@article {pmid41613591,
year = {2025},
author = {Xu, Y and Ma, Y and Huang, Q and Guo, X and Guo, L and Ren, Y and Lu, W and Wu, X and Li, D and Li, S},
title = {The role of bronchoalveolar lavage fluid metagenomic next-generation sequencing in detecting pathogens and optimising antibiotic therapy in paediatric severe community-acquired pneumonia.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1688473},
pmid = {41613591},
issn = {2235-2988},
mesh = {Humans ; *Community-Acquired Infections/drug therapy/microbiology/diagnosis ; Infant ; Child, Preschool ; *High-Throughput Nucleotide Sequencing/methods ; Child ; Male ; Retrospective Studies ; Female ; *Anti-Bacterial Agents/therapeutic use ; *Metagenomics/methods ; Adolescent ; *Bronchoalveolar Lavage Fluid/microbiology/virology ; *Bacteria/genetics/isolation & purification/classification ; Sensitivity and Specificity ; ROC Curve ; *Pneumonia/drug therapy/microbiology/diagnosis ; Severity of Illness Index ; Community-Acquired Pneumonia ; },
abstract = {BACKGROUND: Severe community-acquired pneumonia (SCAP) remains a major cause of mortality in the paediatric population, with current diagnostic and treatment approaches often proving insufficient and contributing to the growing challenge of antibiotic resistance. This study explored the potential of metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid as a tool to enhance the precision of antibiotic management in children with SCAP.

METHODS: A retrospective cohort study of 202 paediatric patients with community-acquired pneumonia (aged 1 month-18 years) admitted to the First Affiliated Hospital of Xinxiang Medical University (November 2020-March 2023) was conducted. Patients were grouped by severity (intensive care unit [ICU]/non-ICU) and mNGS timing (early: ≤72 hours post-admission; late: >72 hours). The diagnostic efficacy of mNGS versus conventional microbiological techniques (CMT) was evaluated using sensitivity, specificity, positive/negative predictive values and area under the receiver operating characteristic curve (AUC) analysis. Antibiotic adjustments and clinical outcomes were analysed via survival statistics.

RESULTS: Metagenomic next-generation sequencing showed a higher positive detection rate (98.51%) than CMT (47.52%) (AUC = 0.82, 95%CI: 0.76-0.88). Of the 202 patients, 127 (62.87%) were male, with a median age of 1.88 years (interquartile range: 0.29-7 years). Early mNGS was associated with fewer extrapulmonary complications (69.63% vs 55.22% in the late group, p < 0.05), and shorter hospitalisation (median 13 vs 15 days, p <0.01). Antibiotic escalation occurred in 50 (24.75%) cases, de-escalation in 22 (10.89%) and same-level adjustment in 25 (12.38%).

CONCLUSION: Metagenomic next-generation sequencing outperforms CMT in pathogen detection. Early mNGS is associated with improved clinical outcomes, suggesting its potential utility in paediatric SCAP management.},
}

Humans
*Community-Acquired Infections/drug therapy/microbiology/diagnosis
Infant
Child, Preschool
*High-Throughput Nucleotide Sequencing/methods
Child
Male
Retrospective Studies
Female
*Anti-Bacterial Agents/therapeutic use
*Metagenomics/methods
Adolescent
*Bronchoalveolar Lavage Fluid/microbiology/virology
*Bacteria/genetics/isolation & purification/classification
Sensitivity and Specificity
ROC Curve
*Pneumonia/drug therapy/microbiology/diagnosis
Severity of Illness Index
Community-Acquired Pneumonia

@article {pmid41613303,
year = {2025},
author = {Huang, J and Lan, C and Liang, Y and Chen, H and Liang, H and He, H and Che, S and Chen, Y},
title = {Case Report: Metagenomic next-generation sequencing diagnosed a rare case of sternal tuberculosis mimicking a malignant tumour.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1708834},
pmid = {41613303},
issn = {2296-858X},
abstract = {This is a case report of a 17-year-old female patient who presented with a painless, palpable swelling on the anterior chest wall. Imaging studies revealed osteolytic lesions involving the manubrium and adjacent ribs, along with multiple enlarged lymph nodes, raising a high suspicion of malignant tumour with metastasis. An ultrasound-guided needle biopsy revealed the pathological finding of "granulomatous inflammation." Multidisciplinary consultation and clinical indicators, including a strongly positive purified protein derivative (PPD) test and markedly elevated erythrocyte sedimentation rate, were taken to indicate a potential diagnosis of tuberculosis. Consequently, subsequent metagenomic next-generation sequencing (mNGS) of the biopsy specimen identified nucleic acid sequences belonging to the Mycobacterium tuberculosis complex, thereby confirming the rare diagnosis of sternal tuberculosis. Following the administration of standardised anti-tuberculosis therapy, a substantial reduction in the size of the lesion was observed, thereby validating the accuracy of the diagnosis. This case underscores the importance of considering extrapulmonary tuberculosis in the differential diagnosis of bone-destructive lesions and demonstrates the critical value of mNGS technology in confirming challenging infectious diseases.},
}

@article {pmid41612676,
year = {2026},
author = {Asin, J and Carvallo, F and Gonzales-Viera, OA and Macías-Rioseco, M and Streitenberger, N and Abdelrazek, S and Crossley, B and Pesavento, PA and Uzal, FA},
title = {Interstitial pneumonias of undetermined etiology in foals in California, 1990-2020.},
journal = {Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc},
volume = {},
number = {},
pages = {10406387251410524},
doi = {10.1177/10406387251410524},
pmid = {41612676},
issn = {1943-4936},
abstract = {Interstitial and bronchointerstitial pneumonias of undetermined etiology in young foals are relatively common in autopsy services with an equine focus. Unknown viruses, toxins, hyperthermia, surfactant or alveolar macrophage function deficiency, certain antibiotics, and aberrant responses to Rhodococcus equi or other bacteria have been proposed as causes. We performed a retrospective study of autopsies on foals with a diagnosis of interstitial or bronchointerstitial pneumonia with an unidentified etiology. Forty-one foals (median age: 3-mo-old) were included. Most were received in summer (n = 28) and spring (n = 10). The most frequently reported clinical signs were dyspnea and/or tachypnea (n = 28) and fever (n = 19). Antibiotic treatment was reported in 21 cases, and the most frequently used antibiotics were penicillin (n = 9) and gentamicin (n = 8). Grossly, most of the lungs were diffusely rubbery-to-firm (n = 35) and did not collapse (n = 22). Histologically, combinations of exudative (E; hyaline membranes), proliferative (P; type II pneumocyte hyperplasia), and fibrotic (F; fibroplasia) phases were common (E + P, n = 15; E + P + F, n = 13) in the interstitial component. Necrosis of the bronchiolar epithelium was rare (n = 4), concurrent suppurative bronchopneumonia was common (n = 22), and a few foals (n = 5) had pulmonary pyogranulomas. Pneumocystis spp. organisms were observed in 8 cases using Grocott-Gomori methenamine silver stain. Bacteria were recovered from the lungs in 22 cases, with R. equi (n = 7) and E. coli (n = 6) being the most common isolates. No unequivocal viral causes were identified during the regular diagnostic work-up and after using novel diagnostic approaches such as herpesvirus consensus PCR and viral metagenomics in a subset of the cases.},
}

@article {pmid41612514,
year = {2026},
author = {Enagbonma, BJ and Pierneef, RE and Modise, DM and Babalola, OO},
title = {Effects of legume-based rotation on subsequent sorghum rhizosphere microbial communities and their drought tolerance-related genes.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-025-00829-9},
pmid = {41612514},
issn = {2524-6372},
support = {CRP/ZAF22-03//ICGEB/ ; },
abstract = {INTRODUCTION: The impacts of incorporating legumes into cereal crops on soil microbial structure, composition, functional genes involved in nitrogen, carbon and phosphorus cycling, signaling pathways and hydraulic conductivity adaptations have been well studied. However, the same cannot be said for functional genes that increase drought tolerance.

OBJECTIVES: Here, we examined the changes in microbial community structure and functional genes involved in drought tolerance in response to legume‒cereal rotation and cereal‒cereal rotation. This study provides a preliminary, exploratory characterization of microbial community and functional gene shifts, without direct evidence of functional impact on plant physiology or productivity.

METHODS: DNA extracted from soil samples collected across cowpea-sorghum treatment (CS) or maize-sorghum treatment (MS) was sequenced via shotgun sequencing.

RESULTS: Nonmetric multidimensional scaling analysis revealed that the microbial communities in the CS treatment significantly differed from those in the MS treatment. Compared with the MS rotation, the CS rotation increased the relative abundances of Pseudomonadota, Acidobacteriota, Chloroflexota, Gemmatimonadota, Euryarchaeota, and Candidatus Bathyarchaeota and reduced the abundances of Actinomycetota, Ascomycota, and Nitrososphaerota at the phylum level. Furthermore, the CS rotation increased the abundance of microbial genera such as Solirubrobacter, Sphingomonas, Nitrosocosmicus, Nitrosotenuis Aspergillus, and Metschnikowia when related to the MS rotation. STAMP analysis revealed that in the CS rotation, genes involved in trehalose biosynthesis, biofilm formation, oxidative stress mitigation (e.g., sodA, katG), stress signaling (e.g., rpoS, ipdC), nutrient provisioning (e.g., nifH, pqqC), membrane fluidity (desA, desB), dormancy (spo0A, spoVF), and ion homeostasis (nhaB, kup) predominated. In the MS rotation, proline biosynthesis (proA, proB, and proC), glycine betaine synthesis (betA and betB), aquaporin (aqpZ), and structural integrity genes (murA and murC) were predominant. The RDA results revealed that crop rotation influenced the soil physicochemical parameters, which in turn impacted both the microbial communities and drought tolerance genes in both treatments, probably creating a favorable environment for resilience under drought.

CONCLUSION: These research findings provide insight into the relationships between cowpea cropping sequences and the soil microbiome and drought-tolerant functional genes fundamental for the productivity of successive crops and this understanding guides sustainable crop selection.},
}

@article {pmid41612472,
year = {2026},
author = {Wang, Y and Shen, Y and Shen, J and Bi, J and Xu, J and Wei, T and Wang, R and Wu, X and Li, F and Bai, J and Jie, Z and Hou, D and Song, Y},
title = {Airway microbiome dysbiosis in severe pneumonia: metagenomic evidence of pathogen expansion and commensal depletion.},
journal = {European journal of medical research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40001-026-03892-1},
pmid = {41612472},
issn = {2047-783X},
support = {ZD2021CY001//Shanghai Municipal Science and Technology Major Project/ ; GWVI-11.1-18//Shanghai Three-year Action Plan to Strengthen the Construction of Public Health System/ ; 82130001//National Natural Science Foundation of China/ ; 2024YFC3044400//National Key Research and Development Program of China/ ; GZNL2024A02003//R&D Program of Guangzhou National Laboratory/ ; W2020-013//The Construction of Multi-Disciplinary Treatment System for Severe Pneumonia/ ; 22Y11900800//Science and Technology Commission of Shanghai Municipality/ ; shslczdzk02201//Shanghai Municipal Key Clinical Specialty/ ; },
abstract = {BACKGROUND: The pulmonary microbiome is increasingly recognized as a key determinant of pneumonia severity, yet its clinical implications remain incompletely understood. Disruption of microbial ecology, or dysbiosis, may impair host immune responses and exacerbate disease progression. This study aimed to characterize microbiome alterations associated with severe pneumonia and their correlation with host inflammatory and coagulative parameters.

METHODS: In this multicenter, prospective observational cohort study conducted across nine hospitals in Shanghai (2021-2025), bronchoalveolar lavage fluid (BALF) samples from 306 patients with clinically diagnosed pulmonary infections were analyzed using metagenomic next-generation sequencing (mNGS). Patients were stratified into severe (n = 196) and non-severe (n = 110) groups using WHO-derived severe pneumonia criteria at the time of bronchoalveolar lavage (BAL). Microbial taxonomic profiles, diversity indices, co-occurrence networks, and correlations with clinical markers were comprehensively assessed using standard bioinformatic and statistical approaches.

RESULTS: Severe pneumonia was associated with marked microbial dysbiosis, including reorganization of co-occurrence network topology with centrality shifting away from commensals toward opportunistic taxa in severe disease, characterized by reduced α-diversity, altered β-diversity, and enrichment of opportunistic Gram-negative pathogens including Acinetobacter and Klebsiella. In contrast, commensals such as Rothia and Prevotella were depleted. Co-occurrence network analysis revealed fragmentation of microbial interactions in severe cases, with centrality shifting from commensals to opportunists like Corynebacterium striatum. Shannon diversity negatively correlated with SOFA scores, and specific taxa positively associated with systemic inflammation (CRP, PCT) and coagulation abnormalities. Nearly all samples demonstrated polymicrobial infection, with distinct microbial patterns observed across monomicrobial and polymicrobial subgroups.

CONCLUSION: Our multicenter observational analysis suggests that severe pneumonia is associated with marked ecological disruption of the lower-airway microbiome, characterized by commensal loss, opportunist expansion, and fragmented interspecies networks, and with concurrent inflammatory and coagulative abnormalities. These hypothesis-generating findings warrant external validation in independent, multi-region cohorts and longitudinal sampling to test directionality and causality before informing clinical decision-making.},
}

@article {pmid41612232,
year = {2026},
author = {Chen, Q and Yin, Q and Chen, J and Jin, L and Guo, W and Huang, M},
title = {Comparison of the diagnostic value of targeted next-generation sequencing, metagenomic next-generation sequencing, and Xpert MTB/RIF in adult pulmonary tuberculosis.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-026-12673-4},
pmid = {41612232},
issn = {1471-2334},
}

@article {pmid41612194,
year = {2026},
author = {Ballandras, V and McNamara, L and Carolan, JC and Pichon, A and Byrne, S},
title = {Whole genome sequencing of 18 economically important aphid pests with photographic vouchers for taxonomic validation.},
journal = {BMC genomic data},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12863-026-01406-w},
pmid = {41612194},
issn = {2730-6844},
}

@article {pmid41611865,
year = {2026},
author = {Ulloa, MA and Serrano, AV and Camelo, LC and Guyot, R and Vela, D and Muñoz, AR},
title = {Bacterial genome reconstruction and community profiling in Neotropical Drosophila.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-36282-y},
pmid = {41611865},
issn = {2045-2322},
abstract = {Drosophila species serve as key models for microbiota research due to their relatively simple microbial communities. However, microbial diversity and dynamics in Neotropical Andean Drosophila remain underexplored. Here we applied shotgun metagenomics to characterize the microbiota of 24 Neotropical Drosophila species from Ecuador, reconstructing 64 high-quality bacterial genomes predominantly from Acetobacteraceae and Enterobacterales. Microbial communities were consistently dominated by yeasts, lactic acid bacteria, acetic acid bacteria, and Wolbachia. Comparative analyses revealed no strong correlation between host phylogeny and microbial community composition, suggesting environmental factors and microbial interactions shape these communities. Notably, shifts in relative abundances indicate dynamic ecological succession and metabolic cooperation among microbes. These findings expand genomic resources for Drosophila-associated bacteria and highlight the complex ecological processes influencing host-microbiota relationships in natural populations.},
}

@article {pmid41611767,
year = {2026},
author = {Jain, AG and Agwan, D and Kumar, A and Pancha, I and Rathod, J and Mohapatra, B},
title = {Mixing regimes shape microbial community composition, nutrient regimes, and plant growth attributes in Jeevamrit: metagenomics and culturomics-based insights.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-36414-4},
pmid = {41611767},
issn = {2045-2322},
support = {GSBTM/JD(R&D)/661/2022-23/00173054//GSBTM/ ; },
abstract = {Jeevamrit, a microbial inoculant widely used in zero-budget natural farming (ZBNF) that relies on local farm-based resources to enhance overall biological health of soil, is reported for inconsistent crop yield enhancements. This is mainly due to variability in its preparation methods, e.g., mixing intensity, incubation regimes, and quality of ingredients used. Hence, the current study aimed to decipher the effect of mixing intensity (extent of oxygenation) on microbial community composition, nutrient transformation, and plant growth attributes of Jeevamrit, using a combined metagenomics-culturomics approach. Frequent mixing (Constant/Intermediate) enhanced nutrient solubilization (Fe, Zn, Cu, Mn) with higher total N and dissolved organic carbon, while less mixing (Anoxic/No-mix) led to accumulation of soluble Fe and NH4[+]-N with higher microbial diversity. Mixing-driven differential enrichment of taxa were noted, i.e., constant mixing (CM) dominated by Acinetobacter (~ 40%), Comamonas, Pseudomonas, and Lysinibacillus, linked to oxidative C/N cycling and metal dissolution. Whereas, anoxic (AO) favored Clostridium sensu stricto, Lactobacillales, Enterococcus, and Enterobacterales (> 60%), correlating to fermentative metabolism-driven reductive elemental cycling. Co-occurrence network analysis identified Acinetobacter, Pseudomonas, Comamonas, Trichococcus, and Stenotrophomonas as hubs, indicating keystone functions in structuring metabolic interactions. The metagenome-recovered MAGs belonged to Acinetobacter sp., Clostridium saccharobutylicum, Trichococcus flocculiformis, and Enterococcus gallinarum with potential to participate in multiple nutrient cycling. Cultivable members of Shigella, Rhodococcus, and Bacillus spp. showed high IAA production (135-145 µg mL[-][1]), NH3 release (~ 0.12 µg mL[-][1]), and K and P solubilization (~ 55.2 µg mL[-][1]). We hypothesize that oxygenation drives the Jeevamrit's microbial guild assembly, where mixing intensity modulates oxido-reductive metabolism and nutrient mobilization efficiency, indicating the requirement for standardization of formulation aligned to soil-specific conditions.},
}

@article {pmid41611691,
year = {2026},
author = {Srivathsan, A and Arzika, AM and Maliki, R and Abdou, A and Lipsitch, M and Blumberg, S and O'Brien, KS and Porco, TC and Hinterwirth, A and Doan, T and Keenan, JD and Lietman, TM and Arnold, BF},
title = {Geographic spillover of antimicrobial resistance from mass distribution of azithromycin.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-68691-y},
pmid = {41611691},
issn = {2041-1723},
abstract = {Large-scale, placebo-controlled, cluster-randomized trials in high-mortality settings in sub-Saharan Africa demonstrated a 14-18% reduction in childhood mortality following twice-annual mass drug administration (MDA) of azithromycin among children aged 1-59 months. Azithromycin MDA also selected for antimicrobial resistance (AMR), particularly macrolide resistance. It is unknown whether the AMR from azithromycin MDA could spill over to neighboring untreated populations. If present, such geographic spillover effects could lead trials to underestimate AMR risks. We assess between-village geographic spillover effects of genotypic macrolide resistance using metagenomic deep sequencing in rectal swabs collected from 300 children in 30 monitoring villages in Niger after two years of MDA in 594 surrounding villages. Conditional permutation tests assess associations between proximal azithromycin treatment intensity and resistance gene abundance. We find no evidence of geographic spillover of macrolide resistance in untreated villages, as the genetic load of AMR remains at baseline levels in placebo-treated villages regardless of surrounding azithromycin treatment intensity (Spearman ρ = -0.05, P = 0.83). Sensitivity analyses confirm robustness across metrics, and no spillover effects are detected for other antibiotic classes. Azithromycin MDA-induced macrolide resistance appears localized to treated villages, mitigating some concerns about geographic spillover of AMR to nearby untreated villages at 24 months.},
}

@article {pmid41611489,
year = {2026},
author = {Li, W and Zhang, N and Li, Z and Cui, L and Wang, X and DU, Y},
title = {[Research progress on nanopore sequencing data alignment analysis methods and reference databases].},
journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology},
volume = {42},
number = {1},
pages = {77-92},
doi = {10.13345/j.cjb.250554},
pmid = {41611489},
issn = {1872-2075},
mesh = {*Nanopore Sequencing/methods ; *Sequence Alignment/methods ; *Nanopores ; *Sequence Analysis, DNA/methods ; *Databases, Genetic ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; },
abstract = {Nanopore sequencing, as an emerging hotspot in sequencing technology, demonstrates tremendous potential in species identification, genome assembly, variant detection, and transcriptome analysis, owing to its distinctive advantages including extended read lengths, rapid detection capabilities, and compact instrumentation. However, nanopore sequencing data are characterized by high error rates and presence of insertions and deletions, which pose novel challenges for the application of conventional sequence alignment tools and the construction of reference databases. Focusing on the characteristics of nanopore data, this paper systematically sorts out sequence alignment tools suitable for nanopore sequencing, and elaborates on their advantages and limitations in processing sequence data for five different application scenarios: long-read sequencing, real-time sequencing, error rate compatibility, metagenomics, and structural variation detection. Meanwhile, from the perspective of data sources, this paper conducts multi-dimensional classification and organization of reference genome databases, and sorts out the key technologies for constructing high-quality nanopore databases. Through the collaborative analysis of alignment tools and databases, this paper provides references for the optimization and innovation of nanopore sequencing data analysis, and promotes the in-depth transformation of metagenomic sequencing from data generation to functional analysis.},
}

*Nanopore Sequencing/methods
*Sequence Alignment/methods
*Nanopores
*Sequence Analysis, DNA/methods
*Databases, Genetic
Metagenomics/methods
High-Throughput Nucleotide Sequencing/methods

@article {pmid41611279,
year = {2026},
author = {Ma, XJ and Wang, F and Han, XT and Fang, F and Han, LY and Liu, HX},
title = {[Clinical characteristics and prognostic factors in patients with cerebrospinal fluid torque teno virus positivity after allogeneic hematopoietic stem cell transplantation].},
journal = {Zhonghua yi xue za zhi},
volume = {106},
number = {5},
pages = {455-460},
doi = {10.3760/cma.j.cn112137-20250711-01704},
pmid = {41611279},
issn = {0376-2491},
mesh = {Humans ; *Torque teno virus/isolation & purification ; *Hematopoietic Stem Cell Transplantation/adverse effects ; Retrospective Studies ; Prognosis ; Male ; Female ; Transplantation, Homologous ; Adult ; Adolescent ; Survival Rate ; Young Adult ; *DNA Virus Infections ; },
abstract = {Objective: To investigate the clinical characteristics and prognostic factors for patients with cerebrospinal fluid positivity for torque teno virus (TTV) after allogeneic hematopoietic stem cell transplantation (allo-HSCT). Methods: A retrospective analysis was conducted on the patients who received allo-HSCT at Hebei Yanda Lu Daopei Hospital from 2022 to 2023 year and showed positive cerebrospinal fluid metagenomic next-generation sequencing (mNGS) results post-transplantation, with their clinical data collected accordingly. The patients were categorized into TTV-negative and TTV-positive groups based on the detection of TTV in cerebrospinal fluid. The TTV-positive group was further subdivided into low-RPM [TTV reads per million sequencing reads (TTV-RPM)<1] and high-RPM (TTV-RPM≥1) subgroups using the threshold of TTV-RPM. The patients were followed until December 9, 2025, to investigate the clinical features of cerebrospinal fluid TTV positive patients after allo-HSCT. The survival curve was drawn to compare the difference of survival rate between groups. The influencing factors of patient prognosis were analyzed using a multivariate Cox regression model. Results: A total of 134 patients were enrolled: sixty in the TTV-negative group, including 35 males and 25 females, aged [M (Q1, Q3)] 30 (14, 42) years, and 74 in the TTV-positive group, including 45 males and 29 females, aged 24 (15, 40) years. Within the TTV-positive group, 44 were classified as low-RPM subgroup and 30 as high-RPM subgroup. Baseline characteristics, including gender, age, primary disease, donor type, neutrophil engraftment time, platelet engraftment time, whether acute graft-versus-host disease (aGVHD) occurred, and other microbial infections in cerebrospinal fluid, showed no significant differences between the TTV-negative and TTV-positive groups, or between the low-RPM and high-RPM subgroups (all P>0.05). The median follow-up time was 30.0(18.0, 35.4) months, the median survival period was not reached in the low-RPM subgroup, while that in the high-RPM subgroup was 25.6 months (95%CI: 5.3-45.9), and the 3-year survival rate was lower than that in the low-RPM subgroup (41.1% vs 76.8%, P=0.014). Multivariate Cox regression analysis confirmed high TTV-RPM level (≥1) in cerebrospinal fluid as a risk factor for mortality in allo-HSCT patients (HR=2.57, 95%CI: 1.09-6.08). Conclusions: There is no difference in clinical characteristics among allo-HSCT patients with or without TTV infection or with different TTV viral loads. A high TTV-RPM value (≥1) in cerebrospinal fluid is a risk factor for mortality in allo-HSCT patients.},
}

Humans
*Torque teno virus/isolation & purification
*Hematopoietic Stem Cell Transplantation/adverse effects
Retrospective Studies
Prognosis
Male
Female
Transplantation, Homologous
Adult
Adolescent
Survival Rate
Young Adult
*DNA Virus Infections

