@article {pmid41730992,
year = {2026},
author = {Escalante, C and Reyes, AM and Zhao, C and Balkcom, KS and Jacobson, AL and Strayer-Scherer, A and Martin, KM and Koebernick, J and Huseth, A and Kozieł, E and Small, I and Greene, JK and Otulak-Kozieł, K and Mulvaney, MJ and Price, PP and Briseño, RIA and Bag, S and Conner, K},
title = {Metatranscriptomics analysis reveals the cotton virome in the southern United States.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41730992},
issn = {2045-2322},
mesh = {*Gossypium/virology/genetics ; *Virome/genetics ; *Plant Viruses/genetics/classification ; High-Throughput Nucleotide Sequencing ; Genome, Viral ; Phylogeny ; Plant Diseases/virology ; *Transcriptome ; United States ; Metagenomics ; Gene Expression Profiling ; },
abstract = {High-throughput sequencing (HTS) has expanded our perspective on the distribution and diversity of plant viruses. Furthermore, improvements in HTS and decreasing sample costs have enabled the discovery of novel plant viruses in field-collected samples. This study examined the putative virome of cotton samples collected from fields across the southern United States. Leaf samples were collected, and total RNA was extracted. Library preparation was performed from pooled samples within locations before sequencing on an Illumina platform. Sequenced libraries were mapped to the cotton reference genome, and the resulting sequences were de novo assembled. A metatranscriptomics analysis revealed complete genome contigs of cotton leafroll dwarf virus in all tested samples. Additionally, 29 putative families of RNA and DNA plant viruses co-infecting cotton were found. Seven families of RNA viruses were more prevalent across all locations. These families included Botourmiaviridae, Hypoviridae, Mitoviridae, Narnaviridae, Partitiviridae, Solemoviridae, and Totiviridae. The information obtained in this investigation will help develop a broader perspective on cotton virus diversity and whether co-infections of viruses can influence (negatively or positively) plant physiology, product quality, and yield.},
}

*Gossypium/virology/genetics
*Virome/genetics
*Plant Viruses/genetics/classification
High-Throughput Nucleotide Sequencing
Genome, Viral
Phylogeny
Plant Diseases/virology
*Transcriptome
United States
Metagenomics
Gene Expression Profiling

@article {pmid41761093,
year = {2026},
author = {Qureshi, A and Wahid, A and Qazi, S and Shahzad, MK and Kiani, HM and Asif, MDA},
title = {DynaBiome: interpretable unsupervised learning of gut microbiome dysbiosis via temporal deep models.},
journal = {BMC bioinformatics},
volume = {27},
number = {1},
pages = {},
pmid = {41761093},
issn = {1471-2105},
abstract = {PURPOSE: Gut microbiome dysbiosis is a critical determinant for autologous fecal microbiota transplantation (Auto-FMT) eligibility, yet current classification approaches rely predominantly on supervised learning with manually annotated sequencing labels, which are often scarce. This study proposes DynaBiome, a framework designed to predict gut dysbiosis by leveraging unsupervised learning and clinical phenotypic proxies as a scalable alternative to ground-truth genomic labeling.

METHODS: Our framework employs an LSTM autoencoder architecture to capture temporal microbiome dynamics within 14-day windows. The model reconstructs normal microbiome patterns, where high reconstruction errors signal potential dysbiosis. To ensure rigorous evaluation and prevent data leakage, the dataset was partitioned via a strict patient-level split. Unsupervised anomaly signals were refined via phenotypic proxy labels (e.g., fever, neutropenia) via weak supervision, and ensemble learning methods were applied to optimize classification performance.

RESULTS: The initial LSTM autoencoder successfully flagged dysbiotic sequences but required refinement to reduce false positives. Ensemble learning significantly enhanced predictive accuracy. The stacked ensemble (with Logistic Regression meta-learner) demonstrated optimal performance with an ROC AUC of 0.8908 and a Weighted F1-score of 0.7909. This approach significantly outperformed the standard One-Class SVM baseline (ROC AUC 0.6033), confirming the superiority of deep temporal modeling over static anomaly detection. Critically, the model achieved performance levels comparable to fully supervised baselines, confirming the efficacy of the proxy-label framework.

CONCLUSION: Integrating unsupervised temporal feature extraction with stacked ensemble methods provides a viable framework for dysbiosis prediction. These results demonstrate that leveraging phenotypic via weak supervision can effectively approximate supervised baselines, thereby reducing the reliance on comprehensive metagenomic annotations for longitudinal patient monitoring.},
}

@article {pmid41895431,
year = {2026},
author = {Ceruti, A and Bisia, M and Balatsos, G and Kobialka, RM and Zamil, MF and Hasan, A and Truyen, U and Lucati, F and Sanpera-Calbet, I and Palmer, JRB and Alam, MS and Michaelakis, A and Wahed, AAE},
title = {MosquitoID: Rapid metagenomic sequencing for offline mosquito surveillance.},
journal = {Acta tropica},
volume = {},
number = {},
pages = {108071},
doi = {10.1016/j.actatropica.2026.108071},
pmid = {41895431},
issn = {1873-6254},
abstract = {Mosquitoes transmit numerous infectious diseases, with climate change expanding their global distribution through warmer environments. Next-generation sequencing offers significant advantages for mosquito genomic surveillance and potential early warning systems. In this study, a portable metagenomic sequencing approach using Oxford Nanopore Technologies (ONT) for field-based mosquito analysis (MosquitoID protocol) was developed, enabling species and host feeding patterns identification, and pathogen detection all coming from a single amplification-free workflow. DNA was extracted from 62 mosquito samples (Aedes albopictus, Aedes cretinus, Culex pipiens, Culiseta longiareolata) from Greece and Spain, either single-species pools (1-19 specimens),mixed-species pools, wirth reverse purification method or archived samples. Additionally, 30 pooled Aedes aegypti samples from Bangladesh underwent cDNA reverse purification. All samples were sequenced using ONT rapid barcoding kits. Offline bioinformatics analysis via Geneious screened custom BLAST databases for species, host, and virus identification. MosquitoID accurately identified mosquito species in 89% of samples overall, with main discrepancies in Aedes cretinus. Virus screening detected Phasi Charoen-like virus in cDNA samples. Host DNA sequences identified multiple species including horses, cattle, and ducks. This study demonstrates metagenomic ONT sequencing's effectiveness for rapid host, species, and virus identification. After further benchmarking, the approach shows potential for real-time disease monitoring and enhanced surveillance systems. Integrating portable next-generation sequencing with offline bioinformatics tools could significantly strengthen mosquito-borne disease prevention strategies, particularly for non-bioinformaticians and in resource-limited settings.},
}

@article {pmid41895455,
year = {2026},
author = {Yin, W and Li, Y and Pan, A and Wu, J and Su, X and Xiao, X and Dong, F and Xu, L and Chen, C and Fu, H and Sun, F},
title = {Synergistic inhibition and microbial adaptation in anammox systems under long-term salinity and fulvic acid stress.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134498},
doi = {10.1016/j.biortech.2026.134498},
pmid = {41895455},
issn = {1873-2976},
abstract = {Salinity and fulvic acid frequently coexist in high-strength wastewater, yet their combined effects on anaerobic ammonium oxidation (anammox) remain unclear. This study evaluated their impacts on reactor performance, microbial community structure, and functional genes. Moderate salinity (5-10 g L[-1] NaCl) slightly enhanced anammox activity, whereas higher salinity (15 g L[-1]) and fulvic acid (> 60 mg L[-1]) significantly inhibited nitrogen removal. Under such combined stress, specific anammox activity decreased by about 40%, indicating a synergistic inhibition. Extracellular polymeric substances increased by 198%, suggesting a microbial stress-response strategy. Microbial community analysis showed a decline in Planctomycetes by 11%, and enrichment of Proteobacteria by 7% and Chloroflexi by 4%. Metagenomic results revealed suppression of key anammox genes and enrichment of denitrification genes, with quorum sensing and polysaccharide biosynthesis genes increased, suggesting EPS-mediated adaptation under combined stress. These findings provide insights for improving anammox stability in saline and humic-rich wastewater treatment systems.},
}

@article {pmid41895928,
year = {2026},
author = {Movsesijan, T and Alcañiz, AJ and Roch, FF and Chaughtai, MS and Dzieciol, M and Stessl, B and Thalguter, S and Strachan, CR and Raindl, M and Wagner, M and Selberherr, E and Quijada, NM},
title = {Biofilm capacity of the psychrophilic bacteria triggers their persistence in the equipment and their spread to beef products throughout processing.},
journal = {Food research international (Ottawa, Ont.)},
volume = {232},
number = {},
pages = {118808},
doi = {10.1016/j.foodres.2026.118808},
pmid = {41895928},
issn = {1873-7145},
mesh = {*Biofilms/growth & development ; Animals ; Cattle ; *Red Meat/microbiology ; *Food Handling/instrumentation ; *Food Microbiology ; *Psychrobacter/genetics/isolation & purification/physiology ; *Equipment Contamination ; Pseudomonas/genetics/isolation & purification/physiology ; Abattoirs ; *Food Contamination/analysis ; *Meat Products/microbiology ; },
abstract = {Microbial contamination in food processing remains a persistent and complex challenge. Understanding the sources, contributing factors, and control measures is essential for effective mitigation. In this study we employed a combination of metagenomic sequencing, targeted culturomics, and whole-genome sequencing of key isolates to gain a comprehensive view of bacterial dynamics and functional capabilities throughout a working shift in a beef slaughter and cutting facility. This allowed us to identify which bacteria are i) most prevalent in the clean facility before the start of the work, ii) able to establish themselves over time, and iii) detectable in the final product. We further generated a functional profile of the microbial community within the facility, with a particular focus on antimicrobial resistance and biofilm formation genes, and the presence of specific pathogens and spoilage organisms. Both culture-based and sequencing data showed that Psychrobacter and Pseudomonas strains present in the final product were also detected on the membrane skinner, a machine used to remove all the excess tissues from meat, and in the drains even after cleaning. We found a high number of genes involved in biofilm formation in Psychrobacter immobilis, a characteristic that may explain their biofilm capacity and the survival of this species during the cleaning process and persistence throughout the facility. Taken together, our findings suggest potential sources of contamination and highlight the advantages of integrating culture-dependent methods with high-throughput sequencing technologies to enhance microbial monitoring and control strategies in food production environments.},
}

*Biofilms/growth & development
Animals
Cattle
*Red Meat/microbiology
*Food Handling/instrumentation
*Food Microbiology
*Psychrobacter/genetics/isolation & purification/physiology
*Equipment Contamination
Pseudomonas/genetics/isolation & purification/physiology
Abattoirs
*Food Contamination/analysis
*Meat Products/microbiology

@article {pmid41895935,
year = {2026},
author = {Li, H and Hu, H and Lu, W and Liu, J and Peng, Q and Wang, S and Dan, T},
title = {Metagenomic analysis of lactic acid bacteria communities in inner Mongolian fermented dairy products: influence of milk source and geography.},
journal = {Food research international (Ottawa, Ont.)},
volume = {232},
number = {},
pages = {118849},
doi = {10.1016/j.foodres.2026.118849},
pmid = {41895935},
issn = {1873-7145},
mesh = {Animals ; *Cultured Milk Products/microbiology ; China ; *Metagenomics/methods ; *Lactobacillales/genetics/classification/isolation & purification ; Cattle ; *Milk/microbiology ; *Food Microbiology ; Fermentation ; Geography ; Horses ; },
abstract = {Inner Mongolia, a key grassland region in China, has a long-standing tradition of fermented dairy products. This study aimed to elucidate the influence of milk source and geographical origin on the community structure and functional characteristics of lactic acid bacteria (LAB) in fermented milk. Twenty-four fermented milk samples from four regions were subjected to metagenomic sequencing analysis including α/β-diversity assessment, taxonomic classification, and functional annotation. The milk source and geographical region jointly shaped the diversity of LAB. The LAB community structure in fermented mare milk displayed more pronounced geographical differentiation than that in fermented cow milk. The core dominant LAB species included Lactobacillus kefiranofaciens, Lactobacillus helveticus, and Lactococcus lactis, with L. helveticus being more abundant in fermented mare milk. The functional profiles of LAB varied depending on the milk source used. The data indicated that milk source was a primary factor associated with the core LAB composition, while geographical origin was associated with the modulation of community diversity and functional attributes. These findings provide region-specific insights into the microbial ecology of traditional Inner Mongolian fermented dairy products.},
}

Animals
*Cultured Milk Products/microbiology
China
*Metagenomics/methods
*Lactobacillales/genetics/classification/isolation & purification
Cattle
*Milk/microbiology
*Food Microbiology
Fermentation
Geography
Horses

@article {pmid41895941,
year = {2026},
author = {Zhang, J and Li, Y and Zhao, X and Wang, Q and Li, J and Xia, Y and Jambal, T and Dorjgotov, D and Zha, M and Chen, Y},
title = {The cheese of Xilingol: A comparative study on microbial diversity and metabolic profiles across typical and meadow steppes.},
journal = {Food research international (Ottawa, Ont.)},
volume = {232},
number = {},
pages = {118860},
doi = {10.1016/j.foodres.2026.118860},
pmid = {41895941},
issn = {1873-7145},
mesh = {*Cheese/microbiology/analysis ; Milk/microbiology ; *Food Microbiology ; Animals ; Moraxella/isolation & purification/metabolism ; Lactococcus lactis/isolation & purification/metabolism ; *Microbiota ; *Metabolome ; Amino Acids/analysis ; China ; },
abstract = {Xilingol cheese (hurood), a traditional product of Inner Mongolia, acquires its superior flavor and quality from region-specific microbial communities. Understanding the microorganisms and metabolites of hurood across different grassland ecosystems is crucial. This study collected milk and hurood samples from typical and meadow steppes. A total of 179 species were identified, with Moraxella osloensis being more abundant in milk and Lactococcus lactis dominant in hurood. Additionally, 26 differential metabolites were screened from different grasslands, with 19 metabolites found in higher concentrations in hurood, such as N-lactoyl-phenylalanine and N-Acetyl-L-Histidine. These differential metabolites are mainly involved in lipid, carbohydrate, amino acid, and energy metabolism. Spearman correlation analysis revealed that L. lactis was significantly and positively correlated with differential metabolites such as O-phospho-l-serine and gluconic acid, which may affect hurood quality through carbohydrate and protein metabolism, especially amino acid metabolism. M. osloensis was positively correlated with metabolites such as 2-Methylhippuric acid and γ-Glu-Cys. Samples from typical steppe showed a richer microbial diversity, while samples from meadow steppe exhibited a higher enrichment of beneficial microorganisms and metabolites. Superior milk quality and the environmental conditions for lactic acid bacteria colonization may both promote the formation of superior flavor characteristics and functional components. This observational study offers valuable insights into the microbial and metabolic characteristics of hurood, thereby supporting efforts to improve hurood quality.},
}

*Cheese/microbiology/analysis
Milk/microbiology
*Food Microbiology
Animals
Moraxella/isolation & purification/metabolism
Lactococcus lactis/isolation & purification/metabolism
*Microbiota
*Metabolome
Amino Acids/analysis
China

@article {pmid41895971,
year = {2026},
author = {Silva, FA and Cabral, L and de Assis, BBT and Ferreira, DP and Egea, MB and Pimentel, TC and Magnani, M},
title = {Microbiota of foods: a comprehensive review of diversity and potential implications.},
journal = {Food research international (Ottawa, Ont.)},
volume = {232},
number = {},
pages = {118899},
doi = {10.1016/j.foodres.2026.118899},
pmid = {41895971},
issn = {1873-7145},
mesh = {*Food Microbiology ; *Fermented Foods/microbiology ; *Microbiota ; Fermentation ; Metagenomics ; Humans ; Metabolomics ; Bacteria/classification/genetics ; RNA, Ribosomal, 16S/genetics ; Biodiversity ; },
abstract = {Microbial communities play a central role in food ecosystems. Fermented foods, in particular, host complex and dynamic microbiomes that are shaped by raw materials, fermentation substrates, processing environments, and regional production practices. This review provides an in-depth analysis of microbial diversity in various spontaneously fermented food products, including beverages, dairy products, and ethnic and other traditional food products. It highlights how microbial composition evolves throughout fermentation and how specific microorganisms contribute to the safety and sensory profiles of the final products. The field has undergone a methodological transformation, moving from classical culture-based methods to advanced omics technologies. Culture-independent approaches such as metataxonomics, metagenomics, metatranscriptomics, metaproteomics, and metabolomics enable a more comprehensive characterization of microbial communities, providing insights not only into their taxonomic composition but also into their functional roles. Despite increasing interest in metagenomics and metatranscriptomics, metataxonomic high-throughput sequencing, particularly 16S rRNA and ITS gene analyses, remains the most widely used technique due to its lower cost and accessibility. However, it provides limited resolution at the species level and cannot distinguish between live and dead cells. Microbiome characterization using omics has practical implications for the food industry, including the identification of microbial signatures in artisanal foods and the improvement of understanding fermentation processes. Our manuscript emphasizes a broad comparative overview of microbial diversity across multiple categories of fermented foods and integrates this with a methodological perspective on omics approaches used to characterize these communities. Findings outline the main methodological approaches, sequencing platforms, primer sets, and bioinformatic tools used in studies, as well as the current limitations and future directions in the field. Integrative multi-omics strategies are expected to significantly enhance food safety, quality, traceability, and functionality across diverse food systems.},
}

*Food Microbiology
*Fermented Foods/microbiology
*Microbiota
Fermentation
Metagenomics
Humans
Metabolomics
Bacteria/classification/genetics
RNA, Ribosomal, 16S/genetics
Biodiversity

@article {pmid41896456,
year = {2026},
author = {Habot-Wilner, Z and Ostrovsky, M and Zur, D and Schwartz, S and Hagin, D and Gadoth, A and Ben-Ami, R and Paran, Y and Goldshmidt, H and Slutzkin, M and Adler, A and Levytskyi, K},
title = {Response to: 'Comment on 'Metagenomic next-generation sequencing: a game changer in the diagnosis of unique intraocular infections''.},
journal = {Eye (London, England)},
volume = {},
number = {},
pages = {},
pmid = {41896456},
issn = {1476-5454},
}

@article {pmid41896477,
year = {2026},
author = {Shaw, J and Marin, MG and Li, H},
title = {High-resolution metagenome assembly for modern long reads with myloasm.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {41896477},
issn = {1546-1696},
support = {R01HG010040//U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI)/ ; PDF-587396//Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada (NSERC Canadian Network for Research and Innovation in Machining Technology)/ ; },
abstract = {Long-read metagenome assembly promises complete genomic recovery from microbiomes. However, the complexity of metagenomes poses challenges. Here we present myloasm, a metagenome assembler for modern long reads such as PacBio HiFi and Oxford Nanopore Technologies (ONT) R10.4 long reads. Myloasm uses polymorphic k-mers to construct a high-resolution string graph and then leverages differential abundance for graph simplification. On real-world ONT metagenomes, myloasm assembled three times more complete circular contigs than the next-best assembler. Myloasm can make ONT and HiFi assemblies comparable. For example, on a jointly sequenced gut metagenome, myloasm with ONT assembled more complete circular genomes than any assembler with HiFi. Myloasm also recovers previously inaccessible within-species diversity. Here, we recovered six complete Prevotella copri single-contig genomes from a gut metagenome and eight complete TM7 (Saccharibacteria) contigs with >93% similarity from an oral metagenome. Overall, we show that myloasm outperforms existing long-read metagenome assemblers across a range of environments and modern sequencing technologies.},
}

@article {pmid41896490,
year = {2026},
author = {Zheng, M and Yang, X and Tian, R and Xia, X and Xu, Q and Hui, Y and Chen, S and Liu, Y and Wang, A},
title = {A Segatella Copri-centered Gut Microbiota-mediated Metabolic Dysregulation Associated with Transition from Asymptomatic to Symptomatic Intracranial Atherosclerosis.},
journal = {Translational stroke research},
volume = {17},
number = {2},
pages = {},
pmid = {41896490},
issn = {1868-601X},
support = {82504498//National Natural Science Foundation of China/ ; 82473699//National Natural Science Foundation of China/ ; 2022YFC3600600//National Key Research and Development Program of China/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; Middle Aged ; *Intracranial Arteriosclerosis/metabolism/microbiology ; Case-Control Studies ; Aged ; Biomarkers/blood ; Metabolomics ; *Ischemic Stroke/metabolism/microbiology ; },
abstract = {The mechanisms underlying the continuum from asymptomatic intracranial atherosclerotic stenosis (aICAS) to symptomatic intracranial large-artery atherosclerotic ischemic stroke (iLAA-IS) remain unclear. We investigated the gut microbiota-metabolite axis in this transition to identify predictive biomarkers and clarify key functional pathways. In a case-control study (63 iLAA-IS cases; 56 aICAS controls), fecal shotgun metagenomics and untargeted plasma metabolomics were profiled. Using machine learning with 10-fold nested cross-validation, we identified five robust biomarkers associated with the transition: Alistipes putredinis (risk-associated) and four protective features (Segatella copri, Gln-Gly, Methionine Sulfoxide, and N6-Acetyl-L-Lysine). Integrated models incorporating these markers significantly improved predictive performance relative to conventional risk factors (e.g., mean AUC of Gln-Gly: 0.9104 vs. 0.7188). Mechanistic analyses revealed a Segatella copri-centered metabolic dysregulation: its depletion coincided with a broad loss of anabolic pathways (BCAA biosynthesis, folate-SAM-methionine metabolism, and tRNA charging), which were positively linked to amino acid-related metabolites. In contrast, the pathways of Alistipes putredinis showed no such coupling. These findings suggest that the aICAS-to-iLAA-IS transition is characterized by chronic metabolic dysregulation, involving a Segatella copri-centered microbiota-metabolite axis. This multi-omic signature offers novel insights into stroke pathogenesis and potential targets for prevention.},
}

Humans
*Gastrointestinal Microbiome/physiology
Male
Female
Middle Aged
*Intracranial Arteriosclerosis/metabolism/microbiology
Case-Control Studies
Aged
Biomarkers/blood
Metabolomics
*Ischemic Stroke/metabolism/microbiology

@article {pmid41896556,
year = {2026},
author = {Walsh, LH and Soni, V and Ancla, J and Somerville, V and Segata, N and Joyce, S and Sinderen, DV and Mahony, J and Shkoporov, AN and Kenny, JG and Cotter, PD and O'Sullivan, O},
title = {Mining of food metagenomes reveals an unexplored diversity of dsDNA bacteriophages.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00941-9},
pmid = {41896556},
issn = {2055-5008},
support = {DOMINO-101060218//European Union's Horizon Europe programme/ ; },
abstract = {Bacteriophages are key drivers of microbial ecology, co-existing and co-evolving with bacteria across diverse environments. Limitations in culturing, alongside advances in sequencing and bioinformatics, have driven the use of metagenomics to explore viral diversity. Viral-specific analysis of >3000 food metagenomes from cFMD produced the FVGC, comprising ~3400 metagenome-assembled viruses, most of which belong to novel Caudoviricetes lineages (n = 91), with only ~15% represented in IMG/VR v4. Together, these findings reveal extensive uncharacterized viral diversity in food systems. Beyond serving as a reference, the FVGC facilitates detailed investigation of virus-host interactions. Viral sequences were pervasive across microbial genomes, with several bacterial families exhibiting near-universal associations with viral elements. Bacterial antiviral defence systems were abundant and taxonomically diverse, dominated by restriction-modification systems, while CRISPR-Cas systems showed pronounced lineage-specific distributions; in contrast, viral anti-defence genes were detected at low frequency (<10% of MAVs). Host prediction linked MAVs to clinically relevant taxa, including expanded ESKAPE pathogens such as Klebsiella pneumoniae, Acinetobacter baumannii, Staphylococcus aureus, and Enterobacter spp., highlighting the ecological connectivity between food-associated viruses and clinically important bacteria. Antimicrobial resistance signals were scarce, suggesting minimal phage-mediated AMR dissemination in food environments. This new publicly available viral database represents a valuable resource for further exploration of viral diversity.},
}

