@article {pmid42555549,
year = {2026},
author = {Eiamthong, B and Srimora, T and Amornloetwattana, R and Uttamapinant, C},
title = {Enhancing the Versatility of Polyethylene Terephthalate (PET) Through Strategic Biomolecular Functionalization.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {65},
number = {37},
pages = {e26115},
pmid = {42555549},
issn = {1521-3773},
support = {//VISTEC/ ; B38G690002//National Science Research and Innovation Fund (NRSF)/ ; },
mesh = {*Polyethylene Terephthalates/chemistry/metabolism ; Biocatalysis ; Surface Properties ; *Proteins/chemistry/metabolism ; },
abstract = {As biocatalytic strategies for PET recycling reach maturation, insights gained from PET hydrolase research can be leveraged to inform the design of proteins and surface-functionalization strategies that promote stable association of functional proteins with PET surfaces, enabling the development of functional protein-plastic hybrid materials. Herein, we examine recent developments in biofunctionalization strategies of PET and related materials, with a focus on chemical biology approaches that offer more precise control of the orientation of proteins on PET and related materials. Biophysical insights from protein-polymer interface chemistry studies can inform protein selection, design, and engineering approaches to minimize denaturation and maximize function of proteins upon attachment to surfaces. Finally, we highlight applications of protein-functionalized PET and related synthetic polymers, including for biomedical applications and scalable biocatalysis, showcasing the potential of integrating biological activity into durable synthetic polymers.},
}

*Polyethylene Terephthalates/chemistry/metabolism
Biocatalysis
Surface Properties
*Proteins/chemistry/metabolism

@article {pmid42705727,
year = {2026},
author = {Xu, S and Li, J and Wang, F and Bian, H and Yan, W and Wang, H and Jiang, C and Sun, J and Wang, Z and Li, X},
title = {Depth-dependent microbial succession and interspecies hydrogen transfer drive pit mud maturation in Chinese strong-flavor baijiu fermentation.},
journal = {Food research international (Ottawa, Ont.)},
volume = {243},
number = {Pt 2},
pages = {120362},
doi = {10.1016/j.foodres.2026.120362},
pmid = {42705727},
issn = {1873-7145},
mesh = {*Hydrogen/metabolism ; *Fermentation ; Bacteria/metabolism/classification/genetics ; Archaea/metabolism/genetics/classification ; *Wine/microbiology/analysis ; *Food Microbiology ; *Microbiota ; Metagenomics ; China ; *Alcoholic Beverages/microbiology ; },
abstract = {Microbial communities in fermentation pit mud play a key role in determining the quality of Chinese strong-flavor baijiu (CSFB). However, the ecological processes underlying pit mud maturation across spatial and temporal scales remain unclear. In this study, amplicon sequencing and metagenomic analyses were employed to investigate the taxonomic succession, community assembly, and metabolic functions of bacterial and archaeal communities during the transition from fresh pit mud (FPM) to new pit mud (NPM) and old pit mud (OPM). A pronounced depth-dependent succession pattern was observed, with 4 cm representing a critical ecological boundary separating distinct community structures and maturation trajectories. During surface-layer maturation, community assembly shifted from stochastic to deterministic processes, accompanied by homogeneous selection and increasing network complexity. In contrast, stochastic processes remained dominant throughout deep-layer maturation. Metagenomic analyses revealed a functional transition from lactate and acetate production, primarily associated with Lactobacillus in FPM and NPM, to butyrate and caproate production associated with Clostridium and Caproiciproducens in OPM. This functional transition was accompanied by enhanced amino acid metabolism, which was associated with the enrichment of Proteiniphilum and Aminobacterium. Notably, methanogen-mediated interspecies hydrogen transfer (IHT) emerged as a key ecological feature during pit mud maturation. In OPM, IHT networks primarily involving Methanobacterium and Methanosarcina linked methanogenesis with reverse β-oxidation through diverse hydrogen-transfer pathways, reinforcing metabolic interactions underlying caproate production. These findings provide new insights into the ecological mechanisms underlying pit mud maturation and offer a theoretical basis for the directed cultivation of high-quality pit mud in CSFB production.},
}

*Hydrogen/metabolism
*Fermentation
Bacteria/metabolism/classification/genetics
Archaea/metabolism/genetics/classification
*Wine/microbiology/analysis
*Food Microbiology
*Microbiota
Metagenomics
China
*Alcoholic Beverages/microbiology

@article {pmid42705729,
year = {2026},
author = {Li, Y and Li, J and Deng, J and Xia, P and Zhou, G and Zhu, Z and Ding, Y and Yang, J and Zhang, F},
title = {Phocaeicola vulgatus alleviates obesity through cross-species arginine production and hepatic retinoic acid signaling.},
journal = {Food research international (Ottawa, Ont.)},
volume = {243},
number = {Pt 2},
pages = {120365},
doi = {10.1016/j.foodres.2026.120365},
pmid = {42705729},
issn = {1873-7145},
mesh = {*Arginine/biosynthesis/metabolism ; Animals ; *Obesity/therapy/microbiology/metabolism ; *Liver/metabolism ; Signal Transduction ; *Tretinoin/metabolism ; Rats ; Humans ; Fecal Microbiota Transplantation ; Male ; Gastrointestinal Microbiome ; Diet, High-Fat ; },
abstract = {Fecal microbiota transplantation (FMT) shows inconsistent clinical efficacy in treating obesity, and the specific microbial determinants dictating its success remain poorly characterized. Our previous clinical FMT trial identified Phocaeicola vulgatus as a key microbe contributing to the therapeutic efficacy of obesity treatment. Here, to investigate its role in obesity, we established an independent clinical cohort comprising obese and lean individuals, revealing that the P. vulgatus-centered network and ornithine synthesis are impaired in the obese group. We then confirmed causality by utilizing a humanized rat model carrying microbiota from a P. vulgatus-deficient obese patient, demonstrating that P. vulgatus supplementation significantly mitigates HFD-induced obesity, including reductions in body weight and serum total cholesterol levels, as well as the alleviation of hepatic steatosis. To further explore the functional mechanisms of P. vulgatus, integrated metagenomic and metabolomic analyses revealed a potential functional association between P. vulgatus and Phascolarctobacterium faecium that is associated with enhanced intestinal arginine biosynthesis and systemic availability. Furthermore, hepatic transcriptomics linked these elevated circulating arginine levels to the upregulation of retinoic acid (RA) signaling. Taken together, our findings outline a potential microbial-host network wherein P. vulgatus mitigates obesity via the arginine-RA axis, providing a valuable scientific basis for exploring this strain as a probiotic candidate for metabolic health.},
}

*Arginine/biosynthesis/metabolism
Animals
*Obesity/therapy/microbiology/metabolism
*Liver/metabolism
Signal Transduction
*Tretinoin/metabolism
Rats
Humans
Fecal Microbiota Transplantation
Male
Gastrointestinal Microbiome
Diet, High-Fat

@article {pmid42705740,
year = {2026},
author = {Zhan, F and Yu, R and Zheng, W and Benjakul, S and Pan, D and Zhang, B},
title = {Intestinal content accelerates muscle protein degradation in red shrimp (Solenocera crassicornis) during refrigeration: Insights from metagenomics and metabolomics.},
journal = {Food research international (Ottawa, Ont.)},
volume = {243},
number = {Pt 2},
pages = {120377},
doi = {10.1016/j.foodres.2026.120377},
pmid = {42705740},
issn = {1873-7145},
mesh = {Animals ; *Refrigeration ; *Muscle Proteins/metabolism ; Proteolysis ; *Metagenomics/methods ; *Metabolomics/methods ; *Intestines/microbiology ; *Shellfish/microbiology/analysis ; Food Storage ; },
abstract = {This study systematically explored the effects of intestinal components on muscle quality deterioration and protein degradation of red shrimp during refrigerated storage. The results demonstrated that refrigeration induced continuous quality degradation and muscle protein breakdown in red shrimp, whereas eliminating intestinal tissues effectively retarded muscle spoilage and protein degradation, and optimized muscle texture. The intestinal microorganisms could secrete extracellular proteases to promote muscle protein degradation were primarily Vibrio, Bacillus, Pseudomonas, Photobacterium, and Shewanella. These microorganisms promote protein degradation by secreting zinc proteases, serine proteases, and aspartyl proteases. This study elucidates the molecular mechanisms of intestinal microbial metabolism influences the muscle protein degradation of red shrimp during refrigeration. The findings provide a theoretical foundation for precise regulation of intestinal-targeted microorganisms, thereby maintaining optimal quality of shrimps during refrigeration.},
}

Animals
*Refrigeration
*Muscle Proteins/metabolism
Proteolysis
*Metagenomics/methods
*Metabolomics/methods
*Intestines/microbiology
*Shellfish/microbiology/analysis
Food Storage

@article {pmid42705742,
year = {2026},
author = {Han, G and Li, K and Wang, J and Xu, P and Liu, T and Xu, X and Zhao, Y},
title = {Mechanistic insights into flavor deterioration in bitter sturgeon caviar: Evidence from lipidomics and metagenomics.},
journal = {Food research international (Ottawa, Ont.)},
volume = {243},
number = {Pt 2},
pages = {120381},
doi = {10.1016/j.foodres.2026.120381},
pmid = {42705742},
issn = {1873-7145},
mesh = {Animals ; *Metagenomics ; *Fishes ; *Lipidomics ; *Taste ; Volatile Organic Compounds/analysis ; Odorants/analysis ; Microbiota ; Bacteria ; *Seafood/analysis/microbiology ; Humans ; },
abstract = {This study systematically compared the flavor and multi-omics differences between normal caviar and bitter caviar based on quantitative descriptive analysis (QDA), volatile compounds (VOCs) analysis, untargeted lipidomics, and metagenomics. The results showed that bitter caviar was characterized not only by increased bitterness, but also by decreased positive sensory attributes, including buttery, nutty, and marine fresh. VOCs analysis indicated that the volatile profile of bitter caviar was reorganized. Compounds such as 3-hydroxy-2-butanone, 1-octen-3-ol, and (E, Z)-2,6-nonadienal showed higher relative odor activity values (rOAVs); however, these changes did not improve its overall sensory experience. Untargeted lipidomics identified 492 differential lipids. These changes were mainly characterized by decreased PC and increased DG and LPC in bitter caviar. KEGG pathways analysis showed that these differential lipids were mainly associated with glycerophospholipid metabolism, choline metabolism in cancer, and retrograde endocannabinoid signaling. Metagenomic analysis showed that bacteria dominated the microbial community of caviar. Among them, Bacillus and Micromonospora showed relatively high abundance in the caviar microbiota. They were also closely associated with lipid metabolic changes involving PC, DG, and LPC, suggesting their potential as candidate targets for future microbiota-directed regulation of caviar quality. These findings provide new insights into the mechanisms underlying sensory deterioration and flavor formation in bitter caviar, and offer a theoretical basis for improving caviar quality in industrial production.},
}

Animals
*Metagenomics
*Fishes
*Lipidomics
*Taste
Volatile Organic Compounds/analysis
Odorants/analysis
Microbiota
Bacteria
*Seafood/analysis/microbiology
Humans

@article {pmid42705761,
year = {2026},
author = {Shi, H and Shen, Y and Ye, Q and Yu, H and Tian, M and Wang, H and Wei, Y and Yan, S and Chen, Y and Zhang, J and Li, S and Yang, Y and Zhao, J},
title = {Spatially resolved multi-omics analysis of indigenous Bacillus-fortified high-temperature Daqu.},
journal = {Food research international (Ottawa, Ont.)},
volume = {243},
number = {Pt 2},
pages = {120404},
doi = {10.1016/j.foodres.2026.120404},
pmid = {42705761},
issn = {1873-7145},
mesh = {*Bacillus/metabolism/genetics ; Multiomics ; *Hot Temperature ; *Food, Fortified/microbiology ; Metabolomics ; Metagenomics ; *Food Microbiology ; },
abstract = {Layer-dependent patterns associated with indigenous Bacillus fortification on high-temperature Daqu remain unclear. Here, six indigenous functional Bacillus strains were combined to fortify Daqu at three inoculation levels (QH4, QH5, QH6), with non-fortified as the control (CK). Upper, middle, and lower shelf-layer samples were profiled by physicochemical measurements, volatilomics, organic acid analysis, untargeted metabolomics, 16S/ITS amplicon sequencing, and metagenomics. PERMANOVA showed significant effects of treatment, spatial layer, and their interaction on physicochemical, volatile, bacterial, and fungal profiles (P = 0.001). Among the three inoculation levels, QH5 showed the most balanced performance: QH5_M exhibited the highest observed mean peak temperature (63.3 °C; +4.5 °C relative to CK_M), and its group-mean temperature remained ≥ 60 °C for seven consecutive days. Multi-omics analyses indicated coordinated, non-linear, and layer-dependent differences associated with indigenous Bacillus fortification, with QH5_M showing the most pronounced combined thermal, pyrazine, substrate, microbial, and predicted functional profile. These findings indicate that moderate indigenous Bacillus fortification was associated with distinct layer-dependent thermal and flavor profiles and coordinated microbial, metabolic, and predicted functional differences.},
}

*Bacillus/metabolism/genetics
Multiomics
*Hot Temperature
*Food, Fortified/microbiology
Metabolomics
Metagenomics
*Food Microbiology

@article {pmid42705847,
year = {2026},
author = {de Paula, BB and Miagostovich, MP and Mannarino, CF and Ribeiro, AVC and Lanzarini, NM and de Oliveira, CS and Novo, SPC},
title = {Metagenomics Reveals Microbial Community Shifts Associated With Contrasting Anthropogenic Impacts in Freshwater Sources of A Coastal Protected Area in Southeastern Brazil.},
journal = {Water environment research : a research publication of the Water Environment Federation},
volume = {98},
number = {9},
pages = {e70567},
doi = {10.1002/wer.70567},
pmid = {42705847},
issn = {1554-7531},
support = {25388.010001/2018-23//Brazilian National Health Foundation (FUNASA)/ ; 0406080/2021//Conselho de Desenvolvimento Científico e Tecnológico/ ; 305737/2023-6//Conselho de Desenvolvimento Científico e Tecnológico/ ; PROEP/IOC441653/2024-3//Conselho de Desenvolvimento Científico e Tecnológico/ ; E26/202.266/2024//Fundação de Amparo à Pesquisa do Rio de Janeiro/ ; },
mesh = {Brazil ; *Fresh Water/microbiology ; *Metagenomics ; *Bacteria/genetics/classification ; *Water Microbiology ; *Anthropogenic Effects ; Environmental Monitoring ; },
abstract = {This study aimed to characterize freshwater microbial communities, environmental drivers, and anthropogenic impact patterns across three sites on Marambaia Island (southeastern Brazil) using metagenomics. Samples collected from freshwater sources used for human consumption were processed through concentration, nucleic acid extraction, and sequencing on the Illumina NextSeq 2000 platform. A total of 67.2 million reads were assembled into 89,230 bacterial contigs, mostly attributed to Gammaproteobacteria, Alphaproteobacteria, and Betaproteobacteria. Sites under lower anthropogenic influence exhibited higher microbial diversity, whereas impacted sites showed enrichment of opportunistic and fecal-associated genera. A heterogeneous anthropogenic impact profile was observed across sites, corroborated by the proposed Anthropogenic Impact Index (AII). Fourteen antimicrobial resistance genes conferring resistance to beta-lactams, quinolones, sulfonamides, tetracyclines, and macrolides were detected predominantly in sewage-impacted areas, indicating potential diffuse contamination. Redundancy analysis revealed that environmental variables explained 88.1% of microbial community variation, with conductivity, salinity, and turbidity as key drivers. These findings demonstrate the applicability of metagenomics as a powerful tool for assessing microbial diversity, ecological dynamics, and contamination risks in vulnerable freshwater systems.},
}

Brazil
*Fresh Water/microbiology
*Metagenomics
*Bacteria/genetics/classification
*Water Microbiology
*Anthropogenic Effects
Environmental Monitoring

@article {pmid42706263,
year = {2026},
author = {He, W and Bobanga, T and Piantadosi, A and Popkin-Hall, ZR and Vulu, F and Collins, MH and Kashamuka, MM and Tshefu, AK and Juliano, JJ and Parr, JB},
title = {Evidence of dengue transmission and a diverse Aedes mosquito virome on the Congo's Angola border.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42706263},
issn = {2041-1723},
support = {INV-050353//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; K24AI134990//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; Yang Biomedical Scholar award//UNC | University of North Carolina at Chapel Hill (UNC-Chapel Hill)/ ; },
mesh = {Animals ; *Aedes/virology ; *Dengue Virus/genetics/isolation & purification ; Humans ; Angola/epidemiology ; *Dengue/transmission/epidemiology/virology ; *Virome/genetics ; *Mosquito Vectors/virology ; Democratic Republic of the Congo/epidemiology ; Female ; Congo ; },
abstract = {Aedes mosquitoes are widely distributed across the Democratic Republic of Congo (DRC), and are major vectors of dengue (DENV), Zika, chikungunya (CHIKV), and yellow fever (YFV) viruses. While the high burden of malaria in the DRC receives considerable attention, arboviruses remain understudied. In the setting of recent CHIKV and YFV outbreaks in southwestern DRC, we collect Aedes mosquitoes in three areas of Kimpese, DRC, near the Angola border, to investigate their virome. Metagenomic and targeted sequencing of eight randomly selected field mosquito pools, comprising 155 mosquitoes from three collection sites, confirm high-confidence DENV reads and human blood meals in six (75%) and eight (100%) pools, respectively. We find diverse mosquito viromes including other known and putative human and animal viruses. Our findings provide strong evidence of endemic DENV transmission along the DRC-Angola border and illustrate the potential of wild-caught mosquitoes for xenosurveillance of emerging pathogens.},
}

Animals
*Aedes/virology
*Dengue Virus/genetics/isolation & purification
Humans
Angola/epidemiology
*Dengue/transmission/epidemiology/virology
*Virome/genetics
*Mosquito Vectors/virology
Democratic Republic of the Congo/epidemiology
Female
Congo

@article {pmid42706541,
year = {2026},
author = {Jundzill, M and Hölzer, M and Mangul, S and Marquet, M and Ehricht, R and Lohde, M and Spott, R and Makarewicz, O and Pletz, MW and Brandt, C},
title = {Large-scale benchmarking of prokaryotic annotation tools across thousands of species.},
journal = {Genome biology},
volume = {27},
number = {1},
pages = {},
pmid = {42706541},
issn = {1474-760X},
support = {FKZ:13N15720//Innovative molecular and biochemical assays for rapid diagnostics, drug development and new therapy concepts (LPI-BT5)/ ; [Projekt-Nr.: 512648189]//German Research Foundation and the Open Access Publication Fund of the Thueringer Universitaets und Landesbibliothek Jena/ ; 760073/23.05.2023, code 285/30.11.2022, within Pillar III, Component C9, Investment 81//Ministry of Research, Innovation and Digitization under Romania's National Recovery and Resilience Plan - Funded by EU - NextGenerationEU program, project "Artificial intelligence-powered personalized health and genomics libraries for the analysis of long-term effects in COVID-19 patients (AI-PHGL-COVID)/ ; Förderkennzeichen: MSP24//University Hospital Jena Young Researchers funding program IZKF/ ; },
mesh = {*Molecular Sequence Annotation/methods ; *Genome, Bacterial ; *Genome, Archaeal ; Benchmarking ; *Software ; Archaea/genetics ; Computational Biology/methods ; Metagenome ; Gene Ontology ; },
abstract = {BACKGROUND: Genome annotation is an important step in deriving functional meaning from prokaryotic sequencing data, yet systematic evaluations guiding tool selection are lacking. We present the first large-scale investigation of four prominent open-source annotation tools (Prokka, Bakta, EggNOG-mapper, and PGAP) across 156,033 diverse genomes. This includes Escherichia coli strains for baseline performance, thousands of archaea and bacteria genomes, as well as frameshifted and metagenome-assembled genomes.

RESULTS: Bakta excels in annotating high-quality bacterial genomes, while PGAP was better for archaeal genomes and challenging bacterial assemblies, including metagenome-assembled, fragmented, or contaminated samples. For Gene Ontology annotation, PGAP consistently provides broader term coverage, whereas EggNOG-mapper offers more terms per feature.

CONCLUSIONS: Our findings highlight tool-specific strengths crucial for selecting optimal solutions based on genome quality, taxonomy, and origin (e.g. MAGs). This study provides an evidence-based guide for users and informs future tool development.},
}

*Molecular Sequence Annotation/methods
*Genome, Bacterial
*Genome, Archaeal
Benchmarking
*Software
Archaea/genetics
Computational Biology/methods
Metagenome
Gene Ontology

@article {pmid42706609,
year = {2026},
author = {Sun, YZ and Su, JW and Elsheikha, HM and Lou, WB and Song, YH and Li, JM and Liu, F and Cai, R and Leng, X and Gong, QL and Zhang, XX},
title = {Farming reshapes the gut resistome, virulome, and mobilome of Cervidae.},
journal = {Virulence},
volume = {17},
number = {1},
pages = {2728506},
doi = {10.1080/21505594.2026.2728506},
pmid = {42706609},
issn = {2150-5608},
mesh = {Animals ; Gene Transfer, Horizontal ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; *Deer/microbiology/virology ; Metagenome ; Interspersed Repetitive Sequences ; Virulence Factors/genetics ; Plasmids/genetics ; Bacteriophages/genetics ; Virome ; Bacteria/genetics/drug effects/classification ; Agriculture ; },
abstract = {The rapid expansion of cervid farming raises concerns about antimicrobial resistance (AMR) dissemination, yet its impact on the Cervidae gut microbiome remains poorly characterized. We integrated 89 newly sequenced fecal metagenomes with 599 publicly available datasets, comprising 285 metagenomes from farmed cervids and 370 from wild cervids, to construct a catalog of 15,494 non-redundant metagenome-assembled genomes (MAGs) representing 2,401 species. Our analysis demonstrates that farming profoundly reshapes the gut microbiome's functional composition. Specifically, farmed cervids exhibited significantly higher relative abundance, diversity, and heterogeneity of antimicrobial resistance genes (ARGs) compared to wild counterparts. We observed a robust synergistic relationship between ARGs, virulence factor genes, and mobile genetic element (MGE)-associated genes, identifying 70 ARG-MGE combinations as evidence of potential horizontal gene transfer. Plasmid profiling further suggested that a subset of ARGs may be associated with conjugative plasmids, with plasmid-associated ARGs being significantly more abundant in farmed than in wild cervids. Virome analyses indicated that bacteriophages, particularly Siphoviridae, may serve as mobile reservoirs for ARGs. Notably, Cervidae shared 268 ARG types with humans, including 23 high-risk genes associated with resistance to clinically important antibiotics (e.g. tetX1, vanRD, and bla-CTX-M-178), with Escherichia coli as a key cross-host carrier. These findings highlight that human-impacted cervid gut microbiomes are significant environmental reservoirs of clinically relevant AMR, underscoring the necessity for enhanced antibiotic stewardship and resistance surveillance in managed wildlife within a One Health framework.},
}

Animals
Gene Transfer, Horizontal
*Gastrointestinal Microbiome/genetics
Feces/microbiology
*Deer/microbiology/virology
Metagenome
Interspersed Repetitive Sequences
Virulence Factors/genetics
Plasmids/genetics
Bacteriophages/genetics
Virome
Bacteria/genetics/drug effects/classification
Agriculture

@article {pmid42706715,
year = {2026},
author = {Sahil, R and Jain, M},
title = {Benchmarking of Reference-Based Tools for Strain-Level Resolution of Plant Microbiome.},
journal = {Molecular ecology resources},
volume = {26},
number = {7},
pages = {e70197},
doi = {10.1111/1755-0998.70197},
pmid = {42706715},
issn = {1755-0998},
support = {BT/PR40261/BTIS/137/55/2023//Department of Biotechnology, Ministry of Science and Technology, India/ ; },
mesh = {*Microbiota ; *Metagenomics/methods/standards ; *Plants/microbiology ; Benchmarking ; *Computational Biology/methods ; Metagenome ; },
abstract = {Strain-level identification of each microbe is crucial for understanding its role in the host. Most of the existing tools have primarily been evaluated on human metagenomic datasets, whereas the plant microbiome exhibits greater diversity and complexity and thus poses a challenge in the strain-level resolution of individual microbes. In this study, we conducted a comprehensive benchmarking of available reference-based tools for strain-level resolution of the plant microbiome. We evaluated seven tools on various performance parameters, like computational requirements, F1-score and relative abundances using synthetic datasets comprising microbes known to have strong associations with plants as well as real plant microbiome datasets. Our results demonstrated a better performance of StrainScan on the synthetic data, achieving higher F1-score and more accurate relative abundance estimates as compared to other tools, but its performance declined gradually with increasing strain diversity. However, StrainGE and StrainScan exhibited competitive performance on real plant metagenome data. Overall, though StrainGE exhibited better performance, it was more computationally expensive. However, StrainScan performed better in detecting low-abundance strains. Our findings suggest the comparative suitability of the available tools for the strain-level analysis of plant metagenome data and highlight the need for the development of more efficient and accurate taxonomic classifiers capable of handling the complex plant metagenome data while maintaining computational efficiency.},
}

*Microbiota
*Metagenomics/methods/standards
*Plants/microbiology
Benchmarking
*Computational Biology/methods
Metagenome

@article {pmid42707077,
year = {2026},
author = {Mello-Grand, M and Gregnanin, I and Peraldo-Neia, C and Ostano, P and Guana, F and Testino, N and Malfitana, V and Marchi, G and Zaramella, S and Robertson, E and Chiorino, G},
title = {Application of PathoChip to urine-derived nucleic acids for broad microbial profiling in men with suspected prostate cancer: setup of a methodological workflow and pilot feasibility study.},
journal = {The journal of liquid biopsy},
volume = {13},
number = {},
pages = {100490},
pmid = {42707077},
issn = {2950-1954},
abstract = {BACKGROUND: Urine-based liquid biopsy is an attractive non-invasive source of prostate cancer (PCa) biomarkers, but urinary microbiome studies have mainly relied on 16S rRNA sequencing or shotgun metagenomics. This pilot study optimized and evaluated a practical workflow using PathoChip - a broad-spectrum microarray designed to detect bacterial, viral, fungal, and parasitic signatures - for microbial profiling of urine sediments from men with suspected PCa, an application not previously established.

METHODS: First-morning urine was collected without prostatic massage from 35 men scheduled for biopsy; 19 were diagnosed with PCa and 16 were biopsy-negative. Different urine volumes and extraction strategies were evaluated to optimize DNA/RNA recovery. A setup phase compared 25 ng versus 50 ng of urine DNA and RNA input. DNA/RNA isolated from human B cells was used as reference control. An analysis pipeline was developed to detect outlier probes and create a presence/absence matrix. Reproducibility was assessed via library yield, Pearson correlation, blank-control subtraction, outlier probe detection. Prevalence comparisons were performed between clinical groups.

RESULTS: An 8 mL starting volume was chosen as consistently available from self-collected urine. Sequential DNA/RNA extraction using the AllPrep DNA/RNA Micro Kit from sediment provided the best balance between nucleic-acid recovery, purity, and clinical compatibility. Reducing the input from 50 ng to 25 ng preserved highly concordant hybridization profiles, with matched samples clustering together with strong correlations. Exploratory analysis revealed PCa- and grade-associated patterns involving Actinomycetaceae, Aerococcaceae, and Streptococcaceae, with Streptococcaceae enriched in PCa of higher grades (ISUP GG ≥ 2). Other signatures, including Mobiluncus, Prevotella, Rhodotorula, Hymenolepis, and JC polyomavirus, were broadly detected but not PCa-discriminating.

