@article {pmid42599548,
year = {2026},
author = {Medeiros, WB and Hidalgo-Martinez, KJ and Penna, DDPS and Oliveira, VM},
title = {Environmental filtering shapes biosynthetic potential and resistome of antarctic microbiomes.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {9},
pages = {},
pmid = {42599548},
issn = {1573-0972},
mesh = {Antarctic Regions ; *Microbiota/genetics ; Multigene Family ; Metagenome ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Metagenomics ; Phylogeny ; Ecosystem ; Drug Resistance, Bacterial/genetics ; },
abstract = {Environmental filtering is a major driver of microbial community assembly in Antarctic ecosystems, yet its influence on biosynthetic potential and antimicrobial resistance remains poorly understood. Here, we analyzed 319 medium- to high-quality metagenome-assembled genomes (MAGs) recovered from four Antarctic sites (Whalers Bay, Crater Lake, Fumarole Bay, and Hannah Point) to investigate the relationship between geochemical gradients, biosynthetic gene clusters (BGCs), and antimicrobial resistance genes (ARGs). Integrating genome-resolved metagenomics, biosynthetic mining, resistome profiling, and environmental analyses, we identified 1,197 BGCs, with terpene clusters representing more than 25% of the total. Several biosynthetic hotspots were detected, including an Acidobacteriota MAG harboring 62 BGCs. Resistome composition exhibited strong site-specific structuring and was significantly associated with geochemical variables, particularly cobalt, iron, organic carbon, and thermal variation. Network analyses revealed highly connected MAGs affiliated with Pseudomonadota and Actinomycetota, linking diverse BGC and ARG classes. At the same time, genomic co-localization of biosynthetic and resistance determinants suggests potential adaptive associations between secondary metabolism and self-resistance mechanisms. Together, these findings demonstrate that environmental filtering shapes both the taxonomic and functional organization of Antarctic microbiomes and highlight polar ecosystems as reservoirs of unexplored biosynthetic diversity with potential biotechnological relevance.},
}

Antarctic Regions
*Microbiota/genetics
Multigene Family
Metagenome
*Bacteria/genetics/classification/metabolism/isolation & purification
Metagenomics
Phylogeny
Ecosystem
Drug Resistance, Bacterial/genetics

@article {pmid42599752,
year = {2026},
author = {Zhou, Y and Shao, Q and Liu, C and Tian, J and Guan, X and Zhang, X and Lu, J},
title = {Seasonal Dynamics of Community and Function of Gut Microbiome in Taihangshan Macaque (Macaca mulatta tcheliensis): Inferred From Metagenomic Data.},
journal = {Integrative zoology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1749-4877.70163},
pmid = {42599752},
issn = {1749-4877},
support = {No.31672302;No.32070446//National Natural Science Foundation of China/ ; },
abstract = {The gut microbiome is a key regulator of host nutritional intake, growth, and health, playing an essential role in mediating host adaptation to environmental changes. The northernmost population of rhesus macaque, Taihangshan macaque (Macaca mulatta tcheliensis), faces severe survival challenges, such as food shortages and harsh temperatures during winter and early spring. Previous studies have shown that they cope with seasonal changes through behavioral adaptations, such as adjusting food resources and flexibly regulating macronutrient intake. However, the role of the gut microbiome in supporting the seasonal adaptation of Taihangshan macaques remains unclear. Herein, we investigated seasonal variations in gut microbiome alpha diversity, composition, and functions from fecal samples of Taihangshan macaques using metagenomic analysis. The results showed that: (1) totally 435 non-redundant metagenome assembled genomes (MAGs) were generated; (2) alpha diversity was significantly higher in spring and winter than in summer and autumn; and (3) in winter, pathways of fatty acid biosynthesis and essential amino acid (EAA) biosynthesis, as well as CAZymes (GH3 and GH5) involved in cellulose and hemicellulose degradation, were significantly enriched. In contrast, pathways related to carbohydrate, energy, and glycan biosynthesis and metabolism, along with CAZymes (GT8 and GH23) potentially facilitating fat synthesis and storage, were enriched in summer. These functional adjustments likely help the host cope with seasonal variations in food availability and environmental conditions. Overall, this study provides new insights into how the gut microbiome responds to seasonal changes in diet and environmental factors in mammals inhabiting temperate forests.},
}

@article {pmid42600417,
year = {2026},
author = {Kasaiyan, S and Mateo, J and Buzzanca, D and Chiarini, E and Alessandria, V and Caro, I},
title = {Technological and microbial changes in cooked sausages incorporating cooked chickpea as a meat replacer and powdered banana pseudostem.},
journal = {Meat science},
volume = {242},
number = {},
pages = {110204},
doi = {10.1016/j.meatsci.2026.110204},
pmid = {42600417},
issn = {1873-4138},
abstract = {This study investigated the quality and microbial dynamics of vacuum-packaged cooked pork sausages reformulated by partially replacing meat protein (13%) with cooked chickpea paste and incorporating powdered banana pseudostem (BPS; 0%-0.4%) as a fibre source. Four sausages: Control (CON), CCP without BPS (CCP-0), and CCP with low (0.2%) or high (0.4%) BPS (CCP-BL and CCP-BH) were analysed over 20 days of refrigerated vacuum storage (3-7 °C). Composition, liquid retention, texture profile, colour, and microbial counts were evaluated. High-resolution shotgun metagenomics was applied to characterize bacterial and fungal dynamics. Composition and cooking yield remained unaffected by the reformulations (p > 0.05). However, substituting meat with cooked chickpea increased centrifugation loss (2 percentage points) and decreased hardness (2-3N), chewiness (∼3 N), and elasticity (0.04-0.05 units). Incorporating BPS increased initial product pH (up to 0.1 units), while decreasing lightness (up to 4 units). Initial total mesophilic bacterial counts were about 1 Log CFU/g higher in sausages with BPS and reached levels near 7 Log CFU/g across all batches by day 10. Adding chickpea supported the growth and survival of Enterobacteriaceae during storage. Shotgun metagenomics revealed that Brochothrix thermosphacta dominated the spoilage microbiota in CON and CCP-0 batches, exceeding 80% relative abundance by day 20. Conversely, BPS inclusion introduces plant-associated taxa (Klebsiella michiganensis and Pantoea rwandensis), significantly elevating alpha diversity and reducing B. thermosphacta percentage (< 20% relative abundance). While cooked chickpeas alter sausage textural characteristics, BPS serves as a functional fibre that modulates vacuum-packaged spoilage ecology.},
}

@article {pmid42600516,
year = {2026},
author = {Hu, Q and Wan, T and Liu, Y and Zhong, H and Chen, Y and Ao, Z and Jin, X and Guo, S},
title = {A real-world retrospective cohort study reveals the clinical utility of metagenomic next-generation sequencing in lower respiratory tract infections.},
journal = {Journal of infection and public health},
volume = {19},
number = {10},
pages = {103332},
doi = {10.1016/j.jiph.2026.103332},
pmid = {42600516},
issn = {1876-035X},
abstract = {BACKGROUND: Lower respiratory tract infections (LRTIs) are complicated by diverse pathogens, posing challenges to traditional diagnostics. However, robust evidence on LRTI pathogen spectra and metagenomic next-generation sequencing (mNGS) clinical utility remains limited.

METHODS: A retrospective analysis was conducted among 815 patients with suspected LRTIs who underwent mNGS and conventional microbiological testing(CMT) of bronchoalveolar lavage fluid. We evaluated the pathogen spectrum, the diagnostic value of mNGS across different infection categories, and its utility in guiding antibiotic therapy.

RESULT: Following exclusions, 754 patients demonstrated 84.5% mNGS positivity. mNGS detected DNA viruses (33.85%, EBV predominating), bacteria (30.83%), fungi (23.30%), mycobacteria (9.43%), and special pathogens (2.59%). Confirmed pathogens included Mycobacterium tuberculosis (n = 124), Candida albicans (n = 118), Pseudomonas aeruginosa (n = 87), Pneumocystis jirovecii (n = 65), Haemophilus influenzae (n = 50) and Aspergillus fumigatus (n = 48). mNGS showed higher positivity than CMT (84.5% vs 53.6%, P < 0.05), with sensitivities of 90.6% (LRTIs), 73.3% (bacterial), 74.7% (fungal), and 81.9% (tuberculosis); specificities were 22.6%, 56.5%, 73.5%, and 96.4%. Its high sensitivity but modest specificity necessitates cautious interpretation. mNGS guided treatment adjustments in 48.4% of patients, with higher rates in critically ill patients (60.1% vs 45.7%, P < 0.05), though clinical improvement was lower in this group (54.7% vs 79.2%, P < 0.05).

CONCLUSIONS: mNGS comprehensively detects pathogens in LRTIs, including bacteria, fungi, mycobacteria, DNA viruses, and special pathogens. While its broad diagnostic value and treatment guidance utility are significant, integration with clinical context is essential to distinguish true pathogens from colonization.},
}

@article {pmid42600761,
year = {2026},
author = {Hong, Z and Lu, Z and Shi, R and Zheng, S and Luo, J and Chen, J and Xie, Z and Zheng, JS and Chen, YM and Zhang, Z},
title = {Prospective associations of tea consumption with skeletal muscle mass and strength: Insights from the gut microbiome and proteomics.},
journal = {Pharmacological research},
volume = {231},
number = {},
pages = {108398},
doi = {10.1016/j.phrs.2026.108398},
pmid = {42600761},
issn = {1096-1186},
abstract = {Tea consumption may be associated with skeletal muscle health, but longitudinal evidence based on repeated assessments remains limited. We examined the associations of tea intake and serum biomarkers with repeated skeletal muscle measures and explored whether these associations might be partly explained by multi-omics features. In this prospective cohort, 3408 adults were followed for approximately 12 years. Skeletal muscle mass was measured by dual-energy X-ray absorptiometry, handgrip strength by digital dynamometry, gut microbial taxonomic and functional profiles by shotgun metagenomic sequencing, serum proteins by data-independent acquisition mass spectrometry, and fecal metabolites by targeted UPLC-MS/MS metabolomics. Linear mixed-effects models examined longitudinal associations, and mediation analyses estimated indirect effects. In longitudinal analyses, higher tea consumption frequency was associated with greater appendicular skeletal muscle mass, appendicular skeletal muscle index, and handgrip strength (β: 0.037-0.140; 95% CI: 0.002-0.205). Higher circulating flavan-3-ols showed similar associations with these muscle-related outcomes (β: 0.085-0.174; 95% CI: 0.007-0.254), whereas no significant associations were observed with walking speed. Exploratory multi-omics analyses identified tea-related differences in gut microbial species and functional pathways, fecal metabolites, and circulating proteins, including Gemmiger formicilis, amino acid biosynthesis pathways, fructose 1,6-bisphosphate, VTN, CFI, CNDP1, and ITIH4. Exploratory mediation analyses identified statistical indirect associations involving multi-omics features, with estimated proportions mediated ranging from 4.5% to 19.0%. Overall, higher tea consumption and circulating biomarkers were associated with greater skeletal muscle mass and strength, accompanied by distinct multi-omics features that may provide potential biological links between tea exposure and muscle-related outcomes.},
}

@article {pmid42600856,
year = {2026},
author = {Li, Y and Chen, L and Zhang, J and Zhang, Y and Wang, M and Zhang, R and Fang, W and Zhang, P and Zhang, G},
title = {Metagenomics reveals rumen residues as a superior inoculum for volatile fatty acid production in vitro.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135627},
doi = {10.1016/j.biortech.2026.135627},
pmid = {42600856},
issn = {1873-2976},
abstract = {Rumen microbiome is widely recognized as an efficient system for lignocellulose degradation. Rumen fluid (RF) has been often used as the inoculum in previous study of bioprocesses, however, the potential of rumen solids (RS) to enhance volatile fatty acid (VFA) production remains underexplored. The anaerobic fermentation performance of RS, RF, and RF + RS mixture as inocula was compared using corn stover as substrate, with RS addition at 5%, 10%, or 20% (w/w) to corn stover and RF addition at 1:2 (v/v) to buffer solution. At a corn stover content of 2.5% (w/v, based on final working volume), the highest VFA concentration of 10.05 g/L was achieved with 20% RS as inoculum, outperforming those with both RF and RF + RS. Metagenomic analysis revealed significant differences in bacterial, fungal, and archaeal community structures with 20% RS and RF. With 20% RS, hydrolytic bacteria (e.g., Enterobacter) dominated the ecological niche, microbial co-occurrence network analysis of the 2,000 most abundant genera revealed a simpler network with fewer negative associations, and functional analysis demonstrated a notable increase in relative abundance of glycosyltransferase (GT) families within carbohydrate-active enzymes (CAZymes). With 20% RS, enrichment in glycolysis-related genes was observed, indicating a preference for carbohydrate degradation, while acid-producing pathways were enriched such as pyruvate metabolism with RF. Rumen solids, as a superior inoculum for VFA production, effectively enhanced lignocellulose bioconversion by enriching specific low-abundance microbial taxa, forming a microbial network with fewer negative associations, increasing the relative abundance of GT families, and strengthening the systemic hydrolysis capacity.},
}

@article {pmid42601406,
year = {2026},
author = {Antman, T and Lewin-Epstein, O and Yerushalmi, T and Broder, YS and Zeevi, D},
title = {Global microbial DNA signatures of temperature and nutrient limitation across ecosystems.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {42601406},
issn = {2058-5276},
abstract = {Microbial genomes continuously adapt to environmental conditions, but identifying universal signatures of adaptation remains challenging. Here we show that environmental temperature can be accurately predicted across ecosystems from DNA composition alone (R[2] = 0.75), using tetranucleotide frequencies from 1,235 marine and soil metagenomes and a machine learning approach. This predictive signal was also apparent within individual taxa, consistent with a fundamental temperature-associated signature. By contrast, GC content exhibited opposite correlations with temperature in soil (positive) and marine (negative) environments. This phenomenon was probably driven by differences in nutrient availability, as GC content increases with nutrients while nutrients decrease with temperature in marine samples. By integrating these observations, we identified specific tetranucleotides, with 50% GC, that displayed consistent and robust temperature correlations across environments and may have contributed to the stability of predictions. This work highlights metagenome-wide DNA-temperature associations, relevant for understanding microbial community responses to global changes.},
}

@article {pmid42601613,
year = {2026},
author = {Lotfi, M and Jalal, D and Sayed, AA},
title = {plsMD: a plasmid reconstruction tool from short-read assemblies.},
journal = {BMC bioinformatics},
volume = {27},
number = {1},
pages = {},
pmid = {42601613},
issn = {1471-2105},
mesh = {*Plasmids/genetics ; *Software ; *Sequence Analysis, DNA/methods ; Genome, Bacterial ; Whole Genome Sequencing/methods ; },
abstract = {BACKGROUND: While whole genome sequencing has become a cornerstone of antimicrobial resistance surveillance, the reconstruction of plasmid sequences from short-read data remains a challenge due to repetitive sequences and assembly fragmentation. Current computational tools for plasmid identification and binning have limitations in reconstructing full plasmid sequences, hindering downstream analyses like phylogenetic studies and antimicrobial resistance gene tracking.

RESULTS: We present plsMD, a tool designed for full plasmid reconstruction from short-read assemblies. plsMD integrates Unicycler assemblies with replicon and full plasmid sequence databases to guide plasmid reconstruction through a series of contig manipulations. Using two datasets - an established benchmark dataset used in previous benchmarking studies and a novel dataset consisting of newly sequenced bacterial isolates - plsMD outperformed existing tools in both. In the benchmark dataset, it achieved excellent recall, precision, and F1 scores of 91.3%, 95.5%, and 92.0%, respectively. In the novel dataset, it achieved recall, precision, and F1 scores of 77.6, 88.9 and 74.5%, respectively. plsMD supports two usage modalities: single-sample analysis for plasmid reconstruction and gene annotation, and batch-sample analysis for phylogenetic investigations of plasmid transmission.

CONCLUSIONS: plsMD represents a significant advancement in plasmid analysis, offering a robust solution for utilizing existing short-read whole genome sequencing data to study plasmid-mediated antimicrobial resistance spread and evolution.},
}

*Plasmids/genetics
*Software
*Sequence Analysis, DNA/methods
Genome, Bacterial
Whole Genome Sequencing/methods

@article {pmid42601633,
year = {2026},
author = {Albastaki, A and Naji, M and Moussa, M and Smith, J},
title = {Soil Microbiomes Across Depth and Ecosystems in Dubai, UAE: Potential Environmental Signatures for Forensic Geolocation.},
journal = {Environmental microbiology reports},
volume = {18},
number = {4},
pages = {e70403},
doi = {10.1111/1758-2229.70403},
pmid = {42601633},
issn = {1758-2229},
mesh = {*Soil Microbiology ; *Microbiota ; *Bacteria/classification/genetics/isolation & purification ; Ecosystem ; Soil/chemistry ; Metagenomics ; Forensic Sciences ; Phylogeny ; },
abstract = {Soil microbial communities exhibit strong sensitivity to environmental gradients, yet their distribution across depth and land-use types in hyper-arid environments remains poorly characterised. Using whole-genome shotgun metagenomics via Oxford Nanopore Technologies long-read sequencing, we profiled soil microbial communities across six contrasting land-use sites in Dubai, UAE: urban, industrial (two locations), marine, desert and agricultural, where each sampled at three depth intervals (0-25 cm, 25-50 cm and 50-100 cm). Marine soils exhibited extreme salinity (EC 23.7-30.7 dS m[-1]) and the highest organic matter content (1.19%-1.76%), while desert soils were nutrient-poor with minimal salinity. Actinomycetota and Pseudomonadota co-dominated across all sites, collectively accounting for 77%-96% of classified sequences. Actinomycetota prevailed in undisturbed desert horizons (up to 53.4%), while Pseudomonadota dominated nutrient-enriched environments, reaching 69.4% at industrial sites. A notable compositional reversal was observed in the desert deep horizon (50-100 cm), where Pseudomonadota increased to 56.8%, departing from the expected oligotrophic depth gradient. PERMANOVA confirmed land use as the primary driver of community composition (p = 0.001), with depth exerting a secondary but significant effect (p ≤ 0.01). NMDS ordination revealed strong site-specific clustering, with each environment harbouring a distinctive microbial fingerprint with promising forensic geolocation potential.},
}

*Soil Microbiology
*Microbiota
*Bacteria/classification/genetics/isolation & purification
Ecosystem
Soil/chemistry
Metagenomics
Forensic Sciences
Phylogeny

@article {pmid42602060,
year = {2026},
author = {Sahu, K and Yao, Q},
title = {metaIVP: an integrative metavirome focused metagenomic processing pipeline.},
journal = {BMC methods},
volume = {3},
number = {1},
pages = {37},
pmid = {42602060},
issn = {3004-8729},
abstract = {BACKGROUND: Metagenomic studies increasingly rely on complex, multi-tool pipelines to recover and characterize viral and non-viral genomes from mixed microbial communities. While these pipelines enable high-resolution genome recovery, limited functionality in downstream post-processing workflows and insufficient logging structures often hinder reproducibility, error tracing, and selective re-analysis. These challenges are particularly critical in metaviral analyses, where viral and non-viral genomes must be processed using distinct methodologies. To address these limitations, we introduce metaIVP, a modular, integrative, and flexible framework designed to systematically manage genome content purification, re-binning, quality assessment, and downstream analyses of viral and non-viral metagenomic contexts.

METHODS: The metaIVP framework is organized into hierarchical modules, each governed by dedicated log files that explicitly control execution state and re-runnability. Contig-level and bin-level analytical and purification steps are implemented as essential modules to isolate genome contents, followed by separate viral and non-viral post-processing workflows. Viral workflows incorporate contamination detection, genome quality evaluation, host prediction, and virus-specific binning. Non-viral analyses include genome binning, alignment and mapping statistics, genome quality assessment, and replication rate estimation. Checkpoints are explicitly defined such that deletion of selected module- or sub-module-level logs enables targeted re-execution of specific analytical steps without rerunning the full pipeline. All analyses are integrated to depict a comprehensive system in the metagenomic samples, with focus on the metaviromic information.

RESULTS: The usage of metaIVP was demonstrated using both a well-controlled human gut virome dataset and a geographically structured environmental metavirome dataset, showing its broad applicability across host-associated and environmental systems. The pipeline effectively separates viral and non-viral genomic content, improves viral bin purity, and preserves sample-specific functional, taxonomic, and host-association features after virome enrichment. Compared with recent state-of-the-art approaches, metaIVP achieves comparable performance, particularly when optional re-binning with vRhyme is applied, while maintaining a higher fraction of high-confidence viral bins.

DISCUSSION: The metaIVP addresses a key gap in metavirome analysis by jointly characterizing viral and non-viral genomic components and supporting integrative downstream analyses within a single framework. Its user-friendly, modular, and controllable design allows flexible execution and provides a foundation for incorporating additional downstream analytical tools as metavirome methodologies continue to evolve.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s44330-026-00090-7.},
}

@article {pmid42602126,
year = {2026},
author = {Ortúzar, M and Formariz, V and Suescún-Sepúlveda, JA and González-Hernández, M and Riesco, R and Garrido-Oter, R and Trujillo, ME},
title = {From natural assemblages to synthetic communities in the Lupinus microbiome.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1891479},
pmid = {42602126},
issn = {1664-462X},
abstract = {INTRODUCTION: Plant roots harbour complex microbial communities that enhance nutrient acquisition, stress tolerance, and pathogen defence, yet their assembly and functional dynamics remain incompletely understood.

RESULTS: In this work, we isolated over 700 bacterial strains from wild Lupinus angustifolius across multiple compartments and soil types, capturing both dominant and rare bacterial taxa. Using co-occurrence network analysis, we selected representative strains to assemble synthetic communities (SynComs) of varying complexity, which were inoculated under sterile and non-sterile conditions. Plants were inoculated with SynComs of increasing complexity under both non-sterile soil and gnotobiotic conditions. SynCom inoculation reshaped root-associated microbiota, moderately influenced the rhizosphere, and had limited impact on bulk soil communities. Increasing SynCom complexity enhanced plant growth and triggered host transcriptional responses involving hormone signaling, defence pathways, and metabolic reprogramming.

DISCUSSION: These findings indicate that soil-driven filtering and microbial interactions govern microbiome assembly and plant responses. Incorporating taxa with distinct ecological roles, including low-abundance members, improves SynCom functionality and advances understanding of plant-microbe interactions in natural and agricultural systems.},
}

@article {pmid42602195,
year = {2026},
author = {Maitray, A and Rishi, P and Conrady, CD and Binkley, E and Williams, BK and Yeh, S and Nicola, MD and Finger, PT},
title = {Vitreoretinal Lymphoma: A Comprehensive Clinical Review and Current Standards in Management.},
journal = {Journal of vitreoretinal diseases},
volume = {},
number = {},
pages = {24741264261474159},
pmid = {42602195},
issn = {2474-1272},
abstract = {PURPOSE: To summarize current evidence on clinical features, multimodal imaging findings, diagnostic techniques, and management strategies for vitreoretinal lymphoma.

METHODS: A literature review was performed to provide updated information on available treatment options for vitreoretinal lymphoma.

RESULTS: Diagnosis of vitreoretinal lymphoma requires vitreous biopsy, with or without retinal/subretinal tissue, for cytology and immunohistochemistry, along with ancillary tests such as flow cytometry, cytokine profiling (interleukin-10/interleukin-6 ratio >1), immunoglobulin heavy chain gene rearrangement analysis, and detection of the MYD88 L265P mutation. Optical coherence tomography and other multimodal imaging techniques have become increasingly useful in raising suspicion, guiding biopsy, and monitoring treatment response. No standardized treatment protocol exists for isolated vitreoretinal lymphoma. Management options include intravitreal chemotherapy (methotrexate and/or rituximab), radiation therapy, and systemic chemotherapy, often showing a good initial response, but relapse and subsequent central nervous system (CNS) involvement are common, resulting in poor overall prognosis and survival. For vitreoretinal lymphoma with CNS disease, current strategies favor high-dose methotrexate-based systemic chemotherapy, with or without intrathecal chemotherapy; whole-brain radiation is generally reserved as rescue therapy. Emerging directions for earlier diagnosis include metagenomic deep sequencing, and chimeric antigen receptor T-cell (CAR-T) therapy has shown promise for treatment of selected relapsed/refractory cases of primary CNS lymphoma with a potential to prolong survival.