@article {pmid41896639,
year = {2026},
author = {Puetz, LC and O Delmont, T and Mitchell, AL and Finn, RD and Zhang, G and Shepeleva, DV and Kharlamova, AV and Kukekova, AV and Trut, LN and Gilbert, MTP},
title = {Gut microbiome community structure correlates with different behavioral phenotypes in the Belyaev Farm-Fox Experiment.},
journal = {Communications biology},
volume = {9},
number = {1},
pages = {},
pmid = {41896639},
issn = {2399-3642},
support = {NIH R35 GM144276//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; RSF-21-44-04405//Russian Science Foundation (RSF)/ ; DNRF143 Center for Evolutionary Hologenomics//Danmarks Grundforskningsfond (Danish National Research Foundation)/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Behavior, Animal ; *Foxes/microbiology/physiology ; Phenotype ; Domestication ; Male ; },
abstract = {Domestication represents one of the largest biological shifts of life on Earth, and for many animal species, behavioral selection is thought to facilitate early stages of the process. The gut microbiome of animals can respond to environmental changes and have diverse and powerful effects on host behavior. As such, we hypothesize that selection for tame behavior during early domestication, may have indirectly selected on certain gut microbiota that contribute to the behavioral plasticity necessary to adapt to the new social environment. Here, we explore the gut microbiome of foxes from the tame and aggressive strains of the "Russian-Farm-Fox-Experiment". Microbiota profiles reveal a significant depletion of bacteria in the tame fox population that have been associated with aggressive and fear-related behaviors in other mammals. Our metagenomic survey allows for the reconstruction of microbial pathways enriched in the gut of tame foxes, such as glutamate degradation, which converge with host genetic and physiological signals, revealing a potential role of functional host-microbiota interactions that could influence behaviors associated with domestication. Overall, by characterizing how compositional and functional potential of the gut microbiota and host behaviors co-vary during early animal domestication, we provide further insight into our mechanistic understanding of this adaptive, eco-evolutionary process.},
}

Animals
*Gastrointestinal Microbiome
*Behavior, Animal
*Foxes/microbiology/physiology
Phenotype
Domestication
Male

@article {pmid41896653,
year = {2026},
author = {Zhao, Z and Yang, Y and Zhang, L and He, X and Ding, K and Chen, Y and Huo, Y and Li, P and Li, R and Ali, T and Zhao, D and Choe, H and Ma, J and Shang, D and Zhang, L},
title = {Multi-omics and network pharmacology reveal the mechanisms of Scutellaria barbata D.Don and Scleromitrion diffusum (Willd.) R.J.Wang against pancreatic cancer.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-45676-x},
pmid = {41896653},
issn = {2045-2322},
support = {2022-BS-244//Liaoning Provincial Doctoral Research Startup Fund Project/ ; XLYC1907113//Liaoning Revitalization Talents Program/ ; 2022RJ19//Distinguished Young Scholars in Dalian/ ; },
abstract = {Pancreatic cancer (PC) is a common gastrointestinal malignancy whose initiation and progression may be closely linked to the gut microbiota. Previous research indicates that Scutellaria barbata D. Don and Scleromitrion diffusum (Willd.) R.J. Wang (SB-SD) exhibit diverse biological activities, such as anti-inflammatory, antioxidant, and antitumor effects, though their precise regulatory mechanisms are not fully elucidated. Here, we treated PC cells with SB-SD to assess its impact on cell viability, apoptosis, migration, and cell cycle progression, while Western blotting analyzed the expression of HSP90AA1, MAPK3, p53, CDK1, and p21. We also established a pancreatic cancer xenograft model in nude mice to evaluate the in vivo inhibitory effect of SB-SD on tumor growth. Furthermore, we employed metagenomic sequencing, untargeted metabolomics, and quantitative proteomics to comprehensively profile changes in the gut microbiota, serum metabolites, and differentially expressed proteins, with Western blotting subsequently validating BCKDK, GATM and p53 expression. The results show that SB-SD significantly inhibited PC cell proliferation, promoted apoptosis, and induced S/G2 phase cell cycle arrest, potentially via modulation of the HSP90AA1/MAPK3 signaling pathway. Measurements of tumor volume and weight, complemented by histopathological analysis, confirmed that SB-SD effectively suppressed the growth of PANC-1 xenograft tumors. Integrated multi-omics analyses suggest that the antitumor effects of SB-SD may involve the modulation of key gut microbes like Bacteroides caccae and Lactobacillus, the promotion of choline metabolism, and the regulation of BCKDK and GATM. Together, these findings not only corroborate the direct antitumor activity of SB-SD against pancreatic cancer but also offer novel mechanistic insights by constructing a microbiota-metabolite-protein interaction network.},
}

@article {pmid41896698,
year = {2026},
author = {Jung, S and Militsi, E and Huck, O},
title = {Oral Microbiome in Systemic Autoimmune Diseases: A Systematic Review.},
journal = {Oral diseases},
volume = {},
number = {},
pages = {},
doi = {10.1111/odi.70215},
pmid = {41896698},
issn = {1601-0825},
abstract = {OBJECTIVE: The oral cavity represents a key but underexplored interface between host immunity and microbial communities. The aim of this systematic review was to synthesize current literature on oral microbiota alterations in systemic autoimmune diseases.

METHODS: PubMed and Web of Science databases were searched for human studies published between January 2000 and April 2025. Eligible observational studies compared adults with diagnoses of systemic autoimmune diseases to controls and characterized oral microbiota diversity and/or composition using sequencing-based methods. Different oral habitats were analyzed (saliva, dental plaque, oral mucosa, gingival crevicular fluid).

RESULTS: 42 studies met inclusion criteria: 19 on rheumatoid arthritis, 18 on primary Sjögren's syndrome, 5 on systemic lupus erythematosus, and 1 on anti-neutrophil cytoplasmic autoantibody-associated vasculitis. 16S rRNA gene sequencing predominated and only 3 studies used shotgun metagenomics, among which one also profiled the oral virome. Across systemic autoimmune diseases, dysbiosis was characterized by enrichment of anaerobic genera (Prevotella, Veillonella) and depletion of commensals (Neisseria, Haemophilus), with distinct β-diversity separation from controls. Periodontal disease and reduced salivary secretion significantly modulated microbial communities but did not fully explain disease-associated alterations.

CONCLUSION: The oral microbiome exhibited shared dysbiotic signatures. However, methodological and clinical heterogeneity limited direct comparison between studies.},
}

@article {pmid41897379,
year = {2026},
author = {Zhang, Y and Zhao, B and Li, J and Yuan, T and Liu, Y and Sun, Z},
title = {Effects and Adaptive Responses of Sulfate-Reducing Biochemical System to Acid Stress.},
journal = {Biomolecules},
volume = {16},
number = {3},
pages = {},
doi = {10.3390/biom16030444},
pmid = {41897379},
issn = {2218-273X},
support = {41772266//State Key Laboratory of Nuclear Resources and Environment, the National Natural Science Foundation of China/ ; },
mesh = {*Sulfates/metabolism ; Hydrogen-Ion Concentration ; *Desulfovibrio/metabolism/genetics ; Oxidation-Reduction ; *Adaptation, Physiological ; *Stress, Physiological ; Acids ; },
abstract = {A decrease in pH can affect the biochemical properties of a sulfate reduction system, but the stress responses to such pH fluctuations and acid-adaptive mechanisms of the microorganisms remain incompletely understood. Here, we compared the sulfate (SO4[2-]) reduction performance of a sulfate-reducing consortium (SRB system) and a pure Desulfovibrio sp. system (Des. system, control) under pH 7.0, 5.5, and 5.0 via batch experiments. A key novelty is the integration of microbial physiology and metagenomics to reveal adaptive mechanisms: the Des. system showed significant inhibition of growth and sulfate reduction with decreasing pH, while the SRB system maintained superior SO4[2-] removal efficiency through three synergistic adjustments: (1) physiological regulation (enhanced H[+]-ATPase activity, stress protein production, and cell membrane cyclopropane fatty acid content); (2) microbial community restructuring (enrichment of acid-resistant Bacillus and Clostridium); and (3) functional gene upregulation (sulfate import, dissimilar sulfate reduction, sulfide oxidation, and SOx system-related genes, p < 0.05). This study links physiological responses to metagenomic functional shifts under acid stress, providing critical theoretical support for applying sulfate-reducing consortia in acidic sulfate-containing wastewater remediation.},
}

*Sulfates/metabolism
Hydrogen-Ion Concentration
*Desulfovibrio/metabolism/genetics
Oxidation-Reduction
*Adaptation, Physiological
*Stress, Physiological
Acids

@article {pmid41897502,
year = {2026},
author = {Khan, A and Xiong, Z and Khan, IA and Cheng, X and Luo, Q and Jia, L and Liu, W and Huang, C and Chen, Z},
title = {Dimercaprol Reprograms Intestinal Redox Homeostasis and Organelle Crosstalk to Combat Iron-Induced Gut Dysbiosis Through NRF2/HO-1 Signaling.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {15},
number = {3},
pages = {},
doi = {10.3390/antiox15030356},
pmid = {41897502},
issn = {2076-3921},
support = {2024YFHZ0325//Zhengli Chen/ ; 32071161//Chao Huang/ ; 2023NSFC1929//Chao Huang/ ; },
abstract = {Gut disorders are largely caused by iron-induced microbial dysbiosis. Excess iron disrupts barrier integrity by inducing oxidative stress, leading to impaired cellular processes. The determination of therapeutic compounds that can reduce iron-induced damage and maintain gut cellular integrity is still a top objective. Dimercaprol (DP) represents a novel iron-chelating strategy for the treatment of iron-induced gut disorders. A chronic iron-overload model was established in mice via intragastric gavage of ferric citrate (FC) (286 mg/kg BW) for 16 weeks. Similarly, IPEC-J2 cells were exposed to FC (50 µmol/L) for 24 h. DP was used as a mechanistic probe to elucidate the pathways involved in iron-induced toxicity. Cells were transfected with or without NRF2 siRNA and exposed to DP post-FC. Colonic contents were assessed via metagenomics and metabolomics. Both in vivo and in vitro experiments were analyzed through a multifaceted analysis, Western blot, RT-qPCR, ELISA, transmission electron microscopy and immunofluorescence assays. Thiols in DP protect gut cells from damage by boosting their natural antioxidant defenses via the NRF2/HO-1 pathway. The DP mechanism of action is multifaceted, including enhancement of barrier integrity, protecting mitochondrial structure and function, suppression of inflammation and endoplasmic reticulum (ER) stress and restoration of gut microbial and metabolic homeostasis. These protective effects are mainly caused by the activation of the NRF2/HO-1 pathway, which makes DP a potential therapeutic agent for disorders caused by chronic gut injury induced by FC. DP provides strong protection against iron-induced gut damage by restoring organelle crosstalk, redox homeostasis and microbial-metabolic balance through NRF2/HO-1 signaling.},
}

@article {pmid41897791,
year = {2026},
author = {Xie, M and Xue, F and Sun, M and Zhuang, Q and Tang, S and Huang, Y and Zhang, Y and Hu, J and Zhou, Y},
title = {Determination of the Modulatory Effects of Selenium-Enriched Egg Powder on the Physiological Immune Response and Cecal Microbiota of Kunming Mice.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/foods15061069},
pmid = {41897791},
issn = {2304-8158},
support = {20252BAC240155//Natural Science Foundation Project of Jiangxi Province/ ; JX-202401//the Open research projects of key laboratories of the Jiangxi Province "Mechanism Research of the Regulation on Immune System by Selenium-enriched Eggs"/ ; },
abstract = {Se-enriched functional eggs are prevalent nowadays, which may help improve body health and anti-oxidant capacities. However, the modulatory effects on cecal microbiota are still limited. This study aims to investigate the underlying mechanism of Se-enriched egg powder in modulating the cecal microbiota of Kunming mice. A total of 72 mice were randomly assigned to a control treatment (CON), a conventional egg powder treatment (EP), and four gradient Se-enriched egg powder treatments (EPS1-EPS4, with the Se content ranging from 0.01 to 0.04% of total dietary content) for a 35-day feeding procedure. Parameters included growth performance, tissue Se content distribution, serum anti-oxidant capacities (GSH-Px, SOD, MDA), and immune cytokines (IgG, TNF-α), and cecal microbiota composition was further measured. Results showed dietary 0.02% (EPS2) significantly improved growth performance, physiological anti-oxidant defenses, and cytokine TNF-α (p < 0.05), while significantly reducing feed conversion ratio and malondialdehyde (MDA) compared with CON (p < 0.05). Metagenomic results revealed that Se-enriched egg powder significantly increased bacterial α-diversity and the abundance of Akkermansia, Bacteroides, and Bifidobacterium (p < 0.05), while significantly decreasing Desulfovibrio and Escherichia-Shigella (p < 0.05). In conclusion, dietary supplementation with Se-enriched egg powder effectively enhances growth performance, anti-oxidant capacity, and immunity, mainly through the promotion of beneficial bacteria diversity and suppression of pathogens.},
}

@article {pmid41897857,
year = {2026},
author = {Yang, Y and Wang, J and Wang, Z and Li, C and Hu, X and Liao, S and Wang, L},
title = {Airborne Microbiome of Tropical Ostrich Farms: Diversity, Antibiotic Resistance, and Biogeochemical Cycling Potential.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {6},
pages = {},
doi = {10.3390/ani16060880},
pmid = {41897857},
issn = {2076-2615},
support = {42367014//The National Natural Science Foundation of China/ ; },
abstract = {The expansion of tropical specialty livestock farming raises urgent concerns about airborne pathogen and antibiotic resistance dissemination. Ostrich farming, characterized by high-density stocking and feed exposure, yet their microbial ecology remain poorly characterized. This study analyzed 48 bioaerosols samples from an ostrich farm in Hainan, China, across dry and rainy seasons using 16S rRNA sequencing and metagenomics. The bacterial community were dominated by Firmicutes, Proteobacteria, and Actinobacteria, followed by Staphylococcus, Bacillus, and Acinetobacter as predominant genera, with particle size significantly shaping their structure. Large particles (>7.0 μm) carried higher species richness, while medium particles (2.1-3.3 μm) exhibited the highest diversity and evenness. Notably, small particles (0.65-1.1 μm), which can penetrate deep into the lungs, were enriched with Brevibacillus and Corynebacterium. Metagenomic analysis identified 638 antibiotic resistance genes (ARGs), dominated by efflux pump-associated determinants. The detection of clinically relevant ARGs (e.g., mcr-1 and blaTEM) reflects the genetic potential of the airborne resistome, rather than confirmed resistance phenotypes or active horizontal gene transfer. Functional analysis revealed a strong potential for organic matter degradation, driven by abundant carbohydrate-active enzymes (CAZymes) and their corresponding CAZyme genes, as well as a nitrogen cycle dominated by assimilation and reduction pathways, while genes for nitrogen fixation and nitrification were absent. Our findings demonstrate that ostrich farming enhanced airborne microbial diversity and functional potential, facilitating the ARG dissemination and nitrogen transformation. This study provides critical insights into the ecological and health risks of bioaerosols in tropical livestock farms, informing environmental monitoring and risk management strategies.},
}

@article {pmid41897913,
year = {2026},
author = {An, Q and Chen, S and Ma, S and Bai, R and Lu, Z and Liu, Y and Wang, F and Wang, Q and Song, Y and Zhang, G and Lyu, Y and Wang, L and Wang, Y and Xia, Z},
title = {Shotgun Metagenomics Reveals Gut Microbiome Remodeling with Altered Taxonomic Composition and Functional Potential in Diabetic Dogs.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {6},
pages = {},
doi = {10.3390/ani16060936},
pmid = {41897913},
issn = {2076-2615},
support = {1051-2225006//General Program of the 2025 Talent Fund, Veterinary Teaching Hospital, China Agricultural University/ ; },
abstract = {Gut microbiota dysbiosis is implicated in metabolic disorders, yet taxonomic and functional alterations in canine diabetes remain incompletely defined. Here, we performed shotgun metagenomic sequencing of fecal samples from 38 diabetic dogs and 37 healthy controls under controlled conditions (no recent antibiotic/probiotic exposure and stable commercial diets). Alpha-diversity indices did not differ between groups, whereas beta-diversity revealed significant separation of community structure at both genus and species levels (p < 0.05). Linear discriminant analysis effect size (LEfSe) identified enrichment of opportunistic-associated taxa in diabetic dogs, including Enterobacterales/Enterobacteriaceae (e.g., Escherichia coli, Klebsiella pneumoniae, Salmonella enterica) and Enterococcus faecalis. In contrast, healthy dogs were enriched for putatively beneficial taxa linked to bile acid and short-chain fatty acid (SCFA) metabolism, including Turicibacter spp. and Romboutsia spp. Functional profiling showed higher abundances of pathways related to carbohydrate/energy metabolism, membrane transport, and virulence/colonization in diabetic dogs; 17 KEGG level-3 pathways and 320 KOs differed at FDR < 0.05, with enriched modules including bacterial secretion systems, lipopolysaccharide biosynthesis, chemotaxis/flagellar assembly, and biofilm formation. Collectively, canine diabetes is associated with a remodeled gut microbiome characterized by expansion of opportunistic pathogens and elevated virulence and metabolic potential, supporting exploration of microbiota-targeted strategies as a complement to conventional management.},
}

@article {pmid41897927,
year = {2026},
author = {Fukuda, EP and Lu, Y and Fowler, E and Jessup, RW and Drewery, ML},
title = {Metagenomic Insights into the Effects of Dietary Thymol on the Structure and Function of the Rumen Microbial Community in Beef Steers Consuming Forage.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {6},
pages = {},
doi = {10.3390/ani16060950},
pmid = {41897927},
issn = {2076-2615},
support = {2021-77040-34881//National Institute of Food and Agriculture/ ; 2020-38422-32250//National Institute of Food and Agriculture/ ; N/a//Translational Health Research Center/ ; },
abstract = {While essential oils are gaining momentum as a strategy to modulate rumen function and potentially reduce enteric methane in cattle, little is known about how their bioactive components, terpenes, affect rumen microbes. Our objective was to evaluate how in vivo doses of thymol affect the structure and function of the rumen microbial community via whole genome shotgun sequencing (WGS). Four beef steers were used in a 4 × 4 Latin square with four 28 d periods. Steers consumed ad libitum forage and received one of four thymol doses (0 [CON], 120 [120-T], 240 [240-T], and 480 [480-T] mg/kg forage intake). Rumen contents were separated into liquid and solid fractions, DNA was extracted, analyzed via WGS, and assessed with orthogonal contrasts. After FDR correction, no taxa were affected by thymol; however, raw p-values demonstrated responses to thymol supplementation for solid-associated uncultured Lachnospiraceae bacterium (p = 0.04), uncultured Methanobrevibacter (p = 0.05), and uncultured Coriobacteriaceae bacterium (p = 0.02). Liquid-associated uncultured Prevotellaceae bacterium (p = 0.03), Prevotella sp. (p = 0.04), and Bacteroides sp. (p = 0.02) also responded to thymol, with the highest abundances observed at various thymol doses. Genes involved in energy production and amino acid metabolism transport were observed at the highest abundances at 240-T, while genes associated with cell cycle control, cell division, and chromosome partitioning were present in the highest abundances at 120-T. The findings suggest that thymol exerts dose-dependent effects on rumen microbial abundances and functional pathways, with 240 mg/kg forage intake appearing to be the most effective dose to downregulate methanogenic enzymes while also enhancing the enzymes associated with metabolism without negatively impacting microbial diversity.},
}

@article {pmid41898277,
year = {2026},
author = {Qiu, D and Suo, L and Wei, T and Lu, Z and Weng, Q and Xiao, J and Wang, X and Xu, Q and Wu, J},
title = {Mediation Role of Gut Microbiota in the Causal Relationship Between m6A Regulatory Genes and Metabolic Dysfunction-Associated Steatotic Liver Disease: A Mendelian Randomization Study.},
journal = {Biomedicines},
volume = {14},
number = {3},
pages = {},
doi = {10.3390/biomedicines14030630},
pmid = {41898277},
issn = {2227-9059},
support = {3502Z20227102//Qinyu Xu/ ; },
abstract = {Background: Metabolic dysfunction-associated steatotic liver disease (MASLD) is a globally prevalent condition with a complex pathogenesis. While both m6A RNA methylation regulators and gut microbiota have been independently implicated in MASLD, their potential causal interplay remains unexplored. This study aimed to investigate the causal relationships among m6A regulatory genes, gut microbiota, and MASLD, and to assess the mediating role of gut microbiota. Methods: We performed a two-sample Mendelian randomization (MR) analysis using publicly available genome-wide association study (GWAS) data. Genetic instruments for m6A regulators were derived from blood expression quantitative trait loci (eQTL) data. Gut microbiota and MASLD data were obtained from large-scale metagenomic and disease GWAS, respectively. The inverse-variance weighted method was the primary analysis, supplemented by sensitivity and mediation analyses to evaluate potential mediating pathways. Results: Genetically predicted levels of four m6A regulators showed significant causal associations with MASLD risk: ALKBH3 increased risk (OR = 1.17), whereas ALKBH5 (OR = 0.89), CBLL1 (OR = 0.76), and RBM15B (OR = 0.83) were protective. Nineteen gut microbial taxa were causally linked to MASLD. Among these, seven taxa were influenced by the four identified m6A genes. Although no mediation effects reached strict statistical significance, the pathway from ALKBH5 to MASLD via Parabacteroides abundance showed a suggestive indirect effect accounting for 21.9% of the total effect (p = 0.068). Given the limited statistical power of mediation analyses in MR settings, this observation should be interpreted with caution and requires validation in larger, well-powered studies. Conclusions: This MR study provides genetic evidence supporting causal roles of specific m6A regulators in MASLD and suggests that gut microbiota may partially mediate these relationships. The findings highlight a potential "m6A-gut microbiota-liver" axis in MASLD pathogenesis.},
}

@article {pmid41898335,
year = {2026},
author = {Schultheiss, HP and Escher, F and Aleshcheva, G and Wiegleb, G and Baumeier, C},
title = {Diagnostic and Therapeutic Options in Myocarditis and Inflammatory Cardiomyopathy.},
journal = {Biomedicines},
volume = {14},
number = {3},
pages = {},
doi = {10.3390/biomedicines14030691},
pmid = {41898335},
issn = {2227-9059},
support = {KK5175802AP2, KK5463501AP2, KK5463901AP2//Federal Ministry of Economic Affairs, Germany/ ; 10169096, 10169098, 10169028//ProFIT grant of the Investitionsbank Berlin/co-funded by EFRE/ ; },
abstract = {Myocarditis and inflammatory cardiomyopathy are inflammatory diseases of the heart muscle that can have both infectious and non-infectious causes. They can be caused by an unresolved viral infection or other infection, or they can be autoimmune, toxic, or allergic in nature. The specific identification of the pathogen and/or confirmation of inflammation can only be achieved through direct tissue analysis using endomyocardial biopsy (EMB), as neither detection of the virus nor assessment of the quality and intensity of the inflammation is possible using non-invasive methods. Accordingly, the removal and analysis of an EMB is considered the diagnostic gold standard in international guidelines and statements. The sudden onset of atypical angina pectoris and initially exertion-dependent dyspnea, as well as arrhythmias, pericardial effusion, and progressive symptoms of heart failure, indicate an acute inflammatory process of the myocardium. In addition, nonspecific symptoms such as fatigue and reduced physical performance may also occur. Diagnostic evaluation includes an electrocardiogram (ECG), cardiac imaging, and laboratory tests. The analysis of the EMB is crucial for a definitive diagnosis and thus for the initiation of an etiology-based, specific and personalized therapy. This includes histological and immunohistochemical inflammation diagnostics as well as molecular virological diagnostics. These enable both the detection of viruses and the assessment of transcriptional virus activity. New analyses using metagenomic next generation sequencing (NGS) techniques provide insights of enormous diagnostic and therapeutic relevance. This applies both to the spectrum of detectable pathogens and to the possibility of confirming transcriptional viral activity. In addition, gene expression profiling enables the differentiation of specific forms of myocardial inflammation (e.g., giant cell myocarditis, cardiac sarcoidosis, and eosinophilic myocarditis) and reduces the influence of "sampling errors" in focal inflammatory processes. The treatment of heart failure or ventricular arrhythmias is always symptomatic according to general evidence-based guidelines. In severe cases, mechanical circulatory support or even a heart transplant may be necessary. Patients with histologically confirmed myocardial inflammation or intramyocardial viral infection can be offered specific, causal, and personalized therapy. These patients can be successfully treated with immunosuppressive or antiviral therapy, which significantly improves the prognosis of the disease.},
}

