@article {pmid41436515,
year = {2025},
author = {Algarni, AD and Abd El-Samie, FE and Soliman, NF and Emara, HM and Algarni, F and Abd-Alhalem, SM and Marie, HS},
title = {Exploiting fuzzy weights in CNN model-based taxonomic classification of 500-bp sequence bacterial dataset.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {44733},
pmid = {41436515},
issn = {2045-2322},
mesh = {Datasets as Topic ; *Fuzzy Logic ; *Convolutional Neural Networks ; DNA, Bacterial/genetics ; *Bacteria/classification/genetics ; Deep Learning ; RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; *Computational Biology/methods ; },
abstract = {Taxonomic classification plays a crucial role in understanding the diversity and evolutionary relationships among bacteria. Accurately classifying bacterial DNA sequences based on a limited 500-bp segment remains challenging. This paper presents an improved Fuzzy-weighted Convolutional Neural Network (F-CNN) for taxonomic classification of bacterial DNA sequences, specifically focusing on the 500-bp segments. The proposed model aims to overcome the limitations of traditional classification methods by leveraging the power of deep learning and fuzzy logic processing. The improved fuzzy deep learning model is proposed to handle the problem of classifying samples with similar probabilities in the classification layer. It incorporates a feature selection stage using various techniques and a fuzzy weighting system to handle the uncertainty associated with similar classes in the classification layer and optimize parameters using fuzzy weights. The experimental results on the Ribosomal Database Project Release 11 (RDP 11) sequences dataset show the superiority of the proposed model, especially at the 500-bp region. Experimental results on the RDP 11 dataset, which includes over 1.4 million bacterial gene sequences, demonstrate the superior performance of the proposed model, achieving a classification accuracy up to 84.03% at the genus level for 500-bp segments and demonstrating high generalization when applied to longer sequences. This paper has significant implications for various fields, including microbiology, epidemiology, and environmental science, where accurate classification of bacteria is crucial for understanding their roles in different ecosystems and disease outbreaks.},
}

Datasets as Topic
*Fuzzy Logic
*Convolutional Neural Networks
DNA, Bacterial/genetics
*Bacteria/classification/genetics
Deep Learning
RNA, Ribosomal, 16S/genetics
*Metagenomics/methods
*Computational Biology/methods

@article {pmid42036837,
year = {2026},
author = {Yancey, CE and Brumfield, KD and Buss, JA and Colwell, RR and Ettwiller, L},
title = {A Bait-and-Switch Strategy Links Phenotypes to Genes Coding for Polymer-Degrading Enzymes in Intact Microbiomes.},
journal = {Microbial biotechnology},
volume = {19},
number = {4},
pages = {e70359},
doi = {10.1111/1751-7915.70359},
pmid = {42036837},
issn = {1751-7915},
support = {//New England Biolabs/ ; OCE1839171//National Science Foundation/ ; CCF1918749//National Science Foundation/ ; CBET1751854//National Science Foundation/ ; R01ES030317A/ES/NIEHS NIH HHS/United States ; 80NSSC20K0814/NASA/NASA/United States ; 80NSSC22K1044/NASA/NASA/United States ; },
mesh = {*Microbiota ; *Chitin/metabolism ; Soil Microbiology ; *Bacteria/enzymology/genetics/classification ; Phenotype ; Chitinases/genetics/metabolism ; Genetic Association Studies ; },
abstract = {Natural microbial communities, with their vast diversity and complexity, are among the richest sources of untapped novel enzymes. Identifying novel enzymes can be challenging because microbiomes often lack clear, measurable phenotypes, unlike laboratory cultures where enzymatic activity can be linked to genetic elements. These constraints have left much of the functional diversity within microbiomes inaccessible to enzyme discovery efforts. Here, we present a genotype/phenotype association framework directly on microbial communities for enzyme discovery. For this, we developed a 'bait-and-switch' treatment strategy that generates measurable dual phenotypes directly within intact microbiomes. Using soil microbiomes as a test system, we applied chitin-rich compost as 'bait' to enrich chitin-degrading organisms, followed by glucose addition to functionally 'switch' the community. This treatment produced a distinct phenotypic signature: prevalence of known chitin degradation genes increases during the bait phase, and their transcripts are rapidly downregulated during the switch phase. By performing hypothesis-free association analysis of protein domains with this dual phenotype, we identified the glycoside hydrolase 18 as the most significantly associated protein domain. Experimental validation confirmed chitinase activity in 63% of tested enzymes, including candidates from unculturable bacteria and those with previously uncharacterized domain architectures. This species-independent, reference-free approach to discover novel enzymes has broad applications in microbiome engineering, biopolymer processing and systems biology, offering a generalizable strategy for functional gene discovery in complex microbial systems.},
}

*Microbiota
*Chitin/metabolism
Soil Microbiology
*Bacteria/enzymology/genetics/classification
Phenotype
Chitinases/genetics/metabolism
Genetic Association Studies

@article {pmid42037322,
year = {2026},
author = {Thouvenot, K and Serrat, F and Lenclume, V and Doussiet, E and Belda, E and Taïlé, J and Alili, R and Rondeau, P and Clément, K and Meilhac, O and Le Moullec, N and Gonthier, MP},
title = {Periodontitis in Patients With Severe Obesity: From the Oral and Gut Microbiota Dysregulation to the Visceral Adipose Tissue Inflammatory and Metabolic Disorders.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {40},
number = {9},
pages = {e71828},
doi = {10.1096/fj.202600054R},
pmid = {42037322},
issn = {1530-6860},
support = {APIDOM-BACTERIOB//CHU de La Réunion/ ; //Institut National de la Santé et de la Recherche Médicale (Inserm)/ ; //University of La Réunion/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Periodontitis/microbiology/metabolism/complications/pathology ; Male ; Female ; *Intra-Abdominal Fat/metabolism/pathology ; Middle Aged ; Adult ; *Obesity, Morbid/microbiology/complications/metabolism ; *Inflammation/metabolism/microbiology/pathology ; *Metabolic Diseases/microbiology/metabolism ; Dysbiosis/microbiology ; Porphyromonas gingivalis ; *Mouth/microbiology ; },
abstract = {During periodontitis, pathogenic oral bacteria like Porphyromonas gingivalis may exert systemic effects directly by translocating into the bloodstream and indirectly by deregulating the gut microbiota, aggravating obesity-related complications. This study aimed to evaluate the links between the periodontal infection, the oral and gut microbiota composition, and the inflammatory and metabolic profile during obesity. Thirty-nine patients suffering from severe obesity, with (n = 23) or without (n = 16) periodontitis, were enrolled. We examined the subgingival microbiota composition, periodontal status and salivary inflammatory response. The fecal microbiota composition was assessed by metagenomic analysis. Inflammatory and metabolic markers were measured in the plasma and epiploon visceral adipose tissue collected during bariatric surgery. Results show that patients with periodontitis exhibited an oral microbiota dysbiosis characterized by an increased abundance of bacteria from the red and orange complexes, worsened periodontal parameters (plaque index, bleeding index, gingival recession, probing depth and clinical attachment level), and higher IL-6 salivary levels. In fecal samples of patients with periodontitis, a higher proportion of the Proteobacteria phylum and changes in functional profile of bacteria were detected. Periodontitis was also linked to higher circulating concentrations of anti-P. gingivalis IgG, total cholesterol and lipoprotein (a). Moreover, periodontitis was associated with an enhanced production of TLR2, MyD88 and TGFβ, as well as higher activities of SOD and catalase antioxidant enzymes in the adipose tissue. Overall, these findings demonstrate that during obesity, the periodontal infection correlates with deregulated oral and gut microbiota composition, higher levels of pro-inflammatory mediators, and altered markers of oxidative stress and lipid metabolism.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Periodontitis/microbiology/metabolism/complications/pathology
Male
Female
*Intra-Abdominal Fat/metabolism/pathology
Middle Aged
Adult
*Obesity, Morbid/microbiology/complications/metabolism
*Inflammation/metabolism/microbiology/pathology
*Metabolic Diseases/microbiology/metabolism
Dysbiosis/microbiology
Porphyromonas gingivalis
*Mouth/microbiology

@article {pmid42037351,
year = {2026},
author = {Chakraborty, S and Mukherjee, D and Sar, P},
title = {Genome-resolved insights into arsenic-impacted paddy soil and microcosm-derived microbiomes from West Bengal, India.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0005926},
doi = {10.1128/mra.00059-26},
pmid = {42037351},
issn = {2576-098X},
abstract = {This study reports 32 metagenome-assembled genomes (MAGs) reconstructed from arsenic (As)-impacted paddy soils of West Bengal, India, and microcosms from these soil samples. These MAGs, represented by 10 bacterial and 2 archaeal phyla, provided critical insights into the metabolic and biogeochemical potential of microbiomes in a highly As-impacted agroecosystem.},
}

@article {pmid42037384,
year = {2026},
author = {Yang, K and King, S and Marshak, A and D'Mello-Guyett, L and Grignard, L and Knee, J and Wong, G and Zhao, L and Lamaka, NG and Save, D and Gose, M and Myers, A and Trehan, I and Cumming, O and Stobaugh, H and Schwartz, DJ},
title = {Gut microbiome associations with acute malnutrition relapse in South Sudan.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0358725},
doi = {10.1128/spectrum.03587-25},
pmid = {42037384},
issn = {2165-0497},
abstract = {Severe acute malnutrition (SAM) is a leading cause of childhood morbidity and mortality that is defined by anthropometric measurements, weight-for-height z score, and mid-upper arm circumference (MUAC) falling significantly below healthy standards. While treatments for SAM and our understanding of this disease have advanced, children experiencing SAM frequently relapse to acute malnutrition (AM) following anthropometric recovery. Little is known about the contribution of the gut microbiome to AM relapse. We hypothesized that features of the gut microbiome, including microbial composition, antimicrobial resistance gene carriage, and predicted microbial functional pathways, of children discharged from treatment for uncomplicated SAM in South Sudan, may be associated with AM relapse at 1-month follow-up. Overall, broad microbiome profiles at discharge were not associated with AM relapse. We evaluated the associations of microbiome features with AM relapse 1-month post-recovery using mixed linear effect models. We identified associations between higher MUAC, which may be a proxy for future health trajectories, and increased Sutterella wadsworthensis and trimethoprim-resistant dihydrofolate reductase antimicrobial resistance genes. These findings suggest that the gut microbiome at discharge of children treated for uncomplicated SAM has limited predictive value as a standalone diagnostic tool for identifying relapse risk at 1 month.IMPORTANCESevere acute malnutrition (SAM) is a devastating illness that impacts the morbidity and mortality of millions of children worldwide. Community-based management of acute malnutrition (CMAM) is the standard of care in South Sudan and many other low-resource settings for children presenting with SAM. Despite this intervention, children treated for SAM under CMAM frequently relapse to acute malnutrition (AM) following treatment. With advancements in our understanding of malnutrition, there has been a strong and growing interest in developing microbiome-based strategies to treat, prevent, and predict relapse to AM following treatment for SAM. Our work characterizes gut microbiome features of children from a geographic area that is traditionally underrepresented in gut microbiome research and shows that in isolation, a child's gut microbiome at discharge likely holds low predictive value for relapse to AM post-CMAM treatment; however, we identified key microbes and microbial features meriting further research.},
}

@article {pmid42037401,
year = {2026},
author = {Wu, Q and Wu, D and Wang, J and Wang, H and Peng, J and Zhao, Y and Chen, J and Yuan, Q},
title = {Lytic viruses drive the decrease in polyphosphate-accumulating and phosphate-solubilizing potential of microbial communities with increasing reservoir age.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0248125},
doi = {10.1128/aem.02481-25},
pmid = {42037401},
issn = {1098-5336},
abstract = {River damming often leads to significant phosphorus enrichment in reservoir sediments and increases the risk of eutrophication with reservoir age. Microorganisms mediate critical steps of phosphorus cycling in ecosystems, and viruses are recognized as key regulators of microbial community structure and function. However, their influence on phosphorus-cycling microorganisms (PCMs) in freshwater environments remains poorly understood. In this study, surface sediment samples were collected from nine reservoirs (12-59 years old) of southwest China and analyzed using metagenomic and metatranscriptomic approaches to profile both PCMs and viral communities. The results demonstrated that the diversity of lytic viruses was the primary factor governing both shifts in the community stability of PCMs and the restructuring of P-cycling gene patterns with increasing reservoir age. Specifically, viral lysis reduced the relative abundance of dominant PCMs, thereby enhancing community diversity and stability. Concurrently, viral activity diminished PCMs' functional potential for phosphate solubilization and polyphosphate accumulation, while stimulating high-affinity inorganic phosphate (Pi) transport. Furthermore, viruses encoded auxiliary metabolic genes (AMGs) related to phosphate solubilization, mineralization, accumulation, and transport, underscoring the viral role in regulating phosphorus retention and release. Compared to polyphosphate-accumulating microorganisms, phosphate-solubilizing microorganisms may be more susceptible to viral infection. Additionally, viral activity was associated with an increase in the relative abundance of Cyanobacteria. Taken together, our results suggest viruses are key regulators of PCMs, highlighting that they should be incorporated into future strategies for assessing and mitigating reservoir eutrophication.IMPORTANCESediment microorganisms are regarded as the engine for endogenous phosphorus release in reservoirs. Therefore, understanding their dynamics and key driving factors is essential for effective eutrophication mitigation. Viral lysis and virus-encoded auxiliary metabolic genes (AMGs) may constitute a critical yet understudied mechanism influencing microbial phosphorus cycling. Our study provides unique, time-series-based mechanistic insights into how viral activity, in the context of large-scale artificial projects (river damming), restructures microbial phosphorus cycling and its potential ecological effects over decades.},
}

