@article {pmid41881444,
year = {2026},
author = {Kringeland, GD and Tangedal, S and Julian, D and Paytuví-Gallart, A and Sanseverino, W and Bertelsen, RJ and Husebø, GR and Knudsen, KS and Lehmann, S and Nielsen, R and Eagan, TML},
title = {Antimicrobial resistance genes and antibiotic use in chronic lung disease: a bronchoscopy study of the lower airways microbiome.},
journal = {BMJ open respiratory research},
volume = {13},
number = {1},
pages = {},
doi = {10.1136/bmjresp-2025-003864},
pmid = {41881444},
issn = {2052-4439},
mesh = {Humans ; Male ; Female ; Cross-Sectional Studies ; Bronchoscopy ; Middle Aged ; Aged ; *Anti-Bacterial Agents/therapeutic use ; *Microbiota/genetics ; Bronchoalveolar Lavage Fluid/microbiology ; Pulmonary Disease, Chronic Obstructive/microbiology/drug therapy ; Case-Control Studies ; *Lung Diseases/microbiology/drug therapy ; *Drug Resistance, Bacterial/genetics ; *Drug Resistance, Microbial/genetics ; Chronic Disease ; },
abstract = {BACKGROUND: Antimicrobial resistance genes (ARGs) in the respiratory microbiome are poorly characterised. We compared the presence of ARGs in healthy controls with patients with chronic lung disease in a cross-sectional study, adjusted for time since antibiotic use.

METHODS: Bronchoalveolar lavage was collected from 100 controls, and 93 patients with chronic obstructive pulmonary disease (COPD), 13 with asthma, 34 with sarcoidosis, 12 with idiopathic pulmonary fibrosis (IPF) and 11 patients with unclassifiable interstitial lung disease (uILD). Participants had not used antibiotics 14 days prior to sampling. Shotgun metagenomic sequencing was performed with Illumina NovaSeq. ARGs were identified using the National Database of Antibiotic-Resistant Organisms. Sample reads were normalised to counts per million.

RESULTS: In total, 38% of controls had at least one ARG, compared with 51%, 39%, 65% and 83% of patients with COPD, asthma, sarcoidosis and IPF, respectively (p=0.01). ARGs against tetracycline (33%) were the most common ARG class, followed by beta-lactam and macrolide resistance (both 26%). In a logistic regression analysis adjusted for sex, age, body composition, smoking and antibiotic use, the OR (95% CI) for having ARGs in the lower airways was 1.30 (0.70 to 2.41) in COPD, 1.00 (0.29 to 3.52) in asthma, 3.52 (1.40 to 8.83) in sarcoidosis, 6.40 (1.25 to 32.73) in IPF and 3.27 (0.76 to 14.16) in uILD compared with controls. Overall mean (SD) ARG counts per million were 403.8 (537.7) in the 35 subjects who had used antibiotics ≤3 months before bronchoscopy, compared with 197.6 (355.9) in the 228 subjects without (p=0.02).

CONCLUSION: The presence of ARGs in the lower airways microbiome was significantly higher in patients with sarcoidosis and IPF than in controls. The counts per million for ARGs were significantly associated with recent antibiotic use.},
}

Humans
Male
Female
Cross-Sectional Studies
Bronchoscopy
Middle Aged
Aged
*Anti-Bacterial Agents/therapeutic use
*Microbiota/genetics
Bronchoalveolar Lavage Fluid/microbiology
Pulmonary Disease, Chronic Obstructive/microbiology/drug therapy
Case-Control Studies
*Lung Diseases/microbiology/drug therapy
*Drug Resistance, Bacterial/genetics
*Drug Resistance, Microbial/genetics
Chronic Disease

@article {pmid41881804,
year = {2026},
author = {Gutiérrez, J and Vergara-Amado, J and Martorell, C and Navedo, JG and Wille, M and Guajardo-Leiva, S and Castro-Nallar, E and Verdugo, C},
title = {Functional Shifts in the Gut DNA Virome in a Long-Distance Migratory Shorebird During the Pre-Migratory Fattening.},
journal = {Molecular ecology},
volume = {35},
number = {6},
pages = {e70315},
doi = {10.1111/mec.70315},
pmid = {41881804},
issn = {1365-294X},
support = {FONDECYT N°1191769//Agencia Nacional de Investigación y Desarrollo/ ; ANILLO ATE220062//Agencia Nacional de Investigación y Desarrollo/ ; Doctoral scholarship N°21201700//Agencia Nacional de Investigación y Desarrollo/ ; //The Pathogen Watchtower Program (Biotia Inc. & The Rockefeller Foundation)/ ; //Universidad Austral de Chile/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Charadriiformes/virology/physiology ; *Animal Migration ; *Virome/genetics ; Feces/virology ; Metagenomics ; Metagenome ; },
abstract = {Migration represents one of the most energetically demanding phases in the life cycle of long-distance migratory birds. Pre-migratory fattening is a critical preparatory stage characterized by hyperphagia, rapid fat accumulation, organ remodelling, and immune modulation. Although the gut microbiome has been recognized as a key contributor to these physiological adaptations, the role of the gut virome remains poorly understood. In this study, the diversity, functional potential, and temporal dynamics of the gut DNA virome in a trans-hemispheric migratory shorebird, the Hudsonian godwit (Limosa haemastica), were assessed during pre-migratory fattening. Adult individuals were maintained under controlled aviary conditions for 15 weeks during the preparation for northbound migration, and faecal samples were collected at two distinct physiological time points: at the beginning and the end of pre-migratory fattening. Shotgun metagenomic sequencing revealed 798 high-quality viral operational taxonomic units (vOTUs), the majority of which were bacteriophages (92%). Potential functional annotation identified auxiliary metabolic genes (AMGs) associated with nucleotide metabolism, redox balance, and host adaptation. Although overall gut virome diversity did not differ between stages, significant changes in potential functional profiles of phages were observed, especially during the final stage of fattening when energy demands are at their highest. In addition to bacteriophages, we report two divergent adenoviruses potentially associated with the Siadenovirus and Aviadenovirus genera. These findings suggest that dynamic viral communities may play underrecognized roles in supporting host physiology during energetically costly life stages.},
}

Animals
*Gastrointestinal Microbiome/genetics
*Charadriiformes/virology/physiology
*Animal Migration
*Virome/genetics
Feces/virology
Metagenomics
Metagenome

@article {pmid41881873,
year = {2026},
author = {Zhao, C and Yao, R and Xiong, M and Liu, X and Yu, J and Jumpponen, A and Romantschuk, M and Ur Rahman, S and Hui, N},
title = {Microbial exposure and antibiotic resistance gene dynamics shift between indoor and outdoor school activities.},
journal = {Ecotoxicology and environmental safety},
volume = {314},
number = {},
pages = {120044},
doi = {10.1016/j.ecoenv.2026.120044},
pmid = {41881873},
issn = {1090-2414},
abstract = {School curricular and extracurricular activities, including indoor study and sports like basketball, significantly impact adolescent physical and mental health. However, their effects on hand and nasal microbiomes, particularly regarding antibiotic resistance genes (ARGs), are underexplored. Here, we recruited 42 junior middle school students in Shanghai to investigate microbial composition and ARGs, collecting 336 hand and nasal samples after handwashing, indoor study, indoor basketball, and outdoor basketball. Our results showed that playing basketball either indoors or outdoors increased microbial diversity in nasal cavities and on hands, compared to post-handwashing. Notably, nasal microbiomes were predominantly derived from hand microbiomes, regardless of the activity performed. Among ARGs, macB genes were more abundant after outdoor basketball than indoor basketball, with this difference more pronounced in nasal cavities than on hands. Metagenomic sequencing identified Aureimonas phyllosphaerae as the primary macB gene host. Although this bacterium harbors ARGs, it is non-pathogenic and lacks mobile genetic elements, indicating a low potential for horizontal gene transfer or interspecies ARG transmission. Collectively, even though students may be exposed to more ARGs during outdoor activities, the health risks are likely minimal because the observed ARG bacteria are non-pathogenic and the likelihood of interspecies ARG transmission is low.},
}

@article {pmid41881888,
year = {2026},
author = {Tuveng, TR and Hagen, LH and Rese, M and Eijsink, VGH and Arntzen, MØ},
title = {Meta-omics profiling of denitrifying bacterial communities with lignin as carbon source.},
journal = {Microbiological research},
volume = {308},
number = {},
pages = {128503},
doi = {10.1016/j.micres.2026.128503},
pmid = {41881888},
issn = {1618-0623},
abstract = {Lignin is the most abundant renewable source of aromatic carbon and its microbial depolymerization and metabolism under aerobic conditions is well studied. However, lignin breakdown in the absence of oxygen remains poorly understood. In this study, we established long-term bacterial enrichment cultures supplied with diverse lignin preparations as the sole carbon source under denitrifying conditions. Denitrification dynamics were followed by monitoring nitrogenous gases. Metagenomics analysis of eight enrichments involving five lignins recovered 62 metagenome-assembled genomes (MAGs), several of which encoded enzymes for both denitrification and anaerobic metabolism of aromatic compounds. Quantitative metaproteomics confirmed expression of such enzymes and additionally showed that several MAGs expressed multiple oxidoreductases and uncharacterised proteins that are potential candidates for involvement in lignin modification. The detection of several oxygen-dependent oxidoreductases despite anaerobic conditions prompts intriguing discussion of potential mechanistic explanations. This systems-level study expands our understanding of bacterial processing of lignin-associated carbon in anaerobic environments and suggests enzymatic targets for further exploration of lignin depolymerization under oxygen-limited conditions.},
}

@article {pmid41882035,
year = {2026},
author = {Kumar, M and Ansari, WA and Singh, A and Kumar, SC and Zeyad, MT and Chakdar, H and Farooqi, MS and Sharma, A and Srivastava, S and Jha, GK and Srivastava, AK},
title = {Impact of genotype and soil fertility on wheat rhizosphere microbiota under the trans-gangetic plain.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-36646-4},
pmid = {41882035},
issn = {2045-2322},
support = {2020//Centre for Agricultural Bioinformatics/ ; 2020//Centre for Agricultural Bioinformatics/ ; 2020//Centre for Agricultural Bioinformatics/ ; 2020//Centre for Agricultural Bioinformatics/ ; 2020//Centre for Agricultural Bioinformatics/ ; 2020//Centre for Agricultural Bioinformatics/ ; },
abstract = {The effects of genotypes (HD3086 and PBW343) and soil physicochemical properties on the wheat rhizospheric bacterial communities along the trans Indo-Gangetic plains were studied. The trans-Indo-Gangetic Plains of India are one of the areas in the country where wheat is grown the most. Despite the agricultural significance of this region, extensive studies on the rhizosphere microbial abundance and community structure related to wheat cultivation in this area are still lacking. To address this knowledge gap, the present study was undertaken to characterize the rhizosphere microbiome using full-length 16 S rRNA-based metagenomic profiling, implementing universal primers, tailed with PacBio Sequel II barcode sequences, providing new insights into microbial dynamics across this major wheat-producing landscape. Statistical analysis revealed significant differences in both abundance and diversity among the different soil samples and wheat genotypes. Four phyla exhibited significant differences in relative abundance between the genotypes (p < 0.05): Proteobacteria (p = 0.002), Planctomycetes (p = 0.000), Verrucomicrobia (p = 0.000), and Firmicutes (p = 0.030). The number of genera identified in genotype HD3086 across all locations was 421, while it was 322 for genotype PBW343. There were 251 genera found common, with 170 genera exclusively present in HD3086 and 71 in PBW343. Significant differences were observed in the relative abundance of eighteen genera (p < 0.05) between the genotypes; some of them include Luteolibacter, Gemmata, Pseudomonas, Stenotrophobacter, Pseudarthrobacter, Devosia, Lacibacter, Gaiella, Luteimonas, and Nitrosospira. Correlation analysis indicated significant associations between microbial diversity and soil parameters like pH, total and available nitrogen, potassium, phosphorus, iron, and organic carbon for both varieties. Core taxa analysis revealed 27 core taxa across both genotypes. The study highlights significant genotype effects on rhizosphere microbiomes, with implications for soil health and crop management strategies.},
}

@article {pmid41882344,
year = {2026},
author = {Muammar, A and Retnaningrum, E and Daryono, BS and Prijambada, ID and Yashima, Y and Peterbauer, C},
title = {A fast workflow to explore active enzymes from environmental samples through functional metagenomics.},
journal = {Applied microbiology and biotechnology},
volume = {110},
number = {1},
pages = {},
pmid = {41882344},
issn = {1432-0614},
mesh = {*Metagenomics/methods ; Feces/microbiology ; Workflow ; Animals ; *Cellulases/genetics/metabolism ; Indonesia ; Multiplex Polymerase Chain Reaction ; Gene Library ; Metagenome ; },
abstract = {Functional metagenomics has emerged as an effective tool for discovering novel enzymes directly from environmental samples, overcoming the limitations of traditional culture-based methods. In this study, we used a functional metagenomic approach on stool samples from Axis kuhlii, an endemic deer species from Indonesia, to identify active cellulases. We created an efficient workflow for expression of metagenomic sequences directly in Komagatella phaffii by combining metagenomic sequencing to investigate enzyme diversity, multiplex PCR to build a genes library, and rolling circle amplification (RCA) to streamline the cloning process, eliminating the need for intermediate Escherichia coli transformation and propagation steps. Furthermore, a semi-high-throughput screening method was used to evaluate multiple samples at once, allowing for the rapid identification of active enzymes. Using this approach, we discovered five endoglucanases and three β-glucosidases with confirmed enzyme activity. This study shows that functional metagenomics can bridge the gap between computational predictions and experimental validation, providing a reliable platform for enzyme discovery and characterization from complex environmental microbiomes. KEY POINTS: • We established K. phaffii expression of metagenomic sequences via multiplex PCR and RCA. • This approach links metagenomic and activity screening to enable enzyme discovery. • Eight active cellulases were obtained from environmental samples through this approach.},
}

*Metagenomics/methods
Feces/microbiology
Workflow
Animals
*Cellulases/genetics/metabolism
Indonesia
Multiplex Polymerase Chain Reaction
Gene Library
Metagenome

@article {pmid41882399,
year = {2026},
author = {Çilkiz, M},
title = {Microbial Biotechnology in Agriculture.},
journal = {Progress in molecular and subcellular biology},
volume = {62},
number = {},
pages = {251-306},
pmid = {41882399},
issn = {0079-6484},
mesh = {*Agriculture/methods ; *Biotechnology/methods ; Soil Microbiology ; Metagenomics/methods ; Crops, Agricultural/growth & development/microbiology ; Metabolomics/methods ; Fertilizers ; },
abstract = {Global food security has become one of the greatest challenges of the twenty-first century due to the rapidly growing world population's food demands and environmental threats such as climate change, soil erosion, and the depletion of freshwater resources. The extensive use of chemical fertilizers and pesticides throughout conventional agriculture has increased productivity significantly, but it has additionally resulted in major ecological and socioeconomic problems, such as soil acidity, groundwater resource pollution, and decreased biodiversity. In this regard, microbial biotechnology is a particularly noteworthy technique that improves agricultural production while promoting environmental sustainability, maintaining ecological balance, and making effective use of resources. This application makes use of microorganisms to enhance soil health and structure, promote plant growth, and minimize both abiotic and biotic stresses. Microbial applications include nitrogen fixation, as well as biofertilizers that reduce the dependency on synthetic materials and biopesticides. Microbial consortia and biostimulants that improve plant physiology by producing phytohormones produce more dependable and durable consequences in the field. Metagenomics and metabolomics are the two types of omic technologies used in these areas of study that provide a thorough description of the variety and roles of microorganisms. Furthermore, the intentional production of microbes targeted at specific organisms has been made practical via synthetic biology and gene editing techniques. In-depth case studies performed in several countries reveal that microbial technologies significantly reduced expenses and improved soil production, advancing the sustainable development goals. Nevertheless, there are several barriers to the widespread use of microbial biotechnology in agriculture. These include unpredictable conditions in the fields, strict regulations, especially related to genetically modified organisms' problems with product quality, and farmers' insufficient understanding. Microbial biotechnology aims to accomplish its full potential as an advancement in technology and as an essential aspect of resource-efficient and environmentally friendly agricultural systems via responsible innovation, adaptable regulations, and worldwide cooperation.},
}

*Agriculture/methods
*Biotechnology/methods
Soil Microbiology
Metagenomics/methods
Crops, Agricultural/growth & development/microbiology
Metabolomics/methods
Fertilizers

@article {pmid41882401,
year = {2026},
author = {Erözden, AA and Tavşanlı, N and Çalışkan, M and Arıkan, M},
title = {Microbial Omics.},
journal = {Progress in molecular and subcellular biology},
volume = {62},
number = {},
pages = {333-366},
pmid = {41882401},
issn = {0079-6484},
mesh = {*Metabolomics/methods ; *Proteomics/methods ; *Genomics/methods ; Metagenomics/methods ; *Computational Biology/methods ; Transcriptome ; Microbiota ; *Bacteria/genetics/metabolism ; },
abstract = {Omics technologies have revolutionized research across diverse fields, and their increasing use in microbiology has provided new opportunities for understanding microbial life. These methods enable detailed investigation of the molecular biology of individual organisms as well as the complex interactions within microbial communities. In this chapter, we describe key single-organism omics approaches, including genomics, transcriptomics, proteomics, and metabolomics, as well as meta-omics techniques such as metagenomics, metatranscriptomics, metaproteomics, and meta-metabolomics. We also discuss integrative multi-omics strategies for studying microbial ecosystems. For each omics method, we outline its main features, experimental and bioinformatic workflows, major applications, and commonly used computational tools, thereby providing a practical guide for researchers aiming to explore microbial structure, function and interactions at multiple molecular levels.},
}

*Metabolomics/methods
*Proteomics/methods
*Genomics/methods
Metagenomics/methods
*Computational Biology/methods
Transcriptome
Microbiota
*Bacteria/genetics/metabolism

@article {pmid41882608,
year = {2026},
author = {Chen, M and Wu, Z and Du, Y and Jiang, J and Feng, J},
title = {Construction of caries risk assessment scale and oral microecology analysis of adolescents with fixed orthodontic treatment.},
journal = {BMC oral health},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12903-026-08114-y},
pmid = {41882608},
issn = {1472-6831},
}

@article {pmid41882673,
year = {2026},
author = {Deng, J and Qiu, Q and Ye, S and Yu, J and Yao, D and Deng, H and Wang, C and Han, L and Deng, Y and Chen, Y and Liu, Y and Liu, C and Shang, X and Fang, X and Lu, C},
title = {Disentangling environmental and disease-specific signatures in the gut microbiome of psoriasis: discovery of Fimenecus sp. as a novel biomarker and characterization of the gut virome.},
journal = {Journal of translational medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12967-026-08013-4},
pmid = {41882673},
issn = {1479-5876},
abstract = {BACKGROUND: The contribution of the gut microbiome to the pathogenesis of psoriasis remains a subject of debate, with inconsistent findings across studies likely confounded by environmental factors. This study aimed to statistically disentangle the effects of a shared household environment from disease-specific microbial signatures in psoriasis. Our objective was to identify novel, multi-kingdom biomarkers, encompassing bacteria and viruses, that hold significant diagnostic and therapeutic potential.

METHODS: We conducted a nested case-control study, performing shotgun metagenomic sequencing on stool samples from 143 participants. The cohort comprised 98 psoriasis patients, 28 healthy cohabiting relatives, and 17 unrelated healthy controls. A comprehensive multi-kingdom analysis of bacteria, viruses, and their associated metabolic pathways was implemented. To ensure the robustness of our findings, a two-stage discovery-validation strategy was employed to identify distinct microbial features associated with psoriasis.