@article {pmid41611053,
year = {2026},
author = {Ma, WJ and Ma, ZS and An, ZJ and Zhang, HM and Tian, Y},
title = {Commercial powdered activated carbon achieves high-efficiency nitrogen removal in sulfur-driven autotrophic denitrification at low temperatures.},
journal = {Environmental research},
volume = {},
number = {},
pages = {123882},
doi = {10.1016/j.envres.2026.123882},
pmid = {41611053},
issn = {1096-0953},
abstract = {Sulfur-driven autotrophic denitrification (SAD), a nitrate removal process, is characterized by low carbon emissions and high sustainability. However, its efficiency is notably affected by low temperatures. This study confirmed that the addition of powdered activated carbon (PAC) could enhance denitrification capacity at low temperatures in the SAD process. At 15-10 °C, the nitrogen removal efficiency was 80.38%, 1.38 times higher than that of the blank reactor. At low temperatures, PAC enhanced the activities of nitrate reductase and nitrite reductase. Meanwhile, PAC stimulated EPS secretion and improved bio-electrochemical properties. Concurrently, both extracellular and intracellular electron transfer were enhanced by the addition of PAC. Microbial analysis indicated that the microbial network with PAC addition exhibited greater stability and robustness. Furthermore, PAC increased the relative abundances of denitrifying bacteria at low temperatures, particularly those of Ferruginibacter and Dokdonella. Metagenomic sequencing indicated that PAC enhanced pathways related to nucleotide sugar metabolism and synthesis, tRNA charging, and coenzyme A biosynthesis. At the genes level, the functional genes narIL, nirS, nasE, norCE, nosZ, soxA, soxZ, and dsrA were enriched with PAC addition. This study proposed and validated the feasibility of using PAC to enhance nitrogen removal efficiency in the wastewater treatment process at low temperatures, and further elucidated the underlying mechanisms.},
}

@article {pmid41611051,
year = {2026},
author = {Shi, J and Sun, C and Su, Y and Wu, Y and Zhan, M and Ji, C and Wang, R and Lv, B},
title = {Ecosystem-specific composition and drivers of plastisphere resistome in freshwater and marine environments.},
journal = {Environmental research},
volume = {},
number = {},
pages = {123858},
doi = {10.1016/j.envres.2026.123858},
pmid = {41611051},
issn = {1096-0953},
abstract = {Microplastics in aquatic environments facilitate the formation of specific plastisphere microbiomes and serve as potential hotspots for antibiotic resistance genes (ARGs) propagation. However, the systematic comparisons of ARG profiles on microplastics from different aquatic ecosystems remain limited, particularly the prevalent ARGs and their bacterial hosts. This study performed a comparative meta-analysis of existing metagenomic datasets to investigate the resistome between freshwater and seawater microplastics (FMP and SMP) and their driving factors. Our results revealed that the ARG profiles on both FMP and SMP were significantly distinct from their surrounding waterbody. Moreover, FMP exhibited a higher diversity and abundance of ARGs rather than SMP. Ten core ARGs were shared on FMP and SMP, while 23 core ARGs were exclusively detected on FMP. The bacterial community on microplastics exhibited an ecosystem-specific composition, and was identified as the primary determinant shaping the ARG profiles. Notably, more complex bacteria-ARG co-occurrence pattern was identified on FMP, involving a broader spectrum of core genera and potential pathogenic hosts (e.g., Mycobacterium, Streptomyces). Furthermore, a significant and specific correlation between mobile genetic elements and ARGs was identified on FMP but not SMP, suggesting a markedly elevated horizontal gene transfer potential, with mechanistic support from the concurrent enrichment of oxidative stress and SOS response genes on FMP. These findings provide a comprehensive characterization of ARGs on aquatic microplastics, and especially highlight the role of FMP on the ARG dissemination.},
}

@article {pmid41611023,
year = {2026},
author = {Li, W and Li, J and Wu, Y and Chen, M and Fu, Y and Li, W and Liu, S and Wang, J and Chen, Y},
title = {Artificial regulation of aerobic and anaerobic layers interface enhanced efficient nitrogen removal by weaving insulating grid and conductive carbon fiber in membrane aerated biofilm reactor.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134074},
doi = {10.1016/j.biortech.2026.134074},
pmid = {41611023},
issn = {1873-2976},
abstract = {Artificial regulation of aerobic and anaerobic biofilm thickness is crucial for enhancing nitrogen removal efficiency of the membrane aerated biofilm reactor (MABR). In this study, conductive aeration membrane modules were fabricated by physical weaving technology to couple MABR with microbial electrochemistry for efficient nitrogen removal. Insulating grids of different thickness and conductive carbon fibers were woven onto the aeration membrane to form aerobic and anaerobic layers. When the total biofilm thickness reached 254 μm (150 μm aerobic layer and 104 μm anaerobic layer), the TN removal efficiency (89.49 ± 2.89 %) was optimal. 16S rRNA gene sequencing and metagenomics analysis confirmed that the aerobic and anaerobic layers in the biofilm were completely separated, but there was a synergistic effect in nitrogen removal. The composite cathode structure provides a mechanism for efficient spatial coupling between the aerobic and anaerobic layers, establishing a basis for regulating biofilm stratification.},
}

@article {pmid41610602,
year = {2026},
author = {Phusathian, B and Pongmanee, K and Theapparat, Y and Saikhwan, N and Trairatapiwan, T and Chaosap, C and Seemacharoensri, A and Tactacan, GB and Wong, LY and Ruangpanit, Y},
title = {Bacterial xylanase supplementation improves nutrient utilization, gut integrity, and microbial metabolism in broilers fed energy-reduced diets.},
journal = {Poultry science},
volume = {105},
number = {4},
pages = {106515},
doi = {10.1016/j.psj.2026.106515},
pmid = {41610602},
issn = {1525-3171},
abstract = {This study evaluated the effects of bacterial xylanase supplementation on growth performance, nutrient digestibility, intestinal integrity, and microbial metabolic function in broilers fed energy-reduced diets. A total of 1,050 one-day-old male Ross 308 broiler chicks were randomly assigned to three dietary treatments, each comprising 14 replicates of 25 birds: a positive control (CON; standard corn-soybean meal diet), a negative control with reduced energy (NC; -85 kcal/kg), and an energy-reduced diet supplemented with bacterial xylanase (NCX; 100 g/ton Belfeed Xylanase™). During the starter phase, broilers fed the NC diet exhibited higher feed intake and FCR compared with those fed the CON and NCX diets (P < 0.05), with no significant difference between the CON and NCX diets. Apparent digestibility of dry matter, crude protein, and fat did not differ among dietary treatments (P > 0.05). However, broilers fed the NCX diet showed higher (P < 0.05) digestibility of crude fiber, NDF, and ADF than those fed the CON or NC diets. Apparent metabolizable energy was higher in broilers fed the CON and NCX diets compared with the NC diet. Furthermore, broilers receiving the CON and NCX diets exhibited significantly lower serum fluorescein isothiocyanate-dextran concentrations than those fed the NC diet, indicating improved intestinal barrier integrity. Bacterial xylanase supplementation increased microbial alpha diversity and altered beta diversity clustering, with enrichment of beneficial taxa such as Bifidobacteriaceae and Lactobacillaceae. Functional metagenomic prediction suggested greater representation of carbohydrate metabolism and energy production pathways in the NCX diet, whereas the NC diet was associated with enrichment of stress-related and xenobiotic degradation pathways. Overall, bacterial xylanase supplementation mitigated the adverse effects of dietary energy reduction by improving fiber utilization, maintaining gut integrity, and modulating the cecal microbiota toward a more favorable metabolic profile.},
}

@article {pmid41610548,
year = {2026},
author = {Zafar, S and Alimohammadi, M and Hatami Moghadam, P and Hadei, M},
title = {Investigating the types of bacterial species with antimicrobial resistance genes in Iran's wastewaters: a systematic review.},
journal = {The Science of the total environment},
volume = {1016},
number = {},
pages = {181385},
doi = {10.1016/j.scitotenv.2026.181385},
pmid = {41610548},
issn = {1879-1026},
abstract = {Antimicrobial resistance (AMR) is a major global health threat, with wastewater systems performing as critical reservoirs and dissemination pathways for antimicrobial-resistant bacteria (ARB) and resistance genes (ARGs). Despite rising AMR rates in Iran, a comprehensive understanding of resistance patterns in wastewater remains limited. This systematic review aimed to investigate the prevalence, bacterial diversity, and resistance gene profiles in hospital, municipal, and industrial wastewater across Iran. A systematic search was conducted in Scopus, PubMed, Web of Science, and Iranian databases for studies published between 1990 and September 2024. Data extraction followed PRISMA guidelines, and study quality was assessed using the JBI checklist. A total of 43 studies from 13 provinces met the inclusion criteria, with nearly half originating from Tehran (21/43, 48.8%), indicating uneven national coverage. Hospital wastewater (18 studies, 41.9%) harbored the highest burden of clinically significant AMR, including MRSA (22%), VRE (17%), and ESBL-producing E. coli (17%). Municipal wastewater (31 studies, 72.1%) frequently contained VRE Enterococcus faecium (32%) and Enterococcus faecalis (23%), ESBL-producing E. coli (19%), and MRSA (10%). Industrial wastewater (10 studies, 23.3%), primarily from slaughterhouses, exhibited high ESBL rates in E. coli (80%), with some studies reporting up to 93% ESBL production among isolates. Across studies, the most recurrent ARGs were blaCTX (16.3%), vanA (20.9%), mecA (9.3%), tetracycline genes, and intI1. Detection methods were predominantly culture- and PCR-based, with limited use of qPCR, molecular typing, or metagenomics. The most frequently detected resistance genes included blaCTX-M, mecA, vanA, tetA, and intI1. Most studies used culture and PCR-based detection; molecular typing and metagenomic approaches were rarely applied. The persistent detection of MDR pathogens and high-priority ARGs highlights significant gaps in AMR surveillance. Strengthening national wastewater monitoring through standardized protocols, broader geographic coverage, and integration of advanced molecular tools is essential to support effective One Health based public-health strategies.},
}

@article {pmid41610462,
year = {2026},
author = {Nagy, EZ and Szeredi, L and Földi, D and Belecz, N and Kovács, ÁB and Sulyok, KM and Grózner, D and Wehmann, E and Bányai, K and Marton, S and Tenk, M and Kreizinger, Z and Gyuranecz, M},
title = {Development and efficacy test of a live, attenuated Mycoplasma hyorhinis vaccine candidate strain.},
journal = {Vaccine},
volume = {75},
number = {},
pages = {128278},
doi = {10.1016/j.vaccine.2026.128278},
pmid = {41610462},
issn = {1873-2518},
abstract = {BACKGROUND: Mycoplasma (M.) hyorhinis causes substantial economic losses in swine. Currently, prevention and treatment rely on minimizing risk factors and administering antibiotics, as no vaccines are commercially available in Europe. However, antibiotics often cannot fully eliminate the bacteria. The development of an effective vaccine could lead to a potentially long-term control method.

MATERIALS AND METHODS: A temperature-sensitive M. hyorhinis strain was developed using 1-methyl-3-nitro-1-nitrosoguanidine (NTG) mutagenesis. The immunogenicity and efficacy of this vaccine candidate clone were evaluated in combination with an adjuvant. Three-week-old piglets were immunized with the candidate vaccine strain, and the vaccination site was monitored daily. At six weeks of age, the pigs were challenged intravenously on two subsequent days. Daily clinical examinations were conducted, with blood and nasal swabs collected weekly throughout the study for M. hyorhinis enzyme-linked immunosorbent assay (ELISA), real-time PCR analysis, and isolation. Three weeks post-challenge, the animals were euthanized for gross and histopathological examinations. Body temperature was recorded daily, and body weight was measured upon arrival, and then at six and nine weeks of age.

RESULTS: Vaccination significantly reduced clinical signs (p = 0.03), as well as gross pathological (p = 0.01) and histopathological (p = 0.005) lesions compared with the positive control group. The vaccinated group exhibited an earlier and higher increase in M. hyorhinis-specific IgG antibody levels post-challenge than the positive control group. However, the vaccine candidate did not mitigate the impact of M. hyorhinis infection on the weight gain. After the challenge (days 21-42), both the vaccinated (p = 0.001) and the positive control (p = 0.003) groups exhibited reduced weight gain compared with the negative control group.

DISCUSSION: Overall, the attenuated M. hyorhinis strain, combined with the adjuvant, provided protection against M. hyorhinis infection. These results form a basis for the development of a novel vaccine candidate that offers effective prevention.},
}

@article {pmid41610081,
year = {2026},
author = {Kiige, JK and Kavoo, AM and Mwajita, MR and Mogire, D and Ogada, S and Wekesa, TB and Kiirika, LM},
title = {Correction: Metagenomic characterization of bacterial abundance and diversity in potato cyst nematode suppressive and conducive potato rhizosphere.},
journal = {PloS one},
volume = {21},
number = {1},
pages = {e0342019},
pmid = {41610081},
issn = {1932-6203},
abstract = {[This corrects the article DOI: 10.1371/journal.pone.0323382.].},
}

@article {pmid41609929,
year = {2026},
author = {Mo, Y and Ahlgren, N and Fuhrman, JA and Sun, F and Hou, S},
title = {A Beginner's Guide to Using DeepVirFinder for Viral Sequence Identification From Metagenomic Datasets.},
journal = {Current protocols},
volume = {6},
number = {2},
pages = {e70310},
doi = {10.1002/cpz1.70310},
pmid = {41609929},
issn = {2691-1299},
support = {549943//Simons Foundation/ ; 42476109//National Natural Science Foundation of China/ ; 42276163//National Natural Science Foundation of China/ ; EF-2125142//National Science Foundation/ ; 3779//Gordon and Betty Moore Foundation/ ; },
mesh = {*Metagenomics/methods ; *Software ; *Viruses/genetics ; *Deep Learning ; Genome, Viral ; Metagenome ; },
abstract = {Identifying viral sequences from metagenomic datasets is critical for investigating their origins, evolutionary patterns, and ecological functions. Previously, we developed a novel deep learning software, DeepVirFinder, to predict viral sequences from shotgun metagenomic assemblies. This method employs a twin convolutional neural network model to extract features from known viral and prokaryotic host genomic sequences for binary classification of input query sequences. With the rapid accumulation of environmental metagenomic data, this approach has accelerated the discovery of novel viruses from diverse environments through an alignment-free and reference-free deep learning strategy. To facilitate the rapid adoption of this software for beginning users, here we have further improved DeepVirFinder by optimizing its runtime performance, while maintaining the essential user interface of the original version. This comprehensive guide provides basic workflows for the most common use cases of DeepVirFinder. Additionally, to assist users in downstream analyses, supplementary scripts were provided in the software for extracting viral sequences and inspecting the results, thereby helping researchers more effectively mine viral information from metagenomic datasets. © 2026 Wiley Periodicals LLC. Basic Protocol 1: Predicting viral sequences in metagenomic assemblies Basic Protocol 2: An integrated pipeline for viral sequence analysis: Prediction, extraction, and visualization Basic Protocol 3: Retraining the DeepVirFinder model using a customized dataset.},
}

*Metagenomics/methods
*Software
*Viruses/genetics
*Deep Learning
Genome, Viral
Metagenome

@article {pmid41609629,
year = {2026},
author = {Huang, R and Wang, Y and Liu, D and Wang, S and Lv, H and Yan, Z},
title = {Retraction for Huang et al., "Long-Read Metagenomics of Marine Microbes Reveals Diversely Expressed Secondary Metabolites.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0238124},
doi = {10.1128/spectrum.02381-24},
pmid = {41609629},
issn = {2165-0497},
}

@article {pmid41609375,
year = {2026},
author = {Yepes-García, J and Falquet, L},
title = {2Pipe starts with a question: matching you with the correct pipeline for MAG reconstruction.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0084425},
doi = {10.1128/msystems.00844-25},
pmid = {41609375},
issn = {2379-5077},
abstract = {Whole-genome sequencing has boosted our ability to explore microbial diversity by enabling the recovery of metagenome-assembled genomes (MAGs) directly from environmental DNA. As a result, the vast availability of sequencing data has prompted the development of numerous bioinformatics pipelines for MAG reconstruction, along with challenges to identify the most suitable pipeline to perform the analysis according to the user needs. This report briefly discusses the computational requirements of these pipelines; presents the variety of interfaces, workflow managers, and package managers they feature; and describes the typical modular structure. Also, it provides a compacted technical overview of 41 publicly available pipelines or platforms to build MAGs starting from short and/or long sequences. Moreover, recognizing the overwhelming number of factors to consider when selecting an appropriate pipeline, we introduce an interactive decision-support web application, 2Pipe, that helps users to identify a suitable workflow based on their input data characteristics, desired outcomes, and computational constraints. The tool presents a question-driven interface to customize the recommendation, a pipeline gallery to offer a summarized description, and a pipeline comparison based on key factors used for the questionnaire. Beyond this and foreseeing the release of novel pipelines in the near future, we include a quick form and detailed instructions for developers to append their workflow in the application. Altogether, this review and the application equip the researchers with a general outlook of the growing metagenomics pipeline landscape and guide the users toward deciding the workflow that best fits their expectations and infrastructure.},
}

@article {pmid41609371,
year = {2026},
author = {Panattoni, A and De Boeck, I and Wittouck, S and Deffner, P and Lillie-Jaschniski, K and Stadler, J and Lebeer, S and Theuns, S},
title = {Exploring the functional microbiome of pigs within the porcine respiratory disease complex: viral-bacterial co-infections and virulence factor profiling.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0191025},
doi = {10.1128/spectrum.01910-25},
pmid = {41609371},
issn = {2165-0497},
abstract = {Respiratory infections are among the most impacting on pigs' health and economic productivity. Despite this, detailed insights into the microbial community of the lower respiratory tract (LRT) are currently lacking, mainly because of difficulties in the processing of respiratory samples. In this study, we characterized the microbiota of the LRT of finisher pigs aged 3-5 months with respiratory symptoms for both the viral and bacterial components, using a previously validated metagenomic diagnostic assay and a full-length 16S rRNA gene sequencing approach, respectively. Functional characterization was carried out using metagenomic shotgun sequencing, revealing the presence of specific virulence factors (VFs). Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) and swine Influenza A Virus (swIAV) were the most prevalent viruses, being detected in 30% and 23% of the tested samples, respectively. Mesomycoplasma hyopneumoniae, Glaesserella parasuis, and Pasteurella multocida were the three most abundant bacterial taxa based on both sequencing approaches, while other detected bacterial taxa consisted mainly of Streptococcus, Clostridium, and Rothia species. Detected virulence factors belonged mainly to Mesomycoplasma and Pasteurella and consisted of adhesion factors such as p102, p97, p146, mhp108, mhp107 and the hemolysin-encoding gene hlyA for Mesomycoplasma, and adhesin-encoding ptfA and endoxtoxin-related gene lpxC for Pasteurella. Our data show how the microbial community of the lower respiratory tract in pigs with respiratory symptoms includes key viral (PRRSV, swIAV) and bacterial pathogens (M. hyopneumoniae, G. parasuis, and P. multocida), along with specific virulence factors likely contributing to disease.IMPORTANCEThe obtained results offer insights into the composition of the swine respiratory tract microflora, opening new perspectives on its correlation with viral infections, functional characteristics, and overall health conditions. Moreover, the present study provides technical advancement on the possibility of extracting and amplifying bacterial DNA from low-biomass respiratory samples, with the resulting possibility of identifying virulence factors and better understanding their contribution to the disease state. These discoveries pave the way for future studies aimed at improving diagnostic accuracy and treatment strategies for respiratory disease in both veterinary and human medicine.},
}

@article {pmid41609355,
year = {2026},
author = {Li, Y and Li, Q and Quan, K and Xie, Y and Yang, N and Ma, T and Zheng, L and Zhou, W and Li, Y and Jin, H and Sun, Z and Chen, Y and Kwok, L-Y and Lu, N and Zhu, W and Liu, W and Zhang, H},
title = {Adjunctive probiotic therapy sustains symptom relief in gastroesophageal reflux disease through gut microbiome-metabolome remodeling.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0156825},
doi = {10.1128/msystems.01568-25},
pmid = {41609355},
issn = {2379-5077},
abstract = {Proton pump inhibitors (PPIs) are standard therapy for gastroesophageal reflux disease (GERD), but long-term use causes dysbiosis, gastrointestinal side effects, and symptom relapse after discontinuation. Probiotics may offer adjunctive benefits by modulating the gut ecosystem. The study aimed to evaluate the efficacy of a multi-strain probiotic (Lihuo) with rabeprazole in GERD and its impact on gut microbiota and metabolome. A randomized, double-blind, placebo-controlled trial was conducted in 120 GERD patients assigned to receive rabeprazole with either Lihuo (n = 64) or placebo (n = 56) for 8 weeks, followed by 4 weeks of probiotic or placebo alone. The primary outcome was change in the Reflux Disease Questionnaire (RDQ) score. Secondary outcomes included Gastrointestinal Symptom Rating Scale, endoscopic healing, and multi-omics profiling (shotgun metagenomics, phageome, and untargeted/targeted metabolomics). Compared with the placebo group, the probiotic group exhibited a pronounced 36.51% reduction in RDQ scores after 12 weeks of intervention (P = 0.017), alongside a higher numerical endoscopic healing rate (36.84% vs 12.50%; P = 0.365). Metagenomics revealed enrichment of Bifidobacterium animalis, Lactiplantibacillus plantarum, and Clostridium sp900540255, with reductions in Bacteroides uniformis and Clostridium Q fessum. Metabolomics showed increased γ-aminobutyric acid, succinate, citrulline, and short-chain fatty acids levels, with interesting microbe-metabolite correlations such as Bifidobacterium animalis-γ-aminobutyric acid and Bacteroides fragilis-succinate (r ≥ 0.30, P < 0.01). Our findings support that adjunctive probiotic therapy sustains post-PPI symptom relief, associated with targeted modulation of gut microbiota and bioactive metabolites.IMPORTANCELong-term proton pump inhibitor use in gastroesophageal reflux disease (GERD) may disrupt gut microbiota and cause symptom relapse after discontinuation. We found that adjunctive probiotic therapy sustained reflux reduction post-proton pump inhibitor. Probiotic use enriched beneficial taxa (Bifidobacterium and Lactiplantibacillus plantarum) and increased γ-aminobutyric acid, succinate, citrulline, and short-chain fatty acids. Strong correlations linked microbial shifts to metabolic and clinical improvements. This study demonstrates that adjunctive probiotic therapy enhances symptom control and supports microbial-metabolic homeostasis in GERD.CLINICAL TRIALSThis study is registered with the Chinese Clinial Trial Registry as ChiCTR2000038409.},
}

@article {pmid41609167,
year = {2026},
author = {Koo, WLY and Thng, KX and Tiew, PY and Chotirmall, SH},
title = {The Airway Microbiome in Chronic Obstructive Pulmonary Disease (COPD): A Guide for Clinicians.},
journal = {British journal of hospital medicine (London, England : 2005)},
volume = {87},
number = {1},
pages = {50163},
doi = {10.31083/BJHM50163},
pmid = {41609167},
issn = {1750-8460},
support = {MOH-001636//National Research Foundation Singapore/ ; MOH-001356//Singapore Ministry of Health's National Medical Research Council/ ; MOH-000710//Singapore Ministry of Health's National Medical Research Council/ ; MOH-001275-00//Singapore Ministry of Health's National Medical Research Council/ ; MOH-000955//Singapore Ministry of Health's National Medical Research Council/ ; RT1/22//Singapore Ministry of Education/ ; },
mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/microbiology/therapy ; *Microbiota ; Dysbiosis/microbiology ; *Lung/microbiology ; Disease Progression ; },
abstract = {Chronic obstructive pulmonary disease (COPD) is a progressive and debilitating respiratory condition marked by chronic symptoms and frequent exacerbations, contributing to significant morbidity and mortality. The advent of molecular microbiology and next-generation sequencing (NGS) has expanded our understanding of the lung microbiome, and integration of microbiome datasets with other omics reveals important microbial-metabolic-immuno-inflammatory interactions that influence COPD pathogenesis. Recent studies have highlighted dysbiosis of the airway microbiome, with shifts in bacterial, viral, and fungal communities playing a crucial role in disease progression, exacerbations and clinical outcomes. Moreover, microbiome changes are observed in COPD associated overlap syndromes, complicating diagnosis and treatment. This review synthesizes current microbiome research in COPD, focusing on its clinical relevance, including its potential as a diagnostic and prognostic tool. We additionally discuss the challenges of integrating microbiome data into clinical practice, emphasizing the need for personalized, precision medicine approaches to optimize COPD management and improve patient outcomes.},
}

Humans
*Pulmonary Disease, Chronic Obstructive/microbiology/therapy
*Microbiota
Dysbiosis/microbiology
*Lung/microbiology
Disease Progression

@article {pmid41608298,
year = {2026},
author = {Aldoori, J and Mitra, S and Davie, A and Toogood, GJ and Edwards, C and Hull, MA},
title = {The effect of omega-3 polyunsaturated fatty acids on short-chain fatty acid production and the gut microbiome in an in vitro colonic fermentation model.},
journal = {Gut microbiome (Cambridge, England)},
volume = {7},
number = {},
pages = {e1},
pmid = {41608298},
issn = {2632-2897},
abstract = {Oral administration of omega-3 polyunsaturated fatty acids (PUFAs) to rodents and humans is associated with an increase in gut bacteria that are predicted to synthesise short-chain fatty acids (SCFAs). We tested the hypothesis that physiological levels of omega-3 PUFAs in the distal intestinal lumen (1-50 μg/mL) are associated with increased SCFA synthesis in an in vitro fermentation model using faecal slurry from 10 healthy participants (mean age 30 years), with and without exogenous dietary fibres. SCFAs were measured by gas chromatography-flame ionisation detection (n = 10), and changes in bacterial composition were analysed by shotgun metagenomic sequencing (n = 6). In the presence of omega-3 PUFAs, there was a mean 9.3% (no inulin; P = 0.03) and 19.3% (+ 0.01 mg/mL inulin; P = 0.01) increase in total SCFA concentration at 24 h compared with paired control fermentations. Omega-3 PUFAs had a limited effect on the fermentation model microbiome in the absence of inulin. However, omega-3 PUFAs (50 μg/mL) were associated with increased abundance of Bifidobacteriaceae compared with paired control fermentations, if inulin (0.01 mg/mL) was present. Prebiotic activity of omega-3 PUFAs drives SCFA synthesis in an in vitro colonic fermentation model and is augmented by the soluble fibre inulin.},
}