CONCLUSIONS: PathoChip can be adapted to urine sediments, generating reproducible microbial profiles from limited DNA/RNA input without prostatic massage. This platform provides a quick and accessible approach to broad screening, extending beyond 16S rRNA sequencing by enabling simultaneous multi-kingdom detection. The observed PCa- and grade-associated patterns are hypothesis-generating and require validation in larger independent cohorts.},
}

@article {pmid42707087,
year = {2026},
author = {Xia, Y and Fu, L and Cao, X and Zheng, X and Nie, B},
title = {Acute Coxiella burnetii infection presenting as sepsis with multisystem involvement in an immunosuppressed patient: a case report.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1899347},
pmid = {42707087},
issn = {2296-858X},
abstract = {Q fever, caused by Coxiella burnetii, rarely presents as severe disseminated disease, and timely diagnosis can be difficult because clinical manifestations are nonspecific and routine microbiological tests are often unrevealing. We report a 68-year-old man with rheumatoid arthritis receiving long-term immunosuppressive therapy who presented with persistent unexplained fever, pancytopenia, hepatic dysfunction, polyserosal effusions, and sepsis with multisystem involvement, without a clear epidemiological exposure history. Blood cultures and routine respiratory pathogen testing were negative. Peripheral-blood metagenomic next-generation sequencing (mNGS) detected C. burnetii nucleic acid sequences, and subsequent antibody testing and targeted qPCR supported the diagnosis of acute Q fever with disseminated manifestations. Doxycycline-based targeted therapy was followed by defervescence and marked clinical and laboratory improvement. This case suggests that, in selected immunocompromised patients with severe infection and persistently negative conventional investigations, mNGS may serve as an adjunctive tool to facilitate timely pathogen identification and guide targeted antimicrobial therapy.},
}

@article {pmid42707228,
year = {2026},
author = {Liang, H and Qin, H and Chen, J and Qin, C and Li, X and Wang, Q and Luo, G and Chen, Y},
title = {Integrating metagenomic next-generation sequencing into a multimodal diagnostic framework for spinal infection: enhancing etiological identification and clinical prediction.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1904634},
pmid = {42707228},
issn = {2235-2988},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; Female ; *Metagenomics/methods ; Retrospective Studies ; Male ; Middle Aged ; Sensitivity and Specificity ; Bacteria/genetics/classification/isolation & purification ; Aged ; *Spinal Diseases/diagnosis/microbiology ; },
abstract = {BACKGROUND: Spinal infection (SI) remains diagnostically challenging because of heterogeneous etiologies, nonspecific clinical manifestations, and the limited sensitivity of conventional microbiological approaches, particularly following empirical antimicrobial exposure. Although metagenomic next-generation sequencing (mNGS) enables unbiased pathogen detection, its incremental clinical value beyond pathogen identification and its role within integrated diagnostic strategies remain incompletely established.

METHODS: We retrospectively analyzed 208 consecutive patients with suspected SI between August 2022 and August 2025. Final diagnoses were established using a multidisciplinary-adjudicated composite reference standard incorporating clinical, radiological, microbiological, and histopathological evidence. The diagnostic performance of mNGS was compared with conventional culture and histopathology. Furthermore, multimodal predictive models integrating clinical variables and microbiological information were developed using L1-regularized logistic regression.

RESULTS: In the comparative cohort, mNGS achieved a significantly higher diagnostic yield than culture (66.5% vs. 27.41%, P < 0.001). Among confirmed SI cases, mNGS demonstrated higher sensitivity than conventional culture (91.67% vs. 40.15%, P < 0.001). mNGS identified a substantially broader pathogen spectrum, ranging from fastidious organisms such as Mycobacterium tuberculosis and Brucella to rare pathogens including Talaromyces marneffei and Coxiella burnetii, and maintained robust sensitivity (98.2%) despite prior antibiotic exposure. While an integrated clinical model achieved an AUC of 0.916, mNGS as a standalone modality provided superior discriminative power (AUC = 0.889) compared to histopathology (AUC = 0.836), the Conventional Biomarker Model (AUC = 0.742), and culture (AUC = 0.693).

CONCLUSIONS: mNGS is a high-yield diagnostic tool for spinal infection, particularly in culture-negative and antibiotic-pretreated scenarios. Integrating mNGS into a multimodal clinical framework facilitates etiological clarity and precision antimicrobial therapy.},
}

Humans
*High-Throughput Nucleotide Sequencing/methods
Female
*Metagenomics/methods
Retrospective Studies
Male
Middle Aged
Sensitivity and Specificity
Bacteria/genetics/classification/isolation & purification
Aged
*Spinal Diseases/diagnosis/microbiology

@article {pmid42707924,
year = {2026},
author = {Wang, J and Wang, Y and Wang, R},
title = {Prognosis of Patients Infected With Talaromyces marneffei Across Various Risk Factors.},
journal = {Journal of general and family medicine},
volume = {27},
number = {5},
pages = {e70171},
pmid = {42707924},
issn = {2189-7948},
abstract = {BACKGROUND: Talaromyces marneffei (TM) is an opportunistic infectious fungus, and more patients in HIV-negative populations are infected with TM.

METHODS: We reviewed the adult patients with TM infections (TMIs) between November 1, 2020 and April 30, 2025. This single-center retrospective study was conducted at a tertiary care hospital located in an urban area, eastern China. Patients with TMI were divided into the following four groups: the HIV group, the non-HIV with solid organ transplant (SOT) group, the non-HIV with stem cell transplantation (SCT) group, and the non-HIV with other factors group.

RESULTS: There were a total of 218 cases of talaromycosis: 165 in the HIV group, 16 in the non-HIV with SOT group, 4 in the non-HIV with SCT group, and 33 in the non-HIV with other factors group. The number (proportion) of patients diagnosed through metagenomic next-generation sequencing (mNGS) in the four groups was as follows: 51 (30.9%), 11 (68.8%), 2 (50.0%), and 25 (75.8%), respectively. The number (proportion) of patients who tested positive in both culture and mNGS was as follows: 19 (11.5%), 1 (6.3%), 0 (0.0%), and 1 (3.0%), respectively. Kaplan-Meier estimates indicated that the patients in the non-HIV with SCT group had the worst prognosis and those in the non-HIV with other factors group had poorer prognosis than the patients in the HIV group.

CONCLUSIONS: TMI in patients who are HIV-negative without SOT may have poorer prognosis. If talaromycosis is suspected, mNGS can be an important supplementary tool for confirming TMI.},
}

@article {pmid42707963,
year = {2026},
author = {Babu, P and Prakash, V and Subhash, S and Vanuopadath, M and Haripriyan, J and Rajan, K and Geetha, AA and P, S and Kumar, GB and Nair, BG and Madhavan, A},
title = {Gut-microbiota-mediated host immune modulation: mechanisms, pathological dysbiosis, and therapeutic frontiers.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1905445},
pmid = {42707963},
issn = {2235-2988},
mesh = {Humans ; *Dysbiosis/immunology/therapy/microbiology ; Animals ; *Gastrointestinal Microbiome/immunology ; Host-Pathogen Interactions/immunology ; *Immunomodulation ; },
abstract = {The mammalian immune system has evolved in constant dialogue with its diverse microbiota, forming an ecological and molecular partnership that is fundamental to health. This review examines how microbial communities shape immunity across developmental and functional axes, the immunological consequences of dysbiosis during infection and inflammatory disease, and emerging microbiota-targeted interventions. The host-microbiota-pathogen triad offers a framework to understand how commensals and pathogens compete for ecological niches and immune recognition, and how disturbances in this balance can cascade into chronic inflammation or infection. Microbial metabolites such as short-chain fatty acids, secondary bile acids, and tryptophan derivatives act as key bioactive intermediaries translating microbial activity into host immune architecture, influencing epigenetic programming, cellular differentiation, and mucosal barrier function. These interactions orchestrate tolerance toward commensals while maintaining effector readiness against pathogens, particularly through regulatory T cell (Treg)-Th17 balance, B cell education, and Immunoglobulin A (IgA) responses. When perturbed, as in infections caused by Clostridioides difficile, Klebsiella pneumoniae, Salmonella enterica, or Listeria monocytogenes, the ensuing dysbiosis reinforces immune dysfunction in a self-perpetuating cycle. Therapeutic frontiers now extend beyond conventional antimicrobial strategies to include live biotherapeutics, bacteriophage therapy, fecal microbiota transplantation, and metabolite-based (postbiotic) interventions. Future efforts must reconcile inter-individual microbiome variability with precision medicine, integrating metagenomic and metabolomic profiling to design safe, effective, and personalized microbiota-centered therapeutics.},
}

Humans
*Dysbiosis/immunology/therapy/microbiology
Animals
*Gastrointestinal Microbiome/immunology
Host-Pathogen Interactions/immunology
*Immunomodulation

@article {pmid42707980,
year = {2026},
author = {Li, ZL and Qu, RN and Liu, SX and Wang, W},
title = {Research progress and clinical translation prospects of the urinary tract microbiome in prostate cancer.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1911969},
pmid = {42707980},
issn = {1664-3224},
mesh = {Humans ; Male ; *Prostatic Neoplasms/microbiology/immunology ; *Microbiota ; *Urinary Tract/microbiology ; Translational Research, Biomedical ; Tumor Microenvironment ; Animals ; },
abstract = {Prostate cancer (PCa) is one of the most common malignancies in men worldwide, and its development is influenced by multiple factors, including genetic susceptibility, hormonal dysregulation, chronic inflammation, immune dysregulation, and remodeling of the tumor microenvironment. In recent years, the urinary tract microbiome has emerged as an important component of the tumor ecosystem and has attracted increasing attention in PCa research. Accumulating evidence indicates that patients with PCa exhibit characteristic microbial alterations in urine, expressed prostatic secretions, semen, and prostate tissue, and that certain taxa are associated with tumor grade, stage, and recurrence risk. These microbes may participate in tumor initiation and progression through a variety of mechanisms, such as inducing chronic inflammation, activating signaling pathways including TLR/NF-κB and STAT3, modulating the Treg/Th17 balance, influencing macrophage polarization, and interfering with androgen metabolism. Meanwhile, advances in 16S rRNA sequencing, metagenomics, metatranscriptomics, and multi-omics integration have provided powerful tools for characterizing host-microbe interactions and their functional relevance. In addition, microbiome-based biomarkers derived from non-invasive samples such as urine, together with artificial intelligence and causal inference approaches applied to multi-cohort data, may offer promising opportunities for early screening, risk stratification, treatment monitoring, and personalized intervention in PCa. However, current evidence remains largely associative, and the causal relationship between microbial changes and PCa has not yet been fully established. Major challenges, including contamination in low-biomass samples and inter-cohort heterogeneity, continue to hinder clinical translation. Future research should focus on longitudinal cohort studies, multicenter validation, standardized sampling workflows, and mechanistic experiments to clarify key microbial signatures and their biological functions, thereby accelerating the clinical application of the urinary tract microbiome in precision diagnosis and treatment of PCa.},
}

Humans
Male
*Prostatic Neoplasms/microbiology/immunology
*Microbiota
*Urinary Tract/microbiology
Translational Research, Biomedical
Tumor Microenvironment
Animals

@article {pmid42708205,
year = {2026},
author = {Cruz, K and Chaudry, TE and McTigue, SM and Huang, H and Bauer, JA and Kim, M},
title = {Opportunistic premise plumbing pathogens (OPPPs) in the built environment: transmission, resistance, and strategies for detection and mitigation.},
journal = {Reviews on environmental health},
volume = {},
number = {},
pages = {},
pmid = {42708205},
issn = {2191-0308},
abstract = {Healthcare associated infections (HAIs) lead to tens of thousands of deaths annually, with 21.6 % being caused by water, according to Collier S, Deng L, Adam E, Benedict K, Beshearse E, Blackstock A, et al. Estimate of burden and direct healthcare cost of infectious waterborne disease in the United States. Emerging Infect Disease J 2021;27:140. This is partially due to Opportunistic Premise Plumbing Pathogens (OPPPs); which may exhibit resistance to disinfection and thrive in pipe biofilms. Evidence found in literature indicates the rate of infections caused by OPPPs are going to increase with time, highlighting the need for better understanding of their detection and mitigation. The aim of this review is to provide insight on the latest status of OPPP research and highlight areas that need further investigation. It also emphasizes the importance of proactive surveillance, extensive water management protocols, and advanced detection technologies in reducing waterborne healthcare-associated infections. Ultimately, it was found there is still extensive research needed to fully mitigate and prevent pathogenic outbreaks.},
}

@article {pmid42708583,
year = {2026},
author = {Yu, H-L and Elsheikha, HM and Wang, H-P and Gao, Y-Q and Liu, R and Ma, H and Jiang, J and Li, Y and Zhang, X-X},
title = {Genome-resolved analysis reveals disruption of gut microbial vitamin B and K2 biosynthesis during Toxoplasma gondii infection in mice.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0156426},
doi = {10.1128/spectrum.01564-26},
pmid = {42708583},
issn = {2165-0497},
abstract = {UNLABELLED: Toxoplasma gondii infection remodels the gut microbiome, yet its impact on microbial vitamin biosynthetic potential and host redox metabolism remains unclear. Here, we integrated mouse gut metagenomes with publicly available metagenome-assembled genomes (MAGs) to construct a genome-resolved atlas of B-vitamin and vitamin K2 biosynthesis. From 45,697 MAGs, we curated 4,771 representative genomes, of which 2,682 met high-quality criteria (completeness ≥90%, contamination <5%). Functional annotation identified 229,717 vitamin-related genes corresponding to 177 Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologs across de novo pathways for eight B vitamins, thiamine (B1), riboflavin (B2), niacin (B3), pantothenate (B5), pyridoxine (B6), biotin (B7), folate (B9), cobalamin (B12), and vitamin K2. Among the high-quality genomes, 1,665 encoded complete de novo pathways for at least one vitamin, highlighting functional specialization and community-level complementarity. Transcripts per million-normalized metagenomic read counts revealed significant differences in KEGG ortholog abundances across six of the nine vitamin pathways. Reanalysis of metagenomic data from infected mice (acute, chronic, and control; n = 10 per group) revealed a stage-dependent reduction in α-diversity of vitamin biosynthesis pathways during acute infection, and a clear β-diversity separation from chronic and control groups. Core niacin biosynthesis genes (nadB, nadA, nadC) displayed phylum-specific redistribution, indicating selective remodeling of microbial NAD[+] precursor production under infection-induced metabolic stress. These results suggest that T. gondii infection disrupts cooperative vitamin biosynthetic networks while specifically modulating niacin pathways linked to host NAD[+] metabolism.

IMPORTANCE: Gut microbes can synthesize essential vitamins, but how infection alters this function is poorly understood. By integrating mouse gut metagenomes with genome-resolved microbial data, we show that Toxoplasma gondii infection reshapes the vitamin biosynthetic potential of the gut microbiome in a stage-dependent manner. Acute infection reduces the diversity of vitamin biosynthesis pathways and shifts the taxonomic distribution of key niacin biosynthesis genes involved in microbial NAD[+] precursor production. These findings identify vitamin metabolism, especially niacin-related pathways, as a sensitive functional axis of microbiome remodeling during infection. Our work links microbial taxonomic changes to functional metabolic consequences and suggests that microbiome-mediated regulation of NAD[+]-related metabolism may contribute to host redox adaptation during T. gondii infection.},
}

@article {pmid42708586,
year = {2026},
author = {Solanki, R and Wiszniak, E and Yi, L and Cabria, G and Strous, M and Davila Aleman, FD},
title = {Genome mining of alkaliphilic cyanobacterial consortia: identification of biosynthetic gene clusters in Sodalinema and associated heterotrophs.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0078026},
doi = {10.1128/aem.00780-26},
pmid = {42708586},
issn = {1098-5336},
abstract = {Alkaline soda lakes are high-pH environments that host specialized microbial communities with potential for biotechnology and natural product discovery. We characterized three Sodalinema-dominated cyanobacterial consortia enriched from Canadian soda lakes over 510 days. Using hybrid metagenomic sequencing and metatranscriptomics across pH, alkalinity, and temperature gradients, we reconstructed high-quality metagenome-assembled genomes and assessed functional activity. All consortia converged toward cyanobacteria dominance and exhibited temperature optima between 21°C and 30°C. Phylogenetic analysis placed Sodalinema genomes within a distinct clade affiliated with Candidatus Sodalinema alkaliphilum. Genomic analysis indicated complete biosynthetic pathways for vitamin B5, vitamin B7, and the molybdenum cofactor, but incomplete pathways for vitamins B1, B9, and B12, consistent with patterns observed in Sodalinema yuhuli. Metatranscriptomic profiles showed increased expression of genes involved in phycocyanin and carotenoid biosynthesis at pH 10.2 relative to pH 8.5. Biosynthetic gene cluster analysis revealed that most secondary metabolic potential resided in heterotrophic community members. Roseinatronobacter encoded pathways for N-acyl homoserine lactones, osmoprotectants, betalactones, and prodigiosin, while Alkalimonas, Wenzhouxiangella, and members of the Kiloniellales encoded clusters for lanthipeptides, cyclodipeptides, hydrogen cyanide, and pyrroloquinoline quinone. These findings indicate functional partitioning within the consortia and highlight the contribution of heterotrophs to secondary metabolism.IMPORTANCEAlkaline soda lakes contain microbial communities adapted to high pH that remain underexplored for biotechnology. This study focuses on Sodalinema, a filamentous cyanobacterium that dominates enriched consortia from Canadian soda lakes, and its associated heterotrophic partners. We show that while Sodalinema drives primary productivity, heterotrophic bacteria encode most of the pathways for antimicrobial and signaling compounds. These interactions may support community stability and defense against competing microorganisms. By linking genomic potential with gene expression, this work identifies alkaline cyanobacterial consortia as a source of bioactive compounds and provides a framework for exploring extremophilic microbial communities for natural product discovery.},
}

@article {pmid42708591,
year = {2026},
author = {Jaffe, AL and Zulli, A and Duong, D and Shelden, B and Goldman, M and Richardson, M and Wolfe, MK and Boehm, AB},
title = {Divergent avian strains drive an off-season influenza A peak in municipal wastewater.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0202726},
doi = {10.1128/spectrum.02027-26},
pmid = {42708591},
issn = {2165-0497},
abstract = {Wastewater sequencing is an increasingly valuable tool in tracking the spread of infectious disease agents across space and time in areas of dense human settlement. Among pathogens that can be readily detected by this approach is influenza A, which follows predictable patterns of prevalence through the winter months in North America. Here, we leverage routine surveillance of a municipal wastewater treatment plant in Northern California to describe an atypical, off-season spike in influenza A concentrations that rivals that of the winter respiratory virus season. Drawing upon metagenomic data generated through hybrid-capture sequencing, we assemble and subsequently characterize fragments of divergent influenza genomes that appear to derive predominantly from the avian H16 clade. These strains exhibit close evolutionary relationships to influenza isolated from migratory shorebirds, hinting at potential host species and mechanisms of geographic spread. Analysis of read abundances suggests that these avian strains dominate the pool of influenza circulating during the summer months, when typical human-infecting strains are essentially absent. Together, our results expand the value of wastewater sequencing to encompass sensitive tracking of outbreaks within animals in interface regions where human settlement abuts wildlands, increasing overall pandemic preparedness.IMPORTANCEResearchers now commonly search municipal wastewater for viral genetic material, which can indicate trends in the diversity and abundance of strains circulating in communities. Here, we show that under certain conditions, municipal wastewater can also capture the signatures of viruses circulating among animal populations, such as birds. Specifically, we draw on a targeted form of nucleic acid sequencing to discover a strain of influenza that is fairly genetically distinct from known relatives and may be circulating among shorebirds in Northern California. These findings both broaden the possible use cases of wastewater sequencing and provide new insights into avian viruses, some of which can jump host species to make other animals or people sick.},
}

@article {pmid42708949,
year = {2026},
author = {Jiang, Y and Chen, L and Dong, H and Li, Q and Zhao, W and Zhu, F and Jiang, J and Zhang, Y and Huang, S and Xue, S},
title = {Ecological Restoration of the Soil-Like Function in the Bauxite Residue: Natural Microbiomes Mediated Molecular Transformation of Dissolved Organic Matter.},
journal = {Environmental science & technology},
volume = {60},
number = {35},
pages = {24764-24775},
doi = {10.1021/acs.est.5c18355},
pmid = {42708949},
issn = {1520-5851},
support = {42030711//National Natural Science Foundation of China (NSFC)/ ; 42477437//National Natural Science Foundation of China (NSFC)/ ; 42671661//National Natural Science Foundation of China (NSFC)/ ; },
mesh = {*Soil/chemistry ; *Microbiota ; *Dissolved Organic Matter ; Soil Microbiology ; Aluminum Oxide ; Carbon ; },
abstract = {Soilization of bauxite residues offers a scalable route for long-term carbon management and ecological restoration. However, the microbial processes that transform exogenous organic inputs into stable soil-like carbon pools remain poorly resolved. Here, we combined cross-ecosystem meta-analysis, machine-learning prediction, native synthetic community (SynCom) construction, 13C-labeled straw microcosms, field validation, Fourier transform ion cyclotron resonance mass spectrometry, and genome-resolved metagenomics to unravel microbiome-mediated carbon transformation at the dissolved organic matter (DOM) molecular scale. Our meta-analysis revealed that alkaline industrial wastes retained soil-like DOM signatures but were enriched in microbial humic- and protein-like components, indicating active yet incomplete carbon processing. Guided by these patterns, native SynCom inoculation increased 13C incorporation into total organic carbon (TOC) and dissolved organic carbon (DOC), enlarged biodegradable and adsorbable DOC fractions, and shifted DOM from recalcitrant aromatic pools toward oxygenated carbohydrate-, tannin-, and phenolic-like molecular classes. Genome-resolved analyses linked this transformation to complementary polymer degradation and nutrient-cycling functions across fungal and bacterial guilds, including enriched carbohydrate-active enzymes in straw-carbon-utilizing metagenome-assembled genomes. Null model and thermodynamic analyses further showed that microbial communities were constrained by homogeneous selection, whereas DOM molecules were diversified through variable selection and redox-dependent transformation. Field-scale validation confirmed that SynCom promoted TOC and DOC accumulation and humic-like, high-density DOM fractions under alkaline conditions. Together, these findings establish a mechanistic framework in which functional microbiomes couple plant carbon depolymerization, DOM molecular diversification, and mineral-interactive carbon stabilization, providing a microbiome-guided strategy for carbon sequestration and soilization in the bauxite residue.},
}

*Soil/chemistry
*Microbiota
*Dissolved Organic Matter
Soil Microbiology
Aluminum Oxide
Carbon

@article {pmid42708950,
year = {2026},
author = {Zhang, X and Yuan, J and Wang, L and Chen, J and Zhang, L and Ding, T and Zheng, G and Li, J and Zeng, EY},
title = {Soil Type Governs the Degradation Dynamics and Microbial Assimilation of Biodegradable Plastic Polybutylene Adipate Terephthalate.},
journal = {Environmental science & technology},
volume = {60},
number = {35},
pages = {24909-24920},
doi = {10.1021/acs.est.6c11170},
pmid = {42708950},
issn = {1520-5851},
support = {22576140//National Natural Science Foundation of China/ ; 42377025//National Natural Science Foundation of China/ ; x2hjD6242050//South China University of Technology/ ; },
mesh = {Biodegradation, Environmental ; *Polyesters ; *Soil/chemistry ; Soil Microbiology ; Biodegradable Plastics ; Soil Pollutants ; },
abstract = {Biodegradable plastics like polybutylene adipate terephthalate (PBAT) are increasingly marketed as alternatives to conventional plastics, yet how soil properties regulate degradation kinetics, how intact films and microplastic fragments differentially affect microbial communities, and which metabolic pathways and functional genes govern mineralization remain unclear. The present study investigated PBAT degradation mechanisms in 10 distinct agricultural soils by integrating metagenomics, microbial community analysis, and strain isolation. The results revealed that the environmental fate of PBAT is critically modulated by soil properties. Neutral-alkaline powdery loam soils exhibited the highest degradation efficiency. Soil physicochemical properties indirectly modulate PBAT weight loss by altering the gene abundance of hydrolases and aromatic-degrading enzymes, with soil nitrogen content serving as a key regulatory factor. Metagenomic correlation analysis suggests that PBAT degradation is associated with specific microbial consortia, including Hydrogenophaga and Ascomycota fungi. Microplastic particles of PBAT induced greater disturbances than intact films, as evidenced by significant reductions in microbial diversity, altered community structure, and shifts in functional gene composition. A complete degradation pathway, including initial polymer cleavage followed by terephthalic acid assimilation via the β-ketoadipate pathway, was elucidated. These results provide mechanistic insights into soil-specific PBAT degradation and facilitate risk assessment and sustainable management of biodegradable plastics.},
}

Biodegradation, Environmental
*Polyesters
*Soil/chemistry
Soil Microbiology
Biodegradable Plastics
Soil Pollutants

@article {pmid42708953,
year = {2026},
author = {Francescato, L and Ghiotto, G and Valerin, MC and De Bernardini, N and Fraulini, S and Sandon, A and Treu, L and Lavagnolo, MC and Campanaro, S},
title = {Adaptive Evolution Reveals Metabolic Plasticity and Functional Redundancy in an Anaerobic Microbiome under Extreme Ammonia Stress.},
journal = {Environmental science & technology},
volume = {60},
number = {35},
pages = {24776-24791},
doi = {10.1021/acs.est.6c05759},
pmid = {42708953},
issn = {1520-5851},
mesh = {*Ammonia ; *Microbiota ; Anaerobiosis ; Methane/metabolism ; },
abstract = {Ammonia toxicity represents a primary biochemical bottleneck governing microbial community structure and performance during the anaerobic digestion of the organic fraction of municipal solid waste. However, the mechanistic basis of microbial adaptation to chronic ammonia levels remains poorly characterized. In this study, a long-term sequential enrichment strategy under progressively increasing ammonia concentrations (350-1500 mgN L-1), integrated with genome-centric metagenomics and metatranscriptomics, was employed to resolve the response of an organic waste-degrading microbiome over a 240 day period. Increasing ammonia pressure induced a progressive decline in methanogenesis and accumulation of volatile fatty acids, particularly acetate. Despite these inhibitory pressures, methane production was only halved relative to the initial baseline reflecting a resilient methanogenic community. This stability was driven by a restructuring of the microbiome, where functional redundancy across divergent taxa preserved core metabolic functions. Key adaptive responses included the reconfiguration of carbon fixation pathways, specifically via a variant of the Wood-Ljungdahl pathway coupled with the glycine cleavage system acting as an alternative acetate oxidation route, as well as sustained osmoprotectant biosynthesis. Cellular homeostasis was preserved through H+ replenishment via multiple energy-converting complexes and K+ influx to maintain cation-proton balance. Collectively, these findings demonstrate that metabolic plasticity and the preservation of core metabolic functions are the primary determinants of ammonia resilience, sustaining methane production under inhibitory conditions.},
}

*Ammonia
*Microbiota
Anaerobiosis
Methane/metabolism

@article {pmid42708973,
year = {2026},
author = {Zhu, X and Zhang, W and Ye, T and Zhang, H and Tan, J and Sun, Y},
title = {Malassezia May Contribute to Basal Cell Carcinoma Development via Inflammatory and Oxidative Stress Pathways.},
journal = {MicrobiologyOpen},
volume = {15},
number = {5},
pages = {e70401},
doi = {10.1002/mbo3.70401},
pmid = {42708973},
issn = {2045-8827},
support = {2023YZ06//Yangtze University Science and Technology Aid to Tibet Medical Talent Training Program Project/ ; 2024BCB043//Key Research and Development Program of Hubei Province/ ; 2024AFC034//Natural Science Foundation of Hubei Province/ ; 2025HD18//Jingzhou Science and Technology Plan Project/ ; },
mesh = {Humans ; *Malassezia/isolation & purification/genetics/pathogenicity ; *Oxidative Stress ; *Basal Cell Carcinoma/microbiology/pathology ; *Skin Neoplasms/microbiology/pathology ; Cell Proliferation ; Superoxide Dismutase 2 ; Keratinocytes/microbiology ; Superoxide Dismutase/genetics ; Cell Line, Tumor ; *Inflammation ; Tumor Necrosis Factor-alpha/genetics ; Superoxide Dismutase-1/genetics ; Gene Expression Profiling ; Interleukin-1beta/genetics ; },
abstract = {Basal cell carcinoma (BCC) is the most common malignant skin tumor. Skin-resident lipophilic Malassezia yeasts are associated with various cutaneous disorders, while their correlative patterns and potential biological effects in BCC tissues remain insufficiently defined. We used RT-qPCR screening of archived FFPE BCC specimens and metagenomic sequencing of three paired fresh tumor and peritumoral tissues to characterize tissue-associated Malassezia colonization. M. globosa was the most abundant species in FFPE samples and was also detectable in fresh tissues. In vitro functional assays (CCK-8, EdU) in HaCaT keratinocytes and A-431 epidermoid carcinoma cells showed that 12 h stimulation with optimal concentrations of M. globosa (1.2 × 10[7] CFU/mL) and M. yamatoensis (1.6 × 10[7] CFU/mL) significantly promoted epithelial cell proliferation. Transcriptome sequencing and subsequent RT-qPCR validation further showed that both strains significantly upregulate pro-inflammatory genes (IL-1β, IL-6, TNF-α) and oxidative stress-related genes (SOD1, SOD2) in these cell lines. Collectively, our findings describe a correlative association between Malassezia colonization and BCC lesions and offer preliminary in vitro mechanistic clues.},
}