RESULTS: Our analysis revealed that the shared household environment was the predominant factor shaping the overall gut microbiome structure. Despite this strong confounding effect, we successfully identified a novel bacterial species, Fimenecus sp000432435, as a robust biomarker for psoriasis, achieving an area under the curve (AUC) of 0.84. Genomic functional prediction indicated that this species encodes pathways with the potential for B-vitamin and secondary bile acid biosynthesis. Furthermore, characterization of the gut virome identified five disease-associated bacteriophages. Among these, vBin_422 exhibited a significant negative correlation with the abundance of Fimenecus sp000432435, suggesting a potential ecological interaction. Notably, the biotin biosynthesis pathway was negatively correlated with disease severity, whereas specific viral taxa showed a positive correlation with systemic inflammatory markers within the patient cohort.

CONCLUSIONS: Controlling for environmental confounders reveals that psoriasis is associated with sparse but distinctmicrobial signatures rather than broad dysbiosis. Fimenecus sp000432435 is a promising candidate for non-invasive diagnostics, while the characterized virome opens new therapeutic avenues targeting bacteriophage-bacteria interactions in psoriasis management.

TRIAL REGISTRATION: ChiCTR-IOR-17011075. Registered 6 April 2017, http://www.chictr.org.cn/showproj.aspx?proj=17334.},
}

@article {pmid41882801,
year = {2026},
author = {Langlois, A and Duplessis, M and Ronholm, J and Vincent, AT and Poulin-Laprade, D and Petri, RM},
title = {Impact of differential dietary concentrations of cobalt, manganese and zinc on gastrointestinal microbiome and resistome of lactating dairy cattle.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-026-00554-9},
pmid = {41882801},
issn = {2524-4671},
}

@article {pmid41883029,
year = {2026},
author = {Dip, SA and Mallick, D and Acharjee Shuvo, U and Barua Soumma, S and Rafsani, F and Kumar Paul, B and Ahmed Moumi, N and Ahmed, S and Zhang, L},
title = {Large language model agents for biological intelligence across genomics, proteomics, spatial biology, and biomedicine.},
journal = {Briefings in bioinformatics},
volume = {27},
number = {2},
pages = {},
doi = {10.1093/bib/bbag110},
pmid = {41883029},
issn = {1477-4054},
support = {2125798//Virginia Tech, the Department of Computer Science, and the U.S. National Science Foundation (NSF)/ ; 2344169//Virginia Tech, the Department of Computer Science, and the U.S. National Science Foundation (NSF)/ ; 2319522//Virginia Tech, the Department of Computer Science, and the U.S. National Science Foundation (NSF)/ ; },
mesh = {*Genomics/methods ; *Proteomics/methods ; Humans ; *Computational Biology/methods ; *Artificial Intelligence ; Large Language Models ; },
abstract = {Large language models (LLMs) are evolving from passive predictors into agentic systems capable of planning, tool-use, and multimodal reasoning. This shift is especially consequential for biology, where complex, noisy, and multi-scale data require adaptive and integrative computational strategies. In this review, we provide the first systematic synthesis of LLM-based agents across genomics, molecular biology, imaging, biomedical analysis, and automated bioinformatics workflows. We analyze >60 emerging systems and organize them within a unifying framework that characterizes agentic traits, such as autonomous decision-making, external tool invocation, memory, and self-correction. Across domains, agentic LLMs show early promise in enabling multi-step analysis, linking heterogeneous evidence, and supporting exploratory scientific tasks. At the same time, our comparative assessment highlights consistent challenges, including unstable reasoning, limited biological grounding, retrieval misalignment, and barriers to reproducibility and biosafety. We conclude by outlining opportunities for trustworthy and collaborative biological agents, including multimodal integration, closed-loop experimental design, and robust evaluation practices. This survey aims to clarify the emerging landscape and chart a path toward reliable agentic systems for biological discovery.},
}

*Genomics/methods
*Proteomics/methods
Humans
*Computational Biology/methods
*Artificial Intelligence
Large Language Models

@article {pmid41883089,
year = {2026},
author = {Duchêne, C and Jaubert, M and Falciatore, A},
title = {Beyond red/far-red sensing: phytochrome perception of the marine light field by microalgae.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.71128},
pmid = {41883089},
issn = {1469-8137},
support = {ANR-25-CE20-4776//Agence Nationale de la Recherche/ ; ANR-20-CE20-0024//Agence Nationale de la Recherche/ ; ANR-25-CE20-1717//Agence Nationale de la Recherche/ ; ANR-11-LABX-0011-01//Agence Nationale de la Recherche/ ; 101082304//Fourth Framework Programme/ ; },
abstract = {Phytochromes (PHYs) are a major group of photoreceptors, described as red and far-red light sensors in land plants. Recent genomic and metagenomic explorations have revealed the presence of PHYs also in various eukaryotic microalgae originating from distinct endosymbiotic events. Growing evidence indicates that these PHYs are spectrally and functionally tuned to shorter wavelengths, which are prevalent in the aquatic environments as depth increases. Investigations using emerging phytoplankton model species, along with environmental surveys, are uncovering new PHY-mediated responses that likely influence their growth and distribution in marine environments. This Tansley Insight explores the implications of these discoveries for understanding the evolution and functional significance of this major photoreceptor class in the upper ocean, where light drives both energy and information flow.},
}

@article {pmid41883376,
year = {2026},
author = {Mao, C and Wang, Y and Li, X and Kong, Q and Al-Farraj, SA and Xu, EG and Grossart, HP and Huang, J and Song, W},
title = {Resistance Gene Dynamics, Biogeochemical Coupling, and Ecological Risks in Sediments of Anthropogenically Impacted Lake Wetlands in China.},
journal = {Environment & health (Washington, D.C.)},
volume = {4},
number = {3},
pages = {420-433},
pmid = {41883376},
issn = {2833-8278},
abstract = {Antibiotic resistance is a growing global threat to both public health and ecosystem stability. While the "One Health" framework emphasizes the need to monitor antibiotic resistance genes (ARGs) across diverse environments worldwide, the risks posed by ARGs in lakes affected by human activities, particularly in lake sediments that serve as natural reservoirs of ARGs, remain poorly understood. Metagenomics enables culture-independent analysis of microbial communities and resistance genes, providing essential insights into ARG dynamics. This study investigates microbial communities, ARGs, metal resistance genes (MRGs), and mobile genetic elements (MGEs) in sediments from Lake Donghu and Lake Weishan in China, two contrasting lake ecosystems subject to urbanization and agricultural activities for over four decades, using high-throughput metagenomic sequencing and assembly. ARGs and MRGs were more strongly influenced by deterministic environmental factors, particularly heavy metals (Cd, Pb, Cu), whereas microbial community structures were predominantly shaped by stochastic processes. Metagenomic binning yielded 293 metagenome-assembled genomes (MAGs), 125 of which were identified as potential ARG hosts, with Proteobacteria and Desulfobacterota being the most common. These hosts frequently cocarried MGEs, virulence factor genes (VFGs), and MRGs and exhibited metabolic pathways linked to carbon, nitrogen, and greenhouse gas (CO2 and N2O) cycling. Dissolved organic carbon (DOC) was determined as a key factor influencing microbial metabolism and promoting resistance gene dissemination. Our findings highlight a tight coupling between ARG dissemination, microbial ecological functions, and biogeochemical processes, underscoring ecosystem-level risks associated with resistance proliferation in human-impacted wetlands of China and elsewhere.},
}

@article {pmid41883694,
year = {2026},
author = {Feigl, V and Röhberg, MZ and Masa, K and Hegedűs, H and Janek, Z and Deák, V and Fehér, C and Buda, K and Medgyes-Horváth, A},
title = {Extremophilic microbial isolates and metagenomic analysis of Greek and Hungarian bauxite residues.},
journal = {Biotechnology reports (Amsterdam, Netherlands)},
volume = {50},
number = {},
pages = {e00956},
pmid = {41883694},
issn = {2215-017X},
abstract = {Bauxite residue (BR) is an extreme environment for microorganisms. The aim of the work was to isolate extremophilic microorganisms for further biotechnological applications, such as bioleaching or waste rehabilitation. At the same time, metagenomic analysis was performed to monitor short-term changes in deposited BR. We isolated and identified alkaliphilic and extreme halotolerant strains of Nesterenkonia massiliensis, N. natronophila, Micrococcus luteus, Aspergillus iizukae, Gibellulopsis serrae, and G. nigrescens from Greek and Hungarian BRs. Most strains were siderophore producers, cellulose degraders and produced oxalic and acetic acids. Metagenomic analysis revealed a shift in the most abundant bacterial classes from the freshly produced BR during 1 month and 3 months of storage: from Gammaproteobacteria (29% relative abundance), to Actinomycetes (31%) and Gammaproteobacteria (39%), respectively. Metagenomic analysis showed the presence of Nesterenkonia species. These results highlight the diverse microbiome of BR and underscore its potential as a valuable reservoir of extremophilic microorganisms.},
}

@article {pmid41883790,
year = {2026},
author = {Way, J and Sherman, T and Leleika, S and Crippen, K and Wilson, R and Fida, TT},
title = {Enrichment and comparative metagenomics of microbes involved in biocorrosion of gas transport or storage steel infrastructure.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1771929},
pmid = {41883790},
issn = {1664-302X},
abstract = {Biocorrosion, also known as microbiologically influenced corrosion (MIC), is the deterioration of metals caused by microbial activities that compromise the structural integrity, reliability, and safety of steel infrastructure. To identify the genetic determinants that MIC-causing microorganisms may use to attack steel infrastructure, field samples from natural gas infrastructure with a potential history of MIC were collected, enriched for different MIC categories, and subjected to whole-genome shotgun sequencing for metagenomic analysis. Biofilms were grown on carbon steel coupons or glass slides as attachment substrates to assess differences in microbial community composition and metabolic activities. The highest corrosion activities were observed in enrichments dominated by acid-producing bacteria (APB) and hydrogen-utilizing bacteria. APB enrichments resulted in the highest accumulation of organic acids and a severe decrease in culture fluid pH. A total of 57 metagenome-assembled genomes were recovered from the biofilms, some of which differed between carbon steel coupons and glass slide substrates. The metagenomes contained most of the known genes implicated in MIC and sulfide production, with substantial variation in estimated gene copy numbers among metagenomes and attachment substrates. Overall, comparative analysis of these biofilm metagenomes enriched from natural gas production and processing infrastructure highlights similarities to microbial communities commonly observed in oil production and processing systems and provides an overview of candidate genes that may be used as molecular probes for MIC.},
}

@article {pmid41883806,
year = {2026},
author = {Peng, L and Zhang, Y and Li, X and Hu, Z},
title = {Integrated multi-omics analysis reveals gut microbiota and metabolic characteristics in coronary heart disease.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1743914},
pmid = {41883806},
issn = {1664-302X},
abstract = {BACKGROUND: Coronary heart disease (CHD) is a leading cause of morbidity and mortality worldwide. Increasing evidence indicates that gut microbiota dysbiosis contributes to CHD pathogenesis through metabolic, inflammatory, and coagulation-related mechanisms. However, comprehensive multi-omics investigations of individuals with CHD remain limited. In this study, we aimed to characterize the multi-omics features of CHD and to identify potential diagnostic biomarkers.

METHODS: The study included 10 patients with clinically diagnosed CHD and 10 healthy controls. Blood and fecal samples were collected for further analysis. The gut microbiota composition was assessed using 16S ribosomal RNA high-throughput sequencing, and shotgun metagenomic sequencing was further performed to evaluate microbial functional potential through the Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation and differential pathway analysis. Non-targeted metabolomic profiling was performed using ultra-high-performance liquid chromatography coupled with Orbitrap mass spectrometry, and quantitative proteomic analysis was conducted using liquid chromatography-tandem mass spectrometry. Functional interaction networks between differentially expressed metabolites and proteins were constructed using Spearman correlation analysis, and the diagnostic potential of candidate biomarkers was evaluated using receiver operating characteristic (ROC) curve analysis.

RESULTS: At the phylum level, the CHD group exhibited an increased abundance of Pseudomonadota and a decreased abundance of Bacillota and Actinomycetota. At the genus level, Escherichia-Shigella, Bacteroides, and Klebsiella were significantly enriched, whereas Bifidobacterium and Faecalibacterium were decreased in abundance. Shotgun metagenomic analysis revealed functional remodeling of gut microbiota in CHD, with upregulation of KEGG pathways related to energy metabolism, inflammatory signaling, and host-microbe interactions. Serum metabolomics and proteomic analyses identified 32 differentially expressed metabolites and 38 differentially expressed proteins, respectively. Correlation analysis revealed significant associations between phospholipid metabolites and apolipoproteins, inflammatory mediators and the complement system, asymmetric dimethylarginine and endothelial function-related proteins, and oxidative stress metabolites and antioxidant proteins. ROC analysis identified several potential biomarkers with high diagnostic value.

CONCLUSION: We demonstrate that individuals with CHD exhibit significant gut microbiota dysbiosis, distinct metabolic pathway alterations, and aberrant expression of coagulation- and inflammatory-related proteins. These findings provide novel insights into potential targets for CHD prevention and treatment strategies.},
}

@article {pmid41884347,
year = {2026},
author = {Liu, H and Li, J and Yang, K and Li, H and Cao, S and Bao, Y and Feng, L and Zhang, L and Niu, J and Tian, T},
title = {Oral microbiome alterations and their association with long-term heavy metal exposure and early health effects.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2647511},
pmid = {41884347},
issn = {2000-2297},
abstract = {BACKGROUND: Long-term heavy metal exposure poses health risks, and non-invasive biomarkers for early detection are needed.

OBJECTIVE: This study investigated whether oral microbiome alterations can serve as a non-invasive indicator of long-term HMs exposure and associated early biological effects.

DESIGN: Soil, buccal mucosa, blood, and urine samples were collected from contaminated (CA) and uncontaminated (UA) areas. Soil contamination was assessed, and internal biomarkers were measured. Oral bacterial diversity was analyzed using metagenomic sequencing.

RESULTS: Severe Cd and Pb contamination was found in CA soil. Participants in CA had elevated internal Cd levels, renal impairment, and immune alterations. Oral microbiome analysis revealed decreased alpha diversity, reduced network complexity, and a shift from beneficial to pathogenic keystone taxa in CA. Functional analysis showed enrichment of stress-response pathways, suppression of metabolic pathways, and increased pathways linked to human diseases. Specific bacterial taxa correlated with internal biomarker levels.

CONCLUSIONS: There is a close association between long-term HMs exposure and reproducible, multi-faceted shifts in the oral microbiome. The oral microbiome may represent a promising, non-invasive biomarker for assessing environmental exposure and its early biological impacts.},
}

@article {pmid41885442,
year = {2026},
author = {Rysava, M and Stredanska, K and Schwarzerova, J and Jakubickova, M and Cejkova, D and Aytan-Aktug, D and Otani, S and Dolejska, M and Palkovicova, J},
title = {Dynamic changes in the plasmidome and resistome in the gastrointestinal tract of chickens.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0407425},
doi = {10.1128/spectrum.04074-25},
pmid = {41885442},
issn = {2165-0497},
abstract = {The expansion of intensive poultry farming has led to a substantial increase in antibiotic use, which, in turn, has promoted the accumulation of antibiotic resistance genes (ARGs). The chicken gut serves as a reservoir for these genes and provides favorable conditions for their horizontal transfer via mobile genetic elements, such as plasmids. Through this process, commensal bacteria can transfer ARGs to pathogens, facilitating their spread and increasing the risk of transmission to humans. In this study, long-read sequencing was used to characterize the plasmidome and resistome in 12 fecal samples from 3 houses of a commercial broiler chicken farm. All chickens received enrofloxacin in the first days of life, with one house additionally treated with sulfamethoxazole/trimethoprim combination. For comparison, metagenomic analysis using short-read sequencing was performed on the same samples. This study revealed the presence of various ARGs associated with resistance to 25 antibiotic classes. A strong genetic association between MOBP-type plasmids and fluoroquinolone resistance was observed within broiler chicken farms. Temporal trends indicated progressive mobilization of these ARGs, suggesting an increasing potential for horizontal gene transfer. While fluoroquinolone resistance expanded over time, diaminopyrimidine resistance remained stable despite the antibiotic treatment. Most ARGs were carried on small plasmids, and complete plasmid reconstructions ranged from 2.6 to 47.6 kb. Our findings demonstrate that plasmidome sequencing enables high-resolution detection of resistance-associated plasmids that may be overlooked by conventional metagenomic approaches. The observed patterns are consistent with an association between fluoroquinolone use in poultry farms and the presence of plasmid-mediated resistance genes with potential for horizontal dissemination.IMPORTANCEDespite the crucial role of plasmids in antimicrobial resistance (AMR) dissemination, studies focusing on plasmidomes, defined as the complete set of plasmids, remain limited. This study is the evidence that chicken farms, where fluoroquinolone treatment is a standard practice, act as an important reservoir of plasmid-mediated antibiotic resistance which may not be revealed by commonly used approaches. Combining a metagenomic approach with a focus on plasmids enhances our ability to understand the genetic context and mechanisms underlying AMR transmission. The findings emphasize the importance of targeted plasmid analysis to improve surveillance and risk assessment of AMR transmission in microbial ecosystems.},
}

@article {pmid41885716,
year = {2026},
author = {Xu, H and Yang, H and Shi, Y and Hu, X and Zhang, L and Li, P and Ma, Y and Yang, T and Xu, Y and Dong, C and Shen, Q},
title = {Genotype-Dependent Rhizosphere Microbiome Assembly Improves Potassium Use Efficiency in Pear Rootstocks Under Low Potassium Stress.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.70499},
pmid = {41885716},
issn = {1365-3040},
support = {32272802//National Science Foundation of China/ ; CARS-28-10//China Agriculture Research System/ ; },
abstract = {Potassium (K) is a vital nutrient for fruit quality in pears (Pyrus spp.), and rhizosphere microbes play a critical role in enhancing plant K uptake and utilization. To investigate the genotype-dependent influences of the rhizosphere microbiome on potassium use efficiency (KUE) in pears, we compared two rootstocks with contrasting KUE (Pyrus betulaefolia and Pyrus ussuriensis) using integrated pot and long-term field experiments, 16S rRNA amplicon sequencing, and metagenomic analyses. Synthetic community (SynCom) inoculation and transcriptome profiling were employed to elucidate the mechanisms underlying enhanced K acquisition. Under low-K conditions, P. betulaefolia recruited distinct microbial communities, which significantly improved K accumulation by upregulating genes (e.g., ATP1A, kdPB, and COG3158) associated with K transport and homoeostasis. Field trials further confirmed that P. betulaefolia-grafted trees sustained higher Bacillaceae abundance, superior fruit quality, and elevated K content than P. ussuriensis under K-deficient conditions. SynComs constructed from five Bacillaceae strains enhanced low-K tolerance by promoting root metabolic activity, stimulating root hair development, modulating K[+] transporter (e.g., NRT2.4) expression, and activating calcium-dependent signalling pathways. Inoculation with SynComs led to substantial improvements under K limitation, including a 105.86% increase in plant biomass, a 164.99% increase in K accumulation, and a 125.91% enhancement in the aboveground K utilisation index. These findings reveal that genotype-driven enrichment of Bacillaceae-dominated microbiomes significantly enhances pear KUE, offering mechanistic insights to guide the development of microbiome-based bioinoculants and breeding of "microbiome-responsive" rootstocks for sustainable fruit production under K-limiting conditions.},
}