@article {pmid41898386,
year = {2026},
author = {Tahtouh Zaatar, M and Othman, R and Abushawish, M and Akl, M and Alachkar, MT and Almatboona, G and Alriyami, F and Alshaibani, A and Ashkanani, D and Basharova, M and Imam, M and Khassay, N and Mikhael, MS and Naderi Far, R and Shaqra, S and Verwey, K and Suleimanova, A and Yousafzada, M and Burmagina, Y},
title = {The Women's Microbiome: Molecular Insights, Clinical Gaps, and Future Frontiers in Precision Health with Implications for Gulf Cooperation Council Populations.},
journal = {International journal of molecular sciences},
volume = {27},
number = {6},
pages = {},
doi = {10.3390/ijms27062521},
pmid = {41898386},
issn = {1422-0067},
mesh = {Humans ; Female ; *Microbiota ; *Women's Health ; *Precision Medicine ; Probiotics ; Pregnancy ; Vagina/microbiology ; Gastrointestinal Microbiome ; },
abstract = {The human microbiome has emerged as a central regulator of health and disease; however, women-specific microbiome research has only recently gained focused scientific attention. Accumulating evidence demonstrates that microbial ecosystems across the gut, vagina, skin, breast tissue, and reproductive tract are dynamically shaped by female hormones, life-stage transitions, and environmental exposures. These interactions influence immune regulation, metabolic homeostasis, reproductive outcomes, mental health, and cancer risk, in part through microbiome-mediated endocrine pathways such as the estrobolome. Advances in high-resolution molecular technologies-including metagenomics, metabolomics, spatial and single-cell profiling, and artificial intelligence-driven modeling-have shifted microbiome research from descriptive taxonomy toward functional, mechanistic, and predictive science. These approaches highlight microbial function and metabolite production as stronger determinants of health outcomes than taxonomic composition alone. Nonetheless, major gaps persist, including limited causal evidence, methodological heterogeneity, underrepresentation of non-Western populations, and barriers to clinical translation. Microbiome-targeted interventions, including probiotics, prebiotics, postbiotics, and emerging microbiota-based therapies, have garnered increasing interest in women's health. Select Lactobacillus and Bifidobacterium strains show potential in modulating vaginal and gastrointestinal health, pregnancy outcomes, and immune function; however, clinical effects remain highly strain-specific and context-dependent. Discrepancies between experimental findings, commercial claims, and validated clinical use underscore the need for rigorous, women-centered trials and standardized outcome measures. This narrative review synthesizes current molecular insights into the women's microbiome across endocrine interactions, pregnancy, reproductive and metabolic health, lifestyle influences, and microbiome-based therapeutic strategies. We integrate clinical perspectives to identify diagnostic and translational challenges and propose future directions emphasizing precision microbiome medicine, validated biomarkers, careful evaluation of microbiome-targeted interventions, and inclusive research frameworks, including populations from the Gulf Cooperation Council (GCC). Collectively, this review positions the microbiome as a critical yet underutilized axis in women's health and outlines a roadmap toward personalized, evidence-based care across the female lifespan.},
}

Humans
Female
*Microbiota
*Women's Health
*Precision Medicine
Probiotics
Pregnancy
Vagina/microbiology
Gastrointestinal Microbiome

@article {pmid41898595,
year = {2026},
author = {Makiel, K},
title = {Anti-Inflammatory Diets in Metabolic Syndrome and Obesity: Multi-Omics Perspectives on the Interplay Between Gut Microbiota, DNA Methylation, and Adipokine Regulation-A Narrative Review.},
journal = {International journal of molecular sciences},
volume = {27},
number = {6},
pages = {},
doi = {10.3390/ijms27062734},
pmid = {41898595},
issn = {1422-0067},
support = {//University of Physical Education, 31-571 Cracow, Poland/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Metabolic Syndrome/diet therapy/metabolism/genetics/microbiology ; *Obesity/diet therapy/metabolism/genetics/microbiology ; *Adipokines/metabolism/genetics ; *DNA Methylation ; *Diet ; Animals ; Inflammation ; Nutrigenomics ; Multiomics ; },
abstract = {An anti-inflammatory dietary pattern represents a key component of non-pharmacological management in obesity and metabolic syndrome (MetS), as it targets chronic low-grade inflammation, adipose tissue dysfunction, insulin resistance, and disturbances of the gut-metabolic axis. In the present work, we outline a framework for an "omics-based" approach that integrates data on gut microbiota composition and function (metagenomics), adipokine profiles, nutrigenomics, epigenetics, and related transcriptomic and metabolomic layers in order to enable more precise characterization of the metabolic phenotype and to support precision nutrition strategies. The proposed dietary model emphasizes the quality rather than merely the quantity of macronutrients, with particular focus on lipid profile optimization. Specifically, total fat intake is recommended to remain below 30% of total energy through the reduction in saturated fatty acids (SFA), trans fats, and excessive omega-6 fatty acids, alongside increased consumption of omega-3 PUFA (EPA/DHA) and plant-based sources of α-linolenic acid (ALA). Concurrently, greater intake of lean protein sources and low-glycemic-index carbohydrates rich in dietary fibre-particularly fermentable fractions-is recommended. The model also highlights the importance of polyphenols with antioxidant and immunomodulatory properties. To enhance feasibility and long-term adherence, recommendations are structured as flexible food substitutions rather than rigid prescriptions. Further well-designed interventional studies are required to confirm the impact of a multi-omics-based anti-inflammatory diet on both molecular and clinical endpoints.},
}

Humans
*Gastrointestinal Microbiome
*Metabolic Syndrome/diet therapy/metabolism/genetics/microbiology
*Obesity/diet therapy/metabolism/genetics/microbiology
*Adipokines/metabolism/genetics
*DNA Methylation
*Diet
Animals
Inflammation
Nutrigenomics
Multiomics

@article {pmid41898625,
year = {2026},
author = {Chaplin, AV and Podoprigora, IV and Shcherbakova, VA and Zakharzhevskaya, NB and Evseev, PV and Vasilyeva, AA and Koshkin, FA and Kardonsky, DA and Vorobyeva, EA and Kashatnikova, DA and Kazakova, VD and Efimov, BA},
title = {Parabacteroides vesiculifaciens sp. nov., a Novel Immunomodulatory, Vesicle-Producing Gut Commensal Isolated from the Human Gut.},
journal = {International journal of molecular sciences},
volume = {27},
number = {6},
pages = {},
doi = {10.3390/ijms27062763},
pmid = {41898625},
issn = {1422-0067},
support = {24-75-10100//Russian Science Foundation/ ; },
mesh = {Humans ; Phylogeny ; *Gastrointestinal Microbiome ; *Bacteroidetes/genetics/classification/isolation & purification ; Feces/microbiology ; Genome, Bacterial ; Animals ; HT29 Cells ; Extracellular Vesicles/metabolism ; Mice ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The genus Parabacteroides comprises widespread gastrointestinal commensals, known to produce immunomodulatory molecules and extracellular vesicles, yet its full diversity is incompletely cataloged. This study describes strain ASD2025[T], isolated from healthy child feces, using a polyphasic taxonomic approach including phenotypic profiling, chemotaxonomy, and comparative genomics. Cells were non-motile, polymorphic rods that produced extracellular vesicles. Phylogenomic analysis placed ASD2025[T] within the genus Parabacteroides within a species complex consisting of P. acidifaciens, P. hominis, "P. massiliensis", P. merdae, and P. johnsonii, with average nucleotide identities to the type strains of 85.5-89.9%. The large genome (5.16 Mbp, 46.2% GC content) contained integrative conjugative elements harboring antibiotic resistance genes and hankyphage-related prophage. The strain produced succinate as the major metabolic end product, and its major fatty acids were anteiso-C15:0, iso-C17:0 3-OH, and C15:0. Conditioned medium from ASD2025[T] antagonized the interleukin-8 response caused by E. coli lipopolysaccharide in HT29 cells. The majority of related metagenome-assembled genomes originate from mouse microbiomes. Based on these distinct characteristics, strain ASD2025[T] (=VKM B-3926[T] = JCM 37967[T]) represents a novel species of the genus Parabacteroides, for which the name Parabacteroides vesiculifaciens sp. nov. is proposed.},
}

Humans
Phylogeny
*Gastrointestinal Microbiome
*Bacteroidetes/genetics/classification/isolation & purification
Feces/microbiology
Genome, Bacterial
Animals
HT29 Cells
Extracellular Vesicles/metabolism
Mice
RNA, Ribosomal, 16S/genetics

@article {pmid41898646,
year = {2026},
author = {Dang, X and Hanson, BA and Lopez, M and Miller, J and Jimenez, M and Koralnik, IJ},
title = {Predictive Utility of ViroFind Detection of Blood and CSF Virome for Viral Presence in Human Brain Tissue.},
journal = {International journal of molecular sciences},
volume = {27},
number = {6},
pages = {},
doi = {10.3390/ijms27062789},
pmid = {41898646},
issn = {1422-0067},
support = {DA048493/DA/NIDA NIH HHS/United States ; },
mesh = {Humans ; *Brain/virology ; *Virome ; HIV Infections/virology/blood/cerebrospinal fluid ; Male ; Female ; Herpesvirus 4, Human/isolation & purification/genetics ; Adult ; High-Throughput Nucleotide Sequencing ; Middle Aged ; Torque teno virus/genetics/isolation & purification ; Viral Load ; Viruses/genetics/isolation & purification ; },
abstract = {Viral presence in the brain may contribute to chronic neurologic diseases. However, investigating these associations is limited by the difficulty of directly sampling brain tissue in living individuals. Here, we evaluated whether peripheral viral detection using unbiased target-enrichment next-generation sequencing could inform viral presence in the brain across a diverse set of viral taxa. We applied ViroFind to matched brain, blood (peripheral blood mononuclear cells, spleen, and/or lymph node), and cerebrospinal fluid (CSF) to assess the predictive utility of viral detection in blood and CSF for identifying viral presence in brain samples obtained from the National NeuroAIDS Tissue Consortium, including both HIV-infected (HIV[+]) and HIV-uninfected (HIV[-]) individuals without known active viral infection of the brain. Blood negativity was generally more informative for predicting the absence of viruses in the brain than blood positivity for predicting viral presence. CSF viral detection demonstrated limited predictive utility for brain presence across most viral taxa examined. Among blood[+] individuals, viral burden differed significantly between brain[+] and brain[-] cases for Epstein-Barr virus (EBV), parvovirus, and torque teno virus (TTV). Blood viral burden showed moderate ability to distinguish brain[+] from brain[-] cases for EBV and parvovirus, and strong discriminatory ability for TTV, with similar decision thresholds across HIV[+] and HIV[-] individuals.},
}

Humans
*Brain/virology
*Virome
HIV Infections/virology/blood/cerebrospinal fluid
Male
Female
Herpesvirus 4, Human/isolation & purification/genetics
Adult
High-Throughput Nucleotide Sequencing
Middle Aged
Torque teno virus/genetics/isolation & purification
Viral Load
Viruses/genetics/isolation & purification

@article {pmid41898837,
year = {2026},
author = {Li, S and Chiodi, C and Maucieri, C and Della Lucia, MC and Zardinoni, G and Ravi, S and Squartini, A and Concheri, G and Geng, G and Wang, Y and Stevanato, P},
title = {Profiling Soil-Plant-Microbial Communities: DNA and Multi-Omics Techniques.},
journal = {Genes},
volume = {17},
number = {3},
pages = {},
doi = {10.3390/genes17030303},
pmid = {41898837},
issn = {2073-4425},
mesh = {*Soil Microbiology ; Rhizosphere ; Metagenomics/methods ; *Microbiota/genetics ; *Plants/microbiology/genetics ; Genomics/methods ; Metabolomics/methods ; Plant Roots/microbiology/genetics ; Crops, Agricultural/microbiology/genetics ; Multiomics ; },
abstract = {Interactions among plant roots, soil, and microorganisms in the rhizosphere regulate nutrient cycling, plant health, and ecosystem resilience. Recent advances in DNA sequencing and multi-omics are contributing to a shift from primarily descriptive surveys toward more mechanistic and predictive frameworks. This review synthesizes methodological developments and conceptual insights spanning microbial ecology, functional genomics, and agricultural applications. We first summarize DNA-based approaches-marker-gene sequencing, shotgun metagenomics, and quantitative nucleic acid assays-and then complementary omics layers, including metatranscriptomics, metaproteomics, metabolomics, epigenomics, ionomics, and phenomics. We next outline computational advances in data integration, network modeling, and visualization that help represent complex multi-layered datasets as biologically interpretable systems. Applications relevant to climate resilience and sustainable agriculture are discussed, including the design of synthetic microbial communities, the identification of biomarkers for soil health and stress tolerance, and case studies in which rhizosphere multi-omics informs crop breeding and soil management strategies. Overall, these developments underscore the potential of treating microbes as functional and, to some extent, manageable components of the plant holobiont. Looking ahead, we identify key research gaps involving standardized workflows, cross-scale causal inference, and real-time monitoring pipelines that integrate molecular diagnostics with remote sensing and edge-cloud analytics. By linking ecological mechanisms with translational practice, multi-omics frameworks may support the development of more sustainable, data-driven agriculture that better aligns productivity with environmental stewardship.},
}

*Soil Microbiology
Rhizosphere
Metagenomics/methods
*Microbiota/genetics
*Plants/microbiology/genetics
Genomics/methods
Metabolomics/methods
Plant Roots/microbiology/genetics
Crops, Agricultural/microbiology/genetics
Multiomics

@article {pmid41898993,
year = {2026},
author = {Tanachaiwiwat, P and Sanscrainte, ND and Okech, BA and Estep, AS},
title = {Insecticide Resistance Mutations, Enzymatic Activity, and Pathogen Infection in Culex quinquefasciatus from Haiti.},
journal = {Insects},
volume = {17},
number = {3},
pages = {},
doi = {10.3390/insects17030331},
pmid = {41898993},
issn = {2075-4450},
support = {P0138_22_HS//Armed Forces Health Surveillance Directorate, Global Emerging Infection Surveillance Program/ ; 6036-10400-002-000-D//United States Department of Agriculture/ ; },
abstract = {Haiti is a Caribbean country of about 11 million people with a high burden of mosquito-transmitted disease and limited vector control, thereby making effective operational mosquito control of high importance. Previous studies have examined vector-borne disease burden and insecticide resistance markers in Haitian Aedes and Anopheles mosquitoes, but not Culex species. In this study, we examined collections of Culex quinquefasciatus from 12 locations in northern and southern Haiti for the presence of markers of insecticide resistance (using a variety of target-site mutations and biochemical assays) and pathogens (using a deep-sequencing microbiome workflow). The metagenomic analysis identified Wolbachia, Rhabdoviridae, and Plasmodium infections in all sample pools at relatively high levels, along with less frequent detections of other potential pathogens. Insecticide resistance marker examination identified variable frequencies of knockdown resistance and acetylcholinesterase resistance mutations, as well as variation in resistance-associated enzymatic activities in these populations. These findings indicate that insecticide resistance to pyrethroid and organophosphate insecticides is likely. Although there was variation among Culex mosquito populations and no clear activity pattern, enzymatic activity was significantly higher at the southern sites than at the northern sites. Similar findings in Cx. quinquefasciatus populations in other locations in the Americas strongly suggest that vector control with pyrethroid and organophosphate adulticides may be of limited efficacy.},
}

@article {pmid41900279,
year = {2026},
author = {De Luca, L and Menna, F and Lupo, S and Vingolo, EM and Carlà, MM and Mancini, M and Oliverio, GW and Minutoli, L and Baldascino, A and Mazzotta, C and Aragona, P and Meduri, A},
title = {The Ocular Surface Bacterial Microbiome and the Impact of Contact Lens Use: A Literature Review.},
journal = {Microorganisms},
volume = {14},
number = {3},
pages = {},
doi = {10.3390/microorganisms14030518},
pmid = {41900279},
issn = {2076-2607},
abstract = {The ocular surface microbiome plays a critical role in maintaining ocular health, preventing infections, and regulating immune responses. Contact lens (CL) wear has been linked to alterations in microbial composition, potentially leading to dysbiosis and increased susceptibility to ocular infections. This review aims to summarize current evidence on the effects of CL use on the ocular microbiome and to discuss strategies to preserve microbial homeostasis. A literature search was conducted in PubMed, Scopus, Web of Science, and Google Scholar for English-language human studies published between January 2005 and January 2025. We included original studies and systematic reviews evaluating the ocular surface bacterial community in contact lens (CL) wearers using either sequencing-based approaches (microbiome; e.g., 16S rRNA gene sequencing/metagenomics) or culture-based methods (microbiota). Two authors screened titles/abstracts and full texts. Overall, 12 studies met the inclusion criteria and were qualitatively synthesized. Across included studies, CL wear was associated with reproducible changes in the ocular surface bacterial community, most commonly a shift toward a skin-like profile and increased detection/relative abundance of opportunistic taxa (e.g., Pseudomonas, Acinetobacter, and Staphylococcus aureus) together with reduced representation of typical ocular commensals in several sequencing-based datasets. Culture-based studies reported increased recovery of opportunistic bacteria from lenses and storage cases, supporting contamination/biofilm-related mechanisms. Lens care solutions and preservatives were reported to modulate bacterial profiles and may contribute to dysbiosis, although evidence remains heterogeneous across study designs and analytic pipelines. CL use is associated with significant alterations in the ocular microbiome, increasing the risk of microbial keratitis and corneal inflammatory events. Strategies to maintain microbial balance, including careful selection of lens care products and development of antimicrobial lenses, may improve ocular surface health in CL wearers. Future longitudinal studies with standardized sampling and analytic workflows are needed to clarify causal links between CL-associated microbial changes and clinical outcomes.},
}

@article {pmid41900290,
year = {2026},
author = {Singh, K and Mitra, S},
title = {Operationalising Genomic Surveillance for Antimicrobial Resistance in Low- and Middle-Income Countries: A One Health Perspective from Bangladesh.},
journal = {Microorganisms},
volume = {14},
number = {3},
pages = {},
doi = {10.3390/microorganisms14030527},
pmid = {41900290},
issn = {2076-2607},
abstract = {Antimicrobial resistance (AMR) represents a critical global health challenge, with low- and middle-income countries (LMICs) disproportionately affected due to limited surveillance capacity. Advances in microbial genomics offer powerful tools for AMR detection and monitoring; however, translating these technologies into sustainable, policy-relevant surveillance systems in resource-constrained settings remains challenging. This review synthesises current approaches to genomic surveillance of AMR in LMICs and presents Bangladesh as a case study to illustrate how genomic, environmental, and clinical data can be integrated within a One Health framework. We examine key barriers to implementation, including laboratory infrastructure, bioinformatics capacity, data governance, and cross-sector coordination, alongside emerging opportunities for capacity building and regional collaboration. Using Bangladesh as a case study, we highlight practical pathways for embedding genomic surveillance into national AMR strategies, integrating human, animal, and environmental reservoirs of antibiotic resistance. We argue that genomic surveillance can move beyond data generation to inform infection prevention, antibiotic stewardship, and public health decision making when supported by context-appropriate infrastructure and interdisciplinary engagement. By focusing on operational and translational considerations rather than technology alone, this review provides actionable insights for microbiologists, public health practitioners, and policymakers seeking to strengthen AMR surveillance systems in LMICs through a One Health approach.},
}

@article {pmid41900318,
year = {2026},
author = {Liu, X and Xiao, N and Yu, J and Geng, X and Zhang, M and Zhang, Y and Xu, H and Nie, C and Wang, M and Li, L},
title = {Divergent Microbial Community and Pathogenicity at a University-Urban Interface: A Comparative Analysis.},
journal = {Microorganisms},
volume = {14},
number = {3},
pages = {},
doi = {10.3390/microorganisms14030557},
pmid = {41900318},
issn = {2076-2607},
support = {grant number 2022YFE0199800//National Key Research and Development Program of China/ ; grant number 24-1-8-smjk-13-nsh//Qingdao Science and Technology Wellness Promotion Demonstration Program/ ; grant number 82271658//the National Natural Science Foundation of China/ ; grant number SKLMTFCP-2023-01//SKLMT Frontiers and Challenges Project/ ; grant numbers ZR2024QD228 and ZR2024QC311//Shandong Provincial Natural Science Foundation/ ; grant number 24-4-4-zrjj-40-jch//Qingdao Natural Science Foundation/ ; grant number FDLAP24008//Opening Project of Shanghai Key Laboratory of Atmospheric Particle Pollution and Prevention (LAP)/ ; },
abstract = {Environmental metagenomics and microbial taxonomy provide essential frameworks to evaluate how population structures shape the evolution of antimicrobial resistance and microbial community dynamics within densely populated environments. To evaluate microbial community composition and pathogenic potential, high-touch surfaces at high-traffic sites on and off campus were analyzed using metagenomics and characterization of 188 bacterial isolates, including antibiotic susceptibility testing, hemolytic assays, and whole-genome sequencing. Off-campus sites showed significantly higher bacterial richness and more complex communities enriched with diverse potential pathogens. Notably, high-risk carbapenemase genes were predominantly identified in these off-campus urban environments. In contrast, on-campus environments harbored less diverse communities dominated by opportunistic, antibiotic-resistant Staphylococcus species, with metagenomic analysis confirming a concentrated enrichment of β-lactam resistance determinants associated with methicillin-resistant staphylococci. Phenotypic profiling revealed extensive antimicrobial resistance, with 84.7% of isolates exhibiting resistance to at least one antibiotic and 35.1% of Staphylococcus showing hemolytic activity. Whole-genome sequencing further revealed that these resistance and pathogenic traits are predominantly localized on mobile plasmids, highlighting a high potential for horizontal gene transfer. These findings indicate that population activities shape distinct microbial communities in closely adjacent environments and highlight the importance of monitoring high-risk resistance determinants in densely populated university settings.},
}

@article {pmid41900320,
year = {2026},
author = {Cheng, H and Han, J and Liu, K and Wang, L and Meng, Q and Liu, C and Liu, X and Wang, M and Yang, F and Li, X},
title = {Integrated Metagenomic and Metabolomic Profiling of Boar Semen During Ambient-Temperature Storage.},
journal = {Microorganisms},
volume = {14},
number = {3},
pages = {},
doi = {10.3390/microorganisms14030560},
pmid = {41900320},
issn = {2076-2607},
support = {2022020101//Agricultural Breeds Research Project of Henan Province/ ; HAAS2023RCQD01//the Key Technology Research and Development Program for Precision and Efficient Breeding of Local Pigs in Hainan Province/ ; },
abstract = {The reproductive efficiency of breeding boars substantially influences swine industry productivity. Sperm viability during ambient-temperature storage is critically affected by environmental factors, including microbial activity. This study aimed to elucidate the dynamics and interactions between the seminal microbiome and metabolome during boar semen storage at 17 °C. Using integrated 16S rRNA sequencing and untargeted metabolomics, we analyzed semen samples from six healthy boars (31-33 months old) collected at day 0 (control), 2, 4, and 6 of storage. Our results demonstrate that storage leads to a marked decline in microbial diversity, progressive enrichment of the opportunistic genus Proteus, depletion of key antioxidant and cofactor metabolites such as vitamin B6, and extensive metabolic reprogramming-including alterations in short-chain fatty acid, purine, and lipid oxidation pathways. Multi-omics correlation analysis further revealed strong associations between microbial succession and metabolic shifts, highlighting their combined role in driving sperm functional decline. These findings provide a mechanistic basis for improving semen preservation strategies through microbiome and metabolite-targeted interventions.},
}