Humans
*Malassezia/isolation & purification/genetics/pathogenicity
*Oxidative Stress
*Basal Cell Carcinoma/microbiology/pathology
*Skin Neoplasms/microbiology/pathology
Cell Proliferation
Superoxide Dismutase 2
Keratinocytes/microbiology
Superoxide Dismutase/genetics
Cell Line, Tumor
*Inflammation
Tumor Necrosis Factor-alpha/genetics
Superoxide Dismutase-1/genetics
Gene Expression Profiling
Interleukin-1beta/genetics

@article {pmid42709036,
year = {2026},
author = {Pilgrim, J and Rzeszutek, A and Cunningham-Oakes, E and Bonner, S and Roberts, L and Darby, AC and Radford, AD},
title = {Expanded detection of canine enteric viruses in UK dogs with diarrhoea.},
journal = {Microbial genomics},
volume = {12},
number = {9},
pages = {},
doi = {10.1099/mgen.0.001799},
pmid = {42709036},
issn = {2057-5858},
mesh = {Animals ; Dogs ; *Diarrhea/veterinary/virology ; *Dog Diseases/virology/epidemiology ; United Kingdom ; Metagenomics/methods ; Feces/virology ; Phylogeny ; *Viruses/genetics/isolation & purification/classification ; },
abstract = {Canine enteric viruses are an important cause of gastrointestinal disease in pet dogs worldwide. Routine diagnosis often relies on pathogen-specific PCR assays, which may fail to detect some viruses, particularly neglected pathogens or genetically divergent variants of established threats. This limits both clinical characterization of affected patients and broader understanding of disease ecology. To address these limitations, we applied metagenomics and a viral discovery bioinformatics pipeline to faecal samples from diarrhoeic dogs in the UK that had been submitted routinely for PCR-based diagnostic testing. Across 80 dogs, we identified 12 viruses known to infect canids, 9 of which have not previously been reported in UK dogs. Among these, several taxa with prior associations to gastrointestinal disease were identified, including canine sapovirus and canine minute virus. By contrast, for other viruses newly detected in the UK, including bufavirus and rotavirus C, clinical relevance in dogs remains unclear. Notably, an identified protoparvovirus fell within the same species as human-canine-associated parvovirus 1, a recently described lineage detected in both canine and human oropharyngeal samples. We also identified a canine parvovirus 2 strain that clustered with a predominantly wildlife-associated lineage, consistent with occasional exposure at the domestic-wildlife interface rather than established circulation in dogs. These two detections illustrate how genome-level surveillance can help prioritize viruses for targeted investigation of host range and transmission context. Overall, these data broaden the catalogue of viruses associated with diarrhoeic dogs in the UK and support periodic review of diagnostic targets informed by viral metagenomic surveillance, while highlighting the need for controlled studies to assess causality and clinical relevance.},
}

Animals
Dogs
*Diarrhea/veterinary/virology
*Dog Diseases/virology/epidemiology
United Kingdom
Metagenomics/methods
Feces/virology
Phylogeny
*Viruses/genetics/isolation & purification/classification

@article {pmid42709542,
year = {2026},
author = {Pinedo-Bardales, M and Erreygers, I and Allonsius, CN and Hiel, M and Eilers, T and Van Rillaer, T and Gehrmann, T and Ahannach, S and Dillen, J and De Boeck, I and Verhoeven, V and Van Puyvelde, S and Segata, N and Wittouck, S and Lebeer, S},
title = {Species and strain sharing in the vaginal microbiome of mothers and their adult daughters.},
journal = {Cell reports},
volume = {45},
number = {9},
pages = {117942},
doi = {10.1016/j.celrep.2026.117942},
pmid = {42709542},
issn = {2211-1247},
abstract = {The vaginal microbiome is key for women's health. However, its establishment, interindividual variation and dynamics remain poorly understood. Here, we investigate bacterial relatedness at species and strain level in adult mother-daughter pairs from the large-scale citizen-science program Isala. Using metagenomic sequencing with quality control including 16S rRNA profile comparison, along with targeted culturing, we assess intergenerational microbiome sharing. At species level, daughters' vaginal microbiomes are significantly more similar to their mothers' than to those of unrelated mothers, with a strong mother-daughter correlation in Lactobacillus crispatus dominance. Strain-level analyses of metagenomes and isolate genomes reveal intraspecies diversity in L. crispatus, with up to two strains observed within the same host, and support intergenerational vaginal bacteria sharing. SNV counts in shared L. crispatus strains show no correlation with daughters' ages. Together, these findings suggest that maternal transmission, host factors, and (shared) environment collectively shape the vaginal microbiome, providing fundamental ecological insights into vaginal microbiome dynamics and perspectives toward lactobacilli-based applications.},
}

@article {pmid42709766,
year = {2026},
author = {Frybortova, V and Satka, S and Jourova, L and Anzenbacher, P and Zapletalova, I and Kraus, M and Kostovcikova, K and Kverka, M and Anzenbacherova, E},
title = {Ketogenic diet-induced changes in hepatic drug metabolism with potential implications for ozanimod pharmacokinetics in mice.},
journal = {PloS one},
volume = {21},
number = {9},
pages = {e0357797},
doi = {10.1371/journal.pone.0357797},
pmid = {42709766},
issn = {1932-6203},
mesh = {Animals ; Female ; *Liver/metabolism/drug effects ; Mice, Inbred C57BL ; Mice ; *Diet, Ketogenic ; *Indans/pharmacokinetics ; *Oxadiazoles/pharmacokinetics ; Cytochrome P-450 Enzyme System/metabolism/genetics ; },
abstract = {Ketogenic diet (KD) is increasingly considered as an adjunctive therapeutic approach across a range of diseases, but its effects on the pharmacokinetics of concomitantly administered drugs remain unclear. Such interactions may be particularly relevant in multiple sclerosis, where KD is being explored as a complementary strategy alongside disease-modifying therapies, such as ozanimod. We therefore investigated whether KD affects ozanimod metabolism and pharmacokinetics and explored potential factors that may contribute to such effects. Specific pathogen-free female C57BL/6 mice were fed either a control diet containing 10% of calories from fat or a ketogenic diet containing 90% of calories from fat for 4 weeks. Metabolic, inflammatory, and hormonal parameters were determined in plasma. Gut microbiota composition was analyzed by whole-metagenome shotgun sequencing. In parallel, hepatic cytochrome P450 (CYP) enzymes were evaluated by mRNA expression and activity together with ozanimod pharmacokinetics. KD induced the expected metabolic adaptation to ketosis and led to a significant increase in plasma cholesterol accompanied by changes in gut microbiota composition. Other metabolic and inflammatory parameters showed only modest changes. In addition, KD altered the expression and activity of hepatic CYP enzymes, including enzymes involved in ozanimod metabolism: CYP1A activity and mRNA expression were significantly increased in KD-fed mice, whereas lower CYP2C activity was observed in pooled samples and CYP3A activity showed a non-significant trend toward lower values. Ozanimod exposure tended to be higher in KD-fed mice, resulting in an approximately 17% increase in area under the concentration-time curve, although this effect did not reach statistical significance. In conclusion, our findings demonstrate that KD altered the expression and activity of hepatic CYP enzymes and revealed a non-significant trend toward increased ozanimod exposure. These observations highlight the potential importance of considering dietary interventions as a factor contributing to variability in drug response.},
}

Animals
Female
*Liver/metabolism/drug effects
Mice, Inbred C57BL
Mice
*Diet, Ketogenic
*Indans/pharmacokinetics
*Oxadiazoles/pharmacokinetics
Cytochrome P-450 Enzyme System/metabolism/genetics

@article {pmid42700609,
year = {2026},
author = {Li, J and Zuo, X and Qiu, L and Meng, F},
title = {Metabolic niche differentiation and napA evolution stabilize partial denitrification in wastewater ecosystems.},
journal = {Water research},
volume = {308},
number = {Pt A},
pages = {126810},
doi = {10.1016/j.watres.2026.126810},
pmid = {42700609},
issn = {1879-2448},
abstract = {Although partial denitrification (PD) is increasingly applied as a nitrite-supplying strategy for anammox-based nitrogen removal, the ecological distribution, metabolic specialization, and genomic determinants of stable nitrite accumulation remain poorly understood at the ecosystem scale. Here, we reconstructed 516 high-quality metagenome-assembled genomes (MAGs) using high-depth metagenomic sequencing of 107 wastewater treatment plants and classified denitrifiers according to their nitrite production or consumption capacities. Of these genomes, 23% (120 MAGs) were classified as partial denitrifiers, 41% (211 MAGs) as complete denitrifiers, and 36% (185 MAGs) as nitrite-reducing denitrifiers, revealing pronounced functional partitioning rather than dominance by complete denitrification pathways. Comparative genomics showed that partial denitrifiers possess metabolic architectures favoring rapid carbon oxidation and NADH generation while exhibiting constrained NADPH production and biosynthetic investment, thereby promoting nitrate-to-nitrite conversion but limiting subsequent nitrite reduction. Nitrite accumulation does not result from incomplete denitrification pathways but from metabolic niche differentiation. These metabolic trade-offs were further associated with the evolutionary divergence of the periplasmic nitrate reductase gene, napA, which displayed distinct sequence characteristics and genomic contexts between partial and complete denitrifiers. Integration of carbohydrate-active enzyme repertoires further revealed metabolic complementarity between partial denitrifiers and anammox bacteria, supporting efficient carbon handoff without direct substrate competition. From an engineering perspective, operating conditions that impose moderate electron limitation, such as low or fluctuating C/N ratios and intermittent carbon feeding, may selectively enrich partial denitrifiers and enhance a stable nitrite supply for PD-anammox systems. Together, these findings identify PD as a predictable ecological state shaped by genome-encoded metabolic specialization and provide a mechanistic basis for designing robust, low-carbon nitrogen-removal processes.},
}

@article {pmid42700718,
year = {2026},
author = {Maglione, A and Rosso, R and Tortarolo, D and Pantini, F and Pernice, S and Contaldo, SG and Lanzillo, R and Spiezia, AL and Cordioli, C and Virgilio, E and Masuzzo, F and Matta, M and Malucchi, S and Cavalla, P and Cocolin, L and Sirovich, R and Beccuti, M and Ferrocino, I and Cordero, F and Clerico, M and Rolla, S},
title = {Gut microbiome profiling at multiple sclerosis onset as a potential early prognostic marker of disease course: evidence from an observational cohort study.},
journal = {EBioMedicine},
volume = {132},
number = {},
pages = {106470},
doi = {10.1016/j.ebiom.2026.106470},
pmid = {42700718},
issn = {2352-3964},
abstract = {BACKGROUND: Alterations in gut microbiome composition have been associated with multiple sclerosis (MS), but their impact on disease severity and early progression remains poorly understood. In this study we investigated whether gut microbiome profiling at diagnosis could identify microbial signatures associated with clinical and radiological features of early MS and provide prognostic information.

METHODS: We analysed the gut microbiome of 53 treatment-naïve patients with MS (pwMS) and 55 healthy donors (HD) using shotgun metagenomic sequencing, combined with clinical features collected over 1 year from diagnosis. To clarify whether gut microbiome composition at MS onset could have prognostic relevance, pwMS were stratified according to lesion burden, lesion localisation, and magnetic resonance imaging (MRI) activity.

FINDINGS: Overall beta diversity in Bacteria, Archaea, and Eukarya differed significantly between pwMS and HD (p-value <0.001, <0.02, <0.03, respectively). Within the MS group, glucocorticoid treatment at disease onset was the clinical factor most strongly associated with gut microbiota diversity. Stratification according to lesion burden, lesion localisation, and MRI activity identified two clinically distinct MS subgroups with different baseline clinical characteristics at onset (p-value <0.03) and different risk of early disease progression. The cluster associated with an unfavourable prognosis showed greater progression within 12 months and was enriched for motor symptoms and spinal cord lesions at diagnosis.

INTERPRETATION: Our findings suggest that gut microbiome alterations are detectable at the earliest stages of MS and are associated with clinical and radiological features linked to short-term disease evolution. Gut microbial profiling may therefore represent a promising early prognostic biomarker and may help to identify candidate targets for early intervention and therapeutic development in MS, although further validation in larger longitudinal cohorts is needed.

FUNDING: This study was supported by grants from the Italian Multiple Sclerosis Foundation, the Cassa di Risparmio di Torino Foundation, and the Italian Ministry of University and Research.},
}

@article {pmid42700855,
year = {2026},
author = {Ning, X and Zhou, L and Zeng, Y and Wang, S and Lv, M and Wang, J and Li, T and Wang, X},
title = {Cable bacteria accelerate nitrogen removal in freshwater sediments by mitigating diffusion limitation via long-distance electron transport.},
journal = {Environmental research},
volume = {308},
number = {Pt 1},
pages = {125593},
doi = {10.1016/j.envres.2026.125593},
pmid = {42700855},
issn = {1096-0953},
abstract = {The sustainable remediation of nitrogen polluted aquatic sediments is often constrained by the spatial separation of electron donors and acceptors, which limits intrinsic microbial nitrogen removal. The long-distance electron transport capacity of cable bacteria offers a natural strategy to overcome this limitation but the kinetic mechanisms remains poorly understood. Herein cable bacteria were enriched from ammonia impacted freshwater sediments and their role in enhancing nitrogen removal was systematically investigated. Biogeochemical analysis showed that cable bacteria reduced ammonium by 93% and increased sulfate accumulation 2.07 times relative to controls. Critically, DGT induced fluxes in sediments and soils (DIFS) modeling at depths of 4 mm and 20 mm revealed that cable bacteria maintained uniformly low nitrate and ammonium diffusion fluxes, whereas in the control nitrate fluxes were 4.5-fold higher and ammonium fluxes were 8.9- to 53-fold higher. This kinetic evidence indicates that cable bacteria accelerate nitrogen removal by enhancing the coupling between nitrification and denitrification, thereby mitigating the classical diffusion limitation that restricts these processes in surface sediments. Metagenomic analysis showed that cable bacteria orchestrated a community shift increasing Nitrospira abundance from 0.4% to 20% and enriching genes for respiratory nitrate reduction (narG) and assimilatory sulfate reduction (cysH, sir), establishing a self-sustaining syntrophic network that coordinated nitrogen and sulfur fluxes. These findings establish cable bacteria as a promising bioremediation tool for cleaner nitrogen management in contaminated aquatic systems.},
}

@article {pmid42700902,
year = {2026},
author = {Li, Z and Li, M and He, X and Zhang, H and Feng, C and Ding, M and Huang, G and Liu, J},
title = {Forty-three years of partial organic substitution shapes microbial assembly and multifaceted network stability in a paddy soil.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135760},
doi = {10.1016/j.biortech.2026.135760},
pmid = {42700902},
issn = {1873-2976},
abstract = {Partial substitution of chemical fertilizers with organic amendments is a promising strategy to sustain soil productivity while reducing chemical inputs. However, the ecological mechanisms by which organic substitution and inorganic reduction reshape soil microbial community assembly, life‑history strategies, and nutrient cycling potential remain poorly understood. A 43-year field experiment with different proportions of organic fertilizer substituting for inorganic nitrogen was conducted. Microbial community structure, assembly processes, keystone taxa, and functional genes involved in nitrogen (N) and sulfur (S) cycles were investigated with high-throughput amplicon and metagenomic sequencing. Our results showed that organic substitution significantly reshapes microbial community composition, increasing community evenness while maintaining species richness. It significantly reduced the proportion of transient and persistent microorganisms while increasing intermittent taxa. Organic substitution significantly reduced (p < 0.05) the contribution of stochastic processes in soil microbes in comparison to those treated only with chemical fertilizers. This shift was accompanied by the enrichment of specific functional phyla such as Actinomycetota (class Thermoleophilia), Myxococcota, and Gemmatimonadota, which served as keystone species in co‑occurrence networks. Functionally, organic substitution significantly upregulated genes involved in organic nitrogen mineralization (glnAB&ureABC&gdhA&GLUL) and anaerobic ammonium oxidation (anammox), while downregulating nitrification, dissimilatory nitrate reduction to ammonium (DNRA), and assimilatory nitrate reduction. Likewise, organic substitution reduced organic sulfur mineralization and hydrogen sulfide production (sreAB) but enhanced assimilatory sulfate reduction. The findings of this study provide new insights into the ecological mechanisms through which organic substitution regulates soil microbiomes and nutrient cycling.},
}

@article {pmid42702111,
year = {2026},
author = {Zhang, M and Wang, Z and Xia, J and Zhen, Y and Jiang, F and Zhang, L},
title = {Magnetite facilitates phage-bacteria interactions and phage-associated metabolic coordination for medium-chain fatty acid biosynthesis under ammonia stress.},
journal = {Water research},
volume = {308},
number = {Pt A},
pages = {126856},
doi = {10.1016/j.watres.2026.126856},
pmid = {42702111},
issn = {1879-2448},
abstract = {Medium-chain fatty acid (MCFA) production from waste activated sludge (WAS) is considered to rely on the syntrophic interactions among distinct functional microorganisms. Whether phages represent an overlooked ecological component involved in MCFA biosynthesis remains unclear. MCFA production is often inhibited by high total ammonia nitrogen (TAN). Conductive materials have been proposed as effective strategies to enhance or recover MCFA production under TAN stress. Therefore, the inhibition-recovery system could provide a useful framework for investigating whether viral ecological responses are associated with MCFA-related metabolic processes. In this study, magnetite (Fe3O4) was selected as the recovery strategy of MCFA production under TAN stress. Results showed that a total of 3915 vOTUs and 118 metagenome-assembled genomes were recovered from the anaerobic bioreactors subjected to three conditions: Control (without TAN stress), TAN stress, and TAN stress with Fe3O4 presence. Under high TAN environment (∼5 g/L), MCFA production reduced by 49% (1.3 g COD/L) in comparison to that without high TAN stress. The ecological coupling between temperate phages and MCFA-related bacterial hosts was weakened, accompanied by substantial decreases in the abundance and transcriptional abundance of phage-associated auxiliary metabolic genes (AMGs) related to MCFA synthesis (e.g., fatty acid biosynthesis, acyl-chain metabolism). In the presence of Fe3O4 (i.e., 10 g/L), MCFA production was four and two times higher than those with and without high TAN stress. In addition to enhanced phage-bacteria ecological coupling and increased the abundance and transcription of AMGs related to MCFA formation, Fe3O4 increased the abundance and expressions of electron-transfer-related AMGs (e.g., cbb3-type cytochrome c oxidase, type IV pilus assembly genes) and QS-related LuxR-family and HTH-type regulators, indicating that such indirect pathway could be largely overlooked during MCFA synthesis. This is also the first-time reporting that phages could represent an ecological layer responsive to iron oxide. Analyses of publicly available metagenomes collected from MCFA-oriented anaerobic systems further confirmed that phages could be broadly associated with the metabolic processes involved in MCFA biosynthesis. Taken together, this study reveals that phages could serve as an overlooked ecological layer associated with MCFA metabolism and provide a viral-ecology perspective for understanding TAN inhibition and iron oxide-mediated recovery during WAS-to-MCFA bioconversion.},
}

@article {pmid42702160,
year = {2026},
author = {Liu, W and Shen, J and Chen, Q and Liu, Z and Han, J and Ni, L},
title = {Metagenomic and physicochemical insights into ultrasound-assisted fermentation: Reprogramming Komagataeibacter intermedius metabolic efficiency for astringency control.},
journal = {Ultrasonics sonochemistry},
volume = {133},
number = {},
pages = {108041},
doi = {10.1016/j.ultsonch.2026.108041},
pmid = {42702160},
issn = {1873-2828},
abstract = {Oral astringency remains a major challenge limiting consumer acceptance of functional fermented beverages. Conventional mitigation strategies often reduce astringency at the expense of bioactive polyphenols, highlighting the need for non-destructive quality improvement approaches. In this study, low-power ultrasound-assisted fermentation (20 kHz, 240 W, 16.68 min/day) was applied to Kombucha, and the underlying mechanisms of astringency alleviation were investigated through integrated physicochemical characterization, metagenomic analysis, and temporal data modeling. Ultrasound significantly reduced sensory astringency and saliva-protein precipitation (OD650, p < 0.05) by Day 7 while preserving monomeric catechins, thereby maintaining antioxidant potential. Small-angle X-ray scattering (SAXS) and spectroscopic analyses revealed that ultrasound promoted the accumulation of water-soluble polysaccharides (1.69 mg/mL on Day 7, p < 0.01), which acted as macromolecular steric barriers and modified the aggregation behavior of polyphenol-salivary protein complexes. Consequently, the radius of gyration (Rg) increased to 608.67 nm, suppressing the formation of large aggregates associated with astringency perception. Furthermore, temporal machine-learning and time-lagged correlation analyses indicated that the reduction in astringency was associated not with increased abundance of Komagataeibacter intermedius, but with upregulated specific metabolic activity during the early fermentation stage. This early-stage metabolic adaptation was strongly associated with subsequent polysaccharide accumulation and sensory improvement. The findings suggest that low-power ultrasound can modulate microbial metabolic activity without altering microbial community structure, thereby influencing polysaccharide biosynthesis and colloidal interactions during fermentation. These results provide new insights into the biological and physicochemical mechanisms underlying ultrasound-assisted fermentation.},
}

@article {pmid42702602,
year = {2026},
author = {Li, Y and Chen, T and Li, P and Zhang, G and Tian, Y and Wang, J and Ni, J},
title = {Elevation-structured viral ecological strategies along glacier-fed rivers on the Qinghai-Tibet Plateau.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42702602},
issn = {2041-1723},
support = {U2240205//National Natural Science Foundation of China (National Science Foundation of China)/ ; 51721006//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Ice Cover/virology ; Tibet ; *Rivers/virology ; Altitude ; Ecosystem ; *Viruses/genetics/classification/isolation & purification ; Metagenome ; *Virome/genetics ; Genome, Viral ; },
abstract = {The Qinghai-Tibet Plateau, a climate-vulnerable source of Asia's major rivers, harbors underexplored viral communities critical to ecosystem functions. By integrating 597 metagenomes from the Yangtze, Yellow, Lancang, and Yarlung Tsangpo rivers with 85 public available glacial metagenomes (Tibetan Glacier Genome and Gene catalog), we built the Glacier-to-River Virome Catalogue, encompassing 36,358 vOTUs and 897,250 viral protein clusters, to decode viral adaptation and ecological influence across elevation gradients. Our results reveal that high-altitude conditions favor viruses with elevated Guanine-Cytosine content, larger genomes and more cold-adaptation genes. A central finding is a systematic viral lifestyle shift from temperate in glaciated regions to lytic viruses downstream, accompanied with decline of pathogens carrying antibiotic resistance genes along the glacier-to-river gradients. Further, viral auxiliary metabolic genes transition from glacier nutrient scavenging (e.g., nitrogen and sulfur transporters) to downstream mineralization processes (e.g., denitrification) in plains highlights their role in biogeochemical cycling. These findings position viruses as pivotal regulators of microbial community structural and functional dynamics to glacier-to-river gradient change and biogeochemistry in the Qinghai-Tibet Plateau, providing critical insights into climate response in vulnerable Asian water towers.},
}

*Ice Cover/virology
Tibet
*Rivers/virology
Altitude
Ecosystem
*Viruses/genetics/classification/isolation & purification
Metagenome
*Virome/genetics
Genome, Viral

@article {pmid42702845,
year = {2026},
author = {Xue, Z and Xu, H and Zhu, L and Zhao, D},
title = {Prevotella melaninogenica Alleviate Mycoplasma pneumoniae Infection Through the Butyrate Based on Multi-Omic Analysis and Experimental Validation.},
journal = {Chemical biology & drug design},
volume = {108},
number = {3},
pages = {e70397},
doi = {10.1111/cbdd.70397},
pmid = {42702845},
issn = {1747-0285},
mesh = {Animals ; Humans ; Multiomics ; *Prevotella melaninogenica/metabolism/physiology ; *Pneumonia, Mycoplasma/microbiology/metabolism/drug therapy ; *Mycoplasma pneumoniae ; Mice ; *Butyrates/metabolism ; Male ; Female ; RNA, Ribosomal, 16S/genetics ; Bronchoalveolar Lavage Fluid/microbiology ; Child ; Child, Preschool ; Disease Models, Animal ; Microbiota ; },
abstract = {Mycoplasma pneumoniae (MP) is one of the main pathogens causing atypical pneumonia in children. The susceptible population is mainly children and adolescents over 5 years old, and the infection rate has increased in recent years. At present, there is limited research on the pulmonary microbiota of patients with Mycoplasma pneumoniae pneumonia, and the characteristics of their microbiota are not yet clear. We included MPP children in stages and established two independent cohorts. Cohort I (n = 175) performed 16S rRNA sequencing on bronchoalveolar lavage fluid (BALF) to explore microbial genus level characteristics, while Cohort II (n = 41) performed metagenomic and transcriptome sequencing to explore microbial species level characteristics and predict inter group differential metabolic pathways. Finally, a murine model infected with MP was established to validate the effects of Prevotella melaninogenica and its metabolite butyrate. Based on Multi-Omic Analysis, we discovered that P. melaninogenica was the most discriminative species enriched in the critically ill group. Functional profiling demonstrated that butanoate metabolism pathways were significantly enriched in the severe group and positively correlated with P. melaninogenica abundance. Transcriptomic analysis revealed that P. melaninogenica-associated host genes were significantly enriched in immune regulation pathways. Animal experiments confirmed that both P. melaninogenica and butyrate pretreatment significantly attenuated MP-induced pulmonary inflammation, pathogen load, and immune cell infiltration. Respiratory microbiota dysbiosis may be associated with MPP severity. Prevotella melaninogenica, a potential protective commensal enriched in severe group MPP patients, may alleviate airway inflammation through its metabolite butyrate.},
}

Animals
Humans
Multiomics
*Prevotella melaninogenica/metabolism/physiology
*Pneumonia, Mycoplasma/microbiology/metabolism/drug therapy
*Mycoplasma pneumoniae
Mice
*Butyrates/metabolism
Male
Female
RNA, Ribosomal, 16S/genetics
Bronchoalveolar Lavage Fluid/microbiology
Child
Child, Preschool
Disease Models, Animal
Microbiota

@article {pmid42703041,
year = {2026},
author = {Zhang, Y and Zhu, D and Gao, F and Chen, Z and Hu, H and Yuan, C},
title = {Soil Acidification Enriches Antibiotic Resistome.},
journal = {Global change biology},
volume = {32},
number = {9},
pages = {e71087},
doi = {10.1111/gcb.71087},
pmid = {42703041},
issn = {1365-2486},
support = {42577555//National Natural Science Foundation of China/ ; 2026A1515010684//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 77000-31610011//Fundamental Research Funds for the Central Universities/ ; GZC20233289//Postdoctoral Fellowship Program of CPSF/ ; },
mesh = {Hydrogen-Ion Concentration ; *Soil Microbiology ; *Soil/chemistry ; *Bacteria/genetics/drug effects ; *Drug Resistance, Microbial/genetics ; *Genes, Bacterial ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Soil acidification represents a critical global change issue. Its impacts on antibiotic resistance genes (ARGs), however, remain poorly understood. Here we first analyzed a published global dataset comprising 1012 sampling sites and found a significant negative correlation between soil pH and the total richness and relative abundance of ARGs. To validate the observed pattern, we subjected three soils (with initial pH 7.8-7.9) each to 4 acidification levels (pH 7, 6, 5, and 4) for 30 days and subsequent recovery for another 30 days in microcosms. Shotgun metagenomic sequencing revealed that acidification (pH 6, 5, and 4) significantly increased the total richness and relative abundance of ARGs, as well as the relative abundances of 175 ARG subtypes, across all three soils. These 175 acidification-enriched ARGs together accounted for more than 70% of all the ARGs under severely acidified conditions (pH 5 and 4). Moreover, 93% of the bacteria carrying acidification-enriched ARGs also carried various virulence factor genes homologs associated with pathogenicity in reference databases, resulting in increased risk score. The total relative abundance of the acidification-enriched ARGs was primarily associated with changes in bacterial community traits (community composition, acidification-enriched metabolic functions, and genome size), followed by the increase in availability of toxic metals. When soil recovered from severe acidification (pH 5 and 4), the total relative abundance of the acidification-enriched ARGs significantly declined, demonstrating that the effect of soil acidification is partially reversible. This study reveals an underrecognized risk of ARGs caused by soil acidification, highlighting that the prevention and mitigation of soil acidification are crucial for combating antibiotic resistance.},
}

Hydrogen-Ion Concentration
*Soil Microbiology
*Soil/chemistry
*Bacteria/genetics/drug effects
*Drug Resistance, Microbial/genetics
*Genes, Bacterial
*Drug Resistance, Bacterial/genetics
Anti-Bacterial Agents/pharmacology

@article {pmid42703182,
year = {2026},
author = {Mansour, MA and Wahid, M and El Molla, MAS and Helmy, MH and Adel, TM and Mostafa, HN},
title = {Central Nervous System Aspergillosis: Advances in Diagnosis, Therapeutics, and Multidisciplinary Management (2026 Update).},
journal = {Mycoses},
volume = {69},
number = {9},
pages = {e70214},
doi = {10.1111/myc.70214},
pmid = {42703182},
issn = {1439-0507},
mesh = {Humans ; *Antifungal Agents/therapeutic use/pharmacokinetics ; *Neuroaspergillosis/diagnosis/drug therapy ; Voriconazole/therapeutic use ; *Central Nervous System Fungal Infections/diagnosis/drug therapy ; },
abstract = {BACKGROUND: Central nervous system (CNS) aspergillosis is a life-threatening infection with mortality rates exceeding 50%, especially in immunocompromised patients. Significant challenges persist due to limited antifungal drug penetration into the CNS, emerging resistance, and diagnostic delays, despite advancements in therapy and diagnostics.