@article {pmid42037579,
year = {2026},
author = {Virtuoso, FAS and Boekhorst, J and van Ravenstein, S and Schouten, D and Juanpere-Borràs, M and Broekhuis, F and Vissia, S and Mazebedi, R and Araldi, A and van Langevelde, F},
title = {DIY: A Practical Field-to-Sequencer Workflow for Metabarcoding the Diet of Terrestrial Carnivore Species.},
journal = {Molecular ecology resources},
volume = {26},
number = {4},
pages = {e70144},
doi = {10.1111/1755-0998.70144},
pmid = {42037579},
issn = {1755-0998},
support = {//Wageningen University and Research/ ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; Feces/chemistry ; *Diet ; *Carnivora/physiology/classification ; Workflow ; *Metagenomics/methods ; },
abstract = {Metabarcoding of faecal samples is a powerful, non-invasive approach for investigating the feeding ecology of carnivores, revealing prey diversity and unexpected dietary components with greater resolution than traditional methods. However, the approach remains technically demanding, as challenges and potential biases arise at every stage, from scat collection and DNA extraction to primer selection, sequencing, and data interpretation. Methodological details for these steps are often scattered across studies, limiting reproducibility and accessibility for ecologists. Here, we present a comprehensive field-to-sequencer workflow for dietary metabarcoding of terrestrial carnivores using Oxford Nanopore Technologies (ONT), covering all stages from sample collection to ecological interpretation. Drawing on field-collected scats of brown (Parahyaena brunnea) and spotted hyenas (Crocuta crocuta) across arid and semi-arid savannas in Botswana, we illustrate practical decisions, technical considerations, and common pitfalls encountered throughout the process. By integrating field, laboratory, and bioinformatic components into a single, accessible framework, this paper provides a pragmatic reference for ecologists aiming to design robust, transparent, and comparable studies of carnivore diet composition.},
}

Animals
*DNA Barcoding, Taxonomic/methods
Feces/chemistry
*Diet
*Carnivora/physiology/classification
Workflow
*Metagenomics/methods

@article {pmid42038227,
year = {2026},
author = {Fu, L and Zhang, Y and Wang, L and Li, X},
title = {Primary amoebic meningoencephalitis caused by Naegleria fowleri in a 6-year-old girl: case report.},
journal = {Frontiers in pediatrics},
volume = {14},
number = {},
pages = {1801355},
pmid = {42038227},
issn = {2296-2360},
abstract = {BACKGROUND: Primary amoebic meningoencephalitis (PAM) is caused by Naegleria fowleri, a rare but highly fatal central nervous system infection with a mortality rate exceeding 95%. Early diagnosis is challenging due to the close similarity of its clinical manifestations and cerebrospinal fluid (CSF) findings to those of acute bacterial meningitis. Metagenomic next-generation sequencing (mNGS) has become a vital tool for identifying rare or unexpected pathogens.

CASE PRESENTATION: A previously healthy 6-year-old girl was admitted with fever, vomiting, and headache of 1 day's duration. Six days before symptom onset, she had played in natural freshwater bodies. After admission, she developed persistent high fever and rapidly progressive altered mental status, followed by two episodes of generalized tonic-clonic seizures, hemoptysis, acute respiratory failure, and circulatory shock. Initial cranial magnetic resonance imaging showed no abnormalities. CSF analysis revealed marked inflammatory changes: a white blood cell count of 3,072 × 10[6]/L, markedly elevated protein (3,667.6 mg/L), and significantly decreased glucose (0.08 mmol/L). Despite administration of broad-spectrum antibiotics, glucocorticoids, osmotherapy, and comprehensive intensive care unit management, the patient died approximately 11 h after admission following three cardiac arrests. Two days postmortem, CSF mNGS confirmed infection with Naegleria fowleri (copy number 3 × 10[5] copies/mL), establishing the diagnosis of PAM.

CONCLUSIONS: This pediatric case serves as a warning that PAM should be considered in children with a history of freshwater exposure and rapidly progressive meningoencephalitis, even when early imaging is normal and CSF findings resemble bacterial meningitis. Early lumbar puncture, rapid molecular diagnostics, and heightened clinician vigilance are critical for the timely initiation of targeted therapy.},
}

@article {pmid42038247,
year = {2026},
author = {Li, X and Jiang, Y and Dai, R and Yang, Y and Wang, W},
title = {Rickettsia felis meningoencephalitis in a child: a case report and literature review.},
journal = {Frontiers in pediatrics},
volume = {14},
number = {},
pages = {1763281},
pmid = {42038247},
issn = {2296-2360},
abstract = {Rickettsia felis (R. felis) infection occasionally invades the central nervous system, causing encephalitis or meningoencephalitis. Although the disease typically presents as mild to moderate illness, delayed diagnosis and treatment may increase the risk of adverse prognosis in pediatric patients. This article reports a case of R. felis meningoencephalitis in a child diagnosed by metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid. mNGS analysis detected high-confidence R. felis-specific sequences, and potential background microbial contamination was effectively excluded through a bioinformatics pipeline, thereby providing critical evidence for etiological confirmation. Due to insufficient clinical awareness, limited pathogen detection methods, and the self-limiting nature of the disease, R. felis infection is prone to missed diagnosis and misdiagnosis in febrile children. The clinical manifestations are nonspecific; even with central nervous system involvement, routine laboratory tests are unlikely to suggest the microbial etiology, contributing to the underrecognition and underreporting of pediatric R. felis meningoencephalitis. Therefore, enhancing diagnostic awareness and achieving early precise diagnosis and treatment may help shorten the disease course and improve patient outcomes.},
}

@article {pmid42038299,
year = {2026},
author = {Liu, HJ and Wang, LF and Li, XY and Li, L},
title = {Toxicity-guided dose modification for disseminated Nocardia farcinica brain abscess in a patient with pneumoconiosis: a brief research report.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1805920},
pmid = {42038299},
issn = {1663-9812},
abstract = {BACKGROUND: Optimal antimicrobial strategies for disseminated nocardiosis with central nervous system (CNS) involvement remain poorly defined, particularly regarding trimethoprim-sulfamethoxazole (TMP-SMX) dosing in immunocompromised patients with severe drug intolerance.

METHODS: This observational case study analyzed the clinical course and pharmacological management of a 55-year-old male gold miner with pneumoconiosis and chronic corticosteroid use who developed Nocardia farcinica brain abscess. Diagnosis was established via metagenomic next-generation sequencing (mNGS) and phenotypic culture. An individualized antimicrobial regimen was designed based on toxicity monitoring.

RESULTS: Diagnosis of N. farcinica was confirmed by mNGS within 48 h. The patient initially failed empirical meropenem but responded to combination therapy with imipenem, amikacin, and TMP-SMX. Due to grade III gastrointestinal toxicity (CTCAE v5.0), TMP-SMX was de-escalated from 15 mg·kg[-1]·d[-1]-11.25 mg·kg[-1]·d[-1], with maintenance at 7.5 mg·kg[-1]·d[-1]. Clinical improvement was observed at Day 120, though durable cure remains unconfirmed.

CONCLUSION: In extreme circumstances of severe dose-limiting toxicity, temporary TMP-SMX dose reduction with intensive monitoring may be feasible as a bridge to complete guideline-concordant therapy, though this approach falls below current recommendations and requires robust therapeutic drug monitoring. Species-directed antimicrobial selection and early molecular diagnosis facilitated initial clinical resolution in this high-risk immunocompromised host.},
}

@article {pmid42038409,
year = {2026},
author = {Nousias, O and Duffy, FG and Duffy, IJ and McCauley, M and Whilde, J and Duffy, DJ},
title = {Long-read nanopore shotgun metagenomic DNA sequencing for river biodiversity, wildlife, pollution, and environmental health monitoring.},
journal = {NAR genomics and bioinformatics},
volume = {8},
number = {2},
pages = {lqag040},
pmid = {42038409},
issn = {2631-9268},
mesh = {Animals ; *Rivers/microbiology ; *Biodiversity ; *Metagenomics/methods ; *Environmental Monitoring/methods ; Humans ; *Nanopore Sequencing/methods ; DNA, Environmental/genetics ; Environmental Health ; Animals, Wild/genetics ; Metagenome ; },
abstract = {As the human population expands and global temperatures rise, species, populations, and biodiversity decline at unprecedented rates, while the frequency of infectious disease emergence increases. Therefore, it is more vital than ever to accurately understand the current state of natural habitats and their constituent species. We assess the feasibility of a single assay: long-read shotgun metagenomic sequencing of environmental DNA (eDNA), to monitor species from across the tree of life, from viruses to complex multicellular organisms, across a representative Irish river system (Avoca River, Co. Wicklow). We conducted aquatic eDNA sampling and long-read shotgun metagenomic sequencing from a mountain tributary through to the sea. This approach could detect and quantify organismal DNA present in environmental samples, from microbes (including DNA viruses) to mammals. Rather than the traditional siloing of microbial and multicellular studies of DNA recovered from environmental samples, simultaneously considering viruses, microbes, and eukaryotes (animals, plants, and fungi) can provide deeper insights. This single assay can simultaneously quantify differences in DNA abundance for a broad range of species and pathogens across sites and sample types, enabling wide-ranging biodiversity assessments. This included human, wildlife, plant, and microbial pathogens and parasites with health, agricultural, and economic importance. The environmental genomic data enabled animal phylogeny and transmissible cancer analysis (blue mussel, Mytilus edulis) even from natural complex community settings. Oxford Nanopore sequencing provides a quantitative approach for river biodiversity, pollution, and environmental health monitoring. Long-read shotgun metagenomic sequencing of environmental samples offers the means to assess whole ecosystems and the ecological, trophic, and host-pathogen interactions occurring within them.},
}

Animals
*Rivers/microbiology
*Biodiversity
*Metagenomics/methods
*Environmental Monitoring/methods
Humans
*Nanopore Sequencing/methods
DNA, Environmental/genetics
Environmental Health
Animals, Wild/genetics
Metagenome

@article {pmid42038418,
year = {2026},
author = {Vlasovets, O and Schaipp, F and Simpson, L and Bolyen, E and Caporaso, JG and Mueller, CL},
title = {Sparse regression, classification, and microbial network estimation in QIIME2 with q2-classo and q2-gglasso.},
journal = {ArXiv},
volume = {},
number = {},
pages = {},
pmid = {42038418},
issn = {2331-8422},
abstract = {MOTIVATION: Statistical analysis of microbial count data derived from 16S rRNA or metagenomics sequencing poses unique challenges due to the sparse, compositional, and high-dimensional nature of the data. While QIIME 2 already provides many tools for data pre-processing and analysis, plugins for statistical regression, classification, and microbial network estimation tailored to compositional count data are relatively scarce.

RESULTS: We present q2-classo and q2-gglasso, two novel QIIME 2 plugins that implement penalized regression, classification, and graphical modeling approaches for microbial compositional data. q2-classo enables the prediction of a continuous or binary outcome of interest using compositional microbiome data as predictors. Both sparse log-contrast regression and classification, as well as tree-aggregated log-contrast models are available. q2-gglasso enables the estimation of taxon-taxon association networks through sparse graphical model estimation, such as, e.g., the SPIEC-EASI framework, as well as adaptive and latent graphical models. The latent model can decompose taxon-taxon associations into a sparse direct interaction matrix and a latent (low-rank) matrix which enables robust principal component embedding of a data set. Within the QIIME 2 ecosystem we demonstrate their application on the Atacama soil microbiome dataset, illustrating robust model selection, classification, and microbial network estimation with covariates and latent factors.

AVAILABILITY: The software is freely available under the BSD-3-Clause License. Source code is available at https://github.com/bio-datascience/q2-gglasso and https://github.com/bio-datascience/q2-classo-latest, with installation through QIIME 2 and Docker.},
}

@article {pmid42038553,
year = {2026},
author = {Rodríguez-Rodríguez, Y and Disla, AMM and Ortega, MER and Gandini, G and Tejada-Tejada, P and Guevara, MÁ and Franco, EF and Dantas, CWD and Ramos, RT and Jáuregui-Haza, UJ},
title = {Microbial Profiling and Biosafety Assessment of a Sargassum-Based Liquid Biofertilizer Using 16S rRNA Metagenomics.},
journal = {International journal of microbiology},
volume = {2026},
number = {},
pages = {3219583},
pmid = {42038553},
issn = {1687-918X},
abstract = {Sargassum seaweed is increasingly abundant in the Caribbean, creating ecological disruption but also providing biomass for agricultural inputs. This study compares the microbial diversity and safety of a Sargassum-based liquid biofertilizer (SBLB-INTEC) with those of a conventional product (LB-BANELINO) using 16S rRNA amplicon sequencing, rather than culture-dependent methods. Both formulations contained key nutrients (K, Ca, and Mg) and low levels of heavy metals. They harbored dense but relatively simple bacterial communities dominated by Firmicutes, particularly Bacilli, with Proteobacteria and other phyla at lower abundances. Staphylococcus (Staphylococcaceae) was highly abundant in both products, while SBLB-INTEC showed a somewhat more balanced community, including Delftia and other Comamonadaceae. Shannon diversity tended to be higher in SBLB-INTEC, but differences in alpha- and beta-diversity between formulations were not statistically significant. Because 16S data cannot distinguish viable from nonviable cells or resolve strain-level pathogenicity, these results do not prove the absence of pathogens; instead, they provide a genus-level baseline to guide targeted culture, qPCR, and functional assays. Overall, the combination of a favorable chemical profile and microbial groups commonly associated with nutrient cycling and plant-associated functions suggests that SBLB-INTEC could become a valuable component of integrated nutrient management in tropical agriculture, offering hope for a more sustainable future pending confirmatory plant-response and biosafety studies. We recommend integrating these microbial data into a national biofertilizer monitoring framework, combining metagenomic surveys with targeted qPCR and resistance gene screening.},
}

@article {pmid42038636,
year = {2026},
author = {Ryder, JH and Turbett, SE},
title = {Mindful diagnostics: a central nervous system infection case study.},
journal = {Antimicrobial stewardship & healthcare epidemiology : ASHE},
volume = {6},
number = {1},
pages = {e96},
pmid = {42038636},
issn = {2732-494X},
abstract = {A clinical case is presented to discuss a framework for use of advanced diagnostics for central nervous system infections. Advantages, limitations, and diagnostic stewardship strategies are discussed for each modality: multiplex molecular meningitis/encephalitis panel, plasma microbial cell-free DNA sequencing, and cerebrospinal fluid metagenomic next generation sequencing.},
}

@article {pmid42039195,
year = {2026},
author = {Liu, Y and Liao, X and Chen, Q and Wang, H and Dai, H},
title = {What is the impact of the virome and mycobiome on female reproductive tract health? A systematic scoping review.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1749584},
pmid = {42039195},
issn = {1664-3224},
mesh = {Female ; Humans ; *Virome ; *Mycobiome ; *Vaginosis, Bacterial/microbiology/virology ; *Microbiota ; Papillomavirus Infections/microbiology/virology ; Vagina/microbiology/virology ; *Reproductive Health ; *Genitalia, Female/microbiology/virology ; Bacteriophages ; },
abstract = {BACKGROUND: Traditional research on the female reproductive tract (FRT) microbiome has focused on the dominance of bacteria, particularly Lactobacillus, as a marker of health. This bacteriocentric paradigm, however, cannot fully explain clinical enigmas like the high recurrence of bacterial vaginosis (BV) or the persistence of HPV infection. This review introduces a new pan-microbiome framework that highlights the overlooked roles of the virome and mycobiome as the ecosystem's neglected components.

