@article {pmid42469164,
year = {2026},
author = {Matsushita, T and Banchev, A and Bovet, J and Chowdary, P and García Fernández, LM and Jiménez-Yuste, V and Kavakli, K and Kremer Hovinga, JA and Windyga, J and Young, G},
title = {Denecimig (Mim8) prophylaxis once every 2 weeks for hemophilia A with or without inhibitors: 26-week results from FRONTIER4.},
journal = {Blood advances},
volume = {10},
number = {20},
pages = {6946-6953},
pmid = {42469164},
issn = {2473-9537},
mesh = {Adolescent ; Adult ; Child ; Humans ; Male ; Middle Aged ; Young Adult ; *Antibodies, Bispecific/therapeutic use/administration & dosage/adverse effects ; Drug Administration Schedule ; *Factor VIII/administration & dosage/therapeutic use ; *Hemophilia A/drug therapy/complications ; Hemorrhage/prevention & control/etiology ; Treatment Outcome ; },
abstract = {Denecimig (Mim8) is a next-generation, activated factor VIII mimetic, fully human bispecific immunoglobulin G4 antibody in development for subcutaneous prophylaxis in bleeding episodes, for patients with hemophilia A (HA) with/without inhibitors. FRONTIER4 is an open-label extension study to assess the safety and efficacy of denecimig. Here we present an interim analysis of patients receiving denecimig once every 2 weeks (Q2W) in FRONTIER4. Patients with HA aged ≥12 years who had participated in the denecimig phase 2 study and ≥12 weeks of its extension and entered arm 1 of the FRONTIER4 phase 3 study received denecimig Q2W for 26 weeks using a tiered dosing approach according to body weight range. The primary end point was the number of treatment-emergent adverse events (TEAEs); secondary end points included injection site reactions, occurrence of anti-denecimig antibodies, denecimig plasma concentrations, and number of treated bleeds. Thirty-seven patients were enrolled who received denecimig for a mean of 1.73 years in the phase 2 study. Sixty TEAEs were reported in 20 patients. Most TEAEs were mild/moderate in severity (98.3%), unlikely to be related to denecimig (75.0%), and resolved during the time frame of this analysis (90.0%). No TEAEs led to permanent discontinuation of denecimig, and none were fatal. Two patients reported 14 injection site reactions. Denecimig plasma concentrations were stable through week 26. The estimated mean annualized bleeding rate was 0.38 bleeds per patient year. Most patients experienced zero treated bleeds (83.8%). In summary, denecimig administered Q2W was well tolerated, with few patients experiencing treated bleeds and no safety concerns. This trial was registered at www.clinicaltrials.gov as NCT05685238.},
}

Adolescent
Adult
Child
Humans
Male
Middle Aged
Young Adult
*Antibodies, Bispecific/therapeutic use/administration & dosage/adverse effects
Drug Administration Schedule
*Factor VIII/administration & dosage/therapeutic use
*Hemophilia A/drug therapy/complications
Hemorrhage/prevention & control/etiology
Treatment Outcome

@article {pmid42901654,
year = {2027},
author = {Guo, Z and Zeng, Z and Ji, L and Shen, Q and Yang, S and Liu, Y and Wang, X and Wu, P and Ni, B and Zhang, W and Sun, R},
title = {Serum metaviromic profiling of yaks and Tibetan sheep provides a pre-harvest viral baseline for food-producing ruminants.},
journal = {Food microbiology},
volume = {142},
number = {},
pages = {105301},
doi = {10.1016/j.fm.2026.105301},
pmid = {42901654},
issn = {1095-9998},
mesh = {Animals ; Cattle/virology/blood ; Sheep/virology/blood ; Tibet ; Phylogeny ; *Virome ; *Viruses/genetics/classification/isolation & purification ; Metagenomics ; },
abstract = {Pre-harvest viral profiles of food-producing ruminants in high-altitude pastoral systems remain poorly defined, limiting the selection of viral targets for monitoring along animal-derived food chains. In this study, we performed viral metagenomic profiling of 142 pooled serum libraries generated from 712 individual blood samples collected from yaks and Tibetan sheep across the Qinghai-Tibet Plateau. A total of 2.87 billion raw reads were obtained, of which 26.34 million were assigned to viral taxa. The serum viromes were dominated by single-stranded DNA and single-stranded RNA viruses, with Parvoviridae being the most abundant family. Yaks harboured significantly greater viral richness and diversity than Tibetan sheep, and community-level analysis showed distinct host-associated virome structures. Phylogenetic reconstruction recovered parvovirus-, astrovirus-, hepacivirus-, and genomovirus-related sequences, including a divergent erythroparvovirus-related lineage; the nepovirus-related sequence was categorized separately as a likely dietary or environmentally derived viral nucleic acid signal. These findings provide a serum-based viral reference for high-altitude pastoral production systems and identify viral lineages that may be considered for exploratory screening in downstream matrices, pending validation of their presence and infectivity. While viral nucleic acids detected in serum do not directly indicate contamination of animal-derived foods or foodborne transmission, they provide baseline data on serum-associated viral diversity that can guide subsequent assessment of potential spillover and food-chain relevance.},
}

Animals
Cattle/virology/blood
Sheep/virology/blood
Tibet
Phylogeny
*Virome
*Viruses/genetics/classification/isolation & purification
Metagenomics

@article {pmid42901661,
year = {2027},
author = {Lau, CH and Yao, L and Madill, R and Richter, R and Lukic, L and Kelly, B},
title = {A quasi-metagenomics approach for subspecies level differentiation of Listeria monocytogenes in foods based on assembly alignment discrepancies.},
journal = {Food microbiology},
volume = {142},
number = {},
pages = {105308},
doi = {10.1016/j.fm.2026.105308},
pmid = {42901661},
issn = {1095-9998},
mesh = {*Listeria monocytogenes/genetics/classification/isolation & purification ; *Food Microbiology/methods ; *Metagenomics/methods ; Genome, Bacterial ; Food Contamination/analysis ; DNA, Bacterial/genetics ; Listeriosis/microbiology ; },
abstract = {Listeriosis is a serious bacterial illness most often caused by consuming food contaminated with Listeria monocytogenes. Rapid response to listeriosis outbreaks, including the identification and tracking of the contamination source, is crucial for safeguarding public health. Despite its utility in foodborne outbreak investigations, high-resolution whole-genome sequencing analysis suffers from inherent delays, as it remains contingent upon recovery of pure isolates via culture-dependent methods. Here, we hypothesize that a quasi-metagenomics approach leveraging bacterial enrichment sequencing can provide preliminary genomic information sufficient to distinguish L. monocytogenes strains. Simulation and sequencing of mock bacterial community samples exposed detectable average nucleotide identity gap and primary metagenome assembly dissimilarity between non-identical L. monocytogenes strains, provided that assembly alignment achieved ≥ 10% proportional coverage of the reference genome. By combining simple Listeria enrichment procedures, a mutanolysin-based bacterial DNA extraction protocol, and multiple displacement amplification technique, an isolate-free sequencing workflow was developed. Using fresh, ready-to-eat microgreens as model food matrices with a challenging microbial background, we present a proof-of-principle demonstration of an end-to-end workflow that utilizes a best-match strategy against a scenario-specific and curated genome reference panel to detect a suspected L. monocytogenes strain in fabricated contamination events. By enabling earlier provision of the genomic fingerprint information pertaining to the implicated L. monocytogenes strain, this quasi-metagenomic sequencing approach may prove useful for supporting time-sensitive outbreak and traceback investigations, with subsequent confirmation achievable through whole-genome sequencing.},
}

*Listeria monocytogenes/genetics/classification/isolation & purification
*Food Microbiology/methods
*Metagenomics/methods
Genome, Bacterial
Food Contamination/analysis
DNA, Bacterial/genetics
Listeriosis/microbiology

@article {pmid42901678,
year = {2027},
author = {Niu, J and Li, W and Chen, X and Zhu, H and Sun, W and Li, X and Sun, B},
title = {Microbial succession and genome-resolved metabolic functions shape flavor evolution during sauce-flavor Baijiu fermentation.},
journal = {Food microbiology},
volume = {142},
number = {},
pages = {105326},
doi = {10.1016/j.fm.2026.105326},
pmid = {42901678},
issn = {1095-9998},
mesh = {Fermentation ; *Bacteria/metabolism/genetics/classification/isolation & purification ; *Flavoring Agents/metabolism ; Taste ; *Fermented Foods/microbiology/analysis ; *Microbiota ; Food Microbiology ; Metagenome ; },
abstract = {Sauce-flavor Baijiu (SFB) fermentation is characterized by a unique multi-round solid-state process, during which complex microbial succession drives flavor formation. However, the functional differentiation and metabolic mechanisms of microbial communities across successive fermentation rounds remain poorly understood. In this study, the physicochemical properties, microbial assembly, and metabolic profiles of fermented grains (FG) were investigated across seven production rounds (R1-R7). The results revealed that as fermentation rounds progressed, the FG environment evolved toward elevated acidity and reduced pH, driving a directional shift in the microbial community from an initially diverse assemblage to a structure dominated by acid-tolerant Acetilactobacillus, which established pronounced ecological dominance in later rounds. Metabolomic analysis further indicated that this dynamic adjustment of microbial structure drove the evolution of the flavor profile, specifically manifesting as differential accumulation of compounds such as esters, alcohols, and pyrazines across the various rounds. Co-occurrence network analysis demonstrated that positive microbial interactions significantly predominated within the fermentation system, and that community function exhibited a convergent trend as the rounds increased. Furthermore, 158 metagenome-assembled genomes (MAGs) were recovered, and metabolic reconstruction elucidated the potential contributions of genera such as Pediococcus, Bacillus, and Oceanobacillus to key metabolic pathways, including glycolysis, phenylalanine metabolism, and pyrazine biosynthesis. This work provides important insights into microbial regulation and quality improvement in SFB fermentation.},
}

Fermentation
*Bacteria/metabolism/genetics/classification/isolation & purification
*Flavoring Agents/metabolism
Taste
*Fermented Foods/microbiology/analysis
*Microbiota
Food Microbiology
Metagenome

@article {pmid42901916,
year = {2026},
author = {Lu, X and Wang, W and Zhang, B and Li, Q and Chen, Y and Hai, Y and Fan, R and Fu, S and Yan, J and Ding, G and Hou, Z and Song, J and Cheng, M and Wei, G},
title = {Nanotherapeutic macrophage reprogramming through immunometabolic and microbial modulation for sepsis treatment.},
journal = {Signal transduction and targeted therapy},
volume = {11},
number = {1},
pages = {},
pmid = {42901916},
issn = {2059-3635},
support = {22577101//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82173682//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82374074//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Sepsis/immunology/drug therapy/microbiology/genetics/pathology/therapy ; *Macrophages/immunology/drug effects ; Animals ; Humans ; Mice ; Succinates/chemistry/pharmacology ; Metabolic Reprogramming ; *Cellular Reprogramming/drug effects ; },
abstract = {Sepsis is a life-threatening syndrome characterized by dysregulated immune responses and metabolic dysfunction, and remains a major cause of global mortality. While nanomedicine offers new opportunities for sepsis therapy, current strategies rarely achieve comprehensive modulation of macrophage immunometabolism and microenvironmental signaling. Here, we develop a glutathione-responsive nanotherapeutic platform (EONPs) by conjugating the stimulator of interferon genes (STING) inhibitor 4-octyl itaconate to polyethylene glycol, followed by encapsulation of the dihydroorotate dehydrogenase (DHODH) inhibitor EA6. Integrated transcriptomic, metabolomic, and metagenomic analyses combined with pharmacological assessments reveal that EONPs suppress systemic hyperinflammation, reprogram macrophages toward an anti-inflammatory phenotype, restore gut microbial homeostasis, and protect against multi-organ injury in septic models. Notably, EONPs enhance the production of the microbiota-derived metabolite 5-hydroxyindoleacetic acid (5-HIAA), which is functionally linked to the anti-inflammatory response and may further support macrophage reprogramming. Our findings establish a previously unrecognized strategy for precise metabolic and microbiota-driven modulation of macrophages, offering a conceptual framework for further investigation of macrophage-targeted nanotherapeutics in sepsis.},
}

*Sepsis/immunology/drug therapy/microbiology/genetics/pathology/therapy
*Macrophages/immunology/drug effects
Animals
Humans
Mice
Succinates/chemistry/pharmacology
Metabolic Reprogramming
*Cellular Reprogramming/drug effects

@article {pmid42901952,
year = {2026},
author = {Gihawi, A and Bampalis, A and Subramanian, S and , and Bova, GS and Butler, A and Corcoran, NM and Favero, F and Gnanapragasam, V and Hamid, A and Jung, C and Kote Jarai, Z and Leeman, G and Loda, M and Reimand, J and Sahli, A and Schlomm, T and Yamaguchi, TN and Weischenfelft, J and Hovens, C and Pope, B and Bristow, R and Brook, MN and Cheng, KCL and Girma, EG and Gruber, AJ and He, HH and Imada, EL and Jakobsdottir, GM and Khani, F and Lutsik, P and Marchionni, L and Molania, R and Papenfuss, AT and Pellegrina, D and Queiroz, LR and Rausch, T and Robinson, B and Zanettini, C and Sørensen, KD and Lamy, P and Cancel-Tassin, G and Cussenot, O and Eeles, RA and Annels, N and Hayes, VM and Hurst, R and Cooper, CS and Brewer, DS},
title = {Recovering anaerobic bacterial genomes in saliva, tumour and blood whole genome sequencing data from patients with prostate cancer.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {},
pmid = {42901952},
issn = {2055-5008},
support = {MA-TIA23-002, MA-ETNA19-003, RIA15-ST2-029 and TLD-CAF22-011/PCUK_/Prostate Cancer UK/United Kingdom ; MA-TIA23-002, MA-ETNA19-003, RIA15-ST2-029 and TLD-CAF22-011/PCUK_/Prostate Cancer UK/United Kingdom ; MA-TIA23-002, MA-ETNA19-003, RIA15-ST2-029 and TLD-CAF22-011/PCUK_/Prostate Cancer UK/United Kingdom ; MA-TIA23-002, MA-ETNA19-003, RIA15-ST2-029 and TLD-CAF22-011/PCUK_/Prostate Cancer UK/United Kingdom ; },
mesh = {Humans ; *Prostatic Neoplasms/microbiology ; Male ; *Saliva/microbiology ; *Genome, Bacterial ; Whole Genome Sequencing ; *Bacteria, Anaerobic/genetics/classification/isolation & purification ; Metagenomics/methods ; Phylogeny ; *Blood/microbiology ; },
abstract = {Microbial constituents in the gastrointestinal tract, the urine and prostate tissue are being linked with clinical differences in prostate cancer, and a recent meta-analysis has linked periodontal disease to this cancer. Several hypotheses exist regarding how specific bacteria can contribute towards the development of prostate cancer. Recovering microbial genomes, and their genomic features, from clinical samples and investigating fine-scale taxonomy is a critical first step in investigating causality. Here, we describe the microbial diversity of samples associated with prostate cancer. Metagenomic assembly of non-human reads from the PanProstate Cancer Group, derived from blood, saliva samples and prostate tissue whole-genome data (N = 247), successfully reconstructed 249 highly complete bacterial genomes, predominantly from oral samples. Our data, reveals eighteen bacterial species from the oral cavity without species level classification, while demonstrating a wide range of known species. This approach enables us to gain additional insights of the microbes in cancer patients at no additional sequencing cost and has the potential to reveal new links that could improve our understanding of cancer initiation and development.},
}

Humans
*Prostatic Neoplasms/microbiology
Male
*Saliva/microbiology
*Genome, Bacterial
Whole Genome Sequencing
*Bacteria, Anaerobic/genetics/classification/isolation & purification
Metagenomics/methods
Phylogeny
*Blood/microbiology

@article {pmid42902048,
year = {2026},
author = {Wang, W and Feng, Y and Wang, Y and Wang, G and Wang, X},
title = {Metagenomic analysis of oral microbiota in Chinese children with obesity.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {42902048},
issn = {1618-1905},
support = {2025JC-YBMS-1085//Natural Science Basic Research Program of Shaanxi Province/ ; },
abstract = {Childhood obesity represents an increasingly severe global public‑health concern, whose precise etiology remains incompletely elucidated and is likely multifactorial. In addition to genetic and lifestyle factors, mounting evidence indicates that the microbes in the digestive tract play a crucial role in the development and progression of obesity. Among them, the oral microbiota may contribute to obesity through mechanisms such as inducing systemic chronic inflammation and promoting gut microbiota dysbiosis. In the present study, saliva samples were collected from 9 obese children and 9 normal-weight children. Using metagenomic sequencing, we aimed to analyze the structural characteristics and functional profiles of the oral microbiota in Chinese school‑age children with obesity, so as to comprehensively dissect the oral microbiome ecology of this population from structural and functional perspectives. The results revealed that the microbiota diversity was similar between the two groups. At the species level, Dialister invisus, Treponema porcinum, Moraxella sp., Moraxella sp. VT 16 12, Moraxella lacunata, and Moraxella caprae were significantly enriched in the normal-weight group. Conversely, Campylobacter concisus, Veillonella sp. oral taxon 158, Veillonella rogosae, Veillonella sp. S13053 19, Streptococcus ilei, and Streptococcus australis were significantly enriched in the obese group. Functional annotation analysis demonstrated significant enrichment of functional genes associated with the hypoxia-inducible factor-1 (HIF-1) signaling pathway, peroxisome proliferator-activated receptor (PPAR) signaling pathway, beta-alanine metabolism, AMP-activated protein kinase (AMPK) signaling pathway, and apoptosis in the normal-weight group. In contrast, functional genes related to biofilm formation-Vibrio cholerae, selenocompound metabolism, RNA polymerase, xylene degradation, and dioxin degradation were significantly enriched in the obese group. Correlation analysis further revealed strong positive correlations between Veillonella sp. oral taxon 158, Veillonella sp. S13053 19, Streptococcus ilei, Streptococcus australis and the functional pathways of biofilm formation-Vibrio cholerae, selenocompound metabolism, xylene degradation, and dioxin degradation. These observations suggest that the oral microbiome undergoes compositional and functional alterations in children with obesity, implying a potential role of oral microbiota in the etiology of childhood obesity.},
}

@article {pmid42902199,
year = {2026},
author = {Zou, W and Yang, H and Xu, N and Wang, G},
title = {Mixed infection with multiple bacteria and microsporidia (Enterocytozoon bieneusi) in a post-renal transplant patient: a case report.},
journal = {BMC infectious diseases},
volume = {26},
number = {1},
pages = {},
pmid = {42902199},
issn = {1471-2334},
support = {2023YFC2307000//National Key Research and Development Program of China/ ; },
mesh = {Humans ; Male ; *Kidney Transplantation/adverse effects ; Adult ; *Microsporidiosis/diagnosis/microbiology/drug therapy ; *Enterocytozoon/isolation & purification/genetics ; *Coinfection/microbiology/diagnosis/drug therapy ; Immunocompromised Host ; Anti-Bacterial Agents/therapeutic use ; *Bacterial Infections/microbiology/diagnosis/drug therapy ; },
abstract = {BACKGROUND: Microsporidia are genetically diverse, obligate intracellular pathogens that are challenging to diagnose due to their resistance to conventional culture methods. Enterocytozoon bieneusi is a primary cause of microsporidiosis, particularly in immunocompromised individuals. This report details a complex case of mixed bacterial and microsporidial infection in a renal transplant recipient, highlighting the utility of advanced molecular diagnostics.

CASE PRESENTATION: A 37-year-old male with a 16-year history of renal transplantation presented with recurrent high fever, chills, and hematochezia. Initial workup revealed severe anemia, thrombocytopenia, and acute kidney injury. Blood cultures grew ESBL-producing Escherichia coli and Klebsiella pneumoniae. CT imaging suggested a duodenobiliary fistula. Due to persistent fever despite broad-spectrum antibiotics, metagenomic next-generation sequencing (mNGS) was performed, identifying E. bieneusi (185 reads) alongside multiple bacteria and viruses. Treatment was adjusted to include meropenem, daptomycin, and albendazole, with careful modulation of immunosuppression. The patient subsequently tested positive for SARS-CoV-2 but showed significant clinical improvement with the adjusted regimen and was discharged after 24 days.

CONCLUSION: This case underscores the diagnostic value of mNGS in identifying rare, opportunistic pathogens in immunocompromised hosts. Successful management requires a multidisciplinary approach, combining targeted antimicrobial therapy, immunomodulation, and aggressive supportive care.

CLINICAL TRIAL NUMBER: Not applicable.},
}

Humans
Male
*Kidney Transplantation/adverse effects
Adult
*Microsporidiosis/diagnosis/microbiology/drug therapy
*Enterocytozoon/isolation & purification/genetics
*Coinfection/microbiology/diagnosis/drug therapy
Immunocompromised Host
Anti-Bacterial Agents/therapeutic use
*Bacterial Infections/microbiology/diagnosis/drug therapy

@article {pmid42902210,
year = {2026},
author = {Li, Y and Chen, X and Wang, J and Yang, M and Zhang, C},
title = {Brucella melitensis infection complicated by secondary hemophagocytic lymphohistiocytosis, meningitis, and multiorgan damage: a case report and literature review.},
journal = {BMC infectious diseases},
volume = {26},
number = {1},
pages = {},
pmid = {42902210},
issn = {1471-2334},
mesh = {Humans ; Female ; *Brucellosis/complications/drug therapy/diagnosis/microbiology ; *Lymphohistiocytosis, Hemophagocytic/diagnosis/microbiology/complications/drug therapy/etiology ; Middle Aged ; *Brucella melitensis/isolation & purification ; *Multiple Organ Failure/microbiology/etiology/diagnosis ; *Meningitis, Bacterial/microbiology/diagnosis/drug therapy/complications ; Anti-Bacterial Agents/therapeutic use ; Animals ; },
abstract = {BACKGROUND: Brucellosis is one of the most widespread zoonotic diseases globally. Of the twelve known Brucella species that affect mammals, Brucella melitensis is the most significant cause of human infection. Others include B. abortus, B. suis, and B. canis, with transmission occurring via unpasteurized dairy, direct animal contact, or occupational exposure (veterinarians, farmers, and laboratory workers). Although hemophagocytic lymphohistiocytosis (HLH) and neurological complications are known sequelae of brucellosis, their simultaneous occurrence with multiorgan failure is rarely reported.

CASE PRESENTATION: A 59-year-old female was admitted with dizziness and fatigue for more than 20 days, accompanied by fever and lethargy for 3 days. An epidemiological history revealed that the patient had close contact with goats, which was considered a key risk factor. On physical examination, the patient appeared lethargic, with petechiae on the skin and mucous membranes, oral blood blisters, gingival bleeding, and splenomegaly. Laboratory results revealed significantly increased ferritin levels, decreased fibrinogen levels, pancytopenia, and elevated transaminase levels. Bone marrow aspiration confirmed the presence of hemophagocytes. Cerebrospinal fluid (CSF) examination supported a diagnosis of meningitis. Blood cultures grew Brucella melitensis, and metagenomic next-generation sequencing (mNGS) of CSF revealed a large number of B. melitensis-specific nucleic acid sequences. Chest computed tomography (CT) revealed bilateral pulmonary infiltrates. The patient was ultimately diagnosed with B. melitensis infection complicated by HLH, meningitis, and multiorgan dysfunction. The patient was treated with ceftriaxone sodium, doxycycline, rifampicin, glucocorticoids, and supportive therapy. Following treatment, her consciousness improved, the fever subsided, the total platelet count rose, and liver enzyme levels gradually decreased. The patient was discharged in stable condition. At the 2-month follow-up, the patient remained in remission with normal haematological indicators, no recurrent fever, and stable neurological function.

CONCLUSIONS: This case reflects the severe nature of brucellosis when atypical multiorgan involvement is present and highlights the diagnostic challenges and the importance of early and standardized treatment. Maintaining a high level of clinical suspicion and achieving an early definite diagnosis are key to improving treatment outcomes and prognosis. In addition, this case report helps expand the known spectrum of clinical complications related to brucellosis.},
}

Humans
Female
*Brucellosis/complications/drug therapy/diagnosis/microbiology
*Lymphohistiocytosis, Hemophagocytic/diagnosis/microbiology/complications/drug therapy/etiology
Middle Aged
*Brucella melitensis/isolation & purification
*Multiple Organ Failure/microbiology/etiology/diagnosis
*Meningitis, Bacterial/microbiology/diagnosis/drug therapy/complications
Anti-Bacterial Agents/therapeutic use
Animals

@article {pmid42902375,
year = {2026},
author = {Yahia, S and Murugesan, S and Al Khodor, S},
title = {Decoding the human milk virome: a comparative analysis of composition, colonization, and health impacts.},
journal = {Journal of translational medicine},
volume = {24},
number = {1},
pages = {},
pmid = {42902375},
issn = {1479-5876},
mesh = {Humans ; *Milk, Human/virology ; *Virome ; Female ; *Health ; },
abstract = {BACKGROUND: Breast milk (BM) is a complex biological system that not only delivers essential nutrition to the baby, but is also a rich collection of microorganisms, including bacteria, viruses and fungi. Dominated by bacteriophages and eukaryotic viruses, the BM virome plays a role in shaping the infant gut microbiome composition, influencing immune development and long-term health outcomes. Emerging research confirms the vertical transmission of bacteriophages from the mother to her infant via breastfeeding, and the shared viral taxa suggest functional roles in modulating bacterial populations and maintaining gut homeostasis. Disruptions in this early life virome, driven by factors such as maternal health, mode of delivery, and geographic location, have been linked to dysbiosis and disease susceptibility for conditions ranging from inflammatory bowel disease to metabolic disorders.

METHODS: A systematic literature search was conducted in NCBI/PUBMED and the European Nucleotide Archive (ENA) using the keywords "Milk virome," "Milk phage," "Milk phageome," and "Milk metagenome". After applying our inclusion and exclusion criteria, two studies remained. This comparative analysis explores the composition and diversity of the BM virome across two geographically distinct cohorts-Turkey and the United States-revealing significant differences in viral diversity and composition.

RESULTS: The Turkish cohort exhibited a significantly higher viral richness and unique taxonomic distributions compared to the USA group. Notably, bacteriophage families like Myoviridae, Siphoviridae, and Podoviridae were shown to be abundant in both populations. The Turkish BM virome featured a higher prevalence of plant- and insect-derived viruses (e.g. Partitiviridae, Tospoviridae), likely tied to dietary or regional agricultural practices.