OBJECTIVE: This comprehensive review aims to synthesize pivotal advances in the management of CNS aspergillosis from 2020 to 2026 and to provide a multidisciplinary framework for addressing these ongoing challenges.

METHODS: We conducted a comprehensive evaluation of the latest clinical data, pharmacokinetic studies, and expert recommendations from the specified period. The review critically appraises evidence on pharmacological therapies, diagnostic technologies, and adjunctive treatment strategies.

FINDINGS: Key findings include: Pharmacotherapy: Voriconazole remains the cornerstone of therapy due to its superior CNS penetration (CSF:Plasma ratio ~50%). The roles of alternatives like isavuconazole, salvage combination regimens, and novel agents (e.g., olorofim, fosmanogepix) are evolving.

DIAGNOSTICS: Cutting-edge tools such as AI-assisted imaging, metagenomic next-generation sequencing (mNGS), and MR spectroscopy for trehalose detection show significant potential for enabling earlier and more accurate diagnosis. Adjunctive Strategies: Neurosurgical intervention, immunomodulation, and therapeutic drug monitoring (TDM) are critical for optimizing outcomes. Emerging strategies like nanoparticle-based drug delivery and host-directed therapies (e.g., PD-1/PD-L1 blockade) offer promising avenues to overcome the blood-brain barrier.

CONCLUSION: This review integrates the latest evidence to provide a timely and actionable resource for clinicians. It bridges gaps in existing guidelines by offering a multidisciplinary approach that addresses the complex management of CNS aspergillosis, with particular relevance for high-risk populations such as COVID-19 and immunocompromised patients.},
}

Humans
*Antifungal Agents/therapeutic use/pharmacokinetics
*Neuroaspergillosis/diagnosis/drug therapy
Voriconazole/therapeutic use
*Central Nervous System Fungal Infections/diagnosis/drug therapy

@article {pmid42703537,
year = {2026},
author = {Wu, J and Luo, X and Fu, S and Zhou, S and He, J and Zhang, D and Zheng, W},
title = {Fatal Pharyngeal Cellulitis Caused by Rhizopus microsporus in a Patient with Acute Myeloid Leukemia.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {608970},
pmid = {42703537},
issn = {1178-6973},
abstract = {INTRODUCTION: Patients with immunodeficiency are highly susceptible to life-threatening fungal infections. Pharyngeal cellulitis caused by Rhizopus microsporus are exceptionally rare.

CASE PRESENTATION: We reported a case of relapsed acute myeloid leukemia (AML) complicated by post-chemotherapy Rhizopus microsporus pharyngeal cellulitis. This cellulitis resulted in severe tissue necrosis, pharyngeal obstruction, and sub-sequent suffocation. Emergency bedside tracheotomy was administered after acute respiratory distress. The metagenomic next-generation sequencing (mNGS) identified Rhizopus microsporus, Klebsiella pneumoniae, Candida albicans, and SARS-CoV-2. Despite surgical intervention and combination antimicrobial therapy (amphotericin B, posaconazole, daptomycin, ceftriaxone, and molnupiravir), the patient stabilized for 2 months before culminating in fatal carotid artery rupture.

CONCLUSION: Rhizopus microsporus-related pharyngeal cellulitis is rare yet highly aggressive, demanding timely diagnosis and close monitoring. This case highlights the critical role of rapid mNGS in diagnosing polymicrobial infections, underscores the necessity of combining aggressive surgical debridement with antifungal/antimicrobial regimens, and stresses rigorous surveillance to prevent life-threatening vascular complications.},
}

@article {pmid42703994,
year = {2026},
author = {Kar, P and Halder, J and Rout, SR and Dash, P and Das, C and Ghosh, G and Rath, G and Kar, B},
title = {Marine-derived Bioactive Compounds: A Promising Frontier against Multidrug-resistant Microbial Infections.},
journal = {Mini reviews in medicinal chemistry},
volume = {26},
number = {12},
pages = {841-858},
pmid = {42703994},
issn = {1875-5607},
mesh = {Humans ; *Biological Products/chemistry/pharmacology/isolation & purification ; *Anti-Bacterial Agents/pharmacology/chemistry/isolation & purification ; Animals ; *Aquatic Organisms/chemistry/metabolism ; *Drug Resistance, Multiple, Bacterial/drug effects ; Bacteria/drug effects ; *Bacterial Infections/drug therapy ; Microbial Sensitivity Tests ; },
abstract = {The global escalation of Multidrug-Resistant (MDR) bacterial infections poses a serious and growing threat to public health, contributing to increased morbidity, mortality, and substantial economic burden worldwide. The widespread and often indiscriminate use of antibiotics in clinical and agricultural settings has accelerated the emergence of resistance, significantly diminishing the efficacy of conventional antimicrobial therapies. This pressing challenge necessitates the exploration of alternative sources for novel antibiotics. Marine ecosystems-renowned for their immense biodiversity and ecological complexity-have gained attention as a rich and largely untapped reservoir of bioactive natural products with potent antimicrobial activity. Marine organisms, such as sponges, tunicates, algae, and bacteria and fungi derived from marine sources, produce structurally diverse and pharmacologically active metabolites, including peptides, polyketides, alkaloids, terpenoids, sterols, lactones, and halogenated compounds. Many of these marine-derived molecules possess unique chemical scaffolds and novel mechanisms of action, offering the potential to circumvent existing resistance pathways. Some compounds have shown promising activity against MDR pathogens, including Staphylococcus aureus, Pseudomonas aeruginosa, and Acinetobacter baumannii. However, challenges such as low natural abundance, difficulty in cultivation, and structural complexity have limited their clinical translation. Recent advancements in marine biotechnology, genomics, metagenomics, and synthetic biology have opened new avenues for the discovery, biosynthesis, and structural optimization of these compounds. These innovative approaches not only facilitate sustainable production but also enhance the pharmacological properties.},
}

Humans
*Biological Products/chemistry/pharmacology/isolation & purification
*Anti-Bacterial Agents/pharmacology/chemistry/isolation & purification
Animals
*Aquatic Organisms/chemistry/metabolism
*Drug Resistance, Multiple, Bacterial/drug effects
Bacteria/drug effects
*Bacterial Infections/drug therapy
Microbial Sensitivity Tests

@article {pmid42704537,
year = {2026},
author = {de Freitas Germano, J and Leite, G and Pimentel, M},
title = {Do Multi-Omics Approaches Improve the Diagnosis of Microbial Overgrowth Syndromes?.},
journal = {Current gastroenterology reports},
volume = {28},
number = {1},
pages = {},
pmid = {42704537},
issn = {1534-312X},
mesh = {Humans ; Multiomics ; *Intestine, Small/microbiology ; Proteomics/methods ; *Blind Loop Syndrome/diagnosis/microbiology ; Breath Tests/methods ; Gastrointestinal Microbiome ; Metagenomics/methods ; Syndrome ; },
abstract = {PURPOSE OF REVIEW: This review investigates how advances in breath testing (BT), small bowel (SB) culture, metagenomics, metatranscriptomics, transcriptomics and proteomics are reshaping the definition and diagnosis of small intestinal bacterial overgrowth (SIBO). It also discusses whether SIBO should be redefined as part of a larger group of microbial overgrowth syndromes.

RECENT FINDINGS: Recent studies identify distinct hydrogen-, methane-, and hydrogen sulfide-associated overgrowth phenotypes, termed SIBO, intestinal methanogen overgrowth (IMO), and intestinal sulfide overproduction (ISO). SB sampling shows that these conditions involve different microbial patterns and functional activity, symptoms, and host responses. Quantitative shotgun metagenomics provides greater taxonomic and functional resolution than culture, while metatranscriptomics reveals active microbial pathways. On top of that, host transcriptomics and proteomics contribute to the better understanding of the predominant microbial effects in host cellular mechanisms in each of the distinct small bowel overgrowth types. SIBO has been increasingly identified as a disorder of microbial ecology and function rather than bacterial quantity alone. Integrating BT with SB sampling and multi-omics approaches may improve classification, clarify symptom mechanisms, and support a more individualized treatment, although standardized methods and further clinical validation remain necessary.},
}

Humans
Multiomics
*Intestine, Small/microbiology
Proteomics/methods
*Blind Loop Syndrome/diagnosis/microbiology
Breath Tests/methods
Gastrointestinal Microbiome
Metagenomics/methods
Syndrome

@article {pmid42704656,
year = {2026},
author = {Bates, KA and Rivera, VB and Glicklich, D and Diflo, T and Chaturvedi, V and Nog, R},
title = {Urinary microbiome in renal transplant patients with BK polyomavirus reactivation.},
journal = {Journal of medical microbiology},
volume = {75},
number = {9},
pages = {},
doi = {10.1099/jmm.0.002196},
pmid = {42704656},
issn = {1473-5644},
mesh = {Humans ; *BK Virus/physiology/genetics ; *Kidney Transplantation/adverse effects ; *Polyomavirus Infections/urine/microbiology/virology ; *Microbiota ; Male ; Female ; Middle Aged ; Adult ; *Virus Activation ; Bacteria/classification/genetics/isolation & purification ; *Tumor Virus Infections/urine/microbiology/virology ; Aged ; DNA, Viral/blood ; *Urine/microbiology ; },
abstract = {Introduction. BK polyomavirus (BKPyV) reactivation is a significant health risk among renal transplant recipients that can lead to nephropathy and allograft loss.Hypothesis/Gap statement. While the microbiota is increasingly recognized as an important determinant of viral infection and pathogenesis, as well as itself undergoing compositional changes in response to infection, the urinary microbiome has yet to be investigated in the context of BK polyomavirus reactivation.Aim. This study aimed to investigate associations between the urinary microbiome and BKPyV-DNAemia in renal transplant patients.Methodology. Shotgun metagenomics of the urinary microbiome was conducted for 22 renal transplant recipients, 11 of whom had BKPyV-DNAemia. Sequence data were analysed using two complementary approaches to identify common microbiome associations with BKPyV-DNAemia: (1) Kaiju - a DNA-to-Protein method that captures bacteria, archaea, fungi, microeukaryotes and DNA viruses and (2) MetaPhlAn4 - a DNA-to-Marker method using a reference database of specific marker genes of prokaryotes.Results. We found increased observed diversity of bacterial taxa in control patients compared to those with BKPyV-DNAemia for data analysed with MetaPhlAn4 (P=0.037) but not Kaiju (P>0.05), which followed a similar trend. Significant differences in microbial beta diversity between the control and BKPyV-DNAemia patient group were identified for the Kaiju dataset (P=0.027) but not for MetaPhlAn4 (P>0.05), with viral reads likely driving these differences in the Kaiju dataset. Both Kaiju and MetaPhlAn4 identified Proteobacteria, Firmicutes and Actinobacteria as bacterial phyla with greatest relative abundance across samples. Screening bacterial species data generated from Kaiju and MetaPhlAn4 against a database of 243 human pathogens identified 8 pathogenic species recovered from both datasets that were present in the urinary microbiome of renal transplant patients.Conclusion. The observed evidence for differences in microbiome diversity and composition associated with BKPyV-DNAemia may play an important role in its pathology and guide the development of diagnostic biomarkers. Our findings warrant further investigation across larger patient cohorts that are more evenly balanced for gender.},
}

Humans
*BK Virus/physiology/genetics
*Kidney Transplantation/adverse effects
*Polyomavirus Infections/urine/microbiology/virology
*Microbiota
Male
Female
Middle Aged
Adult
*Virus Activation
Bacteria/classification/genetics/isolation & purification
*Tumor Virus Infections/urine/microbiology/virology
Aged
DNA, Viral/blood
*Urine/microbiology

@article {pmid42704958,
year = {2026},
author = {Miller, AK and Heremia, L and Waller, SJ and Blanchard, SL and Taylor, JT and Treece, JM and Wille, M and Gemmell, NJ and Winter, D and Dowle, EJ and Geoghegan, JL},
title = {Evaluating sampling strategies for the detection of avian influenza viruses in the environment.},
journal = {Virology},
volume = {625},
number = {},
pages = {111069},
doi = {10.1016/j.virol.2026.111069},
pmid = {42704958},
issn = {1096-0341},
abstract = {Highly pathogenic avian influenza (HPAI) viruses pose an increasing threat to wildlife, livestock and human health, underscoring the need for scalable and early-warning surveillance systems. Environmental RNA (eRNA) monitoring offers a non-invasive, cost-effective alternative to traditional host-based sampling by detecting viral genetic material shed into the environment. Despite its utility, the relative performance of different environmental sampling approaches for avian influenza virus (AIV) detection remains poorly resolved. Here, we conducted a longitudinal study with monthly sampling over approximately one year across two urban waterfowl ponds in Aotearoa New Zealand to evaluate four eRNA sampling strategies - fresh faeces, sediment, active-filtered water and passive-filtered water - for their ability to detect AIV. Using a combination of metagenomic sequencing and RT-qPCR, we show that all sample types can detect AIV, although detections were highly inconsistent across sampling methods, locations and time points. While metagenomic sequencing provided valuable genomic data, including subtype identification and phylogenetic context, RT-qPCR exhibited greater sensitivity, with active-filtered water yielding the highest detection rates, and is currently the more cost-effective approach for large-scale surveillance. Notably, AIV detections were asynchronous among sample types and frequently lacked temporal concordance, suggesting that environmental heterogeneity, RNA persistence, and methodological detection limits strongly influence surveillance outcomes. Despite these inconsistencies, phylogenetic analyses revealed that detected viruses belong to established Australasian lineages, highlighting the ability of environmental surveillance to capture ecologically relevant viral diversity. Our findings demonstrate that while eRNA-based surveillance holds substantial promise as a complementary tool for AIV monitoring, its effectiveness is highly dependent on the environmental sampling strategies and laboratory detection methods used.},
}

@article {pmid42704972,
year = {2026},
author = {Li, J and Shen, F and Chen, Z},
title = {Arbuscular mycorrhizal fungi stabilize ammonium-rich nitrogen removal in constructed wetlands through plant-mediated microbial functional shifts.},
journal = {Water research},
volume = {308},
number = {Pt A},
pages = {126836},
doi = {10.1016/j.watres.2026.126836},
pmid = {42704972},
issn = {1879-2448},
abstract = {Arbuscular mycorrhizal fungi (AMF) are increasingly proposed as a low-energy means of intensifying constructed wetlands (CWs), but whether their benefits depend on influent nitrogen speciation has not been tested. We compared inoculated and uninoculated CWs across three influent N forms at equal N loading. CWs planted with Iris pseudacorus were inoculated with Rhizophagus irregularis (AMF+) or left uninoculated (AMF-) and fed NO3[-]-only (N1), NH4[+]-only (N2), or mixed NO3[-]/NH4[+] (N3) influents at equal total N. Compared with AMF-, AMF+ systems showed higher plant height and chlorophyll content, 30-70% higher SOD/POD activities, and 30-50% lower MDA content and O2·[-] production, especially under N2 and N3. Under N2, AMF prevented TN-removal collapse (83% vs. 26%) and lowered effluent NH4[+]-N (∼3 vs. ∼9 mg N L[-1]). Under N3, AMF maintained ∼88% TN removal (vs. 72%). Selective NH4[+]-N accumulation with negligible effluent NO2[-]-N and NO3[-]-N indicated reduced ammonia-oxidation capacity as the primary N2 bottleneck. Only N2 showed significant AMF-associated community separation (ANOSIM R = 0.77, p = 0.03), accompanied by higher ammonia and nitrite-oxidation potentials (log2FC = 2.20 and 3.99) and increased metagenomic abundances of amoABC, hao, and nxrB. PLS-PM accounted for 68% of the variation in N-removal performance and identified N-cycling functional potential as its strongest positive correlate (β = 0.81), while significant colonization-plant and plant-microbiome paths highlighted host physiological maintenance within the proposed association framework. Overall, AMF benefits were more closely aligned with N-form-specific bottlenecks than with colonization intensity, supporting context-dependent application to stabilize N removal in low-energy CWs treating ammonium-rich or compositionally variable wastewater.},
}

@article {pmid42705201,
year = {2026},
author = {Zhao, X and Meng, T and Zhang, Z and Hu, L and Xiang, X},
title = {Vegetable trimming pellets in laying hen diets drive cecal remodeling and dose-dependent plasma-egg metabolomic dissociation.},
journal = {Poultry science},
volume = {105},
number = {11},
pages = {107637},
doi = {10.1016/j.psj.2026.107637},
pmid = {42705201},
issn = {1525-3171},
abstract = {Vegetable trimming pellets (TVP) provide a potential route for recovering plant biomass as poultry feed, but their dose-dependent effects across production and biological compartments remain unclear. We evaluated diets containing 0% (A), 3% (B), 6% (C), or 9% (D) TVP (80% lettuce and 20% cabbage trimmings) in 240 17-wk-old Hy-Line Grey hens (6 pens of 10 hens per diet) for 12 wk. Diets had similar calculated crude protein, while calculated metabolizable energy decreased from 2.854 to 2.659 Mcal/kg. We assessed production, egg quality, serum, intestine, cecal microbiota and metagenome, and plasma and egg metabolomes. Full-period feed conversion ratio increased from 2.74 in A to 2.88 in D (P = 0.026), and average daily feed intake differed (P = 0.001), while egg production, egg weight, and egg mass remained similar (P > 0.05). At wk 12, shell breaking strength was lower in D than in A to C (3.55 vs. 3.92 to 4.02 kgf/cm[2]; P = 0.030), and yolk color differed among diets (P = 0.007). Serum hormones, several biochemical indices, catalase, and malondialdehyde differed at wk 12 (P < 0.05; marker-specific n = 3 to 6). Cecal community composition differed (permutational multivariate analysis of variance: R[2] = 0.571, P = 0.0006; dispersion P = 0.229), while Shannon diversity remained similar (P = 0.582). Five A-vs.-D metagenomic pathways met a false discovery rate (FDR) < 0.05. In D vs. A, exploratory screening identified 254 annotated plasma and 338 annotated egg candidates, of which 62 and 80, respectively, also met FDR < 0.05; exact annotation matching identified one shared candidate. Graded TVP inclusion maintained major egg-output traits while producing dose-related shifts in feed use, cecal microbial features, and compartment-specific molecular profiles. At the higher inclusion levels, less favorable feed conversion and the lower late-period shell strength at 9% were the principal practical responses.},
}

@article {pmid42705234,
year = {2026},
author = {MacKenzie, C and Seo, H and Schlechte, J and Herik, A and Bains, I and Yu, IL and McCoy, KD and Thornton, CS and McDonald, B},
title = {ON-Time enables rapid microbiome sequencing and analysis for precision medicine.},
journal = {Cell reports methods},
volume = {},
number = {},
pages = {101593},
doi = {10.1016/j.crmeth.2026.101593},
pmid = {42705234},
issn = {2667-2375},
abstract = {Clinical application of microbiome-guided therapies in the intensive care unit (ICU) requires a method to rapidly analyze patient microbiomes to guide urgent treatment decisions. Conventional microbiome sequencing and analysis methods require long turnaround times, methodological complexity, and high costs that are barriers to clinical application. Here, we describe a method for rapid (<5 h turnaround from sample to results) and accurate metagenomic sequencing and taxonomic analysis of microbiomes in individual patient fecal samples, called ON-Time. ON-Time uses a simplified and rapid wet-lab workflow coupled with point-and-click data analysis. Accuracy and precision of ON-Time data were validated using defined mock microbial communities and head-to-head comparison with conventional shotgun metagenomics of ICU patient samples. Key limitations include stochastic identification of functional genes such as antimicrobial resistance and virulence factors. Taken together, ON-Time offers a rapid, accurate, and cost-effective method to analyze individual patient samples for clinically actionable microbiome features to guide personalized therapeutics.},
}

@article {pmid42705487,
year = {2026},
author = {Huang, J and Li, L and Ye, W and Han, L and Liu, Y and Zhan, B and Xu, Y and Peng, X},
title = {Ethanol pretreatment drives microbial community adaptation to overcome acidification in high-solid anaerobic digestion of food waste under rapid organic loading shock.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135803},
doi = {10.1016/j.biortech.2026.135803},
pmid = {42705487},
issn = {1873-2976},
abstract = {This study investigated how ethanol pretreatment (EP) enhances the resilience of high-solid anaerobic digestion against rapid organic loading shocks. Semi-continuous reactors fed with either untreated or EP-treated food waste were compared, and the underlying mechanisms were elucidated by integrating thermodynamic calculations with metagenomic analyses. At an organic loading rate of 6.0 g VS/(Lˑd), the control group (untreated) collapsed due to the accumulation of propionate and other longer-chain volatile fatty acids (VFAs), resulting in a methane yield decrease exceeding 70%. In contrast, the EP group maintained stability, exhibiting a methane yield decrease of less than 5%, with VFAs dominated by readily degradable acetate. Thermodynamic analysis confirmed that EP significantly lowered the energy barriers for VFA degradation. Metagenomic analysis revealed that both propionate/butyrate activation pathways (with lower energy cost or independence from acetyl-CoA) and syntrophic acetate oxidation were activated in the EP group, thereby avoiding the VFA metabolic stress observed in the control group. Furthermore, higher abundances of conductive type IV pili genes, Complex II, and archaeal V/A-type ATPase were detected in the EP group, suggesting the establishment of direct interspecies electron transfer and enhanced electron flux and energy capture efficiency. Moreover, under high loading conditions, only a few high-abundance metagenome-assembled genomes (MAGs) were detected in the control group, while multiple MAGs carrying identical VFA-degrading enzyme systems were identified in the EP group. The functionally redundant microbiota, unobstructed VFA metabolic pathways, and efficient electron transfer and energy supply collectively sustained the stability of the EP group under loading shocks.},
}

@article {pmid42705715,
year = {2026},
author = {Li, G and Shen, L and Nie, L and Tang, P and Shan, Q and Qin, L and Fan, S and Guo, X},
title = {Integrated electronic nose, GC-MS, and metagenomic analyses reveal volatile flavor and microbial community differences in heap-fermented grains of Jiangxiangxing Baijiu across different fermentation degrees.},
journal = {Food research international (Ottawa, Ont.)},
volume = {243},
number = {Pt 2},
pages = {120307},
doi = {10.1016/j.foodres.2026.120307},
pmid = {42705715},
issn = {1873-7145},
mesh = {*Fermentation ; *Volatile Organic Compounds/analysis ; *Gas Chromatography-Mass Spectrometry/methods ; *Electronic Nose ; *Metagenomics/methods ; *Microbiota ; *Food Microbiology/methods ; Taste ; Odorants/analysis ; *Edible Grain/microbiology/chemistry ; *Fermented Foods/microbiology/analysis ; Bacteria/classification/metabolism/genetics ; },
abstract = {The fermentation degree of heap-fermented grains in Jiangxiangxing Baijiu production is a critical factor influencing base Baijiu quality. However, conventional assessment methods largely rely on empirical experience and therefore suffer from limited objectivity and accuracy. In this study, integrated volatile profiling and metagenomic approaches were employed to investigate volatile characteristics and microbial functional potential differentiation in fermented grains with different fermentation degrees (under-fermented, normally fermented, and over-fermented). Significant differences in physicochemical properties were observed among fermentation degrees, particularly in acidity and reducing sugar content. Electronic nose analysis revealed distinct sensor response patterns among different fermentation degrees, indicating differences in overall volatile odor fingerprint patterns. A total of 81 volatile compounds were identified by HS-SPME-GC-MS, with aldehydes, ketones, and pyrazines showing pronounced variations among fermentation degrees, and acetaldehyde exhibiting strong discriminatory potential. LEfSe analysis identified 18 microbial taxa as potential biomarkers associated with different fermentation degrees, including Pichia kudriavzevii, Lentibacillus daiqui, and Acetobacter pasteurianus. Correlation analysis revealed significant positive associations between acetaldehyde levels and Acetobacter abundance. Furthermore, KEGG, CAZy, and eggNOG analyses revealed differentiated functional potentials among fermentation degrees, providing insights into the potential metabolic basis associated with flavor differentiation. Overall, these findings highlight that fermentation degree differentiation is closely associated with coordinated changes in physicochemical conditions, microbial communities, and functional potentials, providing ecological insights into flavor differentiation and theoretical support for objective fermentation degree evaluation and quality control of Jiangxiangxing Baijiu production.},
}

*Fermentation
*Volatile Organic Compounds/analysis
*Gas Chromatography-Mass Spectrometry/methods
*Electronic Nose
*Metagenomics/methods
*Microbiota
*Food Microbiology/methods
Taste
Odorants/analysis
*Edible Grain/microbiology/chemistry
*Fermented Foods/microbiology/analysis
Bacteria/classification/metabolism/genetics

