness of Sustained Release Calcium Butyrate on the microbiome and clinical burden in osteoarthritis of the hand: a proof-of-concept placebo-controlled randomized trial.},
journal = {Osteoarthritis and cartilage},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.joca.2026.01.630},
pmid = {41628665},
issn = {1522-9653},
abstract = {OBJECTIVE: This study primarily assessed effects of Sustained Release Calcium Butyrate (SRCaBu) on gut microbiome composition and function in hand OA patients. Secondary objectives included its impact on hand pain and function, markers of intestinal permeability, systemic inflammation, and safety.

METHOD: A participants, researchers, and pharmacy assistants blinded, randomized, placebo-controlled proof-of-concept trial compared 600mg daily dose SRCaBu with placebo over 4-5 weeks. The primary domain was microbiome composition and function, assessed via fecal 16S rRNA gene- and metagenome sequencing, and short-chain fatty acid analysis. Secondary outcomes included parameters for intestinal barrier function, clinical outcomes and adverse events. Primary analyses followed the per-protocol principle.

RESULTS: 35 participants (mean age 62.5±6.9 years, 82% female) were randomized to SRCaBu (n=18) or placebo (n=17). Two SRCaBu participants discontinued treatment for pre-existing liver impairment and need for pain medication. SRCaBu tended to reduce the relative abundance of Streptococcus (regression coefficient:-0.67, 95%CI:-1.46,0.13) and Faecalibacterium -0.38(-0.83,0.07), increase fecal acetate (median between-group difference: 9.5, [IQR]: [-3.5,22.5]), and was inversely associated with microbial LPS biosynthesis- and virulence genes. SRCaBu increased toxin-related genes, primarily from beneficial Blautia species, without association to pathogenicity. SRCaBu did not significantly affect biomarkers of intestinal permeability, inflammation, or clinical outcomes. Adverse events were mild and comparable between groups.

CONCLUSION: Our study yielded indicative findings that SRCaBu supports microbiome health in patient with hand OA by improving compositional and functional characteristics of the microbiome. Although the treatment was well tolerated, effects on serum markers for intestinal barrier function and systemic inflammation, and clinical symptoms remained unclear.

TRIAL REGISTER: 2020-001071-33 / NL73382.091.21.},
}

@article {pmid41627741,
year = {2026},
author = {Castañeda, S and Ramírez, JD and Poveda, C},
title = {Microbiome Profiling in Chagas Disease: Sample Collection, Sequencing, and Analysis.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3013},
number = {},
pages = {265-297},
pmid = {41627741},
issn = {1940-6029},
mesh = {*Chagas Disease/microbiology/parasitology ; Animals ; Mice ; Trypanosoma cruzi ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Computational Biology/methods ; High-Throughput Nucleotide Sequencing/methods ; *Microbiota ; Sequence Analysis, DNA/methods ; Metagenomics/methods ; },
abstract = {Chagas disease, caused by Trypanosoma cruzi, leads to chronic cardiac and gastrointestinal complications. Emerging evidence shows the gut microbiome plays a key role in modulating disease severity, with shifts in microbial composition influencing immune responses and metabolic pathways. Here, we describe a workflow for microbiome analysis in T. cruzi-infected mice. Methods included sample collection from feces and gastrointestinal tissues, DNA extraction, sequencing, and quality control. Then, we outline bioinformatic analyses covering taxonomic profiling, diversity assessment, and microbial network construction. Finally, protocols for functional prediction tools are also included to explore microbial capabilities and the identification of signatures associated with disease progression.},
}

*Chagas Disease/microbiology/parasitology
Animals
Mice
Trypanosoma cruzi
*Gastrointestinal Microbiome/genetics
Feces/microbiology
Computational Biology/methods
High-Throughput Nucleotide Sequencing/methods
*Microbiota
Sequence Analysis, DNA/methods
Metagenomics/methods

@article {pmid41627733,
year = {2026},
author = {Hałakuc, P and Maciszewski, K and Karnkowska, A},
title = {Euglenid Extrachromosomal DNA: Assembly and Annotation.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3013},
number = {},
pages = {109-120},
pmid = {41627733},
issn = {1940-6029},
mesh = {*Computational Biology/methods ; *Molecular Sequence Annotation/methods ; DNA, Ribosomal/genetics ; Genome, Mitochondrial ; *Euglenozoa/genetics ; Genome, Plastid ; DNA, Mitochondrial/genetics ; Phylogeny ; Genomics/methods ; Sequence Analysis, DNA/methods ; },
abstract = {Euglenids (Euglenozoa) contain several forms of extrachromosomal DNA (ecDNA) in their cells, including the ribosomal DNA operon (rDNA), the mitochondrial genome (mtDNA), and, in photosynthetic species, the plastid genome (ptDNA). These ecDNA elements can be easily and accurately assembled and annotated even from limited sequencing data, such as single-cell genomic or metagenomic datasets. They are an important source of information for phylogenomic analyses, metabarcoding and evolutionary studies. In this chapter, we present a robust and adaptable bioinformatics pipeline for the identification, assembly, and annotation of extrachromosomal DNA from whole-genome datasets. The pipeline was developed with euglenids in mind and takes into account their unique genomic features, but can also be adapted for other Euglenozoa (and protists). This approach enables the recovery of organellar and rDNA sequences with high confidence and supports both targeted studies and large-scale environmental analyses.},
}

*Computational Biology/methods
*Molecular Sequence Annotation/methods
DNA, Ribosomal/genetics
Genome, Mitochondrial
*Euglenozoa/genetics
Genome, Plastid
DNA, Mitochondrial/genetics
Phylogeny
Genomics/methods
Sequence Analysis, DNA/methods

