@article {pmid42930732,
year = {2026},
author = {Tanida, K and Degel-Broßmann, N and Robitaille, A and Heim, D and Glatzel, M and Blümke, P and Aepfelbacher, M and Lütgehetmann, M and Christner, M and Grundhoff, A and Fischer, N},
title = {Disseminated Mucor indicus Infection in a Heart Transplant Recipient: Complementary Conventional and Sequencing-Based Diagnostic Approaches.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {12},
number = {10},
pages = {},
pmid = {42930732},
issn = {2309-608X},
support = {SFB 1648/1 (2024) - 512741711//Deutsche Forschungsgemeinschaft/ ; },
abstract = {Background: Mucormycosis is a rapidly progressive and often fatal invasive fungal infection in immunocompromised patients. Diagnosis remains challenging because microscopy and culture have limited sensitivity, while targeted molecular assays may fail to detect uncommon Mucorales species. Case Presentation: We report a fatal case of disseminated Mucor indicus infection with pulmonary and cerebral involvement in a heart transplant recipient receiving immunosuppressive therapy and posaconazole prophylaxis. Initial microscopy of bronchial secretions demonstrated broad pauciseptate hyphae consistent with Mucorales, whereas targeted PCR assays remained negative. Species identification was subsequently achieved by culture, MALDI-TOF mass spectrometry, and internal transcribed spacer (ITS) sequencing. Following neurological deterioration, brain biopsy confirmed cerebral involvement histopathologically, and ITS sequencing detected M. indicus. Comparative DNA- and RNA-based metagenomic sequencing identified Mucorales sequences, although read abundance remained unexpectedly low despite extensive histopathological fungal burden. Nevertheless, independent mapping of metagenomic reads against databases comprising all genomic viral and fungal reference sequences readily identified Mucor indicus as the sole pathogen receiving significant scores. Conclusions: This case illustrates that targeted Mucorales PCR may fail to detect an uncommon species despite evidence of invasive fungal infection. Microscopy, culture, histopathology, ITS sequencing, and comprehensive metagenomic analyses provided complementary evidence for disseminated Mucor indicus infection. Integrated diagnostics combining histopathology, culture, and complementary molecular methods remain essential for accurate diagnosis of invasive mucormycosis.},
}

@article {pmid42930741,
year = {2026},
author = {Wang, H and Che, Y and Liu, H and Yu, X and Liu, B and Shu, F and Zhou, J and Wu, M},
title = {Arbuscular Mycorrhizal Fungi Inoculation Promotes Growth and Alleviates Fusarium tricinctum-Induced Growth Inhibition in Quercus variabilis Seedlings.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {12},
number = {10},
pages = {},
pmid = {42930741},
issn = {2309-608X},
support = {No. 42430702//National Natural Science Foundation of China/ ; },
abstract = {Quercus variabilis is a key species for reforestation in East Asia, yet the mechanisms by which arbuscular mycorrhizal fungi (AMF) influence seedling growth and responses to soil-borne fungal challenge remain incompletely understood. This study combined physiological and metagenomic approaches to address this gap. Among seven rhizosphere fungal isolates, Fusarium tricinctum (F15) exerted the strongest growth-inhibitory effect on Q. variabilis seedlings and was therefore selected for subsequent experiments. Inoculation with the AMF Rhizophagus intraradices significantly promoted seedling growth (p < 0.05), increasing root length by 4.94% relative to the uninoculated control and increasing ground diameter and aboveground fresh weight by 28.57% and 117.07%, respectively, relative to F15-treated seedlings. AMF inoculation also significantly altered substrate nutrient status (p < 0.05), particularly nitrogen, phosphorus, and potassium, and enhanced the activity of antioxidant enzymes, including peroxidase and catalase (p < 0.05). Metagenomic analysis revealed that AMF significantly reshaped rhizosphere microbial community composition and bacterial α-diversity (p < 0.05), enriching beneficial taxa such as Mesorhizobium. Functional profiling showed differences in predicted microbial functional profiles between AMF-inoculated and F15-treated groups. Together, these results indicate that AMF enhances seedling growth and mitigates the negative effects associated with F15 challenge, potentially through altered substrate nutrient dynamics, enhanced antioxidant capacity, and modulation of the rhizosphere microbial community.},
}

@article {pmid42931080,
year = {2026},
author = {Hudu, SA and Morad, EA and Alhazimi, GM and Othman, RQA and Elboraei, YAE and Jimoh, AO},
title = {Hidden Microbiome of Mining Environments: Implications for Occupational Health, Bioaerosol Exposure, and Antimicrobial Resistance.},
journal = {Journal of xenobiotics},
volume = {16},
number = {6},
pages = {},
pmid = {42931080},
issn = {2039-4713},
support = {NBU-CRP-2026-3770.//Northern Border University/ ; },
abstract = {Mining environments are extreme subsurface ecosystems characterized by elevated concentrations of metals and minerals, limited light, and high particulate loads. Occupational health research in mining has traditionally emphasized physical and chemical hazards, whereas biological exposures remain less well-characterized. This narrative review synthesizes evidence on mining-associated microbial communities, bioaerosols, occupational exposure, respiratory health, and antimicrobial resistance (AMR). The literature search covered PubMed/MEDLINE, Scopus, and Web of Science from database inception through August 2026. Evidence from coal, uranium, metal mining, acid mine drainage, and mine dust environments indicates that geochemical conditions and mining activities shape microbial communities. Drilling, blasting, excavation, and ore transport can aerosolize microbial cells, spores, and dust-associated microbial components, creating plausible inhalation pathways. Metal-rich environments may also favor persistence and co-selection of metal- and antibiotic-resistance determinants within environmental microbial communities. Metagenomic sequencing and environmental DNA approaches have expanded detection of microbial diversity, functional genes, and environmental resistomes. However, environmental detection does not establish microbial viability, effective worker exposure, transmission, or disease causation. Future research should integrate standardized environmental and personal microbial exposure measurements with respirable dust and chemical monitoring, longitudinal occupational epidemiology, and functional validation of resistance determinants to determine the actual occupational-health significance of mining-associated microbiomes.},
}

@article {pmid42931176,
year = {2026},
author = {Bommineni, V and Edison, LK and Kariyawasam, S},
title = {Current Status and Future Trends in Campylobacter Detection and Quantification Across the Food Production Continuum.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {10},
pages = {},
pmid = {42931176},
issn = {2076-0817},
support = {//University of Florida/ ; },
mesh = {*Food Microbiology/methods ; Animals ; *Campylobacter Infections/microbiology/diagnosis ; *Campylobacter/isolation & purification/genetics ; Humans ; Foodborne Diseases/microbiology ; Campylobacter jejuni/isolation & purification/genetics ; Poultry/microbiology ; },
abstract = {Campylobacter spp., particularly Campylobacter jejuni and Campylobacter coli, remain the leading bacterial causes of foodborne gastroenteritis worldwide, with poultry serving as the dominant reservoir and additional transmission routes involving livestock, raw milk, water, fresh produce, and food-processing environments. Accurate detection and quantification are essential for risk assessment, process hygiene monitoring, outbreak investigation, and One Health surveillance; however, reliable measurement is complicated by the organism's fastidious microaerophilic growth requirements, stress sensitivity, low or uneven distribution in complex matrices, and ability to enter viable but non-culturable (VBNC) states. This review examines current and emerging approaches for Campylobacter detection and quantification across the food production continuum, including pre-harvest, harvest and processing, post-harvest, and retail, as well as consumer-level settings. Conventional culture, colony-count enumeration, most probable number (MPN) methods, and immunological assays are compared with molecular approaches, including polymerase chain reaction (PCR), qPCR, digital PCR, viability PCR, whole-genome sequencing, metagenomics, biosensors, microfluidics, and artificial intelligence-assisted surveillance. Regulatory and standardization frameworks, including the International Organization of Standards (ISO), Food and Drug Administration (FDA), United States Department of Agriculture-Food Safety and Inspection Service (USDA-FSIS), and European Union (EU) process hygiene criteria are discussed, together with One Health surveillance systems. Overall, future Campylobacter monitoring will require integrated, matrix-specific strategies that combine standardized culture-based enumeration, viability-informed molecular quantification, genomic source attribution, and harmonized metadata to support more rapid, accurate, and risk-based food-safety decision-making.},
}

*Food Microbiology/methods
Animals
*Campylobacter Infections/microbiology/diagnosis
*Campylobacter/isolation & purification/genetics
Humans
Foodborne Diseases/microbiology
Campylobacter jejuni/isolation & purification/genetics
Poultry/microbiology

@article {pmid42931196,
year = {2026},
author = {Chen, J and Zou, Q and Pan, B and Zhang, Y},
title = {Genomic Surveillance of Respiratory Pathogens: From Molecular Detection to Precision Infection Control.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {10},
pages = {},
pmid = {42931196},
issn = {2076-0817},
support = {32270528//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Respiratory Tract Infections/diagnosis/prevention & control/microbiology/epidemiology ; *Genomics/methods ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing ; Molecular Diagnostic Techniques/methods ; Artificial Intelligence ; },
abstract = {Respiratory pathogens remain a major global public health concern due to factors including their genetic diversity, dynamic transmission patterns, and increasing antimicrobial resistance. Conventional molecular diagnostics, particularly polymerase chain reaction (PCR)-based assays, remain essential for rapid and scalable pathogen detection but provide limited information on pathogen evolution, transmission, and resistance mechanisms. Advances in whole-genome sequencing (WGS), targeted sequencing, and metagenomic next-generation sequencing (mNGS) have expanded respiratory pathogen surveillance from targeted detection toward higher-resolution genomic characterization. However, no single technology can adequately address all surveillance objectives. Instead, molecular diagnostics, genomic sequencing, epidemiological investigation, and clinical assessment provide complementary information that can be integrated according to the pathogen, clinical context, and specific public health question. This review examines the evolution of respiratory pathogen surveillance and emphasizes an integrated framework in which different technologies are selected and combined to support pathogen characterization, transmission investigation, antimicrobial resistance surveillance, and preventive decision-making. We further discuss emerging applications of artificial intelligence (AI) for integrating genomic, epidemiological, and clinical data, with potential roles in genomic interpretation, early risk assessment, and precision infection control. Although AI-enhanced surveillance remains largely at the research and validation stage, advances in data integration, model development, and computational infrastructure may enable more predictive and actionable surveillance systems. Overall, the future of respiratory pathogen surveillance will depend not simply on adopting more advanced technologies, but on integrating complementary detection and analytical approaches to transform pathogen detection into actionable evidence for public health decision-making.},
}

Humans
*Respiratory Tract Infections/diagnosis/prevention & control/microbiology/epidemiology
*Genomics/methods
Metagenomics/methods
High-Throughput Nucleotide Sequencing
Molecular Diagnostic Techniques/methods
Artificial Intelligence

@article {pmid42931227,
year = {2026},
author = {Liu, Q and Jiang, Y},
title = {Diagnosis of Extrapulmonary Tuberculosis at the Interface of Pathogen Detection and Host Response: Molecular, Microbiological, and Histopathological Advances.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {10},
pages = {},
pmid = {42931227},
issn = {2076-0817},
support = {2025SWGKY391//the Preventive Medicine Association of Hubei Province/ ; WF2025Y08//Wuhan Pulmonary Hospital/ ; },
mesh = {Humans ; *Tuberculosis, Extrapulmonary/diagnosis ; *Mycobacterium tuberculosis/genetics/isolation & purification ; Molecular Diagnostic Techniques/methods ; High-Throughput Nucleotide Sequencing ; Biomarkers ; *Host-Pathogen Interactions ; },
abstract = {Extrapulmonary tuberculosis (EPTB) accounts for approximately 16% of notified tuberculosis (TB) cases worldwide and disproportionately affects children and immunocompromised populations. Paucibacillary disease, anatomically diverse sites, and nonspecific presentations make EPTB one of the most persistent diagnostic challenges in TB control. This review integrates microbiological, molecular, sequencing-based, and histopathological approaches to EPTB diagnosis within the context of site-specific immunopathology, including granuloma biology and the microenvironment of caseous necrosis. Comparative evidence is synthesized across osteoarticular, lymph node, pleural, central nervous system, and disseminated EPTB, focusing on Xpert MTB/RIF and Ultra, targeted and metagenomic next-generation sequencing (mNGS), and emerging host-response biomarkers and AI-assisted histopathology. Pragmatic, tiered diagnostic algorithms are proposed for resource-limited settings, where most EPTB occurs, and unresolved gaps in current international guidance are identified. Aligning diagnostic modality choice with anatomical site, specimen quality, pathological subtype, and laboratory capacity can shorten the time to EPTB diagnosis and inform host-directed diagnostic strategies.},
}

Humans
*Tuberculosis, Extrapulmonary/diagnosis
*Mycobacterium tuberculosis/genetics/isolation & purification
Molecular Diagnostic Techniques/methods
High-Throughput Nucleotide Sequencing
Biomarkers
*Host-Pathogen Interactions

@article {pmid42931636,
year = {2026},
author = {Wang, Y and Yu, W and Kanda, K and Iwata, H and Guo, J},
title = {In Ovo Exposure to Phenanthrene Promotes Antimicrobial Resistance Genes and Hemolysin Virulence Factor in Guts of Chicken Embryos.},
journal = {Toxics},
volume = {14},
number = {10},
pages = {},
pmid = {42931636},
issn = {2305-6304},
support = {42571089//National Natural Science Foundation of China/ ; 2026JC-YXQN-119//Natural Science Basic Research Program of Shaanxi/ ; },
abstract = {Antimicrobial resistance genes (ARGs) are increasingly recognized as emerging environmental contaminants that threaten ecological integrity and animal health. Polycyclic aromatic hydrocarbons (PAHs) are widespread pollutants that accumulate in the environment and have been detected in wild bird eggs. Although PAHs have been shown to accelerate ARG dissemination in environmental matrices, their influence on ARG dynamics in birds is unclear. Therefore, it is hypothesized that exposure to elevated levels of PAHs promotes the propagation and enrichment of ARGs in the avian gut. In this study, chicken embryos at Hamburger-Hamilton Stage 1 (HHS 1) were exposed in ovo to phenanthrene (PHE; 1, 100, and 400 nmol/g egg), and the toxic effects were evaluated. High PHE exposure significantly reduced embryonic tarsus length by 14.81% and increased the liver somatic index (LSI) by 26.97%. Functional annotation based on the Virulence Factor Database (VFDB) showed that the relative abundance of hemolysin, a microbial virulence factor associated with gastrointestinal microorganisms, was significantly elevated in the high-PHE group. In a Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, genes involved in nucleotide excision repair (NER) and basal transcription factor (BTF) pathways showed significantly lower relative abundance following high-dose exposure. Additionally, ARGs related to polymyxin and pleuromutilin resistance were significantly enriched in the high-exposure group. Partial least squares path modeling (PLS-PM) indicated that ARG enrichment was jointly shaped by multiple factors. PHE may be directly associated with ARG proliferation or may act indirectly through mobile genetic elements (MGEs), whereas bacterial community abundance might be linked to the potential dissemination of ARGs given its significant positive association with MGEs. Collectively, these findings provide correlative evidence that PHE exposure is associated with increased ARG abundance in avian organisms and highlight the need for an integrated evaluation of PAH-associated hazards to avian health.},
}

@article {pmid42931645,
year = {2026},
author = {Song, F and Bao, S and Chen, C and Xu, M},
title = {Viruses in Soil: A Review of Methods, Distribution and Ecological Functions.},
journal = {Toxics},
volume = {14},
number = {10},
pages = {},
pmid = {42931645},
issn = {2305-6304},
support = {I2023004//Shanghai Science and Technology Development Foundation/ ; },
abstract = {Viruses are the most abundant and active biological organisms in soil ecosystems. However, their spatial distribution and ecological functions remain inadequately addressed owing to a lack of systematic analysis and the complexity of the soil matrix. Therefore, this review systematically summarizes current knowledge of soil viruses through an examination of research methods, spatiotemporal distribution, and ecological functions. Our review indicates that current progress of soil viruses remains constrained by technological inconsistencies and difficulties in viral isolation techniques within complex soil matrices. Therefore, viral distribution analyses are largely limited to small-scale sections of agricultural land, forest, pastureland, and grassland. There is insufficient exploration of viral distribution across large-scale geographic areas and desert soil environments, as well as RNA virus diversity. The characteristics of soil viral communities are primarily influenced by environmental factors such as temperature, moisture, and pH. Overall, we conclude that soil viruses are pivotal drivers of microbial community dynamics and biogeochemical cycling, although our comprehensive understanding is severely bottlenecked by complex soil matrices and inconsistent viral isolation methodologies. Future research should focus on methodological innovations such as long-read sequencing and single-cell approaches to decipher virus-host interaction networks and their ecological roles across large-scale and extreme environments.},
}

@article {pmid42931687,
year = {2026},
author = {Huang, X and Li, Q and Feng, M and Liu, C and Shi, H and Wang, D},
title = {Microbial-Clay Mineral Interactions: Mechanisms and Applications in Environmental Remediation.},
journal = {Toxics},
volume = {14},
number = {10},
pages = {},
pmid = {42931687},
issn = {2305-6304},
support = {2026GXNSFBA00640164//Guangxi Science and Technology Department/ ; Guike AD25069074//Guangxi Science and Technology Department/ ; 42367061//National Natural Science Foundation of China/ ; //Bagui Youth Top Talent Program of Guangxi/ ; },
abstract = {Microbial-clay mineral interactions play a pivotal role in environmental remediation, biogeochemical cycling, and the long-term evolution of the Earth's systems. This review critically synthesizes the fundamental mechanisms, reactive pathways, and environmental implications of microbial-clay mineral interactions. Clay minerals, owing to their large specific surface area, high cation exchange capacity, and tunable surface charge, are shown to sustain microbial metabolism by offering physical shelter and serving as sources of essential nutrients. Concurrently, microorganisms mediate the dissolution, structural alteration, and neoformation of clay phases via proton production, electron transfer reactions, and genetic regulatory networks, thereby establishing a dynamic synergistic relationship. In environmental remediation, clay-microorganism complexes have been demonstrated to promote heavy metal stabilization. They concurrently expedite the breakdown of organic contaminants, including polycyclic aromatic hydrocarbons (PAHs). Nevertheless, major knowledge gaps persist, especially concerning the multiscale complexity of interfacial behaviors and still-elusive molecular-scale interaction mechanisms. Finally, several priority directions for the future are proposed, including the integration of metagenomics and molecular modeling, the design of biomarker-based monitoring tools, and the scalable translation of bench-scale discoveries and laboratory insights into field-scale remediation technologies. Collectively, this work advances fundamental knowledge of key microbe-mineral biogeochemical processes and provides a scientific basis for the development of sustainable, nature-based environmental remediation strategies.},
}

@article {pmid42933050,
year = {2026},
author = {He, X and Zhou, J and Long, S and Liu, H and Zou, G and Song, G},
title = {Nocardia terpenica bacteremia confirmed by blood culture in a patient with granulocytopenia and Aspergillus fumigatus coinfection: a first case report.},
journal = {Diagnostic microbiology and infectious disease},
volume = {117},
number = {1},
pages = {117708},
doi = {10.1016/j.diagmicrobio.2026.117708},
pmid = {42933050},
issn = {1879-0070},
abstract = {BACKGROUND: Nocardia terpenica is a rare environmental actinomycete without prior report of human bloodstream infection. In immunocompromised hosts, it often causes mixed infections, complicating diagnosis and treatment.

CASE PRESENTATION: We report the first bacteremia case of N. terpenica in an adult with severe granulocytopenia after B-ALL induction chemotherapy. Blood culture (positive at 5.9 days) revealed branched Gram-positive rods; species was confirmed by MALDI‑TOF and whole‑genome sequencing (WGS). Plasma mNGS also detected Aspergillus fumigatus, and chest CT showed halo/air‑crescent signs, establishing concurrent invasive pulmonary aspergillosis. The patient cleared infection after combined antibiotics (trimethoprim‑sulfamethoxazole, voriconazole, imipenem/cilastatin, vancomycin) and completed subsequent chemotherapy.

CONCLUSION: We report the first case of N. terpenica bacteremia, highlighting that this species can cause bloodstream infection in severely immunocompromised hosts. Prolonged culture incubation and molecular diagnostics (WGS and mNGS) are essential for timely diagnosis and optimal management.},
}

@article {pmid42933349,
year = {2026},
author = {Qin, H and Zhang, S and Xia, F and Tan, Q and Wan, H and Cai, Y},
title = {Seasonally shifting methane-control regimes across urban rivers and urban wetland rivers in the GBA, China, revealed by environmental, isotopic, and microbial evidence.},
journal = {Journal of environmental management},
volume = {419},
number = {},
pages = {131239},
doi = {10.1016/j.jenvman.2026.131239},
pmid = {42933349},
issn = {1095-8630},
abstract = {Urban rivers (UR) and urban wetland rivers (WR) are increasingly recognized as CH4 sources, yet the processes underlying differences between these aquatic habitats remain poorly resolved. We investigated excess CH4 concentration (ΔCH4), estimated diffusive flux, environmental conditions, stable carbon isotopes, and sediment microbial functional potential in the Guangdong-Hong Kong-Macao Greater Bay Area (GBA), China. CH4 dynamics exhibited a clear seasonal shift between contrasting spatial patterns. UR showed an amplified CH4 state during the first two seasons, the wetland outlet (WO) in wet season 1 and than both WR and WO in dry season 1. In UR, ΔCH4 decreased with dissolved oxygen (β = -0.194, p = 0.020) and increased with total nitrogen (β = 0.272, p = 0.003), indicating strong nutrient-redox control on CH4 accumulation. Stable-isotope signatures overlapped broadly among potential production and oxidation processes, while WR displayed more [13]C-depleted CH4 than UR during wet season 1 despite lower ΔCH4, indicating that source signatures did not translate directly into net CH4 accumulation. Consistently, mcr and CO2-reducing methanogenesis genes and methanogenic taxa were relatively enriched in early UR seasons, whereas pmo-family genes and methane-oxidizing taxa were distributed more broadly across WR and WO. Together, these complementary lines of evidence reveal a seasonally reversible transition from nutrient-redox-driven CH4 amplification in urban rivers to more complex wetland-associated regulation involving carbon supply, redox heterogeneity, and methane-oxidation potential.},
}

@article {pmid42933698,
year = {2026},
author = {Qiao, Z and Wei, Z and Yuan, M and Wei, L and Hu, M and Song, K and Bi, Z and Qin, X and Yin, X},
title = {Start‑up and functional performance assessment of electron-shuttling-driven microalgal-anammox process.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {136132},
doi = {10.1016/j.biortech.2026.136132},
pmid = {42933698},
issn = {1873-2976},
abstract = {The anaerobic ammonium oxidation (anammox) process has received extensive attention because of its low energy consumption and high nitrogen removal efficiency. Nevertheless, its long start-up period limits practical application. In this study, a microalgae-bacteria symbiotic system (ABSS) based on Chlorella vulgaris (C. vulgaris) was established to investigate its effects on anammox start-up and nitrogen and phosphorus removal. The introduction of C. vulgaris shortened the start-up time from 68 to 46 days, corresponding to a 32 % reduction. After 210 days of operation, the nitrogen removal rate (NRR) and phosphorus removal rate (PRR) in the microalgae-bacteria symbiotic reactor (RAM) were 21 % and 25 % higher than those in the control reactor (RA), respectively. The concentration of extracellular polymeric substances (EPS) derived from C. vulgaris, as quantified via total organic carbon measurement, was 297.73 ± 8.55 mg/L. Spectroscopic analyses suggested the presence of humic-like substances and quinone-related structures in the EPS, indicating a potential role in electron transfer. At 100 mg/L, EPS increased hydrazine dehydrogenase (HDH) activity by 49 % relative to the control group. After CoQ extraction, EPS restored HDH activity more effectively than exogenous coenzyme Q (CoQ). Metagenomic analysis showed higher abundances of genes associated with photosynthesis, carbon fixation, and nitrogen metabolism. These findings imply that EPS-mediated electron transfer and strengthened HDH activity may have contributed to the establishment of anammox activity and the shortened start-up period. Overall, this study highlights microalgal integration as a potential strategy for accelerating anammox startup and improving simultaneous nitrogen and phosphorus removal.},
}

@article {pmid42934169,
year = {2026},
author = {Chasapi, IN and Aplakidou, E and Chasapi, MN and Lamari, E and Galaras, A and Diplari, S and Iliopoulos, I and Emiris, IZ and Georgakopoulos-Soares, I and Patalano, S and Stravopodis, DJ and Karatzas, E and Baltoumas, FA and Kyrpides, NC and Pavlopoulos, GA},
title = {ArthroVerse: mapping protein family diversity across arthropod-associated microbiomes.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkag1067},
pmid = {42934169},
issn = {1362-4962},
support = {23592-EMISSION//Hellenic Foundation for Research and Innovation/ ; 28787-VIROMINE//Hellenic Foundation for Research and Innovation/ ; //Penn State College of Medicine and the University of Texas at Austin/ ; //US Department of Energy Joint Genome Institute/ ; DE-AC02-05CH11231//US Department of Energy Office of Science user facilities/ ; 7832-YGIAMEL//Postdoctoral Researcher/ ; //HEAL-Link/ ; },
abstract = {Metagenomic studies of arthropod-associated microbiomes have generated vast amounts of sequence data, yet the functional and structural organization of these proteins remains largely unexplored. Here, we present ArthroVerse, the first comprehensive database of protein families derived from arthropod-associated metagenomes. Non-redundant protein families were generated after rigorous filtering, deduplication, and clustering. The protein families were further annotated with microbial taxonomy, host associations, protein structural information, and carbohydrate-active enzymes predictions. The resulting dataset integrates both metagenomic and reference genome-derived proteins, enabling systematic exploration of functional diversity, evolutionary relationships, and host-microbe interactions in insect microbiomes. ArthroVerse provides a valuable resource for the study of microbial ecology and arthropod physiology, offering unprecedented insight into the protein landscape of insect-associated microbial communities. ArthroVerse is publicly accessible at https://envofams.org/arthroverse/.},
}

@article {pmid42934259,
year = {2026},
author = {Serra Moncadas, L and Ruscheweyh, HJ and Woodhouse, J and Salcher, MM and Okazaki, Y and Ngugi, DK and Pester, M and Posch, T and Ghai, R and Grossart, HP and Sunagawa, S and Pernthaler, J and Andrei, AS},
title = {A global mitochondrial genomic atlas illuminates freshwater microeukaryote diversity.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42934259},
issn = {2041-1723},
support = {PZ00P3_193240//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; PZ00P3_193240//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 31003A_182489//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; GR1540/51_1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; GR1540/51_1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 20-12496X//Grantová Agentura České Republiky (Grant Agency of the Czech Republic)/ ; 20-12496X//Grantová Agentura České Republiky (Grant Agency of the Czech Republic)/ ; },
mesh = {Phylogeny ; *Genome, Mitochondrial/genetics ; *Fresh Water/microbiology ; *Biodiversity ; *Eukaryota/genetics/classification ; Metagenome ; },
abstract = {Environmental genomics has transformed our view of the microbial world, yet progress remains largely prokaryote-centric. Among microbial eukaryotes, inconsistent marker choice and limited species-level resolution blunt diversity estimates and hinder cross-study synthesis. Consequently, regional‑to‑global gradients in richness, turnover, and phylogenetic structure remain poorly resolved. Here we establish a global mitogenome-based framework that converts shotgun metagenomes into species‑resolved, phylogeny‑anchored inventories. From 3,400 metagenomes spanning 362 lakes on seven continents, we reconstruct ~20,000 mitochondrial metagenome-assembled genomes (mitoMAGs), densely populating previously sparse branches of the eukaryotic tree-notably SAR (Stramenopiles-Alveolata-Rhizaria), Cryptophyceae, and Haptista. An empirically calibrated 98.1% mitoMAG‑identity threshold delineates species and tethers community profiles to an evolutionary backbone. On this backbone, coverage‑standardized inventories recover canonical ecological patterns: mesotrophic richness peaks, surface-layer expansion of phylogenetic breadth, and spring maxima with the strongest surface-deep coupling at vernal mixing; supporting the framework. Treating mitoMAGs as primer‑free barcodes yields a single, species‑level, phylogeny‑aware currency that renders richness, evenness, and phylogenetic breadth directly comparable across datasets, depths, seasons, and regions. By placing microbial eukaryotes on an analytical footing comparable to prokaryotes, the resulting atlas brings their diversity into reach and lays the groundwork for future high-throughput, species-aware monitoring and ecological forecasting.},
}

Phylogeny
*Genome, Mitochondrial/genetics
*Fresh Water/microbiology
*Biodiversity
*Eukaryota/genetics/classification
Metagenome

@article {pmid42934712,
year = {2026},
author = {Gu, C and Zhang, R and Rao, YZ and Zhang, X and Zhou, Z and Liu, Y and Dong, X and Wang, L and Wang, Y and Hua, ZS and Krupovic, M and Li, M},
title = {Expansion of the Asgard archaeal virome and defensome provides insights into virus-host interactions.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42934712},
issn = {2049-2618},
mesh = {*Archaeal Viruses/genetics/classification/physiology/isolation & purification ; *Archaea/virology/genetics/classification ; *Virome/genetics ; Metagenomics/methods ; Genome, Viral ; Phylogeny ; *Host Microbial Interactions ; Host-Pathogen Interactions ; },
abstract = {BACKGROUND: Asgard archaea, broadly considered as a group of archaea that exhibit the closest evolutionary relationship with eukaryotes, encode diverse defense systems and are infected by distinct viruses. However, the diversity of Asgard archaeal viruses and their interactions with the hosts remain poorly explored.