CONCLUSIONS: Despite limitations related to sample size and methodological variability, this study emphasizes how dietary habits, environmental exposures, and geographic location may shape the breast milk virome. Further research integrating longitudinal data from a multi-ethnic population, cohorts is essential to fully harness the diagnostic and therapeutic potential of the human milk virome.},
}

Humans
*Milk, Human/virology
*Virome
Female
*Health

@article {pmid42903155,
year = {2026},
author = {Laureano, G and Ramirez, X and Scoles, A and Johne, C and Colón Sáez, CM and Hernández Ortiz, YM and Soleyman, J and Rivera-Vicéns, RE and Arun, A},
title = {Genomic insights into bacterial communities of coenocytic algae using metagenome-assembled genomes.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1851259},
pmid = {42903155},
issn = {1664-302X},
abstract = {Coenocytic algae are organisms that undergo karyokinesis without cytokinesis, resulting in multinucleated cells. Most research on bacterial communities in coenocytic algae has used 16S rRNA sequencing, primarily focusing on the order Bryopsidales of green coenocytic algae. Recent studies have analyzed metagenome-assembled genomes (MAGs) from algal hosts across multiple taxa, such as Chlorophyta, Phaeophyta, and Rhodophyta, revealing further insights into bacterial biosynthetic machinery and potential symbiotic relationships. Given the cosmopolitan distribution of coenocytic algae, such as Bryopsis, Caulerpa, Codium, and the yellow-green alga Vaucheria, and their unique morphology, there is a need to better understand their associated bacterial communities. To address this, filaments of Vaucheria bursata LB2067 were sequenced using the Illumina NovaSeq instrument, and all publicly available short- and long-read datasets from coenocytic algae were screened for MAG recovery. All recovered MAGs from both Bryopsidales and Vaucheriales showed a high dominance of Pseudomonadota at the phylum level, but no consistent patterns at the order or family levels. Core metabolic pathways, including glycolysis, the TCA cycle, and amino acid biosynthesis, were present across MAGs from both coenocytic and non-coenocytic algae. Pathways with significantly higher completeness in coenocytic-associated MAGs included protein secretion (Sec-SRP), which showed the strongest effect, motility (flagellar assembly), thiamin biosynthesis, and polyhydroxybutyrate (PHB) synthesis (Mann-Whitney U, padj < 0.05). Notably, N-acetylglutaminylglutamine amide (NAGGN) biosynthetic gene clusters (BGCs) were found only in MAGs from coenocytic orders, whereas polysaccharide utilization loci (PULs) were present in all MAGs analyzed. These results indicate that bacterial communities associated with coenocytic algae are complex, with diverse survival strategies adapted to challenging and variable environments.},
}

@article {pmid42903157,
year = {2026},
author = {Su, J and Lu, Y and Xia, Y and Xie, C and Kai, J and Huang, L},
title = {Case Report: mNGS-negative Strongyloides hyperinfection syndrome with small bowel obstruction as the initial manifestation in a glucocorticoid-exposed COPD patient: a fatal case.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1940986},
pmid = {42903157},
issn = {1664-3224},
mesh = {Humans ; Male ; *Strongyloidiasis/diagnosis/drug therapy/parasitology ; Animals ; *Pulmonary Disease, Chronic Obstructive/drug therapy/complications ; Aged ; *Intestinal Obstruction/etiology/diagnosis/parasitology ; Fatal Outcome ; *Glucocorticoids/adverse effects ; *Strongyloides stercoralis/genetics ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Immunocompromised Host ; },
abstract = {BACKGROUND: Strongyloides hyperinfection syndrome (SHS) is a life-threatening condition in immunocompromised hosts with an extremely high mortality rate. Metagenomic next-generation sequencing (mNGS) demonstrates limited sensitivity for parasitic detection, and its clinical value remains to be fully elucidated. The conventional microscopy remains an indispensable tool for the diagnosis of parasitic infections.

CASE DESCRIPTION: A 73-year-old male patient with a history of chronic obstructive pulmonary disease (COPD), diabetes mellitus, hypertension, and cerebral infarction presented with abdominal pain and distension for 7 days and no bowel movement for 3 days. He was diagnosed with incomplete small bowel obstruction at an outside hospital and treated with fasting, enemas, meropenem, and methylprednisolone. He was subsequently transferred to our hospital due to acute lower respiratory tract infection. Chest radiography revealed bilateral diffuse infiltrates, and his condition rapidly deteriorated, requiring admission to the intensive care unit (ICU), endotracheal intubation, mechanical ventilation, and continuous renal replacement therapy (CRRT). Stool smear and retrospective sputum examination both identified larvae of Strongyloides stercoralis. However, mNGS of sputum and bronchoalveolar lavage fluid (BALF) obtained upon admission failed to detect any parasitic sequences. The patient was treated sequentially with albendazole and ivermectin, in combination with broad-spectrum antibacterial, antifungal, and antiviral therapy. He ultimately died on February 11, 2025, due to severe pneumonia, sepsis, and bone marrow suppression.

CONCLUSION: For immunocompromised hosts with multiple risk factors, particularly those exposed to glucocorticoids, active parasitic microscopic examination of stool and respiratory secretions should be pursued when unexplained pulmonary infiltrates coexist with gastrointestinal symptoms, even in the setting of negative mNGS results, to avoid missed diagnosis.},
}

Humans
Male
*Strongyloidiasis/diagnosis/drug therapy/parasitology
Animals
*Pulmonary Disease, Chronic Obstructive/drug therapy/complications
Aged
*Intestinal Obstruction/etiology/diagnosis/parasitology
Fatal Outcome
*Glucocorticoids/adverse effects
*Strongyloides stercoralis/genetics
High-Throughput Nucleotide Sequencing
Metagenomics
Immunocompromised Host

@article {pmid42903194,
year = {2026},
author = {Figueroa-Ajraz, F and Bongcam-Rudloff, E and González-Pizarro, K and Dinamarca, MA and Osses-Lobos, L and Sotomayor-Zárate, R and Ibacache-Quiroga, C},
title = {High-fat diet induces an adaptive dysbiosis in the gut microbiota, associated with oxidative stress and the gut resistome profile in a rat model.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1935516},
pmid = {42903194},
issn = {1664-302X},
abstract = {Antibiotic resistance is one of the main public health issues worldwide; therefore, studying the factors contributing to this problem, including the reservoirs of antibiotic resistance genes, is highly relevant. Among these reservoirs, the gut microbiota stands out for its potential to disseminate antibiotic resistance genetic determinants. In this context, identifying the factors shaping the gut resistome is crucial. This study aimed to evaluate the effects of a high-fat diet (HFD) on intestinal and systemic oxidative stress in a rat model and to assess its impact on the gut microbiota, its DNA oxidative damage, and the resistome. Oxidative stress was evaluated by quantifying oxidative stress markers in the host (MDA, T-SOD, and T-GSH/GSSG) and in the gut microbiota (8-OHdG), while the impact on the gut microbiota was determined using a shotgun metagenomic sequencing approach. The effect of HFD on oxidative stress, the gut microbiota, and its resistome was evaluated after 4, 8, and 12 weeks of exposure, with and without supplementation with an antioxidant (N-acetylcysteine). Results showed that a high-fat diet generates a pro-oxidant stimulus in intestinal tissue, with increased lipid peroxidation and superoxide dismutase activity, without systemic effects. In the gut microbiota, HFD altered microbial diversity, without DNA oxidative damage. Analysis of the predominant genera revealed an increased abundance of Mucispirillum, Phocaeicola, and Taurinivorans, among others, and a significant reduction of Segatella, Ligilactobacillus, and Prevotella, which were correlated with intestinal oxidative stress. On the other hand, Mucispirillum showed a significant negative correlation with DNA oxidative damage in the gut microbiota. Resistome characterization showed that a high-fat diet increased the abundance of antibiotic resistance genes (ARGs) in the gut microbiota. ARGs were strongly correlated with significantly modified taxa and showed a mild correlation with oxidative stress, while specific ARGs were associated with the high-fat diet (CblA-1, the vanH gene in the vanM cluster, vanD, and the vanXY gene in the vanE cluster). These findings suggest an adaptive dysbiosis, characterized by a microbial community restructuring associated with oxidative stress tolerance and antibiotic resistance genes.},
}

@article {pmid42903498,
year = {2025},
author = {Liu, Y and Hou, Z and Hao, W and Cui, S and Wang, H and Liu, Y},
title = {Metagenomic mining reveals novel viral histones in dsDNA viruses.},
journal = {hLife},
volume = {3},
number = {6},
pages = {284-296},
pmid = {42903498},
issn = {2949-9283},
abstract = {The compaction of genomic DNA into nucleosomes with the help of histones has long been considered a fundamental feature exclusive to eukaryotic cells. However, it was recently shown that archaea and bacteria also encode histones. A complex picture has emerged with more recent discoveries of eukaryotic-like histones within one phylum of double-stranded DNA (dsDNA) viruses. Nevertheless, the extent to which other dsDNA viruses encode histones remains largely unexplored. Here, we conducted a metagenomic survey of viral histones that were further clustered based on sequence and predicted structural similarities. We identified over 1500 viral histones and histone-fold proteins, including previously undescribed proteins found in the viral class Caudoviricetes. Structural predictions and in vitro assays demonstrated that histone triplets (where three histone folds are fused) and singlets co-occurring in the same viral genome are capable of forming nucleosome-like particles. Beyond nucleosomal histone functions, our analysis revealed six types of structurally and functionally diverse viral histone-fold proteins, some of which do not have known structural or functional homologs. Altogether, our findings reveal a previously unrecognized diversity of viral histones in dsDNA viruses, expanding the known repertoire, structural diversity, and functional versatility of viral histones beyond nucleocytoplasmic large DNA viruses.},
}

@article {pmid42903953,
year = {2026},
author = {Zheng, P and Zhang, Y and Hu, L and Wang, P and Xu, Y},
title = {Severe fever with thrombocytopenia syndrome-associated encephalitis and intracranial hypotension: A case report.},
journal = {Infectious diseases & immunity},
volume = {6},
number = {4},
pages = {315-318},
pmid = {42903953},
issn = {2693-8839},
abstract = {Severe fever with thrombocytopenia syndrome (SFTS) is a natural infectious disease caused by severe fever with thrombocytopenia syndrome virus (SFTSV). Central nervous system (CNS) involvement is not rare in SFTS. In this work, we report a case of SFTS with CNS symptom onset and the metagenomic next-generation sequencing of cerebrospinal fluid (CSF), confirming invasion of SFTSV into the CNS. The case's lumbar puncture indicated an exceptionally low CSF opening pressure-an uncommon finding in other CNS infections and in case reports of SFTS. A spontaneous subdural effusion was observed on the fourth day of hospitalization. Moreover, a flow cytometry analysis of bone marrow revealed a restricted expression of the lambda light chain in monoclonal B cells and plasma cells. The patient succumbed to their severe illness. The early recognition of the disease may be crucial for prognosis despite the disease's current lack of specific treatments.},
}

@article {pmid42903961,
year = {2026},
author = {Xu, L and Zhang, C and Shi, W and Ma, J and Wang, G},
title = {Current status and challenges in the diagnosis and treatment of psittacosis.},
journal = {Infectious diseases & immunity},
volume = {6},
number = {4},
pages = {279-290},
pmid = {42903961},
issn = {2693-8839},
abstract = {Psittacosis is a zoonotic infectious disease caused by the obligate intracellular Gram-negative bacterium Chlamydia psittaci. Despite over a century of research, its global burden remains underestimated owing to non-specific symptoms, poor clinical recognition, and limited diagnostic capacity. This review synthesizes epidemiological evidence from 1879 to 2024, outlining transmission routes, clinical manifestations, diagnostic approaches, and therapeutic strategies, with a focus on advances in molecular diagnostics and the management of high-risk populations and complications. Surveillance data document recurrent outbreaks across Europe, North America, and Asia, with a notable increase in reported cases in China and Europe since 2020. The disease spectrum spans from atypical pneumonia to life-threatening systemic complications, including neurological, cardiac, and pregnancy-related involvement. Conventional methods, such as culture and serology, are constrained by biosafety requirements and cross-reactivity, while polymerase chain reaction, metagenomic next-generation sequencing, and targeted next-generation sequencing provide superior sensitivity but face the challenges of cost and standardization. Tetracyclines remain the mainstay of therapy, macrolides are recommended for pregnant women and children, and newer tetracycline derivatives show promise in severe or refractory cases. Psittacosis should be recognized as a systemic disease of both clinical and public health importance. Future efforts must prioritize standardizing molecular diagnostic workflows, validating novel antimicrobials in clinical practice, and incorporating psittacosis surveillance into public health systems while raising awareness, broadening diagnostic access, and optimizing therapeutic strategies to enable early detection, precision treatment, and effective control.},
}

@article {pmid42904046,
year = {2025},
author = {Zheng, K and Liang, Y and Zhang, Y and Páez-Espino, D and Shao, H and Sung, YY and Mok, WJ and Wong, LL and Wang, S and McMinn, A and Wang, M},
title = {Diversity of reverse-transcriptase-containing viruses through global metagenomics.},
journal = {hLife},
volume = {3},
number = {1},
pages = {52-56},
pmid = {42904046},
issn = {2949-9283},
}

@article {pmid42904108,
year = {2026},
author = {Zhu, K and Wu, S and Deng, H and Liu, C and Zhang, J and Zhu, C and Qiao, Y and Zhang, Y},
title = {Dynamic flavor formation and microbial succession during fermentation of water bamboo shoots: Insights from volatilomics and metagenomics.},
journal = {Food chemistry: X},
volume = {39},
number = {},
pages = {104575},
pmid = {42904108},
issn = {2590-1575},
abstract = {This study investigated the dynamic changes in flavor compounds and microbial communities during fermented water bamboo shoot (FWBS) fermentation by integrating physicochemical analysis, electronic tongue, electronic nose, HS-SPME-GC-MS and metagenomics. These results showed that free amino acids exhibited an initial increase followed by a decrease, reaching a peak on day 5, while lactic acid accumulated rapidly as the predominant organic acid. E-tongue analysis classified FWBS fermentation into early (day1 - day 3), middle (day 5), and late stages (day 7 - day 9). A total of 76 VOCs were detected, mainly esters, phenols and alcohols. Spearman correlation analysis indicated that Lactiplantibacillus, Lactococcus, Leuconostoc, Weissella were positively correlated with 14 key VOCs (VIP > 1, OAV > 1, and P < 0.05) These findings provide new insights into the flavor formation mechanism of FWBS and establish a foundation for quality control and targeted fermentation regulation.},
}

@article {pmid42904169,
year = {2026},
author = {Zhang, Y and Gao, F and Gao, P and Fan, Y and Wang, X and Yang, Y and Gagnon, A and Martinez, G and Gillet, V and Zhu, J and Bellenger, JP and Baccarelli, AA and Takser, L and Shen, Y},
title = {Halogenated flame retardant exposure was associated with pediatric gut microbiome profiles in a Canadian cohort.},
journal = {Gut microbes reports},
volume = {3},
number = {1},
pages = {2747517},
pmid = {42904169},
issn = {2993-3935},
abstract = {Environmental chemical exposures have been linked to gut microbiome dysregulation and adverse health outcomes in children. Halogenated flame retardants (HFRs) are persistent chemicals with substantial early-life exposure, yet evidence on their effects on the pediatric gut microbiome remains limited. We examined associations between HFR exposures and the gut microbiome among 8-12-y-old children from the GESTation and Environment (GESTE) cohort in Sherbrooke, Canada. In a multi-matrix, multi-omics design, 10 HFRs were quantified in plasma (n = 140) and stool (n = 182), with shotgun metagenomic and metatranscriptomic sequencing characterized microbial species and functional pathways. After false discovery rate correction, plasma BDE-47 and BDE-99 were inversely associated with Clostridium sp. CAG:221 and Bacteroides dorei, respectively (q < 0.2). Stool BDE-153 was negatively associated with short-chain fatty acid-producing taxa, including Eubacterium spp. and Roseburia intestinalis, and positively associated with Alistipes putredinis and Faecalibacterium spp. Stool BDE-153 and anti-DP were associated with higher activity of pathways involved in phospholipid homeostasis and 4-aminobutanoate degradation. Mediation analysis suggested that Faecalibacterium spp. partly mediated the association between stool BDE-153 and cytidine diphosphate-diacylglycerol biosynthesis. Our findings suggest that childhood HFR exposure is associated with alterations in gut microbiome composition and function, with potential implications for pediatric health.},
}

@article {pmid42904650,
year = {2026},
author = {Sheriff, J and Capria, A and Bowers, N and Wattam, AR and Poretsky, R},
title = {Exploring antimicrobial resistance in wild and domestic animal populations: combining publicly available data with BV-BRC resources to introduce bioinformatics in an undergraduate classroom.},
journal = {Journal of microbiology & biology education},
volume = {},
number = {},
pages = {e0018226},
doi = {10.1128/jmbe.00182-26},
pmid = {42904650},
issn = {1935-7877},
abstract = {Bioinformatics blends the fields of biology, statistics, computer science, and information technology for the processing and analysis of genomic data. Despite the growing demand for trained bioinformaticians and a positive job market outlook, most undergraduate institutions struggle to integrate bioinformatics into their life science curricula. Educators face numerous barriers to incorporating bioinformatics into their classes, including technical issues and expertise. To address this need, we are developing web-accessible, course-based materials for general microbiology, infectious disease, genomics, and other similar undergraduate and graduate classes that use bioinformatic workflows within the Bacterial and Viral Bioinformatics Resource Center (BV-BRC), one of three National Institute of Allergy and Infectious Diseases (NIAID)-funded Bioinformatics Resource Centers. Here, we present one such activity: a three-part exercise focused on antimicrobial resistance and metagenomics that uses six publicly available metagenomic samples collected from wild and domestic animal populations to explore the distinctions between their gut microbiomes and their respective antibiotic resistance genes. To analyze community composition and identify antibiotic resistance genes, students use two end-to-end services offered by the BV-BRC: Taxonomic Classification and Metagenomic Read Mapping. This assignment was developed to introduce students to core competencies in the field of bioinformatics and to highlight the BV-BRC as an educational resource for integrating bioinformatics without requiring students and instructors to possess the technical proficiencies and computing resources traditionally needed. We successfully implemented this exercise in an upper-level undergraduate microbiology course, demonstrating the feasibility of using the BV-BRC for bioinformatics education in the classroom.},
}

@article {pmid42904653,
year = {2026},
author = {Yang, S and Sun, S and Chen, J and Zhou, Y and Jia, F and Xie, Y and Lu, Y and Ni, Q and Hu, J and Yang, M and Shi, Y and Jia, H and Yang, Y},
title = {Exploratory associations of gut microbiota composition with HBeAg and HBsAg status in nucleos(t)ide analog-treated chronic hepatitis B.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0389625},
doi = {10.1128/spectrum.03896-25},
pmid = {42904653},
issn = {2165-0497},
abstract = {HBeAg and HBsAg reflect viral replication and host immune status and are important determinants of treatment responsiveness in chronic hepatitis B (CHB). The gut microbiota, a key component of the gut-liver axis, may influence immune regulation and antiviral outcomes. This study characterized gut microbiota profiles across different HBeAg and HBsAg statuses in CHB patients receiving nucleos(t)ide analog (NA) therapy. Fecal shotgun metagenomic sequencing was performed in 29 healthy controls (HC) and 101 NA-treated CHB patients without cirrhosis or hepatocellular carcinoma, including 30 HBeAg-positive (EP) and 71 HBeAg-negative (EN) individuals. The EN group was further stratified by serum HBsAg levels into an advantageous subgroup (<1,500 IU/mL, n = 57) and a non-advantageous subgroup (≥1,500 IU/mL, n = 14). Alpha and beta diversity did not differ significantly among EP, EN, and HC groups. Species-level analyses identified nominal group-related differences in several Bacteroidales- and Firmicutes-associated anaerobic commensals, including Bacteroides uniformis, Blautia obeum, Eubacterium ventriosum, Anaerobutyricum, and Parabacteroides timonensis; however, none remained significant after global FDR correction across all detected species. Within the EN group, selected taxa showed directionally consistent associations with HBsAg strata in downsampling, leave-one-out, and CLR-based sensitivity analyses, but these subgroup findings also did not remain significant after FDR correction. NA-treated CHB was associated with exploratory taxonomic differences without detectable loss of microbial diversity. The observed associations with HBeAg status and HBsAg burden were hypothesis-generating and require validation in larger longitudinal cohorts incorporating absolute microbial quantification, targeted metabolomics, host immune profiling, and more complete dietary, anthropometric, and other relevant clinical covariates.},
}

@article {pmid42904657,
year = {2026},
author = {Zhao, Z and Hu, R and Zhou, M and Guan, X and Huang, H and Ding, L and Qian, L and Ming, Y and Niu, M and Wu, K and Yu, X and Yan, Q and Shu, L and He, Q and He, Z},
title = {Competition-dominated microbial interactions and adaptive mutations enhance synthetic denitrifying community functions.},
journal = {mBio},
volume = {},
number = {},
pages = {e0236026},
doi = {10.1128/mbio.02360-26},
pmid = {42904657},
issn = {2150-7511},
abstract = {UNLABELLED: Understanding how interspecific interactions shape ecosystem functioning is a fundamental and longstanding question in ecology, especially along an evolutionary trajectory. Here, we used experimental evolution to evaluate how microbial interactions and adaptive mutations shaped community-level functions in synthetic denitrifying communities (SDCs) along a species richness gradient (one, two, and six species). Our results showed that competitive microbial interactions were observed and significantly (P < 0.05) enhanced denitrification rates in the six-species SDCs during experimental evolution. Genome and metagenome re-sequencing analysis revealed the highest fixed non-synonymous and frameshift mutations within the six-species SDCs, among genes involved in nutrient transport, DNA repair, and secretion pathways. AlphaFold2 protein structure prediction, molecular docking, and Evo 2 host fitness prediction indicated that the fixed mutations could improve host strain fitness, and partial least squares path modeling (PLS-PM) further revealed that interspecific competition accelerated adaptive mutations, thereby reinforcing community-level functions, indicating potential Red Queen dynamics. This study offers novel insights into our understanding of eco-evolutionary mechanisms linking species richness, microbial interactions, adaptive mutations, and community functions, with important implications for active nitrogen removal and greenhouse gas mitigation in diverse ecosystems.

IMPORTANCE: Microbial diversity is widely recognized as a key driver of ecosystem functioning, yet how species interactions shape ecosystem functions through evolutionary processes remains poorly understood. Using synthetic denitrifying communities with different levels of species richness, we show that interspecific competition can accelerate adaptive mutations and enhance community-level denitrification over evolutionary timescales. Communities with higher species richness accumulated more adaptive mutations, particularly in genes associated with nutrient transport, DNA repair, and secretion systems, ultimately improving microbial fitness and denitrification performance. Our findings provide direct experimental evidence that microbial competition can promote functional adaptation, consistent with the Red Queen hypothesis. This study advances our understanding of the eco-evolutionary mechanisms linking species richness, microbial interactions, adaptive evolution, and ecosystem functioning.},
}

@article {pmid42904670,
year = {2026},
author = {Wen, X and Han, S and Wu, M and Show, PL and Liao, B and Cai, Z and Zhou, J},
title = {Functional convergence despite taxonomic turnover across coral-associated microbiomes.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0240126},
doi = {10.1128/spectrum.02401-26},
pmid = {42904670},
issn = {2165-0497},
abstract = {Coral-associated microbiomes are fundamental to holobiont health and resilience, yet their community structures often demonstrate high taxonomic variability across host species. Whether such variability results in functional instability or reflects pervasive metabolic redundancy remains unclear. Here, we investigated microbial taxonomic structure, functional potential, and community assembly mechanisms across 15 coral species using 16S rRNA gene sequencing and shotgun metagenomics. These communities exhibited extreme taxonomic heterogeneity, high beta-diversity, and the absence of a universally shared core genus, indicating strong host-specific filtering that dictates microbial membership. In contrast, Kyoto Encyclopedia of Genes and Genomes pathway-based functional profiles exhibited striking convergence across hosts, revealing a conserved metabolic landscape despite extensive taxonomic turnover. Mantel and Procrustes analyses identified a weak but significant correspondence between taxonomic composition and functional potential, a pattern consistent with functional redundancy across coral-associated microbiomes. Null model-based assembly analyses further revealed a decoupling between taxonomic and functional organization. Taxonomic structure was shaped by a host-dependent balance of stochastic and deterministic processes, whereas functional profiles were predominantly assembled through stochastic processes, maintaining consistently high functional redundancy across hosts. Metagenomic profiling uncovered a two-tier functional architecture underlying this stability: a conserved, high-abundance metabolic core enriched in carbon and phosphorus cycling and stress response functions that support microbial persistence in the coral microenvironment, together with lower-abundance host-specific metabolic modules involved in nitrogen and sulfur transformations that enable niche adaptation. Thus, functional requirements primarily govern the coral-associated microbiome rather than taxonomic identity. This synergy between conserved survival traits and flexible metabolic capacities maintains holobiont homeostasis despite extensive taxonomic turnover.IMPORTANCECoral reefs rely on complex partnerships between corals and their associated microorganisms to maintain health and withstand environmental stress. However, it remains unclear whether changes in microbial communities across different coral species lead to loss of important functions. In this study, we examined microorganisms associated with 15 coral species from the South China Sea and found that coral species hosted highly different microbial communities, while maintaining similar microbial functions. Our findings reveal that different microbial groups can perform similar ecological roles, allowing coral-associated communities to remain functionally stable despite changes in microbial membership. This functional flexibility may help corals maintain biological balance under changing environmental conditions and provides new insights into how coral holobionts preserve resilience in the face of ecological disturbances.},
}

@article {pmid42904690,
year = {2026},
author = {Lücking, D and Manzano-Marín, A and Willemsen, A},
title = {Multilayered network analysis reveals the centrality of newly discovered Nucleocytoviricota in wastewater treatment plant communities.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag267},
pmid = {42904690},
issn = {1751-7370},
abstract = {Viruses of the phylum Nucleocytoviricota are remarkable entities due to their exceptionally large genomes and complex gene repertoires, which blur the lines between viral and cellular life. Previous research has leveraged computational approaches to map their extensive diversity. Experimental work has, in parallel, begun to elucidate their intricate interactions with hosts, bacterial symbionts, co-infecting virophages, and other mobile genetic elements.Although unlikely to replicate all simultaneously within the same host cell, the convergence of these entities within a single environment creates a dense hub of potential interactions that calls for a holistic, topology-based analysis. Here, we recovered high-quality genomes of 61 Nucleocytoviruses, 15 virophages and 14 polinton-like viruses from deeply sequenced metagenomes of 23 Danish wastewater treatment plants, and integrated them into a multilayered interaction network together with microbial contigs. This network recovered putative interactions across multiple levels, including Nucleocytoviruses co-occurring with hyperparasitic elements, associations with abundant activated sludge bacteria, and read-level signals of integration events. We show that the giants among viruses act as centrality-inducing entities, elevating others into highly central positions within the community and therefore are key players shaping the microbial community structure, ecology and evolution in wastewater treatment plants.},
}

@article {pmid42905153,
year = {2026},
author = {Zhang, J and Zhang, Y and Yan, H and Wang, H and Zhou, Y and Zhao, B and Yang, M},
title = {Clinical features and global epidemiological analysis of sparganosis: Based on 5 pediatric cases and a systematic review of 135 literature reports.},
journal = {Parasitology research},
volume = {125},
number = {1},
pages = {},
pmid = {42905153},
issn = {1432-1955},
support = {2026Y0376//the Science Fund of the Yunnan Provincial Department of Education/ ; 2023-SW [GUIDE]-07//the Kunming Health Science and Technology Talent Project - 10 Projects of China/ ; 202102AA100060//the Yunnan Clinical Medical Research Center for Chronic Kidney Disease/ ; N08901329//the "Spring City Plan" High-Level Talent Training - Spring City Famous Medical Special Project/ ; },
mesh = {Humans ; *Sparganosis/epidemiology/diagnosis/drug therapy/parasitology ; Child ; Animals ; Praziquantel/therapeutic use ; Female ; Anthelmintics/therapeutic use ; Retrospective Studies ; Male ; China/epidemiology ; Child, Preschool ; Spirometra ; Adrenal Cortex Hormones/therapeutic use ; },
abstract = {Objective Sparganosis is a rare parasitic disease caused by the larvae of Spirometra mansoni, with pediatric cases being particularly uncommon and prone to misdiagnosis. This study aims to analyze the clinical features, diagnostic strategies, and treatment responses in pediatric sparganosis, and to investigate its global epidemiological trends and diagnostic and therapeutic advancements through a systematic review. Methods We conducted a retrospective analysis of 5 confirmed pediatric sparganosis cases admitted to our center between 2014 and 2023. A systematic search of the PubMed database (1980-2025) for relevant literature was performed, leading to the screening and data extraction of 135 global case reports. Descriptive statistics, correlation analysis, and trend visualization were conducted using R software (version 4.5.1). Results Among the 5 children in our center, the median age was 7 years, and all were from high-parasitic-endemicity areas in Yunnan Province, China. All cases (100%) presented with marked eosinophilia (median value 4.42 × 10[9]/L). Neurological involvement was predominant (60%, 3/5), manifesting as epilepsy, myelitis, etc. All patients received praziquantel treatment, with four also receiving concomitant corticosteroids, and all showed symptom improvement. Analysis of global cases revealed a geographic clustering in East Asia (primarily China, South Korea, Japan, and Thailand), with the central nervous system and subcutaneous tissue being the two major infection sites. Diagnosis relied mainly on MRI ("tunnel sign"), serological testing, and metagenomic Next-Generation Sequencing (mNGS). The highest improvement rate (92.2%) was observed with combination therapy (surgery plus medication), which yielded comparably high improvement rates to single-modality treatments. Conclusion Pediatric sparganosis predominantly involves the nervous system. Diagnosis requires integrating epidemiological history, imaging, and molecular testing. Treatment should be individualized, with a recommended regimen of surgery combined with long-term, weight-based praziquantel therapy, supplemented by corticosteroids when necessary. Strengthening public health education remains the fundamental measure for preventing this disease.},
}