METHODS: We conducted a systematic scoping review following the PRISMA-ScR guidelines. We searched PubMed, Embase, and Web of Science databases for studies published up to October 2025. Inclusion criteria focused on original research and metagenomic studies examining the female reproductive tract (FRT) virome, mycobiome, and bacteriome, specifically their interactions and clinical associations with bacterial vaginosis (BV) and HPV persistence. Data were extracted and synthesized to evaluate the pan-microbiome framework.

RESULTS: The virome and mycobiome, despite their low biomass, are increasingly recognized as potential ecosystem modulators. Bacteriophages, for instance, are proposed to act as community "modulators," either through lytic cycles that maintain bacterial diversity or lysogenic cycles that may contribute to stabilizing pathogenic biofilms in dysbiosis like BV by introducing virulence genes. Similarly, fungi like Candida can transition from harmless commensals to pathogens when the protective bacterial balance is disturbed.

CONCLUSION: FRT health is an emergent property of the complex interactions among bacteria, viruses, and fungi. A comprehensive understanding requires a pan-microbiome perspective. Future therapeutic strategies should move beyond a "one-bug, one-drug" approach toward "ecosystem restoration," using targeted methods like phage therapy or vaginal microbiota transplantation to attempt to restore the balance of the entire microbial community.},
}

Female
Humans
*Virome
*Mycobiome
*Vaginosis, Bacterial/microbiology/virology
*Microbiota
Papillomavirus Infections/microbiology/virology
Vagina/microbiology/virology
*Reproductive Health
*Genitalia, Female/microbiology/virology
Bacteriophages

@article {pmid42039480,
year = {2026},
author = {Liu, J and De Paolis Kaluza, MC and Bromberg, Y},
title = {16S rRNA k-mer composition encodes microbial functional potential.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.16.718937},
pmid = {42039480},
issn = {2692-8205},
abstract = {16S rRNA amplicon sequencing is widely used to profile microbiome taxonomic composition and functional potential. Most 16S rRNA-based analysis methods depend on comparing sequenced reads against reference marker genes from previously characterized organisms. Thus, method accuracy declines in environments dominated by uncharacterized microbes. We uncovered a direct link between 16S rRNA and genome-encoded functions. Using fully sequenced bacterial genomes, we show that (i) whole-genome k-mer composition is predictive of functions encoded in the genome and (ii) 16S rRNA k-mer profiles reflect their source genome k-mer compositions. Leveraging these relationships, we developed embeRNA, a neural network-based framework that predicts functions directly from 16S rRNA k-mer embeddings, without taxonomy assignment or phylogenetic placement. Furthermore, by producing per-function probability scores rather than categorical assignments, embeRNA allows users to adapt decision thresholds to match study goals and sample characteristics, e.g. balancing precision vs. recall or accounting for community novelty. We trained embeRNA on a large collection of bacterial function-omes and evaluated it using a stringent "novel microbes" benchmark, where all test 16S rRNA sequences were dissimilar to those seen in training (all <97% identical). On this test set of phylogenetically novel organisms, embeRNA outperformed reference-based methods overall and achieved significantly better performance for the "hard to label" set of functions. In testing on soil metagenomes with paired 16S rRNA amplicon and whole metagenome shotgun (WMS) sequencing data, embeRNA recovered most WMS-inferred functions and yielded abundance profiles strongly correlated with WMS results. Together, our results indicate that 16S rRNA k-mer composition carries substantial functional signal and that 16S amplicon data can be used to complement WMS-based inference to broaden functional characterization of microbiomes, particularly in understudied environments.},
}

@article {pmid42039609,
year = {2026},
author = {Maldonado Pereira, L and Mutawi, TMA and Singh, A and Sanderson, B and Rekowski, MJ and Barnaba, C and Medina Meza, IG},
title = {Dietary Oxysterols Reprogram Hepatic Lipid Metabolism and Reshape the Gut Metabolome-Microbiome Interface.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.12.717948},
pmid = {42039609},
issn = {2692-8205},
abstract = {Dietary oxysterols are biologically active cholesterol oxidation products ubiquitous in Western diets, yet their systemic effects on host metabolism and the gut microbiome remain largely unexplored. Here, we employed an integrated multi-omics approach - shotgun metagenomics, quantitative proteomics, untargeted metabolomics, and bulk RNA-seq - to characterize the impact of DOxS exposure on the gut-liver axis in rats fed a Western diet (WD vs. WD-DOxS). Hepatic proteomics revealed near-complete suppression of the mevalonate/cholesterol biosynthesis pathway, particularly in males, while de novo lipogenesis enzymes (Scd1, Fasn, Plin2) were paradoxically upregulated, consistent with dual oxysterol signaling through SREBP inhibition and LXR activation. Bile acid synthesis was concurrently suppressed, confirmed by metabolomics. Strikingly, RNA-seq across liver, heart, and brain detected virtually no differentially expressed genes, establishing that DOxS act predominantly through post-transcriptional mechanisms. In the gut, DOxS increased microbial α-diversity while depleting Limosilactobacillus reuteri, with concomitant loss of the barrier-protective metabolite 3-indoleacrylic acid. Tissue-specific responses were widespread, with liver and colon frequently mounting opposing metabolic and immune responses to the same dietary challenge. Cross-omics integration revealed convergent microbiome-metabolite axes connecting microbial remodeling to both hepatic lipid reprogramming and colonic barrier disruption. These findings reposition dietary oxysterols from food-quality markers to active modulators of the gut-liver axis, with implications for metabolic disease and intestinal barrier integrity.},
}

@article {pmid42039751,
year = {2026},
author = {Chen, XG and Zhou, L and Duan, K and Shi, SY and Subi, A and Sun, HW and Lu, YM and Hu, L and Yang, ZT},
title = {Integrative analysis of pathogen detection, antimicrobial resistance, virulence, and host response in severe infections using metagenomic next-generation sequencing.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1786413},
pmid = {42039751},
issn = {2235-2988},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Retrospective Studies ; Male ; Virulence Factors/genetics ; Female ; Middle Aged ; Virulence/genetics ; Aged ; Intensive Care Units ; *Bacteria/genetics/drug effects/pathogenicity/isolation & purification/classification ; *Drug Resistance, Bacterial/genetics ; *Bacterial Infections/microbiology/diagnosis ; *Host-Pathogen Interactions ; Anti-Bacterial Agents/pharmacology ; Adult ; },
abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) offers unbiased pathogen detection. However, its integrative value in simultaneously revealing resistance, virulence, and host-response interplay in Intensive Care Unit(ICU)-infected patients remains underexplored.

METHODS: In this retrospective cohort study of 156 ICU-infected patients, we compared the diagnostic performance of mNGS against conventional microbiological testing (CMT). We analyzed mNGS-derived antibiotic resistance genes (ARGs) and virulence factors (VFs) and correlated them with host immune-inflammatory markers and clinical outcomes.

RESULTS: mNGS demonstrated a significantly higher positive detection rate (89.7% vs. 67.3%, P < 0.001) and clinical concordance (75.6% vs. 35.9%, P < 0.001) than CMT. It revealed a high mixed-infection rate (72.1%). ARGs were detected in 49.0% of bacterial infections, predominantly β-lactamase genes, showing 72.0% concordance with phenotypic susceptibility. Key VFs (e.g., rmpA in K. pneumoniae) were identified. Based on mNGS results, 47.4% of patients had their antimicrobial therapy adjusted.

CONCLUSION: mNGS provides a comprehensive diagnostic tool by integrating pathogen identification, resistance and virulence profiling, and host-response context, enabling more precise and timely management of ICU-infected patients.},
}

Humans
*High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
Retrospective Studies
Male
Virulence Factors/genetics
Female
Middle Aged
Virulence/genetics
Aged
Intensive Care Units
*Bacteria/genetics/drug effects/pathogenicity/isolation & purification/classification
*Drug Resistance, Bacterial/genetics
*Bacterial Infections/microbiology/diagnosis
*Host-Pathogen Interactions
Anti-Bacterial Agents/pharmacology
Adult

@article {pmid42039753,
year = {2026},
author = {Li, X and Fang, J and Li, D and Cai, B and Yin, J and Zheng, Y and Yin, G},
title = {Performance evaluation of mNGS in pathogen diagnosis of skin and soft tissue infections and its optimization effect on antibiotic decision-making.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1771148},
pmid = {42039753},
issn = {2235-2988},
mesh = {Humans ; *Soft Tissue Infections/diagnosis/microbiology/drug therapy ; Retrospective Studies ; Male ; Female ; *Anti-Bacterial Agents/therapeutic use ; Middle Aged ; Adult ; *High-Throughput Nucleotide Sequencing/methods ; Antimicrobial Stewardship ; Aged ; *Metagenomics/methods ; *Bacteria/genetics/isolation & purification/classification/drug effects ; *Skin Diseases, Bacterial/diagnosis/microbiology/drug therapy ; Young Adult ; Coinfection/diagnosis/microbiology/drug therapy ; Adolescent ; Clinical Decision-Making ; },
abstract = {BACKGROUND: Skin and soft tissue infections (SSTIs), often caused by polymicrobial pathogens, pose diagnostic challenges due to the limitations of conventional methods, including low sensitivity and prolonged turnaround time. This diagnostic gap has perpetuated empirical antibiotic use in clinical practice. Metagenomic next-generation sequencing (mNGS), with its unbiased pathogen detection capability, offers a transformative approach for rapid and precise microbial identification in SSTIs.

OBJECTIVE: To evaluate the clinical utility of mNGS compared to conventional microbiological testing in guiding antibiotic stewardship for complex SSTIs.

METHODS: A retrospective cohort study was conducted at the First Affiliated Hospital of Zhengzhou University from April 2023 to May 2025, enrolling 69 patients with clinically diagnosed complex SSTIs. All patients underwent concurrent mNGS testing, conventional bacterial culture, and pathological examination. The diagnostic performance of mNGS was systematically compared with culture methods, with emphasis on culture-negative cases and polymicrobial infections. The impact of mNGS-guided antibiotic adjustments was assessed.

RESULTS: mNGS demonstrated significantly higher pathogen detection rates than conventional culture (P < 0.001), with a concordance of 37.5% between the two methods. Among 24 culture-negative patients, mNGS identified pathogens in 20 cases (83.3% detection rate). For polymicrobial infections (n = 20), culture detected pathogens in only 2 cases, whereas mNGS successfully identified multiple pathogens in the majority. Antibiotic therapy was adjusted based on mNGS results in 11.9% (8/69) of patients.

CONCLUSION: mNGS substantially improves pathogen detection in complex SSTIs compared to conventional methods. Beyond diagnostic accuracy, its clinical value lies in enabling targeted antibiotic therapy, thereby optimizing antimicrobial stewardship and potentially reducing healthcare costs.},
}

Humans
*Soft Tissue Infections/diagnosis/microbiology/drug therapy
Retrospective Studies
Male
Female
*Anti-Bacterial Agents/therapeutic use
Middle Aged
Adult
*High-Throughput Nucleotide Sequencing/methods
Antimicrobial Stewardship
Aged
*Metagenomics/methods
*Bacteria/genetics/isolation & purification/classification/drug effects
*Skin Diseases, Bacterial/diagnosis/microbiology/drug therapy
Young Adult
Coinfection/diagnosis/microbiology/drug therapy
Adolescent
Clinical Decision-Making

@article {pmid42039757,
year = {2026},
author = {Wu, Y and Zhang, J and Su, W and Zhang, Z},
title = {Global epidemiology of tick-borne Alpharhabdovirinae: a meta-analysis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1791903},
pmid = {42039757},
issn = {2235-2988},
mesh = {Animals ; Phylogeny ; *Ticks/virology ; Humans ; *Tick-Borne Diseases/epidemiology/virology ; Genome, Viral ; },
abstract = {INTRODUCTION: The Alpharhabdovirinae subfamily of the family Rhabdoviridae encompasses a diverse and expanding group of tick-borne viruses, some of which pose potential risks as emerging human pathogens. Despite increasing detection through metagenomic surveillance, the global diversity, phylogenetic relationships, and taxonomic framework of tick-borne Alpharhabdovirinae (TBA) remain poorly characterized.

METHODS: This study conducted a comprehensive meta-analysis of all publicly available TBA sequences based on phylogenetic analysis of five structural proteins (N, P, M, G, L), combined with host associations and geographic distributions.