RESULTS: Here, using CRISPR spacer-protospacer matching, we predict 23 viruses associated with Asgard archaea from various habitats. Apart from clusters with known viruses, we report three previously undescribed groups of Asgard viruses with predicted head-tailed virions of the realm Duplodnaviria and filamentous virions characteristic of the archaea-specific realm Adnaviria. Mapping of metagenomic reads to viral and host genomes suggested that most Asgard viruses display relatively low virus-to-host ratios, typically below 10. In addition, we considerably expanded the known defensome of Asgard archaea, among others, detecting putative PARIS and Prometheus defense systems. Finally, the diversity of anti-defense proteins and putative archaeal type IV pilins encoded by some Asgard viruses provide additional insights into the interactions between Asgard archaea and their viruses.

CONCLUSIONS: Overall, this work sheds new light on the Asgard archaeal virome and defensome, and virus-host interactions. Video Abstract.},
}

*Archaeal Viruses/genetics/classification/physiology/isolation & purification
*Archaea/virology/genetics/classification
*Virome/genetics
Metagenomics/methods
Genome, Viral
Phylogeny
*Host Microbial Interactions
Host-Pathogen Interactions

@article {pmid42934726,
year = {2026},
author = {Auguste, M and Bosi, E and Saad, J and Oliveri, C and Doni, L and Marchese, A and Travers, MA and Toulza, E and Boulo, V and Courtay, G and Petton, B and Koechlin, H and Montagnani, C and Di Cesare, A and Corno, G and Andree, KB and Gairin, I and Furones, D and Broquard, C and Wegner, KM and Destoumieux-Garzón, D and Vezzulli, L},
title = {The resistome of European coastal environments revealed by high-resolution targeted metagenomics in oysters.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42934726},
issn = {2049-2618},
mesh = {Animals ; *Metagenomics/methods ; Europe ; *Bacteria/genetics/classification/drug effects/isolation & purification ; *Ostreidae/microbiology ; Metagenome ; Anti-Bacterial Agents/pharmacology ; Microbiota ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Antimicrobial resistance is a major global health threat, and the environment is increasingly recognised as a key reservoir of antibiotic resistance genes (ARGs). In marine ecosystems, filter-feeding organisms such as oysters are sentinel species that reflect the microbiological diversity of their environment. Here, we investigated the ARG content of the Pacific oyster Magallana gigas across four European coastal sites, contrasting anthropogenically impacted aquaculture sites (Bay of Brest, Ebro Delta, Thau lagoon) with natural oyster reefs (Sylt island). ARGs sequencing was enriched using a targeted probe-and-capture metagenomic approach employing 37,826 RNA baits covering over 2000 ARG sequences. Moreover, a novel bioinformatic pipeline ARGifier was specifically designed for sensitive, high-resolution detection and classification of ARGs in metagenomic samples dominated by host DNA.

RESULTS: This strategy was able to overcome limitations of cultivation-based methods and whole metagenomic sequencing, enabling the detection of more than 33,000 ARG sequences in the oyster resistome spanning over 450 genes distributed over 23 resistance classes. Reads assigned to ARGs represented 0.23% of all raw reads and 25.02% of host-depleted reads. Accordingly, comparison of targeted metagenomics and pool-seq analysis of cultured isolates (culturomics) in specific pathogen-free oysters revealed that metagenomics captured dominant, community-wide resistance determinants, whereas culturomics recovered a broader diversity of ARGs due to their presence in genomes of cultivable strains. The oyster resistome across the four farming sites was dominated by multidrug efflux systems associated with intrinsic and housekeeping-related mechanisms, suggesting an environmentally shaped resistance profile. Clinically relevant ARGs, including extended-spectrum Beta-Lactamase, carbapenem, colistin, and vancomycin resistance genes, were detected in low abundance at all sites, with higher enrichment in anthropogenically impacted areas. In addition, several ARGs were associated with plasmids, indicating mobilization potential. Taxonomic analysis revealed that a limited subset of bacteria, particularly Betaproteobacteria and Actinomycetes, carried a disproportionately high number of ARGs despite their low relative abundance in the oyster microbiome.

CONCLUSIONS: Overall, this study delivers a comprehensive inventory of ecologically and clinically relevant ARGs in European coastal environments, positioning farmed and wild oysters as sentinel organisms for monitoring antimicrobial resistance in coastal waters. Our findings highlight the circulation of ARGs within coastal marine ecosystems, which may act as reservoirs and potential sources of mobilisable antimicrobial resistance. Video Abstract.},
}

Animals
*Metagenomics/methods
Europe
*Bacteria/genetics/classification/drug effects/isolation & purification
*Ostreidae/microbiology
Metagenome
Anti-Bacterial Agents/pharmacology
Microbiota
Sequence Analysis, DNA

@article {pmid42934727,
year = {2026},
author = {Liu, Y and Wu, X and Guo, Y and Mei, W and Gao, R and Wang, F and Chen, C and Wang, L and Hao, Y and Wu, T and Yao, X},
title = {Multi-omics analysis reveals that sleep deprivation exacerbates intestinal barrier injury via the microbiota-dependent taurodeoxycholic acid/group 3 innate lymphoid/IL-22 axis.},
journal = {Journal of translational medicine},
volume = {24},
number = {1},
pages = {},
pmid = {42934727},
issn = {1479-5876},
support = {82403215//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Sleep Deprivation/microbiology/immunology/pathology ; Interleukin-22 ; *Interleukins/metabolism ; *Multiomics ; *Intestinal Barrier Function ; *Lymphocytes/metabolism ; *Immunity, Innate ; Mice, Inbred C57BL ; Male ; *Intestines/pathology ; Fecal Microbiota Transplantation ; Mice ; *Gastrointestinal Microbiome ; *Microbiota ; },
abstract = {BACKGROUND: Clinical studies demonstrated a correlation between sleep dysfunction and intestinal diseases. However, the detailed interactions and underlying mechanisms linking sleep disruption to intestinal microenvironment remain poorly understood.

METHODS: We employed the Curling Prevention by Water (CPW) paradigm to establish a mouse model of sleep deprivation (SD) for durations ranging from 0 to 96 h. The dynamic changes in the intestinal microenvironment were systematically profiled using multi-omics approaches, including metagenomic sequencing, untargeted metabolomics and RNA sequencing. The causal role of microbial dysbiosis and the underlying mechanisms were further investigated using germ-free mice, fecal microbiota transplantation (FMT), flow cytometry, and targeted intervention.

RESULTS: The intestinal microenvironment was highly sensitive to SD. Distinct microbial communities and metabolite profiles were observed among brief SD (< 24 h of SD), prolonged SD (24-96 h of SD) and control. Brief SD triggered a self-regulatory response of the gut microbiota, characterized by an increase in certain beneficial bacteria (e.g., Parabacteroides goldsteinii). In contrast, prolonged SD shaped a pro-inflammatory microbial structure, characterized by reduced Akkermansia muciniphila and enriched Pseudomonadota. Multi-omics analysis revealed that SD significantly inhibited microbial bile acid metabolism, particularly taurodeoxycholic acid (TDCA), and impaired intestinal barrier function while suppressing the intestinal immune response to bacteria antigens. Mechanistically, SD exacerbated intestinal barrier damage by inhibiting the TDCA/group 3 innate lymphoid cells (ILC3)/IL-22 axis. Supplementation with TDCA effectively restored ILC3 function, IL-22 production, and barrier integrity in SD mice. Furthermore, FMT from patients with sleep dysfunction significantly disturbed intestinal microenvironment and increased serum cortisol by regulating gut microbiota and inhibiting TDCA/ILC3/IL-22 axis.

CONCLUSION: This study dynamically delineates how SD disrupts intestinal homeostasis by reshaping the gut microbiota and suppressing the TDCA/ILC3/IL-22 axis. These findings provide novel mechanistic insights and identify potential therapeutic targets for sleep dysfunction-associated intestinal complications.},
}

Animals
*Sleep Deprivation/microbiology/immunology/pathology
Interleukin-22
*Interleukins/metabolism
*Multiomics
*Intestinal Barrier Function
*Lymphocytes/metabolism
*Immunity, Innate
Mice, Inbred C57BL
Male
*Intestines/pathology
Fecal Microbiota Transplantation
Mice
*Gastrointestinal Microbiome
*Microbiota

@article {pmid42935434,
year = {2026},
author = {Chen, J and Jiang, YL and Lü, J and Ma, Y and Yang, X and Shen, C and Guo, FL and Yang, ZL},
title = {[Effects of Different Treatment Methods for Printing and Dyeing Sulfate Wastewater on Microbial Structure and Sulfur Cycle Functional Genes].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {47},
number = {10},
pages = {7341-7353},
doi = {10.13227/j.hjkx.202510110},
pmid = {42935434},
issn = {0250-3301},
mesh = {*Wastewater/chemistry ; *Sulfur/metabolism ; *Waste Disposal, Fluid/methods ; *Coloring Agents/isolation & purification ; *Sulfates/isolation & purification/metabolism/chemistry ; Industrial Waste ; Bacteria/genetics/metabolism ; Printing ; Wetlands ; Water Pollutants, Chemical ; },
abstract = {The advantages of Xinjiang raw cotton resources have gradually transformed into manufacturing advantages dominated by textile printing and dyeing， while the high water consumption of the textile printing and dyeing industry conflicts sharply with the water shortage in Xinjiang. The time for comprehensive utilization after the treatment of printing and dyeing wastewater in Xinjiang meets the standards is relatively short， and there is a lack of research support on whether the discharge and utilization will have an impact on the desert ecosystem. This study takes a printing and dyeing wastewater treatment system in an industrial park in Alar City， Xinjiang as the research object and comprehensively analyzes the characteristics and related driving factors of physical and chemical factors of sediment， microbial community， functional structure， sulfur cycle functional genes in drainage outlet （PSK）， constructed wetland （RGSD）， and oxidation pond （YHT）. After the printing and dyeing wastewater was treated by RGSD and YHT， the Na[+]， Cl[-]， SO4[2-]， and electrical conductivity in the water increased significantly. PSK had higher contents of TN， SOC， SO4[2-]， and TDS in sediment， and RGSD had higher contents of Ca[2+]， SO4[2-]， TDS， and TP in sediment， while TN and SOC decreased significantly. YHT had higher contents of Na[+] and Cl[-]， while Ca[2+] and SO4[2-] decreased significantly. The microbial community in sediment was dominated by bacteria， and its α and beta diversity varied significantly among different treatment units， with RGSD having the lowest microbial diversity. Sulfur cycle functional genes analyses showed that assimilatory sulfate reduction was the dominant pathway， dissimilatory sulfate reduction genes were the highest in RGSD， and sulfur oxidation genes were the most abundant at PSK. Structural equation and Mantel analysis indicated that nutrients in sediment promoted microbial diversity and assimilatory sulfate reduction process， while ion concentration had an inhibitory effect on them， and TP， TDS， and SO4[2-] were the key factors driving the variation of microbial community structure. Different ions had different effects on the sulfur metabolic pathway. TN and SOC inhibited dissimilatory sulfate reduction while promoting assimilatory sulfate reduction and sulfur oxidation. Cl[-]， Na[+]， K[+]， and Mg[2+] ions inhibited sulfur oxidation and assimilatory sulfate reduction processes. This study reveals the microbial sulfur metabolism synergy mechanism in different treatment methods of sulfate printing and dyeing wastewater from the perspectives of microbial ecology and functional genes， providing a theoretical basis for the effluent comprehensive utilization of printing and dyeing wastewater treatment and prevention and control of black and odorous water pollution in the Xinjiang Region in the future.},
}

*Wastewater/chemistry
*Sulfur/metabolism
*Waste Disposal, Fluid/methods
*Coloring Agents/isolation & purification
*Sulfates/isolation & purification/metabolism/chemistry
Industrial Waste
Bacteria/genetics/metabolism
Printing
Wetlands
Water Pollutants, Chemical

@article {pmid42935761,
year = {2026},
author = {Whitman, BT and Karimianghadim, R and Auch, B and Liachko, I and , and Monaghan, TM and Pakpour, S and Kao, D},
title = {Metabolic network restoration, not donor microbial engraftment, associates with resolution of recurrent Clostridioides difficile infection.},
journal = {iScience},
volume = {29},
number = {11},
pages = {117907},
pmid = {42935761},
issn = {2589-0042},
abstract = {Fecal microbiota transplantation (FMT) effectively prevents recurrent Clostridioides difficile infection (rCDI). However, the mechanisms underpinning FMT efficacy are incompletely understood. We used proximity-ligation metagenomics, metaproteomics, and metabolomics to profile dynamic changes in rCDI. We analyzed samples collected from the first 7 responders during a clinical trial comparing two donor-based treatments (lyophilized FMT [LFMT] or lyophilized sterile fecal filtrate [LSFF], free of intact microorganisms) to prevent rCDI. LSFF is enriched in Caudoviricetes, lipids, fatty acids, and human and extracellular bacterial proteins compared with LFMT. LFMT recipients had donor microbial engraftment, while LSFF recipients achieved only partial microbial community recovery without donor's contribution. Our multi-omics analyses identified a functional convergence following both treatments, shifting away from oxidative and antibiotic stress survival pathways toward enhanced carbon-nitrogen utilization pathways, suggesting that FMT mechanisms may involve metabolic reprogramming and host-microbial amino acid co-metabolism. Our findings provide important hypothesis-generating insights that warrant further validation.},
}

@article {pmid42935865,
year = {2026},
author = {Abdel Shafi, IR and El Bassiouni, SO and Abdeltawab, MSA},
title = {Living within: endosymbiosis in parasites of medical importance-profits, expenses, and implications for host-parasite interactions.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1956183},
pmid = {42935865},
issn = {2235-2988},
mesh = {*Symbiosis ; Humans ; Animals ; *Host-Parasite Interactions ; *Parasites/microbiology/virology/physiology ; Bacteria ; },
abstract = {Endosymbiosis is a biological relationship, where one organism lives within the body of another. The concept of endosymbiosis was first introduced relevant to the origin and development of organelles in eukaryotes. Later, microorganisms were reported to be associated with different eukaryotes including arthropods, parasitic helminths, and protozoa; subsequently, their role in parasite biology and parasite-human host interactions has been minded. Within this context, filaria-Wolbachia, Leishmania-Leishmania RNA virus (LRV), and Trichomonas-Trichomonas vaginalis virus (TVV) are extensively studied models that demonstrate how endosymbionts can directly drive immunomodulation in human host and worsen the clinical outcome, whereas Acanthamoeba stands out as a reservoir of an array of microorganisms including pathogenic bacteria, and a training hub for bacterial virulence evolution. Despite the progress achieved in understanding these models, the depth of characterization of endosymbionts across parasite taxa is markedly uneven. Disclosing the world of microorganisms living within parasites, especially with the advanced metagenomic analysis, constitutes an emerging field of research of immense scientific significance for parasitology, microbiology, and host-parasite interactions.},
}

*Symbiosis
Humans
Animals
*Host-Parasite Interactions
*Parasites/microbiology/virology/physiology
Bacteria

@article {pmid42936323,
year = {2026},
author = {Li, Y and Fan, M and Hu, Y and Yang, Y and Li, W and Zhang, W and Wang, Y},
title = {Cerebrospinal fluid metagenomic next-generation sequencing for culture-negative anaerobic central nervous system infection involving Prevotella oris: attribution challenges in low-biomass specimens.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1896093},
pmid = {42936323},
issn = {1664-3224},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; *Prevotella/genetics/isolation & purification ; *Bacteroidaceae Infections/diagnosis/cerebrospinal fluid/microbiology ; DNA, Bacterial/genetics ; },
abstract = {Anaerobic central nervous system (CNS) infections are uncommon but diagnostically difficult because fastidious organisms may be suppressed by empirical antimicrobial therapy and conventional cultures may remain negative. Cerebrospinal fluid (CSF) metagenomic next-generation sequencing (mNGS) can recover microbial nucleic acids in this setting, but low microbial biomass creates a central attribution problem: a detected organism may represent active infection, introduced commensal DNA, laboratory background, or bioinformatic misclassification. This narrative Mini Review uses Prevotella oris as a representative oral anaerobe to examine that problem. We synthesize evidence on low-biomass CSF specimen processing and sequencing strategies, including nanopore sequencing, whole-genome amplification, and targeted approaches, alongside contamination control, sequence-level and taxonomic credibility, host-response immunology, neuroimaging and source concordance, antimicrobial timing, and discordant clinical scenarios. We then organize these established principles into an expert-informed two-step pathway that separates technical signal credibility from clinical attribution and explicitly preserves an indeterminate state when evidence conflicts. P. oris is positioned as a useful model of the plausible contaminant paradox rather than as a pathogen with a unique CNS phenotype. We also outline syndrome-based management, source control, and treatment-duration principles. The framework is conceptual and non-validated; its purpose is transparent reasoning and reporting, not diagnostic scoring or probability estimation.},
}

Humans
*High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
*Prevotella/genetics/isolation & purification
*Bacteroidaceae Infections/diagnosis/cerebrospinal fluid/microbiology
DNA, Bacterial/genetics

@article {pmid42937190,
year = {2026},
author = {Quinger, F and Klein, N and Steinhoff-Wagner, J and Camarinha-Silva, A and Rodehutscord, M and Seifert, J},
title = {Field Pea Variants affect Nutrient Digestibility and Gut Microbiome in Pigs.},
journal = {Journal of animal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/jas/skag346},
pmid = {42937190},
issn = {1525-3163},
abstract = {The digestibility of nutrients in different field pea variants in pigs can vary due to characteristics such as anti-nutritional factors. Undigested nutrients can be fermented in the hindgut, and their amount and composition likely affect microbial composition. This study compared a spring field pea variant (SP) with two winter field pea variants (WP1, WP2) with higher trypsin inhibitor activity and a tannic spring forage pea variant (SFP) in terms of nutrient digestibility and effects on the gut microbiome in growing pigs. Four diets containing 40% of one of the four field pea variants were formulated and randomly assigned to 8 ileally cannulated barrows according to a 4 × 4 double Latin square design with the blocking factors animal and period. The experiment consisted of 4 periods, each lasting 11 days. Ileal digesta and feces were collected for 2 days each to determine nutrient digestibility. On the last day of every period, ileal digesta and feces were sampled and analyzed for digestive enzyme activity, metagenomics, metaproteomics, and metabolomics. The data was integrated using DIABLO. The winter field pea variants decreased the prececal digestibility of 16 amino acids (P ≤ 0.032) and increased the activity of carboxypeptidase A (P = 0.002). Pigs fed the SFP showed decreased hindgut disappearance of total dietary fiber (P < 0.001) and concentrations of acetate, propionate, and butyrate in the feces (P ≤ 0.026). More differentially abundant taxa in metagenomic and metaproteomic data were detected in the feces than in ileal digesta among field pea variants. The SFP increased the abundance of host proteins related to innate immune response in ileal digesta and feces (adjusted P ≤ 0.047). Integration of the acquired data layers revealed a negative association of ileal amino acid concentrations with the abundance of Prevotella and proteins related to starch degradation and propionate production in the ileal digesta for winter field pea variants. For SFP, reduced hindgut disappearance of total dietary fiber was associated with a reduction of proteins from Ruminococcus. In conclusion, field pea variants can affect the ileal and fecal microbiome in pigs, potentially due to anti-nutritional factors that either indirectly influence the microbiome by reducing nutrient digestibility or directly affect individual microbial taxa.},
}

@article {pmid42937301,
year = {2026},
author = {Moyo-Heath, B and Chigome, G and Mushamba, R and Onyeaghala, C and Bailey, SF},
title = {Metagenome sequences of unintended bacterial communities from a Pseudomonas fluorescens experimental evolution study.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0085326},
doi = {10.1128/mra.00853-26},
pmid = {42937301},
issn = {2576-098X},
abstract = {We report 16 metagenome sequences from unintended contaminant communities that invaded an evolution experiment initiated with Pseudomonas fluorescens SBW25. Low-diversity bacterial assemblies from center and edge locations across eight populations in contrasting uniform or heterogeneous glucose agar plate environments feature four primary genera: Pseudomonas, Chryseobacterium, Delftia, and Moraxella.},
}

@article {pmid42937321,
year = {2026},
author = {Yagupsky, P},
title = {Diagnosing pediatric skeletal system infections: you are as good as your lab.},
journal = {Journal of clinical microbiology},
volume = {},
number = {},
pages = {e0050826},
doi = {10.1128/jcm.00508-26},
pmid = {42937321},
issn = {1098-660X},
abstract = {Pediatric skeletal system infections are medical emergencies that may cause severe acute complications and long-term orthopedic disabilities. Because the clinical presentation of septic arthritis and osteomyelitis may mimic non-infectious conditions, early identification of the causative agent and determination of its antibiotic susceptibility profile are cornerstones of patient management. The etiology of childhood skeletal system infections has changed over time, reflecting the implementation of conjugate vaccines against Haemophilus influenzae type b and Streptococcus pneumoniae, as well as the development of sensitive molecular detection tests. These novel laboratory methods, coupled with rapid pathogen identification by MALDI-TOF technology, have reduced the fraction of "culture-negative" infections and shortened the turnaround time for pathogen identification from days to hours. However, even today, a substantial fraction of bone and joint infections remains microbiologically unconfirmed. Metagenomic next-generation sequencing holds great promise, but its high cost, the need for technical expertise, and the detection of commensal organisms of dubious significance severely limit its routine use. On the other hand, metagenomic next-generation sequencing has not expanded the list of known pediatric skeletal system pathogens, suggesting that underutilization of current diagnostic methodologies, rather than reduced sensitivity, drives suboptimal diagnosis.},
}

@article {pmid42937368,
year = {2026},
author = {Mishra, S and Mutnuri, S},
title = {Metagenomic and thermodynamic mapping of Ny-Ålesund, Arctic microbiota: harnessing low temperature biohydrogen production.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0145126},
doi = {10.1128/spectrum.01451-26},
pmid = {42937368},
issn = {2165-0497},
abstract = {Biohydrogen produced by psychrophilic dark fermentation has lower energy requirements than conventional methods. In this study, kinetic, thermodynamic, and functional metagenomic analyses were conducted to determine the profiles of microbial consortia from Ny-Ålesund, Svalbard, incubated at 4°C and 20°C in the presence or absence of the methanogenic inhibitor 2-bromoethanesulfonate. Biogas potential values derived from volumetric analyses indicated that pure biohydrogen (>95.6%) was produced, while also confirming the presence of these consortia adapted to operate with lag phases of 4-7 days and exhibiting temperature sensitivity coefficients (Q10) <2.0 at 4°C. While thermodynamic analysis indicated that methanogenic inhibition theoretically disrupted syntrophic electron transfer and yielded a higher activation energy, both anaerobically fermentative acetic and butyric acid pathways remained exergonic. Community succession was observed in functional metagenomic analyses, marked by the enrichment of fermentative genera (Clostridium, Enterobacter, and Klebsiella) harboring the genetic potential for the pyruvate:ferredoxin oxidoreductase (PFOR) and formate hydrogenlyase (FHL) pathways. Metagenomic enrichment for the genes encoding cold-shock defense (cspA, dnaK) and putative electron-bifurcating complexes (rnf, ech) highlights the combined genetic potential to sustain viability and overcome thermodynamic limits at all incubation temperatures. Overall, the biochemical characteristics of native Arctic consortia provide evidence of their potential to serve as viable biocatalysts for biohydrogen production, currently under laboratory batch conditions at low temperatures.IMPORTANCEBiohydrogen production is a potentially sustainable energy source that offers new options for generating carbon-neutral renewable energy. Traditionally, biohydrogen production methods require substantial, continuous heating energy input. This publication describes the examination of the "underutilized" biohydrogen production potential of microbial communities in the Arctic region (Ny-Ålesund, Svalbard) that have separately evolved genetic adaptations necessary to maintain metabolic functions at sub-zero temperatures. Psychrophilic dark-fermentation experiments, combined with thermodynamic modeling and metagenomic analyses, show how unique cold-adapted microorganisms can produce high-purity biohydrogen gas at extreme ambient temperatures under laboratory batch conditions, highlighting a fundamental baseline that could inform future efforts to reduce the energy footprint of biofuel production. While long-term reactor stability and scalability remain to be validated, this work bridges the divide between observational Arctic microbiology and foundational green energy research, demonstrating that the discovery of extreme microbial environments holds promise for developing low-energy biological processes.},
}