Humans
*Sparganosis/epidemiology/diagnosis/drug therapy/parasitology
Child
Animals
Praziquantel/therapeutic use
Female
Anthelmintics/therapeutic use
Retrospective Studies
Male
China/epidemiology
Child, Preschool
Spirometra
Adrenal Cortex Hormones/therapeutic use

@article {pmid42905275,
year = {2026},
author = {Chen, K and Li, J and Chen, J and Zheng, K and Zhou, L and Su, Y and Sun, S and Chen, X and Wang, W and Liang, Y and Shao, H and Liu, Y and Zou, X},
title = {Jestvirus, a Novel Genus in the Family Autotranscriptaviridae Infecting Aeromonas.},
journal = {Current microbiology},
volume = {83},
number = {12},
pages = {},
pmid = {42905275},
issn = {1432-0991},
support = {42120104006 and 42176111//the Natural Science Foundation of China/ ; 2025M770867//the China Postdoctoral Science Foundation/ ; },
mesh = {Phylogeny ; Genome, Viral ; *Bacteriophages/classification/genetics/isolation & purification/ultrastructure ; Viral Proteins/genetics ; DNA, Viral/genetics ; *DNA Viruses/classification/genetics/isolation & purification ; *Aeromonas/virology ; Sequence Analysis, DNA ; },
abstract = {Aeromonas species are ubiquitous, aquatic, opportunistic pathogens; however, their viral predators remain underexplored. Here, we isolated and characterized Aeromonas phage vB_AsaP_JS1, a dsDNA phage with a short non-contractile tail that infects Aeromonas salmonicida. Comparative analyses indicate that vB_AsaP_JS1 diverges from representative T7-like phages, with gene content similarity below 50% and a maximum amino acid identity of 70% or less. It forms a supported monophyletic clade in both phylogenomic and protein-based trees. Gene-sharing network analysis further shows that vB_AsaP_JS1 and its closest relatives form a distinct, isolated cluster, clearly separated from all currently recognized genera within the family Autotranscriptaviridae and related lineages of Caudoviricetes. Collectively, these features satisfy ICTV criteria for genus demarcation and support the establishment of a novel phage genus, tentatively designated Jestvirus. Functional annotation highlights a compact transcriptional module containing a single-subunit T7-like RNA polymerase and a streamlined replication packaging operon. Several putative host-interaction-related genes, including a deoxycytidine kinase homolog, a PelC-like protein, and a putative glycosidase, are encoded in the genome; their possible roles in nucleotide scavenging or host interaction during infection represent hypotheses that require experimental validation. Metagenomic read mapping reveals sequence-level signals related to vB_AsaP_JS1 in wastewater datasets from multiple geographic regions, suggesting a potentially wider environmental distribution for this phage lineage than previously recognized, though confirmation of phage identity and prevalence will require further investigation. Together, our results expand the known genomic diversity of T7-like phages and provide taxonomic, functional, and ecological evidence for a new phage lineage within Caudoviricetes.},
}

Phylogeny
Genome, Viral
*Bacteriophages/classification/genetics/isolation & purification/ultrastructure
Viral Proteins/genetics
DNA, Viral/genetics
*DNA Viruses/classification/genetics/isolation & purification
*Aeromonas/virology
Sequence Analysis, DNA

@article {pmid42899699,
year = {2026},
author = {Du, M and Xue, P and Minasny, B and Tang, Y and Tran, TKA and McBratney, A},
title = {Contrasting edaphic and land-use signatures of microbial phosphorus mobilisation and accumulation genes.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag272},
pmid = {42899699},
issn = {1751-7370},
abstract = {Phosphorus (P) is an essential nutrient that constrains productivity across many terrestrial ecosystems. Soil microorganisms regulate P transformation through distinct functional strategies, yet how these strategies vary with land use and environmental conditions across chronically P-impoverished landscapes remains poorly understood. Here, we combined 268 soil metagenomes from natural, pasture, and cropland systems across Australia with genome-resolved analyses of 1,077 metagenome-assembled genomes (MAGs). Results revealed contrasting genomic distributions among P-cycling strategies. P accumulation genes were widely distributed across bacterial phylogeny, whereas mineralization gene and solubilisation gene were concentrated within specific lineages. Land-use-associated differences were most evident in the relative abundances of mineralisation and solubilisation genes, whereas accumulation genes showed comparatively little variation. Soil properties were stronger predictors of relative P-cycling gene abundance than climatic variables. Among these variables, soil pH was the strongest predictor of both the combined relative abundance of P-cycling genes and mineralisation genes, whereas accumulation genes were negatively associated with the mineral-associated organic carbon fraction. Continental predictions further suggested higher combined relative P-cycling gene abundance in wetter south-western and coastal eastern regions. These analyses reveal contrasting microbial P-cycling gene strategies across Australian soils and provide a genome-resolved framework for understanding their phylogenetic distributions and environmental associations at the continental scale.},
}

@article {pmid42900294,
year = {2026},
author = {Chen, X and Zhang, YS and Yan, D and Doan, T and Shen, LL and Taha, AT and Yang, D and Psaras, C and Callander, JK and Xin, NY and Shivkumar, A and Fawzi, AA and Yiu, G and Telander, DG and Leung, LB and Flaxel, C and Newman, JC and Keenan, JD and Stewart, JM},
title = {An exploratory study of the effect of metformin on the whole blood transcriptome of nondiabetic older adults with age-related macular degeneration.},
journal = {GeroScience},
volume = {},
number = {},
pages = {},
pmid = {42900294},
issn = {2509-2723},
support = {Unrestricted Grant//Research to Prevent Blindness/ ; Core Grant for Vision Research P30 EY037668/EY/NEI NIH HHS/United States ; },
abstract = {Metformin has received increasing attention for benefits beyond blood glucose lowering. The purpose of this study was to identify changes in whole blood transcriptome from a course of metformin in a randomized trial (NCT02684578) of nondiabetic older adults with age-related macular degeneration (AMD). We included patients who were ≥ 55 years of age, nondiabetic, and had geographic atrophy due to AMD. We excluded patients with metformin use for another reason, reduced renal or liver function, or other vitreoretinal diseases. Participants were randomized to metformin or control. The metformin group was prescribed 1000 mg metformin twice daily for 18 months. All eligible patients were approached for consent to blood sample collection. We performed metagenomic sequencing on whole blood samples and conducted differential expression analysis. Fifteen patients underwent blood collection, with eight in the metformin group and seven in the control group. No individual gene achieved statistical significance of difference between groups after correction for multiple comparisons. As a secondary, hypothesis-generating analysis, canonical pathway analysis found downregulation of interferon α/β signaling (P = 0.003, z score = -2.4), cell junction organization (P = 0.03, z score = -2.2), and epithelial mesenchymal transition pathways in the metformin group (P = 0.02, z score = -2.2). There was possible inhibition of upstream proinflammatory molecules and activation of anti-inflammatory molecules by metformin. In this small sub-study of a randomized trial, no gene was significantly changed after metformin exposure. Pathway enrichment analysis identified signals potentially consistent with metformin-associated modulation of "inflammaging" and other biological pathways which require validation in larger cohorts.},
}

@article {pmid42900364,
year = {2026},
author = {You, L and Bai, J and Meng, F and Yin, X},
title = {Clinical characteristics and prognosis of central nervous system Klebsiella pneumoniae infection: a focus on hypervirulent and classical strains.},
journal = {Neurological sciences : official journal of the Italian Neurological Society and of the Italian Society of Clinical Neurophysiology},
volume = {47},
number = {11},
pages = {},
pmid = {42900364},
issn = {1590-3478},
mesh = {Humans ; *Klebsiella Infections/diagnosis/cerebrospinal fluid/complications ; Male ; Female ; *Klebsiella pneumoniae/pathogenicity/genetics ; Retrospective Studies ; Prognosis ; Middle Aged ; Aged ; *Central Nervous System Infections/diagnosis/microbiology ; Adult ; },
abstract = {OBJECTIVE: To investigate the clinical characteristics, diagnosis, treatment, and prognosis of 20 cases of central nervous system (CNS) Klebsiella pneumoniae infection diagnosed by metagenomic next-generation sequencing (mNGS), and to compare the differences between classical Klebsiella pneumoniae (cKP) and hypervirulent Klebsiella pneumoniae (hvKP) in central nervous system infections.

METHODS: Retrospective single-center study of 20 mNGS-diagnosed CNS K. pneumoniae infections (January 2022 - March 2026). Univariate analysis compared hvKP and cKP groups.

RESULTS: Among 20 patients, 19 were diagnosed by CSF mNGS and 1 by abscess fluid mNGS. The cKP group had a higher proportion of tumor history (P = 0.029) and a marginally higher rate of neurosurgery history (P = 0.082). Type 2 diabetes was common in both groups (66.7% vs. 62.5%). The hvKP group had higher rates of focal neurological deficits (77.8% vs. 12.5%, P = 0.015) and bacteremia/sepsis (66.7% vs. 37.5%, P = 0.009), while the cKP group had more delirium (62.5% vs. 11.1%, P = 0.050). CSF mNGS positivity (95%) surpassed culture (23.5%, P < 0.001). Radiologically, hvKP showed more brain abscesses (P = 0.015). hvKP had worse modified Rankin Scale scores (P = 0.002) and higher mortality (44.4% vs. 0%, P = 0.002). No cKP deaths occurred.

CONCLUSION: hvKP and cKP CNS infections differ significantly. hvKP is associated with community-onset severe disease (multiple brain abscesses, pyoventricle, focal deficits) and high mortality, while cKP links to nosocomial factors and better outcomes. mNGS is key for diagnosis, offering high CSF positivity and concurrent virulence/resistance profiling. Potential prognostic factors identified include high CSF mNGS reads, resistance genes, early liver abscess drainage, timely intravitreal injection, and combination therapy.},
}

Humans
*Klebsiella Infections/diagnosis/cerebrospinal fluid/complications
Male
Female
*Klebsiella pneumoniae/pathogenicity/genetics
Retrospective Studies
Prognosis
Middle Aged
Aged
*Central Nervous System Infections/diagnosis/microbiology
Adult

@article {pmid42901005,
year = {2026},
author = {Liu, P and Chen, J and Hu, Z and Gao, J and Chen, X and He, Z and Zhang, D and Pan, X},
title = {Selective upcycling chelated copper from wastewater to Cu2-xSe-rich product: integrating selenium bio-reduction into anaerobic granular sludge technology.},
journal = {Journal of environmental management},
volume = {419},
number = {},
pages = {131199},
doi = {10.1016/j.jenvman.2026.131199},
pmid = {42901005},
issn = {1095-8630},
abstract = {The treatment of wastewater containing chelated copper (Cu), such as Cu-EDTA complexes, remains a persistent challenge owing to the high stability of the chelates and the generation of hazardous heavy metal-bearing sludge. This study proposes a selenium-enhanced anaerobic granular sludge (Se-GS) technology for selective Cu recovery as a Cu2-xSe-rich product. Over 100 days of continuous operation in a single laboratory-scale reactor with synthetic wastewater, the Se-GS reactor achieved a Cu removal efficiency of 98.7%, with dissolved effluent Cu concentrations consistently below 0.5 mg/L, outperforming the unamended control. Sequential extraction, X-ray diffraction and elemental analysis indicated that Cu and Se in the final Se-GS sludge residue may be predominantly present as crystalline Cu2-xSe, which was extracted to obtain a Cu2-xSe-rich product with a Cu recovery efficiency of 62.5%. Metagenomic analysis identified Desulfovibrio as a candidate functional genus associated with selenium transformation and a genome-level pathway for Cu2-xSe biosynthesis was reconstructed. The recovered product exhibited a higher apparent methylene blue (MB) degradation rate under the tested condition than chemically synthesized Cu2-xSe. The process is a selective Cu-recovery unit within a broader treatment train; residual EDTA, Cd and recovery-related streams require further management. Further validation with real wastewater, replicate reactors, and scale-up systems is warranted to confirm the robustness and scalability of the Se-GS process.},
}

@article {pmid42901070,
year = {2026},
author = {Yan, Y and Wang, YN and Wang, F and Gao, Y and Wang, H},
title = {Efficient benzo[a]pyrene bioremediation by a novel halotolerant Rhodococcus ruber TN-1 in salinity environment: Mechanical insight from whole-genome, degradation efficiency and microbial properties.},
journal = {Marine pollution bulletin},
volume = {234},
number = {Pt 1},
pages = {120499},
doi = {10.1016/j.marpolbul.2026.120499},
pmid = {42901070},
issn = {1879-3363},
abstract = {Benzo[a]pyrene (BaP) contamination in highly saline environments has received increasing attention; however, efficient degradation of BaP by halotolerant BaP-degrading bacteria from contaminated water and soils remains poorly understood. In this study, a novel BaP-degrading bacterium, designated Rhodococcus ruber TN-1, was isolated, and its BaP degradation performance was evaluated. Whole-genome sequencing revealed genes and gene clusters associated with benzoate and xylene transport and degradation, naphthalene degradation, and the catabolism of other aromatic compounds. Strain TN-1 exhibited high BaP degradation efficiency in water, with a degradation efficiency exceeding 95% after 3 d of cultivation. Inoculation with strain TN-1 significantly improved the BaP degradation efficiency in three types of saline soil. After 14 d of reaction, the BaP degradation rate increased from 12.08% to 26.94% in the control to 44.03-59.12%. Correlation analysis revealed that the degradation rate of soil BaP was positively correlated with soil catalase (CAT) activity and negatively correlated with salinity. Metagenomic and quantitative real-time PCR (qPCR) analyses demonstrated that the addition of strain TN-1 significantly increased microbial abundance in three saline soils, with strain TN-1 becoming the dominant microorganism and accelerating the microbial degradation of BaP. These findings highlight strain TN-1 as a promising bioaugmentation agent for the remediation of BaP-contaminated saline soils.},
}

@article {pmid42901642,
year = {2027},
author = {Jiang, W and Li, Z and Dong, Y and Ao, Z and Jia, J and Chen, Z and Song, C and Yang, L and Liu, R and Peng, J and Zhang, S and Feng, Z},
title = {Spatiotemporal dynamics of volatile flavor compounds and associated functional microbial communities during strong-flavor Daqu fermentation.},
journal = {Food microbiology},
volume = {142},
number = {},
pages = {105281},
doi = {10.1016/j.fm.2026.105281},
pmid = {42901642},
issn = {1095-9998},
mesh = {Fermentation ; *Volatile Organic Compounds/metabolism/chemistry/analysis ; *Flavoring Agents/metabolism/chemistry ; *Bacteria/genetics/metabolism/classification/isolation & purification ; *Microbiota ; Gas Chromatography-Mass Spectrometry ; Metagenomics ; *Wine/microbiology/analysis ; RNA, Ribosomal, 16S/genetics ; Taste ; Solid Phase Microextraction ; Fungi/metabolism/genetics/classification/isolation & purification ; },
abstract = {Daqu, the essential fermentation starter for Baijiu production, harbors stratified microbial communities that orchestrate flavor formation. This study integrated headspace solid-phase microextraction gas chromatography-mass spectrometry (HS-SPME-GC-MS), metagenomics, and PacBio full-length 16S rRNA and ITS sequencing to characterize the spatiotemporal heterogeneity of volatile flavor compounds (VFCs) and functional microbial communities across three layers-the surface (QP), middle (HQ), and core (QX) of strong-flavor Daqu over a 90-day fermentation period. A total of 47 VFCs were identified, with alcohols, aldehydes, and esters as the predominant components. VFCs peaked at 2-4 days, then declined and stabilized, showing a progressive accumulation gradient from QP to QX. Aldehydes and pyrazines were enriched in HQ and QX, while esters and acids were highest in QX. Metagenomic analysis demonstrated that the abundance of flavor-related enzyme genes followed spatiotemporal trends of VFCs. Although filamentous fungi and Lactobacillaceae constituted the primary microbial sources of flavor-related enzyme genes across all layers, their community composition and successional dynamics exhibited pronounced spatiotemporal specificity. Positive microbial interactions increased from QP (71.70%) to HQ (76.73%) to QX (89.95%), indicating stronger cooperation in QX. These findings provide mechanistic insights into the ecological underpinnings of flavor stratification in Daqu and offer a scientific framework for future targeted optimization of strong-flavor Baijiu fermentation.},
}

Fermentation
*Volatile Organic Compounds/metabolism/chemistry/analysis
*Flavoring Agents/metabolism/chemistry
*Bacteria/genetics/metabolism/classification/isolation & purification
*Microbiota
Gas Chromatography-Mass Spectrometry
Metagenomics
*Wine/microbiology/analysis
RNA, Ribosomal, 16S/genetics
Taste
Solid Phase Microextraction
Fungi/metabolism/genetics/classification/isolation & purification

@article {pmid42895087,
year = {2026},
author = {Aranda, M and Pariente, JA and Terrón, MP and González-Flores, D and Aranda, E and Ruiz-Moyano, S and Velázquez, R and Martín, A},
title = {Comparative dietary profiling of smoked and non-smoked paprika (Capsicum annuum L.) in Wistar rats: metabolomic, biochemical and gut microbiota responses in a healthy animal model.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d6fo03991j},
pmid = {42895087},
issn = {2042-650X},
abstract = {Paprika (Capsicum annuum L.) is a widely consumed spice whose bioactive composition is substantially influenced by processing conditions. Traditional smoking, as applied in the production of PDO Pimentón de la Vera, enriches paprika with wood smoke-derived phenolics while also introducing polycyclic aromatic hydrocarbons (PAHs), warranting an integrated evaluation of processing-related biological responses and safety considerations. This study compared physiological, biochemical, metabolomic, and cecal microbiota responses to dietary supplementation with smoked and non-smoked paprika in healthy Wistar rats. Thirty animals of both sexes (16 females and 14 males) received a control diet or diets supplemented with 5% smoked or non-smoked paprika for 30 days. Histological examination revealed no treatment-related alterations in the organs evaluated. Hematological and biochemical analyses showed diet- and sex-associated differences in hematocrit, plasma glucose, total antioxidant capacity, and lipid-related parameters, although all values remained within normal physiological ranges. Untargeted urinary metabolomics, restricted to males because of insufficient urine volume in females, identified features tentatively annotated as phenolic conjugates and other metabolites associated with paprika intake, with several signals showing higher abundance in the smoked paprika group. Cecal metagenomic analyses showed sex-dependent changes across taxon-level abundance, alpha diversity, and beta diversity. In females receiving smoked paprika, lower TC and LDL-C coincided with higher alpha diversity and lower cecal lipid content, suggesting a potential link between intestinal microbial ecology and lipid handling. Overall, paprika processing was associated with distinct biochemical, metabolomic, and cecal microbiota response patterns in this healthy animal model.},
}

@article {pmid42895327,
year = {2026},
author = {Wittmers, F and Dames, NR and Michelsen, M and Spezzano, R and Comstock, J and Bergauer, K and Vergin, K and Liu, S and Parsons, R and Temperton, B and Saito, MA and Carlson, CA and Worden, AZ},
title = {Seasonal and evolutionary patterns of planktonic Hikarchaeia reveal ecological niches of marine rare biosphere constituents.},
journal = {mBio},
volume = {},
number = {},
pages = {e0175326},
doi = {10.1128/mbio.01753-26},
pmid = {42895327},
issn = {2150-7511},
abstract = {Members of Marine Group IV, now termed Hikarchaeia, hold an important transitional evolutionary position among Archaea but remain uncultivated, and their ecology remains uncharacterized. Over a 5-year period, we performed monthly profile sampling in the North Atlantic Subtropical Gyre and sequenced V4 16S rRNA gene amplicons, while also collecting additional size-fractionated and metagenomic samples. Hikarchaeal relative abundance annually peaked at ~1% of prokaryotic amplicons. Their relative abundances were significantly higher after deep winter mixing when thermal stratification isolated exported dissolved organic matter in the twilight zone (TZ), the boundary region between the epipelagic and mesopelagic. A diminutive 1.17 Mbp complete hikarchaeal genome was recovered by sequencing and co-assembling diel TZ metagenomes from 200 m during summer, where their relative abundances were highest. Phylogenomic reconstruction incorporating our new metagenome-assembled genome (MAG) and public MAGs established five clades. Clades I and III were in subtropical and tropical environments, with vertical partitioning: Clade I dominated the TZ, and Clade III detection initiated in the lower mesopelagic and extended into the bathypelagic. Clade V is polar-associated. Data sparsity makes Clade II and IV distributions unclear. All Hikarchaeia recovered thus far appear to be free-living aerobes capable of heterotrophy. Unlike MGI, MGII, and MGIII Archaea, and most marine pelagic bacteria, the Hikarchaeia encode bacterioruberin biosynthesis, except deep Clade III. Hikarchaeia also have nitrile hydratases alongside enzymes for carbon monoxide oxidation and menaquinone biosynthesis, suggesting previously unrecognized roles in nitrogen and carbon cycling. Collectively, our studies reveal niche partitioning of evolutionarily distinct uncultivated Hikarchaeia clades and patterning within the rare biosphere.IMPORTANCEThe ocean and its vertical water-column structure are changing with planetary warming; yet, there are many enigmatic microbes, especially those that inhabit the deep ocean. Here, we illuminate a group of uncultivated Archaea that were discovered over two decades ago but still lack clear distributions and habitat preferences. With the first complete hikarchaeal genome now in hand, we identified distinct lineages within the Hikarchaeia that occupy different marine niches. Strong reoccurring seasonal patterns were observed that closely followed the annual cycle of temperature-driven ocean stratification. Given rapid natural and anthropogenic perturbations at hand, establishing baselines for these Archaea is critical for improving our understanding and modeling of marine microbiomes and their biogeochemical functions.},
}

@article {pmid42896018,
year = {2026},
author = {Ciappina, G and Maltese, T and Mauro, GD and Fiorentino, V and Ieni, A and Ottaiano, A and Simone, C and Consolo, P and Pollicino, T and Berretta, M},
title = {Gut Microbiota and Immunotherapy: Baseline 16S rRNA Profiling as a Pragmatic Tool for Clinical Stratification.},
journal = {Cancer control : journal of the Moffitt Cancer Center},
volume = {33},
number = {},
pages = {10732748261500279},
doi = {10.1177/10732748261500279},
pmid = {42896018},
issn = {1526-2359},
mesh = {Humans ; *RNA, Ribosomal, 16S/genetics ; *Immunotherapy/methods ; *Gastrointestinal Microbiome/genetics/immunology/drug effects ; *Neoplasms/microbiology/therapy/immunology/drug therapy ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; },
abstract = {The gut microbiota is a complex and dynamic ecosystem involved in the modulation of host immune responses. Accumulating evidence links gut microbial composition to the efficacy and toxicity of immune checkpoint inhibitors (ICIs), although most evidence supporting microbiota-based biomarkers remains observational. Higher baseline alpha-diversity has been associated with favorable outcomes in several cohorts, but these associations are not uniform, and individual taxonomic signatures show substantial inter-study variability. In this perspective, we discuss baseline microbiota profiling as a promising investigational approach to patient stratification in immuno-oncology. Despite its methodological limitations, 16S rRNA sequencing remains a scalable, reproducible, and clinically feasible approach compared with more complex techniques such as shotgun metagenomics. Standardization of sampling procedures, sequencing methodologies, and bioinformatic pipelines is essential for the reliable implementation of microbiota-based biomarkers in routine clinical care. Integrating gut microbiota assessment into pre-treatment evaluation may improve patient selection and support a more biologically informed approach to immunotherapy.},
}

Humans
*RNA, Ribosomal, 16S/genetics
*Immunotherapy/methods
*Gastrointestinal Microbiome/genetics/immunology/drug effects
*Neoplasms/microbiology/therapy/immunology/drug therapy
*Immune Checkpoint Inhibitors/therapeutic use/pharmacology

@article {pmid42896326,
year = {2026},
author = {Shen, H and Pang, C and Mei, H and Wang, Y and He, C and Wang, W},
title = {Synergistic enhancement of quinoline degradation and nitrogen removal in a coupling FeS-ZVI microelectrolysis and partial denitrification-anammox system: performance and mechanisms.},
journal = {Journal of hazardous materials},
volume = {518},
number = {},
pages = {143923},
doi = {10.1016/j.jhazmat.2026.143923},
pmid = {42896326},
issn = {1873-3336},
abstract = {Quinoline in coal chemical wastewater severely inhibits the performance of partial denitrification-anammox (PD/A) process. This study innovatively developed a FeS-ZVI microelectrolysis coupled PD/A system to simultaneously enhance quinoline degradation and nitrogen removal under quinoline stress. The coupled system achieved quinoline and nitrogen removal efficiencies of 92.0 ± 2.4% and 81.7 ± 1.7%, respectively, outperforming the control (32.8 ± 6.0% and 17.8 ± 9.5%), FeS (73.3 ± 6.8% and 53.8 ± 5.4%), and ZVI (75.3 ± 9.3% and 51.6 ± 5.6%) groups. Mechanistically, the FeS-ZVI microelectrolysis facilitated reactive species generation, thereby enhancing the abiotic removal of quinoline (30.0 ± 0.7%). Meanwhile, FeS-ZVI microelectrolysis maintained higher microbial electron transport and energy metabolism, with electron transport system activity, electron-donating capacity, and ATPase activity being 31.9-133.1%, 30.4-116.5%, and 104.1-771.3% higher, respectively, than those in the other groups. Crucially, quinoline degradation into chain compounds and the release of Fe[2 +]/S[2-] via FeS-ZVI microelectrolysis, enhanced heterotrophic and autotrophic partial denitrification, respectively, ultimately supporting anammox. Metagenomics analysis revealed enrichment of the electroactive bacteria (Pseudomonas), quinoline-degrading bacteria (Exiguobacterium), and genes involved in carbon (Ior A/B, PcaD, LigC), nitrogen (hdh, hzs, narB), and sulfur (Sox) metabolism. Therefore, the FeS-ZVI microelectrolysis-PD/A system achieved synergistic carbon and nitrogen removal under quinoline stress.},
}

@article {pmid42896375,
year = {2026},
author = {Li, B and Pang, H and Huang, D and Ruan, C and Ijaz, UZ and Yin, H and Lin, H and Qiu, Y and Yu, P},
title = {Phage preferential infection of antibiotic-susceptible bacteria enriches antibiotic-resistant bacteria in activated sludge microbiomes.},
journal = {Water research},
volume = {309},
number = {Pt A},
pages = {127160},
doi = {10.1016/j.watres.2026.127160},
pmid = {42896375},
issn = {1879-2448},
abstract = {Despite the significance of phages in microbial ecosystems, the contribution of lytic phages to the propagation of antibiotic resistance genes (ARGs) within activated sludge microbiomes remains unclear. By integrating global metadata analysis and metagenomics, we first demonstrated that lytic phages exhibit a strong infection preference for antibiotic-susceptible bacteria (ASB, 70.84%) over antibiotic-resistant bacteria (ARB, 29.16%). This preferential phage infection was consistent with ARB carrying an exceptionally higher abundance of antiviral defense systems than ASB (averaging 1.83 versus 0.03 systems per whole genome). Furthermore, phage transplant experiments revealed that elevated phage predation pressure (phage-to-bacteria ratios ≥100) drove significant shifts in community composition toward highly defended lineages, thereby enriching the relative abundance of ARGs and mobile genetic elements (MGEs) by 25∼30-fold compared to controls. Additionally, real-time microfluidic tracking confirmed a "Kill-the-Winner" ecological dynamic, where phages selectively eradicate fast-growing ASB, thereby indirectly promoting ARB survival and increasing ARG transfer frequency. Overall, these findings highlight an underappreciated ecological risk driven by selective predation of lytic phages, which indirectly accelerates ARG dissemination in complex environmental microbiomes.},
}

@article {pmid42896558,
year = {2026},
author = {Wernike, K and Hoffmann, B and Link, EK and Rotheneder, S and Eshak, M and Pfaff, F and Höper, D and Beer, M},
title = {Emergence of Shamonda Orthobunyavirus, Central Europe, 2026.},
journal = {Emerging infectious diseases},
volume = {32},
number = {12},
pages = {},
doi = {10.3201/eid3212.261496},
pmid = {42896558},
issn = {1080-6059},
abstract = {Since mid-June 2026, an acute, nonfatal syndrome characterized by high herd illness rate, reduced milk yield, diarrhea, fever, and lethargy has affected dairy cattle in southern Germany and Switzerland. After major viral pathogens were excluded, pan-Simbuvirus reverse transcription PCR detected an orthobunyavirus, confirmed by metagenomic sequencing, enabling recovery of a complete Shamonda virus genome.},
}

@article {pmid42896727,
year = {2026},
author = {Dian, S and Johar, E and Witari, D and Sriyani, IY and Dewi, YP and Antonjaya, U and Ganiem, AR and Yudhaputri, FA and van Crevel, R and Masyeni, S and Ledermann, JP and Powers, AM and Mossel, EC and Myint, KSA},
title = {Recovery of Human Pegiviruses from Patients with Acute Febrile Illness and Sub-acute Central Nervous System Infection.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {109200},
doi = {10.1016/j.ijid.2026.109200},
pmid = {42896727},
issn = {1878-3511},
abstract = {OBJECTIVE: To describe two cases of HPgV-1 identified during high-throughput sequencing (HTS)-based investigation of previously undiagnosed acute febrile illness (AFI) and central nervous system infection.