@article {pmid41900339,
year = {2026},
author = {Malik, PK and Mohapatra, A and Trivedi, S and Kolte, AP and Sahoo, A and Bhatta, R},
title = {In Vitro Degradation of Chlorpyrifos by the Ruminal Microbes: Insights from the Rumen Metagenome.},
journal = {Microorganisms},
volume = {14},
number = {3},
pages = {},
doi = {10.3390/microorganisms14030581},
pmid = {41900339},
issn = {2076-2607},
abstract = {In vitro studies were conducted in a series to investigate if the ruminal microbes are capable of degrading chlorpyrifos. This in vitro study presents the results from three experiments: Exp. I was conducted without feed, while Exp II and III were conducted with feed, either with or without methanol for dissolving chlorpyrifos, respectively. A basal diet comprising finger millet straw and concentrate was prepared. Incubation medium with feed but without chlorpyrifos served as the control. A total of six replicates each of control and chlorpyrifos spiked were used for the incubation. The pesticide concentration in the incubation medium before and after 24 h of incubation was analyzed using GC-MS/MS. The genomic DNA was isolated from the incubation fluid of the individual samples, and the shotgun metagenomic sequencing was performed. The clean reads were taxonomically classified using the Kraken2 database, and microbial classification at different taxonomic ranks was separated using Pavian v1.0. The microbial genes in the metagenome data were predicted and assigned functional roles using the MetaErg v1.2.3 pipeline. The assigned KEGG Orthology (KO), EC numbers (Enzyme Commission number), Gene Ontology (GO), and corresponding NCBI taxonomy information relevant to chlorpyrifos metabolism/degradation were retrieved. Results from the study revealed that the chlorpyrifos concentration was decreased from 5.78 to 1.64 ppm over 24 h of in vitro incubation with feed. Similar alpha and beta diversity indices between control and chlorpyrifos treatments revealed that the richness and the evenness of the microbial population were not affected by the presence of chlorpyrifos in the rumen fluid. There was no difference in the microbiota affiliated to the major phyla such as Bacteroidota, Fibrobacterota, Bacillota, and Pseudomonadota. The EC 3.1.8.1, EC 3.1.3.1, EC 1.14.13.-, and EC 1.1.1.- reported for chlorpyrifos degradation were not detected in the metagenome, and only EC 3.1.1.1 was identified, which demonstrated that degradation of chlorpyrifos was carried out by the affiliated enzyme carboxylesterase. The presence of GO:0004035, GO:0004364, GO:0019637, GO:0016791, and GO:0042178 in the metagenome strengthens that the chlorpyrifos degradation in the present study was primarily assigned to the rumen microbiota. This in vitro study provided insights into the rumen microbiota involved in the chlorpyrifos degradation and the initial clue that the rumen microbes are capable of degrading chlorpyrifos. Further, the animal studies in different species with the variable levels of chlorpyrifos are also warranted to confirm the efficacy of rumen microbes in mixed syntrophy and determine the threshold capabilities of the ruminal microbes.},
}

@article {pmid41900342,
year = {2026},
author = {Ntzouvaras, A and Koletti, A and Zografaki, ME and Marka, S and Skliros, D and Vasilakis, G and Karavidas, I and Koukouvinis, AK and Efrose, RC and Kalloniati, C and Tzovenis, I and Flemetakis, E},
title = {Isolation and Characterization of Microalgae Isolates from Hydroponic Effluent Water: Metagenomics and Biotechnological Insights.},
journal = {Microorganisms},
volume = {14},
number = {3},
pages = {},
doi = {10.3390/microorganisms14030582},
pmid = {41900342},
issn = {2076-2607},
support = {PRIMA2019-04//European Union research and innovation Horizon 2020/ ; },
abstract = {Hydroponic systems are gaining prominence in sustainable agriculture, yet their nutrient-rich effluents remain an underexplored source of microbial biodiversity with potential biotechnological interest. In this study, shotgun metagenomic sequencing was employed to profile, with a high taxonomic resolution, the photosynthetic microbial community in hydroponic effluent before and after a natural algal bloom, revealing pronounced shifts in microbial composition. Notably, relative abundance increased sixfold for Chlamydomonas reinhardtii and tenfold for Bigelowiella natans. Four dominant microalgal strains (PR1-PR4) were subsequently isolated and characterized through integrative morphological and molecular taxonomy, with phylogenetic analyses based on four genetic markers (18S rRNA, ITS, rbcL and tufA) confirming that each isolate represents a distinct lineage within Chlorophyceae families, including Chlorella sp., Chlamydomonas sp., and Scenedesmus sp. Growth kinetics under three temperature regimes, typical of Greek environmental conditions from spring to autumn (15 °C, 23 °C, 32 °C), demonstrated broad ecological plasticity and rapid biomass production, highlighting strains with strong adaptive resilience. Biochemical profiling of the isolates revealed significant inter-strain differences in primary and secondary metabolite content, including proteins (up to 43% DW), lipids (up to 31% DW), carbohydrates (up to 44% DW), photosynthetic pigments, phenolics, flavonoids, and antioxidant activity. The observed metabolic diversity of autochthonous microalgal strains from hydroponic environments, combined with their high growth rates, underscores their potential for applications in bioremediation, bioenergy, and the development of value-added products within a circular bioeconomy framework.},
}

@article {pmid41900399,
year = {2026},
author = {Yi, X and Lin, Y and Peng, Y and Liu, Y and Ning, C and Lei, J and Wang, L and Chen, C and Wu, L and Liao, J},
title = {Urbanization-Induced Shifts in Microbial Functional Genes of Wetland Nitrogen Cycling Promote Nitrous Oxide (N2O) Emissions.},
journal = {Microorganisms},
volume = {14},
number = {3},
pages = {},
doi = {10.3390/microorganisms14030640},
pmid = {41900399},
issn = {2076-2607},
support = {32401392//National Natural Science Foundation of China/ ; OT-S-KTA4//Hunan Forest Quality Improvement and Efficiency Enhancement Demonstration Project Funded by the European Investment Bank Loan/ ; XLKY202216//Forestry Science and Technology Innovation Project of Hunan Province/ ; XLKY202319//Forestry Science and Technology Innovation Project of Hunan Province/ ; 2024JJ5235//Hunan Provincial Natural Science Foundation of China/ ; },
abstract = {Urban wetlands are assumed to contribute to nitrous oxide (N2O) emissions; however, the microbial mechanisms underlying enhanced N2O fluxes in urban wetlands and differences in microbial responses between aquatic and soil compartments have not been clearly identified. Here, we characterized the nitrogen (N) cycling microbial communities and their functional metabolic pathways in urban and rural wetlands using metagenomics and N2O flux measurements. Results showed that urbanization drove a 6~8-fold increase in N2O fluxes from urban wetlands compared to rural wetlands. Structural equation modeling (SEM) confirmed that urbanization intensity was a primary driver (standardized coefficients: 0.72 for soil and 0.92 for water). In wetland water, N2O emissions were negatively correlated with inorganic nutrient concentrations (coefficient = -0.62). Aquatic microbial communities exhibited substantial taxonomic shifts but preserved network connectivity, indicating adaptive strategies for surviving urban perturbations at the cost of reduced functional redundancy. In wetland soil, microbial communities maintained stability under urbanization, which was attributed to environmental buffering from heterogeneous microenvironments. Soil N2O emissions were positively linked to microbial alpha diversity (coefficient = 0.79). Furthermore, urban wetlands enriched genes mediating nitrification and denitrification while depleting genes associated with N fixation and organic N metabolism. This functional shift reflects microbial specialization in processing elevated reactive N (Nr) inputs from urban sources, trapping urban wetlands in an "N loss loop" that reinforces high N2O fluxes. This study elucidates the microbial mechanisms governing wetland N2O emissions under urbanization, thereby enhancing understanding of microbially mediated N cycling in the urban wetland ecosystem.},
}

@article {pmid41900403,
year = {2026},
author = {Zhang, W and Fan, C and Yang, L and Sun, Y and Tang, L},
title = {Integrated Metagenomic and Metabolomic Analyses Reveal Rhizosphere Soil Microecological Changes in Thlaspi arvense L. Lines with Different Alkaloid Contents.},
journal = {Microorganisms},
volume = {14},
number = {3},
pages = {},
doi = {10.3390/microorganisms14030643},
pmid = {41900403},
issn = {2076-2607},
support = {CARS-16-S3//The China Agriculture Research System of MOF and MARA/ ; },
abstract = {Pennycress (Thlaspi arvense L.), a representative and economically valuable cover crop, supports and enhances key ecological processes throughout its life cycle via its root system. It is hypothesized that pennycress selectively modulates its rhizosphere microbial community through root-derived metabolites, which may influence both the crop's growth and the subsequent crops in rotation. However, systematic investigations comparing the rhizosphere microbiomes and metabolomes among different pennycress lines remain limited. This study employed metagenomic and metabolomic approaches to examine the dynamic changes in the rhizosphere microbial community and metabolite profiles of three pennycress lines with significantly different total alkaloid contents. The goal was to elucidate the interactions between microbes and metabolites. Results indicated significant differences in microbial community structure across the cultivars. JiL67 maintained stable community diversity, while LiN54 (with the lowest alkaloid content) showed reduced diversity. HeL43 (with the highest alkaloid content) exhibited increased diversity but also potential community homogenization, accompanied by the significant enrichment of microbial taxa capable of alkaloid tolerance. Metabolomic analysis identified metabolites such as Portulacaxanthin II, Oleanolic acid, and Soraphen A as significantly enriched in the rhizosphere soil of pennycress. This study reveals the shifts in rhizosphere microbial communities and metabolites linked to different pennycress lines and uncovers their interactive mechanisms, providing a scientific foundation for developing more economically efficient pennycress cultivation strategies.},
}

@article {pmid41900432,
year = {2026},
author = {Guerrero-Torres, LE and García-Galindo, JJ and Gómez-Galindo, MF and Delgado, DIR and Retolaza Carlos, CE and Suárez-Rico, DO and Beltrán-Ramírez, A and Balleza Alejandri, LR},
title = {The Gut Microbiota in Parkinson's Disease: Mechanistic Insights into Microbial-Host Interactions.},
journal = {Microorganisms},
volume = {14},
number = {3},
pages = {},
doi = {10.3390/microorganisms14030673},
pmid = {41900432},
issn = {2076-2607},
abstract = {Parkinson's disease (PD) is a multifactorial neurodegenerative disorder characterized by progressive motor and non-motor manifestations, including early gastrointestinal dysfunction. Growing evidence implicates the gut microbiota as an active modulator of host immune tone and neurodegenerative vulnerability, extending beyond descriptive taxonomic associations toward functional and metabolic mechanisms. PD-associated dysbiosis is consistently characterized by altered microbial functional capacity, including reduced short-chain fatty acid (SCFA) production, enrichment of pro-inflammatory metabolic traits, and sustained immune stimulation at the intestinal interface. These shifts promote chronic low-grade inflammation and intestinal barrier perturbations, creating conditions that may facilitate abnormal α-synuclein aggregation within the enteric nervous system. Current management predominantly relies on dopaminergic replacement and related symptomatic strategies, such as levodopa combinations, dopamine agonists, monoamine oxidase-B and catechol-O-methyltransferase (COMT) inhibitors, and device-aided therapies, which alleviate symptoms but do not halt underlying neurodegeneration or modify long-term disease course. These therapeutic limitations have intensified interest in upstream mechanisms that might be amenable to disease-modifying interventions, particularly those arising at the level of the gut microbiota and gut-immune-brain axis. This narrative review integrates clinical, metagenomic, metabolomic, and mechanistic evidence to propose a unified model in which microbiota-driven immune and metabolic perturbations may act as upstream drivers converging on α-synuclein pathology, neuroinflammation, and neurovascular dysfunction.},
}

@article {pmid41900479,
year = {2026},
author = {Park, H and Kim, JS and Kim, DJ and Suk, KT},
title = {Strain Diversity in the Human Microbiome: Personal Variation, Pathobionts, Therapeutics, and Methodological Challenges.},
journal = {Microorganisms},
volume = {14},
number = {3},
pages = {},
doi = {10.3390/microorganisms14030720},
pmid = {41900479},
issn = {2076-2607},
support = {NRF-2020R1I1A3073530//National Research Foundation of Korea/ ; NRF-2020R1A6A1A03043026//National Research Foundation of Korea/ ; },
abstract = {Advances in sequencing technologies have transformed human microbiome research, yet most analyses still rely on species-level profiles. However, strains rather than species represent the true ecological and functional units of the microbiome. Individual strains can vary substantially in gene content, metabolic capacity, virulence factors, antimicrobial resistance, and host-interaction properties. These differences critically influence immune responses, epithelial barrier integrity, disease susceptibility, and therapeutic outcomes. Here, we synthesize recent human microbiome studies that provide robust strain-resolved evidence, focusing on three major themes: (i) the emergence and long-term persistence of personalized strain repertoires, (ii) strain-specific pathobiont traits that drive host pathology, and (iii) the implications of strain-level ecology for the development of next-generation microbiome therapeutics. We also highlight key methodological innovations including high-resolution amplicon profiling, advanced metagenomic and single-cell genomics, and culture-based functional approaches that collectively enable strain-level resolution and are reshaping the field.},
}

@article {pmid41901034,
year = {2026},
author = {Lee, YK and Kim, HY and Shim, D},
title = {A Triple-Hit Multi-Omics Framework for Psoriasis: Microbial Metabolic Remodeling and Immune Cell Methylome Signature Associated with an AMP-Dominant Lesional Program.},
journal = {Life (Basel, Switzerland)},
volume = {16},
number = {3},
pages = {},
doi = {10.3390/life16030516},
pmid = {41901034},
issn = {2075-1729},
support = {RS-2023-00263429//Ministry of Science and ICT (MSIT), South Korea/ ; },
abstract = {The gut-skin axis is increasingly implicated in psoriasis pathogenesis, yet the cross-compartment convergence of molecular programs remains incompletely defined. We constructed a conceptual "Triple-Hit" multi-omics framework by integrating five independent public datasets spanning gut microbial functional remodeling (shotgun metagenomics), systemic immune cell methylomes (PBMC and CD8+ T-cell EPIC 850K), and lesional skin regulatory layers (miRNA and bulk RNA-seq). In the gut compartment, functional profiles exhibited a selective reduction in microbial lipid catabolic potential, including decreased fatty acid degradation and a lowered composite lipid degradation score, alongside heterogeneous shifts across SCFA-associated metabolic pathways. Systemically, PBMC methylomes revealed widespread regional remodeling (45,396 DMRs) enriched for membrane-proximal signaling and cytoskeletal programs, while CD8+ T cells showed specific epigenetic alterations in lipid- and glycosphingolipid-associated loci, suggesting a systemic metabolic-epigenetic alignment. In the skin, we identified a compact miRNA signature (168 DE-miRNAs) and a mechanistically interpretable, directionality-constrained miRNA-mRNA bridge that aligns with an AMP-dominant inflammatory transcriptome, consistent with reduced post-transcriptional restraint. Collectively, these findings support a convergent multi-omics framework linking putative microbial metabolic remodeling, systemic immune priming, and cutaneous effector programs. This study provides a systems-level perspective on psoriasis pathogenesis, highlighting the metabolic-epigenetic-transcriptional convergence as a potential avenue for therapeutic intervention.},
}

@article {pmid41901100,
year = {2026},
author = {Kim, HJ and Park, J and Oh, S and Kim, D and Kim, HJ and Jo, C and Kim, EB and Jang, A},
title = {Effect of Alpha-Lipoic Acid, Betaine, and L-Carnitine Supplementation on Gut Microbiota and Obesity Biomarkers in Mice.},
journal = {Nutrients},
volume = {18},
number = {6},
pages = {},
doi = {10.3390/nu18060925},
pmid = {41901100},
issn = {2072-6643},
support = {2022R1A2C1005235//National Research Foundation of Korea/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Carnitine/pharmacology/administration & dosage ; *Obesity/microbiology/metabolism ; *Betaine/pharmacology/administration & dosage ; Male ; *Thioctic Acid/pharmacology/administration & dosage ; Mice, Inbred C57BL ; *Dietary Supplements ; Diet, High-Fat/adverse effects ; Biomarkers/blood ; Mice ; Disease Models, Animal ; Leptin/blood ; },
abstract = {Background/Objectives: This exploratory study (n = 6 per group) investigated the associations between supplementation with α-lipoic acid (AL), betaine (BT), and L-carnitine (LC) and gut microbiota composition in a high-fat diet (HFD)-induced obesity mouse model. Methods: Four-week-old male C57BL/6J mice were fed a control diet (10% fat), HFD (60% fat), or HFD supplemented with AL, BT, or LC (300 mg/kg BW/day) for nine weeks. Results: All three compounds were associated with shifts in microbial composition compared to the HFD-only group. While AL and BT supplementation moderately modulated specific Firmicutes and Bacteroidetes taxa, LC supplementation was linked to a more pronounced reduction in the Firmicutes/Bacteroidetes ratio and a decreased abundance of genera such as Christensenellaceae, Lachnospiraceae, and Coprococcus 3. These microbial changes were correlated with obesity-related metabolic and adiposity markers, including leptin and lipid parameters. Furthermore, functional profiling via PICRUSt suggested potential alterations in amino acid metabolism; however, these findings represent inferred metabolic potential rather than direct metagenomic measurements. Conclusions: Collectively, these results indicate differential associations between dietary supplementation and gut microbiota composition in HFD-fed mice. Although this study was conducted within an exploratory framework and utilized a modest sample size, the observed microbial shifts consistently paralleled metabolic alterations, supporting biologically plausible associations that warrant further mechanistic investigation.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Carnitine/pharmacology/administration & dosage
*Obesity/microbiology/metabolism
*Betaine/pharmacology/administration & dosage
Male
*Thioctic Acid/pharmacology/administration & dosage
Mice, Inbred C57BL
*Dietary Supplements
Diet, High-Fat/adverse effects
Biomarkers/blood
Mice
Disease Models, Animal
Leptin/blood

@article {pmid41901112,
year = {2026},
author = {Solano-Aguilar, G and Lakshman, S and Chen, C and Beshah, E and Molokin, A and Vinyard, B and Dawson, HD and Santin-Duran, M and Bruna, G and Smith, A and Urban, JF},
title = {Fruit and Vegetable Supplemented-Diet Ameliorates Dextran Sodium Sulfate (DSS)-Induced Colitis by Modulating Host Transcriptome and Gut Metagenome Response.},
journal = {Nutrients},
volume = {18},
number = {6},
pages = {},
doi = {10.3390/nu18060937},
pmid = {41901112},
issn = {2072-6643},
support = {Cris 8040-51000-058-00D//United States Department of Agriculture/ ; },
mesh = {Animals ; Dextran Sulfate ; *Fruit ; *Colitis/chemically induced/prevention & control/microbiology/diet therapy ; *Transcriptome ; *Gastrointestinal Microbiome ; *Dietary Supplements ; *Vegetables ; Swine ; *Metagenome ; Disease Models, Animal ; *Diet ; Colon/pathology ; },
abstract = {Background/Objectives: Dietary intake of fruits and vegetables (FVs) has been inversely associated with a lower risk of ulcerative colitis. Using a pig model, we evaluated the effect of FV supplementation on dextran sulfate sodium (DSS)-induced colitis. Methods: Six-week-old pigs were fed a grower diet (negative control), grower diet + 4% DSS (positive control), half-FV diet + DSS, or full-FV diet + DSS. FV levels matched half or full daily recommendations from the Dietary Guidelines for Americans (DGA). Clinical signs were monitored; proximal colon contents (PCs) and mucosa (PCM) were analyzed for metagenome, transcriptome and histopathology. Results: Full-FV pigs showed no diarrhea, less fecal occult blood (FOB), crypt hyperplasia, but no changes in gene expression or microbiome diversity (p < 0.05). Half-FV pigs had increased FOB, differentially expressed genes (DEGs) linked to tissue remodeling, crypt/goblet cell hyperplasia and two cases of diarrhea (p < 0.05). DSS controls showed reduced immune-related DEGs, altered microbiome, PCM erosion, FOB, and persistent diarrhea in one pig (p < 0.05). Conclusions: A three-week full-FV diet conferred protection against DSS-induced colitis, with a dose-dependent protection of intestinal tissue and gut metagenome under inflammatory challenge.},
}

Animals
Dextran Sulfate
*Fruit
*Colitis/chemically induced/prevention & control/microbiology/diet therapy
*Transcriptome
*Gastrointestinal Microbiome
*Dietary Supplements
*Vegetables
Swine
*Metagenome
Disease Models, Animal
*Diet
Colon/pathology

@article {pmid41901564,
year = {2026},
author = {Gonzalez, A and Argotsinger, J and Oram, RJ and Miller, JL},
title = {Impact of Metagenomic Next-Generation Sequencing on Antibiotic Management in Pediatric Patients.},
journal = {Medicina (Kaunas, Lithuania)},
volume = {62},
number = {3},
pages = {},
doi = {10.3390/medicina62030482},
pmid = {41901564},
issn = {1648-9144},
mesh = {Humans ; Retrospective Studies ; *High-Throughput Nucleotide Sequencing/methods/statistics & numerical data ; Child ; Male ; Female ; Child, Preschool ; *Metagenomics/methods ; Infant ; *Anti-Bacterial Agents/therapeutic use ; Adolescent ; Pediatrics/methods ; },
abstract = {Background and Objectives: Metagenomic next-generation sequencing (mNGS) is an emerging diagnostic tool used to guide the management of infectious diseases. However, clinical criteria in which there is a clear benefit have not been identified, and more real-world clinical experience is needed to identify patient populations in which mNGS testing may have the most benefit. The aim of this article is to evaluate the utilization of mNGS to determine the impact on clinical practice for pediatric patients. Materials and Methods: This retrospective analysis included pediatric patients that had a mNGS test performed between January 2020 and September 2024. The primary outcome was the clinical impact of the mNGS test on patient management defined as either a positive impact or no impact. Secondary outcomes included test turnaround time, agreement or discordance between conventional testing and mNGS, and hospital length of stay. Results: Forty-six mNGS tests in 42 patients were evaluated. Of 60 organisms identified from the 46 tests, 27 organisms (45%) were considered clinically significant. mNGS had a positive clinical impact in 18 (39.1%) patients, primarily due to antimicrobial modifications (16, 34.8%) and new diagnoses (6, 13.0%). The majority of patients with a positive clinical impact were immunosuppressed (15/18, 83.3%). Conclusions: mNGS demonstrated utility in a subset of pediatric patients, particularly those considered immunosuppressed. Its ability to confirm or exclude infections, particularly fungal infections in this patient population, contributed to its impact. However, its limited benefit in immunocompetent patients underscores the importance of careful patient selection to optimize diagnostic and antimicrobial stewardship.},
}

Humans
Retrospective Studies
*High-Throughput Nucleotide Sequencing/methods/statistics & numerical data
Child
Male
Female
Child, Preschool
*Metagenomics/methods
Infant
*Anti-Bacterial Agents/therapeutic use
Adolescent
Pediatrics/methods

@article {pmid41887505,
year = {2026},
author = {Wang, Q and Zhang, J and Xia, Y and Zha, M and Li, J and Jambal, T and Dorjgotov, D and Tseveen, S and Chen, Y},
title = {Traditional fermented goat milk products in Mongolia: Analysis from the perspective of metagenomics to metabolomics.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2025-27796},
pmid = {41887505},
issn = {1525-3198},
abstract = {Mongolia is known for its rich dairy traditions, with goat milk representing a distinctive and valuable dairy resource. Fermentation improves the quality and nutritional value of goat milk, which is closely associated with microbial activity. As traditional Mongolian fermented dairy products primarily depend on natural fermentation, investigating the microbial and metabolic changes during this process is essential for understanding product quality. In this observational study, raw goat milk (RGM) and fermented goat milk (FGM) samples were collected from Mongolia, and a total of 102 microbial species were identified using shotgun metagenomic sequencing. The RGM contained a higher proportion of viruses and nonlactic acid bacteria (non-LAB), including Macrococcus caseolyticus. Following fermentation, the microbial community composition shifted, becoming dominated by LAB species such as Lactobacillus helveticus and Lactobacillus delbrueckii, with beneficial microorganisms attaining predominant abundance. A total of 22 differential metabolites were identified between RGM and FGM. Approximately half of these metabolites were related to AA metabolism, while the remainder were involved in energy metabolism, antioxidant processes, and lipid metabolism. Spearman correlation analysis suggested that LAB, primarily Lactobacillus species, were positively associated with the abundance of metabolites such as organic acids and AA in the fermented products. In contrast, the presence of pathogenic microorganisms such as viruses showed a negative correlation with fermentation efficiency markers. It was hypothesized as a potential factor affecting product quality, possibly through disrupting host microbial metabolism. Overall, this observational study identifies understanding of the factors governing FGM quality and provides a scientific foundation for improving the goat milk industry and harnessing microbial resources in traditional fermented dairy products.},
}