@article {pmid41627460,
year = {2026},
author = {Do, TH and Dao, TK and Pham, TTN and Nguyen, MH and Nguyen, TQ and To, LA and Nguyen, TVH and Phung, TBT},
title = {Understanding the bacteriome, phageome and phage-associated bacteriome in healthy Vietnamese children under two years of age.},
journal = {Archives of microbiology},
volume = {208},
number = {4},
pages = {167},
pmid = {41627460},
issn = {1432-072X},
support = {DTDLCN.63/22//Ministry of Science and Technology/ ; },
mesh = {Humans ; Infant ; Vietnam ; *Gastrointestinal Microbiome ; Feces/microbiology/virology ; *Bacteria/classification/genetics/isolation & purification/virology ; *Bacteriophages/genetics/isolation & purification/classification ; Child, Preschool ; Male ; Female ; Metagenome ; Diarrhea/microbiology ; Southeast Asian People ; },
abstract = {The establishment of the intestinal microbiota during early life plays an important role in physical and mental development and in shaping disease susceptibility in adult. However, knowledge of the gut microbiota in healthy Vietnamese children remains limited. In this study, real-time PCR was used to detect 24 diarrheal pathogens in stool samples, revealing that 41% of healthy infants aged 6-24 months living in Hanoi, Hung Yen were asymptomatic carriers of Escherichia coli (29.1%), Clostridioides difficile (10.3%) and Sapovirus. Pooled metagenomes of gut bacteria (HMG1, HMG2) and viruses (HV1, HV2) from two groups of pathogen-negative infants aged 6-11 months (n = 17) and 12-24 months (n = 13) were subsequently sequenced. As expected, from the classified reads, HMGs comprised of 99.99% bacterial reads, while HVs comprised of bacteria (78.5% in HV1, 42.3% in HV2), phages (8.3% in HV1, 41.0% in HV2) and viruses. The gut microbiota was formed by core bacteria: Actinobacteria (82.6-84.5%), Firmicutes, Proteobacteria and Bacteroidetes, with abundance of Bifidobacterium (> 80%), phages: Podoviridae (65.5-70.2%), Siphoviridae, Myoviridae with dominant crAssphage. The HMGs and HVs shared core bacterial composition but differed in relative abundance. The gut microbiota of older children was characterized by an increase of probiotic bacteria, Escherichia phage, Lactococcus phage and decrease of bacterial pathogens and phages targeting Lactobacillus, Klebsiella, Acinetobacter. Bacterial genes in the gut phage fraction may reflect bacterial community in recent past. Overall, this study provides a scientific basis for understanding the gut microbiome in relation to health and diseases in children particularly within the Vietnamese population.},
}

Humans
Infant
Vietnam
*Gastrointestinal Microbiome
Feces/microbiology/virology
*Bacteria/classification/genetics/isolation & purification/virology
*Bacteriophages/genetics/isolation & purification/classification
Child, Preschool
Male
Female
Metagenome
Diarrhea/microbiology
Southeast Asian People

@article {pmid41627458,
year = {2026},
author = {Jiang, F and Gu, H and Song, P and Zhang, J and Cai, Z and Liang, C and Gao, H and Zhang, R and Zhang, T},
title = {Post-defecation exposure alters gut microbiota of forest musk deer with implications for conservation metagenomics.},
journal = {Applied microbiology and biotechnology},
volume = {110},
number = {1},
pages = {53},
pmid = {41627458},
issn = {1432-0614},
support = {32200408//National Natural Science Foundation of China/ ; 2023-ZJ-952Q//Natural Science Foundation of Qinghai Province/ ; 2023M743743//China Postdoctoral Science Foundation/ ; },
mesh = {Animals ; *Deer/microbiology ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; *Metagenomics ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation & purification ; Forests ; DNA, Bacterial/genetics ; Endangered Species ; Conservation of Natural Resources ; Time Factors ; Sequence Analysis, DNA ; },
abstract = {In endangered species conservation, fecal samples are a vital non-invasive tool for gut microbiota analysis. Yet, the influence of external exposure time on microbial composition and function remains unclear, constraining data accuracy and reliability. To address this, we investigated the time-gradient effect in the globally endangered forest musk deer (Moschus berezovskii). Using non-invasive sampling under standardized captive conditions, fecal samples were collected at six storage times: (0, 1, 2, 4, 6, 8 days). Gut microbiota composition, diversity, enterotypes, and functional differences were assessed through 16S rRNA gene sequencing on the Illumina MiSeq platform. In total, 147,013 valid ASVs (amplicon sequence variants) were obtained showing significant shifts in microbial composition with storage time. Dominant phyla included Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria. Increasing storage time led to declining α-diversity, reduced community stability, and more unique genera. PCoA (principal coordinates analysis) and NMDS (non-metric multidimensional scaling) indicated progressive separation of experimental groups from control groups, with Anosim and Adonis confirming progressive separation with storage time. Structurally, Firmicutes decreased while Proteobacteria, specifically the Acinetobacter genus, increased with storage time. Community assembly shifted from deterministic to stochastic processes, reflecting stronger environmental disturbance effects. These results demonstrate that the gut microbiota composition, diversity, and ecological functions in forest musk deer feces are highly sensitive to storage time. Thus, preservation duration must be strictly controlled as a critical variable in microbiome studies. This work establishes methodological standards for non-invasive fecal metagenomics in endangered species, providing theoretical insights and practical guidance for improving scientific rigor in conservation-related microbiome research. KEY POINTS: Fecal microbiota diversity and stability decline significantly with longer storage. Firmicutes decrease while Proteobacteria, especially Acinetobacter, increase over time. Storage duration strongly impacts microbiome data, requiring strict sampling control.},
}

Animals
*Deer/microbiology
*Gastrointestinal Microbiome/genetics
Feces/microbiology
*Metagenomics
RNA, Ribosomal, 16S/genetics
*Bacteria/classification/genetics/isolation & purification
Forests
DNA, Bacterial/genetics
Endangered Species
Conservation of Natural Resources
Time Factors
Sequence Analysis, DNA

@article {pmid41627236,
year = {2026},
author = {Yu, M and Wang, Y and Huangfu, K and Wu, S and Huang, H and Ma, Z and Wang, Y and Qiu, Y and Liu, S},
title = {Oxygen Vacancy-Engineered High-Entropy Oxide Nanozymes for Spatiotemporal Cascading Antifouling in Marine Environments.},
journal = {Small (Weinheim an der Bergstrasse, Germany)},
volume = {},
number = {},
pages = {e13363},
doi = {10.1002/smll.202513363},
pmid = {41627236},
issn = {1613-6829},
support = {52272271//National Natural Science Foundation of China/ ; },
abstract = {The catalytic versatility and compositional tunability of oxidative attack-based nanozymes offer a promising strategy for marine antifouling, yet their performance is often constrained by insufficient active-site accessibility, transient catalytic intermediates and restricted diffusion. Inspired by haloperoxidases (HPOs) in marine organisms, this study reports oxygen vacancy (Vo)-enriched high-entropy oxides (Vo-HEO) as multifunctional nanozymes to address these challenges. The entropy-stabilized multicomponent lattice, synergistically coupled with abundant Vo sites, reconfigures electronic structures and diversifies catalytic pathways, enabling efficient HPO-mimetic generation of hypobromous acid (HOBr), which is a selective and long-lived biocide (half-life > 36 days) capable of disrupting bacterial quorum sensing (QS) signals and oxidizing key biomolecules. By further integrating persistent HOBr with highly reactive hydroxyl radicals, Vo-HEO establishes a spatiotemporally cascading protective regime at the substrate interface, combining long-range QS suppression in the bulk phase with rapid oxidative eradication at the nano-biological interface, ultimately reducing bacterial adhesion by 90%. Microbiological characterization and metagenomic sequencing analyses further verify that Vo-HEO systematically collapses the coordination of microbial communication and energy metabolism across temporal and spatial scales. Collectively, this work demonstrates intelligent regulation of marine microecology and establishes a paradigm for adaptive antifouling design.},
}