@article {pmid41885787,
year = {2026},
author = {Ayed, M and Cadavez, V and Gonzales-Barron, U},
title = {Current research trends towards the control of protozoans in foods.},
journal = {Italian journal of food safety},
volume = {},
number = {},
pages = {},
doi = {10.4081/ijfs.2026.15114},
pmid = {41885787},
issn = {2239-7132},
abstract = {Protozoan parasites such as Cryptosporidium spp., Giardia duodenalis, Toxoplasma gondii and Cyclospora cayetanensis remain difficult-to-control hazards in food due to environmental persistence, low infectious doses, and the interpretability gap between nucleic acid detection and infectivity. This review synthesizes 4-year research trends shaping protozoan control in food systems, focusing on three critical pillars: matrix-adapted front-end processing (concentration, lysis, inhibitor management); inhibitor-resilient quantification; and sequencing-based attribution for outbreak investigation and source tracking. Recent benchmarking across wastewater, the water-soil-produce nexus, and food-relevant matrices repeatedly indicates - depending on matrix and study design - that upstream workflow steps often dominate analytical sensitivity and reproducibility. Accordingly, tiered analytical strategies are emerging in which the quantitative polymerase chain reaction (PCR) technique supports scalable screening, droplet digital PCR is used for decision-grade confirmation/quantification under inhibition and low-template conditions, and targeted sequencing or metagenomics is deployed selectively for traceback and contextual investigation. We integrate these developments into an actionable control framework that links prevention at the water-soil-plant interface with tiered analytics and viability-aware interpretation of post-intervention results. Research priorities ahead include harmonized performance reporting (recovery, inhibition controls, limit of detection/quantification), transparent endpoint hierarchy for intervention claims (detectability versus viability/infectivity), and interoperable sequence databases to enable cross-laboratory attribution and program-level learning. The field is moving from "can we detect?" towards "can we decide? - requiring reproducible front-end processing, inhibitor-resilient quantification, interoperable attribution resources, and endpoint discipline for intervention efficacy claims.},
}

@article {pmid41886617,
year = {2026},
author = {Qiao, Z and Chen, Z and Gong, H and Guo, X and Yu, H and Chen, L},
title = {Exogenous Elemental Sulfur Promoting Methane Production and Simultaneous Ammonia Nitrogen Removal in Anaerobic Digestion of Food Waste: Experimental Verification and Mechanism Analysis.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c18148},
pmid = {41886617},
issn = {1520-5851},
abstract = {The treatment of food waste (FW) via anaerobic digestion (AD) is frequently plagued by a low methane yield and ammonia (NH4[+]) inhibition. This study demonstrates that the addition of elemental sulfur (S[0]) effectively mitigates both of these issues. Through batch and continuous experiments, it was found that the specific methane yield was enhanced by up to 48.1% and the NH4[+] concentration decreased by 26.9% at the optimal S[0] dosages of 20 mg/L. Metagenomic analysis revealed a dual mechanism underlying this enhancement: at low dosages, S[0] provides a sulfur-containing functional group for the biosynthesis of methyl-coenzyme M, thereby accelerating the rate-limiting "methyl-transfer" step in methanogenesis; at high dosages, it promotes the biosynthesis of coenzyme A, which markedly enhances acidogenesis. Furthermore, S[0] alleviates NH4[+] inhibition by fostering a synergistic interaction between sulfate-reducing bacteria and anammox bacteria, which convert NH4[+] to N2. Continuous operation over 140 days confirmed the long-term stability and effectiveness of this S[0] addition strategy. This study provides mechanistic insights into S[0]-driven methanogenesis in complex organic waste (FW) and offers a cost-effective, sustainable approach to enhancing AD efficiency and stability.},
}

@article {pmid41886785,
year = {2026},
author = {Tian, M and Li, J and Dai, S and Ma, L},
title = {Clinical Characteristics and Management of Four Cases of Visceral Leishmaniasis-Associated Hemophagocytic Lymphohistiocytosis.},
journal = {The American journal of tropical medicine and hygiene},
volume = {},
number = {},
pages = {},
doi = {10.4269/ajtmh.25-0530},
pmid = {41886785},
issn = {1476-1645},
abstract = {The aim for the present study was to analyze clinical features, diagnostic approaches, and therapeutic strategies for visceral leishmaniasis (VL)-associated hemophagocytic lymphohistiocytosis (HLH) in pediatric patients. The clinical characteristics and test results of the children were summarized. Among the four patients, three resided in VL-endemic regions, and one had traveled to a VL-endemic region. All patients presented with recurrent fever (>38.5°C), hepatosplenomegaly, and decreased hemoglobin (HGB) levels ([78.75 ± 8.50] g/L) and platelet (PLT) counts ([59.50 ± 17.48] × 109/L). Before a definitive diagnosis could be made, patients exhibited progressive declines in white blood cell counts, HGB levels, and PLT counts, along with elevated triglyceride, serum cytokine (interleukin [IL]-6, IL-10, IL-2R, and tumor necrosis factor α) levels. Bone marrow aspirate smears revealed hemophagocytosis and Leishmania donovani (LD) bodies in all cases: two were diagnosed via direct identification of LD bodies, one was diagnosed through re-examination of bone marrow smears after confirming a travel history, and one was diagnosed via re-examination prompted by metagenomic next-generation sequencing, which revealed leishmaniasis. All the patients were initially diagnosed with HLH and received HLH-directed immunochemotherapy before VL diagnosis, with suboptimal response. After confirmation of VL, sodium stibogluconate therapy was initiated, resulting in a partial response in all cases. Etiological investigation is critical for HLH diagnosis. For VL-associated HLH, sodium stibogluconate as targeted therapy rapidly controls HLH, facilitates immunosuppression withdrawal, and significantly improves patient outcomes. White blood cell count, HGB level, PLT count, and lactate dehydrogenase level may serve as critical prognostic biomarkers for VL-associated HLH.},
}

@article {pmid41886955,
year = {2026},
author = {Ling, GC and Chen, SJ and Li, ZL and Yang, S and Xiao, YY and Xiao, M and Zhang, YY and Zhong, HJ and Zhang, JY and Li, Y and Xie, JJ},
title = {A microbiota-tryptophol-AhR axis mediates the gut-kidney protective effects of Hushen Tongfengtai Granules in hyperuricemic nephropathy.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {155},
number = {},
pages = {158089},
doi = {10.1016/j.phymed.2026.158089},
pmid = {41886955},
issn = {1618-095X},
abstract = {BACKGROUND: Hyperuricemia (HUA) may result in hyperuricemic nephropathy (HN), and gut dysbiosis with barrier dysfunction can worsen disease progression. Hushen Tongfengtai granules (HSTFT), a traditional Chinese herbal prescription, have been used clinically to mitigate HUA and related renal injury. However, the mechanisms behind their effects remain to be explored.

OBJECTIVE: To find HSTFT to mitigate HN through mechanisms dependent on gut microbiota.

METHODS: Fecal metagenomics and UPLC-ESI-MS/MS metabolomics were employed to identify key microbial taxa and metabolites modulated by HSTFT. Antibiotic-treated mice were used to investigate the gut microbiota-dependent mechanisms of HSTFT. In vivo and in vitro experiments were further conducted to validate the ameliorative effects of HSTFT on gut dysbiosis and barrier dysfunction in HUA mice.

RESULTS: HSTFT could improve renal injury and intestinal barrier dysfunction in HUA. Fecal metagenomic analysis revealed enrichment of Bifidobacterium breve. Antibiotic depletion could abolish the therapeutic efficacy of HSTFT, while Bifidobacterium breve (B.breve) recolonization could restore intestinal and renal protection. Metabolomic analysis identified tryptophol as a key HSTFT-associated metabolite. Exogenous tryptophol (TOL) recapitulated the protective effects and may activate the aryl hydrocarbon receptor (AhR) pathway. The AhR antagonist CH223191 could inhibit the TOL/HSTFT-mediated protective effects on intestinal barrier integrity and renal function.

CONCLUSION: HSTFT could ameliorate HN by enhancing intestinal barrier integrity and renal protection, with the underlying mechanism involving upregulation of intestinal B.breve and its metabolite TOL via AhR pathway activation.},
}

@article {pmid41887041,
year = {2026},
author = {Huang, J and Fu, Z and Zhou, S and Hu, J and Yu, G and Qin, C and Ma, Z},
title = {Metagenomic insights into sex-specific taxonomic and functional differentiation of epidermal mucus microbiota in the humphead wrasse (Cheilinus undulatus).},
journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics},
volume = {59},
number = {},
pages = {101810},
doi = {10.1016/j.cbd.2026.101810},
pmid = {41887041},
issn = {1878-0407},
abstract = {The humphead wrasse (Cheilinus undulatus) is a large coral reef fish of high ecological and economic importance, whose epidermal mucus microbiota plays a critical role in host defense, immune regulation, and environmental adaptation. However, the influence of host sex on the structure and functional potential of epidermal mucus microbiota remains poorly understood. In this study, epidermal mucus samples were collected from sexually mature female and male humphead wrasse, and shotgun metagenomic sequencing was performed to systematically compare microbial community composition, diversity, and functional gene profiles between sexes. The results showed no significant differences in alpha diversity (ACE and Shannon indices) between female (FM) and male (M) groups. In contrast, beta diversity analyses and hierarchical clustering revealed clear sex-related separation of microbial community structures at both phylum and genus levels. Although both groups were dominated by Pseudomonadota, Bacillota, Bacteroidota, and Verrucomicrobiota, their relative abundances and sex-specific taxa differed markedly. Functional annotation based on KEGG indicated that female-specific taxa harbored a greater number and broader range of functional genes, mainly associated with carbohydrate, amino acid, energy, and cofactor metabolism, as well as disease-related pathways. Furthermore, Comprehensive Antibiotic Resistance Database (CARD) and the Virulence Factor Database (VFDB) analyses revealed that female-specific taxa exhibited higher diversity of antibiotic resistance genes and virulence factors, whereas male-specific taxa showed a more limited functional repertoire, primarily related to basic metabolism and biofilm formation. Overall, this study demonstrates pronounced sex-associated differences in both the taxonomic composition and functional potential of epidermal mucus microbiota in humphead wrasse, highlighting the importance of host sex in shaping host-microbiome interactions and providing new insights for health management and conservation of coral reef fishes.},
}

@article {pmid41887065,
year = {2026},
author = {Song, J and Hou, YN and Li, R and Feng, Z and Wang, AJ and Ren, N and Wei, W and Ni, BJ and Huang, C},
title = {Ectoine modulates mixotrophic denitrification pathway partitioning to sustain stable nitrogen and phenol removal under hypersaline stress.},
journal = {Water research},
volume = {298},
number = {},
pages = {125764},
doi = {10.1016/j.watres.2026.125764},
pmid = {41887065},
issn = {1879-2448},
abstract = {Hypersaline wastewater containing phenolic compounds imposes coupled osmotic and cytotoxic stresses that severely disrupts biological treatment processes. While compatible solutes are known to enhance cellular osmoprotection, their capacity to regulate microbial metabolic, particularly the balance between autotrophic and heterotrophic denitrification pathways under combined salinity stress remain poorly understood. This study reveals that the compatible solute ectoine modulates pathway partitioning in mixotrophic denitrification systems, enabling efficient nitrogen and phenol removal under 4% salinity. The ectoine amended reactor maintained nitrogen removal above 95% and phenol degradation above 80%, whereas the unprotected control collapsed to 34% and 33% respectively. Multi-scale mechanistic investigations revealed a coordinated protection cascade. First, ectoine enhanced cellular resilience by suppressing reactive oxygen species (ROS) by 88.2%, maintaining ATP level and electron transport activity, thereby preserving bioenergetic integrity. Second, structural fortification was achieved through intensified extracellular polymeric substance (EPS) production. The protein-to-polysaccharide ratio increased from 0.70 to 1.51 creating a protective matrix that stabilized membrane permeability and preserved catalytic enzymes, with nitrate reductase and nitrite reductase activities increasing 2.16- and 2.93-fold. Third, metagenomic profiling revealed community reconfiguration, with selective enrichment of halotolerant heterotrophs (Halomonas, Marinobacter) to 49% relative abundance. Aromatic‑degradation genes (catA, benB) rose by 7‑ and 48‑fold, while nitrogen‑metabolism genes (nasA, norC) remained high representation. This restructuring reversed pathway contributions from 81% sulfur-autotrophic dominance to 82% heterotrophic dominance. Ectoine thus functions as a metabolic modulator that links cellular stress alleviation and community-level functional potential to pathway repartitioning, offering a feasible strategy for the biotreatment of saline phenolic wastewater.},
}

@article {pmid41887066,
year = {2026},
author = {Wang, H and Wu, Y and Weng, H and Zhang, L and Peng, Y},
title = {Denitrification mode management selects resource-conserving consortia for low-carbon municipal wastewater treatment.},
journal = {Water research},
volume = {298},
number = {},
pages = {125775},
doi = {10.1016/j.watres.2026.125775},
pmid = {41887066},
issn = {1879-2448},
abstract = {Low-carbon municipal wastewater treatment increasingly relies on carbon-limited denitrification, yet how carbon limitation reorganizes denitrifying communities and their greenhouse-gas footprint remains poorly resolved. We implemented denitrification mode management in a municipal wastewater sequencing batch reactor by switching from anaerobic-aerobic (AO) to anaerobic-aerobic-anoxic (AOA) operation. This shift moved denitrification from an pre-anaerobic stage with higher carbon availability to a post-anoxic stage where readily available carbon was limited. We combined metagenomics and metatranscriptomics to link process performance with microbial traits and gene expression. The mode switch improved nitrogen removal from 67.1 ± 1.8% to 88.5 ± 3.9% and reduced carbon requirement from 4.9 ± 0.5 to 3.3 ± 0.4 mg COD per mg N removed, while decreasing the N2O emission factor from 0.024 to 0.005 mg N2O-N per mg NO3[-]-N and lowering CO2 and CH4 emissions by 20-30%. Carbon-limited post-denitrification selected taxa with smaller genomes, reduced metabolic redundancy and a pronounced shift from broad extracellular carbon catabolism and complete denitrification towards intracellular carbon storage and truncated denitrification. Intracellular carbon pools insulated organics at the single-cell level and buffered electron delivery across denitrification steps, enabling a division-of-labour network that prevents electron imbalance and suppresses N2O build-up. Together, these findings link denitrification mode management to trait-based community restructuring and offer a process-level framework for understanding low-carbon, low-emission nitrogen removal under carbon-limited conditions.},
}

@article {pmid41887069,
year = {2026},
author = {Qiang, H and Xu, X and Liu, Z and Heo, S and Yue, X and Zhou, A and Makinia, J},
title = {New insights into the interplay between chain elongation and homoacetogenesis in microbial electrosynthesis: Chloroform-enhanced medium-chain carboxylate production.},
journal = {Water research},
volume = {298},
number = {},
pages = {125790},
doi = {10.1016/j.watres.2026.125790},
pmid = {41887069},
issn = {1879-2448},
abstract = {Microbial electrosynthesis (MES)-assisted chain elongation (CE) is a promising strategy for sustainable medium-chain carboxylic acid (MCCA) production from waste streams. However, MES induces inevitable H2 evolution, and the understudied interaction between H2-driven homoacetogenesis and CE creates a critical knowledge gap. To resolve this metabolic conflict, chloroform (CHCl3) at 0.0075%-0.045% was used to inhibit homoacetogenesis, with systematic investigations on carbon flux distribution, functional microbial communities, and key metabolic pathways. Results showed 0.03% CHCl3 optimized MCCA production to 2902.8 ± 116.1 mg COD/L (103.0% increase), with electron efficiency (40.8%) and acetate utilization efficiency (94.3%) significantly higher than the Control (21.8% and 43.5%, respectively). Homoacetogenesis inhibition conserved reducing power (moderated H2, lowered NAD[+]/NADH) and redirected acetyl-CoA to drive CE. Microbial community analysis revealed enriched chain-elongating bacteria with more modular, cooperative interaction networks. Metagenomic analysis confirmed elevated abundances of reverse β-oxidation genes (e.g., ACAT, crt) and reduced homoacetogenesis genes (e.g., cooF, cooS) after treatment. Taxon-function contribution analysis identified Clostridium_kluyveri as the dominant functional agent for CE-related key genes. Economic and life-cycle assessments demonstrated a net economic gain of $1.61-4.22/m[3] and mitigated key environmental impacts due to improved product yield. This study elucidates how regulating the competition between homo-acetogens and chain-elongating bacteria directionally enhances CE, providing a novel ecological perspective and strategy for optimizing electricity-driven biomanufacturing processes.},
}

@article {pmid41887245,
year = {2026},
author = {Reddy, K and Sinha, P and Antcliffe, DB and McDowell, C and Bradley, PA and Black, L and Murphy, L and Barbaras, J and Conlon, J and Camporota, L and Ostermann, M and Hopkins, P and Szakmany, T and Cherian, S and Welters, I and Brealey, D and Parekh, D and Rostron, AJ and Bos, LDJ and Nichol, A and Shankar-Hari, M and Gordon, AC and Delucchi, K and O'Kane, CM and Matthay, MA and Calfee, CS and McAuley, DF and , },
title = {Bedside identification of subphenotypes in acute respiratory failure (PHIND): a multicentre, observational cohort study.},
journal = {The Lancet. Respiratory medicine},
volume = {},
number = {},
pages = {},
doi = {10.1016/S2213-2600(26)00040-8},
pmid = {41887245},
issn = {2213-2619},
abstract = {BACKGROUND: Acute respiratory distress syndrome (ARDS) is a clinically defined, biologically heterogeneous condition with no proven disease-modifying therapies. Retrospective analyses have identified two biologically distinct subphenotypes (hyperinflammatory and hypoinflammatory) of ARDS, with differing outcomes and responses to therapy. Rapid identification of these subphenotypes in an actionable timeframe has previously not been possible. The PHIND study aimed to prospectively identify these subphenotypes and to demonstrate differing 60-day mortality.

METHODS: The PHIND study was a prospective, multicentre, observational cohort study conducted in intensive care units (ICUs) within the National Health Service in the UK and the Health Service Executive in Ireland. Adult patients aged 18 years and older with ARDS or acute hypoxaemic respiratory failure (AHRF) were enrolled within 72 h of onset of the syndrome. Eligible patients were required to be receiving invasive mechanical ventilation, non-invasive ventilation, or high-flow nasal oxygen. Plasma interleukin (IL-6) and soluble TNF receptor-1 (TNFR1) were quantified at enrolment using a near-patient benchtop immunoanalyser (Randox multiSTAT) with a run time of approximately 1 h. Together with plasma bicarbonate measured from an arterial blood sample, these values were used to prospectively determine subphenotypes on an individual patient basis using a validated parsimonious logistic regression model. The primary outcome was 60-day mortality. The study was registered on ClinicalTrials.gov, NCT04009330.

FINDINGS: Between Nov 22, 2019, and Sept 28, 2023, 1853 patients from 30 centres were screened for eligibility. Of these, 1328 were excluded and 525 were recruited into the study, with 512 individuals included. 308 (60%) patients were male, 204 (40%) were female, and mean age was 57·0 years (SD 15·1). 443 (87%) patients were white, 18 (4%) were Black, and 16 (3%) were Asian. 490 were subphenotyped using the near-patient assay: 89 (18%) were classified as hyperinflammatory and 401 (82%) as hypoinflammatory. The primary outcome of 60-day mortality was measured in 486 patients after four patients withdrew consent for confirmation of vital status. 60-day mortality was significantly higher in the hyperinflammatory group (45 [51%] of 88) than in the hypoinflammatory group (111 [28%] of 398; risk ratio 1·8 [95% CI 1·4-2·4], p<0·0001). After adjustment, hyperinflammatory patients had increased odds of 60-day mortality (adjusted odds ratio 2·7 [95% CI 1·6-4·4], p=0·0002).

INTERPRETATION: Rapid identification of ARDS inflammatory subphenotypes using a near-patient assay was feasible and associated with many clinical characteristics and outcomes consistent with those described in earlier retrospective studies, including mortality, prevalence of sepsis, and incidence of metabolic acidosis. These findings support the implementation of precision medicine approaches in ARDS and the urgent need for prospective, subphenotype-stratified interventional trials.