CONCLUSIONS: Treatment of vitreoretinal lymphoma requires a multidisciplinary, individualized approach that integrates multimodal imaging, cytologic and molecular diagnostics, CNS evaluation, and tailored local or systemic therapy. Prospective multicenter studies are needed to refine diagnostic algorithms and standardize management.},
}

@article {pmid42594461,
year = {2026},
author = {Lu, D and Chen, B and Nie, E and Lian, S and Li, R and Guo, R and Fu, S},
title = {Indole inhibits anaerobic digestion by disrupting AHLs-mediated quorum sensing.},
journal = {Journal of hazardous materials},
volume = {516},
number = {},
pages = {143267},
doi = {10.1016/j.jhazmat.2026.143267},
pmid = {42594461},
issn = {1873-3336},
abstract = {The emerging understanding highlights indole as a disruptive factor to quorum sensing (QS) mechanisms, prompting further investigation into its role in anaerobic digestion (AD) system inhibition. However, relevant studies are still scarce and the potential mechanism linking indole and AD inhibition remains unclear. This study showed that indole (1, 2, and 3 mM) significantly reduced cumulative methane production by 8.47-51.89% and extended the lag phase by 1.34-6.68 days. Time-series AHLs quantification, metagenomics, and circular clustering heatmaps analysis revealed that indole might disrupt microbial communication between hydrolysis-acidification bacteria and acetoclastic methanogens by reducing the AHLs level (C6-HSL, 3-oxo-C8-HSL, C10-HSL, C12-HSL, 3-oxo-C10-HSL, and C18-HSL). Notably, indole degradation alleviated the inhibition of C10-HSL, C18-HSL, and 3-oxo-C10-HSL, which might restore hydrolysis and acidification and mitigate AD inhibition. Exogenous AHLs (1 and 5 µM) restored methane production by 48.44-55.59% in 3 mM indole-inhibited reactors (p < 0.05), while the quorum quenching agent vanillin further reduced methane production by 72.55%, suggesting that AHLs play an important role in helping microorganisms resist indole stress. These findings highlight the importance of AHLs-mediated inter-microbial communication in counteracting indole-inhibited methanogenesis inhibition, suggesting potential practical strategies to enhance AD stability and efficiency in challenging conditions.},
}

@article {pmid42595035,
year = {2026},
author = {Mao, H and Deng, Y and Wang, X and Yu, Q and Zhao, Z and Zhang, Y},
title = {Two-phase anaerobic digestion with sub-thermophilic hydrolysis: Regulating metabolites to accelerate electron transfer and enhance methanogenesis.},
journal = {Environmental research},
volume = {307},
number = {},
pages = {125448},
doi = {10.1016/j.envres.2026.125448},
pmid = {42595035},
issn = {1096-0953},
abstract = {Sub-thermophilic anaerobic digestion accelerates the hydrolysis and acidogenesis of complex substrates to improve methane production, but methanogens may be inhibited under such condition. Two-phase anaerobic digestion (TPAD) system can decouple the hydrolytic-acidogenic and methanogenic phases to optimize microbial activity in each phase. Therefore, in this study, a novel temperature-phased strategy combining a 45°C hydrolytic-acidogenic phase with a 37°C methanogenic phase (TPAD45°C/37°C) was developed to accelerate the degradation of agricultural waste and avoid the sub-thermophilic temperature-induced inhibition of methanogenesis. Results showed that 45°C hydrolytic phase increased ethanol and acetate production, and decreased propionate production compared to the 37°C control. Consequently, at a solid retention time of 20 days, the methane yield in the TPAD45°C/37°C group was 31.8% and 13.0% higher than that in the TPAD37°C/37°C and TPAD45°C/45°C groups, respectively. Mechanistically, the TPAD45°C/37°C group exhibited the highest McrA activity and coenzyme F420 content, indicating superior methanogenic activity. Furthermore, Tafel polarization and temperature-dependent conductivity analyses revealed that the higher levels of ethanol from 45°C hydrolysate provided a stronger thermodynamic driving force to minimize the energy barrier and improve intrinsic electron transfer rates, thereby enhancing methanogenesis. Additionally, the TPAD45°C/37°C group exhibited the highest overall metabolic potential. Microbial community analysis revealed that this system enriched the methanogens, which in turn promoted the degradation of complex substrates and increased methane production. This study provided an economically viable, energy-positive, and highly resilient technological strategy for the sustainable valorization of agricultural waste.},
}

@article {pmid42595117,
year = {2026},
author = {Hashimoto, M and Oki, H and Kawahara, K and Fujii, KK and Koide, T},
title = {Molecular basis of collagen triple helix recognition by VWF A-like domain 2 of collagen VII: Implications for interlaced anchoring fibril formation.},
journal = {The Journal of biological chemistry},
volume = {},
number = {},
pages = {113448},
doi = {10.1016/j.jbc.2026.113448},
pmid = {42595117},
issn = {1083-351X},
abstract = {Anchoring fibrils formed by collagen VII play a critical role in stabilizing the dermal-epidermal junction. The N-terminal non-collagenous (NC1) domain of collagen VII binds firmly to basement membrane components including collagen IV and has also been reported to interact with mesenchymal fibrillar collagens via its von Willebrand factor A-like domain 2 (A2 domain). To elucidate how collagen VII recognizes fibrillar collagen, we performed yeast two-hybrid screening using a triple-helical random peptide library, which resulted in the identification of a Met-Gly-Φ (Φ; aromatic amino acid residue) motif. Biochemical analysis with synthetic triple-helical peptides revealed a binding preference of Trp > Phe as the Φ residue by the A2 domain despite Trp being absent in native collagens. The crystal structure of the A2 domain in complex with the Nle (Met surrogate)-Gly-Trp-containing peptide revealed a unique mechanism by which two distinct hydrophobic pockets of the A2 domain accommodate the Nle and Trp residues corresponding to the Met-Gly-Φ motif, engaging all three chains of the triple helix. Subsequent molecular dynamics simulations demonstrated that the A2 domain recognizes the corresponding native Met-Gly-Phe motif in a similar manner, but with lower affinity, implying a transient interaction with mesenchymal collagens. The findings obtained in this work suggest models in which transient A2-triple helix interaction promotes the recruitment of collagen I and III fibrils into the arc-shaped structure of anchoring fibrils. This also provides a foundation for linking structural understanding to skin fragility diseases caused by collagen VII dysfunction.},
}

@article {pmid42595349,
year = {2026},
author = {Yang, Z and Ramakrishnan, M and Wang, B and Wei, Q and Ahmad, Z},
title = {Optimized Controlled-Release Fertilization Improves Productivity and Reshapes the Rhizosphere Microbiome in Lei Bamboo: A Metagenomic Assessment.},
journal = {Environmental microbiology},
volume = {28},
number = {8},
pages = {e70401},
pmid = {42595349},
issn = {1462-2920},
support = {2018YFD060010403//National Key Research and Development Program of China/ ; 2021F1065-10//Special Project of Zhejiang Provincial Scientific Research Institutes/ ; },
mesh = {*Fertilizers/analysis ; *Rhizosphere ; *Microbiota ; *Soil Microbiology ; *Poaceae/microbiology/growth & development ; Nitrogen/metabolism ; Metagenomics ; Bacteria/classification/genetics/isolation & purification/metabolism ; Soil/chemistry ; Urea/metabolism ; },
abstract = {Intensive nitrogen fertilization in Lei bamboo (Phyllostachys praecox) plantations has increased productivity but has also reduced nitrogen-use efficiency (NUE), accelerated nutrient losses, and contributed to soil degradation. How nutrient-release strategies influence rhizosphere microbiome assembly and ecosystem functioning remains poorly understood. Here, we developed a bamboo shoot-specific controlled-release fertilizer (CRF) and evaluated different urea-CRF blending ratios to identify sustainable fertilization strategy for Lei bamboo production. Mixed CRF-urea treatments outperformed both sole-fertilizer applications and the unfertilized control. T2 (30% urea + 70% CRF) achieved the highest shoot yield, whereas T3 (50% urea + 50% CRF) enhanced NUE. Optimized fertilization improved soil nutrient availability and organic matter accumulation without significantly affecting soil pH. Metagenomic analysis revealed the enrichment of taxa associated with nutrient transformation, organic matter turnover, and plant growth. However, pathway-level analysis revealed shifts in carbon, nitrogen, and sulfur cycling activities under optimized nutrient-release regimes. Our results demonstrate that synchronizing nitrogen release with plant and microbial demand enhances rhizosphere function, productivity and NUE. T2 delivered the strongest overall agronomic performance by maximizing shoot yield while maintaining improved nutrient retention and ecological stability. These findings provide a mechanistic link between fertilization strategy, rhizosphere microbial dynamics, and ecosystem function, supporting sustainable Lei bamboo production.},
}

*Fertilizers/analysis
*Rhizosphere
*Microbiota
*Soil Microbiology
*Poaceae/microbiology/growth & development
Nitrogen/metabolism
Metagenomics
Bacteria/classification/genetics/isolation & purification/metabolism
Soil/chemistry
Urea/metabolism

@article {pmid42595408,
year = {2026},
author = {McQueen, AD and Calomeni-Eck, AJ and Cicerrella, AS and Chung, SH and Malmfeldt, MP and Lindsay, DL and Gong, P},
title = {Enhancing early-season detection of harmful algal blooms caused by sediment-borne overwintering cyanobacteria using metagenomic and qPCR tools.},
journal = {Harmful algae},
volume = {158},
number = {},
pages = {103160},
doi = {10.1016/j.hal.2026.103160},
pmid = {42595408},
issn = {1878-1470},
mesh = {*Harmful Algal Bloom ; *Cyanobacteria/genetics/classification/physiology ; *Geologic Sediments/microbiology ; *Metagenomics/methods ; RNA, Ribosomal, 16S/genetics/analysis ; Seasons ; Lakes/microbiology ; Real-Time Polymerase Chain Reaction/methods ; Polymerase Chain Reaction ; },
abstract = {To better inform adaptive management strategies for harmful algal blooms (HABs), there is a critical need to improve detection capabilities of bloom risks earlier in the growing season. Emerging molecular tools such as metagenomic Next-Generation Sequencing (NGS) and amplification-based quantitative polymerase chain reaction (qPCR) can accurately identify the taxonomy of cyanobacteria and akinetes of which the latter are particularly challenging to distinguish morphologically and estimate their abundance. This study aimed to evaluate the contribution of these advanced molecular tools to assessing the presence, density, and planktonic growth potential of overwintering cyanobacterial cells in sediments from historically HAB-impacted waterbodies in the USA. We conducted 14-day incubation experiments using field-collected lake sediments and characterized cyanobacterial taxonomy and abundance in the sediments (pre-incubation) and overlying water (post-incubation) using light microscopy, genus-specific qPCR, and 16S rRNA amplicon sequencing. By analyzing qualitative and quantitative results, we not only identified the prevailing cyanobacterial genera that moved from sediment to water column over the incubation but also determined their relative abundance and the cyanobacterial genera consistent between sediment and water column. This study demonstrated that metagenomic and qPCR tools provided additional lines of evidence to augment traditional microscopy and improved taxonomic identification and quantification. Our approach can better inform planktonic growth potential of problematic cyanobacteria to enhance early detection capabilities, and guide targeted countermeasures taken to improve preventative or remedial HAB management, reducing environmental and public health impacts.},
}

*Harmful Algal Bloom
*Cyanobacteria/genetics/classification/physiology
*Geologic Sediments/microbiology
*Metagenomics/methods
RNA, Ribosomal, 16S/genetics/analysis
Seasons
Lakes/microbiology
Real-Time Polymerase Chain Reaction/methods
Polymerase Chain Reaction

@article {pmid42595551,
year = {2026},
author = {Wang, L and Yang, J and Li, D and Zhang, F and Yan, JA and Wang, YY and Sun, J and Cao, H},
title = {[Tremella fuciformispolysaccharide retards the progression of colorectal cancer by regulating the gut microbiota-metabolome axis].},
journal = {Zhonghua zhong liu za zhi [Chinese journal of oncology]},
volume = {48},
number = {8},
pages = {975-982},
doi = {10.3760/cma.j.cn112152-20250925-00485},
pmid = {42595551},
issn = {0253-3766},
support = {MS2024064//Jiangsu Province Science and Technology Development Program of Traditional Chinese Medicine (General Project)/ ; YJZ202305//the Jiangnan University Affiliated Hospital Research-Oriented Hospital Medical Research Project (General Project)/ ; KX-25-C166//Wuxi City 2025 Soft Science Research Project/ ; },
mesh = {Animals ; *Colorectal Neoplasms/pathology/metabolism/microbiology/drug therapy/chemically induced ; Humans ; Mice ; HT29 Cells ; *Gastrointestinal Microbiome/drug effects ; Mice, Inbred C57BL ; *Polysaccharides/pharmacology ; NF-kappa B/metabolism ; Male ; *Basidiomycota/chemistry ; *Metabolome/drug effects ; Azoxymethane ; Apoptosis/drug effects ; Dextran Sulfate ; Cell Proliferation/drug effects ; Feces/chemistry/microbiology ; Disease Progression ; Colon/pathology/metabolism ; },
abstract = {Objective: To investigate the anti-colorectal cancer effect of tremella fuciformis polysaccharides (TFP) via the gut microbiota-metabolite axis. Methods: Colorectal cancer was induced in C57BL/6J mice using azoxymethane/dextran sulfate sodium. TFP or distilled water was administered by gavage for 3 weeks. Disease activity index (DAI), colon length, tumor burden, histopathology, gut microbiota (metagenomics), fecal metabolites (untargeted metabolomics), and colonic protein expression (Western blot) were assessed. Pyridoxic acid's effect on HT-29 cells was tested in vitro. Results: TFP significantly reduced DAI [2.0(1.8, 3.3) vs. 3.5(2.8, 4.5), P＜0.01], increased colon length [(7.2±1.1) vs. (5.5±0.5) cm, P＜0.05], lowered pathological score [6(3, 8) vs. 9(8, 10), P＜0.05], and decreased tumor number [2(1, 3) vs. 4(3, 4), P＜0.05] and volume [(11.02±7.88) vs. (24.99±3.38), P＜0.01]. Metagenomics revealed that TFP significantly reshaped gut microbiota (R[2]=0.173, P=0.027), enriching Candidatus Amulumruptor, Helicobacter, and Akkermansia. Metabolomics showed distinct profiles (R[2]=0.159, P=0.004), with pyridoxic acid elevated 1.20 fold (P＜0.001). Pyridoxic acid suppressed HT-29 cell viability and migration, and correlated positively with several upregulated bacteria, suggesting a microbiota-metabolite axis underlying its anti-tumor effect. TFP downregulated nuclear factor-κB (NF-κB) (P＜0.01) and upregulated phosphorylated AMP-activated protein kinase alpha (p-AMPKα) (P＜0.001), BAX (P＜0.001), and cleaved caspase-3 (P＜0.05). Conclusion: TFP inhibits colorectal cancer progression by modulating gut microbiota, elevating pyridoxic acid, suppressing NF-κB, and activating AMPK-mediated apoptosis.},
}

Animals
*Colorectal Neoplasms/pathology/metabolism/microbiology/drug therapy/chemically induced
Humans
Mice
HT29 Cells
*Gastrointestinal Microbiome/drug effects
Mice, Inbred C57BL
*Polysaccharides/pharmacology
NF-kappa B/metabolism
Male
*Basidiomycota/chemistry
*Metabolome/drug effects
Azoxymethane
Apoptosis/drug effects
Dextran Sulfate
Cell Proliferation/drug effects
Feces/chemistry/microbiology
Disease Progression
Colon/pathology/metabolism

@article {pmid42595815,
year = {2026},
author = {Vasquez, YM and Nardi, T and Terasaki, GM and Byl, P and Brůna, T and Villada, JC and Romero-Gutiérrez, MF and Mock, T and James, TY and , and Woyke, T and Schulz, F},
title = {Genomic catalogue of giant viruses reveals expanded diversity and functional potential.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {42595815},
issn = {2058-5276},
support = {Contract No. DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; Contract No. DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; Contract No. DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; Contract No. DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; Contract No. DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; Contract No. DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; },
abstract = {Nucleocytoplasmic large DNA and Mirusviricota viruses exhibit taxonomic richness which continually expands due to metagenomic sequencing. Here we curate a database of giant virus metagenome-assembled genomes (GVMAGs V2), comprising 8,508 species-level representatives from 18,727 GVMAGs, a sixfold increase from the previous giant virus phylogenetic frameworks. Phylogenomics revealed 712 previously undescribed genera, 13 previously unknown viral families and an order we propose named Mycodnavirales. By accounting for alternative and custom genetic codes, we improved gene calling in over 1,300 GVMAGs, enabling more accurate identification of protein-coding genes. Database mining uncovered putative endogenous viral elements in hosts spanning algae, fungi and parasitic protists, highlighting that giant virus integration is widespread and evolutionarily persistent. Protein-level analysis revealed enriched genes for pollutant degradation in Algavirales and widespread biosynthetic gene clusters linked to antimicrobial-like and antibiotic resistance gene-like activity. This public resource will serve as a foundation for expanding giant virus diversity, uncovering virus-host interactions and exploring viral evolution.},
}

@article {pmid42595818,
year = {2026},
author = {Cumbo, F and Blankenberg, D},
title = {Characterization of microbial dark matter at scale with MetaSBT and taxonomy-aware Sequence Bloom Trees.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {42595818},
issn = {1546-1696},
support = {U24HG006620//U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI)/ ; U24CA231877//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; },
abstract = {Accurately characterizing metagenome-assembled genomes remains a substantial challenge due to the presence of sequencing errors, incomplete assembly and contamination. Here, we present MetaSBT, a tool for organizing, indexing and characterizing microbial reference genomes and metagenome-assembled genomes, demonstrated in this study using viruses. MetaSBT identifies clusters of genomes across all seven taxonomic levels using the Sequence Bloom Tree data structure, which relies on Bloom filters to index large amounts of genomes based on their k-mer composition. We built an initial set of databases composed of over 190,000 viral genomes from public sources, grouped into sequence-consistent clusters at different taxonomic levels. We defined over 40,000 candidate species, ~80% of which, to our knowledge, do not match viral species in reference databases to date. Furthermore, we showed that our databases are useful to existing quantitative metagenomic profilers to unlock the detection of unknown microbes and the estimation of their abundance in metagenomic samples. The open-source framework and databases are fully integrated into the Galaxy platform.},
}

@article {pmid42595876,
year = {2026},
author = {Knuth, D and Mäder, P and Boekhorst, J and Poll, C and Kandeler, E and Alaoui, A and Pasković, I and Polić Pasković, M and Baldi, I and Bureau, M and Alcon, F and Contreras, J and Glavan, M and Abrantes, N and Campos, I and Norgaard, T and Huerta Lwanga, E and Geissen, V and Harkes, P},
title = {Beneath the surface: non-target effects of multiple pesticides on the soil microbiome in organic and conventional agricultural European fields.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {42595876},
issn = {1614-7499},
support = {862568//HORIZON EUROPE Framework Programme/ ; },
abstract = {Previous studies have shown that diverse cocktails of pesticide mixtures are omnipresent in agricultural soils yet miss a clear link to the effects on the soil microbiome. In this study, we linked the occurrence of pesticides in conventional and organic agricultural soils of the SPRINT (Sustainable plant protection transition) projects' Case Study Sites to the composition and function of soil microbial communities. Metagenomic sequencing, phospholipid fatty acids analysis and enzyme activity measurements were used to characterize the soil microbiome and effects of site-specific parameters such as pH and SOC, and pesticide residues. Differences in the soil microbiome were strongly influenced by the geographic origin of the samples, with the pH value as dominant driver. Against our hypothesis, effects of the investigated management systems were limited, yet significant at the European level. Notably, an association between some pesticides could still be observed after accounting for the variation explained by the environmental factors. Among these, especially fungicides, with modes of action that aim to interfere with processes in microorganisms, seemed to affect the soil microbiome. This might occur either by directly affecting these processes in non-target organisms or by changing co-dependencies between fungi and bacteria. Next to fungicides, aminomethylphosphonic acid showed a significant effect on the soil microbial composition and an interactive, possibly synergistic effect with the persistent pesticide hexachlorobenzene. The latter raises concerns about a possible interaction of recently applied pesticides and persistent "legacy" pesticides. This work highlights that even though environmental parameters can overshadow the effects of pesticides, especially the identity of the pesticides present, can have an influence on the soil microbiome.},
}

@article {pmid42597171,
year = {2026},
author = {Wang, T and Liang, H and Wu, Y and Zhang, X and Zhang, S and Wei, Z and Li, W and Song, W and Luo, Z and Al-Dalali, S},
title = {Multi-omics profiling of microbial ecology and non-volatile compounds across fermentation stages of spontaneous litchi (Litchi chinensis Sonn.) fermented vinegar-like beverage.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1908193},
pmid = {42597171},
issn = {2296-861X},
abstract = {INTRODUCTION: Litchi fruit vinegar-like beverages (LVBs) are notable processed products derived from litchi fruit, yet few studies have focused on the systematic characterization of microbial and metabolic dynamics during their natural fermentation process.

METHODS: This work employed a comprehensive methodology integrating metagenomics and untargeted metabolomics based on UHPLC-MS/MS (Orbitrap Q Exactive HF-X) to elucidate the dynamic profiles of the microbial community and non-volatile metabolites, as well as their interrelations, across the various spontaneous fermentation stages of LVBs.

RESULTS: Metagenomic analysis indicated reduced microbial diversity and substantial structural changes within the community. Bacteria dominated the fermentation, accounting for 69.16 - 99.04% of the microbial community based on the taxonomically classified reads at the kingdom level. During the preliminary stage, Leuconostoc, Enterobacter, and Klebsiella were the prevalent genera. During the mid-fermentation stage, Komagataeibacter and Lactiplantibacillus emerged as the predominant genera in acid production. In the final stage, the microbial community was dominated primarily by Zymomonas and the Acetobacteriaceae family, including Acetobacter and Komagataeibacter. The non-targeted metabolomics study identified 2,382 metabolites through comprehensive database matching (in-house library, HMDB, KEGG, and metDNA algorithm) and stringent quality filtering (identification score > 0.5 and QC CV < 0.5), which were categorized into 20 distinct groups. Thirty seven metabolites, including amino acids, organic acids, and benzene derivatives, were identified as probable distinct differential metabolites based on a p-value threshold of p < 0.05, VIP > 1.0, and a fold change (FC ≥ 2 or ≤ 0.5) between consecutive fermentation stages in pairwise OPLS-DA of litchi vinegar-like beverage fermentation. Spearman correlation analysis revealed a highly organized ecological interaction network among dominant bacteria, physicochemical parameters, and non-volatile taste metabolites in the LVB fermentation system. Zymomonas mobilis, Acetobacter pasteurianus, Leuconostoc suionicum, and Lactiplantibacillus plantarum facilitated fermentation through metabolic synergy. Meanwhile, stage-specific enrichment of distinct Enterobacteriaceae species (Enterobacter hormaechei, and Enterobacter quasiroggenkampii) reflected species-level niche differentiation and resource competition, rather than a unified family-wide competitive behavior.

DISCUSSION: These findings provide a theoretical framework for engineering synthetic consortia and bioaugmentation approaches, informing the selection of starters and co-cultures to enhance LVB sensory and bioactive properties, alongside facilitating sfruit valorization.},
}

@article {pmid42597276,
year = {2026},
author = {Ding, Y and Li, Q and He, F and Zheng, Q and Zhao, G and Wan, J and Fang, Y and Yang, T and Zou, L and Yu, W and Dai, J},
title = {The Impact of Human Immunodeficiency Virus Co‑Infection on the Pathogen Spectrum and Outcomes of Severe Community‑Acquired Pneumonia: Insights from Metagenomic Next‑Generation Sequencing.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {599541},
pmid = {42597276},
issn = {1178-6973},
abstract = {PURPOSE: Severe community-acquired pneumonia (SCAP) causes high morbidity and mortality. Metagenomic next-generation sequencing (mNGS) data comparing pathogen profiles in SCAP between people living with human immunodeficiency virus (HIV) (PLWH) and HIV-uninfected individuals remain scarce.

PATIENTS AND METHODS: We retrospectively enrolled 72 SCAP patients at Kunming Third People's Hospital. We compared alpha diversity of respiratory microbiota, pathogen spectrum and healthcare resource utilization (HRU) between the two groups. We also assessed whether HIV infection was an independent risk factor for 30-day mortality.

RESULTS: mNGS detected pathogens in 70 of 72 patients (97.2%). PLWH showed higher detection rates of Pneumocystis jirovecii (p < 0.001), Human gammaherpesvirus 4 (EBV) (p = 0.013), and Human betaherpesvirus 5 (CMV) (p < 0.001). Among the 54 SCAP patients who survived 30 days, HRU metrics did not differ between groups. Elevated D-dimer level was an independent risk factor for 30-day mortality in SCAP patients (hazard ratio [HR]: 1.02, 95% confidence interval [CI]: 1.004-1.030; p = 0.0127).