@article {pmid41607944,
year = {2025},
author = {Gao, YQ and Hou, QY and Hou, XW and Wei, YJ and Shang, KM and Ma, H and Geng, HL and Liu, R and Yang, LH and Elsheikha, HM and Ni, HB and Huang, YF},
title = {Metagenomics-based characterization of fecal microbiome and resistome of laying hens during the production cycle.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1740567},
pmid = {41607944},
issn = {2297-1769},
abstract = {The extensive use of antimicrobials in livestock has accelerated the emergence of antimicrobial resistance (AMR), raising serious global concerns. Poultry feces are recognized as important reservoirs of antibiotic resistance genes (ARGs) and their associated mobile genetic elements (MGEs); however, the microbial community characteristics and ARG profiles of laying hens across different laying stages remain poorly understood. In this study, 40 fecal samples were collected from laying hens at five sampling points, including the early laying stage (HE), three peak laying stages (HPI, HPII, and HPIII), and the late laying stage (HL), with eight randomly selected samples per stage. Shotgun metagenomic sequencing was conducted to characterize the taxonomic structure and functional profiles of the intestinal microbiota and to systematically analyze the diversity and distribution patterns of ARGs. The results showed that most ARGs were harbored by bacteria belonging to the phyla Pseudomonadota and Bacillota, with Escherichia coli serving as the primary carrier of antibiotic resistance genes. Moreover, significant correlations were observed between the co-abundance and co-occurrence of ARGs and MGEs, suggesting that MGEs play a key role in facilitating ARG dissemination. Overall, these findings provide novel insights into the prevalence of ARGs in laying hens across different laying stages and may inform strategies to mitigate the spread of antimicrobial resistance in poultry production systems.},
}

@article {pmid41604101,
year = {2026},
author = {Nihel, AB and Rania, AD and Hamadou, OH and Ghiles, G and Imen, B and Fatma, A and Ali, A and Basma, M and Hayet, S and Radhouan, G and Leila, AK and Mokdad-Gargouri, R},
title = {Nanopore sequencing of the Tunisian gut microbiome: effect of the DNA extraction methods.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {57},
number = {1},
pages = {47},
pmid = {41604101},
issn = {1678-4405},
support = {952583//H2020 European Research Council/ ; },
abstract = {UNLABELLED: High-throughput sequencing technologies have revolutionized the field of microbiome research, offering unprecedented insights into microbial diversity, community structure, and evolution. In this study, we compared three DNA extraction methods including; enzymatic lysis (ELM), commercial kit (CKM) and Phenol/Chloroform (PCAI) for their efficacy in microbiome taxonomy using Nanopore Sequencing. Metagenomic analysis of DNA extracted from stool samples were analyzed to determine the variability in microbial compositions. Our results revealed significant differences in DNA yield, microbial diversity, and community structure among the extraction methods tested. Globally, Phocaeicola_vulgatus, Ruminococcus_bicirculans, Faecalibacterium_prausnitzii, Prevotella copri, and Bacteroides ovatus are the most abundant identified species in all the samples. Further, the results showed that Ruminococcus_bicirculans is the most abundant specie identified in ELM, whereas the richness of Bacteroides_fragilis is higher in PCAI than ELM and CKM-processed samples. Our findings underscore the importance of methods selection in microbiome research and provide insights into optimizing DNA extraction protocols for nanopore sequencing.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42770-025-01866-9.},
}

@article {pmid41455901,
year = {2025},
author = {Li, X and Zhao, Y and Wu, K and Li, X and Lv, G and Chen, Y and He, L and Sun, W},
title = {Responses of cotton roots and soil microbiota adaptation to drought hardening.},
journal = {BMC plant biology},
volume = {26},
number = {1},
pages = {184},
pmid = {41455901},
issn = {1471-2229},
support = {2022ZD0115801//National Science and Technology Major Project/ ; },
abstract = {BACKGROUND: Global climate change has intensified the frequency and severity of drought events, posing significant threats to agriculture in arid regions. As an important economic crop, cotton is highly vulnerable to drought stress, which adversely affects its growth, yield, and associated soil microbial communities.

AIMS: This study aimed to conduct an in-depth investigation the effects of drought hardening on cotton root physiology and rhizosphere microbial dynamics by integrating physiological and metagenomic analyses. By analyzing aboveground responses and yield performance of cotton, this study sought to elucidate the comprehensive impact of drought hardening on cotton growth and yield, with the goal of providing a scientific basis for water-saving irrigation strategies in cotton fields in arid regions.

METHODS: The experiment was conducted in 2024 at Huaxing Farm in Changji, Xinjiang, using the Zhongmian 113 variety. The experiment used the field water requirement as the control (CK, including the water for seedling emergence, totaling 4950 m³/ha), and set three different drought hardening treatments: mild (D1, with 20% water saving during the seedling stage), moderate (D2, with 30% water saving during the seedling stage), and severe (D3, with 40% water saving during the seedling stage). Compared with the control, the total water savings for the entire growth period of treatments D1, D2, and D3 were 12.5%, 15%, and 17.5%, respectively.

RESULTS: Based on the performance of cotton growth, development, and yield, the D1 treatment significantly enhanced the antioxidant capacity of cotton roots and effectively maintained cell membrane integrity. Additionally, the D1 treatment significantly altered the diversity of soil fungi, to some extent, this water management practice optimized the structure of the microbial community, and promoted the formation of the dominant bacterial group, Gemmatimonadales.

CONCLUSIONS: The study preliminarily revealed the interaction between Gemmatimonadales and cotton roots during the budding stage. Meanwhile, through a comprehensive analysis of cotton growth characteristics, root physiological and biochemical processes, and yield performance, it was shown that the stress resistance of cotton was enhanced under the D1 treatment. This research provided a scientific basis for water-saving irrigation strategies in cotton fields in arid regions, demonstrating that under the D1 condition, it is possible to enhance the stress resistance of cotton while conserving water.},
}

@article {pmid41607902,
year = {2025},
author = {Song, Z and Huang, Y and Gu, Y and Che, L and Zhang, K and Liu, Q and Guan, Q and Sui, L},
title = {Genetic characterization of the respiratory tract viruses in Jilin, Northeast China, 2023.},
journal = {Frontiers in public health},
volume = {13},
number = {},
pages = {1756127},
pmid = {41607902},
issn = {2296-2565},
mesh = {Humans ; China/epidemiology ; *Respiratory Tract Infections/virology/epidemiology ; Adult ; Phylogeny ; Child ; Female ; Male ; Child, Preschool ; High-Throughput Nucleotide Sequencing ; Middle Aged ; Adolescent ; Infant ; Respiratory Syncytial Virus, Human/genetics ; Influenza B virus/genetics ; },
abstract = {OBJECTIVE: Respiratory viral infections impose a significant global health burden, necessitating continuous regional surveillance to understand pathogen circulation. This study aimed to characterize the spectrum of respiratory pathogens and identify potential causative agents in Jilin Province, northeast China, during 2023.

METHODS: Using metagenomic next-generation sequencing, we analyzed 250 respiratory samples and 195 blood samples, sequencing of all samples yielded 399,256 viral reads. Bioinformatic and phylogenetic analyses were conducted to identify and characterize the detected viruses.

RESULTS: Severe acute respiratory syndrome coronavirus 2 (lineage BA.2), human respiratory syncytial virus B (lineage GB5.0.5a), and influenza B virus (lineage V1A.3a.2) were identified as common respiratory pathogens across both pediatric and adult populations. Influenza A virus (lineage 3C.2a1b.2a.2a.3a.1), rhinovirus (subtype C), human respiratory syncytial virus A (lineage GA2.3.5), human respiratory syncytial virus B (lineage GB5.0.5a), and human metapneumovirus (lineage A2c) were detected in pediatric or adult respiratory samples. Human Pegivirus (genotype 3) was detected exclusively in adult blood samples. Strikingly, a novel picobirnavirus was identified in adult sputum samples, sequence and structural analyses consistently indicate that this picobirnavirus is closely related to human-associated strains, exhibiting ≥70% amino acid identity and an RdRP structure nearly identical to that of picobirnaviruses previously identified in human upper respiratory swabs from Cambodia. This finding was validated by nested RT-PCR, representing the first documented detection of picobirnavirus in respiratory specimens from China. As most identified strains were first reported in northeast China, we also conducted comprehensive phylogenetic analyses of representative viruses, revealing high sequence similarity with epidemic strains from other regions of China.

CONCLUSION: These findings delineate the respiratory viruses of northeast China, providing data for region-specific surveillance to mitigate future public health risks.},
}

Humans
China/epidemiology
*Respiratory Tract Infections/virology/epidemiology
Adult
Phylogeny
Child
Female
Male
Child, Preschool
High-Throughput Nucleotide Sequencing
Middle Aged
Adolescent
Infant
Respiratory Syncytial Virus, Human/genetics
Influenza B virus/genetics

@article {pmid41607747,
year = {2026},
author = {Luo, L and Huang, G and Yang, H and Chi, H},
title = {Revisiting multi-region 16S sequencing in gastric cancer.},
journal = {World journal of gastrointestinal oncology},
volume = {18},
number = {1},
pages = {114708},
pmid = {41607747},
issn = {1948-5204},
abstract = {Wu et al recently applied multi-region 16S rRNA sequencing to characterize the gastric cancer microbiome, demonstrating improved taxonomic resolution and detection sensitivity over conventional single-region approaches. While the study represents a valuable methodological step forward, it remains limited by single-center design, lack of quantitative calibration, and insufficient control for contamination and inter-laboratory variability. This editorial critically appraises these methodological gaps and emphasizes that future efforts must focus on harmonized, consensus-driven workflows to ensure reproducibility and clinical reliability. The translational potential of multi-region 16S lies in moving from descriptive microbial profiling to actionable clinical integration, particularly for recurrence prediction, treatment-response monitoring, and perioperative complication risk assessment. By addressing these methodological, economic, and ethical challenges, the field can advance toward evidence-based and clinically deployable microbiome-guided precision oncology.},
}

@article {pmid41606855,
year = {2025},
author = {Yang, J and He, Y and Huang, J and Li, M and Wu, X and Pei, X and Yang, X},
title = {Decoding resistome profiles and horizontal transfer of antibiotic resistance genes across the pork production chain under One Health sectors.},
journal = {Food research international (Ottawa, Ont.)},
volume = {221},
number = {Pt 1},
pages = {117259},
doi = {10.1016/j.foodres.2025.117259},
pmid = {41606855},
issn = {1873-7145},
mesh = {*Gene Transfer, Horizontal ; Animals ; Swine ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Microbial/genetics ; *One Health ; *Drug Resistance, Bacterial/genetics ; *Pork Meat/microbiology ; Food Microbiology ; Abattoirs ; Metagenome ; Microbiota/genetics ; Metagenomics ; Bacteria/genetics ; },
abstract = {The emergence of antimicrobial resistance has become a global threat to public health. Intensive antibiotic use in swine farming has accelerated the proliferation of antibiotic resistance genes (ARGs) in animal-derived foods, making the production chain a potential ARG transmission route to humans. However, shared resistome profiles and horizontal gene transfer (HGT) mechanisms along this chain remain unclear. Here, we systematically investigated the resistome profile, ARGs' host, and potential HGT of ARGs across interconnected swine farm, slaughterhouse, and retail market by metagenomic assembly and binning. From 42 metagenomes, 1354 ARG subtypes were identified, with 303 shared across all interfaces. Both microbiome and mobile genetic elements (MGEs) contributed to the variation in ARG profiles. Pseudomonadota were the dominant drivers that shape the resistome through plasmid-mediated HGT. Among the 133 reconstructed ARG-carrying genomes (ACGs), 38 of them carried multiple ARGs, indicating the potential mobility of ARGs. Notably, 3 ACGs taxonomically assigned to Pseudomonas_E alcaligenes, Serratia_J grimesii, and Escherichia coli carrying 9, 13, and 41 ARGs, respectively. Furthermore, MetaCHIP analysis uncovered 445 potential HGT events, and ARGs including CpxR, macB, fusA, and vanR were annotated as potentially transferred subtypes. This study decodes the resistome profiles and tracks horizontal ARG transfer at the community level across the entire pork supply chain - from swine farms to retail outlets. To our knowledge, few studies have explored ARG transmission subtypes and directional flows among humans, pigs, and environmental compartments in the pork production chain using metagenomic approaches. These findings highlight the important role of the pork production chain as a critical transmission vector for ARGs under One Health framework.},
}

*Gene Transfer, Horizontal
Animals
Swine
Anti-Bacterial Agents/pharmacology
*Drug Resistance, Microbial/genetics
*One Health
*Drug Resistance, Bacterial/genetics
*Pork Meat/microbiology
Food Microbiology
Abattoirs
Metagenome
Microbiota/genetics
Metagenomics
Bacteria/genetics

@article {pmid41606854,
year = {2025},
author = {Okoye, CO and Abhadiomhen, SE and Ezenwanne, BC and Chen, X and Jiang, H and Wu, Y and Jiang, J},
title = {Machine learning-based predictive modeling of foodborne pathogens and antimicrobial resistance in food microbiomes using omics techniques: A systematic review.},
journal = {Food research international (Ottawa, Ont.)},
volume = {221},
number = {Pt 1},
pages = {117255},
doi = {10.1016/j.foodres.2025.117255},
pmid = {41606854},
issn = {1873-7145},
mesh = {*Machine Learning ; *Food Microbiology ; *Foodborne Diseases/microbiology ; *Microbiota ; *Drug Resistance, Bacterial/genetics ; Animals ; Genomics/methods ; Metagenomics ; Salmonella/pathogenicity/genetics ; Food Safety ; Humans ; },
abstract = {The globalization of food systems has heightened the risk of foodborne pathogens such as Salmonella, Listeria monocytogenes, and Campylobacter, exacerbated by rising antimicrobial resistance (AMR). Traditional pathogen identification and AMR risk surveillance methods are often labor-intensive and low-throughput, while single-omics approaches fail to capture microbial complexity. Moreover, reliance on individual machine learning (ML) models limits predictive robustness, posing challenges to food safety and public health. This systematic review evaluates ML-based predictive modeling integrated with omics techniques (genomics, metagenomics, and transcriptomics) for foodborne pathogen and AMR risk surveillance. Following PRISMA guidelines, 1245 articles from PubMed, Scopus, and other databases (2015-2025) were screened, selecting 13 relevant studies. These studies applied ML algorithms, including Random Forest (RF), Extreme Gradient Boosting (XGBoost), and Support Vector Machines (SVM), to enhance predictive accuracy. The selected studies demonstrated predictive accuracies up to 99 % and AUROC scores above 0.90. Key discoveries include genetic markers for Salmonella virulence, Listeria attribution to fruits and dairy, and 145 mobile antimicrobial resistance genes (ARGs) in poultry. Despite these advancements, limitations such as small sample sizes, inconsistent metadata, overfitting, and computational scalability hinder real-world implementation. This review underscores the potential of ML-driven omics frameworks to revolutionize foodborne pathogen and AMR risk monitoring, paving the way for smarter, more resilient food safety systems. However, methodological inconsistencies necessitate standardized protocols, larger datasets, and explainable AI (XAI) to improve reliability and applicability in global food safety monitoring.},
}

*Machine Learning
*Food Microbiology
*Foodborne Diseases/microbiology
*Microbiota
*Drug Resistance, Bacterial/genetics
Animals
Genomics/methods
Metagenomics
Salmonella/pathogenicity/genetics
Food Safety
Humans

@article {pmid41606550,
year = {2026},
author = {Zhang, X and Xu, J and Chen, M and Wu, Y and Chen, D and Xu, X and He, X},
title = {Aspergillus fumigatus in mechanically ventilated pneumonia- independent mortality risk and synergistic microbiome signatures from a multicenter mNGS cohort.},
journal = {BMC pulmonary medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12890-026-04131-3},
pmid = {41606550},
issn = {1471-2466},
support = {2022GYX28//Lishui Public Welfare Technology Application Research Program Project/ ; },
}

@article {pmid41606218,
year = {2026},
author = {Abdelhameed, A and Hussein, RH and Hatem, ZA and Bağcı, C and Ziemert, N},
title = {From niche to niche: investigating microbial communities and their specialised metabolite gene clusters in human microbiomes.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {2},
pages = {65},
pmid = {41606218},
issn = {1573-0972},
mesh = {Humans ; *Multigene Family ; *Microbiota/genetics ; *Bacteria/genetics/metabolism/classification/isolation & purification ; Metagenomics ; Biosynthetic Pathways/genetics ; Metagenome ; },
abstract = {Diverse microbial communities within the human microbiome perform vital functions which influence both health and disease in hosts. Specialized metabolites produced by microbes via biosynthetic gene clusters (BGCs) drive ecological interactions and offer possibilities for therapeutic application. The biosynthetic capabilities of microorganisms present in human microbiomes are still mostly unexplored despite metagenomics advancements. The study examines the variety of microbial communities and BGC locations through metagenomic data from 1,191 samples across eight human microbiomes taken from the IMG/M database. Kraken2 executed taxonomic classification while antiSMASH v6.1.1 identified BGCs. The study used BiG-SCAPE to build a sequence similarity network while Bracken and Pavian tools analyzed microbial diversity. A total of 25,681 BGCs were identified, of which 97.5%, showed no significant match to existing clusters in MIBIG database, indicating substantial potential for novel biosynthetic discoveries . Showing no match to existing clusters in the MIBiG database which shows huge potential for new biosynthetic discoveries. New strains were discovered that produce unique RiPPs, NRPs, and siderophores primarily within the microbiomes of the large intestine, oral cavity, and skin. The large intestine showed maximum microbial and biosynthetic diversity compared to other areas while the biliary tract and nasal cavity displayed minimal diversity. New BGCs associated with antibiotic, cytotoxic, and immune-modulating functions present potential therapeutic uses. The investigation uncovers essential information about how microbial communities develop specific functions within various body regions. Uncharacterized BGC discoveries present new opportunities for drug development and treatments that target microbiomes.},
}

Humans
*Multigene Family
*Microbiota/genetics
*Bacteria/genetics/metabolism/classification/isolation & purification
Metagenomics
Biosynthetic Pathways/genetics
Metagenome

@article {pmid41606121,
year = {2026},
author = {Duttagupta, S and Messaoudene, M and Hunter, S and Desilets, A and Jamal, R and Mihalcioiu, C and Belkaid, W and Marcoux, N and Fidelle, M and Suissa, D and Ponce, M and Geiger, M and Malo, J and Piccinno, G and Punčochář, M and Filin, A and Heidrich, V and Rusu, D and Mbaye, B and Durand, S and Ben Aissa, I and Puller, V and de Lahondès, R and Blais, N and Tehfe, M and Owen, S and Bélanger, K and Parvathy, SN and Shieh, B and Raphael, J and Lenehan, J and Breadner, D and Rothenstein, J and Rozza, N and Maillou, J and Nili, S and Prifti, DK and Pinto, F and Armanini, F and Kim-Schulze, S and Marron, TU and Kroemer, G and Derosa, L and Zitvogel, L and Silverman, M and Segata, N and Vareki, SM and Routy, B and Elkrief, A},
title = {Fecal microbiota transplantation plus immunotherapy in non-small cell lung cancer and melanoma: the phase 2 FMT-LUMINate trial.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
pmid = {41606121},
issn = {1546-170X},
abstract = {Immune checkpoint inhibitors (ICI) have improved outcomes for patients with non-small cell lung cancer (NSCLC) and melanoma, yet over half of patients exhibit primary resistance. Fecal microbiota transplantation (FMT) may overcome resistance to anti-programmed cell death protein 1 (PD-1) therapy. The clinical activity and safety of FMT plus anti-PD-1 in NSCLC or anti-PD-1 plus anti-cytotoxic T-lymphocyte antigen 4 (CTLA-4) therapy in melanoma have not been evaluated. Here we report results from FMT-LUMINate, a multicenter, open-label, phase 2 trial assessing healthy donor FMT plus anti-PD-1 in NSCLC (n = 20) or anti-PD-1 plus anti-CTLA-4 (dual ICI) in melanoma (n = 20), in the first-line setting. Eligible patients received a single FMT via oral capsules prior to ICI initiation. The primary endpoint was objective response rate (ORR) in NSCLC. Secondary endpoints included ORR in melanoma, safety and donor-host microbiome similarity. In NSCLC, the ORR was 80% (16/20), meeting the study primary endpoint. In melanoma, the ORR was 75% (15/20). FMT was deemed safe in both cohorts by an independent data and safety monitoring committee, with no grade 3 or higher adverse events (AEs) in NSCLC and 13 (65%) patients experiencing grade 3 or higher AEs in melanoma. Shotgun metagenomic sequencing revealed that responders developed a distinct post-FMT gut microbiome composition, independent of acquired donor-recipient similarity or strain-level engraftment. Responders exhibited significantly greater loss of baseline bacterial species compared to non-responders, with frequent depletion of Enterocloster citroniae, E. lavalensis and Clostridium innocuum. This finding was reproduced across three published FMT oncology trials. We recolonized antibiotic-treated, tumor-bearing mice with post-FMT stool from two responder patients, and reintroduction of the specific bacterial species that were lost after FMT abrogated the antitumor effect of ICI. Taken together, these findings confirm the clinical activity of FMT in combination with ICI and suggest that the elimination of deleterious taxa is required for FMT-mediated therapeutic benefit. ClinicalTrials.gov identifier: NCT04951583 .},
}

@article {pmid41605932,
year = {2026},
author = {Raethong, N and Patumcharoenpol, P and Vongsangnak, W},
title = {Modeling diet-gut microbiome interactions and prebiotic responses in Thai adults.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00921-z},
pmid = {41605932},
issn = {2055-5008},
support = {N42A660907//National Research Council of Thailand/ ; },
abstract = {The impact of diet on gut microbial metabolism is essential for advancing microbiome-based health interventions. This study introduces a novel systems biology pipeline that integrates genome-scale metabolic models (GSMMs) with Thai dietary intake data to simulate gut microbiome metabolism and assess prebiotic responses. Utilizing metagenomic data from healthy Thai adults and an average Thai diet derived from national surveys, community-scale metabolic models (CSMMs) were developed and simulated under both typical dietary and prebiotic-supplemented condition. Flux variability analysis was employed to assess metabolic capacities, short-chain fatty acids (SCFAs) production in relation to microbial taxonomy. The results promisingly revealed inter-individual variability in SCFA profiles, with Bacteroides and Phocaeicola notably linked to isobutyrate production and Bifidobacterium emerged as a key responder to prebiotic supplementation. This integrative framework offers biological insights into diet-gut microbiome interactions and provides a foundation for the development of precision nutrition strategies tailored to the Thai population.},
}

@article {pmid41605275,
year = {2026},
author = {Wu, L and Li, H and Gu, Y and Zhou, Y and Shen, Z and Zuo, J},
title = {In situ ammonia recovery relieves ammonia stress in anaerobic digestion and multi-omics elucidate community-dominant and functionally dominant genera of methanogens.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134098},
doi = {10.1016/j.biortech.2026.134098},
pmid = {41605275},
issn = {1873-2976},
abstract = {The accumulation of endogenous ammonia nitrogen in anaerobic digestion (AD) is widely recognized as a critical factor inhibiting methanogenesis. Gas-permeable membranes (GPM), leveraging their selective permeation properties, provide a large gas-liquid mass transfer interface and demonstrate significant potential in preventing ammonia accumulation. In this study, integrating GPM into AD achieved in situ ammonia removal and recovery, fundamentally alleviating ammonia inhibition and enabling ammonia valorization. GPM reactors (with H2SO4 absorption/vacuum distillation) maintained ammonia at 1300-1500 mg/L (vs. >5000 mg/L in controls) and sustained biogas yield 0.67-0.72 L/g VS at 7 g VS/(L·d) OLR (controls inhibited at 5 g VS/(L·d)). Multi-omics revealed microbial mechanisms: community-dominant Methanobacterium contributed little to methanogenesis, while functionally dominant Methanothrix retained robust activity via dual methanogenic pathways and upregulated biosynthesis-related proteins. This study validates GPM-AD efficacy and provides theoretical support for optimization.},
}

@article {pmid41605063,
year = {2026},
author = {Tang, B and Lin, L and Li, W and Li, Z and Zhao, J and Zhao, W and Zhao, C},
title = {Successful treatment with oseltamivir of an atypical influenza B-associated encephalitis identified by mNGS: A case report.},
journal = {Diagnostic microbiology and infectious disease},
volume = {115},
number = {1},
pages = {117286},
doi = {10.1016/j.diagmicrobio.2026.117286},
pmid = {41605063},
issn = {1879-0070},
abstract = {This case report describes a 51-year-old female with influenza B-associated encephalitis (IBAE) presenting primarily with insomnia, headache, and dizziness, but without fever, following an initial cough. Routine microbiological tests (cultures, staining, multiplex PCR) on cerebrospinal fluid (CSF) and initial brain/chest CT scans were negative. Diagnosis was confirmed by metagenomic next-generation sequencing (mNGS) detecting influenza B virus in the CSF. Treatment involved oral oseltamivir and fluid replacement for headache/intracranial pressure. Symptoms significantly improved after eight days of oseltamivir, leading to discharge. This case highlights sleep disturbances and headache as primary IBAE symptoms without fever. Routine CSF testing often fails to detect influenza B; early mNGS enables definitive diagnosis, allowing precise, timely treatment (like oseltamivir) and avoiding ineffective empiric therapy or disease worsening.},
}