FUNDING: Innovate UK, Randox Laboratories, and Belfast Health & Social Care Trust.},
}

@article {pmid41887297,
year = {2026},
author = {Lin, X and Yang, J and Kong, H and Pu, L and Ma, P and Mu, W and Sheng, H and He, J and Zou, Y and Wang, Y and Guo, X and Zhang, S and Wang, S},
title = {Metagenomic analysis of the gut microbiota in Cryptosporidium-infected Tibetan sheep.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {108461},
doi = {10.1016/j.micpath.2026.108461},
pmid = {41887297},
issn = {1096-1208},
abstract = {Cryptosporidium are important causative parasitic protozoa that cause gastrointestinal discomfort and diarrhea in humans and animals, posing a huge threat to public health. Ruminants serve as the main source of Cryptosporidium infection. However, the relationship between this intestinal parasite and host gut microbiota in Tibetan sheep remains almost unknown. In the present study, using nested PCR targeting the SSU rRNA gene, we detected Cryptosporidium in 9% (38/420) of fecal samples. The positive rate was significantly higher in 4-7 month-old lambs than in adult sheep. Infection of Cryptosporidium spp. was associated with limited overall structural and functional alterations of the host gut microbiota, characterized by increased the relative abundance of Escherichia and reduced functional pathways related to amino acid biosynthesis and nucleotide/nucleoside biosynthesis. Additionally, the data indicates that age served as a primary determinant of the gut microbiota, whereas Cryptosporidium load showed no significant association with microbial variation. Machine learning model analysis revealed that these differential microbial features could effectively discriminate between infected and uninfected animals. These findings elucidate that Cryptosporidium infection is associated with specific and limited gut microbiota alterations in sheep.},
}

@article {pmid41887416,
year = {2026},
author = {Zhang, L and Xie, J and Lu, Y and Kong, L and Zhou, L and Wu, S and Wang, W and Huang, J and Li, J and Cheng, S},
title = {Enhanced nitrogen removal and mitigated greenhouse gas emissions in bioelectrochemical system-modular moving bed wetland at low temperature: Functional zonation and multi-pathway electron transfer.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134493},
doi = {10.1016/j.biortech.2026.134493},
pmid = {41887416},
issn = {1873-2976},
abstract = {This study integrated bioelectrochemical systems (BESs) into modular moving bed constructed wetlands (MMBCWs) to mitigate low temperature constraints on nitrogen removal and greenhouse gas emissions. Conventional MMBCW, microbial fuel cell-MMBCW (MFC-MMBCW), and microbial electrolysis cell-MMBCW (MEC-MMBCW) were constructed to assess feasibility. Results showed that MEC-MMBCW achieved superior nitrogen removal and the lowest global warming potential under cold conditions. Biofilm characteristics and metagenomic analyses revealed that MEC-MMBCW established spatially stratified functional zones. Specifically, the anode promoted organic matter and ammonia oxidation, while enhanced denitrification outcompeted compensatory anammox in the cathode. Furthermore, a multi-pathway extracellular electron transfer (EET) network mediated by extracellular polymeric substances (EPS), cytochrome c, and conductive pili accelerated electron transfer rates. These mechanisms synergistically boosted metabolic potential and activated latent degradation pathways, enhancing treatment resilience. Consequently, MEC-MMBCW represents a viable strategy for sustainable wastewater treatment in cold regions.},
}

@article {pmid41887490,
year = {2026},
author = {Li, Z and Fu, J and Hu, J and Li, T and Xu, Y},
title = {Sediment-water interface reoxygenation by NO3-LDH promotes tetracycline degradation in sediments and modulates antibiotic resistance gene dynamics.},
journal = {Environmental research},
volume = {},
number = {},
pages = {124357},
doi = {10.1016/j.envres.2026.124357},
pmid = {41887490},
issn = {1096-0953},
abstract = {The widespread presence of antibiotics in aquatic sediments, together with hypoxic conditions, constrains oxygen-driven natural degradation, thereby prolonging their environmental persistence. In this work, nitrate-intercalated layered double hydroxide (NO3-LDH) was employed as a controlled-release nitrate amendment to alleviate interfacial oxygen limitation while minimizing the secondary environmental risks associated with the high release peaks of conventional nitrate reagents. As a result, NO3-LDH increased dissolved oxygen (DO) from 1.05 to 3.39 mg/L, enhanced TC removal from 64.5% to 89.8% within 15 d, and reduced the combined abundance of tetracycline resistance genes (tetA, tetQ, and tetS) by 53.0%. Mechanistically, DO enrichment increased •OH generation 1.94-fold and upregulated cytochrome P450-related genes, supporting coupled enhancement of abiotic oxidation and oxygen-dependent microbial transformation. The improved oxidative microenvironment also favored the enrichment of aerobic aromatic-degrading taxa, further promoting TC attenuation. Although overall antibiotic resistance genes (ARGs) levels declined, fluoroquinolone- and macrolide-associated ARGs exhibited a transient early increase, likely triggered by an abrupt redox perturbation upon oxygen recovery that imposed oxidative stress on anaerobic microorganisms, intensified ATP-demanding stress responses, and increased membrane permeability. As interfacial redox conditions stabilized and TC concentrations decreased, these stress responses subsided and ARGs abundances declined at later stages. Overall, restoring interfacial DO strengthens oxygen-driven natural antibiotic degradation and inhibits the long-term accumulation of ARGs, providing a mechanistically grounded strategy for in situ remediation of antibiotic-contaminated sediments.},
}

@article {pmid41876075,
year = {2026},
author = {Wu, H and Wang, H and Man, S and Yan, Q},
title = {Biogenic FeS Reshapes microbial interactions to regulate acetogenesis in CO2-Fed microbial electrosynthesis.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134480},
doi = {10.1016/j.biortech.2026.134480},
pmid = {41876075},
issn = {1873-2976},
abstract = {Inefficient electron transfer and poorly coordinated microbial communities often limit stable CO2-to-acetate conversion in microbial electrosynthesis (MES). Herein, Shewanella oneidensis MR-1 was introduced to induce in situ biogenic FeS formation at the cathode to regulate microbial interactions and enhance acetogenesis. Under the acetogenesis dominant condition (RAT: sludge to MR-1 ratio of 2:1, Fe/S = 5/10 mM, initial MR-1 inoculation), acetate production reached 1330.6 mg L[-1] with the carbon recovery efficiency of 62.9%. Community and metagenomic analyses showed that FeS selectively enriched acetogens and Fe/S transforming microorganisms while restructuring functional pathways related to redox metabolism and energy conservation. Co-occurrence network analysis further revealed that FeS promoted coordinated, function oriented microbial interactions rather than competitive associations. This study highlights the role of biogenic FeS in linking electron transfer with microbial cooperation, providing a mechanistic basis for improving MES performance through community level regulation.},
}

@article {pmid41876513,
year = {2026},
author = {Jovicic, D and Anestis, K and Fiutowski, J and Jørgensen, BB and Kjeldsen, KU and Rotaru, AE},
title = {Genome-centric metagenomics reveals electroactive syntrophs in a conductive particle-dependent consortium from coastal sediments.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {41876513},
issn = {2041-1723},
support = {1026-00159B//Natur og Univers, Det Frie Forskningsråd (Natural Sciences, Danish Council for Independent Research)/ ; 101045149//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; },
mesh = {*Geologic Sediments/microbiology ; *Metagenomics/methods ; Acetates/metabolism ; Oxidation-Reduction ; Electron Transport ; Phylogeny ; *Microbial Consortia/genetics ; Methane/metabolism ; Methanosarcina/metabolism/genetics ; Charcoal ; Cytochromes/metabolism/genetics ; Genome, Bacterial ; },
abstract = {Conductive particles are common in coastal sediments, yet their role in shaping methane-producing communities and pathways remains unclear. We applied genome-resolved metagenomics to a sediment-derived consortium serially transferred for a decade and obligately dependent on granular activated carbon (GAC). We discovered a particle-obligate food web composed of electrogenic syntrophic acetate oxidizers (SAO), an electrotrophic methanogen, and necromass recyclers. The primary SAO electrogen, Candidatus Geosyntrophus acetoxidans, represents a new genus and possesses a complete acetate oxidation pathway and extracellular electron-transfer (EET) machinery, including two porin-cytochrome conduits, 43 additional multiheme cytochromes and conductive pili. A secondary SAO, a Lentimicrobium sp. with a giant PCC-cluster, supplies an alternative EET-linked acetate-oxidation route. Electrons from electrogens transfer via GAC to a Methanosarcina equipped with the heptaheme cytochrome MmcA and flagellin for electron uptake. These results provide a genomic blueprint of this particle-obligate environmental consortium and suggest an overlooked acetate-to-methane electron-transfer route in geoconductor-rich anoxic sediments.},
}

*Geologic Sediments/microbiology
*Metagenomics/methods
Acetates/metabolism
Oxidation-Reduction
Electron Transport
Phylogeny
*Microbial Consortia/genetics
Methane/metabolism
Methanosarcina/metabolism/genetics
Charcoal
Cytochromes/metabolism/genetics
Genome, Bacterial

@article {pmid41876637,
year = {2026},
author = {Wang, R and Ma, R and Cai, Y and Zhang, L and Lu, W and Zheng, W and Kong, J and Miao, Q and Li, X and Guan, L and Gao, Y and Chen, K and Kwan, ATH and McIntyre, RS and Xu, G and Yu, CK and Lam, BY and So, KF and Lin, K},
title = {Exploratory characterization of gut microbiota and cognitive profiles in adolescents with subthreshold depression: a shotgun metagenomics sequencing study.},
journal = {Npj mental health research},
volume = {5},
number = {1},
pages = {},
pmid = {41876637},
issn = {2731-4251},
support = {No. 2021A1515011361//Natural Science Foundation of Guangdong Province/ ; No. 202102020735//Science and Technology Program of Guangzhou/ ; No. 2024SRP208//Guangzhou Medical University Research Capacity Enhancement Program/ ; No. 202007030012//Science and Technology Program of Guangzhou, China/ ; No. 202007030012//Science and Technology Program of Guangzhou, China/ ; No. 82171531//National Natural Science Foundation of China/ ; No. PX-66221557//Guangzhou Medical University student innovation ability enhancement Program/ ; STG STG1/M-501/23-N//the Hong Kong RGC theme-based Strategic Target Grant Scheme/ ; },
abstract = {Subthreshold depression (SD) in adolescents is a prevalent condition associated with significant functional impairment and an increased risk of developing major depressive disorder. Currently, the lack of reliable objective markers complicates its accurate identification. Investigating the gut microbiome may offer novel insights into its underlying mechanisms. This study aimed to investigate the association between gut microbiome and cognitive function in adolescents with subthreshold Depression (SD). Thirty-eight adolescents with SD and 139 clinically-well (CW) adolescents were recruited. Gut microbiome and cognitive function were assessed by metagenomic sequencing and the MATRICS Consensus Cognitive Battery (MCCB), respectively. Compared with the CW adolescents, the SD group showed higher relative abundance of Spirochaetes, Synergistetes, Spirochaetia, Synergistia, Spirochaetales, Rhizobiales, Synergistales, Thermoanaerobacterales, Rhodospirillales, Synergistaceae, and Oxalobacteraceae at four levels. The Spatial Span scores were higher in the SD group compared to the CW group. Moreover, EggNOG analyses showed a significant negative correlation of the intracellular trafficking secretion, and vesicular transport with the Spatial Span scores. The KEGG pathway of the neurodegenerative diseases and translation was depleted in the microbiome of adolescents with SD. The higher abundance of Spirochaetes, Spirochaetia, and Spirochaetales was the best predictor of SD in adolescents. Our findings suggest that gut microbiome abnormalities, depressive symptoms, and cognitive influences co-occur in adolescents with SD, which may play a crucial role in the pathogenesis of SD and cognitive function in adolescent. Gut microbiome may serve as a potential biomarker for the identification and treatment of adolescents with SD.},
}

@article {pmid41876857,
year = {2026},
author = {Peñuelas, J and Zheng, B and Tariq, A and Sardans, J},
title = {Microbial phosphorus cycling in terrestrial ecosystems.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
pmid = {41876857},
issn = {1740-1534},
abstract = {Phosphorus is an essential yet often limiting macronutrient that shapes primary productivity and microbial activity in terrestrial ecosystems. Unlike carbon and nitrogen cycles, which have gaseous phases, the terrestrial phosphorus cycle is primarily governed by soil biogeochemistry, wherein microorganisms orchestrate key transformations. This Review synthesizes current knowledge of the microbial phosphorus cycle, emphasizing the diverse mechanisms used by bacteria, fungi and archaea to mobilize phosphorus (for example, via phosphatases such as PhoA and PhoD and organic acids such as citrate) and to directly enhance plant phosphorus uptake. We explore the ecological significance of these processes in maintaining soil health, supporting ecosystem productivity and influencing carbon sequestration. We propose the Microbial Phosphorus Adaptive Evolution Theory (MPAET): chronic phosphorus scarcity drives evolutionary and ecological shifts in microbial communities towards higher scavenging investment, polyphosphate handling and lipid remodelling. Furthermore, we examine how environmental factors, land use and climate modulate these shifts (for example, phoD expression increases under phosphorus stress), with cascading effects on ecosystem function and global phosphorus availability. New technologies such as metagenomics, [18]O-phosphate tracing and nanoscale secondary ion mass spectrometry are now revolutionizing our understanding of these dynamics. This Review underscores the critical need to integrate microbial phosphorus cycling into ecosystem models and to develop sustainable strategies for phosphorus smart management. Such approaches are essential for addressing global challenges related to soil degradation, food security and environmental change.},
}

@article {pmid41877267,
year = {2026},
author = {Peirson, LE and McKenney, EA and Patterson, JR and Beasley, JC and Périquet-Pearce, S and Cloete, C and Melton, MH and PetersonWood, B and Portas, R and Aschenborn, O and Lafferty, DJR},
title = {African carnivore gut bacterial diversity and composition are associated with sample condition but not storage technique.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-026-00553-w},
pmid = {41877267},
issn = {2524-4671},
support = {Financial Assistance Award no. DE-EM0005228//U.S. Department of Energy/ ; Peter White Scholar Award//Northern Michigan University/ ; },
abstract = {Non-invasive fecal sampling is essential for molecular wildlife studies such as gut microbiome (GMB) research, yet field conditions often limit preservation options. To test the effects of preservation methods on the results of GMB community composition, we compared gut bacterial communities in paired fecal samples preserved in stabilization tubes and air-dried in paper bags collected from anesthetized African lions (Panthera leo) and spotted hyenas (Crocuta crocuta) in Etosha National Park, Namibia. Additional opportunistic samples from the ground around carnivore feeding sites that varied in moisture content were also analyzed. No differences in alpha or beta diversity were detected between preserved and dried samples, although bacterial beta diversity differed between preserved and opportunistic samples, supported by NMDS ordinations and PERMANOVA results. Core bacterial communities remained consistent across opportunistic sample conditions, indicating that host-associated taxa persist despite environmental exposure supporting the use of opportunistic samples for GMB studies in remote arid settings. However, consistent sampling protocols and future field-based desiccation studies remain critical for comparative analyses. These findings highlight that rapid air-drying offers a reliable, low-cost preservation option that maintains core microbiome patterns, expanding the feasibility of GMB research in remote or resource-limited field contexts where refrigeration and preservatives may be unavailable.},
}

@article {pmid41877288,
year = {2026},
author = {Wei, G and Liu, M and Huang, L and Chen, C},
title = {Metagenomic sequencing reveals the dynamic changes of pig gut fungal composition following the ages and identifies fungal species associated with diarrhea in piglets.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-026-00551-y},
pmid = {41877288},
issn = {2524-4671},
support = {32272831//National Natural Science Foundation of China/ ; },
}

@article {pmid41877461,
year = {2026},
author = {Tagliabue, A and Furfaro, G and Pallavicini, A and Martino, F and Zane, L and Sattin, E and Valle, G and Piraino, S and Turon, X},
title = {Comparative Multi-Marker Environmental DNA Metabarcoding of Marine Metazoan Communities: Water vs. Sediment.},
journal = {Molecular ecology resources},
volume = {26},
number = {3},
pages = {e70126},
doi = {10.1111/1755-0998.70126},
pmid = {41877461},
issn = {1755-0998},
support = {MCIU/AEI/10.13039/501100011033//BlueDNA PID2023-146307OB/ ; CCI 2014IT16M2OP005//Programma Operativo Nazionale Ricerca e Innovazione 2014-2020/ ; ECS00000043//Interconnected Nord-Est Innovation Ecosystem/ ; //European Regional Development Fund/ ; 2020J3W3WC//Italian Ministry of Education, Universities and Research/ ; D33C22000960007//National Recovery and Resilience Plan/ ; C93C22002810006//National Recovery and Resilience Plan/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; *DNA, Environmental/genetics ; Animals ; *Geologic Sediments ; *Biodiversity ; *Aquatic Organisms/classification/genetics ; RNA, Ribosomal, 18S/genetics ; Electron Transport Complex IV/genetics ; *Metagenomics/methods ; *Seawater ; },
abstract = {This study investigates the metazoan biodiversity in the Southern Adriatic Sea using environmental DNA (eDNA) metabarcoding. Sediment and adjacent water samples were collected from three sites (one pristine, two impacted by human activities) at three distances from the coast across two seasons. The complex four-factor experimental design (576 samples) addresses key sources of eDNA variability and provides a valuable comparison of markers (COI and 18S) and sample types, which remain rare in the literature. Results showed differences in the number and type of taxa identified, taxonomic resolution, and number of amplicon sequence variants (ASV) per operational taxonomic unit (OTU) across markers. The obtained overall community structure (beta-diversity) was similar for both markers. Sediment samples had higher OTU richness, but lower diversity than water samples. The two sample types provided distinct and only partially overlapping views of biodiversity. Sediment samples were rich in benthic species, whereas water samples featured mostly planktonic and nektonic species. Biodiversity varied by site and season, with sediment samples showing less seasonal variability. The pristine site did not host higher biodiversity than impacted sites, likely because of the latter's habitat heterogeneity. This study confirms the effectiveness of eDNA metabarcoding for biodiversity assessment in coastal ecosystems and provides a foundational dataset for future monitoring. By highlighting the complementary nature of COI and 18S markers and the role of sample type, this research supports integrating eDNA metabarcoding into routine environmental monitoring programs while emphasising the need for further standardisation and improved reference databases.},
}

*DNA Barcoding, Taxonomic/methods
*DNA, Environmental/genetics
Animals
*Geologic Sediments
*Biodiversity
*Aquatic Organisms/classification/genetics
RNA, Ribosomal, 18S/genetics
Electron Transport Complex IV/genetics
*Metagenomics/methods
*Seawater

@article {pmid41877907,
year = {2026},
author = {Xie, S and Zhang, H and Xie, Y and Liu, F and Ye, S and Liu, X and Lai, Z},
title = {Analysis of the Clinical Features of HSV-2 Encephalitis Confirmed by the mNGS Technique: Insights Derived from Seven Patient Studies.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {567731},
pmid = {41877907},
issn = {1178-6973},
abstract = {BACKGROUND: Herpes simplex virus type 2 (HSV-2) encephalitis is rare in immunocompetent adults. Diagnosis typically depends on cerebrospinal fluid (CSF) polymerase chain reaction (PCR), which has limited sensitivity and potential for false negatives. Metagenomic next-generation sequencing (mNGS) provides unbiased pathogen detection, facilitating rapid HSV-2 identification in CSF and minimizing misdiagnosis risks, especially in atypical cases or immunocompetent individuals. This study examines the diagnostic value of mNGS in a cohort of patients with HSV-2 encephalitis presenting atypically.

METHODS: A retrospective analysis was performed on patients diagnosed with HSV-2 encephalitis using mNGS at our institution between January 2022 and January 2025. Clinical characteristics, ancillary test results, and patient outcomes were analyzed to evaluate the diagnostic value of mNGS.