CONCLUSION: HIV co‑infection in SCAP patients is associated with a distinct pathogen spectrum but does not affect HRU or 30‑day mortality. Elevated D‑dimer level is an independent risk factor for 30‑day mortality in SCAP patients.},
}

@article {pmid42597328,
year = {2026},
author = {Wu, B and Lu, S and Liu, H},
title = {Precision diagnostics in bronchiectasis: current advances in imaging, microbiology, biomarkers, and digital health.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1907636},
pmid = {42597328},
issn = {2296-858X},
abstract = {Bronchiectasis is a complex, chronic airway syndrome driven by a vicious cycle of irreversible bronchial dilatation, impaired mucociliary clearance, recurrent infection, and tissue-destructive inflammation. Reflecting its profound clinical heterogeneity, patients with identical structural damage on high-resolution computed tomography (HRCT) often exhibit divergent profiles in airway microbiology, inflammatory endotypes, exacerbation frequencies, and therapeutic responses, indicating that static anatomical classification fails to capture disease complexity. Sole reliance on visual CT inspection, standard sputum cultures, and subjective symptom tracking misses the driving mechanisms of individual disease progression. Emerging modalities-artificial intelligence (AI)-driven quantitative imaging, molecular microbiology, high-throughput biomarker profiling, and digital remote monitoring-aim to address these gaps. Our analysis shows that while these tools cannot substitute for bedside clinical acumen, they clarify obscure phenotypes, expose actionable treatable traits, and enable earlier, preemptive strategies. This review evaluates these contemporary diagnostic frameworks in non-cystic fibrosis bronchiectasis, dissecting their clinical utility, evidentiary maturity, and the economic and logistical barriers to routine adoption. Given that current evidence remains fragmented, advancing the field demands standardized imaging protocols, transparent algorithmic pipelines, clinically actionable metagenomic reporting, and robust validation in underrepresented Asian and Chinese cohorts. The real challenge lies not in generating more data, but in integrating these heterogeneous, high-dimensional datasets into pragmatic, point-of-care decision pathways that improve patient outcomes without widening disparities in global healthcare delivery.},
}

@article {pmid42597565,
year = {2026},
author = {Okonta, EO and Nnadi, CO and Paul-Chima, UO},
title = {The gut microbiome as a plausible but unproven moderator of cinnamon trial outcomes in type 2 diabetes: toward phytochemical standardization and precision nutraceuticals.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1874182},
pmid = {42597565},
issn = {2296-861X},
abstract = {Cinnamon (Cinnamomum spp.) has been widely investigated as an adjunctive nutraceutical for glycemic management in type 2 diabetes mellitus, yet clinical findings remain inconsistent. This variability is commonly attributed to differences in cinnamon species, dosage, intervention duration, baseline glycemic status and phytochemical standardization, alongside methodological factors such as trial quality, dietary patterns, medication use, adherence and endpoint selection. One potential contributor that has received limited attention is the gut microbiome. We propose a testable hypothesis that a substantial proportion of the marked inter-trial heterogeneity observed in cinnamon meta-analyses (I[2] > 75%) may reflect underlying gut-microbial metabotypes differing in their ability to convert cinnamon polyphenols and procyanidins into bioactive metabolites. Type 2 diabetes is associated with altered microbial composition, reduced butyrate-producing taxa and disrupted metabolic pathways. Cinnamon phytochemicals, including polyphenols, cinnamaldehyde, procyanidins and coumarin, undergo microbial biotransformation that may influence their bioavailability and metabolic effects. Because cinnamaldehyde is rapidly absorbed in the proximal gastrointestinal tract, colon-targeted delivery systems may be required to rigorously evaluate microbiome-mediated mechanisms. No randomized controlled trial has directly examined whether microbiome composition modifies cinnamon's glycemic effects in type 2 diabetes. Future studies should therefore incorporate microbiome-informed designs, including phytochemical fingerprinting, safety monitoring and, where feasible, metagenomic and metabolomic profiling, to distinguish true biological non-response from intervention heterogeneity and advance precision nutraceutical approaches for diabetes management.},
}

@article {pmid42597686,
year = {2026},
author = {Annaswamy, V and Mikesh, M and Dinkeloo, K},
title = {The Microbiome of Nurdles: Life on the Primary Microplastics of the Texas Gulf Coast.},
journal = {microPublication biology},
volume = {2026},
number = {},
pages = {},
pmid = {42597686},
issn = {2578-9430},
abstract = {Nurdles are small, pre-production plastic pellets. Globally, nurdles are the second largest source of microplastic pollution due to release during manufacture and transport. As these nurdles persist in the environment, they undergo weathering-a process that significantly increases surface area and colonization by microbes. To gain an understanding of the composition of the microbiome found on nurdles, full-length 16S targeted metagenomic sequencing was performed on DNA extracted from nurdles collected from the Texas Gulf Coast. Sequencing data showed a greater amount and diversity of microbes found to be associated with nurdles than with the sand from which the nurdles were collected.},
}

@article {pmid42597889,
year = {2026},
author = {Ren, S and Ren, S and Chen, H and Zhang, W and Zhang, T and Chong, H and Wang, Z and Cao, W and Yong, X and Zhou, J},
title = {SuSha: A multi-model ensemble learning framework for predicting microbial salinity adaptation.},
journal = {Engineering microbiology},
volume = {6},
number = {3},
pages = {100292},
pmid = {42597889},
issn = {2667-3703},
abstract = {Current research on microbial salinity adaptation faces substantial challenges, including the limited predictive accuracy of traditional single-gene models and difficulty in dissecting systemic biological responses to salinity stress in complex natural habitats. To overcome these bottlenecks, the multi-model ensemble learning tool SuSha, which leverages genome-wide amino acid composition features, was developed. By extracting features from the whole-genome data of 123 bacterial and archaeal species with well-defined salinity adaptations, a 24-dimensional feature vector was constructed, comprising the frequencies of 20 standard amino acids and four aggregated functional categories. Based on this, an ensemble model was developed by integrating algorithms such as random forest, bagging, and extra trees. Five-fold cross-validation demonstrated that this 24-dimensional feature-based ensemble model achieved a global accuracy of 0.765 and an area under the curve of 0.941, significantly outperforming individual baseline models. Furthermore, the model was externally validated using 2678 metagenomic samples from six global regions, encompassing freshwater, marine, and hypersaline habitats. SuSha exhibited high robustness, ecological consistency across diverse salinity gradients, and a classification accuracy of over 90% for extreme halophiles, particularly within the extreme halophilic range. By enabling high-precision genotype-to-phenotype predictions using a habitat-adaptive algorithm-switching strategy, SuSha provides a robust computational framework for inferring the physiological potential of uncultivated microorganisms and mining microbial resources in extreme environments.},
}

@article {pmid42598143,
year = {2026},
author = {Mollick, SA and Khual, GK and Ghosh, A and Patel, SK and Bhattacharyya, S and Roy, CS and Maile, A and Nagarajaram, HA and Longkumer, M and Babu, MN and Kundapur, AR and Uniyal, S and Chattterjee, A and Mitra, M and Sikdar, M and Urade, BP and Pulamaghatta, VN},
title = {Gut microbial diversity and candidate keystone taxa in Indian tribes: Insights across lifestyle-ecological continuum and health associations.},
journal = {Current research in microbial sciences},
volume = {11},
number = {},
pages = {100650},
pmid = {42598143},
issn = {2666-5174},
abstract = {Despite the critical role of the gut microbiome in host physiology and health, it remains poorly characterized in Indigenous populations undergoing rapid acculturation. This study presents high-resolution, whole-genome metagenomic profiling of gut microbiota from five Particularly Vulnerable Tribal Groups (PVTGs) of Southern India, Irula, Jenu Kuruba, Kurumba, Chenchu, and Konda Savara, spanning distinct ecological zones and cultural transitions. Using an ecology-lifestyle continuum framework, we investigated taxonomic and functional diversity with a focus on identifying computationally inferred candidate keystone taxa, defined by their association with variation in community ordination structure. A leave-one-taxon-out ordination framework identified 121 candidate keystone taxa, many of which were population-specific and have not been widely reported. Functional analyses revealed a conserved core of metabolic pathways, including glycolysis and folate biosynthesis, alongside group-specific enrichment in xenobiotic degradation, amino acid biosynthesis, mucin metabolism, and lipid processing, associated with differences in dietary and environmental exposures across populations. Large-scale disease-association mapping (n = 5,625) linked 50 candidate keystone taxa to 14 conditions, with 44 associated with health and 6 with disease. While Fusicatenibacter saccharivorans and Alistipes shahii were enriched in healthy states, Ruminococcus gnavus, Bifidobacterium longum, Flavonifractor plautii, and Blautia wexlerae were enriched in disease-associated profiles. Cross-cohort validation against an independent set of traditional metagenomes (n = 119) further showed that a subset of Indian tribal core candidate keystone taxa was consistently identified across geographically distinct populations, with partial conservation of community associations and health associations, indicating reproducible context-dependent microbial association patterns across traditional populations. Alpha diversity was highest in minimally acculturated groups, with higher degrees of acculturation associated with reduced microbial diversity and greater enrichment of disease-associated taxa. Overall, this study provides a context-aware framework for understanding gut microbiome dynamics in culturally transitioning populations, emphasizing the conservation of microbial heritage and informing population-specific microbiome-based interventions.},
}

@article {pmid42598172,
year = {2026},
author = {Udahemuka, JC and Cassidy, H and Schuele, L and Uwibambe, E and Ngabo, MG and Masirika, LM and Sindayiheba, R and Otani, S and Gashegu, M and Twizere, JC and Aarestrup, F and Ndayisenga, F and Oude Munnink, BB and Koopmans, MPG and Ndishimye, P},
title = {Persistent circulation of Rift Valley fever virus lineage C in Rwanda, 2022-2025.},
journal = {One health (Amsterdam, Netherlands)},
volume = {23},
number = {},
pages = {101529},
pmid = {42598172},
issn = {2352-7714},
abstract = {Rwanda has experienced recurrent Rift Valley fever virus outbreaks in the last decade. In this study, we investigated whether these outbreaks resulted from repeated introductions or sustained local circulation. We generated RVFV whole-genome sequences from livestock samples collected between 2022 and 2025 using Nanopore sequencing. Genomic analyses indicated the outbreaks resulted from sustained local circulation of lineage C rather than repeated introductions, suggesting ongoing transmission likely driven by sporadic spillover. This study underscores the importance of continuous genomic One Health surveillance in endemic settings.},
}

@article {pmid42598412,
year = {2026},
author = {Wang, X and Chen, W and Zhang, H and Cao, D and Sun, J and Hu, H},
title = {Gut microbial biomarkers for major depressive disorder: a cross-sectional study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1690285},
pmid = {42598412},
issn = {2235-2988},
mesh = {Humans ; *Major Depressive Disorder/microbiology/diagnosis/virology ; *Biomarkers/analysis/blood ; Cross-Sectional Studies ; *Gastrointestinal Microbiome ; Female ; Adult ; Male ; Metagenomics ; Bacteria/genetics/classification/isolation & purification ; Middle Aged ; Viruses/genetics/classification/isolation & purification ; Feces/microbiology/virology ; },
abstract = {BACKGROUND: Alterations in the gut microbiota have been associated with a variety of psychiatric disorders, including major depressive disorder (MDD). However, the relationship between MDD and gut microbial communities remains incompletely understood. Most previous studies have primarily focused on gut bacteria, with relatively limited attention to other microbial components.

METHODS: In this study, we analyzed gut microbial profiles from 36 patients with MDD and 36 healthy controls using metagenomic sequencing data. The MaAsLin2 algorithm was applied to identify potential microbial biomarkers associated with MDD.

RESULTS: A total of 6 bacterial biomarkers and 7 viral biomarkers were identified. The models based on these features demonstrated strong predictive performance, with area under the curve (AUC) values of 0.891 for bacteria and 0.878 for viruses. Notably, the combined bacterial-viral model achieved an AUC of 0.946. These findings were further evaluated through external testing in two unrelated research cohorts. In the Shanxi cohort, the AUC values were 0.825 (bacteria), 0.803 (viruses), and 0.972 (combined model). In the Wuhan cohort, the AUC values were 0.683 (bacteria), 0.693 (viruses), and 0.784 (combined model).

CONCLUSION: In summary, our results highlight the potential of gut bacterial and viral biomarkers as candidate biomarkers and potential auxiliary tools for MDD assessment and suggest that integrating multi-domain microbial features may improve prediction accuracy.},
}

Humans
*Major Depressive Disorder/microbiology/diagnosis/virology
*Biomarkers/analysis/blood
Cross-Sectional Studies
*Gastrointestinal Microbiome
Female
Adult
Male
Metagenomics
Bacteria/genetics/classification/isolation & purification
Middle Aged
Viruses/genetics/classification/isolation & purification
Feces/microbiology/virology

@article {pmid42598558,
year = {2026},
author = {Abbasi, H and Hawn, SE and Javanbakht, A and Seedat, S and Bourassa, K and Sinnott, SM and Seligowski, AV and Hemmings, S and Kimbrel, NA and Wolf, E and Smith, AK and Brick, L and Mehta, D},
title = {From molecules to minds: Integrative multi-omics in psychiatry.},
journal = {Journal of mood and anxiety disorders},
volume = {15},
number = {},
pages = {100194},
pmid = {42598558},
issn = {2950-0044},
abstract = {Psychiatric disorders are biologically complex conditions arising from interactions across genomic, epigenomic, transcriptomic, proteomic, metabolomic, and metagenomic layers. Single-omics approaches rarely capture more than a fraction of the variance in complex conditions, underscoring the importance of integrative multi-omics frameworks. This mini-review summarizes key methodologies and their application in psychiatric research, with a focus on systems-level integration of genomic risk scores, transcriptomic networks, and neuroimaging data to advance biological understanding of disorders such as depression, schizophrenia, and Alzheimer's disease. We also outline the infrastructural requirements for effective multi-omics research, including standardized biobanking, Laboratory Information Management Systems, adherence to FAIR data principles, and federated learning approaches for privacy-preserving analysis. Importantly, we highlight the need for greater global inclusivity in psychiatric genomics. Current datasets are heavily biased toward relatively high-resourced and predominantly White, non-Hispanic populations, limiting generalizability. Initiatives such as the Psychiatric Genomics Consortium-Africa and H3ABioNet demonstrate how locally led efforts can strengthen capacity, promote data sovereignty, and support equitable research practices. Advancing multi-omics psychiatry will require coordinated investment in infrastructure, training, and inclusive international collaboration. This mini-review serves primarily as a conceptual roadmap, highlighting what integrative approaches have demonstrated so far and future directions for the field.},
}

@article {pmid42598885,
year = {2026},
author = {Baidya, AK and Aich, P},
title = {Serum-Cecal Metabolome Integration Predicts Gut Microbial Communities and Reveals Pathway-Level Host-Microbe Crosstalk Under Disease-Induced Dysbiosis.},
journal = {Omics : a journal of integrative biology},
volume = {},
number = {},
pages = {15578100261479266},
doi = {10.1177/15578100261479266},
pmid = {42598885},
issn = {1557-8100},
abstract = {The gut microbiome shapes systemic physiology through metabolites that enter circulation, yet most computational approaches focus on predicting metabolite profiles from microbial features rather than inferring microbial composition from host metabolomes. Here, we investigate whether host-derived metabolomic profiles can be leveraged to predict gut microbial community structure and to determine how disease-associated dysbiosis reshapes metabolite-microbe interactions and gut-to-systemic metabolic communication. We developed an integrative multi-omics framework combining serum and cecal metabolomics with 16S rRNA-based microbiome profiling. Supervised learning models demonstrated that cecal metabolites carry predictive signals for microbial abundances across conditions. Regularized canonical correlation analysis (rCCA) revealed cross-compartment metabolite-microbe networks. These analyses showed both conserved and condition-specific interaction patterns, indicating substantial network reorganization under disease-associated dysbiosis. Pathway-level integration further identified metabolic pathways linking the gut microbiome, the cecal environment, and the systemic circulation, representing coordinated gut-to-systemic communication axes. Together, our results establish a multi-omics strategy for predictive inference of gut microbial composition from host metabolomes and provide a framework for identifying pathway-level mechanisms underlying host-microbe metabolic crosstalk.},
}

@article {pmid42599000,
year = {2026},
author = {Wang, W and Jiang, L and Niu, T and Zhang, M and Chen, L and Jia, X and Yuan, L and Tian, K and Li, X},
title = {Resolving the Phylogenetic Placement of the FSfaCV/PCV5-Related Viruses Within the Genus Macochavirus.},
journal = {Transboundary and emerging diseases},
volume = {2026},
number = {1},
pages = {e8481347},
doi = {10.1155/tbed/8481347},
pmid = {42599000},
issn = {1865-1682},
support = {2023YFD1800500//National Key Research and Development Program of China/ ; 32500538//National Natural Science Foundation of China/ ; D18007//111 Project/ ; //Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; },
mesh = {Animals ; *Phylogeny ; Genome, Viral ; Swine ; *Swine Diseases/virology/epidemiology ; China/epidemiology ; *DNA Viruses/genetics/classification ; Circovirus/genetics ; },
abstract = {Metagenomic analysis of fecal samples from diarrheic pigs in China identified 10 complete circular single-stranded DNA viral genomes previously designated as putative porcine circovirus 5 (PCV5)-like viruses. Genome characterization revealed a typical cressdnavirus organization with bidirectionally oriented Rep and Cap genes. Phylogenetic analyses based on complete genomes and encoded proteins showed that these viruses do not cluster with members of Circoviridae but instead form a distinct lineage within the family Pecoviridae, closely related to the genus Macochavirus. Sequence identity, genetic distance, and nucleotide diversity analyses supported their classification as a coherent viral group. Comparative analyses indicated greater sequence divergence in the Rep region than in the Cap region. These findings support reclassification of putative PCV5 as a porcine-associated lineage within the genus Macochavirus, designated porcine Macochavirus (PMV), thereby resolving their long-standing taxonomic ambiguity and expanding the recognized diversity of cressdnaviruses within the family Pecoviridae.},
}

Animals
*Phylogeny
Genome, Viral
Swine
*Swine Diseases/virology/epidemiology
China/epidemiology
*DNA Viruses/genetics/classification
Circovirus/genetics

@article {pmid42599081,
year = {2026},
author = {Buddhasiri, S and Singhla, T and Pengpanun, S and Eiamsam-Ang, T and Thiennimitr, P},
title = {Shotgun metagenomic sequence data from milk and fecal samples of dairy cattle in Thailand.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0056426},
doi = {10.1128/mra.00564-26},
pmid = {42599081},
issn = {2576-098X},
abstract = {We report shotgun metagenomic sequence data from milk and fecal samples of dairy cattle in Thailand. This data set captures microbial genetic profiles from mammary- and gut-associated sample types and provides a resource for future comparative microbiome, functional, and antimicrobial resistance gene analyses in dairy cattle.},
}

@article {pmid42599332,
year = {2026},
author = {Lee, SY and Hwang, S and Cho, I and Lee, H and Lee, J and Koo, D and Kim, JW and Cho, KS},
title = {Functional dynamics and interactions within the bacterial community responsible for biodegradable plastic degradation during aerobic composting.},
journal = {Biodegradation},
volume = {37},
number = {4},
pages = {},
pmid = {42599332},
issn = {1572-9729},
support = {RS-2025-02311604 & RS-2025-07902968//Ministry of Trade, Industry and Energy/ ; },
mesh = {*Composting ; Biodegradation, Environmental ; Aerobiosis ; *Bacteria/metabolism/genetics/classification ; *Biodegradable Plastics/metabolism ; Polyesters/metabolism ; Polyhydroxybutyrates ; Sewage/microbiology ; *Plastics/metabolism ; },
abstract = {Though biodegradable plastics have been widely developed as sustainable alternatives to petroleum-based plastics, their degradation behavior and microbial interactions in composting environments remain insufficiently understood. In this study, the degradation characteristics of polyhydroxybutyrate (PHB), polylactic acid (PLA), polybutylene adipate terephthalate (PBAT), and polybutylene succinate (PBS), and the interactions between bacterial communities and functional genes, were evaluated in a 41-day aerobic composting system using anaerobically digested sewage sludge as substrate. Composting parameters were similarly affected by all biodegradable plastics, and the final compost reached a Solvita compost maturity index of 8.0 with no detectable pathogenic bacteria and a CO2 index of 7.83, indicating stable composting. After 41 days of composting, microcracks and microbial attachment were observed on all biodegradable plastic surfaces, with PHB and PBAT showing the most pronounced structural damage and biofilm formation, whereas microbial attachment to PLA was limited. Although biodegradable plastic addition did not greatly alter the overall bacterial community structure, it selectively promoted specific bacterial genera (Symbiobacterium, Paenibacillus, and Psychrobacillus). PICRUSt2-based functional gene prediction revealed that PHB degradation-related genes exhibited the highest predicted abundance, whereas PLA- and PBS-related genes showed low abundance, indicating differences in functional degradation potential among plastic types. Positive correlations among esterase- and hydrolase-related genes under biodegradable plastic-amended conditions suggest that coordinated microbial functional responses to biodegradable plastic addition. Network analysis further indicated that biodegradable plastic addition influenced interactions between specific bacterial genera and degradation-related functional genes. Overall, this study provides insights into bacterial functional adaptation during biodegradable plastic degradation under aerobic composting conditions.},
}

*Composting
Biodegradation, Environmental
Aerobiosis
*Bacteria/metabolism/genetics/classification
*Biodegradable Plastics/metabolism
Polyesters/metabolism
Polyhydroxybutyrates
Sewage/microbiology
*Plastics/metabolism

@article {pmid42586034,
year = {2026},
author = {Ibarbalz, FM and Pierella Karlusich, JJ},
title = {Genes from the deep: Evolution's untapped biotechnology.},
journal = {Cell host & microbe},
volume = {34},
number = {8},
pages = {1486-1488},
doi = {10.1016/j.chom.2026.07.004},
pmid = {42586034},
issn = {1934-6069},
mesh = {*Biotechnology ; Metagenomics/methods ; Evolution, Molecular ; *Bacteria/genetics ; },
abstract = {The deep sea, Earth's largest yet least-explored biome, harbors vast microbial diversity. In this issue of Cell Host & Microbe, Guo et al. uncover its hidden functional potential through metagenomics guided by AI-predicted protein folds, while Eriksson et al. reveal how microbial diversity is structured across latitude and depth.},
}

*Biotechnology
Metagenomics/methods
Evolution, Molecular
*Bacteria/genetics

@article {pmid42586263,
year = {2026},
author = {Zhou, Y and Guo, Q and Zhao, X and Zhang, W and Zhang, H and Huang, S and He, Z and Xie, Y and Zhang, W and Gu, J and Pan, S and Li, W},
title = {Blood and gut virome remodeling in gastric cancer: Anellovirus expansion and novel virus discovery.},
journal = {Virologica Sinica},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.virs.2026.08.010},
pmid = {42586263},
issn = {1995-820X},
abstract = {Gastric cancer (GC) is a prevalent malignancy worldwide, yet effective early diagnostic tools remain lacking, and the role of the virome, a key component of the tumor microenvironment, in GC progression is largely unknown. This study aimed to characterize the virome landscapes in peripheral blood and feces of GC patients versus healthy controls, and to identify viral signatures associated with GC onset and metastasis. We performed viral metagenomic sequencing on pooled libraries from 100 GC patients (45 non-metastatic, 55 metastatic) and 50 healthy controls, followed by taxonomic annotation, diversity assessment, LEfSe differential abundance testing, and co-occurrence network analysis. In blood, the GC virome shifted from a bacteriophage-dominated profile in controls to one overwhelmingly dominated by Anelloviridae (> 80%), with significantly decreased alpha diversity. In contrast, the gut virome of GC patients showed increased alpha diversity and coexistence of diverse bacteriophages. LEfSe identified betatorquevirus in blood as a key discriminatory taxon for GC. Network analysis revealed negative correlations between Anelloviridae and multiple bacteriophage families, suggesting niche competition. We also discovered 67 provisional novel anellovirus species and one novel gemykibivirus in GC patient blood. Collectively, our findings indicate that GC is associated with compartment-specific virome remodeling in blood and gut, and that expansion of blood anelloviruses holds promise as a non-invasive biomarker. This study provides a foundational resource for understanding the virome's role in GC.},
}

@article {pmid42586379,
year = {2026},
author = {Zhuo, Q and Wei, R and Su, Y and Shao, H and Han, L and Huang, G},
title = {Responses of biogeochemical cycles to polyethylene microplastics exposure during aerobic fermentation of dairy manure.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135605},
doi = {10.1016/j.biortech.2026.135605},
pmid = {42586379},
issn = {1873-2976},
abstract = {Microplastics (MPs) are emerging contaminants that may disrupt Earth's biogeochemical cycles of elements, yet their effects on multi-element cycling during aerobic fermentation of livestock manure remain unclear. This study evaluated how polyethylene (PE) MPs and fermentation strategy affected multi-element functional potential during aerobic fermentation of dairy manure solids by integrating metagenomic functional profiling, co-occurrence networks, and other complementary approaches. Fermentation time dominated functional gene succession, with treatment separation becoming most evident on day 30. Biomarkers were confined to the C cycling and detected only in the low concentration treatments, with none at the higher concentration. Network analysis revealed predominantly positive associations among genes involved in different elemental cycles. The membrane-covered treatment at the lower concentration formed the most connected network. The pathway profiles and network topology in the membrane-covered treatment at the higher concentration were similar to those of the blank control. This suggests that, under high MPs exposure, the membrane-covered treatment retained a functional profile similar to the blank control, likely in association with the more stable fermentation conditions in the membrane-covered treatment. Physicochemical properties, process variables, and gas emissions jointly explained 78% of functional gene variation. Mantel tests and structural equation modelling further linked fermentation conditions, gas emissions, and multi-element functional potential. Overall, multi-element functional responses to MP exposure varied with fermentation stage, strategy, and PE MP concentration. These findings highlight the importance of fermentation management when assessing multi-element functional responses to MP exposure during manure valorization.},
}

@article {pmid42586589,
year = {2026},
author = {Carsello, EA and Liston, K and Maust, B and Deutsch, G and Wright, J and Wong, S and Morgan, L and Vora, S},
title = {Balamuthia mandrillaris presenting as central nervous system vasculitis in a young child.},
journal = {BMJ case reports},
volume = {19},
number = {8},
pages = {},
doi = {10.1136/bcr-2026-275051},
pmid = {42586589},
issn = {1757-790X},
mesh = {Humans ; *Vasculitis, Central Nervous System/parasitology/diagnosis ; Male ; *Balamuthia mandrillaris/isolation & purification/genetics ; *Amebiasis/diagnosis/parasitology/complications/drug therapy ; Brain/pathology/parasitology ; Diagnosis, Differential ; },
abstract = {Balamuthia mandrillaris is a rare and difficult-to-diagnose infection with high mortality. We present the case of an immunocompetent toddler presenting with central nervous system (CNS) vasculitis. He was initially diagnosed with Takayasu arteritis and had an initial period of improvement following immunosuppressive therapy. Subsequently, he had rapid decompensation with diffuse intracranial lesions progressing to severe neurological injury and compassionate extubation. Metagenomic sequencing of the CSF and pathology and PCR from brain biopsy were positive for B. mandrillaris To our knowledge, this is the first case of Balamuthia presenting as a mixed vessel CNS vasculitis and highlights the importance of consideration of this infection in cases of vasculitis, particularly in mixed vessel disease. It further demonstrates the potential use of newer diagnostics, namely CSF metagenomic testing and amoeba PCR, in earlier diagnosis and treatment.},
}

Humans
*Vasculitis, Central Nervous System/parasitology/diagnosis
Male
*Balamuthia mandrillaris/isolation & purification/genetics
*Amebiasis/diagnosis/parasitology/complications/drug therapy
Brain/pathology/parasitology
Diagnosis, Differential

@article {pmid42586639,
year = {2026},
author = {Humayun, S and Justine, EE and Rjabovs, V and Lee, HJ and Darko, CNS and Reile, I and Kim, YJ and Tuvikene, R},
title = {Gut-protective efficacy of red algal galactans: The role of structure and molecular weight.},
journal = {Carbohydrate polymers},
volume = {389},
number = {},
pages = {125609},
doi = {10.1016/j.carbpol.2026.125609},
pmid = {42586639},
issn = {1879-1344},
mesh = {Molecular Weight ; Humans ; *Galactans/chemistry/pharmacology/isolation & purification ; *Rhodophyta/chemistry ; Animals ; Caco-2 Cells ; Oxidative Stress/drug effects ; Rheology ; Mice ; },
abstract = {Linking structure, rheology, and bioactivity, this study demonstrates how red algal galactans can be tailored as functional food ingredients with gut-protective potential. Funoran and furcellaran were isolated from Gloiopeltis furcata and Furcellaria lumbricalis, respectively, and characterized using chromatographic and NMR spectroscopic techniques. Funoran was identified as a highly sulfated, methoxylated agaran (22.7% sulfate), whereas furcellaran exhibited a hybrid κ-/β-carrageenan structure (17.4% sulfate). High molecular weights (3955 and 2966 kDa) were observed and reduced via controlled autohydrolysis without sulfate loss. Structural variations governed rheological behavior, with furcellaran showing ion-dependent gelation and funoran forming weaker networks. Both native and depolymerized galactans were non-cytotoxic to Caco-2 cells, maintained tight junction integrity, and reduced oxidative stress. In a DSS-induced colitis model, treatments alleviated clinical symptoms, decreased pro-inflammatory cytokines and MPO activity, and restored barrier-related proteins. Metagenomic analysis revealed partial correction of dysbiosis, including enrichment of short-chain fatty acid producing taxa, particularly in depolymerized funoran. Overall, structural features and molecular weight critically determine both rheological and biological functions. Depolymerization enhances fermentability while preserving bioactivity, highlighting red-algal galactans as promising multifunctional hydrocolloids for food and gut health applications.},
}