@article {pmid42705723,
year = {2026},
author = {Tong, W and Wang, H and Yang, Y and Xu, J and Huang, Z and Huang, D and Luo, H and Zhao, L and Zhang, S},
title = {Enzyme-driven synthesis and metabolic mechanism of ferulic acid in strong-flavor Daqu: pathway elucidation and microbial drivers.},
journal = {Food research international (Ottawa, Ont.)},
volume = {243},
number = {Pt 2},
pages = {120354},
doi = {10.1016/j.foodres.2026.120354},
pmid = {42705723},
issn = {1873-7145},
mesh = {*Coumaric Acids/metabolism/analysis ; Fermentation ; Carboxylic Ester Hydrolases/metabolism ; *Alcoholic Beverages/microbiology/analysis ; *Flavoring Agents/metabolism ; Carboxy-Lyases/metabolism ; Bacteria/metabolism ; Metabolic Networks and Pathways ; Microbiota ; },
abstract = {Ferulic acid (FA) is a bioactive phenolic compound in strong-flavor Baijiu with important health functions. Its microbial synthesis and metabolic mechanisms in strong-flavor Daqu remain unclear, limiting the understanding of its production. This study explored FA synthesis and metabolic dynamics during Daqu fermentation from D0-D90 using physicochemical detection, feruloyl esterases (FAEs) activity assay, and metagenomic sequencing. Results indicated that FA content fluctuated dynamically throughout fermentation, reaching a final level of 4.39 ± 0.17 mg/kg, and FAEs activity was significantly positively correlated with FA content. Genera significantly associated with FA dynamics were identified. High-abundance genera including Lichtheimia, Saccharopolyspora, Aspergillus, Byssochlamys and Rasamsonia exhibited significantly positive correlations with FA accumulation at respective fermentation stages. This phenomenon may be attributed to their capacity to secrete FAEs, thereby promoting the release of FA. The dynamic change of free FA content was also associated with the expression of ferulic acid decarboxylase, a key enzyme potentially involved in free FA degradation. A comprehensive FA metabolic network in Daqu was constructed, including the cell wall release pathway and the shikimate biosynthesis pathway. A metabolic association model was established based on the phasic succession of fungal and bacterial communities and their coupling with FA metabolic enzyme systems, which suggested a potential division of labor. Fungi are likely to participate in free FA release through secretion of FAEs and auxiliary degrading enzymes, while bacteria may mainly participate in the metabolic turnover and consumption of free FA. This study expands the current understanding of phenolic acid metabolism in strong-flavor Daqu, and provides a theoretical basis for interpreting FA metabolic characteristics during Daqu fermentation.},
}

*Coumaric Acids/metabolism/analysis
Fermentation
Carboxylic Ester Hydrolases/metabolism
*Alcoholic Beverages/microbiology/analysis
*Flavoring Agents/metabolism
Carboxy-Lyases/metabolism
Bacteria/metabolism
Metabolic Networks and Pathways
Microbiota

@article {pmid42705725,
year = {2026},
author = {Xiao, L and Wan, Y and Jiang, M and Liu, Z and Chen, G and Ke, S and Jiang, J and Guo, S and Yu, P and Wu, H and Wang, A and Ning, M and Zhou, Z},
title = {Effects of extraction methodologies on structural characterization and gut microbiota fermentation properties of Apocynum venetum polysaccharides.},
journal = {Food research international (Ottawa, Ont.)},
volume = {243},
number = {Pt 2},
pages = {120357},
doi = {10.1016/j.foodres.2026.120357},
pmid = {42705725},
issn = {1873-7145},
mesh = {*Fermentation ; *Polysaccharides/chemistry/isolation & purification/metabolism/pharmacology ; *Gastrointestinal Microbiome/physiology ; *Apocynum/chemistry ; Prebiotics ; Bacillus/metabolism ; *Plant Extracts/chemistry ; Hydrogen-Ion Concentration ; },
abstract = {Apocynum venetum L. polysaccharides are classified into neutral-to-acidic heteropolysaccharides rich in glucuronic acid, exhibiting antioxidant, immunomodulatory, and potential prebiotic activities. Different extraction methods have a significant impact on the structural characterization and biological activity of polysaccharides. This study aims to compare the structural characteristics and in vitro prebiotic activity of the Apocynum venetum L. polysaccharides BAC and CEL-U obtained via Bacillus velezensis fermentation and the combined ultrasonic-cellulase method, respectively. The results showed that BAC and CEL-U were acidic heteropolysaccharides composed of rhamnose, arabinose, galactose, glucose and galacturonic acid, and they all showed linear branching structure. Compared with CEL-U, BAC had lower molecular weight (17.51 kDa), higher uronic acid content (27.27%) and typical triple helix structure. In vitro fermentation showed that BAC can produce more propionic acid and butyric acid, maintain a lower pH, promote the proliferation of beneficial bacteria (Segatella and Prevotella), and inhibit potentially harmful bacteria. Metagenome analysis further revealed that BAC played a prebiotic role by activating specific glycosidase-mediated degradation pathways and enriching functional pathways related to carbohydrate metabolism. These findings clarify the structure-activity relationship of Apocynum venetum polysaccharide and provide a theoretical basis for its targeted application in the field of intestinal health.},
}

*Fermentation
*Polysaccharides/chemistry/isolation & purification/metabolism/pharmacology
*Gastrointestinal Microbiome/physiology
*Apocynum/chemistry
Prebiotics
Bacillus/metabolism
*Plant Extracts/chemistry
Hydrogen-Ion Concentration

@article {pmid42700597,
year = {2026},
author = {Pan, M and Shen, L and Feng, J and Li, Z and Wu, L and Wu, R and Du, S and Liu, H},
title = {Metagenomic analysis of florfenicol and microplastics effects on microbial function and antibiotic resistome in rice seedling rhizosphere soil.},
journal = {Journal of hazardous materials},
volume = {517},
number = {},
pages = {143454},
doi = {10.1016/j.jhazmat.2026.143454},
pmid = {42700597},
issn = {1873-3336},
abstract = {Antibiotics enrich antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) in farmland, but the contribution of microplastics (MPs) to this process remains unclear. Here, through metagenome analysis, we revealed the add-on effects of PE and PLA on ARGs and VFGs enrichment in rice seedling rhizosphere soil under florfenicol (FF) stress. Compared with controls, root iron plaque content decreased by 35%, 66% and 69% under FF, FF + PE and FF + PLA treatments, disrupting microbial iron balance and activating ABC transporter pathways. Loss of beneficial/core microbes weakened community resistance; bacteria were more sensitive to stress than fungi. Among 945 ARGs and 391 VFs detected, antibiotic efflux abundance rose by 184% under FF, while mobile genetic elements (MGEs) increased from 0.5% to 38.1%, facilitating horizontal ARG transfer. In addition to horizontal gene transfer (HGT) mediated by mobile genetic elements (MGEs), our finding suggests a potential mechanism by which virulence factors (VFs) may promote ARG enrichment through the accumulation of tissue-damaging free radicals. Only one ARG-carrying human pathogen existed in controls, whereas six multi-drug-resistant pathogens emerged under combined pollution. This study provides new insights into the environmental risks of the add-on effects of MPs under antibiotics stress and contributing to the "One Health" goal.},
}

@article {pmid42700605,
year = {2026},
author = {Su, R and Zhao, D and Zhang, X and Wu, QL and Zeng, J},
title = {Trade-off mechanisms between N2O emissions and nitrogen multifunctionality in a lake littoral mesocosm wetland under seasonal water-level fluctuations: insights from metagenomics and machine learning.},
journal = {Water research},
volume = {308},
number = {Pt A},
pages = {126777},
doi = {10.1016/j.watres.2026.126777},
pmid = {42700605},
issn = {1879-2448},
abstract = {Freshwater littoral wetlands are hydrologically dynamic interfaces that regulate nitrogen (N) metabolism (e.g., removal, retention, and N2O emission); however, the effect of seasonal water-level fluctuations on N2O emissions and nitrogen multifunctionality (NMF) remains poorly quantified. This hydrological variability challenges accurate estimates of greenhouse gas (GHG) emissions and complicates ecosystem management strategies that aim to balance climate mitigation with ecosystem functions and sustainability. Here, using a water-level controlled mesocosm at Poyang Lake Wetland Research Station, China, we combine static-chamber measurements, [15]N isotope pairing, metagenomic binning, and an interpretable causal machine learning framework to elucidate the microbial mechanisms and environmental thresholds governing the trade-off between limiting N2O emissions and maintaining NMF. N2O flux (-27.678 to 86.791 μg m[-][2] h[-][1]) was observed at the source-sink transition with rising water levels, whereas NMF was higher in both the continuously dry (0.379) and wet (0.158) zones than in zones subject to water-level fluctuations. A functional quadrant plot revealed the asynchronous relationship between N2O emissions and NMF maintenance. Metagenomic binning demonstrated that distinct dominant microbial taxa mediated N2O and NMF and their trade- off via cooperative and competitive interactions. Moreover, key thresholds, including soil organic matter contents and abundances of hao, hzsABC, nosZII, nirKS, and nasAB genes, drive the system toward a low-emissions and high-function state. This study clarifies the trade-off mechanisms between N2O emissions and NMF maintenance, and provides an ecological basis for reconciling climate mitigation with ecosystem functions in aquatic ecosystems.},
}

@article {pmid42697040,
year = {2026},
author = {Frangieh, MR and Saad, M and Fattouh, N and Sawan, S},
title = {Antibiotics and nanoparticles in Parkinson's disease: From gut microbiota dysbiosis to neuroprotection and targeted nanotherapies.},
journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie},
volume = {203},
number = {},
pages = {119903},
doi = {10.1016/j.biopha.2026.119903},
pmid = {42697040},
issn = {1950-6007},
abstract = {Parkinson's disease (PD) is increasingly linked to gut-brain axis dysfunction. While broad-spectrum antibiotics may contribute to gut dysbiosis, which has been associated with an increased abundance of curli-producing Enterobacteriaceae and processes implicated in α-synuclein aggregation, certain antibiotic classes, particularly tetracyclines and β-lactams, have demonstrated neuroprotective properties in pre-clinical models of PD. This creates a therapeutic paradox: antibiotics may exert either beneficial or detrimental effects depending on many factors including host microbiome composition. Importantly, much of the current evidence remains observational or pre-clinical, and a direct causal relationship between antibiotic exposure and PD has not yet been established. This review synthesizes current epidemiological, mechanistic, and pre-clinical evidence regarding this paradox and explores the emerging role of nanotechnology in resolving it. Preclinical studies suggest that nanoparticle-based drug delivery systems may enhance BBB penetration and enable more targeted drug release. Such approaches have been proposed as a means to reduce systemic exposure and potentially limit microbiota disruption, although these benefits have not yet been demonstrated in clinical PD populations. We further discuss the translational hurdles, including nanotoxicity and regulatory requirements, and propose a roadmap for future research that integrates metagenomics with precision nanomedicine. Collectively, these findings provide a framework for future investigation of targeted therapeutic strategies for PD. However, substantial mechanistic, clinical, and translational validation is required before their therapeutic potential can be established.},
}

@article {pmid42697290,
year = {2026},
author = {Ansari, SK and Shah, NH and Elboughdiri, N and Chaudhary, AA and Ali, MAM and Wani, AK},
title = {Extremozymes for food fermentation: Integrating AI, metagenomics, and protein engineering.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {154351},
doi = {10.1016/j.ijbiomac.2026.154351},
pmid = {42697290},
issn = {1879-0003},
abstract = {Climate change-induced fluctuations in temperature, pH, salinity, and water activity are increasingly compromising microbial metabolism and fermentation efficiency, exposing the limitations of conventional mesophilic enzymes in maintaining process stability and product consistency. Extremozymes, derived from extremophilic microorganisms, exhibit exceptional structural stability and catalytic activity under harsh physicochemical conditions, making them promising biocatalysts for climate-resilient food fermentation. Although considerable progress has been achieved in extremozyme discovery and engineering, challenges remain in bridging computational prediction with experimental validation, functional characterization, large-scale production, and industrial deployment. This review critically examines the diversity, biochemical properties, and functional roles of extremozymes in food fermentation while evaluating the influence of climate-induced process stresses on microbial performance, enzyme functionality, and fermentation outcomes. It further synthesizes recent advances in Artificial Intelligence (AI)-assisted metagenomics, machine learning, transformer-based protein modelling, generative protein design, multi-omics (MO) integration, and high-throughput screening platforms, including microfluidics, droplet-based systems, and cell-free expression technologies, that are accelerating enzyme discovery, engineering, and validation. Particular emphasis is placed on the integration of computational and experimental workflows to improve the accuracy, scalability, and industrial translation of next-generation extremozymes. Unlike previous reviews that primarily describe individual enzyme classes or AI methodologies, this review provides a comprehensive and critical framework linking climate-driven fermentation challenges with emerging computational and biotechnological solutions. It identifies current knowledge gaps, technological bottlenecks, and future research priorities for developing robust, programmable, and energy-efficient fermentation systems capable of sustaining product quality, process reliability, and sustainable food production under increasingly variable environmental conditions.},
}

@article {pmid42697635,
year = {2026},
author = {Shan, M and Wang, J and Chen, W and Zheng, C and Zhang, L and Yu, Y and Han, L and Fang, H},
title = {Hexaconazole enantiomers drive the dissemination and risks of antibiotic resistance genes in the soil-earthworm system.},
journal = {Pesticide biochemistry and physiology},
volume = {223},
number = {},
pages = {107319},
doi = {10.1016/j.pestbp.2026.107319},
pmid = {42697635},
issn = {1095-9939},
mesh = {Animals ; *Triazoles/chemistry/pharmacology/toxicity ; *Oligochaeta/drug effects/microbiology/genetics ; Soil Microbiology ; Stereoisomerism ; *Soil Pollutants/chemistry ; *Drug Resistance, Microbial/genetics ; *Fungicides, Industrial/chemistry/pharmacology ; Soil/chemistry ; *Genes, Bacterial ; },
abstract = {Chiral fungicides constitute a substantial proportion of commonly used pesticides; however, the spread of antibiotic resistance genes (ARGs) in agricultural settings under repeated exposure to different enantiomers is still unclear. Here, the prevalence and potential risks of ARGs were investigated in the soil-earthworm ecosystem when exposed to hexaconazole (HEX) enantiomers. Metagenomic analysis indicated that R-HEX and S-HEX facilitated the dissemination of ARGs in soil without earthworms, but this effect diminished with successive exposures. Notably, S-HEX exhibited a greater effect on ARG profiles compared to R-HEX. Furthermore, HEX enantiomers, particularly S-HEX, increased the mobility potential of ARGs and enhanced host pathogenicity, thereby contributing to elevated ecological risks. Specifically, exposure to the HEX enantiomer led to an enrichment of dominant pathogenic ARG hosts, such as Enterobacteriaceae. Importantly, earthworms alleviated the enantiomer-driven dissemination of ARGs and weakened their association with mobile genetic elements (MGEs). Overall, this study offers novel perspectives on the enantiomer-driven propagation of ARGs induced by the chiral pesticide hexaconazole in soil and highlights the role of earthworms in mitigating ARG contamination. These findings contribute significantly to the risk assessment and remediation strategies for chiral pesticides.},
}

Animals
*Triazoles/chemistry/pharmacology/toxicity
*Oligochaeta/drug effects/microbiology/genetics
Soil Microbiology
Stereoisomerism
*Soil Pollutants/chemistry
*Drug Resistance, Microbial/genetics
*Fungicides, Industrial/chemistry/pharmacology
Soil/chemistry
*Genes, Bacterial

@article {pmid42697647,
year = {2026},
author = {Huang, C and Dai, X and Chen, Y and Ge, H and Zhang, L and Yu, Y and Fang, H},
title = {Chitosan mitigates the dissemination of antibiotic resistance genes caused by metalaxyl in the soil-earthworm system.},
journal = {Pesticide biochemistry and physiology},
volume = {223},
number = {},
pages = {107278},
doi = {10.1016/j.pestbp.2026.107278},
pmid = {42697647},
issn = {1095-9939},
mesh = {Animals ; *Chitosan/pharmacology ; *Oligochaeta/drug effects ; Soil Microbiology ; *Alanine/analogs & derivatives/toxicity/pharmacology ; *Fungicides, Industrial/toxicity/pharmacology ; *Drug Resistance, Microbial/genetics ; *Soil Pollutants/toxicity ; Soil/chemistry ; Bacteria/genetics/drug effects ; Gene Transfer, Horizontal/drug effects ; },
abstract = {The widespread use of agricultural fungicides can lead to residual contamination and accelerate the emergence and spread of antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARBs) in soil ecosystems. Developing green remediation strategies that simultaneously reduce fungicide residues and mitigate antibiotic resistance risks is therefore beneficial for soil pollutant control. Here, we investigated the effects of chitosan (CHI) on the dissipation of metalaxyl (MET) enantiomers and their influence on the soil-earthworm resistome and microbiome through pot experiments and metagenomics analysis. The results showed that CHI significantly accelerated MET dissipation in soil and reduced its bioaccumulation in earthworms. MET enantiomers, particularly S-MET, promoted the dissemination of ARGs, including high-risk ARGs, in the soil-earthworm system, whereas CHI suppressed these effects, likely by limiting the potential for mobile genetic element (MGE)-mediated horizontal gene transfer (HGT). Compared with the corresponding treatments without CHI amendment, CHI amendment reduced the total relative abundance of ARGs by 16.8%-24.7% in soil and by 34.1%-58.3% in earthworm guts. Furthermore, CHI reshaped microbial community structure in both soil and earthworm gut samples by driving ecological niche differentiation of Actinomycetota and Pseudomonadota and reduced ARG host abundance. These findings offer practical insights for controlling contamination by fungicides and ARGs in agricultural soils.},
}

Animals
*Chitosan/pharmacology
*Oligochaeta/drug effects
Soil Microbiology
*Alanine/analogs & derivatives/toxicity/pharmacology
*Fungicides, Industrial/toxicity/pharmacology
*Drug Resistance, Microbial/genetics
*Soil Pollutants/toxicity
Soil/chemistry
Bacteria/genetics/drug effects
Gene Transfer, Horizontal/drug effects

@article {pmid42697668,
year = {2026},
author = {Zhu, S and Liu, X and Yang, X and Wu, W and Ahmed, T and Jiang, H and Ding, T},
title = {Amplicon and metagenomic sequencing reveal thifluzamide drive rhizosphere microbial structural shifts and functional adaption.},
journal = {Pesticide biochemistry and physiology},
volume = {223},
number = {},
pages = {107299},
doi = {10.1016/j.pestbp.2026.107299},
pmid = {42697668},
issn = {1095-9939},
mesh = {*Rhizosphere ; Fungi/drug effects/genetics ; Oryza/microbiology ; Bacteria/drug effects/genetics ; Metagenomics ; *Fungicides, Industrial/pharmacology ; Soil Microbiology ; *Microbiota/drug effects ; Metagenome ; },
abstract = {Thifluzamide (TF) is a widely used phenyl urea fungicide in rice production; however, its impacts on the structural composition and functional dynamics of the rhizosphere microbiome remain poorly understood. Here, we systematically investigated the effects of TF on the structure, interactions, and functional potential of the rice (Oryza sativa L.) rhizosphere microbiome using integrated amplicon sequencing and metagenomic approaches. TF application significantly altered both bacterial and fungal community composition, bacterial diversity was markedly reduced, whereas fungal diversity increased. With bacterial diversity markedly reduced while fungal diversity increased. Beta-diversity analyses revealed strong treatment-driven community separation, indicating pronounced TF-induced microbial restructuring. Co-occurrence network analysis demonstrated reduced complexity and connectivity in bacterial networks but increased negative co-occurrence patterns within fungal communities, suggesting contrasting stability responses between microbial kingdoms. Metagenomic profiling further revealed substantial functional shifts, including the differential enrichment of KEGG and COG pathways associated with xenobiotic metabolism. Notably, while total ARG abundance remained stable, TF exposure altered the resistome profile by selectively enriching specific classes of antibiotic resistance genes (ARGs), biocide resistance genes (BRGs), and mobile genetic elements (MGEs). Strong positive correlations between MGEs and ARGs highlighted an elevated potential for horizontal gene transfer. Metagenome-assembled genome (MAG) analysis identified specific TF-enriched bacterial taxa, including Methylophilus, Sulfurospirillum, and Azospirillum, which harbored genes involved in pesticide degradation and xenobiotic transformation. Collectively, these findings demonstrate that TF profoundly reshapes the rice rhizosphere microbiome by altering microbial diversity, interaction networks, resistance gene profiles, and functional capacities. This study provides genomic insights into fungicide-microbiome interactions, underscoring the potential ecological implications associated with TF application, while identifying candidate microbial taxa that may contribute to pesticide degradation and rhizosphere microecology resilience.},
}

*Rhizosphere
Fungi/drug effects/genetics
Oryza/microbiology
Bacteria/drug effects/genetics
Metagenomics
*Fungicides, Industrial/pharmacology
Soil Microbiology
*Microbiota/drug effects
Metagenome

@article {pmid42697801,
year = {2026},
author = {Htut, M and Lee, K and Nathwani, N and Rosenzweig, M and Janakiram, M and Goldsmith, S and Sanchez, JF and Scott, M and Keats, J and Krishnan, A and Rosen, ST and Wang, SS},
title = {Gut Microbiome Composition Is Associated With Response to CD38 Antibody (Daratumumab) Treatment Among Relapsed Multiple Myeloma Patients.},
journal = {Clinical lymphoma, myeloma & leukemia},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.clml.2026.08.004},
pmid = {42697801},
issn = {2152-2669},
abstract = {INTRODUCTION: Growing data support interactions between host-gut microbes and treatment responses in multiple myeloma (MM), where a higher abundance of Eubacterium hallii in stool samples has been found among MM patients with negative minimal residual disease after induction therapy. Here, we evaluated changes in the gut microbiome associated with daratumumab (dara) based therapy in 40 MM patients, before and after therapy.

PATIENTS AND METHODS: Patients with relapsed MM and prior autologous transplantation who had received 1 to 4 prior lines of therapy were eligible. Two stool samples were collected, one within 1 week prior to dara (predara) and one immediately after 4 doses of dara (postdara). Metagenomics sequencing was conducted. Microbiome taxonomic analyses were performed using MetaPhlAn4, and microbial functional pathway analyses were conducted using HUMAnN3.6. QIIME2 was used for compositional and statistical analyses.

RESULTS: Of 40 participants enrolled, there were 5 nonresponders; 35 patients achieved partial response (PR) or better (responders). Among responders, 10 patients achieved complete remission (CR), and 25 patients achieved either very good partial response (VGPR) or PR. There were no statistically significant differences between overall pre and postdara gut microbiomes. Differential abundance analysis (ANCOM-BC) showed statistically significant (q ≤ 0.05) overgrowth of Alistipes finegoldii and Acidaminococcus intestini species in responders and Ruminococcus torques, Sellimonas intestinalis and Clostridium symbiosum in nonresponders. Compared to non-CR, CR samples showed enrichment of Faecalibacterium prausnitzii; non-CR samples were enriched in Segatella copri and Faecalimonas umbilicata.

DISCUSSION/CONCLUSION: Our results suggest differences in species between clinical responders and nonresponders, but larger prospective studies are needed to confirm these results.},
}

@article {pmid42698579,
year = {2026},
author = {Murugesan, M and Thankappan, S and Mageshwaran, V and Ramasamy, R and Singaram, A},
title = {Decoding the functional diversity of plant growth-promoting bacterial communities in the soils of Western Ghats, Tamil Nadu, India.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1865342},
doi = {10.3389/fmicb.2026.1865342},
pmid = {42698579},
issn = {1664-302X},
abstract = {Western ghats in India, one of the world's biodiversity hot spots is the reservoirs of microbial resources having agricultural and industrial significance. However, the diversity of plant growth-promoting microbial communities associated with the plants and soil in the Western Ghats is untapped vault. The current emphasis on natural farming is more depending on the indigenous microbial communities and their metabolic functions towards sustainable one -health. With this background, the present study examines the bacterial diversity of soils from the Western Ghats of Nilgiris, Coimbatore and Dindigul regions. Among the 10 soil samples collected (S1 to S10), three soil samples (S2, S4 and S6) representing respective three regions were subjected for metagenomic studies based on their distinct soil chemical and biological properties. The computational analysis of the metagenome revealed the core genus Bradhyrhizobium in all soil samples, while Trebonia, Arthrobacter, Streptomyces, and Pseudomonas are the next most abundant genera, which varied substantially. The results collectively demonstrate that soil sample from Dindigul harbours the richest and most diverse microbial community among the three regions. In culturable studies, a total of 101 bacterial isolates were obtained from 10 soil samples (S1 to S10). Among them four Gram-negative bacterial isolates showed potential plant growth-promoting attributes, such as Ammonia, Indole Acetic Acid, Hydrogen cyanide and siderophore production, phosphorus, potassium, and zinc solubilization. The 16S rDNA analysis revealed that the bacterial isolates were Pseudomonas glycinae S6B1, Pseudomonas tolaasii S2B3, Pseudomonas azotoformans S9H10, and Pseudomonas poae S10B2. The isolate, S10B2, exhibited the maximum inhibition, with 81.25%, 70.1%, and 35% against plant pathogenic fungi, Rhizoctonia solani, Sclerotium rolfsii, and Fusarium oxysporum, respectively, indicating strong biocontrol potential. The effect of bacterial inoculants on chick pea (Cicer arietinum var. JG 62), showed that P. glycinae S6B1 significantly promoted plant growth such as root length, shoot length, and fresh/dry biomass. These findings unlock the core microbiome of soils of Western Ghats, which can be utilized to develop a synthetic microbial consortium to boost agricultural productivity.},
}

@article {pmid42698876,
year = {2026},
author = {Wang, X and Gao, R and Shen, W and Wu, X},
title = {Clinical characteristics of Tropheryma whipplei pneumonia: A retrospective analysis based on five cases.},
journal = {IDCases},
volume = {45},
number = {},
pages = {e02730},
doi = {10.1016/j.idcr.2026.e02730},
pmid = {42698876},
issn = {2214-2509},
abstract = {OBJECTIVE: Acute pulmonary infection caused by Tropheryma whipplei (TW) is rare. This article summarizes the medical records of TW pneumonia patients to provide clinical insights into diagnosis and treatment.

METHODS: A retrospective analysis was conducted on five patients diagnosed with TW pneumonia from 2021 to 2023 in Changzhou No. 2 People's Hospital. The study focused on clinical symptoms, imaging characteristics, diagnostic methods, and treatment approaches.

RESULTS: Patients aged 35-65 years had underlying diseases and presented with fever, cough, expectoration, and chest tightness. Laboratory tests showed white blood cells, procalcitonin, C-reactive protein, and erythrocyte sedimentation rate increased, and the patients had anemia and hypoalbuminemia. Chest CT showed nodular lesions, cavities and patchy shadows. TW was detected in bronchoalveolar lavage fluid (BALF) by metagenomic next-generation sequencing (mNGS). Four patients received ceftriaxone combined with doxycycline or compound sulfamethoxazole tablets, while one treated empirically with cefotetan. All patients showed significant improvement.