@article {pmid41604988,
year = {2026},
author = {Zhou, Y and Wu, Y and Shu, B and Xu, F},
title = {Resourceful utilization of Bougainvillea horticultural waste for synchronous degradation and power generation in MFCs.},
journal = {Bioelectrochemistry (Amsterdam, Netherlands)},
volume = {170},
number = {},
pages = {109237},
doi = {10.1016/j.bioelechem.2026.109237},
pmid = {41604988},
issn = {1878-562X},
abstract = {The disposal of horticultural waste derived from Bougainvillea species poses substantial environmental challenges in coastal cities of southeastern China. This study innovatively employs Bougainvillea horticultural waste (BHW) as the main substrate in microbial fuel cells (MFCs) for simultaneous organic degradation and bioenergy recovery, with an acid-pretreated BHW-fed MFC (MFC-ABG) included for comparison. Results indicated that the untreated BHW-fed MFC (MFC-BG) achieved a peak voltage of 0.401 V and sustained operation for 19 days, coupled with 78.7% polysaccharide removal. Metagenomics showed that MFC-BG significantly enriched electroactive Geobacter (29.39%) and hydrolytic Proteiniphilum (2.69%), driving lignocellulose decomposition through oxidative auxiliary enzymes (AA4/AA6). Comparatively, MFC-ABG achieved an enhanced voltage of 0.706 V and a high polysaccharide reduction efficiency of 85.6%, benefits attributable to acid-induced substrate solubilization and glycoside hydrolase (GH)-dominated enzymatic shifts. Although microbial community diversity declined in both MFC systems, MFC-BG retained a higher species richness (MFC-BG: Sobs = 28,209; MFC-ABG: Sobs = 25,746), reflecting the adaptive resilience of the associated microbial community. This study confirms BHW as a viable feedstock for MFCs and clarifies the microbial mechanisms underlying the synergistic coupling of substrate degradation and electron transfer.},
}

@article {pmid41604303,
year = {2026},
author = {Guo, Z and Cheng, H and Shi, H and Liu, D and Zhai, X and Li, X and Zhang, X and Liu, L and Zhang, XH and Zhang, Y},
title = {Potential for microbial methanethiol-dependent dimethylsulfide production in different marine sediments.},
journal = {Cell reports},
volume = {45},
number = {2},
pages = {116891},
doi = {10.1016/j.celrep.2025.116891},
pmid = {41604303},
issn = {2211-1247},
abstract = {Dimethyl sulfide (DMS) plays a pivotal role in sulfur cycling and climate regulation. This study investigates microbial DMS production via the methylation of hydrogen sulfide (H2S) and methanethiol (MeSH) in nearshore, pelagic deep-sea, and cold-seep sediments using culture-dependent and -independent methods. DMS production is detected in all sediments with exogenous MeSH addition. High mdd abundance is found in pelagic deep-sea sediments (24.55%-26.73%) from the Kuroshio-Oyashio Extension region, as well as in the nearshore sediments (25.78%). Metagenomic analyses reveal previously unrecognized Mdd-encoding taxa, such as Polyangia, and eight Bacteroidota and Bacillota isolates may possess unknown Mdd enzymes. Importantly, a widespread alternative pathway that converts H2S to MeSH is identified, representing a significant source of MeSH. These findings reveal a prevalent and diverse microbial pathway for DMS production in marine sediments, underscoring the need for further investigation to discover Mdd[+] microbial contributors.},
}

@article {pmid41604225,
year = {2026},
author = {Bilhalva, LC and Yacoub, MN and Dos Santos, AP and Manley, SR and Guasch, PM and Krumbeck, JA and Brinker, EJ and Martinez-Romero, G and Conrado, FO and Knoll, JS and Sharkey, LC},
title = {First report of Castellaniella spp. infection in dogs and the genomic evidence of a novel species.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxag033},
pmid = {41604225},
issn = {1365-2672},
abstract = {AIMS: This study reports the first documented cases of Castellaniella spp. infection in dogs, describing associated clinical and pathological findings and characterizing a novel species within this genus.

METHODS AND RESULTS: Pleural effusions from two dogs presenting with acute respiratory distress and systemic illness were evaluated via cytology, bacterial culture, and next-generation sequencing. Both cases exhibited neutrophilic-macrophagic inflammation with intracellular gram-negative rods, primarily within macrophages. Bacterial culture failed to identify the organisms. Metagenomic analysis identified organisms belonging to the genus Castellaniella in both cases. In case 2, an unclassified Castellaniella species was detected, suggesting the presence of a previously undescribed species within the genus. Both dogs died shortly after presentation, and necropsy and histopathology findings were described.

CONCLUSIONS: Castellaniella spp. warrant consideration as potential emerging pathogens in domestic animals, challenging their previous classification as non-pathogenic environmental bacteria. The identification of a novel species also underscores the genus's genetic diversity and adaptive potential.},
}

@article {pmid41604220,
year = {2026},
author = {Yao, ML and Lin, P and Hua, K and Zhang, W},
title = {The biosynthetic gene cluster landscape of the oral microbiome across health and dental caries.},
journal = {Journal of industrial microbiology & biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jimb/kuag005},
pmid = {41604220},
issn = {1476-5535},
abstract = {Specialized metabolites encoded by biosynthetic gene clusters (BGCs) in the oral microbiome remain largely unexplored in the context of oral health and disease. Previous genome-centric surveys have identified hundreds of uncharacterized BGCs in the oral cavity associated with health and disease, but these studies relied on reference genomes and did not capture strain-level variation or the native distribution of BGCs. Here, we assembled three independently sourced metagenomic datasets from healthy and dental caries samples, extracted BGCs, and quantified their metagenomic abundance and transcriptional activity. We found that aryl polyene, ribosomally synthesized and post-translationally modified peptide (RiPP), and nonribosomal peptide (NRP) encoding BGCs were the most prominent BGCs identified across the three metagenomic datasets. We grouped the identified BGCs into homology-based gene cluster families (GCFs) and found that specific GCFs were consistently associated with either health or caries across diverse taxa, suggesting that some specialized metabolites may perform conserved ecological functions. Conversely, other BGCs showed more restricted taxonomic distributions and were linked to disease-associated taxa, such as Propionibacterium acidifaciens, suggesting niche-specific biosynthetic capacities within the oral environment. Applying elastic-net regression to the metatranscriptomic dataset further identified a subset of 51 BGCs out > 3 000 that distinguished healthy from caries samples, reinforcing the discriminatory power of BGC expression patterns. Together, these results demonstrate that BGCs provide functional resolution beyond taxonomic profiling and that BGC expression, rather than genomic presence alone, differentiates oral microbial community states. This underscores the relevance of specialized metabolism to oral health and supports the use of BGC-centric analyses to interrogate microbial interactions underlying community stability and disease-associated shifts.},
}

@article {pmid41604102,
year = {2026},
author = {Rocha, LBA and Gonçalves, VN and de Oliveira, FS and Corrêa, GR and Senra, EO and Duarte, EB and Lopes, FAC and Silva, MC and Convey, P and Câmara, PEAS and Rosa, LH},
title = {Endolithic fungal diversity is present in the unique phosphatized rocks of an environmentally extreme equatorial archipelago revealed by DNA amplicon metagenomics.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {57},
number = {1},
pages = {46},
pmid = {41604102},
issn = {1678-4405},
}

@article {pmid41603859,
year = {2026},
author = {Ahmed, N and Abdjan, MI and Aminah, NS and Helianti, I},
title = {Computational design of carbohydrate binding modules-fused PETase like enzyme for enhanced polycaprolactone (PCL) degradation: structural insights, molecular dynamics, and QM/MM simulations.},
journal = {Journal of biomolecular structure & dynamics},
volume = {},
number = {},
pages = {1-28},
doi = {10.1080/07391102.2026.2619892},
pmid = {41603859},
issn = {1538-0254},
abstract = {A novel PET hydrolase-like enzyme identified from metagenomic databases using HMMR search was computationally fused with five different carbohydrate-binding modules (CBMs). AlphaFold3 predicted the 3D structures of the fused enzyme-CBM, which were validated using ERRAT, Verify3D, and PROCHECK. Molecular docking was performed with polycaprolactone triol using AutoDock Vina, followed by 100 ns molecular dynamics (MD) simulations using AMBER. Trajectory analyses and binding free energy calculations (QM/MM-GBSA) were conducted. The putative PET hydrolase-like enzyme shared 49.62% similarity with Ideonella sakaiensis PETase (5XJH). The fused models exhibited the best stability, with an instability index of <40 and a thermostability aliphatic index between 58.83 and 68.27. Structure validation confirmed high-quality 3D models, with >90% of the residues in the allowed Ramachandran regions. All the fused models showed favourable binding to PCL-triol, exhibiting strong interactions. In MD simulations, BlCBM5 and TrCBM complexes displayed a minimal fluctuation: all-atom RMSD ∼0.35 and ∼0.45 nm, backbone RMSD ∼0.48, ∼0.41 nm, atom contacts ∼4.2-5, ∼2-6, and H-bonds ∼2-5, ∼1-2, respectively. The BlCBM5 and TrCBM complexes showed the lowest binding energies, with MM-GBSA values of -36.66 ± 0.12 and -21.48 ± 0.11 kcal/mol, and QM/MM-GBSA values of -37.36 ± 0.13 and -21.70 ± 0.11 kcal/mol, respectively. Residue-level analysis identified key contributors (M133, W157, and F62) in both models. BlCBM5 and TrCBM complexes were the top candidates for enhancing PCL plastic degradation. The findings of this study were based on predictive insights, and experimental validation is required in the future.},
}

@article {pmid41603547,
year = {2026},
author = {Gschwind, R and Bonnet, M and Abramova, A and Jarquín-Díaz, VH and Wenne, M and Löber, U and Godron, N and Kampouris, ID and Tskhay, F and Nahid, F and Debroucker, C and Bui-Hai, M and El Aiba, I and Klümper, U and Berendonk, TU and Forslund-Startceva, SK and Zahra, R and Bengtsson-Palme, J and Ruppé, E},
title = {Cefiderocol resistance genes identified in environmental samples using functional metagenomics.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag010},
pmid = {41603547},
issn = {1751-7370},
abstract = {Antibiotic resistance poses a global public health threat, which can originate from the transfer of environmental antibiotic resistance genes to pathogenic bacteria, as highlighted by the "One Health" framework. Cefiderocol is a siderophore cephalosporin recently introduced in clinical practice which displays a "Trojan Horse" mechanism, utilizing bacterial iron transportation systems for cell entry. Although it is only used as a last-line antibiotic, resistance has already been observed in clinical isolates. Yet, cefiderocol resistance genes are difficult to monitor as resistance mechanisms remain mostly undescribed in antibiotic resistance gene databases and therefore uncharacterized in the environment. To address this critical gap, we applied functional metagenomics to diverse environmental samples (wastewater, freshwater, and soil) from France, Germany, Sweden, and Pakistan. Four antibiotic resistant genes were identified as responsible for increased cefiderocol minimum inhibitory concentrations to clinically-relevant levels (ranging from 1 to 4 mg/L), including ꞵ-lactamases (VEB-3, OXA-372 homolog, and YbxI homolog) and a partial penicillin-binding protein homolog. None of these genes had been previously reported as a cefiderocol resistance gene. Three out of four had their closest homologs in pathogenic bacteria. The blaVEB-3 gene was associated with a mobile genetic element and distributed across all wastewater metagenomes analyzed in this study. We therefore highlight the critical need for functional metagenomics, to characterize previously uncharacterized last-line antibiotic resistance mechanisms which will be used to enrich antibiotic resistance gene databases and thereby improving antibiotic resistance surveillance in all One Health compartments.},
}

@article {pmid41603333,
year = {2026},
author = {Tiwari, P and Gupta, A and Kaushik, M and Dwivedi, R and Tripathi, M and Dada, R},
title = {Association of yoga with cognitive and gut microbiome changes in Alzheimer's disease: An exploratory case-control study.},
journal = {Journal of Alzheimer's disease : JAD},
volume = {},
number = {},
pages = {13872877261415612},
doi = {10.1177/13872877261415612},
pmid = {41603333},
issn = {1875-8908},
abstract = {BackgroundAlzheimer's disease (AD) is marked by cognitive decline, depressive symptoms, and gut microbial dysbiosis. Yoga may support cognitive and emotional health while modulating gut microbiota, but integrative clinical evidence is limited.ObjectiveTo evaluate the effects of a 12-week yoga intervention on cognition, depressive symptoms, and gut microbial diversity, composition, and function in Indian patients with mild AD.MethodsIn this hospital-based case-control study, 16 AD patients and 17 cognitively healthy controls (HCs) were recruited at AIIMS, New Delhi. AD diagnosis followed NIA-AA criteria, supported by Montreal Cognitive Assessment (MoCA) and Patient Health Questionnaire-9 (PHQ-9) assessments. AD participants underwent 60-min supervised yoga sessions daily for 12 weeks. Cognitive performance, depressive symptoms, and stool microbiota were assessed pre- and post-intervention. Metagenomic sequencing enabled taxonomic and functional profiling, with alpha diversity, beta diversity (Bray-Curtis distance), and differential abundance analyses performed using standard bioinformatics tools.ResultsYoga was associated with improved cognition (MoCA: 22.33 ± 2.34 → 25.44 ± 2.01; p = 0.001) and reduced depressive symptoms (PHQ-9: 5.78 ± 3.11 → 2.22 ± 1.71; p = 0.007). Alpha diversity remained stable, while beta diversity shifted post-yoga AD samples toward the HC cluster. Beneficial taxa (Faecalibacterium prausnitzii, Roseburia intestinalis, Bifidobacterium, Akkermansia) increased, whereas pro-inflammatory taxa (Collinsella aerofaciens, Klebsiella spp.) decreased. Functional analysis showed partial recovery of metabolic and short-chain fatty acid pathways.ConclusionsA 12-week yoga intervention was associated with cognitive and mood improvements and partial normalization of gut microbial function in mild AD. Larger randomized trials with lifestyle monitoring and multi-omics integration are warranted to confirm causal mechanisms.},
}

@article {pmid41602901,
year = {2025},
author = {Sun, Y and Yuan, L and Hu, T and Sun, C and Yang, D and Tian, M and Dong, S and Gu, H},
title = {Isavuconazole as initial antifungal therapy combined with surgical management of pediatric pulmonary mucormycosis: a case report and literature review.},
journal = {Frontiers in pediatrics},
volume = {13},
number = {},
pages = {1701905},
pmid = {41602901},
issn = {2296-2360},
abstract = {Invasive mucormycosis (IM) in pediatric patients is a rare but life-threatening fungal disease with limited treatment options. Isavuconazole is a new triazole that has shown efficacy and safety in adults for both primary and salvage treatment of mucormycosis. However, data regarding the initial use of isavuconazole in children are rare. In this study, we report a case of a 6-year-old girl with diabetes mellitus. Metagenomic next-generation sequencing detected Rhizopus oryzae in her bronchoalveolar lavage fluid , and a chest computed tomography revealed a reversed halo sign. Oral isavuconazole was given as primary monotherapy with continuous control of blood glucose. After the lesion partially shrank and became confined, the patient visited the thoracic surgery department to undergo lobectomy; she recovered well after the procedure. This report highlights the importance of quick diagnosis of mucormycosis and may provide a reference for providing the initial antifungal treatment in pediatric mucormycosis. All of the aforementioned interventions helped buy time for subsequent surgical treatment, leading to the curing of the child. Isavuconazole may represent an effective and safe therapeutic option as first-line monotherapy for pediatric mucormycosis.},
}

@article {pmid41602774,
year = {2025},
author = {Zhang, M and Zhu, Y and Sun, Z and Wang, B and Chen, J and Zhou, F and Zeng, J and Li, M and Zou, D and Jiang, Z},
title = {Correction: Chemoautotrophic Thermodesulfobacteriota as a key genomic potential group in the hypoxic diazotrophic community of the Changjiang (Yangtze River) estuary.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1766907},
doi = {10.3389/fmicb.2025.1766907},
pmid = {41602774},
issn = {1664-302X},
abstract = {[This corrects the article DOI: 10.3389/fmicb.2025.1671267.].},
}

@article {pmid41602763,
year = {2025},
author = {Xu, J and Li, J and Kong, X and Zhang, C and Qi, B and Zhu, X and Zhu, Y and Xu, Y},
title = {Dysbiosis and metabolic pathway shifts in the gut microbiome of children with sepsis: a comparative analysis.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1715990},
pmid = {41602763},
issn = {1664-302X},
abstract = {BACKGROUND: The newly published Phoenix Sepsis Score in 2024 for assessing sepsis in children mainly focuses on respiratory, cardiological, coagulation and neurological indicators, whereas the gut microbiome also plays key roles in the occurrence and progression of sepsis. Additionally, emerging evidence suggests that specific biomarkers in gut microbiome are associated with disease progression. This study aimed to explore the differences in gut microbiome diversity, composition and function between septic and healthy children, and to establish correlations with clinical indicators and outcomes, providing new possibilities for the diagnosis and treatment of sepsis.

RESULTS: Analysis of gut microbiome was performed in 20 sepsis children and 9 healthy controls aged between 3 and 18 years old. The anal swab samples were analyzed by metagenomic next-generation sequencing. Significant differences were observed in α and β diversity of gut microbiome between sepsis group and healthy controls groups. Especially, Shannon diversity was significantly correlated with white blood cell count, serum lactate, length of pediatric intensive care unit stay and length of hospital stay (all R > 0, p < 0.05). Firmicutes and Bacteroidetes were both dominant in most of children in SG and HC groups, while three in SG showed extremely low combined abundances of Firmicutes and Bacteroidetes (<10%), which might be associated with chemistry therapy and death outcome. Bacteria associated with nosocomial infections, including genus taxa Acinetobacter, Prevotella, Escherichia, Klebsiella, Bacteroides, and Corynebacterium, can be dominant (relative abundance>70%) in sepsis group, which were absent in healthy control group. Enterococcus abundance not only predicted sepsis risk (AUC = 0.85) but also was correlated with 28-day mortality (R > 0, p = 0.004). Gene function prediction based on Kyoto Encyclopedia of Genes and Genomes pathway analysis indicated significant differences profile in SG and sepsis-deaths groups. The enriched gut microbiome genes were related to cellular proliferation, energy metabolism, signal transduction, the oxidative stress response and arginine metabolism.

CONCLUSION: Significant differences in diversity, taxa composition and gene function in the gut microbiome existed between septic and healthy children. The associations between gut microbiome dysbiosis and clinical indicators were identified. Enterococcus could be a biomarker to predict sepsis risk.},
}

@article {pmid41602756,
year = {2025},
author = {Chisompola, D and Luwaya, E and Nzobokela, J and Mwansa, P and Chakulya, M},
title = {AI-powered analysis of viral metagenomic sequencing data for rapid outbreak investigation and novel pathogen discovery.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1717859},
pmid = {41602756},
issn = {1664-302X},
abstract = {Emerging viral outbreaks continue to pose a persistent global health threat, underscoring the urgent need for a shift from reactive to proactive health security strategies. Viral metagenomic next-generation sequencing (mNGS) offers an unbiased, powerful approach to pathogen detection and discovery, yet its utility has been constrained by the computational complexity and slow turnaround time of data analysis during outbreak crises. The integration of artificial intelligence (AI) and mNGS is dismantling these barriers, enabling faster, more scalable outbreak response. This review synthesizes how AI-driven analytics are transforming mNGS applications, from genome assembly to sequence classification, using advanced architectures such as convolutional neural networks, recurrent neural networks, and transformers. Beyond accelerating workflows, AI's capacity for pattern recognition outperforms traditional homology-based methods, facilitating the discovery of novel viral families and tracing hidden transmission chains through anomaly detection. Nonetheless, critical challenges remain, including limited training data, the interpretability of AI models, and resource-intensive computational demands that risk widening an "AI divide" in global health. We evaluate these obstacles and highlight forward-looking strategies, including federated learning for privacy-preserving data sharing and explainable AI for improving trust and biological insight. Looking ahead, we envision an "AI-first" paradigm for outbreak preparedness, anchored in integrated "Digital Immune Systems" for continuous, global-scale surveillance. By framing the synergy between mNGS and AI as a transformative leap, this review underscores its potential to strengthen resilience against future pandemics.},
}

@article {pmid41602753,
year = {2025},
author = {Nissan, I and Peretz, A},
title = {Editorial: Innovation in tackling the global challenge of eradicating antibiotic-resistant microorganisms.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1774105},
doi = {10.3389/fmicb.2025.1774105},
pmid = {41602753},
issn = {1664-302X},
}

@article {pmid41602101,
year = {2025},
author = {Deng, Q and Liu, Y and Zhang, J and Zhang, H and Zhang, Y and Wang, M and Jia, M and Ding, D and Fang, Y and Wang, Y and Gu, H and Wang, H},
title = {Clinical validation and utility of targeted nanopore sequencing for rapid pathogen diagnosis and precision therapy in lung cancer patients with pulmonary infections.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1730098},
pmid = {41602101},
issn = {2235-2988},
mesh = {Humans ; *Lung Neoplasms/complications/microbiology ; *Nanopore Sequencing/methods ; Male ; Female ; Middle Aged ; Aged ; Sputum/microbiology ; *Precision Medicine/methods ; High-Throughput Nucleotide Sequencing ; *Respiratory Tract Infections/diagnosis/microbiology/drug therapy ; Metagenomics/methods ; Microbiota ; Bacteria/genetics/isolation & purification/classification ; Sensitivity and Specificity ; Adult ; Aged, 80 and over ; },
abstract = {BACKGROUND: Pulmonary infections are common in patients with lung cancer (LC), complicating diagnosis and treatment. This study explored the diagnostic performance and clinical utility of targeted nanopore sequencing (TNPseq) for detecting pathogens in LC-related pulmonary infections.

METHODS: A total of 143 patients with LC or benign pulmonary diseases complicated by pulmonary infections were included and stratified into diagnostic and therapeutic cohorts. Sputum samples underwent conventional culture, metagenomic next-generation sequencing (mNGS), and TNPseq analyses. Microbiota profiles were compared across disease groups and correlated with tumor therapy responses. In the therapeutic cohort, clinical outcomes were assessed between empirical therapy and TNPseq-guided therapy.

RESULTS: TNPseq identified a significantly higher proportion of clinically relevant pathogens compared to mNGS (48.76% vs. 16.80%, p < 0.001) and demonstrated superior sensitivity (81.25% vs. 68.75%), with a 40.7% reduction in turnaround time (16 hours vs. 27 hours). Both sequencing methods revealed an enrichment of Lactobacillus species in non-initial diagnosis lung cancer (NDLC) patients (p < 0.01). Patients exhibiting partial response or stable disease (PR/SD) showed increased abundance of Neisseria, Veillonella, and Prevotella species (p < 0.05). Clinical remission was achieved in all patients; however, 68.4% of those initially receiving empirical therapy subsequently required a switch to TNPseq-guided treatment due to its ineffectiveness. Compared to this empirical-to-TNPseq group, the median treatment duration was significantly shorter under direct TNPseq guidance (total: 6 days vs. 13 days, p < 0.01; LC subgroup: 5 days vs. 15.5 days, p < 0.05), thereby reducing unnecessary antibiotic exposure.