Molecular Weight
Humans
*Galactans/chemistry/pharmacology/isolation & purification
*Rhodophyta/chemistry
Animals
Caco-2 Cells
Oxidative Stress/drug effects
Rheology
Mice

@article {pmid42586789,
year = {2026},
author = {Deas, G and Macgregor, K and Kite, D and Ward, H and May, A and Powell, M and Jenkins, M},
title = {HIV-associated CD8 encephalitis: role of metagenomics in complex CNS presentations.},
journal = {Practical neurology},
volume = {},
number = {},
pages = {},
doi = {10.1136/pn-2026-005308},
pmid = {42586789},
issn = {1474-7766},
abstract = {We describe a 54-year-old woman living with HIV who presented with a tonic-clonic seizure and rapidly progressive encephalitis. Despite an undetectable plasma viral load while taking Biktarvy, initial investigations revealed cerebrospinal fluid escape with an HIV viral load of 474 copies/mL. Extensive testing for opportunistic infections and autoantibodies was negative. Brain biopsy and metagenomic next-generation sequencing identified frequent CD8+ T-cell infiltration and human pegivirus, though the latter was deemed a bystander. The patient's condition improved significantly, notably without the high-dose corticosteroids typically required for CD8+ encephalitis. This recovery suggests a moderate, self-limiting phenotype of the disease. The case highlights the diagnostic utility of metagenomics in complex presentations while cautioning against the misinterpretation of non-pathogenic commensals.},
}

@article {pmid42587158,
year = {2026},
author = {Sinha, T and Brushett, S and Fernández-Pato, A and Garmaeva, S and Andreu-Sánchez, S and Spreckels, JE and Mallon, CA and Kuzub, N and Gois, MB and Wu, J and Kruk, M and Jankipersadsing, SA and Dekens, JAM and Gacesa, R and Vila, AV and Bang, C and Perenboom, C and Franke, A and Tytgat, HLP and Mottaz, SC and Peters, L and de Jonge, A and Verkade, HJ and Swertz, MA and Wijmenga, C and Kuipers, F and Scherjon, S and Sikkema, J and Sprikkelman, AB and de Kroon, MLA and Prins, JR and Gordijn, SJ and Koppelman, GH and Reijneveld, SA and , and Fu, J and Yassour, M and Kurilshikov, A and Zhernakova, A},
title = {Maternal influences on infant gut microbiome and health.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {42587158},
issn = {1476-4687},
abstract = {The establishment of the infant gut microbiome is critical for later health[1,2], yet how it is shaped by maternal and early-life factors remains unclear. Here we metagenomically sequenced 4,526 longitudinal faecal samples from 714 mother-infant pairs in the Dutch birth cohort Lifelines NEXT, spanning 12 weeks of pregnancy to 1 year postpartum. We integrated these data with 474 clinical and exposure variables, and with ultra-deep sequencing of breast milk and vaginal microbiomes. We observe that the maternal gut microbiome undergoes only subtle changes during pregnancy and postpartum, influenced by diet, infections and pre-pregnancy smoking. The maternal gut microbiome is a major reservoir for infant gut strains, with only occasional transmission from vaginal and breast milk microbiomes. Mother-infant gut strain sharing is time dependent, and higher maternal gut species abundance increases the likelihood of strain transmission. We find that the maternal gut microbiome is a predictor of infant eczema. Mode of delivery and feeding mode primarily shaped the infant gut microbiome and its functional profiles, with maternal exposures also having a role. Of 585 vaginally delivered infants, 155 were born at home, but home delivery was only moderately associated with infant gut microbiome composition, similar to other birth parameters such as duration of pushing and ruptured membranes. Overall, we highlight the central role of the mother and her microbiome in shaping the infant gut ecosystem and early health outcomes.},
}

@article {pmid42587419,
year = {2026},
author = {Chang, H and Yang, Y and Zhang, P and Lei, Z and Zhang, Y and Li, S and Wang, L and Wang, Y and Jiang, J and Li, L and Shi, H and Shi, A},
title = {Disrupted Gut Viral-Bacterial Ecology of Patients With Liver Cirrhosis.},
journal = {Liver international : official journal of the International Association for the Study of the Liver},
volume = {46},
number = {9},
pages = {e70836},
pmid = {42587419},
issn = {1478-3231},
support = {2025JC-YBQN-1179//Natural Science Basic Research Program of Shaanxi Province/ ; 2025SCIPT-63//Scientific Research Supporting Fund of the Second Affiliated Hospital of Xi'an Jiaotong University/ ; },
mesh = {Humans ; *Liver Cirrhosis/microbiology/virology ; *Virome ; *Gastrointestinal Microbiome ; Feces/microbiology/virology ; *Bacteria/genetics ; Case-Control Studies ; Metagenome ; Metagenomics ; Male ; },
abstract = {BACKGROUND: The gut microbiota contributes to liver cirrhosis (LC), yet the gut virome and its cross-kingdom ecology with bacteria are less well defined.

METHODS: To characterize LC-associated virome alterations and assess their clinical relevance, we reanalyzed publicly available faecal metagenomes from patients with LC and healthy controls. After quality control and removal of human reads, sequences were mapped to the Chinese Gut Viral Catalogue at 95% nucleotide similarity, viral operational taxonomic units (vOTUs) were annotated using the latest ICTV framework, and viral functions were inferred by KEGG annotation. Differential vOTUs and bacterial species, virus-bacteria networks and random forest classifiers were constructed with internal and external validation.

RESULTS: LC showed reduced viral richness and Shannon diversity, and a distinct Bray-Curtis separation from controls. Ten viral families and 473 vOTUs differed between groups (59 LC-enriched). KEGG-based profiling highlighted functional shifts in LC-enriched viruses, including increased K01185 (lysozyme) and K02172 (blaR1). Virus-bacteria networks were markedly sparser in LC than in controls (130 vs. 509 significant correlations). A virome-based random forest model distinguished patients from controls with high accuracy in internal (optimal AUC = 0.911) and external (optimal AUC = 0.773) validation cohorts, and the model combining viral and bacterial features achieved similarly robust performance.

CONCLUSIONS: LC is associated with disrupted gut viral-bacterial ecology, and virome features show promise as non-invasive biomarkers, warranting longitudinal and mechanistic follow-up.},
}

Humans
*Liver Cirrhosis/microbiology/virology
*Virome
*Gastrointestinal Microbiome
Feces/microbiology/virology
*Bacteria/genetics
Case-Control Studies
Metagenome
Metagenomics
Male

@article {pmid42587714,
year = {2026},
author = {Becherucci, V and Romano, F and Russo, E},
title = {Artificial Intelligence for Integrated Analysis of Non-Blood Biological Fluids: From Biomarker Discovery to Clinical Decision-Support Systems.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {16},
number = {15},
pages = {},
doi = {10.3390/diagnostics16152478},
pmid = {42587714},
issn = {2075-4418},
abstract = {The analysis of non-blood biological fluids, including cerebrospinal fluid (CSF), serous effusions, and synovial fluid, plays a central role in laboratory medicine by providing essential diagnostic and prognostic information for neurological, infectious, inflammatory, and neoplastic diseases. However, the interpretation of these specimens remains challenging because it requires the integration of heterogeneous biochemical, cytological, microbiological, molecular, and clinical data, often in the absence of standardized analytical workflows. Artificial intelligence (AI), particularly Machine Learning (ML) and Deep Learning (DL), is emerging as a powerful approach for extracting clinically relevant information from complex multidimensional datasets beyond the capabilities of conventional analytical methods. AI-driven Clinical Decision-Support Systems (CDSSs) can integrate laboratory findings with clinical, demographic, imaging, and multi-omics data, supporting diagnostic interpretation, patient stratification, and personalized clinical decision-making. At the same time, the convergence of AI with proteomics, metabolomics, metagenomics, and other omics technologies is accelerating biomarker discovery and advancing precision laboratory medicine. Current evidence indicates different levels of maturity across biological fluids. AI-assisted interpretation of CSF biomarkers and digital cytology of serous effusions currently show the strongest clinical evidence, whereas applications involving synovial fluid and integrated multi-omics remain largely exploratory. Although important technical, methodological, and regulatory challenges still limit widespread clinical implementation, AI has the potential to improve diagnostic accuracy, reduce interpretative variability, and support more integrated diagnostic workflows. This mini-review summarizes current and emerging AI applications in non-blood biological fluid analysis, with particular emphasis on biomarker discovery, CDSS, multi-omics integration, current evidence, existing limitations, and future perspectives for precision laboratory medicine.},
}

@article {pmid42587989,
year = {2026},
author = {Zhang, X and Sun, L and Yang, L and Li, X and Cao, Z and Pan, C},
title = {Identification of Key Microorganisms and Metabolic Pathways Associated with the Formation of Off-Flavour Compounds in the Pit Mud of Strong-Flavour Baijiu.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {15},
pages = {},
doi = {10.3390/foods15152731},
pmid = {42587989},
issn = {2304-8158},
support = {231111112000//Henan Province/ ; },
abstract = {Off-flavours represent one of the most prevalent and severe causes of deteriorating pit mud quality in Strong-Flavour Baijiu production. However, the key compounds responsible for these off-flavours and their formation mechanisms remain poorly understood, thereby limiting quality control in the production process of Strong-Flavour Baijiu pit mud. To investigate the origin of off-flavours in pit mud, this study employed gas chromatography-mass spectrometry coupled with metagenomic methods to compare samples from normal and off-flavoured pit mud. The results show that the main cause of off-flavours in pit mud is the abnormal accumulation of acids such as heptanoic acid and hexanoic acid due to imbalanced nutrient ratios, along with insufficient synthesis of key esters including ethyl hexanoate, ethyl butyrate, and ethyl lactate; microorganisms such as Fermentimonas, Methanoculleus, Hortaea and Proteiniphilum, which are non-strictly anaerobic and acid-sensitive in the pit mud, are key microbes associated with these odour compounds. Furthermore, based on the annotation from the KEGG database, this study further inferred the possible microbial metabolic pathways that could lead to the formation of these off-flavour compounds, including starch and cellulose degradation pathways, biosynthesis pathways of valine, leucine, and isoleucine, pyruvate metabolism pathways, and butyric acid metabolism pathways. In summary, the study systematically analysed the key substances related to the odour of the pit mud of strong-flavour Chinese Baijiu and its microbial sources, providing a theoretical basis for the quality regulation of the pit mud during production and developing high-quality artificial pit mud.},
}

@article {pmid42587998,
year = {2026},
author = {Lefèvre, H and Fadhlaoui, K and Guez, JS and Lainé, E and Beyssac, E},
title = {Resistance of Bamboo Fibers to Gastrointestinal Digestion and Their Nutrient-Dependent Fermentation by Human Gut Microbiota.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {15},
pages = {},
doi = {10.3390/foods15152740},
pmid = {42587998},
issn = {2304-8158},
abstract = {Bamboo fibers are increasingly incorporated into food products as sustainable dietary fiber ingredients, yet their gastrointestinal digestion resistance and fermentative behavior by human gut microbiota remain insufficiently characterized. This study combined an INFOGEST-based in vitro digestion protocol with colonic fermentation using fecal microbiota from three healthy donors as an exploratory donor panel. Bamboo fibers were resistant to salivary, gastric, and intestinal enzymatic hydrolysis, as demonstrated by the absence of structural modifications in FTIR spectra, preserved morphology observed by scanning electron microscopy, and negligible release of reducing sugars (<0.1 g/L across all digestive phases), in contrast to extensively hydrolyzed wheat starch used as a positive control. During in vitro colonic fermentation, microbial responses were strongly dependent on substrate availability. In nutrient-limited minimal medium, bamboo fiber supplementation increased gas production, acidification, and SCFA formation compared with control conditions. Concomitantly, SCFA concentrations increased under minimal-medium conditions, although the magnitude of the response varied among donors, with the strongest changes observed for donor 1 (acetate reaching 5.4 vs. 3.3 g/L and propionate 1.48 vs. 0.76 g/L). These effects were markedly attenuated in nutrient-rich medium, indicating competition with readily fermentable substrates. Beta-diversity analyses and metagenomic profiling revealed that microbial community composition clustered primarily according to donor identity rather than experimental conditions. SEM further showed surface erosion and microbial attachment on fermented fibers, supporting partial structural alteration. Overall, bamboo fibers are resistant to upper gastrointestinal digestion but display context-dependent fermentative activity by human gut microbiota under carbohydrate-limited conditions, highlighting the importance of inter-individual variability, dietary context and substrate availability in determining their fermentative potential.},
}

@article {pmid42588064,
year = {2026},
author = {De Sales-Millan, A and Reyes-Ferreira, P and González-Cervantes, RM and Luna-Álvarez, M and Guillén-López, S and Cobo-Díaz, JF and Ramos, S and Aguirre-Garrido, JF and Velázquez-Aragón, JA},
title = {Clinical Improvement and Taxonomic-Functional Gut Microbiome Remodeling After Six Months of Multi-Strain Synbiotic Supplementation in Mexican Children with Autism Spectrum Disorder.},
journal = {Nutrients},
volume = {18},
number = {15},
pages = {},
doi = {10.3390/nu18152441},
pmid = {42588064},
issn = {2072-6643},
support = {E022 Program Recursos Fiscales para la Investigación//Instituto Nacional de Pediatria/ ; },
mesh = {Humans ; *Autism Spectrum Disorder/microbiology/therapy ; Male ; *Gastrointestinal Microbiome/genetics ; Female ; Mexico ; Longitudinal Studies ; *Synbiotics/administration & dosage ; Child ; Feces/microbiology ; Child, Preschool ; Probiotics/administration & dosage ; Dietary Supplements ; Treatment Outcome ; RNA, Ribosomal, 16S/genetics ; Dysbiosis/microbiology ; },
abstract = {Background/Objectives: Gut dysbiosis in children with autism spectrum disorder (ASD) has been associated with alterations in microbial ecology and metabolic function that may contribute to gastrointestinal dysfunction and the severity of clinical manifestations. Synbiotic and probiotic supplementation has emerged as a promising microbiome-targeted strategy for ASD; however, its effects on gut microbiome composition, functional potential, and clinical outcomes remain incompletely understood. We conducted a longitudinal study of Mexican children diagnosed with ASD to analyze changes in the composition, diversity, and functional potential of the gut microbiome during six months of multi-strain synbiotic supplementation. Methods: Stool samples were collected from 25 children with ASD at baseline and after 3 and 6 months of multi-strain synbiotic supplementation. Gut microbiome composition and diversity were analyzed by 16S rRNA gene sequencing, whereas whole metagenome sequencing (WMS) was performed in a subset of samples to evaluate the functional potential of the fecal microbiome. Gastrointestinal symptoms were assessed using the Rome IV criteria, and ASD severity was evaluated with the Childhood Autism Rating Scale (CARS). Results: Twenty-five children with ASD completed the 6 months of synbiotic supplementation. Overall, ASD severity decreased, reflected by a reduction in total CARS score, and improvements in several CARS domains. Gastrointestinal symptoms also decreased significantly. Longitudinal microbiome profiling revealed significant taxonomic and diversity changes over the supplementation period, while WMS identified changes in microbial metabolic potential, including enrichment of tryptophan biosynthesis pathways and reduced L-rhamnose degradation. Conclusions: This exploratory research provides proof-of-concept evidence supporting multi-strain synbiotic supplementation in children with ASD. Larger controlled studies are needed to confirm these findings and clarify their relevance to microbiota-gut-brain axis interactions. The observed concordance between clinical improvements and microbiome remodeling supports further investigation of microbiome-targeted interventions according to ASD severity and duration of supplementation.},
}

Humans
*Autism Spectrum Disorder/microbiology/therapy
Male
*Gastrointestinal Microbiome/genetics
Female
Mexico
Longitudinal Studies
*Synbiotics/administration & dosage
Child
Feces/microbiology
Child, Preschool
Probiotics/administration & dosage
Dietary Supplements
Treatment Outcome
RNA, Ribosomal, 16S/genetics
Dysbiosis/microbiology

@article {pmid42588960,
year = {2026},
author = {Kiss, J and Libisch, B and Ozoaduche, CL and Fébel, H and Rasschaert, G and Lambrecht, E and Heyndrickx, M and Szabó, M and Keresztény, T and Posta, K and Olasz, F},
title = {Genetic Elements Associated with the Acquired Resistome of the Gut Microbiota in a Broiler Rooster Flock in Hungary.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {15},
pages = {},
doi = {10.3390/ani16152322},
pmid = {42588960},
issn = {2076-2615},
support = {TKP2020-NKA-24//National Research, Development and Innovation Office/ ; RRF-2.3.1-21-2022-00007//National Research, Development and Innovation Office/ ; 2019-2.1.11-TÉT-2020-00141//National Research, Development and Innovation Office/ ; GINOP_PLUSZ-2.1.1-21-2022-00221//National Research, Development and Innovation Office/ ; },
abstract = {Antibiotic resistance in Gram-negative bacteria poses a global health threat, and poultry farming provides an important reservoir for multidrug-resistant pathogens. Our study aimed to characterize the faecal microbiota and acquired resistome of Ross-308 roosters in Hungary. Amplicon and shotgun metagenomics revealed a faecal microbiota dominated by the Firmicutes, Bacteroidota, and Proteobacteria and a diverse faecal resistome, including qnrB and an aadA1-bearing integron. Culture-based screening of an antibiotic-free rooster yielded the MDR Escherichia coli strain K1G, displaying resistance also to third-generation cephalosporins and fluoroquinolones. Whole-genome sequencing classified K1G as a serotype O23:H16-ST453 avian pathogenic E. coli (APEC) strain featuring a set of chromosomal virulence factors (including astA, hlyE, lpfA, and iss) and three plasmids: a phage-like plasmid, a mosaic virulence plasmid (carrying blaTEM-1b, hlyF, iutA, ompT, iucD, and cvaC), and an IncC type 1 resistance plasmid harbouring blaCMY-2. The detection of identical or closely related ST453 E. coli strains also in broiler meat in Hungary highlights a potential risk of transmission to humans through the food chain. Moreover, the carriage of multiple acquired antibiotic resistance genes in E. coli K1G indicates that individual chickens can harbour or transmit antibiotic resistance even in the absence of direct antibiotic exposure.},
}

@article {pmid42589241,
year = {2026},
author = {Wang, Q and Wang, BY and Wilus, D and Xie, H},
title = {Effects of Non-Surgical Periodontal Therapy on Dental Plaque Microbiome.},
journal = {International journal of molecular sciences},
volume = {27},
number = {15},
pages = {},
doi = {10.3390/ijms27156584},
pmid = {42589241},
issn = {1422-0067},
support = {R16GM149359/GM/NIGMS NIH HHS/United States ; U54MD007586/MD/NIMHD NIH HHS/United States ; },
mesh = {Humans ; *Dental Plaque/microbiology ; *Microbiota/genetics ; Female ; Male ; Adult ; Middle Aged ; *Periodontitis/microbiology/therapy ; Metagenome ; Dental Scaling ; Root Planing ; Metagenomics/methods ; },
abstract = {Periodontitis, a chronic inflammatory disease affecting approximately 40% of U.S. adults aged 30 years and older, is characterized by dysbiosis of the dental plaque microbiome. However, although scaling and root planing (SRP) is the cornerstone of periodontal treatment, its effects on the taxonomic composition and functional potential of the dental plaque microbiome remain incompletely understood. In this study, we used whole-metagenome shotgun sequencing to characterize taxonomic composition and functional potential in dental plaque microbiomes collected from 39 patients with Stage II or III generalized periodontitis before and 3-4 months after SRP. Consistent with clinical improvement, periodontal therapy significantly reduced probing depth, clinical attachment level, bleeding on probing, and plaque index. Whole-metagenome shotgun sequencing identified 3.18 million non-redundant genes and 12,353 microbial species across 78 samples, revealing increased gene and species richness after treatment, along with a significant restructuring of the microbial community. Established periodontal pathogens, including Porphyromonas gingivalis, as well as the emerging pathogens Escherichia coli and Burkholderia multivorans, decreased following treatment. Tannerella forsythia also showed a marked reduction after treatment, although this decrease was not significant after false discovery rate (FDR) correction. In contrast, health-associated early colonizers, including multiple Actinomyces species and Streptococcus cristatus, increased. Functional annotation using the Carbohydrate-Active Enzymes (CAZy) database identified significant treatment-associated differences in carbohydrate-active enzymes, including multiple glycosyltransferases, indicating remodeling of the predicted functional potential of the dental plaque microbiome. These findings demonstrate that successful SRP promotes coordinated taxonomic and predicted functional remodeling of the dental plaque microbiome and highlight the value of shotgun metagenomic sequencing for characterizing both taxonomic and functional recovery following periodontal therapy.},
}

Humans
*Dental Plaque/microbiology
*Microbiota/genetics
Female
Male
Adult
Middle Aged
*Periodontitis/microbiology/therapy
Metagenome
Dental Scaling
Root Planing
Metagenomics/methods

@article {pmid42589351,
year = {2026},
author = {Shen, H and Huang, S and Wang, Z and Zhou, S and Huang, L and Zhang, H and Han, Y and Jiang, J and Guo, H},
title = {Glycyrrhizic Acid Alleviates Atherosclerosis in ApoE[-/-] Mice via Microbial Indole-3-Lactic Acid-Mediated AhR-p65 Interaction in the Endothelium.},
journal = {International journal of molecular sciences},
volume = {27},
number = {15},
pages = {},
doi = {10.3390/ijms27156694},
pmid = {42589351},
issn = {1422-0067},
support = {No. 3332025150//Fundamental Research Funds for the Central Universities/ ; No. 2025-I2M-KJ-016//CAMS Innovation Fund for Medical Sciences/ ; },
mesh = {Animals ; *Atherosclerosis/drug therapy/metabolism/microbiology/etiology/pathology ; Mice ; *Glycyrrhizic Acid/pharmacology/therapeutic use ; *Receptors, Aryl Hydrocarbon/metabolism ; *Indoles/metabolism ; Male ; *Transcription Factor RelA/metabolism ; *Apolipoproteins E/deficiency/genetics ; Gastrointestinal Microbiome/drug effects ; Diet, High-Fat/adverse effects ; Mice, Inbred C57BL ; Humans ; Fecal Microbiota Transplantation ; Endothelium, Vascular/metabolism/drug effects ; Mice, Knockout ; },
abstract = {Glycyrrhizic acid (GL), a natural triterpenoid glycoside extracted from the "medicine food homology" herb Glycyrrhiza glabra L., exhibits potent anti-atherosclerotic effects; yet its underlying mechanisms remain unclear due to its poor oral bioavailability. The gut microbiota plays a pivotal role in the development of atherosclerosis (AS). In this study, the microbiota-dependent anti-AS effects of GL were evaluated in high-fat diet (HFD)-fed ApoE[-/-] mice using antibiotic depletion and fecal microbiota transplantation (FMT). Integrated metagenomic and metabolomic analyses were performed to identify the key bioactive microbial metabolite. Further in vivo and in vitro experiments, including co-immunoprecipitation and dual-luciferase reporter assays, were utilized to elucidate the underlying molecular mechanisms. It was demonstrated that oral administration of GL alleviated AS in a microbiota-dependent manner by reversing gut dysbiosis, improving intestinal barrier function, and reducing pro-inflammatory lipopolysaccharide (LPS) levels. GL shifted intestinal tryptophan metabolism toward bacterial-derived indole-3-lactic acid (ILA) production, suppressing LPS-induced vascular endothelial adhesion dysfunction by activating the aryl hydrocarbon receptor (AhR). Mechanistically, ILA-activated AhR interacted with the NF-κB subunit p65 in the cytoplasm, effectively preventing the nuclear translocation of p65 and suppressing the promoter activities of adhesion molecules (VCAM1 and ICAM1), resulting in the amelioration of HFD-induced AS. These findings elucidate the microbiota-dependent mechanism of orally administered GL against AS, and highlight the therapeutic potential of targeting the ILA-AhR-p65 axis in the vascular endothelium as a strategy for AS.},
}

Animals
*Atherosclerosis/drug therapy/metabolism/microbiology/etiology/pathology
Mice
*Glycyrrhizic Acid/pharmacology/therapeutic use
*Receptors, Aryl Hydrocarbon/metabolism
*Indoles/metabolism
Male
*Transcription Factor RelA/metabolism
*Apolipoproteins E/deficiency/genetics
Gastrointestinal Microbiome/drug effects
Diet, High-Fat/adverse effects
Mice, Inbred C57BL
Humans
Fecal Microbiota Transplantation
Endothelium, Vascular/metabolism/drug effects
Mice, Knockout