@article {pmid42937679,
year = {2026},
author = {Ran, J and Qiu, G and Jin, J and Zhang, P and Hu, H and Liu, Y and Liu, X and Li, C and Xi, Y},
title = {Clinicopathologic Features of Stress-Associated Sudden Death in Three Captive Crested Ibis (Nipponia nippon).},
journal = {Avian diseases},
volume = {70},
number = {3},
pages = {349-358},
doi = {10.1637/aviandiseases-D-26-00005},
pmid = {42937679},
issn = {1938-4351},
mesh = {Animals ; *Death, Sudden/veterinary/etiology ; *Stress, Physiological ; *Birds ; *Bird Diseases/pathology/etiology ; Female ; Male ; Endangered Species ; Animals, Zoo ; Corticosterone/analysis ; },
abstract = {The endangered crested ibis (Nipponia nippon), once reduced to just seven individuals in the wild worldwide in 1981, has rebounded to more than 10,000 through intensive conservation. Yet the species remains highly vulnerable to acute environmental disturbance, with stress-induced sudden death (SISD) posing persistent challenges for captive management and reintroduction programs. We investigated three SISD cases, integrating behavioral context with necropsy and histopathology in all cases, and computed tomography/magnetic resonance imaging neuroimaging and metagenomic pathogen screening in a subset. Major organs showed no diagnostic lesions, with only mild, nonspecific digestive tract changes. Neuroimaging identified localized subdural hemorrhage without diffuse parenchymal damage. Metagenomic screening detected no high-pathogenicity avian viruses, fungi, or parasites and only trace environmental bacteria. Using published datasets, we also compared baseline corticosterone (CORT) from feathers and blood across five avian species; crested ibis occupied the lower end of baseline CORT distributions, consistent with reduced endocrine buffering capacity. These observations suggest that peracute death may occur in association with acute disturbance even in the absence of overt infectious or major degenerative lesions, with panic flight and collision trauma likely contributing to the terminal events. Framing SISD as a failure of physiological tolerance thresholds highlights actionable management: minimizing startle stimuli, reducing predator cues and human disturbance during sensitive periods, carefully staging transfers to new enclosures, managing group dynamics to limit social transmission of stress, designing for safe flight, and early-warning monitoring. Taken as case-based evidence, this work may help refine captive husbandry and reintroduction protocols aimed at improving survival and long-term population resilience.},
}

Animals
*Death, Sudden/veterinary/etiology
*Stress, Physiological
*Birds
*Bird Diseases/pathology/etiology
Female
Male
Endangered Species
Animals, Zoo
Corticosterone/analysis

@article {pmid42937876,
year = {2026},
author = {Hioki, Y and Klapper, M and Ibrahim, A and Hübner, A and Steinacker, M and Willing, K and Nachawati, R and Hildebrandt, D and Reimer, L and Zimmermann, A and Mantke, J and Sato, M and Warinner, C and Stallforth, P},
title = {Reconstruction of a 30,000-Year-Old Biosynthetic Gene Cluster Reveals Lasso Peptides Formed by a Highly Tolerant Cyclase.},
journal = {Journal of the American Chemical Society},
volume = {148},
number = {38},
pages = {40629-40635},
pmid = {42937876},
issn = {1520-5126},
support = {NA//Werner Siemens-Stiftung/ ; 390713860//Deutsche Forschungsgemeinschaft/ ; JP24KJ1884//Japan Society for the Promotion of Science/ ; NA//Astellas Foundation for Research on Metabolic Disorders/ ; },
mesh = {*Multigene Family ; *Peptides/chemistry/genetics/metabolism ; Humans ; *Actinomyces/genetics/enzymology ; Amino Acid Sequence ; Phylogeny ; },
abstract = {Microbial metagenomes preserved in prehistoric dental calculus samples provide access to past bacterial biodiversity and evolutionary dynamics across archeological time scales. Consequently, this sequence space represents a largely unexplored resource for natural product discovery. Phylogeny-guided genome mining of human dental calculus metagenomes spanning recent times to the Middle and Upper Paleolithic revealed a distinct lasso cyclase lineage associated with oral Actinomyces species. Heterologous expression of a biosynthetic gene cluster reconstructed from an approximately 30,000-year-old sample yielded two lasso peptides, palassoptides A1 and A2. Structure analyses established a canonical class II lasso topology with an eight-residue macrolactam ring. Notably, both palassoptides feature an unprecedented amino acid composition for lasso peptides. Mutational analysis of the PalA2 precursor further showed that PalC accepts all possible substitutions at core position 1 except for Pro, revealing the broadest respective tolerance reported for a lasso cyclase to date. Homologous gene clusters with highly conserved yet variable precursor sequences are widespread among modern oral Actinomyces, indicating long-term preservation of this biosynthetic lineage within the human oral microbiome. The two palassoptides exhibited combination-dependent antibacterial activity against selected Gram-positive bacteria. These findings demonstrate that ancient metagenomes can reveal chemically uncharacterized natural products and expand the known structural diversity of natural products.},
}

*Multigene Family
*Peptides/chemistry/genetics/metabolism
Humans
*Actinomyces/genetics/enzymology
Amino Acid Sequence
Phylogeny

@article {pmid42938079,
year = {2026},
author = {Pallasdies, L and Barber, H and Lee, M and Burchill, L and Ho, HNN and Stewart, AWE and Nastasovici, A and Sanne-Wander, H and Rathnayake, DT and Hofferek, V and Jebeli, L and McDaniels, TA and McConville, MJ and Field, RA and Pidot, S and Scott, NE and Jin, Y and Williams, SJ},
title = {A Bacterial Pathway for Homotaurine Catabolism via Sulfopropanoate.},
journal = {Journal of the American Chemical Society},
volume = {148},
number = {37},
pages = {39900-39910},
doi = {10.1021/jacs.6c10662},
pmid = {42938079},
issn = {1520-5126},
support = {NA//Australian Government/ ; 218568/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; MX31850//Diamond Light Source/ ; NA//Australian Government/ ; 218568/Z/19/Z//Royal Society/ ; NA//University of Manchester/ ; DP210100362//Department of Education and Training/ ; DP230102668//Department of Education and Training/ ; DP240100126//Department of Education and Training/ ; FT200100270//Department of Education and Training/ ; GNT2018980//Australian Government/ ; GNT2021638//Australian Government/ ; NA//Australian Academy of Science/ ; NA//University of Melbourne/ ; },
mesh = {*Taurine/metabolism/analogs & derivatives/chemistry ; Models, Molecular ; },
abstract = {Small aminoorganosulfonates are reservoirs of carbon, nitrogen, and sulfur in marine and host-associated ecosystems. Homotaurine, a C3-aminoorganosulfonate produced by marine algae and present in algal-derived foods, is comparatively well documented, but its complete microbial catabolism has remained unresolved. Here we identify a complete bacterial pathway for homotaurine catabolism in Caballeronia jiangsuensis strain McCoy, isolated by metabolic enrichment from soil by growth on homotaurine. Growth, proteomic, metabolomic, biochemical, structural, and heterologous-expression analyses show that homotaurine is imported and oxidatively deaminated to sulfopropanoate, then converted to sulfolactate through E-sulfoacrylate by SpuABCD and SpuIJ, enzymes related to succinate dehydrogenase and fumarase. Sulfolactate is cleaved by redundant SuyAB sulfolyases to release pyruvate and sulfite, which is oxidized and excreted as sulfate, completing biomineralization. Crystal structures of the HtaA homotaurine-binding protein and SuyAB2 sulfolyase reveal ligand recognition and provide a structural framework for sulfolactate cleavage. Hidden Markov model searches and Tara Oceans and human gut metagenomes show that the core sulfopropanoate-to-sulfolactate module is widespread in marine Proteobacteria, especially Roseobacter-lineage bacteria, and occurs more narrowly in human gut-associated sulfur-metabolizing taxa such as Bilophila wadsworthia. This pathway connects algal, dietary, and xenobiotic C3-aminoorganosulfonates to microbial carbon, nitrogen, and sulfur cycling, and identifies sulfopropanoate turnover as a conserved module in organosulfonate metabolism.},
}

*Taurine/metabolism/analogs & derivatives/chemistry
Models, Molecular

@article {pmid42938125,
year = {2026},
author = {Andonov, V and Velchov, V and Nikolov, Y and Cherkezov, N and Tenev, D and Dimitrov, M and Tsenkov, T and Dimitrov, N},
title = {From Measured Accuracy to Patient Outcome: Navigation in Total Hip Arthroplasty and Molecular Diagnosis of Periprosthetic Joint Infection: A Narrative Review.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {16},
number = {20},
pages = {},
pmid = {42938125},
issn = {2075-4418},
abstract = {Background: Total hip arthroplasty (THA) and the diagnosis of periprosthetic joint infection (PJI) have each acquired a technology that measures with high precision: intraoperative navigation, which reports component position to within a few degrees, and molecular methods, which identify the infecting organism and the host response at genomic resolution. Objective: To establish whether the measured accuracy has been shown to reach the patient as a clinical outcome. Methods: This is a narrative review, reported according to SANRA. MEDLINE, Scopus, and Web of Science databases were searched from inception to 31 August 2026. English-language studies in humans were eligible if they reported positional or diagnostic accuracy, a patient-level clinical or economic outcome after THA or after treatment of PJI or osteomyelitis, or a factor modifying the relation between the two. Animal, in vitro, and cadaveric studies, conference abstracts, and reports without extractable data were excluded. Forty studies were included. No pooled estimate was calculated, and no new statistical analysis was performed. Results: Navigation reduced positional outliers consistently, but in two matched claims-based cohorts of patients with morbid obesity (4499 and 5835 patients), it was not associated with lower rates of PJI, dislocation, periprosthetic fracture, mechanical loosening, or revision within two years. Candidate immunogenetic variants in osteomyelitis have never been tested against a treatment decision. Metagenomic sequencing was no more accurate than culture (sensitivity 63.2% versus 68.4%; specificity 80.0% versus 95.0%) except after antibiotic exposure. Reported infection rates and test accuracy both change with the case definition applied. Conclusions: In both settings, the limiting factor is the design of the studies linking measurement to outcome rather than the precision of the measurement.},
}

@article {pmid42938214,
year = {2026},
author = {Bratosin, F and Branea, HS and Hogea, E},
title = {Plasma and Serum Metagenomic Sequencing of Microbial Cell-Free Nucleic Acids for Suspected Central Nervous System Infection: A Systematic Review.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {16},
number = {20},
pages = {},
pmid = {42938214},
issn = {2075-4418},
abstract = {Background/Objectives: Untargeted metagenomic sequencing of microbial cell-free DNA or RNA in plasma or serum offers pathogen detection without lumbar puncture or biopsy, but its value in suspected central nervous system (CNS) infection is uncertain. We reviewed diagnostic yield, agreement with CNS-site testing, clinical impact, and failure modes. Methods: PubMed/MEDLINE was searched with seven documented strings (inception to 2 September 2026), supplemented by citation and web searching. Eligible reports were primary human studies of untargeted plasma or serum metagenomic sequencing with a separable result in patients with suspected or confirmed infectious CNS syndromes. Selection, extraction, and design-specific risk-of-bias appraisal followed PRISMA 2020 and were performed independently by two authors with disagreements resolved by discussion; the search was restricted to PubMed/MEDLINE and no protocol was registered. Synthesis was narrative because designs and reference standards were incompatible. Results: Of 190 reports assessed, 69 studies were included (18 denominator-based cohorts, 8 small series, 43 case reports; 51 from the United States). Positive CNS-specific clinical impact in commercial assay cohorts ranged from 0 of 24 adult to 5 of 24 pediatric meningoencephalitis tests. Among 51 case-level reports, the plasma or serum result was concordant with CNS-site testing in 28, positive when CNS-site testing was negative in 5, unconfirmed in 12, and negative or missed the pathogen in 6. All five plasma-only detections came from single case reports, which contributed to no yield or agreement denominator; excluding the four abstract-level case reports moved no proportion by more than 1.3 percentage points. RNA viruses, low-burden focal mould disease, and chromosomally integrated HHV-6 were recurrent sources of false-negative or misleading results. Conclusions: Plasma or serum metagenomic sequencing is a useful adjunct in selected difficult CNS infections, particularly disseminated, fungal, amoebic, or fastidious bacterial disease, but it does not replace CNS-site diagnostics.},
}

@article {pmid42938241,
year = {2026},
author = {Zhang, B and Zhang, Y and Wu, Y and Gao, Y and Li, X and Wu, H and Li, Y and Song, N},
title = {Application Value and Cognitive Challenges of PET/CT in the Diagnosis and Treatment of Visceral Leishmaniasis: A Retrospective Single-Center Case Series and Literature Review.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {16},
number = {20},
pages = {},
pmid = {42938241},
issn = {2075-4418},
abstract = {Background and Clinical Significance: The role of [18]F-fluorodeoxyglucose positron emission tomography/computed tomography (PET/CT) in visceral leishmaniasis (VL) remains undefined. We sought to characterize the PET/CT features of VL and assess its diagnostic and therapeutic value. Case Presentation: Four VL patients undergoing PET/CT at our hospital (2022-2025) were retrospectively analyzed as a single-center case series, combined with a literature review of published VL PET/CT cases up to December 2025. Three of the four cases exhibited increased [18]F-fluorodeoxyglucose ([18]F-FDG) uptake in the spleen, bone marrow, and lymph nodes, with additional tonsillar uptake in one case and hepatic uptake in another; one case presented with isolated lymph node uptake. In three cases, initial bone marrow smears were negative for amastigotes, and PET/CT was performed for fever of unknown origin (FUO). One case was diagnosed within one week via metagenomic next-generation sequencing (mNGS) prompted by PET/CT and epidemiological history. In the other two, VL was not suspected; they received chemotherapy/corticosteroids for presumed hemophagocytic syndrome (HPS) or connective tissue disease, and the time from symptom onset to VL diagnosis ranged from 2.5 to 4.5 months. The fourth case, confirmed by bone marrow smear, underwent PET/CT for suboptimal treatment response to exclude other diseases. Among 99 published VL cases undergoing PET/CT, indications were documented in 35, with FUO representing 83%. Initial bone marrow smears were negative in 69% of 64 evaluable cases. Of the 88 cases with evaluable PET/CT findings, 5 showed no abnormal FDG uptake. The predominant pattern was increased [18]F-FDG uptake in the reticuloendothelial system (RES), most frequently involving the spleen (73/88, 83%), bone marrow (44/88, 50%), lymph nodes (29/88, 33%), and liver (15/88, 17%); other sites (lungs/pleura, colon, tonsils) were rarely involved. Accompanying enlargement of the spleen or liver was seen in approximately 50% of cases. The most common involvement patterns were combined splenic and bone marrow (23/88, 26%) and isolated splenic (20/88, 23%). Conclusions: PET/CT can provide diagnostic clues for VL, screen for comorbidities, and guide biopsy. Typical PET/CT findings-increased RES uptake without significant other organ involvement-reflect the parasite's RES tropism. However, these findings mimic lymphoma, HPS, hematological disorders, and connective tissue diseases, risking misdiagnosis. Thus, VL should be promptly excluded in such patients using epidemiological history and etiological testing before considering alternative diagnoses.},
}

@article {pmid42938719,
year = {2026},
author = {Schroeder, TH and Eliwi Alsaffan, M and Bondarenko, A and Dervishi, A},
title = {Integrating Plasma mNGS into ICU Antimicrobial Stewardship: A Four-Phase Framework.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {10},
pages = {},
pmid = {42938719},
issn = {2079-6382},
abstract = {Background: Plasma metagenomic next-generation sequencing (mNGS) may complement conventional microbiology in critically ill patients, yet its contribution to antimicrobial stewardship in the intensive care unit (ICU) remains unclear. Methods: In this retrospective, single-center observational study, we analyzed 243 paired mNGS-blood culture episodes from 180 ICU patients. We applied a four-phase stewardship framework that integrated clinical severity, biomarker kinetics, blood culture results, mNGS findings, and clinical assessment. Treatment adaptations were classified as escalation, de-escalation, discontinuation, or no change. Multivariable regression identified factors associated with stewardship modification and mortality. Results: Active treatment adaptation occurred in 121 of 243 episodes (49.8%), comprising 61 escalations, 39 de-escalations, and 21 discontinuations. mNGS positivity was independently associated with treatment modification (OR 2.66, 95% CI 1.23-5.75; p = 0.014), whereas blood culture positivity showed an inverse association (OR 0.45, 95% CI 0.20-1.04; p = 0.062). Mortality was primarily linked to physiologic severity and host-response markers, particularly SAPS II and procalcitonin. In-hospital survival did not differ between patients who received stewardship-guided adaptation and those in whom empirical antibiotic therapy was maintained (HR 1.02, 95% CI 0.57-1.81; log-rank p = 0.951). Conclusions: Microbiological findings, particularly mNGS, were associated with antimicrobial treatment adaptation but not independently with mortality. Because mNGS was embedded within a multimodal diagnostic and clinical pathway, its independent contribution cannot be fully separated from concurrent microbiological, biomarker, and clinical information. These findings should be regarded as exploratory and require prospective multicenter validation.},
}

@article {pmid42938727,
year = {2026},
author = {Vulpie, S and Ceachir, P and Craciun, AM and Varan, I and Magiar, O and Dugăeșescu, D and Muntean, D and Licker, M},
title = {Carbapenemases in Gram-Negative Bacilli: Classification, Detection, Therapeutic Options, and Resistance to Novel Antimicrobials.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {10},
pages = {},
pmid = {42938727},
issn = {2079-6382},
abstract = {Carbapenem-resistant Gram-negative bacilli (CR-GNB), particularly Enterobacterales, Pseudomonas aeruginosa, and Acinetobacter baumannii, remain a major clinical challenge and serious threat to modern medicine, with carbapenemase production representing a particular clinical and epidemiological concern. This structured narrative review integrates three clinically linked areas: the evolution and classification of clinically important carbapenemases; phenotypic and molecular methods for their detection and characterization; and the organism- and enzyme-specific activity of recently introduced antimicrobial agents and β-lactam-β-lactamase inhibitor combinations, including ceftolozane-tazobactam, ceftazidime-avibactam, meropenem-vaborbactam, imipenem-cilastatin-relebactam, cefiderocol, plazomicin, eravacycline, cefepime-enmetazobactam, sulbactam-durlobactam (FDA 2023), aztreonam-avibactam (EMA 2024; FDA 2025), and cefepime-zidebactam (FDA 2026). Particular emphasis is placed on baseline, experimentally selected and treatment-emergent resistance mechanisms and their clinical implications. Although these agents have substantially expanded the therapeutic armamentarium against CR-GNB, important gaps persist, particularly for metallo-β-lactamase-producing organisms, carbapenem-resistant A. baumannii, and metallo-β-lactamase-producing P. aeruginosa. Their activity may be compromised by pre-existing resistance determinants, target alterations, permeability defects, efflux-pump overexpression, β-lactamase evolution or overproduction, and combinations of these mechanisms, while treatment-emergent resistance threatens long-term effectiveness. By linking laboratory carbapenemase detection with a comparative, mechanism-based assessment of antimicrobial activity, resistance determinants, and clinical limitations, this review provides a practical framework for mechanism-directed therapy and antimicrobial stewardship and identifies priorities for future research, including improved direct inhibition of metallo-β-lactamases, more reliable therapeutic options for CR-GNB, prospective studies stratified by resistance mechanisms, strengthened epidemiological surveillance and infection-prevention strategies, and continued therapeutic innovation.},
}

@article {pmid42938781,
year = {2026},
author = {Shuvo, MSH and Ju-Young, W and Jo, S and Ahmed, I and Aziz, MT and Atashi, A and Raihan, MA and Yeji, P and Hyunhee, C and Kim, T and Yu, H and Bae, H and Kim, S and Seo, H and Song, HY},
title = {Hospital Drain Microbiomes as Distinct Microbial Signatures Within Urban Wastewater Networks in the Han River Watershed.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {15},
number = {10},
pages = {},
pmid = {42938781},
issn = {2079-6382},
support = {RS-2023-00219563//Ministry of Science and ICT/ ; P0027492//Korea Institute for Advancement of Technology/ ; NA//Korea Bio Associations/ ; NA//Soonchunhyang University/ ; },
abstract = {Background: Hospital drainage systems represent an important interface between healthcare facilities and urban wastewater networks and may contribute distinct microbial inputs to downstream aquatic environments. This issue is particularly relevant in Seoul, Republic of Korea, where urban wastewater discharges into receiving waters within the Han River watershed. Methods: In this study, we characterized hospital drain microbiomes to evaluate their microbial and environmental signatures, using residential drains as a non-clinical comparison. Results: Hospital drains exhibited a distinct taxonomic profile, with greater relative abundances of Bacteroidota and Firmicutes and several genera of environmental or potential public health relevance, including Mycobacterium, Legionella, and Pseudomonas. Although microbial richness was comparable between the two environments, Simpson diversity was significantly lower in hospital drains, indicating reduced community evenness. Bray-Curtis and Jaccard analyses showed clear separation between hospital and residential microbial communities, and hierarchical clustering further supported environment-associated community structuring. LEfSe analysis identified distinct hospital-associated taxonomic biomarkers, and predicted functional profiling revealed substantial metabolic differentiation, with 19 of the 25 most significantly differentiated pathways enriched in hospital samples. Conclusions: These microbial and functional differences underscore the ecological uniqueness of hospital drains and support their inclusion in future wastewater-based microbial surveillance strategies. Collectively, these findings establish hospital drains as distinct microbial ecosystems within urban wastewater networks and provide a baseline for future studies examining the persistence of hospital-associated microbial signatures within the Han River watershed.},
}

@article {pmid42939021,
year = {2026},
author = {Vieira, MS and Dias, RS and Lima, HS and Sousa, MP and Silva, CCD and Paula, SO},
title = {Influence of a Bacteriophage Cocktail as a Biocontrol Strategy on Sulfate-Reducing Bacteria in a Pilot-Scale System.},
journal = {Bioengineering (Basel, Switzerland)},
volume = {13},
number = {10},
pages = {},
pmid = {42939021},
issn = {2306-5354},
support = {00000//Petrobras (Brazil)/ ; 00000//Coordenação de Aperfeicoamento de Pessoal de Nível Superior/ ; 0000//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
abstract = {Sulfate-reducing bacteria (SRB) play crucial roles in microbiologically induced corrosion (MIC), especially in anaerobic environments where the production of hydrogen sulfide (H2S) and biofilm formation accelerate metal degradation. Conventional treatments, such as THPS-based biocides, while effective, face limitations relating to the development of resistance and poor biofilm penetration. In this study, we evaluated the use of a non-specific bacteriophage cocktail as a biological control strategy against a mixed SRB culture (AP) biofilm and related corrosion, utilizing a pilot-scale system with AISI 1020 carbon steel coupons. Over 38 days, we monitored H2S production, optical density, and ATP concentrations, along with the surface characterization of steel coupons through scanning electron microscopy (SEM) and profilometry. Metagenomic sequencing revealed changes in microbial community composition, including reductions in sulfate consumers and shifts in dominant taxa. SEM and profilometric analyses showed disrupted and less aggressive biofilms on treated surfaces, often exhibiting filamentous structures. Diversity indices indicated the modulation of microbial richness and composition over time. These findings demonstrate the potential of bacteriophage cocktails to reshape complex microbial communities and reduce MIC, providing a sustainable alternative to chemical biocides in large-scale industrial settings.},
}

@article {pmid42939184,
year = {2026},
author = {Ho, ST and Chen, MJ},
title = {From Microbiome Associations to Deployable Precision Probiotics in Animals: A Critical Narrative Review and Proposed Causal Evidence Framework for Next-Generation Probiotic Development.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {20},
pages = {},
pmid = {42939184},
issn = {2076-2615},
support = {NSTC 115-2313-B-002-006-MY3//National Science and Technology Council/ ; },
abstract = {Next-generation probiotics (NGPs) are promoted as precision tools for animal health, yet the term is often applied to uncommon taxa before causality, safety and target-species efficacy are established. This critical narrative review reframes animal NGPs as a development pathway rather than a taxonomic category. A structured PubMed search was last run on 14 September 2026 with a publication date cutoff of 1 September 2026 and was supplemented by citation tracing and targeted searches of authoritative sources. From the screened literature, 45 representative and conceptually informative sources were purposively selected for the final narrative synthesis; the review was not intended to provide systematic or exhaustive coverage. The detailed synthesis focused on terrestrial farm and companion animals, whereas equine, rabbit and aquaculture studies were treated as boundary evidence. We evaluate how strain-resolved metagenomics, culturomics, metatranscriptomics, metaproteomics, metabolomics, host transcriptomics, machine learning, metabolic modeling and perturbation systems can move discovery beyond association. Studies across animal sectors show many biomarkers but limited causal validation, strain tracking, formulation data, multisite trials and ecological safety assessment. We propose an author-developed conceptual framework comprising a cumulative evidence ladder, from reproducible associations to field-ready deployment, and the ANIMAL-NGP reporting checklist (Animal endotype, Native ecological fit, Identity and genomic safety, Mechanism, Administration and manufacturing, and Longitudinal validation). These tools are intended to align claims with evidence and require prospective application and external validation. Multi-omics should therefore function as an evidence-navigation system, not as a substitute for causality.},
}

@article {pmid42939670,
year = {2026},
author = {Dawson, ZD and Martin, T and Ji, E and Lee, KE and Chen, X and Zhou, X and St Jean, S and Li, Y and Ma, J},
title = {PAD2 Deficiency Reveals Sex-Divergent Colonic Homeostasis, β-Catenin Remodeling, and Antibiotic-Sensitive Phenotypes.},
journal = {Biomolecules},
volume = {16},
number = {10},
pages = {},
pmid = {42939670},
issn = {2218-273X},
support = {R01AG071676/AG/NIA NIH HHS/United States ; R01AG072430/AG/NIA NIH HHS/United States ; R01EY036243/EY/NEI NIH HHS/United States ; R01HL157215//National Heart Lung and Blood Institute/ ; },
mesh = {Animals ; *beta Catenin/metabolism ; Female ; Male ; Mice ; Colitis/chemically induced/metabolism/genetics/pathology ; *Anti-Bacterial Agents/pharmacology ; Humans ; Homeostasis/drug effects ; *Protein-Arginine Deiminase Type 2/deficiency/genetics/metabolism ; Mice, Knockout ; *Colon/metabolism/pathology/drug effects ; Phenotype ; Intestinal Mucosa/metabolism ; Dextran Sulfate ; Gastrointestinal Microbiome/drug effects ; },
abstract = {Peptidylarginine deiminase 2 (PAD2) catalyzes protein citrullination and is implicated in inflammatory bowel disease and colorectal cancer. However, its role in regulating the intestinal epithelium and the influence of biological sex and the microbiome remain poorly defined. This study investigated the relationships among PAD2 deficiency, sex-divergent epithelial states, β-catenin regulation, and the intestinal microbiome. Global PAD2 knockout and wild-type littermate mice of both sexes were characterized under basal conditions and following dextran sodium sulfate-induced colitis. Intestinal epithelial phenotypes were assessed by histology, immunofluorescence, immunoblotting, quantitative RT-PCR, and immunoprecipitation. Gut microbial communities were evaluated by shotgun metagenomics, while broad-spectrum antibiotic treatment, fecal protein immunoblotting, and recombinant human PAD2 exposure in vitro were used to examine relationships among antibiotic-sensitive factors, β-catenin regulation, and epithelial phenotypes. PAD2 deficiency was associated with distinct epithelial states in male and female colons before injury. Male KO mice displayed increased β-catenin phosphorylation and increased susceptibility to DSS colitis, whereas female KO mice demonstrated increased total β-catenin abundance and preservation of structural epithelial features following injury. Female KO microbiota exhibited genotype-associated differences in microbial community composition by exploratory Bray-Curtis PERMANOVA. Broad-spectrum antibiotic treatment altered the female epithelial phenotype, reduced active β-catenin, and progressively depleted luminal PAD2-immunoreactive proteins. Exogenous recombinant human PAD2 increased epithelial protein citrullination and altered active β-catenin abundance in HT29 cells. Collectively, these findings demonstrate both sex-specific and sex-divergent colonic phenotypes while supporting a framework connecting PAD2 biology, epithelial architecture, and the microbial environment during intestinal maintenance and injury.},
}