CONCLUSIONS: By enabling rapid pathogen detection and profiling of the pulmonary microbiome, TNPseq facilitates targeted therapy and reduces antibiotic overuse in LC patients. These findings highlight the potential of TNPseq as a promising, rapid, and non-invasive diagnostic candidate for first-line use, offering a comprehensive view of both infection and host-microbe interactions in immunocompromised patients.},
}

Humans
*Lung Neoplasms/complications/microbiology
*Nanopore Sequencing/methods
Male
Female
Middle Aged
Aged
Sputum/microbiology
*Precision Medicine/methods
High-Throughput Nucleotide Sequencing
*Respiratory Tract Infections/diagnosis/microbiology/drug therapy
Metagenomics/methods
Microbiota
Bacteria/genetics/isolation & purification/classification
Sensitivity and Specificity
Adult
Aged, 80 and over

@article {pmid41601644,
year = {2025},
author = {Song, DJ and Dong, R and Liu, YM and Wang, T and Ma, J},
title = {Autoimmune cerebellar ataxia with anti-Homer3 antibodies associated with herpesvirus infection: a case report and literature review.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1709326},
pmid = {41601644},
issn = {1664-3224},
mesh = {Humans ; Female ; *Cerebellar Ataxia/immunology/diagnosis/etiology/drug therapy ; Adolescent ; *Autoantibodies/immunology/blood ; *Autoimmune Diseases/immunology/diagnosis ; *Herpesviridae Infections/immunology ; },
abstract = {Autoimmune cerebellar ataxia (ACA) is a cerebellar syndrome mediated by autoimmune mechanisms. ACA is particularly rare, and cases of ACA with anti-Homer-3 antibodies associated with herpesvirus infection are even rarer. In this study, we report a case of a 15-year-old girl who was admitted with a one-month history of progressive vertigo and unsteady gait. Metagenomic next-generation sequencing (mNGS) of her cerebrospinal fluid (CSF) revealed eight sequences of human herpesvirus 7 (HHV-7). Anti-Homer-3 antibodies were detected in both serum and CSF samples. Following a series of immunotherapy, the patient showed improvements in dizziness and gait stability. However, her symptoms recurred during the tapering of corticosteroids. The patient developed three episodes of generalized seizures. Concurrently, gait instability significantly worsened. Repeat first-line immunotherapies including corticosteroid and IVIG were not effective. Rituximab was initiated and symptoms were partial improved. In this study, we present the clinical symptoms of this patient with anti-Homer-3 antibody-associated ACA, conduct long-term follow-up, and review relevant literature. Our aim is to enhance the understanding of this rare disease by summarizing key clinical features, thus providing valuable insights into the diagnosis and treatment of ACA.},
}

Humans
Female
*Cerebellar Ataxia/immunology/diagnosis/etiology/drug therapy
Adolescent
*Autoantibodies/immunology/blood
*Autoimmune Diseases/immunology/diagnosis
*Herpesviridae Infections/immunology

@article {pmid41601218,
year = {2025},
author = {Li, CT},
title = {[Applications and challenges of forensic microbiomics].},
journal = {Fa yi xue za zhi},
volume = {41},
number = {5},
pages = {441-442},
doi = {10.12116/j.issn.1004-5619.2025.551105},
pmid = {41601218},
issn = {1004-5619},
mesh = {Humans ; *Metagenomics/methods ; *Microbiota/genetics ; *Forensic Medicine/methods ; *Gastrointestinal Microbiome ; China ; Genomics ; Human Genome Project ; *Forensic Sciences ; Metagenome ; },
}

Humans
*Metagenomics/methods
*Microbiota/genetics
*Forensic Medicine/methods
*Gastrointestinal Microbiome
China
Genomics
Human Genome Project
*Forensic Sciences
Metagenome

@article {pmid41601044,
year = {2026},
author = {Sun, X and Zheng, L and Qi, R and Li, H},
title = {Salinity and redox-driven niche differentiation of ammonia-oxidizing microbes in a saline-alkaline river system.},
journal = {Ecotoxicology and environmental safety},
volume = {309},
number = {},
pages = {119613},
doi = {10.1016/j.ecoenv.2025.119613},
pmid = {41601044},
issn = {1090-2414},
mesh = {*Ammonia/metabolism ; Oxidation-Reduction ; *Rivers/microbiology/chemistry ; *Salinity ; *Bacteria/metabolism/genetics ; *Archaea/metabolism/genetics ; Nitrification ; Geologic Sediments/microbiology ; Wetlands ; China ; Ecosystem ; Soil Microbiology ; },
abstract = {The ammonia oxidation process constitutes a critical step in the nitrogen cycle within river ecosystems. Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) are the major contributors to this process; however, their relative contributions differ substantially across different environments, particularly in saline-alkaline regions. To investigate the differences in ammonia oxidation processes between soil and sediment across various riparian zones in the Yinbei Irrigation District in Ningxia, samples were collected from five representative riparian types along the Third Drainage Ditch: a gravel-reed mixed zones, a reed zones, a high-salt Kochia scoparia zones, an Iris lactea embankment zones, and a bare soil zone. The potential nitrification rate (PNR) and associated environmental factors were quantified, and the community structure of microorganisms was analyzed by metagenomic sequencing, while the abundances of AOA and AOB functional genes (amoA) were quantified by quantitative PCR (qPCR). Through a multi-dimensional investigation of the ammonia oxidation process in riparian zones and sediments of saline-alkali wetlands, this study provided critical evidence for the mechanisms underlying habitat-specific nitrogen transformations. Pronounced physical and chemical differences were observed between sediments and riparian zones. Whereas the sediments exhibited strong reducing conditions, the riparian zones were characterized by pronounced saline-alkali stress. PCoA analysis revealed a clear separation between AOA and AOB communities, with saline-alkali-tolerant AOA predominating in riparian zones and AOB predominating in sediments. The strong reducing condition impedes the activity of AOB in sediments, thereby resulting in the accumulation of NH4[+] -N. AOA contributed 67-68.9 % of the total PNR in riparian zones, thereby driving substantial NO3[-]-N production. Seasonal variations exhibited no significant influence on the partitioning of microbial functions, which were jointly regulated by the saline-alkali gradient and redox state. This study demonstrates that the ammonia oxidation process of saline-alkali wetlands exhibits a pronounced mechanism of habitat-specific functional differentiation: AOB in sediments are constrained by the anoxic conditions induced by elevated total organic carbon (TOC), whereas AOA in riparian zones overcome the inhibition of nitrification under high pH or electrical conductivity (EC) through evolved salt-tolerant adaptations This discovery provides a novel theoretical framework for elucidating the microbial mechanisms driving the nitrogen cycle in saline-alkaline environments.},
}

*Ammonia/metabolism
Oxidation-Reduction
*Rivers/microbiology/chemistry
*Salinity
*Bacteria/metabolism/genetics
*Archaea/metabolism/genetics
Nitrification
Geologic Sediments/microbiology
Wetlands
China
Ecosystem
Soil Microbiology

@article {pmid41601042,
year = {2026},
author = {Sun, Y and Tu, Q and Shao, Z and Li, H},
title = {The normalization of gene abundance affects the discovery: A case of metal resistance genes in coastal sediments.},
journal = {Ecotoxicology and environmental safety},
volume = {309},
number = {},
pages = {119608},
doi = {10.1016/j.ecoenv.2025.119608},
pmid = {41601042},
issn = {1090-2414},
mesh = {*Geologic Sediments/microbiology/chemistry ; China ; Metagenomics/methods ; *Environmental Monitoring/methods ; *Water Pollutants, Chemical/toxicity/analysis ; *Metals/toxicity ; Estuaries ; },
abstract = {The advent of metagenomic technologies has given rise to a plethora of gene abundance calculation methods, which have emerged in a successive manner. Nevertheless, the extent to which these approaches are appropriate for metagenomic data and the specific research objectives remain subjects of debate. In this study, metagenomics sequencing was utilised to analyse the sediments from two coastal regions of China: the Beibu Gulf (BBG) and the Liaohe Estuary (LHE). The abundance of metal resistance genes (MRGs), which are critical genetic elements that influence ecosystem functioning and health, in the regions under study was obtained by two different calculation methods: the cell-normalized abundance (copies per prokaryotic cell) and the ppm abundance (sequences per million sequences). The application of diverse abundance calculation methodologies yielded markedly divergent outcomes. The cell-normalized and ppm abundances indicated a substantial elevation of total MRG abundance in the BBG and LHE sediments, respectively. Furthermore, disparate comparison outcomes were identified based on the varied abundance calculation methodologies employed across distinct MRG types, including genes demonstrating resistance to Fe, Al, Cr, Se, and multi-metals. These disparities can be ascribed to the variations in the prokaryotic biomass among different sediments, signifying that it is imperative to select an appropriate abundance calculation method according to whether the research objective necessitates the consideration of biomass differences. Furthermore, the results of multiple correlation analyses indicated that petroleum content was the key factor, and the ruvB gene was identified as an indicator for the MRG level based on both two abundance calculation methods. These findings establish a methodological foundation for metagenomics-based research and offer insights into the MRGs present in coastal sediments.},
}

*Geologic Sediments/microbiology/chemistry
China
Metagenomics/methods
*Environmental Monitoring/methods
*Water Pollutants, Chemical/toxicity/analysis
*Metals/toxicity
Estuaries

@article {pmid41600881,
year = {2026},
author = {Li, J and Baumgartner, W and Wang, L},
title = {Histopathologic and Genomic Characterization of a Novel Caprine Astrovirus Identified in a Boer Goat Kid in Illinois, United States.},
journal = {Viruses},
volume = {18},
number = {1},
pages = {},
pmid = {41600881},
issn = {1999-4915},
mesh = {Animals ; Goats/virology ; *Goat Diseases/virology/pathology ; *Astroviridae Infections/veterinary/virology/pathology ; Phylogeny ; Genome, Viral ; *Astroviridae/genetics/classification/isolation & purification ; Genomics ; High-Throughput Nucleotide Sequencing ; },
abstract = {Astroviruses are non-enveloped, positive-sense single-stranded RNA viruses known to infect various mammals and birds, including humans, often causing gastrointestinal disorders. In recent years, astroviruses have also been linked to neurological and respiratory diseases across several species, including ruminants, mink, deer, and other mammals. Notably, astrovirus infections in goats have been documented in countries such as Switzerland and China, where novel genotypes have been identified in fecal samples. However, their role in the context of disease remains unclear, and reports focusing solely on goat astrovirus in the United States have not been published. A necropsy case of a Boer goat kid with a history of diarrhea was submitted for investigation following death in January 2025. Fresh tissues were received and used for histopathology and enteric pathogen testing, including parasitic, bacterial, and viral workups. Metagenomic-based next-generation sequencing (mNGS) was also applied for this case. Histological examination revealed severe necrotizing enterocolitis. The small intestine exhibited epithelial ulcerations, villus atrophy, hyperplastic and dilated crypts with necrotic debris, few intraenterocytic coccidian parasites, and increased inflammatory cells in the lamina propria. The large intestine showed similar findings with pleomorphic crypt enterocytes. Standard enteric pathogen tests were negative except for aerobic culture that identified Escherichia.coli and Enterococcus hirae. mNGS and bioinformatic analysis identified a novel astrovirus in the intestinal content that showed the highest nucleotide identity (86%) to the sheep strain Mamastrovirus 13 sheep/HA3 from China based on BLAST analysis. Phylogenetic analysis indicated that the newly identified caprine astrovirus IL90175 clustered with astrovirus strains from small ruminants in Asia and Europe. This research reports the discovery, histopathologic features, and genetic characteristics of a gastrointestinal disease-causing astrovirus in a goat kid, which had not been previously described in the United States.},
}

Animals
Goats/virology
*Goat Diseases/virology/pathology
*Astroviridae Infections/veterinary/virology/pathology
Phylogeny
Genome, Viral
*Astroviridae/genetics/classification/isolation & purification
Genomics
High-Throughput Nucleotide Sequencing

@article {pmid41600842,
year = {2026},
author = {Hake, N and von Holtum, C and Höper, D and Nijhof, AM and Dietze, K and Hoffmann, B},
title = {Identification and Long-Term Detection of Hepacivirus bovis Genotype 1 and 2 on a Cattle Farm in Germany.},
journal = {Viruses},
volume = {18},
number = {1},
pages = {},
pmid = {41600842},
issn = {1999-4915},
mesh = {Animals ; Cattle ; Germany/epidemiology ; *Cattle Diseases/virology/epidemiology/diagnosis ; *Genotype ; Phylogeny ; High-Throughput Nucleotide Sequencing ; Farms ; Genome, Viral ; Female ; Real-Time Polymerase Chain Reaction ; },
abstract = {In 2020, a dairy farm in northwest Germany reported several cows with severe respiratory disease, fever, and reduced milk production. Multiple direct and indirect diagnostic methods were used to identify the cause of the disease. However, the pathogens detected could not be correlated with the severity of the clinical symptoms, so further diagnostic steps were taken. Blood and nasal swab samples were examined using next-generation sequencing (NGS) as part of a metagenomic analysis. For the first time in Germany, Hepacivirus bovis genotype 2 was detected. Real-time RT-PCR assays confirmed the presence of BovHepV genotypes 1 and 2 in the herd between 2020 and 2023. Analyses of complete and partial genome sequences demonstrated the presence of different virus variants in the herd over several years. In addition, the sequence data indicated that cattle can be reinfected with viruses belonging either to different BovHepV subtypes or to the same subtype. Although no direct link could be established between the detection of bovine hepaciviruses and the observed clinical symptoms, the PCR and sequence data obtained provide valuable insights into the epidemiology and pathogenesis of BovHepV infections.},
}

Animals
Cattle
Germany/epidemiology
*Cattle Diseases/virology/epidemiology/diagnosis
*Genotype
Phylogeny
High-Throughput Nucleotide Sequencing
Farms
Genome, Viral
Female
Real-Time Polymerase Chain Reaction

@article {pmid41591600,
year = {2026},
author = {Bilecen Şen, D and Ertürkmen, P and Alp Baltakesmez, D},
title = {Microbiota and quality profiling of fermented goat meat sausages (sucuk) under nitrite-reduced and mixed-culture strategies.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {2},
pages = {64},
pmid = {41591600},
issn = {1573-0972},
abstract = {The bioprotective activity of lactic acid bacteria (LAB) to modulate the microbiota and quality of nitrite-reduced fermented goat meat sucuk was investigated. Antagonistic activity of LAB strains against foodborne pathogens was evaluated using agar well diffusion, spot-on lawn, and cross-streak assays. Three LAB isolates affiliated with the genera Weissella, Limosilactobacillus, and Lactiplantibacillus, exhibiting inhibition zones > 18 mm, were selected and applied as a mixed culture (MC; 2:1:1). Sucuk formulations with 150, 75, and 0 ppm sodium nitrite were produced in the presence or absence of a MC and analyzed during fermentation (days 0 and 7) and refrigerated storage (days 7 and 14). Among the treatments, 75 ppm nitrite combined with MC (75-MC) exhibited the highest LAB counts, enhanced acidification (pH 4.7 on fermentation day 7), inhibited pathogens and spoilage microorganisms, and improved moisture and color stability (> 90% of initial L[*] and a[*]), with a significant treatment × day interaction (P < 0.05). Metagenomic analysis of the 16 S rRNA (V3–V4) and ITS2 regions revealed a LAB-dominated sucuk microbiota, characterized by Levilactobacillus (69.5%), Lactiplantibacillus (12.1%), Psychrobacter (8.8%), and Lacticaseibacillus (3.0%) among bacteria, and Yarrowia (46%), Kurtzmaniella (11.8%), Geotrichum (6.7%), and Cladosporium (5.5%) among fungi. This microbial composition was associated with enhanced microbial stability and technological quality, while mixed-culture strategies under nitrite-reduced conditions promoted a Lactobacillaceae-enriched microbiota, highlighting their potential role in bioprotection and product quality.},
}

@article {pmid41408163,
year = {2025},
author = {Yang, G and He, W and Ma, B and La, Y and Ma, X and Wu, X and Chu, M and Zhao, M and Liu, X and Zhao, Y and Guo, X and Wang, L and Liang, C},
title = {Effects of dietary supplementation with astragalus polysaccharides on growth performance, serum parameters, and rumen microbial function of yaks.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {64},
pmid = {41408163},
issn = {1471-2180},
support = {CARS-37//Modern Beef Yak Industry Technology System/ ; 25ZYJA008//Central Guidance Funds for Local science and technology Development projects/ ; },
abstract = {BACKGROUND: Astragalus polysaccharide (APS) has become a natural feed additive that has attracted much attention in animal husbandry due to its significant immunomodulatory activity, low toxicity and promotion of animal growth performance. In this study, in order to explore the effects of dietary APS on the growth performance and rumen microorganisms of yaks, 20 male yaks aged 2–3 years were selected and randomly divided into two groups: experimental group (1.0 g/kg APS were added to the diet, AG) and control group (no APS were added to the diet, CG), with 10 yaks in each group. After 60 days of continuous feeding, 5 animals were randomly selected from each group to collect rumen fluid. Comparative analysis of rumen microbial composition, function, and metabolites was conducted using metagenomic and metabolomic approaches.

RESULTS: The analysis of yak body weight index showed that the body weight of yak in the AG group was significantly higher than that in the CG group on the 60 th day (P < 0.05). In addition, APS significantly increased the immune indexes of IgA, IgM, IgG, IL-10, IGF1, GH, and NOS in yaks (P < 0.05). Metagenomic analysis showed that the beneficial bacteria (such as Euryarchaeota, Methanobrevibacter and Butyrivibrio) in the rumen of yaks were significantly increased after the addition of astragalus polysaccharides in the experimental group. Differential metabolites were significantly enriched in pathways such as Purine metabolism, Galactose metabolism and Tryptophan metabolism that may have a positive impact on the growth and development of yaks. This may promote the production of immune and growth-related metabolites by regulation, and ultimately enhance the immune function and growth performance of yak.

CONCLUSIONS: The results showed that the addition of APS could significantly improve the growth performance and immune function of yak. It can also optimize the rumen microbial community. It shows that polysaccharides such as APS can be used as effective substitutes for antibiotics and other drugs for long-term improvement of yak growth performance and rumen health.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-025-04581-5.},
}

@article {pmid41600629,
year = {2026},
author = {Wang, D and Sun, J and Zhang, Y and Yuan, L and Xu, X and Xue, Y and Sun, H},
title = {Integrated 13C-DNA Stable Isotope Probing and Metagenomics Approaches to Identify Bisphenol A Assimilating Microorganisms and Metabolic Pathways in Biofilms.},
journal = {Toxics},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/toxics14010080},
pmid = {41600629},
issn = {2305-6304},
support = {52100082//National Natural Science Foundation of China/ ; KYCX25_3358//Postgraduate Research & Practice Innovation Program of Jiangsu Province/ ; SJCX25_1722//Postgraduate Research & Practice Innovation Program of Jiangsu Province/ ; BK20240983//Natural Science Foundation of Jiangsu Province/ ; ZMF23020040//Changzhou University Research Start-up Fund Project/ ; },
abstract = {Bisphenol A (BPA) is a persistent environmental contaminant requiring effective removal strategies. Biofilms offer advantages over conventional activated sludge for refractory compound degradation, yet the specific microorganisms and mechanisms driving BPA removal in biofilms remain poorly understood. This study employed an integrated approach, combining [13]C-DNA stable isotope probing (SIP) and metagenomics to identify BPA-assimilating microorganisms and elucidate their metabolic pathways in biofilms. Two moving bed biofilm reactors (MBBRs) were operated at contrasting BPA concentrations (500 μg/L and 10 mg/L) to enrich distinct microbial communities. Using DNA-SIP, we revealed differences in assimilating bacteria across diverse concentrations of BPA-enriched biofilms. Simultaneously, we reconstructed the genomes of these assimilating bacteria, dissecting the functional genes essential to the degradation process and identifying significant gene variations among different assimilating bacteria. By integrating these gene functions, we constructed the BPA metabolic pathway, which surprisingly comprised genes from various assimilating bacteria. This research significantly advances our understanding of BPA-assimilating bacteria within biofilms and provides valuable insights for refining biofilm technologies aimed at BPA removal from wastewater.},
}

@article {pmid41599943,
year = {2026},
author = {Rocha, HR and Ribeiro, P and Rodrigues, PM and Gomes, AM and Pintado, M and Coelho, MC},
title = {Bioinformatic Insights into the Carotenoids' Role in Gut Microbiota Dynamics.},
journal = {Nutrients},
volume = {18},
number = {2},
pages = {},
doi = {10.3390/nu18020330},
pmid = {41599943},
issn = {2072-6643},
mesh = {*Gastrointestinal Microbiome/drug effects ; *Carotenoids/pharmacology/chemistry ; *Computational Biology ; Humans ; Fermentation ; Lycopene/pharmacology ; Lutein/pharmacology ; Bacteria/drug effects/genetics/classification ; beta Carotene/pharmacology ; },
abstract = {Background/Objectives: Carotenoids are bioactive pigments with well-established antioxidant and immunomodulatory properties, yet their impact on gut microbiota remains poorly understood from a chemical standpoint. This study explores how carotenoid structure and gastrointestinal stability shape microbial responses combining in vitro fermentation with bioinformatic analyses. Methods: Individual carotenoids (beta (β)-carotene, lutein, lycopene) and combined carotenoids, as well as algal-derived extracts were subjected to 48 h in vitro fermentation, and microbial composition and activity were assessed through sequencing and computational analysis. Results: β-carotene and lycopene promoted acid-tolerant taxa such as Escherichia-Shigella, whereas lutein, due to its higher polarity, supported more transient fluctuations. Mixtures and algal carotenoids exhibited synergistic effects, sustaining beneficial genera including Bifidobacterium and Bacteroides and promoting structured ecological trajectories. Conclusions: These findings provide a chemistry-driven perspective on how carotenoids act as modulators of microbial ecosystems, with direct implications for the formulation of carotenoid-enriched functional foods and dietary interventions.},
}

*Gastrointestinal Microbiome/drug effects
*Carotenoids/pharmacology/chemistry
*Computational Biology
Humans
Fermentation
Lycopene/pharmacology
Lutein/pharmacology
Bacteria/drug effects/genetics/classification
beta Carotene/pharmacology

@article {pmid41599039,
year = {2026},
author = {Wang, Z and Chen, G and Yang, M and Wang, S and Fang, J and Shi, C and Gu, Y and Ning, Z},
title = {Host-Filtered Blood Nucleic Acids for Pathogen Detection: Shared Background, Sparse Signal, and Methodological Limits.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {1},
pages = {},
doi = {10.3390/pathogens15010055},
pmid = {41599039},
issn = {2076-0817},
support = {2024-PWXZ-04//New Quality Clinical Specialty Program of High-end Medical Disciplinary Construction in Shanghai Pudong New Area/ ; 2024ZDXK0019//Shanghai Municipal Health Commission, Key Discipline of Shanghai Health System, Cardiology/ ; PW2025D-01//The Scientific Research Program of Shanghai Pudong New Area Health Commission (the Joint Research and Development Program)/ ; },
mesh = {Humans ; *Metagenomics/methods ; *Tuberculosis/microbiology/diagnosis/blood ; Microbiota/genetics ; *Cell-Free Nucleic Acids/blood/genetics ; *Coronary Artery Disease/microbiology/diagnosis/blood ; Mycobacterium tuberculosis/genetics/isolation & purification ; Male ; Female ; Cohort Studies ; },
abstract = {Plasma cell-free RNA (cfRNA) metagenomics is increasingly explored for blood-based pathogen detection, but the structure of the shared background "blood microbiome", the reproducibility of reported signals, and the practical limits of this approach remain unclear. We performed a critical re-analysis and benchmarking ("stress test") of host-filtered blood RNA sequencing data from two cohorts: a bacteriologically confirmed tuberculosis (TB) cohort (n = 51) previously used only to derive host cfRNA signatures, and a coronary artery disease (CAD) cohort (n = 16) previously reported to show a CAD-shifted "blood microbiome" enriched for periodontal taxa. Both datasets were processed with a unified pipeline combining stringent human read removal and taxonomic profiling using the latest versions of specialized tools Kraken2 and MetaPhlAn4. Across both cohorts, only a minority of non-host reads were classifiable; under strict host filtering, classified non-host reads comprised 7.3% (5.0-12.0%) in CAD and 21.8% (5.4-31.5%) in TB, still representing only a small fraction of total cfRNA. Classified non-host communities were dominated by recurrent, low-abundance taxa from skin, oral, and environmental lineages, forming a largely shared, low-complexity background in both TB and CAD. Background-derived bacterial signatures showed only modest separation between disease and control groups, with wide intra-group variability. Mycobacterium tuberculosis-assigned reads were detectable in many TB-positive samples but accounted for ≤0.001% of total cfRNA and occurred at similar orders of magnitude in a subset of TB-negative samples, precluding robust discrimination. Phylogeny-aware visualization confirmed that visually "enriched" taxa in TB-positive plasma arose mainly from background-associated clades rather than a distinct pathogen-specific cluster. Collectively, these findings provide a quantitative benchmark of the background-dominated regime and practical limits of plasma cfRNA metagenomics for pathogen detection, highlighting that practical performance is constrained more by a shared, low-complexity background and sparse pathogen-derived fragments than by large disease-specific shifts, underscoring the need for transparent host filtering, explicit background modeling, and integration with targeted or orthogonal assays.},
}

Humans
*Metagenomics/methods
*Tuberculosis/microbiology/diagnosis/blood
Microbiota/genetics
*Cell-Free Nucleic Acids/blood/genetics
*Coronary Artery Disease/microbiology/diagnosis/blood
Mycobacterium tuberculosis/genetics/isolation & purification
Male
Female
Cohort Studies

@article {pmid41598945,
year = {2026},
author = {Hirata, K and Suzuki, T and Yura, K and Asahi, T and Kataoka, K},
title = {Gut Microbiome Differences Across Mixed-Sex and Female-Only Social Rearing Regimes in Female Field Crickets Teleogryllus occipitalis (Orthoptera: Gryllidae).},
journal = {Insects},
volume = {17},
number = {1},
pages = {},
doi = {10.3390/insects17010091},
pmid = {41598945},
issn = {2075-4450},
support = {24KJ2101//Japan Society for the Promotion of Science/ ; JPJ009237//Cabinet Office/ ; },
abstract = {The insect gut microbiome contributes to various host physiological processes and behaviors, such as digestion, nutrient absorption, immunity, mate choice, and fecundity. The social environment can shape gut microbial communities. Mixed-sex vs. female-only rearing is an important social context because it differs in exposure to the opposite sex and mating opportunities, which may in turn affect female physiology that may influence their gut microbiome. Despite the growing recognition of these social-microbial interactions, most studies have relied on 16S rRNA amplicon sequencing or qPCR, which provide only coarse taxonomic resolution and limited functional insight. In this study, we used whole-genome shotgun metagenomics to examine changes in microbial diversity and functional gene composition in the female field cricket Teleogryllus occipitalis (Serville) (Orthoptera: Gryllidae) reared under two social conditions: mixed-sex rearing and female-only rearing. Species richness and diversity analyses revealed that community composition separated between females from mixed-sex and female-only rearing. Functional profiling indicated higher relative abundances of genes annotated to nutrient processing and inter-bacterial competition in females from mixed-sex rearing, whereas females from female-only rearing showed relative enrichment of genes annotated to stress resistance and nitrogen fixation. These findings provide a genome-resolved foundation for testing how social rearing conditions covary with gut microbiome composition and functional potential in female crickets.},
}