RESULTS: Seven patients (2 males, 28.57%; 5 females, 71.43%) with a mean age of 33.57 years were included; one had pre-existing immunodeficiency (14.28%). Most presented atypical symptoms; six treated within three days fully recovered, while one with delayed treatment died. Mean follow-up was 14.71 ± 5.82 months. Higher viral sequence counts correlated with worse outcomes. Initial CSF analysis showed normal cell counts in one patient; all exhibited lymphocytic pleocytosis and elevated protein levels.

CONCLUSION: This study contributes to the limited clinical data on adult HSV-2 encephalitis by summarizing clinical manifestations and treatment outcomes, thereby informing improved diagnostic and management strategies. It also highlights the prognostic importance of early diagnosis and immune status assessment through the application of mNGS.},
}

@article {pmid41877920,
year = {2026},
author = {Zeng, F and Zhu, T and Chen, X and Huang, K and Liu, L and Wang, G and Mai, J and Zhang, S},
title = {Gut microbiota and metabolic status during pregnancy in captive Asian elephants.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1749490},
pmid = {41877920},
issn = {2297-1769},
abstract = {BACKGROUND: The gut microbiota is regarded as one of the key factors regulating host health. The gut microbiota and its connection to fecal metabolites are crucial for supporting fetal development and ensuring maternal health during reproductive stages. Although studies have examined Asian elephants, the composition and function of the gut microbiota in pregnant and non-pregnant captive Asian elephants have not been reported.

METHODS: We compared the fecal microbiota and fecal metabolites of pregnant (G1), non-pregnant (never gotten pregnant after reaching sexual maturity, G2), and subadult (G3) captive Asian elephants using metagenomic sequencing and untargeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) metabolomics.

RESULTS: We found significant differences in the gut microbiota among the G1, G2, and G3 groups. The phylum Bacteroidetes showed notable differences between G1 and G2. The analysis of fecal metabolomics revealed significant differences in 49 metabolites between G1 and G2, of which 25 were upregulated and 24 were downregulated. These results suggested significant differences in the composition of gut microbiota and fecal metabolites during reproductive stages, while gut microbial diversity remained stable. These findings inform our ongoing research on the potential health conditions of captive Asian elephants, with the aim of better understanding the role of the gut microbiota in reproductive regulation.},
}

@article {pmid41877937,
year = {2025},
author = {Zhang, M and Pak, H and King, SD and Zuniga, AA and Hassan, YA and King, MD},
title = {Mitigating airborne pathogen risks in a full-scale meat processing facility.},
journal = {Total environment microbiology},
volume = {1},
number = {3},
pages = {},
pmid = {41877937},
issn = {3050-6417},
abstract = {Foodborne illnesses caused by Shiga toxin-producing Escherichia coli (STEC) and Salmonella represent a major public health concern, particularly in meat processing facilities where bioaerosols generated during processes like carcass spraying and dehiding can lead to contamination. In this study, we assessed airborne concentrations of STEC and Salmonella at multiple locations within a full-scale meat processing facility using quantitative polymerase chain reaction (qPCR) and Illumina MiSeq sequencing. Additionally, we utilized computational fluid dynamics (CFD) simulations to model airflow within the facility and evaluated the effectiveness of air curtains in mitigating the transfer of bioaerosols between high-risk (dehiding and tripe) and low-risk (chiller and fabrication) areas. qPCR results showed that pathogen concentrations in the dehiding rooms were 126 GCN/m[3] for STEC and 105 GCN/m[3] for Salmonella during spring, with levels rising significantly in summer (2198 GCN/m[3] for STEC and 1799 GCN/m[3] for Salmonella). Simulated airflow patterns revealed that entrained bioaerosols could be transported from unclean to clean areas, increasing the risk of cross-contamination. The use of air curtains effectively reduced this spread by creating barriers between high- and low-risk areas. Our findings suggest that bacterial survivability and aerosolization was enhanced in summer, highlighting the critical role of environmental factors and airflow management in controlling contamination risks. This study demonstrates the value of integrating experimental data with CFD simulations to assess pathogen spread and identify effective mitigation strategies in meat processing facilities.},
}

@article {pmid41878086,
year = {2026},
author = {Luo, D and Jia, S and He, W and Fan, Z and Yin, W},
title = {Periplaneta americana Powder Alleviates Neuropathic Pain and is Associated with Gut Microbiota Changes in Rats.},
journal = {Journal of pain research},
volume = {19},
number = {},
pages = {564911},
pmid = {41878086},
issn = {1178-7090},
abstract = {BACKGROUND: This study aims to evaluate the therapeutic potential of Periplaneta americana powder (PAP) in alleviating neuropathic pain in a rat model of sciatic nerve injury induced by chronic constriction injury (CCI), and to systematically analyze its effects on the composition and structure of the gut microbiota during the intervention process, with the goal of elucidating the mechanisms underlying the analgesic effects of PAP.

METHODS: A rat model of CCI was established (n = 12 per group), and PAP was administered for intervention. The analgesic effects were evaluated using mechanical withdrawal threshold (MWT) and thermal withdrawal latency (TWL). Pathological changes in the spinal cord and colon tissues were examined via hematoxylin-eosin (HE) staining, and the expression of the astrocyte marker glial fibrillary acidic protein (GFAP) in the spinal cord was detected by immunohistochemistry. The expression levels of pro-inflammatory cytokines TNF-α and IL-1β in spinal cord tissues were measured using enzyme-linked immunosorbent assay (ELISA). Fecal samples were collected at the endpoint of treatment for metagenomic sequencing and analysis.

RESULTS: After PAP treatment, behavioral tests in CCI rats showed a significant increase in MWT and TWL (P < 0.05). Histological analysis revealed marked alleviation of spinal cord and colon tissue damage as well as reduced inflammatory cell infiltration (P < 0.05). Immunohistochemistry further demonstrated a significant decrease in GFAP expression in the spinal cord (P < 0.05). ELISA results showed that the expression levels of TNF-α and IL-1β in spinal cord tissues were significantly decreased (P < 0.05).Metagenomic analysis indicated that PAP reshaped the gut microbiota structure, increased the abundance of SCFA-producing bacteria, and was associated with the butyrate metabolism pathway.

CONCLUSION: This study indicates that PAP can significantly alleviate neuropathic pain in a rat model of sciatic nerve chronic constriction injury (CCI) and suppress the central inflammatory response.Notably, this effect is accompanied by changes in the gut microbiota, particularly characterized by a significant alteration in the abundance of short-chain fatty acid-producing bacteria. These results suggest that PAP not only possesses substantial analgesic effects but may also mediate the intervention of CCI-induced neuropathic pain by regulating the structure of the gut microbiota.},
}

@article {pmid41878266,
year = {2026},
author = {Huang, J and Yan, X and Su, Q and Tu, H and Yu, Z and Liu, D and Wu, B},
title = {Temporal dynamics of gut microbiota and virome in preterm infants: insights from longitudinal metagenomic analysis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1598786},
pmid = {41878266},
issn = {2235-2988},
mesh = {Humans ; *Infant, Premature ; *Gastrointestinal Microbiome/genetics ; Infant, Newborn ; *Metagenomics ; *Virome ; *Bacteriophages/genetics/isolation & purification/classification ; Longitudinal Studies ; *Bacteria/classification/genetics/isolation & purification ; Female ; Male ; Feces/microbiology/virology ; Enterococcus faecalis ; Gastrointestinal Tract/microbiology ; },
abstract = {INTRODUCTION: Preterm infants exhibit heightened vulnerability to morbidity and mortality due to their underdeveloped immune systems and immature gastrointestinal tract. The gut microbiota plays a pivotal role in neonatal health, yet its establishment is influenced by multiple factors, including prematurity, antibiotic exposure, and feeding modalities. This study aimed to examine the interactions among gut bacteriophages, bacterial communities, and clinical variables in preterm infants to identify potential microbial biomarkers associated with health outcomes.

METHODS: We employed metagenomic shotgun sequencing and co-occurrence network analysis to characterize the virome and bacterial communities in 12 preterm neonates at 14 and 28 days post-birth. This approach enabled the identification of dynamic microbial colonization patterns and key bacterial species and bacteriophages associated with clinical parameters.

RESULTS: Staphylococcus epidermidis exhibited a significant decline over time, whereas Enterococcus faecalis and its associated bacteriophages showed progressive enrichment, becoming predominant by day 28. In contrast, the relative abundances of Clostridioides difficile and Klebsiella pneumoniae remained statistically stable between the two time points (14 vs. 28 days).

DISCUSSION: These findings suggest that microbial changes during the first month of life may reflect a combination of host developmental processes and external influences, such as antibiotic exposure or delivery mode. The observed microbial signatures provide preliminary insights into early gut microbiota and virome development in preterm infants. However, their functional relevance and long-term stability require confirmation in larger, well-powered longitudinal studies with denser temporal sampling. The enrichment of Enterococcus faecalis may indicate its opportunistic colonization potential in the preterm gut and warrants further investigation regarding its role in gut homeostasis and immune system maturation.},
}

Humans
*Infant, Premature
*Gastrointestinal Microbiome/genetics
Infant, Newborn
*Metagenomics
*Virome
*Bacteriophages/genetics/isolation & purification/classification
Longitudinal Studies
*Bacteria/classification/genetics/isolation & purification
Female
Male
Feces/microbiology/virology
Enterococcus faecalis
Gastrointestinal Tract/microbiology

@article {pmid41878461,
year = {2026},
author = {Li, Z and Zhang, Y and Xu, D and Huang, B},
title = {Diagnostic and therapeutic journey of infantile endobronchial tuberculosis: a case report.},
journal = {Frontiers in pediatrics},
volume = {14},
number = {},
pages = {1778717},
pmid = {41878461},
issn = {2296-2360},
abstract = {BACKGROUND: Endobronchial tuberculosis (EBTB) in infants is rare and is often overlooked because of nonspecific clinical manifestations. Coexisting primary immunodeficiency and opportunistic infections further increased diagnostic and therapeutic complexity.

CASE PRESENTATION: We reported a male infant aged 40 days who presented with fever and mild cough. Chest imaging showed progressive bilateral nodular and granulomatous lesions despite broad-spectrum antibacterial therapy. Microbiological evaluation revealed positive T-SPOT.TB and GeneXpert MTB/RIF results from bronchoalveolar lavage fluid (BALF), while metagenomic next-generation sequencing identified Pneumocystis jirovecii. Genetic testing demonstrated a heterozygous IKZF1 mutation, consistent with underlying immunodeficiency. Serial bronchoscopies confirmed necrotizing endobronchial tuberculosis with airway stenosis. The patient received standard anti-tuberculosis therapy, systemic corticosteroids, trimethoprim-sulfamethoxazole, intravenous immunoglobulin, and repeated bronchoscopic intraluminal drug delivery. Clinical and radiological remission was achieved, with no airway sequelae during 18-month follow-up.

CONCLUSIONS: This case highlighted the unique coexistence of infantile EBTB, IKZF1-related immunodeficiency, and P. jirovecii coinfection. Early bronchoscopy played a pivotal diagnostic and therapeutic role. Repeated intraluminal bronchoscopic therapy combined with systemic treatment might prevent irreversible airway damage in severe pediatric EBTB.},
}

@article {pmid41878469,
year = {2026},
author = {de Azevedo, PS and Vedovatto, MM and de Freitas, PCG and Luz, RBS and Streit, RSA and Persinoti, GF},
title = {parsomics: a data-driven framework for metagenomics data integration powered by a local relational database.},
journal = {Bioinformatics advances},
volume = {6},
number = {1},
pages = {vbag049},
pmid = {41878469},
issn = {2635-0041},
abstract = {MOTIVATION: Metagenomics enables the analysis of complex microbial communities directly from environmental samples, resulting in massive datasets that are processed using multiple tools and workflows. Data integration is key for metagenomics research, however, challenges in data organization and management locally remain open in existing workflows.

RESULTS: We present parsomics, a lightweight and extensible data management tool designed for efficient local storage, organization, and integration of metagenomic analysis results. Built upon PostgreSQL and implemented in Python, parsomics leverages a user-defined configuration file to automatically construct a relational database tailored to metagenomics-based data. It is user-friendly, easy to deploy, and implements modular plugin-based extensions to support diverse data types and outputs. parsomics can be installed in every major GNU/Linux environment and currently focuses on prokaryotic metagenomics analysis.

parsomics is an open-source project and its source code is available at https://gitlab.com/parsomics under the GPLv3 license. Comprehensive documentation can be found at https://parsomics.org and https://api.parsomics.org.},
}

@article {pmid41878742,
year = {2026},
author = {Armijo-Godoy, G and Cottet, L and Rupayan, A and Carrasco, M and Levicoy, D and Salvo-Garrido, H},
title = {Functional and ecological characterization of Labrys methylaminiphilus subsp. lupini subsp. nov., associated with Lupinus luteus nodules in acidic soils of southern Chile.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1759558},
pmid = {41878742},
issn = {1664-302X},
abstract = {BACKGROUND: Members of the genus Labrys are widely distributed in soil and plant-associated environments, yet their ecological roles and functional contributions within plant-associated microbiomes remain poorly understood. Labrys methylaminiphilus strain La1 was isolated from nodules of Lupinus luteus growing in acidic soils of southern Chile, providing an opportunity to investigate strain-level traits relevant to plant-microbe interactions under environmental stress.

METHODS: Strain La1 was characterized using physiological and biochemical, chemotaxonomic, and genomic approaches, including whole-genome sequencing and comparative genomics. Functional traits related to plant interaction were assessed through in vitro assays for indole-3-acetic acid (IAA) production, antifungal activity against lupine pathogens, and in planta experiments evaluating plant growth under salinity and osmotic stress. The ecological distribution of closely related taxa was inferred from screening of publicly available environmental microbiomes using protologger pipeline.

RESULTS: Although strain La1 showed high genomic similarity to L. methylaminiphilus JLW10[T], it exhibited distinct phenotypic, metabolic, and ecological features. These included tolerance to acidic and moderately saline conditions, utilization of rhizosphere-associated carbon sources, and a fatty acid profile consistent with adaptation to terrestrial environments. Genomic analyses revealed genes related to stress tolerance, exopolysaccharide biosynthesis, carbohydrate-active enzymes, siderophore production, IAA synthesis, and non-ribosomal peptide synthetases. Consistent with these traits, La1 inhibited the growth of Colletotrichum lupini and Pleiochaeta setosa and significantly enhanced L. luteus biomass under osmotic and salinity stress. Metagenomic screening indicated that sequences closely related to La1 are predominantly associated with soil, rhizosphere, and plant-associated habitats.

CONCLUSION: This study demonstrates that strain La1 represents a functionally versatile and ecologically specialized lineage within L. methylaminiphilus, contributing traits relevant to plant-associated microbiomes in acidic soils. This integrated functional and ecological evidence supports the designation of Labrys methylaminiphilus subsp. lupini subsp. nov. and highlights the relevance of strain-level analyses for understanding plant-microbe interactions.},
}

@article {pmid41878750,
year = {2026},
author = {Du, Z and Li, L and Liu, J and Wang, H and Li, J and Xu, Y and Cui, L and Yin, J},
title = {Wheat-Dependent Exercise-Induced Anaphylaxis Patients on a Wheat-Free Diet Exhibit a Gut Microbiota Composition More Similar to Healthy Individuals.},
journal = {Journal of asthma and allergy},
volume = {19},
number = {},
pages = {464532},
pmid = {41878750},
issn = {1178-6965},
abstract = {PURPOSE: There are limited studies on the intestinal microbiome in patients with wheat-dependent exercise-induced anaphylaxis (WDEIA), and changes in the gut microbiome in WDEIA patients after wheat-free diet have not been studied.

METHODS: This is a cross-sectional analysis. Fecal samples and clinical data were collected from 26 non-wheat-free patients with WDEIA, 11 wheat-free patients with WDEIA, and 24 healthy controls (HCs). The gut microbiota was evaluated through metagenomic sequencing.

RESULTS: The sequencing revealed differences in the gut microbiome between patients with WDEIA on a non-wheat-free diet and HCs; more specifically, the non-wheat-free group exhibited a downregulation of two families (Rikenellaceae and Odoribacteraceae), three genera (Alistipes, Odoribacter, and Catenibacterium), and four species (Bacteroides_stercoris, Alistipes_putredinis, Bacteroides_intestinalis, and Bacteroides_cellulosilyticus). A wheat-free diet is associated with intestinal flora more similar to the structure of healthy individuals. The species Bacteroides_stercoris was negatively correlated with T-IgE, and the genus Catenibacterium was negatively correlated with T-IgE, as well as wheat, gluten, or gliadin-specific IgE. The genus Catenibacterium was positively correlated with the healthy control-enriched "Apoptosis (ko04210)" pathway and negatively correlated with the non-wheat-free WDEIA group-enriched "Thyroid hormone signaling pathway (ko04919)" pathway.

CONCLUSION: Patients with WDEIA exhibit a specific gut microbiota signature and function, which demonstrated the potential association between the gut microbiome and WDEIA development. WDEIA patients on a wheat-free diet exhibit a gut microbiome composition more similar to healthy individuals.},
}

@article {pmid41878990,
year = {2026},
author = {Sun, Y and Li, Y and Temur, B and Lin, Y and Liu, Y and Yi, L and Sun, Z and Zhang, G and Li, J and Guo, Y and Li, L and Cai, J and Tian, W and Meng, G and Jiang, L and Fang, M and Ding, F and Zhou, X and Tu, C and He, B},
title = {Diversity Patterns of Domestic Herbivore Viruses in China Reveal Transmission Dynamics with Disease Management Implications.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e17444},
doi = {10.1002/advs.202517444},
pmid = {41878990},
issn = {2198-3844},
support = {32130104//National Natural Science Foundation of China/ ; 2025-NK-112//Qinghai Science and Technology Achievement Transformation Special Project/ ; },
abstract = {Domestic herbivores have complex interactions with humans and wildlife, playing important roles in zoonotic and epizootic disease emergence and transmission. Yet their viral diversity and cross-species transmission dynamics remain understudied. Through pan-viromic profiling of 10,225 swabs and 4,304 serum samples from 5,710 adult individuals across China's five major herbivore-rearing provinces, we prepare the domestic herbivore viromic catalog of China (DhCN-Virome) comprising 1,085,360 viral metagenomes, nearly capturing their family-level viral diversity while expanding by 2.3-fold global subgenus-level viral diversity. Distinct viromic signatures emerge across herbivore species and sample types. Viral communities generally follow a "higher openness, greater stability" pattern, with animals raised in confined settings being more susceptible to external influences. Viral circulations, particularly involving viruses of health concern, occur primarily within herbivore species but also extensively between herbivores and other species, including potential human-herbivore and avian-horse viral transmission. Bacteriophages constitute the most abundant viral entities, characterized by lytic replication strategies with some targeting pathogenic bacterial hosts. These findings expand our knowledge of herbivore viral diversity patterns and ecological transmission dynamics, underscoring the need for unified disease management strategies across all herbivore species. Particularly, the risk viruses represent potential triggers for future outbreaks, necessitating urgent epidemiological surveillance and vaccination programs.},
}

@article {pmid41879294,
year = {2026},
author = {Liu, Y and Zhao, X and Gao, J and Xu, K},
title = {Therapeutic Evolution and Outcomes in EGPA Complicated by Diffuse Alveolar Hemorrhage: case-based review.},
journal = {Modern rheumatology case reports},
volume = {},
number = {},
pages = {},
doi = {10.1093/mrcr/rxag028},
pmid = {41879294},
issn = {2472-5625},
abstract = {BACKGROUND: Eosinophilic granulomatosis with polyangiitis (EGPA) is a rare systemic vasculitis characterized by asthma, eosinophilia, and multi-organ involvement. Diffuse alveolar hemorrhage (DAH) is an uncommon but life-threatening pulmonary complication in EGPA.