@article {pmid41628276,
year = {2026},
author = {Habib, I and Hernandez-Valencia, JC and Martinu, J and Novakova, E},
title = {Viral metagenome characterization reveals species-specific virome profiles in Triatominae populations from the southern United States.},
journal = {PLoS neglected tropical diseases},
volume = {20},
number = {2},
pages = {e0013576},
doi = {10.1371/journal.pntd.0013576},
pmid = {41628276},
issn = {1935-2735},
abstract = {Kissing bugs (Triatominae) are hematophagous insects and the principal vectors of Trypanosoma cruzi, the causative agent of Chagas disease. While their bacterial microbiomes have received considerable attention, the diversity of viruses associated with these insects remains poorly understood. To address this gap, we investigated the metavirome of five Triatominae species from the southern United States (Triatoma rubida, T. sanguisuga, T. gerstaeckeri, T. indictiva, and Hospesneotomae protracta), sampled in Texas, New Mexico, and Arizona. We sequenced 23 samples, including abdomen, gut and reproductive tissues from 13 field-collected individuals and assembled 41 viral operational taxonomic units (vOTUs), 40 of which are novel and together constitute 13 viral families, including Chuviridae, Arenaviridae, Orthomyxoviridae, Partitiviridae, Solemoviridae, Circoviridae, Rhabdoviridae, Microviridae, Xinmoviridae, Astroviridae, Narnaviridae, Tombusviridae, and the order Elliovirales. The vOTUs composition and abundance analysis examined variables including species, sex, tissue type, blood meal, and T. cruzi infection status, showing that metavirome diversity varied significantly among Triatominae species. Our findings demonstrate a species-specific metavirome and the presence of virus taxa linked to insects, plants, and vertebrates, highlighting the complex ecological interactions between viruses and triatomines. This study uncovers a diverse and largely novel set of metaviromes within North American Triatominae, providing a foundation for future research on virus-vector interactions.},
}

@article {pmid41626594,
year = {2026},
author = {Sapino, R and Fernández-González, Á and Castresana, J},
title = {Development of Metagenomic Methods for Health Monitoring of Endangered Species Using Fecal Samples.},
journal = {Evolutionary applications},
volume = {19},
number = {2},
pages = {e70199},
pmid = {41626594},
issn = {1752-4571},
abstract = {Metagenomic analysis of fecal samples is emerging as a powerful tool for monitoring endangered species, particularly in assessing the burden of pathogens and parasites that can threaten population viability. However, accurate identification in non-model species remains challenging due to the frequent absence of host-specific pathogen reference genomes. In this study, we developed a robust computational framework for detecting potentially pathogenic bacteria from metagenomic sequences by mapping them to available reference genomes in databases. Several key parameters affecting the analysis, including mapping algorithm, database configuration, and identification parameters, were analyzed to optimize detection sensitivity and specificity. Applying this approach to fresh fecal samples of the Iberian desman (Galemys pyrenaicus), a critically endangered semi-aquatic mammal, we identified 26 potentially pathogenic bacterial species, with prevalences ranging from isolated cases to nearly half of the individuals examined. Furthermore, our analysis revealed that some desmans had atypical compositions of potential pathogens, suggesting variations in environmental exposure or host genetic factors. This work demonstrates a novel application of fecal metagenomics for species-level detection of microorganisms implicated in disease, providing a powerful approach to gain essential insights into the health and epidemiology of endangered species and to support the development of more effective conservation strategies.},
}

@article {pmid41626263,
year = {2026},
author = {Liu, Y and Fu, H},
title = {Pulmonary Tropheryma whipplei Infection Presenting With Multiple Thick-Walled Cavities on Chest CT: A Case Report and Literature Review.},
journal = {Respirology case reports},
volume = {14},
number = {2},
pages = {e70487},
pmid = {41626263},
issn = {2051-3380},
abstract = {Whipple's disease (WD) is a rare chronic multisystem infectious disease caused by the actinomycete Tropheryma whipplei. Pulmonary involvement is uncommon, and its clinical manifestations lack specificity, with diverse imaging findings, making it prone to misdiagnosis. We report a rare case of a 50-year-old woman who presented with a 2-week history of cough. Chest CT showed multiple thick-walled cavities in both lungs, a highly unusual presentation for WD pneumonia. Routine microbiological tests, including acid-fast staining and culture of bronchoalveolar lavage fluid (BALF), were negative, which made the diagnosis challenging. Metagenomic next-generation sequencing (mNGS) of BALF detected T. whipplei, confirming the diagnosis of WD pneumonia. After oral doxycycline treatment, follow-up chest CT showed complete resolution of the pulmonary cavities. This case demonstrates that multiple thick-walled cavities may be a characteristic imaging manifestation of WD pneumonia, highlights the diagnostic value of mNGS for this rare infection, and supports oral doxycycline monotherapy as an effective treatment option for isolated pulmonary TW infection.},
}

@article {pmid41626090,
year = {2026},
author = {Chen, L and Tang, M and Wang, Q and Jiang, H},
title = {Why a Mycobacterium Avium Infected Patient Showed a Positive Xpert MTB/RIF Result?.},
journal = {Clinical case reports},
volume = {14},
number = {2},
pages = {e71965},
pmid = {41626090},
issn = {2050-0904},
abstract = {This article discusses whether a MAC infected patient with a positive Xpert MTB/RIF test has a co-infection with Mycobacterium tuberculosis (MTB). The patient presented with chronic, indolent pulmonary patchy shadows on imaging but lacked typical symptoms. The MTB antigen-specific interferon-gamma enzyme-linked immunospot assay (T-SPOT.TB) was negative. Bronchoalveolar lavage fluid (BALF) testing yielded conflicting results: Xpert MTB/RIF assay detected trace levels of MTB DNA, whereas reverse dot blot hybridization confirmed the presence of Mycobacterium avium complex (MAC); in contrast, metagenomic next-generation sequencing (mNGS) returned a negative result for all pathogens. Mycobacterial culture ultimately returned positive; however, the MPB64 assay-employed for species identification-yielded a negative result, indicating a probable nontuberculous mycobacterial (NTM) infection. Despite contradictory lab results, the patient's symptoms and culture findings favored MAC infection. However, MTB infection could not be definitively ruled out in this patient, so a treatment regimen combining anti-tuberculosis and anti-MAC medications (isoniazid, rifampicin, ethambutol, and azithromycin) was initiated, leading to significant radiographic improvement. The discordance between the positive Xpert MTB/RIF result and other diagnostic evidence highlights important diagnostic challenges, underscoring the need for integrated clinical interpretation and providing actionable insights for clinicians.},
}