Animals
*beta Catenin/metabolism
Female
Male
Mice
Colitis/chemically induced/metabolism/genetics/pathology
*Anti-Bacterial Agents/pharmacology
Humans
Homeostasis/drug effects
*Protein-Arginine Deiminase Type 2/deficiency/genetics/metabolism
Mice, Knockout
*Colon/metabolism/pathology/drug effects
Phenotype
Intestinal Mucosa/metabolism
Dextran Sulfate
Gastrointestinal Microbiome/drug effects

@article {pmid42939710,
year = {2026},
author = {Ascari, F and Baldelli, L and Scicchitano, D and Pellegrini, C and Ravaioli, F and De Fanti, S and Esposito, E and Porru, E and Di Laudo, F and Lodi, R and Bacalini, MG and Candela, M and Provini, F and Fiori, J and Interino, N},
title = {Exploratory Metabolomic and Metagenomic Profiling of Fecal Samples in Isolated REM Sleep Behavior Disorder.},
journal = {Biomolecules},
volume = {16},
number = {10},
pages = {},
pmid = {42939710},
issn = {2218-273X},
support = {//Ministero della Salute/ ; 2024.0058//Fondazione Del monte di Bologna e di Ravenna/ ; },
mesh = {Humans ; *REM Sleep Behavior Disorder/metabolism/microbiology/genetics ; *Feces/chemistry/microbiology ; *Metabolomics/methods ; Female ; Male ; Cross-Sectional Studies ; *Metabolome ; Middle Aged ; *Metagenomics/methods ; Multiomics ; Gastrointestinal Microbiome ; Aged ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Isolated REM sleep behavior disorder (iRBD) is among the most reliable prodromal markers of α-synucleinopathies. Under the body-first (gut-first) model of α-synuclein pathology, in which pathology may originate in the enteric nervous system and ascend to the brain, the gut is a biologically plausible compartment in which early and accessible molecular alterations might be detectable; however, the fecal metabolome remains poorly investigated in this population. In this exploratory, cross-sectional study of 21 iRBD patients and 15 healthy controls, we characterized fecal samples through an integrated multi-omics framework. The fecal metabolome was profiled on two complementary mass spectrometry platforms: HS-SPME GC-EI-high-resolution MS, used for both untargeted volatilomics and targeted quantification of linear and branched short-chain fatty acids, and untargeted LC-MS/MS for the non-volatile fraction. Gut microbial community composition was characterized on the same material by 16S rRNA gene sequencing, and the metabolomic and microbial layers were combined by DIABLO multi-omics integration. Linear short-chain fatty acids were preserved, whereas branched-chain fatty acids were selectively increased in iRBD, indicating a shift toward proteolytic fermentation. Volatile indole was reduced, while p-cresol and 2-octanone were increased, paralleled at the LC-MS/MS level by attenuation of the tryptophan-indole axis, class-level bile acid depletion, and increased acylcarnitines. The microbiome was depleted of Blautia and Faecalibacterium and enriched in Oscillospirales. Integration resolved a coherent host-microbe signature that discriminated iRBD patients from controls within this discovery cohort (84.8% cross-validated accuracy). These cross-sectional findings characterize candidate fecal signatures associated with iRBD; given the exploratory design and the limited sample size, they are hypothesis-generating, and their value for predicting phenoconversion remains to be established in prospective studies.},
}

Humans
*REM Sleep Behavior Disorder/metabolism/microbiology/genetics
*Feces/chemistry/microbiology
*Metabolomics/methods
Female
Male
Cross-Sectional Studies
*Metabolome
Middle Aged
*Metagenomics/methods
Multiomics
Gastrointestinal Microbiome
Aged
RNA, Ribosomal, 16S/genetics

@article {pmid42939852,
year = {2026},
author = {Kim, JW and Lee, YJ and Kim, K and Ko, SH},
title = {Interplay Between the Gut Microbiome and Oxidative Stress in Type 2 Diabetes.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {15},
number = {10},
pages = {},
pmid = {42939852},
issn = {2076-3921},
support = {No. RS-2024-00338024//National Research Foundation of Korea/ ; },
abstract = {Type 2 diabetes (T2D) develops when pancreatic beta cells progressively fail to compensate for insulin resistance in a host environment shaped by diet, adiposity, aging, medications, and genetics. Gut microbial dysbiosis and oxidative stress are often treated as parallel abnormalities; however, evidence increasingly supports a bidirectional microbiome-redox axis. Reduced butyrate production, altered bile-acid and amino-acid metabolism, intestinal barrier failure, and microbial products can promote mitochondrial dysfunction, NADPH oxidase activity, inflammation, and impaired insulin signaling. Conversely, hyperglycemia, lipotoxicity, inflammation, and reactive oxygen and nitrogen species remodel the intestinal habitat, favoring inflammation-adapted organisms and reinforcing dysbiosis. This review synthesizes evidence linking this circuit to insulin-responsive tissues, pancreatic islets, regulated cell death, and diabetic complications and critically examines dietary, microbiome-directed, antioxidant, glucose-lowering, and metabolic-surgical interventions. Human evidence is strongest for reproducible functional shifts, medication-microbiome interactions, and modest benefits of selected dietary and biotic interventions, whereas redox mediation and durable clinical efficacy remain heterogeneous. Future studies should integrate longitudinal metagenomics, metabolomics, validated redox biomarkers, strain-level and spatial sampling, and causal designs to identify patients with T2D most likely to benefit from microbiome-redox precision therapy.},
}

@article {pmid42940926,
year = {2026},
author = {Kuprin, A and Baklanova, V and Rechits, A},
title = {First Shotgun Metagenomic Characterization of the Gut Microbiome of the Endangered Longhorn Beetle Callipogon relictus (Coleoptera: Cerambycidae).},
journal = {Insects},
volume = {17},
number = {10},
pages = {},
pmid = {42940926},
issn = {2075-4450},
abstract = {The gut microbiome of Callipogon relictus, a rare member of the family Cerambycidae, was characterized for the first time using shotgun metagenomic sequencing. The aim of this study was to compare the taxonomic diversity and structure of the gut microbial communities in larvae and adults. Bacteria dominated the metagenomic profiles, accounting for 92.47% of the taxonomic composition in adults and 85.31% in larvae. Proteobacteria predominated in the bacterial component of both pooled profiles, accounting for 87.88% and 89.43%, respectively. The pooled adult profile had the highest relative abundances of Gammaproteobacteria and Enterobacterales, whereas the pooled larval profile had higher relative abundances of Alphaproteobacteria and Rickettsiales. In the pooled samples analyzed, 155 bacterial and 69 fungal genera were detected in the larval profile, compared with 85 and 17 genera, respectively, in the adult profile; the fungal component accounted for 10.46% of the larval profile and 0.18% of the adult profile. The two profiles shared 77 bacterial, 17 fungal, and 15 protist genera. The virus-like/retroelement sequence fraction was dominated by sequences related to Errantivirus, a member of the family Metaviridae. Because Metaviridae comprise LTR retrotransposons, this signal was interpreted as endogenous retroelement DNA rather than evidence of a free-virus gut virome. These results provide a preliminary description of a shared bacterial core accompanied by differences between the pooled profiles in lower-rank bacterial composition and in the structure of the fungal and protist components of the C. relictus microbiome.},
}

@article {pmid42940937,
year = {2026},
author = {Zulian, L and Peruzzo, A and Bertola, M and Scopel, G and Albertin, E and Martinello, M and Manzinello, C and Moressa, A and Petrin, S and Gallocchio, F and Dacasto, M and Pauletto, M and Mutinelli, F and Bordin, F and Granato, A},
title = {Honey Bees as Bioindicators of Environmental PFASs Contamination and Potential Effects on Gut-Microbial Communities.},
journal = {Insects},
volume = {17},
number = {10},
pages = {},
pmid = {42940937},
issn = {2075-4450},
support = {IZS VE 06/23 RC//Ministry of Health/ ; },
abstract = {Honey bees are valuable bioindicators of environmental contamination due to their wide foraging range and exposure to diverse biotic and abiotic stressors. This study evaluates the use of honey bees as bioindicators for detecting per- and polyfluoroalkyl substances (PFASs) in areas with varying levels of exposure risk (high-, intermediate-, and low-), as well as their potential effects on gut-microbial communities. Analytical chemistry to detect PFASs and pesticide residues were combined with molecular and metagenomic analyses to identify common honey bee pathogens and characterize gut-microbial communities. Short-chain PFASs were predominated over long-chain compounds, particularly in high-risk areas, while pesticide residues occurred in only a few apiaries. Molecular analyses revealed several widespread pathogens, while metagenomics showed a stable gut microbiome mainly composed of the genera Lactobacillus, Bartonella, Bombilactobacillus, Snodgrassella, Gilliamella, Bifidobacterium, and Gluconacetobacter. However, microbial-community composition differed significantly between apiaries with high- versus low-risk PFAS exposure. These results support honey bees as effective bioindicators for environmental PFAS monitoring and suggest that PFAS exposure may be associated with alterations in their gut-microbial communities. Further research is needed to elucidate the impact of PFASs on honey bee toxicity, gut-microbiota composition, and overall health.},
}

@article {pmid42941196,
year = {2026},
author = {Pizzocaro, E and Soverini, M and Salvagno, GL and Lotfollahzadeh, A and Santacroce, B and Bruno, G and Frigerio, I and Di Renzo, L and Castagnetti, A and Butturini, G},
title = {Gut Microbiome Compositional and Functional Signatures Associated with Chemotherapy Response in Pancreatic Ductal Adenocarcinoma: An Exploratory Cohort Study.},
journal = {Metabolites},
volume = {16},
number = {10},
pages = {},
pmid = {42941196},
issn = {2218-1989},
support = {NA//Fondazione Unipancreas ETS/ ; },
abstract = {Background/Objectives: The gut microbiome modulates chemotherapy efficacy in pancreatic ductal adenocarcinoma (PDAC), yet its relationship with the clinically relevant endpoint of post-chemotherapy surgical eligibility remains poorly characterised. We explored whether baseline gut microbiome composition and metagenomically predicted metabolic function differ between chemotherapy responders and non-responders in PDAC. Methods: In this prospective single-centre exploratory cohort study, faecal samples were collected from 15 patients with non-immediately resectable PDAC at diagnosis, before chemotherapy. Whole-genome shotgun metagenomics was performed, and microbial functional capacity was inferred through an assembly-based pipeline. Patients were classified as responders (achieved surgical eligibility, n = 6) or non-responders (n = 9). Results: At baseline, responders showed enrichment of Collinsella aerofaciens (p = 0.026) and Butyrivibrio fibrisolvens (p = 0.012), while non-responders were enriched in oral-origin bacteria (Streptococcus gordonii, Actinomyces spp., Rothia dentocariosa). Predicted butyrate showed the largest effect size difference between groups but did not reach significance (p = 0.179); responders also had broadly elevated predicted SCFAs and bile acids. However, chemotherapy regimen (mFOLFIRINOX in 5/6 responders vs. 2/9 non-responders; Fisher p = 0.041) and disease stage were unevenly distributed between groups. Conclusions: This exploratory study identifies the compositional and functional microbiome features distinguishing PDAC chemotherapy responders from non-responders. These associations are confounded by disease stage and regimen and require validation in larger, regimen-stratified cohorts before predictive or mechanistic claims can be made.},
}

@article {pmid42941936,
year = {2026},
author = {Vacaras, C and Vacaras, V and Nistor, C and Vesa, SC and Jucan, C and Furdui, IM and Strilciuc, S and Stefanescu, E and Chira, D and Rafila, A and Muresanu, DF},
title = {Limited Gut Microbiome Differences Between Relapsing-Remitting and Secondary Progressive Multiple Sclerosis: A Shotgun Metagenomic Study.},
journal = {International journal of molecular sciences},
volume = {27},
number = {20},
pages = {},
pmid = {42941936},
issn = {1422-0067},
support = {//Foundation for the Study of Nanoneurosciences and Neuroregeneration and by the Romanian Society of Microbiology./ ; },
mesh = {Humans ; *Multiple Sclerosis, Relapsing-Remitting/microbiology ; *Multiple Sclerosis, Chronic Progressive/microbiology ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; Female ; Male ; Middle Aged ; Adult ; Biomarkers/blood ; Cross-Sectional Studies ; Shotgun Sequencing ; },
abstract = {The gut microbiome may contribute to multiple sclerosis (MS) pathophysiology, but its relationship with disease phenotype and progression remains unclear. To characterize taxonomic and functional gut microbiome differences between relapsing-remitting MS (RRMS) and secondary progressive MS (SPMS) and their associations with neurological disability and circulating biomarkers. This cross-sectional study included 89 participants (30 healthy controls, 29 RRMS, and 30 SPMS). Shotgun metagenomic sequencing was used to assess microbial diversity, taxonomic profiles, and predefined short-chain fatty acid (SCFA)-related pathways, integrated with disability measures and serum GFAP, NfL, and S100B. SPMS participants were substantially older than those with RRMS (median 49.0 vs. 31.0 years), prompting age-adjusted analyses and an age-overlap sensitivity analysis. Alpha diversity and overall microbial community composition were similar across groups. SPMS showed greater interindividual microbial community dispersion than RRMS in the full cohort, with a similar direction and magnitude but attenuated statistical significance in the age-overlap sensitivity analysis. Exploratory taxonomic signals were not confirmed by FDR-controlled analyses. No robust phenotype-specific differences in predicted SCFA-related pathways or associations of taxonomic or functional features with disability or circulating biomarkers were identified. Greater microbial community dispersion in SPMS was observed in the full cohort, but this finding was attenuated in the age-overlap sensitivity analysis and should be considered preliminary. Overall, these findings do not support a distinct SPMS-associated gut microbiome signature, although potential phenotype-related differences cannot be excluded.},
}

Humans
*Multiple Sclerosis, Relapsing-Remitting/microbiology
*Multiple Sclerosis, Chronic Progressive/microbiology
*Gastrointestinal Microbiome/genetics
*Metagenomics/methods
Female
Male
Middle Aged
Adult
Biomarkers/blood
Cross-Sectional Studies
Shotgun Sequencing

@article {pmid42942211,
year = {2026},
author = {Zhao, Z and Luo, J and Zhao, Z and Liu, G and Feng, S and Chen, X and Cai, K and Song, Z},
title = {Effects of Arbuscular Mycorrhizal Fungi and Clay Minerals on Soil Nitrogen and Phosphorus Availability and Microbial Community Responses.},
journal = {Life (Basel, Switzerland)},
volume = {16},
number = {10},
pages = {},
pmid = {42942211},
issn = {2075-1729},
support = {2023YFD2301500//National Key Research and Development Program of China/ ; },
abstract = {Efficient management of soil nitrogen and phosphorus availability is important for soil fertility and crop productivity, but the field responses of rhizosphere microbial communities to arbuscular mycorrhizal fungi (AMF) and clay-mineral amendments remain unclear. A wheat-field experiment compared four treatments: an untreated control (A), bentonite (B; 39 kg plot-1), sepiolite (C; 39 kg plot-1), and AMF inoculation (E; 2.25 kg inoculum plot-1; 120 spores g-1). Each treatment comprised six 4 × 7.5 m plots. Soil physicochemical properties were evaluated using all six plots, whereas rhizosphere microbial sequencing used three plots per treatment (plots 2, 4, and 6; n = 3). Treatment E showed higher mean alkali-hydrolyzable nitrogen (101.50 vs. 93.33 mg kg-1) and available phosphorus (56.00 vs. 20.98 mg kg-1) than the control, whereas treatment B showed a 32.8% higher mean available potassium. None of the bacterial or AMF alpha-diversity indices differed significantly among treatments. Taxonomic summaries showed descriptive variation among treatments, whereas principal component analysis (PCA) and analysis of similarities (ANOSIM) did not detect significant treatment-level separation of either the bacterial or AMF communities. Shotgun metagenomic annotation, rather than 16S-based functional inference, further showed descriptive differences in nitrogen- and phosphorus-related gene-abundance profiles and functional potential; Pseudomonadota and Actinomycetota accounted for substantial shares of several nutrient-cycling gene categories, while pstB showed comparatively pronounced numerical variation among treatments. These metagenomic profiles represent genetic functional potential and do not demonstrate transcript abundance or metabolic activity. Overall, AMF inoculation and clay-mineral amendments were associated with descriptive differences in nutrient availability, taxonomic profiles, and metagenomic functional potential in alkaline wheat farmland, but significant treatment-level separation of the overall bacterial and AMF communities was not detected.},
}

@article {pmid42942900,
year = {2026},
author = {Pătru, O and Luca, S and Păunescu, A and Enache, B and Văcărescu, C and Cozma, D and Crișan, S and Bena, A},
title = {The Gut Microbiome-Estrogen Axis in Menopause: Implications for Body Composition, Cardiometabolic Health and Nutrition.},
journal = {Nutrients},
volume = {18},
number = {20},
pages = {},
pmid = {42942900},
issn = {2072-6643},
mesh = {Humans ; *Menopause/physiology/metabolism ; Female ; *Estrogens/metabolism ; *Gastrointestinal Microbiome/physiology ; *Body Composition/physiology ; *Nutritional Status ; Aging ; Cardiometabolic Risk Factors ; },
abstract = {Background/Objectives: Menopause is associated with profound endocrine, metabolic, immune, and microbial changes that may contribute to accelerated biological aging and increased cardiometabolic risk. The gut microbiome represents a potential interface between estrogen biology, host metabolism, inflammation, and systemic organ function. This narrative review examines the role of menopause-associated gut microbiome remodeling in microbiome-mediated metabolic aging, focusing on the estrobolome, microbial metabolites, organ crosstalk, and microbiome-targeted interventions. Methods: Relevant literature was identified through searches of PubMed/MEDLINE, Scopus, and Web of Science, supplemented by reference-list screening. Human observational and clinical studies, mechanistic investigations, systematic reviews, meta-analyses, and relevant guidelines were critically evaluated and synthesized narratively. No formal meta-analysis was performed. Results: Menopause-associated changes in gut microbial composition and function may influence estrogen metabolism through the estrobolome and modify the production of short-chain fatty acids, lipopolysaccharides, trimethylamine N-oxide, and bile acid metabolites. These pathways may contribute to chronic low-grade inflammation, insulin resistance, endothelial dysfunction, dyslipidemia, hepatic metabolic dysfunction, adipose tissue inflammation, adverse changes in body composition, sarcopenia, neuroinflammation, and urogenital microbial instability. Dietary patterns, fermentable fiber, physical activity, probiotics, synbiotics, phytoestrogens, and menopausal hormone therapy may influence components of this network, although the strength of evidence remains variable. Current data do not support the use of microbiome characteristics to select or dose hormone therapy. Conclusions: The gut microbiome may act as a dynamic mediator linking estrogen decline with metabolic and systemic aging after menopause. However, causality, individual variability, and clinical translation remain insufficiently established. Longitudinal studies integrating shotgun metagenomics, metabolomics, hormone measurements, standardized hormone therapy exposure, and clinical outcomes are needed to determine whether microbiome-derived biomarkers can support risk stratification and personalized interventions for healthier aging in postmenopausal women.},
}

Humans
*Menopause/physiology/metabolism
Female
*Estrogens/metabolism
*Gastrointestinal Microbiome/physiology
*Body Composition/physiology
*Nutritional Status
Aging
Cardiometabolic Risk Factors

@article {pmid42943305,
year = {2026},
author = {Spathakis, M and Kolios, G and Paspaliaris, V and Dovrolis, N},
title = {Colorectal Cancer-Associated Microbiome Remodeling Implicates Host Microbial Metabolite-Receptor Axes.},
journal = {Pharmaceuticals (Basel, Switzerland)},
volume = {19},
number = {10},
pages = {},
pmid = {42943305},
issn = {1424-8247},
support = {//BioGut Technologies Inc./ ; },
abstract = {Background/Objectives: Colorectal neoplasia is accompanied by reproducible changes in the gut microbiome and fecal metabolome, but the receptor systems through which altered microbial metabolic outputs may interface with the host remain incompletely defined. We investigated whether disease-associated microbial functional remodeling converges on metabolite-sensing receptor axes that could prioritize mechanistic and pharmacological hypotheses across the adenoma-to-carcinoma sequence. Methods: We analyzed 1534 publicly available stool shotgun metagenomes from 11 colorectal neoplasia cohorts, including 624 controls, 209 adenomas and 701 colorectal cancers (CRCs). Study-adjusted species and unstratified MetaCyc pathway models were combined with stage-pattern classification and mapping of microbial pathways to predefined metabolite-receptor axes. Findings were examined in two independent fecal metabolomics datasets. Results: CRC was associated with 68 species and 249 unstratified pathways at false discovery rate q < 0.05. Among CRC-associated features, 17 species and 36 pathways were adenoma-concordant, whereas 37 species and 170 pathways were CRC-specific. Of 136 pathways mapped to seven receptor-linked ligand classes, 79 were FDR-supported. Nucleotide/purinergic metabolism contained 39 FDR-supported pathways, predominantly lower in CRC, whereas fatty-acid/short-chain fatty acid signaling contained 21 FDR-supported pathways, predominantly higher in CRC. Independent fecal metabolomics showed the strongest axis-level convergence for these two axes. Conclusions: Colorectal neoplasia is associated with reproducible microbial functional remodeling that can be organized into biologically defined metabolite-receptor axes. Fatty-acid/SCFA and nucleotide/purinergic pathways emerge as the leading candidates for prospective functional and pharmacological investigation. The analysis prioritizes testable host-microbiome signaling modules but does not establish metabolite flux, receptor activation or therapeutic efficacy.},
}

@article {pmid42943340,
year = {2026},
author = {Cheng, M and Zhang, M and Wang, W and Jia, X and Cong, B},
title = {Multi-Omics Analysis Identifies Gut-Associated Metabolic Signatures Associated with Metformin-Mediated Protection Against LPS-Induced Lung Injury.},
journal = {Pharmaceuticals (Basel, Switzerland)},
volume = {19},
number = {10},
pages = {},
pmid = {42943340},
issn = {1424-8247},
support = {30705010094//Hebei Medical University/ ; 2019-I2M-5-055//Chinese Academy of Medical Sciences & Peking Union Medical College/ ; 82304360//National Natural Science Foundation of China/ ; },
abstract = {Background/Objectives: Lipopolysaccharide (LPS)-induced lung injury involves pulmonary inflammation, metabolic disturbance, and intestinal dysregulation. This study investigated whether metformin attenuates LPS-induced lung and colonic injury and characterized associated gut microbiota-metabolite changes. Methods: Male C57BL/6J mice were assigned to control (CON), LPS, metformin 200 mg/kg (MET 200 mg/kg), and metformin 400 mg/kg (MET 400 mg/kg) groups. Metformin was administered by gavage for 7 days before intranasal LPS challenge. Lung and colon injury were assessed by histology, immunostaining, ELISA, and RT-qPCR. Untargeted serum metabolomics, colonic-content metabolomics, and colonic-content shotgun metagenomics were performed in the CON, LPS, and MET 400 mg/kg groups. Differential-feature, pathway-enrichment, and exploratory Spearman correlation analyses were conducted. Results: Metformin reduced LPS-induced lung injury, inflammatory cytokine production, F4/80- and MPO-positive immune-cell infiltration, and colonic inflammatory and barrier-related abnormalities. Serum metabolomics identified 468 differential features in LPS versus CON and 286 in MET versus LPS, with 218 overlapping features. Colonic-content metabolomics identified 1000 and 554 differential features, respectively, with 328 overlapping features. Eight metabolites showed metformin-associated directional shifts toward control levels in both serum and colonic contents. Metagenomics showed metformin-associated remodeling of gut microbial composition and predicted gene-content functional potential. Exploratory integrated analyses linked metformin-responsive genera and shared metabolites with pulmonary inflammatory indicators. Conclusions: Metformin was associated with attenuated LPS-induced lung and colonic injury and coordinated gut-associated microbiota-metabolite remodeling. Because the study did not include a metformin-only group or causal perturbation experiments, these findings identify candidate associations rather than demonstrating a causal gut microbiota-metabolite-lung mechanism.},
}

@article {pmid42943366,
year = {2026},
author = {Moreira, J and Bettencourt, R},
title = {Deciphering Macroalgal Microbiomes: Metagenomic Insights, Ecological Roles and Bioprospecting Potential.},
journal = {Microorganisms},
volume = {14},
number = {10},
pages = {},
pmid = {42943366},
issn = {2076-2607},
support = {UID/05634/2025 (DOI: 10.54499/UID/05634/2025); UID/PRR/05634/2025 (DOI: 10.54499/UID/PRR/05634/2025); UID/PRR2/05634/2025 (DOI: 10.54499/UID/PRR2/05634/2025)//Fundação para a Ciência e Tecnologia/ ; PROSCIENTIA Incentive System-project M1.1.A/FUNC.UI&D/014/2025//Regional Directorate for Science, Innovation and Development of the Azores Government-PROSCIENTIA Incentive System/ ; ACORES-01-0145-FEDER-000138//European Regional Development Fund (ERDF)/ ; M3.1.b context emp/F/017/2024//Fundo Regional para a Ciência e Tecnologia/ ; },
abstract = {Macroalgae host complex microbial communities that influence surface colonization, development, nutrient transformation, carbohydrate turnover, environmental responses, and the production of potentially valuable metabolites. Advances in shotgun metagenomics and genome-resolved analysis have greatly expanded access to this functional diversity, but they have also increased the risk of conflating genomic potential with biological activity or host benefit. This narrative review evaluates the bacterial component of macroalgal microbiomes-the component for which mechanistic and experimentally validated evidence is most extensive-through a framework that separates what has been proven from what is merely predicted, distinguishing functional prediction from expression, biochemical activity, metabolite exchange, host response, and experimental causality. Particular attention is given to bacteria-dependent morphogenesis, metabolic complementarity, environmental acclimation, carbohydrate-active enzymes and polysaccharide-utilization loci, biosynthetic gene clusters, and the translational potential of seaweed-associated microorganisms. Comparative perspectives from microalgal and cyanobacterial systems are used to identify principles that generalize across algal microbiomes while emphasizing the distinctive spatial and chemical complexity of macroalgal surfaces. Invasive and bloom-forming macroalgae provide an additional ecological context in which microbial functional redundancy, recruitment flexibility, and dominant populations may shape whole-community profiles. An illustrative, hypothesis-generating taxon-attribution case study, based on single metagenomic datasets from Rugulopteryx okamurae and Sargassum sp. holobionts in the Azores, which confounds host identity with sampling location, time, and thallus condition, shows that the disproportionate genomic contribution of the genus Cobetia measurably alters the interpretation of a specific subset of community-level KEGG pathway contrasts, while the majority of pathway-level and taxon-specific signals discussed retain their direction after this taxon's exclusion and residual-community renormalization. Together, these analyses argue that macroalgal microbiome research should move beyond inventories of predicted functions toward explicit taxonomic attribution, experimental validation, and ecological context. Such integration will be essential for establishing which microbial functions are ecologically consequential and which can be translated reproducibly into biotechnology.},
}