METHODS: RNA metagenomic HTS was applied to clinical samples that had previously tested negative by PCR targeting alphaviruses, flaviviruses, enteroviruses, herpesviruses, and paramyxoviruses. Specimens were also tested for IgM antibodies against chikungunya virus, dengue virus, and Japanese encephalitis virus.

RESULTS: A complete HPgV-1 genotype 4 was recovered from a child with undifferentiated AFI. In a middle-aged man with HIV and severe neurological disorder, complete genomes of HPgV-1 (genotype 4), HPgV-2, and hepatitis C virus (genotype 3k) were identified.

CONCLUSION: To our knowledge, this is the first report of HPgV-2 detection in Indonesia, expanding its known geographic distribution. These findings underscore the complexity of viral co-infections in immunocompromised patients and the uncertain clinical significance of human pegiviruses. This further highlights the utility of metagenomic HTS for pathogen discovery and genomic surveillance in unexplained clinical syndromes.},
}

@article {pmid42896801,
year = {2026},
author = {Li, J and Deng, Y and Yu, Y and He, W and Feng, Y},
title = {Moisture-induced pore restriction reveals a lower initial moisture window for aerobic composting of aquaculture-derived particulates.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125977},
doi = {10.1016/j.envres.2026.125977},
pmid = {42896801},
issn = {1096-0953},
abstract = {Aerobic composting offers a sustainable route for recycling aquaculture-derived particulates, but appropriate moisture conditions for these fine and adhesive materials remain unclear because conventional criteria are mainly derived from terrestrial wastes. Aquaculture-derived particulates were composted for 28 d at initial moisture contents of 40%, 45%, and 50%. The 40% treatment maintained the highest porosity and more favorable oxygen conditions, entered the thermophilic phase (>50 °C) on day 8, and remained thermophilic for 13 d. In contrast, the 45% treatment sustained thermophilic conditions for only 6 d, whereas the 50% treatment never exceeded 50 °C and reached a minimum O2 concentration of 5.3%. The 40% treatment achieved a 52.47% decrease in C/N ratio, a final germination index of 81.7 ± 6.3%, and an HA/FA ratio of 1.87 ± 0.06, indicating enhanced organic matter stabilization and humification. Higher moisture caused persistent oxygen limitation, prolonged NH4[+]-N accumulation, ammonia loss, and increased greenhouse gas emissions. Microbial and metagenomic analysis were consistent with faster succession toward thermotolerant and aerobic degraders under 40% moisture, whereas higher moisture favored oxygen-limited metabolic potentials. Aquaculture-derived particulates also contained higher mucin-equivalent levels than the conventional substrates examined, suggesting that mucin may increase moisture-dependent adhesion and pore restriction. These findings demonstrate that aquaculture particulate-based composting requires a lower initial moisture level than commonly applied to conventional substrates, highlighting the importance of balancing water availability and pore aeration to improve compost stability and mitigate greenhouse gas emissions.},
}

@article {pmid42896957,
year = {2026},
author = {Newton, JP and Allentoft, ME and Bateman, PW and Ferrier, S and Thomsen, PF and Nevill, P},
title = {Car-Mounted Airborne eDNA Sampling Detects Landscape Scale Biodiversity Turnover Along Environmental Gradients.},
journal = {Molecular ecology resources},
volume = {26},
number = {7},
pages = {e70217},
doi = {10.1111/1755-0998.70217},
pmid = {42896957},
issn = {1755-0998},
support = {//Mineral Resources/ ; },
mesh = {*DNA, Environmental/genetics/isolation & purification ; *Biodiversity ; Animals ; Extrachromosomal DNA ; Plants/genetics/classification ; Western Australia ; DNA Barcoding, Taxonomic ; Ecosystem ; *Metagenomics/methods ; },
abstract = {Documenting accelerating global biodiversity decline requires monitoring tools that can operate across large spatial scales and repeated timeframes. Analysis of airborne environmental DNA (eDNA) is an emerging method used to track species distributions, but it is unknown whether airborne eDNA retains coherent ecological signals across terrestrial landscapes, or whether atmospheric mixing and DNA transport make it too spatially diffuse to resolve meaningful macroecological patterns. To address this question, we conducted a biodiversity survey using car-mounted airborne eDNA sampling along a repeated 1155 km route across south-western Western Australia, spanning the Southwest Australian biodiversity hotspot and adjacent inland regions. This extensive and environmentally heterogeneous region faces ongoing pressures from habitat loss, invasive species and climate change, highlighting the need for scalable biodiversity monitoring approaches. Samples were collected at ~26 km intervals and analysed using metabarcoding assays targeting plants, vertebrates and arthropods, with generalised dissimilarity modelling used to assess environmental drivers of community turnover. We detected a broad range of plants and animals, including species of ecological and biosecurity importance. Different taxonomic groups showed distinct spatial scales of airborne eDNA community similarity and beta diversity was structured primarily by habitat and environmental gradients rather than geographic distance alone. This indicates that airborne eDNA did not simply reflect spatially homogenised biological material but retained ecological structure informative of macroecological patterns. Together, these findings demonstrate that car-mounted airborne eDNA can recover ecologically meaningful patterns of community turnover across heterogeneous terrestrial landscapes and support landscape-scale biodiversity assessment.},
}

*DNA, Environmental/genetics/isolation & purification
*Biodiversity
Animals
Extrachromosomal DNA
Plants/genetics/classification
Western Australia
DNA Barcoding, Taxonomic
Ecosystem
*Metagenomics/methods

@article {pmid42897202,
year = {2026},
author = {Zelik, L and Levin, Y and Sawaed, J and Telpaz, S and Zigdon, M and Nuriel-Ohayon, M and Rubin, E and Gordon, A and Mogilevski, Z and Yehuda, A and Awad, A and Shaalan, H and Ben-Simon, S and Modilevsky, S and Naama, M and Dalvi, J and Moadi, L and Kurtz, M and Perez, S and Turjeman, S and Werbner, M and Khatib, S and Koren, O and Erez, A and Bel, S},
title = {Disentangling microbiota-dependent and -independent impacts of antibiotics on host physiology.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {42897202},
issn = {2058-5276},
abstract = {Antibiotics are believed to affect host physiology by altering the gut microbiota. However, it remains unclear which effects of antibiotics are microbiota dependent and which are microbiota independent. Here we present a resource encompassing host and microbiota responses to antibiotic treatment and a computational tool with which to analyse them. Metagenomic and transcriptomic analyses of conventional and germ-free mice revealed that antibiotic administration routes and their combinations affect host and microbiota responses. We developed CompoRes-a computational tool that distinguishes the microbiota-independent impact of antibiotic-induced perturbations, revealing that antibiotics directly impact host physiology. We found that diurnal expression of major histocompatibility complex class II in the mouse colon is controlled by glucose via feeding. This pattern was lost during antibiotic treatment as vancomycin altered feeding behaviour in a microbiota-independent and evolutionarily conserved manner. Together, our study establishes a direct, non-microbial pathway by which antibiotics reshape host immunity and circadian physiology.},
}

@article {pmid42897351,
year = {2026},
author = {Vijande, C and Fuentes-González, C and Lazzari, M and Lema, JM and Balboa, S},
title = {Industrial WWTP Sludge as a Reservoir of Putative Plastic-Degrading Enzymes: Insights Into Microbial Community Structure.},
journal = {Microbial ecology},
volume = {89},
number = {1},
pages = {},
pmid = {42897351},
issn = {1432-184X},
support = {ED481A 2022/391//Xunta de Galicia/ ; ED431F2024/302//Xunta de Galicia/ ; RYC2021-031220-I//Agencia Estatal de Investigación/ ; },
mesh = {*Sewage/microbiology ; *Plastics/metabolism ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/enzymology/isolation & purification/metabolism ; Biodegradation, Environmental ; Metagenomics ; Biofilms/growth & development ; *Microbiota ; Proteobacteria/genetics/enzymology/isolation & purification ; *Wastewater/microbiology ; },
abstract = {Plastic pollution has emerged as a major environmental challenge. While various microorganisms and enzymatic mechanisms involved in plastic degradation have been described, the microbial communities present in wastewater treatment plants (WWTPs) - particularly those linked to the oil industry - remain largely underexplored as potential reservoirs of plastic-associated metabolic functions. This study evaluated the potential of microbial communities from an industrial WWTP located in an oil refinery complex to colonise different plastic polymers, as well as their genetic potential for plastic-associated transformations. Industrial sewage sludge was incubated with four polymeric substrates: low-density polyethylene, polyamide, polypropylene, and polystyrene. Metagenomic analysis of the inoculum was performed to assess its potential to harbour genes encoding proteins with sequence similarity to enzymes previously associated with plastic transformation or degradation. Additionally, 16S rRNA amplicon sequencing studied changes in microbial community composition during biofilm formation. Proteobacteria accounted for approximately 50% of the microbial relative abundance in the inoculum. Metagenomic screening identified 773 genes encoding proteins with homology to enzymes previously associated with plastic degradation. Biofilms developed on plastic surfaces were dominated by Proteobacteria and Bacteroidota, although differences in dominant classes and orders were observed depending on the polymer type. Correlation analyses further indicated associations between specific microbial taxa and individual plastic types. Overall, the results highlight industrial WWTP sludge as a potential reservoir of microorganisms associated with plastic colonisation, providing new insights into plastisphere community assembly in engineered environments.},
}

*Sewage/microbiology
*Plastics/metabolism
RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification/enzymology/isolation & purification/metabolism
Biodegradation, Environmental
Metagenomics
Biofilms/growth & development
*Microbiota
Proteobacteria/genetics/enzymology/isolation & purification
*Wastewater/microbiology

@article {pmid42897585,
year = {2026},
author = {Tanatani, K and Suzuki, H and Fujita, M and Araki, T and Suzuki, Y and Michinobu, T and Otsuka, Y and Nakamura, M and Masai, E and Kamimura, N},
title = {A 2-pyrone-4,6-dicarboxylic acid biosensor for lignin valorization based on a newly identified transcriptional regulatory system.},
journal = {Biotechnology for biofuels and bioproducts},
volume = {19},
number = {1},
pages = {},
pmid = {42897585},
issn = {2731-3654},
support = {JPMJCR23L4//JST CREST/ ; JPMJPF2104//JST COI-NEXT/ ; 24K01891//JSPS KAKENHI/ ; 21K05872//JSPS KAKENH/ ; JPJS00420240017//JSPS J-PEAKS/ ; },
abstract = {BACKGROUND: Lignin is the most abundant renewable aromatic resource on Earth, yet its efficient conversion into value-added chemicals through biological funneling remains a key challenge. Sphingobium lignivorans SYK-6 exhibits broad metabolic capacity for lignin-derived aromatic compounds, ranging from monomers to dimers, making it a suitable host for biological funneling. Production systems for the polymer building block 2-pyrone-4,6-dicarboxylic acid (PDC) from lignin-derived aromatic compounds have been constructed using SYK-6. In this study, we developed a PDC-responsive biosensor to facilitate high-throughput screening of improved PDC-producing strains.

RESULTS: PDC-assimilating bacteria were isolated from environmental samples, and their genomes were analyzed to obtain candidate PDC-responsive transcriptional regulatory systems. Among these, the LysR-type transcriptional regulator PdcR and its target promoter PPDC from Cupriavidus sp. 8B were identified and characterized as a PDC-responsive system, in which PdcR is suggested to act as both a repressor and an activator. A reporter plasmid pCup1 carrying these components was introduced into a PDC hydrolase gene-deficient strain (ΔligI) of SYK-6 to construct the PDC biosensor ΔligI(pCup1). The biosensor was specific for PDC, with no response observed for its upstream metabolites. When vanillic acid or protocatechuic acid was supplied as a substrate, concentration-dependent fluorescence responses were observed over a range of 0.1-5 mM, demonstrating that PDC production from lignin-derived aromatic compounds can be monitored. Fluorescence increased synchronously with PDC accumulation, suggesting real-time monitoring of PDC production. Furthermore, the biosensor responded to PDC produced from aromatic compounds in softwood black liquor extract.

CONCLUSIONS: ΔligI(pCup1) enables real-time, specific detection of PDC produced from lignin-derived aromatic compounds, including those in black liquor extract derived from lignocellulosic biomass, demonstrating applicability to screening for lignin valorization. Integration of this biosensor with diverse strain engineering approaches, including random mutagenesis, adaptive laboratory evolution, and metagenomics-based enzyme discovery, would provide a platform for efficient selection of SYK-6 strains with enhanced PDC production capability.},
}

@article {pmid42897614,
year = {2026},
author = {Gattei, A and Vettorazzo, S and Pindo, M and Salmaso, N and Manghi, P and Larsen, S and Donati, C},
title = {Metagenomics identifies distinct functional and taxonomic profiles between freshwaters and associated sediments in alpine habitats.},
journal = {Environmental microbiome},
volume = {21},
number = {1},
pages = {},
pmid = {42897614},
issn = {2524-6372},
support = {PNRR, Mission 4 Component 2, Investment 1.4, D.D. 1034 17/06/2022, Project CN00000033//Ministero dell'Istruzione, dell'Università e della Ricerca/ ; },
abstract = {BACKGROUND: Alpine freshwater habitats are biodiversity hotspots, home to uniquely adapted microbial communities. However, our understanding of how taxonomic composition and metabolic potential of microbial communities varies across habitat type and physiography remains limited.

RESULTS: Using metagenomic sequencing, we examined microbial diversity and functions in sediment and water habitats across a physiographic gradient, including deep and shallow lakes, pasture ponds, ponds and peat bogs. Overall, sediments supported more diverse and even microbial communities. Conversely, waters displayed higher heterogeneity across the physiographic gradient in both taxonomic and functional composition. Notably, water communities from small water bodies, especially peat bogs and ponds, showed comparable diversity to their respective sediment communities, with higher taxonomic richness than aquatic communities from larger water bodies. Sediment microbial communities showed higher functional potential for nitrogen and methane metabolism, a pattern related to the likely anoxic conditions. By contrast, water bodies favored higher potential for carbohydrate metabolism, carbon oxidation and photosynthesis. Lastly, we recovered 496 bacterial and archaeal metagenome-assembled genomes and found that 73% could not be assigned at the species level.

CONCLUSIONS: Our findings shed new light on the microbial diversity and metabolic potential of alpine freshwater ecosystems, highlighting the vast and unknown diversity harbored by these fragile alpine ecosystems.},
}

@article {pmid42898413,
year = {2026},
author = {Yuan, Y and Wang, J and Feng, N and Wu, F and Dong, X and Xu, Y and Zhao, S and Tan, T},
title = {Pathogen-targeted quick multiplex PCR identification of Chlamydia psittaci and Haemophilus influenzae coinfection in pneumonia: a case report.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1890644},
pmid = {42898413},
issn = {2296-858X},
abstract = {This study describes a rare case of pneumonia induced by coinfection with Chlamydia psittaci (C. psittaci) and Haemophilus influenzae (H. influenzae). The patient had a history of chronic nephritis and long-term pigeon breeding. The initial manifestation was slurred speech, followed by rapid progression to high fever and respiratory failure. Chest computed tomography revealed bilateral interstitial pneumonia, predominantly in the right lung. Pathogen-targeted quick multiplex polymerase chain reaction (pt-qPCR) confirmed the pathogens as C. psittaci and H. influenzae, and metagenomic next-generation sequencing (mNGS) further verified consistent results. After 7-days of combination therapy with doxycycline and azithromycin, the treatment was switched to doxycycline combined with moxifloxacin for an additional 8-days. The patient achieved complete recovery and was discharged from the hospital. This case suggests that pt-qPCR may facilitate early identification of mixed infections in patients with severe pneumonia and a history of avian exposure, thereby providing valuable information to guide clinical decision-making.},
}

@article {pmid42898572,
year = {2026},
author = {Choi, Y and Kang, A and Kang, MG and Lee, DJ and Kyoung, D and Heo, JM and Song, M and Oh, S and Kim, Y},
title = {Exploring synergistic effect of bacteriophages with probiotics against multidrug resistant Salmonella Typhimurium in a simulated chicken gastrointestinal system using metagenomic- and culturomic approaches.},
journal = {Journal of animal science and technology},
volume = {68},
number = {4},
pages = {1213-1238},
pmid = {42898572},
issn = {2055-0391},
abstract = {Salmonella is a critical foodborne pathogen that significantly affects global food safety and the poultry industry. The reliance on antibiotics to control Salmonella infections has led to the emergence of antibiotic-resistant bacteria, necessitating the development of alternative strategies. The present study explored the synergistic potential of combining bacteriophages and probiotics as a dual approach for Salmonella suppression and gut microbiota modulation. Using a multi-omics approach integrating culture and metagenomics, we isolated Lactobacillus reuteri J2M1, a robust probiotic strain with strong acid and bile tolerance, intestinal adhesion, and a safety profile. Concurrently, two bacteriophages, SLAM_phiST45 and SLAM_phiST56, targeting Salmonella Typhimurium were selected based on their broad host range, enhanced inhibitory effects as a cocktail, and genomic safety validated through whole-genome sequencing. In a model that simulated the gut environment of poultry, the combined application of bacteriophages and L. reuteri J2M1 resulted in significant changes in the microbial community at the genus level. Although the application of bacteriophages alone effectively reduced Salmonella populations, it also led to the proliferation of genera that contain potential pathogens, such as Clostridium perfringens. In contrast, the co-application of L. reuteri J2M1 mitigated these negative effects by promoting the growth of beneficial genera, including Oscillibacter and Clostridium butyricum, which are associated with anti-inflammatory properties and gut health. These findings demonstrate that combining bacteriophages with probiotics suppresses pathogens as well as contributes to the establishment of a balanced gut microbial community. This study highlights the utility of a multi-omics approach for probiotic discovery, the efficacy of bacteriophage cocktails in pathogen suppression, and the benefits of their synergistic application with probiotics. Although in vivo validation is required, these in vitro results provide a robust foundation for the development of sustainable and effective alternatives to antibiotics for poultry production.},
}

@article {pmid42898582,
year = {2026},
author = {Keum, GB and Cho, J and Song, M and Choi, Y and Kang, J and Doo, H and Kwak, J and Kim, H and Chae, Y and Yang, H and Lee, S and Kim, ES and Kim, S and Kim, HB},
title = {Effects of fructooligosaccharides and inulin on growth performance, immunity and the gut microbiome in weaned piglets.},
journal = {Journal of animal science and technology},
volume = {68},
number = {5},
pages = {1444-1459},
pmid = {42898582},
issn = {2055-0391},
abstract = {Prebiotics such as fructooligosaccharides and inulin are biological activators that selectively stimulate the growth and activity of beneficial bacteria in the gastrointestinal tract. However, their specific effects when applied during the weaning period in piglets remains limited. Therefore, this study evaluated the effects of fructooligosaccharides and inulin supplementation in weaned piglets on growth performance, nutrient digestibility, immune response, and gut microbiota composition with the aim of exploring their potential benefits for piglet health during the weaning transition. A total of 72 weaned piglets (28 days of age) were allocated to three dietary groups: CON (basal diet), FOS (CON + 0.3% fructooligosaccharides), and INU (CON + 3% inulin) to investigate the effects of fructan supplementation. Growth performance, nutrient digestibility, blood profiles, immune responses, and fecal microbiota were evaluated. Although fructan supplementation did not induce significant changes in growth performance or nutrient digestibility, it significantly increased serum immunoglobulin A levels. Furthermore, the fecal microbiota of the fructan supplemented piglets was enriched with short-chain fatty acid-producing bacteria, including Phascolarctobacterium, Agathobacter, Clostridium sensu stricto, and Flavonifractor. Fructan supplementation in the diets of weaned piglets positively influenced immune response and gut microbiota composition, suggesting its potential to enhance gut health during the weaning period.},
}

@article {pmid42898979,
year = {2026},
author = {Gong, C and Jing, X and Jiang, S and Yu, C},
title = {Parvimonas micra and central nervous system infections: mechanisms of transformation from oral commensal to intracranial pathogen and clinical evidence.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1971569},
pmid = {42898979},
issn = {2235-2988},
mesh = {Humans ; *Brain Abscess/microbiology ; *Bacillota/pathogenicity/genetics/drug effects ; *Gram-Positive Bacterial Infections/microbiology ; *Central Nervous System Infections/microbiology ; *Mouth/microbiology ; Animals ; },
abstract = {Parvimonas micra (P. micra), an anaerobic oral coccus long dismissed as a culture contaminant, is increasingly recognized as a causative agent of pyogenic central nervous system (CNS) infections, yet its neuropathogenesis remains poorly defined. This narrative review synthesizes 41 peer-reviewed studies identified via a structured comprehensive literature search of PubMed, Embase and Web of Science through June 2026. Epidemiologically, pooling available case reports and small series (n=64 confirmed CNS cases), P. micra is among the most frequently isolated Gram-positive anaerobic cocci in reported brain abscess series, with proportions ranging from approximately 4% to over 10% in individual cohorts; species-level data are inconsistently reported and a precise pooled estimate cannot be derived. A male predominance (approximately 2.7:1) is observed among reported cases, though this should be interpreted cautiously given the small sample size and potential reporting bias. Approximately two-thirds of patients have no documented immunosuppressive condition. Brain abscess represents ~80% of CNS manifestations, with 60-70% presenting as polymicrobial infection. We propose a five-step pathogenic cascade-periodontal dysbiosis, epithelial barrier breach, intravascular survival, blood-brain barrier (BBB) translocation, and intracranial suppuration-as a conceptual framework. Virulence factors including the TmpC-AppA axis and extracellular vesicle DnaK have been characterized in non-CNS models (oral carcinoma, periodontitis, oral lichen planus); their relevance to CNS infection is inferred, and BBB translocation mechanisms remain entirely hypothetical. Metagenomic next-generation sequencing (mNGS) outperforms conventional culture in selected brain abscess cohorts (~85% vs ~50% in pus; ~84% vs ~8% in CSF across CNS infections), though performance varies by specimen type, prior antibiotic exposure, and sequencing platform. All-cause mortality is 5-10% and 20-25% of survivors sustain neurological sequelae, though these estimates may overestimate true population rates due to publication bias. P. micra shows consistently low in vitro minimum inhibitory concentrations to metronidazole and β-lactams. Early empirical anaerobic coverage and consideration of mNGS as a complementary diagnostic tool are recommended for suspected odontogenic brain abscess.},
}

Humans
*Brain Abscess/microbiology
*Bacillota/pathogenicity/genetics/drug effects
*Gram-Positive Bacterial Infections/microbiology
*Central Nervous System Infections/microbiology
*Mouth/microbiology
Animals

@article {pmid42899037,
year = {2026},
author = {Selleri, E and Longhi, G and Tarracchini, C and de Carolis, E and Petraro, S and Mancabelli, L and Milani, C and Turroni, F and Ventura, M and Lugli, GA},
title = {Genome-scale insights into the metabolic landscape and evolutionary development of Bifidobacterium bifidum.},
journal = {Microbiome research reports},
volume = {5},
number = {3},
pages = {18},
pmid = {42899037},
issn = {2771-5965},
abstract = {Background: Bifidobacterium bifidum (B. bifidum) is an infant gut symbiont specialized in degrading host-derived glycans. Despite its relevance in early life, the species' genomic diversity has not yet been comprehensively surveyed, and current reference collections capture only a fraction of the global B. bifidum pangenome. Methods: In this study, we reconstructed the first comprehensive pangenome of B. bifidum using 1,351 high-quality genomes, including metagenome-assembled genomes. This dataset was used for in silico comparative genomics analyses to identify species-specific genetic and functional features. In vitro transcriptomics analyses were further performed to validate and functionally characterize selected species-specific traits. Results: Comparative genomic analysis with other human-associated bifidobacteria species identified 667 B. bifidum-specific clusters of orthologous genes mostly involved in carbohydrate utilization, osmotic regulation, and host interaction. Notably, B. bifidum displays the most extensive enzymatic repertoire for host-glycan degradation, dedicating 43% of its conserved glycoside hydrolases to these substrates. We identified significant gain-of-function events, including two unique phosphotransferase systems (PTS) for disaccharide uptake. Transcriptomic profiling corroborated the functional relevance of these PTS clusters, which were significantly up-regulated during growth on human milk oligosaccharides, mucin, and N-acetylglucosamine. While the species exhibits high genomic stability, a localized divergence (average nucleotide identitiy, ANI < 98.5%) was identified in rural, non-Westernized populations, reflecting niche-specific adaptations. Conclusion: The identified genomic framework highlighted a distinct evolutionary path of B. bifidum, placing this taxon as a metabolic cornerstone in the neonatal gut via extensive metabolic specialization toward glycan hosts.},
}

@article {pmid42899262,
year = {2026},
author = {Zhang, X and Yi, H and Zheng, J and Yin, Y},
title = {dbcan-nf: a Nextflow pipeline for accurate CAZyme annotation in metagenomes.},
journal = {Bioinformatics advances},
volume = {6},
number = {1},
pages = {vbag304},
pmid = {42899262},
issn = {2635-0041},
abstract = {MOTIVATION: Carbohydrate-active enzymes (CAZymes) are crucial for carbohydrate degradation in any ecological environment. However, CAZyme annotation is not easy in whole-genome shotgun (WGS) metagenomes, due to the lack of accurate, scalable, robust, and reproducible workflows. We previously published dbCAN as a web server and associated standalone tool run_dbcan that performs CAZyme annotation with assembled genomes as the input but not with raw WGS reads.