RESULTS: 345 TBA strains were classified into 12 distinct phylogenetic clusters, each exhibiting unique evolutionary and ecological characteristics. These clusters include: (1) seven species-level lineages within the genus Alpharicinrhavirus, predominantly associated with Hyalomma and Haemaphysalis ticks across Eurasia; (2) a cluster related to Manly virus, widely distributed in Amblyomma, Haemaphysalis, and Rhipicephalus ticks acrossAustralia and China, exhibiting additional protein-coding genes of unknown function; (3) the genus Ledantevirus (21 species), characterized by broad host tropism including bats, rodents, and humans, with some members displaying phosphoprotein phylogenetic anomalies suggestive of recombination; (4) the genus Lostrhavirus, together with Tongliao Rhabd tick virus 1, forming a cluster associated with Hyalomma and Amblyomma ticks; (5) a Mononegavirus cluster comprising Alpharicinrhavirus heilongjiang, Alpharicinrhavirus skanevik (Norway mononegavirus 1), and Mononegavirales sp. specifically associated with Ixodesticks in Eurasia; and (6) one clusters with incomplete protein repertoires and uncertain taxonomic positions, including Tahe rhabdovirus 3 and Yanbian Rhabd tick virus 1 which lacks phosphoprotein entirely. This study provide a refined phylogenetic framework for TBA viruses, clarify their evolutionary relationships, and highlight critical knowledge gaps, including numerous uncharacterized hypothetical proteins and incomplete genomes that warrant further investigation.

DISCUSSION: This study underscores the importance of enhanced global surveillance and genomic characterization to assess the emergence potential and public health threat posed by this diverse group of tick-borne viruses.},
}

Animals
Phylogeny
*Ticks/virology
Humans
*Tick-Borne Diseases/epidemiology/virology
Genome, Viral

@article {pmid42039802,
year = {2026},
author = {Adhikary, K and Selim, S and Sarkar, R and Ganguly, K and Das, J and Almuhayawi, MS and Alruhaili, MH and Gattan, HS and Karak, P},
title = {Synthetic microbiomes in bioengineered rhizospheres: new frontiers for climate-resilient agriculture.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1780132},
pmid = {42039802},
issn = {1664-302X},
abstract = {Climate change poses significant threats to global agricultural productivity, necessitating innovative strategies to ensure food security and ecological sustainability. One promising avenue lies in the deliberate design and deployment of synthetic microbiomes and engineered rhizospheres to enhance plant resilience under environmental stress. This review places particular emphasis on multi-kingdom microbial interactions including bacteria, fungi, protists, and archaea and their potential for tailored, stress-specific applications within engineered rhizosphere systems. By integrating knowledge from microbial ecology, genomics, and systems biology, researchers have begun to unravel the complex interactions between plants and their associated microbial communities. Engineered microbial assemblies tailored to specific host plants and environmental conditions have shown potential in stabilizing crop performance during drought, salinity, and nutrient limitations. Moreover, the manipulation of root exudation patterns and soil physicochemical properties can be harnessed to recruit beneficial microbes and suppress harmful ones. The review also examines the role of synthetic biology tools, such as CRISPR-based genome editing and metabolic pathway engineering, in optimizing microbial traits for enhanced plant support. However, knowledge gaps remain in understanding multi-kingdom dynamics, optimizing SynComs for specific environmental contexts, and translating laboratory successes to reliable, field-scale applications. Additionally, advances in high-throughput screening, machine learning, and metagenomic profiling are accelerating the identification of key microbial taxa and functions relevant to plant health. Despite these promising developments, challenges remain in scaling these approaches for field applications and ensuring their ecological safety and consistency. This review explores the need for interdisciplinary efforts to translate laboratory insights into field-ready technologies, ultimately contributing to the development of climate-resilient and sustainable agricultural systems.},
}

@article {pmid42039826,
year = {2026},
author = {Gini, C and Tiezzi, F and Jiang, J and Byrd, MH and Wen, H and Johnson, JS and Brito, LF and van Vliet, S and Maltecca, C},
title = {Data-driven enterosignatures link gut microbiome reorganization to heat stress responses in lactating sows.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1797687},
pmid = {42039826},
issn = {1664-302X},
abstract = {BACKGROUND: Heat stress (HS) can disrupt the gut microbiome, yet most livestock studies rely on taxonomic summaries that overlook the ecological structure of microbial communities. Enterosignatures (ES) as latent, co-occurring microbial assemblages learned from metagenomic data, offer a framework to capture these dynamics but have scarcely been applied in livestock HS research.

METHODS: Shotgun metagenomes were obtained from 25 lactating sows, belonging to two genetic lines (TOL, n = 13; SEN, n = 12), which were divergently selected based on genomic breeding values (GEBVs) for heat tolerance, and exposed to HS conditions. Results were decomposed using non-negative matrix factorization (NMF), yielding 8 taxonomic (T-ES) and 5 functional (F-ES) subcommunities. Functional profiles (based on KEGG Orthology, KOs) were mapped to metagenome-assembled genomes (MAGs) to integrate metabolic attributes within each ES.

RESULTS: Temporal shifts dominated T-ES variation, with limited genetic-line effects. T-ES 1 (p = 5.42 × 10[-4], Cohen's d = 0.723) and T-ES 7 (p = 0.007, Cohen's d = 0.303) showed increases from day 4 to day 14. Despite modest overall genetic line effects, TOL animals progressively transitioned toward phylogenetically diverse and balanced communities, whereas SEN animals shifted toward imbalanced states characterized by enrichment of taxa with pathobiont potential or single-taxon dominance. Other T-ES displayed small to moderate effects, and T-ES 8 showed a potentially noteworthy genetic line-specific effect size at late lactation (Cohen's d = 0.960; 95% CI: -1.80 to -0.10), though omnibus tests were non-significant (p = 0.757), and the wide confidence interval underscores substantial uncertainty at this sample size. No F-ES reached statistical significance (p > 0.05); moderate effect sizes (up to d = 0.638) suggest possible functional restructuring warranting investigation in larger cohorts.

CONCLUSION: This work presents the first use of ES to track microbiome responses to HS in lactating sows. ES revealed latent taxonomic and functional subcommunities with clear temporal reorganization, offering insights not detectable with standard clustering or diversity metrics. Although genetic-line effects were modest, several ES showed biologically relevant shifts, supporting ES as a hypothesis-generating exploratory framework for linking microbial ecology to physiological adaptation under HS conditions, while warranting validation in larger, controlled trials.},
}

@article {pmid42039832,
year = {2026},
author = {Sola, L and Candeliere, F and Busi, E and Raimondi, S and Amaretti, A and Rossi, M},
title = {A genomic atlas of gut clostridia: phylogeny, butyrate, and propionate production.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1761627},
pmid = {42039832},
issn = {1664-302X},
abstract = {INTRODUCTION: Clostridia is a major microbial class in the human gut, crucial for fermenting undigested carbohydrates and proteins, which produce short-chain fatty acids essential for gut health and immune balance. This study revised the taxonomic classification and phylogeny of all the species of intestinal Clostridia catalogued in the Unified Human Gastrointestinal Genome database using a whole-genome approach and assessed butyrate and propionate producing species.

METHODS: A total of 1,897 Clostridia species, including those with recognised binomial nomenclature and those lacking formal taxonomic classification, were retrieved and reclassified using GTDB-Tk. Their phylogeny was determined by identifying, concatenating, and aligning the 120 ubiquitous single-copy proteins defined in the GTDB. Average amino acid identity (AAI), percentage of conserved proteins (POCP), and phylogenetic relationships were used to organize the species into genera and families. The presence of enzymes belonging to the biosynthetic pathways for butyrate and propionate production was investigated in all genomes with the tool GapSeq.

RESULTS: Reclassification of the genomes resulted in 404 recognised species and 1,493 species lacking formal taxonomic classification. Oscillospirales and Lachnospirales encompassed most of the species. The pathways leading to butyrate and propionate production were analyzed in their entirety, revealing 519 species as potential butyrate producers, 257 as potential propionate producers and 77 capable of producing both. To assess the abundance of each species, 151 faecal metagenomes of healthy subjects were profiled, indicating that butyrate producing Clostridia accounted on average for 28.0% of each microbiome.

CONCLUSIONS: This study offers a comprehensive overview of intestinal Clostridia diversity, emphasising their role in gut ecosystems and their potential for butyrate and propionate production.},
}

@article {pmid42040306,
year = {2026},
author = {Yang, R and Zhu, J and Zhang, Y and Liu, Y and Li, Z and Zhang, H and Li, Q and Wang, X and Chen, X and Chen, D and Liu, Q},
title = {Organic amendments boost maize yield (Zea mays L.) in karst soils via a hierarchical process driven by soil phosphorus enhancement and microbial-mediated nutrient cycling.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1782544},
pmid = {42040306},
issn = {1664-462X},
abstract = {INTRODUCTION: Sustainable food production in fragile karst landscapes requires moving beyond input-intensive agriculture.

METHODS: This study investigated how long-term organic amendments affected maize yield, using a 15-year field trial on karst yellow soil. Integrating soil analysis, metagenomics, and causal modeling, revealed that adding farmyard manure or bio-organic fertilizer to mineral NPK increased yield by 12.08% and 11.48%, respectively, and improved key soil properties, most notably available phosphorus.

RESULTS: Organic inputs shifted the soil microbiome toward copiotrophic taxa and enriched genes for organic matter decomposition and phosphorus mobilization. However, statistical modeling revealed that these biological changes did not directly drive yield. Instead, the primary pathway was hierarchical: amendments first enhanced the soil's chemical habitat, which then directly boosted crop growth while simultaneously shaping the microbial community and its functional potential. The interaction of soil, microbes, and genes together explained 81% of the yield variation.

DISCUSSION: Our findings demonstrate that in phosphorus-limited karst soils, organic amendments act foremost as soil conditioners. Microbial processes, though crucial, are secondary mediators that translate improved soil conditions into efficient nutrient cycling. Therefore, sustainable intensification in these vulnerable agroecosystems should prioritize managing soil health over directly targeting microbial processes.},
}

@article {pmid42040505,
year = {2026},
author = {Collado, C and Romero-Tena, P and Wegener, G and Elvert, M and Menapace, W and Laso-Pérez, R},
title = {Anaerobic oxidation of methane supports a minimal microbial community in a subsurface biofilm at Ginsburg mud volcano.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag072},
pmid = {42040505},
issn = {2730-6151},
abstract = {Deep marine sediments generate large amounts of methane, but most of this gas is consumed by the anaerobic oxidation of methane (AOM) mediated by microscopic consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). In this study, we investigated the AOM within a sulfate-methane transition zone (SMTZ) at a depth of ~9.6 m at the rim of the Ginsburg mud volcano in the Gulf of Cádiz. The SMTZ is supplied with sulfate from both overlying seawater and an underlying evaporitic deposit, and it coincides with a fracture zone that hosts a visible biofilm. Here, carbon dioxide shows the strongest [13]C-depletion, indicating intense methane consumption. Metagenomic and lipid biomarker analysis of the biofilm revealed an exceptionally simple microbial community dominated by ANME-1b archaea (63%), which predominantly produce strongly [13]C-depleted glycerol dialkyl glycerol tetraethers and, to a lesser extent, the less common macrocyclic archaeols. The putative partner bacterium Seep-SRB1c (Desulfobacterota) is less abundant (9%). Additionally, the biofilm contained five low-abundance heterotrophs that likely rely on biomass or metabolites released from the ANME-SRB consortium. Our study highlights the presence of active methanotrophic biofilms in subsurface sediments and suggests that these communities may play an overlooked role in mitigating seafloor methane emissions.},
}

@article {pmid42040506,
year = {2026},
author = {Zhang, T and Pan, J and Palomo, A and Ouyang, Z and Wen, X and Li, J and Wang, C and Zheng, M},
title = {Unique characteristics of acid-tolerant comammox bacteria revealed by multi-omics analyses.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag070},
pmid = {42040506},
issn = {2730-6151},
abstract = {Complete ammonia oxidation (comammox) is a critical biogeochemical process in the nitrogen cycle. In this study, we utilized comammox Nitrospira to convert urine wastewater into ammonium nitrate by operating a laboratory-scale membrane bioreactor at pH 3 ~ 4. During the process, the acid-tolerant comammox Nitrospira was highly enriched. The metagenomic and metatranscriptomic analyses were applied to reveal its unique characteristics. Comparative genomic analysis among previously reported comammox Nitrospira demonstrated that this species was phylogenetically novel, named Candidatus Nitrospira aciditolerans. Key mechanisms were further identified to enable this species to thrive in acidic environments. These include active proton efflux, regulation of proton consumption, inhibition of proton influx, and cellular strategies for acid stress management and repair. Remarkably, different from other comammox Nitrospira and acid-tolerant ammonia-oxidizing bacteria (AOB), Candidatus Nitrospira aciditolerans possesses highly expressed V-type ATPases that are typically associated with acidophilic ammonia-oxidizing archaea (AOA). This may indicate an ecologically significant role for comammox bacteria and AOA in co-maintaining ammonia oxidation activity in low pH environments. Kinetic characterization revealed an apparent ammonium half-saturation coefficient K m of 0.50 ± 0.05 μM NH3 and an apparent ammonium inhibition constant K i of 241.43 ± 45.64 μM NH3. The enrichment culture demonstrated optimal ammonia oxidation activity at neutral pH but maintained functionality across a broader pH range between 4 and 8. Like other nitrifying bacteria, this comammox culture was sensitive to temperature and salinity changes. The findings enhance our understanding of the nitrogen cycle under acidic conditions and also present opportunities for engineering applications of acid-tolerant ammonia oxidizers.},
}

@article {pmid42040549,
year = {2026},
author = {Chen, Q and Yang, Z and Ren, D and Bao, C and Zhao, Y and Shi, Z},
title = {Case Report: Pulmonary tuberculosis with pneumocystis jirovecii colonization in a non-HIV patient: a cautionary tale on interpreting mNGS results.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1782843},
pmid = {42040549},
issn = {2296-858X},
abstract = {The diagnosis and treatment process of this case highlights that mNGS, as a powerful pathogen detection tool, provides a rapid method for the early detection of Pneumocystis jirovecii. However, mNGS testing of lavage specimens alone cannot distinguish between colonization and infection by the pathogen, particularly when a high number of sequences are present. Clinicians should therefore interpret laboratory results with caution to avoid unnecessary treatment that may cause adverse effects to the patient. CT scans offer strong evidence for differentiating between Pneumocystis jirovecii infection and/or Mycobacterium tuberculosis infection. Performing a biopsy at the site of infection, collecting pathological samples, and submitting them for mNGS testing can further assist clinicians in making a definitive diagnosis.},
}