@article {pmid42943375,
year = {2026},
author = {Anema, RF and Francis, FL and Smith, ZK and St-Pierre, B},
title = {Enrichment of Candidate Formate and Acetaldehyde-Producing Ruminal Bacteria in Response to Corn-Based Diets.},
journal = {Microorganisms},
volume = {14},
number = {10},
pages = {},
pmid = {42943375},
issn = {2076-2607},
support = {7010068, SD00H866-26//South Dakota State University Agricultural Experiment Station Hatch/ ; },
abstract = {In ruminant production systems, feeding diets with easily digestible and energy-dense compounds during the finishing phase is a common strategy to ensure optimal growth and performance. As ruminal microbial communities are responsible for fermenting feed into nutrients that the animal host can absorb and use, concentrate-based diets favor specialists that can utilize starch, as well as other cross-feeding species that benefit from their metabolic activities and their end products. Currently, a gradual increase in the proportion of concentrate in rations remains the best strategy towards developing resilience to undesirable end products, thus mitigating their adverse effects on the host. In an effort to gain further insights into the mechanisms involved in the adaptation of ruminal microbial communities to starch-rich diets, we used a 16S rRNA gene-based approach to identify eight highly represented species-level Operational Taxonomic Units (OTUs) that were more abundant in the rumen of finishing lambs fed a whole corn-based diet for 56 (D56, n = 7) or 63 days (D63, n = 8) compared to samples collected from lambs on a forage diet (p < 0.05) that were harvested prior to the dietary transition (D0, n = 4). To assess their metabolic capabilities, a metagenomics-based approach was used for OTUs corresponding to uncharacterized bacterial species, while publicly available genomes were analyzed as a proxy for OTUs closely related to known bacterial species. As anticipated, the potential to hydrolyze starch and metabolize glucose into pyruvate was found in all datasets analyzed, but more diverse capabilities were observed for other functions, such as the types of end products synthesized. For instance, lactate was not the only undesirable microbial end product predicted, as the potential to generate formate, acetaldehyde and ethanol was also found across datasets. While the impact of these compounds on the rumen remains poorly explored, ongoing research on how they can affect gut health in humans indicates that they may have undesirable effects. Together, these and other results from this study provide further insight into how ruminal bacterial communities in finishing lambs adapt to starch-based ingredients and how they can in turn affect the ruminal environment.},
}

@article {pmid42943376,
year = {2026},
author = {Wang, Z and Cui, R and Tong, J and Liu, P and Huang, S and Gu, Y and Luo, G},
title = {Impact of Residual Glutaraldehyde-Didecyldimethylammonium Bromide on Fermentation Performance and Microbial Community in Ectopic Fermentation System.},
journal = {Microorganisms},
volume = {14},
number = {10},
pages = {},
pmid = {42943376},
issn = {2076-2607},
support = {32472888//National Natural Science Foundation of China/ ; XZ202501ZY0147//the Science and Technology Projects of Xizang Autonomous Region/ ; 2024ZHXC0005//the Sichuan Science and Technology Program/ ; 2026-YF05-00039-SN//the Chengdu Municipal Science and Technology Bureau Key R&D Support Program/ ; sccxtd-2026-08//the Program for Pig Industry Technology System Innovation Team of Sichuan Province/ ; ZYN2025261//the Fundamental Research Funds for the Central Universities of Southwest Minzu University/ ; },
abstract = {Ectopic fermentation systems (EFSs) are widely applied to treat livestock manure, yet residual disinfectants transferred from production areas into the manure collection system may compromise their performance, and the consequences of such continuous low-dose input remain unclear. Here, we aimed to determine whether long-term input of the widely used disinfectant glutaraldehyde-didecyldimethylammonium bromide (GD) impairs EFS operation, and to identify the changes in microbial communities and organic matter underlying these effects. Pig manure slurry containing 20 mg/kg GD was supplied continuously, and physicochemical parameters, enzyme activities, microbial communities, antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and three-dimensional excitation-emission matrix (3D-EEM) spectra were monitored throughout the fermentation period. GD significantly reduced total nitrogen accumulation (p < 0.05) and suppressed lignocellulose-degrading enzyme activities during the late fermentation stage. Microbial richness declined significantly (Chao index, p < 0.05), accompanied by enrichment of thermotolerant taxa such as Thermobifida and Bacillus, while soluble microbial by-products decreased markedly. Unexpectedly, MGEs including intI1, intI2 and Tn916/1545 were less abundant under GD exposure, likely reflecting the overall inhibition of microbial growth. These findings demonstrate that GD residues exert cumulative adverse effects on EFS performance, and highlight the need to coordinate on-farm disinfection with downstream manure treatment.},
}

@article {pmid42943377,
year = {2026},
author = {Quiñonez Álvarez, CP and Berutti-Suárez, L and Mafla Andrade, SX},
title = {Association of Helicobacter pylori Infection with the Gastric Microbiota: A Scoping Review from a Molecular Diagnostic Perspective.},
journal = {Microorganisms},
volume = {14},
number = {10},
pages = {},
pmid = {42943377},
issn = {2076-2607},
abstract = {Helicobacter pylori infection remains globally one of the main causes of chronic gastritis, gastroduodenal ulcer disease, and gastric adenocarcinoma. Although the stomach has been considered an almost sterile environment, molecular techniques have revealed a complex and dynamic gastric microbiome whose composition may vary with H. pylori infection status. This review presents current knowledge on the impact of H. pylori on the composition, diversity, and functional implications of the gastric microbiome, focusing on studies applying molecular diagnostic techniques such as conventional PCR, quantitative real-time PCR (qPCR), 16S rRNA gene sequencing, and shotgun metagenomics. A systematic literature search was conducted between January and March 2025, including all eligible studies published from 2006 to 2025 following the PRISMA methodology for exploratory reviews. Thirty studies met the inclusion criteria and were integrated into the qualitative synthesis, which included primary studies, secondary sources, and methodological studies. The evidence suggests that H. pylori infection is generally associated with decreased alpha diversity and increased relative abundance of Proteobacteria (especially Helicobacter), along with decreased abundances of Firmicutes, Actinobacteria, and Bacteroidetes. Several studies have reported associations between virulence factors (e.g., CagA and VacA) and alterations in the gastric microenvironment, reflecting microbial and host-related changes relevant to chronic inflammation and gastric carcinogenesis. From a diagnostic perspective, qPCR and sequencing-based methods enable detection of H. pylori, evaluation of virulence- and resistance-associated targets, and broader taxonomic and functional analyses. However, significant methodological heterogeneity, particularly concerning sample types, DNA extraction, 16S hypervariable regions, and bioinformatics platforms, limits comparability between studies. These findings underscore the need for standardized molecular methods to improve understanding of interactions between H. pylori and the microbiome, as well as their clinical implications.},
}

@article {pmid42943391,
year = {2026},
author = {Chang, W and Ma, W and Du, J and He, W and Zhu, N},
title = {Warming and Nitrogen Addition Induce Asynchronous Taxonomic and Functional Responses and Reorganize Microbial C, N, P Cycling Potential in an Alpine Wetland on the Qinghai-Tibet Plateau.},
journal = {Microorganisms},
volume = {14},
number = {10},
pages = {},
pmid = {42943391},
issn = {2076-2607},
support = {32660405, 31860143//National Natural Science Foundation of China/ ; 26ZDFG001//Gansu Provincial Science and Technology Plan/ ; 2024RCXM82//the Priority Talent Project of Gansu Province/ ; 24ZYQA023//the Central Government Guide Local Science and Technology Development Funds/ ; 2021CYZC-15//the Gansu Provincial Department of Education Industrial Support Program Project/ ; 2026CXZX-793//the Innovation Star Project for Graduate Students in Universities in Gansu Province/ ; 26JDWA001//the innovation Platform Plan Program of Gansu Province/ ; },
abstract = {Climate warming and atmospheric nitrogen deposition are altering carbon (C), nitrogen (N), and phosphorus (P) cycling in alpine wetlands. However, how these drivers jointly reorganize microbial communities and their biogeochemical cycling potential remains poorly understood, particularly in cold, nutrient-limited alpine wetlands. We conducted a four-year field experiment combining open-top chamber warming and nitrogen addition. Soil physicochemical measurements were integrated with shotgun metagenomic sequencing to assess microbial community structure and the functional potential associated with C, N, and P cycling. The results showed that archaeal and bacterial community composition remained stable following warming and nitrogen addition, whereas fungal composition changed. Functional gene richness was positively correlated with archaeal and bacterial richness but was not correlated with fungal richness, indicating asynchronous responses between taxonomic-functional dimensions. Warming and nitrogen addition did not consistently increase the overall abundance of C, N, and P cycling functional genes. Instead, they induced pathway-specific responses: compensatory shifts among C fixation pathways, decreases in complex C degradation genes, increases in nitrification genes, and decreases in genes associated with P acquisition and homeostatic regulation. Soil moisture and enzyme activities were significantly correlated with C, N, and P cycling genes. These findings highlight domain-specific taxonomic responses and process-specific re-organization of microbial functional potential and emphasize the importance of hydro-thermal constraints when predicting alpine-wetland biogeochemical responses to future warming and increasing N inputs.},
}

@article {pmid42943393,
year = {2026},
author = {Senok, A and Verma, S and Shouqair, D and Alghafri, R and Moradigaravand, D and Nassar, R and Everett, D and Goering, R and Khan, M},
title = {Resolving Host-Associated Antimicrobial Resistance in Municipal Wastewater Using Hi-C Metagenomics.},
journal = {Microorganisms},
volume = {14},
number = {10},
pages = {},
pmid = {42943393},
issn = {2076-2607},
support = {AJF-NIH-1-MBRU//This work was funded by Grant# AJF-NIH-1-MBRU as part of the UAE-NIH Collaborative Research Initiative (UAE-NIH-CRI) which comprises four collaborating UAE institutes: Al Jalila Foundation, Mohammed Bin Rashid University of Medicine and Health Sciences, K/ ; },
abstract = {Conventional wastewater metagenomics enables population-level surveillance of antimicrobial resistance (AMR) but provides limited insight into the bacterial hosts, genomic context, and the mobility of resistance determinants. In this study, we applied high-throughput chromosome conformation capture (Hi-C) metagenomics, a proximity-ligation approach, to resolve host-associated AMR. Six influent wastewater samples collected from two municipal wastewater treatment plants over a four-month sampling period were investigated. Integrated shotgun metagenomic and Hi-C sequencing were used to reconstruct metagenome-assembled genomes (MAGs), plasmid bins, and viral bins, and to link AMR, stress-response, and virulence-associated genes to their bacterial hosts through Hi-C contacts. From 12,877 genome bins, 454 met quality thresholds (139 MAGs, 130 plasmid bins, 185 viral bins) spanning 70 bacterial and archaeal families. AMRFinderPlus identified 771 resistance and fitness-associated gene hits (517 AMR, 232 stress-response, 22 virulence-associated), dominated by macrolide-lincosamide-streptogramin B (n = 117), β-lactam (n = 114), and tetracycline (n = 96) determinants. Hi-C linked 490 gene hits to host families; Enterobacteriaceae had the highest number of host-assigned detections (n = 131), while Aeromonadaceae carried the broadest AMR repertoire (n = 102; 72% AMR). The host-plasmid network comprised 137 AMR-positive plasmid bins linked to 106 MAGs through 166 Hi-C-supported associations. Five plasmid contigs, including one harbouring blaCMY-4, were linked to MAGs from two distinct bacterial classes, suggestive of cross-lineage plasmid carriage. Viral AMR attribution was limited, with erm(B) as the sole resistance determinant identified on a viral contig. Hi-C metagenomics extends wastewater resistome profiling beyond gene inventories by resolving bacterial hosts, plasmid associations, and genomic context, strengthening the ecological interpretation of wastewater-based AMR surveillance.},
}

@article {pmid42943414,
year = {2026},
author = {Kimura, H and Kimura, R and Mizukoshi, F and Shikichi, A and Tsukagoshi, H and Tomita, H and Ryo, A},
title = {Molecular Public Health for Infectious Disease Prevention and Control.},
journal = {Microorganisms},
volume = {14},
number = {10},
pages = {},
pmid = {42943414},
issn = {2076-2607},
abstract = {Molecular technologies have transformed infectious disease surveillance, but their public health value depends on whether molecular signals can be converted into timely and effective action. Unlike molecular epidemiology, which primarily uses molecular variation to characterize distribution, relatedness, transmission, and evolution, molecular public health is defined here as an end-to-end operational framework that connects molecular evidence to population-level decisions, interventions, and evaluation. This narrative review integrates molecular detection, pathogen genomics, bioinformatics, metagenomics, wastewater and environmental surveillance, One Health monitoring, antimicrobial resistance genomics, multi-omics, and artificial intelligence. The framework progresses from detection and analytical interpretation to prediction, intervention, and feedback. Implementation maturity is heterogeneous: targeted PCR, short-read pathogen genomics, and bioinformatics-supported outbreak investigation are established in many defined use cases, whereas pathogen-agnostic metagenomics, multi-omics, and AI-enabled decision support remain more context dependent or emerging. Actionability is operationalized through analytical validity, epidemiological interpretability, sample-to-decision time relative to the intervention window, decision impact, and measurable post-intervention outcomes. Persistent barriers include sampling bias, uneven global capacity, incomplete metadata, insufficient standardization, governance concerns, and poorly defined trigger thresholds. The central criterion for the field should therefore be whether molecular information measurably improves prevention and control.},
}

@article {pmid42943417,
year = {2026},
author = {Pericàs, JM and Cañas, MA and Goenaga, MA and Nevado, C and Kestler, M and De La Villa, S and Muñoz, P and Blanes, R and Tasias, M and Escudero-Sánchez, R and Moreno-García, J and Alonso-Socas, MM and Rodríguez-Esteban, Á and Calderón-Parra, J and Diego-Yagüe, I and Boix-Palop, L and García-Álvarez, L and Gasch, O and Careta, O and Paredes, R and Luzko, IS and Garcia-De-La-Mària, C and Hernández-Meneses, M and Cuervo, G and Moreno, A and Arias, CA and Miró, JM and , },
title = {A Multicenter Prospective Protocol to Explore the Relationship Between Enterococcus faecalis Bloodstream Infections and Colorectal Neoplasms (EnteroColonus-GAMES Project).},
journal = {Microorganisms},
volume = {14},
number = {10},
pages = {},
pmid = {42943417},
issn = {2076-2607},
support = {PI19/01898//Instituto de Salud Carlos III, Proyectos de Investigación en Salud/ ; 2017-26//Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)/ ; },
abstract = {Preliminary evidence suggests that patients with Enterococcus faecalis bacteremia and infective endocarditis, particularly those without an identifiable source, may have an increased prevalence of colorectal neoplasia. Whether systematic colonoscopy should be recommended in this population remains unresolved. EnteroColonus is a multicenter, prospective, observational matched cohort study that will recruit adults aged 50 years or older with E. faecalis bacteremia and/or infective endocarditis from 22 Spanish centers, together with asymptomatic controls undergoing colorectal cancer screening. Cases will be stratified into E. faecalis bacteremia/endocarditis of unknown origin (EFBEUO) and with suspected source (EFBESS). The original planned sample size initially was 414 participants: 276 cases and 138 matched controls. Under the amended protocol, the current confirmatory sample-size target is 165 participants (110 cases and 55 matched controls; 2:1 case-to-control allocation). Core procedures include colonoscopy, histopathology, clinical and microbiological phenotyping of colonic samples, fecal microbiome profiling by shotgun metagenomics, detection of E. faecalis genetic material in colorectal biopsy specimens using 16S sequencing and species-specific qPCR, and whole-genome, SNP, and phylogenetic analyses of clinical isolates. Secondary endpoints include microbiome profiles, biopsy positivity for E. faecalis, genomic traits of bloodstream isolates, mortality, relapse/recurrence, and development of a colorectal neoplasia risk score. This protocol is designed to clarify which patients with E. faecalis bloodstream infection might benefit from systematic colonoscopy evaluation and to explore host-microbe mechanisms underlying the observed association with colorectal neoplasia.},
}

@article {pmid42943445,
year = {2026},
author = {Wen, J and Huang, J and Liu, G and Liang, S and Zeng, L and Huang, R and Yu, N and Qin, G and Chen, Q and Yan, S},
title = {Taxonomic and Functional Profiles of the Gastrointestinal Microbiome Across Digestive Tract Segments in Growing Water Buffaloes.},
journal = {Microorganisms},
volume = {14},
number = {10},
pages = {},
pmid = {42943445},
issn = {2076-2607},
support = {2024YFD1301300//National Key Research and Development Program of China/ ; AA23026004//Guangxi Buffalo Breeding Key Technology R&D Talent Introduction Project/ ; AA22068099//uangxi Science and Technology Major Project/ ; },
abstract = {Gastrointestinal segments in ruminants differ in physiological environment and substrate availability. This study characterized taxonomic and gene-encoded functional profiles in 54 shotgun metagenomes from 30 growing male water buffaloes assigned to five dietary formulations. The dataset comprised 30 rumen-fluid samples, six per group, and 24 post-slaughter samples from six gastrointestinal sites in five animals. Comparisons among groups A-E yielded p = 0.9816 for final body weight, p = 0.9315 for overall average daily gain, and p = 0.2832 for rumen-fluid pH. Genus-level principal coordinate analysis (PCoA) used Bray-Curtis dissimilarities calculated from Hellinger-transformed relative abundances. In the 30 rumen-fluid samples, PERMANOVA yielded R[2] = 0.1554, pseudo-F = 1.1499, and p = 0.327. The cross-site profiles were described separately from the dietary-group comparison. Post-slaughter rumen contents had larger proportions of Bacteroidota than the other sampled sites, whereas Bacillota accounted for the largest proportions in the cecum and colon. Kyoto Encyclopedia of Genes and Genomes (KEGG) Level 2 profiles and carbohydrate-active enzyme (CAZyme) profiles described the distribution of annotated functions across sites. These data characterize taxonomic assignments and carbohydrate-utilization-related gene profiles from the rumen to the colon in growing water buffaloes.},
}

@article {pmid42943450,
year = {2026},
author = {Huang, JK and Wu, PH and Chen, ZF and Liu, PY and Chuang, YS and Kuo, MC and Chiu, YW and Hsu, PC and Kuo, TH and Lin, YT},
title = {Identification of Gut Microbiome Signatures Associated with the Kynurenine Pathway in Tryptophan Metabolism in Patients Undergoing Hemodialysis.},
journal = {Microorganisms},
volume = {14},
number = {10},
pages = {},
pmid = {42943450},
issn = {2076-2607},
support = {MOST 111-2314-B-037-032-MY3 and MOST 111-2314-B-037 -083 -MY3//Ministry of Science and Technology/ ; KMUH109-9R17, KMUH110-0R19, KMUH111-1R14, KMUH112-2R21 and KMUH113-3R18//Kaohsiung Medical University Hospital/ ; NHRIKMU-111-I003-2, NHRIKMU-113-I005, NYCUKMU-112-I006, KT112P012, KT113P006, NHRIKMU-114-I001 and S11209//Kaohsiung Medical University/ ; },
abstract = {Patients with chronic kidney disease (CKD) and hemodialysis (HD) often experience gut microbiota dysbiosis, which may influence tryptophan metabolism through the kynurenine pathway. We aimed to investigate the specific gut microbiota signatures associated with metabolites involved in the kynurenine pathway in HD patients. In this cross-sectional study, we analyzed serum metabolite concentrations and fecal shotgun metagenomic profiles from 85 patients receiving maintenance hemodialysis at Kaohsiung Medical University Hospital. Fecal samples were analyzed using shotgun metagenomic sequencing to characterize microbiome composition and functional pathways. We measured kynurenine pathway metabolites (kynurenine, kynurenic acid, nicotinuric acid, and trigonelline) by liquid chromatography tandem mass spectrometry and analyzed their associations with microbial species abundance and genomic metabolic modules (GMM). Several bacterial species displayed associations with kynurenine pathway metabolites. Ruminococcus gnavus and Eubacterium sp. CAG:180 demonstrated correlations with kynurenine and kynurenic acid levels, respectively; however, these associations did not persist after adjustment. Distinct levels of metabolites corresponded to distinct patterns of genomic metabolic modules. High kynurenine levels correlated with increased pathways for pectin and arginine degradation. Elevated nicotinuric acid levels were associated with enhanced pathways for anaerobic fatty acid beta-oxidation and propionate production. Trigonelline levels correlated with homocysteine metabolism and various amino acid degradation pathways. Specific microbial taxa and predicted functional modules were associated with circulating kynurenine- and niacin-related metabolites. These cross-sectional findings are hypothesis-generating and do not establish directionality, causality, or therapeutic efficacy. Interpretation is limited by the modest sample size and the absence of a non-hemodialysis control group.},
}

@article {pmid42943474,
year = {2026},
author = {Ghiba, MTA and Alsheikh-Hussain, A and Alzahrani, TE and Alhamdoosh, M and Alhetheel, AF and Hanif, A and Eifan, SA},
title = {Complementary Use of Shotgun Metagenomics and Multiplex PCR for Pathogen Detection on High-Touch Surfaces.},
journal = {Microorganisms},
volume = {14},
number = {10},
pages = {},
pmid = {42943474},
issn = {2076-2607},
support = {ORF-2026-797//King Saud University/ ; },
abstract = {Shotgun metagenomics is being increasingly promoted as a pathogen-agnostic alternative to targeted PCR for environmental surveillance, yet its practical value on dry, low-biomass, host-dominated surfaces remains uncertain. In a companion study, we reported QIAstat-Dx multiplex PCR screening of 55 pooled high-touch surface samples from Riyadh, identifying 19 positive pools (34.5%). Here, in a retrospective exploratory comparison, we use those previously reported PCR calls as the targeted comparator and ask what unenriched shotgun metagenomic sequencing adds. Ten archived pools, each with at least one PCR-detected viral target, were sequenced (Illumina NovaSeq X Plus, 2 × 150 bp). Human-mapped reads constituted a substantial fraction of every library (mean 59.1%; range 42.1-80.2%). Among 14 evaluable PCR-positive target events, metagenomics assigned at least one read pair to the corresponding target taxon in 10 (71.4%; exact 95% CI, 41.9-91.6%). Because the cohort was preselected for viral PCR positivity, this value represents positive agreement/taxonomic concordance within the selected cohort and not diagnostic sensitivity. At the same ≥1 read-pair threshold, target taxa were also assigned to 91 of 246 (37.0%) evaluable pool-by-target cells in which PCR was negative; raising the threshold to ≥10 read pairs reduced positive agreement to 35.7% while background assignment remained 24.8%. Of six target categories with PCR-positive events, only coronavirus 229E was assigned more read pairs in its PCR-positive pool than in any PCR-negative pool. Across all ten pools, the three respiratory RNA-virus taxa represented among the PCR-positive calls accounted for only 105 classified read pairs in total-including assignments in both PCR-positive and PCR-negative pool-target cells-equivalent to 0.12% of the viral fraction. Even the broadest viral reference coverage was limited, as adenovirus in HP10 reached 16.39% (23 distinct alignment spans), while SARS-CoV-2 in CP17 reached 8.83% (12 spans); these partial, discontinuous alignments did not support robust whole-genome consensus reconstruction or genome-wide variant or phylogenetic analysis. Metagenomics nevertheless provided a broader taxonomic context beyond the targeted panel. Under this retrospective unenriched workflow, target recovery was variable, no tested assignment threshold separated a PCR-positive target signal from the background assignment, and shotgun metagenomics added ecological context rather than providing a reliable replacement for targeted multiplex PCR in this dataset.},
}

@article {pmid42943483,
year = {2026},
author = {Pan, Z and Wang, Z and Zhao, S and Chen, G and Wu, D and Xia, Q},
title = {Escherichia marmotae Dominates the Global Distribution of cdtABC Carriers in the Human Gut.},
journal = {Microorganisms},
volume = {14},
number = {10},
pages = {},
pmid = {42943483},
issn = {2076-2607},
support = {ZR2023QC225//Shandong Academy of Sciences/ ; },
abstract = {The gut microbiota can influence colorectal cancer through microbial metabolism, immune regulation and direct damage to host DNA. Previous experimental studies have shown that cytolethal distending toxin (CDT) can damage host DNA and promote colorectal tumorigenesis in model systems. However, the distribution of bacteria carrying intact cdtABC systems in human gut populations remains poorly characterized. Here, we integrated systematic screening of 60,008 complete bacterial genomes with analyses of 12,238 human gut metagenomes from 45 countries. We identified 871 intact cdtABC loci in 783 genomes, revealing a taxonomically restricted but genetically diverse carrier landscape. Carriers were detected worldwide, but the population signal was strongly dominated by an Escherichia marmotae lineage, a pattern that remained robust across minimum abundance thresholds. Most carrier-detected samples contained a single carrier, indicating pronounced lineage dominance. After carrier species were removed from the taxonomic profiles, the surrounding microbiome consistently distinguished samples with and without carriers across studies. This community signal was strongest for E. marmotae but remained detectable for other carriers and involved reproducible associations with Escherichia, Faecalibacterium and other gut taxa. By connecting intact loci with carrier lineages, global gut distribution and microbial community context, our study extends CDT research beyond isolated bacterial strains. These findings provide a basis for prioritising cdtABC carriers for functional validation and evaluating their potential relevance to colorectal cancer.},
}

@article {pmid42943488,
year = {2026},
author = {Song, Y and Jia, Z},
title = {Comparative Genomics of Ecologically Differentiated Nitrososphaera-Related Ammonia-Oxidizing Archaea.},
journal = {Microorganisms},
volume = {14},
number = {10},
pages = {},
pmid = {42943488},
issn = {2076-2607},
support = {92251305//National Natural Science Foundation of China/ ; XDA28020203//Chinese Academy of Sciences/ ; },
abstract = {Soil acidification strongly influences the ecology of terrestrial ammonia-oxidizing archaea (AOA). Within this group, the Nitrososphaera-related alpha (NS-α) and delta (NS-δ) lineages exhibit pronounced pH-associated ecological differentiation. In the preceding microcosm experiment, NS-α populations showed greater persistence than NS-δ during ammonium-driven soil acidification, yet the genomic basis underlying this ecological differentiation remains poorly understood. In this study, metagenomic sequencing of one near-neutral baseline microcosm (pH 7.35) and one acidified microcosm (pH 4.73) was used to reconstruct 12 Nitrososphaera-affiliated metagenome-assembled genomes (MAGs), including 2 NS-α and 10 NS-δ MAGs. These genomes were compared using genome-based phylogenetic analysis, amoA phylogeny, average amino acid identity (AAI), average nucleotide identity (ANI), and KEGG functional annotation to investigate lineage-level genomic differentiation and candidate functional genomic features. Genome-based phylogenetic and whole-genome similarity analyses supported clear differentiation between NS-α and NS-δ, while also revealing substantial genomic heterogeneity within NS-δ. Functions related to nitrogen acquisition and regulation, respiratory energy metabolism, autotrophic carbon fixation, and oxidative-stress defense were broadly distributed across both lineages and showed no clear NS-α-specific pattern. In contrast, Mre11, HerA, NurA, and RadA were detected in both reconstructed NS-α MAGs. Comparison with representative NS-α reference genomes, including the neutrophilic Nitrososphaera viennensis EN76, further showed that this DNA-repair-related gene repertoire is not restricted to acidic environments and is more consistent with a broader NS-α-associated genomic feature. Na[+]/H[+] antiporters and Trk/Ktr-type K[+] transport systems were not detected within either reconstructed NS-α MAG, although MAG-level non-detection was not interpreted as definitive lineage-level absence. Overall, the results identify genomic differences between NS-α and NS-δ but do not establish a functional advantage under acidification. The potential physiological significance of the DNA-repair-related pattern therefore remains to be experimentally tested.},
}