CONCLUSION: TW pneumonia often occurs in patients with underlying diseases, and immunocompromised patients have more severe lung damage. Most chest CT shows nodular lesions with atypical distribution and shape. Early diagnosis requires relies on mNGS, and treatment mainly bases on the third-generation cephalosporin combined with tetracycline or sulfonamides. Sequential therapy with sulfamethoxazole and clarithromycin is effective, and close follow-up needs to determine the total course of treatment.},
}

@article {pmid42698879,
year = {2026},
author = {Cioletti, G and Kenney, S and Hovingh, E and Springer, H and Haley, BJ and Ganda, E},
title = {Nasopharyngeal microbiome and resistome profiles in dairy calves fed milk replacer with low-level β-lactams.},
journal = {JDS communications},
volume = {7},
number = {5},
pages = {670-677},
doi = {10.3168/jdsc.2025-0994},
pmid = {42698879},
issn = {2666-9102},
abstract = {Feeding waste milk (WM) to preweaning dairy calves is a common management practice that offers economic benefits but may influence the microbiome and antimicrobial resistance (AMR) due to the presence of antibiotic residues. The objective of this study was to describe longitudinal patterns in the nasopharyngeal microbiome and AMR gene profiles of dairy calves fed either nonsupplemented milk replacer or milk replacer supplemented with low-level β-lactam antibiotics to simulate WM exposure during the preweaning period. Using shotgun metagenomic sequencing, we profiled the nasopharyngeal microbiome and resistome of 11 Holstein bull calves fed milk replacer with (MR+A; n = 6) or without (MR; n = 5) low levels of β-lactam antibiotics. Antibiotic concentrations were selected to reflect residue levels reported in WM. Deep nasopharyngeal swabs were collected every 2 wk from 1 to 15 wk of age; samples from wk 3 and 15 were excluded due to elevated contaminant burden, resulting in 6 retained time points. No significant differences in microbial α-diversity, β-diversity, or community structure were detected by dietary treatment or sampling age. Tetracycline, macrolide-lincosamide-streptogramin, aminoglycoside, metal, acid, and biocide resistance classes were among the most prominent, with descriptive differences in z-score patterns between groups but no significant differences detected. Larger-scale studies are needed to evaluate the long-term effects of WM feeding on respiratory health and AMR dynamics in dairy calves.},
}

@article {pmid42699185,
year = {2026},
author = {McGregor, K and Okaeme, N and Khorasaniha, R and Veniamin, S and Jovel, J and Miller, R and Mahmood, R and Graham, M and Bonner, C and Bernstein, CN and Arnold, DL and Bar-Or, A and Marrie, RA and O'Mahony, J and Yeh, EA and Zhao, Y and Banwell, B and Waubant, E and Knox, N and Van Domselaar, G and Zhu, F and Mirza, AI and Tremlett, H and Armstrong, H},
title = {Proportionality-based association metrics in count compositional data.},
journal = {NAR genomics and bioinformatics},
volume = {8},
number = {3},
pages = {lqag102},
doi = {10.1093/nargab/lqag102},
pmid = {42699185},
issn = {2631-9268},
mesh = {Animals ; Mice ; Single-Cell Analysis ; Metagenomics/methods ; Sequence Analysis, RNA ; Algorithms ; },
abstract = {Compositional data comprise vectors that describe the constituent parts of a whole. Data arising from various -omics platforms such as 16S and RNA sequencing are compositional in nature. In this kind of data, correlations between features on raw counts have no meaningful interpretation. Metrics of proportionality were formulated to address this problem. However, an inherent bias arises when these metrics are calculated empirically on count-based measures due to variability in read depths. We quantify the bias introduced by empirically calculating proportionality-based association metrics in count data. Additionally, we propose a means of estimating these metrics within a logit-normal multinomial model in pursuit of more accurate estimates. The model-based estimates are shown to outperform empirical estimates in simulated data and are applied to a mouse embryonic stem cell single-cell sequencing dataset, as well as a pediatric-onset multiple sclerosis metagenomic dataset.},
}

Animals
Mice
Single-Cell Analysis
Metagenomics/methods
Sequence Analysis, RNA
Algorithms

@article {pmid42699249,
year = {2026},
author = {Xue, Z and Li, H and Wang, X and Cai, Y and Huang, Z and Li, W and Su, Y and Wu, Z and Fang, X and Zhang, W},
title = {Diagnostic and Therapeutic Impact of Metagenomic Next-Generation Sequencing in Tuberculous Osteoarticular Infections with Negative or Confounding Conventional Cultures.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {620236},
doi = {10.2147/IDR.S620236},
pmid = {42699249},
issn = {1178-6973},
abstract = {PURPOSE: Diagnosing tuberculous osteoarticular infections (TB-OAI) remains challenging due to frequent false-negative or confounding conventional culture results. This study evaluated the diagnostic and therapeutic utility of metagenomic next-generation sequencing (mNGS) for occult TB-OAI in patients presenting with negative or misleading culture outcomes.

PATIENTS AND METHODS: We retrospectively analyzed 13 patients with confirmed TB-OAI, encompassing periprosthetic, fracture-related, and native joint infections. Patients were stratified by conventional culture results into strictly culture-negative (n=8) and culture-confounded (n=5; yielding non-mycobacterial organisms) groups. A composite reference standard of mNGS positivity combined with histopathological or clinical validation established the definitive diagnosis. We assessed diagnostic yield, therapeutic modifications, and clinical outcomes.

RESULTS: Conventional culture failed to identify Mycobacterium tuberculosis in all 13 cases (0% sensitivity) and yielded misleading non-mycobacterial flora in 5 cases (38.5%). Conversely, mNGS successfully identified the pathogen in 100% (13/13) of patients, corroborated by histopathology in all cases. Consequently, mNGS results changed clinical management from empirical antibiotics to targeted anti-tuberculosis therapy in all cases (100%). Postoperative erythrocyte sedimentation rate (ESR) and C-reactive protein (CRP) levels decreased significantly (P < 0.05). Over a mean follow-up of 17.5 ± 3.0 months, 12 patients achieved durable infection eradication. One patient experienced early recurrence requiring a two-stage revision, ultimately achieving successful infection control.

CONCLUSION: mNGS serves as a promising diagnostic rescue tool for occult TB-OAI when conventional cultures are negative or misleading. While limited by sample size, these preliminary findings suggest mNGS effectively guides the transition from empirical to targeted anti-tuberculosis therapy and limits diagnostic delays.},
}

@article {pmid42699313,
year = {2026},
author = {Prachansuwan, A and Sukkha, P and Thiyajai, P and Chamtim, P and Kitdumrongthum, S and Sridonpai, P and Dee-Uam, A and Tongdonpo, K and Trachootham, D and Srichamnong, W and Thaipisuttikul, I and Raethong, N},
title = {Gut microbiome and metabolic responses to cricket powder supplementation in Thai subjects with high or borderline-high LDL cholesterol: an exploratory, randomized, crossover controlled trial.},
journal = {Current research in food science},
volume = {13},
number = {},
pages = {101536},
doi = {10.1016/j.crfs.2026.101536},
pmid = {42699313},
issn = {2665-9271},
abstract = {Edible insects are emerging as sustainable functional foods, yet human evidence for microbiome-mediated effects remains limited, particularly in Asian populations. Therefore, this study investigated whether cricket powder supplementation modulates gut microbiome composition and metabolic outputs in Thai subjects with high or borderline-high LDL cholesterol. In a randomized, crossover controlled trial, 17 subjects received cricket powder or control products for 21 days, separated by a 4-week washout. Gut microbiome composition was profiled using full-length 16S rRNA gene sequencing, and fecal short-chain fatty acids (SCFAs) were quantified by gas chromatography-mass spectrometry. Blood lipids and gastrointestinal tolerance were also assessed. As a result, cricket powder did not alter overall microbial diversity or community structure but induced targeted species-level shifts, including enrichment of Blautia faecis and Mediterraneibacter glycyrrhizinilyticus. Despite these compositional changes, fecal SCFAs remained unchanged. Notably, branched-chain SCFAs were not increased, indicating no shift toward proteolytic fermentation and preservation of microbial metabolic balance. Gastrointestinal tolerance was maintained without adverse effects. Blood lipid parameters were unchanged, with a modest trend toward increased high-density lipoprotein cholesterol (HDL-C). Collectively, cricket powder induces selective microbiome remodeling without disrupting metabolic homeostasis, supporting its potential as a sustainable, microbiome-targeted functional food.},
}

@article {pmid42699484,
year = {2026},
author = {Chen, J and Zhou, Q and Zhang, Y and Chen, J and Zheng, X and Ye, F},
title = {What constitutes a true polymicrobial periprosthetic joint infection? From multiple detections to organism-level causality.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1936444},
doi = {10.3389/fmicb.2026.1936444},
pmid = {42699484},
issn = {1664-302X},
abstract = {Polymicrobial periprosthetic joint infection (PJI) is often defined by recovery of two or more microorganisms from the same clinical episode, but this numerical definition is biologically incomplete. A second organism may represent a true co-pathogen, colonization, contamination, reagent background, nonviable DNA after antimicrobial exposure, or an analytically plausible signal of uncertain clinical importance. Established PJI definitions determine whether infection is present but do not provide a validated organism-level rule for assigning causality to every detection. We therefore propose a sequential approach: first establish PJI using accepted episode-level criteria, then adjudicate each detected microorganism separately before classifying the episode as polymicrobial. This Mini Review examines evidence relevant to organism-level causal attribution, including sampling integrity, reproducibility across independent deep specimens, anatomical coherence, orthogonal confirmation, quantitative and temporal signal, organism biology, and clinical concordance. We also consider how tissue culture, synovial fluid culture, sonication, blood culture, PCR, and metagenomic sequencing generate different interpretive challenges, particularly after antimicrobial exposure. Finally, we propose a pragmatic four-category vocabulary-strongly supported participant, probable participant, uncertain detection, and likely contaminant-to make organism-level causal confidence explicit in multidisciplinary interpretation and research reporting. This framework is intended as an interpretive aid rather than a validated diagnostic score. Whether it improves inter-rater consistency, antimicrobial precision, or organism-specific outcomes requires prospective validation.},
}

@article {pmid42699605,
year = {2026},
author = {Yue, Y and Wei, W and Wu, C and Suo, N and Zhang, Z and Liu, W and Su, Q and Wang, M and Zhang, Y and Xie, B},
title = {Four-domain gut metagenomics reveals archaeal-centered cross-kingdom remodeling across coronary artery disease and acute myocardial infarction.},
journal = {iScience},
volume = {29},
number = {9},
pages = {117227},
doi = {10.1016/j.isci.2026.117227},
pmid = {42699605},
issn = {2589-0042},
abstract = {Cardiovascular microbiome research has focused mainly on bacterial taxa and pathways. We profiled stool archaea, bacteria, fungi, and viruses in patients with acute myocardial infarction (AMI) and healthy controls. Paired plasma metabolomics was examined in a subset. An independent angiography-defined cohort included angiographically normal controls, severe coronary artery disease (CAD), and AMI. No archaeal genus remained differentially abundant after multiple-testing correction. In the discovery cohort, archaeal-bacterial correlations were predominantly positive in healthy controls and negative in AMI, while archaeal-fungal rewiring was prominent. The extension cohort identified sign-flip archaeal-virome edges between severe CAD and AMI, while severe CAD showed the lowest archaeal-bacterial connectivity. Plasma metabolomics captured a broad AMI-associated systemic shift. These findings show that gut archaeal signals are expressed through multi-kingdom ecological organization across coronary disease states.},
}

@article {pmid42700527,
year = {2026},
author = {Yin, Z and Ping, H and Li, C},
title = {Antimony species-dependent enrichment and transcriptional activity of antibiotic and metal resistance genes in the gut microbiome of male mice.},
journal = {Journal of environmental management},
volume = {417},
number = {},
pages = {130867},
doi = {10.1016/j.jenvman.2026.130867},
pmid = {42700527},
issn = {1095-8630},
abstract = {The gut microbiome is a reservoir for antibiotic resistance genes (ARGs) and is sensitive to environmental pollutants. ARGs in environmental and host-associated microbiomes can be enriched by metal(loid)s through co-selection with metal resistance genes (MRGs). However, as a ubiquitous toxic metalloid, antimony (Sb) induced alterations of ARGs in the gut microbiome and the underlying mechanisms remain unclear. Here, by integrating genome-resolved metagenomics and metatranscriptomics, we characterized the genomic potential and transcriptional activity of ARGs and MRGs in the gut microbiome of mice exposed to Sb(III)- and Sb(V)-contaminated drinking water. We found that both Sb(III) and Sb(V) significantly increased ARGs abundance, whereas only Sb(III) enhanced ARGs transcription (288.40 ± 41.67 TPM, P < 0.05). Co-selection of ARGs and MRGs was observed through metagenome-assembled genomes (MAGs) analysis, and key taxa driving this process were identified (e.g., Eubacterium_J and Lachnospiraceae_COE1). Sb(III), but not Sb(V), induced co-regulation of macrolide-lincosamide-streptogramin resistance genes and arsRABC operon. A potentially higher risk of ARG dissemination under Sb(III) stress was suggested by the increased abundance and transcription of mobile genetic elements (MGEs). This study advances our understanding of the interactions between Sb and ARGs in the gut microbiome and highlights the potential chemical species-dependent enrichment and transcriptional activation of ARGs.},
}

@article {pmid42692700,
year = {2026},
author = {Li, Z and Guo, Y and Zhang, X and Xie, N and Zhang, F and Zhen, Z},
title = {Integrated microbiome and metabolome analysis reveals microbial and metabolic dynamics associated with goose foie gras spoilage during refrigerated storage.},
journal = {Food research international (Ottawa, Ont.)},
volume = {243},
number = {Pt 1},
pages = {120303},
doi = {10.1016/j.foodres.2026.120303},
pmid = {42692700},
issn = {1873-7145},
mesh = {Animals ; *Metabolome ; *Food Storage/methods ; *Refrigeration ; *Microbiota ; *Geese/microbiology ; Thiobarbituric Acid Reactive Substances/analysis ; *Food Microbiology ; Metabolomics ; RNA, Ribosomal, 16S/genetics ; Colony Count, Microbial ; Bacteria ; Chromatography, High Pressure Liquid ; },
abstract = {Goose foie gras spoils rapidly under refrigeration, yet its microbial and metabolite dynamics during storage are poorly described. Samples from a single Landes production batch were stored at 4 °C in air-sealed polyethylene pouches and analysed on days 0, 2, 4, 6, 8, 10 and 12. Three biological replicates per time point were processed for total viable count (TVC), total volatile basic nitrogen (TVB-N), thiobarbituric acid reactive substances (TBARS), 16S ribosomal RNA (rRNA) amplicon sequencing, and ultra-high-performance liquid chromatography-mass spectrometry (UHPLC-MS)-based untargeted metabolomics. TVC increased from 3.85 to 6.16 log CFU/g, TVB-N from 8.99 to 27.77 mg/100 g and TBARS from 0.18 to 0.72 mg MDA/kg between day 0 and day 12, with the steepest changes appearing after day 6. The maximum TVC reached 6.16 log CFU g[-1] on day 12, below the 7 log CFU g[-1] level cited for some meat products; no sensory evaluation was performed. The late storage period is therefore described as a phase of concurrent rises in TVC, TVB-N and TBARS rather than as a confirmed spoilage endpoint. The 14 most abundant genera were retained for multivariate analysis. Seven genera, including Brochothrix, Pseudomonas, Lactobacillus and Lactococcus, met the operational definition of candidate spoilage-associated taxa. Forty candidate metabolites were screened by random forest. Five (tyramine, 4-hydroxyphenylacetaldehyde, adenosine monophosphate, oxidized glutathione and γ-glutamylcysteine) were prioritized on the joint basis of random forest importance, Benjamini-Hochberg-adjusted Kruskal-Wallis p < 0.05, ROC AUC ≥ 0.85 and KEGG pathway interpretability. Microbe-metabolite co-variation was quantified through Benjamini-Hochberg-adjusted Spearman correlation, yielding 108 microbe-metabolite pairs at BH-adjusted P < 0.05 (|ρ| ≥ 0.6), and canonical correlation analysis explained 73.39% of the joint cross-covariance in the first two variates. This study establishes a quantitative microbial-metabolic deterioration signature for refrigerated goose foie gras under air-sealed storage, provides a set of biomarker candidates with defined ROC performance, and identifies shifts in specific tyrosine, glutathione, purine and phospholipid pathways. The concordance between microbial succession and these pathway changes is hypothesis-generating and requires metagenomic confirmation, and these findings are presented as preliminary biochemical anchors for future targeted validation and preservation research.},
}

Animals
*Metabolome
*Food Storage/methods
*Refrigeration
*Microbiota
*Geese/microbiology
Thiobarbituric Acid Reactive Substances/analysis
*Food Microbiology
Metabolomics
RNA, Ribosomal, 16S/genetics
Colony Count, Microbial
Bacteria
Chromatography, High Pressure Liquid

@article {pmid42692847,
year = {2026},
author = {Budinská, E},
title = {Microbiome in early cancer detection - biomarker potential and limitations.},
journal = {Klinicka onkologie : casopis Ceske a Slovenske onkologicke spolecnosti},
volume = {39},
number = {Supplementum 1},
pages = {63-66},
doi = {10.48095/ccko2026S63},
pmid = {42692847},
issn = {1802-5307},
mesh = {Humans ; *Early Detection of Cancer/methods ; *Neoplasms/diagnosis/microbiology ; *Microbiota ; *Biomarkers, Tumor ; },
abstract = {BACKGROUND: Microbiome analysis in cancer research has experienced a surge in interest comparable to the introduction of microarrays for tumor gene expression profiling 25 years ago. Associative studies investigating the composition of the microbiome in stool, tumor tissue swabs and tumor biopsies of oncology patients have been conducted across most cancer types, and their number continues to grow. Screening approaches based on non-invasive or minimally invasive sampling, including the analysis of stool, saliva, urine, and buccal and rectal swabs, are from a clinical perspective among the most promising, owing in part to simpler logistics and the possibility of repeated sampling. These types of specimens are commonly used in microbiome studies, making the microbiome an attractive target for both screening and diagnostic applications.

AIM: This review aims to summarize current knowledge regarding the potential of the microbiome in the early detection of cancer, emphasizing its clinical applicability and limitations in the context of population-based prevention.},
}

Humans
*Early Detection of Cancer/methods
*Neoplasms/diagnosis/microbiology
*Microbiota
*Biomarkers, Tumor

@article {pmid42692903,
year = {2026},
author = {Hejndorf, S and Gulay, A and Zheng, C and Nielsen, RV and Rasmussen, SB and Grønlykke, L and Nørgaard, JC and Rasmussen, KK and Rafiq, S and Català-Moll, F and Ravn, HB and Lundgren, J and Murray, DD and Ilett, E},
title = {The Relationship Between the Preoperative Gut Microbiome and Systemic Inflammatory Response Syndrome After Cardiac Surgery: A Prospective Cohort Study.},
journal = {Journal of cardiothoracic and vascular anesthesia},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.jvca.2026.08.119},
pmid = {42692903},
issn = {1532-8422},
abstract = {OBJECTIVES: To determine whether preoperative intestinal microbiome characteristics are associated with the development of systemic inflammatory response syndrome (SIRS) after cardiac surgery.

DESIGN: Single-center prospective observational cohort study.

SETTING: Tertiary university hospital.

PARTICIPANTS: A total of 196 adults undergoing elective cardiac surgery with extracorporeal circulation between 2018 and 2019.

INTERVENTIONS: No microbiome-targeted intervention was performed.

MEASUREMENTS AND MAIN RESULTS: Shotgun metagenomic sequencing was used to assess microbial diversity (inverse Simpson index, gene richness, dominance), taxonomic composition, and functional potential. The primary outcome was development of SIRS within 24 hours postoperatively. Associations were evaluated using Wilcoxon rank-sum tests, χ[2] tests, and logistic regression adjusted for age and sex. Forty-four patients (22%) developed SIRS. Microbiome diversity did not differ significantly between patients with and without SIRS (median inverse Simpson index 20.4 v 19.3, p = 0.12; gene richness, p = 0.30; dominance, p = 0.61). In adjusted analyses, diversity was not associated with SIRS risk (odds ratio, 1.04; 95% confidence interval, 0.99-1.07). Descriptive analyses of taxonomic composition and functional potential similarly revealed no significant differences between SIRS and non-SIRS groups.

CONCLUSIONS: In this cohort of elective cardiac surgery patients, preoperative gut microbiome diversity, composition, and functional potential were not associated with the development of postoperative SIRS. These findings do not support a strong causal or predictive role of the presurgical gut microbiome in postoperative inflammatory responses after cardiac surgery.},
}

@article {pmid42692915,
year = {2026},
author = {Pushpakumara, BLDU and Coffey, MJ and Hudson, J and Halim, J and Chuang, S and Prentice, B and Jaffe, A and Edwards, R and Day, AS and Oliver, M and Ranganathan, S and Wainwright, C and Selvadurai, H and van Dorst, J and Ooi, CY},
title = {The cystic fibrosis gut microbial dysbiosis index (CF-GMDI): a quantitative measure of gut microbial imbalance in children with cystic fibrosis.},
journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jcf.2026.08.007},
pmid = {42692915},
issn = {1873-5010},
abstract = {BACKGROUND: Gut dysbiosis is a hallmark of cystic fibrosis (CF), typically characterised using non-specific diversity metrics and study-specific taxonomic lists, limiting comparability across studies. We aimed to develop a metagenomic, species-level CF Gut Microbial Dysbiosis Index (CF-GMDI) to standardise measurement of gut microbial imbalance in children with CF (cwCF) METHODS: CF-GMDI was derived using stool metagenomic data from the PEARL-CF study (70 cwCF; 67 healthy controls (HC); 0-6 years). Differentially abundant taxa were identified between cwCF and HC using MaAsLin2. The index was calculated as the log10 ratio of the summed relative abundances of taxa enriched in CF vs HC to those depleted in CF vs HC. Reproducibility was assessed in the independent EARTH cohort (56 cwCF; 56 HC; 0-18 years). Responsiveness to therapy was evaluated using publicly available metagenomic data from an Elexacaftor/Tezacaftor/Ivacaftor (ETI) study (39 cwCF; 6-18 years).

RESULTS: CF-GMDI was significantly higher in cwCF than HC (p < 0.001), inversely correlated with species richness (ρ = -0.74, p < 0.001), and higher in pancreatic-insufficient vs pancreatic-sufficient cwCF in the PEARL-CF cohort (p = 0.01). Key ecological and clinical associations were replicated in the EARTH cohort. In the ETI study, CF-GMDI decreased significantly at 6 and 12 months post-treatment, whereas alpha diversity remained unchanged.

CONCLUSIONS: CF-GMDI is a CF-associated metric that captures clinically relevant gut microbiome restructuring not detected by standard diversity measures in cwCF (0-18 years). It differentiates disease and pancreatic status and tracks therapeutic modulation, supporting its use as a novel endpoint in CF intervention studies.},
}

@article {pmid42693003,
year = {2026},
author = {Quesada-Ocampo, LM and Miles, T and Prieto-Torres, M and Chilvers, MI and Crandall, SG and Gent, D and Gold, KM and Heger, L and Kudenov, M and Naegele, RP and Xiang, L},
title = {Invisible Threats, Relentless Hunters: Biosurveillance of Airborne Plant Pathogens.},
journal = {Annual review of phytopathology},
volume = {64},
number = {1},
pages = {493-519},
doi = {10.1146/annurev-phyto-011325-093123},
pmid = {42693003},
issn = {1545-2107},
mesh = {*Air Microbiology ; *Plant Diseases/microbiology/prevention & control ; *Biosurveillance/methods ; Metagenomics ; *Plants/microbiology ; },
abstract = {Airborne dispersal enables plant pathogens to travel across fields, regions, and continents, fueling rapid epidemics and emerging disease threats. Biosurveillance, the systematic monitoring of airborne inoculum, offers the opportunity to detect pathogens before symptoms appear and informs timely, risk-based management. Recent advances in air sampling, molecular diagnostics, metagenomics, and imaging technologies have expanded the scale and resolution of pathogen monitoring, from single-species qPCR assays to community-level aerobiome surveys. Integration of biosurveillance data with decision-support systems, remote sensing, and artificial intelligence is transforming early-warning capabilities and providing novel insights into pathogen ecology, evolution, and fungicide resistance. Yet major challenges remain, including assay standardization, data interpretation, and translation into actionable tools for growers. This review synthesizes current approaches, highlights case studies in which biosurveillance has advanced disease management, and outlines future directions toward coordinated surveillance networks and precision agriculture applications.},
}

*Air Microbiology
*Plant Diseases/microbiology/prevention & control
*Biosurveillance/methods
Metagenomics
*Plants/microbiology

@article {pmid42693026,
year = {2026},
author = {Han, R and Gu, YW and Dong, J and Zhang, XZ and Cao, L and Wang, ZZ and Xiao, W and Jiang, S},
title = {[Mechanism of Tianshu Capsules in treating migraine rats based on gut microbiota].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {51},
number = {16},
pages = {4734-4743},
doi = {10.19540/j.cnki.cjcmm.20260509.701},
pmid = {42693026},
issn = {1001-5302},
mesh = {Animals ; *Migraine Disorders/drug therapy/metabolism/genetics/microbiology ; Rats, Sprague-Dawley ; Rats ; *Gastrointestinal Microbiome/drug effects ; *Drugs, Chinese Herbal/administration & dosage ; Calcitonin Gene-Related Peptide/genetics/metabolism ; Male ; Humans ; Disease Models, Animal ; Endothelin-1/metabolism/genetics/blood ; Capsules/administration & dosage ; Serotonin/blood/metabolism ; Proto-Oncogene Proteins c-fos/metabolism/genetics ; },
abstract = {This study aims to investigate the therapeutic effect of Tianshu Capsules(TS) on migraine rat model and explore its potential mechanism of action from the perspectives of the structure of the gut microbiota and functional pathway regulation. A migraine rat model was established via subcutaneous injection of nitroglycerin. The Sprague-Dawley rats were randomly divided into a control group, a model group, a low-dose TS group, a medium-dose TS group, a high-dose TS group, and an ibuprofen group. The efficacy of TS in improving migraine was evaluated by general condition observation and measurement of the craniofacial pain threshold. The expression of the gene c-fos in the trigeminal ganglion was determined by quantitative real-time polymerase chain reaction(PCR). The contents of endothelin-1(ET-1), calcitonin gene-related peptide(CGRP), and 5-hydroxytryptamine(5-HT) in serum were measured by enzyme-linked immunosorbent assay(ELISA). Fecal samples were subjected to metagenomic sequencing for systematic analysis of gut microbial diversity, taxonomic composition difference, and functional pathway changes of Kyoto Encyclopedia of Genes and Genomes(KEGG), and their correlations with behavioral and biochemical indices were further evaluated. The results show that TS significantly improves the increased body temperature and decreased craniofacial pain threshold in migraine rats. It also markedly suppresses the elevated expression levels of the gene c-fos in the trigeminal ganglion and reduces the levels of ET-1, CGRP, and 5-HT in serum. Metagenomic beta diversity analysis and differential taxonomic abundance analysis reveal that the migraine model induces significant gut microbiota dysbiosis, characterized by enrichment of harmful genera, including Streptococcus and Enterococcus, as well as a decline in the abundance of beneficial bacteria such as Allobaculum, Eubacterium, and Muribaculum. Functional pathway analysis results of KEGG further reveal that the relative abundances of pathways associated with biosynthesis of phenylalanine, tyrosine, and tryptophan, bacterial secretion system, citrate cycle, and biosynthesis of secondary metabolites are significantly decreased in the model group. TS intervention increased the abundance of the genus, such as Parabacteroides, Eubacterium, Allobaculum, and Muribaculum, while decreasing levels of microbiota, including Staphylococcus. TS also significantly upregulated pathways associated with barrier function(tight junction), amino acid biosynthesis pathways, and biosynthesis pathways of neurotransmitter precursors such as cysteine and methionine metabolism. In addition, it downregulated inflammatory pathways(Toll and IMD signaling) and pathways related to Staphylococcus aureus infection, thereby restoring the structure and function of the microbiota to a state close to those of the normal group. Spearman correlation analysis reveals that partial gut microbiota are significantly associated with migraine-related behavioral and biochemical indices(c-fos, ET-1, CGRP, and 5-HT). In conclusion, TS can regulate the disrupted gut microbiota structure and microbial functions related to neurotransmitter metabolism, intestinal barrier function, and inflammatory regulation in migraine model rats, which may be one of the potential key ways through which TS exert its anti-migraine effect.},
}

Animals
*Migraine Disorders/drug therapy/metabolism/genetics/microbiology
Rats, Sprague-Dawley
Rats
*Gastrointestinal Microbiome/drug effects
*Drugs, Chinese Herbal/administration & dosage
Calcitonin Gene-Related Peptide/genetics/metabolism
Male
Humans
Disease Models, Animal
Endothelin-1/metabolism/genetics/blood
Capsules/administration & dosage
Serotonin/blood/metabolism
Proto-Oncogene Proteins c-fos/metabolism/genetics

@article {pmid42693476,
year = {2026},
author = {O'Brien, PA and Bell, SC and Negri, AP and Kjeldsen, SR and Zaugg, J and Webster, NS and Wahab, MA and Vanwonterghem, I and Rix, L},
title = {Metagenomic insights into mechanisms of coral larval settlement induction and inhibition by marine biofilms.},
journal = {Environmental microbiome},
volume = {21},
number = {1},
pages = {},
pmid = {42693476},
issn = {2524-6372},
abstract = {BACKGROUND: Biofilms are essential to larval settlement in many marine invertebrates, yet the mechanisms driving settlement induction or inhibition in corals remain poorly resolved. This challenge lies in the vast taxonomic and functional diversity of marine biofilms, making it difficult to identify cues associated with settlement. To address this, we analysed the metagenomes of biofilms used to induce settlement (attachment and metamorphosis) of four broadcast-spawning non-acroporid coral species: Dipsastrea favus, Platygyra sinensis, Echinophyllia aspera and Porites lobata. Biofilms were developed for one or two months, under light or dark treatments, with light biofilms inducing significantly higher settlement than dark biofilms.