RESULTS: Here, we present dbcan-nf, an accurate and scalable Nextflow pipeline integrating run_dbcan as a component step, for automated CAZyme annotation in metagenomes. dbcan-nf supports multiple analytical routes, including individual sample assembly (IA), multisample coassembly (CA), assembly-free (AF), and subsampling (SS), and accepts both short and long reads. Using five benchmark datasets, we showed that dbcan-nf (IA and AF routes) had a much higher accuracy (recall and F1 score) and detected more CAZyme families than the competing tool Cayman. Among the different routes, dbcan-nf-IA produced the most accurate CAZyme annotation, especially when the sequencing depth is sufficient (e.g., >1.0 Gb). However, as a read assembly-based method, dbcan-nf-IA had a higher computational cost than Cayman. Finally, dbcan-nf leverages Nextflow-supported high-performance computing execution for workflow-level scalability through concurrent processing of multiple samples.

https://github.com/bcb-unl/dbcan-nf.},
}

@article {pmid42899356,
year = {2026},
author = {Fatawou, MA and Pierre, C and Arnaud, L and Justine, C and Henri, MM and Toutou, TD and Ibrahim, T and Ripa, N and Gwladys, MC and Richard, N},
title = {Use of Metagenomic Next-Generation Sequencing to Investigate Respiratory Pathogens in Influenza-Negative Nasopharyngeal Swabs From Cameroon's National Influenza Surveillance.},
journal = {Influenza and other respiratory viruses},
volume = {20},
number = {10},
pages = {e70336},
doi = {10.1111/irv.70336},
pmid = {42899356},
issn = {1750-2659},
support = {101046133//European Union Research and Innovation program Horizon Europe/ ; CCD/SA/783//Islamic Development Bank (IsDB) through the IsDB Merit Postdoctoral Scholarship Program 2023/ ; },
mesh = {Humans ; Cameroon/epidemiology ; *High-Throughput Nucleotide Sequencing ; *Metagenomics/methods ; *Nasopharynx/virology/microbiology ; *Respiratory Tract Infections/virology/epidemiology ; Female ; Male ; Child, Preschool ; *Viruses/isolation & purification/genetics/classification ; Child ; Infant ; Adolescent ; Influenza, Human/epidemiology/virology ; Young Adult ; Epidemiological Monitoring ; },
abstract = {BACKGROUND: In Cameroon, national influenza surveillance identifies influenza-positive cases, but the causes of non-influenza ARIs remain poorly characterized. We applied metagenomic next-generation sequencing (mNGS) to investigate respiratory pathogens in influenza-negative nasopharyngeal swabs collected through national influenza surveillance.

METHODS: We analyzed 199 influenza-negative nasopharyngeal swabs collected between September and December 2023 from patients with influenza-like illness or severe acute respiratory infection. Mixed DNA/RNA libraries were prepared and sequenced on an Illumina NovaSeq platform. Taxonomic classification was performed using METAMIC (v2.0) and SPAdes (V3.15.5) bioinformatic pipelines.

RESULTS: Viral sequences were detected in 120/199 samples (60.3%, 95% CI: 53.5%, 67.1%), representing 15 viral species. The most frequent viruses were rhinovirus (43/131), respiratory syncytial virus (33/131), influenza virus, parainfluenza virus and enterovirus. Two non-respiratory viruses (Rotavirus and Papillomavirus) were also detected. Sequencing generated an average of 26.1 million reads per sample, with a mean depth of 870.3 per sample and an average genomic coverage of 82%. Eleven viral co-infections were identified. Several bacterial and fungal genera were also detected.

CONCLUSION: Our study shows that mNGS provides a powerful, unbiased approach for characterizing respiratory pathogens in Cameroon, revealing substantial viral diversity among influenza-negative ARI cases. However, cost and bioinformatics capacity remain major barriers to routine implementation. Longitudinal studies and clinical correlation are needed to strengthen interpretation and guide integration of mNGS into national surveillance.},
}

Humans
Cameroon/epidemiology
*High-Throughput Nucleotide Sequencing
*Metagenomics/methods
*Nasopharynx/virology/microbiology
*Respiratory Tract Infections/virology/epidemiology
Female
Male
Child, Preschool
*Viruses/isolation & purification/genetics/classification
Child
Infant
Adolescent
Influenza, Human/epidemiology/virology
Young Adult
Epidemiological Monitoring

@article {pmid42899645,
year = {2026},
author = {Yang, K and Xie, Z and Li, W and Ren, Y and Chen, XY and Wang, X and Ren, H and Xiong, S and Zhang, X},
title = {Niche Divergence-Based Identification of Microbial Indicators Tracking Cyanobacterial Bloom Succession: A Metagenomic and Machine Learning Framework.},
journal = {Environmental science & technology},
volume = {60},
number = {41},
pages = {29569-29582},
doi = {10.1021/acs.est.6c04563},
pmid = {42899645},
issn = {1520-5851},
support = {2022ZZ06//National Observation and Research Station of Erhai Lake Ecosystem in Yunnan/ ; 42577128//Natural Science Foundation of China/ ; },
mesh = {*Machine Learning ; *Cyanobacteria ; Lakes ; Metagenomics ; Harmful Algal Bloom ; },
abstract = {Cyanobacterial harmful algal blooms (CyanoHABs) pose significant environmental and public health risks through toxin production, antibiotic resistance gene dissemination, and the disruption of biogeochemical cycles. Although extensive metagenomic investigations have explored microbial interactions between Cyanobacteria and coexisting members, the potential of incorporating functional indicators into early CyanoHAB monitoring systems remains underexplored. In this study, we employed metagenomic binning combined with machine learning approaches to analyze seasonal cyanobacterial succession and coexisting microbial communities across 19 sites in Erhai Lake across four seasons. We documented distinct niche shifts driven by the spatiotemporal heterogeneity in seasonal cyanobacterial succession alongside the formation of unique niches triggered by this asynchrony. Specialized microbial members (SN-MAGs) were identified as candidate bioindicators associated with early-stage cyanobacterial proliferation. Functional profiling showed r/K selection and metabolic adaptations in these SN-MAGs, including stress resistance and altered carbon metabolism, linked to cyanobacterial dynamics. Machine learning models leveraging these features were constructed and retrospectively evaluated. Cross-lake validation using an independent Lake Taihu dataset confirmed associations among these features and microbial community shifts preceding Microcystis proliferation. Our findings highlight the potential value of the dynamics of specific bacteria as a sensitive indicator of cyanobacterial dynamics. Moreover, we propose that these identified functional markers could potentially be developed into targeted molecular assays (e.g., qPCR assays), offering possible utility in predicting Microcystis population expansion.},
}

*Machine Learning
*Cyanobacteria
Lakes
Metagenomics
Harmful Algal Bloom

@article {pmid42899671,
year = {2026},
author = {Ke, X and Huang, X and Zhang, N and Yang, X and Chen, Y and Shao, J and Shi, J and Xu, J and He, Y},
title = {Combined Residues of Frequently Detected Herbicides are Stronger Predictors of Soil Resistome and Virulence Potential than Single Residues.},
journal = {Environmental science & technology},
volume = {60},
number = {41},
pages = {29555-29568},
doi = {10.1021/acs.est.6c03454},
pmid = {42899671},
issn = {1520-5851},
support = {2023C02004//Key Research and Development Program of Zhejiang Province/ ; 226-2025-00064//Fundamental Research Funds for the Central Universities/ ; 42225705//National Natural Science Foundation of China (NSFC)/ ; CARS-04//the earmarked fund for CARS/ ; JYB2025XDXM703//Fundamental and Interdisciplinary Disciplines Breakthrough Plan of the Ministry of Education of China/ ; },
mesh = {*Herbicides ; Soil Microbiology ; Soil/chemistry ; China ; Virulence ; },
abstract = {Overuse of herbicides has resulted in a global epidemic of evolved resistance in soil ecosystems. While single herbicide risk has been documented, the impact of multiple herbicide residues on the soil resistomes remains poorly understood. Our study quantified the residues of 24 herbicides, profiled antibiotic resistance genes (ARGs) and virulence factor genes (VFGs), and reconstructed 1086 metagenome-assembled genomes (MAGs) from 93 agricultural soils across China. The analytical results demonstrate that the frequently detected herbicide residues (e.g., 60-90% detection frequency) are stronger predictors of soil antibiotic resistomes than total herbicide load, unsupervised mixture based on principal component analysis (PCA), or single-herbicide models. For VFG abundance, the same mixture outperformed the best single herbicide and total herbicide concentration, although PCA-PC1 showed a moderately stronger correlation. Specifically, these commonly detected herbicides showed positive associations with ARG abundance through both direct linkages and bacterial community-dependent indirect pathways. Similar patterns were observed for virulence potential, where frequently detected residues maintained strong predictive performance and were predominantly associated with indirect pathways. Functional annotation patterns further suggest a concurrent enrichment of traits related to antioxidant defense, mobility, adherence, and immune modulation under elevated herbicide exposure. Notably, multiple herbicide residues were linked to the abundance of a Trinickia taxon, which was identified as a candidate ARG-VFG co-occurrence MAG carrying a high ARG load. Our findings highlight the need to integrate compound exposure of frequently detected herbicides into future risk assessment methodology for preventing the dissemination of ARGs in agricultural soils.},
}

*Herbicides
Soil Microbiology
Soil/chemistry
China
Virulence

@article {pmid42891347,
year = {2026},
author = {Serrana, JM and Nascimento, FJA and Posselt, M},
title = {Metagenomic mining of environmental resistomes: Comparative performance of deep learning and alignment-based annotation methods.},
journal = {iMetaOmics},
volume = {3},
number = {2},
pages = {e70107},
pmid = {42891347},
issn = {2996-9514},
abstract = {Antimicrobial resistance (AMR) in marine environments poses intricate challenges due to the ecological complexity of microbial communities and environmental gradients. This study compares various antimicrobial resistance gene (ARG) annotation tools and databases, focusing on deep learning approaches versus traditional alignment-based methods, to evaluate their effectiveness in profiling the resistome of a complex marine ecosystem. Our report not only highlights the utility of deep learning methods for environmental applications but also proposes pathways for future improvements that can bridge the gap between comprehensive detection and clinically relevant risk interpretation.},
}

@article {pmid42891357,
year = {2026},
author = {Zhang, H and Luo, Z and Zhang, J and Wang, C and Tian, Y and Li, D and Guo, Y and Zhang, Y and Li, W and Gong, Y and Kang, X and Jiang, R},
title = {Changes in the gut microbiome during fasting-induced molting and its effects on gut-liver function.},
journal = {iMetaOmics},
volume = {3},
number = {2},
pages = {e70103},
pmid = {42891357},
issn = {2996-9514},
abstract = {Fasting-induced molting (FIM) rejuvenates the laying cycle in hens; however, the fasting process may result in intestinal dysbiosis, which compromises host immunity and disrupts the intestine-liver function. Consequently, investigating the changes in gut microbiota during FIM and its impacts on gut-liver metabolic homeostasis is crucial for enhancing the efficiency of FIM in laying hens. Here, a total of 90 laying hens, aged 60 weeks, were selected for the FIM. Samples were collected at four time points: the day before fasting, the 15th day of fasting, the 5th day of refeeding, and the 47th day of refeeding. Metagenomic sequencing and non-targeted metabolomics were employed to investigate the roles of the gut microbiota and metabolites in the remodeling of gut-liver function, focusing on intestinal injury-repair mechanisms and changes in liver function. During the fasting period, the abundance of harmful microbiota and metabolites increase, leading to intestinal injury. This process activates the TGF-beta signaling pathway, promoting intestinal stem cell proliferation. Simultaneously, liver function dysfunction as evidenced by elevated bile acid levels in the liver and serum and activation of the non-classical bile acid synthesis pathway. During the refeeding period, the previously observed effects were reversed, leading to the remodeling of the intestinal microbiota and gut-liver function. We identified key microorganisms (Liquorilactobacillus mali and Tissierellia bacterium KA00581) and functional metabolites (d-Panthenol and 3-hydroxyanthranilic acid (3-HAA)) involved in intestinal-liver function during FIM. Notably, d-Panthenol promotes chicken small intestinal organoid branching and growth, enhances barrier function, and reduces inflammation. Our study underscores the role of gut microbiota in gut-liver injury during FIM in laying hens, suggesting potential probiotic- or metabolite-based interventions to mitigate gut-liver injury and facilitate recovery.},
}

@article {pmid42892135,
year = {2026},
author = {Zhu, Y and Yin, J and Guo, Y and Yu, Y and Wang, K and Yu, Z and Zhang, J and Han, D and Wang, Y and Li, W and Liu, P and Rong, C},
title = {Multilayer defense collapse model and rare taxa-based early warning for solid-state vinegar fermentation stagnation: A time-series metagenomic study.},
journal = {International journal of food microbiology},
volume = {463},
number = {},
pages = {112122},
doi = {10.1016/j.ijfoodmicro.2026.112122},
pmid = {42892135},
issn = {1879-3460},
abstract = {Fermentation stagnation is a persistent challenge in industrial vinegar production, yet its microecological mechanisms remain poorly understood. Here, we conducted time series metagenomic analysis comparing normal and stagnant solid state acetic acid fermentation, and propose the Multilayer Defense Collapse (MDC) model as a unifying framework for stagnation mechanisms. We found fermentation stagnation represents a cascade collapse of four progressive defense layers rather than a single-point failure. Initial perturbation first impairs community network resilience, manifesting as community simplification with 72% reduction in species richness and synchronous viral diversity loss. Metabolic monopoly by core functional bacteria then weakens through triple reconfiguration involving genus-level replacement of lactic acid bacteria, reduced acetic acid bacterial contribution, and limited pathogen penetration. The acidic chemical barrier subsequently fails through both barrier weakening and quorum sensing-mediated active breakthrough. Antimicrobial peptide defense ultimately collapses with 74% AMP decline, driving the system into a dysregulated steady state characterized by broad-spectrum resistome expansion. Random forest analysis further showed that rare taxa, rather than core bacteria, serve as the most sensitive early warning indicators, with 20-50 sentinel species sufficient for high-accuracy classification. This study provides a mechanistic framework for fermentation stagnation and offers potential early-warning indicator and graded intervention.},
}

@article {pmid42892166,
year = {2026},
author = {Palanisamy, H and Vidyalakshmi, S},
title = {Deploying machine learning and metagenomics for predicting gut microbial drug biotransformation in colorectal cancer.},
journal = {Computational biology and chemistry},
volume = {126},
number = {Pt 2},
pages = {109495},
doi = {10.1016/j.compbiolchem.2026.109495},
pmid = {42892166},
issn = {1476-928X},
abstract = {Colorectal cancer (CRC) is one of the leading causes of death globally. Chemotherapy is considered as one of the standard treatment option for CRC. Although effective in many cases, drugs used in chemotherapy are often associated with adverse toxicity. Inter-individual variations in drug response are often attributed to pharmacogenomic associations, and current evidence suggests involvement of gut microbes as a contributor to drug response variations. While several studies have implemented machine learning to predict drug responses mediated by gut microbial enzymes, these predictions mainly rely on substrate information and bacterial genome data. In this study, we have developed CRCGMMeta Predictor, a tool that predicts gut microbial enzymes and species capable of biotransforming drugs. Unlike existing tools, CRCGMMeta Predictor integrates enzyme prediction with species-level abundance in CRC metagenomes using eight geographically diverse metagenomic studies. The tool was trained on 437,079 species-specific enzyme data, incorporating 3457 substrate and protein-encoding features. Multiple machine learning models were evaluated, with the random forest model achieving 99% accuracy, precision, recall, F1 score and ROC-AUC metrics. Validation of the generated model with a blind set achieved 97% accuracy, while 10-fold cross-validation achieved an accuracy of 0.831 ± 0.068. Based on the above results, the random forest model was selected to build the CRCGMMeta Predictor tool. This was further assessed against fluoropyrimidine drugs and its ability to predict enzymes supported by literature evidence and those predicted by existing computational tools. These findings highlight the potential of CRCGMMeta Predictor in identifying microbiome-mediated drug responses.},
}

@article {pmid42892321,
year = {2026},
author = {Ma, J and Hao, T and Bai, Y and Xiao, L and Yang, Q and Dai, P and Wang, H},
title = {Optimizing Pathogen Detection in Clinical Metagenomics: A Comprehensive Benchmarking of Bioinformatic Pipelines for Single-End Short Reads.},
journal = {The Journal of molecular diagnostics : JMD},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jmoldx.2026.09.003},
pmid = {42892321},
issn = {1943-7811},
abstract = {Metagenomic next-generation sequencing for identifying pathogens has been increasingly utilized as a diagnostic tool. Prior research mostly emphasizes the selection of classification software based on reads above 100bp, neglecting the influence of sequencing data pre- and post-processing stages. Independently assessment was performed assessed the efficacy and effects of tools for each phase, encompassing quality control, host read elimination, taxonomic classification, and false positive removal, utilized in a metagenomics analysis pipeline employing single-end 50bp reads derived from sequencing 13 positive-control mock community samples. The efficacy of tool combinations was assessed using single-end 50 bp data from identical mock samples processed using different wet-lab methodologies. The findings indicate that the selection of quality control and host-removal techniques is essential, significantly influencing the extraction of microbial reads from clinical metagenomic sequencing data and resulting in elevated alpha diversity. While false-positive filtering enhances precision for trimming tool-based combinations without impacting recall, its effect is limited for combinations utilizing the bt2 aligner. The tool combination pipelines integrated with various false positive methodologies for four microbial categories: no filtering for bacteria, bracken for fungi, relative abundance (>0.1%) for DNA viruses, and z-score (z > 3) for RNA virus identification, as implemented in the prior R Shiny application for forthcoming benchmarking. This study highlights the critical role of preprocessing and classifier selection in accurate metagenomic pathogen identification.},
}

@article {pmid42892362,
year = {2026},
author = {Xiong, J and Yan, M and Tan, W and Sun, Y and Chen, L and Tian, H and Tan, Q},
title = {Genome-centric metagenomic analysis revealed the microbial superiority of the developed anaerobic digestion startup strategy based on combination of raw and concentrated digestate.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {136090},
doi = {10.1016/j.biortech.2026.136090},
pmid = {42892362},
issn = {1873-2976},
abstract = {Concentrating the digestate as inoculum to initiate new anaerobic digestion (AD) reactors has been proven to be feasible. However, functional microorganisms after centrifugal concentration have poor activity in the initial stage, resulting in a long startup period. In this study, AD was initiated through addition of centrifugal concentrated digestate combined with different proportions of raw digestate (0%, 9%, 18%, and 27%, in terms of total working volume), aiming to restore the metabolic activity rapidly with a minimum amount of raw digestate to reduce the startup cost. The result showed that Cen-18% (bioaugmentation of 18% raw digestate on the top of concentrated digestate) was the most suitable startup strategy in terms of methane production rate and methane yield. Metagenomic absolute quantitative analysis revealed that methane metabolism (ko00680) was enhanced in Cen-18% (2.9 × 10[10] copies/g V.S. (1.5-1.8) × 10[10] copies/g in other groups) along with the AD progress by upregulating the abundance of key functional genes in carbohydrate metabolism (gapA, fbaA and eno) and amino acid metabolism (carB, argG and argH). Moreover, genome-centric metagenomic analysis implied that the Cen-18% accelerated carbon conversion by enriching higher abundance of the identified key carbohydrate and protein degraders (i.e., Bacteroidales_MAG2 and Bacteroidales_MAG8) in Cen-18% than other experimental groups. Hydrogenotrophic methanogenesis performed by Methanomicrobiales_MAG1 and Methanomicrobiales_MAG2 was the dominant methanogenic pathway in Cen-18%, which was highly symbiotic with the acetate oxidation bacteria DUMP01_MAG3, DUMP01_MAG1, and Thermosediminibacterales_MAG2. This study provides practical support for the startup of newly built biogas digesters.},
}

@article {pmid42892428,
year = {2026},
author = {Wu, H and Xiao, W and Li, X and Fu, M and Xu, CY and Zhou, X},
title = {Single biochar application enhances soil methane sink and underlying microbial mechanisms in a subtropical forest after twelve years of treatments.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125968},
doi = {10.1016/j.envres.2026.125968},
pmid = {42892428},
issn = {1096-0953},
abstract = {Biochar is an effective amendment for enhancing soil carbon sequestration and regulating soil greenhouse gas emissions, such as methane (CH4), yet its decadal-scale effects in forest ecosystems remain unclear. Here, based on a 12-year field experiment in a subtropical forest where biochar was applied once at rates of 0 (CK), 10 (Bio10), and 30 t ha[-1] (Bio30), we monitored in-situ CH4 fluxes over one year and simulated daily soil CH4 fluxes using a Soil Methanotrophy Model (MeMo). Combined with laboratory incubations and metagenomic absolute quantification sequencing, we found that a single biochar application enhanced the soil CH4 sink even after twelve years, in a dose-dependent manner. Compared with CK, Bio10 increased the annual cumulative CH4 uptake by 24.9% (P < 0.05), although its mean annual CH4 uptake flux showed no statistically significant increase (10.3%). In contrast, Bio30 significantly increased both the mean annual flux and annual cumulative uptake by 56.0% and 76.4%, respectively. Biochar addition significantly increased soil extractable organic carbon (EOC) contents, but significantly decreased ammonium nitrogen (NH4[+]-N) content (P < 0.05). Furthermore, relative to CK, Bio30 increased methanotrophic abundance (e.g., pmoA gene abundance) by 56.5% and methane oxidation potential by 170.5%. Biochar did not significantly alter the overall methanotrophic community structure. Structural equation modeling revealed that biochar enhanced methane oxidation potential directly, and indirectly through increasing soil EOC contents, and methanotrophic abundance, thereby promoting CH4 uptake (total effect = 0.60). In summary, a single application of 30 t ha[-1] biochar still exerts a significant enhancement of the soil CH4 sink in subtropical forest soils twelve years after application. These findings provide critical scientific evidence for evaluating the long-term climate mitigation benefits of biochar in forest ecosystems and offer theoretical support for nature-based strategies to enhance forest soil CH4 sinks.},
}

@article {pmid42893466,
year = {2026},
author = {Jiang, Y and Jiang, H and Xie, Y and Zheng, T},
title = {Covariation of DOM molecular characteristics and bacterial carbon metabolism potential along a reservoir-agricultural river nutrient gradient.},
journal = {Environmental geochemistry and health},
volume = {48},
number = {16},
pages = {},
pmid = {42893466},
issn = {1573-2983},
support = {2024ZD1004405//Deep Earth Probe and Mineral Resources Exploration National Science and Technology Major Project/ ; 2026NSFSC0268//Sichuan Science and Technology Program/ ; },
mesh = {*Rivers/chemistry/microbiology ; *Bacteria/metabolism/genetics/classification ; *Carbon/metabolism ; *Dissolved Organic Matter/analysis/chemistry ; RNA, Ribosomal, 16S/genetics ; Agriculture ; Nutrients/analysis ; Nitrogen/analysis ; Phosphorus/analysis ; },
abstract = {Agricultural nutrient loading is associated with variation in dissolved organic matter (DOM) composition and microbial communities across reservoir-agricultural river continuums, yet the covariation among nutrient conditions, DOM molecular heterogeneity, and bacterial metabolic potential remains insufficiently understood. This study integrated optical spectroscopy, ultrahigh-resolution mass spectrometry, nitrate dual-isotope tracing, end-member mixing analysis (EMMA), 16S rRNA sequencing, and metagenomic functional profiling to characterize DOM sources and composition and their associations with bacterial communities in a typical reservoir-agricultural river continuum. Our results showed that nitrogen and phosphorus enrichment within agricultural river reaches systematically rearranges DOM source apportionment, with relative abundance of humic-like components (C1, C3) rising alongside elevated abundances of heteroatomic molecular formulas (CHOS, CHONS) relative to oligotrophic reservoirs. Nutrient loading reshaped DOM via exogenous input of heteroatom-rich anthropogenic organics and boosted in-situ microbial humification. EMMA modeling further indicated that anthropogenic sources contributed 37.9% to riverine DOM. Principal coordinates analysis showed that reservoir-river community differentiation coincided with nutrient and fluorescent DOM gradients. Reservoir samples were dominated by Acinetobacter, Exiguobacterium, and Clade_III and showed higher relative abundances of several genes associated with carbohydrate and aromatic compound degradation. In contrast, river communities featured humic-adapted genera (Mycobacterium, hgcl_clade, Limnohabitans, and unclassified_Sporichthyaceae) and showed higher relative abundances of genes associated with lipid utilization and terrestrial-polymer degradation. This study highlighted coordinated spatial variation in nutrient conditions, DOM characteristics, bacterial community composition, and genomic carbon metabolism potential across the reservoir-agricultural river continuum, supplying theoretical guidance for pollution control and carbon cycling regulation in anthropogenic-disturbed inland water catchments.},
}

*Rivers/chemistry/microbiology
*Bacteria/metabolism/genetics/classification
*Carbon/metabolism
*Dissolved Organic Matter/analysis/chemistry
RNA, Ribosomal, 16S/genetics
Agriculture
Nutrients/analysis
Nitrogen/analysis
Phosphorus/analysis

@article {pmid42893623,
year = {2026},
author = {Ali, F and Ali, A and Nadeem, MA and Baloch, FS and Kurt, C and Do, MC and Yu, JK and Chung, YS},
title = {Omics-driven improvement of safflower (Carthamus tinctorius L.) for climate resilience, oil quality, and high-value metabolites under changing environments.},
journal = {Plant physiology and biochemistry : PPB},
volume = {239},
number = {},
pages = {111867},
doi = {10.1016/j.plaphy.2026.111867},
pmid = {42893623},
issn = {1873-2690},
abstract = {Safflower is an Asteraceae oilseed crop valued for its high-quality unsaturated fatty acids (≈90% oleic and linoleic acids), natural floral pigments, and diverse bioactive compounds. These attributes underpin its applications in functional foods, nutraceuticals, pharmaceuticals, and various industrial sectors. Safflower inherent tolerance to drought, heat, cold, and salinity positions it as a climate-resilient alternative to more temperature-sensitive oilseeds; however, omics-based research in this crop remains comparatively fragmented. This review consolidates recent advances across major omics domains. Genomics covers chromosome-scale assemblies, GWAS panels, QTL mapping, and diagnostic candidate genes for molecular breeding. Transcriptomics summarizes regulatory networks for flavonoid and oil biosynthesis, stress-responsive transcription factors (NAC, WRKY, bZIP, AP2/ERF), and seed developmental programs. The proteomics section addresses stress-inducible, therapeutic, and storage/lipid metabolic proteins linked to quality and stress adaptation. Metabolomics outlines quinochalcone and flavonoid pathway architecture, color-specific metabolic profiles, and emerging clinical and nutraceutical applications. Phenomics highlights UAV-based high-throughput phenotyping, RGB and multispectral imaging for salt and drought screening, and machine-learning-assisted germplasm authentication. Epigenomics focuses on DNA methylation and miRNA-mediated regulation. Finally, lipidomics and metagenomics consider oil authentication biomarkers, refining optimization, and microbiome-driven nutrient cycling shaping medicinally important compounds. Despite these advances, critical gaps remain in multi-omics integration, CRISPR-based functional validation, genomic selection pipelines, and detailed characterization of root-shoot architecture under combined stresses. Addressing these gaps will advance mechanistic understanding of climate resilience and enable the development of stress-tolerant, high-yielding safflower cultivars with improved oil quality and bioactive profiles, thereby supporting climate-resilient production systems and high-value safflower-based products at scale.},
}