@article {pmid41887507,
year = {2026},
author = {Scott, J and Brouard, JS and Drouin, G and Ouellet, DR and Ster, C and Petri, RM},
title = {Microbiota Changes in Rumen and Milk Corresponding to Dietary Protein Intake in Transition Dairy Cows.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2025-27576},
pmid = {41887507},
issn = {1525-3198},
abstract = {During the transition period in dairy cows, the incidence of disease increases due to a negative energy balance affecting both the metabolic and immune health status. Limiting milk production at the beginning of lactation improves the metabolic status of cows. However, past strategies tested to achieve this reduction either negatively impacted milk yield for the rest of the lactation or were difficult to implement on large-scale dairy farms. This study evaluated the impact of a temporary reduction in metabolizable protein (MP) supply during the transition period on the rumen and milk microbiota and their metabolic composition. Treatment cows (n = 5) were fed 80% of their MP needs (80MP) from 14 d before calving to 14 d after calving, before being switched to a 100% MP diet (100MP) for an additional 14 d. Control cows (n = 6) were fed 100MP for the entire experiment. Samples of rumen content and milk were taken in the immediate Postpartum phase (PP) on d 2 and 7, as well as after dietary change in the experimental Recovery phase (RP) on d 21 and 28 postpartum. All samples were extracted for DNA and analyzed using shotgun metagenomic sequencing (Illumina NovaSeq). Milk samples were additionally analyzed for composition, and rumen fluid was analyzed for short-chain fatty acids and ammonia-N. Significant changes to the microbial composition were almost exclusively associated to effect of day of sampling, with the exception being the family Micrococcaceae, which was found to be differentially abundant in the 100MP compared with the 80% group in PP milk samples. This study used a metagenomics approach to understanding the impact of altered protein supply on rumen and milk microbiota, to better understand impacts on these separate ecosystems.},
}

@article {pmid41887601,
year = {2026},
author = {Wei, Y and Liu, Q and Gong, Z and Han, GZ},
title = {Unveiling the cryptic diversity and distribution of elements related to virophage mavirus through deep mining of pPolB proteins.},
journal = {Virologica Sinica},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.virs.2026.03.009},
pmid = {41887601},
issn = {1995-820X},
abstract = {Virophages are unique double-stranded DNA (dsDNA) viruses that parasitize viruses of Nucleocytoviricota (NCVs). While conventionally viewed as a viral group, growing evidence suggests that "virophage" is better understood as a parasitic lifestyle, rather than a natural group. Despite this conceptual shift, their diversity and evolution remain largely obscure and contentious. Through deep mining of protein-primed type B DNA polymerase (pPolB) in 7,041 eukaryotic genomes and 12,053 metagenomes sampled globally, we expand the diversity of pPolB-carrying mavirus virophage-related elements (pMVREs), which include virophages, transpovirons, and Polinton-like viruses (PLVs). Our phylogenomic and metagenomic mining reveals the widespread distribution of pMVREs in eukaryotic genomes (97/7,041, 1.38%) and global environments (2,450/12,053, 20.33%). pMVREs possess genome architectures of high plasticity and promiscuity. The presence of pMVREs and NCVs is statistically correlated in both eukaryotic genomes and global metagenomes, supporting a specific co-occurrence association between pMVREs and NCVs. Moreover, pMVRE diversity and composition exhibit strong heterogeneity across global ecosystems. Together, this study unveils a vast diversity of virophage-related elements and provides insights into the intricate relationship among virophages, transpovirons, PLVs, pMVREs, and NCVs.},
}

@article {pmid41887858,
year = {2026},
author = {Zheng, D and Li, D and Wang, J},
title = {Beyond ammonia-oxidizing bacteria-centric paradigms: Geobacter-assisted anodic anaerobic ammonia oxidation.},
journal = {Journal of environmental sciences (China)},
volume = {163},
number = {},
pages = {399-408},
doi = {10.1016/j.jes.2025.07.035},
pmid = {41887858},
issn = {1001-0742},
mesh = {*Geobacter/metabolism/physiology ; *Ammonia/metabolism ; Oxidation-Reduction ; Electrodes ; Anaerobiosis ; Biofilms ; Bacteria/metabolism ; *Anaerobic Ammonia Oxidation ; },
abstract = {Anodic anaerobic ammonium oxidation (anodic anammox) presents a sustainable approach for nitrogen removal, yet its bioelectrochemical mechanisms remain unclear due to biofilm complexity and undefined roles of electroactive microorganisms (EAMs). This study reveals that nitrite (NO2[-]) is the direct product of ammonia-oxidizing bacteria (AOB)-driven anodic anammox, with extracellular electron transfer (EET) mediated by indirect mechanisms via redox shuttles. Metagenomic analysis identified two ammonia oxidation pathways: (1) a novel short-range nitrification pathway (NH4[+] → NO2[-]) governed by ncd2 genes, and (2) a traditional ammonia oxidation pathway (NH4[+] → NH2OH) facilitated by amoABC. Intriguingly, Geobacter exhibited potential NH2OH oxidation capability, bridging AOB activity and electrode respiration. Functional inhibition experiments demonstrated that EAMs-derived electron shuttles and reactive oxygen species (ROS) are critical for enhancing EET efficiency, with ROS serving as a key electron acceptor for AOB under anaerobic conditions. Spatial and metabolic synergy between EAMs and AOB-via substrate cross-feeding, cofactor provision, and electron transfer-was essential for maintaining biofilm stability. These findings challenge the conventional view of AOB-driven anodic anaerobic anammox mechanisms and provide new insights into sustainable nitrogen removal in engineered bioelectrochemical systems.},
}

*Geobacter/metabolism/physiology
*Ammonia/metabolism
Oxidation-Reduction
Electrodes
Anaerobiosis
Biofilms
Bacteria/metabolism
*Anaerobic Ammonia Oxidation

@article {pmid41887859,
year = {2026},
author = {Chen, J and Li, G and Liu, J and Yuan, X and Zhao, G and Yang, X and Huang, S and Zheng, Z},
title = {Comparative assessment of novel nematicide trifluenfuronate and fosthiazate on soil ecosystem: From microbial community structure to KEGG functional pathways.},
journal = {Journal of environmental sciences (China)},
volume = {163},
number = {},
pages = {409-419},
doi = {10.1016/j.jes.2025.05.033},
pmid = {41887859},
issn = {1001-0742},
mesh = {*Soil Microbiology ; *Soil Pollutants/toxicity ; Soil/chemistry ; *Antinematodal Agents/toxicity ; Ecosystem ; *Microbiota/drug effects ; RNA, Ribosomal, 16S ; Bacteria ; Organophosphorus Compounds ; Thiazolidines ; },
abstract = {In recent years, the increasing demand for environmentally friendly pesticides in agricultural production has driven the development of novel pesticides characterized by high efficiency, low toxicity, and improved environmental compatibility. Simultaneously, greater emphasis is being placed on evaluating their impact on the soil ecosystem to ensure sustainable pesticide use and the stability of agroecosystems. In this study, we employed 16S rRNA gene high-throughput sequencing and metagenomic analysis to compare the effects of the novel nematicide trifluenfuronate and the commonly used nematicide fosthiazate on soil physicochemical properties, bacterial community structure, and metabolic functions in cucumber cultivation soils. Results showed that soil enzyme activity, microbial community structure and diversity exhibited the most significant differences on day 7 following nematicide application but stabilized by day 100. Both nematicide type and concentration were key factors influencing bacterial community structure. Compared to fosthiazate, trifluenfuronate more significantly enhanced soil bacterial community abundance while exerting fewer negative impacts on related enzyme activities and KEGG pathways. In addition, fosthiazate preferentially regulated membrane-associated efflux genes, whereas trifluenfuronate primarily interfered with the transcriptional regulation of target genes to mitigate antibiotic stress. These alterations in microbial community structure and function led to changes in soil nutrient bioavailability. This made the trifluenfuronate treatment group have higher available nitrogen and phosphorus content to supply to cucumber. This research contributes to understanding their ecological effects and paves the way for future sustainable pesticide research.},
}

*Soil Microbiology
*Soil Pollutants/toxicity
Soil/chemistry
*Antinematodal Agents/toxicity
Ecosystem
*Microbiota/drug effects
RNA, Ribosomal, 16S
Bacteria
Organophosphorus Compounds
Thiazolidines

@article {pmid41887904,
year = {2026},
author = {Jin, R and Chen, C and Zhang, J and Li, Y and Wu, Y and Wang, F and Chen, Z and Huang, T and Cheng, Q and Yu, X and Jia, P},
title = {Solid waste dumping differentially impacts soil prokaryotic, fungal, and viral communities: Insights from metagenomics.},
journal = {Journal of environmental sciences (China)},
volume = {163},
number = {},
pages = {867-879},
doi = {10.1016/j.jes.2025.10.021},
pmid = {41887904},
issn = {1001-0742},
mesh = {*Soil Microbiology ; Metagenomics ; *Microbiota ; Fungi ; *Solid Waste ; Soil/chemistry ; Soil Pollutants/analysis ; *Refuse Disposal ; Environmental Monitoring ; },
abstract = {Rapid urbanization and industrialization have dramatically increased global solid waste generation, placing immense pressure on waste management systems. In many developing countries, illegal and uncontrolled dumping remains widespread, yet its ecological impacts, particularly on soil microbial communities, are still poorly understood. To address this knowledge gap, we applied high-throughput amplicon sequencing and metagenomic profiling to analyze soil microbiomes across three categories of solid waste dumping. Our results show that solid waste dumping significantly altered both biotic and abiotic components of soil ecosystems. Soil properties shifted abruptly, with elevated pH and increased concentrations of pollutants such as petroleum hydrocarbons and fluorides. Microbial communities were extensively restructured, exhibiting both taxonomic turnover and functional adaptations. Viral communities displayed greater sensitivity to dumping-induced disturbances than prokaryotic or fungal communities. These findings provide new insights into soil microbiome responses to anthropogenic pollution and highlight taxon-specific adaptation strategies. To our knowledge, this is among the first comparative studies integrating prokaryotic, fungal, and viral responses to solid waste dumping using high-throughput molecular approaches. Our findings present a novel perspective that may guide future monitoring efforts and enhance approaches to environmental damage identification and assessment.},
}

*Soil Microbiology
Metagenomics
*Microbiota
Fungi
*Solid Waste
Soil/chemistry
Soil Pollutants/analysis
*Refuse Disposal
Environmental Monitoring

@article {pmid41888119,
year = {2026},
author = {Rodríguez-Varela, R and Pochon, Z and Mas-Sandoval, A and Yaka, R and Fortes-Lima, CA and García Rubio, A and Márquez-Grant, N and Marí, J and Graziani, G and Ferrer Abárzuza, A and Vicente, M and Lorca-Francisco, L and Linderholm, A and Lagerholm, VK and Arauna, LR and Pérez-Ramallo, P and Krzewińska, M and Schlebusch, CM and Götherström, A},
title = {Analysis of medieval burials from Ibiza reveals genetic and pathogenic diversity during the Islamic period.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {41888119},
issn = {2041-1723},
support = {2019-00849_VR//Vetenskapsrådet (Swedish Research Council)/ ; },
mesh = {Humans ; History, Medieval ; *Islam/history ; Spain ; *Burial/history ; *Genetic Variation ; Metagenomics ; Gene Flow ; *Leprosy/microbiology/history/genetics ; DNA, Ancient/analysis ; Male ; Cemeteries ; },
abstract = {Ibiza, an island in present-day Spain, was conquered in 902 CE by the Umayyad Emirate of Córdoba. The island remained under Islamic rule until 1235. Here, we analyse the genetic and metagenomic profiles of 13 individuals from an Islamic cemetery in Ibiza, dated to 950-1150 CE. Genome-wide analyses reveal heterogeneity, with ancestry components from Europe, North Africa, and Sub-Saharan Africa. Our analyses estimate that North African gene flow occurred two to seven generations before these individuals lived, suggesting admixture following the Islamic conquest of Iberia and potentially on Ibiza itself. Notably, two individuals trace their Sub-Saharan origins to distinct regions, Senegambia and present-day southern Chad, providing direct evidence of trans-Saharan connections via military and slave networks documented in contemporary Arabic sources. Metagenomic analyses detect several pathogens in this community, with one individual carrying Mycobacterium leprae, offering insight into the presence of leprosy in Ibiza. Our findings align with the historically documented two-pulse demographic model, indicating an initial settlement following the early tenth-century conquest and a second influx associated with Almoravid movements in the twelfth century. These securely dated genomes offer insights into medieval population dynamics and health in the Balearics.},
}

Humans
History, Medieval
*Islam/history
Spain
*Burial/history
*Genetic Variation
Metagenomics
Gene Flow
*Leprosy/microbiology/history/genetics
DNA, Ancient/analysis
Male
Cemeteries

@article {pmid41888125,
year = {2026},
author = {Fu, J and Zhang, J and He, R and Dong, Q and Mao, H and Shen, W and Wu, W and Chen, X and Ma, W and Zhai, Q and Chen, L and Zhou, H and Hu, S and He, Y and Qi, C},
title = {A global metagenomic atlas of aging identifies a microbiota phase transition associated with disease risk.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00970-4},
pmid = {41888125},
issn = {2055-5008},
support = {2023A1515012538//Basic and Applied Basic Research Foundation of Guangdong Province/ ; NSFC82300623//National Natural Science Foundation of China/ ; NSFC82272391//National Natural Science Foundation of China/ ; NSFC82302610//National Natural Science Foundation of China/ ; 2019YFA0802300//National Key Research and Development Program of China/ ; },
abstract = {Biological aging has been associated with altered risk of aging-related diseases, but the contribution of the gut microbiota to this process remains poorly understood. Here, we constructed an interpretable gut microbiota age clock using metagenomic data from 8115 fecal samples across five continents. We discovered a key microbial perturbation occurring at 56-60 years of chronological age, which was validated in an independent cohort of 2263 metagenomes. This perturbation was associated with a decline in ecological stability and substantial changes in the abundance of core species. Notably, the association between gut microbiota age and diseases was identified to be significantly altered before and after this inflection time. Moreover, within-species analyses uncovered phylogenetic divergence for seven age-related species, such as Escherichia coli, alongside functional alterations in older individuals, including enhanced cell motility, carbohydrate metabolism and horizontal gene transfer. Overall, our global gut microbiome atlas uncovers a critical age transition phase, highlighting opportunities for microbiota-based therapies and offering novel insights into evolutionary dynamics during aging.},
}

@article {pmid41888178,
year = {2026},
author = {Ariaeenejad, S and Abedanzadeh, S},
title = {Enhanced stability and reusability of metagenomic laccase via immobilization on functionalized mesoporous silica for antibiotic contaminant removal.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41888178},
issn = {2045-2322},
mesh = {*Laccase/chemistry/metabolism/genetics ; *Silicon Dioxide/chemistry ; *Enzymes, Immobilized/chemistry/metabolism ; *Anti-Bacterial Agents/chemistry/isolation & purification/metabolism ; Enzyme Stability ; Porosity ; *Metagenome ; Water Pollutants, Chemical/chemistry ; Biodegradation, Environmental ; Metagenomics ; Doxycycline/chemistry ; Imidazoles/chemistry ; },
abstract = {The extensive application of tetracycline antibiotics in agriculture and medicine has led to persistent contamination of aquatic and terrestrial ecosystems, disrupting microbial communities and contributing to the spread of antibiotic resistance. Conventional treatment methods often suffer from poor efficiency, limited stability, and high environmental costs, underscoring the need for robust and sustainable alternatives. Here, we present a biocatalytic platform in which a metagenome-derived laccase (PersiLac1) is covalently immobilized onto imidazole-functionalized SBA-15 mesoporous silica to overcome the limitations of free laccase, including low stability and high leaching. Immobilization markedly enhanced thermal stability, reusability, and catalytic efficiency toward the degradation of doxycycline (DC) and tetracycline (TC). The optimized system exhibited minimal enzyme leaching (9.6% at 25 °C; 22.0% at 80 °C) and achieved removal efficiencies of 76.7 ± 2.8% for DC and 53.7 ± 2.1% for TC within 24 h. High removal performance was maintained even at elevated antibiotic concentrations (200 mg L[-1]), with 43.9% and 42.8% removal for DC and TC, respectively. The immobilized laccase retained over 83% (DC) and 73% (TC) of its initial activity after 10 consecutive reuse cycles. To the best of our knowledge, this is the first report of integrating a metagenomic laccase with an imidazole-functionalized SBA-15 support for antibiotic degradation, offering a unique combination of enhanced stability, high reusability, and environmentally relevant performance. These findings highlight the potential of this immobilization strategy as a sustainable and high-performance solution for the remediation of antibiotic contaminants in water systems.},
}

*Laccase/chemistry/metabolism/genetics
*Silicon Dioxide/chemistry
*Enzymes, Immobilized/chemistry/metabolism
*Anti-Bacterial Agents/chemistry/isolation & purification/metabolism
Enzyme Stability
Porosity
*Metagenome
Water Pollutants, Chemical/chemistry
Biodegradation, Environmental
Metagenomics
Doxycycline/chemistry
Imidazoles/chemistry

@article {pmid41888223,
year = {2026},
author = {Afshar Jahanshahi, D and Ariaeenejad, A and Hasannejad, A and Zabihi, MR and Ghaffari, MR and Ariaeenejad, S and Kavousi, K},
title = {MiGPC: a comprehensive catalog of enzybiotics from environmental metagenomes.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-44250-9},
pmid = {41888223},
issn = {2045-2322},
support = {4020052//Center for International Scientific Studies & Collaborations (CISSC)/ ; },
abstract = {Antimicrobial agents play a vital role in human and environmental health, with applications spanning medicine, food preservation, agriculture, and biotechnology. Among them, enzybiotics enzyme-based antimicrobials have emerged as powerful alternatives to conventional antibiotics due to their targeted mechanisms and lower propensity for resistance. Beyond their medical relevance, enzybiotics have emerging applications in food preservation, animal health, and agriculture, thereby broadening their industrial and environmental value. To support the discovery and characterization of these versatile biomolecules, we present the first genome-resolved metagenomic gene and protein targeted enzybiotic catalog focused on enzybiotics, derived from diverse environmental microbiomes. The Microbial Enzybiotic Gene and Protein Catalog (MiGPC), integrates 15 whole-metagenome datasets from oceans, soils, fecal samples, vegetation, and plastic-contaminated environments, capturing a wide ecological spectrum. Enzybiotic sequences were compiled through a hybrid strategy combining public database mining and manual literature curation, yielding over 136,000 enzybiotic sequences, 7654 metagenome-assembled genomes (MAGs), and ~ 100 million unique genes and proteins. MiGPC integrates taxonomic and enzybiotic gene profiles, offering a robust platform for the discovery, annotation, and ecological mapping of antimicrobial enzymes. Functional analyses using KEGG and eggNOG revealed that approximately 62% of the genes remained uncharacterized, highlighting a rich source of potentially novel functions. Glycoside hydrolases and glycosyl transferases were the most prevalent CAZyme families, while the dominant enzybiotic-producing taxa belonged primarily to the Pseudomonadota and Bacillota phyla. Statistical modeling uncovered two major ecological clusters that distinguished polluted from relatively pristine environments. MiGPC enables high-throughput screening of previously unexplored metagenomes, facilitating the identification of novel antimicrobial agents from under characterized ecosystems. Overall, MiGPC represents a landmark resource that will support multi-omics research, microbial ecology, and the development of next-generation biotechnological solutions based on enzybiotics.},
}

@article {pmid41888360,
year = {2026},
author = {Belay, G and Suarez, C and Simachew, A and Paul, CJ},
title = {Microorganisms and functional genes in an aerobic-anoxic integrated gold mine wastewater treatment system.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {4},
pages = {},
pmid = {41888360},
issn = {1573-0972},
}

@article {pmid41888867,
year = {2026},
author = {Tao, M and Fan, Y and Qian, L and Liu, H and Ming, Y and Yu, X and Wu, K and Niu, M and Yan, Q and Huang, X and He, Z},
title = {Microbially driven methane and sulfur cycling processes and coupling mechanisms in mangrove sediments.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00877-9},
pmid = {41888867},
issn = {2524-6372},
support = {2021M703751//China Postdoctoral Science Foundation/ ; SML2023SP205, SML2024SP002, SML2024SP022//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; 42430707, 52070196, 32370113 and 92251306//National Natural Science Foundation of China/ ; 2024A1515010931//Guangdong Basic and Applied Basic Research Foundation/ ; },
abstract = {BACKGROUND: Methane (CH4) as a powerful greenhouse gas is the second largest contributor to global climate warming. Mangrove sediments are an important natural source of biogenic CH4 with rich organic carbon (C) and diverse sulfur (S) compounds, ideally for studying CH4 and S cycling processes and coupling mechanisms. Here we sampled mangrove sediment cores and analyzed their key microbial groups, key environmental factors and possible coupling mechanisms for CH4 and S cycling by metagenome sequencing approaches.

RESULTS: Our results showed that Methanomicrobiales and Methanophagales were predominant methanogens, Methanospirareceae was a representative of anaerobic methanotrophic archaea (ANME), and Desulfobacteraceae and Desulfobulbaceae were abundant sulfate-reducing bacteria (SRB), while Ectothiorhodospiraceae, Chromatiaceae and Comamonadaceae were dominant S-oxidizers. Correlation network analysis revealed positive interactions among methanogens, ANME and SRB. Also, metagenome-assembled genome (MAG) analysis indicated interspecies hydrogen transfer and extracellular electron exchange via conductive pili, flagella, and cytochromes were potential coupling mechanisms between methanogens and SRB. ANME could form consortia with SRB by intermediate metabolites (e.g., acetate) and/or direct interspecies electron transfer (e.g., flagella, pili, cytochromes). Furthermore, methanogen MAGs encoded thiosulfate oxidation and partial sulfate reduction pathways, while the ANME MAGs possessed potentials for S disproportionation and incomplete sulfate reduction. Additionally, SO4[2-], total sulfur, moisture content and salinity were important environmental factors affecting the microbial community structure and gene families involved in CH4 and S cycling.

CONCLUSION: This study provides novel insights into coupling mechanisms of CH4 and S cycling processes in mangrove sediments, having important implications for mitigating global warming.},
}

@article {pmid41888912,
year = {2026},
author = {Krull, J and Sidhu, C and Solanki, V and Bligh, M and Rößler, L and Singh, RK and Huang, G and Robb, CS and Teeling, H and Seeberger, PH and Schweder, T and Crawford, CJ and Hehemann, JH},
title = {Sulfated mannan of diatoms selects host-specific microbiota in the sunlit ocean.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02379-9},
pmid = {41888912},
issn = {2049-2618},
support = {101029842//MSCA/ ; Project number 570219261//Deutsche Forschungsgemeinschaft/ ; HE 7217/5-1//DFG/ ; 101044738//ERC/ ; },
abstract = {BACKGROUND: Diatoms, a keystone phylum in Earth's ecosystems, are responsible for substantial oxygen production and the fixation of carbon dioxide in the form of carbohydrates that fuel global food webs. They host diverse prokaryotes, yet how diatoms preferentially recruit those with complementary metabolic traits remains unknown.

RESULTS: We discovered that diatoms exude a C6-sulfated α-1,3-mannan that serves as a selective carbon source for adapted Polaribacter. Its structure was resolved using NMR spectroscopy, chromatography, chemical synthesis, and enzymatic dissection. Biochemical, physiological, and structural analyses demonstrated, that specialized Bacteroidota employ a four-enzyme pathway to metabolize this glycan. Metagenomic and transcriptomic data revealed that sulfated mannan utilization loci are globally abundant and actively expressed in surface ocean bacterioplankton. Because this mannan provides only carbon, oxygen, sulfur, and hydrogen, bacteria must obtain other essential elements elsewhere, reinforcing metabolic interdependence.