RESULTS: Gene composition varied strongly among treatments, with light biofilms enriched in genes encoding carotenoid biosynthesis and nitrate reduction, while dark biofilms encoded more genes for denitrification and nitric oxide production. Modelling revealed the abundance of genes encoding GABA biosynthesis and the type III secretion system (SS) were positively associated with settlement, while genes encoding the type II secretion system, flagellar and lipopolysaccharides were negatively associated. Genes predicted to promote settlement were concentrated in metagenome assembled genomes (MAGs) assigned to Flavobacteriaceae, Rhodobacteraceae and Pirellulaceae, consistent with previous research identifying these lineages as potential inducers. While we detected homologues of some biosynthesis genes for the settlement-inducing compounds cycloprodigiosin and tetrabromopyrrole in the MAGs, pathways were incomplete suggesting additional compounds promote settlement on these biofilms.

CONCLUSIONS: These findings link biofilm metagenomics to coral larval settlement for the first time, suggesting carotenoids may attract larvae to biofilm surfaces, while GABA may promote searching and attachment. Additional compounds, for example cycloprodigiosin, tetrabromopyrrole or effector proteins, may be required to complete metamorphosis, however the specific compounds responsible likely vary across biofilm communities and suggest multiple mechanisms can lead to settlement. Simultaneously, elevated levels of nitric oxide, type II SS exudates or an abundance of flagellar potentially inhibit the settlement process. This study advances our understanding of the complex microbial processes underpinning coral larval settlement.},
}

@article {pmid42693766,
year = {2026},
author = {Baños, E and Segura, CR and De Boer, EJ and Cundy, AB and Barrera, XT and Nogué, S and Holman, LE and Rius, M},
title = {Getting to the Core of the Matter-Assessing the Role of Replication in Metabarcoding-Based sedaDNA.},
journal = {Molecular ecology resources},
volume = {26},
number = {7},
pages = {e70200},
doi = {10.1111/1755-0998.70200},
pmid = {42693766},
issn = {1755-0998},
support = {TED2021-132228B-C21//TEMPOINVASIONS/ ; TED2021-132228B-C22//TEMPOINVASIONS/ ; PID2023-146307OB//TEMPOINVASIONS/ ; },
mesh = {*DNA Barcoding, Taxonomic/methods ; *Geologic Sediments/microbiology ; *Metagenomics/methods ; RNA, Ribosomal, 18S/genetics ; Electron Transport Complex IV/genetics ; *Biota ; },
abstract = {Replication is central to most experimental and sampling designs, increasing inferential power and capturing fine-scale data heterogeneity. However, its importance remains poorly evaluated in some ecological and evolutionary settings. This is the case of metabarcoding studies using DNA recovered from sedimentary archives, in which biological signals integrate ecological information through depositional and burial processes, yet are commonly inferred from a single sediment core per site. Here, we evaluated the effect of different types of replication using sedimentary DNA metabarcoding data from two genetic markers (mitochondrial COI and nuclear 18S) using a nested sampling design. The design included three intertidal sites, three spatially separated sediment cores per site (biological replicates), two sediment horizons per core, and eight PCR (technical) replicates per sediment sample. Variance partitioning showed that site identity and sediment age group together explained > 70% of the variation in beta diversity, indicating that among-site spatial and stratigraphic differences were the dominant drivers of community composition. PERMANOVA likewise identified non-significant effects of biological replication. Among PCR replicates from the same sediment sample, richness varied substantially, whereas Shannon diversity was more consistent. Despite this variability, differences in community composition among technical replicates remained smaller than those associated with biological replication or site identity, indicating a limited influence on broader ecological patterns. Community composition was highly similar among replicate cores within sites, consistent with stratigraphic coherence. These results indicate limited within-site heterogeneity and suggest that, under stratigraphically coherent conditions, increasing biological replication may provide little additional information, whereas enhancing technical replication and stratigraphic resolution can improve ecological inference from sedimentary DNA metabarcoding datasets.},
}

*DNA Barcoding, Taxonomic/methods
*Geologic Sediments/microbiology
*Metagenomics/methods
RNA, Ribosomal, 18S/genetics
Electron Transport Complex IV/genetics
*Biota

@article {pmid42694210,
year = {2026},
author = {Oberdorfer, J and Tesani, J and Tagliaferri, TL and Schmitz, SM and Buhl, EM and Kraft, F and Krüttgen, A and Horz, HP},
title = {Genome-guided isolation and characterization of a novel bacteriophage infecting Escherichia coli reveal a putative new genus.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1909709},
pmid = {42694210},
issn = {1664-302X},
abstract = {We have isolated and characterized a novel bacteriophage termed Jab, with lytic activity against multidrug-resistant clinical isolates of Escherichia coli. Phage Jab was identified from liquid manure by means of metagenome sequencing of a phage community enrichment using an E. coli clinical isolate ECH07 as host. The initial enrichment was composed of four phages, of which phage Jab represented only a minute fraction (less than 1%). Jab isolation strategy comprised a targeted approach using iterative replication rounds while equipping ECH07 with resistance against the numerically dominant phages coupled with a subsequent host switch to E. coli BL21. Whole-genome sequence analysis revealed only a remote evolutionary distance to known phages within the subfamily Vequintavirinae. The dsDNA genome of phage Jab comprises 142,100 bp (GC content 40.09%) and encodes 264 proteins and five transfer RNAs (tRNAs). No lysogeny-associated proteins were detected, suggesting an obligate lytic lifestyle. In silico genome analysis revealed the presence of at least four putative depolymerases. The closest homology of phage Jab is with members of the new genus Septuagintavirus with around 34% nucleotide identity. VIRIDIC and network analyses strongly suggest that phage Jab belongs to a putative novel genus. The host range of phage Jab is likely restricted to E. coli, displaying a moderately narrow host range (i.e., productive lysis in 8 out of 27 isolates tested). Notably, transmission electron microscopy (TEM) revealed the occurrence of conspicuous unique spherical structures attached at the end of the tail fibers when propagated on BL21 but not when propagated on ECH07. Although their function remains enigmatic, the possible role of those structures as a bacterial (vesicle-based) defense mechanism warrants further investigation.},
}

@article {pmid42694408,
year = {2026},
author = {Young, D and Stüer-Patowsky, K and Huang, L and Elshahed, MS and Youssef, NH and Hanafy, R and Cheng, Y and Moon, CD and Soni, P and Joshi, A and Stabel, M and Ochsenreither, K and Dagar, SS and Hillman, E and Solomon, KV and Fliegerová, KO and Griffith, GW and Callaghan, TM and Podmirseg, SM and Sczyrba, A and Flad, V and Lebuhn, M and Wurzbacher, C},
title = {Full ribosomal operon sequencing of anaerobic gut fungi (phylum Neocallimastigomycota): insights on its markers and phylogenetic resolution.},
journal = {IMA fungus},
volume = {17},
number = {},
pages = {e195921},
pmid = {42694408},
issn = {2210-6340},
abstract = {The phylogenetic affiliations of anaerobic gut fungi (Neocallimastigomycota) are typically evaluated using single-gene markers. However, this approach often fails to resolve relationships between closely related lineages. To address this issue and identify alternative markers, we created a curated database comprising the complete ribosomal operon sequences of 156 isolates, representing 20 of the 22 recognized genera and two new genus-level clades. Using long-read sequencing, we obtained ~9 kbp operon sequences and developed a robust analysis pipeline. Incorporating both coding genes and non-coding regions (excluding IGS1) improved phylogenetic resolution. This phylogenetic approach successfully resolved the Cyllamyces and Caecomyces clades (hard-to-distinguish genetically), as well as seven analysed Piromyces species. We also scanned the operon for markers that are suitable for short-read sequencing platforms, with the aim of enhancing biodiversity and phylogenetic studies. Notably, the ETS1 genetic region also enabled the distinction between these lineages, indicating its phylogenetic value within the ribosomal operon. The resulting database is a valuable resource for expanding and strengthening phylogenetic frameworks.},
}

@article {pmid42694564,
year = {2026},
author = {Lu, P and Liu, M and Zhang, L and Fan, JJ and Sun, Y},
title = {Synergistic Regulation of Alzheimer's Disease and Intestinal Microbiota Metabolism Mediated by the Gut-Brain Axis: A Comprehensive Analysis from a Multidisciplinary Perspective.},
journal = {International journal of medical sciences},
volume = {23},
number = {9},
pages = {2939-2962},
pmid = {42694564},
issn = {1449-1907},
mesh = {Humans ; *Alzheimer Disease/microbiology/metabolism/immunology/therapy ; *Gastrointestinal Microbiome/immunology/physiology ; *Brain/metabolism/immunology ; Animals ; Multiomics ; *Brain-Gut Axis/immunology/physiology ; *Dysbiosis/microbiology/immunology ; },
abstract = {Alzheimer's disease (AD), as a neurodegenerative disease with the interaction of multiple factors, has a close association between its pathological process and the metabolic imbalance of the gut microbiota mediated by the gut-brain axis. This review systematically summarizes the molecular mechanisms by which the gut microbiota regulates the functions of the central nervous system bidirectionally through molecular pathways such as metabolites (e.g., short-chain fatty acids, tryptophan-kynurenine metabolites), immunomodulatory mediators (e.g., cytokines, chemokines), and bioactive substances (e.g., γ-aminobutyric acid, 5-hydroxytryptophan) via the gut-brain axis. It synthesizes current evidence suggesting the imbalance of microbiota homeostasis may be closely associated with the core pathologies of AD (including β-amyloid deposition and tau protein hyperphosphorylation) through mechanisms such as the activation of the C/EBPβ-AEP signaling pathway, induction of chronic neuroinflammation, oxidative stress cascade reactions, and metabolic network remodeling. These findings, primarily derived from preclinical models and correlational human studies, indicate potential mechanisms but require further causal validation and rigorous clinical translation, including the downregulation of butyrate synthesis pathways and their associated epigenetic and immunomodulatory consequences (as mechanistically dissected in Section 5.2). Multi-omics integration (metagenomics, metabolomics, spatial transcriptomics) has delineated characteristic microbial and metabolic alterations in AD, while computational approaches are beginning to elucidate the complex networks underlying these associations (see Sections 6 and 7 for details).Intervention strategies based on microbiota regulation (such as microbiota-targeted dietary interventions and postbiotics) are emerging as promising approaches, although their clinical applications remain in early stages. Preliminary evidence suggests that fecal microbiota transplantation may improve cognitive outcomes in AD patients with comorbid conditions; however, rigorous randomized controlled trials are essential to validate its efficacy and safety. Critically, translating these mechanistic insights into clinical practice requires overcoming three translational bottlenecks: inferring causality from correlational multi-omics data, resolving species/strain-level functional heterogeneity masked by genus-level taxonomy, and establishing standardized safety protocols for live biotherapeutic products. Addressing these challenges defines the near-term roadmap for precision medicine in AD. However, current research still faces challenges such as the heterogeneity of cross-omics data, the lack of technical standardization, and insufficient interdisciplinary cooperation mechanisms. In the future, it is necessary to promote the early molecular diagnosis and personalized targeted treatment of AD through longitudinal multi-omics dynamic monitoring, modeling of the microbiota-host interaction network, and optimization of the ethical-translational medicine framework.},
}

Humans
*Alzheimer Disease/microbiology/metabolism/immunology/therapy
*Gastrointestinal Microbiome/immunology/physiology
*Brain/metabolism/immunology
Animals
Multiomics
*Brain-Gut Axis/immunology/physiology
*Dysbiosis/microbiology/immunology

@article {pmid42694612,
year = {2026},
author = {Davis, EE and Younger, J and Burridge, C and Armbrecht, L},
title = {How low can you go? Establishing detection limits for rare eukaryotes in Southern Ocean sedimentary ancient DNA.},
journal = {Bioinformatics advances},
volume = {6},
number = {1},
pages = {vbag113},
pmid = {42694612},
issn = {2635-0041},
abstract = {MOTIVATION: Sedimentary ancient DNA (sedaDNA) is genetic material extracted from paleoarchives. It provides insights into the composition and dynamics of ecosystems over time. Such information can be crucial in anticipating how ecological communities may respond to environmental shifts within the context of the current climate crisis. However, challenges exist in accurately verifying ancient DNA from ecologically significant vertebrate species (e.g. fishes, aquatic birds, and mammals). These species occur only in trace amounts in sedimentary records. Here, we benchmark a stringent bioinformatic pipeline using synthetic and empirical metagenomic sedaDNA data from IODP Expedition 382 (Scotia Sea). Our objectives are threefold: (i) test taxonomic assignment precision for rare marine eukaryotes, (ii) evaluate taxonomic assignment sensitivity across different sediment ages, and (iii) establish the minimum sequence quantity necessary for robust identification.

RESULTS: We demonstrate that taxonomic assignment precision varied significantly with sequence quantity and metagenomic context. Assignment sensitivity decreased with taxonomic rank and database representation. Reliable detection of low-abundance taxa in sedaDNA is achievable with 250 and 500 DNA fragments at the family and genus level, respectively. The reanalysis of IODP Exp. 382 sedaDNA data, using a custom built marine vertebrate-focused reference database, resulted in the first genetic reconstruction of the vertebrate community in the Scotia Sea. This lays the groundwork for future investigations into the presence and biodiversity of Southern Ocean vertebrates using sedaDNA.

All project related scripts and generated simulated datasets are available in ae_fishing_benchmark repository (https://github.com/33davis/ae_fishing_benchmark). The demultiplexed raw data in relation to the IODP Exp. 382 U1538 reanalysed during this study is available in the NCBI Sequence Read Archive database (https://www.ncbi.nlm.nih.gov/sra) under Accession code/BioProject PRJNA861836 (BioSamples SAMN29928044 - SAMN29928123) and includes metadata for each sediment and control sample.},
}

@article {pmid42694670,
year = {2026},
author = {Zhu, X and Gao, Y and Zhang, J and Sun, L and Peng, M and Cui, Y and Xie, K},
title = {Fatal Tension Pneumocephalus Associated with Central Nervous System Infection Caused by an Extended-Spectrum β-Lactamase-Producing Klebsiella pneumoniae Harboring Hypervirulence-Associated Genes.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {631108},
pmid = {42694670},
issn = {1178-6973},
abstract = {BACKGROUND: Central nervous system (CNS) infections caused by Klebsiella pneumoniae harboring hypervirulence-associated genes usually arise from metastatic dissemination from an extracranial focus. Cases lacking an overt extracranial source remain uncommon. Furthermore, the spontaneous development of tension pneumocephalus in this context is exceptionally rare.

CASE PRESENTATION: We report a fatal case of a 49-year-old female with a 40-year history of polycystic liver and kidney disease who presented with fulminant meningoencephalitis. Despite aggressive systemic meropenem therapy and neuroprotective measures, she developed refractory intracranial hypertension (780 mmH2O) and rapidly progressive tension pneumocephalus without evidence of neurotrauma or external anatomical breach. Blood and cerebrospinal fluid (CSF) cultures, alongside CSF metagenomic next-generation sequencing (mNGS), identified an extended-spectrum β-lactamase (ESBL)-producing K. pneumoniae. The isolate exhibited a hypermucoviscous phenotype and harbored multiple hypervirulence-associated genes (eg, rmpA, iucA, and iroB) alongside resistance determinants (CTX-M-15-like and AAC(6')-Ib-cr), supporting a probable convergent phenotype. The patient ultimately died from irreversible multiple organ dysfunction syndrome on day 7.

CONCLUSION: The rapid evolution of tension pneumocephalus in this case highlights the potential for abrupt neurological deterioration in CNS infections associated with convergent K. pneumoniae phenotypes. While the exact etiology of intracranial gas is likely multifactorial, this case underscores the critical need to integrate phenotypic assays with molecular diagnostics to identify hypervirulence, while maintaining rigorous differential diagnoses for spontaneous pneumocephalus in the neurocritical care setting.},
}

@article {pmid42694775,
year = {2026},
author = {Shouq, MI and Saleem, HGM and Wang, Y and Sohail, M and Hussain, A and Zhang, H and Zheng, H},
title = {Lesion-specific oral microbiome signatures and predicted carcinogenic pathways in oral squamous cell carcinoma: a paired-site study in Pakistan.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2721025},
pmid = {42694775},
issn = {2000-2297},
abstract = {BACKGROUND: Oral squamous cell carcinoma accounts for over 90% of oral neoplasms. Despite therapeutic advances, the lack of reliable, non-invasive biomarkers and delayed diagnosis continues to impede effective clinical management. By combining paired lesion and non-lesion sampling with predictive metagenomics analysis, our study addresses this gap and advances the current understanding of microbiome‒tumor interactions.

METHODS: We analyzed 92 buccal swab samples from 39 OSCC patients and 14 healthy controls using 16S rRNA gene (V3-V4) sequencing. Taxonomic profiling was conducted using QIIME2 and SILVA/eHOMD databases, functional pathways were predicted using PICRUSt2, and hub taxa were identified through co-abundance network analysis.

RESULTS: Microbial community structure differed significantly across lesion, non-lesion, and healthy sites (PERMANOVA, p = 0.001). Lesions were enriched with Selenomonas infelix and Treponema vincentii, while healthy controls harbored Streptococcus oralis and Gemella haemolysans. Co-abundance network analysis revealed lesion-specific hub species, notably T. vincentii, strongly correlated with predicted activation of pyrimidine biosynthesis pathways (r = 0.69, q < 1E-6), suggesting predicted metabolic alterations in the tumor microenvironment. Non-lesion sites were also characterized by two hub species, Prevotella melaninogenica and Segatella oulorum.

CONCLUSION: Our findings define a lesion-specific microbial signature of OSCC characterized by the depletion of health-associated taxa, enrichment of pro-inflammatory pathobionts, and predicted associations with metabolic pathways implicated in carcinogenesis. These alterations reflect a predicted functionally altered tumor microenvironment.},
}

@article {pmid42694997,
year = {2026},
author = {Abboud, E and Rossi, P and Crouzy, B and Evangeliou, N and Nenes, A and Violaki, K},
title = {Characterization of the atmospheric microbiome in a semi-rural area of Central Europe using flow cytometry.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag167},
pmid = {42694997},
issn = {2730-6151},
abstract = {Characterizing bioaerosols is important for understanding their potential impacts on the environment and public health. In this study, we developed a novel flow cytometry-based approach to determine the low nucleic acid (LNA), high nucleic acid (HNA), dead, and intact bioaerosol populations in samples collected with a wet cyclone at Payerne, Switzerland, during spring and summer 2024. We found that the average bioaerosol number concentration reached (2.47 ± 3.35)×10[4] m[-3]. The HNA and intact populations were the most abundant populations, representing the largest fraction of total bioaerosols within 65% and 97% of the samples, respectively. Our results show that the LNA can be composed of dead bioaerosols, which correlated strongly with atmospheric particulate mass. Quantitative Polymerase Chain Reaction (qPCR) and metagenomic analysis reveal significant correlations and associations (Spearman, PERMANOVA, and Mantel) between the different kingdoms analyzed, reflecting complex ecological interactions in the atmosphere among the communities. Despite this complexity, LNA was mainly associated with the archaea Nitrososphaerota and bacteria Actinomycetota, whereas HNA was enriched by fungal classes such as Pichiomycetes and Ustilaginomycetes. Pollen abundance was positively correlated with temperature and negatively correlated with relative humidity and pollution (NOx and NO2), as these conditions promote the formation of sub-pollen particles (pollen fragments) through osmotic (bursting) and oxidative stress. Factor analysis indicates a seasonal dynamics transition from plant-associated bioaerosols in the spring season, to other bioaerosol types to be co-emitted during summer. Overall, the integration of flow cytometry with molecular analysis provides a framework to characterize and quantify bioaerosols and provides new insights into the ecological structure, variability, and sources of the atmospheric microbiome.},
}

@article {pmid42695007,
year = {2026},
author = {Pan, Q and Tsompanidou, E and Hu, W and Khan, MT and van Dijl, JM},
title = {Faecalibacterium harmsenii sp. nov., an abundant but previously overlooked Faecalibacterium in the human gut.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag221},
pmid = {42695007},
issn = {2730-6151},
abstract = {Faecalibacterium is one of the most abundant anaerobes in the human colon. At the genus level, this bacterium shows a strong positive association with human health. Expanding collections of isolates and metagenome-assembled genomes have revealed its species diversity, yet species-level functions remain so far underexplored. Here, we describe a novel species, Faecalibacterium harmsenii. In addition, we reclassify another isolate as a member of the recently reported Faecalibacterium langellae species. Despite close genomic relatedness, these isolates exhibit distinct physiological and biochemical traits, including differences in carbohydrate utilization, stress tolerance, enzymatic activity, Gram-staining and fatty acid composition. Our present comparative genomics analyses further uncover extensive functional diversity and plasticity across type strains, with F. harmsenii being distinguished by an expanded carbohydrate gene repertoire and reduced defense systems, mobile genetic elements and antibiotic resistance genes. Extending to the species, we identify species-specific ecological niches across hosts and differential sensitivities to human diseases, highlighting certain species as reliable biomarkers of gut health. Together, these findings refine our understanding of Faecalibacterium diversity and provide a framework for its use in microbiome-based diagnostics and therapeutic development.},
}

@article {pmid42695179,
year = {2026},
author = {Nett, N and Dumack, K},
title = {A Pan-European Whole-Microbiome Study of Wastewater Influent: Prokaryotes, Protists, Fungi, and Metazoa.},
journal = {The Journal of eukaryotic microbiology},
volume = {73},
number = {5},
pages = {e70112},
doi = {10.1111/jeu.70112},
pmid = {42695179},
issn = {1550-7408},
support = {556896378//Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)/ ; },
mesh = {*Wastewater/microbiology/parasitology ; *Fungi/classification/genetics/isolation & purification ; *Bacteria/classification/genetics/isolation & purification ; Europe ; *Microbiota ; *Eukaryota/classification/genetics/isolation & purification ; Seasons ; Animals ; },
abstract = {Microbial communities entering wastewater treatment plants (WWTPs) through untreated sewage represent an important interface between human, environmental, and treatment-associated microbiomes, yet our understanding of their biogeography remains poorly resolved, particularly for microbial eukaryotes. Using shotgun metagenomic time-series data from influent samples of seven WWTPs across a European latitudinal gradient, we analyzed the taxonomic composition and dynamics of bacteria, protists, fungi, and microscopic metazoa. Influent community composition varied with geographic location and season, with a pronounced north-south divergence driven by dominant taxa and stronger seasonal shifts observed at higher latitudes. Cross-domain associations were pervasive, suggesting that co-varying bacterial and eukaryotic components structure the incoming microbial pool. Our findings provide a pan-European baseline for whole-microbiome wastewater surveillance and highlight that influent communities differ regionally and seasonally. These patterns may be relevant for downstream treatment-stage microbiomes, but direct effects on reactor community assembly and treatment performance require targeted sampling across treatment stages.},
}

*Wastewater/microbiology/parasitology
*Fungi/classification/genetics/isolation & purification
*Bacteria/classification/genetics/isolation & purification
Europe
*Microbiota
*Eukaryota/classification/genetics/isolation & purification
Seasons
Animals

@article {pmid42695323,
year = {2026},
author = {Dong, S and Li, T and Li, C and Li, L and Wu, T and Ren, Y and Jiao, Y and Wang, L and Zhu, T and Li, P},
title = {Integrating Metagenomics and Network Pharmacology Reveals That Hypericum perforatum L. Alleviates Depressive-Like Behaviors via Gut Microbiota-Associated Inflammatory and PI3K-Akt Signaling.},
journal = {Combinatorial chemistry & high throughput screening},
volume = {},
number = {},
pages = {},
doi = {10.2174/0113862073500203260805052728},
pmid = {42695323},
issn = {1875-5402},
abstract = {INTRODUCTION: Hypericum perforatum L. (HP) is a well-known herbal antidepressant with reliable antidepressant effects. However, its underlying mechanism, particularly the interplay with the gut-brain axis, remains poorly elucidated. In this study, aimed to explore the potential mechanism by which HP relieves depressive-like behaviors by integrating metagenomic sequencing and network pharmacology, with a focus on gut microbiota and host signaling pathways.

METHODS: A rat model of depressive-like behaviors was established using Chronic Restraint Stress (CRS). Sucrose Preference Test (SPT), Open Field Test (OFT), and Forced Swimming Test (FST) were applied to evaluate behavioral performance. Histopathological changes in the hippocampus and colon were assessed by Hematoxylin and Eosin (HE) staining. Serum levels of inflammatory cytokines were measured by ELISA. Gut microbiota composition was profiled by metagenomic sequencing; intestinal barrier integrity was evaluated by assessing the expression of tight junction proteins Zona Occludens 1 (ZO-1) and occludin. Network pharmacology was used to predict active components, targets, and pathways of HP. Key hippocampal pathway proteins were validated by western blot analysis.

RESULTS: HP intervention ameliorated CRS-induced depressive-like behaviors, alleviated hippocampal neuronal damage, and restored intestinal barrier integrity. Serum levels of proinflammatory cytokines were also reduced. Metagenomic analysis revealed that HP reversed CRS-induced gut dysbiosis, notably by increasing the relative abundance of beneficial bacteria (e.g., Prevotella) and decreasing pro-inflammatory taxa. Redundancy Analysis (RDA) revealed close correlations between microbial alteration and inflammatory cytokine levels. Network pharmacology identified six active components and 42 potential therapeutic targets; the phosphoinositide 3- Kinase-Protein Kinase B (PI3K-Akt) signaling pathway was determined as the core pathway. Experimental verification confirmed that HP could regulate the PI3K-Akt signaling pathway and modulate the expression of its downstream protein Nuclear Factor Kappa B (NF-κB) in the hippocampus.

DISCUSSION: Our work provides integrative insight into the pharmacological characteristics of HP and supports that gut microbiota may be potentially involved in its antidepressant-like effects.

CONCLUSION: This study provides evidence that HP ameliorates CRS-induced depressive-like behaviors, which is closely associated with the restoration of gut microbial homeostasis, suppression of systemic inflammation, and regulation of the brain PI3K-Akt signaling pathway.},
}

@article {pmid42695693,
year = {2026},
author = {Claiborne, C and Lyu, Z},
title = {Meta-CD: a metagenomic sequencing coverage and depth calculator for target species.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0081126},
doi = {10.1128/mra.00811-26},
pmid = {42695693},
issn = {2576-098X},
abstract = {Metagenomic Coverage and Depth Calculator (Meta-CD) is a convenient, biologist-friendly tool for determining coverage and depth to enhance taxonomic detection, functional profiling, and metagenome-assembled genome (MAG) recovery in metagenomics. It supports experimental design and post-sequencing analysis, modeling how genome size, relative abundance, sequencing depth, and DNA quantity influence detection of target species.},
}

@article {pmid42695919,
year = {2026},
author = {Chen, Y and Kuan, AS and Liao, PH and Wang, WH and Chen, YC},
title = {Rapid diagnosis of Fusobacterium nucleatum-associated brain abscess using metagenomic next-generation sequencing: A case series.},
journal = {Journal of neuropathology and experimental neurology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jnen/nlag047},
pmid = {42695919},
issn = {1554-6578},
support = {T21006//Taipei Veterans General Hospital/ ; },
}

@article {pmid42695976,
year = {2026},
author = {de Kreek, F and Hertzberger, R and van Eeden, F and Illidge, S and Teunis, EJ and Hanemaaijer, M and Lievens, E and Rienstra, F and Wiedhaup, DE and Lisotto, P and Butler, D and Molenaar, D and Kort, R},
title = {Intra-individual genetic diversity of vaginal Lactobacillus crispatus revealed through citizen science-driven isolation and pangenome analysis.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxag218},
pmid = {42695976},
issn = {1365-2672},
abstract = {AIMS: A vaginal microbiome dominated by Lactobacillus crispatus is associated with positive reproductive and sexual health outcomes, yet intra-individual genetic diversity within this species remains largely unexplored. This study characterised inter- and intra-individual genomic variation in L. crispatus strains isolated through a citizen science initiative and assessed implications for multi-strain probiotic development.