@article {pmid42894046,
year = {2026},
author = {Song, JL and Wu, RC and Sun, R and Gao, YX and He, BQ and Xie, YJ and Xie, JS and Li, XR and Tong, FX and Liu, Y and Li, H and Wang, ZQ},
title = {Gastrodin alleviates acute colitis with comorbid anxiety- and depression-like behaviours rather than cognitive dysfunction by modulating gut microbiota and suppressing inflammation.},
journal = {Naunyn-Schmiedeberg's archives of pharmacology},
volume = {},
number = {},
pages = {},
pmid = {42894046},
issn = {1432-1912},
abstract = {Inflammatory bowel disease (IBD) patients frequently suffer from emotional disturbances, predominantly anxiety- and depression-like symptoms, and may also have cognitive dysfunction, but the mechanisms remain unclear, and no therapies targeting the gut or nervous system exist. Gastrodin (GAS), the primary active component of Gastrodia elata, has anti-inflammatory and neuroprotective effects. Whether GAS can alleviate acute colitis with comorbid anxiety- and depression-like behaviours or cognitive dysfunction via the gut-brain axis is unknown. Using a 3% dextran sulfate sodium (DSS)-induced mouse model, we administered GAS (240 mg/kg) by gavage for 7 days. The open field, elevated plus maze, tail suspension, and forced swimming tests showed that GAS improved behavioural abnormalities (including anxiety- and depression-like behaviours); it also restored colon length and reduced colonic histopathological injury. Metagenomic sequencing revealed that GAS reshaped the gut microbiota, increasing Sporosarcina and Nitrospirae while decreasing Clostridiaceae and Lachnospiraceae. Untargeted metabolomics indicated that GAS shifted the metabolic profile away from DSS and normalized taurine levels, and KEGG pathway analysis suggested that GAS may partially ameliorate DSS-induced metabolic disturbances by downregulating virulence-related pathways and upregulating energy metabolic pathways such as the TCA cycle and oxidative phosphorylation relative to DSS. Western blot confirmed that GAS restored the tight junction protein Occludin and decreased TNF-α. Quantitative proteomics demonstrated that GAS reversed the aberrant expression of 191 colonic proteins. These results demonstrate correlative associations between GAS treatment and the alleviation of acute colitis and behavioural abnormalities, alongside concurrent changes in gut microbiota composition, metabolite profiles, and intestinal barrier proteins. Whether these associations reflect a causal gut-brain axis mechanism requires direct experimental validation. GAS modulates the microbiota, partially restores metabolism, repairs the gut barrier, and suppresses local inflammation, suggesting a potential gut-brain axis mechanism. These findings position GAS as a promising candidate for further mechanistic and translational investigation in IBD-associated behavioural comorbidities.},
}

@article {pmid42894517,
year = {2026},
author = {Degnan, SM and Wong, ZS and Degnan, BM and Erpenbeck, D and Hentschel, U and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , },
title = {The chromosomal genome sequence of the sponge, Rhabdastrella globostellata (Carter, 1883) (Tetractinellida: Ancorinidae) and its associated microbial metagenome sequences.},
journal = {Wellcome open research},
volume = {11},
number = {},
pages = {459},
pmid = {42894517},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual Rhabdastrella globostellata (sponge; Porifera; Demospongiae; Tetractinellida; Ancorinidae). The genome sequence has a total length of 155.58 megabases. Most of the assembly (98.97%) is scaffolded into 21 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 18.12 kilobases. Gene annotation of this assembly by Ensembl identified 17 532 protein-coding genes. From the metagenome data, we recovered 131 bins, of which 55 were high-quality MAGs, representing 19 phyla (i.e., Pseudomonadota, Chloroflexota, Acidobacteriota) and candidate phyla (including Ca. Poribacteria).},
}

@article {pmid42894575,
year = {2026},
author = {Fu, T and Hu, SY and Chen, JZ and Sun, QW and Liao, XF and Huang, XL},
title = {Biases in high throughput sequencing methods affect microbial molecular ecology networks and keystone taxa identification in the Cinnamomum migao rhizosphere and phyllosphere.},
journal = {Current research in microbial sciences},
volume = {11},
number = {},
pages = {100666},
pmid = {42894575},
issn = {2666-5174},
abstract = {The rhizosphere and phyllosphere microbial symbiotic interactions are crucial factors affecting plant health and productivity. How to authentically reflect the species interactions and assembly processes that shape shaping microbial communities has attracted extensive attention from ecologists. The construction of most microbial networks relies on amplicon sequencing data, neglecting both total microbial biomass and inter-domain interactions. The impacts of sequencing resolution ratio, microbial domain, and quantification methods on microbial interspecies interactions and network parameters still require further exploration. In this study, the rhizosphere and phyllosphere microbial communities of Cinnamomum migao-a rare medicinal plant in the Lauraceae family endemic to China, were annotated using amplicon, spike-in absolute amplicon, 2bRAD-M, and metagenomic sequencing. Concurrently, VOCs were extracted from the roots and leaves of C. migao through SPME and analyzed using GC-MS. Multivariate analysis was performed on the obtained dataset. Our results showed that all sequencing methods consistently revealed differences in community composition, diversity, and network structure between the rhizosphere and phyllosphere microbial communities. Furthermore, differences in community domain, sequencing resolution, and microbial quantification from sequencing technologies significantly the influenced network parameters of C. migao rhizosphere and phyllosphere microbiomes, subsequently influencing the topological identification of Zi-Pi (putative keystone taxa) within microbial co-occurrence networks. We emphasize that these identifications are based on network centrality metrics and should be considered as hypotheses for biological keystone potential, pending experimental validation. Remarkably, the VOCs in rhizosphere and phyllosphere environments showed correlations with microbial community composition and were potentially linked to microbial community assembly processes. Our findings highlight the critical importance of considering annotation resolution, quantification methods, microbial domain boundaries, and Zi-Pi (keystone taxa) identification when constructing microbial networks using different sequencing methods. This study raises higher standards for utilizing sequencing data to decipher interspecies relationships within microbial communities.},
}

@article {pmid42895014,
year = {2026},
author = {Tian, M and Wang, Y and Li, C and Fan, J and Chen, Q and Bu, H and Fan, X and Liu, Q},
title = {Gut microbial and metabolomic alterations associated with herpetic trigeminal neuralgia: an exploratory multi-omics study.},
journal = {Journal of oral & facial pain and headache},
volume = {40},
number = {5},
pages = {130-145},
doi = {10.22514/jofph.2026.067},
pmid = {42895014},
issn = {2333-0376},
support = {2025M773964//China Postdoctoral Science Foundation/ ; 262300422312//Henan Provincial Natural Science Foundation for Young Scholars (Category C)/ ; LHGJ20250266//Henan Provincial Medical Science and Technology Joint Research Project/ ; },
mesh = {Humans ; *Trigeminal Neuralgia/microbiology/metabolism/virology ; Multiomics ; *Gastrointestinal Microbiome ; *Metabolomics ; Female ; Male ; Middle Aged ; Feces/microbiology ; Aged ; Case-Control Studies ; },
abstract = {BACKGROUND: Herpetic trigeminal neuralgia (HTN) is a neuropathic pain disorder caused by varicella-zoster virus invasion of the trigeminal nerve, but its mechanisms remain poorly elucidated. Accumulating evidence implicates gut microbiota dysbiosis and metabolic perturbations in modulating chronic pain via the gut-brain axis, yet their roles in HTN have not been systematically explored.

METHODS: Integrated multi-omics analysis was performed on 19 patients with HTN and 18 healthy controls. Fecal metagenomic sequencing characterized gut microbial composition and function. Untargeted metabolomics profiled metabolic signatures in fecal and circulating samples. Weighted gene co-expression network analysis (WGCNA) and random forest modeling screened pivotal microbial and metabolic features associated with HTN. Correlation analysis between differential metabolites and clinical pain scores validated the translational potential of identified alterations.

RESULTS: HTN patients showed significantly reduced gut microbial diversity, with enriched Proteobacteria, depleted butyrate-producing bacteria (including Faecalibacterium, Roseburia, and Lachnospira), and expanded opportunistic pathogens (Escherichia coli and [Ruminococcus] gnavus). Microbial pathways for pH homeostasis and oxidative stress defense were downregulated. Metabolomic analysis identified differential metabolites, primarily involving nicotinate/nicotinamide metabolism and retrograde endocannabinoid signaling. WGCNA and random forest analyses suggested fecal metabolites as potential candidate features, with associations between gut microbial dysregulation and systemic metabolic changes. Furthermore, screened metabolites correlated significantly with pain scores.

CONCLUSIONS: This study provides multi-omics evidence of gut microbial and metabolic dysregulation in HTN, generating hypotheses for further mechanistic research. Large-scale, multicenter prospective cohorts with standardized metadata collection are needed to validate these findings.},
}

Humans
*Trigeminal Neuralgia/microbiology/metabolism/virology
Multiomics
*Gastrointestinal Microbiome
*Metabolomics
Female
Male
Middle Aged
Feces/microbiology
Aged
Case-Control Studies

@article {pmid42891312,
year = {2026},
author = {Ban, S and He, B and Song, Y and An, XL and Xu, Y and Wu, Q and Shi, Y},
title = {Biosynthesis gene cluster-containing species drive microbial community stability under thermal stress through enhanced ecological cohesion.},
journal = {iMetaOmics},
volume = {3},
number = {1},
pages = {e70082},
pmid = {42891312},
issn = {2996-9514},
abstract = {Understanding the mechanisms that govern the ecological stability of microbial communities is critical to elucidating how microbes adapt to changes in their environment. Here, we investigated microbial assembly and changes during spontaneous fermentation, in which the temperature naturally increased from 20°C to 65°C, to determine how thermal stress shapes community dynamics and resilience. Longitudinal metagenomic sampling revealed that heterogeneous selection favored thermotolerant taxa, while ecological drift exerted a stronger influence on fungal communities, indicating that both deterministic and stochastic processes jointly contributed to the community assembly. Specifically, bacterial turnover was primarily driven by heterogeneous selection and dispersal limitation, while fungal assembly was driven by homogeneous selection and drift. Furthermore, the infer Community Assembly Mechanisms by Phylogenetic-bin-based null model analysis identified 27 bacterial and 140 fungal groups that exhibited significant compositional shifts along the thermal gradient. Among these, 11 biosynthesis gene cluster (BGC)-containing species could enhance the microbial community stability by strengthening positive cohesion among species (all species: 0.303-0.464; without BGC-containing species: 0.289-0.461). By removal simulations, we further identified six BGC-containing species (two bacteria and four fungi) that were critical for maintaining robustness to the changes under thermal stress. Co-culture experiments confirmed that their presence increased community biomass by at least 50.08% compared with the control without these six species. Taken together, our results suggest that BGC-containing species can maintain the microbial community stability by reinforcing ecological cohesion and increasing biomass production under high-temperature stress.},
}

@article {pmid42891316,
year = {2026},
author = {Chen, K and Wan, X and Guo, W and Yu, H and Tong, Y and Ke, H and Fang, J and Luo, X and Che, D and Hou, C and Mei, X and Hu, B and Liu, Y and Yu, X and Xiang, D and Chen, W and Zeng, Y and Xu, Y and Shen, J and Chen, Q and Pi, L and Fu, L and Zhou, H and Liang, B and Zhang, M and Dong, Y and Chen, Y and Zhou, W and Gu, X},
title = {Comprehensive spatial profiling reveals transitional microbiome dynamics and microbial heterogeneity in pediatric adenoid hypertrophy.},
journal = {iMetaOmics},
volume = {3},
number = {2},
pages = {e70101},
pmid = {42891316},
issn = {2996-9514},
abstract = {This study characterizes the upper respiratory microbiome in 276 children (101 Adenoid hypertrophy (AH) 119 Adenotonsillar hypertrophy (ATH), 11 Tonsil hypertrophy (TH), and 45 healthy controls by analyzing 1149 samples across five distinct niches: nasopharyngeal swabs (NS), adenoid swab (AS), and tonsil swabs (TS), plus adenoid tissues (AT) and tonsil tissues (TT). Utilizing a workflow of 16S rRNA sequencing, qPCR, and metagenomics, we identified significant spatial heterogeneity and niche-specific dominance, such as Staphylococcus in the nasopharynx and Streptococcus on mucosal surfaces. AT exhibited a transitional microbiome with intermediate composition and unique Ralstonia enrichment. Machine learning models demonstrate that AT microbial profiles (area under curve, AUC = 0.752) offer superior predictive power for AH severity compared to surface swabs. SHAP analysis identified key contributing genera, such as Roseburia and Flavobacterium, as primary drivers of these predictive outcomes. These findings highlight how tissue-infiltrating microbial dynamics drive chronic inflammation and pediatric hypertrophy.},
}

@article {pmid42891323,
year = {2026},
author = {Asif, M and Bilal, H and Xiao, M and Dong, L and Li, WJ},
title = {Microbiome-mediated plant-soil feedbacks as a tool for resilient agriculture.},
journal = {iMetaOmics},
volume = {3},
number = {3},
pages = {e70112},
pmid = {42891323},
issn = {2996-9514},
abstract = {Conventional agricultural intensification has eroded the biological foundations of productive soil by disrupting the reciprocal interactions, plant-soil feedback (PSF), through which plants actively shape and are continuously shaped by the soil microbiome. Although the molecular mechanisms governing PSF direction are increasingly well-characterized, deliberate PSF management as a practical tool for resilient crop production remains underdeveloped. This is largely because no integrative framework has translated these ecological insights into state-contingent, field-deployable decision rules. This review addresses that gap by first synthesizing the molecular basis of microbiome assembly, encompassing host genetic control of root exudate chemistry, receptor-mediated microbial recognition, and the bidirectional chemical dialogue between plant and rhizosphere. Building from this mechanistic foundation, we move beyond cataloging mechanisms to present a novel, integrative three-pillar management framework for actively steering PSF. This framework operationalizes PSF management by strategically combining: (i) engineering the plant partner (leveraging genetics to recruit beneficial microbiomes), (ii) managing the soil habitat (using agronomic practices to engineer suppressive ecological legacies), and (iii) deploying advanced microbial consortia. Critically, we argue that the recent meta-omics revolution, integrating metagenomics, metatranscriptomics, metaproteomics, and metabolomics, is the enabling technology that transforms this framework from a conceptual model into a quantifiable, diagnosable, and agriculturally deployable system. Multi-omics tools provide the empirical foundation for diagnosing soil feedback states, monitoring intervention outcomes, and building predictive models. By bridging the lab-field gap and evaluating key translational challenges, this review provides a coherent, actionable roadmap for harnessing PSF to achieve cultivated resilience in modern agriculture.},
}

@article {pmid42891330,
year = {2026},
author = {Hong, W and Zhang, R and Lin, X and Wang, Y and Yang, S and Mufti, FUD and Yao, Y and Zhou, G and Xi, C and Shu, W and Price, G and Zhao, Y and Song, L},
title = {Resistome flow in global landfill systems.},
journal = {iMetaOmics},
volume = {3},
number = {1},
pages = {e70075},
pmid = {42891330},
issn = {2996-9514},
abstract = {Antibiotic resistance genes (ARGs) represent a critical global public health threat. Effective resistome management within the One Health framework requires a comprehensive understanding of the sources and movement of ARGs across environmental media. This study provides a detailed analysis of resistome characteristics and dynamics in global landfill systems. Landfill systems were found to harbor diverse and highly mobile ARGs, with multidrug-resistant genes (MDRGs) comprising 32.63% of total ARGs, and comparable or even higher levels of associated ARG subtypes than in other environmental media, such as acidic mine wastewater. The ARG density on plasmids was 3.5 times higher than that on chromosomal sequences, with five times more abundant ARG-carrying plasmid-associated contigs in landfill systems than that in wastewater. At the metagenome-assembled genome level, members of the phylum Pseudomonadota were identified as the most abundant hosts (29.72%), harboring 47.74% and 56.47% of the total ARGs and MDRGs, respectively. Genomic analysis of 35 Pseudomonas spp. strains revealed unique Pseudomonas species in landfill systems, including P. aeruginosa. Resistome flow pathways were further mapped, including inflows into landfill (via soil, wastewater, freshwater, and the human and pig gut), movement within landfills (across landfill refuse, leachate, and airborne particles), and outflows from landfills (via landfill leachate effluent, gas emissions, and refuse evacuation). The results emphasized diverse resistome development and movement within landfill systems, ultimately contributing to the environmental spread of ARGs. Thus, our study highlights the urgent need for comprehensive policies and management strategies to mitigate resistome proliferation at every stage of municipal solid waste management.},
}

@article {pmid42891333,
year = {2026},
author = {Li, Y and Wang, M and Liu, X and Wu, J and Mao, Y and Zhang, C and Chen, Q and Wang, Z and Jing, G and Han, M},
title = {L-EasyARG: A long-read metagenomics tool for rapid antibiotic-resistance-gene profiling.},
journal = {iMetaOmics},
volume = {3},
number = {2},
pages = {e70098},
pmid = {42891333},
issn = {2996-9514},
abstract = {l-EasyARG is a pipeline for long-read metagenomic profiling of antibiotic resistance genes (ARGs) and their genetic context. It integrates ARG identification, plasmid and mobile genetic element (MGE) detection, taxonomic classification, and further identifies ARGs carried by human bacterial pathogens (HBPs) defined in the WHO and ESKAPE pathogen lists. Benchmarking on simulated datasets with error rates ranging from 0% to 15% demonstrates optimal F1-scores at ≤5% errors, outperforming existing tools such as ARGpore2 and DeepARG. Application to hospital wastewater samples validates its ability to capture disinfection-induced shifts in ARG composition, ARG-MGE co-occurrence, and ARG-host associations. l-EasyARG generates comprehensive outputs including abundance profiles, co-occurrence networks, and interactive visualizations, enabling efficient resistome surveillance and risk assessment. The pipeline is user-friendly and locally executable.},
}

@article {pmid42891342,
year = {2026},
author = {Shen, Z and Li, X and Gong, Z and Hu, Y and Cai, Y and Shao, K and Gao, G and Martin, RM and Tang, X},
title = {Warm-wet transition restructures arid lake microbiomes and functional potential.},
journal = {iMetaOmics},
volume = {3},
number = {3},
pages = {e70119},
pmid = {42891342},
issn = {2996-9514},
abstract = {Over the past six decades, northwestern China has undergone a pronounced climatic transition from a "warm-dry" to a "warm-wet" regime, driving substantial shifts in lake water level (WL), salinity, and nutrient conditions. However, how this hydroclimatic transition restructures lake microbiomes and their functional potential remains poorly understood. Here, we used Lake Bosten, the largest inland lake in arid northwestern China, as a model ecosystem to examine the long-term impacts of climate-driven environmental change on microbial diversity, community assembly, network structure, and functional potential. We combined (1) meteorological and aquatic environmental records from 1958 to 2022, (2) decade-separated field surveys of microbial communities (2010-2011 vs. 2021-2022) using amplicon sequencing and metagenomics, and (3) mesocosm experiments simulating projected future hydroclimatic conditions. Warm-wet conditions influenced the Lake Bosten ecosystem through two main pathways: direct temperature effects and indirect WL mediated effects on hydrological connectivity and water chemistry. Field observations showed that the warm-wet period was characterized by higher WL, lower salinity and total nitrogen, and increased bacterial and eukaryotic diversity. Community assembly shifted toward stronger homogeneous selection and weaker dispersal limitation in both bacterial and eukaryotic communities, consistent with enhanced hydrological connectivity. At the same time, both microbial domains showed reduced community stability, and their co-occurrence networks exhibited lower complexity and structural stability. In contrast, broad metagenomic functional composition showed no significant shift despite pronounced taxonomic and network reorganization. Nitrogen cycling genes showed pathway-specific redistribution, with enhanced nitrogen fixation and selected nitrification related genes but reduced nitrate reduction, denitrification, and dissimilatory nitrate reduction to ammonium (DNRA). Taxon-function linkage further indicated that functional compensation was mainly mediated by replacement within bacterial functional guilds. Overall, our study links warm-wet hydroclimatic change to altered water level, salinity, nutrient conditions, microbiome restructuring, cross domain network rewiring, and buffered functional potential in an arid lake.},
}

@article {pmid42891346,
year = {2026},
author = {Luo, XQ and Dong, X and Li, JL and Yao, JC and Peng, Z and Li, Q and Yang, ZW and Yuan, Y and Li, WJ and Wang, P},
title = {Diversity, transfer potential, and transcriptional activity of virus-carried antibiotic resistance genes in global estuaries.},
journal = {iMetaOmics},
volume = {3},
number = {1},
pages = {e70074},
pmid = {42891346},
issn = {2996-9514},
abstract = {Estuaries, the transition zones between terrestrial and marine ecosystems, are vital hotspots for antibiotic resistance genes (ARGs) due to substantial antibiotic pollution. Although viruses have been considered as reservoirs and vectors of ARGs in various environments, the composition, transmission, and ecological drivers of virus-carried ARGs (vARGs) in estuarine ecosystems remain poorly understood. Here, we constructed a Global Estuarine Virome (GEV) dataset by recovering 136,443 viral operational taxonomic units (vOTUs) from 534 worldwide estuarine metagenomes. Based on this GEV dataset, we identified 282 (temperate: 217; lytic: 65) vOTUs that carried 462 ARGs. These ARGs encompassed 108 ARG subtypes conferring resistance to 13 antibiotic classes, with their richness and abundances in estuaries being directly and indirectly correlated with changes in temperatures and coastal human activities. Network approach further revealed temperature-dependent vARG transfers between viruses and prokaryotes. Moreover, ARG-carrying vOTUs could target abundant prokaryotic taxa (e.g., Rhodobacteraceae and Flavobacteriaceae) and potential pathogens, including Acinetobacter venetianus and Pseudomonas marginalis. Notably, leveraging 188 estuarine metatranscriptomes, we found that over half of the vARGs (51%) were active in estuaries, and the expression levels of vARGs were sometimes comparable to their prokaryotic counterparts. The relative contribution of viruses to ARG expression also increased under warmer conditions. Overall, although the ARGs were only detected in a small fraction (0.2%) of the estuarine vOTUs, this study reveals that the potential risks of vARGs in estuarine ecosystems warrant attention, especially in the context of global warming and socioeconomic development. This underscores the necessity of incorporating vARGs into future surveillance and management of estuaries.},
}

@article {pmid42886419,
year = {2026},
author = {Bagul, SY and Sarkar, R and Suthar, MK and Kumar, V and S, S and Rana, VS and Sircar, D and Reddy, NRR},
title = {Culturomics and amplicon-based insights into the endophytic microbiome of Kalmegh (Andrographis paniculata (Burm.f.) Nees) and its implications in plant growth promotion.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {11},
pages = {},
pmid = {42886419},
issn = {1573-0972},
support = {NASF/MA-10007/2023-24//ICAR - National Agricultural Science Fund/ ; (NASF/MA-10007/2023-24//ICAR - National Agricultural Science Fund/ ; (NASF/MA-10007/2023-24//ICAR-National Agricultural Science Fund (NASF)/ ; },
mesh = {*Endophytes/classification/isolation & purification/genetics/metabolism ; *Bacteria/classification/isolation & purification/genetics/metabolism ; *Microbiota/genetics ; *Andrographis/microbiology/growth & development ; Diterpenes/metabolism ; Plant Leaves/microbiology/chemistry ; Plants, Medicinal/microbiology/growth & development ; Plant Development ; Metagenomics ; Phylogeny ; Plant Stems/microbiology ; Andrographis paniculata ; Plant Extracts ; },
abstract = {Leaf and stem endophytic microorganisms play an important role in plant physiology and secondary metabolite biosynthesis of plants, particularly in medicinal plants. Kalmegh (Andrographis paniculata (Burm.f.) Nees) is an important medicinal plant with liver-protective, anti-inflammatory, ovicidal, larvicidal, and anti-urolithatic properties. The medicinal activities are due to presence of andrographolides. This study investigated the culture-independent diversity of endophytic bacteria associated with Kalmegh at nursery, vegetative, and flowering stages using a metagenomic approach. The results revealed that Sphingomonas was the dominant bacterial genus during nursery and vegetative stages, whereas Halobacterium predominated during the flowering stage. Microbial abundance was highest in the nursery stage, followed by flowering and vegetative stages. Functional analysis showed that flowering stage endophytes were enriched with specialized carbon metabolism and aromatic compound degradation pathways, potentially influencing andrographolide biosynthesis. Chemical analysis supported these findings, showing the highest andrographolide content in leaves during flowering (3.1%). Gene expression analysis further demonstrated that increased andrographolide accumulation was associated with upregulation of methyl erythritol phosphate pathway (MEP) pathway and diterpene biosynthetic genes. Bacterial endophytes isolated from flowering-stage leaves exhibited plant growth-promotion, antifungal, and seed germination-enhancing activities. In vitro assays against Fusarium wilt and Rhizoctonia disease showed that Bacillus cereus strains KL11, KL12, and KL5 inhibited pathogen growth by 60-65%. Biopriming with strains KL3 and KL5 of Bacillus cereus improved seed germination and plant growth. Pot trials with Micrococcus luteus KES1 increased herbage yield, plant height, and andrographolide content by 43%. These findings highlight the potential of leaf and stem endophytes for sustainable improvement of Kalmegh productivity and andrographolide content in the plant.},
}

*Endophytes/classification/isolation & purification/genetics/metabolism
*Bacteria/classification/isolation & purification/genetics/metabolism
*Microbiota/genetics
*Andrographis/microbiology/growth & development
Diterpenes/metabolism
Plant Leaves/microbiology/chemistry
Plants, Medicinal/microbiology/growth & development
Plant Development
Metagenomics
Phylogeny
Plant Stems/microbiology
Andrographis paniculata
Plant Extracts

@article {pmid42886518,
year = {2026},
author = {Sharif, B and Kutschera, VE and Oskolkov, N and Guinet, B and Lord, E and Chacón-Duque, JC and Oppenheimer, J and van der Valk, T and Del-Molino, DD and Heintzman, PD and Dalén, L},
title = {DNAharvester: A Nextflow Pipeline for Analysing Highly Degraded DNA from Ancient and Historical Specimens.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btag782},
pmid = {42886518},
issn = {1367-4811},
abstract = {MOTIVATION: Ancient DNA (aDNA) research has advanced rapidly with the development of high-throughput sequencing, enabling genome-wide analyses of large collections of prehistoric specimens. However, analysing palaeontological and archaeological material with highly degraded DNA constitutes a major bioinformatic challenge. DNA from such samples is characterized by short fragment lengths, low endogenous content, post-mortem damage, and cross-species contamination, which can increase spurious mapping and reference bias, affecting downstream population genetic inferences.

RESULTS: We present DNAharvester, a modular and reproducible pipeline designed specifically for processing highly degraded DNA from ancient and historical specimens. DNAharvester integrates metagenomic filtering, competitive mapping, adaptive aligner selection (incorporating BWA-aln, BWA-mem, and Bowtie2), and systematic evaluation of reference bias and spurious mapping. By incorporating flexible mapping and filtering strategies, the pipeline can be adapted to varying sample preservation, focusing on maximizing authentic data recovery. DNAharvester features subworkflows for iterative assembly of mitogenomes, identification of genomic repeats and CpG sites, taxonomic classification, microbial/pathogen screening, genetic sex determination, and variant calling. To accommodate varying sequencing depths, the pipeline supports diploid variant calling, genotype likelihood estimation, and pseudo-haploid random allele calling. We validated the pipeline using simulated and empirical datasets, demonstrating its ability to systematically mitigate complex background contamination while preserving authentic genomic signals. By streamlining complex bioinformatic tasks through simple configuration files, DNAharvester establishes a standardized approach for analysing aDNA datasets and makes genomic analyses of ancient remains accessible to the broader research community.