@article {pmid42589520,
year = {2026},
author = {Dima, V and Calomfirescu Avramescu, A and Mirea, A and Toma, AI and Bohiltea, RE and Bivoleanu, A and Stewart, DL},
title = {Ureaplasma Species in Perinatal Disease: From the Age of Innocence to the Missing Villain.},
journal = {International journal of molecular sciences},
volume = {27},
number = {15},
pages = {},
doi = {10.3390/ijms27156865},
pmid = {42589520},
issn = {1422-0067},
mesh = {Humans ; *Ureaplasma Infections/microbiology ; *Ureaplasma/pathogenicity/physiology ; Female ; Pregnancy ; Infant, Newborn ; Chorioamnionitis/microbiology ; Animals ; },
abstract = {Ureaplasma urealyticum and Ureaplasma parvum occupy an odd place in perinatal medicine: dismissed for decades as harmless residents of the female genital tract, they are now recognized as pathogens with real consequences for preterm newborns. This review traces that paradigm shift, from organisms once dismissed as harmless colonizers to pathogens now implicated in chorioamnionitis, preterm birth, and a range of serious neonatal morbidities, and describes the molecular mechanisms that underlie their pathogenicity: Toll-like receptor (TLR1/2/6/9)-mediated NF-κB and MyD88/IRAK4/TRAF6 signaling, NLRP3 inflammasome activation and pyroptosis, and blood-brain barrier disruption via claudin-5/occludin downregulation and MMP-mediated tight junction cleavage. We also review the evidence for biofilm-conferred antibiotic tolerance and the clinical associations between Ureaplasma colonization and intraventricular hemorrhage (pooled OR 1.62, 95% CI 1.23-2.13), bronchopulmonary dysplasia (pooled OR 2.30, 95% CI 1.65-3.20), late-onset sepsis, and neurodevelopmental impairment. Diagnosis remains a weak point: culture sensitivity is below 10% compared with polymerase chain reaction (PCR) testing, and no randomized trial has yet shown that microbiological eradication translates into better clinical outcomes-a gap we examine critically. Whether these organisms cause disease seems to depend on gestational age, bacterial load, serovar-specific virulence, and host immune competence. We argue that this conditionality calls for risk stratification rather than dismissal whenever Ureaplasma is identified in clinical specimens, and that the field needs a paradigm shift toward Ureaplasma screening in high-risk pregnancies and targeted neonatal PCR testing, backed by adequately powered interventional trials.},
}

Humans
*Ureaplasma Infections/microbiology
*Ureaplasma/pathogenicity/physiology
Female
Pregnancy
Infant, Newborn
Chorioamnionitis/microbiology
Animals

@article {pmid42589527,
year = {2026},
author = {Coppini, M and Mauceri, R and Vacca, D and Bertolazzi, G and Caponio, VCA and Rodolico, V and Belmonte, B and Campisi, G},
title = {Longitudinal Exploratory Analysis of Salivary Microbiota Profiles in Patients with Oral Squamous Cell Carcinoma Before and After Surgery: A Pilot Study.},
journal = {International journal of molecular sciences},
volume = {27},
number = {15},
pages = {},
doi = {10.3390/ijms27156873},
pmid = {42589527},
issn = {1422-0067},
mesh = {Humans ; *Saliva/microbiology ; Pilot Projects ; *Mouth Neoplasms/microbiology/surgery ; Female ; Male ; *Microbiota ; *Carcinoma, Squamous Cell/surgery/microbiology ; Middle Aged ; Aged ; Longitudinal Studies ; Metagenomics/methods ; Bacteria/genetics/classification ; Adult ; Metagenome ; },
abstract = {Salivary microbiome profiling may represent a promising non-invasive approach for characterizing OSCC-associated microbial patterns and longitudinal microbiome dynamics during patient management. This exploratory pilot study aimed to longitudinally assess salivary microbiota profiles in patients with oral squamous cell carcinoma (OSCC) before and after tumor resection using Oxford Nanopore Technology. Unstimulated saliva samples were collected from 16 patients with OSCC at two time points (before and after tumor resection) and from 10 OSCC-free reference subjects. Microbial DNA was extracted using the QIAamp DNA Blood Kit (QIAGEN GmbH, Hilden, Germany) and subjected to long read metagenomic sequencing using the Oxford Nanopore MinION platform (v. 20.06.4, Oxford Nanopore Technologies, Oxford, UK). Taxonomic profiling was performed to longitudinally characterize salivary microbiota composition within patients and to provide descriptive comparisons with the OSCC-free reference cohort. Longitudinal analysis identified differences in salivary microbiota profiles between pre- and post-resection samples. Before surgery, an increased relative abundance of Neisseria subflava and Leptotrichia buccalis was observed. Post-surgical samples showed higher levels of Glaesserella parasuis, Streptomyces anulatus, and Lactobacillus species. Distinct microbial patterns were also descriptively observed between OSCC patients and OSCC-free controls, suggesting disease-associated dysbiosis. This exploratory longitudinal pilot study suggests differences in salivary microbiota profiles between samples collected before and after tumor resection in patients with OSCC, including changes in taxonomic composition and reduced alpha diversity. Given the limited sample size and the potential influence of unmeasured perioperative factors, these findings should be considered hypothesis-generating. Larger, well-controlled longitudinal studies incorporating standardized oral health assessment and detailed perioperative metadata are required to clarify the biological and clinical relevance of these observations.},
}

Humans
*Saliva/microbiology
Pilot Projects
*Mouth Neoplasms/microbiology/surgery
Female
Male
*Microbiota
*Carcinoma, Squamous Cell/surgery/microbiology
Middle Aged
Aged
Longitudinal Studies
Metagenomics/methods
Bacteria/genetics/classification
Adult
Metagenome

@article {pmid42589560,
year = {2026},
author = {Valenzuela, B and Navarrete-Diaz, I and Cayo, M and Solís-Cornejo, F and Zamorano, P},
title = {Genome-Resolved Metagenomics Reveals Thermophilic Microbial Diversity and Putative Hydrolase-Encoding Genes in the El Tatio Geothermal Field.},
journal = {International journal of molecular sciences},
volume = {27},
number = {15},
pages = {},
doi = {10.3390/ijms27156905},
pmid = {42589560},
issn = {1422-0067},
support = {Fondo para el Desarrollo en Investigación: en artes, ciencias y/o tecnología para actividades de titulación de pregrado": "Bioprospección de Genes de Enzimas Hidrolíticas mediante Análisis Metagenómico en el Campo Geotermal El Tatio"//University of Antofagasta/ ; },
mesh = {*Metagenomics/methods ; *Metagenome ; Phylogeny ; *Archaea/genetics/classification/enzymology ; *Hydrolases/genetics ; *Hot Springs/microbiology ; *Bacteria/genetics/classification/enzymology ; Chile ; },
abstract = {Geothermal ecosystems constitute important reservoirs of thermophilic microorganisms and their associated metabolic functions; however, the genome-resolved diversity and enzymatic potential of high-altitude geothermal systems remain poorly characterized. Here, we applied shotgun metagenomics and genome-resolved approaches to investigate thermophilic microbial communities inhabiting geothermal sediments from the El Tatio geothermal field, a polyextreme hydrothermal system located at ~4300 m above sea level in the Andean Altiplano of northern Chile. Genome reconstruction yielded 657 metagenome-assembled genomes (MAGs), including 190 near-complete and 273 high-quality genomes, providing a comprehensive genome-resolved view of microbial diversity in this environment. Taxonomic analyses revealed diverse archaeal and bacterial communities dominated by members of Thermoproteota, Methanobacteriota, Deinococcota, and Actinomycetota. Functional screening identified 612 high-confidence putative hydrolase-encoding genes distributed across multiple thermophilic lineages, including genes associated with esterases, lipases, proteases, and glycoside hydrolases. Notably, several candidates were recovered from archaeal MAGs affiliated with Thermoproteus, Sulfolobales, Pyrobaculum, and Acidilobaceae, expanding the genomic repertoire of putative hydrolytic functions in thermophilic archaea. Sequence-based thermostability prediction identified proteins with estimated melting temperatures exceeding 80 °C, with the highest predicted value reaching 87.6 °C. Collectively, these results expand current knowledge of microbial diversity and functional potential in high-altitude geothermal ecosystems and identify El Tatio as a rich source of putative hydrolase-encoding genes for future biochemical and biotechnological exploration.},
}

*Metagenomics/methods
*Metagenome
Phylogeny
*Archaea/genetics/classification/enzymology
*Hydrolases/genetics
*Hot Springs/microbiology
*Bacteria/genetics/classification/enzymology
Chile

@article {pmid42589672,
year = {2026},
author = {Zeng, C and Chen, J and Yong, X and Xie, Y},
title = {Convergent Gut Microbiome Remodeling Across Ischemic Stroke, Myocardial Infarction, and Longevity Reveals a Shared Ecological Signature of Aging and Disease.},
journal = {International journal of molecular sciences},
volume = {27},
number = {15},
pages = {},
doi = {10.3390/ijms27157020},
pmid = {42589672},
issn = {1422-0067},
support = {cstc2021jcyj-msxmx0848//Natural Science Foundation of Chongqing/ ; BSKJ2022006//Bishan District Science and Technology Bureau/ ; 81773954//National Natural Science Foundation of China (NSFC)/ ; 202310617015//National College Student Innovation and Entrepreneurship Program/ ; X2024160170123, X2026106170029//Chongqing College Students' Innovation and Entrepreneurship Project/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Aging ; *Myocardial Infarction/microbiology ; *Longevity ; *Ischemic Stroke/microbiology ; Male ; Female ; Aged ; Dysbiosis/microbiology ; },
abstract = {Gut microbiota dysbiosis has been associated with ischemic stroke (IS), myocardial infarction (MI), and aging, but whether these contexts share reproducible microbial features remains unclear. We conducted an exploratory and hypothesis-generating descriptive study of genus-level microbiota patterns across an internal IS cohort and publicly available external IS, MI, and age-stratified or longevity-associated datasets. Analyses were performed within predefined age strata and interpreted cautiously because of the small internal cohort, cross-cohort heterogeneity, and the absence of direct metabolite, intestinal barrier, inflammatory, or microbial activity measurements. No taxon in the internal cohort remained statistically significant after false-discovery-rate correction; therefore, all taxonomic observations were treated as descriptive. Candidate overlapping features included repeated detection of Escherichia-Shigella and Klebsiella and non-uniform patterns among genera previously associated with short-chain fatty acid metabolism, including Faecalibacterium, Blautia, and Roseburia. Lachnoclostridium and Bacteroides showed opposite abundance gradients in selected cross-dataset comparisons. These observations suggest possible ecological overlap across ischemic disease and age-associated microbiome contexts, but they do not establish causality, disease-specific biomarkers, or shared microbial function. The mechanistic models discussed in this manuscript are literature-informed hypotheses based on exploratory compositional data and require future validation in larger, harmonized longitudinal cohorts using metagenomic, metabolomic, clinical, and experimental measurements.},
}

Humans
*Gastrointestinal Microbiome
*Aging
*Myocardial Infarction/microbiology
*Longevity
*Ischemic Stroke/microbiology
Male
Female
Aged
Dysbiosis/microbiology

@article {pmid42590140,
year = {2026},
author = {Guo, F and Zhang, L and Liu, Z and Zhou, B and Fan, H and Zhang, D and Yang, Q and Li, T and Ge, Y},
title = {Clinical Utility of Metagenomic Next-Generation Sequencing in Adult Patients with Fever of Unknown Origin: A Retrospective Real-World Study.},
journal = {Journal of clinical medicine},
volume = {15},
number = {15},
pages = {},
doi = {10.3390/jcm15156038},
pmid = {42590140},
issn = {2077-0383},
support = {2022-PUMCH-B-043.//Peking Union Medical College Hospital/ ; },
abstract = {Background: Fever of unknown origin (FUO) remains a major diagnostic challenge due to its heterogeneous etiologies and nonspecific clinical manifestations. Although metagenomic next-generation sequencing (mNGS) represents a promising diagnostic tool, its clinical utility in adult patients with FUO remains incompletely characterized. Methods: In this study, we retrospectively analyzed adult FUO patients who underwent mNGS testing at Peking Union Medical College Hospital between March 2022 and April 2024. Clinically meaningful diagnostic contribution was determined according to the final clinical diagnosis following multidisciplinary adjudication. Diagnostic performance, pathogen spectrum, therapeutic impact, specimen type, and predictors of clinically meaningful mNGS results were evaluated. Results: A total of 127 FUO patients were included in the study. Infectious diseases accounted for 53.5% of final diagnoses, followed by noninfectious inflammatory diseases (11.0%), malignancies (10.2%), and undiagnosed conditions (19.7%). mNGS made a clinically meaningful diagnostic contribution in 31.5% (40/127) of patients, despite an overall positivity rate of 56.7% (72/127), and showed a higher sensitivity than conventional culture for infectious etiologies (69.1% vs. 16.9%), though with a lower specificity (57.6% vs. 96.0%). Diagnostic contribution varied significantly by specimen type, with drainage fluid/abscess samples showing the highest diagnostic yield (90.9%). Lower white blood cell count was independently associated with clinically meaningful mNGS results (OR 0.87, 95% CI 0.77-0.98). Conclusions: mNGS provides clinically meaningful diagnostic value in adult patients with FUO, particularly for identifying occult infectious etiologies. Lesion-directed sampling, whenever feasible, and careful interpretation of sequencing results in the clinical context are essential to maximize the diagnostic utility of this approach. A lower white blood cell count was independently associated with clinically meaningful mNGS results, although this finding requires validation in larger prospective studies.},
}

@article {pmid42591141,
year = {2026},
author = {Szeitz, A and Pinto, J and Pieters, A},
title = {Editorial: Advances in mass spectrometry: transforming analytical chemistry in molecular and spatial biology, multimodal omics, and bioanalysis.},
journal = {Frontiers in molecular biosciences},
volume = {13},
number = {},
pages = {1926838},
pmid = {42591141},
issn = {2296-889X},
}

@article {pmid42591156,
year = {2026},
author = {Kütahya, C and Pániker, CC and Ly, F and Jerath, A and Little, E and Gali, R and Haimi, MZBD and Malek, AHBA and Muhamad, KB and Supian, SB and Young, TB and Lawrence, S and Bell, T and Nee, TY and Jiménez, JI and Huynh, F},
title = {Masterbatch-enabled acceleration of polyolefin biodegradation under open air terrestrial environmental conditions.},
journal = {Npj Materials degradation},
volume = {10},
number = {1},
pages = {90},
pmid = {42591156},
issn = {2397-2106},
abstract = {Polyolefins, commonly used in packaging and single-use products, are notoriously persistent in the environment, contributing significantly to environmental pollution. In scientific literature to date, polyolefins have not been reported to fully biodegrade. This study examines the biodegradation potential of polyolefin materials, specifically polyethylene (PE) and polypropylene (PP), enhanced through the incorporation of Biotransformation Masterbatch technology. The inclusion of the Biotransformation Masterbatch accelerated and enabled the full biodegradation of PE and PP, as demonstrated by laboratory weathering, and biodegradation studies in soil at mesophilic temperatures. Ecotoxicity tests revealed no adverse effects on test organisms in both soil and water environments, while metagenomics analysis demonstrated that biodegradation of these polyolefins did not significantly change the soil microbiota composition, which showed higher metabolic activity compared to virgin plastic controls. These findings demonstrate that Biotransformation technology provides an effective solution for delivering polyolefin-based materials with reduced environmental impact. It offers a sustainable alternative to conventional plastics, preserving the performance characteristics of traditional polyolefins while addressing the problem with fugitive plastic waste in the environment.},
}

@article {pmid42591585,
year = {2026},
author = {Chen, G and Pan, Y and Bai, Z and Zheng, Y and Wei, Y},
title = {Synergistic algae-bacteria interactions in a novel membrane aeration biofilm system: performance and microbial function.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1900925},
pmid = {42591585},
issn = {1664-302X},
abstract = {Low carbon-to-nitrogen (C/N) ratio wastewater poses a major challenge to biological nitrogen removal due to insufficient electron donors for denitrification. In this study, an algae-bacteria membrane-aerated biofilm reactor (AB-MABR) was established to enhance nitrogen removal under carbon-limited conditions, and its performance was compared with that of a conventional bacterial MABR (B-MABR). The results showed that the AB-MABR achieved superior pollutant removal performance, with COD, NH4 [+]-N, and TN removal efficiencies being 4.0, 21.9, and 12.3% higher, respectively, than those of the B-MABR. Overall, AB-MABR outperformed B-MABR in pollutant removal. The removal efficiencies of COD, NH4 [+]-N, and TN were 92.3, 77.2, and 66.6%, respectively, which were markedly higher than those achieved by B-MABR (88.8, 55.3, and 54.3%). The incorporation of microalgae significantly enhanced microbial metabolic activity, as evidenced by higher ATP content, electron transport system activity (ETSA), and cytochrome c (Cyt-c) levels. Meanwhile, EPS production increased by 25% in the AB-MABR, accompanied by greater accumulation of protein-like and humic-like substances. SEM and CLSM analyses revealed that microalgae promoted the formation of a denser and more stratified biofilm with higher biomass and stronger structural stability. Metagenomic analysis further demonstrated that pathways associated with microbial metabolism, secondary metabolite biosynthesis, and environmental adaptation were enriched in the AB-MABR system, indicating enhanced metabolic potential and ecological resilience. Overall, microalgal incorporation strengthened electron transfer, stimulated EPS secretion, improved biofilm development, and enhanced microbial metabolic functions, thereby promoting nitrogen transformation and removal under low C/N conditions. These findings provide new insights into the synergistic mechanisms of algae-bacteria biofilms and demonstrate the potential of AB-MABR technology for sustainable nitrogen removal from carbon-limited wastewater.},
}

@article {pmid42591617,
year = {2026},
author = {Mukhedkar, D and Stosic, MS and Székely, AJ and Avershina, E and Arroyo Mühr, LS},
title = {Strong catchment-specific structuring of Swedish wastewater microbiomes in a paired two-timepoint metagenomic survey.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1907599},
pmid = {42591617},
issn = {1664-302X},
abstract = {INTRODUCTION: Wastewater microbial communities integrate signals from human populations, environmental inputs, and sewer infrastructure, but the extent to which these communities vary between wastewater catchments compared with individual sampling occasions remains incompletely understood.

METHODS: We analyzed influent wastewater from 16 wastewater treatment plant sites across Sweden, collected at two paired within-year timepoints, Week 3 and Week 21, using shotgun metagenomic sequencing and compositional data analysis.

RESULTS: Classified genus-level profiles were dominated by bacteria (96.54%), with smaller contributions from viruses (2.03%), eukaryota (1.05%) and archaea (0.40%). Genus-level alpha diversity increased between the two sampled timepoints, with median within-site changes of +10 genera in richness and +0.21 in Shannon diversity (p < 0.003). In contrast, overall community composition was primarily structured by wastewater treatment plant site: site explained 58.3% of total variance (p = 0.0003), whereas sampling timepoint explained 3.7% and was not significant (p = 0.106). Within-site compositional change between the two timepoints was nevertheless evident (p = 4.8 × 10[-4]), but the magnitude and direction of change varied across sites, indicating heterogeneous local shifts rather than a synchronized national temporal pattern. Genera detected in at least 75% of sites at both sampled timepoints accounted for most classified community abundance, whereas most measured within-site Aitchison turnover was accounted for by genera outside the high-prevalence shared fraction. Geographic distance and the number of connected inhabitants showed no significant association with genus-level community composition.

DISCUSSION: These findings indicate that Swedish influent wastewater microbiomes are strongly catchment-specific across paired sampling timepoints and support the use of site-specific reference profiles when interpreting wastewater metagenomic data. Denser temporal sampling and additional catchment metadata will be needed to assess seasonality, long-term stability, and the local drivers of wastewater microbiome variation.},
}

@article {pmid42591668,
year = {2026},
author = {Dell'Alma, M and Cesana, M and Kenny, P and Peron, G and Cafarella, C and Rigano, F and Mondello, L and Mangieri, N and Pizzi, S and Russo, P and Mora, D and Gargari, G},
title = {Multi-omic characterization of microbial dynamics during spontaneous fermentation of sweet wine Picolit variety.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1857803},
pmid = {42591668},
issn = {1664-302X},
abstract = {INTRODUCTION: Spontaneous wine fermentation is driven by the ecological succession of vineyard-derived microorganisms, yet little is known about how this process unfolds in Picolit, a grape variety characterized by acinellatura (berry millerandage) and elevated sugar concentration. This study aimed to characterize the microbial and metabolic dynamics of spontaneous Picolit fermentation and to identify the ecological and functional transitions occurring throughout the process.

METHODS: An integrated multi-omic approach combining shotgun metagenomics and untargeted metabolomics was applied to spontaneous fermentations of Picolit grapes produced at Aquila del Torre, an organic and biodynamic winery located in Savorgnano del Torre (Friuli-Venezia Giulia, Italy), within the newly established "Friuli Colli Orientali Sottozona Savorgnano D.O.C." Five fermentation stages were sampled and analyzed to investigate microbial succession, functional pathways and metabolomic changes.

RESULTS: The initial must displayed high microbial richness dominated by non-Saccharomyces yeasts, oxidative bacteria and Botrytis cinerea. An atypical persistence and increasing abundance of B. cinerea suggested a strong interaction between grape physiology and fungal activity. Early fermentation stages were characterized by diverse non-Saccharomyces taxa, including Lachancea, Pichia, Torulaspora and Schizosaccharomyces, which were associated with acid modulation, aromatic precursor release and phenolic turnover. From mid-fermentation onward, a multi-species Saccharomyces consortium established functional dominance, coinciding with a marked reduction in bacterial diversity and a transition from aroma-related metabolic pathways to stress adaptation functions. Multi-omic network analyses revealed a progressive loss of modularity as fermentation progressed and the system became more stable.

DISCUSSION: These findings demonstrate that spontaneous Picolit fermentation follows a distinctive ecological trajectory shaped by grape physiology, terroir and native microbial diversity. The persistence of B. cinerea, together with the succession of non-Saccharomyces and Saccharomyces populations, highlights unique microbial interactions that may contribute to wine identity. Overall, the results support the enological value of spontaneous fermentation and provide a microbial and functional framework for understanding and valorizing wines produced under the Savorgnano Bianco D.O.C.},
}

@article {pmid42591980,
year = {2026},
author = {Zhao, X and Ming, X and Shang, Z and Zhou, M and Xiao, Y},
title = {Epstein-Barr Virus-Positive B-Cell Lymphoproliferative Disorder Complicated by Septic Shock in Activated PI3Kδ Syndrome: A Pediatric Case Report and Literature Review.},
journal = {Case reports in hematology},
volume = {2026},
number = {},
pages = {3644513},
pmid = {42591980},
issn = {2090-6560},
abstract = {Activated phosphoinositide 3-kinase delta syndrome (APDS) is a rare inborn error of immunity caused by gain-of-function variants in PIK3CD and characterized by recurrent infections, lymphoproliferation, and impaired viral control. We report a 17-year-old male with a heterozygous PIK3CD c.3061G > A (p.E1021K) variant who presented with progressive edema, extensive hypermetabolic lymphadenopathy, splenomegaly, and Epstein-Barr virus (EBV) DNAemia. A core needle biopsy of the right inguinal lymph node demonstrated an immunodeficiency-associated EBV-positive B-cell lymphoproliferative disorder with extensive monotypic plasmacytoid differentiation. Because the biopsy contained limited mature B-cell tissue, the pathological findings favored a polymorphic B-LPD although EBV-positive diffuse large B-cell lymphoma with plasmacytic differentiation could not be excluded. The patient received anti-B-cell-directed therapy and supportive treatment. He was subsequently readmitted with septic shock and acute respiratory distress syndrome. Blood metagenomic next-generation sequencing detected Escherichia coli and Klebsiella pneumoniae, together with antimicrobial-resistance genes including blaNDM. Despite intensive antimicrobial and organ-supportive treatment, the patient remained critically ill and was discharged at his family's request for transfer to a local hospital; his subsequent outcome was unavailable. This case highlights the diagnostic difficulty of classifying EBV-positive B-cell proliferations using limited biopsy tissue in APDS and the competing risks of lymphoproliferative disease and severe infection. Adequate tissue sampling and pathological characterization, close microbiological surveillance, and individualized multidisciplinary management are essential in this setting.},
}

@article {pmid42592599,
year = {2026},
author = {Tao, G and Tang, W and Zhao, Y and Ma, Y and Xu, Y},
title = {A case report of ocular infection caused by Aspergillus fumigatus.},
journal = {AME case reports},
volume = {10},
number = {},
pages = {154},
pmid = {42592599},
issn = {2523-1995},
abstract = {BACKGROUND: Aspergillus fumigatus (A. fumigatus) can cause invasive infections in various sites of the body, including invasive pulmonary, hematogenous disseminated, and intracranial infections, posing substantial challenges for diagnosis and treatment. The methods of identification in this laboratory are worthy of study.

CASE DESCRIPTION: A 44-year-old male was admitted to our hospital with a 1.5-month history of bilateral scleral icterus accompanied by progressive visual deterioration. The patient was previously diagnosed with acute liver failure [hepatitis B e-antigen (HBeAg)-negative chronic hepatitis B] at another hospital. During hospitalization, his vision in the left eye decreased. Slit-lamp examination during ophthalmologic consultation suggested left endophthalmitis, with concurrent suspicion of retinal detachment. Examinations at admission confirmed the presence of hepatitis B virus (HBV) DNA, acute liver failure (Child-Pugh Class C), moderate anemia. The levels of the inflammatory markers were significantly elevated, including interleukin (IL-6, IL-8, IL-1β), and interferon-gamma (IFN-γ). After obtaining informed consent, emergency vitrectomy of the left eye was performed, retinal detachment repositioning and laser photocoagulation for retinal lesions, cryotherapy for retinal lesions, and vitreous silicone oil implantation in the left eye. The vitreous was cultured, then identified using next-generation metagenomic sequencing (mNGS) technology, enabling the detection of Aspergillus within a short period of time. This enabled a rapid diagnosis of Aspergillus endophthalmitis, guiding subsequent clinical management. After undergoing anti-infection and liver-protective treatment, the patient's condition stabilized and he was discharged from the hospital.

CONCLUSIONS: mNGS is a technology that can directly perform high-throughput sequencing of all the genetic material (DNA and/or RNA) of microorganisms in clinical samples (such as blood, bronchoalveolar lavage fluid, cerebrospinal fluid, etc.). The combination of mNGS and conventional detection methods effectively improves the detection rate of fungi.},
}

@article {pmid42592806,
year = {2026},
author = {Saavedra-Lozano, J and Agüera, M and Velasco-Arnaiz, E},
title = {Evolving paradigms in pediatric osteomyelitis: modern insights into an old disease.},
journal = {Current opinion in infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1097/QCO.0000000000001231},
pmid = {42592806},
issn = {1473-6527},
abstract = {PURPOSE OF REVIEW: Acute hematogenous osteomyelitis (AHO) remains a potentially devastating infection in children, in which delayed diagnosis or inadequate therapy can result in significant long-term sequelae. This review provides an update of the epidemiology, diagnosis and management of pediatric AHO, with particular emphasis on emerging diagnostic tools and evolving therapeutic strategies aimed at preventing complications.