@article {pmid41598908,
year = {2026},
author = {González-Peña, R and Hidalgo-Martínez, DO and Laredo-Tiscareño, SV and Huerta, H and de Luna-Santillana, EJ and Adame-Gallegos, JR and Rodríguez-Alarcón, CA and Rubio-Tabares, E and García-Rejón, JE and Muñoz-Ramírez, ZY and Tangudu, C and Garza-Hernández, JA},
title = {Characterization of the Bacteriome of Culicoides reevesi from Chihuahua, Northern Mexico: Symbiotic and Pathogenic Associations.},
journal = {Insects},
volume = {17},
number = {1},
pages = {},
doi = {10.3390/insects17010052},
pmid = {41598908},
issn = {2075-4450},
support = {419- 395 24-23//Secretaría de Ciencia, Humanidades, Tecnología e Innovación (SECIHTI)/ ; SIP20250075//Secretaría de Investigación y Posgrado from Instituto Politécnico Nacional/ ; },
abstract = {Culicoides biting midges are vectors of veterinary and zoonotic pathogens, yet the bacteriome of several species remains unexplored. Culicoides reevesi, a poorly studied species in northern Mexico, represents an opportunity to investigate microbial associations that may influence vector biology. Adults of C. reevesi were analyzed using 16S rRNA amplicon sequencing, followed by functional prediction with PICRUSt2. Heatmaps and pathway summaries were generated to highlight dominant taxa and functions. The bacteriome was dominated by Pseudomonadota, followed by Actinomycetota, Bacillota, and Bacteroidota. Symbiotic taxa such as Asaia and Cardinium were identified alongside potentially pathogenic bacteria, including Escherichia coli, Mycobacterium avium, Vibrio parahaemolyticus, and Enterococcus faecalis. Functional predictions indicated metabolic versatility, with abundant pathways related to aerobic respiration, the TCA cycle, amino acid biosynthesis, and quorum sensing. Despite all samples being collected from the same site and date, apparent differences in bacterial composition were observed across pools, suggesting microhabitat or host-related variability. This study provides the first taxonomic and functional baseline of the C. reevesi bacteriome. The detection of both symbiotic and pathogenic bacteria highlights the dual ecological role of the microbiome in host fitness and pathogen transmission potential. In conclusion, we suggest that these microbial associations influence vector physiology and competence, providing a basis for future microbiome-based control strategies. These findings emphasize the importance of integrating microbiome analyses into entomological surveillance and vector control strategies in endemic regions.},
}

@article {pmid41598312,
year = {2026},
author = {Thant, EP and Klaysubun, C and Suwannasin, S and Dechathai, T and Singkhamanan, K and Yaikhan, T and Chaichana, N and Pomwised, R and Wonglapsuwan, M and Chusri, S and Surachat, K},
title = {Global Comparative Genomics of Stenotrophomonas maltophilia Reveals Cryptic Species Diversity, Resistome Variation, and Population Structure.},
journal = {Life (Basel, Switzerland)},
volume = {16},
number = {1},
pages = {},
doi = {10.3390/life16010158},
pmid = {41598312},
issn = {2075-1729},
abstract = {Background:Stenotrophomonas maltophilia is an increasingly important multidrug-resistant opportunistic pathogen frequently isolated from clinical, environmental, and plant-associated niches. Despite its medical relevance, the global population structure, species-complex boundaries, and genomic determinants of antimicrobial resistance (AMR) and ecological adaptation remain poorly resolved, partly due to inconsistent annotations and fragmented genomic datasets. Methods: Approximately 2400 genome assemblies annotated as Stenotrophomonas maltophilia were available in the NCBI Assembly database at the time of query. After pre-download filtering to exclude metagenome-assembled genomes and atypical lineages, 1750 isolate genomes were retrieved and subjected to stringent quality control (completeness ≥ 90%, contamination ≤ 5%, ≤500 contigs, N50 ≥ 10 kb, and ≤1% ambiguous bases), yielding a final curated dataset of 1518 high-quality genomes used for downstream analyses. Genomes were assessed using CheckM, annotated with Prokka, and compared using average nucleotide identity (ANI), pan-genome analysis, core-genome phylogenomics, and functional annotation. AMR genes, mobile genetic elements (MGEs), and metadata (source, host, and geographic origin) were integrated to assess lineage-specific genomic features and ecological distributions. Results: ANI-based clustering resolved the S. maltophilia complex into multiple distinct genomospecies and revealed extensive misidentification of publicly deposited genomes. The pan-genome was highly open, reflecting strong genomic plasticity driven by accessory gene acquisition. Core-genome phylogeny resolved well-supported clades associated with clinical, environmental, and plant-related niches. Resistome profiling showed widespread intrinsic MDR determinants, with certain lineages enriched for efflux pumps, β-lactamases, and trimethoprim-sulfamethoxazole resistance markers. MGE analysis identified lineage-specific integrative conjugative elements, prophages, and transposases that correlated with source and geographic distribution. Conclusions: This large-scale analysis provides the most comprehensive genomic overview of the S. maltophilia complex to date. Our findings clarify species boundaries, highlight substantial taxonomic misannotation in public databases, and reveal lineage-specific AMR and mobilome patterns linked to ecological and clinical origins. The curated dataset and evolutionary insights generated here establish a foundation for global genomic surveillance, epidemiological tracking, and future studies on the evolution of antimicrobial resistance in S. maltophilia.},
}

@article {pmid41598263,
year = {2026},
author = {Liu, Y and Zhao, M and Zhong, S and Wu, G and Yang, F and Zhou, J},
title = {Review on Mining Robust Lactic Acid Bacteria for Next-Generation Silage Inoculants via Multi-Omics.},
journal = {Life (Basel, Switzerland)},
volume = {16},
number = {1},
pages = {},
doi = {10.3390/life16010108},
pmid = {41598263},
issn = {2075-1729},
support = {2023J06019//Fujian Provincial Outstanding Youth Fund Projects/ ; KFB25053A and KFB25010A//Science and Technology Innovation Specia Fund Project of Fujian Agriculture and Forestry University/ ; },
abstract = {Lactic acid bacteria (LAB), as the core microorganisms in silage fermentation, play a crucial role in improving silage quality and ensuring feed safety, making the screening, identification, and functional characterization of LAB strains a significant research focus. Researchers initially isolate and purify LAB from various samples, followed by identification through a combination of morphological, physiological, biochemical, and molecular biological methods. Systematic screening has been conducted to identify LAB strains tolerant to extreme environments (e.g., low temperature, high temperature, high salinity) and those possessing functional traits such as antimicrobial activity, antioxidant capacity, production of feruloyl esterase and bacteriocins, as well as cellulose degradation, yielding a series of notable findings. Furthermore, modern technologies, including microbiomics, metabolomics, metagenomics, and transcriptomics, have been employed to analyze the structure and functional potential of microbial communities, as well as metabolic dynamics during the ensiling process. The addition of superior LAB inoculants not only facilitates rapid acidification to reduce nutrient loss, inhibit harmful microorganisms, and improve fermentation quality and palatability but also demonstrates potential functions such as degrading mycotoxins, adsorbing heavy metals, and reducing methane emissions. However, its application efficacy is directly constrained by factors such as strain-crop specific interactions, high dependence on raw material conditions, limited functionality of bacterial strains, and relatively high application costs. In summary, the integration of multi-omics technologies with traditional methods, along with in-depth exploration of novel resources like phyllosphere endophytic LAB, will provide new directions for developing efficient and targeted LAB inoculants for silage.},
}

@article {pmid41597762,
year = {2026},
author = {Xiong, Y and Dai, Z and He, F and Liu, R and Wang, J and Zhan, Z and Jia, H and Chen, S and Cai, L},
title = {Effect of Hantavirus Infection on the Rodent Lung Microbiome: Specific Regulatory Roles of Host Species and Virus Types.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010244},
pmid = {41597762},
issn = {2076-2607},
support = {2024JJ9472//The natural science foundation of Hunan provincial/ ; },
abstract = {The lung-targeting characteristic of Hantavirus infection and the unclear mechanism underlying its interaction with the lung microbiome hampers the development of effective prevention and control strategies. In this study, lung tissues from Apodemus agrarius and Rattus norvegicus were collected at Hantavirus surveillance sites in Hunan Province. Metagenomic sequencing was subsequently applied to compare microbiome diversity, community structure, and function between infected and uninfected groups. Then the linear discriminant analysis effect size (LEfSe) was employed to identify key biomarkers. The results indicated that after infection with Hantaan virus (HTNV), Apodemus agrarius exhibited significantly increased evenness but markedly decreased richness of lung microbial communities, as reflected by consistent reductions in the number of observed species, Abundance-based Coverage Estimator (ACE) index, and Chao1 index. In contrast, Rattus norvegicus infected with Seoul virus (SEOV) showed no significant difference in microbial richness compared with uninfected controls, and even a slight increase was observed. These findings suggest that host species and virus type may play an important role in shaping microbial community responses. Furthermore, β-diversity analysis showed that the community structure was clearly separated by the host rodent species, as well as by their virus infection status. LEfSe analysis identified taxa with discriminatory power associated with infection status. Streptococcus agalactiae and Streptococcus were associated with SEOV-infected Rattus norvegicus, while Chlamydia and Chlamydia abortus were relatively enriched in uninfected Apodemus agrarius. This exploratory study reveals preliminary association between specific host-Hantavirus pairings (HTNV-Apodemus agrarius and SEOV-Rattus norvegicus) and the rodent lung microbiome, offering potential insights for future research into viral pathogenesis.},
}

@article {pmid41597751,
year = {2026},
author = {Liu, PY and Tang, HJ and Lee, SS and Liao, CH and Huang, CH and Kuo, HY and Sheng, WH and Taiwan Metagenomic Sequencing Microbiology Study Group, },
title = {Comparative Analysis of Microbial Detection in Traditional Culture Versus Metagenomic Next-Generation Sequencing in Patients with Periprosthetic Joint Infection: A Prospective Observational Study.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010233},
pmid = {41597751},
issn = {2076-2607},
support = {M09A7321 and MOHW113-TDU-B-211-114006//the Ministry of Health and Welfare of Taiwan/ ; NSTC 113-2321-B-002-016//the National Science and Technology Council of Taiwan/ ; },
abstract = {Identifying pathogens causing periprosthetic joint infection (PJI) is a challenge for clinicians. We aimed to evaluate the application of metagenomic next-generation sequencing (mNGS) to identify pathogens in PJI. A prospective analysis was conducted of patients diagnosed PJI between 2022 and 2024 at twelve hospitals in Taiwan. Both conventional bacterial culture (CMT) and mNGS of joint fluid and debrided tissue were performed. Demographic characteristics, laboratory results and clinical outcomes were collected. The diagnostic performance of these two methods was analyzed. A total of 42 patients with a mean age of 67.9 years were enrolled in analysis. The knee was the most common joint involved (69.1%). A high proportion of patients (78.6%) received prior antibiotics within the two weeks at sample collection. mNGS identified pathogens in 28 out of 42 patients (66.7%), whereas CMT yielded positive results in 12 out of 42 patients (28.6%) (McNemar's test, p = 0.01). Staphylococcus species was the most common genus detected (n = 11), followed by Cutibacterium (n = 4). Other detected genera included Escherichia, Mycobacterium, Enterobacter, Klebsiella (n = 2 each), Acinetobacter, and Corynebacterium (n = 1 each). Our results support the idea that mNGS could serve as a valuable diagnostic tool for PJI in addition to traditional culture methods.},
}

@article {pmid41597740,
year = {2026},
author = {Lowell, JL and Brown, L},
title = {Metals and Microbes: Microbial Community Diversity and Antibiotic Resistance in the Animas River Watershed, Colorado, USA.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010222},
pmid = {41597740},
issn = {2076-2607},
support = {RL5GM118990//NIH Building Infrastructure Leading to Diversity (BUILD) Initiative (U54)/ ; },
abstract = {Antimicrobial resistant (AMR) infections are a persistent public health issue causing excess death and economic impacts globally. Because AMR in clinical settings is often acquired from nonpathogenic bacteria that surround us, environmental surveillance must be better characterized. It has been well established that metals can co-select for bacterial AMR. Furthermore, recent studies have shown that compromised microbial community diversity may lead to community invasion by antibiotic resistance genes (ARGs). Widespread legacy mining has led to acid mine drainage and metal contamination of waterways and sediments throughout the western United States, potentially compromising microbial community diversity while simultaneously selecting for AMR bacteria. Our study objectives were to survey metal contaminated sediments from the Bonita Peak Mining District (BPMD) in southwestern Colorado, USA, compared to sites downstream in Durango, CO for bacterial and ARG diversity. Sediment bacteria were characterized using 16S rRNA Ilumina and metagenomic sequencing. We found that overall, bacterial diversity was lower in metal-contaminated, acidic sites (p = 0.04). Metagenomic sequencing revealed 31 different ARGs, with those encoding for efflux pumps (mex and spe gene families) substantially more prevalent in the BPMD sites, elucidating a specific AMR marker fingerprint from the high metal concentration sediments. Raising awareness and providing antimicrobial tracking techniques to resource limited communities could help provide information needed for better antibiotic use recommendations and environmental monitoring.},
}

@article {pmid41597738,
year = {2026},
author = {Xi, D and Zhu, F and Zhang, Z and Zhou, S and Zhang, J},
title = {Forest Type Shapes Soil Microbial Carbon Metabolism: A Metagenomic Study of Subtropical Forests on Lushan Mountain.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010220},
pmid = {41597738},
issn = {2076-2607},
support = {20232BAB205020//Jiangxi Provincial Natural Science Foundation/ ; 22-315-6-18//the Science and Technology Program of Shenyang/ ; JJXC2023010//Jiujiang City's "Xuncheng Talent" Program/ ; 20242BCC32138//Jiangxi Provincial Key Laboratory of Carbon Neutrality and Ecosystem Carbon Sinks/ ; },
abstract = {Forest type strongly influences soil microbial community composition and associated carbon cycling, yet its influence on microbial functional traits remains poorly understood. In this study, metagenomics sequencing was used to investigate soil microbial communities and carbon metabolism genes across three forest types: deciduous broadleaf (DBF), mixed coniferous-broadleaf (CBMF), and coniferous forest (CF) at two soil depths (0-20 cm and 20-40 cm) on Lushan Mountain in subtropical China. The results showed that CF exhibited higher bacterial diversity and a distinct microbial composition, with an increase in Actinomycetota and Bacteroidota and a decrease in Acidobacteriota and Pseudomonadota. The Calvin cycle was the dominant carbon fixation pathway in all forests, while the relative abundance of secondary pathways (i.e., the 3-hydroxypropionate bi-cycle and reductive citrate cycle) varied significantly with forest type. Key carbon fixation genes (sucD, pckA) were more abundant in CF and CBMF, with higher levels of rpiA/B and ackA in DBF. Functional profiling further indicated that CF soils, especially in the surface layer, were enriched in glycoside hydrolases (GHs) and carbohydrate esterases (CEs), while CBMF showed a greater potential for starch and lignin degradation. Multivariate statistical analyses identified soil available phosphorus (AP) and pH as primary factors shaping microbial community variation, with AP emerging as being the dominant regulator of carbon-related functional gene abundance. Overall, the prevalence of these distinct genetic potentials across forest types underscores how vegetation composition may shape microbial functional traits, thereby influencing the stability and dynamics of the soil carbon pool in forest ecosystem.},
}

@article {pmid41597735,
year = {2026},
author = {Moser, K and Ballif, A and Pillonel, T and Concu, M and Montenegro-Borbolla, E and Nickel, B and Stampfli, C and Ruf, MT and Audry, M and Kapel, N and Gerber, S and Jacot, D and Bertelli, C and Galpérine, T},
title = {Fecal Microbiota Transplantation Donor Screening: Is Dientamoeba fragilis a Valid Criterion for Donor Exclusion? A Longitudinal Study of a Swiss Cohort.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010217},
pmid = {41597735},
issn = {2076-2607},
support = {//internal funding at the Lausanne University Hospital (CHUV)/ ; grant number 51NF40 180575//he salaries of K.M. and E.M.-B. were supported as a part of NCCR Microbiomes, a National Centre of Competence in Research, funded by the Swiss National Science Foundation/ ; },
abstract = {Dientamoeba fragilis is a protozoan of the human digestive tract, yet its transmission and pathogenic role remain poorly understood. This study aimed to evaluate its impact on the efficacy and safety of fecal microbiota transplantation (FMT) in treating recurrent Clostridioides difficile infection (rCDI). This longitudinal cohort study analyzed stool samples from FMT donors and recipients pre-treatment and at 2 and 8 weeks post-FMT. All samples were retrospectively tested using real-time PCR. Shotgun metagenomics was also performed on selected donor-recipient pairs to explore transmission. CDI cure rates, gastrointestinal adverse events (AEs), and serious adverse events (SAEs) were assessed prospectively. A total of 53 FMT were analyzed (179 samples), with 23 (43%) derived from D. fragilis-positive donor stool (4 of 10 donors, 40%). Four of 52 recipients (18.2%), initially negative and who received treatment from positive donors, tested positive post-FMT. Shotgun metagenomics could not definitely confirm transmission due to the lack of a good reference genome. No significant differences in efficacy, AE, or SAE were observed between FMT from D. fragilis-positive versus -negative donors, even in immunocompromised patients. No SAEs were attributed to FMT. D. fragilis may be transmitted via FMT without evidence of short-term clinical impact. Consequently, RT-PCR detection should be interpreted cautiously in the context of donor exclusion decisions.},
}

@article {pmid41597726,
year = {2026},
author = {Lee, HJ and Park, SH and Han, SY and Lee, JH and Kim, DU and Seo, HI},
title = {Differences in the Biliary Microbiome Between Biliary Tract Cancer and Benign Biliary Disease.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010208},
pmid = {41597726},
issn = {2076-2607},
support = {202100350001//Biomedical Research Institute, Pusan National University Hospital/ ; },
abstract = {Bile contains many bacteria that can contribute to various diseases. Therefore, identifying bile microbiome differences between benign and malignant conditions is essential. In this study, bile samples were collected aseptically from 141 patients with biliary tract cancer (BTC) or benign biliary diseases (BBDs) who underwent endoscopic retrograde cholangiopancreatography or biliary tract surgery. Quality control PCR was performed to amplify the V3-V4 region of the bacterial 16S rRNA gene. Metagenomic sequencing of bile was successfully performed in 35 of 56 samples collected from patients with BTC and 24 of 85 samples from patients with BBD. The mean alpha diversity values comprised 2.788 ± 2.833 and 2.319 ± 1.355 in the BBD and BTC groups, respectively (p = 0.399). The bacterial species (4.7%) were shared between groups, whereas 12.3% and 83% were indicated to patients with BTC and BBD, respectively. Bacteroides coprocola, Prevotella copri, and Bacteroides plebeius were more frequently identified in the bile of patients with BTC, whereas Bacteroides vulgatus and Bacteroides uniformis were more abundant in the bile of patients with BBD. Distinct patterns of microorganism abundance between the two groups of patients suggest association of bile microbiome with disease status, so its diagnostic potential should be validated in further studies.},
}

@article {pmid41597714,
year = {2026},
author = {Isgandarov, I and Abilda, Z and Kanat, R and Daurov, D and Sapakhova, Z and Daurova, A and Zhambakin, K and Volkov, D and Begaly, A and Shamekova, M},
title = {Long-Read Metagenomics Profiling for Identification of Key Microorganisms Affected by Heavy Metals at Technogenic Zones.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010196},
pmid = {41597714},
issn = {2076-2607},
support = {BR24992837//Ministry of Agriculture of the Republic of Kazakhstan/ ; },
abstract = {Heavy metal pollution poses a serious threat to soil ecosystems worldwide, as long-term exposure can alter microbial community functioning and reduce overall ecosystem resilience. This study investigated the impact of heavy metal contamination in technogenic industrial areas of the East Kazakhstan Region on soil microbial communities. Soil samples were collected for chemical and metagenomic analyses. Concentrations of Zn, Pb, Cu, and Cd were quantified by flame atomic absorption spectrometry (FAAS). Using long-read whole-metagenome nanopore sequencing, we conducted strain-level profiling of soils with different levels of metal contamination. This approach provided high-resolution taxonomic data, enabling detailed characterization of microbial community structure. Heavy metal exposure did not significantly reduce microbial diversity or richness but influences the quality of community composition. Metal-resistant taxa dominated contaminated soils. Overall, the results highlight the value of long-read sequencing for resolving strain-level responses to environmental contamination.},
}

@article {pmid41597701,
year = {2026},
author = {Mollova, D and Baev, V and Borisova, T and Rusinova, M and Iliev, I},
title = {A Metagenomic Comparison of the Colostrum Microbiome in Bulgarian Mothers by Delivery Mode: A Pilot Study.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010184},
pmid = {41597701},
issn = {2076-2607},
support = {KP-06-M81/6//Bulgarian Science Fund/ ; },
abstract = {Colostrum harbors a highly diverse microbial community, predominantly composed of genera such as Staphylococcus, Streptococcus, Lactobacillus, Bifidobacterium, and Enterococcus. The composition and diversity of this microbiota are influenced by maternal factors-including age, body mass index, lactation activity, stress levels, and gestational diabetes-as well as external factors such as mode of delivery, antibiotic exposure, diet, and geographic location. This microbial community plays a critical role in maternal and neonatal health by contributing to early gut colonization, supporting digestion, promoting immune system development, and protecting against pathogenic microorganisms through mechanisms such as antimicrobial peptide production by lactic acid bacteria. The primary aim of this study was to evaluate the impact of mode of delivery on colostrum microbiota by comparing mothers who delivered vaginally with those who underwent cesarean section. Colostrum samples from 15 mothers were subjected to DNA extraction, high-throughput sequencing, and bioinformatic analyses to characterize microbial composition and predicted functional profiles. Although substantial inter-individual variability was observed, no statistically significant differences were detected in overall microbial diversity or community structure between the two delivery groups. However, distinct bacterial taxa and functional characteristics were identified that were specific to each mode of delivery, suggesting subtle delivery-related influences on colostrum microbiota composition.},
}

@article {pmid41597665,
year = {2026},
author = {Khachatryan, A and Vardanyan, A and Zhang, R and Zhang, Y and Shi, X and Willscher, S and Nguyen, NHA and Vardanyan, N},
title = {Metagenome Insights into Armenian Acid Mine Drainage: A Novel Thermoacidophilic Iron-Oxidizing Bacterium with Perspectives for Copper Bioleaching.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010146},
pmid = {41597665},
issn = {2076-2607},
support = {22rl-031//Higher Education Science Committee of Armenia/ ; 23-YSIP-012//Higher Education Science Committee of Armenia/ ; },
abstract = {The microbial ecology of acid mine drainage (AMD) systems in Armenia, with a long mining history, remains unexplored. This study aimed to characterize the microbial diversity and functional potential of AMD in the Syunik region and to isolate novel microorganisms with biotechnological value. A comprehensive analysis of the microbial communities' structure of Kavart abandoned, Kapan exploring mines effluent, and Artsvanik tailing was conducted. Metagenomics revealed bacterial-dominated communities, comprising Pseudomonadota (previously "Proteobacteria") (68-72%), with site-specific variations in genus abundance. A high abundance and diversity of metal resistance genes (MRGs), particularly for copper and arsenic, were identified. Carbohydrate-active enzyme (CAZy) analysis showed a dominance of GT2 and GT4 genes, suggesting a high potential for extracellular polymeric substances (EPS) production and biofilm formation. A novel strain of iron-oxidizing bacteria Arm-12 was isolated that shares only ~90% similarity with known Leptospirillum type species, indicating it may represent a new genus without culturable representatives. The strain exhibits enhanced copper extraction from concentrate. This study provides the first metagenomic insights into Armenian AMD systems and tailing, revealing a unique community rich in metal resistance and biofilm-forming genes. The isolation of a novel highly effective iron-oxidizer Arm-12 highlights the potential of AMD environments as a source of novel taxa with significant applications in biomining and bioremediation processes.},
}

@article {pmid41597664,
year = {2026},
author = {Liepa, E and Ustinova, M and Gudra, D and Roga, A and Kalnina, I and Dejus, B and Dejus, S and Strods, M and Tomsone, LE and Kibilds, J and Bartkevics, V and Berzins, A and Dumpis, U and Juhna, T and Fridmanis, D},
title = {Urban Wastewater Metagenomics Reveals the Antibiotic Resistance Gene Distribution Across Latvian Municipalities.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010145},
pmid = {41597664},
issn = {2076-2607},
support = {VPP-COVID-2020/1-0008//Latvian Council of Science/ ; No.5.2.1.1.i.0/2/24/I/CFLA/001//CFLA/ ; },
abstract = {Antimicrobial resistance (AMR) poses a global health threat, with urban wastewater systems serving as key reservoirs for resistance dissemination. This study aimed to investigate the relationships among urban environments, bacterial communities, and AMR patterns, and evaluate the specific municipal-scale drivers of resistance gene distribution. Shotgun metagenomic analysis was conducted on 45 wastewater samples collected from 15 municipalities across Latvia to determine the composition of the resistome and its correlation with local factors. The analysis identified 417 distinct antibiotic resistance genes (ARGs) belonging to 108 families, with geographic location serving as the primary driver of ARG distribution, which explained 65.87% of community variation (p = 0.001). Local industrial factors demonstrated significant effects, with food industry wastewater significantly influencing both bacterial taxonomy and ARG profiles (p < 0.05). While the presence of a regional hospital did not shape the overall municipal resistome, hospital-associated wastewater showed 19 overlapping ARGs, including clinically critical carbapenemases. Municipal wastewater systems function as geographically structured reservoirs of AMR that are shaped by localized industrial and healthcare outputs. These findings support wastewater-based AMR surveillance as a valuable tool for tracking specific resistance sources.},
}