Implemented in Nextflow, DNAharvester provides a highly scalable, containerized framework that enhances reproducibility, portability, and robustness in aDNA analyses. DNAharvester is open source under the GNU General Public License v3.0 and freely available at https://github.com/NBISweden/DNAharvester.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online and Zenodo repository: https://doi.org/10.5281/zenodo.22725211.},
}

@article {pmid42886573,
year = {2026},
author = {Hou, S and Jiang, Y and Zhang, D and Xu, Z and Li, Y and Liu, X and Zhang, H and Zhang, J and Zhai, Q and Zhang, C and Wang, X and Huang, S},
title = {A high-resolution spatial model of the primate gut microbiome defines niche-specific functions and host-adapted microbial metabolism.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2748153},
doi = {10.1080/19490976.2026.2748153},
pmid = {42886573},
issn = {1949-0984},
mesh = {Animals ; Humans ; *Macaca mulatta/microbiology ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Gastrointestinal Tract/microbiology ; Bile Acids and Salts/metabolism ; Metagenomics ; *Host Microbial Interactions ; },
abstract = {The spatial organization of the gastrointestinal microbiome is shaped by strong physicochemical gradients along the gut, yet many region-associated microbial niches remain poorly resolved in humans. Here, we used the rhesus macaque (Macaca mulatta) as a spatially resolved primate model to profile 148 luminal and mucosal samples across the gastrointestinal tract using shotgun metagenomics, 2bRAD-M sequencing, and targeted bile acid metabolomics, complemented by comparative human datasets. Microbial communities exhibited strong spatial stratification along the gastrointestinal tract, while host species explained greater variation than anatomical location in our comparative datasets. Despite broad phylum-level similarity between humans and monkeys, substantial divergence emerged at species and functional levels. Monkey-associated Segatella copri encoded expanded carbohydrate-active enzyme (CAZyme) repertoires specialized for degradation of complex plant polysaccharides, consistent with dietary and other host-associated adaptation. Along the gastrointestinal tract, microbial load and diversity followed pronounced spatial gradients, although the low-biomass stomach retained unexpectedly high taxonomic and functional diversity. Mucosal communities largely mirrored luminal microbiota at broad taxonomic scales but exhibited distinct species-level signatures associated with niche-specific functional specialization. The monkey large intestine was further enriched in the immunomodulatory bile acid isoallo-lithocholic acid (isoalloLCA), with candidate biosynthetic genes identified in previously uncharacterized microbial lineages. Together, these findings establish a high-resolution framework of the primate gut microbiome and reveal how spatial organization and host-associated selection shape microbial metabolism and host-microbe interactions relevant to gut health.},
}

Animals
Humans
*Macaca mulatta/microbiology
*Gastrointestinal Microbiome
*Bacteria/classification/genetics/isolation & purification/metabolism
Gastrointestinal Tract/microbiology
Bile Acids and Salts/metabolism
Metagenomics
*Host Microbial Interactions

@article {pmid42887104,
year = {2026},
author = {Yang, S and Luo, Y and Zou, X and Zhang, W and Su, Y and Luo, J and Wang, F},
title = {Thiamphenicol decouples acidogenesis from methanogenesis and redirects carbon flux toward volatile fatty acids in sludge anaerobic digestion.},
journal = {Journal of hazardous materials},
volume = {518},
number = {},
pages = {143930},
doi = {10.1016/j.jhazmat.2026.143930},
pmid = {42887104},
issn = {1873-3336},
abstract = {Antibiotic residues in waste activated sludge (WAS) may disrupt anaerobic carbon conversion, yet how phenicol antibiotics redistribute carbon between acidogenesis and methanogenesis remains unclear. At 10 mg/g TSS, methane production decreased by 63.2% while VFAs reached 131-fold the control. This functional decoupling was underpinned by microbial fates: hydrolytic-acidogenic bacteria were largely retained or enriched, whereas methanogenic archaea and syntrophic bacteria were severely depleted. Concurrently, bacteria-archaea ecological networks underwent reorganization, with positive correlations partially rebounding at moderate TAP exposure. The network collapsed at high TAP, with substantial loss of connector taxa mediating inter-module metabolite exchange. Metagenomic evidence further revealed a functional asymmetry: genes involved in substrate transport and amino acid metabolism were maintained or showed increased relative abundance, while methanogenic genes and AI-2-associated communication genes exhibited decreased relative abundance. PLS-PM revealed that TAP was positively associated with the acidogenic bacterial community (β = 0.960) but negatively with methanogenic potential (β = -0.998). Accordingly, the methane share dropped from 98.7% to 18.1%, while VFAs increased to 81.9% of the COD-equivalent product pool. This work advances the understanding of antibiotic-driven functional imbalance and carbon flux redirection in sludge anaerobic digestion, providing a mechanistic basis for managing antibiotic-laden sludge prior to energy recovery.},
}

@article {pmid42887308,
year = {2026},
author = {Zhang, L and Ye, M and Dong, Y and Yuan, L and Qiu, S and Shao, H and Zhang, D},
title = {Modulation of the gut microbiome and resistome in Taihe Black-Boned Silky Fowls by different dietary selenium forms.},
journal = {Poultry science},
volume = {105},
number = {12},
pages = {107919},
doi = {10.1016/j.psj.2026.107919},
pmid = {42887308},
issn = {1525-3171},
abstract = {Selenium is a widely utilized supplement in poultry production. Its bioavailability and tissue deposition vary with chemical form and may affect the gut microenvironment. Taihe Black-Boned Silky Fowl (TBSF), a Chinese endemic breed with systemic melanin deposition, exhibit enhanced absorption and enrichment of diverse compounds. As a metalloid, selenium may also promote antimicrobial resistance in microbiomes, including those of the gut. However, its impact on the TBSF gut microbiota and resistome remains unknown. We therefore investigated how selenium chemical form influences the cecal microbiome and resistome. Four dietary treatment groups of TBSF (n = 120 birds per group; 60 males and 60 females) were fed for 80 days: CK (selenium-deficient control), YS (sodium selenite), JS (yeast-derived selenium), and DS (selenomethionine), with measured dietary selenium concentrations of 0.05 ± 0.002, 0.33 ± 0.023, 0.35 ± 0.017, and 0.36 ± 0.042 mg/kg, respectively. We performed metagenomic sequencing analysis to assess alterations in microbial composition and resistome profiles in cecum. Results demonstrated that selenium supplementation significantly modulated cecal microbiota structure in both male and female birds(Bray-Curtis distance-based analysis, Wilcoxon rank-sum test, P < 0.05), with pronounced sex-dependent differences. The relative abundances of three prevalent antibiotic resistance genes (ARGs), bcrA, efrA, and fusA, were significantly elevated in selenium-supplemented groups compared with the CK group (Kruskal-Wallis H test, FDR-adjusted P < 0.05). Selenium supplementation reduced mobile genetic element (MGE) type diversity while increasing overall MGE relative abundance. Transposases and recombinases were the two most abundant MGE-associated functional classes. Mantel correlation analysis revealed strong associations between cecal microbiota composition and both ARG and MGE profiles (r ≥ 0.5, P ≤ 0.001). The sexually dimorphic cecal microbiota composition in TBSF may underlie the observed sex-dependent resistome response: sodium selenite exerted the strongest effect on ARG and MGE enrichment in roosters, whereas yeast-derived selenium induced the strongest effect in hens. Further network analysis revealed that sodium selenite exerted the most pronounced influence on resistome-microbiota co-occurrence patterns. These findings underscored the dual-sided nature of selenium supplementation from the perspective of ARGs, indicating that selenium supplementation may alter the composition of the cecal microbiota, thereby modulating the relative abundance and community structure of ARGs and MGEs in the TBSF cecum. Given selenium's essential role and narrow therapeutic index, its chemical form and dosage must be evidence-based and rigorously optimized to minimize potential unintended contributions to antimicrobial resistance. This represents a potential ecological and antimicrobial resistance concern from a One Health perspective that warrants further investigation.},
}

@article {pmid42887325,
year = {2026},
author = {Cao, X and Zang, Z and Liu, J and Zhan, G and Shi, G and Zhang, L},
title = {Synergistic effects of biochar and organic fertilizer on the regulation of microbial carbon and nitrogen metabolism in paddy soil to reduce net greenhouse gas emissions.},
journal = {Journal of environmental management},
volume = {419},
number = {},
pages = {131181},
doi = {10.1016/j.jenvman.2026.131181},
pmid = {42887325},
issn = {1095-8630},
abstract = {Biochar and organic fertilizer have been widely applied to improve soil carbon sequestration and mitigate greenhouse gas (GHG) emissions in rice production systems. However, the synergistic mechanisms through which these amendments regulate microbial carbon/nitrogen (C/N) metabolism, net GHG emissions, and crop productivity in dry direct-seeded rice (DDSR) systems remain insufficiently understood. In this study, a two-year field experiment was conducted with combined treatments of organic fertilizer substitution (0% and 20%) and biochar application (0, 5, and 10 t/hm[2]) to evaluate their integrated effects on GHG emissions, soil properties, rice yield, and microbial functional genes involved in C/N cycling. Biochar and organic fertilizer significantly reduced CH4 and N2O emissions, leading to lower global warming potential (GWP), greenhouse gas emission intensity (GHGI), and net greenhouse gas emissions (NGHGE), while simultaneously increasing rice yield. The combined application of 20% organic fertilizer substitution with 5 t/hm[2] biochar achieved the optimal performance, increasing yield by 11.64%-15.44% and reducing GWP and GHGI by 7.58%-16.56% and 17.21%-27.72%, respectively. Metagenomic analysis revealed that the combined application modified microbial community structure while regulated microbial C/N metabolism by reshaping key functional pathways. The enhancement of Calvin-Benson-Basham (CBB) pathway was related to the increased abundance of PRK and prkB under biochar conditions; meanwhile, reduced abundances of aclA, aclB, and ccsA were associated with suppressed reductive tricarboxylic acid (rTCA) cycle. Concurrently, denitrification and nitrification pathways showed positive correlations with increased abundances of nirK, norB, and nosZ. Redundancy analysis (RDA) and mantel analyses indicated that soil organic carbon (SOC), pH, ammonium nitrogen (NH4[+]-N), and nitrate nitrogen (NO3[-]-N) were the primary drivers shaping microbial functional gene structure. Overall, the synergistic application of biochar and organic fertilizer effectively coordinated carbon sequestration, emission reduction, and yield enhancement, providing a feasible strategy for low-carbon and sustainable management of DDSR.},
}

@article {pmid42887796,
year = {2026},
author = {Liu, L and Liu, L and Qiu, C and Yu, J and Wang, C and Wang, S},
title = {Mechanistic insights into riboflavin-mediated recovery of the single-stage partial nitritation-anammox system under tetracycline stress.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {136039},
doi = {10.1016/j.biortech.2026.136039},
pmid = {42887796},
issn = {1873-2976},
abstract = {Tetracycline (TC) contamination poses a potential threat to the stability of anammox-based wastewater treatment systems, yet effective strategies for accelerating functional recovery remain poorly understood. This study explored the inhibitory effects of 5 mg/L TC on a single-stage partial nitritation-anammox (SPNA) system, and further unraveled its functional potential and underlying mechanisms of exogenous riboflavin for restoring system performance. TC exposure substantially impaired nitrogen removal, with total nitrogen removal efficiency decreasing from 53.39 % to 34.44 %, accompanied by a pronounced decline in anammox activity. Supplementation with 0.5 mg/L riboflavin accelerated system recovery, partially restoring total nitrogen removal efficiency to 48.15 %, by enhancing anammox activity and suppressing nitrite-oxidizing bacteria proliferation. Riboflavin alleviated these disturbances by enhancing electron transfer, mitigating oxidative stress, and restoring nitrogen metabolism-related functional genes. Metagenomic analysis further revealed that riboflavin recovered extracellular electron transfer and amino acid and nucleotide metabolism pathways disrupted by TC stress, while promoting the enrichment of tetracycline resistance and degradation-related genes and putative tetracycline-degrading bacteria, including Sphingobacterium and Bacillus. These responses were accompanied by enhanced tetracycline removal, suggesting potential mechanisms of improved microbial adaptation to antibiotic stress.},
}

@article {pmid42887801,
year = {2026},
author = {Zhang, S and Wang, Q and Zhang, X and Tian, Z and Xu, X and Wang, S and Lv, G and Chen, Y and Ma, Y and Gao, A},
title = {Short-chain perfluorobutyric acid (PFBA) disrupts anaerobic ammonium oxidation in riverbed sediments and reshapes the functional microbial community.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {136077},
doi = {10.1016/j.biortech.2026.136077},
pmid = {42887801},
issn = {1873-2976},
abstract = {Perfluorobutanoic acid (PFBA), a representative short-chain perfluoroalkyl carboxylic acid, is increasingly detected in aquatic environments, yet its impacts on anaerobic nitrogen cycling remain poorly understood. Here, a laboratory-scale simulated river sediment system was established to investigate the concentration-dependent effects of PFBA (1 ng/L-50 mg/L) on Anammox performance, microbial communities, functional genes, and PFBA transformation. Low PFBA concentrations (≤1 μg/L) stimulated nitrogen removal, with NH4[+]-N conversion and NO2[-]-N removal increasing by 30.8% and 38.9%, respectively. In contrast, inhibition emerged at 1 mg/L and became pronounced at ≥ 10 mg/L. At 50 mg/L, NO2[-]-N and TN removal rates decreased to 7.58 and 5.22 μg/(g·h), respectively, and remained suppressed during recovery. High PFBA exposure reduced extracellular polymeric substances (EPS) -associated protein content and key Anammox enzyme activities, accompanied by downregulation of hao, hdh, and hzs and increased relative abundance of nrf, indicating a shift from autotrophic Anammox toward heterotrophic dissimilatory nitrate reduction to ammonium (DNRA). Notably, 91.7% of PFBA was apparently transformed at 50 mg/L, with shorter-chain products such as perfluoropropanoic acid and trifluoroacetic acid being qualitatively identified, suggesting sequential dealkylation and decarboxylation. However, a complete mass balance was not established because the transformation products were not quantified. These findings demonstrate that PFBA exerts concentration-dependent effects on sedimentary nitrogen cycling by disrupting Anammox metabolism and reshaping microbial functional pathways, providing new insights into per- and polyfluoroalkyl substances (PFAS) ecological risks and sediment bioremediation.},
}

@article {pmid42887802,
year = {2026},
author = {Liu, H and Li, L and Peng, Y and Peng, X and Li, Z and Zhao, B},
title = {Nitrogen removal mechanisms in improved hybrid activated sludge-membrane aerated biofilm reactor: Insights from metagenomics and metaproteomics.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {136070},
doi = {10.1016/j.biortech.2026.136070},
pmid = {42887802},
issn = {1873-2976},
abstract = {Simultaneous nitrification-denitrification (SND) is a promising process for low C/N wastewater treatment. A hybrid activated sludge-membrane aerated biofilm reactor (H-MABR) capable of achieving two‑stage SND was developed and exhibited satisfactory nitrogen removal performance; however, the underlying mechanisms remain unclear. To address this, an improved H-MABR was developed and integrated metagenomic and metaproteomic analyses were performed to systematically elucidate the spatial distribution of microbial communities and their functions in the reactor. The results showed that the improved H-MABR achieved removal efficiencies of 94.4 ± 0.4% for chemical oxygen demand, 92.9 ± 0.7% for total nitrogen, and 97.8 ± 0.8% for ammonia nitrogen. Multi‑omics analysis identified seven dominant microbial genera and three highly expressed nitrogen metabolic pathways. The outer ring was the primary nitrogen removal zone, where the aerobic zone mainly mediated nitrification and the anoxic zone exhibited significantly upregulated activities of NosZ, NirK, NirS, and NorC (ORA vs. ORO), strongly supporting the denitrification function in this zone. The inner ring served as an important auxiliary nitrogen removal unit, showing particularly strong ammonia nitrogen removal performance, which was attributed to the highly expressed hydroxylamine dehydrogenase. This study provides a foundation for advancing the understanding and application of SND systems.},
}

@article {pmid42888205,
year = {2026},
author = {Hoozemans, JB and de Jonge, PA and Guman, MSS and Haal, S and Aydin, Ö and Meijnikman, AS and Bäckhed, F and de Brauw, M and Acherman, YIZ and Nieuwdorp, M and Groen, AK and Gerdes, VEA},
title = {Understanding pathophysiology of gallstone disease: a multi-omic analysis focused on adult women with obesity.},
journal = {International journal of obesity (2005)},
volume = {},
number = {},
pages = {},
pmid = {42888205},
issn = {1476-5497},
abstract = {BACKGROUND: Gallstone disease has a complex, multifactorial pathophysiology. Both the gut microbiome and the liver have been implicated as potential contributors. Because obesity is associated with alterations in gut microbial composition and is itself a risk factor for gallstone formation, we investigated the relative roles of the gut microbiome, the liver, and adipose tissue in gallstone disease in female patients with obesity.

METHODS: From the BARIA cohort, 108 consecutive female patients with obesity were included, of whom at baseline 39 had ultrasound proven gallstones (cases), whereas 69 did not have gallstones (controls). Fecal shotgun metagenomics, untargeted fasting plasma metabolomic analysis, and bulkRNAseq transcriptome analyses of liver, visceral (VAT), and subcutaneous (SAT) biopsies (taken during surgery) were analyzed.

RESULTS: Especially VAT showed differences in expression of 57 genes, whereas liver gene expression revealed differences only after secondary analysis. In contrast to other publications, in liver "classic" ABC transporter gallstone genes were not identified in this cohort. Instead, the cholesterol transporter ABCG1 emerged, and expression was decreased in patients with gallstone disease. Plasma metabolomic profiling demonstrated increased levels of primary and secondary bile acids in the gallstone group. In contrast, gut microbiome differences between groups were limited.

CONCLUSIONS: This integrated multi-omics analysis suggests that visceral adipose tissue may play a more prominent role in gallstone disease pathophysiology in women with obesity than previously appreciated. The observed selective molecular alterations and persistent bile acid differences highlight the complex metabolic interplay underlying gallstone formation and provide insight into tissue-specific mechanisms associated with obesity-related gallstone disease.},
}

@article {pmid42888449,
year = {2026},
author = {He, P and Zhang, K and Khan, J and Ouyang, H and Hu, S and Qian, S and Shu, B and Li, X and Lin, D},
title = {Metagenomic analysis of developmental-category-associated fungal communities in the gut contents of Achatina fulica, an intermediate host of Angiostrongylus cantonensis.},
journal = {Parasites & vectors},
volume = {19},
number = {1},
pages = {},
pmid = {42888449},
issn = {1756-3305},
support = {18MDZ02//Major Project Cultivation Plan of Xizang Minzu University/ ; XZ202401ZR0017//the Tibet Natural Science Foundation/ ; No. SKXRC2025159//the Youth S&T Talent Support Programme of Guangdong Provincial Association for Science and Technology/ ; 82672963 and 82202560//the National Natural Science Foundation of China/ ; 23360095 and 23360208//College Students' Innovative Entrepreneurial Training Plan Program/ ; },
mesh = {Animals ; Metagenomics ; *Mycobiome ; *Snails/microbiology/parasitology ; *Angiostrongylus cantonensis/physiology ; China ; *Fungi/genetics/classification/isolation & purification ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; },
abstract = {BACKGROUND: The invasive giant African snail (Achatina fulica) poses serious agricultural and ecological threats and serves as an important intermediate host of the zoonotic parasite Angiostrongylus cantonensis, which causes human eosinophilic meningitis. While its gut bacterial microbiome has been extensively characterized, the gut mycobiome remains largely uncharacterized. In particular, variations in gut fungal communities across developmental stages remain unknown, limiting our understanding of the A. fulica gut holobiont.

METHODS: In November 2025, giant African snails were collected from Guangzhou, Guangdong Province, China. Genomic DNA was extracted from the gut contents of the collected snails. Metagenomic sequencing was conducted to characterize variations in the gut mycobiota across different snail sample types.

RESULTS: Metagenomic sequencing of 18 snail gut samples across three developmental stages showed lower fungal alpha diversity in adults than in juveniles, whereas PCoA visualized differences in community composition among developmental categories and PERMANOVA confirmed that these differences were statistically significant. Ascomycota dominated the mycobiome, with developmental-category-associated differences in taxonomic composition. LEfSe and DESeq2 identified differentially abundant taxa associated with developmental categories, while SIMPER analysis identified several taxa contributing to the observed dissimilarity, including Synchytrium taraxaci, Aspergillus flavus and Cladosporium cladosporioides. These taxa are interpreted as contributors to community dissimilarity rather than as causal drivers of developmental-category-associated differences. Co-occurrence networks analysis identified six highly connected taxa (Hanseniaspora uvarum, Apiospora montagnei, Aureobasidium thailandense, Colletotrichum aenigma, Truncatella angustata, and Calonectria ilicicola) within the inferred fungal association network.

CONCLUSIONS: Gut fungal community composition differed significantly among the sampled developmental categories of A. fulica, although the cross-sectional design does not establish that the host development itself causes these differences. The identified developmental-category-associated and highly connected taxa provide a baseline for gut mycobiota ecology and a foundation for future controlled studies investigating their functional roles and potential relevance to A. cantonensis infection.},
}

Animals
Metagenomics
*Mycobiome
*Snails/microbiology/parasitology
*Angiostrongylus cantonensis/physiology
China
*Fungi/genetics/classification/isolation & purification
*Gastrointestinal Microbiome
Gastrointestinal Tract/microbiology

@article {pmid42888864,
year = {2026},
author = {Schlager, JG and Stiefel, D and Patzer, K and Schloter, M and Foesel, BU and Zelzer, NM and French, LE and Gschwendtner, S and Hartmann, D},
title = {Basal Cell Carcinoma May Be Associated With Staphylococcus Dysbiosis.},
journal = {Experimental dermatology},
volume = {35},
number = {10},
pages = {e70371},
doi = {10.1111/exd.70371},
pmid = {42888864},
issn = {1600-0625},
support = {//Verein zur Förderung von Wissenschaft und Forschung an der Medizinischen Fakultät der LMU München e.V. (WiFoMed)/ ; },
mesh = {Humans ; *Dysbiosis/microbiology/complications ; *Basal Cell Carcinoma/microbiology ; *Skin Neoplasms/microbiology ; Skin Microbiome ; *Staphylococcus/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Female ; Aged ; Male ; Middle Aged ; Skin/microbiology ; Aged, 80 and over ; Microbiota ; },
abstract = {There is growing evidence that a dysbiosis of the skin microbiome has an impact on carcinogenesis in cutaneous squamous cell carcinoma. However, the role of the microbiome in basal cell carcinoma (BCC) remains unclear due to limited, inconsistent, ex vivo studies. Here, we analysed the skin microbiome of patients with BCC, including the tumour lesion as well as perilesional skin from the same subject. Skin swabs from BCC and perilesional skin were taken prior to tumour surgery. After DNA extraction, we used a metabarcoding approach based on 16S rRNA gene amplicon sequencing to analyse the cutaneous bacterial communities. In total, 63 patients with BCC were included for analysis. Most tumour lesions were located on sun-exposed, sebaceous areas such as the nose, cheeks, and forehead. The genera Corynebacterium, Cutibacterium, and Staphylococcus predominated both in BCC and perilesional skin. However, the microbiome of BCC was reduced in overall bacterial richness, with a significant overabundance of amplicon sequence variants (ASV) assigned to the genus Staphylococcus, resulting in a reduced complexity in microbial networks. The dominating ASV assigned to Staphylococcus was also detected in perilesional skin regions, indicating that the microbial dysbiosis in BCC affected regions is caused by natural members of the healthy skin microbiome. The BCC microbiome is characterised by microbial dysbiosis, reflected by a reduced overall bacterial richness, fewer microbe-microbe interactions and a significant over-representation of Staphylococcus species compared with perilesional skin. Further long-read metagenomics and cultivation-based studies are needed to identify Staphylococcus species driving dysbiosis.},
}

Humans
*Dysbiosis/microbiology/complications
*Basal Cell Carcinoma/microbiology
*Skin Neoplasms/microbiology
Skin Microbiome
*Staphylococcus/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
Female
Aged
Male
Middle Aged
Skin/microbiology
Aged, 80 and over
Microbiota

@article {pmid42888868,
year = {2026},
author = {Xie, S and Yang, Y and Tang, S and Zhou, L and Wang, J and Chan, JWY and Or, B and Li, N and Gong, S and He, Z and Ni, J and Liu, Y and Zhang, J and Chan, PKS and Chen, Z and Wong, SH and Mok, VCT and Chan, NY and Chau, SWH and Wing, YK and Huang, B},
title = {Habitual Diet, Gut Microbiome Dysbiosis, and α-Synucleinopathy Conversion in Isolated Rapid Eye Movement (REM) Sleep Behavior Disorder.},
journal = {Movement disorders : official journal of the Movement Disorder Society},
volume = {},
number = {},
pages = {},
doi = {10.1002/mds.70562},
pmid = {42888868},
issn = {1531-8257},
support = {05162876//Health and Medical Research Fund/ ; 06170676//Health and Medical Research Fund/ ; C4044-21G//Research Grants Council of Hong Kong/ ; //Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong/ ; },
abstract = {BACKGROUND: Accumulating evidence indicates that habitual diet, including plant-based dietary patterns, is associated with neurodegenerative α-synucleinopathy risk. However, the role of diet and its correlation with the gut microbiome in prodromal α-synucleinopathy, specifically among patients with isolated rapid eye movement (REM) sleep behavior disorder (iRBD), remains unclear.

OBJECTIVE: To evaluate dietary patterns, their interplay with gut microbial dysbiosis, and longitudinal effects on neurodegenerative progression in iRBD patients.

METHODS: We recruited 287 iRBD patients and 208 age- and sex-matched controls. Plant-based diet indices (PDIs) were derived from food frequency questionnaires. Shotgun metagenomic sequencing was performed in 456 subjects for diet-microbiome analyses. After a median follow-up of 4.2 years, 45 (15.7%) iRBD patients converted to α-synucleinopathies. Cox proportional hazards models assessed the associations between diet and neurodegenerative outcomes.

RESULTS: We found that iRBD patients exhibited lower healthful PDIs (adjusted odds ratio [aOR] 95% confidence interval [95% CI]: 0.48 [0.29-0.80], P = 0.005) but higher consumption of unhealthful plant-based foods (refined grains, sweets, and sweeteners). Diet-microbiome interaction analysis identified dietary associations for 84.3% of iRBD-related gut microbes, including co-occurrence between healthful PDI and Clostridium sp. AF20-17LB. Longitudinally, four dietary factors and five iRBD-related microbes were associated with neurodegenerative outcomes; specifically, higher coffee consumption was linked to a lower risk of progression to α-synucleinopathy (aHR [95% CI]: 0.30 [0.11-0.78], P = 0.01). Furthermore, mediation analyses indicated that the iRBD-enriched species Ruthenibacterium lactatiformans mediated the association between unhealthful PDI and dementia-first conversion.