RECENT FINDINGS: Improved recognition by clinical and laboratory algorithms of age-specific pathogens, like Kingella kingae in young children or highly virulent organisms including methicillin-resistant Staphylococcus aureus (MRSA), may allow for individualized therapy. Novel molecular techniques, such as metagenomic next-generation sequencing (mNGS), offer the potential for broader and faster microbiological diagnosis. Multidisciplinary protocols that integrate early MRI may enhance anatomic delineation of infection and lead to faster detection of complications. Antibiotic stewardship programs based on local epidemiology support optimized empiric and targeted therapy, while early transition to oral antibiotics has been shown to improve quality of life and reduce healthcare resource utilization without compromising clinical outcomes.

SUMMARY: Although AHO continues to pose diagnostic and therapeutic challenges, its management is shifting toward individualized, evidence-based care driven by advances in diagnostics, risk stratification and antimicrobial stewardship. Future research should focus on developing and validating multidisciplinary protocols to further improve the accuracy of diagnosis.},
}

@article {pmid42593076,
year = {2026},
author = {Ramos Romano, AL and Coutouné, N and Rego-Costa, A and Desai, MM and Carazzolle, MF and Gombert, AK},
title = {Dynamics of contaminant microbes in bioethanol production from sugarcane.},
journal = {Journal of industrial microbiology & biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jimb/kuag020},
pmid = {42593076},
issn = {1476-5535},
abstract = {The dynamics and impact of microbial contaminants in industrial sugarcane bioethanol production in Brazil were investigated through a two-year metagenomic study across two biorefineries. Shotgun metagenomic sequencing revealed that temporal shifts in the contaminant microbiome dynamics within production seasons were more pronounced than inter-annual or inter-mill variations. While Saccharomyces spp. dominated, bacterial communities, primarily within the Firmicutes phylum and dominated by the genera Lactobacillus, Limosilactobacillus, and Bacillus, exhibited dynamic changes. Correlation analyses with industrial process parameters revealed a complex interplay: lower Lactobacillus levels in one mill were associated with increased ethanol yield, whereas higher levels in another mill correlated with reduced yeast viability and increased flocculation. The presence of Limosilactobacillus was linked to decreased yeast viability, whereas Bacillus showed potential for inhibiting both Lactobacillus and Limosilactobacillus. These findings highlight the nuanced and species-specific impacts of bacterial contaminants on bioethanol production, underscoring the need for strain-level functional studies and targeted interventions to optimize fermentation efficiency and stability in industrial settings.},
}

@article {pmid42593705,
year = {2026},
author = {Wei, W and Zhou, L and Huang, Y and Lu, Z and Zhang, R and Zeng, M and Wang, X},
title = {Association Between Gut Microbiota Dysbiosis and Bilirubin Metabolism Dysregulation in Children with Heart Failure.},
journal = {Journal of cardiovascular translational research},
volume = {19},
number = {1},
pages = {},
pmid = {42593705},
issn = {1937-5395},
mesh = {Humans ; *Heart Failure/microbiology/diagnosis/blood ; *Bilirubin/blood ; *Dysbiosis ; *Gastrointestinal Microbiome ; Female ; Child, Preschool ; Male ; Child ; Case-Control Studies ; Biomarkers/blood ; Feces/microbiology ; Age Factors ; Metabolomics ; Infant ; Ribotyping ; Clostridium/genetics ; Adolescent ; Eubacteriales ; },
abstract = {Patients with heart failure (HF) demonstrate dysregulation in bilirubin metabolism. The specific characteristics of intestinal bilirubin metabolism in HF remain unclear. This study involved metagenomic sequencing and metabolomic profiling of fecal samples from 45 children with HF and 32 healthy children. Serum total bilirubin levels were 11.3umol/L, 19.4umol/L and 5.0umol/L in HF New York Heart Association (NYHA) I-II, NYHA III-IV and control group (p < 0.001), and the median gut microbiome health index (GMHI) were - 0.78, -1.53 and 0.09 in each (p < 0.001). The abundance of 2 bacteria species containing bilirubin reductase, Ruminococcus gnavus (p = 0.028) and Clostridium sp.M62/1 (p = 0.002) significantly decreased in NYHA III-IV group. The gut downstream bilirubin products, urobilinogen and stercobilin were decreased in the HF group; while the upstream bilirubin products, unconjugated and conjugated bilirubin increased. Dysbiosis of the gut microbiome and the decrease of bilirubin reductase containing bacteria in pediatric HF patients related to a reduction in gut bilirubin metabolism.},
}

Humans
*Heart Failure/microbiology/diagnosis/blood
*Bilirubin/blood
*Dysbiosis
*Gastrointestinal Microbiome
Female
Child, Preschool
Male
Child
Case-Control Studies
Biomarkers/blood
Feces/microbiology
Age Factors
Metabolomics
Infant
Ribotyping
Clostridium/genetics
Adolescent
Eubacteriales

@article {pmid42594431,
year = {2026},
author = {Huo, P and Li, Y and Han, T and Zhang, T and Gao, P},
title = {Labile carbon supply modulates H2O2-mediated N2O emissions during sediment denitrification: Insights from metagenomics.},
journal = {Journal of environmental management},
volume = {415},
number = {},
pages = {130690},
doi = {10.1016/j.jenvman.2026.130690},
pmid = {42594431},
issn = {1095-8630},
abstract = {Reactive oxygen species (ROS), particularly hydrogen peroxide (H2O2), are critical yet complex regulators of the nitrogen cycle. While H2O2 is known to modulate nitrous oxide (N2O) emissions during heterotrophic denitrification, how this regulation interacts with labile carbon supplies remains poorly understood. Here, we investigated the response of N2O emissions to exogenous H2O2 gradients under varying carbon-to-nitrogen (C/N) ratios in riverine sediments. We found that labile carbon addition (glucose) significantly broadened the tolerance window of denitrification to H2O2 stress and altered the dose-response relationship of N2O emissions across H2O2 concentrations ranging from 49 to 1960 μmol kg[-1] dry soil. Under carbon-limited conditions (NC), H2O2 reduced cumulative N2O emissions by 36.98% during the initial 6 h, coinciding with decreased relative genomic representation of Class I complete-repertoire genera and Class II nosZ-bearing genera lacking at least one upstream module. Conversely, under high-carbon conditions, H2O2 addition resulted in a 20.74% increase in cumulative N2O emissions compared to the control. Metagenomic analysis revealed a concurrent enrichment of denitrification and antioxidant genes (e.g., katG, trxB). This enriched genetic potential, contrasted with the observed N2O accumulation, highlights an apparent uncoupling between genomic capacity and phenotypic activity. This suggests that while the microbial community retains the genetic potential for denitrification, acute oxidative stress likely constrains terminal N2O reduction. These findings indicate that the convergence of labile carbon supply and ROS generation represents an important trigger for transient N2O pulses. This study deepens the understanding of the role of H2O2 in regulating denitrification-derived N2O emissions.},
}

@article {pmid42594433,
year = {2026},
author = {Fan, Y and Wei, Q and Zhang, P and Zou, L and Aisikaier, A and Ma, X and Dai, Z and Tian, Y and Li, Y and Wang, F and Yang, S and Cao, W},
title = {Hydrological regime modulates nitrogen retention-removal shifts in a glacier-oasis alpine river by restructuring multi-trophic interactions and microbial assembly.},
journal = {Journal of environmental management},
volume = {415},
number = {},
pages = {130604},
doi = {10.1016/j.jenvman.2026.130604},
pmid = {42594433},
issn = {1095-8630},
abstract = {Nitrogen (N) cycling in glacier-oasis alpine rivers exhibits distinct spatiotemporal patterns driven by multi-trophic community interactions. This study integrated 16S/18S rRNA sequencing with metagenomic analysis to investigate N-transformation dynamics across trophic levels and their response to varying hydrological regimes. The α-diversity of multi-trophic communities exhibited trophic-level-specific longitudinal patterns, with bacteria and algae generally showing higher diversity in the oasis reach (OR), whereas protozoans and metazoans were more diverse in the glacial reach (GR). In the OR, the species turnover of microeukaryotes exceeded 40%, and the pooled OR-irrigation channel reach (ICR) group exhibited 9.1-22.6-fold greater network complexity than the GR. The abundances of functional genes associated with nitrification and denitrification were 12.3-13.8 and 4.7-9.6 times higher in the OR than in the GR, respectively; N fixation potential was 2.4-14.1 times greater and bacterial α-diversity was 0.94-1.42 times higher in the OR than in the GR. Notably, only during the dry season did the GR exhibit 63-84% higher nitrate assimilation than the OR. Path analysis revealed that algae-protozoan symbiosis promoted N assimilation and retention (β = 0.87), whereas bacterial communities enhanced dissimilatory nitrate reduction and denitrification, facilitating N removal (β > 0.66). In contrast, metazoan predation (β = -0.78) and dissolved oxygen (β = -0.24) suppressed denitrification. The differentiation of N-cycling functions was governed by high α- and β-diversity within microbial communities. Heterogeneous selection and dispersal limitation during community assembly, acting through cross-trophic cascading effects, collectively balanced N retention against removal and ultimately determined the fate of N in the river ecosystem. Climate change may redistribute N-cycling hotspots along alpine rivers by altering hydrological regimes and riverine gradients, potentially increasing eutrophication risk by reducing N removal and enhancing N retention.},
}

@article {pmid42580113,
year = {2026},
author = {Zhang, Y and Xu, Z and Chu, W and He, H and Ma, L and Zhang, J and Ye, C},
title = {Underappreciated role of polluted storm sewer discharge in the accumulation of antibiotic resistance genes in downstream sediments.},
journal = {Journal of hazardous materials},
volume = {515},
number = {},
pages = {143253},
doi = {10.1016/j.jhazmat.2026.143253},
pmid = {42580113},
issn = {1873-3336},
abstract = {Polluted storm sewers (PSSs) are important pathways for contaminant transport to receiving waters, yet the association between PSS discharge and antimicrobial resistance in downstream sediments remains poorly understood. We investigated antibiotic resistance gene (ARG) distributions in paired upstream-downstream stream water and sediments around six PSS outfalls, together with PSS outfall samples, using metagenomic sequencing and binning. Downstream sediments exhibited transitional ARG profiles between upstream and PSS sediments, indicating a compositional linkage with PSS sediments. Acquired ARGs (sulfonamide and tetracycline resistance genes) were enriched in downstream sediments, while the intrinsic chromosomal resistance determinant mexB showed a similar pattern, consistent with their higher abundances in PSS discharges. SourceTracker indicated that sediment sources (87%) from upstream and PSSs contributed more to downstream sediment ARG profiles than water sources. The intermediate suspended solid levels in downstream water between PSS water and upstream water further supported particle-associated transport. Sulfonamide resistance genes were associated with putative plasmid contigs and co-occurred with qacEdelta1 and IS91, suggesting potential mobility. Azonexus was the dominant potential host of sulfonamide and tetracycline resistance genes, whereas Pseudomonas_E was associated with mexB enrichment. Collectively, these findings highlighted PSS discharge as an important anthropogenic pathway associated with ARGs in downstream sediments.},
}

@article {pmid42580122,
year = {2026},
author = {Gao, Z and Xue, L and Ma, Y and Chen, C and Ling, H and Wang, L and Zhang, W and Qian, J and Yang, Z and Hua, M and Pan, B},
title = {Mechanistic insights into low-dose nZVI-enhanced process stability under variable industrial loads in field-scale anaerobic treatment: Interfacial evolution and strain-resolved adaptation.},
journal = {Water research},
volume = {307},
number = {},
pages = {126665},
doi = {10.1016/j.watres.2026.126665},
pmid = {42580122},
issn = {1879-2448},
abstract = {Anaerobic treatment of industrial wastewater is limited by high variability and low biodegradability, which compromise process stability under varying industrial loads. A low-dose nanoscale zero-valent iron (nZVI)-augmented continuous-flow strategy was proposed and evaluated long-term in an on-site 3000 L reactor coupled to a full-scale expanded circulating granular sludge bed (ECSB). nZVI increased the mean chemical oxygen demand (COD) removal efficiency from 12.96% to 25.94% and reduced effluent fluctuation by 49%. Concurrently, sludge aggregation intensified, accompanied by protein enrichment in tightly bound extracellular polymeric substances (T-EPS) and a shift in dissolved organic matter (DOM) fluorescence toward humic-like hydrolytic intermediates. Metagenome-assembled genomes indicated a stable community core without structural replacement, alongside enriched iron-metabolism pathways. Incomplete electron-output pathways in key populations further suggest a possible contribution of nZVI-derived iron phases to conductive-material-mediated direct interspecies electron transfer (cDIET). Nonsynonymous single-nucleotide variant (SNV) trajectories and strain deconvolution further identified population-level selection in genes for iron homeostasis, oxidative stress, and electron transfer. These findings reposition nZVI from a reactive supplement to an interfacial stability regulator. More broadly, they provide field-scale evidence that refined nanomaterial dosing strategies can stabilize anaerobic treatment under real industrial loads by coupling interfacial reorganization with within-population adaptation.},
}

@article {pmid42580131,
year = {2026},
author = {Liu, C and Zhang, H and Guo, Z and Jiang, L and Yu, L and Zhu, C and Zhu, G},
title = {Electron flow boosted highly selective ammonium production from microbial nitrate reduction.},
journal = {Water research},
volume = {307},
number = {},
pages = {126656},
doi = {10.1016/j.watres.2026.126656},
pmid = {42580131},
issn = {1879-2448},
abstract = {Microbial dissimilatory nitrate reduction to ammonium (DNRA) process is considered as a bridge connecting nitrification and denitrification processes, which helps to improve the removal efficiency of nitrate wastewater. However, the competitiveness of DNRA was weaker than the denitrification, resulting in over 60-70% of nitrogen loss each year as N2 or N2O via denitrification. Here, we report a strategy of employing electron flow to rapidly initiate DNRA process (e-DNRA) with no external energy input. This e-DNRA strategy lies in establishing a high carbon-to-nitrogen ratio habitat to create favorable conditions for the growth and reproduction of DNRA bacteria. Subsequently, DNRA functional bacteria are enriched under reducing microenvironment induced by electron flow, ultimately forming a stable biofilm with high DNRA activity. By controlling extracellular electron flow, a nitrate reduction efficiency, conversion efficiency of nitrate to ammonium, and yield rate of 93.2%, 92.7%, and 1.23 µmmol N d[-1] g[-1] (MLSS) m[-3] were achieved, respectively. Transcriptome analysis and [15]N isotope tracing technology demonstrated that electron flow promoted the expression of nrfA gene by an order of magnitude. Genus-level microbial community structure revealed species Lentimicrobium, Geobacter, and Thauera are the primary determinants for the high DNRA efficiency. Moreover, metagenome-assembled genomes found that the electron flow increased the expression of cyt b and cyt c1 subunits in complex III by 1-2 orders of magnitude which sustained the high-rate DNRA. The proposed e-DNRA strategy provides a new solution for the synergistic treatment of nitrate wastewater and ammonium recovery.},
}

@article {pmid42580322,
year = {2026},
author = {Yang, L and Xiang, L and Rilong, J and Yihe, H},
title = {Tuberculous Arthritis Diagnosed by Metagenomic Sequencing after Negative Microbiology Studies and a 4-Year Delay.},
journal = {The American journal of tropical medicine and hygiene},
volume = {},
number = {},
pages = {},
doi = {10.4269/ajtmh.26-0309},
pmid = {42580322},
issn = {1476-1645},
abstract = {Tuberculous arthritis of the knee is a rare form of extrapulmonary tuberculosis that often presents with nonspecific symptoms, leading to delayed or missed diagnosis, particularly in elderly patients with comorbidities. We report the case of a 70-year-old man with a 2-year history of left knee pain and recurrent swelling. The patient was under therapy for lung cancer. He underwent two arthroscopic procedures for both diagnostic and therapeutic purposes. Repeated standard tests for tuberculosis were negative before metagenomic next-generation sequencing (mNGS) identified Mycobacterium tuberculosis nearly 2 years later. After 1-year triple-antituberculous therapy, he remained asymptomatic at the 2-year follow-up. This case highlights a high index of suspicion for indolent infection in culture-negative chronic arthropathy. The use of mNGS-increasingly accessible and cost effective-enables rapid and sensitive diagnosis of paucibacillary extrapulmonary tuberculosis.},
}

@article {pmid42580423,
year = {2026},
author = {Song, W and Shang, H and Yang, H},
title = {Performance stability and adaptability of embedded phosphorus removal biofillers: insights from microbial community responses and regulatory mechanisms.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135602},
doi = {10.1016/j.biortech.2026.135602},
pmid = {42580423},
issn = {1873-2976},
abstract = {Given the typically low phosphorus (P) concentrations in municipal wastewater, this study established a reactor employing embedded P removal biofillers (EBPAOs). The P removal performance of the system was systematically evaluated under three aerobic-phase operating modes: high-P batch feeding (Experiment S), low-P batch feeding (Experiments T10-T2), and low-P continuous feeding (Phases A-E). The results exhibited that, under the low-P batch feeding mode, the aerobic P uptake rate (Pup-rate) of the EBPAOs followed the Michaelis-Menten equation (R[2] = 0.940). Under the continuous feeding mode, the Pup-rate remained stable throughout the aerobic phase. When the influent PO4[3-]-P concentrations were sequentially adjusted to 10, 8, 6, 4, and 2 mg/L, with corresponding hydraulic retention times (HRTs) of 60, 50, 40, 30, and 25 min, respectively, the aerobic effluent PO4[3-]-P concentration remained below 0.3 mg/L in all cases. The volumes of wastewater treated per cycle were 2.5, 3, 3.75, 5, and 6 times the nominal reactor volume, respectively. Microbial community analysis revealed that Candidatus_Accumulibacter (48.59-58.82%) was the dominant genus in the EBPAOs. Metagenomic analysis further showed that, as the influent PO4[3-]-P concentration decreased, polyphosphate-accumulating organisms (PAOs) consumed more COD to synthesize additional polyhydroxyalkanoates (PHA), thereby providing the energy required for efficient P uptake under aerobic low-P conditions. Concurrently, the abundances of the PstS gene and genes associated with the Embden-Meyerhof-Parnas (EMP) pathway, the tricarboxylic acid (TCA) cycle, and PHA synthesis were significantly upregulated. In conclusion, EBPAOs enable efficient and stable P removal from low-P wastewater.},
}

@article {pmid42580547,
year = {2026},
author = {Wei, Y and Zhu, L and Jin, X and Yao, H and He, S and Feng, P and Yu, F and Xiang, Y and Li, Z and He, S},
title = {Metagenomic indications of potential pathogen-associated and antibiotic resistance risks following UV-chlorine disinfection in sprout production.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {128943},
doi = {10.1016/j.envpol.2026.128943},
pmid = {42580547},
issn = {1873-6424},
abstract = {Hydroponic agriculture commonly relies on low-pressure UV combined with chlorination (LPUV-chlorine) disinfection for water reuse, yet its impacts on non-coliform pathogens and associated resistance risks remain insufficiently understood. Here, metagenomic analysis of a commercial sprout production system revealed that LPUV-chlorine treatment did not completely remove pathogen-associated DNA signals and was associated with an increased relative abundance of Pseudomonas aeruginosa, accompanied by increased abundance of antibiotic resistance genes (ARGs) and virulence factor genes (VFGs). The relative abundances of VFGs related to biofilm formation and exoenzyme activity increased by 16∼18-fold compared to source water (SW), while β-lactam resistance genes showed marked increases in relative abundance. Network analysis revealed statistical associations between several pathogen-associated taxa and ARG profiles but did not establish their genomic hosts or transfer pathways. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis further revealed higher relative representation of genes associated with two-component systems and flagellar assembly, suggesting potential stress-adaptive functions and preferential persistence. In contrast, medium-pressure UV (MPUV) achieved ≥ 4-log reductions of P. aeruginosa, Escherichia coli, and Salmonella enterica within seconds, with 40.24%, 2.29%, and 26.44% lower fluence than LPUV, respectively. Transcriptomic analysis revealed decreased expression of selected virulence-associated genes and increased expression of phage-associated genes, suggesting potential effects on virulence-related functions and prophage responses. These findings highlight a potential pathogen-selection risk under LPUV-chlorine disinfection and indicate MPUV as a promising chlorine-free microbial risk control strategy in hydroponic water reuse systems.},
}

@article {pmid42581103,
year = {2026},
author = {Wang, R and Tabrizian, T and Wang, D and English, J and Ayer, A and Gal, M and Yang, WL and Wu, Z and Mao, K and Novaj, A and Zhang, X and Basu, I and Brodin, NP and Koba, W and Saxena, D and Choi, J and Augenlicht, LH and Ericsson, A and Gavathiotis, E and Guha, C and Huffman, DM},
title = {TNFR1 signaling connects inflammation to impaired fatty acid oxidation to drive intestinal stem cell aging.},
journal = {Nature aging},
volume = {},
number = {},
pages = {},
pmid = {42581103},
issn = {2662-8465},
support = {P30CA013330//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; 1210OD023591-01//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; P30DK020541//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; T32AG23475//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; R56AG052981//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; P30AG038072//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; T32AG23475//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; },
abstract = {Aging is characterized by a decline in function of intestinal stem cells (ISCs), but the extent to which this is shaped by systemic factors is unclear. Here we show that the ISC aging phenotype can be propagated from old to young mice utilizing heterochronic parabiosis, and implicate a role for inflammation in these effects, as anti-inflammatory drugs, including TNF antibodies, restored function. Parabiotic rescue experiments demonstrate that TNFR1 knockout protected young ISCs from the old environment. In young organoids, TNF downregulated crypt budding, while impairing mitochondrial pathways and fatty acid oxidation (FAO). However, aged ISC function was enhanced by boosting mitochondrial fusion, whereas FAO in aged crypts was improved by countering inflammation with salicylate treatment. Thus, these data identify the old environment through the progeronic factor TNF, as a driver of ISC aging phenotypes through intestinal epithelial cell TNF receptor 1 signaling to downregulate FAO, proliferation and regenerative capacity in these cells.},
}

@article {pmid42581991,
year = {2026},
author = {Song, X and Liu, X and Lou, M and Xu, J and Gong, X and Yang, Q and Chen, G and Mei, J},
title = {Atypical cat-scratch disease with acute high-grade fever and neuropsychiatric symptoms: a case report.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1810698},
pmid = {42581991},
issn = {2297-1769},
abstract = {OBJECTIVE: To report an atypical case of neurological cat-scratch disease (NCSD) presenting with acute-onset fever and prominent neuropsychiatric manifestations in an older adult.

PATIENT: An 85-year-old East Asian man with a history of hypertension and coronary artery disease.

RESULTS: Three months after a cat scratch, the patient developed abrupt high-grade fever, followed by nocturnal delirium with visual hallucinations and a witnessed seizure-like episode, and later complained of occipital headache. Physical examination revealed mild bilateral axillary and left supraclavicular lymphadenopathy without focal neurologic deficits. Cerebrospinal fluid cultures and stains were negative for bacteria and fungi. Serum metagenomic next-generation sequencing (mNGS) detected Bartonella henselae. After antibiotic therapy, the fever and headache resolved.

CONCLUSION: Cat-scratch disease should be considered as a rare but important infectious etiology in patients presenting with febrile illness accompanied by delirium or other neuropsychiatric symptoms. Clinicians should carefully inquire about recent cat exposure or scratch history and consider early pathogen-directed empiric antibiotic therapy to minimize diagnostic delay and improve outcomes.},
}

@article {pmid42582033,
year = {2026},
author = {Shi, P and Liu, Z and Wu, X and Zhao, F and Xu, J and Li, Q and Ye, M and Nian, D},
title = {Clinical utility of CSF metagenomic next-generation sequencing in suspected CNS infection: performance against a composite reference standard and read-count stratification.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1905481},
pmid = {42582033},
issn = {2235-2988},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; Female ; *Metagenomics/methods ; Retrospective Studies ; *Central Nervous System Infections/diagnosis/cerebrospinal fluid/virology ; Male ; Reference Standards ; Adult ; Middle Aged ; Sensitivity and Specificity ; Aged ; *Cerebrospinal Fluid/virology ; Meningitis/diagnosis/cerebrospinal fluid ; Young Adult ; Adolescent ; },
abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF) is increasingly used to identify pathogens in suspected central nervous system (CNS) infections. However, integrating these results into real-world clinical decision-making remains problematic, particularly given the lack of standardized quantitative metrics beyond raw read counts.

METHODS: We retrospectively analyzed 46 patients with suspected encephalitis, meningitis, or meningoencephalitis who underwent CSF mNGS testing. Etiologic certainty was classified using a composite clinical reference standard as Definite, Probable, or Unlikely. We assessed concordance between mNGS findings and the Likely etiology category (Definite or Probable), calculated diagnostic performance metrics, characterized the detected pathogens, and explored a tiered interpretation framework based on maximum read counts per patient (<10, 10-49, and >=50). Trends across read-count strata were evaluated using the Cochran-Armitage test, and exact binomial 95% confidence intervals (CIs) were calculated.

RESULTS: CSF mNGS detected pathogens in 13 of 46 patients (28.3%). Positivity increased with greater adjudicated diagnostic certainty, from 0% in Unlikely cases to 11.8% in Probable cases and 73.3% in Definite cases. Within the composite reference framework, mNGS showed 40.6% sensitivity, 100% specificity, 100% positive predictive value, and 42.4% negative predictive value, indicating stronger rule-in than rule-out performance. Viral detections predominated, with herpes simplex virus type 1 and varicella-zoster virus as the most frequent pathogens; all findings should be interpreted in the context of DNA-only testing. Among mNGS-positive patients with Likely etiologies, the proportion classified as Definite increased across higher max-read strata, but these tier-specific estimates were imprecise and should be viewed as exploratory.