@article {pmid42040584,
year = {2026},
author = {Li, CB and Tang, S and Wen, Y},
title = {Case Report: The complete radiological resolution of diffuse cholangitis in a HIV-positive patient with cryptosporidium infection after anti-retroviral therapy.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1686336},
pmid = {42040584},
issn = {2296-858X},
abstract = {We present a case of an HIV-positive patient with AIDS cholangiopathy secondary to Cryptosporidium infection. Imaging examination showed intrahepatic and extrahepatic cholangitis without papillary stenosis and extrahepatic bile duct strictures, indicating mild bile duct disease. However, it failed to obtain positive results in fecal microscopy examinations. Alternatively, metagenomic next-generation sequencing (mNGS) of a blood sample identified Cryptosporidium infection. The diagnostic power of mNGS is highly sensitive and can simultaneously identify various pathogens. To avoid irreversible damage to the biliary system, the rapid initiation of anti-HIV therapy restored the function of the immune system and led to the clinical resolution of cryptosporidiosis.},
}

@article {pmid42040837,
year = {2026},
author = {Sander, MM and Stoof-Leichsenring, KR and Liu, S and Shen, W and Lisovski, S and Herzschuh, U},
title = {Sedimentary Metagenomics Reveal Avian Community Transitions From the Last Glacial Maximum to the Holocene.},
journal = {Ecology and evolution},
volume = {16},
number = {4},
pages = {e72064},
pmid = {42040837},
issn = {2045-7758},
abstract = {The transition from the Last Glacial to the Holocene was marked by significant warming. This forced a compositional turnover of terrestrial plant and mammal communities discovered by diverse palaeoecological techniques. In this study, we analysed ancient environmental DNA with shotgun metagenomics from eight lake sediment cores, collected in northern Eurasia and Alaska, to elucidate the relationship of past bird communities and vegetation structure across the last 21,000 years. We leveraged all DNA reads assigned to the class 'Aves' to characterise the compositional changes of the bird community. The dominance of chicken birds (Galliformes, mainly ptarmigans) during the Last Glacial Maximum turned into a higher taxonomic bird diversity with increased numbers of songbird, raptor and waterfowl abundances and genera. This went along with the late glacial loss of the steppe-tundra and the increase of shrub and tree cover. Compared to the northern boreal areas, vegetation and bird communities were more stable in the northern tundra sites, where open landscapes prevailed throughout. Metagenomics significantly contribute to the reconstruction of past avian community changes and thus have high potential to support the predictions of distribution changes in the course of future ecosystem change.},
}

@article {pmid42041249,
year = {2026},
author = {Marroquin, SM and Cohen, S and Neely, MN and Doran, KS},
title = {Akkermansia muciniphila impacts group B Streptococcus vaginal colonization.},
journal = {mBio},
volume = {},
number = {},
pages = {e0286825},
doi = {10.1128/mbio.02868-25},
pmid = {42041249},
issn = {2150-7511},
abstract = {Streptococcus agalactiae, or group B Streptococcus (GBS), is an opportunistic pathogen that asymptomatically colonizes the vaginal tract of up to 30% of healthy individuals. However, during pregnancy, it is associated with adverse pregnancy outcomes, and GBS can be transmitted to the fetus in utero or the newborn during vaginal birth, resulting in invasive neonatal disease. Previously, we identified that Akkermansia muciniphila increases GBS vaginal persistence in a cohort of human vaginal microbiome samples collected throughout pregnancy and promotes GBS vaginal colonization in a murine model. However, the mechanisms responsible for these observations are unknown. Here, we analyze additional vaginal shotgun metagenomic data sets and show that across independent studies with diverse populations, A. muciniphila-positive samples had higher GBS abundance. We determined that A. muciniphila aggregates with human vaginal isolates of GBS across all serotypes and promotes GBS attachment to human vaginal epithelial cells (hVECs). RNA-sequencing analysis reveals that A. muciniphila changed the expression of 281 unique GBS genes during hVEC co-colonization, many of which are involved in cell wall/membrane/envelope biogenesis. We demonstrate the importance of the GBS capsule and pili for direct interaction with A. muciniphila and increased attachment to hVECs, respectively. Lastly, we found that A. muciniphila promoted GBS aggregation in the murine vaginal lumen and that continual treatment with A. muciniphila reduced GBS vaginal persistence. Our results provide mechanistic insights and further evidence of the impact of A. muciniphila on GBS vaginal colonization and also demonstrate a beneficial potential of A. muciniphila treatment in the vaginal environment.IMPORTANCEGroup B Streptococcus (GBS) is a frequent colonizer of the vaginal tract of healthy people; however, during pregnancy, maternal colonization is associated with adverse pregnancy outcomes. GBS is a leading cause of neonatal sepsis and meningitis, with transmission to neonates occurring either during vaginal delivery or through ascension into the uterus during pregnancy. The influence of the vaginal microbiota on GBS pathogenesis remains greatly underappreciated. We have found that GBS is associated with the mucin-degrading intestinal commensal Akkermansia muciniphila, a newly identified colonizer of the vaginal tract. Our research identifies the mechanistic impact of this commensal organism on GBS aggregation, cell adherence, and gene expression, as well as its therapeutic potential during GBS vaginal colonization. Unraveling relationships between GBS and the vaginal microbiota will improve maternal-fetal health and may facilitate the development of alternative methods to reduce GBS in utero complications and neonatal disease.},
}

@article {pmid42041251,
year = {2026},
author = {Gador-Whyte, AP and Sherry, NL and Brischetto, A and Andersson, P and Bond, KA and van Hal, SJ and Harris, PNA and Howden, BP and , },
title = {Implementation of pathogen genomics in clinical microbiology laboratories.},
journal = {Clinical microbiology reviews},
volume = {},
number = {},
pages = {e0017725},
doi = {10.1128/cmr.00177-25},
pmid = {42041251},
issn = {1098-6618},
abstract = {SUMMARYPathogen genomics, including whole-genome sequencing (WGS) and clinical metagenomics, is a transformative technology increasingly being implemented in clinical microbiology, including in hospital laboratories. Pathogen genomics can improve the control of healthcare-associated infections, provide rapid infection diagnosis, and could enable replacement of laborious microbiology tests. To date, real-world implementation of pathogen genome sequencing has primarily been limited to public health laboratories, but sequencing in the clinical microbiology setting has the potential to provide advantages, including turnaround time and ability to focus on local priorities. In this review, we consider the factors that represent barriers to, and potential enablers of, the implementation of pathogen genomics in clinical microbiology, including the availability of funding and genomics-trained staff. We outline key use cases and implementation models of pathogen genomics in clinical microbiology and suggest a broad framework for labs commencing sequencing. Finally, we consider future opportunities, including direct-from-specimen sequencing, the role of machine learning in genomics analysis, and the application of pathogen genomics to clinical decision support.},
}

@article {pmid42041878,
year = {2026},
author = {Carlone, J and Ribeiro, ÁCDS and Parisi, A and Giampaoli, S and Fasano, A},
title = {Profiling the Athletes' Gut Microbiome: A Critical Methodological Perspective on 16S Metabarcoding and Shotgun Metagenomics.},
journal = {Biology},
volume = {15},
number = {8},
pages = {},
doi = {10.3390/biology15080600},
pmid = {42041878},
issn = {2079-7737},
abstract = {The growing interest in the role of the gut microbiome in athletic performance has led to the application of various sequencing technologies in this field. This review critically examines the sequencing methodologies used in microbiome studies on physical performance and sport, comparing their advantages, limitations, and applicability. In particular, the focus is on 16S metabarcoding and shotgun metagenomics, evaluating how these methodological approaches influence the interpretation of results in sports contexts. Close attention is directed toward technical challenges, methodological biases, and future perspectives, including emerging technologies and multi-omics approaches. This review aims to bridge the gap between methodological rigor and sports-specific applicability, providing evidence-based methodological guidance to support researchers in designing robust athlete microbiome studies and translating sequencing-derived findings into concrete applications for performance and sports health.},
}

@article {pmid42041929,
year = {2026},
author = {Ma, Y and Hu, Y and Zhang, J and Sun, Q and Wang, H and Liu, X and Tian, W and Wang, W and Ma, X and Shao, D and Liu, K and Li, B and Qiu, Y and Ma, Z and Li, Z and Wei, J},
title = {The Gut Microbiome and Metabolome of Domestic Cats Were Altered by the Oral Administration of Complex Probiotics.},
journal = {Biology},
volume = {15},
number = {8},
pages = {},
doi = {10.3390/biology15080652},
pmid = {42041929},
issn = {2079-7737},
abstract = {Probiotics are commonly applied to maintain the balance of gut microbiota and regulate the intestinal metabolic function of companion animals. In the present study, complex probiotics (Bacillus coagulans SNZ-1969, Bacillus subtilis, and Bacillus licheniformis) were added into the basal diet of domestic cats to investigate their influence on the intestinal microbiome and metabolic characteristics. Results revealed that the alpha diversity of the gut microbiota in the probiotic group was enhanced when compared to the control group. The beta diversity of the gut microbiota was also altered by the oral consumption of the complex probiotics. Compared to the control group, the relative abundance of beneficial microbes (such as Clostridium, Bacteroides, Phocaeicola, and Ruminococcus) in the probiotic group was enhanced, while the relative abundance of opportunistic pathogens (such as Escherichia, Gallibacter, Corynebacterium) was decreased. Additionally, the intestinal metabolic characteristics of domestic cats were also changed. The metabolomic analysis identified 408 differential metabolites between the two groups, and the KEGG function pathway analysis proved that the dominant pathway related to the differential metabolites were the amino acid metabolism, lipid metabolism, carbohydrate metabolism, energy metabolism, endocrine system, digestive system, immune system, and other metabolic pathways. Spearman's correlation analysis revealed that the beneficial microbes had positive correlations with the differential metabolites. In conclusion, the current study demonstrated that oral administration of complex probiotics could regulate overall health and well-being in domestic cats through modulating the gut microbiome and metabolic characteristics.},
}

@article {pmid42043232,
year = {2026},
author = {Geng, M and Wang, X and Huang, X and Li, Y and Wei, Y and Cai, Y and Li, J and Jiang, C and Wu, W and Liu, S and Guo, N and Zhang, X and Wu, W and Han, G and Han, X and Liu, T and Li, Q and Wang, S},
title = {Metatranscriptomic Analysis of Tick Virome Diversity in Hebei Province, China.},
journal = {Viruses},
volume = {18},
number = {4},
pages = {},
doi = {10.3390/v18040443},
pmid = {42043232},
issn = {1999-4915},
support = {ZDGWNLJS25-25//Surveillance and Early Warning Technologies for Unknown and Emerging Pathogens/ ; 20260864//Hebei Provincial Medical Science Research Project/ ; },
mesh = {Animals ; China ; Phylogeny ; *Virome/genetics ; *Ticks/virology ; Genome, Viral ; *RNA Viruses/genetics/classification/isolation & purification ; Metagenomics ; },
abstract = {Ticks serve as primary vectors for a wide array of RNA viruses, yet the diversity and distribution of tick-associated RNA viruses remain incompletely characterized in Hebei province. To address this gap, we conducted a systematic metatranscriptomic investigation of 986 ticks representing six species, collected from the diverse ecological landscapes of Hebei Province in northern China. Our analysis recovered 25 complete or near-complete viral genomes spanning 12 families, including Phenuiviridae, Flaviviridae, and Nairoviridae. Of critical public health significance, we identified Severe Fever with Thrombocytopenia Syndrome Virus (SFTSV) in both Haemaphysalis longicornis and Dermacentor nuttalli. Phylogenetic reconstruction revealed marked geographic stratification where strains from the coastal plains clustered with the dominant Genotype F, while those from the mountainous north formed a characteristic and divergent lineage phylogenetically linked to isolates from Inner Mongolia. Furthermore, a novel viral agent provisionally named Zhangjiakou Hepacivirus was discovered in Haemaphysalis japonica. This virus shared less than 80% nucleotide identity with the rodent-associated Hepacivirus P, consistent with a rodent origin and possible cross-species transmission. Collectively, these findings reveal descriptive variation associated with vector identity, physiological status, and ecological context in shaping viral evolution and underscore the need for continuous metagenomic surveillance to mitigate emerging tick-borne disease risks within a One Health framework.},
}

Animals
China
Phylogeny
*Virome/genetics
*Ticks/virology
Genome, Viral
*RNA Viruses/genetics/classification/isolation & purification
Metagenomics

@article {pmid42043279,
year = {2026},
author = {Rūmnieks, J and Baltā, I and Šišovs, M and Tārs, K},
title = {ssRNA bacteriophage metagenomes reveal a diverse set of novel protein families.},
journal = {Protein science : a publication of the Protein Society},
volume = {35},
number = {5},
pages = {e70582},
doi = {10.1002/pro.70582},
pmid = {42043279},
issn = {1469-896X},
support = {5.2.1.1.i.0/2/24/I/CFLA/001//European Commission/ ; },
mesh = {Open Reading Frames ; *Viral Proteins/genetics/chemistry ; *Metagenome ; Genome, Viral ; *Bacteriophages/genetics ; },
abstract = {The bacteriophages with single-stranded RNA (ssRNA) genomes (class Leviviricetes) are among the simplest known viruses that encode only three core proteins: a receptor-binding protein, a capsid protein, and an RNA-dependent RNA polymerase. The number of isolated ssRNA phages has remained very low, but the accumulating RNA metagenome data have uncovered a large variety of these viruses in many environments. Besides the core proteins, many of these genomes putatively encode additional proteins, which up to now have remained uncharacterized. We looked for non-conserved open reading frames (ORFs) in Leviviricetes sequences from the IMG/VR virus metagenome database and used sequence- and structure-based clustering to organize them into similarity groups. Potential ORFs were found throughout the ssRNA phage genomes but almost exclusively on the positive-sense RNA strand, suggestive of their protein-coding potential. The prevalence of the non-conserved ORFs varied in various phage lineages, and their distribution among different genome positions was markedly uneven. Most of the identified ORFs encode all-α proteins, a portion of which contain transmembrane segments that resemble a group of known ssRNA phage lysis proteins, while many others represent previously uncharacterized families of globular or semi-globular α-helical proteins. We additionally uncovered a major class of globular α/β proteins and experimentally determined the structure of a representative protein of this group. These results pave the way for further functional studies of novel ssRNA phage proteins for a better understanding of this diverse virus group.},
}