@article {pmid41625985,
year = {2026},
author = {Taboada, S and Riesgo, A and Busch, K and Erpenbeck, D and Hentschel, U and Galià, C and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , },
title = {The chromosomal genome sequence of the sponge Phakellia ventilabrum (Linnaeus, 1767) and its associated microbial metagenome sequences.},
journal = {Wellcome open research},
volume = {11},
number = {},
pages = {15},
pmid = {41625985},
issn = {2398-502X},
abstract = {We present a genome assembly from a specimen of Phakellia ventilabrum (Porifera; Demospongiae; Bubarida; Bubaridae). The genome sequence has a total length of 211.92 megabases. Most of the assembly (99.97%) is scaffolded into 25 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 24.36 kilobases in length. Gene annotation of this assembly by Ensembl identified 21 622 protein-coding genes. Thirty-three binned genomes were generated from the metagenome assembly, of which eight were classified as high-quality metagenome assembled genomes (MAGs) and of which four of the MAGs are fully circular. The MAGs were taxonomically assigned to Pseudomonadota (i.e. Candidatus Poriferihabitaceae), Nitrospirota, Nitrospinota, and the archaeal Nitrosopumilus clade.},
}

@article {pmid41625959,
year = {2026},
author = {de Melo Pereira, GV and da Silva Vale, A and Ribeiro-Barros, AI and Rodrigues, LRS and de França Bettencourt Mirção, GM and Camilo, B and da Piedade Ernesto Tapaça, I and de Mello Sampaio, V and Brar, SK and Soccol, CR},
title = {Integrated microbial-metabolomic analysis reveals how fermentation contributes to the unique flavor of African Arabica coffee.},
journal = {Food chemistry. Molecular sciences},
volume = {12},
number = {},
pages = {100344},
pmid = {41625959},
issn = {2666-5662},
abstract = {Post-harvest fermentation is a decisive stage in shaping the flavor complexity of Arabica coffee. In this study, we mapped for the first time the microbial-driven flavor metabolic network underlying the fermentation of high-quality African coffee, using a combined metabolomic, meta-barcoding, and metagenomic approach applied to samples from Chimanimani National Park, Mozambique. Over 72 h of spontaneous fermentation, chemical analyses revealed rapid sucrose hydrolysis, lactic acid accumulation, and the formation of 74 volatile compounds. These transformations were driven by a previously unreported core microbiome (Leuconostoc-Hanseniaspora-Galactomyces axis), whose functional repertoire (1791 genes) highlighted the Ehrlich pathway and ester biosynthesis as central flavor routes. Among the volatiles formed, linalool, phenylethyl alcohol, and ethyl acetate were most abundant, emerging as predictive drivers of the floral and fruity notes identified in the resulting high-quality coffee beverage (score 87.25 ± 0.25). This study underscores microbial terroir as a key factor adding value to emerging African origins.},
}

@article {pmid41625836,
year = {2025},
author = {Matsukawa, M and Sakai, Y and Aoki, K and Ishii, Y},
title = {Urinary Microbiome Profiling by Shotgun Metagenomic Sequencing in Women Having Acute Cystitis-Like Symptoms With Negative Urine Cultures.},
journal = {Cureus},
volume = {17},
number = {12},
pages = {e100451},
pmid = {41625836},
issn = {2168-8184},
abstract = {BACKGROUND: Women presenting with typical symptoms of acute cystitis but with negative urine cultures, termed acute cystitis-like symptoms with negative urine cultures (ACNCs) in this study, are not uncommon. Despite previous attempts to detect bacterial DNA in urine, the etiology remains unclear. Although alterations in the urinary microbiome have been linked to other urological disorders, its involvement in ACNC has not been thoroughly investigated.

METHODS: Between September 2016 and December 2017, midstream urine samples were collected from women aged ≥16 years who had at least one typical symptom of acute cystitis and a negative urine culture. Samples were obtained at the initial (V1) and follow-up (V2) visits. Shotgun metagenomic sequencing (SMG) was performed via an Illumina MiSeq system. Taxonomic analysis at the genus level included taxa with ≥10 assigned reads in samples with ≥10,000 human-subtracted reads (HSRs).

RESULTS: Of 206 eligible women, 15 (7.3%; median age, 65 years) met the ACNC criteria and were enrolled. SMG was conducted for 15 samples at V1 and nine samples at V2. At V1, the HSR varied widely, and only five samples met the criteria for reliable interpretation. Seven samples, particularly those with high-grade pyuria, contained fewer than 1,000 HSRs, indicating potentially very low microbial loads or technical limitations. ACNC microbiomes demonstrated marked interindividual variation in taxonomic composition. The predominant taxa most frequently observed were Lactobacillus spp., Gardnerella spp., and JC polyomavirus. Conventional uropathogens, such as Escherichia spp., were not identified at interpretable levels. At V2, microbial diversity remained heterogeneous, but eight samples yielded sufficient read counts for interpretation.

CONCLUSIONS: While conventional uropathogens below interpretable criteria are unlikely to be responsible for most ACNCs, it is not necessarily recommended to regard the leading taxon in each case as the cause or to exclude microbiological involvement simply due to a low HSR because no validated metagenomic signature distinguishes pathogens from commensals. However, the observed diversity in ACNC microbiome profiles may reflect a heterogenous group of microbial conditions, including potentially viral, and nonmicrobial etiologies.},
}

@article {pmid41625740,
year = {2025},
author = {Su, J and Liu, K and Wu, X and Lin, B and Ying, F and Zhu, Y and Li, M and Guo, P},
title = {Case Report: Confocal microscopy in the early diagnosis of microsporidial keratitis.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1745070},
pmid = {41625740},
issn = {2296-858X},
abstract = {This report describes a rare case of microsporidial stromal keratitis (MSK) complicated by corneal perforation in a 69-year-old male farmer with a 5-month history of ocular redness, pain, photophobia, and epiphora. In vivo confocal microscopy (IVCM) revealed pathognomonic findings-hyperreflective double-walled spore casings and vesicular clusters, providing the earliest diagnostic clues for microsporidia infection. Subsequent metagenomic next-generation sequencing (mNGS) and histopathology confirmed Microsporidia species. The patient underwent therapeutic penetrating keratoplasty followed by targeted anti-microsporidial therapy, achieving globe preservation and visual improvement. This case underscores IVCM's pivotal role in diagnosing MSK, particularly in atypical presentations. Because MSK remains a rare corneal disorder, its insidious progression necessitates high clinical vigilance. In summary, IVCM's ability to detect microsporidial structures in real-time significantly enhances early diagnosis, complementing molecular methods like mNGS. We conclude that IVCM, as a non-invasive and rapid diagnostic tool, provides a convenient and efficient means for the early differentiation of challenging corneal infections.},
}