CONCLUSION: In this real-world cohort, positive CSF mNGS results supported an infectious etiology more strongly than negative results excluded it. Max-read-based stratification may have exploratory interpretive value for positive findings, but it should not be considered a validated clinical decision rule and requires confirmation in larger multicenter studies with standardized reference standards.},
}

Humans
*High-Throughput Nucleotide Sequencing/methods
Female
*Metagenomics/methods
Retrospective Studies
*Central Nervous System Infections/diagnosis/cerebrospinal fluid/virology
Male
Reference Standards
Adult
Middle Aged
Sensitivity and Specificity
Aged
*Cerebrospinal Fluid/virology
Meningitis/diagnosis/cerebrospinal fluid
Young Adult
Adolescent

@article {pmid42582222,
year = {2026},
author = {Zhang, Q and Zhang, Z and Zhang, Z and Qin, G and Jin, M and Chen, B and Yu, Y and Wang, T and Wang, M and Lu, T and Zhu, D and Cui, L and Qian, H and Rillig, MC and Zhu, YG},
title = {Potential plastic biodegradation in lakes worldwide.},
journal = {Innovation (Cambridge (Mass.))},
volume = {7},
number = {8},
pages = {101338},
pmid = {42582222},
issn = {2666-6758},
abstract = {Plastic pollution is ubiquitous, yet the biodegradation of plastic waste remains poorly understood due to limited knowledge of microbial plastic degradation potential. Here, we demonstrate that plastic waste shapes the global distribution of plastic-degrading potential across 182,661 lakes worldwide using integrated metagenomic and machine learning analyses and identify a tipping point (≥7.44 particles/m[3]) for effective in situ bioremediation. We constructed, for the first time, a catalog of candidate plastic-degrading bacteria, including 15,715 nonredundant enzyme homologs and 4,856 metagenome-assembled genomes. To facilitate future applications, we developed a computational approach to categorizing candidate plastic-degrading bacteria according to their degradation potential, ecological risk, environmental adaptation, and competition capacity. Furthermore, we customized eight template culture media based on the growth factor biosynthesis profiles of high-priority candidate plastic-degrading bacteria. Using these media, we successfully enriched the plastic-degrading microbial communities and isolated a high-priority strain, Serratia ficaria HfyG-1, from Xiazhu Lake, which harbors a wide variety of previously uncharacterized putative degrading enzymes that effectively degrade polylactic acid and polyethylene terephthalate. Our study provides a molecular resource for the bioremediation of plastic-polluted environments worldwide and highlights a proof-of-concept framework for identifying, investigating, and exploiting unknown functional microorganisms for practical applications.},
}

@article {pmid42582600,
year = {2026},
author = {Chen, J and Fan, W and Chen, X and Zhang, H and Feng, M and He, S and Song, C and Wang, J},
title = {Domestication shapes the gut microbial structure and metabolic function in felids: a metagenomic study of wild and domestic cats.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1828152},
pmid = {42582600},
issn = {1664-302X},
abstract = {INTRODUCTION: The domestication process has profoundly altered the dietary patterns and living conditions of cats, with corresponding effects on their gut microbiome.

METHODS: This study compared the gut microbiota composition and metabolic functions between wild felids (Otocolobus manul and Felis bieti) and domestic cats using metagenomic sequencing.

RESULTS: Taxonomic analysis revealed significantly higher microbial alpha diversity and distinct community structure in wild felids compared to domestic cats. The gut microbiota of domestic cats was characterized by a higher relative abundance of Bacteroidota (when compared to F. bieti) and of Pseudomonadota, Uroviricota, and Cyanobacteriota, as well as an enrichment of carbohydrate-associated genera such as Segatella. In contrast, wild felids exhibited enrichment of potential pathogens (e.g., Clostridium perfringens, Escherichia coli) and genera including Clostridium and Fusobacterium, alongside a higher abundance of microbial genes linked to protein degradation and fermentation. Functional metagenomic analysis further identified consistent differences in microbial metabolic potential across both wild species comparisons. Wild felids showed higher abundances of genes involved in butyrate production, lysine degradation, and de novo synthesis of vitamins and cofactors. Domestic cats, in contrast, exhibited enrichment of genes for plant polysaccharide hydrolysis, ketone body formation, aromatic amino acid biosynthesis, and salvage of folate derivatives.

DISCUSSION: These results suggest that domestication is associated with a shift in the gut microbial functional repertoire - from a butyrogenic, protein-catabolic, and de novo-synthesizing profile in wild felids toward a more carbohydrate-hydrolyzing, ketogenic, and salvage-oriented profile in domestic cats, reflecting dietary and environmental adaptations.},
}

@article {pmid42582632,
year = {2026},
author = {Tshisekedi, KA and Van Den Bossche, T and Martens, L and De Maayer, P and Botes, A},
title = {Temporal and Functional Profiling of the Microbiome of High and Low Nitrogen Content Barley Seed in Silo Storage.},
journal = {Food science & nutrition},
volume = {14},
number = {8},
pages = {e72179},
pmid = {42582632},
issn = {2048-7177},
abstract = {Barley grain quality is influenced by nitrogen content and storage conditions; however, their impact on the composition and function of the grain microbiome is not well understood. This study combined metataxonomic (16S rRNA and ITS) profiling, metagenome sequencing, and metaproteome analyses to characterize the structure and function of the barley grain microbiome. Grains with high (> 1.5%) and low (< 1.5%) nitrogen content from a single barley cultivar (Kadie) were sampled at harvest and after 3, 6, and 9 months of storage. Amplicon sequencing revealed a community dominated by Proteobacteria, Firmicutes, and Ascomycota, while metagenomics confirmed the abundance of genera such as Erwinia, Pantoea, and Pseudomonas, aligning with previous reports of barley endophytes. While a consistent set of core microbial genera was identified, their relative abundances varied throughout storage. Metagenomic analysis revealed the high-nitrogen grain microbiome had potential for rapid metabolic activity that declined post-harvest, whereas the low nitrogen grain community sustained prolonged metabolic potential. Metaproteomics confirmed that these functional shifts revealed a temporal transition from active growth to stress tolerance. Findings from this work contribute to a better understanding of the barley grain microbiome during prolonged storage, offering insights that could help optimize storage for malting and brewing.},
}

@article {pmid42583033,
year = {2026},
author = {Bi, D and Yu, S and Zhang, M and Huang, Y and Dou, Z and Tian, B and Lu, J},
title = {The gut virome and regulatory T cell axis in health and systemic disease.},
journal = {Microbiome research reports},
volume = {5},
number = {2},
pages = {14},
pmid = {42583033},
issn = {2771-5965},
abstract = {The gut virome, comprising bacteriophages and eukaryotic viruses, represents a complex and dynamic component of the intestinal microbiome whose functional significance has long been underestimated. Emerging evidence highlights the gut virome as a pivotal modulator of the host immune system, particularly in regulating the balance and function of regulatory T cells (Tregs), which are essential for maintaining immune homeostasis. This review distinguishes two mechanistic axes by which the virome influences Tregs: (i) an indirect 'virome-bacteriome-metabolite-Treg axis', and (ii) a direct 'viral pathogen-associated molecular patterns (PAMPs)-pattern recognition receptors (PRRs)-Treg' signaling axis. This review comprehensively examines the dualistic role of the gut virome in preserving intestinal equilibrium and its involvement in the pathogenesis or amelioration of intestinal inflammatory disorders such as inflammatory bowel disease (IBD). Furthermore, the influence of the gut virome extends beyond the gut, potentially impacting systemic immune-related diseases. By integrating recent advances in metagenomics, viromics, and immunology, we elucidate the molecular mechanisms through which the gut virome orchestrates immune regulation. This synthesis aims to provide a comprehensive understanding of the gut virome as a critical immune regulator and to explore its potential as a biomarker for disease diagnosis and a novel target for therapeutic intervention.},
}

@article {pmid42583788,
year = {2026},
author = {Han, L and Wu, X and Gong, B and Li, X and Li, X and Wang, Z},
title = {A Two-Sample Mendelian Randomisation Analysis of the Oral Microbiome and Oral/Oropharyngeal/Tongue Cancers.},
journal = {Oral health & preventive dentistry},
volume = {24},
number = {},
pages = {613-621},
doi = {10.3290/j.ohpd.c_2778},
pmid = {42583788},
issn = {1757-9996},
mesh = {Humans ; *Mendelian Randomization Analysis ; *Microbiota/genetics ; *Tongue Neoplasms/microbiology ; *Oropharyngeal Neoplasms/microbiology ; Polymorphism, Single Nucleotide ; Genome-Wide Association Study ; *Mouth Neoplasms/microbiology ; Saliva/microbiology ; *Mouth/microbiology ; Tongue/microbiology ; },
abstract = {OBJECTIVE: To assess the potential causal relationships of the oral microbiome with the risks of oral cancer, oropharyngeal cancer, and tongue cancer using two-sample Mendelian randomisation (MR) analysis, while distinguishing these from reverse causal effects of the cancers on microbial abundance.

METHODS AND MATERIALS: Using single-nucleotide polymorphisms as instrumental variables, we applied the MR inverse-variance-weighted approach to evaluate the effects of the dorsal-tongue and salivary microbiomes on oral, oropharyngeal, and tongue cancers. Analyses were conducted with the R package TwoSampleMR, leveraging genome-wide association study (GWAS) summary statistics from CNGBdb, the FinnGen consortium, and other sources. Sensitivity, heterogeneity, and pleiotropy assessments were performed. Additionally, reverse MR sensitivity analyses were conducted to explore the possible causal influence of cancers on the oral microbiota.

RESULTS: Using a single nucleotide polymorphism (SNP) significance threshold of p 5 × 10-6, our large-scale MR study revealed genetically supported causal relationships between microbial taxa derived from saliva and the tongue and the risk of oral, oropharyngeal, and tongue cancers. Integrating these results, we found that both 's Veillonella_rogosae_mgs_2008' and 's unclassified_mgs_1048' conferred a reduced risk of oropharyngeal and tongue cancers. Sensitivity analyses based on heterogeneity tests and pleiotropy evaluations further corroborated the robustness of our findings, lending additional credibility to the conclusions.

CONCLUSION: This study leveraged large-scale publicly available genetic data and identified significant causal relationships between the oral microbiota and cancers of the oral cavity, oropharynx, and tongue. Reverse MR analyses indicated that oral and tongue cancers may in turn alter the abundance of specific oral microbes, suggesting a potential bidirectional causal loop. Future work should integrate metagenomic data to further validate these microbiota-cancer associations.},
}

Humans
*Mendelian Randomization Analysis
*Microbiota/genetics
*Tongue Neoplasms/microbiology
*Oropharyngeal Neoplasms/microbiology
Polymorphism, Single Nucleotide
Genome-Wide Association Study
*Mouth Neoplasms/microbiology
Saliva/microbiology
*Mouth/microbiology
Tongue/microbiology

@article {pmid42583799,
year = {2026},
author = {Lee, I and Suk, KT and Park, JY and Yong, D and Kim, DJ and Kim, BS and Lee, SS},
title = {Fecal microbiota transplantation accelerates clearance of carbapenemase-producing Enterobacterales intestinal carriage: influence of recipient gut microbiome ecology.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiag414},
pmid = {42583799},
issn = {1537-6613},
abstract = {BACKGROUND: Persistent intestinal carbapenemase-producing Enterobacterales (CPE) carriage challenges infection prevention and antimicrobial stewardship. We evaluated fecal microbiota transplantation (FMT) for decolonization and response-associated recipient microbiome features.

METHODS: This prospective cohort study assessed intestinal CPE clearance in 131 adult carriers (68 receiving FMT; 63 under observation). Responders achieved clearance, defined as three consecutive negative rectal surveillance cultures for CPE, obtained at 3-day intervals within 1 month after FMT. Following least absolute shrinkage and selection operator (LASSO)-based covariate selection, Cox proportional hazards models estimated associations between FMT and time to successful decolonization within prespecified 0-30-day and 0-90-day windows. A longitudinal metagenomic subcohort of 21 FMT recipients (102 fecal samples) underwent shotgun sequencing to characterize taxonomic composition, microbial network organization, functional pathways, antimicrobial resistance genes (ARGs), and donor engraftment.

RESULTS: After LASSO-based covariate selection, FMT was associated with faster CPE clearance than observation at 1 month (hazard ratio, 4.02; 95% confidence interval, 1.84-8.79), with effects sustained at 3 months. Responders showed relatively preserved baseline microbial network organization and enrichment of taxa annotated with arginine-related pathway features, suggesting metabolic relevance to microbial niche competition. After FMT, responders had greater engraftment of donor-associated taxa and donor-like ecological reassembly, with reduced Klebsiella pneumoniae dominance and ARG abundance.

CONCLUSIONS: FMT may accelerate intestinal decolonization in CPE carriers; response variability was associated with recipient gut-microbiome ecology, suggesting microbiome-guided patient selection could optimize microbiota-based strategies.},
}

@article {pmid42584065,
year = {2026},
author = {Roush, C and Whiteley, M},
title = {Dental wastewater reveals a hidden reservoir of oral bacteriophage diversity.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0182026},
doi = {10.1128/spectrum.01820-26},
pmid = {42584065},
issn = {2165-0497},
abstract = {Bacteriophages (phages) are being explored as alternatives or complements to antibiotics because of their ability to selectively kill bacterial pathogens. However, phages that infect many oral bacteria remain undiscovered. Here, we discovered that dental wastewater harbors previously underexplored phage diversity. Viral particles concentrated from dental wastewater displayed diverse morphologies, including abundant filamentous phage-like particles. Deep long-read metagenomic sequencing of concentrated viral particles generated 7.4 billion bases of sequence data and yielded 255 medium- to high-quality viral operational taxonomic units (vOTUs), including 46 predicted complete genomes. Comparison with large phage databases revealed that 63 of these 255 vOTUs had no detectable match, indicating that extensive sequencing of dental wastewater substantially expands the number of potential bacteriophages associated with the human oral microbiome. Host prediction linked many vOTUs to oral-associated bacterial taxa, including species with few or no previously reported phages, such as Porphyromonas gingivalis, Tannerella forsythia, and Candidatus Saccharibacteria. Functional annotation identified diverse genes associated with antiphage defense systems within a subset of vOTUs, suggesting that oral phages may contribute to the movement of genes encoding bacterial immune functions within the oral microbiome. Together, these findings expand the known oral phageome and show that dental wastewater contains a largely untapped diversity of phages.IMPORTANCEThe human oral cavity contains a diverse microbial community, but the bacteriophages (phages) that infect many oral bacteria remain poorly characterized. This gap limits our understanding of how phages shape oral microbial communities. Here, we show that dental wastewater is an underexplored source of oral phage diversity. Deep long-read metagenomic sequencing revealed 255 medium- to high-quality phage operational taxonomic units, many of which are not present in existing oral phage databases. These genomes include predicted phages of periodontal disease-associated bacteria and other oral taxa with few or no known phages. Dental wastewater therefore expands the known human oral phageome and reveals candidate phages linked to bacteria associated with oral health and disease.},
}

@article {pmid42584072,
year = {2026},
author = {Eiler, A},
title = {Rethinking evolutionary inference in metagenomic time series.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0069326},
doi = {10.1128/msystems.00693-26},
pmid = {42584072},
issn = {2379-5077},
abstract = {As ecologists increasingly use metagenomic time series to track evolution in the wild, there is a risk of misinterpreting ecological dynamics as rapid adaptation. This Perspective identifies methodological limitations that generate misleading signatures of microbial evolution. A primary issue is confusing evolutionary change (driven by de novo mutation or horizontal gene transfer) with ecological lineage turnover, such as seasonal oscillations or the reactivation of dormant lineages. Current metagenome-assembled genomes can collapse micro-diverse lineages and decouple adaptive mobile elements, creating inaccurate genomic signatures of sweeps or stasis. To address these issues, I propose a framework integrating long-read sequencing, pangenome graph theory, and forward-time simulations to model populations as temporal genetic networks and better resolve microbial evolutionary dynamics.},
}

@article {pmid42584101,
year = {2026},
author = {Yu, D and Zhang, L and Agu, D and Gao, N and Xiao, Y and Zhang, M and Zhang, J and Yan, J},
title = {Temporal succession of microbiomes and resistomes during buried rat carcass decomposition.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0043726},
doi = {10.1128/msphere.00437-26},
pmid = {42584101},
issn = {2379-5042},
abstract = {Burial is a prevalent approach for disposing of human and animal carcass. Carcass decomposition is a key natural disturbance that reshapes microbial communities and modulates biogeochemical cycles. Animal intestines serve as critical natural reservoirs of antibiotic resistance genes (ARGs), and carcass decomposition concurrently remodels intestinal bacterial assemblages and resistome profiles. Most previous studies have characterized microbial succession in surface-exposed carcasses, yet the coordinated temporal shifts of intestinal microbiota, resistomes, and horizontal gene transfer (HGT) signatures within buried carcasses remain underexplored. We established a buried rat carcass model and performed metagenomic sequencing to characterize temporal dynamics of intestinal bacteria, ARGs, mobile genetic elements (MGEs), and HGT events. Bacterial communities underwent directional succession accompanied by reduced α-diversity and stage-specific β-diversity. Proteobacteria gradually outcompeted Firmicutes and Bacteroidetes to become dominant taxa. The resistome followed regular temporal changes: tetracycline and macrolide-lincosamide-streptogramin (MLS) ARGs prevailed in early decomposition, while multidrug, β-lactam, polymyxin, and quinolone ARGs accumulated in mid-late stages, with ARG richness peaking on day 28. Approximately 83% of temporally dynamic ARG subtypes were positively correlated with decomposition duration. Procrustes analysis (R[2] = 0.859) revealed strong correlations between bacterial succession and resistome dynamics, with Proteobacteria as potential multidrug-resistant hosts and major HGT donors. This study identifies a correlative cascade of microbial succession that drives MGE functional shift, which in turn increased HGT potential and ultimately leads to resistome accumulation in buried carcass intestinal habitats. These findings expand the theoretical framework of disturbance-driven microbial-resistome co-succession and offer insights into drivers of antibiotic resistance propagation in terrestrial cadaver systems.IMPORTANCEAnimal carcass burial is a ubiquitous natural terrestrial disturbance, and carcass intestinal contents represent a major endogenous reservoir of environmental antibiotic resistance genes (ARGs). Although extensive research has characterized microbial succession of exposed carcasses, the co-occurrence patterns of gut microbiome and resistome together with associated horizontal gene transfer (HGT) under buried conditions remain underexplored. Using metagenomic profiling of decomposing rat intestinal feces, this study explores a potential correlative cascade spanning bacterial succession, mobile genetic element (MGE) functional shifts, increased HGT potential, and gradual ARG enrichment. Our findings expand the ecological data set focused on subsurface buried carcass habitats and advance mechanistic knowledge of coupled microbiome-resistome succession driven by postmortem decomposition.},
}

@article {pmid42584108,
year = {2026},
author = {Vaziri, GJ and Pritchard, JC and Howard, JI and Stamm, GE and O'Connor, DH and Newman, CM and Aliota, MT and Dzikwi-Emennaa, A},
title = {Metagenomic sequencing detects viruses and bacteria in a cross-sectional clinical cohort of undifferentiated febrile illness in Nigeria.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0015726},
doi = {10.1128/msphere.00157-26},
pmid = {42584108},
issn = {2379-5042},
abstract = {UNLABELLED: Molecular and microscopy-based diagnostic capacity is often insufficient or unavailable in places where infectious disease burdens are highest, such as in West Africa. Rapid diagnostic testing (RDT) can provide quick and affordable diagnoses of common infections but is an imperfect solution due to limitations around detecting and dealing with false-negative and false-positive results. An alternative to RDT is unbiased metagenomic sequencing for pathogen surveillance. Here, we present data from unbiased metagenomic sequencing used to identify causes of undiagnosed febrile illness in Jos, Plateau State, Nigeria. Proof of concept for this approach has been demonstrated by several groups who have identified epidemic and endemic viral diseases like Lassa fever, yellow fever, and chikungunya. We show that unbiased deep sequencing and metagenomic analysis can be used to identify RNA viruses in clinical samples. We sequenced RNA from sera of patients (n = 343), many of whom were acutely febrile (76%), in a survey of clinics in Jos. We detected five human-infecting viruses in 39 (11 %) specimens. Among these were hepatitis B virus, human pegivirus, and several anelloviruses. While most of the viruses identified are unlikely to cause clinical symptoms in the patients we sampled, their presence demonstrates the validity of our approach. Additionally, our sequencing data allowed us to identify genetic material from potentially pathogenic bacteria, another possible etiological agent of febrile illness.

IMPORTANCE: In low-resource areas, fevers due to infectious pathogens are a major source of illness, but tools for detecting and identifying such pathogens are often limited. Unbiased approaches for identifying genetic material from all potentially infectious organisms in a sample represent an opportunity for discovering sources of fever. Metagenomic sequencing can improve insight into pathogen landscapes in low-resource settings, potentially providing early detection of disease outbreaks. However, unbiased metagenomic sequencing (mNGS) is no panacea; it is susceptible to contamination and false positives. We used mNGS to evaluate serum from >300 Nigerian clinic-goers in Jos, Nigeria, most of whom (>70%) had fevers of unknown origin. Our goal was to understand arbovirus prevalence in Jos, Nigeria, and identify the sources of infection not routinely monitored for at clinics. We detected hepatitis B virus, as well as nonpathogenic anelloviruses. Our study provides insight into the utility and limitations of mNGS for pathogen surveillance.},
}

@article {pmid42584675,
year = {2026},
author = {Tozluyurt, A and Acar, A},
title = {Postoperative Nocardia cyriacigeorgica infection after glioblastoma resection: correlating metagenomic next-generation sequencing with conventional microbiology.},
journal = {Naunyn-Schmiedeberg's archives of pharmacology},
volume = {},
number = {},
pages = {},
pmid = {42584675},
issn = {1432-1912},
abstract = {Postoperative nocardial infection after cranial surgery is rare and difficult to diagnose because Nocardia spp. grow slowly in conventional culture. Metagenomic next-generation sequencing (mNGS) can shorten the interval to microbial detection, but read abundance is influenced by commensal DNA and by contamination during sampling, laboratory processing, and sequencing. mNGS findings therefore require correlation with conventional microbiology and with the clinical context. An 84-year-old woman developed purulent surgical wound discharge with epidural empyema approximately 2 weeks after resection of a World Health Organization grade 4 glioblastoma and postoperative corticosteroid exposure. Revision surgery comprised extensive debridement, removal of the infected bone flap and fixation screw, and evacuation of the empyemas. Direct Gram and modified acid-fast stains of the operative specimen showed branching, acid-fast filamentous organisms on day 1. mNGS of abscess fluid reported 196,785 reads assigned to Nocardia cyriacigeorgica on day 7, and culture on buffered charcoal yeast extract agar yielded N. cyriacigeorgica on day 18, confirmed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. More than 20 million reads were assigned to Corynebacterium tuberculostearicum, yet no corresponding coryneform predominance was seen microscopically; its significance was therefore interpreted cautiously as a possible skin-derived or background contribution, although a true polymicrobial contribution could not be excluded. Surgical source control with intravenous meropenem and amikacin was followed by resolution of the infection. Additionally, three multimodal artificial intelligence systems were each queried five times with the same prompt. mNGS enabled earlier species-level recognition of N. cyriacigeorgica than culture, but direct microscopy gave the earliest diagnostic clue and culture remained essential for confirmation and isolate recovery. Taxonomic read abundance must not be equated with causality. The artificial intelligence outputs were discordant between systems and, in one system, incorrect in a stable and reproducible way; this illustrates current limitations rather than clinical readiness and supports the need for prespecified, blinded, multi-case validation before clinical deployment.},
}

@article {pmid42584818,
year = {2026},
author = {Sharma, S and Sharma, PK and Gupta, E and Dash, PK and Srivastava, A},
title = {Simplified Inhouse Nanoweb Membrane Enrichment Coupled Viral Whole Genome Shotgun Metagenomics Approach for Waste Water Surveillance.},
journal = {Food and environmental virology},
volume = {18},
number = {3},
pages = {},
pmid = {42584818},
issn = {1867-0342},
mesh = {*Genome, Viral ; *Wastewater/virology ; *Metagenomics/methods ; *Sewage/virology ; SARS-CoV-2/genetics/isolation & purification ; India ; *Viruses/genetics/isolation & purification/classification ; *Environmental Monitoring/methods ; COVID-19/virology ; Shotgun Sequencing ; Animals ; },
abstract = {Wastewater/sewage represents a highly complex environmental matrix and harbors various viruses including viruses of epidemic and pandemic potential like Influenza A and, SARS-CoV-2. The limitations of available methods for sample concentration are cost, efficiency and time. NGS- metagenomics offer sample to virus genomic characterization for even non-cultivable viruses at highest resolution. In this study, we have collected samples from sewage treatment plants located in Gwalior region of Central India (December 2023 to March 2025). In this study a novel in house nanoweb membrane-based sample enrichment followed by magnetic bead based nucleic acid extraction was optimized in conjunction to shotgun whole genome metagenomics on Nanopore and ion torrent NGS. Both the methods were found comparable with commercially available methods by virus specific TaqMan qPCR. Both the methods were found successful in virus recovery at two log through 10[2]GC/50 ml feline calicivirus, Influenza A virus, Zika virus, SARS-CoV-2 spiked in sewage matrix alone or in mixture), suggesting the optimized protocol found working for virus characterization at strain level. Here, we have standardized a simple field amenable waste water sample enrichment followed by nucleic acid extraction protocol, that can easily be integrated with latest onsite downstream molecular diagnostic platforms. The developed method is very simple, cost effective and field deployable. This will help to develop a suitable strategic plan for sewage surveillance towards early warning/microbial forensics and future decisions for prevention and therapeutic interventions.},
}

*Genome, Viral
*Wastewater/virology
*Metagenomics/methods
*Sewage/virology
SARS-CoV-2/genetics/isolation & purification
India
*Viruses/genetics/isolation & purification/classification
*Environmental Monitoring/methods
COVID-19/virology
Shotgun Sequencing
Animals