Open Reading Frames
*Viral Proteins/genetics/chemistry
*Metagenome
Genome, Viral
*Bacteriophages/genetics

@article {pmid42044527,
year = {2026},
author = {Rabasco, JT and Bolyen, E and Caporaso, JG and Sapers, H and Callahan, BJ},
title = {Identify contaminants with decontam on the QIIME 2 Framework.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0126125},
doi = {10.1128/mra.01261-25},
pmid = {42044527},
issn = {2576-098X},
abstract = {Here, we present the integration of the decontam method for contaminant identification and a supplemental approach for identifying the source of contaminants in sequencing data within the QIIME 2 Framework for microbiome data science. We demonstrate its use in a tutorial based on the QIIME 2 "Moving Pictures Tutorial" data.},
}

@article {pmid42044543,
year = {2026},
author = {Zhang, X and Chen, J and Li, Y and Tang, R and Zhu, T and Yuan, Y},
title = {Aerobic biodegradation of acesulfame by sediment-enriched microbial consortia: Kinetics, pathway, and microbial mechanism.},
journal = {Journal of environmental management},
volume = {405},
number = {},
pages = {129734},
doi = {10.1016/j.jenvman.2026.129734},
pmid = {42044543},
issn = {1095-8630},
abstract = {Artificial sweetener acesulfame (ACE), an emerging pollutant frequently detected in aquatic environments, exhibits potential ecological toxicity and risk accumulation effects. However, its environmental fate and microbial degradation mechanisms within sedimentary environments remain inadequately characterized. Herein, we established a sediment-based microcosm system to quantitatively characterize the degradation kinetics of ACE, track associated shifts in microbial community structure and function, and decipher the underlying molecular mechanisms. The results showed that successive enrichment cycles significantly augment the aerobic biodegradation of ACE by sediment microbial communities. Under aerobic conditions, the degradation rate constant increased from 0.58 to 3.60 d[-1] following enrichment, significantly exceeding the rate under the anoxic conditions. Metagenomic analysis revealed that ACE treatment reshaped the microbial community structure, with Pseudomonadota remaining the dominant phylum (60.2-65.8%). Genes encoding ACE-degrading sulfatase and amidase were linked to Chelatococcus and Devosia, both of which showed dramatic enrichment in treated samples, underscoring their critical contribution to ACE degradation. A two-step hydrolytic pathway for ACE degradation via sulfonate ester and amide bond hydrolysis was elucidated through combined product analysis. This biodegradation process coincided with significant changes in the abundance of genes governing carbon, nitrogen, and sulfur metabolism, reflecting a functional restructuring of the microbial community. Toxicity assessment indicated that most transformation products exhibited lower toxicity than the parent compound, suggesting an overall reduction in environmental risk. These findings elucidate the microbial degradation mechanisms of ACE, facilitating the assessment of its environmental risks and the development of effective bioremediation strategies.},
}

@article {pmid42044779,
year = {2026},
author = {Zhang, Y and Zeng, M and Guo, P and Zhang, Z and Chen, X and Li, X and Hao, F and Jiao, X and Wu, Y and Feng, W and Zheng, X},
title = {Effects of Rehmannia glutinosa Libosch. Rhizome Water Extract and Rehmapicrogenin on Pulmonary Hypertension: Multi-Omics Insights into Epidermal Growth Factor Receptor/Pyruvate Kinase M2 Pathway and Metabolic Regulation.},
journal = {Journal of ethnopharmacology},
volume = {},
number = {},
pages = {121775},
doi = {10.1016/j.jep.2026.121775},
pmid = {42044779},
issn = {1872-7573},
abstract = {Rehmannia glutinosa Libosch. (RG), as one of the 'Four Famous Chinese Medicinal Herbs', has a long history of medicinal use and is classified as belonging to the meridians of the heart, liver, and kidney. RG has the effects of clearing heat and cooling blood, nourishing yin, and generating fluids. Pulmonary hypertension (PH) is a cardiovascular disease, and its pathogenesis can be summarized as 'yin deficiency', 'blood stasis', and 'qi deficiency'. The efficacy of RG is highly compatible with this disease, and the compounds isolated from RG can significantly inhibit the proliferation of pulmonary arterial smooth muscle cells (PASMCs). However, the mechanism by which it intervenes in PH remains unclear.

OBJECTIVE: In this study, the mechanisms and active components of RG were investigated for treating PH by using multi-omics analysis and surface plasmon resonance (SPR) technology, providing experimental support for clinical application.

METHODS: A PH mouse model was established through 5 weeks of hypoxia, with RG administration starting in week four. Cardiorespiratory function was evaluated after treatment. The therapeutic targets of RG were identified via 16S rDNA sequencing, metagenomics, and metabolomics. SPR ligand fishing was performed to isolate rehmapicrogenin (Reh), an RG-derived compound that targets the epidermal growth factor receptor (EGFR). The effects and mechanisms of Reh were assessed by measuring cardiac and pulmonary function, oxidative stress, apoptosis, immune cell activity, and glycolysis. An in vitro model of hypoxia-induced PASMC proliferation was used to validate Reh's mechanism with an EGFR agonist (NSC).

RESULTS: RG extracts improved cardiorespiratory function and regulated gut microbiota, correcting the Firmicutes/Bacteroidetes (F/B) ratio in PH mice. RG also mitigated metabolic disturbances and inhibited glycolysis through pyruvate kinase M2 (PKM2) regulation, as confirmed using immunofluorescence analysis, western blotting, and PCR. SPR identified Reh as the active ingredient, which improved cardiorespiratory function, reduced oxidative stress and apoptosis, and suppressed EGFR and PKM2 expression and glycolysis. In vitro, Reh inhibited PASMC migration and proliferation, alleviated oxidative stress, and reduced mitochondrial damage. These effects were reversed upon NSC addition, confirming the role of EGFR in the mechanism.

CONCLUSION: RG and its active compound Reh mitigate hypoxia-induced PH by targeting the EGFR/PKM2 pathway, reducing glycolysis, and regulating gut microbiota dysbiosis.},
}

@article {pmid42044791,
year = {2026},
author = {Dai, Y and Li, J and Wang, X and Xia, F and Zheng, J and Shen, C},
title = {Synergistic Mechanisms of Bacteria and Fungi in the Biodegradation of Benzo[a]pyrene: Insights from Metagenomic and Metabolomic Analyses.},
journal = {Environmental research},
volume = {},
number = {},
pages = {124602},
doi = {10.1016/j.envres.2026.124602},
pmid = {42044791},
issn = {1096-0953},
abstract = {Polycyclic aromatic hydrocarbons (PAHs) are pervasive organic pollutants, with benzo[a]pyrene (BaP), a prominent heavy-weight PAH, drawing considerable attention due to its high toxicity and resistance to degradation. While both bacteria and fungi have been demonstrated to effectively remediate BaP, their synergistic mechanisms remain poorly understood. In this study, we employed Pseudomonas nicosulfuronedens DY-8 (bacterium) and Arthrinium acutiapicum DL-5 (fungus) to explore the mechanisms underlying PAH bioaugmentation using metagenomic and metabolomic approaches. Although both strains individually enhanced BaP degradation, their combined application significantly reduced BaP residuals. qPCR analysis revealed that the bacteria promote BaP dissipation by stimulating the abundance of PAH-RHD GP genes in the soil. Correlations between metabolite abundance, enriched microbial populations, functional gene abundance, and fungal growth suggest that fungi enhance the growth of indigenous bacteria, further boosting the degradation of BaP metabolites. Additionally, the synergistic treatment of bacteria and fungi further altered the diversity of soil functional microorganisms, metabolic products, and functional genes. These findings provide insights into potential synergistic mechanisms by which bacterial-fungal interactions drive the degradation of high-molecular-weight PAHs, underscoring the potential of microbial consortia in the bioremediation of persistent organic pollutants in soil environments.},
}

@article {pmid42044793,
year = {2026},
author = {Zhou, Y and Hu, X and Du, L and Gu, Y and Li, J and Jia, M and Zhang, G and Wang, Y},
title = {Antibiotic Resistance Genes Across Divergent Wetland Types: Profiles, Driving Mechanisms, and Risk Assessment.},
journal = {Environmental research},
volume = {},
number = {},
pages = {124601},
doi = {10.1016/j.envres.2026.124601},
pmid = {42044793},
issn = {1096-0953},
abstract = {Wetlands are critical reservoirs and hotspots of antibiotic resistance genes (ARGs). Metagenomic sequencing was employed to profile the ARG and mobile genetic element (MGE) abundance and diversity in coastal (B), constructed (R), and swampy (W) wetlands. In total, 560 ARGs were detected across all sites, primarily conferring resistance to cephalosporins and tetracyclines, with antibiotic efflux being the dominant mechanism of resistance. ARG richness was significantly higher in wetlands R and W than in wetland B (p < 0.001). Non-metric multidimensional scaling (NMDS) further indicated significant differences in ARG β-diversity among the wetlands. Pseudomonadota were identified as the primary hosts of both ARGs and MGEs. Soil salinity and Cr content were the key environmental factors regulating ARG profiles, with salinity exhibiting the broadest influence and linearly correlating with multiple ARG types. In addition, plasmid and insertion sequence (IS) richness positively correlated with ARG richness, showing the strongest explanatory power for ARG richness variation. Risk assessment revealed that rank I and II ARGs were significantly enriched in wetland W (p < 0.05), whereas rank IV ARGs were dominant across most sites. This study demonstrated that soil physicochemical properties, plasmids, and ISs jointly and differentially shaped ARG abundance and diversity in wetlands, accompanied by an assessment of their risk. These findings support the development of targeted strategies to mitigate ARG dissemination in wetland ecosystems.},
}

@article {pmid42044853,
year = {2026},
author = {Weng, H and Wang, H and Zhang, Q and Li, X and Zhang, L and Peng, Y},
title = {Enrichment of comammox Nitrospira with urea: comparative genomics reveals divergent urea response mechanisms among ammonia-oxidizing microorganisms.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134722},
doi = {10.1016/j.biortech.2026.134722},
pmid = {42044853},
issn = {1873-2976},
abstract = {Urea is a major nitrogen form in natural and engineered ecosystems, yet the traits driving niche partitioning among nitrifiers during urea nitrification remain poorly understood. In this work, a stable urea nitrification microbial community was successfully established over prolonged cultivation characterized using 16S rRNA gene amplicon sequencing, qPCR and genome-resolved metagenomics coupled with comparative genomics. A clade A comammox Nitrospira closely related to Candidatus Nitrospira nitrosa became dominant (OTU330, 13.9%) and yielded the most abundant nitrifier metagenome-assembled genome (MAG). Genomes indicate comammox Nitrospira couples ATP-dependent urea ABC uptake to a streamlined urease-only module characterized by slow substrate turnover, whereas Nitrosomonas relies on passive urea channels and redundant urease/urea-amidolyase pathways, enabling rapid urea metabolism. These contrasting urea acquisition strategies suggest an affinity-capacity trade-off that underpins niche partitioning in urea-fed, oligotrophic nitrifying systems and provide targets for enhancing urea-based wastewater treatment processes.},
}

@article {pmid42045408,
year = {2026},
author = {Kutuzova, S and Piera Líndez, P and Danielsen, LS and Nielsen, KN and Olsen, NS and Riber, L and Gobbi, A and Forero-Junco, LM and Erdmann Dougherty, P and Westergaard, JC and Browne, PD and Christensen, S and Hestbjerg Hansen, L and Nielsen, M and Nybo Andersen, J and Rasmussen, S},
title = {Improving metagenome binning by integrating intrinsic features and taxonomy.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {42045408},
issn = {1546-1696},
support = {NF23SA0084103//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF20OC0062223//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF21SA0072102//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF14CC0001//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF23SA0084103//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NF23SA0084103//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF20OC0062223//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF14CC0001//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NF23SA0084103//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF20OC0062223//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF14CC0001//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF23SA0084103//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059348//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF20OC0062223//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF23SA0084103//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF14CC0001//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; 7076-00129B//Innovationsfonden (Innovation Fund Denmark)/ ; },
abstract = {A common procedure for studying the microbiome is binning the sequenced contigs into metagenome-assembled genomes. State-of-the-art binning methods use coabundance and sequence-based motifs such as tetranucleotide frequencies, whereas taxonomic labels derived from alignment based classification have not been widely used. Here we propose TaxVAMB, a metagenome binning tool based on semisupervised bimodal variational autoencoders, combining tetranucleotide frequencies and contig coabundances with taxonomic information. TaxVAMB outperformed all other binners on CAMI2 human microbiome datasets, returning on average 29% more high-quality assemblies than the next best binner, and performed on par with the best binners on short-read datasets. On a human gut long-read dataset, TaxVAMB recovered 29% more high-quality bins. In a typical single-sample setup, TaxVAMB on average returns 83% more high-quality bins compared to VAMB. Lastly, TaxVAMB binned incomplete genomes better than any other tool, returning on average 300% more high-quality bins of incomplete genomes than the next best binner.},
}