CONCLUSIONS: Together, these results define a chemically specific interaction between diatoms and specialized bacteria that is mediated by a single sulfated polysaccharide and a dedicated four-enzyme degradation pathway. Presence of this pathway in marine metagenomes and transcriptomes indicates that a sulfated mannan from diatoms exerts selection pressure in the sunlit ocean microbiome.},
}

@article {pmid41889037,
year = {2026},
author = {Muddiman, KJ and Doble, A and Stephen, AS and Bescos, R and Illsley, CS and Nicholas, TL and Hanks, S and Toit, LD and Brookes, ZLS},
title = {A Pilot Study Assessing the Oral Microbiome in Women of Menopausal Age: Do Oral Nitrate-Reducing Bacteria Play a Role?.},
journal = {International dental journal},
volume = {76},
number = {3},
pages = {109518},
doi = {10.1016/j.identj.2026.109518},
pmid = {41889037},
issn = {1875-595X},
abstract = {INTRODUCTION: The links between oral health and female ageing are poorly understood, but many changes occur in the oral cavity of menopausal women that affect quality of life, and few current oral health interventions consider gender as part of their approach. The aim of this pilot study was to test the hypothesis that the oral microbiome and microenvironment change during female ageing and are thus worthy of further consideration both experimentally and clinically.

METHODS: This observational pilot study retrospectively assessed women aged 18 to 89 years (n = 60) attending a UK primary care dental school facility for blood pressure screening, further analysing the salivary oral microbiome using metagenomics and the biochemical microenvironment using high-performance liquid chromatography. Periodontal health screening (Basic Periodontal Examination [BPE]) was then conducted as part of routine clinical care.

RESULTS: The cross-sectional design classified women into <32 years (n = 18), 40 to 49 years (n = 10), 50 to 59 years (n = 20), and 60+ years (n = 12), but the differences in salivary oestradiol levels between groups were inconclusive. Small numbers were not enough to detect differences in oral microbiome abundance, but nitrate-reducing species (P < .05), nitrate-nitrite-reducing activity (P < .05), and buffering capacity all increased as women aged 60+ years (P < .01), warranting increased numbers. Ageing women also had higher blood pressure (P > .05), were more likely to have periodontal pockets >5.5 mm (BPE4), and had an increased abundance of Porphyromonas (P < .05), but a full periodontal assessment is needed.

CONCLUSIONS: These observations suggest that the composition of the oral microbiome changes as women age, and thus, prospective and longitudinal oral microbiome studies with larger numbers are needed, including concurrent full periodontal assessment, plasma hormonal levels, and salivary flow. However, this study suggests that the oral microbiome in older women may require special consideration, with an increased focus on tailored oral hygiene interventions for this group.},
}

@article {pmid41889316,
year = {2026},
author = {Niyazi, HA and Niyazi, HA and AbdulMajed, H and Juma, N and Helmi, N and Alqarni, M and Saleh, BH and Zubair, M and Alfadil, A and Alhazmi, W and Alharbi, OS and Halabi, WS and Altalhi, R and Moglad, E and Alharbi, MT and Gazzaz, M and Alharthi, TM and Altayb, HN and Ibrahem, K},
title = {Pan-genome analysis and phylogenetic characterization of Klebsiella pneumoniae from global isolates.},
journal = {Future microbiology},
volume = {},
number = {},
pages = {1-12},
doi = {10.1080/17460913.2026.2617118},
pmid = {41889316},
issn = {1746-0921},
abstract = {AIMS: This study aimed to investigate the global genetic diversity, evolutionary relationships, and antimicrobial resistance (AMR) profiles of Klebsiella pneumoniae by performing a comprehensive pan-genome and phylogenetic analysis across worldwide isolates.

MATERIALS AND METHODS: A total of 72,057 K. pneumoniae genomes were retrieved from the NCBI database, from which 91 high-quality representative genomes each from a unique country were selected based on completeness, metadata availability, and sequence quality. Genomic assemblies were assessed using QUAST, annotated with PROKKA, and analyzed for pan-genomic composition and phylogenetic relatedness using standard bioinformatics pipelines.

RESULTS: The pan-genome revealed a large accessory component, reflecting extensive genomic plasticity and adaptability. QUAST analysis indicated significant variability in genome size and contig number, while PROKKA annotation identified diverse coding sequences, tRNA, rRNA, and AMR genes. Phylogenetic clustering demonstrated both geographically localized and globally disseminated lineages, suggesting regional adaptation and intercontinental transmission.

CONCLUSIONS: This study provides a global perspective on the genomic diversity and evolutionary patterns of K. pneumoniae. The widespread presence of AMR determinants underscores the urgent need for continuous genomic surveillance and integration of metagenomic approaches to improve monitoring, infection control, and therapeutic strategies against multidrug-resistant strains.},
}

@article {pmid41889516,
year = {2026},
author = {Mao, J and Jin, Q and Ye, D and Yang, Y},
title = {Case Report: A rare presentation of pulmonary tuberculosis with extensive ground-glass opacities in an immunocompetent patient: lessons from metagenomic next-generation sequencing.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1696371},
pmid = {41889516},
issn = {2296-858X},
abstract = {Pulmonary tuberculosis (PTB) is typically diagnosed through sputum smear microscopy and culture. However, diagnosis is challenging in patients with atypical radiological features and negative conventional tests. Ground-glass opacities (GGOs) are common but non-specific computed tomography (CT) findings and are rarely observed in immunocompetent PTB patients. We report the first case of an immunocompetent 53-year-old female presenting with extensive bilateral GGOs without classic clinical symptoms. Conventional microbiological cultures, acid-fast staining, and serological assays were all negative. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid identified Mycobacterium tuberculosis, further supported by a positive T-spot TB assay. Standard anti-tuberculosis therapy led to complete resolution of GGOs over nine months, confirmed by follow-up CT imaging. This case underscores the diagnostic challenge of atypical PTB presenting with non-classical CT manifestations in an immunocompetent host. It highlights the decisive role of mNGS as a complementary tool in cases where conventional methods fail, enabling timely diagnosis, precise treatment, and improved patient outcomes.},
}

@article {pmid41889550,
year = {2026},
author = {Xiu, Q and He, H and Liu, Z and Ou, X and Meng, Y and Zhao, K and Yang, Q and Zhang, X and Hou, Y and Yao, S and Gao, P and Xia, W},
title = {Biosurfactant-driven desorption and remediation of heavy oil contaminated soils underpinned by molecular simulations and microbial dynamics.},
journal = {RSC advances},
volume = {16},
number = {18},
pages = {16316-16328},
pmid = {41889550},
issn = {2046-2069},
abstract = {This study integrates molecular dynamics simulations and bench-scale experiments to investigate the adsorption and desorption behaviors of heavy oil on five mineral substrates: SiO2, kaolinite, muscovite, and Ca[2+]-/Na[+]-montmorillonite. Adsorption followed Langmuir isotherms, with montmorillonite exhibiting the highest capacities (0.061-0.062 molecules per Å[2] for aromatics in simulations; 0.086-0.091 g g[-1] in bench-scale tests) and SiO2 the lowest (0.027 pcs per Å[2]; 0.013 g g[-1]). Among four biosurfactants evaluated-rhamnolipid, sophorolipid, trehalose lipid, and mannosylerythritol lipid-sophorolipid consistently achieved the greatest desorption efficiency, removing up to 99.63% of adsorbed oil from Na[+]-montmorillonite and 96.04% from field-contaminated soil. 16S rRNA and metagenomic sequencing revealed an increased abundance of hydrocarbon-degrading bacteria within the soil microbial community, highlighting a synergistic effect between biosurfactant-induced desorption and biodegradation. These findings underscore the critical roles of mineralogical properties, oil fraction characteristics, and biosurfactant selection in soil washing treatment. This work presents a viable and eco-friendly strategy for remediating crude oil-contaminated soils, with important implications for optimizing large-scale environmental restoration efforts.},
}

@article {pmid41889698,
year = {2026},
author = {Almatrafi, R and Alasiri, A and Almuneef, G and Al-Hazzani, AA and Alghoribi, MF and Hakami, M and Arafah, AM and Alotibi, RS and Alrabiah, S and Alqurainy, N and Ajina, R and Aldriwesh, MG},
title = {First metagenomic analysis of age-associated changes in the gut microbiome among healthy Saudi adults: SAMS pilot study.},
journal = {Frontiers in aging},
volume = {7},
number = {},
pages = {1733638},
pmid = {41889698},
issn = {2673-6217},
abstract = {INTRODUCTION: The gut microbiome undergoes dynamic changes with aging across diverse healthy populations. However, data from Saudi Arabia remain limited. This pilot study investigated age-related variations in the gut microbiome among healthy Saudi adults to characterize region-specific microbial signatures and identify taxa potentially associated with aging in a healthy population.

METHODS: We established the Saudi Aging and Microbiome Study (SAMS) to investigate age-related changes in fecal microbiome of Saudi adults. In this pilot phase, 145 healthy participants aged 19-69 years were enrolled. Shotgun metagenomic sequencing was performed to profile fecal microbiome at the species level. Microbial diversity and taxonomic composition were compared across five age groups. Spearman and confounder-adjusted partial Spearman correlation were applied to identify taxa significantly associated with chronological age.

RESULTS: We analyzed fecal microbiome of 145 healthy adults distributed among five age groups: G1 (19-29 years, n = 33; 22.7%), G2 (30-39 years, n = 30; 20.7%), G3 (40-49 years, n = 27; 18.6%), G4 (50-59 years, n = 31; 21.4%), and G5 (60-69 years, n = 24; 16.6%). Of these, 75 (51.7%) were male, and 70 (48.3%) were female. Alpha diversity increased from young to older adulthood for observed richness and Shannon indexes (all q < 0.05). Beta diversity also varied significantly with age (PERMANOVA R [2] = 0.13, q = 0.023), indicating distinct microbial community structures in healthy older adults. At the phylum level, Firmicutes significantly increased with age (FC = 1.35; q = 0.026), whereas Bacteroidota decreased (FC = 0.59; q = 0.01). Consistent with these trends, Blautia obeum showed positive correlations, while Bacteroides thetaiotaomicron and Phocaeicola vulgatus showed negative correlations with chronological age.

CONCLUSION: In healthy Saudi adults, increasing age was associated with higher microbial diversity and compositional shifts at phylum and species levels. These age-associated microbial taxa might represent biomarkers of healthy aging and suggest an enhanced community capacity for short-chain fatty acids (SCFAs) production, a hypothesis warranting validation through future functional analyses.},
}

@article {pmid41889866,
year = {2026},
author = {Van Camp, AG and Park, J and Ozcelik, E and Eskiocak, O and Ozler, KA and Papciak, K and Subhash, S and Alwaseem, H and Ergin, I and Chung, C and Shah, V and Yueh, B and Fein, MR and Durmaz, C and Mozsary, C and Kilic, E and Garipcan, A and Damle, N and Najjar, D and Nelson, TM and Ryon, KA and Butler, DJ and Patel, CJ and Thaiss, CA and Birsoy, K and Mason, CE and Meydan, C and Tierney, BT and Beyaz, S},
title = {Diverse high-fat diets drive multi-omic reprogramming that persists after dietary reversal.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.17.708620},
pmid = {41889866},
issn = {2692-8205},
abstract = {Dietary fat composition modulates host physiology and the gut microbiome, but the long-term effects of specific fat sources and the extent to which these changes resolve after dietary reversal remain incompletely defined. Here, we present a longitudinal multi-omic resource of mice maintained for one year on a purified control diet, seven high-fat diets differing in predominant fat source, or reversal regimens in which animals were switched from high-fat to control diet after 4 or 9 months. We further incorporated two cohorts with distinct pre-existing microbiome configurations to determine how baseline community structure shapes diet-induced remodeling of the gut microbiome ecosystem. By integrating longitudinal phenotyping, fecal metagenomics, fecal metabolomics, plasma metabolomics and lipidomics, and intestinal single-cell RNA sequencing, we defined the shared and dietary fat-specific responses across host and microbiome compartments. Baseline microbiome composition strongly influenced microbial responses to diet, indicating that pre-existing community structure is a major determinant of dietary ecosystem remodeling. Although many altered features shifted toward baseline after dietary reversal, only approximately half of diet-associated microbial changes recovered within the study window. A subset of taxa exhibited persistent alterations, including sustained depletion of Lactobacillus johnsonii and Bifidobacterium pseudolongum and sustained enrichment of Alistipes finegoldii , consistent with a "microbiome memory" of prior high-fat diet exposure. This memory effect is mirrored in the host, by sustained suppression of major histocompatibility complex class II (MHC-II) gene expression in intestinal epithelial cells after dietary reversal. These findings indicate that dietary fats leave a lasting imprint on the host-microbiome interactome that survives dietary intervention. Together, these data establish a resource for defining how dietary fat source, baseline microbiome composition, and dietary history shape host-microbiome states. The entire resource is available online as an RShiny app.},
}

@article {pmid41890171,
year = {2026},
author = {Zhao, S and Sai, Y and Jia, M and Qiao, Y and Guo, W and Ding, W and Shao, X and Zheng, Y},
title = {Comprehensive insights into the mechanism of flavor formation in Cheonggukjang: Integration of metagenomics, volatomics, and metabolomics.},
journal = {Food chemistry: X},
volume = {35},
number = {},
pages = {103756},
pmid = {41890171},
issn = {2590-1575},
abstract = {Microbial metabolism shapes the unique flavor profile of Cheonggukjang; however, the formation pathways of characteristic flavor compounds mediated by microbiota remain unclear, hindering precise quality control. To fill this gap, this study innovatively integrated metagenoics, volatilomics, and metabolomics to systematically decode the flavor formation mechanism during Cheonggukjang fermentation. Volatile compound analysis defined three fermentation stages for Cheonggukjang (0-18, 18-60, and 60-72 h), identifying the 60-72 h period as the most critical for flavor formation. A total of 15 key flavor compounds were identified, with 10 designated stage-specific flavor markers. LefSe analysis revealed that Bacillus subtilis, Bacillus velezensis, Caldibacillus thermoamylovorans, and Bacillus licheniformis were the key biomarkers across different fermentation stages, while redundancy analysis (RDA) indicated that total sugar as the key driver of microbial succession. Additionally, this study reconstructed the metabolic network responsible for characteristic flavor formation and identified C. thermoamylovorans, B. licheniformis, B. velezensis, B. subtilis, Bacillus paralicheniformis, and Caldibacillus hisashii as core functional microbiota modulating amino acid metabolic to drive flavor development. This study lays a theoretical framework for standardizing Cheonggukjang production and targeted regulating its flavor quality.},
}

@article {pmid41890980,
year = {2026},
author = {Shi, Y and Sanderson, H and Chuan, J and Khan, IUH and Sunohara, M and Craiovan, E and Lapen, DR and Diarra, M and Chen, W},
title = {Dual-platform metagenomic surveillance distinguishes pathogen and resistome hotspots across agricultural and mixed-use watersheds.},
journal = {One health (Amsterdam, Netherlands)},
volume = {22},
number = {},
pages = {101384},
pmid = {41890980},
issn = {2352-7714},
abstract = {Freshwater systems embedded in agricultural landscapes serve as dynamic reservoirs and conduits for fecal-associated microbes, zoonotic pathogens, and antimicrobial resistance (ARG) and virulence factor (VF) genes. Yet factors that govern their densities and diversity remain a research challenge. From 2016 to 2021, we conducted a longitudinal water surveillance in an agriculturally dominated river basin in eastern Ontario, Canada; characterizing fecal-associated bacterial communities using 16S rRNA gene amplicon and shotgun metagenomic sequencing. Agricultural drainage ditches consistently harbored higher fecal-associated bacterial diversity with pronounced seasonal shifts; i.e., higher levels during larger flow periods in spring and fall. Elevated discharge was associated with enrichment of genera containing zoonotic or opportunistic pathogens, such as those in Pseudomonas, Sphingomonas, and Massilia. Conditionally rare taxa (CRTs), although typically low in abundance, accounted for ∼12.6% of all pathogen-associated genera and disproportionately contributed to community turnover, highlighting their role as transient reservoirs of microbial risk. Shotgun metagenomics detected 27 ARGs, primarily at mixed-use sites, and 14 VFs, mainly in agricultural ditches. Clinically relevant β-lactamase genes (e.g., oxa, imp, sme) co-occurred with metal-resistance operons, a pattern suggestive of possible co-selection, although selective agents were not directly measured. Although the prevalence of ARG and VF was low (<5% of samples), their ecological context indicates potential transmission pathways. Limited overlap in ARGs between short-read and metagenome-assembled genome (MAG)-based profiling reflects their complementary strength: gene-level sensitivity versus host-resolved analysis. Together, these findings demonstrate the utility of integrated amplicon and shotgun metagenomic surveillance for proactive One Health risk assessment in agricultural watersheds.},
}

@article {pmid41891006,
year = {2026},
author = {Mills, EG and Evans, KM and Dorazio, AJ and Squires, KM and Sundermann, AJ and Stellfox, ME and Culyba, MJ and Shields, RK and Van Tyne, D},
title = {Culture-enriched metagenomic sequencing reveals within-patient diversity and transmission of vancomycin-resistant Enterococcus faecium.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.11.26348025},
pmid = {41891006},
abstract = {UNLABELLED: Colonization of the gastrointestinal (GI) tract by vancomycin-resistant Enterococcus faecium (VREfm) often precedes bloodstream infection and serves as a reservoir for onward patient transmission in healthcare settings. Routine clonal isolate-based sequencing often underestimates within-patient diversity, and can miss transmission involving low-abundance and co-colonizing strains. Here we applied culture-enriched metagenomic sequencing to matched GI tract and blood VREfm populations collected ≤14 days apart from 35 patients with positive VREfm blood cultures collected between 2020 and 2025 at a single hospital. GI populations exhibited greater within-patient diversity than bloodstream populations, including multi-strain colonization in five patients. Among single-strain populations, variant analysis suggested distinct environment-specific pressures between the GI tract and bloodstream environments. To assess transmission using culture-enriched metagenomic sequencing, we compared all 70 VREfm populations against 470 contemporary clinical VREfm isolate genomes collected from the same hospital and identified 19 putative transmission clusters, including six clusters involving multi-strain populations. Together, these results demonstrate how culture-enriched metagenomic sequencing improves resolution for assessing within-patient VREfm diversity and enhances the detection of transmission events that could be missed by clonal isolate-based surveillance.

IMPACT STATEMENT: VREfm bloodstream infection is often seeded from bacteria colonizing the gut. The genetic diversity within gut and blood VREfm populations, and the role of this diversity in bacterial transmission, has been difficult to resolve as genomic surveillance typically relies on sequencing a clonal clinical isolate from each patient. Using culture-enriched metagenomic sequencing of matched GI tract and bloodstream VREfm populations from 35 patients at a single hospital, we found that the GI tract reservoir contained VREfm populations with greater strain and variant diversity than populations collected from the bloodstream. By integrating population sequencing with a large collection of VREfm clinical isolate genomes, we further demonstrate that different strains co-colonizing the GI tract of the same patient can reside in multiple putative transmission clusters, revealing potential transmission links that clone-based approaches are likely to miss. These findings demonstrate the potential utility of culture-enriched metagenomic sequencing for higher-resolution hospital surveillance of bacterial transmission. Applying this approach to other bacterial pathogens could improve our ability to detect and interpret transmission involving heterogeneous microbial populations that colonize and infect hospitalized patients.

DATA SUMMARY: Patient demographic data and clinical characteristics can be found in Table S1 (online Supplementary Material). All sequencing data generated in this study has been deposited in the National Center for Biotechnology Information (NCBI) under BioProject PRJNA901969, with sample accession numbers listed in Table S2 . Sequences used to construct the local reference strain database are available at NCBI BioProject PRJNA475751, with accession numbers listed in Table S3 . Variants identified in single-strain blood and GI populations are listed in Table S4 . Accession numbers for clinical isolate genomes included in transmission analyses are listed in Table S5 .

REPOSITORIES: Sequencing data generated in this study is deposited in the National Center for Biotechnology Information (NCBI) under BioProject PRJNA901969.},
}

@article {pmid41891018,
year = {2026},
author = {Basso, M and Hildebrand, F and Winder, C and Baker, DJ and Manders, R and Barberis, M and Gibbons, SM and Cohen Kadosh, K},
title = {Anxiety associated with dietary intake and gut microbiome features in a cross-sectional cohort of sub-clinically anxious young women.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.18.26348688},
pmid = {41891018},
abstract = {Background Emerging evidence highlights the gut-brain axis as a key pathway linking diet and anxiety, yet the key determinants remain unclear. Most studies have focused on single components of diet and rarely integrate long- and short-term intake. Furthermore, prior gut-brain work has focused on microbiome composition, while functional features remain underexplored. In this study, we investigated associations between long- and short-term dietary intake, gut microbiome composition and functions, and anxiety in a subclinical cohort of 46 females (18-24 years) from the United Kingdom. Results Long-term diet quality was assessed using the Healthy Eating Index (HEI-2020) derived from a food frequency questionnaire, stratifying participants into lower and higher diet quality clusters. Short-term dietary intake was assessed via 24-hour recalls. Shotgun metagenomics of stool samples was used to assess differences in alpha and beta diversity indices, species abundances, and bacterial pathways putatively metabolizing gut-brain-axis-relevant molecules. Anxiety was measured using the State-Trait Anxiety Inventory (state subscale STAI-s). Regression models identified diet quality (HEI cluster) as the primary dietary feature of anxiety variation. The presence of Ruminococcus gnavus and Flavonifractor plautii and the abundances of Bilophila wadsworthia and Bacteroides thetaiotaomicron were positively associated with anxiety. The presence of Feacalibacterium prausnitzii and greater abundances of butyrate, propionate, and GABA synthesis pathways were inversely associated with anxiety. Non-linear models revealed a U-shaped relationship between inositol synthesis and STAI-s. Finally, we found that habitual diet quality may modulate anxiety-related responses to short-term dietary variation. Conclusions These findings reveal widespread links between long-term diet quality, microbiota composition and function, and anxiety symptoms. These results point towards several promising targets for prebiotic, probiotic, postbiotic, and dietary interventions aimed at reducing anxiety.},
}

@article {pmid41891399,
year = {2026},
author = {Elsheikh, M and Ibrahim, MA and Fares, S and Bhongade, M and Adhem, K and Ramirez-Morales, XI and Kaseb, AO and Petrosino, J and Hassan, MM and Jalal, PK},
title = {Influence of Gut Microbiota on Response to Immune Check Point Inhibitors in MASLD Patients With HCC: Unraveling the Connection.},
journal = {Cancer medicine},
volume = {15},
number = {4},
pages = {e71738},
doi = {10.1002/cam4.71738},
pmid = {41891399},
issn = {2045-7634},
support = {R21CA293626/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome/immunology/drug effects ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; *Liver Neoplasms/drug therapy/immunology/microbiology/complications ; *Carcinoma, Hepatocellular/drug therapy/immunology/microbiology/complications ; Dysbiosis/microbiology ; Drug Resistance, Neoplasm ; Fecal Microbiota Transplantation ; Probiotics/therapeutic use ; },
abstract = {Immune checkpoint inhibitors (ICIs) have emerged as a promising treatment for various cancers, including advanced hepatocellular carcinoma (HCC). However, a significant proportion of patients with HCC, particularly those with metabolic dysfunction-associated liver disease (MASLD), exhibit resistance to ICI therapy. Studies have revealed that the presence of specific gut bacteria, such as Akkermansia, Bifidobacterium, and Lachnoclostridium, is associated with improved outcomes with ICI-treated HCC patients. Conversely, the overgrowth of bacteria like Enterobacteriaceae is linked to resistance to therapy. This review investigates the role of gut microbiota in shaping immune checkpoint inhibitor responses in MASLD-related hepatocellular carcinoma, focusing on how dysbiosis may contribute to ICI resistance and exploring microbiome modulation strategies, such as fecal microbiota transplantation and probiotics, aiming to optimize therapeutic outcomes.},
}

Humans
*Gastrointestinal Microbiome/immunology/drug effects
*Immune Checkpoint Inhibitors/therapeutic use/pharmacology
*Liver Neoplasms/drug therapy/immunology/microbiology/complications
*Carcinoma, Hepatocellular/drug therapy/immunology/microbiology/complications
Dysbiosis/microbiology
Drug Resistance, Neoplasm
Fecal Microbiota Transplantation
Probiotics/therapeutic use

@article {pmid41891696,
year = {2026},
author = {Toth, CRA and Molenda, O and Nesbø, CL and Luo, F and Devine, CE and Chen, X and Wu, K and Xiao, JZ and Puri, R and Guo, S and Bawa, N and Wang, P-H and Wei, Y and Flick, R and Edwards, EA},
title = {Identification of a highly expressed gene cluster likely coding for benzene activation enzymes in a methanogenic enrichment culture.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0208325},
doi = {10.1128/aem.02083-25},
pmid = {41891696},
issn = {1098-5336},
abstract = {UNLABELLED: The oil refinery (OR) consortium is a model methanogenic enrichment culture used to study anaerobic benzene degradation. Over half of the culture's bacterial community consists of two closely related Desulfobacterota strains, designated ORM2a and ORM2b, whose mechanisms of benzene activation are unknown. Three proteomics data sets were integrated and analyzed using high-quality OR metagenomes and metagenome-assembled genomes (MAGs), including a complete circularized ORM2a MAG, to identify active metabolic pathways and proteins expressed during methanogenic benzene degradation. Among the proteins identified were Bam-like subunits of an ATP-independent benzoyl-CoA degradation pathway, as well as downstream β-oxidation proteins yielding acetate. The most abundant proteins identified mapped to two ORM2a gene clusters of unknown function. Homologous and syntenic gene clusters were identified in the MAGs of ORM2b and a sulfate-reducing Pelotomaculum that also degrades benzene, as well as in nine contigs assembled from hydrothermal vent metagenomes. Extensive homology and structural predictions suggest that the first cluster-termed the "Magic" gene cluster-encodes for enzymes catalyzing the chemically challenging activation of benzene and subsequent transformation steps yielding benzoyl-CoA. The second ("Nanopod") gene cluster encodes a transmembrane complex that may facilitate benzene transport across the cell membrane. Phylogenomic analyses place ORM2a and ORM2b within a novel genus of strict anaerobes specialized for benzene degradation, which we propose naming "Candidatus Anaerobenzenivorax."