@article {pmid42584931,
year = {2026},
author = {Kaszecki, E and Azimychetabi, Z and Emery, RJN and Saville, BJ},
title = {Integrated transcriptomic and hormonomic insights into cadmium tolerance of a Euglena mutabilis fungal-algal-bacterial consortium.},
journal = {Microbiology (Reading, England)},
volume = {172},
number = {8},
pages = {},
doi = {10.1099/mic.0.001750},
pmid = {42584931},
issn = {1465-2080},
mesh = {*Cadmium/metabolism/toxicity ; *Transcriptome ; *Euglena/genetics/metabolism/drug effects ; *Microbial Consortia/genetics ; *Fungi/genetics/metabolism ; Gene Expression Profiling ; *Bacteria/genetics/metabolism/classification ; Chloroplasts/metabolism ; },
abstract = {Acidic, metal-contaminated environments harbour specialized microbial consortia adapted to extreme stress. We examined an environmental Euglena mutabilis culture naturally associated with Talaromyces and Acidiphilium acidophilum and exposed it to cadmium (Cd). Integrated transcriptomic, hormonal, structural and taxonomic analyses revealed a coordinated Cd-tolerance strategy. RNA sequencing showed differential regulation of metal transporters consistent with a shift from Cd uptake to intracellular sequestration. Transmission electron microscopy confirmed Cd compartmentalization within chloroplasts and increased paramylon granules. Cd exposure suppressed light-harvesting complex genes and formate/nitrite transporters while maintaining core photosynthetic function. Hormone profiling indicated strong repression of bioactive auxin and cytokinin (CK) free bases, alongside accumulation of CK nucleotides and downregulation of CK biosynthetic and activation genes. Metagenomics revealed Cd-driven enrichment of Talaromyces and Acidiphilium, implicating them in detoxification and stress support. Together, these responses highlight early Cd uptake followed by chloroplast-based detoxification, metabolic buffering via paramylon, hormonal downregulation of growth and community-mediated resilience.},
}

*Cadmium/metabolism/toxicity
*Transcriptome
*Euglena/genetics/metabolism/drug effects
*Microbial Consortia/genetics
*Fungi/genetics/metabolism
Gene Expression Profiling
*Bacteria/genetics/metabolism/classification
Chloroplasts/metabolism

@article {pmid42585057,
year = {2026},
author = {de Oliveira, FF and A C Fernandes, M},
title = {BIKE: A Binary $K$-mer Exact Counter with Alphabet-Independent Memory and Deterministic Parallelism.},
journal = {IEEE transactions on computational biology and bioinformatics},
volume = {PP},
number = {},
pages = {},
doi = {10.1109/TCBBIO.2026.3723002},
pmid = {42585057},
issn = {2998-4165},
abstract = {K-mer counting is a fundamental computational task in bioinformatics, underpinning genome assembly, metagenomic classification, error correction, and similarity analysis. Existing exact-counting methods rely on hash tables or static allocation strategies whose memory requirements grow exponentially with the alphabet size and substring length, rendering them impractical for amino acid sequences at moderate-to-large values of $k$. We propose BIKE (Binary K-mer Exact Counter), a novel exact k-mer counting algorithm whose memory footprint depends exclusively on the input sequence length $n$, independently of the alphabet size m or the $k$-mer length $k$. BIKE decomposes the counting problem into $n-1$ mutually independent pivot-based comparison blocks operating entirely on binary matrices, requiring only one bit per entry, and employs a union-find aggregation mechanism that guarantees exact counts for $k$-mers of arbitrary multiplicity. This structural regularity yields a fully deterministic degree of parallelism, enabling closed-form analytical models that provide accurate execution-time predictions under ideal parallel execution assumptions. Experimental results on real biological sequences confirm functional correctness and demonstrate memory reductions of up to three orders of magnitude over classical exact methods for amino acid alphabets. Analytical performance projections, derived from the closed-form parallel model, indicate that an FPGA realisation of BIKE would be expected to outperform CPU-based dynamic allocation at moderate sequence lengths; however, these remain theoretical estimates pending hardware implementation. BIKE is therefore presented as a theoretical and data-structural contribution, establishing a new algorithmic foundation for alphabet-independent, exactly-counted, and deterministically parallel $k$-mer analysis.},
}

@article {pmid42585229,
year = {2026},
author = {Fellows Yates, JA and Hübner, A and Borry, M and , and Warinner, C},
title = {De novo assembly and authentication of ancient DNA metagenomes with nf-core/mag.},
journal = {PLoS computational biology},
volume = {22},
number = {8},
pages = {e1014591},
doi = {10.1371/journal.pcbi.1014591},
pmid = {42585229},
issn = {1553-7358},
mesh = {*DNA, Ancient/analysis ; *Metagenomics/methods ; *Metagenome/genetics ; *Sequence Analysis, DNA/methods ; Computational Biology/methods ; Software ; Humans ; },
abstract = {Ancient DNA provides a direct window into the evolutionary processes that have shaped living microbial species today, as well as their now extinct relatives. Advances in both sequencing methods and de novo assembly techniques have not only resulted in a flood of modern metagenomic sequencing data, but they have also allowed palaeogenomicists to retrieve vast amounts of ancient DNA from past microorganisms, including species and strains without modern reference genomes. However, the degraded nature of ancient DNA means that the standard techniques of genome assembly developed for modern DNA are unlikely to perform effectively, unless heavily modified. This hinders the incorporation of ancient data into broader metagenomic studies that would otherwise benefit from having deep time information on the evolution of different microbial species. In this primer and protocol paper, we provide guidance on ways to adapt existing metagenomic de novo assembly processes, including data input, tools, and settings, in order to perform more robustly and effectively on ancient DNA. After assembly, we then further describe how ancient DNA contigs can be identified and validated. The key steps of ancient metagenomic assembly are now integrated in a dedicated ancient DNA mode in the established pipeline nf-core/mag. By introducing support for ancient DNA data in nf-core/mag, we aim to improve the ability of researchers to more regularly integrate de novo assembled ancient microbial data into broader metagenomics studies of microbial ecology and evolution.},
}

*DNA, Ancient/analysis
*Metagenomics/methods
*Metagenome/genetics
*Sequence Analysis, DNA/methods
Computational Biology/methods
Software
Humans

@article {pmid42585836,
year = {2026},
author = {Cao, Y and Du, P and Zhai, R and Guo, Y and Lin, M and Wang, Z},
title = {Drought stress adaptation in Ficus carica L.: Modulation of ROS scavenging, nitrogen uptake, and rhizosphere bacterial community assembly and functions.},
journal = {Microbiological research},
volume = {313},
number = {},
pages = {128678},
doi = {10.1016/j.micres.2026.128678},
pmid = {42585836},
issn = {1618-0623},
abstract = {Rhizosphere microorganisms are crucial for plant drought resistance; however, their response to drought stress in fig plants remains poorly understood. In this study, potted 'BoJi Red' fig plants were utilized to systematically investigate drought-induced changes in the structure, assembly processes, and functional potential of rhizosphere bacterial communities. The results showed that drought significantly inhibited fig growth, photosynthesis, and nitrogen uptake, while increasing reactive oxygen species (ROS) content and antioxidant enzyme activities, although these enzyme activities declined under severe drought conditions. Bacterial community richness and diversity significantly increased under moderate and severe drought, shifting toward drought-resistant groups, notably Actinomycetota and Bacillota. The number of nodes, links, and key species in the microbial co-occurrence network decreased as drought intensified, with stochastic processes dominating community assembly. Moreover, ecological niche breadth and the proportion of generalist species increased with drought severity. Notably, Nocardioidaceae was significantly enriched under drought, and metagenomic profiling indicated this taxon is strongly associated with carbohydrate metabolism pathways, with predicted genetic potential to participate in soil carbon turnover and nutrient transformation. Additionally, drought significantly reduced the abundance of nitrogen-fixing genes (nifD, nifK) and weakened the relative contribution of Rhizobiaceae to nitrogen fixation; correlative functional profiling suggests Nocardioidaceae may possess alternative nitrogen cycling pathways that could partially offset suppressed rhizosphere nitrogen fixation capacity. Overall, these findings indicate that the fig plant response to drought stress involves both physiological adjustments in the host and functional reconfiguration of the rhizosphere microbial community, with Nocardioidaceae playing a key role in maintaining rhizosphere functions and enhancing drought tolerance.},
}

@article {pmid42585873,
year = {2026},
author = {Wang, H and Liang, Z and Guo, W and Ni, L and Lv, X},
title = {Mechanized Qu-making may contribute to lactic acid bacteria overproliferation in Hongqu rice wine brewing: Insights into microbial dysbiosis and flavor quality deterioration.},
journal = {International journal of food microbiology},
volume = {461},
number = {},
pages = {112013},
doi = {10.1016/j.ijfoodmicro.2026.112013},
pmid = {42585873},
issn = {1879-3460},
abstract = {Hongqu (HQ) serves as the core saccharification and fermentation starter (commonly referred to as "Qu") for Hongqu rice wine (HQW), a traditional Chinese fermented alcoholic beverage celebrated for its unique sensory characteristics and potential health-promoting properties. Driven by industrialization, mechanized Qu production has been progressively implemented to enhance process reproducibility, scalability, and operational efficiency. However, the implications of this technological transition on microbial community assembly, metabolic function and flavor formation during HQW brewing remain insufficiently characterized. To address this gap, this study employed an integrated metagenomic and metabolomic approach to comparatively analyze the taxonomic composition and functional metabolic profiles of mechanized Hongqu (MHQ) and traditional Hongqu (THQ), and further monitored their dynamic succession throughout HQW brewing process. Results demonstrated that MHQ exhibited significantly higher saccharification capacity and markedly enriched abundance of Saccharomyces cerevisiae, yet displayed a substantial reduction in Aspergillus niger compared with THQ (1.06% versus 43.41%). Paradoxically, despite these favorable starter attributes, HQW fermentation inoculated with MHQ induced an uncontrollable proliferation of lactic acid bacteria (LAB), predominantly represented by Pediococcus acidilactici, Lactiplantibacillus plantarum and Weissella paramesenteroides. This LAB-dominant consortium proliferated markedly during HQW fermentation, resulting in a community compositional shift toward bacterial dominance, evidenced by a fungi-to-bacteria ratio of 1.00:5.88 in MHQW, whereas THQW retained fungal dominance, with a corresponding ratio of 1.00:0.26. This structural shift coincided with significant declines in the relative abundances of functional fungi, including Saccharomyces cerevisiae and Monascus purpureus, possibly involving changes in niche occupation and acidification. These microbial community changes were associated with a metabolic shift characterized by excessive accumulation of organic acids, dysregulated biogenic amine profiles, depletion of free amino acids, and diminished synthesis of key volatile flavor compounds. Quantitatively, MHQW exhibited significantly higher final titratable acidity (12.67 g/L vs. 5.76 g/L), lower ethanol yield (17.29% v/v vs. 20.39% v/v), elevated total organic acid content (16.62 g/L vs. 6.28 g/L), and reduced total free amino acid concentration (3366.23 mg/L vs. 4303.93 mg/L) relative to THQW. Collectively, these findings indicate that mechanized Qu-making may disrupt the delicate "fungi-bacteria" ecological equilibrium essential for robust and balanced HQW fermentation, potentially favoring LAB proliferation. This study highlights the potential value of rational microbiome design to control LAB proliferation while maintaining functional fungi, which is important for optimizing mechanized Qu-making processes and improving flavor quality and fermentation robustness in HQW production. Collectively, our work provides a mechanism-informed framework for advancing Huangjiu modernization through rational microbiome engineering.},
}

@article {pmid42585927,
year = {2026},
author = {Ma, J and Qin, K and Qiao, Z and Ren, Z and Yang, X and Liu, Y},
title = {Integrative multi-omics reveals comprehensive gut-liver-adipose metabolic changes in peak laying hens with high or low egg production.},
journal = {Poultry science},
volume = {105},
number = {11},
pages = {107493},
doi = {10.1016/j.psj.2026.107493},
pmid = {42585927},
issn = {1525-3171},
abstract = {Eggs serve as an indispensable global nutritional resource, sustaining the economic foundation of the commercial poultry industry. To meet this continuous demand, egg formation involves an exceptionally energy-intensive biological process requiring continuous yolk precursor synthesis, which imposes a massive metabolic burden on laying hens. However, the comprehensive metabolic differences across the gut-liver-adipose axis between peak laying hens with high or low egg production remain incompletely characterized. A total of 180 healthy Hy-Line Brown laying hens (45-week-old) were continuously fed and monitored for production performance over a 6-week period. Following the exclusion of individuals with extremely low egg production (≤10 eggs during the 6-week monitoring period; n = 5) and candidate hens that repeatedly produced unqualified eggs over multiple weeks (n = 20), the remaining hens were ranked by 6-week average laying rate and allocated into FH (high-production hens at 50 weeks of age, n = 15) and FL (low-production hens at 50 weeks of age, n = 14) groups. Initial body weight did not differ significantly between groups (FH: 1936 ± 29.0 g; FL: 1894 ± 48.2 g; P-value = 0.446). We integrated transcriptomic, untargeted metabolomic, targeted bile acid metabolomics, and microbiome (16S rRNA and metagenomic) profiles to characterize comprehensive metabolic changes across the gut-liver-adipose axis associated with divergent egg-production phenotypes. The results showed that: (1) FH hens exhibited higher serum APOB and lower conjugated bile acids (TCDCA, TCA, and THDCA), with hepatic upregulation of FASN, PPARA, CPT1A, and VTG1 along with downregulation of CYP7A1, CYP7B1, CYP8B1, and CYP27A1; (2) intersecting module hub genes (MHGs) with differentially expressed genes (DEGs) identified 354 upregulated and 299 downregulated core genes, with EEF2 identified as the primary hepatic downregulated hub gene; (3) in abdominal fat, GSEA revealed significant enrichment in fatty acid transport (NES = 1.54), long-chain fatty acid metabolic process (NES = 1.39), and steroid hormone biosynthesis (NES = 1.85), accompanied by significant downregulation of ANGPTL4 and upregulation of HSD3B1, VTG1, VTG2, and VTG3; (4) ileal mucosal transcriptomics identified 619 DEGs (502 upregulated), with GSEA highlighting enrichment in cell junction organization (NES = 1.52) and tube morphogenesis (NES = 1.39), which were further categorized into functional modules including enteric synaptic signaling, epithelial adhesion, mucosal vascularization, and tissue renewal; (5) the functional profile of the ileal microbiota in FH hens showed enrichment of functions related to complex carbohydrate degradation and carbohydrate-binding modules, with keystone taxa including Blautia and Bifidobacterium associated with production and lipid markers. Collectively, these findings suggest that high egg production during the peak laying period is associated with coordinated metabolic differences across the liver, abdominal fat tissue, and intestine. The observed profiles included reduced hepatic translation-related and primary bile acid synthesis-related signatures, adipose endocrine-related changes and microbial functional potential related to carbohydrate utilization and antioxidant-related functional potential. These findings provide candidate multi-omics features for precision nutritional strategies and genetic improvement in commercial poultry.},
}

@article {pmid42585954,
year = {2026},
author = {Yang, S and Zhang, X and Wang, K and Zhao, X and Li, X},
title = {Pyrite fuels electron fluxes to accelerate hydrocarbon removal in coastal wetland soil.},
journal = {Journal of hazardous materials},
volume = {515},
number = {},
pages = {143275},
doi = {10.1016/j.jhazmat.2026.143275},
pmid = {42585954},
issn = {1873-3336},
abstract = {Natural sulfide minerals drive subsurface electron flow, but their role in hydrocarbon turnover is poorly understood. Here, we investigated whether pyrite (FeS2) can sustain electron transfer and accelerate petroleum hydrocarbon degradation in coastal wetland soils using a microbial electrochemical system (MES). High-dose pyrite amendment markedly enhanced long-term voltage output and increased cumulative charge by 34% over 120 days, indicating persistent subsurface electron release. Since pyrite improved soil conductivity and stimulated extracellular electron transfer, as reflected by elevated cytochrome c, extracellular polymeric substances production, and electroactive protein-like components. These electron transfer processes nearly doubled total petroleum hydrocarbon removal and promoted dissolved organic matter transformation from recalcitrant lignin-like compounds toward more bioavailable lipid- and protein-like components. Meanwhile, pyrite oxidation intensified Fe[2 +]/Fe[3+] cycling, secondary iron mineral formation, and coupled carbon-iron-sulfur transformations. Metagenomic analysis further revealed enrichment of hydrocarbon degraders, electroactive microorganisms, sulfate reducers, and methanogens, together with upregulation of genes involved in carbon metabolism, nitrogen cycling, iron-sulfur transformation, conductive pili assembly, and ubiquinone biosynthesis. These findings identify pyrite as a geological energy node that fuels persistent subsurface electron fluxes to enhance hydrocarbon removal in coastal wetland soils, highlighting the potential of activating natural iron-sulfur minerals for in situ bioremediation in anoxic coastal zones.},
}

@article {pmid42585955,
year = {2026},
author = {Han, X and Gao, Y and Chen, J and Yang, P and Liang, X and Wang, L and Ge, Y and Gui, H and He, Y and Zhan, F and Zhang, X and Kuzyakov, Y},
title = {Microplastics disrupt bacterial defense within the plant-AMF-bacteria continuum to amplify Cd bioavailability.},
journal = {Journal of hazardous materials},
volume = {515},
number = {},
pages = {143257},
doi = {10.1016/j.jhazmat.2026.143257},
pmid = {42585955},
issn = {1873-3336},
abstract = {The plant-arbuscular mycorrhizal fungi (AMF)-bacteria continuum provides a critical barrier against heavy-metal toxicity, but how microplastics (MPs) disrupt rhizosphere functions and exacerbate phytotoxicity remains unresolved. Using a maize-AMF-bacteria system in cadmium (Cd)-contaminated soil, we investigated two MP fractions differing in size and morphology added at increasing Cd contents. Although AMF colonization remained resilient, MPs induced fraction-dependent bacterial functional decoupling. Small MPs shifted the microbiome from extracellular Cd-immobilizing taxa (Sphingomonadaceae and Rhizobiaceae) toward intracellular stress-tolerant lineages. Large MPs restricted bacterial contacts, suppressing density-dependent cooperation. Metagenomic profiling and analysis of metagenome-assembled genomes (MAGs) revealed reduced potential for quorum sensing, ABC transporters, and alpha-linolenic acid metabolism under large MP exposure, compromising biofilm formation and extracellular Cd sequestration. Partial least squares path modeling indicated that bulk-soil chemistry did not define Cd uptake by plants. Instead, depletion of available Cd in soil reflected a biological sink associated with enhanced plant uptake. Enhanced Cd accumulation was associated with loss of rhizosphere defense mechanisms: potential root-barrier disruption by large MPs and weakened microbial buffering. Consequently, large MPs increased the Cd bioconcentration factor by 57.5%, compared with 32.1% for small MPs. These findings show that MPs amplify legacy Cd risks without increasing bulk-soil Cd availability, through disruption of root-interface integrity and microbial protection.},
}

@article {pmid42585962,
year = {2026},
author = {Xian, ZN and Hu, J and Wang, Z and Gong, H and Dai, X and Zhu, N},
title = {Process-resolved effects of dibutyl phthalate on sludge anaerobic fermentation: Enzyme inhibition and metabolic disruption underlie the suppression of acidogenesis.},
journal = {Journal of hazardous materials},
volume = {515},
number = {},
pages = {143232},
doi = {10.1016/j.jhazmat.2026.143232},
pmid = {42585962},
issn = {1873-3336},
abstract = {Growing evidence suggests that leaching of plasticizers such as dibutyl phthalate (DBP) from microplastics inhibits methanogenesis in anaerobic digesters treating waste activated sludge. However, how DBP influences upstream anaerobic fermentation (AF) remains unclear. This study evaluated the effects of DBP on overall sludge AF and separately on solubilization, hydrolysis, and acidogenesis processes. Volatile fatty acid (VFA) production showed a V-shaped response to environmentally relevant DBP concentrations. A reduction of 45.3% was observed at 0.5 mg/L DBP, whereas reductions exceeded 95% at 1-2 mg/L. The inhibition then weakened with increasing DBP, with a 60.5% reduction at 200 mg/L, an upper-bound level selected to bracket the maximum concentration reported in sludge. Stage-specific effects intensified with DBP concentration and peaked at 200 mg/L, where solubilization increased by 34.6%, whereas hydrolysis and acidogenesis decreased by 30.8% and 11.2%, respectively. The combined influence of these processes explained the nonmonotonic VFA response. Notably, enzyme assays and molecular simulations indicated that DBP inhibited ACK in a competitive-like manner and reduced its activity. Metagenomic analysis further indicated that DBP reduced genetic potential for downstream pathways converting pyruvate and acetyl-CoA to fermentation products. Collectively, these results reveal a DBP-induced fluctuating AF response and provide mechanistic insights into optimizing anaerobic treatment of plasticizer-laden sludge.},
}

@article {pmid42585964,
year = {2026},
author = {Wang, X and Liao, H and Wang, X and Wang, Y and Li, D and Ma, H and Yang, J and Qian, X and Wang, H and Li, Q and Xiu, Z and Yang, Y},
title = {Cobalamin-autonomous Trichlorobacter facilitates robust In situ bioremediation of halogenated solvents.},
journal = {Journal of hazardous materials},
volume = {515},
number = {},
pages = {143046},
doi = {10.1016/j.jhazmat.2026.143046},
pmid = {42585964},
issn = {1873-3336},
abstract = {Organohalide-respiring bacteria (OHRB) are key mediators of chlorinated solvent detoxification in anoxic groundwater, yet their practical application is often constrained by vitamin B12 (cobalamin) auxotrophy and the requirement for strictly controlled anoxic and nutrient conditions. Here, we report the enrichment and characterization of a Trichlorobacter-dominated consortium (NB-12) that sustains efficient dihaloelimination of halogenated alkanes under minimal nutrient and relaxed anoxic constraints. The NB-12 enrichment completely transformed 1,2-dichloroethane (1,2-DCA) to ethene within 40 h (≥3.3 μmol h[-1]) and also dechlorinated 1,2-dichloropropane and 1,1,2-trichloroethane, as well as debrominated 1,2-dibromoethane and 1,2-dibromopropane. Exogenous vitamin B12 supplementation did not enhance dechlorination kinetics or product yields. Amplicon sequencing and metagenomic analyses identified Trichlorobacter lovleyi as the dominant population (>60% relative abundance) and revealed a complete anaerobic cobalamin biosynthesis pathway in the corresponding metagenome-assembled genome, indicating corrinoid autonomy at the community level. Notably, the NB-12 consortium retained sustained dehalogenation activity in non-sterile, unbuffered, and oxygen-leaky mesocosms prepared using only tap water, trace elements, and lactate-conditions mimicking challenging in situ environments. Field bioaugmentation using this "low-input" inoculant resulted in successful aquifer colonization and a reduction in 1,2-DCA concentrations in contaminated groundwater. Together, these results demonstrate that corrinoid-autonomous, Trichlorobacter-dominated enrichments can relax key physiological and operational constraints of OHR-based remediation, expanding the applicability of low-input, cost-effective strategies for in situ treatment of halogenated alkane-contaminated groundwater.},
}

@article {pmid42586007,
year = {2026},
author = {López-Cañizares, J and Truchado, P and Macrì, M and Cobo-Díaz, JF and Álvarez-Ordóñez, A and Bonetta, S and Allende, A},
title = {Water reuse within a circular economy: Long-read metagenomics reveals distinct residual resistome profiles across full-scale wastewater-reclamation systems in Murcia, Spain.},
journal = {Chemosphere},
volume = {411},
number = {},
pages = {145063},
doi = {10.1016/j.chemosphere.2026.145063},
pmid = {42586007},
issn = {1879-1298},
abstract = {Water reuse is a key pillar of circular economy strategies, particularly in water-scarce regions, by preserving freshwater resources and supporting agricultural production. Current regulations promote the use of reclaimed water for irrigation, placing wastewater treatment plants (WWTPs) at the center of this transition. However, emerging risks related to antibiotic-resistant bacteria (ARB) and antibiotic-resistance genes (ARGs) challenge the safety of reuse as these determinants may persist after treatment. This study evaluated the effectiveness of ozonation, sodium hypochlorite, UV-C irradiation, and membrane bioreactor (MBR) systems in reducing ARGs in effluents from the Region of Murcia (Spain) across five sampling campaigns between 2023 and 2024. Metagenomic sequencing identified ARGs associated with 17 antibiotic classes, with macrolide-, β-lactam-, and tetracycline-ARGs dominating. Total ARG abundance was lower in treated effluents than in influents, with the greatest percentage reduction in MBR system, although based on only two effluent samples. Selected macrolide-, sulfonamide-, tetracycline- and β-lactam-ARGs nevertheless remained detectable after treatment, with distinct gene-specific profiles among the wastewater-reclamation systems. Effluent samples differed in the taxonomic composition of ARG-carrying reads and in the detection of ARGs putatively co-localized on mobilome associated contigs. These findings show that total ARG reduction alone does not fully characterize wastewater-reclamation performance because substantial decreases in total ARG burden were accompanied by different residual resistome profiles. Combining ARG abundance, identity, potential hosts, and genomic context enables a fuller assessment of reclaimed-water treatment. These metagenomic associations indicate potential persistence and mobility but do not constitute direct evidence of horizontal gene transfer or quantitative environmental risk.},
}

@article {pmid42575184,
year = {2026},
author = {Zha, Y and Wang, Z and Sun, W and Meng, J and Liu, Y and Wang, B},
title = {Metagenomic insights into biogeochemical functional potential and resistome dynamics of PM2.5 microbial communities.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125444},
doi = {10.1016/j.envres.2026.125444},
pmid = {42575184},
issn = {1096-0953},
abstract = {Atmospheric particulate matter harbors diverse microorganisms, yet their functional potential in biogeochemical cycling and the associated risks of resistome remain poorly understood. Here, we performed metagenomic sequencing on PM2.5 samples collected across four months to unravel the microbial genetic repertoire involved in methane, nitrogen, phosphorus, and sulfur cycling, as well as the resistome, and pathogen composition. A broad range of functional genes was detected for each biogeochemical cycle, with more than 65% of gene subtypes shared across all months, indicating conserved functional signatures. In contrast, more than 80% of the resistome showed temporal variation in abundance, with the lowest richness observed in March. Temporal shifts were also observed in resistome composition, with several resistance determinants reaching higher abundances in April and May. Network analysis indicated frequent co-occurrence among several pathogenic and opportunistic taxa. Contig-based profiling identified 51 potential pathogenic taxa, including 32 human- or animal-associated taxa. In addition, both PM10 and PM2.5 concentrations were associated with pathogen abundance and functional gene richness (e.g., antibiotic resistance genes and virulence factors). Together, this metagenomic survey suggests contrasting temporal patterns between conserved biogeochemical functional potential and more variable resistome-related traits in PM2.5 microbial communities. While constrained by limited temporal coverage and sample size, this study provides preliminary insights into the ecological and potential public health relevance of airborne microbial communities in urban environments.},
}