@article {pmid41625489,
year = {2026},
author = {Zhou, L and Liu, J and Li, S and Xiong, Y and Qin, F and Luo, Z and Huang, D and Chen, H and Wang, X},
title = {Association between anxiety symptoms on risky e-biking riding behavior among adolescents: based on gut-brain axis.},
journal = {Comprehensive psychoneuroendocrinology},
volume = {25},
number = {},
pages = {100337},
pmid = {41625489},
issn = {2666-4976},
abstract = {OBJECTIVE: This study aimed to investigate the association between anxiety symptoms and risky e-bike riding behavior (RERB) among adolescents and to explore whether gut microbiota mediates this relationship.

METHODS: Adolescents using e-bikes were recruited through a combined online and offline recruitment approach. Data collection involved supervised electronic questionnaire completion in face-to-face settings, with biological samples collected independently by participants. Anxiety symptoms were assessed using the Generalized Anxiety Disorder-7 scale. RERB were evaluated via a structured questionnaire, yielding separate scores for aggressive behaviors (ABS), violation behaviors (VBS), and negligent behaviors (NES), along with total behavior scores (TBS). Fecal samples were obtained for metagenomic sequencing to characterize gut microbiota composition. Multiple linear regression was employed to elucidate the associations between anxiety symptoms and RERB. Partial Least Squares Path Modeling (PLS-PM) was applied to evaluate the potential mediating role of gut microbiota in these associations.

RESULTS: A total of 71 adolescents were included in this cross-sectional study. Anxiety symptoms were significantly associated with RERB, including TBS and VBS (both P < 0.05). Among the 15 microbial genera identified from fecal samples, 17 species showed significant association with both anxiety symptoms and RERB. PLS-PM modeling revealed a significant mediating effect of specific gut microbiota in the anxiety→behavior pathway, particularly for TBS and VBS. In contrast, for ABS, a reverse pathway-microbiota→anxiety→behavior-was found significant.

CONCLUSIONS: Anxiety symptoms were significantly associated with RERB among adolescents. Specific gut microbiota may mediate these associations, suggesting a potential microbiota-brain-behavior pathway.},
}

@article {pmid41624871,
year = {2025},
author = {Zhu, H and Hu, L and Feng, Z and Zhang, Z and Zhu, H and Li, H},
title = {Case Report: Murine typhus complicated by symmetrical peripheral gangrene: first report and diagnostic insights from metagenomic next-generation sequencing.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1746919},
pmid = {41624871},
issn = {1664-3224},
mesh = {Humans ; Female ; High-Throughput Nucleotide Sequencing ; Aged ; *Gangrene/diagnosis/etiology ; Metagenomics/methods ; *Typhus, Endemic Flea-Borne/diagnosis/drug therapy/complications/microbiology ; Anti-Bacterial Agents/therapeutic use ; *Rickettsia typhi/genetics ; Doxycycline/therapeutic use ; },
abstract = {BACKGROUND: Murine typhus, a flea-borne infection caused by Rickettsia typhi, often presents with nonspecific symptoms that delay diagnosis. While usually self-limiting, it can rarely progress to multiple organ dysfunction syndrome (MODS). We report the first case of murine typhus complicated by symmetrical peripheral gangrene (SPG), in which metagenomic next-generation sequencing (mNGS) enabled rapid diagnosis and guided timely doxycycline therapy.

CASE PRESENTATION: A 69-year-old female from South China was hospitalized with persistent abdominal pain and low-grade fever. She was a farmer and had suspected animal exposure. Laboratory investigations revealed hypoxia, abnormal coagulation profile, hepatorenal impairment, and thrombocytopenia. Despite empirical antibiotic therapy, her condition deteriorated progressively, manifested as hemodynamic instability, respiratory failure, and the emergence of purpuric-petechial cutaneous eruptions. Immediate interventions were initiated, including administration of vasoactive agents and mechanical ventilation. Based on mNGS, R. typhi was confirmed, she received targeted antibiotic treatment with intravenous doxycycline (100 mg twice daily). On the hospital day 16, gangrene of all four extremities became evident. The patient underwent amputation of all four extremities and survived, with systemic symptoms gradually resolving during 6-months follow-up.

CONCLUSION: This first reported case of murine typhus complicated by symmetrical peripheral gangrene (SPG) establishes its potential to cause life-threatening multiorgan failure. Metagenomic next-generation sequencing (mNGS) resolved the diagnostic challenge by rapidly identifying Rickettsia typhi, guiding life-saving doxycycline therapy and underscoring its value in severe zoonotic infections.},
}

Humans
Female
High-Throughput Nucleotide Sequencing
Aged
*Gangrene/diagnosis/etiology
Metagenomics/methods
*Typhus, Endemic Flea-Borne/diagnosis/drug therapy/complications/microbiology
Anti-Bacterial Agents/therapeutic use
*Rickettsia typhi/genetics
Doxycycline/therapeutic use

@article {pmid41624426,
year = {2026},
author = {Santi, I and Pavloudi, C and Abagnale, M and Azua, I and Baña, Z and Bastianini, M and Belser, C and Berg, K and Bilbao, J and Bird, K and Broudin, C and Camusat, M and Cancio, I and Caray-Counil, L and Casotti, R and Castel, J and Comtet, T and Cox, CJ and Cunliffe, M and Daguin, C and Deneudt, K and Díaz de Cerio, O and Exter, K and Fauvelot, C and Fontana, Y and Frada, MJ and Galand, PE and Gallia, R and Garczarek, L and González Fernández, J and Guillou, L and Heynderickx, H and Koplovitz, G and Labrune, C and Lagaisse, R and Laroquette, A and Lescure, L and Lopes, E and Loulakaki, M and Louro, B and Magalhães, C and Margiotta, F and Moal, H and Moussy, A and Not, F and Percopo, I and Paredes Rosendo, E and Péru, E and Poulain, J and Praebel, K and Rigaut-Jalabert, F and Romac, S and Rzeznik-Orignac, J and Sarno, D and Souza Troncoso, J and Thiébaut, E and Thomas, W and Tkacz, A and Tramontano, F and Trano, AC and Wincker, P and Pade, N},
title = {Next release of the European Marine Omics Biodiversity Observation Network (EMO BON) shotgun metagenomic data from water and sediment samples (Release 2).},
journal = {Biodiversity data journal},
volume = {14},
number = {},
pages = {e178484},
pmid = {41624426},
issn = {1314-2828},
abstract = {The European Marine Omics Biodiversity Observation Network (EMO BON) is a long-term genomic observatory run by the European Research Infrastructure European Marine Biological Resource Centre (EMBRC). It was established in 2021 to support the challenges of biodiversity observation and unsystematic management of biodiversity data in the European seas. EMO BON introduced and coordinated the systematic and harmonised observation of biodiversity amongst more than fourteen marine stations in the European coastline. Here, we report the next release (Release 2) of shotgun metagenomic data from seawater and sediment microbial communities.},
}