CASE PRESENTATION: We report a 49-year-old previously healthy woman who presented initially with asthma-like symptoms and later developed fever, hemoptysis, cutaneous purpura, and periorbital edema. Laboratory evaluation revealed marked eosinophilia, anemia, elevated inflammatory markers, and strongly positive MPO-ANCA. Bronchoalveolar lavage fluid (BALF) was hemorrhagic and contained hemosiderin-laden macrophages, indicating DAH. Broad-spectrum antibiotics were empirically initiated but discontinued after metagenomic next-generation sequencing (mNGS) of BALF excluded infection. Bone marrow biopsy showed eosinophilic hyperplasia without clonal mutations. A diagnosis of MPO-ANCA positive EGPA with DAH was established. The patient received pulse methylprednisolone, prednisone, intravenous immunoglobulin, mepolizumab, and rituximab. Clinical symptoms improved rapidly, and radiological signs of alveolar hemorrhage nearly resolved within days.

CONCLUSION: Our case illustrates that integration of rituximab and mepolizumab with corticosteroids can achieve rapid remission and steroid sparing in EGPA-DAH. While evidence remains limited to case reports and small series, targeted biologics may fundamentally improve outcomes in this high-risk subset. Prospective studies are warranted to define optimal treatment strategies.},
}

@article {pmid41879323,
year = {2026},
author = {Mortensen, GA and Schmidt, H and Radivojac, P and Ye, Y and Haas, DM},
title = {Metagenomic profiling and predictive modeling of the gut microbiome reveal signatures of gestational disease.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0315525},
doi = {10.1128/spectrum.03155-25},
pmid = {41879323},
issn = {2165-0497},
abstract = {The gut microbiome plays a vital role in maternal health and pregnancy outcomes, yet its impact on conditions like gestational hypertension (GH) and gestational diabetes mellitus (GDM) remains poorly understood. This study explores how the gut microbiome differs between pregnant women with these conditions and healthy controls, using metagenomic sequencing to analyze microbial composition and function. Our findings reveal that women with GH and GDM exhibit greater microbiome variability and distinct shifts in bacterial communities compared to healthy pregnancies. Key beneficial bacteria, such as Bacteroides fragilis and Roseburia intestinalis, were reduced in cases, suggesting potential disruptions in gut-related metabolic and immune functions. In addition to multiple differentially abundant species of Sphingobacterium in cases versus controls, functional analysis indicated changes in carbohydrate and lipid metabolism, reinforcing the microbiome's connection to metabolic health. Furthermore, machine learning models demonstrated promising results in predicting disease status based on microbiome data, underscoring the potential for gut bacteria as potential predictive biomarkers for pregnancy-related conditions. These insights highlight the gut microbiome's role in pregnancy health and suggest it may be a promising target for future interventions aimed at reducing complications and improving maternal-fetal outcomes.IMPORTANCEGut microbial dysbiosis has been implicated in pregnancy complications, yet most studies rely on 16S rRNA sequencing, which limits resolution and functional insight. Here, using shotgun metagenomic sequencing and machine learning, we identified robust microbial taxonomic and functional signatures that distinguish gestational hypertension and gestational diabetes from healthy pregnancies. A combined feature set enabled accurate classification of disease status, with overlapping features between statistical and predictive frameworks underscoring biological relevance. Altogether, our study defines high-resolution microbiome signatures with translational potential as predictive biomarkers for maternal health, while also providing an open, reproducible analysis pipeline to support future investigations.},
}

@article {pmid41879886,
year = {2026},
author = {Chen, W and Li, X and Zhao, X and Zuo, Z and Wang, D and Zhao, F},
title = {GMW: a hybrid graph-based approach for post-assembly metagenome analysis and decontamination.},
journal = {Science China. Life sciences},
volume = {},
number = {},
pages = {},
pmid = {41879886},
issn = {1869-1889},
abstract = {Accurate genome assembly from metagenomic sequencing data remains challenging, particularly in mixed infections involving multiple pathogens, due to data complexity and contaminant sequences. Here, we present GMW (Genomic Microbe-Wise), a novel computational tool that improves pathogen genome assembly accuracy and enhances contaminant removal capabilities by simplifying the post-assembly graph. GMW leverages community detection algorithms, sequence similarity analysis, and coverage patterns to resolve strain mixtures and improve assembly accuracy. Using datasets of influenza A virus subtypes, we demonstrate GMW's ability to disentangle mixed infections and reconstruct complete viral genomes with high precision. Additionally, GMW outperforms traditional sequence similarity methods in classifying target contigs from contaminants. This tool also provides interactive visualization modules to streamline the inspection of assembly outputs, including simplified representations of complex assembly graphs. By enhancing assembly quality and contamination filtering, GMW emerges as a versatile solution for applications in clinical diagnostics, microbial ecology, and pathogen surveillance.},
}

@article {pmid41880538,
year = {2026},
author = {Consuegra-Asprilla, JM and Cuesta-Astroz, Y and González, Á},
title = {Characterization of the vaginal microbiome and its metabolic potential in Colombian patients with recurrent vulvovaginal candidiasis.},
journal = {Medical mycology},
volume = {},
number = {},
pages = {},
doi = {10.1093/mmy/myag026},
pmid = {41880538},
issn = {1460-2709},
abstract = {Recurrent vulvovaginal candidiasis (RVVC) is a multifactorial condition in which vaginal microbiota dysbiosis plays a key role. This study aimed to characterize the vaginal microbiome of patients with RVVC using metagenomic sequencing. Vaginal scraping samples were collected from 34 women aged 20-47 years and classified into three groups: (1) 14 women with RVVC who had experienced 3-7 episodes of VVC in the previous year; (2) 9 women with severe RVVC, defined as ≥8 episodes in the last year; and (3) 11 healthy women as controls. The results revealed an increased relative abundance of bacteria associated with bacterial vaginosis-including Gardnerella vaginalis, Gardnerella swidsinskii, and Prevotella bivia-as well as higher levels of Lactobacillus iners in both RVVC groups. In contrast, healthy women showed greater abundance of Lactobacillus crispatus and Lactobacillus gasseri. Diversity analyses indicated lower α-diversity in the healthy group compared to RVVC patients. Metabolic potential profiling showed a differential increase in sequences related to the phosphotransferase system (PTS), fructose/mannose metabolism, pentose phosphate pathway, and cysteine/methionine and purine metabolism in RVVC groups relative to controls; no significant differences were observed between RVVC groups, indicating that microbial profiles alone do not correlate with the degree of disease severity. These findings provide relevant insights into the taxonomic and functional characteristics of the vaginal microbiome in women with RVVC and may support the development of targeted therapeutic strategies.},
}

@article {pmid41880703,
year = {2026},
author = {Liang, H and Liu, J and Huang, Y and Wang, Z and Wang, J and Liu, H and Zhang, L and Peng, Y},
title = {Engineering the anammox pathway in a full-scale AOA process for industrial wastewater treatment.},
journal = {Water research},
volume = {298},
number = {},
pages = {125793},
doi = {10.1016/j.watres.2026.125793},
pmid = {41880703},
issn = {1879-2448},
abstract = {The anammox process holds significant potential for municipal wastewater treatment, yet its full-scale application in industrial wastewater treatment plants (IWTP), particularly within endogenous denitrification-based processes, remains challenging. This study demonstrates the successful establishment of the anammox pathway in a full-scale (16,000 m[3]/d) anaerobic-aerobic-anoxic (AOA) process IWTP by implementing a synergistic control strategy that integrates low dissolved oxygen (DO: 0.5 - 1.4 mg/L) with residual ammonia (1.6 - 2.9 mg/L) at the aerobic outlet. During 450 days of operation, the system achieved stable and advanced nitrogen removal, with effluent NH4[+]-N and total nitrogen (TN) averaging only 0.2 mg/L and 5.7 mg/L, respectively. Metagenomic and isotope tracing analyses identified that the anoxic zone biofilm as a functional hotspot for anammox, where the relative abundance of anammox bacteria (AnAOB), predominantly Candidatus Brocadia, was significantly enriched to 0.074%. This community contributed to 36.7% of the TN removal via dual pathways coupling anammox with endogenous and exogenous partial denitrification. Economically, the incorporation of anammox reduced aerobic zone aeration energy consumption by 18.2% and decreased external carbon dosage by 44.4%. This work provides a pioneering demonstration of anammox under complex water quality conditions and offers a viable technological route toward low-carbon wastewater treatment.},
}

@article {pmid41881056,
year = {2026},
author = {Chetruengchai, W and Sriwattanapong, K and Manaspon, C and Fakhruddin, KS and Samaranayake, L and Shotelersuk, V and Porntaveetus, T},
title = {Metagenome and Metabolic Pathways in Plaque Biofilms of Thai ELANE-Associated Neutropenic Patients: An Original Study and Scoping Review.},
journal = {European journal of dentistry},
volume = {},
number = {},
pages = {},
doi = {10.1055/s-0046-1818559},
pmid = {41881056},
issn = {1305-7456},
abstract = {Congenital neutropenia, particularly ELANE-associated forms, is associated with recurrent oral infections and aggressive periodontitis. While ELANE deficiency compromises oral health, its relationship to plaque biofilm ecology and metabolic function remains unclear. The oral microbiome-metabolome interplay in this condition remains largely uncharacterized globally. Here, we address this gap by characterizing the dental plaque metagenome and inferred metabolic pathways in a defined cohort of Thai neutropenia patients.In this exploratory study, we sequenced dental plaque samples from a defined cohort of nine individuals: three patients with severe congenital neutropenia or cyclic neutropenia (CyN) with confirmed ELANE variants, and six from age- and gender-matched healthy controls. Shotgun metagenomics was used for genomic analysis, followed by comprehensive microbiota examination. Subsequently, MetaCyc, a curated database, was used for in silico analysis and comparisons of the predicted functional pathways between the test and control plaque biofilms.The principal coordinate analysis plot and heat map revealed distinct segregation of microbial profiles between the patients and control groups. A significant variation in the proportions of the five core phyla was noted in patients and controls. Two commensal species, Aggregatibacter sp oral taxon 458 and Leptotrichia sp oral taxon 212, were enriched in the controls. Conversely, four species were significantly enriched in the patients, Selenomonas flueggei, Streptococcus milleri, Kingella oralis, and Actinobaculum sp oral taxon 183; the latter being notably elevated across all patients. The MetaCyc in silico analyses suggested predicted enrichment of functional pathways associated with inflammation and oxidative stress in patients, including L-methionine biosynthesis IV, formaldehyde assimilation III, L-rhamnose degradation, and the superpathway of (R,R)-butanediol biosynthesis pathways.Our study advances the understanding of ELANE-associated periodontitis by moving beyond descriptive microbiota analysis to suggest potential associations between host immune deficiency, microbial dysbiosis, and the microbiota-associated metabolic pathway alterations. These findings provide preliminary insights into targeted periodontal care in neutropenic patients, though further validation in larger cohorts is required.},
}

@article {pmid41881128,
year = {2026},
author = {Song, Z and Yang, J and Zhang, L and Peng, Y},
title = {Photocatalytic Fe3O4@CDs Drives Nitrite-Independent extracellular respiration of anammox via efficient bidirectional electron transfer.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134489},
doi = {10.1016/j.biortech.2026.134489},
pmid = {41881128},
issn = {1873-2976},
abstract = {Anaerobic ammonium oxidation (Anammox) process relying on extracellular electron transfer (EET) overcomes nitrite scarcity in practical wastewater, but inefficient EET rate constrains nitrogen removal. Herein, Fe3O4 with carbon dot shell (Fe3O4@CDs) was self-assembled with anammox bacterial as a photocatalytic hybrid. Building on bacteria inward uptake of photogenerated electrons from CDs and outward transfer of respiratory electrons to Fe3O4, a bidirectional electron pathway was established firstly. This novel route achieved efficient nitrite-independent Anammox, enabling direct and rapid removal of 80 mg/L NH4[+]-N. To elucidate efficient nitrogen removal essence, metagenomics was employed to reveal photogenerated electrons fate and their mediated nitrogen metabolism mechanism. Results showed that, following assembly via -P-O bonds, bacteria internalized CDs photogenerated electrons (0.82 µA/cm) into menaquinone (MQ) pool. This influx activated energy-generation route constructed by bc1 and Rnf enzymes, increasing intracellular ATP level by 3.36---6.51-fold. Consequently, energy drove electrons pumping from MQ pool to cytochrome c, followed by transport outward via CDs, pili and flavin, amplifying electrons eflux by 1.77-fold. Such efflux generated MQ pool electron vacancies, which were efficiently replenished by electrons from hydrazine synthase- and hydrazine dehydrogenase-catalyzed NH4[+]-N oxidation to N2 without nitrite. Underpinned by the photogenerated electron-driven EET process, Anammox bacteria was enriched from 25.26% to 48.02%, thus sustaining a total nitrogen removal efficiency of > 97% for over 80 days-far exceeding the performance of existing system. This technology provides an efficient and sustainable theoretical framework for the application of anammox in practical wastewater treatment.},
}

@article {pmid41881328,
year = {2026},
author = {Zhang, N and Wang, J and Yang, S and Liu, F},
title = {Biogeochemical and genomic drivers of groundwater DNRA: predictability of ammonium accumulation risk.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {128006},
doi = {10.1016/j.envpol.2026.128006},
pmid = {41881328},
issn = {1873-6424},
abstract = {Widespread ammonium (NH4[+]-N) contamination in groundwater, with local concentrations exceeding 20 mg/L, challenges traditional nitrogen removal, which is dominated by denitrification. Dissimilatory nitrate reduction to ammonium (DNRA), a nitrogen-retaining pathway, competes with denitrification. However, the environmental conditions that promote DNRA in aquifers and its quantitative contribution to NH4[+]-N loading remain critical knowledge gaps in groundwater nitrogen cycling research. We investigated how C/N ratios, Fe[2+] concentrations, initial NO3[-]-N, hydrochemical types, total dissolved solids (TDS), and pH influenced DNRA efficiency and its competition with denitrification. We found that DNRA efficiency peaked in organic-rich aquifers (15.70-26.69%) and was minimum in industrially and agriculturally contaminated groundwater (0.71%). High Fe[2], high initial NO3[-]-N, and HCO3[-]-type environments markedly promoted DNRA, whereas Cl[-]-type water inhibited it. Competition analysis revealed that elevated C/N ratios, Fe[2+], and TDS increased the relative contribution of DNRA to nitrate reduction. Metagenomic analysis further demonstrated that high C/N ratios and Fe[2+]-rich conditions promoted DNRA dominance via selective enrichment of Enterobacteriaceae carrying the abundant nrfA gene. Conversely, high mineralization and Na-Cl water types drastically reduced DNRA efficiency by suppressing the expression of key functional genes. Furthermore, under intermittent nitrate input, NH4[+]-N accumulated even with low DNRA efficiency, posing long-term water quality risks. We developed a DNRA efficiency prediction model using the Extreme Gradient Boosting algorithm (R[2] = 0.92), thereby enabling accurate assessment across diverse groundwater conditions. This work advances mechanistic understanding and provides an innovative predictive methodology for assessing DNRA-driven NH4[+]-N enrichment risks in groundwater.},
}

@article {pmid41871945,
year = {2026},
author = {Vázquez-Castellanos, JF and Yoon, SJ and Won, SM and Raes, J and Kwon, HC and Si, J and Suk, KT},
title = {Stage-dependent gut microbiome and functional signatures across the liver disease spectrum: an integrative multicohort study.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-337436},
pmid = {41871945},
issn = {1468-3288},
abstract = {BACKGROUND: The gut-liver axis plays a critical role in liver disease progression; however, how gut microbial ecology and function vary across disease stages remains unclear.

OBJECTIVE: To define stage-specific microbial and functional signatures and evaluate their diagnostic potential.

DESIGN: We analysed faecal samples from 1168 individuals spanning healthy controls, fatty liver, hepatitis, cirrhosis and hepatocellular carcinoma by 16S rRNA sequencing, with a subset (n=141) profiled by shotgun metagenomics. To increase statistical power and enable external validation, 2376 publicly available metagenomic datasets, including 734 liver-related, were integrated. Machine learning-based multicohort analysis was used to identify microbial biomarkers, assess risk factors and classify disease stages.

RESULTS: Microbial diversity declined and a low-richness enterotype expanded with disease severity. Machine learning revealed a discordance in hepatitis, which lacked taxonomic markers but was defined by a conserved functional signature of biosynthetic upregulation. In contrast, advanced stages featured consistent markers like Ligilactobacillus and Veillonella, with strain-level evidence confirming oral-gut transmission. Functional profiling delineated a metabolic continuum from anabolic precursor synthesis in hepatitis to virulence factor production in cirrhosis and putrefactive metabolism in carcinoma. Comparative analysis confirmed that these signatures were distinct from those in non-liver metabolic and oncologic disorders. Importantly, the expansion of oral-derived Veillonella spp and the low-richness enterotype were significantly associated with increased mortality.