@article {pmid41597613,
year = {2026},
author = {Jarrín-V, P and Carrión-Olmedo, JC and Loján, P and Reyes-Barriga, D and Lara, M and Oña, A and Quiroz-Moreno, C and Castillejo, P and Tenea, GN and Díaz, M and Monfort-Lanzas, P and Molina, CA},
title = {Predicted Bacterial Metabolic Landscapes of the Sumaco Volcano: A Picrust2 Analysis of 16S rRNA Data from Amazonian Ecuador.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010094},
pmid = {41597613},
issn = {2076-2607},
support = {NA//National Institute of Biological Resources (NIBR) and the Korea International Cooperation Agency (KOICA) of the Republic of Korea/ ; },
abstract = {The Sumaco volcano in Ecuador, which has a distinct geological origin from the Andes and is located in the Amazon basin, offers an opportunity to study untouched microbiomes. We explored comparative patterns of abundance from predicted functional profiling in soil samples collected along the elevation and sulfur gradients on its slopes. Using 16S rRNA gene metabarcoding, we inferred metagenome functional profiles, contrasting sample groups by altitude or soil sulfur concentration. We inferred that high-altitude communities may have higher predicted abundance for anaerobic metabolism (crotonate fermentation), coenzyme B12 synthesis, and degradation of diverse carbon sources (sugars and octane). High-sulfur soils were associated with an inferred enrichment of pathways for degrading complex organic compounds and nitrogen metabolism, reflecting adaptation to unique geochemical conditions. In contrast, low-sulfur soils are consistent with a higher predicted abundance of glycerol degradation. Within the limitation imposed by the potential weak associations of the applied predicted functional profiling to actual gene content, we propose that the inferred metabolic changes represent different ecological strategies for resource acquisition, energy generation, and stress tolerance, and they are optimized for varying conditions in this unique volcanic ecosystem. Our findings highlight how environmental gradients shape soil microbiome functional diversity and offer insights into microbial adaptation in Sumaco's exceptional geochemistry within the Amazon. Further efforts linking functional predictions back to specific taxa will offer a complete ecological perspective of the microbiome exploration in the Sumaco volcano.},
}

@article {pmid41597576,
year = {2025},
author = {Wang, L and Zhao, Y},
title = {The Response of Substrate Microbial Communities to the Addition of Mineral Nutrients During the Growth Period of Straw Mushroom Volvariella volvacea.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010056},
pmid = {41597576},
issn = {2076-2607},
support = {No. 2024YFD1200204//National Key R&D Program of China/ ; No. 21N51900500//Shanghai Committee of Science and Technology/ ; 2020-02-08-00-12-F01479//Shanghai Agricultural Commission Program/ ; KFKT2023-03//the Shanghai Key Laboratory of Agricultural Genetics and Breeding/ ; },
abstract = {Volvariella volvacea were grown on an abandoned cotton-based substrate, which was divided into two conditions: a group with added nutrients (N3P3) and a control group (CK). Using metagenomic sequencing technology, the study investigated the effect of nutrient addition during the growth process of V. volvacea on the microbial community and metabolic pathways of the substrate. The study found that the main bacteria in the N3P3 group were Proteus and Microsporidium, while in the CK group, Bacillus marinosus and Microsporidium globosa were more common. At all stages of V. volvacea growth, Proteobacteria and Firmicutes dominated. Metabolic function analysis showed that the N3P3 group significantly increased amino acid metabolism, nitrogen metabolism, genetic information processing, and cellular processes, while reducing the contents of pathogenic and saprophytic symbiotic fungi. Nitrogen metabolism, phosphorus metabolism, and carbon metabolism were closely related to the growth of V. volvacea, and nutrient addition significantly improved microbial community diversity and metabolic levels, which can be used as a substrate optimization formula. This is of great significance for the development of sustainable agriculture.},
}

@article {pmid41597535,
year = {2025},
author = {Wang, Y and Liu, S and Zheng, Z and Ma, J and Xiang, Y and Wu, L and Ding, C and Shi, Y},
title = {Deciphering the Structure and Genetic Basis of Adaptive Mechanism of Soil Microbial Communities in a Manganese Electrolysis Plant.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010015},
pmid = {41597535},
issn = {2076-2607},
support = {QKHJCZK [2021] 224//Science and Technology Program of Guizhou Province/ ; QKHCG [2023] ZD008//Guizhou Provincial Science and Technology Projects/ ; No. [2023] 026//Guizhou Key Laboratory of Green Metallurgy and Process Strengthening/ ; No. [2023] 70//Science and Technology Major Project of Tongren/ ; },
abstract = {The development of China's manganese (Mn) industries has caused severe water and soil pollution, threatening ecological and human health. Microbes are usually regarded as an important indicator of environmental pollution assessment. However, the current understanding of microbial community characteristics and their formation mechanisms in Mn production areas remains limited. In order to address this, soil properties and microbial structural characteristics across different functional zones in a typical Mn electrolysis plant in China's "Manganese Triangle" were investigated via metagenomic sequencing. Results showed soil Mn levels significantly exceeded background values, indicating high environmental risk. Acidobacteria and Proteobacteria were dominant phyla. Microbial abundance was lowest in the adjacent natural reservoir, whereas diversity was highest in the sewage treatment plant. Correlation analyses identified Mn, nitrate nitrogen, ammonium nitrogen, pH, and moisture as key environmental drivers, with Mn being the primary one. Metagenomic analysis revealed abundant Mn resistance genes, enabling microbial survival under high Mn stress. This study demonstrated that excessive Mn exposure enriched Mn-resistant genes, thereby shaping unique microbial communities dominated by Mn-resistant bacteria. These findings clarified the structural characteristics and adaptive mechanisms of soil microbial communities in Mn-contaminated areas, providing a theoretical basis for ecological risk management and bioremediation.},
}

@article {pmid41597231,
year = {2026},
author = {Feng, Y and Geng, Y and Liu, S and Huang, X and Mou, C and Zhao, H and Zhou, J and Li, Q and Deng, Y},
title = {Overwinter Syndrome in Grass Carp (Ctenopharyngodon idellus) Links Enteric Viral Proliferation to Mucosal Disruption via Multiomics Investigation.},
journal = {Cells},
volume = {15},
number = {2},
pages = {},
doi = {10.3390/cells15020157},
pmid = {41597231},
issn = {2073-4409},
support = {2024YFD2401102//National Key R&D ProgramNational Key R&D Program/ ; 2025ZNSFSC1081//Sichuan Provincial Natural Science Foundation/ ; NKYRCZX2025031//Research Initiation Funding from the Sichuan Academy of Agricultural Sciences/ ; SCCXTD-2025-15//Sichuan Freshwater Fish Innovation Team of the National Modern Agricultural Industrial Technology System/ ; },
mesh = {Animals ; *Carps/virology/microbiology ; *Fish Diseases/virology/microbiology/genetics ; *Intestinal Mucosa/virology/pathology/microbiology ; Gastrointestinal Microbiome ; Metagenomics ; Transcriptome ; Multiomics ; },
abstract = {Overwinter Syndrome (OWS) affects grass carp (Ctenopharyngodon idellus) aquaculture in China, causing high mortality and economic losses under low temperatures. Failure of antibiotic therapies shows limits of the 'low-temperature-pathogen' model and shifts focus to mucosal barrier dysfunction and host-microbiome interactions in OWS. We compared healthy and diseased grass carp collected from the same pond using histopathology, transcriptomics, proteomics, and metagenomics. This integrated approach was used to characterize intestinal structure, microbial composition, and host molecular responses at both taxonomic and functional levels. Results revealed a three-layer barrier failure in OWS fish: the physical barrier was compromised, with structural damage and reduced mucosal index; microbial dysbiosis featured increased richness without changes in diversity or evenness, and expansion of the virobiota, notably uncultured Caudovirales phage; and mucosal immune dysregulation indicated loss of local immune balance. Multi-omics integration identified downregulation of lysosome-related and glycosphingolipid biosynthesis pathways at transcript and protein levels, with disrupted nucleotide metabolism. Overall gut microbial richness, rather than individual taxa abundance, correlated most strongly with host gene changes linked to immunity, metabolism, and epithelial integrity. Although biological replicates were limited by natural outbreak sampling, matched high-depth multi-omics datasets provide exploratory insights into OWS-associated intestinal dysfunction. In summary, OWS entails a cold-triggered breakdown of intestinal barrier integrity and immune homeostasis. This breakdown is driven by a global restructuring of the gut microbiome, which is marked by increased richness, viral expansion, and functional shifts, ultimately resulting in altered host-microbe crosstalk. This ecological perspective informs future mechanistic and applied studies for disease prevention.},
}

Animals
*Carps/virology/microbiology
*Fish Diseases/virology/microbiology/genetics
*Intestinal Mucosa/virology/pathology/microbiology
Gastrointestinal Microbiome
Metagenomics
Transcriptome
Multiomics

@article {pmid41597216,
year = {2026},
author = {Mamun, MAA and Rakib, A and Mandal, M and Li, W and Miller, DD and Chen, H and Nagarkatti, M and Nagarkatti, P and Singh, UP},
title = {VERU-111 Promotes an Anti-Tumor Response Through Restoration of Gut Microbial Homeostasis and Associated Metabolic Dysregulation.},
journal = {Cells},
volume = {15},
number = {2},
pages = {},
doi = {10.3390/cells15020141},
pmid = {41597216},
issn = {2073-4409},
support = {AI140405//National Institute of Allergy and Infectious Diseases/ ; },
mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; Mice ; *Homeostasis/drug effects ; *Colorectal Neoplasms/drug therapy/microbiology/metabolism/pathology ; RNA, Ribosomal, 16S/genetics ; Mice, Inbred C57BL ; Azoxymethane ; Dextran Sulfate ; *Antineoplastic Agents/pharmacology ; Male ; Humans ; },
abstract = {The rising global burden of colorectal cancer (CRC) has now positioned it as the third most common cancer worldwide. Chemotherapy regimens are known to disrupt the composition of the gut microbiota and lead to long-term health consequences for cancer patients. However, the alteration of gut microbiota by specific chemotherapeutic agents has been insufficiently explored until now. The purpose of this study was to assess changes in the gut microbiota following treatment with VERU-111 as a chemotherapy agent for the treatment of CRC. We thus performed a metagenomic study using 16S rRNA gene amplicon sequencing of fecal samples from different experimental groups in the azoxymethane (AOM) and dextran sodium sulfate (DSS)-induced murine model of CRC. To predict the functional potential of microbial communities, we used the resulting 16S rRNA gene sequencing data to perform Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. We found that the administration of VERU-111 led to a restructured microbial community that was characterized by increased alpha and beta diversity. Compared to the mice treated with DSS alone, VERU-111 treatment significantly increased the relative abundance of several bacterial species, including Verrucomicrobiota species, Muribaculum intestinale, Alistipes finegoldii, Turicibacter, and the well-known gut-protective bacterial species Akkermansia muciniphila. The relative abundance of Ruminococcus, which is negatively correlated with immune checkpoint blockade therapy, was diminished following VERU-111 administration. Overall, this metagenomic study suggests that the microbial shift after administration of VERU-111 is associated with suppression of several metabolic and cancer-related pathways that might, at least in part, facilitate the suppression of CRC. These favorable shifts in gut microbiota suggest a novel therapeutic dimension of using VERU-111 to treat CRC and emphasize the need for further mechanistic exploration.},
}

*Gastrointestinal Microbiome/drug effects
Animals
Mice
*Homeostasis/drug effects
*Colorectal Neoplasms/drug therapy/microbiology/metabolism/pathology
RNA, Ribosomal, 16S/genetics
Mice, Inbred C57BL
Azoxymethane
Dextran Sulfate
*Antineoplastic Agents/pharmacology
Male
Humans

@article {pmid41596861,
year = {2026},
author = {Iturritxa, E and Mesanza, N and Torija, MJ},
title = {Wild Yeasts as Reservoirs of Bacterial Diversity: Biotechnological Insights from 16S rRNA Metabarcoding.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {2},
pages = {},
doi = {10.3390/foods15020262},
pmid = {41596861},
issn = {2304-8158},
abstract = {Recently acquired evidence indicates that bacteria can utilise yeasts as survival niches. This study investigated the presence of hidden, intracellular bacteria (endobacteria) within wild yeasts collected from natural ecosystems and evaluated whether biotechnological processes influenced these bacterial communities. We examined the microbiotas of 28 axenic cultures of wild yeasts; these were selected due to their potential brewing and biocontrol uses and were isolated from habitats associated with Quercus and Vitis. We also analysed the microbiotas present after these strains were used to ferment beer wort. Bacterial communities were characterised using 16S rRNA gene amplicon metagenomics. The results indicate that yeast strains and their endobacterial partners have coevolved, and their compositions are shaped by the environmental conditions. Substantial bacterial diversity was detected across strains in both axenic cultures and post-fermentation samples. The ecological origin of the yeast (oak- or grape-associated) did not significantly affect the endobacterial community structure. Across all samples, the dominant phyla were Proteobacteria, Actinobacteria, Firmicutes, and Cyanobacteria, with Proteobacteria representing over 90% of sequences. Most bacterial genera were shared between axenic and fermentation conditions. However, Escherichia and Comamonas predominated in axenic cultures, while Parvibaculum dominated after fermentation. These findings suggest that yeasts constitute stable microhabitats for bacterial communities, and their relative abundances can shift during fermentation processes.},
}

@article {pmid41596857,
year = {2026},
author = {Tsouggou, N and Korozi, E and Pemaj, V and Drosinos, EH and Kapolos, J and Papadelli, M and Skandamis, PN and Papadimitriou, K},
title = {Advances in Shotgun Metagenomics for Cheese Microbiology: From Microbial Dynamics to Functional Insights.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {2},
pages = {},
doi = {10.3390/foods15020259},
pmid = {41596857},
issn = {2304-8158},
abstract = {The cheese microbiome is a complex ecosystem strongly influenced by both technological practices and the processing environment. Moving beyond traditional cultured-based methods, the integration of shotgun metagenomics into cheese microbiology has enabled in-depth resolution of microbial communities at the species and strain levels. The aim of the present study was to review recent applications of shotgun metagenomics in cheese research, underscoring its role in tracking microbial dynamics during production and in discovering genes of technological importance. In addition, the review highlights how shotgun metagenomics enables the identification of key metabolic pathways, including amino acid catabolism, lipid metabolism, and citrate degradation, among others, which are central to flavor formation and ripening. Results of the discussed literature demonstrate how microbial composition, functional traits, and overall quality of cheese are determined by factors such as raw materials, the cheesemaking environment, and artisanal practices. Moreover, it highlights the analytical potentials of shotgun metagenomics, including metagenome-assembled genomes (MAGs) reconstruction, characterization of various genes contributing to flavor-related biosynthetic pathways, bacteriocin production, antimicrobial resistance, and virulence, as well as the identification of phages and CRISPR-Cas systems. These insights obtained are crucial for ensuring product's authenticity, enabling traceability, and improving the assessment of safety and quality. Despite shotgun metagenomics' advantages, there are still analytical restrictions concerning data handling and interpretation, which need to be addressed by importing standardization steps and moving towards integrating multi-omics approaches. Such strategies will lead to more accurate and reproducible results across studies and improved resolution of active ecosystems. Ultimately, shotgun metagenomics has shifted the field from descriptive surveys to a more detailed understanding of the underlying mechanisms shaping the overall quality and safety of cheese, thus bringing innovation in modern dairy microbiology.},
}

@article {pmid41596659,
year = {2026},
author = {Sánchez-Recillas, E and Almanza-Aguilera, E and Bars-Cortina, D and Zamora-Ros, R and Godínez-Santillán, RI and Sánchez-Tusié, AA and Vergara-Castañeda, HA},
title = {Effect of Garambullo (Myrtillocactus geometrizans) Consumption on the Intestinal Microbiota Profile in an Early-Phase Rat Model of Colon Cancer.},
journal = {International journal of molecular sciences},
volume = {27},
number = {2},
pages = {},
doi = {10.3390/ijms27021014},
pmid = {41596659},
issn = {1422-0067},
support = {1560335//Secretaría de Ciencia, Humanidades, Tecnología e Innovación/ ; FME202404//Autonomous University of Queretaro - FONFIVE/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Colonic Neoplasms/microbiology/chemically induced/pathology/drug therapy ; Male ; Rats ; Rats, Sprague-Dawley ; Disease Models, Animal ; Azoxymethane ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Dextran Sulfate ; *Plant Extracts/pharmacology ; Bacteria/genetics/classification ; },
abstract = {Bioactive compounds in food contribute to reducing the risk of developing colon cancer by modulating the gut microbiota. We have recently demonstrated that garambullo (Myrtillocactus geometrizans), an endemic fruit of Mexico rich in bioactive compounds, attenuates aberrant crypt foci in an animal model. However, its potential to modulate the gut microbiota is unknown. The main objective of this study was to evaluate whether its consumption modulates colon carcinogenesis by altering the microbiota in an in vivo model induced by azoxymethane and dextran sulfate sodium (AOM/DSS). Fecal samples were collected from twelve male Sprague-Dawley rats and analyzed for microbiota composition after 0, 8, and 16 weeks of treatment with saline (control), AOM/DSS, garambullo (G), or residue of garambullo (RG) with AOM/DSS (G+AOM/DSS and RG+AOM/DSS, respectively). Characterization of the microbiome was based on the conserved region of the 16S rRNA V3-V4 gene, and analyzed by the ZymoBIOMICS' Targeted Metagenomics Sequencing (Zymo Research) service. In an animal model induced with AOM/DSS for 8 weeks, consumption of G and its residue increased the bacterial genera Shuttleworthiia, Subdoligranulum, Lactobacillus, Faecalibacterium, and Alloprevotella (p < 0.05). Consumption of G and its residue allowed the proliferation of bacteria that produce short-chain fatty acids and are associated with protective mechanisms of the colon.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Colonic Neoplasms/microbiology/chemically induced/pathology/drug therapy
Male
Rats
Rats, Sprague-Dawley
Disease Models, Animal
Azoxymethane
Feces/microbiology
RNA, Ribosomal, 16S/genetics
Dextran Sulfate
*Plant Extracts/pharmacology
Bacteria/genetics/classification

@article {pmid41596633,
year = {2026},
author = {Tamayo-Ordóñez, YJ and Rosas-García, NM and Bello-López, JM and Tamayo-Ordóñez, MC and Tamayo-Ordóñez, FA and Calzada-Mendoza, CC and Ayil-Gutiérrez, BA},
title = {A Possible Recently Identified Evolutionary Strategy Using Membrane-Bound Vesicle Transfer of Genetic Material to Induce Bacterial Resistance, Virulence and Pathogenicity in Klebsiella oxytoca.},
journal = {International journal of molecular sciences},
volume = {27},
number = {2},
pages = {},
doi = {10.3390/ijms27020988},
pmid = {41596633},
issn = {1422-0067},
mesh = {Gene Transfer, Horizontal ; *Klebsiella oxytoca/genetics/pathogenicity ; Virulence/genetics ; Phylogeny ; Evolution, Molecular ; Virulence Factors/genetics ; Genome, Bacterial ; Klebsiella Infections/microbiology ; *Drug Resistance, Bacterial/genetics ; Humans ; COVID-19 ; },
abstract = {Klebsiella oxytoca has emerged as an important opportunistic pathogen in nosocomial infections, particularly during the COVID-19 pandemic, due to its capacity to acquire and disseminate resistance and virulence genes through horizontal gene transfer (HGT). This study presents a genome-based comparative analysis of K. oxytoca within the genus Klebsiella, aimed at exploring the evolutionary plausibility of outer membrane vesicle (OMV) associated processes in bacterial adaptation. Using publicly available reference genomes, we analyzed pangenome structure, phylogenetic relationships, and the distribution of mobile genetic elements, resistance determinants, virulence factors, and genes related to OMV biogenesis. Our results reveal a conserved set of envelope associated and stress responsive genes involved in vesiculogenic pathways, together with an extensive mobilome and resistome characteristic of the genus. Although these genomic features are consistent with conditions that may favor OMV production, they do not constitute direct evidence of functional OMV mediated horizontal gene transfer. Instead, our findings support a hypothesis generating evolutionary framework in which OMVs may act as a complementary mechanism to established gene transfer routes, including conjugation, integrative mobile elements, and bacteriophages. Overall, this study provides a genomic framework for future experimental and metagenomic investigations into the role of OMV-associated processes in antimicrobial resistance dissemination and should be interpreted as a recently identified evolutionary strategy inferred from genomic data, rather than a novel or experimentally validated mechanism.},
}

Gene Transfer, Horizontal
*Klebsiella oxytoca/genetics/pathogenicity
Virulence/genetics
Phylogeny
Evolution, Molecular
Virulence Factors/genetics
Genome, Bacterial
Klebsiella Infections/microbiology
*Drug Resistance, Bacterial/genetics
Humans
COVID-19

@article {pmid41596486,
year = {2026},
author = {Sá, L and Machado, E and Ginani, V and Timbó, R and Romiti, R and Kurizky, P and Gomes, C},
title = {Species-Level Comparative Metagenomic Analysis of the Bacterial Abundance of the Gut Microbiome in Psoriasis, Hidradenitis Suppurativa, and Pemphigus Foliaceous Patients Using Shotgun Next-Generation Sequencing.},
journal = {International journal of molecular sciences},
volume = {27},
number = {2},
pages = {},
doi = {10.3390/ijms27020838},
pmid = {41596486},
issn = {1422-0067},
support = {00193-00000279/2023-70//Fundação de Apoio à Pesquisa do Distrito Federal (FAP-DF)/ ; 445040/2023-8//National Council for Scientific and Technological Development/ ; 21/2023//Departamento de Ciência e Tecnologia, da Secretaria de Ciência, Tecnologia, Inovação e Com-plexo da Saúde, do Ministério da Saúde (Decit/SECTICS/MS)/ ; },
mesh = {Humans ; *Psoriasis/microbiology ; *Pemphigus/microbiology ; Female ; Male ; *Gastrointestinal Microbiome/genetics ; High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Middle Aged ; Adult ; *Hidradenitis Suppurativa/microbiology ; Feces/microbiology ; *Bacteria/genetics/classification ; Aged ; },
abstract = {Recent studies have revealed a specific relationship between gut bacteria and inflammatory skin profiles. We aimed to perform a species-level comparative metagenomic analysis of the gut microbiome in patients with psoriasis, hidradenitis suppurativa (HS), and pemphigus foliaceus (PF). We included omnivorous nonsmokers and nondrinkers with psoriasis (n = 24), HS (n = 10), and PF (n = 11), as well as healthy controls (n = 10). We collected faecal samples from all patients for classic parasitological analysis. Gut microbiome analysis was conducted using shotgun next-generation sequencing. We used the Deseq2, Limma_voom, LinDA, and MaAMaAsLin 2 bioinformatics tools to evaluate concordance and differential abundance between patients. Thirteen patients (23.64%) were diagnosed with active intestinal parasitosis. The presence of intestinal parasitosis was significantly related to immunosuppression (p = 0.009). The most abundant microorganism species found in the faeces of the patients evaluated was Escherichia coli. Psoriasis patients presented a greater abundance of bacteria from the Veillonellaceae family, whereas PF patients presented a greater abundance of Firmicutes bacteria. Patients with PF showed increased E. coli virulence and antibiotic resistance functional markers. Immunosuppression significantly influenced the presence of intestinal parasitosis as well as increased the virulence of functional markers in patients with PF receiving systemic corticosteroid therapy.},
}

Humans
*Psoriasis/microbiology
*Pemphigus/microbiology
Female
Male
*Gastrointestinal Microbiome/genetics
High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
Middle Aged
Adult
*Hidradenitis Suppurativa/microbiology
Feces/microbiology
*Bacteria/genetics/classification
Aged

@article {pmid41596119,
year = {2026},
author = {Patanè, GT and Moreira, RJ and Almeida-Santos, M and Putaggio, S and Barreca, D and Oliveira, PF and Alves, MG},
title = {Anthocyanins and Metabolic Disease: A New Frontier in Precision Nutrition.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {15},
number = {1},
pages = {},
doi = {10.3390/antiox15010061},
pmid = {41596119},
issn = {2076-3921},
support = {2024.03012.BD//Fundação para a Ciência e Tecnologia/ ; UIDB/50006/2020//Laboratório Associado para a Química Verde/ ; CEECINST/00026/2018//Fundação para a Ciência e Tecnologia/ ; CDL-CTTRI-267-SGRH/2022//Fundação para a Ciência e Tecnologia/ ; UIDB/04501/2020-DOI 10.54499/UIDB/04501/2020 and UIDP/04501/2020-DOI 10.54499/UIDP/04501/2020//iBiMED/ ; },
abstract = {Metabolic syndrome (MetS) represents a global health challenge mainly driven by chronic low-grade inflammation and persistent oxidative stress (OS). Current therapeutic and nutritional strategies often fail to resolve these interconnected core pathologies due to the multifactorial nature of MetS. Anthocyanins (ACNs), a class of potent dietary flavonoids, offer significant promise due to their established pleiotropic effects, including robust antioxidant activity through modulation of the Nrf2/ARE pathway, anti-inflammatory effects via NF-κB suppression, and overall support for glucose and lipid homeostasis. However, the therapeutic efficacy of ACNs is characterized by interindividual variability, which is intrinsically linked to their low systemic bioavailability. This heterogeneity in the response is due to the complex interplay between genetic polymorphisms affecting absorption, distribution, metabolism, and excretion (ADME), as well as the specific biotransformation capacity of the gut microbiome. This review proposes that achieving the full clinical potential of ACNs requires moving beyond conventional nutritional advice. We propose that precision nutrition, which integrates multi-omics data (e.g., genomics, metagenomics, and metabolomics), can determine the individual phenotype, predict functional metabolic response, and tailor safer and effective ACN-rich interventions. This integrated, multifactorial approach is essential for optimizing the antioxidant and metabolic benefits of ACNs for the prevention and management of MetS and its associated pathologies.},
}