@article {pmid42943547,
year = {2026},
author = {Branda, F and Maria, F and Alexiev, I and Demir, AB and Limon, Ö and Ceccarelli, G and Scarpa, F and Russo, A and Spoto, S and Ciccozzi, M},
title = {Surveillance, Detection and Therapeutic Innovation in Antimicrobial Resistance in the Age of Polycrisis: From Genomic and Digital Innovation to One Health Integration.},
journal = {Microorganisms},
volume = {14},
number = {10},
pages = {},
pmid = {42943547},
issn = {2076-2607},
abstract = {Antimicrobial resistance (AMR) surveillance is increasingly strained by interconnected global crises, i.e., pandemics, climate change, armed conflicts, population mobility, and health inequalities, that disrupt healthcare delivery, diagnostic capacity, and laboratory infrastructure. In parallel, artificial intelligence (AI), machine learning, whole-genome sequencing, metagenomics, and digital surveillance offer the potential to shift from reactive reporting to predictive intelligence that anticipates resistance threats, although current implementations remain sector-specific, retrospective, and project-funded. Environmental surveillance, particularly wastewater monitoring coupled with genomic epidemiology, provides early warnings at population and ecosystem levels. The future integration of AI across human, animal, and environmental sectors could enable unified One Health intelligence; no such integrated platform is currently operational. This review focuses primarily on bacterial AMR. It examines how global drivers strain surveillance, how genomic, metagenomic, digital, and AI-enabled technologies reshape AMR detection and prediction, and the emerging non-antibiotic therapeutic landscape, including bacteriophage therapy, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-based antimicrobials, antimicrobial peptides, microbiota-directed interventions, nanomedicine, host-directed therapies, photodynamic therapy, and vaccines. It then explores how these innovations can be integrated within a One Health framework to support coordinated global preparedness. Addressing the AMR crisis will require not only technological innovation but also equitable implementation, interdisciplinary collaboration, and resilient systems.},
}

@article {pmid42943560,
year = {2026},
author = {Pappa, S and Tsioka, K and Sotiraki, S and Pervanidou, D and Papa, A},
title = {Detection and Genetic Analysis of Jingmen Tick Virus in Greece.},
journal = {Microorganisms},
volume = {14},
number = {10},
pages = {},
pmid = {42943560},
issn = {2076-2607},
support = {101102733//European Union/ ; 101132974//European Commission/ ; },
abstract = {Jingmen tick virus (JMTV) is an emerging, segmented RNA virus in the Flaviviridae family. Since its first identification in 2010 in China, JMTV has been detected in several parts of the world, primarily in ticks, but also in other arthropods, mammals, and even humans. The study included 400 adult ticks (333 Rhipicephalus bursa, 40 Ixodes ricinus and 27 Ixodes gibbosus) previously collected from livestock and the environment in various administrative regions of Greece. The ticks were grouped into 107 pools and screened for JMTV using an in-house real-time RT-PCR protocol. JMTV was detected in 41 (38.3%) tick pools (minimum infection rate 10.2%) in five of the seven regions tested. The virus positivity differed among tick species, hosts and regions. A single JMTV-positive R. bursa tick has been previously found co-infected with Aigai virus. Five positive pools with the highest viral load (Ct range 14.61-20.36) were subjected to metagenomic next-generation sequencing. Genetic analysis based on the complete coding sequences of all four RNA segments revealed that the sequences of the Greek strains cluster within JMTV Group 1, sharing 95.41% to 97.16% nucleotide identity with their closest relatives from Kosovo, Romania, and Türkiye. The results of the study confirm the wide distribution of JMTV in ticks in Greece, providing the first comprehensive genomic data for the virus in the country and highlighting the need for surveillance studies to assess any public health risk.},
}

@article {pmid42943562,
year = {2026},
author = {Hu, Y and Cheng, S and Fang, H and Lu, M},
title = {Short-Term Simulated NH4[+]/NO3[-] Inputs Reorganize Soil Microbial Communities and Modify N-Cycling Functional Potential in Temperate Forests.},
journal = {Microorganisms},
volume = {14},
number = {10},
pages = {},
pmid = {42943562},
issn = {2076-2607},
support = {32371725//National Natural Science Foundation of China/ ; 32501531//National Natural Science Foundation of China/ ; 20222-051244//"Unveiling the List of Hanging" and Technology Project of Jinggangshan Agricultural High-tech Industral Demonstration Zone/ ; XDA0440404//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; XDA28130100//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 20244-018652//Ji'an City Science and Technology Plan Project/ ; 2024H-090166//Ji'an City Science and Technology Plan Project/ ; 20255-061606//Ji'an City Science and Technology Plan Project/ ; },
abstract = {Forest soil nitrogen (N) turnover and nitrous oxide (N2O) release are strongly influenced by atmospheric N deposition. Although the effects of individual inorganic N species on soil biogeochemistry are well documented, the consequences of changing their relative supply for N2O formation and the underlying microbial pathways remain less clear. We therefore examined soil N2O emissions, microbial communities, and N-transformation potential across a gradient of ammonium-to-nitrate (NH4[+]/NO3[-]) inputs in a temperate forest soil from Northeast China. Seven treatments covering NH4[+]/NO3[-] ratios from 1:5 to 5:1 were established. Soil physicochemical properties and N2O emissions were measured, while microbial taxonomic profiles and N-cycling genes were characterized by metagenomic sequencing. Altering the composition of inorganic N reorganized the microbial community, including the relative representation of archaeal, bacterial, and eukaryotic groups. N2O release was greatest when NH4[+] and NO3[-] were supplied in equal proportions, a pattern that may reflect a stronger contribution of nitrification-associated processes. Across the treatment gradient, the response of N2O emissions to inorganic N composition was nonlinear. By contrast, the 1:2.5 NH4[+]/NO3[-] treatment produced comparatively low N2O emissions and contained a greater representation of genes associated with N2O reduction, consistent with enhanced microbial potential for N2O consumption. Under the more nitrate-dominated 1:5 treatment, genes involved in dissimilatory nitrate reduction to ammonium (DNRA) were enriched, indicating a shift in the potential routes of nitrate transformation. Metagenomic data further revealed marked variation in genes linked to nitrification, denitrification, and biological N fixation. In comparison with these compositional and functional responses, microbial diversity changed relatively little, possibly because overlapping functions were distributed among different taxa under contrasting N inputs. Overall, the findings show that the balance between ammonium and nitrate can affect forest-soil N2O emissions by restructuring microbial assemblages and their potential to transform N. These responses emphasize the need to consider the composition, rather than only the amount, of N deposition when evaluating microbial regulation of ecosystem N cycling and greenhouse-gas release. Field studies are still needed to test the generality of these patterns and their relevance to N management.},
}

@article {pmid42943568,
year = {2026},
author = {Wang, Y and Li, J and Yang, X and Liu, F and Pei, G and Cui, M and Guo, Y and Jia, Y and Zhang, S and Bao, L and Cui, Y and Huang, Y},
title = {Soil Microbiome Signatures Associated with Epidemiological Heterogeneity Across Natural Plague Foci in Inner Mongolia, China.},
journal = {Microorganisms},
volume = {14},
number = {10},
pages = {},
pmid = {42943568},
issn = {2076-2607},
support = {2024YFC2310101//National Key Research and Development Program of China/ ; 2025ZD01900105//the National Science and Technology Major Project of China/ ; },
abstract = {Plague persistence relies on complex host-vector-environment interactions, yet the ecological contribution of soil microbiomes to natural foci remains poorly understood. We performed shotgun metagenomic sequencing of 143 soil samples across four distinct plague foci in Inner Mongolia, China, to characterize microbiome features associated with contrasting epidemiological states. Taxonomic, functional, and network analyses showed that the three active plague foci exhibited lower microbial diversity, simplified co-occurrence networks, and enrichment of specific taxa, particularly Streptomyces. Conversely, the quiescent Marmota sibirica focus harbored a more complex and interconnected microbial network with greater richness and exclusive detection of Yersinia bacteriophages, showing significant concordance with bacterial community structure. These patterns indicate distinct microbiome configurations associated with specific host and geographic settings, highlighting the need to disentangle host- and site-specific effects from broader epidemiological status. Compared with surface and deep soil, burrow-associated soil exhibited greater microbial differentiation and higher richness of bacteriophages, antimicrobial resistance genes, and virulence-associated genes, suggesting its potential as a sensitive environmental matrix for ecological monitoring. Overall, our findings identify distinct soil microbiome signatures-specifically taxonomic shifts, altered network complexity, exclusive Yersinia phage detection, and functional gene enrichment-associated with epidemiological heterogeneity across natural plague foci, providing a baseline for understanding ecological variation among endemic habitats.},
}

@article {pmid42943582,
year = {2026},
author = {Zhu, WJ and Zhang, Y and Mu, M and Pei, T and Wang, H and Liang, X and Tang, Y and Wang, C and Dai, Y and Wang, Z and Liu, Z and Yu, Z and Wang, T},
title = {Integrated Metagenomic and Metatranscriptomic Analysis Reveals Microbiome Differences Between Bisexual and Parthenogenetic Populations of Haemaphysalis longicornis.},
journal = {Microorganisms},
volume = {14},
number = {10},
pages = {},
pmid = {42943582},
issn = {2076-2607},
support = {32201274//National Natural Science Foundation of China/ ; BJK2023017//Science Research Project of the Hebei Education Department/ ; },
abstract = {The tick Haemaphysalis longicornis is an important vector of human and animal pathogens in East Asia that comprises both bisexual (Bis) and parthenogenetic (Par) populations. While previous studies have documented differences between these reproductive groups in genome ploidy, host transcription, and vector capacity, it remains unclear whether reproductive strategy is accompanied by systematic divergence in the tick-associated microbiome, including microbial community composition, transcriptional activities, and functional outputs. Here, we profiled laboratory-maintained Bis and Par populations using metagenomic (MG) and metatranscriptomic (MT) sequencing to integrate community composition, core taxa, functional potential, and RNA/DNA relative activity (RNA abundance normalized to corresponding DNA abundance). Par populations exhibited higher MG alpha diversity, whereas Bis populations showed higher MT alpha diversity, indicating a decoupling between the microbial DNA reservoir and the active RNA transcript community. MG functional analysis revealed that Par populations possessed a higher potential for environmental sensing, membrane transport, biofilm formation, porphyrin metabolism, and iron acquisition. Conversely, Bis populations exhibited enhanced potential in biotin metabolism, lipoic acid metabolism, and oxidative phosphorylation. MT analysis identified significant differences in a limited number of species and CAZy families, while selected KEGG pathways showed no significant variance, suggesting restricted rather than systemic transcriptional differentiation. By integrating DNA and RNA profiles, we classified 279 shared species into four activity states, revealing higher RNA/DNA relative activity ratios for thiamine metabolism in Par, and for biofilm formation, flagellar assembly, sulfur metabolism, and fatty acid degradation in Bis. Overall, Bis and Par populations exhibit distinct differences in their microbial reservoirs, transcript compositions, and relative transcriptional activities, providing critical microbiome insights into the symbiosis and vector adaptation associated with reproductive strategies in H. longicornis.},
}

@article {pmid42943597,
year = {2026},
author = {Atuahene, PY and Stevenson, B and Sang, Y},
title = {AI-Facilitated Discovery of Microbiome-Originated Antimicrobial Peptides: A Perspective on Combating Antibiotic Resistance Within Public Health and Food Safety Frameworks.},
journal = {Microorganisms},
volume = {14},
number = {10},
pages = {},
pmid = {42943597},
issn = {2076-2607},
support = {Evans-Allen-1013186//USDA NIFA/ ; 2020-67016-31347//NIFA AFRI/ ; 2025-38821-45500//NIFA AFRI/ ; },
abstract = {The escalating crisis of antimicrobial resistance (AMR) demands innovative therapeutic strategies beyond conventional antibiotics. Antimicrobial peptides (AMPs), particularly those originating from the human, animal, and environmental microbiome, represent a promising frontier within public health microbiology and microbial food safety. Recent advances in artificial intelligence (AI) and machine learning (ML) have revolutionized the discovery pipeline, enabling high-throughput mining of metagenomic data and de novo generation of novel peptide sequences. This perspective review synthesizes recent breakthroughs in AI-driven discovery of microbiome-originated AMPs, examines their preclinical efficacy against multidrug-resistant (MDR) pathogens under One Health and climate-sensitive frameworks and application in infectious disease treatment and discusses translational challenges including pharmacokinetics, toxicity, manufacturing scalability, and applications in food preservation and water safety. We argue that the convergence of microbiome science, deep learning, and synthetic biology positions AI-discovered AMPs as viable next-generation interventions against antibiotic resistance across human, animal, and environmental domains.},
}

@article {pmid42943600,
year = {2026},
author = {Kim, A and Moon, SB and Kim, JS and Kim, MS and Lee, Y and Kang, G and Kim, KH and Roh, H},
title = {Long-Read Metagenomics Reveals Temporal DNA Virome Dynamics and Recovers Sequences of a Major Viral Pathogen at a Sea-Cage Fish Farm.},
journal = {Microorganisms},
volume = {14},
number = {10},
pages = {},
pmid = {42943600},
issn = {2076-2607},
support = {//National Institute of Fisheries Science/ ; R2026058//Ministry of Oceans and Fisheries/ ; },
abstract = {Coastal sea-cage aquaculture environments support dynamic microbial communities, yet their viral components remain poorly characterized. This study profiled DNA viral-like reads recovered from total metagenomes of iron-flocculated seawater concentrates (operationally termed DNA virome) at a rock bream (Oplegnathus fasciatus) sea-cage farm off Geoje Island, Korea, at five time points between July 2024 and May 2025 using long-read Nanopore metagenomics. Multivariate analyses of DNA virome composition indicated temporal patterning in virome composition; samples collected within the cages tended to group together. The DNA virome was dominated overall by bacteriophages of abundant marine bacteria and by viruses infecting picoeukaryotic phytoplankton, and it showed marked temporal turnover during the investigated year: Micromonas-associated viruses became prominent in December, whereas Ostreococcus- and Bathycoccus-associated viruses increased during seasonal rewarming in May, suggesting that environmentally driven changes in microbial host communities may contribute to temporal virome turnover. Pelagibacter phage abundance was positively correlated with that of its potential host Pelagibacter ubique, and both Synechococcus T7-like virus and Synechococcus virus were positively correlated with Parasynechococcus marenigrum, associations that are consistent with, but do not demonstrate, taxon-specific virus-host relationships. Nanopore reads assigned to infectious spleen and kidney necrosis virus, now classified within the species Megalocytivirus pagrus 1, were recovered from samples collected in September 2024 (12,960 bp) and May 2025 (340 bp). Average nucleotide identity analysis indicated that the seawater-derived sequence was most closely related to red seabream iridovirus subtype II, the subtype predominant in Korean cultured marine fish. The seawater virome results and the bioinformatic pipelines developed in this study together may provide a non-invasive approach for tracking temporal virome dynamics and for environmental screening of viral pathogen DNA in sea-cage aquaculture.},
}

@article {pmid42943608,
year = {2026},
author = {Xie, M and Shang, H and Wang, F and Yang, J and Geer, N and Zhang, Q and Xu, X and Baolige, D},
title = {Exploratory Shotgun Metagenomic Analysis of the Fecal Microbiome and Antimicrobial-Resistance Potential in Simmental Calves with Different Diarrheal Statuses.},
journal = {Microorganisms},
volume = {14},
number = {10},
pages = {},
pmid = {42943608},
issn = {2076-2607},
support = {2025ZY0147//Central Government Guiding Local Science and Technology Development Fund Project/ ; 2025YFDZ0091//Inner Mongolia Autonomous Region Science and Technology Plan/ ; 2020ZD0006//Inner Mongolia Autonomous Region Major Science and Technology Project/ ; },
abstract = {Calf diarrhea is frequently accompanied by disruption of the gastrointestinal microbiota, but the relationships between clinical status and microbial community composition, gene-content functional potential, and antimicrobial-resistance-associated features remain incompletely characterized. This exploratory study aimed to characterize these features in calves with different diarrheal statuses using shotgun metagenomics. Six approximately 2-month-old Simmental calves from Chahar Right Middle Banner, Inner Mongolia, were included, comprising two healthy calves, two calves with mild diarrhea, and two calves with severe diarrhea. Read-based taxonomic profiling was complemented by gene-abundance-weighted taxonomic annotation, and microbial functional potential was characterized using eggNOG/COG, KEGG, and CAZy annotations, together with conservatively screened CARD-associated sequence-homology candidates. The two severe-diarrhea samples exhibited lower bacterial richness and Shannon diversity, although PCoA did not show clear separation according to clinical severity. These two samples showed high representation of Proteobacteria and Enterobacteriaceae-related taxa, particularly Escherichia-related assignments, together with lower representation of Ruminococcaceae, Faecalibacterium, and Prevotella. Gene-content profiles showed higher representation of selected functions related to transport, environmental sensing, motility, secretion, and bacterial cell-envelope processes, whereas several glycan- and complex-carbohydrate-associated functions showed lower representation. Selected CARD-associated candidates were also more abundant in the severe-diarrhea samples. Within this small exploratory cohort, the two severe-diarrhea samples therefore showed concordant taxonomic and gene-content differences; however, these observations should not be interpreted as a general severity-specific microbiome signature and require validation in larger longitudinal cohorts.},
}

@article {pmid42943609,
year = {2026},
author = {Naito, A and Kondratowicz, J and Hanger, S and Koulenti, D and Katsounas, A},
title = {Pneumocystis jirovecii Pneumonia in Critical Care: Evolving Host Populations, Diagnostic Uncertainty, and Management Controversies.},
journal = {Microorganisms},
volume = {14},
number = {10},
pages = {},
pmid = {42943609},
issn = {2076-2607},
abstract = {Pneumocystis jirovecii pneumonia (PCP) remains a major cause of acute respiratory failure in immunocompromised patients and is increasingly encountered in critical care outside the traditional human immunodeficiency virus (HIV) population. This narrative review examines the evolving epidemiology, diagnosis, management, prophylaxis, and prognosis of PCP in critically ill adults. The epidemiological landscape has shifted toward patients with haematological and solid malignancies, solid organ or haematopoietic stem-cell transplantation, autoimmune and inflammatory diseases, and exposure to corticosteroids or other immunosuppressive therapies. Emerging data also implicate states of immune dysregulation such as cirrhosis. Diagnosis remains challenging because Pneumocystis cannot be routinely cultured and molecular detection alone cannot reliably distinguish colonisation from active infection. Accordingly, respiratory polymerase chain reaction (PCR) results require interpretation alongside host factors, imaging, serum β-D-glucan, microscopy, and, increasingly, metagenomic sequencing. Trimethoprim-sulfamethoxazole remains first-line therapy. Lower-dose regimens may reduce toxicity while maintaining efficacy, but current evidence is largely retrospective and prospective trials are needed. The benefit of adjunctive corticosteroids in non-HIV PCP remains uncertain, with conflicting observational data and no definitive mortality benefit demonstrated in the first randomised trial. Echinocandins remain investigational adjuncts, whereas venovenous extracorporeal membrane oxygenation may provide rescue support in selected patients with refractory acute respiratory distress syndrome. Prophylaxis is effective but remains inconsistently applied in several at-risk groups. Mortality among intensive care unit (ICU) patients remains high, particularly in non-HIV PCP, and varies substantially according to underlying disease, immune phenotype, co-infection, and severity of respiratory failure. Improved risk stratification and adequately powered prospective studies are priorities.},
}

@article {pmid42943633,
year = {2026},
author = {Oshima, A and Sekiguchi, S and Uchikawa, S and Fujita, N and Yoshida, H and Yamada, S and Fujita, N and Shiwa, Y and Tsuji, A and Tanaka, N and Okada, S and Nishida, A},
title = {Shotgun Metagenomics Reveals Systemic Metabolic Pathways Promoting Organic Acid Production in Traditional Sunki Fermentation.},
journal = {Microorganisms},
volume = {14},
number = {10},
pages = {},
pmid = {42943633},
issn = {2076-2607},
abstract = {Salt-free lacto-fermentation is gaining attention owing to the global demand for sodium reduction. Sunki, a traditional unsalted Japanese turnip pickle, provides a unique ecological model. In this study, we investigated the microbial balance and systemic metabolic pathways that promote organic acid accumulation using shotgun metagenomics. We revealed that a high-quality sunki cluster exhibiting an abundant accumulation of organic acids (lactic acid 8.58 ± 2.42 g/L, acetic acid 2.70 ± 0.76 g/L, succinic acid 1.50 ± 0.52 g/L) and low pH (3.91 ± 0.15) was characterized by the co-dominance of specific lactic acid bacteria along with the foundational species Limosilactobacillus fermentum. This co-dominance enables the synergistic operation of both the homofermentative and heterofermentative pathways, whose functional potentials positively correlated with lactic acid (r = 0.50) and acetic acid (r = 0.48) concentrations, respectively, thereby achieving both effective preservation and flavor complexity. Furthermore, we propose a dual-pathway model for succinic acid production involving the reductive tricarboxylic acid cycle from malate and the γ-aminobutyric acid (GABA) shunt. Succinic acid positively correlated with the functional potential of the GABA shunt enzyme (puuE, r = 0.57) and negatively correlated with that of glutamate dehydrogenase (gdhA, r = -0.51), suggesting a metabolic switch redirecting glutamate flux toward the GABA shunt. This mechanism highlights an advanced ecological adaptation for pH homeostasis, emphasizing that a balanced co-dominance structure determines the quality of salt-free fermented foods.},
}

@article {pmid42943641,
year = {2026},
author = {Funada Barbosa, MR and Foro Ramos, EDS and Villanova, F and Silva, RLO and Zhang, W and Ferreira, NE and Tozetto-Mendoza, TR and Mendes-Correa, MC and Pandey, RP and Sato, MIZ and Leal, E and da Costa, AC},
title = {Molecular Characterization of Previous Unclassified Dicistroviruses in Water Reservoir in São Paulo, Brazil.},
journal = {Microorganisms},
volume = {14},
number = {10},
pages = {},
pmid = {42943641},
issn = {2076-2607},
abstract = {In this study, viral metagenomics was applied to identify viruses related to the Dicistroviridae family in freshwater samples collected from urban reservoirs of the state of São Paulo, Brazil. Through next-generation sequencing, five complete RNA genomes similar to Dicistroviridae were detected. These genomes range from 8.032 to 9.425 nucleotides in length, and each contains two open reading frames (ORFs) with conserved protein domains and internal ribosome entry sites (IRES) characteristic of Dicistroviridae. Phylogenetic and genetic identity analyses based on the amino acid sequences of the nonstructural (ORF1) and structural (ORF2) polyproteins suggest that these five genomes represent four putative novel species provisionally named Hydro virus 1 to Hydro virus 4. These findings enhance our understanding of the diversity and distribution of Dicistroviridae in aquatic environments.},
}

@article {pmid42943642,
year = {2026},
author = {Chen, S and Li, S and Li, Y and Zhang, Y and Duan, X and Xu, C and Qian, W and Si, H and Liu, H and Li, Z},
title = {Comparison of Fecal Microbiome of Wild Red Deer in Different Regions Reveals Geographic Differentiation.},
journal = {Microorganisms},
volume = {14},
number = {10},
pages = {},
pmid = {42943642},
issn = {2076-2607},
support = {20240101012JJ//Natural Science Foundation of Jilin provinces/ ; 2023YFD1302000//National Key Research and Development Program of China/ ; CARS-43//earmarked fund/ ; JLARS-2026-080204//Jilin Agricultural Research System/ ; },
abstract = {The gut microbiome plays critical roles in nutrient metabolism and host adaptation in ruminants, yet genome-level functional differences in the fecal microbiomes across geographic populations of wild red deer remain underexplored. Here, we integrated 16S rRNA gene sequencing and shotgun metagenomics to characterize the fecal microbiome of wild red deer populations in Inner Mongolia (NMG, n = 16) and Gansu Province (GS, n = 16), China. The NMG population exhibited significantly higher α-diversity and a distinct microbial community compared to GS (adjusted p < 0.05). NMG was enriched in Clostridium, Eubacterium, and Bacillus, while GS harbored higher abundances of Ruminococcus, Oscillospira, and Faecalibacterium (adjusted p < 0.05). Functional profiling revealed that the fecal microbiome in NMG showed greater functional potential associated with amino acid, pyruvate, and butanoate metabolism pathways, whereas the fecal microbiome in GS was enriched in the genetic potential of starch/sucrose metabolism, glycan degradation, and bile acid biotransformation (adjusted p < 0.05). CAZyme analysis demonstrated that GS was enriched in glycoside hydrolases, polysaccharide lyases, and carbohydrate esterases, while NMG showed higher auxiliary activity family abundance (adjusted p < 0.05). Genome-resolved metagenomics recovered 456 species-level genome bins (SGBs), revealing that GS-enriched SGBs (Rikenellaceae, Oscillospirales CAG-272) contained CAZyme genes associated with pectin degradation, whereas NMG-enriched SGBs contained genes associated with lignin modification and chitin degradation. These findings demonstrate the significant differences in the fecal microbiomes between the two geographically distinct wild red deer populations.},
}

@article {pmid42943856,
year = {2026},
author = {Yao, P and Huang, J and Liu, W and Yuan, Q and Lv, J},
title = {Astragalus Polysaccharides Alleviate Inflammatory Damage in Murine Rheumatoid Arthritis by Modulating Th17/Treg Balance via the Gut-Joint Axis.},
journal = {Molecules (Basel, Switzerland)},
volume = {31},
number = {20},
pages = {},
pmid = {42943856},
issn = {1420-3049},
support = {CSTB2022NSCQ-MSX0199//Natural Science Foundation of Chongqing/ ; 81903888//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Th17 Cells/drug effects/immunology/metabolism ; *T-Lymphocytes, Regulatory/drug effects/immunology/metabolism ; *Polysaccharides/pharmacology/chemistry ; *Arthritis, Rheumatoid/drug therapy/pathology/immunology/metabolism ; Mice ; *Astragalus Plant/chemistry ; Gastrointestinal Microbiome/drug effects ; Cytokines/metabolism ; *Arthritis, Experimental/drug therapy/pathology/immunology ; *Joints/drug effects/pathology ; Inflammation/drug therapy ; Disease Models, Animal ; Male ; },
abstract = {Astragalus polysaccharides (APSs) have demonstrated protective effects in RA models; however, the underlying microbe-host crosstalk remains unclear. In this study, collagen-induced arthritis (CIA) was established in mice, followed by prophylactic and therapeutic APS administration. The following were then assessed: articular histopathology, splenic Th17/Treg frequencies via flow cytometry, serum and joint cytokine profiles via ELISA and immunohistochemistry, gut microbial metagenomes, and bone erosion via Safranin O-fast green staining. It was found that APS treatment significantly attenuated joint inflammation and bone destruction, rebalanced the Th17/Treg ratio, and reduced pro-inflammatory cytokines (TNF-α and IL-17) while elevating anti-inflammatory IL-10 both systemically and locally. Subsequently, fecal microbiota from APS-treated donor mice was transplanted via oral gavage into CIA recipient mice. APS reversed RA-associated gut dysbiosis by enriching Ligilactobacillus, Lactobacillus, Limosilactobacillus, and Bacteroides, and these microbial shifts closely paralleled diminished articular inflammation and preserved bone architecture. Collectively, these findings indicate that APS mitigates RA progression by reconfiguring the gut microbial ecosystem-favoring beneficial taxa while curbing pathobionts-thereby restoring intestinal homeostasis, normalizing the Th17/Treg axis, and suppressing systemic and articular inflammatory responses.},
}