METHODS AND RESULTS: Fifty-three women participated in this citizen science project. Self-sampling resulted in 48 shotgun metagenomes. Twenty-two participants isolated their own L. crispatus strains using selective enrichment and LAMP-based species confirmation, resulting in 53 whole-genome-sequenced isolates. L. crispatus dominated 20 of 48 metagenomes (50.1-99.6% relative abundance). Pangenome analysis revealed 3 456 gene families, of which 43.7% were core and 56.3% accessory. A 14-kb plasmid harbouring a Fic-domain toxin-antitoxin protein, but devoid of antimicrobial resistance genes, was present in 44 of 53 strains. Strains from the same individual clustered closely together yet harboured 1-123 gene differences. Intra-individual variation was observed in the pullulanase type I gene required for glycogen degradation: 40 strains were predicted to grow on glycogen, six showed genetic disruptions with unknown consequences, and seven were predicted to lack this ability entirely. Variation within individuals was also found for bacteriocin classes and CRISPR-Cas genes.

CONCLUSIONS: Substantial functional diversity exists within L. crispatus, even among strains from the same individual, supporting the rationale for multi-strain vaginal probiotics. This citizen science approach enabled discovery of host-specific adaptations while ensuring participant ownership of their strains.},
}

@article {pmid42696316,
year = {2026},
author = {Jiang, J and Huang, Q and Wu, F and Liang, P and Fan, L and Zhou, X and Zheng, C and Shi, X and Song, H and Wang, J and Luo, JX and Chen, J and Yang, Q and Peng, S and Yin, L and Zeng, D and Jie, H and Zhu, G},
title = {Gut Microbiota Analysis and Comparison in Forest Musk Deer (Moschus berezovskii) of Different Ages and Musk-Secreting Periods.},
journal = {Integrative zoology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1749-4877.70181},
pmid = {42696316},
issn = {1749-4877},
support = {2025ZNSFSC0280//Sichuan Provincial Natural Science Foundation/ ; 82274046//National Natural Science Foundation of China/ ; 2024jbky- 019//Chongqing Basic Research Projects/ ; },
abstract = {Under homeostatic conditions, the gut microbiota are closely associated with host health, undergoing co-evolution with the host through complex interactions to maintain mutually beneficial symbiosis. However, dynamic changes in the gut microbiota of forest musk deer (Moschus berezovskii; FMD) at different age stages and musk-secreting periods remain unclear. In this study, we analyzed the fecal microbiota of FMD using metagenomic sequencing across four age groups (subadult, young adult, adult, and old) and four musk-secreting period groups (before musk-secreting period, during musk-secreting period, after musk-secreting period, and musk collection). The results showed that the gut microbiota structure of FMD demonstrated stability across different age stages and musk-secreting periods and was dominated by Firmicutes. Moreover, changes in musk-secreting periods had a greater effect on the gut microbiota of subadult and old FMD, while age-associated differences in gut microbial composition were mainly evident during AMSP. LDA effect size (LEfSe) and STAMP analyses further revealed significant age-associated and musk-secreting period-associated differences in the structure and function of the gut microbiota in FMD. In addition, subadult FMD showed enhanced immune response-associated and potential pathogen-associated functions during musk collection, accompanied by the enrichment of potential opportunistic pathogenic bacteria, suggesting that musk collection may be associated with host stress responses and gut microecological disturbance. In summary, this study explored the relationships among age stages, musk-secreting periods, and gut microbiota of FMD, providing a certain strategic reference for the healthy captive breeding of FMD and the improvement of musk production.},
}

@article {pmid42696374,
year = {2026},
author = {Fang, Y and Fan, C and Liu, P and Wang, S and Zhang, W},
title = {Computed tomography-guided precision biopsy combined with metagenomic next-generation sequencing for etiological diagnosis in patients with blood culture-negative systemic infections.},
journal = {The Journal of international medical research},
volume = {54},
number = {9},
pages = {3000605261481695},
doi = {10.1177/03000605261481695},
pmid = {42696374},
issn = {1473-2300},
mesh = {Humans ; Female ; *High-Throughput Nucleotide Sequencing/methods ; Male ; *Tomography, X-Ray Computed/methods ; Retrospective Studies ; *Image-Guided Biopsy/methods ; *Metagenomics/methods ; Middle Aged ; *Sepsis/diagnosis/microbiology/drug therapy ; Blood Culture ; Aged ; Adult ; },
abstract = {ObjectiveTo evaluate the diagnostic efficacy of computed tomography-guided percutaneous biopsy combined with metagenomic next-generation sequencing in patients with blood culture-negative systemic infections and to assess the clinical impact of using this combined strategy for etiological confirmation and guidance of targeted antimicrobial therapy.MethodsThis single-center retrospective observational cohort study enrolled 78 patients who met the Sepsis-3 consensus criteria for suspected systemic infection and had negative conventional microbiological work-ups (at least two sets of blood cultures) between April 2022 and March 2025. All patients underwent computed tomography-guided biopsy of radiologically identified infectious foci, with specimens processed concurrently for conventional culture and metagenomic next-generation sequencing. Diagnostic performance was benchmarked against the final comprehensive clinical diagnosis, and the influence of metagenomic next-generation sequencing findings on antimicrobial therapy modification was analyzed. Sample size calculation, based on a prior study estimating an metagenomic next-generation sequencing detection rate of 85% (α = 0.05, β = 0.2), indicated a minimum of 68 cases; accordingly, 78 patients were enrolled.ResultsComputed tomography-guided biopsy was technically successful in all 78 patients (100%). The pathogen detection rate of metagenomic next-generation sequencing (91.0%, 71/78) was significantly higher than that of conventional culture (55.1%, 43/78; p < 0.001). Using the final clinical diagnosis as the reference standard, metagenomic next-generation sequencing achieved a sensitivity of 94.7% (95% confidence interval: 86.9-98.5), specificity of 100.0% (95% confidence interval: 29.2-100.0), positive predictive value of 100.0% (95% confidence interval: 94.9-100.0), and negative predictive value of 42.9% (95% confidence interval: 9.9-81.6). Among the 35 culture-negative specimens, metagenomic next-generation sequencing established a definitive microbiological diagnosis in 28 cases (80.0%) and detected polymicrobial infections in 11 cases (14.1% of the cohort). Antimicrobial therapy was rationally adjusted based on metagenomic next-generation sequencing results in 69.2% (54/78) of the patients.ConclusionsThe integration of computed tomography-guided precision biopsy with metagenomic next-generation sequencing offers a highly effective diagnostic approach for blood culture-negative systemic infections. This synergistic strategy improves etiological diagnosis by providing high-yield target specimens that enable comprehensive, unbiased pathogen screening, facilitates differentiation between infectious and non-infectious etiologies, and supplies critical evidence for guiding precision antimicrobial therapy. These findings highlight the growing role of interventional radiology in the contemporary framework of precision infectious disease management.},
}

Humans
Female
*High-Throughput Nucleotide Sequencing/methods
Male
*Tomography, X-Ray Computed/methods
Retrospective Studies
*Image-Guided Biopsy/methods
*Metagenomics/methods
Middle Aged
*Sepsis/diagnosis/microbiology/drug therapy
Blood Culture
Aged
Adult

@article {pmid42696471,
year = {2026},
author = {Pinder, H and Rudkin, JK and Quail, NPA and Wall, DM and Young, P and Rooney, LM},
title = {Convergent methodologies in prosthetic joint infection research: integrating transdisciplinary approaches to understand and prevent biofilm-driven failure of orthopaedic prostheses.},
journal = {Journal of medical microbiology},
volume = {75},
number = {9},
pages = {},
doi = {10.1099/jmm.0.002206},
pmid = {42696471},
issn = {1473-5644},
mesh = {*Prosthesis-Related Infections/microbiology/prevention & control ; *Biofilms/growth & development ; Humans ; *Joint Prosthesis/microbiology ; Prosthesis Failure ; },
abstract = {Prosthetic joint infections (PJIs) remain among the most devastating complications of arthroplasty, imposing substantial clinical, economic and patient burdens. Although culture-based diagnostics underpin current clinical practice, PJIs are biofilm-driven infections shaped by taxonomic diversity, spatial organization, host responses and surface interactions, meaning conventional approaches provide only a partial and often decontextualized view of the infection process. We examine how convergent methodologies can transform PJI research by integrating approaches that have traditionally been studied in isolation, including sequencing, transcriptomics, metabolomics, advanced imaging and culture-based characterization. We discuss how whole-genome sequencing, shotgun metagenomics, transcriptomic and metabolomic approaches resolve pathogen identity, functional activity and adaptive persistence and how cross-scale imaging and spatial biology techniques reveal where microbes colonize, interact and survive across implant surfaces. We highlight emerging opportunities to unify these datasets into coherent frameworks that capture both the molecular and physical dimensions of PJIs. Integrating these complementary approaches will enable a multi-layered understanding of PJIs that link composition, function and spatial organization. Ultimately, this provides a foundation for predictive diagnostics, precision antimicrobial strategies and improved implant design and supports a shift towards more effective, mechanism-informed management of implant-associated infection.},
}

*Prosthesis-Related Infections/microbiology/prevention & control
*Biofilms/growth & development
Humans
*Joint Prosthesis/microbiology
Prosthesis Failure

@article {pmid42696749,
year = {2026},
author = {Cisneros-Martínez, AM and Varela, MÁF and González-Serrano, F and Rebollar, EA},
title = {Exploring the ecological drivers of bacteriophage diversity and functional viral potential in the skin of the axolotl Ambystoma altamirani.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiag103},
pmid = {42696749},
issn = {1574-6941},
abstract = {Bacteriophages play important roles in shaping microbial community dynamics across diverse environments. In the amphibian skin, most microbiome studies have focused on bacteria and their interactions with the fungus Batrachochytrium dendrobatidis (Bd), leaving other microbial components, including viruses, largely unexplored. Here, we present the first characterization of the viral community in the amphibian skin microbiome, focusing on ecological drivers of bacteriophage diversity and functional potential in the axolotl Ambystoma altamirani. Using public shotgun metagenomes, we found that the viral fraction was dominated by bacteriophages of the class Caudoviricetes. Bacteriophage diversity was significantly associated with local physicochemical parameters at the time of sampling, and showed a strong positive correlation with bacterial diversity, whereas no significant associations were detected with the presence of Bd. In addition, seasonality influenced the composition and properties of bacteria-bacteriophage co-abundance networks. Functional annotation of assembled bacteriophage sequences revealed a diverse functional potential, including putative auxiliary metabolic genes, superinfection exclusion, toxin-antitoxin, and virulence factors. Overall, these findings highlight the ecological relevance of bacteriophages in amphibian skin microbiomes and underscore the need for further studies on their role in the amphibian host's health.},
}

@article {pmid42696789,
year = {2026},
author = {Kan, Y and Fu, Y and Yang, W and Harindintwali, JD and Liu, Q and Jiang, X and Wang, C and Hu, J and Chen, L and Wang, C and Tian, D and Ye, M and Jiang, X},
title = {Rhizosphere microbiome assembly and functional enrichment drive salt tolerance in wheat.},
journal = {Journal of environmental management},
volume = {417},
number = {},
pages = {130869},
doi = {10.1016/j.jenvman.2026.130869},
pmid = {42696789},
issn = {1095-8630},
abstract = {Soil salinization is a major constraint on wheat production, as seedling-stage stress strongly constrains early growth and potential yield. However, the mechanisms by which the rhizosphere microbiome mediates varietal differences in salt tolerance remain poorly understood. Here, we compared a salt-tolerant wheat cultivar (Jimai60, JM60) and a salt-sensitive cultivar (Guomai301, GM301) grown in saline-alkali soil. Integrating soil physicochemical, enzymatic analyses and 16S rRNA gene and shotgun metagenomic sequencing, we investigated rhizosphere microbiome assembly, network structure, and functional potential at the seedling stage. JM60 assembled a distinct rhizosphere microbiome enriched in Bacteroidota, with Sphingobacterium acting as a keystone taxon in a more stable co-occurrence network. In contrast, GM301 was dominated by Zobellella and exhibited increased negative microbial interactions, indicating a reduced network that is structurally more cooperative. Metagenomic analyses showed enrichment in JM60-associated microbiomes of genes linked to oxidative stress resistance (katE), central carbon metabolism (pdhD), and nitrogen utilization (hutF), suggesting enhanced redox homeostasis, nutrient cycling, and ion balance regulation. These functional traits aligned with higher leaf antioxidant enzyme activity and altered rhizosphere nutrient profiles in JM60. Our findings demonstrate that wheat salt tolerance is linked to assembly of a functionally enriched rhizosphere microbiome, highlighting microbiome-driven mechanisms for improving crop resilience in saline soils.},
}

@article {pmid42685249,
year = {2026},
author = {Zhang, B and Xu, X and Zhang, M and Qi, B and Ma, H and Yan, P and Lens, PNL and Shi, W},
title = {Free Ammonia Stress Rewires Microbial Signaling Networks and Constrains Metabolic Cooperation in Oxygenic Photogranules.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag225},
pmid = {42685249},
issn = {1751-7370},
abstract = {Free ammonia (FA) is a prevalent chemical inhibitor in wastewater ecosystems, yet its ecological impacts on microbial communication and cooperation remain poorly understood. Here, we demonstrated that FA stress restructured the community function of oxygenic photogranules (OPGs) by rewiring signaling-associated regulatory networks and redirecting cellular energy allocation. Temporal profiling of extracellular signaling molecules and intracellular regulatory molecules, integrated with metagenomic and metatranscriptomic analyses, revealed a concentration-dependent reconfiguration of microbial signaling. Under low FA exposure (≤ 1.0 mg/L), diffusible signal factor (DSF)- and indole-3-acetic acid (IAA)-associated pathways were more active, coinciding with photogranules consolidation and efficient nitrogen removal. At moderate FA stress (5.0 mg/L), the regulatory landscape shifted toward acyl-homoserine lactone (AHL)-associated signaling and bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP)-mediated intracellular regulation, consistent with enhanced aggregation and stress adaptation. In contrast, severe FA stress (25.0 mg/L) broadly attenuated signaling-associated pathways, weakened metabolite cross-feeding networks, impaired energy generation, and increased maintenance-related energetic demands. Under these constraints, microbial populations appeared to shift from cooperative metabolism toward self-maintenance-oriented carbon metabolism, evidenced by activation of the carbon-efficient glyoxylate shunt. Collectively, these findings suggest that FA-induced signaling disruption constrains microbial cooperation through cellular energy limitation, highlighting energy allocation as a key determinant of microbial social stability in phototrophic wastewater microbiomes.},
}

@article {pmid42685266,
year = {2026},
author = {Colajanni, A and Uricaru, R and Darko, S and Subramanian, R and Douek, DC and Thiébaut, R and Thebault, P},
title = {Benchmarking methods for extracting microbial signal from host-dominated metatranscriptomes.},
journal = {Briefings in bioinformatics},
volume = {27},
number = {5},
pages = {},
doi = {10.1093/bib/bbag454},
pmid = {42685266},
issn = {1477-4054},
mesh = {Humans ; *Microbiota/genetics ; Benchmarking ; *Transcriptome ; *Gene Expression Profiling/methods ; Sequence Analysis, RNA/methods ; *Computational Biology/methods ; },
abstract = {Human RNA sequencing (RNA-seq) data originally generated for human transcriptome profiling are overwhelmingly dominated by host sequences, yet they often contain a small fraction of non-human reads that can be exploited for microbial detection. When such datasets are repurposed for secondary microbiome-oriented analyses, extracting and accurately classifying this weak microbial signal becomes technically challenging, and no ready-to-use pipeline currently exists. In this study, we evaluate computational strategies for filtering host reads and classifying microbial transcripts in host-dominated RNA sequencing data. We compare assembly-based approaches similar to those used in a previous study focusing on microbial translocation with state-of-the-art assembly-free methods, and assess their respective strengths and limitations using simulated datasets reflecting low microbial abundance. Our results show that assembly-based methods yield accurate taxonomic predictions but struggle at low read depth, whereas assembly-free methods are more robust in sparse settings at the cost of reduced precision. To leverage the complementarity of both approaches, we propose a hybrid pipeline that integrates assembly-based and assembly-free classification. On simulated data, this hybrid strategy improves microbial classification performance compared with either approach alone. Application to a real human metatranscriptomic dataset analyzed in a microbial translocation context illustrates the broader microbial signal captured by the hybrid approach, despite intrinsic challenges related to the absence of reliable ground truth and the risk of host read misclassification. Our work provides a framework for extracting microbial signals from host-dominated human metatranscriptomes, enabling the reuse of existing transcriptomic datasets for microbiome-related analyses, including but not limited to microbial translocation studies.},
}

Humans
*Microbiota/genetics
Benchmarking
*Transcriptome
*Gene Expression Profiling/methods
Sequence Analysis, RNA/methods
*Computational Biology/methods

@article {pmid42685579,
year = {2026},
author = {Hartono, S and Røder, HL and Boeren, S and Swarts, DC and Abee, T and Smid, EJ and van Mastrigt, O},
title = {Stressostat cultivation of Lactococcus lactis improves lactate stress resistance through mutations in RNA polymerase.},
journal = {Microbiological research},
volume = {314},
number = {},
pages = {128706},
doi = {10.1016/j.micres.2026.128706},
pmid = {42685579},
issn = {1618-0623},
abstract = {Adaptive laboratory evolution is used to improve the phenotypes of microorganisms and to characterise the mechanisms underlying resistance against complex growth inhibition. Here we focused on lactic acid bacteria (LAB) as starter cultures for food fermentations. Production of LAB starter cultures is challenging due to growth inhibition by organic acids, mainly lactate, produced during fermentation. By utilising stressostat cultivation we generated Lactococcus lactis isolates with enhanced lactate resistance. Using a combination of (meta)genomics, proteomics and pH-controlled batch fermentations, we deciphered the lactate resistance mechanisms of these L. lactis isolates. Proteome responses of L. lactis, combined with similar growth inhibition at high salt, suggest that high lactate mainly causes osmotic stress. We identified RNA polymerase (RNAP) mutations in subunits β (rpoB) and β' (rpoC) as key mutations, causing pleiotropic effects in the proteome. These proteome adaptations are linked to enhanced lactate resistance, particularly the resistance to hyperosmotic stress in absence of glycine-betaine. Combined, our study shows that RNAP mutations enhanced lactate resistance through pleotropic effects in the proteome that changed L. lactis responses against multiple stresses.},
}

@article {pmid42685687,
year = {2026},
author = {Zou, X and Ni, Y and Zhang, Q and Chang, K and Li, S and Zhang, Y and Yu, H and Wang, C and Yao, X and Chen, S and Nie, X and Zhao, J and Lu, B and Li, Y and Gan, N and Wang, Z and Yan, Q and Cao, B},
title = {The human oral and airway viral genome catalog from metagenomes enables virome characterization informing respiratory health.},
journal = {Med (New York, N.Y.)},
volume = {},
number = {},
pages = {101269},
doi = {10.1016/j.medj.2026.101269},
pmid = {42685687},
issn = {2666-6340},
abstract = {BACKGROUND: Viral communities of the upper aerodigestive tract represent an important component of the human microbial ecosystem but remain poorly characterized due to the limited availability of habitat-specific reference resources.

METHODS: We integrated 19,997 public and 2,673 newly sequenced oral and airway metagenomes to establish the Oral and Airway Viral Genome Catalogue (OAVGC). Viral genomes were reconstructed and characterized through taxonomic assignment, prokaryotic host prediction, functional annotation, and assessment of putative antibacterial activity. Our prospective longitudinal aging cohort, alongside 5 in-house datasets and publicly cohorts, were analyzed to investigate associations between airway virome profiles and respiratory health.

FINDINGS: The OAVGC comprised 141,459 high-quality viral genomes (completeness ≥90%) clustered into 68,708 viral operational taxonomic units (vOTUs). Approximately half of these viruses and families are previously undescribed, with independent cross-cohort detection and PCR assays providing additional support for their occurrence. Across multiple respiratory infection cohorts, the virome exhibited convergent diversity reductions and compositional signatures. In the prospective cohort, the baseline airway virome was correlated with host lung function and geriatric health scores. Virome-based machine learning classifiers demonstrated potential for predicting the future occurrence of upper respiratory tract infections up to 12 months in advance, outperforming bacteriome-based models in our prediction analyses.

CONCLUSIONS: The OAVGC provides an unprecedented genomic and functional resource for investigating the ecological and clinical associations of the oral-airway virome, revealing its potential impact on respiratory health and capacity to predict future infections.

FUNDING: National Natural Science Foundation of China (82341113) and National Key R&D Program of China (2022YFA1304303).},
}

@article {pmid42685930,
year = {2026},
author = {Babenkova, PI and Golovina, NA and Reprintseva, VN and Karaulova, SO and Vostrikova, AD and Burakova, IY and Pogorelova, SV and Smirnova, YD and Morozova, PD and Shutikov, VA and Mikhailov, EV and Kozin, SV and Dzhimak, SS and Gureev, AP and Syromyatnikov, MY},
title = {Comenic acid as a modulator of the gut-testis axis in pyridaben-induced toxicity.},
journal = {Reproductive toxicology (Elmsford, N.Y.)},
volume = {},
number = {},
pages = {109342},
doi = {10.1016/j.reprotox.2026.109342},
pmid = {42685930},
issn = {1873-1708},
abstract = {Pyridaben is an acaricide that inhibits mitochondrial complex I, which disrupts mitochondrial viability and causes oxidative stress. Pyridaben administration was associated with significant damage to mitochondrial DNA (mtDNA) in mice. The oxidative stress related to pyridaben exposure also co-occurred with alterations in the morphology of the testes and intestines, leading to the activation of the Nrf2-dependent protective pathway in testicular tissue, reduction of the seminiferous tubule lumen accompanied by interstitial tissue swelling, and adaptive changes in the intestinal epithelial tissue. Comenic acid (CA) exhibits active antioxidant properties; in the group receiving CA, the mtDNA copy number increased. Functionally, pyridaben considerably reduced the alpha diversity of the intestinal microbiome, while CA administration appeared to normalize this indicator, also mitigating shifts in beta diversity. Taxonomic analysis revealed that pyridaben elevated the abundance of the families Bacteroidaceae and Muribaculaceae, which aligned with a functional upregulation of endotoxic dTDP-β-L-rhamnose and L-lysine biosynthesis pathways. Conversely, CA treatment attenuated these shifts, reducing opportunistic taxa while concurrently upregulating protective pathways, including folate transformations and CDP-diacylglycerol biosynthesis. These findings suggest that CA, potentially due to its antioxidant properties and modulation of the intestinal microbial and functional profiles, may exert a compensatory effect against pyridaben-induced toxicity via the gut-testis axis.},
}

@article {pmid42685938,
year = {2026},
author = {Zhao, Z and Zhou, J and Li, H and Yu, C and Zhou, L and Luo, Z and Wang, Y and Liang, D and Li, W and Yang, J},
title = {Modulating bile acid isomerization and brain distribution by multiflorin A mitigates neuroendocrine stress and ameliorates anxiety-like behavioral alterations.},
journal = {Journal of ethnopharmacology},
volume = {},
number = {},
pages = {122338},
doi = {10.1016/j.jep.2026.122338},
pmid = {42685938},
issn = {1872-7573},
abstract = {Bile acids (BAs) have long been recognized in traditional ethnic medicines as a regulator of emotion and mental states; however, the underlying biological mechanisms by which BAs influence neuropsychological functions remain largely unclear. Multiflorin A (MA), an acetylated flavonoid glycoside and the signature bioactive constituent of Pruni Semen, is believed to ameliorate psychological stress via targeting the bile system.

AIM OF THE STUDY: This study aimed to investigate alterations in bile acid metabolism and distribution in SPS-induced PTSD-associated anxiety-like behavioral alterations and the therapeutic effects of MA and ursodeoxycholic acid (UDCA).

MATERIALS AND METHODS: SPS-stressed mice exhibiting anxiety-like behaviors were treated with MA. Behavioral tests, histopathology, targeted BAs metabolomics, metagenomics, neurotransmitter profiling, proteomics, and immunofluorescence were performed. UDCA was used as a reference compound to explore the involvement of BAs in MA-mediated neuroprotective effects.

RESULTS: SPS exposure induced anxiety-like behavioral deficits, accompanied by dysregulation of systemic BAs homeostasis, characterized by peripheral BAs depletion, central accumulation of hydrophobic BAs, partial blood-brain barrier disruption, and synaptic impairment. MA and UDCA treatment significantly improved behavioral performance, alleviated histopathological damage, and partially restored gut microbiota composition and BAs profiles, including increased levels of isomerized bile acids such as UDCA and alloLCA. These changes were accompanied by restoration of tight junction, PSD-95 expression, and neurotransmitter balance. Proteomics showed partial reversal of SPS-induced synaptic and neurotransmitter dysregulation, consistent with reduced neural hyperexcitability.

CONCLUSION: MA may ameliorate PTSD-associated anxiety-like behavioral alterations through modulation of the gut microbiota-bile acid-brain interactions, supporting a role for BAs metabolism in neuropsychiatric regulation.},
}

@article {pmid42687165,
year = {2026},
author = {Wang, Y and Wang, L and Cai, Z and Yu, L and Guo, Y and Zhang, L and Zhu, M and Liu, Z and Zhao, Y and Liu, L and Cao, A},
title = {Comparison of clinical efficacy and gut microbiota characteristics in children with ASD treated with fecal microbiota transplantation and ketogenic diet.},
journal = {BMC psychiatry},
volume = {26},
number = {1},
pages = {},
pmid = {42687165},
issn = {1471-244X},
mesh = {Humans ; *Diet, Ketogenic ; *Fecal Microbiota Transplantation ; Female ; Male ; *Gastrointestinal Microbiome ; *Autism Spectrum Disorder/therapy/microbiology/diet therapy ; Child ; Child, Preschool ; Treatment Outcome ; },
abstract = {OBJECTIVE: Autism Spectrum Disorder (ASD) is a neurodevelopmental disorder characterized by impairments in social communication and interaction, along with restricted, repetitive patterns of behavior. It is often accompanied by gastrointestinal dysfunction and gut microbiota dysbiosis. Fecal Microbiota Transplantation (FMT) and the Ketogenic Diet (KD) are interventions targeting the gut microbiota for ASD.

METHODS: 30 participants were diagnosed with ASD according to DSM-5 and ADOS-2. ASD core symptoms were evaluated with CARS and ABC. Gut microbiota composition was analyzed by shotgun metagenomic sequencing.

RESULTS: Both groups demonstrated significant improvements in core symptoms. In the FMT group, the mean CARS score significantly decreased from 34.87 to 33.53 (p < 0.01); in the KD group, it declined from 35.13 to 33 (p < 0.01). The mean ABC score reduced from 79.93 to 69.33 (p = 0.064) in the FMT group and from 63.07 to 42.73 (p < 0.01) in the KD group. Following the intervention, no statistically significant changes were observed in α-diversity or β-diversity within either group. LEfSe analysis revealed distinct post-intervention microbial signatures: FMT significantly enriched butyrate-producing taxa (Wujia chipingensis, Eubacterium sp. MSJ-33, and Butyrivibrio crossotus), while KD elevated Blautia massiliensis and decreased propionate metabolism -associated taxa (Veillonella sp. S12025-13 and Veillonella nakazawae). KEGG enrichment analysis revealed that KD enriched propionate metabolism (Fold enrichment = 3.747, q = 0.010) and aromatic compound degradation (Fold enrichment = 3.591, q = 0.010).

CONCLUSIONS: Both interventions significantly improved clinical symptoms among children with ASD, potentially through distinct patterns of gut microbiota modulation.

CLINICAL TRIALS NUMBER: NCT06348433 (03/21/2024).},
}

Humans
*Diet, Ketogenic
*Fecal Microbiota Transplantation
Female
Male
*Gastrointestinal Microbiome
*Autism Spectrum Disorder/therapy/microbiology/diet therapy
Child
Child, Preschool
Treatment Outcome