CONCLUSION: This large-scale study delineates stage-dependent ecological and functional remodelling of the gut microbiome across liver diseases. These findings highlight the potential of microbiome-based markers for non-invasive diagnosis and prognostic risk stratification in liver diseases.},
}

@article {pmid41872229,
year = {2026},
author = {Ji, M and Li, Y and Wang, M and Liu, X and Gong, X and Tu, Q},
title = {Unveiling the biodiversity of large DNA viruses in intertidal mudflats via metagenomics.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-71095-7},
pmid = {41872229},
issn = {2041-1723},
abstract = {Large DNA viruses (LDVs) are unique members of the Earth's virosphere, remarkable for their extra-large genome sizes and broad metabolic potential. However, our knowledge of this viral group remains very limited, particularly in complex dynamic habitats. In this study, 237 metagenome-assembled LDV genomes are comprehensively recovered from intertidal mudflats using multiple sampling and sequencing strategies totaling 5.3 TB data. A phylogenetically distinct subgroup within Imitervirales is identified, showing broad associations with multiple eukaryotic lineages. Certain LDV populations can persist locally and exhibit significant genomic variations potentially driven by dynamic intertides. Ecological patterns are observed at both community and genetic levels, with giant viruses showing steeper community turnover but weaker nucleotide diversity variations than large phages. Moreover, LDVs exhibit similar macroecological patterns to their potential hosts, which substantially shape LDV community assembly. The intertidal LDVs encode diverse functional genes, most of which remain uncharacterized, with a 27.32% improvement for unknown phage genes using a protein language model. Although giant viruses and large phages share comparable functional gene composition, they exhibit distinct preferences for specific metabolic pathways, especially those associated with carbon and nitrogen cycling. This study broadens our understanding of the biodiversity and ecology of LDVs in the understudied intertidal ecosystems.},
}

@article {pmid41872577,
year = {2026},
author = {Shan, X and Cao, K and Jeckel, H and Alcalde, RE and Trindade, IB and Kwiecinski, JV and Newman, DK},
title = {Drought drives elevated antibiotic resistance across soils.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41872577},
issn = {2058-5276},
support = {2R01AI127850-06A1//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 2R01AI127850-06A1//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 2R01AI127850-06A1//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 2R01AI127850-06A1//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 2R01AI127850-06A1//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 2R01AI127850-06A1//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 2R01AI127850-06A1//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 2209379//National Science Foundation (NSF)/ ; ALTF 191-2023//European Molecular Biology Organization (EMBO)/ ; },
abstract = {Antibiotic resistance is a growing threat to human health and is often attributed to excessive clinical usage that selects for resistance. Although many antibiotics are derived from soil microorganisms, how environmental changes to soil ecosystems might promote resistance is poorly understood. Here we establish drought as a driving force of antibiotic resistance in the soil, with potentially far-reaching public health consequences. Across various geographic regions and soil types, we consistently observe metagenomic signatures of enrichment for antibiotic producers under drought conditions. Experimentally, we demonstrate that drought-induced lowering of water content concentrates natural antibiotics, thereby intensifying selection against sensitive strains and favouring antibiotic-resistant bacteria. Using clinical surveillance data from 116 countries, we show that the average frequency of hospital antibiotic resistance is strongly correlated with the local aridity index, even after controlling for regional income differences. Together, our findings reveal an underrecognized link between climate factors and antibiotic resistance.},
}

@article {pmid41872600,
year = {2026},
author = {Segev, T and Barak, D and Zahavi, L and Godneva, A and Rein, M and Krongauz, D and Samocha-Bonet, D and Rossman, H and Weinberger, A and Segal, E},
title = {Diet-microbiome associations in 10,068 individuals from the Human Phenotype Project to guide personalized nutrition.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
pmid = {41872600},
issn = {1546-170X},
abstract = {Diet is a major environmental factor influencing the human gut microbiome. However, the effects of specific foods and dietary patterns on microbial composition, diversity and function is not fully understood, limiting progress toward personalized dietary strategies. Here, leveraging 10,068 participants from the Human Phenotype Project with app-based diet logs and shotgun metagenomics, we predicted diet-microbiome associations at species-level resolution. Diet significantly predicted microbial diversity (richness r = 0.26, Shannon Index r = 0.24), the relative abundance of 669 of 724 species tested (92.4%, false discovery rate <0.05), and 313 of 320 pathways (97.8%, false discovery rate <0.05). Feature attribution identified distinct food-microbe links, including coffee with Lawsonibacter asaccharolyticus (r = 0.43), yogurt with Streptococcus thermophilus (r = 0.42) and milk with Bifidobacterium species (r = 0.31-0.36). In parallel, broader dietary patterns, especially the degree of food processing, emerged as predictors of microbial diversity and composition. We also show that diet-microbiome associations persist over four years, with 82.5% of species exhibiting significant longitudinal tracking between predicted and observed abundances. Finally, we developed an exploratory analysis for simulating personalized dietary interventions with predicted microbiome shift effects that are associated with improvements in cardiometabolic health. Our findings demonstrate that diet is strongly associated with microbiome composition, diversity and function, and highlight its potential for guiding personalized interventions.},
}

@article {pmid41872963,
year = {2026},
author = {Kim, B and Kim, HN and Cheong, HS and Jeong, S and Kim, J and Park, DI and Joo, EJ},
title = {Fecal microbiota from hepatitis B-infected individuals alters triglyceride metabolism and microbial pathways in mice.},
journal = {Gut pathogens},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13099-026-00825-5},
pmid = {41872963},
issn = {1757-4749},
support = {RS-2023-KH135855//Korea Health Industry Development Institute/Republic of Korea ; NRF-2021R1A2C4002454//National Research Foundation of Korea/ ; },
}

@article {pmid41874180,
year = {2026},
author = {Garzon, A and Miramontes, C and Weimer, BC and Profeta, R and Hoyos-Jaramillo, A and Fritz, HM and Pereira, RV},
title = {Characterizing the nasopharyngeal microbiome and resistome of dairy cattle with and without bovine respiratory disease.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0264825},
doi = {10.1128/spectrum.02648-25},
pmid = {41874180},
issn = {2165-0497},
abstract = {Bovine respiratory disease (BRD) remains a significant economic challenge in dairy cattle despite extensive vaccination programs that have been developed and implemented during the last few decades. This study investigated the nasopharyngeal microbiome and resistome of dairy cattle across various life stages to understand the roles of microbial communities associated with BRD. A case-control study was conducted on three commercial dairy farms in Northern California, collecting nasopharyngeal swabs from 69 animals, including preweaned calves, weaned heifers, and lactating cows with and without BRD. Shotgun metagenomic sequencing was used to characterize both microbiome and resistome profiles observed at the time of BRD diagnosis. Results revealed that BRD is associated with distinct microbial community patterns, rather than the increased abundance of a specific pathogen. Age was a critical factor influencing microbial diversity, with adult cows showing the highest diversity and weaned heifers with BRD showing the lowest. A total of 1,164 bacterial species were identified, with BRD cases harboring 14 unique species compared to control animals. BRD cases were characterized by the co-occurrence of multiple respiratory pathogens, including Mannheimia haemolytica, Pasteurella multocida, Histophilus somni, and Mesomycoplasma species, which showed positive correlation with BRD cases but negative correlations in BRD controls, while BRD control animals showed significantly higher abundance of commensal Staphylococcus species. Resistome analysis identified 65 antimicrobial resistance genes, with BRD cases harboring more unique resistance genes than BRD controls. These findings challenge traditional single-pathogen models and demonstrate that BRD is likely the result of complex microbial community interactions and changes in community abundance, providing new potential targets to explore when considering prevention strategies toward promoting microbial communities that prevent or reduce the risk of BRD.IMPORTANCEBovine respiratory disease (BRD) represents one of the most economically challenging conditions in cattle production, with an estimated direct cost that exceeds $165 million annually in the United States alone. Despite decades of vaccination efforts targeting known pathogens, BRD prevalence remains unchanged, indicating an incomplete understanding of disease pathogenesis. This study provides critical insights by shifting focus from individual pathogens to entire microbial communities, revealing that BRD involves complex bacterial interactions, as well as the role of the understudied nasal commensal microbiome in healthy animals. The identification of distinct "pathobiomes" associated with disease and protective commensal communities in healthy animals fundamentally changes approaches to BRD prevention and treatment. The discovery that age significantly influences microbiome stability highlights critical intervention periods. Furthermore, the association between BRD and increased antimicrobial resistance genes raises concerns about current treatment and overall management practices, selecting for drug-resistant communities. This research provides a foundation for developing microbiome-based diagnostic tools and interventions supporting healthy microbial ecosystem development.},
}

@article {pmid41874256,
year = {2026},
author = {Lam, WKJ and Chan, KKP and Wang, G and Lai, CKC and Kang, G and Chan, C and Leung, ACY and Wong, NHL and Tso, CSN and Chow, KM and Ramakrishnan, S and Wong, KT and Lau, CHY and Ng, JKC and Lo, RLP and Yip, WH and Ngai, JCL and To, KW and Tse, IOL and Cheng, SH and Shang, H and Chan, KW and Lai, A and Chan, CML and Lee, VCT and Malki, Y and Choy, LYL and Ma, ML and Zhou, Q and Yu, SCY and Jiang, P and Ko, FWS and Chan, KCA and Hui, DSC and Lee, YCG and Lo, YMD},
title = {Sequencing of Pleural Fluid and Plasma for Tuberculous Pleuritis.},
journal = {NEJM evidence},
volume = {5},
number = {4},
pages = {EVIDoa2500237},
doi = {10.1056/EVIDoa2500237},
pmid = {41874256},
issn = {2766-5526},
mesh = {Humans ; *Tuberculosis, Pleural/diagnosis/microbiology/blood ; Male ; Female ; Middle Aged ; *Mycobacterium tuberculosis/genetics/isolation & purification ; *Pleural Effusion/microbiology ; *DNA, Bacterial/analysis ; Prospective Studies ; Sensitivity and Specificity ; Aged ; Adult ; High-Throughput Nucleotide Sequencing ; },
abstract = {BACKGROUND: The laboratory diagnosis of tuberculous pleuritis (TBP) is hindered by the paucibacillary nature of Mycobacterium tuberculosis in the pleural space, resulting in low sensitivity of microbiological culture and polymerase chain reaction-based analyses on pleural fluid. The use of metagenomic next-generation sequencing for diagnosing TBP may be limited by the background noise of DNA from nontuberculous mycobacteria.

METHODS: We performed targeted sequencing to analyze M. tuberculosis DNA in paired pleural fluid and plasma from prospectively enrolled consecutive patients with new-onset pleural effusion. We used a bioinformatics alignment algorithm to the M. tuberculosis genome that was masked for regions with high sequence similarity to nontuberculous mycobacteria. Our primary outcome was a comparison of diagnostic sensitivity between M. tuberculosis sequencing as described above and culture using McNemar's test.

RESULTS: Among the included 329 patients with pleural effusion, 34 patients with TBP were identified. Targeted sequencing detected M. tuberculosis DNA fragments in the pleural fluid of all TBP cases (median, 267.6 reads per 10 million [RP10M]; interquartile range [IQR], 30.8-2644.3) but absent in 288 out of 295 (97.6%) non-TBP samples (median, 0 RP10M; IQR, 0-0). Targeted sequencing of pleural fluid achieved a sensitivity of 97.1% for TBP detection at a cutoff of 2 RP10M, in contrast to 47.1% by M. tuberculosis culture (P<0.001, McNemar's test). Sequencing yielded an area-under-the-curve value of 0.9996 (95% confidence interval, 0.9988-1.0000) for differentiating TBP and non-TBP. Plasma analysis by targeted sequencing with the same alignment algorithm reported an area-under-the-curve value of 0.9475 (95% confidence interval, 0.8929-1.0000).

CONCLUSIONS: Targeted sequencing of pleural fluid with selectively masked M. tuberculosis genomic alignment accurately diagnosed TBP and outperformed conventional diagnostic tests. (Supported by InnoHK and the Hong Kong Tuberculosis, Chest and Heart Diseases Association; ClinicalTrials.gov number, NCT05397730.).},
}

Humans
*Tuberculosis, Pleural/diagnosis/microbiology/blood
Male
Female
Middle Aged
*Mycobacterium tuberculosis/genetics/isolation & purification
*Pleural Effusion/microbiology
*DNA, Bacterial/analysis
Prospective Studies
Sensitivity and Specificity
Aged
Adult
High-Throughput Nucleotide Sequencing

@article {pmid41874416,
year = {2026},
author = {Koseli, E and Tyc, KM and Buzzi, B and Akbarali, HI and Damaj, MI},
title = {The Role of the Gut Microbiome in Nicotine Withdrawal and Dependence.},
journal = {Nicotine & tobacco research : official journal of the Society for Research on Nicotine and Tobacco},
volume = {},
number = {},
pages = {},
doi = {10.1093/ntr/ntag057},
pmid = {41874416},
issn = {1469-994X},
abstract = {INTRODUCTION: Smoking is considered a global pandemic with more than 1.3 billion people being active smokers. Increasing evidence suggests that nicotine exposure can lead to changes in the gut microbiome, increases in permeability, and impaired mucosal immune responses in the gastrointestinal tract. However, the literature on behavioral aspects of nicotine-microbiome interaction, such as dependence and withdrawal, is limited. In this study, we used homologous fecal material transplants (FMT) to modify the gut microbiome and its impact on the intensity of nicotine withdrawal in mice.

METHODS: We used osmotic minipumps as an application of chronic nicotine for 15 days and orally gavaged FMT 2x a day to the mice. We assessed the nicotine withdrawal by measuring the number of somatic signs and anxiety-like behaviors at 24 h and 1 week after the mini pump removal. Fecal samples were also collected points to identify the gut microbiome changes.

RESULTS: Fecal transplants reduced the number of somatic signs and anxiety-like behaviors in nicotine-treated mice up to a week after the removal of minipumps. The shotgun metagenomic results of the fecal samples from 24 h after minipumps removal time point show altered gut microbiome with a significant shift in the species composition between the nicotine treated and its homologous FMT treatment.

CONCLUSIONS: Our results indicate that under our experimental conditions fecal transplant can reduce the severity of nicotine withdrawal. This suggests that interactions along the gut-brain axis are important for the development of nicotine dependence and might help lower the risk of cancer and other serious health problems in humans.},
}

@article {pmid41874421,
year = {2026},
author = {Wang, J and Lu, L and Sun, Y and Messer, LF and Wu, M and Duan, Z and Shi, J and Yang, Y and Li, C and Mao, Y and Zhu, D and Rillig, MC and Wang, X},
title = {AHL-mediated quorum sensing drives plastisphere formation and elevates pathogenic potential.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag066},
pmid = {41874421},
issn = {1751-7370},
abstract = {The biofilm colonizing plastic debris, termed 'the plastisphere', is of growing global concern due to escalating plastic pollution. However, the biological mechanisms underpinning plastisphere formation remain poorly understood. Here, we analyzed public global metagenomes, revealing a significant enrichment of genes associated with quorum sensing (QS) and biofilm formation, with a pronounced signal for acyl-homoserine lactone (AHL) QS. Using controlled microfluidic and tubular column experiments, we further demonstrate that exogenous AHL actively promotes plastisphere formation, biomass accumulation, and extracellular polymeric substance production on microplastics, whereas a quorum quenching agent (AHL acylase) effectively inhibits these processes. Multi-omics analyses revealed that AHLs can transcriptionally activate genes involved in adhesion, motility, chemotaxis, and matrix production, fundamentally reshaping community structure, restructuring inferred microbial interaction networks, and driving community assembly toward stronger deterministic selection. AHL stimulation also increased the relative abundance and expression of pathogen-associated and virulence-related functions, suggesting an elevated virulence potential within the plastisphere under QS-promoting conditions. Together, our findings establish AHL-mediated QS as a central driver of plastisphere assembly and a key determinant of risk profile, highlighting its critical role in understanding and potentially mitigating the growing environmental and health hazards associated with microplastic pollution.},
}

@article {pmid41874457,
year = {2026},
author = {Mohr, AE and Berryman, CE and Harris, MN and Lawrence, AB and Chakraborty, N and Campbell, R and Dimitrov, GI and Gautam, A and Hammamieh, R and Lieberman, HR and Rood, JC and Pasiakos, SM and Karl, JP},
title = {Testosterone administration partially modulates gut microbiota responses to severe energy deficit.},
journal = {American journal of physiology. Endocrinology and metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajpendo.00291.2025},
pmid = {41874457},
issn = {1522-1555},
support = {W81XWH-14-1-0335//DOD | OSD | Defense Technical Information Center (ADD)/ ; W81XWH-17-2-0026//DOD | OSD | Defense Technical Information Center (ADD)/ ; Joint Program Committee-5//Military Operational Medicine Research Program (MOMRP)/ ; //DOE | Oak Ridge Institute for Science and Education (ORISE)/ ; T32DK137525//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; },
abstract = {Severe diet- and exercise-induced energy deficit (SED) suppresses androgen production in healthy men, altering metabolism and driving muscle loss. The gut microbiota modulates host metabolism, yet the community's response to SED and any role of androgen hormones are unclear. Herein, healthy, physically-active men were randomized to receive 200mg/wk testosterone enanthate (n = 24) or placebo (n = 26) during a 28-day residential intervention that restricted energy intake and increased energy expenditure inducing a ~2000 kcal/d SED. Multi-omic analyses revealed altered gut microbiota composition, reduced fecal short-chain fatty acids (SCFA), and shifts in bacterial metabolic pathways toward lipid utilization and mucin degradation during SED, suggesting adverse effects of SED on gut microbiota metabolic functions. Testosterone administration preserved certain SCFA-producing taxa and bioenergetic pathways without fully counteracting effects of SED indicating a limited but potentially important interplay between androgen status and the gut microbiota under conditions of SED.},
}

@article {pmid41874663,
year = {2026},
author = {Hu, C and Lin, M and Hu, T and Zeng, Y and Zeng, R and Wang, C},
title = {Linking Bacterial r/k Ecological Shifts to Spatiotemporal Nitrogen Removal Dynamics in Recirculating Aquaculture Systems.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02742-1},
pmid = {41874663},
issn = {1432-184X},
support = {NO.2024SJRC4//the Central Public-interest Scientific Institution Basal Research Fund, CAFS/ ; NO.LTO2326//State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences/ ; NO.2023A04J0897//Guangzhou Science and Technology Program Project/ ; NO.SL2023E04J00185//Demonstration and Promotion of Key Technologies for Land-based Factory Farming of Hybrid Eleotris oxycephala/ ; },
}

@article {pmid41874734,
year = {2026},
author = {de Medeiros Azevedo, T and Aburjaile, FF and Pandolfi, V and Ferreira-Neto, JRC and Fracetto, GGM and de Oliveira Silva, RL and Gonçalves-Oliveira, RC and de Carvalho Azevedo, VA and Brenig, B and Benko-Iseppon, AM},
title = {Unlocking the microbiome of an extremophile plant: metagenomic insights into Calotropis procera's endo-rhizosphere communities.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {4},
pages = {},
pmid = {41874734},
issn = {1573-0972},
}

@article {pmid41874898,
year = {2026},
author = {Son, JS and Lee, SY and Sang, MK and Spinelli, F and Ryu, CM},
title = {Protective holobiome promotes strawberry tolerance of biotic stresses.},
journal = {Stress biology},
volume = {6},
number = {1},
pages = {},
pmid = {41874898},
issn = {2731-0450},
support = {. RS-2022-RD010288//RDA/ ; CN00000022//Italian Academy for Advanced Studies in America, Columbia University/ ; KRIBB202434//Korea Research Institute of Bioscience and Biotechnology/ ; },
abstract = {The commercial cultivation of strawberry (Fragaria × ananassa) is increasingly challenged by biotic stresses such as plant pathogens and insect pests, while climate change exacerbates abiotic stresses. Reliance on chemical fumigants and broad-spectrum pesticides presents risks to human health, environmental quality, and microbial diversity. The strawberry holobiome, defined as the integrated community of plant-associated microorganisms that inhabit the rhizosphere, phyllosphere, endosphere, and fruit surface, is emerging as a key determinant of plant health and productivity. Recent metagenomic and metabolomic studies have identified cultivar-specific microbial consortia that suppress plant disease, enhance stress tolerance via induced systemic resistance, and modulate fruit quality. The engineering of synthetic microbial communities (SynComs) offers a targeted approach to microbiome augmentation, but the lack of high-resolution functional data hinders the development of effective SynComs, especially in hydroponic and substrate culture systems. This review synthesizes recent advances in holobiome profiling, evaluates microbial biocontrol strategies against major pathogens, and outlines future directions, including AI (artificial intelligence)-driven community design, integrated multi-omics analysis, and microbiome-assisted breeding. Addressing these gaps will enable precision management of the strawberry microbiome to sustain yield, quality, and resilience under dynamic environmental conditions.},
}

@article {pmid41874931,
year = {2026},
author = {Gong, K and Xie, Z and Zhang, P and Xu, J and Huang, J and Li, X and Huang, L},
title = {Limosilactobacillus reuteri LR-99 Modulates Gut Microbiota and Core Symptoms in Children with Autism Spectrum Disorder: A Single-arm Pilot Study.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {41874931},
issn = {1867-1314},
support = {3502Z202372073//Xiamen Natural Science Foundation of China/ ; },
}

@article {pmid41875072,
year = {2026},
author = {van der Heyde, M and Curran, M and Floeckner, S and Nevill, P and White, NE and Austin, AD and Guzik, MT},
title = {Validating COI eDNA Metabarcoding Primers for Detection of Subterranean Fauna.},
journal = {Molecular ecology resources},
volume = {26},
number = {3},
pages = {e70127},
doi = {10.1111/1755-0998.70127},
pmid = {41875072},
issn = {1755-0998},
support = {LP190100555//Australia Research Council Linkage Project/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; *DNA Primers/genetics ; *DNA, Environmental/genetics ; *Electron Transport Complex IV/genetics ; Animals ; Biodiversity ; *Metagenomics/methods ; },
abstract = {Subterranean ecosystems host a diverse range of ancient fauna, but studying these ecosystems is challenging due to significant sampling difficulties. Environmental DNA (eDNA) metabarcoding offers a promising approach for monitoring subterranean biodiversity, yet issues such as primer bias and non-target amplification can complicate its effectiveness. Thus, thorough validation of metabarcoding primers is crucial for accurate and comprehensive assessments of subterranean faunal diversity. This study aimed to address the need for robust primer validation through in silico, in vitro and in situ analyses, shedding light on primer performance across various subterranean taxa. The primary objective was to evaluate the effectiveness of COI metabarcoding primers for assessing subterranean faunal diversity. In silico analyses involved curating COI sequences from the Barcode of Life Database (BOLD) and selecting 14 primer combinations for in vitro testing using mock communities. Results revealed varying primer performance in terms of PCR efficiency and detection limits across different taxa. One primer combination (BF1/jgHCO2198) detected 82% of taxa in the mock community, but only at high DNA concentrations of the target taxa. The highest proportion of subterranean taxa detected in a diluted mock community was 68% using the fwhF2/fwhR2n primer combination. For in situ field validation, this same primer set detected 13 out of 16 subterranean taxa identified in haul net samples, along with an additional four taxa not identified by haul net. These findings highlight the potential of COI metabarcoding and the critical importance of primer selection for eDNA studies aimed at conserving subterranean biodiversity.},
}