@article {pmid41623646,
year = {2025},
author = {Thagulisi, F and Baatjies, L and Sharma, A and Ngom, JT and Nyambo, K and Jooste, T and Tapfuma, KI and Mavumengwana, V},
title = {Antimycobacterial activity of intertidal sediment-derived bacteria from False Bay, South Africa.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1745248},
pmid = {41623646},
issn = {1664-302X},
abstract = {Tuberculosis (TB), caused by Mycobacterium tuberculosis, remains a global health burden due to the pathogen's ability to develop resistance to current treatment options. Consequently, drug discovery studies are essential for identifying new antimycobacterial agents with novel mechanisms of action. This study investigated the antimycobacterial activity of crude extracts derived from mixed culturable bacteria isolated from intertidal marine sediments. The bacterial diversity of the bioactive mixed cultures was characterized using 16S rRNA gene-based metagenomic analysis. Their pathogen-targeted effects were evaluated against Mycobacterium smegmatis mc[2]155 and M. tuberculosis H37Rv, and THP-1-derived macrophages infected with M. smegmatis mc[2]155. Of the 48 mixed bacterial crude extracts derived from 17 intertidal marine sediments, five-PPB1, GCR1, BB1, PPB2, and CR1-demonstrated strong antimycobacterial activity against M. smegmatis mc[2]155 and M. tuberculosis H37Rv with minimum inhibitory concentrations ranging from 31.25 to 62.50 μg/mL and 7.8125 to 15.625 μg/mL, respectively. At 62.50 μg/mL, CR1 significantly reduced the intracellular M. smegmatis mc[2]155 burden in THP-1-derived macrophages, resulting in 28.08 ± 4.25% mean decrease in bacterial survival (p < 0.0001) and 94.4% ± 1.14 mean growth inhibition. From the CR1 mixed cultures, nine axenic bacterial isolates were cultivated, and their resulting crude extracts were evaluated for bioactivity. The identified isolates included Marinobacter maritimus, Psychrobacter celer, Pseudomonas benzenivor, Bacillus altitudinis, Bacillus aerius, Bacillus stratosphericus, and Paenibacillus glucanolyticus. Metabolite profiling of axenic crude extracts identified several compounds, including tenacibactin B, maremycin D1, and tubercidine. These findings suggest that South African intertidal marine sediments host diverse microbial communities capable of producing novel antimycobacterial agents.},
}

@article {pmid41623642,
year = {2025},
author = {Kuang, HF and Jiang, XY and Tie, SY and Lian, K and Hao, MY and Xu, H and Huang, X and Yang, Y and Guo, Q and Li, J and Chen, LL},
title = {Global research trends in bacteriophage and gut microbiota: a bibliometric and visual analysis from 2012 to 2025.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1738456},
pmid = {41623642},
issn = {1664-302X},
abstract = {BACKGROUND: The gut microbiota constitutes a complex microbial ecosystem that plays a fundamental role in host metabolism and immune homeostasis. As the most abundant viral entities in the gut, bacteriophages are increasingly recognized as key modulators of microbial community structure and function. Nevertheless, the global research landscape and thematic evolution of bacteriophage-gut microbiota studies have not been systematically evaluated.

METHODS: Publications related to bacteriophages and the gut microbiota published between 2012 and 2025 were retrieved from the Web of Science Core Collection and Scopus databases. Bibliometric and visual analyses were conducted using CiteSpace, VOSviewer, and Scimago to examine publication trends, countries/regions, institutions, authors, journals, references, and research hotspots.

RESULTS: A total of 687 articles and reviews were included. The annual number of publications increased steadily, with accelerated growth after 2018 and a peak in 2023. China ranked first in publication output, while the United States demonstrated strong centrality in global collaboration networks. The University of California, San Diego and the University of Copenhagen were identified as leading institutions. Highly productive authors included Colin Hill, Bernd Schnabl, Zhang Yue, Li Shenghui, and Ross R. Pau. Frontiers in Microbiology and Nature are the most influential journals in this field. Keyword analyses revealed major research hotspots, including viral metagenomics, antimicrobial resistance, phage-microbiota-immune interactions, and the transition from phage therapy toward microecological and immunomodulatory interventions.

CONCLUSION: Research on bacteriophage-gut microbiota interactions has shifted from descriptive profiling to mechanistic and translational studies, driven by advances in viral metagenomics and phage culturomics. Increasing attention has been directed toward disease-associated phage-microbiota interactions, particularly in inflammatory bowel disease, as well as the development of precision interventions such as phage therapy and engineered phages. This bibliometric analysis provides a comprehensive overview of global research trends and highlights emerging directions for future microbiome research.},
}

@article {pmid41623638,
year = {2025},
author = {Kane, Y and Ma, Y and Yan, B and Zhao, X and Ge, T and Li, Y and Cao, L and Zhang, M and Wan, Z and Zhang, T and Zhang, C},
title = {The human plasma anellome exhibits age- and sex-dependent patterns with links to cardiometabolic health in older adults.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1716110},
pmid = {41623638},
issn = {1664-302X},
abstract = {The human plasma virome is dominated by anelloviruses which are increasingly associated with several clinical conditions including among others HIV-1, COVID-19, autoimmune diseases, and cardiovascular and metabolic diseases. Due to their high genetic divergence, most studies investigated human anellome at broad family or genus level. These approaches obscure the contributions of specific anellovirus species to clinical conditions. We conducted plasma metagenomics in 218 individuals from young (0-16 years) and old (63-100 years) cohorts to resolve the anellome at the species level and examine its patterns across age, sex, and associations with cytokines and cardiometabolic outcomes. Older adults exhibited near-universal anellovirus detection and significantly higher abundance compared with youth. Species-specific analysis revealed that Alphatorquevirus_homin1 and Alphatorquevirus_homin13 were markedly enriched in diseased older adults. Predictive modeling based on machine learning algorithms distinguished disease status in the young cohort with high accuracy (AUC = 0.86), but performance was limited in the elderly (AUC = 0.58), suggesting a lack of diagnostic value in advanced age. Specific species abundances and diversity were associated with stroke and coronary heart disease, while cytokine correlations revealed module-specific immune signatures: Gammatorquevirus-dominated modules associated positively with pro-inflammatory cytokines and growth factors (e.g., IL-1β, IL-15, VEGF), whereas Beta- and some Alphatorquevirus-dominated modules showed predominantly negative correlations with several inflammatory and regulatory mediators (e.g., IL-6, TNF-α, IL-10). These findings demonstrate that the anellome is influenced by age and immune status and shows associations with cardiometabolic health, although these relationships do not guarentee diagnostic or causal significance. Additonally, we found no significant differences of Human endogenous retrovirus K Env expression between disease and healthy controls. This work underscores the importance of resolving human anollome to species level in future longitudinal studies to strengthen their clinical significance and biomarker potential.},
}