@article {pmid42045553,
year = {2026},
author = {Wei, D and Xing, C and Zeng, S and Hou, D and Deng, Z and Long, X and Wang, H and Zhou, R and Yu, L and Shu, N and Tao, Z and Zhou, X and Weng, S and He, J and Huang, Z},
title = {The crayfish-rice coculture model contributes to regulating the soil fertility of rice fields and maintaining the stability of soil microbial community composition and function.},
journal = {Advanced biotechnology},
volume = {4},
number = {2},
pages = {},
pmid = {42045553},
issn = {2948-2801},
support = {2023YFD2401705//National Key Research and Development Program of China/ ; 2024YFD2401202//National Key Research and Development Program of China/ ; AA23062047//Earmarked Fund for CARS-48-20; Guangxi Science and Technology Major Special Project/ ; SML2021SP203//Innovation Group Project of Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; },
abstract = {Rice-fish coculture represents a classic sustainable agricultural paradigm; however, the microecological mechanisms underlying its capacity to maintain soil fertility and microbial community stability remain poorly understood. We conducted a 13-month field experiment comparing three cultivation systems:crayfish-rice coculture (CRCE), crayfish-waterweed coculture (CWCE), and rice monoculture (RME)-by integrating physicochemical analysis, 16S rRNA sequencing, metagenomics, microbial network analysis, and null model simulations. Our results demonstrated that coculture systems, particularly CRCE, enhanced soil fertility through carbon sequestration (total carbon: 25.0-45.0 mg/g; total organic carbon: 15.0-35.0 mg/g) and sustained redox homeostasis (consistently low oxidation-reduction potential: - 150 to - 50 mV), in stark contrast to the extreme redox fluctuations observed in RME. These stable edaphic conditions imposed deterministic selection on microbial communities (homogeneous selection contribution: 30%-50% in CRCE vs. 10%-20% in RME), shifting community assembly from stochastic drift dominance toward predictable succession. This assembly shift enriched functionally coupled keystone taxa, including iron reducers (Geobacter), sulfur oxidizers (Sulfuricurvum), and nitrifiers (Nitrospira), which formed ecological networks characterized by 98.6% positive interactions and enhanced functional gene repertoires associated with carbon, nitrogen, and sulfur biogeochemical cycles. Metagenomic analysis corroborated these findings, revealing enrichment of functional genes involved in polymer degradation, nitrification, and sulfate reduction in CRCE, supporting enhanced nutrient cycling capacity. We establish a hierarchical causal pathway in which bioturbation-induced environmental stabilization drives deterministic community assembly, which in turn promotes keystone taxon enrichment and functional integration. This framework provides a mechanistic explanation for how crayfish-rice coculture regulates soil fertility and sustains microbial community compositional and functional stability in anthropogenically designed agricultural ecosystems.},
}

@article {pmid42045683,
year = {2026},
author = {Boppana, LKT and Bag, R},
title = {Metagenomic Microbial Next-Generation Gene Sequencing as a Noninvasive Diagnostic Tool in Adult Lung Transplantation: A Retrospective Case Series.},
journal = {Lung},
volume = {204},
number = {1},
pages = {},
pmid = {42045683},
issn = {1432-1750},
}

@article {pmid41850677,
year = {2026},
author = {Mi, X and Liu, R and Jiang, Z and Tang, M and Yan, J and Liu, J and Li, Y and Zheng, J and Yang, W and Gong, L and Shi, J},
title = {Gut Microbiota-Derived Propionate Governs Hepatic N2 Neutrophils in Wilson's Disease.},
journal = {Cellular and molecular gastroenterology and hepatology},
volume = {20},
number = {7},
pages = {101770},
doi = {10.1016/j.jcmgh.2026.101770},
pmid = {41850677},
issn = {2352-345X},
abstract = {BACKGROUND & AIMS: Neutrophil functions play a pivotal role in hepatic pathogenesis. Our previous work has established that N2-polarized neutrophils promote hepatic fibrogenesis in Wilson's disease depends on hepatic transforming growth factor-β1 (TGF-β1) production. However, the regulators governing TGF-β1 production in orchestrating disease-associated N2 neutrophils remain elusive. In this study, we investigated the immunomodulatory effects of gut microbiota-derived short-chain fatty acids (SCFAs) on neutrophil polarization.

METHODS: Fecal metagenomic sequencing and short-chain fatty acid (SCFA) profiling were performed on ATP7B-knockout (ATP7B-KO) mice and their wild-type (WT) littermate controls. Fecal microbiota transplantation (FMT) experiments were conducted by transferring feces from WT mice or Akkermansia muciniphila into recipient mice. Additionally, propionate or trichostatin A (TSA) was administered to both ATP7B-KO and WT groups. Mice were assessed using histological analyses, Sirius Red staining, flow cytometry, biochemical assays, immunohistochemistry, measurement of TGF-β1 levels, immunofluorescence, and quantitative real-time polymerase chain reaction (qRT-PCR) for gene expression profiling. To elucidate the underlying molecular mechanisms, 4D label-free quantitative acetylated proteomics, site-directed mutagenesis, plasmid transfection, co-immunoprecipitation (IP), and luciferase reporter assays were employed.

RESULTS: We report that Akkermansia muciniphila was markedly reduced in the gut microbiota of mice with Wilson's disease, accompanied by decreased SCFA levels, especially propionate. Additionally, transplantation of fecal bacteria from wild-type mice or A muciniphila could promote an antifibrotic effect, elevate propionate levels, reduce TGF-β1 secretion, and decrease hepatic N2 neutrophils in mice with Wilson's disease. Moreover, administration of propionate also significantly enhanced antifibrotic immunity. Mechanistically, propionate reduced the production of TGF-β1 in hepatocytes by inhibiting histone deacetylase activity, increasing the acetylation of DNAJA3 at sites K134 and K385, thus decreasing expression of DNAJA3. Consistently, gut-derived propionate inversely correlated with hepatic injury severity in patients with Wilson's disease, which could be functionally mediated by TGF-β1.

CONCLUSIONS: Gut microbiota are pivotal for hepatic neutrophil polarization and liver fibrosis in Wilson's disease. Our findings suggest that therapeutic modulation of gut microbiota, SCFA profiles, and TGF-β1 production, particularly when combined with histone deacetylase inhibitors, may represent promising therapeutic approaches for Wilson's disease.},
}

@article {pmid42033828,
year = {2026},
author = {Liu, X and Li, N and Wu, WM and Ambrosini, R and Zhong, B and Mei, X and Liu, R and Zhou, L and Yi, S and He, Y},
title = {Freeze-thaw aging and microbial colonization converts microplastics into nitrogen cycling hotspots.},
journal = {Journal of hazardous materials},
volume = {511},
number = {},
pages = {142170},
doi = {10.1016/j.jhazmat.2026.142170},
pmid = {42033828},
issn = {1873-3336},
abstract = {As global warming intensifies, the frequency of freeze-thaw events increases, significantly impacting microbial metabolism and biogeochemical cycling. However, the synergistic effects of freeze-thaw cycles (FTCs) and pervasive microplastics (MPs) on microbial community assembly and nitrogen cycling remain poorly understood. Here, we conducted a microcosm experiment integrating metagenomic and random forest model to elucidate the co-regulatory mechanisms of FTCs and MPs on plastisphere microbial communities and nitrogen metabolism. Results revealed that FTCs accelerated the environmental aging of MPs, inducing surface cracking and oxidation, thereby creating microenvironments favorable for microbial colonization. In the experimental microcosms, the combined effects of FTCs and presence of MPs increased microbial richness and diversity, promoted community differentiation between sediment and plastisphere, and increased microbial niche specialization. Functional analyses showed that FTCs induced a functional reconfiguration of the plastisphere nitrogen metabolism, with a selective enrichment of key enzyme genes, such as nitrite reductase, which may enhance nitrite redox activity and N2O emission capacity. In the plastisphere, the contribution of Acinetobacter to nitrogen cycling increased, whereas Nitrospira declined, possibly due to oxygen limitation. Overall, our findings suggested that FTCs may facilitate transformation of MPs from inert pollutants into potentially metabolically active microhabitats, providing critical insights for assessing emerging pollutants and climate change.},
}

@article {pmid42033834,
year = {2026},
author = {Su, S and Lin, M and Li, K and Lin, J and Chen, Z},
title = {Soil aggregates as functional units for cadmium sequestration: Differential regulation by nitrogen enrichment and labile carbon inputs.},
journal = {Journal of hazardous materials},
volume = {511},
number = {},
pages = {142196},
doi = {10.1016/j.jhazmat.2026.142196},
pmid = {42033834},
issn = {1873-3336},
abstract = {While cadmium (Cd) speciation in soil is known to control its environmental risk, how nitrogen (N) enrichment and labile organic carbon (LOC) inputs redistribute Cd fractions within soil aggregates remains unclear. This study examined how ammonium enrichment (AT), nitrate enrichment (NT), and glucose input (CT) altered carbonate-bound Cd (CB-Cd) and organic matter-bound Cd (OM-Cd) within soil aggregates. Both N enrichment and glucose input enhanced CB-Cd formation, with CT increasing CB-Cd by 39.19% via stimulated microbial activity and carbonate precipitation. Different sources of enriched N regulated OM-Cd, with AT decreasing OM-Cd by 15.55%, and NT increasing OM-Cd by 24.61%. This was attributed to competitive adsorption and suppressed microbial decomposition of recalcitrant organic matter. Aggregate hierarchy was also crucial in determining Cd speciation, where macroaggregates, with higher LOC and genes involved in carbonate precipitation, favored CB-Cd partitioning, whereas microaggregates, with greater surface area and enriched alkyl/aromatic C, served as the major OM-Cd sink. Microbial community analysis revealed that glucose reshaped communities, enriching r-strategists like Amycolatopsis and Trichoderma, which were positively correlated with CB-Cd and OM-Cd. Metagenomic data indicated that glucose stimulated genes for labile C degradation, reinforcing CB-Cd formation, while N addition suppressed C-degradation genes. Random forest and PLS path models identified alkyl C, O-alkyl C, and polysaccharide derivatives as primary SOC components regulating CB-Cd, while alkyl C, phenolic, and aromatic compounds regulating OM-Cd. These findings reveal a mechanism for stabilizing Cd in less bioavailable fractions via SOC and N management, leveraging soil aggregates' role in long-term metal sequestration.},
}

@article {pmid42033969,
year = {2026},
author = {Tian, J and Wang, L and Wang, Y and Zheng, M and Sun, C},
title = {Distribution characteristics of emerging contaminants and microbial communities in Bohai Sea sediments.},
journal = {Marine environmental research},
volume = {219},
number = {},
pages = {108068},
doi = {10.1016/j.marenvres.2026.108068},
pmid = {42033969},
issn = {1879-0291},
abstract = {As a semi-enclosed marginal sea in China, the Bohai Sea has long been influenced by substantial pollutant inputs from surrounding rivers, making it an important region for investigating the distribution patterns of pollutants and microbial communities. In this study, the concentrations of emerging contaminants (ECs) in 19 sediment samples were determined, and metagenomic sequencing was employed to systematically analyze the structure and functional characteristics of microbial communities. The results showed that the detected ECs included synthetic musks (SMs, 7.96-22.85 ng/g dw), dominated by tonalide (AHTN) and galaxolide (HHCB); organophosphate esters (OPEs, not detected-282.27 ng/g dw), were not detected in most samples, but relatively high concentrations were observed at the NS-33 station; and polyhalogenated carbazoles (PHCZs, 0.70-4.36 ng/g dw), with 3,6-dichlorocarbazole (36-CCZ) constituting 61.87% of PHCZs. The microbial community was dominated by Proteobacteria (68.36%). Further network analysis indicated significant correlations between PHCZs and nitrogen metabolism genes, suggesting that PHCZs may inhibit nitrogen fixation and nitrification, while enhancing denitrification. Overall, this study reveals the distribution patterns of ECs and microbial communities in Bohai Sea sediments and their potential associations, providing insights into their interactions in coastal ecosystems.},
}

@article {pmid42033990,
year = {2026},
author = {Wu, Q and You, J and Li, D and Tang, S and Wu, S and Wang, Q and Teng, W},
title = {Oxygen vacancy-rich nanosystems eradicate stubborn periodontal biofilms by synergistic EPS degradation, metabolic activation and microbiome restoration.},
journal = {Biomaterials},
volume = {333},
number = {},
pages = {124234},
doi = {10.1016/j.biomaterials.2026.124234},
pmid = {42033990},
issn = {1878-5905},
abstract = {Periodontitis-associated biofilms pose a severe public health threat due to a dual defense mechanism. This involves a protective physical matrix barrier and biological interference from persistent bacteria and microbial dysbiosis. Current strategies often fail to penetrate deeply, eradicate dormant persisters and resolve microbial dysbiosis, leading to biofilm resistance and disease recurrence. In this study, we develop a multifunctional nanoplatform combining photothermal, photodynamic therapy and peroxidase-like catalysis to execute a sequential strategy. This system integrates molybdenum oxide nanodots rich in oxygen vacancy (MoO3-x) with the photosensitizer indocyanine green (ICG). It exhibits improved optical and enzymatic performance due to the introduced oxygen vacancies. Upon irradiation, the system produces localized hyperthermia and ROS storms to destabilize the biofilm matrix and promote ultrasmall nanodots penetration. The thermal and oxidative stress increase membrane permeability and reactivate metabolism of dormant persisters. Metagenomic analyses confirms that MoO3-x/ICG-treated biofilms show decreased abundance of key persistence-related genes and great enrichment in metabolic pathways. Additionally, the platform exhibits therapeutic effects and a successful shift towards a healthier oral microbiota in periodontitis model. Overall, MoO3-x/ICG demonstrates excellent biofilm eradication and successfully prevents biofilm regrowth or secondary infection. This work targets the entire biofilm lifecycle and presents a nanoplatform for long-term management of periodontal infections.},
}