*DNA Barcoding, Taxonomic/methods
*DNA Primers/genetics
*DNA, Environmental/genetics
*Electron Transport Complex IV/genetics
Animals
Biodiversity
*Metagenomics/methods

@article {pmid41875156,
year = {2026},
author = {Shen, LQ and Wang, L and Yao, Z and Lin, D and Ye, YQ and Zhang, WR and Ye, M and Sun, MM and Du, S and Wu, D and O'Connor, P and Zhu, D},
title = {Phages drive the dissemination of antibiotic resistance genes by facilitating host adaptation to heavy metal stress.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {13},
pages = {e2535653123},
doi = {10.1073/pnas.2535653123},
pmid = {41875156},
issn = {1091-6490},
support = {22193062//MOST | National Natural Science Foundation of China (NSFC)/ ; 2024YFE0106300//MOST | National Key Research and Development Program of China (NKPs)/ ; 2023321//Youth Innovation Promotion Association of the Chinese Academy of Sciences (CAS YIPA)/ ; 2022A-163-G//Ningbo Yongjiang Talent Project/ ; },
mesh = {*Metals, Heavy/toxicity/metabolism ; *Bacteriophages/genetics/physiology ; Soil Microbiology ; *Drug Resistance, Microbial/genetics ; *Adaptation, Physiological/genetics ; *Drug Resistance, Bacterial/genetics ; *Bacteria/genetics/virology/drug effects ; Stress, Physiological ; Genes, Bacterial ; China ; Gene Transfer, Horizontal ; },
abstract = {Heavy metals are increasingly recognized as major drivers of antibiotic resistance gene (ARG) dissemination in soil ecosystems. However, the role of phages in heavy metal-driven ARG dissemination and the underlying mechanisms remain poorly understood. Here, through integrative metagenomic, viromics, and metabolomic analyses of paddy soils across China, we reveal that soil phages promote ARG dissemination under heavy metal stress, likely through two potential mechanisms. First, phage-encoded auxiliary metabolic genes (AMGs) reprogram host metabolism to enhance bacterial survival and adaptation, thereby facilitating the cotransfer of adjacent ARGs and indirectly promoting horizontal dissemination. Second, phage-encoded heavy metal detoxification genes (HDGs) directly mediate metal detoxification, driving the cotransfer of neighboring ARG fragments and inducing lipid peroxidation-associated increases in membrane permeability, which collectively enhance ARG mobilization. We further identify a significant enrichment of lysogenic phages coharboring ARGs with AMGs or HDGs (AMG-ARG and HDG-ARG fragments), underscoring their contribution to ARG dissemination. Phage transplantation experiments confirm that elevated heavy metal stress triggers lysogenic phage-mediated ARG transduction to bacterial hosts. Cumulatively, our experiments highlight the pivotal role of phages in mediating ARG transfer under heavy metal pressure and underscore the necessity of incorporating phage dynamics into ARG risk assessments.},
}

*Metals, Heavy/toxicity/metabolism
*Bacteriophages/genetics/physiology
Soil Microbiology
*Drug Resistance, Microbial/genetics
*Adaptation, Physiological/genetics
*Drug Resistance, Bacterial/genetics
*Bacteria/genetics/virology/drug effects
Stress, Physiological
Genes, Bacterial
China
Gene Transfer, Horizontal

@article {pmid41875508,
year = {2026},
author = {Estrada, CSD and de Oliveira, OA and Lopes, TAC and Maria, CRC and Avelino-Alves, D and Lima, M and Vidal, LM and de Siqueira Campos, L and Dias, GM and Thompson, C and Tschoeke, D and Thompson, F},
title = {Rhodolith metagenome diversity shifts across the Great Amazon System.},
journal = {The Science of the total environment},
volume = {1027},
number = {},
pages = {181652},
doi = {10.1016/j.scitotenv.2026.181652},
pmid = {41875508},
issn = {1879-1026},
abstract = {Rhodolith-forming coralline algae in the Great Amazon Reef System (GARS) occur under strong light and redox gradients imposed by the Amazon River plume. We tested whether a conserved microbial and metabolic core persists across sectors while functions reorganize with local conditions. We conducted shotgun metagenomics on rhodolith holobionts collected in the South, Central, and North sectors and profiled taxonomic composition and pathway markers (KEGG/SEED; METABOLIC). Bacteria dominated the holobiont, with Proteobacteria, Chloroflexi, and Bacteroidetes prevailing, and Thaumarchaeota as the main archaeal lineage. Functional profiles showed structured not random variation among sectors. In the South, high water transparency supported oxygenic phototrophy (psa/psb, rbcL/S; phycobiliproteins) and stronger coupling between carbon fixation and respiration. The Central sector displayed a transitional configuration combining oxygenic and anoxygenic phototrophy (pufL/M; bch genes) with co-occurring nitrification-denitrification (amoA, nxrAB, nirK, nosZ), indicating tight NS cycling. The North was enriched in sulfur redox pathways linked to suboxic microzones, with sulfate-reducing and sulfur-oxidizing lineages and contributions from methanogenic archaea. Across sectors, high diversity and functional redundancy likely underpin holobiont persistence in mesophotic settings. Our results indicate a resilient, sector-specific reorganization of rhodolith-associated microbiomes along plume-driven gradients, with implications for biogenic calcification and biogeochemical stability under climate change and ocean acidification scenarios.},
}

@article {pmid41875555,
year = {2026},
author = {Lu, L and Li, M and Kang, G and Wu, P and Wang, N and Tan, Y and Su, G and Ruan, J and Zhang, S},
title = {Fate of per- and polyfluoroalkyl substances (PFAS) and microbial communities in wastewater treatment: Disinfection-driven changes in microbial dynamics and PFAS profiles.},
journal = {Ecotoxicology and environmental safety},
volume = {314},
number = {},
pages = {120059},
doi = {10.1016/j.ecoenv.2026.120059},
pmid = {41875555},
issn = {1090-2414},
abstract = {Municipal wastewater treatment plants (MWWTPs) are both sinks and sources of per- and polyfluoroalkyl substances (PFAS) due to limited removal efficiency in current treatment systems. However, the role of treatment processes, especially disinfection, in altering PFAS and microbial communities remains underexplored. In this study, we investigated the occurrence of 17 PFAS in two MWWTPs in Northwest China and characterized microbial communities through metagenomic sequencing. Results showed that total PFAS concentrations increased from 56.8 to 60.3 ng/L in MWWTPA and from 5.1 to 19.1 ng/L in MWWTPB, indicating ineffective removal. Perfluoropentanoic acid (PFPeA) and perfluorononanoic acid (PFNA) dominated the influent, accounting for 86.6% and 33.3% in MWWTPA and MWWTPB, respectively. In contrast, perfluorooctanesulfonic acid (PFOS, 46.8-52.4%) and perfluorooctanoic acid (PFOA, 5.1-8.9%) concentrations increased markedly in the effluent, becoming the predominant PFAS. Meanwhile, disinfection also altered microbial diversity and homogenized community structures between the two MWWTPs. Further analysis revealed strong associations (p < 0.01) between elevated PFAS levels and specific microbial taxa, including Actinomycetia and Thermoprotei, alongside increased relative abundance of genes annotated as haloacid dehalogenases, monooxygenases, and cytochrome P450. These associations may reflect potential influences on PFAS precursor dynamics. Overall, these findings highlight the importance of considering both chemical and microbial shifts when evaluating PFAS behavior during wastewater treatment.},
}

@article {pmid41875615,
year = {2026},
author = {Kesavan, D and Meenatchi, R and Mohanakrishna, R and Tripathi, A and B S, Y and Narayanane, S and Gupta, S and Yadav, P and Pasupuleti, M and Mani, G and Balachandran, KRS and Rangamaran, VR and Verma, P and Kumar, AG and Vinithkumar, NV and Gopal, D and Pazhani, GP and Arockiaraj, J},
title = {Metagenomic mining of microbial communication genes from Indian deep-sea sediments using a quorum sensing- and quenching-related protein database.},
journal = {Marine genomics},
volume = {86},
number = {},
pages = {101245},
doi = {10.1016/j.margen.2026.101245},
pmid = {41875615},
issn = {1876-7478},
abstract = {Cell-to-cell communication among microbes plays a key role in environmental adaptation and highly contributes to global biogeochemical cycling. However, microbial communication systems in deep-sea sediments, where diverse microbial communities employ quorum sensing (QS) and quorum quenching (QQ) mechanisms to regulate ecological interactions, remain largely understudied. Their distribution patterns and functional dynamics in deep-sea ecosystems are poorly understood. This study investigated QS and QQ communication systems alongside microbial community distribution in Arabian Sea sediments collected from depths of 334, 492, 550, and 992 m across the northern and southern Arabian Sea. Shotgun metagenomic sequencing was performed in conjunction with a curated QS- and QQ-related protein (QSP) database. Both individual assemblies and metagenome-assembled genomes (MAGs) were analyzed to comprehensively identify communication-associated proteins. In total, around 359 QSPs were detected across four sediment samples. Shallow sediments (334 and 492 m) exhibited greater abundance and diversity of QS and QQ elements, particularly acyl-homoserine lactone (AHL)-driven QS systems and acylase/lactonase-based QQ systems, indicating active microbial interactions. In contrast, deeper sediments (550 and 992 m) displayed reduced diversity of canonical QS elements with enrichment of autoinducer-2 (AI-2), diffusible signal factor (DSF), and cyclic-di-GMP signalling pathways, suggesting adaptive mechanisms conducive to oligotrophic and high-pressure conditions of deep-sea. Correlation analyses revealed potential intra- and inter-system associations among QS regulators and QQ enzymes, indicating complex regulatory networks. MAG-derived protein analyses detected conserved catalytic motifs, and molecular docking supported functional interactions with signal molecules. Overall, these findings provide a preliminary overview of QS and QQ related genes in deep sea sediments of the Arabian Sea and suggest potential variability in microbial communication systems within these environments.},
}

@article {pmid41875710,
year = {2026},
author = {Gadoin, E and Massot, M and Callens, M and Arnout, P and Bedhomme, S and Rajkovic, A},
title = {Shotgun metagenomic profiling reveals a high diversity of taxa and genes within biofilms formed on microplastics incubated in urbanised aquatic ecosystems.},
journal = {Marine pollution bulletin},
volume = {228},
number = {},
pages = {119569},
doi = {10.1016/j.marpolbul.2026.119569},
pmid = {41875710},
issn = {1879-3363},
abstract = {Microplastics (MPs) are ubiquitous in aquatic ecosystems, where they are colonized by microbial communities, called the plastisphere. Of great concern is the detection of potential pathogens and antimicrobial resistance genes (ARG) in the plastisphere, which might be transported across ecosystems through MPs drifting. We used shotgun metagenomic profiling to assess taxa diversity, ARG and virulence genes (VG), within biofilm formed on polypropylene (PP) particles incubated in situ in five locations, following an anthropic gradient around Ostend (Belgium). Our results demonstrated significant variability of the plastisphere across incubation sites, but not between PP and control glass beads. Potential pathogenic bacteria (PPB) represented about 7% of bacterial reads within biofilms and VG were mainly involved in nutrition and adherence. Using dqPCR results to normalize metagenomic reads, we demonstrated a selective enrichment of ARG and VG in biofilms, while these were less abundant but more diverse in surrounding water. These findings highlight the presence of PPB, ARG and VG across all sites, likely driven by anthropogenic pressures. Although no substrate-specific effect was detected, the ability of PP particles to act as microbial reservoirs, coupled with their high mobility, reinforces concerns about their potential role in the transport and dissemination of microbial hazards.},
}

@article {pmid41875745,
year = {2026},
author = {Zhang, H and Li, B and Ni, R and Ye, L and Bai, G and Zhao, J},
title = {Stable functional consortium assembly via uncoupled SAD/anammox inoculation drives synergistic nitrogen‑sulfur removal in sediment.},
journal = {Water research},
volume = {297},
number = {},
pages = {125768},
doi = {10.1016/j.watres.2026.125768},
pmid = {41875745},
issn = {1879-2448},
abstract = {The remediation of black‑odorous sediments remains challenging due to the intricate sediment matrix, the co-occurrence of multiple pollutants, and the difficulty in maintaining stable functional microbial consortia under fluctuating redox conditions. Although calcium nitrate (CN) is a used chemical oxidant, its sole application often results in incomplete nitrogen removal and risks of secondary pollution. While the integration of CN with sulfur-autotrophic denitrification (SAD) and anaerobic ammonia oxidation (anammox) presents a promising alternative, the microbial, especially concerning the assembly and efficacy of different microbial inoculation strategies, are poorly understood. This study systematically compared two distinct bioaugmentation approaches: the pre-coupled addition of a SAD and anammox consortium versus an uncoupled strategy involving separate additions of SAD and anammox consortium, both in combination with CN. Results demonstrated that the CN+S+A (uncoupled) treatment achieved optimal performance, enhancing the removal of NH4[+], NO3[-], and total nitrogen by 42%, 40%, and 35%, respectively, compared to CN alone, while also effective oxidizing acid‑volatile sulfide. Mechanistic analysis revealed that CN first optimized the sediment microenvironment. The uncoupled inoculation uniquely fostered a stable, dual-core microbial consortium dominated by Thiobacillus (3.00%) and Candidatus Brocadia (0.83%), which established a sustainable "sulfur-driven nitrogen removal" cycle. Metagenomic and isotopic tracing confirmed the enrichment of key functional genes and elevated process rates underpinning this synergy. These findings highlight that CN combined with uncoupled bioaugmentation is a novel and effective strategy for rebuilding stable nitrogen-sulfur cycles in black-odorous sediments.},
}

@article {pmid41875962,
year = {2026},
author = {Rector, A and Karatas, M and Bloemen, M and De Coninck, L and Swinnen, J and Close, L and Thijssen, M and Pourkarim, MR and Matthijnssens, J and Desmet, S and Van Ranst, M and Johnson, MC and Wollants, E},
title = {Airplane wastewater as a gateway for pathogen surveillance wastewater surveillance in airplane.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {},
number = {},
pages = {105930},
doi = {10.1016/j.meegid.2026.105930},
pmid = {41875962},
issn = {1567-7257},
abstract = {BACKGROUND: Air travel plays a key role in the global spread of many diseases, including COVID-19. Surveillance of international travelers is useful for the detection of emerging viruses and variants of concern, especially in a context of global relaxations in testing policy. We aimed to assess the feasibility of using wastewater surveillance from airplanes as a method for monitoring SARS-CoV-2 variants and other pathogens entering Belgium.

METHODS: From January to March 2023, in the wake of the COVID pandemic, 32 wastewater samples were collected at Brussels Airport from direct flights originating in Beijing, China. We applied various qPCR panels and sequencing methods, including hybrid-capture metagenomic sequencing (Twist Bioscience) targeting more than fifteen thousand strains of known human and animal viruses.

RESULTS: Nineteen out of 32 samples tested positive for SARS-CoV-2. Various other pathogens, including enterovirus/rhinovirus, adenovirus, norovirus, adenovirus 40/41, and multiple clinically relevant bacteria, were identified using respiratory and gastrointestinal qPCR panels. In 7 samples, SARS-CoV-2 variants could be determined, belonging to known lineages BA4/BA5, BA4.6/BF7, and XBB. Moreover, hybrid-capture approach allowed us to recover complete genomes of viruses from families Polyomaviridae, Papillomaviridae, Herpesviridae as well as Aichivirus A and Hepatitis B virus.

CONCLUSION: This pilot project demonstrates the feasibility of detecting SARS-CoV-2 and its variants in wastewater of commercial airplanes. This method offers a valuable means of obtaining information from regions with limited SARS-CoV-2 genomic surveillance data. Moreover, using a hybrid-capture approach, a broad range of viruses of concern can be detected. The implementation of this novel screening approach is promising for enhancing traveler-based surveillance.},
}

@article {pmid41876072,
year = {2026},
author = {Shen, Q and Xiong, JQ and Wang, Q and Yang, L and Shen, Z and Lei, Z and Ru, S},
title = {Cyanobacteria-driven morphology and adaptive microbial succession: Resilience mechanisms in algal-bacterial granular sludge under tripartite stress.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134481},
doi = {10.1016/j.biortech.2026.134481},
pmid = {41876072},
issn = {1873-2976},
abstract = {Algal-bacterial granular sludge (ABGS) is a promising wastewater treatment technology, yet its practical application is constrained by its unknown stability under realistic multi-stressor conditions. This work demonstrated that ABGS could withstand combined low temperature (< 15°C), carbon scarcity, and sulfamethoxazole (SMX) exposure (0-100-1000 μg/L) through the defense strategy that integrated morphological, microbial and metabolic adaptations. Metagenomics revealed a metabolic trade-off, characterized by the downregulation of energy-intensive pathways (e.g., oxidative phosphorylation and TCA cycle), and the upregulation of biosynthetic and stress-responsive pathways (e.g., glyoxylate shunt and amino sugar metabolism), redirecting carbon towards extracellular polymeric substances (EPS) production. This was synergized by the protective cyanobacterial surface barrier and reconfigured protein-rich EPS for SMX sequestration. Microbial community restructuring enhanced functional resilience, as exemplified by the shift from Nitrospira to Candidatus Nitrotoga, which sustained stable nitrification. This coordinated adaptation not only enabled the robust removal of COD (> 90%) and NH4[+]-N (> 97%), but also suppressed the proliferation of antibiotic resistance genes (ARGs) under 100 μg/L SMX stress. These findings position ABGS as self-engineering ecosystems that actively modulate microbial community assembly and metabolic networks to remove nutrients and mitigate the dissemination of ARGs.},
}

@article {pmid41876074,
year = {2026},
author = {Zhang, Y and Wu, J and Yue, C and Wang, X and Qu, Y and Zhang, X and Sun, Y and Liu, Z and Qu, J and Xu, X},
title = {Enhancing anaerobic digestion of agricultural waste via a stable Fe-Emodin-Biochar composite: Kinetic performance, energy recovery, and metabolic insights.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134463},
doi = {10.1016/j.biortech.2026.134463},
pmid = {41876074},
issn = {1873-2976},
abstract = {Anaerobic digestion (AD) efficiency is often constrained by energy transfer in interspecies electron transfer. To address this, a cost-effective electron mediator was engineered by immobilizing industrial-grade Emodin onto an Fe-biochar matrix via one-step hydrothermal synthesis. The optimal composite (Fe/Emodin molar ratio 1.5:1) achieved a 43.3 % increase in cumulative methane yield and shortened the lag phase by 38.1 %. According to biochemical tests, the composite reduced energy barriers on the breakdown of volatile fatty acids, as shown by a 2.2-fold rise in ATP levels and increased expression of Coenzyme F420. A community shift marked by the co-enrichment of Methanothrix and syntrophic bacteria was revealed by metagenomic analysis. A change from energetically constrained hydrogen transfer to pathways mediated by the composite was suggested by the abundance of Type IV pili genes and Cytochrome c genes, which suggested the possible activation of direct interspecies electron transfer (DIET). By utilizing low-cost precursors and overcoming the instability of free mediators, this study offers a scalable biotechnological method for agricultural residue valorization. Furthermore, this approach demonstrates economic viability and potential life-cycle sustainability.},
}

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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