@article {pmid41623634,
year = {2025},
author = {Zeng, J and Gong, L and Qin, S and Fang, P and Shu, F and Zhang, W and Zhou, Y and Li, X and He, Q and Sun, P and Deng, H},
title = {Multi-omics reveals glutinous rice varieties shape Baijiu flavor via microbial and metabolic modulation.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1721127},
pmid = {41623634},
issn = {1664-302X},
abstract = {INTRODUCTION: Glutinous rice significantly influences Baijiu flavor, yet standardized brewing-specific indicators are lacking.

METHODS: In this study, metagenomic, metaproteomic, and non-targeted GC-MS analyses of Zaopei, along with HS-SPME-GC-MS analysis of Baijiu, were used to compare the effects of three glutinous rice varieties with distinct nutritional profiles on microbial diversity and flavor formation.

RESULTS: The Wuliangye-specific variety Dajiugu, with high sucrose, high amino acids, and low fatty acids, promoted early growth and metabolic activity of Saccharomycopsis, Enterobacter, and Klebsiella. Functional genera such as Saccharopolyspora, Pediococcus, and Clostridium enhanced fatty acid and amino acid accumulation in Zaopei and increased ethyl acetate, 4-vinylphenol, and dimethyl trisulfide in Baijiu.

DISCUSSION: These findings highlight the pivotal role of glutinous rice variety in shaping Baijiu flavor and offer a scientific basis for breeding brewing-specific glutinous rice.},
}

@article {pmid41484707,
year = {2026},
author = {Zhou, Z and Zheng, X and Yang, W and Cui, Y and Gao, Y and Xia, J and Wang, Y and Gao, Y and Lu, M and Zhang, D and Wang, H and Chen, L},
title = {A rare case of peritoneal dialysis-associated peritonitis caused by Coxiella burnetii diagnosed by mNGS.},
journal = {BMC infectious diseases},
volume = {26},
number = {1},
pages = {233},
pmid = {41484707},
issn = {1471-2334},
abstract = {We report a rare case of peritoneal dialysis (PD)-associated peritonitis caused by Coxiella burnetii, an intracellular pathogen typically associated with Q fever. A 28-year-old female with lupus nephritis and end-stage kidney disease on PD presented with cloudy effluent and abdominal pain after consuming undercooked lamb. Despite initial empirical broad-spectrum antibiotic therapy (cefazolin/ceftazidime protocol), clinical symptoms persisted. Conventional bacterial, fungal, and mycobacterial cultures were negative. Metagenomic next-generation sequencing (mNGS) of the peritoneal effluent identified C. burnetii DNA. The treatment was transitioned to doxycycline and hydroxychloroquine resulted in clinical improvement and normalization of inflammatory markers. This case underscores the diagnostic value of mNGS in culture-negative peritonitis and emphasizes C. burnetii as an emerging pathogen in immunocompromised PD patients, particularly with zoonotic exposure histories.},
}

@article {pmid41623622,
year = {2025},
author = {Li, Y and Cheng, Y and Liu, W and Li, J and Li, S and Suriguga, and Ma, T and Kwok, LY and Cai, Z and Sun, Z},
title = {Gut microbial and functional signatures in breast cancer: an integrated metagenomic and machine learning approach to non-invasive detection.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1722632},
pmid = {41623622},
issn = {1664-302X},
abstract = {INTRODUCTION: Breast cancer is associated with significant restructuring of the gut ecosystem. Gut microbial composition and function may influence cancer development and progression through immune modulation, metabolic regulation, and inflammation-related pathways.

METHODS: Using shotgun metagenomic sequencing of fecal samples from 38 stage I-III breast cancer patients and 36 age- and body mass index-matched healthy controls. Machine learning models were constructed to evaluate the diagnostic potential of integrated microbial and metabolic features.

RESULTS: Significant alterations were observed in gut microbiota composition, including depletion of beneficial taxa (Limosilactobacillus fermentum, Blautia sp.) and enrichment of Prevotella copri. Pathways involved in short-chain fatty acid and purine metabolism were reduced. The gut phageome exhibited structural changes and altered correlations with bacterial hosts. Predictive analysis revealed depletion of short-chain fatty acids (butyrate, propionate), purine intermediates (hypoxanthine, xanthine), and nicotinate in patients. A machine learning model integrating microbial and predicted metabolic features achieved an area under the curve values of 0.78 in the discovery cohort and 0.73 (recall = 0.74) in an independent validation cohort.

DISCUSSION: Coordinated gut microbiome, phageome, and metabolome alterations characterize breast cancer, offering potential non-invasive biomarkers and mechanistic insights for disease detection and intervention.},
}

@article {pmid41623619,
year = {2025},
author = {Wei, T and Qian, N and Wang, H and Song, Y and Wang, W and Li, Y and Zhao, Z and Xu, F and Yang, W},
title = {Wilson's disease-associated gut dysbiosis: novel insights into microbial functional alterations, virulence changes, and resistance markers.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1714276},
pmid = {41623619},
issn = {1664-302X},
abstract = {BACKGROUND: Although the gut microbiota is associated with a variety of metabolic, inflammatory, and neurological disorders through microbial dysbiosis, current studies on the gut microbiota in Wilson's disease (WD) remain limited. Critical gaps exist in understanding the roles of key functional microbial factors in WD pathogenesis, which hinders the acquisition of mechanistic insights into this disease.

OBJECTIVE: This study aims to characterize alterations in the gut microbiome associated with WD, with a particular emphasis on virulence factors (VFs) and antibiotic resistance genes (ARGs), as well as functional mobile genetic elements (MGEs), in order to elucidate their potential roles in disease progression and clinical manifestations.

METHODS: We analyzed fecal samples from 37 patients with WD and 33 healthy controls (HCs) using metagenomic sequencing, with a specific focus on examining virulence gene profiles and antibiotic resistance patterns and MGE composition in relation to liver function markers.