CONCLUSIONS: Habitual diet in iRBD is associated with gut microbiome dysbiosis and predicts neurodegenerative progression. These findings highlight diet-microbiome interactions as modifiable targets for intervention in prodromal α-synucleinopathy. © 2026 The Author(s). Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.},
}

@article {pmid42888920,
year = {2026},
author = {Hardy, SMC and Aguilar-Pine, EJ and Gulick, S and Ahmad, A and Baker, BJ and Scott, N and Aitolo, G and Felton, N and Cockell, CS},
title = {Impact Crater Hydrothermal Systems Support Rapid Microbial Enrichment and Diverse Metabolic Potential.},
journal = {Geobiology},
volume = {24},
number = {6},
pages = {e70070},
doi = {10.1111/gbi.70070},
pmid = {42888920},
issn = {1472-4669},
support = {73592LPI//Simons Foundation/ ; LI-SIAME-00002001//Simons Foundation/ ; ST/V000586/1//Science and Technology Facilities Council/ ; ST/Y001788/1//Science and Technology Facilities Council/ ; },
mesh = {*Hydrothermal Vents/microbiology ; *Bacteria/metabolism/classification/genetics ; Germany ; *Archaea/metabolism/classification/genetics ; },
abstract = {Impact crater hydrothermal systems, formed after asteroid and comet impacts, have been proposed as promising habitats for life on early Earth and as key targets in the search for life on planetary bodies such as Mars, since they provide liquid water and active geochemical turnover. Because no newly formed impact structures exist on Earth, studies of microbial establishment in impact-crater hydrothermal systems have largely relied on the direct observation of fossil microbial life or its isotopic signatures. To address this limitation, we established simulated microcosm hydrothermal systems in the laboratory using melt-bearing impact breccia (suevite) from the Ries impact structure, Germany, and temperate soils. Within weeks, these systems hosted taxonomically diverse communities, with broad metabolic potential, partitioned among oxidized impact glass, endolithic suevite habitats, and sedimentary environments. Dominant taxa included thermophiles from primarily heterotrophic lineages (e.g., Meiothermus and Aneurinibacillus spp.), as well as lineages with potentially chemolithotrophic metabolisms (e.g., Brockia spp.). Metagenomic annotations identified genes associated with methane, iron, and sulfur cycling, including sulfate-reduction, indicating metabolic potential for biogeochemically relevant processes under hydrothermal conditions. These results show that impact-generated hydrothermal systems can rapidly support diverse thermophilic microbial communities with habitat-specific community structure and metabolic potential, supporting their relevance as analogue environments for studying early microbial establishment and biosignature formation in planetary impact settings.},
}

*Hydrothermal Vents/microbiology
*Bacteria/metabolism/classification/genetics
Germany
*Archaea/metabolism/classification/genetics

@article {pmid42888984,
year = {2026},
author = {Wei, E and Shang, P and Li, F and Yan, K and Zhang, M and Fang, X and Jia, P and Wang, J and Zhao, J and Li, N and Wang, H and Xie, N},
title = {Clinical and metagenomic characterization of HHV-6 versus HHV-7 encephalitis in immunocompetent children.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1909287},
doi = {10.3389/fcimb.2026.1909287},
pmid = {42888984},
issn = {2235-2988},
mesh = {Humans ; *Herpesvirus 7, Human/genetics ; *Herpesvirus 6, Human/genetics ; Male ; Female ; Child, Preschool ; Child ; Infant ; *Encephalitis, Viral/virology/cerebrospinal fluid/diagnosis ; Retrospective Studies ; *Roseolovirus Infections/virology/cerebrospinal fluid/diagnosis ; Metagenomics ; High-Throughput Nucleotide Sequencing ; Adolescent ; Immunocompetence ; DNA, Viral/cerebrospinal fluid ; Cerebrospinal Fluid/virology ; },
abstract = {BACKGROUND: Human herpesvirus 6 (HHV-6) and human herpesvirus 7 (HHV-7) are betaherpesviruses that can cause encephalitis/encephalopathy in immunocompetent children. However, early clinical manifestations, routine laboratory tests, and neuroimaging findings often lack specificity, making etiological characterization challenging. This study aimed to characterize the clinical features and metagenomic findings of HHV-6 and HHV-7 encephalitis in immunocompetent children.

METHODS: This single-center retrospective cohort study included children (<18 years) with suspected central nervous system infection who underwent lumbar puncture and cerebrospinal fluid (CSF) next-generation sequencing (mNGS) testing at The First Affiliated Hospital of Zhengzhou University between January 2020 and December 2024. Patients with HHV-6 or HHV-7 sequences detected in CSF by mNGS, together with compatible clinical features and exclusion of other more likely etiologies, were included. Demographic characteristics, clinical manifestations, laboratory and CSF findings, neuroimaging features, mNGS results, treatments, and short-term outcomes were analyzed.

RESULTS: A total of 20 children with CSF HHV-6 or HHV-7 sequence detection were included (HHV-6, n=5; HHV-7, n=15). HHV-6 cases mainly occurred in infants and young children, whereas HHV-7 cases were predominantly observed in older children. Fever and seizure-related symptoms were the most common clinical manifestations. Peripheral inflammatory markers, CSF parameters, and neuroimaging findings showed heterogeneous patterns among patients. CSF mNGS detected HHV-6 or HHV-7 sequences in all included cases, with variable sequencing read counts (HHV-6: median 257 reads, range 55-52, 686; HHV-7: median 2, 635 reads, range 457-26, 355). The median turnaround time of mNGS reporting was 1 day (range, 1-2 days). All patients received antiviral therapy, with some receiving adjunctive corticosteroids and/or intravenous immunoglobulin. Short-term outcomes at discharge were generally favorable, and only one patient developed secondary autoimmune encephalitis.

CONCLUSIONS: HHV-6 and HHV-7 encephalitis in immunocompetent children share overlapping clinical characteristics and lack specific early laboratory or imaging features. CSF mNGS enabled rapid and unbiased detection of HHV-6 and HHV-7 sequences and provided complementary etiological information when interpreted together with clinical and ancillary findings.},
}

Humans
*Herpesvirus 7, Human/genetics
*Herpesvirus 6, Human/genetics
Male
Female
Child, Preschool
Child
Infant
*Encephalitis, Viral/virology/cerebrospinal fluid/diagnosis
Retrospective Studies
*Roseolovirus Infections/virology/cerebrospinal fluid/diagnosis
Metagenomics
High-Throughput Nucleotide Sequencing
Adolescent
Immunocompetence
DNA, Viral/cerebrospinal fluid
Cerebrospinal Fluid/virology

@article {pmid42889167,
year = {2026},
author = {Zhao, C and Chen, J and Wu, P and Zhang, W and Ning, S},
title = {Viral metagenomic characterization of HAdV-B-related signals in bronchoalveolar lavage fluid from pediatric and adult clinical cohorts.},
journal = {Frontiers in public health},
volume = {14},
number = {},
pages = {1961482},
doi = {10.3389/fpubh.2026.1961482},
pmid = {42889167},
issn = {2296-2565},
mesh = {Humans ; *Bronchoalveolar Lavage Fluid/virology ; *Metagenomics ; *Adenoviruses, Human/genetics/isolation & purification ; Phylogeny ; Child ; Adult ; Female ; Male ; Child, Preschool ; High-Throughput Nucleotide Sequencing ; *Adenovirus Infections, Human/virology ; Cohort Studies ; Infant ; },
abstract = {Human adenovirus (HAdV) is an important respiratory virus in children, but sequence-level evidence for HAdV-related signals in lower respiratory tract samples remains limited. In this study, we analyzed metagenomic next-generation sequencing data from 189 bronchoalveolar lavage fluid (BALF) libraries from pediatric and adult clinical cohorts, including 30 pediatric and 159 adult patients, together with laboratory environmental controls. MEGAN read-level classification was used to screen for Adenoviridae-related signals. HAdV-related contigs were further reviewed, and a BALF-derived HAdV-B-related representative contig was selected for read recruitment and coverage analysis. Phylogenetic trees were reconstructed using penton base, hexon, and fiber protein sequences. Adenoviridae-classified signals were more apparent in pediatric BALF libraries than in adult BALF libraries or environmental controls. Several pediatric BALF libraries showed broad read coverage across the HAdV-B-related representative contig, whereas adult libraries and environmental controls mainly showed low-coverage-breadth signals. Phylogenetic analysis placed BALF-derived penton base, hexon, and fiber sequences within HAdV-B-related lineages. Twenty-seven capsid protein sequences from 12 pediatric samples had best BLASTp matches to references annotated as HAdV-B3 (n = 23) or HAdV-B7 (n = 4). These findings provide sequence evidence for HAdV-B-related sequence signals in clinically selected pediatric BALF samples and support further investigation using targeted assays and genome sequencing.},
}

Humans
*Bronchoalveolar Lavage Fluid/virology
*Metagenomics
*Adenoviruses, Human/genetics/isolation & purification
Phylogeny
Child
Adult
Female
Male
Child, Preschool
High-Throughput Nucleotide Sequencing
*Adenovirus Infections, Human/virology
Cohort Studies
Infant

@article {pmid42889534,
year = {2026},
author = {Al-Fatlawi, A and Schroeder, M},
title = {UniProt data pruning and the growing invisibility of the dark proteome.},
journal = {NAR genomics and bioinformatics},
volume = {8},
number = {4},
pages = {lqag115},
doi = {10.1093/nargab/lqag115},
pmid = {42889534},
issn = {2631-9268},
mesh = {*Proteome/genetics ; *Databases, Protein ; Proteomics/methods ; },
abstract = {The protein resource UniProtKB has undergone a major, multi-stage reorganization of its protein space, implemented from release 2025_04 through release 2026_02. Analysis of UniProtKB and UniParc records accessed on 20 January 2026 showed that 125.9 million entries were last present in UniProtKB in 2025 and are now represented in UniParc, while ~200.0 million entries remained in UniProtKB at the access date. Of these, 58.9 million were designated for removal in release 2026_02, whereas 141.2 million were classified as retained. The reorganization retains all reviewed UniProtKB/Swiss-Prot entries (the expert-curated subset of UniProtKB), along with proteins from selected reference proteomes and unreviewed entries with additional biologically important data, including experimentally determined three-dimensional structures. The expected benefits include reduced redundancy, easier navigation, and a protein set that is more tractable for annotation and routine searches. However, the reorganization may reduce the visibility of protein sequences from uncultured microorganisms and metagenomic surveys, phylogenetically underrepresented lineages, particularly many archaeal groups, proteins belonging to the so-called "dark proteome," and strain-level variants of well-studied species such as Escherichia coli. We argue that the main consequence is not the loss of the sequences themselves, because affected proteins remain recoverable through UniParc and related resources, but a reduction in their discoverability, annotation context, and accessibility within routine workflows. These effects are likely to be most important for biodiversity-oriented analyses, retrospective reuse of older datasets, studies of specialized protein families, and downstream pipelines that rely on UniProtKB as an annotation hub. As UniProt shifts toward a more explicitly reference-proteome-centered model, a critical question arises: What are the implications of UniProtKB contraction for the representation of evolutionary diversity across the tree of life, particularly in under-sampled and uncultured lineages?},
}

*Proteome/genetics
*Databases, Protein
Proteomics/methods

@article {pmid42890506,
year = {2026},
author = {Yang, X and Chen, J and Song, J and Liu, H and Wang, L and Li, T and Yan, H and Gao, X and Ding, S},
title = {A nested case-control study on the relationship between gut microbiota and non-alcoholic fatty liver disease.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1917815},
doi = {10.3389/fendo.2026.1917815},
pmid = {42890506},
issn = {1664-2392},
mesh = {Humans ; *Non-alcoholic Fatty Liver Disease/microbiology/epidemiology ; Female ; Male ; *Gastrointestinal Microbiome ; Case-Control Studies ; Middle Aged ; Biomarkers/analysis ; Adult ; Metagenomics ; Boosting Machine Learning Algorithms ; },
abstract = {BACKGROUND: The gut microbiota plays an important role in non-alcoholic fatty liver disease (NAFLD). This study aimed to explore gut microbiota-associated biomarkers for incident NAFLD and evaluate their predictive value, providing preliminary evidence for early risk identification.

METHODS: From an initial cohort of 1,772 participants, 404 were included in the final analysis, comprising 101 incident NAFLD cases and 303 age-matched controls (1:3). Gut microbiota composition and function were characterized by metagenomic sequencing. Microbial features were compared between participants who developed NAFLD (NAFLD -/+) and those who did not (NAFLD -/-). A CatBoost model integrating gut microbiota, functional pathways, and clinical indicators was constructed to predict NAFLD, with a random forest (RF) model on the same features for comparison. Progressively enriched feature sets assessed the incremental value of microbiota-related features beyond clinical indicators, and SHapley additive exPlanations (SHAP) values interpreted the model outputs.

RESULTS: The NAFLD (-/+) group had significantly lower species-level beneficial gut microbiota (P < 0.05), and the two groups differed markedly in gut microbiota metabolic enrichment. The CatBoost model achieved an area under the curve (AUC) of 0.762, indicating moderate predictive performance for incident NAFLD. We also identified significant intergroup differences in gut microbiota composition within the diagnostic model, including the key species Coprobacillus unclassified and the metabolic pathway PWY-5030.

CONCLUSION: Gut microbiota alterations may serve as potential early biomarkers for incident NAFLD and contribute to its pathogenesis. The CatBoost model integrating multi-omics and clinical data shows moderate predictive ability, supporting the potential of gut microbiota-based approaches for non-invasive risk stratification.},
}

Humans
*Non-alcoholic Fatty Liver Disease/microbiology/epidemiology
Female
Male
*Gastrointestinal Microbiome
Case-Control Studies
Middle Aged
Biomarkers/analysis
Adult
Metagenomics
Boosting Machine Learning Algorithms

@article {pmid42890539,
year = {2026},
author = {Yao, H and Chen, J and Liu, C and Huang, J and Liu, L and Wang, Q and Wang, F},
title = {Structural and functional characterization of the gut microbiota in women with early pregnancy loss in Northwest China.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1895733},
doi = {10.3389/fmicb.2026.1895733},
pmid = {42890539},
issn = {1664-302X},
abstract = {BACKGROUND: Early pregnancy loss (EPL) is a common adverse pregnancy outcome with a complex and incompletely understood etiology. Moreover, metagenomic studies of the gut microbiota in women with EPL in Northwest China remain limited.

OBJECTIVE: This study aimed to characterize differences in gut microbial composition and predicted functional potential between women with EPL (EPL group) and normal controls (NCs) using shotgun metagenomic sequencing.

METHODS: We collected fecal samples from 216 women in Northwest China (EPL group, n = 72; NCs, n = 144). Shotgun metagenomic sequencing was performed to analyze gut microbiota composition and assess the functional potential of the microbiota.

RESULTS: Our study revealed significant differences in the composition of the gut microbiota between the EPL group and NCs, as assessed by alpha and beta diversity analyses (p < 0.001). Bacteroides was significantly more abundant in the EPL group, whereas Coprococcus, Bifidobacterium, and Roseburia were significantly more abundant in NCs. Compared to NCs, the EPL group had higher relative abundances of species such as Bacteroides stercoris, Bacteroides plebeius, and Bacteroides uniformis, but lower relative abundances of Bifidobacterium adolescentis, Megamonas funiformis, and Fusicatenibacter saccharivorans. Partial correlation analysis showed that Bacteroidetes was positively correlated with EPL at the phylum level. At the genus level, Odoribacter, Parabacteroides, and Haemophilus were positively correlated with EPL, whereas Corynebacterium, Lactobacillus, and Roseburia were negatively correlated with EPL. Metabolic pathway analysis revealed that pathways such as L-rhamnose degradation I, L-arginine biosynthesis III and 2-oxobutanoate degradation I exhibited significant positive correlations with EPL. In contrast, pathways including purine nucleobases degradation I (anaerobic) and chitin derivatives degradation showed significant negative correlations with EPL.

CONCLUSION: The results of our study revealed significant differences in gut microbiota composition and metabolic pathways between the EPL group and NCs, indicating that gut microbiome alterations are associated with EPL.},
}

@article {pmid42890753,
year = {2026},
author = {Li, Y and Liu, Y and Chen, Y and Xiang, B and Fu, H and Pan, H and Xu, T and Li, Z and Zhang, Y and Yuan, H and Zhang, C},
title = {High-fiber diet altered gut microbiota, improved glycemic control, and reduced body weight in newly diagnosed type 2 diabetes and obesity.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1972983},
doi = {10.3389/fmicb.2026.1972983},
pmid = {42890753},
issn = {1664-302X},
abstract = {Type 2 diabetes and obesity commonly coexist, making glycemia and body weight both central treatment goals. Few trials have directly compared a high-fiber dietary intervention with metformin. The factors associated with individual responses to high-fiber diet also remain unclear. In this single-center, open-label, head-to-head clinical trial, 48 adults with newly diagnosed type 2 diabetes and overweight or obesity were randomized to a high-fiber dietary intervention without glucose-lowering medication (n = 36) or metformin (n = 12) monotherapy for 84 days; 46 completed the trial. Clinical outcomes and 184 fecal samples were assessed longitudinally using shotgun metagenomic and metabolite profiling. At Day 84, the high-fiber group had greater reductions in glycated hemoglobin and body mass index and lower glycemic variability than the metformin group. The diet altered gut microbiota by Day 28, enriching genomes from Bifidobacterium and Lactobacillus and depleting genomes from Bilophila wadsworthia, but metformin produced little detectable microbiota change. These changes included increased acetate-production functions and decreased hydrogen sulfide-production functions; fecal hydrogen sulfide was lower at Days 28 and 56, although short-chain fatty acid concentrations did not differ between groups at matched time points. Within the high-fiber group, participants with increased fecal acetate (25 of 34) had larger glycated hemoglobin reductions at Days 28 and 56, and baseline microbial features differed between acetate-response subgroups. These findings support high-fiber diet as a non-pharmacologic strategy for diabesity, with baseline microbial features as candidate markers of response. Clinical trial registration: ChiCTR-INR-17011752.},
}

@article {pmid42890803,
year = {2026},
author = {Yang, Y and Yang, J and Zhang, W and Zhou, L and Zhu, C and Zhang, X and Mao, Y and Zhang, M},
title = {Host-microbiota interaction drives 5-hydroxyindole-3-acetic acid production to promote linear growth in infant mice.},
journal = {iMetaOmics},
volume = {3},
number = {1},
pages = {e70062},
doi = {10.1002/imo2.70062},
pmid = {42890803},
issn = {2996-9514},
abstract = {This study discovered that Lactiplantibacillus plantarum Hi188 promoted linear growth in postweaning mice. Transcriptomic analysis, untargeted metabolomics, and in vitro experiments showed that the elevated levels of 5-hydroxyindole-3-acetic acid (5-HIAA) activated the hepatic aryl hydrocarbon receptor (AhR) and subsequently promoted insulin-like growth factor-1 (IGF-1) production via the IRS1/PI3K/Akt pathway. Integrated metagenomics and reverse transcription quantitative polymerase chain reaction (RT-qPCR) analysis of host colonic genes revealed that 5-HIAA was cooperatively produced by the gut microbiota and the host. These findings offered novel perspectives on the therapeutic potential of microbiota-targeted interventions for growth regulation.},
}

@article {pmid42890805,
year = {2026},
author = {Coche-Miranda, J and Arros, P and Canales, N and Berríos-Pastén, C and Azziz, G and Lagos, R and Orlando, J and Chávez, FP and Marcoleta, AE},
title = {Antarctic soil microbiomes encode structurally conserved and phylogenetically diverse beta-lactamases.},
journal = {iMetaOmics},
volume = {3},
number = {3},
pages = {e70118},
doi = {10.1002/imo2.70118},
pmid = {42890805},
issn = {2996-9514},
abstract = {Antimicrobial resistance is a major global health threat shaped not only by clinical settings but also by environmental reservoirs, in line with the One Health framework. Antarctic and Subantarctic soils represent a largely unexplored component of the environmental resistome, particularly beta-lactamases, whose diversity, structural features, and biogeographic patterns remain poorly resolved. Here, we applied an integrative metagenomic approach combining sequence-, structure-, and function-based similarity to systematically identify putative beta-lactamase orthologs across an extensive collection of Antarctic and Subantarctic soil metagenomes. We detected multiple beta-lactamase classes and families, with a predominance of class A serine beta-lactamases and subclass B3 metallo-beta-lactamases. Several previously uncharacterized families and divergent variants were identified, many of which retain conserved catalytic architectures. Beta-lactamase diversity and relative abundance were strongly patterned across three major biogeographic clusters: Subantarctic islands, the Antarctic Peninsula and surrounding islands, and continental cold deserts, mirroring shifts in microbial community composition. The Antarctic Peninsula and maritime Antarctica exhibited the highest overall beta-lactamase abundance. Analysis of more than 3500 metagenome-assembled genomes indicated that most beta-lactamases were encoded by members of p_Pseudomonadota and p_Bacteroidota, with additional representatives distributed across other bacterial phyla. A subset was linked to mobile genetic elements, suggesting a latent but limited potential for horizontal gene transfer. Together, these findings reveal a geographically organized and compositionally diverse repertoire of beta-lactamases in (sub)Antarctic soils, underscoring the evolutionary persistence of conserved catalytic frameworks in cold environments and highlighting the contribution of remote ecosystems to global resistome diversity.},
}

@article {pmid42890814,
year = {2026},
author = {Chen, P and Taylor, JW and Gao, C},
title = {Arbuscular mycorrhizal fungal community abundance, functions, and symbiotic interactions revealed by root metatranscriptomes.},
journal = {iMetaOmics},
volume = {3},
number = {2},
pages = {e70087},
doi = {10.1002/imo2.70087},
pmid = {42890814},
issn = {2996-9514},
abstract = {Arbuscular mycorrhizal (AM) fungal communities are often profiled by metabarcoding, but this approach can bias abundance estimates and provide limited insight into community function and interactions with the host. Here, using weekly, field-based multi-omics, we find metatranscriptomes and metagenomes increase estimates of AM fungal relative abundance 6-15-fold over rDNA metabarcoding and that root AM fungal relative abundance correlates strongly with sorghum forage yield (R > 0.9) and moderately with grain yield/quality. AM fungal relative abundance is impacted directly by sorghum development and indirectly by drought via suppressed sorghum fatty acid gene expression. Gene co-expression network revealed coordinated plant and AM fungal functions in structural reorganization, resource exchange, and signal communication between the symbiotic partners. We found that early-season co-transcriptions of AM fungal and host genes feature cytoskeletal genes essential for arbuscule formation, the fungal-plant organs of nutrient and mineral exchange. Late-season plants downregulate cytoskeletal genes, but AM fungi continue their upregulation, which is associated with fungal sporulation and putative mating. Our study identifies previously ignored massive underestimation of AM fungal relative abundance, highlights the predictive role of AM fungal relative abundance for crop productivity, and uncovers symbiotic life history dynamics underpinned by coupled and decoupled co-expression of plant and AM fungal genes.},
}

@article {pmid42890823,
year = {2026},
author = {Han, Y and Peng, Y and Li, M and Wei, X and Chai, J and Zhao, J and Li, Y and Deng, F},
title = {Evidence tiers for strain-resolved long-read metagenomics.},
journal = {iMetaOmics},
volume = {3},
number = {3},
pages = {e70130},
doi = {10.1002/imo2.70130},
pmid = {42890823},
issn = {2996-9514},
abstract = {Long-read metagenomics links variants, repeats, and mobile elements across individual molecules and can reveal lineage turnover that is obscured at the species level. The strength of the resulting inference, however, depends on the type and genomic span of the recovered linkage. We distinguish four evidence units-strain profiles, local haplotype blocks, genome-scale strain candidates, and host-linkage evidence-and describe the diagnostics appropriate to each. Confidence is reported separately as candidate, supported, or high confidence in context, based on read assignment, allele coherence, coverage continuity, boundary support, and independent confirmation. Ambiguous placement, contamination, consensus collapse, coverage breaks, reference bias, or unresolved linkage should prompt more conservative terminology. Aligning terms with the available evidence reduces overstatement in claims of strain reconstruction, host assignment, persistence, replacement, and engraftment, while making analyses easier to compare and review.},
}

@article {pmid42890888,
year = {2026},
author = {Bian, P and Han, B and Zhu, H and Zhou, Y and Qi, Z and Gao, W and Wang, Y and Chen, N},
title = {Effects of cultivation of herbaceous perennials on soil microbial community structure and nitrogen cycling functions.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1961532},
doi = {10.3389/fpls.2026.1961532},
pmid = {42890888},
issn = {1664-462X},
abstract = {This study aimed to elucidate the impacts of cultivating different herbaceous perennials on the rhizosphere microenvironment, nitrogen-cycling microbial communities, and functional genes in black soils of urban green spaces in Northeast China, thereby providing a scientific basis for rational urban plant configuration and interspecific differences in soil nutrient cycling. Focusing on five commonly utilized herbaceous perennials in Changchun (Lycopus lucidus [P-LL], Salvia japonica [P-SJ], Hemerocallis fulva [P-HF], Hosta ensata [P-HE], and Pseudolysimachion spicatum [P-PS]), this study integrated conventional physicochemical analyses, metagenomic sequencing, co-occurrence networks, and Random Forest modeling to analyze rhizosphere soil nutrient profiles, nitrogen-cycling microbial community structures, and key functional gene abundances after two years of continuous cultivation. Different floral treatments significantly altered rhizosphere nutrient status and microbial community composition. The P-LL treatment exhibited relatively higher contents of total nitrogen (TN), soil microbial biomass nitrogen (SMBN), available phosphorus, and available potassium, demonstrating a high-level soil multifunctionality index (SMI). The P-PS treatment showed higher available nitrogen and ammonium nitrogen but lower SMBN, accompanied by a higher relative abundance of Actinomycetota and the assembly of a microbial co-occurrence network with enhanced connectivity and robustness, indicating a potent organic nitrogen mineralization potential in its rhizosphere. The composition of nitrogen-cycling genes remained broadly stable across treatments, dominated by ammonia assimilation genes (glnA and gltB), with a relatively low abundance of denitrification genes (nirK). Multivariate and Random Forest analyses revealed that SMBN exerted the strongest positive regulatory effect on nitrogen-sensing genes (e.g., ntrY and ntrX), whereas TN, nitrate nitrogen (NO3 [-]-N), and available potassium (AK) emerged as the paramount direct drivers determining the abundance variations of core ammonia assimilation genes. Different herbaceous perennials shaped species-specific rhizosphere nutrient and microbial functional profiles. P-LL and P-PS exhibited superior comprehensive nutrient traits and potential nitrogen mineralization characteristics, respectively, making them excellent candidate species for urban green space configuration and future mixed-planting trials in cold regions.},
}

@article {pmid42890922,
year = {2026},
author = {Lee, DH and Kim, YS and Kim, DW and Kim, DS and Cha, CJ},
title = {Long-term spatiotemporal dynamics of β-lactamase resistome in the Han River, South Korea.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1903212},
doi = {10.3389/fmicb.2026.1903212},
pmid = {42890922},
issn = {1664-302X},
abstract = {The global dissemination of antimicrobial resistance, particularly resistance to widely prescribed β-lactam antibiotics, is a critical public health threat worldwide. Aquatic ecosystems act as key reservoirs where antibiotic resistance genes accumulate and are transmitted between environmental bacteria and human pathogens within a One Health framework. To move beyond short-term observations and better understand these cross-sectoral dynamics, we conducted 5-year longitudinal surveillance using shotgun metagenomics across different seasons along the Han River, South Korea. Our analysis revealed a diverse repertoire of β-lactamases, predominantly belonging to Ambler classes A and D, which also accounted for most mobile β-lactamase genes and were enriched in densely populated downstream regions. Furthermore, β-lactamase genes exhibited clear seasonal fluctuations, with a pronounced winter surge in total and mobile β-lactamase gene abundances. We also identified a substantial fraction of novel variants, whose abundance and composition varied across spatial and seasonal gradients. Network analysis revealed that the genera Pseudomonas and Klebsiella acted as primary hosts, with their mobile β-lactamase genes highly connected to multiple taxa, suggesting important roles in β-lactamase gene transmission. These findings suggest that preemptive management of aquatic β-lactamase genes is a fundamental strategy for mitigating future resistance crises within a One Health framework and provide critical evidence for identifying transmission pathways and tracking resistance evolution between natural and clinical environments.},
}