IMPORTANCE: Benzene is a widespread, persistent, and toxic pollutant that can accumulate in anoxic environments such as groundwater and sediments. Benzene can be metabolized in the absence of oxygen; however, despite decades of research, the biochemical mechanisms for benzene activation under anaerobic conditions remain unproven. This study provides strong genetic and proteomic evidence for a new suite of enzymes that initiate anaerobic benzene activation. These findings lay a foundation for future biochemical studies and expand our understanding of how microbes carry out difficult chemical reactions in the absence of oxygen.},
}

@article {pmid41891698,
year = {2026},
author = {Li, Y and Ji, M and Tu, Q},
title = {Patterns and drivers of macro- and micro-diversity of mudflat intertidal archaeomes along the Chinese coasts.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0143425},
doi = {10.1128/msystems.01434-25},
pmid = {41891698},
issn = {2379-5077},
abstract = {Archaea are widespread in Earth's ecosystems, contributing to ecosystem multifunctioning and stability. Compared to bacteria, our understanding of the biodiversity and underlying drivers of archaeal communities in representative ecosystems remains much less tapped. In this study, the macro- and micro-diversity of mudflat intertidal archaeomes were comprehensively analyzed at a large geographic scale, aiming to resolve the ecological drivers determining the variations in archaeal biodiversity. The compositions of mudflat intertidal archaeal taxa highly varied, especially the dominant Thaumarcheota and Euryarchaeota, but maintained relatively stable functional potential across space, demonstrating that functional traits were selected by the ecosystem in priority. While archaeal communities carried important functional traits mediating various biogeochemical cycling processes, horizontal gene transfer played critical roles in endowing functional genes for many archaeal lineages, such as the citric acid cycle in Methanosarcinia and various amino acid metabolism genes in Thermoplasmata. Spatial scaling, including latitudinal diversity gradient and distance-decay patterns (DDR), was clearly observed for archaeal taxonomic groups, but only DDR was weakly observed for functional traits. Intra-population genetic variations were significantly and positively associated with community macro-diversity, demonstrating covariations between nucleotide-level micro- and community-level macro-diversity. The compositions of intertidal archaeomes were mainly structured by homogeneous selection, with different phylogenetic bins being shaped by distinct ecological processes and remarkable variations across different sites. The study contributes to a comprehensive insight into the mechanisms shaping archaeal diversity and ecological characteristics within a fluctuating ecosystem.IMPORTANCEThe dynamic intertidal mudflat ecosystems host intense biogeochemical activities mediated by microbial communities, among which archaea contribute as an essential component but remain much less understood compared to bacteria. To gain better insights into the diversity, functional potential, and ecological drivers of archaeal communities in intertidal mudflats, archaeal phylogenetic signatures and genomic sequences were recovered via amplicon sequencing of 16S rRNA genes and shotgun metagenomes, targeting both macro- and micro-diversity. The results showed that archaeal taxonomic composition highly varied across space, whereas the functional potential remained relatively stable. Horizontal gene transfer served as an important source of archaeal metabolic diversity, obtaining additional genes linked to key biochemical pathways. The dominance of environmental selection further demonstrated the ecological forces governing archaeal communities in highly variable coastal habitats. This study established a large-scale framework for understanding the microbial ecology of intertidal archaeomes in dynamic coastal ecosystems.},
}

@article {pmid41892210,
year = {2026},
author = {Liang, X and Li, X and Mi, N and Wu, Y and Wu, J and Chen, H and Liu, D},
title = {Early-Life Diarrhea Disrupts Antioxidant-Immune Homeostasis and Gut Microbiota in Suckling Calves.},
journal = {Biology},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/biology15060450},
pmid = {41892210},
issn = {2079-7737},
support = {YLXKZX-NND-012//First-class Disciplines of Inner Mongolia Scientific Research Special Program/ ; 2023-JSGG-5//National Center of Technology Innovation for Dairy/ ; BR22-11-17//Basic Scientific Research Business Project of Universities directly under the Inner Mongolia Au-tonomous Region/ ; 2024LHMS03054//nner Mongolia Natural Science Foundation Project/ ; },
abstract = {Calf diarrhea is a common early-life disorder that adversely affects growth, oxidative balance, immune function, and intestinal microbiota, thereby compromising health and production performance. This study systematically investigates the effects of naturally occurring diarrhea in 7-day-old suckling calves on oxidative stress, immune responses, intestinal barrier integrity, and gut microbiota structure and function. Fecal scores, serum antioxidant and immune indices, and intestinal permeability markers were measured, and fecal samples were subjected to metagenomic sequencing. Diarrhea-affected calves exhibited higher fecal scores, increased oxidative stress indicated by reduced total antioxidant capacity, elevated lipid peroxidation, and altered antioxidant enzyme activities. Humoral immunity was impaired, inflammatory responses were dysregulated, and intestinal barrier function was disrupted. Gut microbial diversity declined, showing a depletion in health-associated taxa and the enrichment of opportunistic pathogens. Correlation analyses revealed that pathogenic bacteria abundance positively associated with diarrhea severity, oxidative stress, inflammation, and barrier disruption, while beneficial genera correlated with antioxidant and immune function. Functional profiling indicated a microbial shift from amino acid metabolism and antioxidant homeostasis toward carbohydrate and energy metabolism under diarrheic conditions. These findings highlight the pivotal role of gut microbiota dysbiosis in diarrhea pathogenesis and provide a foundation for developing microbiome-targeted interventions to improve calf health.},
}

@article {pmid41892424,
year = {2026},
author = {Gomes, E and Mesquita, TG and Serra, P and Araújo, D and Almeida, C and Machado, A and Oliveira, R and Castro, J},
title = {Antimicrobial Resistance in the Food Chain: Bridging Knowledge Gaps for Effective Detection and Control.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {3},
pages = {},
doi = {10.3390/antibiotics15030262},
pmid = {41892424},
issn = {2079-6382},
support = {https://doi.org/10.54499/2024.13640.PEX//Fundação para a Ciência e Tecnologia/ ; https://doi.org/10.54499/2022.07654.PTDC//Fundação para a Ciência e Tecnologia/ ; APTA4shiga (number 14840)//Fundação para a Ciência e Tecnologia/ ; },
abstract = {Antimicrobial resistance (AMR) poses a critical global public health threat, with the food chain serving as a significant transmission route connecting animals, environment, and humans. This review adopts a One Health perspective to analyze the key drivers of AMR dissemination across animal agriculture, aquaculture and food processing. We evaluate detection methodologies, contrasting the regulatory gold standard of culture-based phenotypic testing with rapid molecular advancements, including Whole Genome Sequencing (WGS), metagenomics, and emerging CRISPR-Cas diagnostics. While molecular tools offer unprecedented speed and resolution, challenges such as matrix interference, the viable but non-culturable (VBNC) state, and the genotype-phenotype disconnect remain. Finally, integrated mitigation strategies are also described, ranging from on-farm antimicrobial stewardship and innovative biofilm control to consumer hygiene practices. It is essential to bridge the technical and regulatory gaps in AMR surveillance in order to develop effective interventions and ensure a safer food system.},
}

@article {pmid41892439,
year = {2026},
author = {Gomes-Gonçalves, S and Bento, JT and Moreira, G and Mourão, J and Cruz, R and Esteves, F and Baptista, AL and Pereira, MA and Caseiro, P and Carreira, P and Figueira, L and Mesquita, JR},
title = {Comprehensive Shotgun Metagenomic Profiling of Antibiotic Resistance Genes in Sheep and Goat Farming Environments.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {3},
pages = {},
doi = {10.3390/antibiotics15030277},
pmid = {41892439},
issn = {2079-6382},
support = {PRR-C05-i03-I-000190//RumiRes project-"Vigilância epidemiológica de resistências antimicrobianas e resíduos medicamentosos em Pequenos ruminantes da Região Centro"/ ; },
abstract = {BACKGROUND: Antimicrobial resistance (AMR) is a growing global health concern, driven in part by antibiotic use in animal production systems. Despite its relevance, the microbiome and resistome of small ruminant farm environments remain largely underexplored.

METHODS: In this study, shotgun metagenomics was applied to environmental samples from 46 sheep, goat and mixed-species farms across 14 municipalities in central Portugal.

RESULTS: Microbial profiling revealed a well-preserved microbiome with Pseudomonadota, Actinomycetota, Bacteroidota and Bacillota (syn. Proteobacteria, Actinobacteria, Bacteroidetes and Firmicutes respectively) as the most dominant phylum across different farm types. Regarding AMR, a total of 706 unique antimicrobial resistance genes (ARGs), covering 15 antibiotic classes, were detected. Tetracycline, aminoglycoside and macrolide resistance genes dominated across all samples, forming a conserved core resistome. While overall resistome profiles were broadly similar among farm types, significant differences were observed in specific ARG classes, such as pleuromutilin and fosfomycin.

CONCLUSIONS: These findings highlight small ruminant farm environments as potential reservoirs of clinically relevant ARGs, including WHO highest priority critically important antimicrobial (HPCIA) resistance genes for macrolides (mph(c), erm(f), erm(b)) and fluoroquinolones (qnrD1), as well as critically important antimicrobial (CIA) resistance genes for glycopeptides (vanR-SC, vanR-O) and aminoglycosides (str, aadA), supporting the need to incorporate these environments into surveillance strategies.},
}

@article {pmid41892455,
year = {2026},
author = {Dashti, AA and Vali, L and Walsh, F},
title = {Metagenomic Profiling of Soil Microbiomes and Resistomes in Arid Ecosystems of Kuwait.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {3},
pages = {},
doi = {10.3390/antibiotics15030294},
pmid = {41892455},
issn = {2079-6382},
support = {(RN01/15))//Kuwait University/ ; (code EASREF).//University of Gloucestershire/ ; },
abstract = {Background/Objective: This study addresses a significant knowledge gap in the literature concerning antibiotic resistance genes (ARGs) in arid soils by employing metagenomic approaches to characterise their diversity, using Kuwait as a model environment. Methods: Soil samples were collected from two agriculturally managed sites (K1 and K3) and one coastal unmanaged site (K2), representing distinct ecological conditions. Results: Taxonomic profiling revealed notable variation in microbial communities at both the phylum and genus levels. Alpha diversity analyses based on the Chao1 and Shannon indices indicated that agricultural soils exhibited greater microbial richness and diversity than the coastal soil. Beta diversity analysis further demonstrated substantial differences in microbial community composition among the sites. Consistent with previous soil microbiome studies, ARGs such as tetA, aac(3)-Ib, sul1, qep, muxB, mexW, mexB, and macB were detected across the sites. However, the identification of distinct clinically relevant resistance genes, including ugd, blaOXA-18, blaCMY-19, blaMOX-7, blaFOX-7, blaLRA-12, and novA, suggests the influence of site-specific or extreme selective pressures. Conclusions: Several of the detected ARGs appear to be rare or previously unreported in soil environments. Although the sample size is too small to support broad generalisations, the detection of ugd in soil is particularly noteworthy, suggesting that soils may serve as reservoirs of polymyxin resistance, potentially undermining the effectiveness of polymyxin antibiotics.},
}

@article {pmid41892478,
year = {2026},
author = {Scarlata, GGM and Belančić, A and Štimac, D and Fajkić, A and Meštrović, T and Abenavoli, L},
title = {Bacteriophage Therapy Against Shigella spp.: A Precision Antimicrobial Strategy.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {3},
pages = {},
doi = {10.3390/antibiotics15030317},
pmid = {41892478},
issn = {2079-6382},
abstract = {Shigellosis remains a significant global cause of infectious colitis, increasingly complicated by multidrug-resistant strains and the microbiota-disrupting effects of broad-spectrum antibiotics. Although conventional antimicrobial therapy can reduce symptom duration and bacterial shedding, it also contributes to gut dysbiosis, loss of colonization resistance, and further selection for antimicrobial resistance. These challenges have renewed interest in precision antimicrobial strategies, particularly bacteriophage therapy, which provides strain-level specificity and preserves the gut microbiota. This narrative review evaluates the biological rationale, preclinical and early clinical evidence, safety considerations, and translational challenges associated with bacteriophage therapy targeting Shigella spp. The historical development and mechanistic basis of phage therapy are summarized, with emphasis on the advantages of obligately lytic phages, receptor-specific targeting, self-amplification at infection sites, and activity against both planktonic and biofilm-associated bacteria. Recent microbiota research indicates that shigellosis is closely associated with early and persistent disruption of gut ecology, including depletion of short-chain fatty acids-producing taxa and reduced microbial resilience. Phage-based approaches may reduce pathogen burden while preserving beneficial microbial communities. Evidence from in vitro systems, animal models, human intestinal organoids, and a Phase 1 clinical trial demonstrates targeted efficacy and favorable safety profiles for Shigella-specific phages and phage cocktails. Major barriers to clinical adoption include immune interactions, phage resistance dynamics, genomic safety screening, regulatory classification, and the need for standardized susceptibility testing. Future directions emphasize the development of personalized phage therapy platforms that integrate rapid diagnostics, phage libraries, metagenomics, and artificial intelligence-assisted matching to enable scalable, precision treatment.},
}

@article {pmid41892488,
year = {2026},
author = {Mise, K and Wasai-Hara, S and Itoh, H},
title = {Global terrestrial distribution of N2O-reducing Acidobacteriota members.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag073},
pmid = {41892488},
issn = {1751-7370},
abstract = {Nitrous oxide (N2O) is a potent greenhouse gas, and soil is its largest terrestrial source. Microbial N2O reductase (NosZ) is the only known enzyme capable of reducing N2O to N2, making nosZ-harboring prokaryotes important sinks in terrestrial ecosystems. Despite being among the most abundant and ubiquitous bacterial phyla in soil, the potential role of Acidobacteriota in N2O reduction remains largely unexplored. In this study, we addressed this gap using genomic, metagenomic, and physiological analyses. We first analyzed 199,602 prokaryotic genomes, including genomes from both isolated strains and metagenome-assembled genomes. We found that 491 Acidobacteriota genomes harbored nosZ, predominantly the Sec-dependent NosZ gene (nosZII). Global metagenomic analysis of 321 soil samples revealed that Acidobacteriota nosZII is one of the most abundant groups of nosZ and distributed across different continents. Among Acidobacteriota, nosZII from the class Vicinamibacteria was the most prevalent in the soils. Finally, we provide the physiological evidence of N2O-reducing activity in Acidobacteriota by demonstrating that the Vicinamibacteria type strain, Luteitalea pratensis KCTC52215T, can reduce N2O. Taken together, these findings highlight the previously overlooked potential role of Acidobacteriota as a global N2O sink and underscore the need to include them in future studies on soil N2O dynamics.},
}

@article {pmid41892593,
year = {2026},
author = {Krasenbrink, J and Chen, SC and Tanabe, TS and Sarikeçe, H and Meurs, P and Borusak, S and Samrat, R and Guan, G and Priemer, C and Osvatic, J and Séneca, J and Hausmann, B and Speth, DR and Selberherr, E and Wanek, W and Schleheck, D and Mussmann, M and Loy, A},
title = {Sulfoquinovose degradation by cow rumen microbiota.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag069},
pmid = {41892593},
issn = {1751-7370},
abstract = {Sulfoquinovose, a sulfonated sugar derived from the thylakoid membrane lipid sulfoquinovosyl diacylglycerol, is abundant in photosynthetic organisms and plays a key role in global sulfur cycling. Its degradation in nature is mediated by specialized bacteria, many of which rely on the enzyme sulfoquinovosidase (YihQ) to release sulfoquinovose from sulfoquinovosyl (diacyl)glycerol. Despite its ecological importance, the diversity and functional roles of sulfoquinovose-degrading microorganisms remain poorly characterized in natural environments. Here, we developed a yihQ-targeted amplicon sequencing approach to investigate the richness and distribution of SQ-degrading bacteria across selected environments. We revealed high richness of yihQ-containing microorganisms in the analyzed cow rumen samples, far exceeding that observed in human and mouse gut microbiomes, suggesting an important role of sulfoquinovose metabolism in ruminant digestion. Anoxic microcosm experiments with sulfoquinovose-amended rumen fluid revealed cooperative microbial degradation of sulfoquinovose to sulfide via isethionate cross-feeding. Amplicon sequencing and genome-resolved metagenomics and metatranscriptomics identified yet undescribed and uncultured sulfoquinovose-degrading taxa. Members of Caproiciproducens (Acutalibacteraceae), Candidatus Limivicinus (Oscillospiraceae), and Sphaerochaetaceae transcribed the isethionate-producing sulfo-transketolase pathway, whereas isethionate was likely respired by a Candidatus Mailhella bacterium (Desulfovibrionaceae). This study presents a functional gene-based assay for tracking environmental yihQ richness, highlights sulfoquinovose degradation as a central metabolic process in the cow rumen, describes previously unknown sulfoquinovose-metabolizing bacteria, and advances understanding of sulfur physiology in complex microbial communities.},
}

@article {pmid41892682,
year = {2026},
author = {Murgina, O and Stafeeva, K and Karaulova, S and Vostrikova, A and Kononova, S and Chursina, D and Pozdeeva, S and Makogonova, A and Burakova, I and Pogorelova, S and Morozova, P and Smirnova, Y and Syromyatnikov, M and Shutikov, V and Mikhailov, E and Gureev, A},
title = {Probiotic Bacillus subtilis, but Not a Lactobacillus spp., Ameliorates Cognitive Impairment in a Mouse Model of LPS and Zidovudine-Induced Neuroinflammation.},
journal = {Brain sciences},
volume = {16},
number = {3},
pages = {},
doi = {10.3390/brainsci16030340},
pmid = {41892682},
issn = {2076-3425},
support = {FZGW-2024-0003//Mikhail Syromyatnikov/ ; },
abstract = {Background/Objectives: The gut-brain axis is increasingly recognized as a critical modulator of cognitive function. This study investigated the neurotoxic effects of combined exposure to bacterial lipopolysaccharide (LPS) and the antiretroviral drug zidovudine (ZDV) in a mouse model, and evaluated the protective potential of two probiotic interventions: Bacillus subtilis and a mixture of lactobacilli. Methods: Cognitive function was assessed using the Morris water maze (MWM). Gut microbiota composition was analyzed by 16S rRNA sequencing, and intestinal morphology was examined histologically. Gene expression of neuroinflammatory markers and mitophagy-related genes in brain tissue was quantified by RT-PCR. Plasma levels of cell-free mitochondrial DNA (cf-mtDNA) were measured as a marker of mitochondrial damage. Results: Combined LPS + ZDV exposure induced systemic inflammation, impaired spatial memory, damaged the intestinal mucosa, and caused dysbiosis characterized by an increase in pro-inflammatory Muribaculaceae. In the brain, LPS + ZDV significantly upregulated Tnfa expression, confirming neuroinflammation. Bacillus subtilis administration prevented cognitive deficits, maintained Tnfa at control levels, and significantly reduced Il1b and Il6 expression compared to the LPS + ZDV group. This was accompanied by activation of the PINK1/PTEN-dependent mitophagy pathway, prevention of cf-mtDNA release, and restoration of gut microbial diversity. In contrast, the Lactobacilli mixture not only failed to improve outcomes but was associated with exacerbated intestinal damage, more pronounced cognitive dysfunction, and no reduction in neuroinflammatory markers. Conclusions: Combined exposure to LPS and ZDV induces gut-brain axis dysfunction characterized by neuroinflammation, cognitive impairment, intestinal damage, and dysbiosis. Bacillus subtilis effectively preserves cognitive function through activation of PINK1/PTEN-dependent mitophagy and suppression of neuroinflammation, highlighting its potential as a therapeutic candidate for cognitive impairments associated with gut-brain axis dysfunction. The contrasting effects of the lactobacilli mixture underscore the critical importance of strain-specificity in probiotic interventions.},
}

@article {pmid41893096,
year = {2026},
author = {Fan, J and Liu, S and Zhang, H and Jin, C and Wu, N},
title = {Dysbiosis of the Gut-Lung Axis and Its Immune Correlates During Pulmonary Cryptococcus neoformans Infection.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {12},
number = {3},
pages = {},
doi = {10.3390/jof12030163},
pmid = {41893096},
issn = {2309-608X},
support = {Grant No. 2023YFC2506004//National Key Research and Development Program of China/ ; },
abstract = {Cryptococcus neoformans is a major fungal pathogen responsible for life-threatening meningitis, especially in immunocompromised individuals. Although the gut-lung axis is known to regulate immune responses in respiratory infections, its role in cryptococcosis remains unclear. This study aimed to define the dynamic changes in the gut and lung microbiota and their relationship with host immunity during C. neoformans infection. Using a mouse model, we found that pulmonary infection induced significant dysbiosis in both the lung and gut microbiota, marked by decreased beneficial commensals and increased opportunistic pathogens. Integrated analysis showed these microbial shifts were closely associated with distinct immune responses: lung dysbiosis correlated with a strong IL-17-mediated pulmonary inflammatory response, while gut dysbiosis was linked to systemic immune activation in the spleen. Functional metagenomic prediction further revealed widespread disruption in microbial metabolic pathways, including energy metabolism and biosynthesis, in both sites. Importantly, a positive correlation was observed between lung and gut dysbiosis, indicating an interconnected gut-lung axis during cryptococcosis. These findings demonstrate that C. neoformans infection causes coordinated disruptions in microbiota and immunity across the gut-lung axis, underscoring the microbiome as a critical modulator of host response and suggesting potential avenues for microbiome-targeted therapies.},
}

@article {pmid41893137,
year = {2026},
author = {Francis, DV and Kishorkumar, M and Ahmed, ZFR and Neumann, EG and Kurup, SS},
title = {Molecular Advances and Sustainable Strategies in Mushroom Production for Food Security: A Review.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {12},
number = {3},
pages = {},
doi = {10.3390/jof12030205},
pmid = {41893137},
issn = {2309-608X},
support = {21R097//ARIFSID/ ; },
abstract = {Mushrooms offer a promising solution for sustainable food production due to their nutritional value, low resource requirements, and ability to grow in diverse environments. As interest in mushrooms grows, it is important to understand where current research is focused and where key gaps remain. A bibliometric analysis of 776 research articles indexed in Web of Science revealed a strong emphasis on yield, substrate reuse, and enzymatic degradation, but limited attention to molecular approaches, climate adaptation, and studies from arid regions such as the Middle East. Building on these findings, this review explores the ecological diversity of mushrooms and their adaptations across tropical, temperate, boreal, and arid ecosystems. It discusses the role of mycorrhizal and microbial interactions in nutrient cycling and environmental resilience, including desert truffle symbioses. Key pathways and genetic regulation involved in lignin degradation are outlined, along with recent advancements in transcriptomics, proteomics, genomics, metabolomics, and metagenomics that support improved cultivation and bioactive compound production. The review also addresses sustainable practices, such as microbiome integration and resource recycling, to enhance mushroom farming. The aim is to bring together ecological insights and molecular strategies to support sustainable mushroom production, particularly in regions facing resource and climate challenges.},
}