@article {pmid41595535,
year = {2026},
author = {Ma, Y and Wang, L and Hu, H and Shieh, AR and Li, E and He, D and He, L and Liu, Z and Paing, TM and Chen, X and Cao, Y},
title = {Composition and Function of Gut Microbiome: From Basic Omics to Precision Medicine.},
journal = {Genes},
volume = {17},
number = {1},
pages = {},
doi = {10.3390/genes17010116},
pmid = {41595535},
issn = {2073-4425},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Precision Medicine/methods ; Animals ; Genomics/methods ; Probiotics ; },
abstract = {The gut microbiome is defined as the collective assembly of microbial communities inhabiting the gut, along with their genes and metabolic products. The gut microbiome systematically regulates host metabolism, immunity, and neuroendocrine homeostasis via interspecies interaction networks and inter-organ axes. Given the importance of the gut microbiome to the host, this review integrates the composition, function, and genetic basis of the gut microbiome with host genomics to provide a systematic overview of recent advances in microbiome-host interactions. This encompasses a complete technological pipeline spanning from in vitro to in vivo models to translational medicine. This technological pipeline spans from single-bacterium CRISPR editing, organoid-microbiome co-culture, and sterile/humanized animal models to multi-omics integrated algorithms, machine learning causal inference, and individualized probiotic design. It aims to transform microbiome associations into precision intervention strategies that can be targeted and predicted for clinical application through interdisciplinary research, thereby providing the cornerstone of a new generation of precision treatment strategies for cancer, metabolic, and neurodegenerative diseases.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Precision Medicine/methods
Animals
Genomics/methods
Probiotics

@article {pmid41595438,
year = {2025},
author = {Vougiouklaki, D and Letsiou, S and Ladias, K and Tsakni, A and Mavrokefalidou, I and Siateli, Z and Halvatsiotis, P and Houhoula, D},
title = {Lactobacillus-Dominated Cervical Microbiota Revealed by Long-Read 16S rRNA Sequencing: A Greek Pilot Study.},
journal = {Genes},
volume = {17},
number = {1},
pages = {},
doi = {10.3390/genes17010018},
pmid = {41595438},
issn = {2073-4425},
mesh = {Female ; Humans ; *RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Pilot Projects ; *Cervix Uteri/microbiology ; Greece ; *Lactobacillus/genetics/isolation & purification/classification ; Adult ; Middle Aged ; Vagina/microbiology ; },
abstract = {Background/Objectives: The vaginal microbiota constitutes a highly dynamic microbial ecosystem shaped by the distinct mucosal, hormonal, and immunological environment of the female genital tract. Accumulating evidence suggests that shifts in cervical microbial composition and function may influence host-microbe interactions and contribute to gynecological disease risk. Within this framework, the present study aimed to perform an in-depth genomic characterization of the cervical microbiota in a well-defined cohort of Greek women. The primary objective was to explore the functional microbial landscape by identifying dominant bacterial taxa, taxon-specific signatures, and potential microbial pathways implicated in cervical epithelial homeostasis, immune modulation, and disease susceptibility. Methods: Microbial genomic DNA was isolated from 60 cervical samples using the Magcore Bacterial Automated Kit and analyzed through full-length 16S rRNA gene sequencing using the Nanopore MinION™ platform, allowing high-resolution taxonomic assignment and enhanced functional inference. In parallel, cervical samples were screened for 14 HPV genotypes using a real-time PCR-based assay. Results: The cervical microbial communities were dominated by Lactobacillus iners, Lactobacillus crispatus, and Aerococcus christensenii, collectively representing over 75% of total microbial abundance and suggesting a functionally protective microbiota profile. A diverse set of low-abundance taxa-including Stenotrophomonas maltophilia, Stenotrophomonas pavanii, Acinetobacter septicus, Rhizobium spp. (Rhizobium rhizogenes, Rhizobium tropici, Rhizobium jaguaris), Prevotella amnii, Prevotella disiens, Brevibacterium casei, Fannyhessea vaginae, and Gemelliphila asaccharolytica-was also detected, potentially reflecting niche-specific metabolic functions or environmental microbial inputs. No HPV genotypes were detected in any of the cervical samples. Conclusions: This genomic profiling study underscores the functional dominance of Lactobacillus spp. within the cervical microbiota and highlights the contribution of low-abundance taxa that may participate in metabolic cross-feeding, immune signaling, or epithelial barrier modulation. Future large-scale, multi-omics studies integrating metagenomics and host transcriptomic data are warranted to validate microbial functional signatures as biomarkers or therapeutic targets for cervical health optimization.},
}

Female
Humans
*RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
Pilot Projects
*Cervix Uteri/microbiology
Greece
*Lactobacillus/genetics/isolation & purification/classification
Adult
Middle Aged
Vagina/microbiology

@article {pmid41595429,
year = {2025},
author = {Wu, H and Li, J and Long, J and Liao, H and Zhan, K and Chen, H and Lei, F},
title = {Enhancing Ecological Functions in Chinese Yellow Earth: Metagenomic Evidence of Microbial and Nitrogen Cycle Reassembly by Organic Amendments.},
journal = {Genes},
volume = {17},
number = {1},
pages = {},
doi = {10.3390/genes17010009},
pmid = {41595429},
issn = {2073-4425},
support = {Grants 2022YFD1901500 and 2022YFD1901505//the National Key R&D Program of China/ ; Grant U2420626//the National Natural Science Foundation of China (NSFC)/ ; },
mesh = {*Soil Microbiology ; Soil/chemistry ; *Nitrogen Cycle/genetics ; Metagenomics/methods ; Nitrogen/metabolism ; China ; Zea mays/growth & development ; Fertilizers ; *Microbiota/genetics ; Metagenome ; Bacteria/genetics/classification ; Charcoal ; },
abstract = {BACKGROUND: Chinese Yellow Earth is a key subtropical agricultural resource in southwestern China; however, its productivity is limited by acidity and poor nutrient retention. This study examined how reduced nitrogen plus organic amendments affect its soil microbial structure and maize yield.

METHODS: A field experiment with four treatments evaluated reduced nitrogen fertilization amended with rice husk plus rapeseed cake (RS) or RS with biochar (BC). Soil properties (pH, nitrogen, organic matter) and maize yield were analyzed. Metagenomic analysis (NR database) characterized microbial communities, and correlation analysis with Mantel tests identified key relationships.

RESULTS: Combined organic amendments under reduced N significantly increased soil pH, nitrogen components, and organic matter, increasing maize yield by 4.41-8.97%. Metagenomics revealed enriched beneficial genera including Sphingomonas and Bradyrhizobium. Yield positively correlated with nitrate nitrogen and a beneficial microbial cluster containing Lysobacter and Reyranella, whereas Steroidobacter negatively correlated with key fertility indicators. Mantel tests revealed nitrate nitrogen as the primary correlate of functional gene community succession.

CONCLUSIONS: This study reveals that reduced nitrogen with organic amendments promotes soil improvement and microbial modulation, demonstrating potential as a sustainable practice to maintain crop productivity in Chinese Yellow Earth. The observed trend toward yield improvement underscores its promise and warrants further validation through additional trials. Overall, the findings highlight the beneficial effects of these amendments on soil health and their role in supporting sustainable subtropical agriculture under reduced nitrogen input.},
}

*Soil Microbiology
Soil/chemistry
*Nitrogen Cycle/genetics
Metagenomics/methods
Nitrogen/metabolism
China
Zea mays/growth & development
Fertilizers
*Microbiota/genetics
Metagenome
Bacteria/genetics/classification
Charcoal

@article {pmid41594879,
year = {2026},
author = {Han, H and Yang, Y and Zhu, X and Wangdwei, M and Yang, L},
title = {Age-Specific Composition and Predicted Function of Gut Microbiota in Plateau Pikas (Ochotona curzoniae).},
journal = {Biology},
volume = {15},
number = {2},
pages = {},
doi = {10.3390/biology15020144},
pmid = {41594879},
issn = {2079-7737},
support = {202401ZR0101//Natural Science Foundation of the Xizang Autonomous Region/ ; 2021-GSP-B015//High-level Personnel Training Program of Xizang University/ ; },
abstract = {Gut microbes play a crucial role in regulating physiological processes such as host energy metabolism, nutrient absorption, and environmental adaptation. The predicted functions of gut microbes can be influenced by many factors, both extrinsic and intrinsic to the hosts. The plateau pika is a key species in the alpine ecosystem of the Qinghai-Tibet Plateau. Previous research on the plateau pika primarily examined how extrinsic factors affected its gut microbiota. However, studies on intrinsic factors are scarce. Here, we used live-trapping to capture plateau pikas and collect cecum contents. Using metagenomic sequencing of cecum content samples, we characterized and compared the gut microbial composition and predicted function of plateau pika in adult (n = 9) and juvenile (n = 9) populations. The results indicated that Bacillota and Bacteroidete were the major bacterial phyla. The core gut microbial genera were the same, but the relative abundance of Oscillospira in juveniles was significantly lower than that in adults. The changes in the proportion of cellulose-degradation-related bacterial communities in juveniles suggest that they tend to choose low-fiber diets. In this study, we found no significant differences in the gut microbial composition and diversity, KEGG level 1 metabolic pathways, or CAZy class level between adult and juvenile plateau pikas. In total, the composition and predicted functions of cecal microorganisms in juvenile and adult male plateau pikas were not different. Regarding KEGG level 2 metabolic pathways, the juvenile group had a higher relative abundance of metabolic pathways for cofactors and vitamins, terpenoids, and polyketides, whereas the adult group had a higher relative abundance of energy metabolism. However, the resulting differences remain unclear. Therefore, future research should validate the above findings on a broader spatio-temporal scale and conduct cross-species comparisons to construct a microbial ecological framework for the health management of plateau wild animals.},
}

@article {pmid41594852,
year = {2026},
author = {Zhao, Q and Li, B and Ma, J and Wei, J and Qin, W},
title = {The Gut Microbiome of the Goitered Gazelle Enables Plasticity by Responding to Environmental Factors in the Qaidam Basin.},
journal = {Biology},
volume = {15},
number = {2},
pages = {},
doi = {10.3390/biology15020118},
pmid = {41594852},
issn = {2079-7737},
support = {32160316//National Natural Science Foundation of China/ ; },
abstract = {The Qaidam Basin on the Qinghai-Tibet Plateau is an extreme arid environment, posing severe survival challenges. The goitered gazelle (Gazella subgutturosa) is a keystone species in this fragile ecosystem, yet the ecological role of its gut microbiota and its associations with environmental drivers remain poorly understood. We collected fecal samples from gazelles across seven regions of the basin. Metagenomic sequencing was employed to characterize the gut microbiome. Statistical analyses (Mantel tests, multiple regression on matrices, co-occurrence networks) were used to link microbial composition and function with key environmental factors. The gut microbiota was dominated by fiber-degrading phyla (Firmicutes, Bacteroidota) and enriched in metabolic pathways, aligning with a high-fiber diet. Regarding environmental drivers of gut microbial composition variations, isothermality and soil organic carbon were significant predictors, likely via vegetation and environmental inoculation. Regarding environmental drivers of gut microbial function variations, winter solar radiation was uniquely associated with metabolic function without altering microbial composition, suggesting a functional plasticity-the capacity to shift metabolic profiles independently of taxonomic turnover-in response to environmental variation. The gut microbiota of the goitered gazelle exhibits a stable core composition alongside environmentally responsive functional modules. This suggests the microbiome may serve as a significant mediator of host resilience, highlighting adaptation as a dynamic interplay between host, microbiome, and environment. These insights are crucial for microbiome-assisted conservation.},
}

@article {pmid41594560,
year = {2025},
author = {Dissanayaka, DMS and Jayasinghe, TN and Sohrabi, HR and Rainey-Smith, SR and Taddei, K and Masters, CL and Martins, RN and Fernando, WMADB},
title = {Gut Microbial Composition and Short-Chain Fatty Acid Metabolism in Cognitively Unimpaired Adults Stratified by Amyloid-β Status.},
journal = {Biomolecules},
volume = {16},
number = {1},
pages = {},
doi = {10.3390/biom16010018},
pmid = {41594560},
issn = {2218-273X},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Fatty Acids, Volatile/metabolism ; Female ; Male ; *Amyloid beta-Peptides/metabolism ; Aged ; Feces/microbiology/chemistry ; Middle Aged ; Alzheimer Disease/metabolism ; Cognition ; },
abstract = {Short-chain fatty acids (SCFAs) produced by gut microbial fermentation influence host metabolism and neuroinflammatory processes implicated in Alzheimer's disease (AD). However, the relationship between fecal SCFAs, microbial taxa, and cerebral amyloid-β (Aβ) burden in cognitively unimpaired individuals remains unclear. Fecal SCFAs were quantified using GC-MS, and microbial species were profiled by shotgun metagenomics in 87 participants. Associations between SCFAs, demographics, APOE ε4 status, and Aβ burden were tested using nonparametric statistics and multivariable regression. Microbial-SCFA links were evaluated using Spearman correlations and multivariate ordinations, with mediation analysis exploring potential indirect pathways. Acetate was the predominant SCFA and demonstrated the most robust microbial associations. Higher acetate concentrations were positively associated with Bacteroides ovatus and Faecalibacterium prausnitzii, whereas lower acetate levels were linked to species such as Bifidobacterium animalis and Lachnoclostridium scindens. Stratified analyses indicated that individuals with elevated Aβ burden exhibited more pronounced species-SCFA relationships, including a notable association between Bacteroides thetaiotaomicron and butyrate. Multivariate ordination further identified a significant overall coupling between SCFA profiles and microbial community structure. Mediation analysis suggested that an Oscillospiraceae species may represent a potential intermediary linking valerate concentrations with Aβ status. SCFA concentrations were not strongly influenced by demographic or genetic factors, but specific species demonstrated robust associations with acetate levels. Distinct SCFA-microbial interaction patterns in Aβ High individuals suggest subtle early gut microbial alterations linked to amyloid burden. These findings highlight the potential role of SCFA-related microbial pathways in preclinical AD.},
}

Humans
*Gastrointestinal Microbiome
*Fatty Acids, Volatile/metabolism
Female
Male
*Amyloid beta-Peptides/metabolism
Aged
Feces/microbiology/chemistry
Middle Aged
Alzheimer Disease/metabolism
Cognition

@article {pmid41594301,
year = {2026},
author = {Camatti, J and Bonasoni, MP and Santunione, AL and Cecchi, R and Radheshi, E and Carretto, E},
title = {Postmortem Microbiology in Forensic Diagnostics: Interpretation of Infectious Causes of Death and Emerging Applications.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {16},
number = {2},
pages = {},
doi = {10.3390/diagnostics16020325},
pmid = {41594301},
issn = {2075-4418},
abstract = {Background/Objectives: Postmortem microbiology has traditionally been regarded with caution in forensic practice due to concerns related to contamination, bacterial translocation, and postmortem microbial overgrowth. As a result, microbiological findings obtained after death have often been considered unreliable or of limited diagnostic value. However, growing evidence indicates that, when appropriately interpreted and integrated with autopsy findings, histopathology, and circumstantial information, postmortem microbiology can provide crucial support for cause-of-death determination. This narrative review critically examines the current role of postmortem microbiology in forensic diagnostics, with a focus on its diagnostic applications, interpretative challenges, and future perspectives. Methods/Results: The transition from conventional culture-based techniques to molecular approaches-including polymerase chain reaction, microbiome analysis, and metagenomic methods-is discussed, highlighting both their potential advantages and inherent limitations within the forensic setting. Particular attention is devoted to key interpretative issues such as postmortem interval, sampling strategies, contamination, and bacterial translocation. In addition to cause-of-death attribution, emerging applications-including postmortem interval estimation, trace evidence analysis, and artificial intelligence-based models-are reviewed. Although these approaches show promising research potential, their routine forensic applicability remains limited by methodological heterogeneity, lack of standardization, and interpretative complexity. Conclusions: In conclusion, postmortem microbiology represents a valuable diagnostic tool when applied within a multidisciplinary forensic framework. Its effective use requires cautious interpretation and integration with pathological and contextual evidence, avoiding standalone or automated conclusions. Future progress will depend on standardized methodologies, multidisciplinary collaboration, and a clear distinction between experimental research and routine forensic practice.},
}

@article {pmid41594136,
year = {2026},
author = {Kitano, T and Matsunaga, N and Akiyama, T and Azuma, T and Fujii, N and Tsukada, A and Hibino, H and Kuroda, M and Ohmagari, N},
title = {Environmental Dissemination of Antimicrobial Resistance: A Resistome-Based Comparison of Hospital and Community Wastewater Sources.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {1},
pages = {},
doi = {10.3390/antibiotics15010099},
pmid = {41594136},
issn = {2079-6382},
support = {JP22fk0108131//Japan Agency for Medical Research and Development/ ; JP25fk0108666//Japan Agency for Medical Research and Development/ ; },
abstract = {Background/Objectives: Comparative analysis of antimicrobial resistomes in hospital and community wastewater can provide valuable insights into the diversity and distribution of antimicrobial resistance genes (ARGs), contributing to the advancement of the One Health approach. This study aimed to characterize and compare the resistome profiles of wastewater sources from a hospital and community. Methods: Longitudinal metagenomic analysis was conducted on wastewater samples collected from the National Center for Global Health and Medicine (hospital) and a shopping mall (community) in Tokyo, Japan, between December 2019 and September 2023. ARG abundance was quantified using reads per kilobase per million mapped reads (RPKM) values, and comparative analyses were performed to identify the significantly enriched ARGs in the two sources. Results: A total of 46 monthly wastewater samples from the hospital yielded 825 unique ARGs, with a mean RPKM of 2.5 across all detected genes. In contrast, 333 ARGs were identified in the three shopping mall wastewater samples, with a mean RPKM of 2.1. Among the ARGs significantly enriched in the hospital samples, 23, including genes conferring resistance to aminoglycosides (nine groups) and β-lactam antibiotics (eight groups), exhibited significantly high RPKM values. No ARGs were found to be significantly enriched in the community wastewater samples. Conclusions: This study highlights the higher diversity and abundance of ARGs, particularly those conferring resistance to aminoglycosides and β-lactam antibiotics including carbapenems, in hospital wastewater than in community wastewater. These findings underscore the importance of continuous resistome monitoring of hospital wastewater as part of the integrated One Health surveillance strategy.},
}

@article {pmid41594088,
year = {2026},
author = {Soto-López, JD and Velásquez-González, O and Barrios-Izás, MA and Belhassen-García, M and Muñoz-Bellido, JL and Fernández-Soto, P and Muro, A},
title = {Metagenomic Comparison of Bat Colony Resistomes Across Anthropogenic and Pristine Habitats.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {1},
pages = {},
doi = {10.3390/antibiotics15010051},
pmid = {41594088},
issn = {2079-6382},
abstract = {BACKGROUND/OBJECTIVES: The mammalian microbiota constitutes a reservoir of antimicrobial resistance genes (ARGs), which can be shaped by environmental and anthropogenic factors. Although bat-associated bacteria have been reported to harbor diverse ARGs globally, the ecological and evolutionary determinants driving this diversity remain unclear.

METHODS: To characterize ARG diversity in wildlife exposed to contrasting levels of human influence, we analyzed homologs of resistance mechanisms from the Comprehensive Antibiotic Resistance Database in shotgun metagenomes of bat guano. Samples were collected from a colony exposed to continuous anthropogenic activity in Spain (Salamanca) and from a wild, non-impacted bat community in China (Guangdong). Metagenomic analyses revealed marked differences in taxonomic and resistome composition between sites.

RESULTS: Salamanca samples contained numerous hospital-associated genera (e.g., Mycobacterium, Staphylococcus, Corynebacterium), while Guangdong was dominated by Lactococcus, Aeromonas, and Stenotrophomonas. β-lactamases and MurA transferase homologs were the most abundant ARGs in both datasets, yet Salamanca exhibited higher richness and functional diversity (median Shannon index = 1.5; Simpson = 0.8) than Guangdong (Shannon = 1.1; Simpson = 0.66). Salamanca also showed enrichment of clinically relevant ARGs, including qacG, emrR, bacA, and acrB, conferring resistance to antibiotics critical for human medicine. In contrast, Guangdong exhibited a more restricted resistome dominated by β-lactamase and MurA homologs. Beta diversity analysis confirmed significant compositional differences between resistomes (PERMANOVA, R[2] = 0.019, F = 1.33, p = 0.001), indicating ecological rather than stochastic structuring.

CONCLUSIONS: These findings suggest that anthropogenic exposure enhances the diversity and evenness of resistance mechanisms within bat-associated microbiomes, potentially increasing their role as reservoirs of antimicrobial resistance.},
}

@article {pmid41594081,
year = {2026},
author = {Mohamed, FA and Al-Bulushi, M and Melegh, S and Timmer, B and Meszéna, R and Freytag, C and Laczkó, L and Miló, L and Urbán, P and Bőkényné-Tóth, R and Gyenesei, A and Kardos, G and Nyul, A and Urbán, E and Pál, T and Sonnevend, Á},
title = {Emergence of OXA-48-like Carbapenemase-Producing Escherichia coli in Baranya County, Hungary.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {1},
pages = {},
doi = {10.3390/antibiotics15010044},
pmid = {41594081},
issn = {2079-6382},
support = {300852//University of Pécs Medical School, Hungary/ ; },
abstract = {Background: Carbapenem-resistant Escherichia coli (CREC) producing OXA-48-like carbapenemase was first detected in Hungary in 2022. The aim of the present study was to characterize such strains isolated in 2022-2025 in Baranya County, Hungary. Methods: Antibiotic susceptibility and the whole-genome sequence (WGS) of E. coli isolates, identified as OXA-48-like carbapenemase producers using the CARBA-5 NG test, were established. The transferability of blaOXA-48-like plasmids was tested by conjugation. Results: Of the 6722 non-repeat E. coli isolates, 6 produced an OXA-48-like carbapenemase. They exhibited variable resistance to ertapenem and were susceptible to imipenem and meropenem. WGS revealed that all OXA-48-like producer E. coli belonged to high-risk clones: two clonally related OXA-181-producer E. coli ST405 were isolated in Hospital A, three OXA-244-producing E. coli ST38 (two identical via cgMLST from Hospital B), and an OXA-48-producing E. coli ST69. The blaOXA-48 and blaOXA-244 genes were chromosomally located, while blaOXA-181 was on a non-conjugative IncFIB-IncFIC plasmid. So far, the blaOXA-181-bearing plasmid of this incompatibility type has only been described in Ghana, but all blaOXA-48-like gene-carrying transposons in this study have already been identified in Europe and other continents. The E. coli ST38 isolates, showing close association based on core genome SNP distances to European and Qatari strains, belonged to Cluster A and harbored blaCTX-M-27. All but the E. coli ST69 isolate had cephalosporinase gene(s). Conclusions: This study describes small-scale intra-hospital transfers of OXA-48-like carbapenemase-producer E. coli. Interestingly, E. coli ST405 of Hungary carried blaOXA-181 on an IncFIB-IncFIC plasmid, which has only been reported from Africa so far.},
}

@article {pmid41594066,
year = {2025},
author = {Domingues, CPF and Rebelo, JS and Dionisio, F and Nogueira, T},
title = {Clinical and Environmental Plasmids: Antibiotic Resistance, Virulence, Mobility, and ESKAPEE Pathogens.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {1},
pages = {},
doi = {10.3390/antibiotics15010029},
pmid = {41594066},
issn = {2079-6382},
support = {UI/BD/153078/2022//Fundação para a Ciência e Tecnologia/ ; SFRH/BD/04631/2021//Fundação para a Ciência e Tecnologia/ ; UIDP/00329/2025//Fundação para a Ciência e Tecnologia/ ; },
abstract = {BACKGROUND/OBJECTIVES: Plasmids are autonomous DNA molecules that can replicate independently and transfer horizontally between bacterial cells. They play a key role in disseminating adaptive traits, such as antimicrobial resistance and virulence. Our study investigates the fundamental differences between plasmid populations originating from clinical/isolates and environmental/metagenomes.

METHODS: We compare three distinct plasmid genome datasets-the NCBI Reference Sequence Database (RefSeq), the Integrated Microbial Genomes & Microbiomes system (IMG/PR) from bacterial isolates (I) and microbiomes (M)-to assess how plasmid origin shapes their characteristics, including mobility types, antimicrobial resistance genes (ARGs), virulence genes (VGs) and host taxonomy.

RESULTS: We show that plasmids originating from bacterial isolates, more enriched in clinical samples, are fundamentally distinct from recovered from metagenomic data. Plasmids from isolates are larger, enriched in conjugative plasmids and display a higher frequency of ARGs and VGs than the ones assembled from metagenomes. Furthermore, ARGs are more frequently associated with highly mobile plasmids, particularly pCONJ.

CONCLUSIONS: These findings highlight the importance of plasmid origins in studies of plasmid epidemiology, functional potential and mobility.},
}