Animals
*Th17 Cells/drug effects/immunology/metabolism
*T-Lymphocytes, Regulatory/drug effects/immunology/metabolism
*Polysaccharides/pharmacology/chemistry
*Arthritis, Rheumatoid/drug therapy/pathology/immunology/metabolism
Mice
*Astragalus Plant/chemistry
Gastrointestinal Microbiome/drug effects
Cytokines/metabolism
*Arthritis, Experimental/drug therapy/pathology/immunology
*Joints/drug effects/pathology
Inflammation/drug therapy
Disease Models, Animal
Male

@article {pmid42944006,
year = {2026},
author = {Wyler, M and Darpel, K and Berset, R and Renzullo, S and Huber, H and Bauer, J and Peter-Egli, J and Bachofen, C and Kubacki, J},
title = {Identification, Isolation and Genomic Characterization of an Emerging Shamonda Virus Variant Associated with Bovine Disease in Switzerland.},
journal = {Viruses},
volume = {18},
number = {10},
pages = {},
pmid = {42944006},
issn = {1999-4915},
mesh = {Animals ; Cattle ; Switzerland/epidemiology ; *Cattle Diseases/virology/epidemiology ; *Genome, Viral ; Phylogeny ; Disease Outbreaks/veterinary ; *Orthobunyavirus/genetics/isolation & purification/classification ; *Bunyaviridae Infections/veterinary/virology/epidemiology ; RNA, Viral/genetics ; High-Throughput Nucleotide Sequencing ; },
abstract = {In July 2026, an outbreak of a cattle illness characterized by high fever, diarrhea and reduced milk production, often affecting whole herds, was detected across several regions of northern Switzerland. To investigate the cause of the outbreak, a broad range of diagnostic methods was applied, including pathogen-specific RT-qPCRs, ELISA, serum neutralization test, virus isolation and metagenomic next-generation sequencing. A Shamonda virus (SHAV) was detected in samples from affected cattle, followed by successful virus isolation and complete genome sequencing of all three segments. Viral RNA was also detected in tissue samples from aborted calves, including the brain and spleen, supporting the need for further investigation of the virus in the context of reproductive disease. These findings document the first detection and molecular characterization of a SHAV in Switzerland and demonstrate its widespread circulation in cattle during the 2026 outbreak.},
}

Animals
Cattle
Switzerland/epidemiology
*Cattle Diseases/virology/epidemiology
*Genome, Viral
Phylogeny
Disease Outbreaks/veterinary
*Orthobunyavirus/genetics/isolation & purification/classification
*Bunyaviridae Infections/veterinary/virology/epidemiology
RNA, Viral/genetics
High-Throughput Nucleotide Sequencing

@article {pmid42944039,
year = {2026},
author = {Socha, W and Krzysiak, MK and Moniuszko, E and Kulik, P and Tomana, J and Larska, M},
title = {Next-Generation Sequencing in Practical Wildlife Disease Investigation: Metagenomic Insights into European Bison and Gazelle Mortality and Morbidity Events.},
journal = {Viruses},
volume = {18},
number = {10},
pages = {},
pmid = {42944039},
issn = {1999-4915},
support = {101136346 EUPAHW//European Food Safety Authority/ ; },
mesh = {Animals ; *Bison/microbiology/virology ; *Metagenomics/methods ; *Animals, Wild/microbiology/virology ; *High-Throughput Nucleotide Sequencing ; Phylogeny ; *Animal Diseases/mortality/microbiology/epidemiology ; Metagenome ; Pasteurella multocida/genetics/isolation & purification ; *Ruminants/microbiology/virology ; },
abstract = {Wildlife disease investigations require diagnostic methods capable of detecting diverse and previously unrecognized pathogens. Metagenomic next-generation sequencing (mNGS) was applied to samples from three Dorcas gazelles (Gazella dorcas osiris) affected by sudden mortality and four European bison (Bison bonasus) with respiratory disease or necrotic balanoposthitis (NBP). No dominant bacterial species was detected in gazelles. In European bison, respiratory disease was associated with Pasteurella multocida, whereas NBP samples were dominated by Porphyromonas levii and other anaerobes. Dorcas gazelle samples contained mainly Retroviridae-related sequences of undetermined pathogenic significance. Parapoxvirus-related annotations were not confirmed by PCR, suggesting non-specific or host-related sequence similarity. Macavirus-related sequences were consistent with previous PCR findings and enabled reconstruction of an approximately 51.1 kb fragment of a divergent gammaherpesvirus genome. These findings demonstrate the value of mNGS for wildlife disease investigation and genomic surveillance, while emphasizing the need for independent validation of metagenomic taxonomic assignments.},
}

Animals
*Bison/microbiology/virology
*Metagenomics/methods
*Animals, Wild/microbiology/virology
*High-Throughput Nucleotide Sequencing
Phylogeny
*Animal Diseases/mortality/microbiology/epidemiology
Metagenome
Pasteurella multocida/genetics/isolation & purification
*Ruminants/microbiology/virology

@article {pmid42944051,
year = {2026},
author = {Ghidini, M and Sberna, G and Guerrera, LP and Maggi, F and Novazzi, F},
title = {The Gut Virome in Gastrointestinal Cancers: Mechanisms, Biomarkers, and Translational Opportunities.},
journal = {Viruses},
volume = {18},
number = {10},
pages = {},
pmid = {42944051},
issn = {1999-4915},
mesh = {Humans ; *Gastrointestinal Neoplasms/virology/therapy ; *Virome ; *Gastrointestinal Microbiome ; Animals ; Bacteriophages ; Gastrointestinal Tract/virology ; Translational Research, Biomedical ; Biomarkers, Tumor ; Oncogenic Viruses ; Bacteria/virology ; },
abstract = {The gastrointestinal tract contains a dense multi-kingdom ecosystem in which bacteria, fungi, archaea, viruses, the mucosa, and the immune system interact. Although cancer microbiome research has focused mainly on bacteria, the gut virome dominated by bacteriophages may influence gastrointestinal carcinogenesis by reshaping bacterial communities, transferring functional genes, modulating inflammation, and altering treatment response. The strongest evidence comes from colorectal cancer, where multiple cohorts show altered phage diversity, temperate-phage enrichment, disrupted phage-bacteria networks, and reproducible stool-based diagnostic signals. Emerging studies in pancreatic cancer, esophageal adenocarcinoma, hepatocellular carcinoma, and precursor lesions suggest that virome disruption extends beyond colorectal cancer, although evidence remains uneven. Classic oncogenic viruses, including Epstein-Barr virus and hepatitis viruses, provide complementary examples of direct viral carcinogenesis in digestive organs. Anelloviruses are widespread in healthy individuals and are not established causes of cancer, but their abundance and composition may reflect immune status, inflammation, tissue injury, and altered host viral ecology. Virome-related interventions remain clinically immature: fecal microbiota transplantation has reached small phase I/II studies in gastrointestinal cancers, whereas phage, fecal-filtrate, and fecal virome approaches remain preclinical or non-oncology; direct oncolytic viruses have reached late-phase testing. Major barriers include viral dark matter, specimen and assay heterogeneity, disease-related confounding, limited external validation, and weak causal evidence. Standardized, mechanistically anchored, multi-kingdom studies are needed to establish clinical utility.},
}

Humans
*Gastrointestinal Neoplasms/virology/therapy
*Virome
*Gastrointestinal Microbiome
Animals
Bacteriophages
Gastrointestinal Tract/virology
Translational Research, Biomedical
Biomarkers, Tumor
Oncogenic Viruses
Bacteria/virology

@article {pmid42944114,
year = {2026},
author = {Ma, Q and Tharwat, M and Ullah, A and Liu, J and Alkheraif, AA and Khan, MZ},
title = {Integrating Host Transcriptomics and Metagenomics in the Periparturient Dairy Cow: From Molecular Signatures to Host-Microbiome Interfaces.},
journal = {Veterinary sciences},
volume = {13},
number = {10},
pages = {},
pmid = {42944114},
issn = {2306-7381},
support = {QU-APC-2026//Qassim University/ ; },
abstract = {The periparturient or transition period-roughly three weeks before to three weeks after calving-compresses the most severe metabolic, endocrine and immunological demands of the production cycle into a few weeks and accounts for most clinical disease and involuntary culling in dairy herds. Conventional surveillance relies on downstream indicators-non-esterified fatty acids, β-hydroxybutyrate, calcium and acute-phase proteins-that document failed adaptation without resolving its regulatory origins. Two omics platforms now close that gap. Transcriptomics shows that the liver, adipose tissue, mammary gland, endometrium, rumen epithelium and circulating leukocytes each execute a distinct, temporally ordered program organized around lipid mobilization, gluconeogenesis, endoplasmic reticulum stress, redox defense and inflammatory resolution, layered over a regulatory tier of non-coding RNAs. Metagenomics shows in parallel that rumen, hindgut, uterine, vaginal, teat-apex and colostrum communities are restructured by parturition and by the dietary shift into lactation, with reproducible dysbiotic signatures accompanying ketosis, fatty liver, metritis, endometritis and intramammary infection. Critically, the two layers are mechanistically coupled: microbial short-chain fatty acids, secondary bile acids, purine derivatives and amino acids reprogram hepatic and immune cell transcription, while host lipolysis, inflammation and mineral demand reshape community structure. This review synthesizes both groups of literature within a single framework, formalizes five host-microbiome interfaces supported by paired measurements and identifies the biomarker, nutritional and genetic-selection opportunities that emerge only when host and microbial evidence are read together.},
}

@article {pmid42944646,
year = {2026},
author = {Lynggaard, C and Bodawatta, KH and de Fraga, R and Martins, VCC and Aleixo, A and Tavares, VDC and Trevelin, LC and Gastauer, M and Bohmann, K},
title = {Active Filtration of Airborne eDNA for Vertebrate Surveys in Tropical Caves.},
journal = {Molecular ecology resources},
volume = {26},
number = {8},
pages = {},
doi = {10.1111/1755-0998.70218},
pmid = {42944646},
issn = {1755-0998},
support = {CF21-0411//Carlsbergfondet/ ; R100603.NNL.04//Instituto Tecnológico Vale/ ; R100603.CR.04//Instituto Tecnológico Vale/ ; VIL41390//Villum Fonden/ ; 309243/2023-8//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 313429/2025-1//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 310865/2022-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 441201/2023-7//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
mesh = {Animals ; *Caves ; Brazil ; *Vertebrates/classification/genetics ; *DNA, Environmental/genetics/isolation & purification ; *DNA Barcoding, Taxonomic/methods ; Biodiversity ; Extrachromosomal DNA ; *Filtration/methods ; Tropical Climate ; *Metagenomics/methods ; },
abstract = {Hidden from sunlight, caves are remarkable subterraneous ecosystems that host a wide range of animals, including unique species. Conventional cave biodiversity surveys can be physically challenging, disturb sensitive vertebrate communities, or require animal collection. Here we evaluate the use of metabarcoding of airborne environmental DNA (eDNA) as a non-invasive method for surveying cave vertebrates. We collected 55 samples by filtering air for 24 h at three light zones (outside, and in twilight and dark zones inside the cave) in three tropical caves in Amazonian Brazil. Using two metabarcoding primer sets targeting mammal and vertebrate DNA, we detected 123 wild vertebrate taxa encompassing mammals, birds, amphibians, and a reptile, of which 74 were identified to genus level. Genus richness in the twilight zone was significantly higher than outside the caves. Vertebrate diversity was also highest in the twilight zone, and community composition differed significantly between light zones and caves. Mammals and amphibians were mostly detected in the twilight and dark zones, whereas birds were more frequently detected outside the cave and in the twilight zone. While preliminary, our results show that caves with smaller entrances yielded more homogeneous communities in the twilight and dark zones. We detected eight of the 13 bat species and one of the four amphibian species recorded in previous surveys, while also detecting taxa not previously recorded in the caves, demonstrating complementarity with conventional surveys. As airborne eDNA requires minimal human presence in cave interiors, it reduces disturbance to sensitive fauna, lowers safety risks to surveyors, and offers a scalable method to complement conventional cave biodiversity surveys in tropical regions.},
}

Animals
*Caves
Brazil
*Vertebrates/classification/genetics
*DNA, Environmental/genetics/isolation & purification
*DNA Barcoding, Taxonomic/methods
Biodiversity
Extrachromosomal DNA
*Filtration/methods
Tropical Climate
*Metagenomics/methods

@article {pmid42786310,
year = {2026},
author = {Chen, J and Ren, Y and Zhou, Y and Wang, Z and Li, J and Guo, X and Xu, H and Wang, Y and Tang, H and Han, JJ},
title = {Multi-modality profiling identifies Neisseria flavescens as a central geroprotective oral commensal in humans.},
journal = {Nature aging},
volume = {6},
number = {10},
pages = {2202-2217},
pmid = {42786310},
issn = {2662-8465},
support = {32330017//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82361148130//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2025YFA1805300//Ministry of Science and Technology of the People's Republic of China (Chinese Ministry of Science and Technology)/ ; 2024YFF0729200//Ministry of Science and Technology of the People's Republic of China (Chinese Ministry of Science and Technology)/ ; 2025YFC3409300//Ministry of Science and Technology of the People's Republic of China (Chinese Ministry of Science and Technology)/ ; L2604004//Natural Science Foundation of Beijing Municipality (Beijing Natural Science Foundation)/ ; GZC20230084//China Postdoctoral Science Foundation/ ; },
mesh = {*Neisseria/physiology ; Humans ; *Aging/physiology ; Animals ; Mice ; Caenorhabditis elegans/physiology ; *Mouth/microbiology ; Multiomics ; Metagenome ; *Senotherapeutics ; Gastrointestinal Microbiome ; Biosynthetic Pathways ; Liver/metabolism ; Probiotics/administration & dosage ; Akkermansia/physiology ; Bifidobacterium/physiology ; Lactobacillaceae/physiology ; Random Allocation ; Male ; Mice, Inbred C57BL ; Tongue/microbiology ; },
abstract = {Aging is accompanied by progressive physiological decline, yet the microbiome determinants that modulate aging remain unclear. Here, we identify Neisseria flavescens (Nf) as an oral commensal associated with decelerated aging in humans. Using AURORA, a generative multi-modality framework, we developed multi-modality aging clocks, performed in silico screening for age-gap-reducing interventions and predicted Nf as a top hit. In silico perturbations linked increased Nf abundance to favorable physiological signatures, beneficial gut taxa and biosynthesis of beneficial metabolites. We isolated two Nf strains and validated their production of beneficial metabolites. Functional assays demonstrated that live Nf extended lifespan and healthspan in Caenorhabditis elegans. In aged mice, heat-killed Nf supplementation restored the serum metabolome, liver transcriptome and gut microbiome toward younger states. By establishing an AI-driven intervention discovery engine and identifying Nf as a geroprotective microorganism, these findings highlight the oral microbiome as an underestimated axis of systemic aging and a candidate for geroprotective interventions.},
}

*Neisseria/physiology
Humans
*Aging/physiology
Animals
Mice
Caenorhabditis elegans/physiology
*Mouth/microbiology
Multiomics
Metagenome
*Senotherapeutics
Gastrointestinal Microbiome
Biosynthetic Pathways
Liver/metabolism
Probiotics/administration & dosage
Akkermansia/physiology
Bifidobacterium/physiology
Lactobacillaceae/physiology
Random Allocation
Male
Mice, Inbred C57BL
Tongue/microbiology

@article {pmid42925771,
year = {2026},
author = {Pradeep, A and Mathew, AI and Koyyappurath, S and Vemula, PK and Bhat, SG and Narayanan, S},
title = {An exploratory study of gut microbiota and humoral immune responses following bacterial ghost administration in rats.},
journal = {Vaccine},
volume = {95},
number = {},
pages = {129284},
doi = {10.1016/j.vaccine.2026.129284},
pmid = {42925771},
issn = {1873-2518},
abstract = {The rise of multidrug-resistant pathogens necessitates innovative immunotherapeutic approaches. Bacterial ghosts (BGs) are non-viable empty cell envelopes retaining antigenic determinants, offer a safe and potent immunomodulatory alternative to live bacterial vaccines. This exploratory study examined the selected tolerability parameters, humoral immune responses, and gut microbiota profiles potential of Staphylococcus aureus-derived ghost cells (GCs) in Sprague Dawley rats. Animals received three doses at one-week intervals via oral and intramuscular (IM) administration at low (10[6] units/mL) and high (10[9] units/mL) doses over a 21-day period. Hemocompatibility, serum biochemistry, and histopathology of key organs provided preliminary insights into the tolerability of the formulation under the experimental conditions. Serum immunoglobulin profiling revealed increases in GC-specific IgG and IgA levels with oral administration, while IM delivery showed less systemic variations in antibody production. qRT-PCR analyses indicated a minimal but detectable pro-inflammatory cytokine expression, notably TNF-α, especially in high-dose IM groups. Gut microbiome analysis via 16S rRNA sequencing identified differences in microbial diversity indices and the relative abundance of selected bacterial taxa across experimental groups. Histological assessments of gut tissue indicated mild, non-pathological mucosal changes only at high oral doses. Overall, the findings provide preliminary observations on humoral immune responses, selected tolerability parameters, and gut microbiota profiles following GC administration. These preliminary findings encourage further investigation of BGs as engineerable platforms with potential applications in immunomodulation, mucosal vaccine development, and microbiome-targeted interventions.},
}

@article {pmid42926052,
year = {2026},
author = {Wang, W and Chu, W and Lan, S and He, Y and Chen, Y and Zhou, H and Wang, L and Yu, Y and Wang, Z and Tan, Z and Zhang, Y and Li, X},
title = {Stage-dependent nutrient assimilation, protein accumulation and microbial instability during fed-batch cultivation of Chlorella mutant strain in Chinese Baijiu brewing wastewater.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {136122},
doi = {10.1016/j.biortech.2026.136122},
pmid = {42926052},
issn = {1873-2976},
abstract = {Chinese Baijiu brewing wastewater (CBBW) is a high-strength organic wastewater rich in recoverable nutrients, but its direct conversion into microalgal protein remains limited by unstable loading and microbial succession. This study established a photobioreactor using real CBBW and the heavy-ion-mutagenized Chlorella mutant SLJ-Q1 under fed-batch culture. During the early phase (Days 0-10), SLJ-Q1 achieved a specific growth rate of 0.069/d, with total nitrogen (TN) and chemical oxygen demand (COD) removal rates of 12.6 and 332.8 mg/(L·d). This phase featured enhanced bacterial network complexity and genetic potential for carbon-nitrogen co-metabolism and amino acid biosynthesis, promoting nutrient conversion into protein-rich biomass. The harvested biomass reached 1.85 g/L, containing 65.5% crude protein with an essential amino acid index (EAAI) of 0.94-0.99 and heavy metals below feed safety limits. However, the bacterial count (5.93 × 10[7] CFU/g) exceeded GB 13078-2017, indicating that post-harvest hygienic treatment is required. Prolonged feeding caused oxygen-limiting conditions, Clostridium enrichment, enhanced genetic potential for anaerobic nitrogen metabolism, nutrient accumulation, and photobioreactor (PBR) destabilization. These findings suggested the feasibility of producing microalgal protein from CBBW and highlight feed loading control, dissolved oxygen balance, and post-harvest hygienic treatment as key considerations for sustainable scale-up.},
}

@article {pmid42926093,
year = {2026},
author = {Li, X and Liu, H and Wu, J and Xi, C},
title = {Source Apportionment and Resistome Signatures of Community and Hospital Effluents in Urban Sewer Networks.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {129378},
doi = {10.1016/j.envpol.2026.129378},
pmid = {42926093},
issn = {1873-6424},
abstract = {Antibiotic resistance surveillance has traditionally focused on clinical settings, potentially overlooking broader microbial reservoirs in the community. Wastewater-based epidemiology (WBE) provides a powerful tool for capturing these population-level signals. This study aimed to identify source-specific resistome characteristics and estimate the relative compositional contributions of hospital and residential wastewater to the downstream wastewater treatment plant (WWTP). By integrating droplet digital polymerase chain reaction (ddPCR) with metagenomic sequencing, spatiotemporal dynamics across an urban sewer network were characterized. Bacterial 16S rRNA gene concentrations did not differ significantly between hospital and residential wastewater. Under the specified flow scenarios, hospital wastewater represented a small fraction of the estimated total influent volume. Bayesian source tracking further indicated that residential sources collectively accounted for nearly 80% of the inferred source contribution to the influent antibiotic resistance genes (ARGs) profile and 70.9% of the influent microbial community composition, whereas hospital wastewater accounted for only 5.5% of the inferred resistome contribution. These findings show that hospital wastewater contained clinically important resistance genes (e.g., blaKPC-2), whereas the sampled residential references accounted for the largest combined inferred contribution to the influent microbiome and resistome. Together, these results highlight the importance of incorporating community surveillance through wastewater-based approaches within the One Health framework.},
}

@article {pmid42926479,
year = {2026},
author = {Norton, GJ and Dudek, AM and Gerner, RR and Guo, C and Castillo, V and Argueta, FA and Beebout, CJ and Kamyabi, G and Drushell, J and Walker, GT and Hsu, CY and Bessho, S and Nuccio, SP and Chu, H and Zengler, K and Nolan, EM and Raffatellu, M},
title = {Targeting catecholate siderophore systems enables precision depletion of gut enterobacteria during colitis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.10.02.756324},
pmid = {42926479},
issn = {2692-8205},
abstract = {Adherent-invasive Escherichia coli (AIEC) is frequently isolated from the dysbiotic gut microbiome in inflammatory bowel disease and is implicated in disease progression, highlighting its potential as a therapeutic target. Here we show that iron acquisition is essential for AIEC colonization of the inflamed gut. Mechanistically, four catecholate siderophore receptors act redundantly to support AIEC growth under iron-limited conditions and during colitis. Immunization of colitis-prone Il10 [-/-] mice against catecholate siderophores reduced intestinal AIEC colonization, particularly its association with the mucosa, while largely preserving overall gut microbiome composition. Longitudinal metagenomic profiling identified immunization-associated shifts in Akkermansiaceae and Lactobacillaceae , and experiments in gnotobiotic Il10 [-/-] mice demonstrated that Limosilactobacillus reuteri , a member of the Lactobacillaceae , limited AIEC colonization, whereas Akkermansiaceae exacerbated disease. Our findings establish catecholate siderophore-mediated iron acquisition as a therapeutic target in AIEC and provide proof-of-principle that virulence-targeted immunization can selectively antagonize a disease-associated bacterium while preserving the gut microbiota.},
}

@article {pmid42926633,
year = {2026},
author = {Oliver, A and Podell, S and Allen, EE},
title = {Conserved synteny reveals a saccharolytic lifestyle across Kiritimatiellia.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.10.06.756941},
pmid = {42926633},
issn = {2692-8205},
abstract = {Kiritimatiellia are a class of Verrucomicrobiota whose few cultured representatives are known for hosting large repertoires of carbohydrate-active enzymes and sulfatases. Many families of this class are restricted to metagenome-assembled genomes not yet discussed in literature, leaving their genome organization undescribed. Here, we survey 898 Kiritimatiellia genomes using similarity-colocalization networks (SCoNes), a data structure that captures conserved synteny among homologous genes across genomes. Using this approach, we investigate four metabolic adaptations to a glycan-rich environment: complex polysaccharide degradation, nitrogen cycling, hydrogenase activity, and natural product biosynthesis. Rather than unrelated functions, these capacities envelop a single anaerobic and saccharolytic strategy where sulfated glycan hydrolysis fuels fermentation, hydrogenases balance redox, and excess carbon supports nitrogen fixation.},
}

@article {pmid42926716,
year = {2026},
author = {Jiang, AK and Arp, G and Kato, M and Brunner, T and Grant, MR and Clarke, AM and Sidebottom, AM and McMillin, M and Lehmann, CJ and Odenwald, MA and Wolfe, KS and Patel, BK and Odenike, O and Li, Y and Light, SH and Hall, B and Jiang, X},
title = {SpiE is a distinct gut microbial 4-cholesten-3-one 5β-reductase that acts with SpiR to convert cholesterol to coprostanol.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.10.06.757028},
pmid = {42926716},
issn = {2692-8205},
abstract = {Gut microbes convert cholesterol into coprostanol, a poorly absorbed sterol that is largely excreted in feces and is linked to lower serum cholesterol levels. However, the enzymes responsible for this process remain poorly characterized. The second step of the pathway, cholestenone reduction into coprostanone, has long been established, yet the enzyme(s) responsible were unknown. Here, we use comparative genomics to identify SpiE, a cholestenone (4-cholesten-3-one) reductase that is part of the steroid processing (spi) pathway with SpiR. We confirm that SpiE binds to and reduces both cholestenone and progesterone into 5β-reduced forms. SpiR and SpiE together convert cholesterol into coprostanol, indicating that both enzymes are sufficient for coprostanol formation. SpiE belongs to the short-chain dehydrogenase (SDR) family and represents an evolutionarily distinct lineage of SDR ene-reductases. Metagenomic analyses reveal that spiE relative abundance is strongly correlated with stool coprostanol (Spearman's ρ=0.81, p =5.99e-65). In longitudinal patient cohorts, antibiotic treatment coincided with loss of SpiE and coprostanol production. Post antibiotics, the emergence of distinct SpiE-encoding genera rescued coprostanol production in some individuals. Our findings provide the biochemical basis of the cholesterol to coprostanol pathway and lay the groundwork for future studies linking it to host physiology.},
}

@article {pmid42926794,
year = {2026},
author = {Faure, R and Nakshi, AH and Abrar, MH and Chikhi, R and Lemane, T and Taheri, M and Won, S and Wu, H and Koslicki, D and Medvedev, P},
title = {Sketching the SRA: experiment-wide similarity search across 4.8 million metagenomes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.10.07.757297},
pmid = {42926794},
issn = {2692-8205},
abstract = {Recent efforts have demonstrated that systematic analysis of the millions of metagenomes in the Sequence Read Archive (SRA) enables groundbreaking biological discoveries. However, SRA-scale comparison of whole metagenomes has remained elusive. Here, we introduce the most comprehensive resource to date for experiment-to-experiment analysis of all SRA metagenomes, comprising FracMinHash sketches (470GB), hypergen sketches (19GB), and an all-pairs Jaccard similarity matrix (90GB), which we release online at https://github.com/RolandFaure/SRA-metagenome-sketches-databases . These resources enable a wide range of analyses, which we demonstrate with several applications. First, we use the FracMinHash sketches to uncover temporal trends, finding that the amount of newly discovered microbial sequence continues to grow, rather than saturate or shrink. Second, we use the hypergen sketches, which enable nearest-neighbor search, to identify co-assembly candidates and thereby improve assembly quality. Third, we use the similarity matrix to analyze all SRA metagenomes, identifying duplicated submissions and over 50K candidates for metadata correction. Together, our resources unlock systematic analysis of metagenomic data at unprecedented scale.},
}