RESULTS: Beta diversity analysis revealed significant differences in the gut microbial community structure between patients with WD and HCs, and a distinct set of microbial taxa was identified that showed significant associations with clinical indicators. A gut microbial co-occurrence network identified key species playing central roles in the microbial community structure, including Prevotella stercorea, Firmicutes bacterium CAG 110, Bacteroides salyersiae, Lactococcus petauri, Streptococcus cristatus, Actinomyces sp. HMSC035G02, and Streptococcus viridans. Widespread functional dysbiosis was detected across multiple biological levels in patients with WD, with significant correlations identified between these microbial alterations and clinical indicators. Significant disruptions were identified in key metabolic pathways, including the Pentose Phosphate Pathway, Pyruvate Metabolism, and Starch and Sucrose Metabolism, which were associated with the dysregulation of carbohydrate-active enzymes (CAZymes). These alterations showed significant correlations with clinical markers of liver dysfunction (e.g., procollagen III N-terminal peptide PIIINP, aspartate transaminase/alanine transaminase AST/ALT). A total of 54 virulence factor (VF) genes exhibited differential abundance in WD, with 36 genes depleted and 18 enriched. Notably, these included colibactin genes (clbB, clbH) from Escherichia coli and type IV secretion system genes (aec19, pilB). These VFs were significantly associated with indicators of liver function (e.g., bilirubin levels) and coagulation abnormalities. Among the detected antibiotic resistance genes (ARGs), 21 exhibited disease-specific patterns in WD, notably tetQ (encoding tetracycline resistance), ErmB (conferring macrolide resistance), and cfxA6 (mediating cephamycin resistance). Furthermore, ARG profiles were associated with Bifidobacterium enrichment and showed significant correlations with lipid metabolism markers [e.g., triglycerides (TG), high-density lipoprotein cholesterol (HDL-C)]. Critically, we identified significant enrichment of 60 functional mobile genetic elements (MGEs) in WD, spanning categories involved in DNA replication/repair, phage activity, and conjugative transfer, indicating heightened genomic plasticity and horizontal gene transfer potential. Strikingly, correlation network analysis revealed strong and specific co-occurrence between key ARGs (e.g., ErmX) and defined suites of MGEs, suggesting MGE-facilitated dissemination of resistance determinants.

CONCLUSION: Wilson's disease (WD) patients exhibit significant alterations in gut microbial community structure and functional dysbiosis, wherein the enrichment of virulence genes (such as colibactin genes clbB/clbH) and the specific antibiotic resistance genes (such as tetQ and ErmB), and the activation of mobile genetic elements are closely associated with clinical indicators including liver function impairment, coagulation abnormalities, and lipid metabolism disorders.},
}

@article {pmid41623458,
year = {2026},
author = {Li, QM and He, LS and Wang, Y},
title = {Small proteins from prokaryotes in the marine water column at full ocean depth.},
journal = {iScience},
volume = {29},
number = {2},
pages = {114585},
pmid = {41623458},
issn = {2589-0042},
abstract = {Small proteins (SPs, ≤50 aa) are often overlooked in genomics. We conducted the first systematic analysis of prokaryotic SPs across the full ocean-depth gradient. From 433,311 short open reading frames (sORFs) predicted from 71 western Pacific metagenomes, we identified 193,281 SP clusters. Filtration yielded 75,581 prevalent SPs, including 4,307 high-confidence clusters (RfSPs). Notably, 87.09% of RfSPs lacked non-marine homologs, and ∼70% contained unknown domains. While most (65.57%) were phylum-specific, twelve were distributed across ≥5 phyla, and some were prophage-associated. Geographically, twenty-three core RfSPs were universally present. Co-occurrence analysis revealed that interacting RfSPs typically originated from the same or adjacent zones. Finally, we confirmed the transcription of 8.20% RfSP clusters in deep-sea metatranscriptomes. The zone-specific transcription of certain RfSPs suggests adaptive functions, such as stress response and molecular chaperoning, in distinct marine environments. Our study reveals SPs as a critical strategy for prokaryotic adaptation to deep-sea stressors.},
}

@article {pmid41623309,
year = {2026},
author = {Luo, Y and Ding, H and Pan, J and Xu, G},
title = {Use of metagenomic next-generation sequencing to diagnose Tropheryma whipplei infection-related pneumonia: A case report.},
journal = {Experimental and therapeutic medicine},
volume = {31},
number = {3},
pages = {75},
pmid = {41623309},
issn = {1792-1015},
abstract = {Whipple's disease is caused by Tropheryma whipplei (T. whipplei), an uncommon pathogen that is often related to gastrointestinal symptoms. Extraintestinal involvement, particularly pulmonary manifestations, is rare and poses notable diagnostic challenges. An objective technique for identifying undiscovered infections is the application of metagenomic next-generation sequencing (mNGS). The present case report described a 55-year-old female presenting with community-acquired pneumonia (CAP), who received empirical treatment with moxifloxacin, ultimately diagnosed through mNGS performed on bronchoalveolar lavage fluid. The results indicated that the patient was infected with T. whipplei and that the patient exhibited notable clinical improvement within 2 weeks following intravenous moxifloxacin during hospitalization and continuation of oral moxifloxacin following discharge. The present case report highlighted the utility of mNGS in diagnosing atypical infections and identified T. whipplei as a potential etiological agent of CAP in immunocompetent hosts.},
}

@article {pmid41622335,
year = {2026},
author = {Ota, C and Bamba, M and Sato, S and Tsuchimatsu, T},
title = {Soil microbial composition and abundance influence the growth of Lotus japonicus.},
journal = {Journal of plant research},
volume = {},
number = {},
pages = {},
pmid = {41622335},
issn = {1618-0860},
abstract = {In mutualistic symbiosis between plants and bacteria, the abundance and composition of symbiotic bacterial groups in the soil microbiota can be important for plant growth. Here, we focused on the nitrogen-fixing mutualism between Lotus japonicus and nodule bacteria to investigate whether and how much the abundance of symbiotic rhizobia in the soil microbiota of natural environments contributes to variations in host plant growth. An inoculation experiment of soil microbiota revealed extensive variations in plant growth phenotypes, even between microhabitats. We found that the local presence of L. japonicus and the relative abundance of Mesorhizobium bacteria showed positive correlations with plant growth supported by both 16S amplicon sequencing and shotgun metagenome analyses. Among bacteria investigated, the abundance of Mesorhizobium was most strongly associated with plant growth phenotypes, supporting its role as the primary symbiotic rhizobia in natural environments. Given the specificity and the selectivity of plants for favorable rhizobia, legume-rhizobia interactions could trigger a positive plant-soil feedback that enriches favorable rhizobia into the soil surrounding legume plant habitats.},
}