@article {pmid41893308,
year = {2026},
author = {Yeerjiang, B and Manaer, T and Liu, X and Bieerdimulati, R and Nabi, X},
title = {Mechanistic Insights into Lactobacillus harbinensis and Other Probiotics Regulating Lipid Metabolism in T2DM Mice via the PPARγ-LXRα-NPC1L1 Signaling Pathway Based on Multi-Omics Analysis.},
journal = {Metabolites},
volume = {16},
number = {3},
pages = {},
doi = {10.3390/metabo16030157},
pmid = {41893308},
issn = {2218-1989},
support = {No. 82260640//National Natural Science Foundation of China/ ; },
abstract = {Background/Objectives: Intestinal dysbiosis is a pivotal trigger of type 2 diabetes mellitus (T2DM). Our previous studies confirmed that composite probiotics derived from fermented camel milk (CPCM), containing Lactobacillus harbinensis and 13 other strains, can ameliorate glucose and lipid metabolism in T2DM mice by reshaping bile acid profiles, and its effect may be associated with the PPARγ-LXRα-NPC1L1 signaling pathway. Methods: Metagenomic analysis characterized alterations in intestinal microbiota structure and functional genes post-CPCM intervention, proteomic analysis detected changes in protein expression profiles related to glucose and lipid metabolism in mice, and Caco-2 cells were used for in vitro validation to clarify the regulatory effect of exopolysaccharides (EPS) (the active component of CPCM) on the PPARγ-LXRα-NPC1L1 signaling pathway. Results: The results showed that CPCM significantly improved glucose and lipid metabolism and remodeled the intestinal flora structure in mice, markedly enriching beneficial bacteria such as Lactobacillus and Akkermansia and enhancing the expression of functional genes related to the peroxisome proliferator-activated receptor (PPAR) signaling pathway and short-chain fatty acid synthesis in the microbiota. Proteomic analysis revealed that CPCM reversed the expression of key proteins involved in fatty acid oxidation and transport, thereby restoring the function of the PPAR signaling pathway. In vitro experiments validated that extracellular polysaccharides, the active component of CPCM, significantly upregulated the expression of PPARγ and liver X receptor α (LXRα) and inhibited the expression of Niemann-Pick C1-Like 1 (NPC1L1), a cholesterol absorption transporter, in Caco-2 cells. Conclusions: In conclusion, CPCM ameliorates glucose and lipid metabolic disorders in T2DM through multiple mechanisms: reshaping the intestinal probiotic community, enhancing its beneficial metabolic functions, restoring the activity of the PPARγ-LXRα signaling pathway, and subsequently downregulating NPC1L1.},
}

@article {pmid41893658,
year = {2026},
author = {Lisjak, A and Correa Lopes, B and Pilla, R and Nemec, A and Lampreht Tratar, U and Suchodolski, JS and Tozon, N},
title = {Assessment of Fecal Microbiota in Healthy Dogs and Dogs with Cutaneous Mast Cell Tumors Treated with Electrochemotherapy Combined with Gene Electrotransfer of IL-12.},
journal = {Veterinary sciences},
volume = {13},
number = {3},
pages = {},
doi = {10.3390/vetsci13030241},
pmid = {41893658},
issn = {2306-7381},
support = {P3-0428, P4-0053, P3-0003, and J4-2546//The Slovenian Research and Innovation Agency/ ; The microbiome research at the Gastrointestinal Laboratory at Texas A&M University is in part funded through Purina PetCare Research Excellence Fund//Purina PetCare Research Excellence Fund/ ; },
abstract = {Cancer is a major health concern, with its incidence rate continuing to increase. There is growing interest in the microbiota and its role in carcinogenesis, as it significantly influences physiological and pathological processes. Various aspects of the microbiome have been shown to have both anti-tumor and pro-tumor effects. Advances in techniques such as high-throughput DNA sequencing have greatly improved our understanding of microbial populations in the human and canine gut. We aimed to (1) characterize the intestinal microbiota of healthy dogs and dogs with cutaneous mast cell tumors (MCTs), (2) assess changes in the intestinal microbiota of dogs undergoing electrochemotherapy (ECT) combined with gene electrotransfer (GET) of the IL-12 plasmid (IL-12), and (3) explore possible associations with the expression of immune markers Programmed cell death protein 1 (PD-1), Programmed death-ligand 1 (PD-L1), and Granzyme B (GZMB) in MCT tissue. Stool samples were collected from healthy dogs (n = 24) and dogs with MCTs (n = 24) before and after ECT and IL-12 GET. DNA was extracted from the samples, and shallow shotgun sequencing was performed. Immunohistochemistry was performed on the tumors to assess the expression of PD-1, PD-L1, and GZMB. The dysbiosis index, alpha diversity, and beta diversity did not differ between groups. Regarding microbial composition, Bifidobacterium animalis, Corynebacterium variabile, Lactobacillus johnsonii, Pediococcus pentosaceus, Streptococcus anginosus, Streptococcus equinus, Streptococcus intermedius, Clostridium thermobutyricum, Megasphaera elsdenii, and Anaerobiospirillum sp. were found in lower relative abundance in feces of dogs with MCTs, while Bacteroides togonis, Lactobacillus amylolyticus, Prevotella sp. CAG:279, and Megamonas hypermegale were more abundant compared to healthy dogs. Our study provides further insight into the composition of the gut microbiota in dogs with MCTs, where ECT and IL-12 GET did not lead to major shifts. We were unable to establish any association between the expression of immune markers and the microbiota.},
}

@article {pmid41893667,
year = {2026},
author = {Karakaya, E and Satıcıoğlu, İB and Yarım, D and Güran, Ö and Güran, C and Alpman, U and Atalan, G and Abay, S and Aydın, F},
title = {Culture and Metagenomic Insights into the Ear Microbiota in Dogs with Healthy Ears and Otitis Externa.},
journal = {Veterinary sciences},
volume = {13},
number = {3},
pages = {},
doi = {10.3390/vetsci13030250},
pmid = {41893667},
issn = {2306-7381},
support = {TSA-2022-12342 and THD-2024-13751//Erciyes University/ ; },
abstract = {The canine ear microbiota plays an important role in ear health, and dysbiosis is associated with otitis externa (OE) and antimicrobial resistance (AMR). This study aims to investigate the ear microbiota of dogs with healthy ears and OE using bacterial culture-based methods and shotgun metagenomic sequencing, and to screen for AMR and virulence-associated genetic signatures. Ear swab specimens from 100 healthy and 100 OE-affected dogs were analyzed. The isolates obtained via bacterial culture were identified by MALDI-TOF MS and 16S rRNA sequencing. Metagenomic analysis was performed via Illumina shotgun sequencing. The most commonly defined species in healthy dogs in culture were Staphylococcus pseudintermedius (24.5%) and Staphylococcus epidermidis (5.7%); in dogs with OE, the most commonly defined species were S. pseudintermedius (30.5%), and Clostridium perfringens (4.5%). In healthy samples, metagenomic analysis revealed higher relative abundances of Bacteroides fragilis (15.8%) and Ezakiella coagulans (8.2%), while S. pseudintermedius (38.7%) dominated in OE. AMR profiling demonstrated diverse resistance determinants, including efflux pump systems and methicillin resistance-associated genes. In conclusion, the present study shows that S. pseudintermedius is a predominant member of canine ear microbiota, with higher presence in OE highlighting microbial shifts, and demonstrates that combining culture and metagenomic analyses provides a concise view of microbial communities and clinical relevance.},
}

@article {pmid41893692,
year = {2026},
author = {Shehla, S and Obaid, MK and Niaz, S and Khan, MA and Ahmad, AA and Abdel-Maksoud, MA and Alamri, A and Alrokayan, S and Shoaib, M and Shams, S and Ren, Q},
title = {Shotgun Metagenomics Reveals Microbial Diversity, Resistome, and Plasmidome in Dairy Cattle Feces.},
journal = {Veterinary sciences},
volume = {13},
number = {3},
pages = {},
doi = {10.3390/vetsci13030275},
pmid = {41893692},
issn = {2306-7381},
support = {ORF-RC-2026-2600//King Saud University/ ; },
abstract = {Fecal microbiota are shaped by upstream digestive processes and reflect the outcome of host-microbe interactions, including the resistant microbial fraction that survives to be excreted. This is particularly crucial for assessing zoonotic risks and environmental contamination, as feces are the primary source of dissemination, which is considered an emerging One Health threat. Therefore, we conducted a pilot study to obtain the exploratory findings regarding the cattle GIT microbial composition, potential resistome, and their transmission drivers, such as plasmids, using metagenomic analysis from different districts in Khyber Pakhtunkhwa (KP) province, Pakistan. For this purpose, a total of 150 fecal samples (50 from each district) of healthy cattle were collected from various farms in Mardan (FC1), Peshawar (FC2), and Dera Ismail Khan (FC3) districts. Total DNA from each sample was extracted, pooled (FC1, FC2, and FC3), and sequenced via the Illumina platform. Bacteria were the highly abundant kingdom, while Pseudomonadota and Bacillota were dominant phyla in all samples. Caryophanon latum and Escherichia coli were highly abundant at the species level. A large resistome (40-49 genes), including critical genes, such as tet(X), blaOXA-427, and plasmidomes (16-22), such as IncF, was detected in the samples. The prominence of certain commensal or opportunistic pathogens in the fecal microbiota may indicate the presence of sub-clinical gastrointestinal disruptions or disease that may affect cattle herds. The fecal resistome is extensive, identifying dairy cattle in these regions as important reservoirs for AMR genes capable of spreading via HGT. This pilot study establishes that the fecal microbiota of dairy cattle in this region are not merely a waste product but a complex ecosystem, rich in microbiota of One Health significance.},
}

@article {pmid41893724,
year = {2026},
author = {Qiu, Q and Gong, T and Du, L and Li, W and Hu, Y and Li, D and Zhou, C and Liu, W},
title = {Comparative Analysis of Microbial Community Structure and Function in the Gut of South China Tigers Under Different Dietary Treatments.},
journal = {Veterinary sciences},
volume = {13},
number = {3},
pages = {},
doi = {10.3390/vetsci13030307},
pmid = {41893724},
issn = {2306-7381},
support = {2110499//Diagnosis and Treatment of Genetic Diseases and Training for Stereotypic Behaviors in South China Tigers at Changsha Ecological Zoo/ ; 2110499//Artificial breeding of Reeves's pheasant (Syrmaticus reevesii) at Changsha Ecological Zoo/ ; },
abstract = {The gut microbiota is a crucial component of a tiger's health and plays a significant role in adapting to changes in food and the environment. Although extensive studies have been carried out on the gut microbiota of tigers, investigating the responses of gut microbial composition and function to preadaptation to wild predation patterns under captive conditions is particularly significant for South China tigers, given that it is the only tiger subspecies existing solely in captive settings at present. Here, we performed shotgun metagenomic sequencing for a comprehensive analysis of the gut microbiota of South China tigers assigned to two dietary groups (live prey group, LP group; frozen meat group, FM group), thereby generating abundant valuable data for this endangered subspecies. The results indicated that the core intestinal microbial composition was similar between the two dietary groups. Differential analysis revealed associations between dietary treatments and microbial abundance in the intestines of South China tigers. Functional gene analysis revealed that the LP group exhibited upregulation of genes and pathways related to antimicrobial resistance, bacterial infection-related disease, cell motility and proliferation, while the FM group displayed efficient energy metabolism. A total of 1251 antibiotic resistance genes (ARGs) were identified in the gut microbiome of South China tigers. The core resistome mainly included resistance to peptides, glycopeptides, tetracyclines, fluoroquinolones, and macrolides. In addition, the differences in ARGs between the LP group and FM group may be related to a broader range of animal tissues of live prey and the processing conditions of frozen meat. In summary, although feeding live prey did not change the core framework of the gut microbiota in South China tigers, it was associated with differences in microbial abundance, metabolic pathways, and antibiotic resistance gene profiles.},
}

@article {pmid41894043,
year = {2026},
author = {Tian, X and Feng, Y and Wang, C and Zhao, W and Xue, L and Zhu, L and Ji, X and Wang, H and Gu, Y and Jiang, Q and Zhang, J},
title = {Analysis of the characteristics of rumen microorganisms and their metabolites and plasma metabolites in crossbred beef cattle at different stages.},
journal = {Veterinary research communications},
volume = {50},
number = {3},
pages = {},
pmid = {41894043},
issn = {1573-7446},
support = {2021BEF01002//Major Project of Science and Technology ofNingxia Autonomous Region/ ; 2023AAC03050//Natural Science Foundation of Ningxia Hui Autonomous Region/ ; },
}

@article {pmid41894133,
year = {2026},
author = {Zhang, X and Chen, L and Wang, F and Xu, X and Wu, Y and Xu, J and Xu, Y and He, X},
title = {Torque teno virus in the lower respiratory tract: association with immunosuppression but not mortality in severe pneumonia-a multicenter retrospective cohort study.},
journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {},
number = {},
pages = {},
pmid = {41894133},
issn = {1435-4373},
support = {2024C3186//Key Research and Development Program of Zhejiang Province/ ; GZY-ZJ-KJ-24030//Major Project of National-Zhejiang Provincial Administration of Traditional Chinese Medicine/ ; },
}

@article {pmid41894264,
year = {2026},
author = {Yu, Y and Hong, S and Wang, Z and Li, S and Zhang, S},
title = {Leptospirosis-induced diffuse alveolar hemorrhage: A rare case report from a non-epidemic area and literature review.},
journal = {Medicine},
volume = {105},
number = {13},
pages = {e48131},
doi = {10.1097/MD.0000000000048131},
pmid = {41894264},
issn = {1536-5964},
support = {No. LY21H100002//Zhejiang Natural Science Foundation Project/ ; No.2024C31025//Science and Technology Plan Project of zhoushan/ ; },
mesh = {Humans ; Female ; *Leptospirosis/complications/diagnosis/drug therapy ; Aged ; *Hemorrhage/etiology/diagnosis/microbiology ; *Pulmonary Alveoli/pathology ; *Lung Diseases/etiology/diagnosis/microbiology ; Shock, Septic/etiology ; Anti-Bacterial Agents/therapeutic use ; },
abstract = {RATIONALE: Leptospirosis is an uncommon cause of severe pneumonia and diffuse alveolar hemorrhage (DAH), particularly in non-endemic areas, posing a significant diagnostic challenge. This case highlights the critical role of advanced molecular diagnostics in identifying this rare and life-threatening presentation.

PATIENT CONCERNS: A 65-year-old woman presented with an acute onset of high fever, chest tightness, and rapidly progressive shortness of breath.

DIAGNOSES: The patient was initially misdiagnosed with severe community-acquired pneumonia. She subsequently developed septic shock and multiple organ dysfunction syndrome. A definitive diagnosis of leptospirosis-induced DAH was confirmed through metagenomic next-generation sequencing, reverse transcription quantitative PCR, and subsequent seroconversion shown by immunoglobulin M enzyme-linked immunosorbent assay.

INTERVENTIONS: Upon diagnosis, targeted antimicrobial therapy with intravenous penicillin was initiated. Supportive care included management of septic shock and lung-protective ventilation for concomitant acute respiratory distress syndrome.

OUTCOMES: Following the confirmation of leptospirosis and initiation of targeted treatment, the patient's condition gradually stabilized. After a course of intensive care, she made a full recovery and was successfully discharged.

LESSONS: This case underscores that leptospirosis can present as fulminant DAH even in non-endemic regions. A high index of suspicion, aided by epidemiological clues and the rapid application of metagenomic next-generation sequencing/reverse transcription quantitative PCR, is crucial for timely diagnosis. Prompt targeted antimicrobial therapy combined with intensive organ support is essential for a favorable outcome in severe cases.},
}

Humans
Female
*Leptospirosis/complications/diagnosis/drug therapy
Aged
*Hemorrhage/etiology/diagnosis/microbiology
*Pulmonary Alveoli/pathology
*Lung Diseases/etiology/diagnosis/microbiology
Shock, Septic/etiology
Anti-Bacterial Agents/therapeutic use

@article {pmid41894564,
year = {2026},
author = {McCartin, LJ and Vohsen, SA and Wood, AL and Horowitz, J and Orozco-Juarbe, JJ and Pittoors, N and Morrissey, D and Vaga, CF and Hansel, CM and Collins, AG and Quattrini, AM and Herrera, S},
title = {Accounting for Intra- and Intergenomic Sequence Variation in Reference Barcodes Improves eDNA Metabarcoding Biodiversity Assessment.},
journal = {Molecular ecology resources},
volume = {26},
number = {3},
pages = {e70130},
doi = {10.1111/1755-0998.70130},
pmid = {41894564},
issn = {1755-0998},
support = {NA18OAR0110289//NOAA Ocean Exploration/ ; NA21OAR0110202//NOAA Ocean Exploration/ ; NA18NOS4780166//National Centers for Coastal Ocean Science/ ; //Smithsonian Institution/ ; //Smithsonian Women's Committee/ ; //Bureau of Ocean Energy Management/ ; 2000013668//National Academies of Sciences, Engineering, and Medicine/ ; //NOAA Fisheries Office of Science and Technology/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; *Biodiversity ; Animals ; *DNA, Environmental/genetics ; Puerto Rico ; *Anthozoa/genetics/classification ; *Genetic Variation ; *Metagenomics/methods ; RNA, Ribosomal, 28S/genetics ; },
abstract = {Environmental DNA (eDNA) metabarcoding can rapidly characterise biodiversity, yet its accuracy and effectiveness are limited by incomplete DNA barcode reference databases. We evaluated how comprehensive reference databases that include sequence variation within genomes (intragenomic) and across individuals and species (intergenomic) improve eDNA-based biodiversity assessments. We collected coral tissue and water samples at deep sites offshore Puerto Rico for reference barcoding and eDNA metabarcoding. Genome skimming coral specimens yielded 28S barcodes for 314 of 346 samples (90.8%) and revealed divergent intragenomic 28S lineages in multiple octocoral families. Incorporating local reference barcodes substantially changed ASV taxonomic classifications: 22 ASVs (8.9%) gained genus-level resolution, 19 ASVs (7.7%) were reassigned to different genera, and 14 ASVs (5.7%) lost incorrect genus-level classifications. Thus, incomplete reference databases produce not only unclassified ASVs but also false positive detections and ecologically meaningful misclassifications. When intragenomic 28S lineages were excluded from the reference database, 18 ASVs (7.4%) could not be classified to family or genus, demonstrating that unrecognised intragenomic variation can be mistaken for unsampled taxa. Integrating reference genome skimming and eDNA metabarcoding expanded known coral family richness by 36% at depths shallower than 1000 m and by 181% at depths greater than 1000 m. eDNA also detected two coral families previously unknown off Puerto Rico and nearby islands, underscoring its potential for biodiversity discovery.},
}

*DNA Barcoding, Taxonomic/methods
*Biodiversity
Animals
*DNA, Environmental/genetics
Puerto Rico
*Anthozoa/genetics/classification
*Genetic Variation
*Metagenomics/methods
RNA, Ribosomal, 28S/genetics

@article {pmid41894872,
year = {2026},
author = {Chen, H and Chai, Z and Chen, J and Song, C and Zheng, M},
title = {Anthraquinone-2-sulfonate enhances endogenous denitrification and phosphorus removal: Electron shuttle-mediated syntrophic partnerships.},
journal = {Water research},
volume = {298},
number = {},
pages = {125783},
doi = {10.1016/j.watres.2026.125783},
pmid = {41894872},
issn = {1879-2448},
abstract = {Endogenous denitrification (EnD) and denitrifying phosphorus removal (DPR) offer distinct advantages for low-carbon wastewater treatment, yet the nutrient removal performance is often constrained by inefficient electron transfer and nitrite/free nitrous acid (FNA) inhibition. Here, we demonstrate that anthraquinone-2-sulfonate (AQS) acts as an effective redox mediator to overcome these bottlenecks. With nitrate (NO3[-]-N) as the electron acceptor, the addition of 0.05 mmol/L AQS significantly amplified the electron transfer system activity (ETSA) by 3.66-fold. Consequently, this enhancement promoted the NO3[-]-N removal rate to 25.90 mg/(g VSS·h) (12.65-fold increase) and increased the phosphorus uptake rate to 3.69 mg/(g VSS·h) (1.95-fold improvement), achieving removal efficiencies of 96.22±1.00 % and 96.03±2.98 % for phosphorus and nitrogen, respectively. Moreover, when nitrite (NO2[-]-N) served as the electron acceptor, AQS enhanced the phosphorus uptake rate and nitrogen removal rate by 1.69-fold and 1.54-fold, respectively. Microbial analysis revealed a robust syntrophic partnership wherein Thauera, Candidatus Competibacter and Defluviicoccus (functioning as denitrifying glycogen-accumulating organisms) efficiently reduced NO3[-]-N to NO2[-]-N, which was subsequently scavenged by Dechloromonas and Candidatus Accumulibacter clade Ⅱ (functioning as denitrifying polyphosphate-accumulating organisms) for coupled phosphorus uptake. Metagenomic analysis further indicated that AQS facilitated electron transfer from Complexes I/Ⅱ to nitrate reductase and Complex Ⅲ, accelerating NO2[-]-N generation while alleviating FNA toxicity via coupled electron transfer from Cyt c to nitrite reductase. Crucially, this accelerated electron flux potentially intensified the proton motive force, suggesting an enhanced capacity for ATP generation to fuel the upregulation of phosphate transport (pit/pst) and polyphosphate synthesis (ppk) genes. These findings highlight AQS as a promising strategy to regulate electron transfer kinetics and metabolic coupling for advanced nutrient removal.},
}

@article {pmid41894881,
year = {2026},
author = {Zhao, Y and Li, Y and Zheng, Y and Yan, P and Lai, Y and Wang, X and Zhuang, LL and Zhang, J},
title = {Enhanced co-removal of nutrients and glyphosate from rural sewage in siphon-driven constructed wetlands: Optimization and mechanisms.},
journal = {Water research},
volume = {298},
number = {},
pages = {125812},
doi = {10.1016/j.watres.2026.125812},
pmid = {41894881},
issn = {1879-2448},
abstract = {Constructed wetlands (CWs) often suffer from limited carbon/oxygen availability and poorly controlled redox conditions, constraining pollutant removal from rural sewage. Hence, siphon-driven CWs (S-CWs) were optimized for the co-removal of the typical rural pollutant glyphosate (N-(phosphonomethyl)glycine, PMG) and typical wastewater pollutants (carbon (C), nitrogen (N), phosphorus (P)). S-CWs exhibited strong PMG resilience, tolerating up to 8 mg/L, and achieved 50.91-92.14%, 50.93-56.82% and 96.19-97.18% for PMG, N and P removal, respectively. These results indicated superior performance compared with unaerated and aerated CWs. Mechanistic analysis showed that PMG removal was dominated by biodegradation in the aerobic, carbon-enriched inlet area of S-CWs. This process was driven by genera such as Alcaligenes and Geobacillus, and enzymes like PhnI, PhnJ via aminomethylphosphonic acid (AMPA) and C-P lyase pathways, as confirmed by metagenomics and AlphaFold 3 predictions. PMG transiently inhibited N removal by suppressing denitrification but not nitrification. However, microbial adaptation over 135 days restored N removal along the first 50% pathway, even under high PMG stress (10 mg/L). In contrast, P removal was more persistently inhibited throughout the system, as the additional PMG-derived P increased total P load and accelerated substrate adsorption saturation. Long-term operation confirmed the robustness of S-CWs, including reduced effluent toxicity, healthier plant growth, lower oxidative stress, and minimal clogging (only 1.40-13.53% porosity decline). These observations highlight the hydraulic stability and long-term suitability of S-CWs for treating PMG-laden rural wastewater.},
}

@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.},
}