@article {pmid42926836,
year = {2026},
author = {Guo, J and Tran, HTT and Cai, Q and Hoang, MV and Tran, TV and Shu, XO and Nguyen, SM},
title = {Rural-urban differences in gut microbiome among Vietnamese women.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.10.04.26364707},
pmid = {42926836},
abstract = {Gut microbiome plays an important role in human health. Urbanization has been suggested to alter the gut microbiome. We comprehensively evaluated differences in gut microbiome profiles of 76 urban and 81 rural female residents of Vietnam using shotgun metagenomic data. We evaluated rural-urban differences in gut microbial diversity, individual microbial taxa, and metabolic pathways. Rural residents had higher alpha and beta diversities in age-adjusted models (p<0.05). Additionally, significant rural-urban differences were observed for 35 microbial taxa in age-adjusted models (FDR<0.1). Rural residents had higher relative abundance of classes, orders, and families of FGB2982 and FGB38642 and strain SGB15332 of the species Faecalibacterium prausnitzii , whereas urban residents had higher relative abundances of species Bacteroides thetaiotaomicron, Coprobacter fastidiosus, Bilophila wadsworthia, Enterobacter cloacae, Enterobacter hormaechei, Klebsiella aerogenes , Dielma fastidiosa, and Holdemania massiliensis. Notably, these associations were attenuated after further adjustment for socioeconomic characteristics, lifestyle, dietary factors, and comorbidity (FDR>0.1). In the fully adjusted model, significant rural-urban differences were observed in the abundance of 17 microbial taxa, including Ruminococcus sp AF13 28 and Prevotella pectinovora, as well as in three metabolic pathways (FDR<0.1). This study suggests that urbanization-related factors may contribute to differences in the gut microbiome between urban and rural Vietnamese women.},
}

@article {pmid42926938,
year = {2026},
author = {Vatanen, T and Kreuze, K and Björkgren, L and Turkington, C and Nezam-Abadi, N and Seymour, S and Shkoporov, A and Hill, C and Friman, V and Knip, M},
title = {Maternal transmission and limited virulent phage replication shape early infant gut virome maturation.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-11232673/v1},
pmid = {42926938},
issn = {2693-5015},
abstract = {Early life gut microbiome dynamics are increasingly recognized as important determinants of microbiome maturation, yet the ecological dynamics of its associated bacteriophages remain poorly resolved. Here, we performed bulk and virus like particle (VLP)-enriched metagenomic sequencing and fecal metabolomic profiling of longitudinal fecal samples from 32 mother-infant dyads, incorporating an exogenous phage spike in to enable absolute quantification of viral loads. Our results show that early infant gut phageome is defined by a profound lack of virulent phage genome copies while temperate phages remain relatively stable, challenging previous assumptions. We further identified extensive maternal sharedness of mainly virulent phages predicted to infect Bacteroidaceae, which could explain recovery of virulent phage absolute abundances. Virulent phage concentrations were further associated with several fecal metabolites including primary bile acids. These findings revise the current model of infant phageome assembly highlighting the underappreciated role of virulent phages.},
}

@article {pmid42927839,
year = {2026},
author = {Li, X and Cai, Y and Yin, F and Chen, WS and Huang, S and Li, A and Zhou, T and Fernandes, TV and Dong, H},
title = {Staged waste-based lactic acid broth redistributes multi-gas emission windows during swine manure composting.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {136127},
doi = {10.1016/j.biortech.2026.136127},
pmid = {42927839},
issn = {1873-2976},
abstract = {Composting recycles livestock manure, but temporally distinct ammonia, nitrous oxide and methane emissions can obscure trade-offs between nitrogen conservation and climate mitigation. We evaluated staged supplementation with waste-based lactic acid fermentation broth (LA) during 42-d forced-aeration rotary-drum composting of swine manure and maize straw, using three parallel reactors per treatment and equal-mass water addition (WA) as the control. LA showed a short initial heating/decomposition lag followed by thermophilic and carbon-transformation catch-up. Reactor-mean ammonia release during temperature-defined days 2-6 was 49.9% lower; the sampled peak shifted from day 3 to day 5 and was 17.3% lower. Later compensation limited the day-42 mean difference to 7.8%, indicating early-window attenuation and redistribution. Observed cumulative means of nitrous oxide and methane were 41.5% and 37.3% lower, respectively, producing a 38.5% lower direct non-CO2 greenhouse-gas mean. Lower early pH was consistent with a lower estimated free-ammonia fraction and temporary maintenance of an ammoniacal pool. Higher early nosZ/(nirK + nirS) and nosZ/nirK ratios indicated greater annotated terminal nitrous-oxide-reduction potential relative to nitrite-reduction potential. After day 21, methane approached zero despite a higher sampled methane peak under LA, as late carbon dioxide release weakened and mcrA, mcrB and mcrG abundances remained low. These DNA profiles represent functional potential rather than gene activity. Both germination index (GI) means exceeded the 70% criterion by day 7; late temperature, carbon dioxide, total organic carbon (TOC) and humic-like dissolved organic matter (DOM) supported progressive stabilization. Strong early ammonia attenuation is promising for recurrent-feed thermophilic semi-continuous systems with captured exhaust, based on batch results.},
}

@article {pmid42927840,
year = {2026},
author = {Yi, MM and Lv, PL and He, SY and Li, Q and Chen, R},
title = {How acetate alleviates ammonium inhibition and enhances methane-fed single-cell protein production.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {136124},
doi = {10.1016/j.biortech.2026.136124},
pmid = {42927840},
issn = {1873-2976},
abstract = {Anaerobic digestion produces methane-rich biogas and ammonium-rich digestate, but their joint conversion into single-cell protein (SCP) requires coordinated carbon and nitrogen utilisation. Here, a methane-fed mixed consortium was operated in a membrane biofilm reactor to determine how acetate regulates carbon-nitrogen coordination under ammonium stress. Ammonium addition impaired nitrogen conversion and protein enrichment without eliminating methylotrophs. Acetate restored these functions, increasing protein content to 61.25 % and the apparent N-based SCP yield from 0.34 to 1.46 g SCP/g N. Nitrogen balances showed greater incorporation of inorganic nitrogen into cellular organic nitrogen with acetate, consistent with the increased metagenomic potential for the glyoxylate shunt and ammonium assimilation. Excess acetate, however, promoted soluble microbial products and extracellular polymeric substances, lowering the apparent carbon-based SCP yield. These findings suggest that acetate improves nitrogen incorporation and protein production in a methane-fed mixed consortium while methane utilisation remains active. Controlled acetate retention in anaerobic digestate may therefore support the joint recovery of waste-derived carbon and nitrogen as microbial protein.},
}

@article {pmid42928761,
year = {2026},
author = {Liu, J and Wang, X and Xie, P and Dong, L and Bai, P and Liu, Y and Chen, G and Hao, D},
title = {Tropheryma whipplei Pneumonia with Myelofibrosis: A Rare Actinomycetia Case Report and Literature Review.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {636054},
pmid = {42928761},
issn = {1178-6973},
abstract = {Tropheryma whipplei (T. whipplei) is an uncommon pathogen that infects multiple sites, predominantly the gastrointestinal tract. However, pulmonary involvement is uncommon, and its clinical manifestations and imaging features lack specificity, making it prone to misdiagnosis. However, with the development of metagenomic next-generation sequencing (mNGS), clinicians have a potent tool at their disposal for detecting T. whipplei infections. We report a case of an elderly woman with a history Myelofibrosis who presented with a dry cough, fever, fatigue and difficulty breathing. Routine microbiological tests were negative; mNGS of bronchoalveolar lavage fluid (BALF) suggested T. whipplei infection. Following a definitive diagnosis, the patient was treated with a regimen of meropenem in combination with trimethoprim-sulfamethoxazole (TMP-SMX) for 16 days followed by 2 weeks of TMP-SMX maintenance, after which the patient improved and was discharged uneventfully.},
}

@article {pmid42928806,
year = {2026},
author = {Chaumeil, PA and Hugenholtz, P and Parks, DH},
title = {gTranslate: rapid and accurate translation table prediction for prokaryotic genomes.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e21825},
pmid = {42928806},
issn = {2167-8359},
mesh = {*Computational Biology/methods ; *Genome, Bacterial ; *Protein Biosynthesis ; *Software ; Machine Learning ; },
abstract = {BACKGROUND: Bioinformatic tools often require the prediction of protein-coding genes to make inferences about prokaryotic genomes. Typically, the genetic code used for translating genes to proteins must be specified by the user based on the taxonomic classification of a genome assembly or, for some widely used tools, established using a heuristic rule based on gene coding densities. Manual specification is at best inconvenient, but more challenging is that many bioinformatic tools are applied before taxonomic classifications have been established making specifying the translation table impractical.

METHODS: Here we provide a computationally efficient tool, gTranslate, that uses an ensemble of five machine learning methods to accurately predict translation tables for prokaryotic genomes. The feature vector used by gTranslate takes advantage of differences in gene coding densities when predicting genes under different translation tables along with features that consider the number and ratio of UGA stop codon reassignments to tryptophan or glycine. gTranslate is freely available at https://github.com/cmc-aau/gTranslate and archived on Zenodo.

RESULTS: We demonstrate that gTranslate correctly predicts the translation table of prokaryotic genomes >99.99% of the time (i.e., <1 error per 10,000 genomes) and outperforms a more computationally expensive prediction method and a coding density heuristic used by popular bioinformatic tools. Using gTranslate, we identify a basal lineage of Ca. Stammera capleta that uses the standard bacterial genetic code instead of the UGA stop codon to tryptophan reassignment common to other members of this species. We also identify the first instances of UGA-to-tryptophan reassignment in the Patescibacteriota making this the first bacterial phylum with members capable of using translation tables 4, 11, and 25.},
}

*Computational Biology/methods
*Genome, Bacterial
*Protein Biosynthesis
*Software
Machine Learning

@article {pmid42929531,
year = {2026},
author = {Zhang, J and Fang, L and Ma, C and Hu, Z and Chen, C and Zhu, T and Ying, J and Zhu, W and Huang, G and Ni, J and Zhang, C and Yu, G},
title = {Gut Clostridium aminophilum as a protective microbe in never-smoker lung cancer: insights from metagenomics and machine learning.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0099426},
doi = {10.1128/spectrum.00994-26},
pmid = {42929531},
issn = {2165-0497},
abstract = {Lung cancer in never-smoking patients (LCINS) has gradually gained attention in recent years, and emerging evidence points to a potential role of the gut microbiota in LCINS by modulating host immunity and metabolism. In this study, metagenomics was performed on stool samples from 24 LCINS patients and 18 healthy individuals. LCINS patients exhibited reduced microbial richness in α-diversity compared with healthy controls, and differences in principal component distribution were observed. Pathway enrichment analyses revealed that LPS biosynthesis capacity was significantly increased, whereas the fatty acid biosynthesis pathway was significantly decreased in LCINS. A total of 317 differentially abundant species were identified, including 29 assigned to the module most strongly associated with LCINS based on weighted gene co-expression network (WGCNA). Then, 36 machine learning-based diagnostic models were constructed based on these 29 species, with the glmBoost + Ridge model showing the best performance for LCINS discrimination (AUC = 0.855). SHAP (SHapley Additive exPlanations) identified Clostridium aminophilum as a protective factor and the top contributor to model performance (SHAP value = 0.068), with a single-species AUC of 0.743. In vitro, the culture supernatant of Clostridium aminophilum markedly suppressed A549 cell proliferation and migration. In vivo, oral administration of Clostridium aminophilum (5 × 10[6] CFU) for 21 days significantly suppressed tumor growth in subcutaneous A549-derived xenograft models. These findings suggest a significant association between LCINS and the gut microbiota, characterized by a marked depletion of Clostridium aminophilum. Notably, metabolites derived from Clostridium aminophilum were shown to inhibit lung cancer progression.IMPORTANCELung cancer remains the leading cause of cancer incidence and mortality worldwide, and the proportion of lung cancer in patients who have never smoked (LCINS) has been steadily increasing. However, the potential role of the gut microbiota in this disease has not been fully explored. In this study, we characterized the gut microbial spectrum of LCINS patients using metagenomic sequencing and developed a lung cancer predictive model with translational potential. Importantly, we identified a beneficial bacterium, Clostridium aminophilum, which may be developed as a probiotic to support conventional lung cancer treatments. These findings offer promising avenues for early diagnosis, adjunctive therapy, and personalized management of gut microbiota in LCINS patients.},
}

@article {pmid42930067,
year = {2026},
author = {Liakopoulou, G and Koutsiaris, AG},
title = {Artificial Intelligence in Virus Detection: From Metagenomic Discovery to Clinical Decision Support and Population Surveillance.},
journal = {Biotech (Basel (Switzerland))},
volume = {15},
number = {4},
pages = {},
doi = {10.3390/biotech15040090},
pmid = {42930067},
issn = {2673-6284},
abstract = {Artificial intelligence (AI) is increasingly central to modern virus detection, particularly as metagenomic next-generation sequencing (mNGS) expands diagnostic and surveillance capabilities beyond targeted assays. This paper reviews how AI supports virus detection across three interconnected levels. The metagenomic layer forms the technical core of the review, while the clinical and population sections examine how sequence-level AI outputs are translated into patient-level and public-health decision support. At the metagenomic level, AI addresses key bottlenecks caused by fragmented assemblies and weak homology signals. Foundation-model approaches such as ViraLM leverage pretrained genome representations to improve viral contig discrimination under short-contig conditions, whereas LucaProt integrates sequence- and structure-informed learning to detect highly divergent RNA viruses via RdRP (RNA-dependent RNA polymerase)-focused discovery. At the clinical level, targeted molecular tests remain effective when the suspected pathogen is known, while mNGS provides a complementary, hypothesis-free approach that can broaden etiological investigation in complex infections when laboratories apply appropriate quality control and clinicians interpret results in context. At the population level, early warning systems combine heterogeneous data sources (epidemiological, open-source, digital, environmental, and wastewater signals) with AI methods to enhance outbreak detection and forecasting. Across all levels, robust contamination control, transparent reporting, external validation, and standardized interpretation criteria determine real-world value. Overall, hybrid pipelines that integrate molecular evidence, clinical metadata, and population-scale surveillance within governed, reproducible workflows are likely to provide the greatest impact.},
}

@article {pmid42925753,
year = {2026},
author = {Zhang, Q and Yang, Y and Hou, L and Ng, HY},
title = {Sequential quorum-sensing regulation mitigates the trade-off between methane production and biofouling in anaerobic membrane bioreactors.},
journal = {Water research},
volume = {309},
number = {Pt A},
pages = {127167},
doi = {10.1016/j.watres.2026.127167},
pmid = {42925753},
issn = {1879-2448},
abstract = {Anaerobic membrane bioreactors (AnMBRs) enable simultaneous wastewater treatment and methane recovery, but their long-term operation is constrained by the conflict between enhanced microbial activity and membrane biofouling. Acyl-homoserine lactone (AHL)-mediated quorum sensing (QS) regulates anaerobic metabolism, extracellular polymeric substance (EPS) production, and biofilm formation, making microbial signaling a potential means of balancing methane production and membrane fouling control. Here, we developed a sequential QS modulation strategy that couples metabolic activation with signal attenuation in AnMBRs. C10-HSL, a medium-chain AHL, was first introduced to activate LuxR-type QS signaling and strengthen methanogenic electron transfer, while a naringenin-β-cyclodextrin inclusion complex (NAR-β-CD) was subsequently applied to attenuate biofilm-associated QS responses with improved system stability. C10-HSL stimulation increased sludge electron-transfer activity by 19.95 % and cumulative methane production by 18.42 %, confirming the effectiveness of QS activation in intensifying anaerobic conversion. Subsequent NAR-β-CD addition reduced EPS accumulation and alleviated membrane fouling while maintaining methane recovery. Metagenomic profiling revealed distinct regulatory outcomes: C10-HSL enriched genes associated with secretion systems, redox mediator biosynthesis, and biofilm formation, whereas NAR-β-CD altered QS-associated signaling, transport, and metabolic functions, accompanied by reduced EPS production. These findings establish sequential QS modulation as a microbial signaling-oriented strategy to balance methanogenic intensification from biofouling development, offering a new route toward stable energy recovery in AnMBRs.},
}

@article {pmid42925759,
year = {2026},
author = {Yue, H and Guan, X and Shen, Y},
title = {Sewer-relevant aging of microplastics drives plastic-class-dependent N2O emissions from denitrifying sludge.},
journal = {Water research},
volume = {309},
number = {Pt A},
pages = {127194},
doi = {10.1016/j.watres.2026.127194},
pmid = {42925759},
issn = {1879-2448},
abstract = {Microplastics (MPs) accumulate in sewer systems and wastewater treatment plants (WWTPs), where they undergo aging processes distinct from photo-oxidation in surface waters. How such sewer-relevant aging impacts denitrification-associated nitrous oxide (N2O) emissions remains unknown. Here, we simulated sewer-relevant aging (sulfidation and mechanical abrasion) for non-biodegradable, compostable and biodegradable MPs (NMPs, CMPs, BMPs) and evaluated their effects on N2O emissions relative to pristine MPs, while linking MP-derived dissolved organic carbon (DOC) characteristics to microbial physiological and community responses. Aging increased DOC release from CMPs and BMPs by 30.0% and 115.8%, respectively, and generated plastic-dependent molecular signatures enriched in aromatic and sulfur-containing compounds. Rather than bioavailable carbon sources, aged MP-derived DOC could barely be consumed as the electron donor yet acted as a potent physiological disruptor. Correspondingly, aged CMPs and BMPs increased N2O emissions to 2.5- and 8.0-fold those of their pristine counterparts, with a stimulation order of BMPs > CMPs > NMPs under carbon-sufficient conditions (C/N = 4:1). Stronger N2O stimulation was associated with more severe membrane damage and greater impairment of electron supply. Metagenomic analysis further revealed enrichment of Paracoccus under stronger N2O stimulation, together with shifts in denitrification-related genomic potential. As a genus capable of degrading diverse plastic additives while harboring a complete denitrification pathway, Paracoccus could favor N2O accumulation under electron-limited conditions, where N2O reduction is disadvantaged relative to upstream denitrification steps. These findings showed that sewer-relevant aging reshaped MP effects on denitrification-associated N2O emissions in a plastic-dependent manner and challenged the presumed environmental benignity of compostable and biodegradable plastics, underscoring the need to incorporate MPs aging into risk assessment for WWTPs.},
}

@article {pmid42923188,
year = {2026},
author = {Wang, X and Li, J and Cheng, Y and Liu, Y and Li, H and Tan, H and Hu, Y and Zhao, M and Liu, J},
title = {Microbiota-assisted screening for colorectal neoplasia: advanced adenoma as the key translational endpoint-a narrative review.},
journal = {American journal of translational research},
volume = {18},
number = {9},
pages = {8227-8253},
pmid = {42923188},
issn = {1943-8141},
abstract = {Microbial differences between established colorectal cancer (CRC) and cancer-free controls are reproducible, but screening translation depends on detecting advanced adenoma and early CRC in asymptomatic populations. We examined the gut microbiota as an adjunct to fecal immunochemical testing (FIT), stool deoxyribonucleic acid (DNA) testing, and colonoscopy, with advanced adenoma as the prevention-relevant endpoint. This narrative review used a structured, purposive search of PubMed, Embase, Web of Science, Scopus, and the Cochrane Library through April 10, 2026, prioritizing human neoplasia cohorts, stage-specific biomarkers, multi-omics studies, FIT comparators, and reporting standards. Across studies, microbial signals were strongest for established CRC and weaker and less consistently reported for advanced adenoma. Quantitative evidence supports selected adjunctive approaches, including fecal Fusobacterium nucleatum and multitaxon panels combined with FIT, but external validation remains sparse. The 2025 pooled analysis of 3,741 metagenomes demonstrated reproducible CRC-related features across 18 cohorts but did not report advanced-adenoma-specific accuracy. Clinical utility cannot be inferred from sensitivity, specificity, or the area under the receiver operating characteristic curve alone: prevalence-dependent positive predictive value (PPV), negative predictive value (NPV), calibration, a prespecified action threshold, decision-curve net benefit, and colonoscopy burden are decisive. Translation therefore requires a locked assay and model tested prospectively before bowel preparation in a representative screening cohort, with advanced adenoma reported separately and performance compared directly with FIT or stool DNA testing. Microbiota-based markers currently merit evaluation as adjuncts, not replacements, within established screening pathways.},
}

@article {pmid42923191,
year = {2026},
author = {Li, Z and Wang, Y and Lai, L and Huang, Y and Li, L},
title = {A novel multiplex assay for species-level identification of non-tuberculous mycobacteria in culture-positive respiratory specimens based on capillary electrophoresis: development and clinical validation.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1966137},
pmid = {42923191},
issn = {1664-302X},
abstract = {Nontuberculous mycobacterial pulmonary disease (NTM-PD) is rising globally, driven predominantly by Mycobacterium avium complex (MAC), yet treatment is highly species-dependent. We developed a Multiplex assay targeting four clinically important non-tuberculous mycobacteria (NTM) species-M. avium, M. intracellulare, M. abscessus, and M. fortuitum-and compared it with metagenomic next-generation sequencing (mNGS), using colony-based multigene Sanger sequencing as the reference method. Among 101 specimens, 63 (62.4%) yielded polymicrobial results, of which mixed-species detection of M. avium-M. intracellulare accounted for 46 (73.0%). The Multiplex assay and mNGS showed no statistically significant difference in overall accuracy in this cohort (82.2% vs. 81.2%; raw agreement 83.2%, P = 1.000). The Multiplex assay achieved 100.0% sensitivity for all four species, with specificity of 87.8% and 87.5% for M. avium and M. intracellulare, respectively, and >98% for M. abscessus and M. fortuitum; mNGS showed the converse pattern, with lower MAC sensitivity (88.5%, 92.2%) but higher MAC specificity (93.9%, 95.8%). Requiring only a single PCR reaction without sequencing or bioinformatic analysis, the Multiplex assay showed no statistically significant difference in diagnostic accuracy from mNGS in this culture-positive cohort, without requiring library preparation or sequencing, representing a promising candidate for further evaluation as a routine NTM species-identification tool.},
}

@article {pmid42923215,
year = {2026},
author = {Luo, Y and Wang, Y and Shi, Z and Li, Z and Pu, T and Wang, Y and Ni, M and He, X and Li, J and Li, C and Li, X and Yang, P},
title = {Metagenomic and culture-dependent characterization of between-field variation in phosphorus-cycling microbial communities and functional potential across tobacco-safflower rotation fields.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1983930},
pmid = {42923215},
issn = {1664-302X},
abstract = {INTRODUCTION: Rhizosphere microorganisms contribute to soil phosphorus (P) transformation and plant P acquisition, but P-cycling microbial communities and functional associations across tobacco-safflower rotation fields remain poorly characterized.

METHODS: Twenty-one safflower rhizosphere soil samples were collected from seven tobacco-safflower rotation fields in Lijiang, China. Soil physicochemical properties were measured, and shotgun metagenomics was used to characterize P-cycling bacterial communities and genes associated with P solubilization, mineralization, regulation, and transport. Culturable phosphate-solubilizing bacteria were isolated, preliminarily assigned taxonomically using 16S rRNA gene sequences, and evaluated by plate and liquid-culture assays.

RESULTS: Soil properties and P-cycling bacterial communities showed pronounced between-field variation. Metagenomic screening identified 6,019 non-redundant gene sequences assigned to 38 predefined P-cycling KO terms, with 460 genus-level bacterial taxa. Among 124 taxa shared across all fields, Nocardioides, Arthrobacter, Streptomyces, Gaiella, and Marmoricola were major dominant genera. PCoA and PERMANOVA showed significant field differences at the phylum (R [2] = 0.983, p = 0.001) and genus (R [2] = 0.964, p = 0.001) levels. Soil pH was associated with all four P-cycling functional modules. Exploratory random-forest analysis identified Sphingomonas, Streptomyces, Nocardioides, and Arthrobacter as candidate indicator taxa associated with variation in soil available P. Eighty-six culturable phosphate-solubilizing isolates representing 45 putative species-level taxa were obtained, with Streptomyces the most abundant genus (22.1%). Streptomyces isolates had solubilization index values of 1.10-1.89. The isolate with the highest SI, Streptomyces sp. LG-4, provisionally affiliated with S. endophyticus, reached a maximum net phosphate solubilization of 354.60 ± 7.22 mg L[-1] on day 3.

CONCLUSION: Soil physicochemical heterogeneity, particularly pH, was associated with between-field differences in P-cycling microbial communities and metagenomically inferred functional potential. Because no non-rotation or monoculture controls were included, these patterns should be interpreted as field-associated variation rather than effects of the rotation system itself. Both metagenomic and culture-dependent analyses highlighted Streptomyces as a candidate group of interest, while Streptomyces sp. LG-4 showed phosphate-solubilizing capacity under laboratory conditions and requires further taxonomic and functional validation.},
}

@article {pmid42923306,
year = {2026},
author = {Gao, X and Dong, Q and Shin, AS},
title = {Associations of colonic transit with the gut microbiota and short-chain fatty acids in health and irritable bowel syndrome.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1953842},
pmid = {42923306},
issn = {2296-861X},
abstract = {Gut bacteria are known to influence short-chain fatty acid (SCFA) levels through direct metabolic activity. Colonic transit also affects substrate contact time, fermentation duration, and SCFA absorption. But it is unclear whether some bacteria influence SCFA levels indirectly, by altering transit, rather than only directly, and whether this differs across health and irritable bowel syndrome (IBS) subtypes. Using data from 56 participants [17 healthy volunteers (HV), 15 IBS-C, 24 IBS-D] with concurrent stool metagenomes, stool SCFA, and segmental colonic transit measurements, we applied mediation analysis to test whether each bacterial taxon's association with SCFA levels may be transit-mediated statistically. Three taxa showed a potential transit-mediated association with at least one SCFA: Faecalibacterium prausnitzii in HV, Bacteroides thetaiotaomicron in IBS-C, and Phascolarctobacterium succinatutens in IBS-D. For F. prausnitzii, the transit-mediated pathway was the only detectable association with SCFA. The remaining two taxa, B. thetaiotaomicron and P. succinatutens, additionally showed a direct, transit-independent effect alongside the transit-mediated one. Separately, an analysis of direct, non-mediated effects identified 15 additional taxa (5 in HV, 2 in IBS-C, and 8 in IBS-D) whose associations with SCFA levels were not explained by colonic transit. Together, these findings suggest that colonic transit may potentially mediate specific associations between gut bacteria and SCFA levels, in addition to the direct metabolic effects of the bacteria. However, because the present study is cross-sectional, these findings should be interpreted as statistical associations rather than established biological or directional relationships. In addition, this was an exploratory post-hoc analysis of a single relatively small cohort, and independent validation will be required before the biological or clinical significance of these findings can be established.},
}