@article {pmid42034087,
year = {2026},
author = {Liao, S and Lin, X and Wang, X and Lin, J and Lu, Y and Deng, W and He, Q and Chi, Y and Xu, Z},
title = {Insights into the salt-dependent mechanisms of physicochemical changes, microbial succession, and biogenic amine formation during Doubanjiang fermentation.},
journal = {Food chemistry},
volume = {516},
number = {},
pages = {149287},
doi = {10.1016/j.foodchem.2026.149287},
pmid = {42034087},
issn = {1873-7072},
abstract = {Excessive biogenic amine formation is a major safety concern in salt-reduced Doubanjiang fermentation. This study compared high- (12%), medium- (9%), and low-salt (6%) systems to elucidate physicochemical dynamics, microbial succession, and mechanisms promoting biogenic amine accumulation. Salt reduction accelerated acidification and proteolysis, with the low-salt system showing the highest total acidity (0.73 g/100 g) and free amino acids (2684.86 mg/100 g), accompanied by excessive biogenic amine accumulation (1456.95 mg/kg). Microbial communities responded strongly to salinity, with Weissella and Bacillus dominating under low-salt conditions, whereas Tetragenococcus and Millerozyma prevailed at higher salinities. Metagenomic and culturomic analyses further identified key functional strains associated with biogenic amine metabolism. Microbially driven acid accumulation and increased amino acid availability, together with activation of decarboxylases induced by acid stress, jointly promoted biogenic amine formation in the low-salt system. These findings clarify salt-dependent mechanisms of biogenic amine formation and provide guidance for designing safe reduced-salt fermentation strategies.},
}

@article {pmid42034426,
year = {2026},
author = {Zhou, N and Wei, R and Yang, S and Hu, F and Feng, Y and Zheng, H},
title = {Antibiotic resistance gene profiles in the gut microbiomes of Apis cerana, Apis mellifera, and Bombus terrestris.},
journal = {Pesticide biochemistry and physiology},
volume = {220},
number = {},
pages = {107059},
doi = {10.1016/j.pestbp.2026.107059},
pmid = {42034426},
issn = {1095-9939},
mesh = {Animals ; Bees/microbiology ; *Gastrointestinal Microbiome/genetics ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Metagenome ; China ; },
abstract = {The gut microbiota of honeybees has been increasingly recognized as a reservoir of antibiotic resistance genes (ARGs). However, comprehensive comparisons of ARG profiles between honeybees and bumblebees inhabiting the same environments are limited. Moreover, the diversity of mobile genetic elements (MGEs) in bee gut microbiomes and their potential role in mediating the horizontal transfer of ARGs have not yet been fully elucidated. In this study, metagenomic sequencing of 48 gut samples from farmed Apis mellifera, Apis cerana, and Bombus terrestris across four regions in China revealed 127 ARG subtypes, which collectively conferred resistance to nine major antibiotic classes. We found that A. mellifera, which carried the highest load of ARGs, concurrently harbored the greatest abundance of MGEs among the three species. Although ARG abundance varied significantly by region, no consistent geographical pattern emerged across the bee species. Importantly, strong positive correlations were detected between the abundances of ARGs and MGEs, particularly between the insertion sequence gene Tn3 and plasmid gene IncQ1. Metagenome-assembled genome analyses further confirmed the co-occurrence of ARGs (sul2, aph(3″)-Ib, and aph(6)-Id) with MGEs (Tn3 and IncQ1) across the three bee species, providing direct evidence that horizontal gene transfer mediated by MGEs contributes to the dissemination of ARGs within bee gut microbiomes. Overall, these findings highlight the critical role of the bee microbiome as a reservoir for ARGs and as a bioindicator for environmental pollutants, providing important insights into the mechanisms of ARG dissemination in ecosystems.},
}

Animals
Bees/microbiology
*Gastrointestinal Microbiome/genetics
*Drug Resistance, Microbial/genetics
Anti-Bacterial Agents/pharmacology
Metagenome
China

@article {pmid42034448,
year = {2026},
author = {Zhang, Y and Zhao, L and Zhang, P and Yang, Y and Wang, A and Xue, C and Yao, Y and Zhang, J and Zhao, M},
title = {Paenibacillus polymyxa EP-4 can effectively control southern corn leaf blight and affect the selectivity of Spodoptera frugiperda to corn.},
journal = {Pesticide biochemistry and physiology},
volume = {220},
number = {},
pages = {107047},
doi = {10.1016/j.pestbp.2026.107047},
pmid = {42034448},
issn = {1095-9939},
mesh = {Animals ; *Zea mays/microbiology ; *Plant Diseases/microbiology/prevention & control ; *Spodoptera/physiology/microbiology ; *Paenibacillus polymyxa/physiology ; *Pest Control, Biological/methods ; Plant Leaves/microbiology ; Ascomycota ; Biological Control Agents ; },
abstract = {Southern corn leaf blight (SCLB) and Spodoptera frugiperda pose serious threats to corn yield. In recent years, an increasing number of studies have investigated biological control agents to control plant diseases and insect pests. However, research on the use of one biocontrol bacterium to control plant diseases and insect pests simultaneously is very limited. In this study, the bacterium EP-4, which can significantly inhibit the growth of Bipolaris maydis, was identified as Paenibacillus polymyxa. EP-4 metabolites inhibited hyphal growth, caused hyphal deformities, significantly reduced the spore germination of B. maydis, and damaged cell membranes, leading to DNA leakage. In the greenhouse, EP-4 significantly reduced the disease index of SCLB and the feeding and oviposition preferences of S. frugiperda to corn. Metabolite analysis revealed that inoculation with B. maydis and S. frugiperda after EP-4 pretreatment affected the production of corn resistance-related substances such as brassinolide, quercetin, 2-undecanone and naringin. Metagenomic analysis revealed that EP-4 pretreatment and subsequent inoculation with pests and diseases could induce the recruitment of Pseudomonas, Burkholderia, Azotobacter and Mesorhizobium in corn. EP-4 could significantly reduce the occurrence of SCLB and significantly affect the feeding and oviposition of S. frugiperda on corn. The mechanism of action of EP-4 on pests and diseases has been shown to differ. This strain has great application potential in corn.},
}

Animals
*Zea mays/microbiology
*Plant Diseases/microbiology/prevention & control
*Spodoptera/physiology/microbiology
*Paenibacillus polymyxa/physiology
*Pest Control, Biological/methods
Plant Leaves/microbiology
Ascomycota
Biological Control Agents

@article {pmid42034850,
year = {2026},
author = {Gupta, E and Sharma, S and Dash, PK and Parida, M},
title = {Metagenomic profiling unveils the viral diversity in field-collected Aedes larvae from Central India employing nanopore sequencing.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-49112-y},
pmid = {42034850},
issn = {2045-2322},
}

@article {pmid42034975,
year = {2026},
author = {Wang, H and Chen, Z and Qi, L and Wang, Z and Xu, D and Mao, Y and Shen, Z and Chen, K},
title = {Metagenomic profiling of Poa alpigena rhizosphere and bulk soil microbiomes across differing land-use contexts in the Qinghai lake alpine wetland.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-04999-5},
pmid = {42034975},
issn = {1471-2180},
support = {This work was supported by the Natural Science Foundation Project of Anhui Provincial Universities (No. 2022AH052150 and 2024AH051553). Research on Ecosystem Changes in the Qinghai Lake Littoral Zone Under Water Level Rise and Their Impacts on Carbon Cycle (2023-ZJ-905T).//This work was supported by the Natural Science Foundation Project of Anhui Provincial Universities (No. 2022AH052150 and 2024AH051553). Research on Ecosystem Changes in the Qinghai Lake Littoral Zone Under Water Level Rise and Their Impacts on Carbon Cycle (2023-ZJ-905T)./ ; },
}

@article {pmid42034994,
year = {2026},
author = {Chen, Y and Bao, R and Jin, W and Yin, X and Qin, L and Pan, J and Yao, Y and Shen, J and Fang, T and Ma, Y and Zhou, C and Miao, Q and Hu, B},
title = {Metagenomic and genomic characterization of extrapulmonary Mycobacterium abscessus infections: a comparative cohort study.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-026-13117-9},
pmid = {42034994},
issn = {1471-2334},
support = {SHDC22024315//Shanghai Shen Kang Hospital Development Center/ ; },
}

@article {pmid42035444,
year = {2026},
author = {Lopez, C and Banker, A and Venkatasamy, V and Garcia, J and Mattiazzi, A and Eidam, L and Preczewski, L and Anjan, S and Nasrallah, A and Vianna, R and Morsi, M and Natori, Y},
title = {Diagnosing Hyperammonemia Syndrome in Non-Lung Solid Organ Transplant Recipients With Metagenomic Next-Generation Sequencing: Utility and Limitations From Two Clinical Cases.},
journal = {Clinical transplantation},
volume = {40},
number = {4},
pages = {e70550},
doi = {10.1111/ctr.70550},
pmid = {42035444},
issn = {1399-0012},
}

@article {pmid42035799,
year = {2026},
author = {Chen, S and Zhu, B and Lu, X and Huang, Y and Wang, S and Wang, W and Chen, G and Wu, X and Zhou, J and Wu, F and Wu, K},
title = {Integrative multi-kingdom gut microbiome analysis uncovers clinical signatures of major depressive disorder.},
journal = {Journal of affective disorders},
volume = {},
number = {},
pages = {121858},
doi = {10.1016/j.jad.2026.121858},
pmid = {42035799},
issn = {1573-2517},
abstract = {BACKGROUND: Accumulating evidence indicates that gut microbiome is significantly altered in major depressive disorder (MDD). However, most studies have focused on bacteria, while the functional and ecological contributions of eukaryotes, archaea, and viruses in MDD remain poorly understood.

METHODS: Fecal samples were collected from 121 first-episode, drug-naïve young adults with MDD and 117 healthy controls (HC) with matched demographic characteristics for shotgun metagenomic sequencing. Clinical data included the Hamilton Depression Scale (HAMD) and the MATRICS Consensus Cognitive Battery (MCCB). We systematically explored the multi-kingdom gut microbiome, functional genes, and metabolic pathways in MDD and their clinical associations, further assessing their diagnostic potential via machine learning.

RESULTS: MDD patients showed significant alterations in multi-kingdom microbiota diversity, accompanied by coordinated diversity relationships across microbial kingdoms relative to HC. In addition, we further identified 19 bacterial, 16 eukaryotic, 15 archaeal, and 10 viral species, as well as 22 functional genes and 32 metabolic pathways, that differed between groups. Importantly, five bacterial and four viral species were significantly associated with cognitive function, such as a positive correlation between Bifidobacterium pseudocatenulatum and attention/vigilance in MDD. Finally, validation demonstrated that a Random Forest model integrating multi-kingdom microbiota and functional features achieved superior diagnostic performance, significantly outperforming models based solely on bacterial features.

CONCLUSION: This study revealed extensive multi-kingdom microbial dysbiosis in MDD, providing deeper insight into disease-associated ecological disruption and highlighting the potential of microbial markers for enhancing clinical auxiliary diagnosis.},
}

@article {pmid42035921,
year = {2026},
author = {Liu, H and Xie, B and Zhuo, H and He, B and Dai, J and Zhou, Z and Shen, G and Chen, B and Tang, J and Ren, H and Jiang, X},
title = {Molecular Traces of Microbial Cross-Kingdom Migration: From the Gut Ecosystem to the Intervertebral Disc Microenvironment.},
journal = {The spine journal : official journal of the North American Spine Society},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.spinee.2026.04.027},
pmid = {42035921},
issn = {1878-1632},
abstract = {BACKGROUND CONTEXT: Low back pain is a leading cause of disability worldwide, and lumbar intervertebral disc degeneration (IVDD) is strongly associated with its development. Recent studies have shown that the gut microbiota (GM) and its metabolites may be involved in the occurrence and development of IVDD through the gut-disc axis. However, the key microbes mediating this process and their specific molecular mechanisms remain unclear.

PURPOSE: This study aimed to identify the gut microbes that play a key role in the progression of IVDD using multi-omics approaches and clarify the specific mechanisms by which these microbes participate in IVDD by regulating host cell functions.

STUDY DESIGN/SETTING: A single center, prospective cross-sectional study.

PATIENT SAMPLE: We prospectively included 113 patients who underwent surgical treatment for symptomatic lumbar degenerative diseases from May 2022 to May 2023, and their degenerated lumbar intervertebral disc (IVD) tissues as well as paired feces samples were collected.

OUTCOME MEASURES: Metagenomic next-generation sequencing (mNGS), modified Pfirrmann typing, Single-cell RNA sequencing (scRNA-seq), Bulk RNA sequencing (Bulk RNA-seq).

METHODS: Clinical IVD samples and paired fecal samples were prospectively collected and subjected to multi-omics bioinformatics analysis. mNGS was used to analyze the microbial composition in IVD and paired fecal samples. scRNA-seq was employed to resolve the cellular heterogeneity of IVD tissues. Bulk RNA-seq was utilized to identify the characteristics of host response genes related to microbial exposure. Subsequent AUCell scoring was performed to evaluate the abundance of microbes in cell subsets. The CellChat algorithm was applied to analyze the microbe-mediated intercellular communication network of host cells.

RESULTS: The raw detection rate of mNGS in IVD tissues was 100%, with a positive rate of 60.2% (68/113) after excluding background bacteria. A total of 505 genera and 1,528 microbial species were detected, with dominant species including Stutzerimonas stutzeri and Moraxella osloensis. The mNGS detection rate in fecal samples was 100% (322 genera and 789 species), among which Phocaeicola vulgatus (PV) was a dominant species. A total of 7 bacterial species shared by GM and IVD were identified; however, only the relative abundances of PV and Bacteroides thetaiotaomicron (BT) increased gradually with the severity of IVDD. Single-cell RNA-seq identified 10 cell clusters, annotated as chondrocytes, macrophages, fibroblasts, and endothelial cells, with the proportions of the latter three non-chondrocyte populations being significantly higher in the severe IVDD group. Chondrocytes were further divided into subsets. Subsets MDC1 and MDC5 were related to mild degeneration with high expression of ACAN and SOX9, whereas SDC2, SDC3, SDC4, SDC6, and SDC7 were related to severe degeneration. AUCell scoring revealed that PV showed a significantly higher abundance in these pathological subsets, while BT was evenly distributed. Furthermore, chondrocytes with high PV abundance significantly upregulated matrix degradation genes including MMP13 and COL1A1, as well as cell adhesion genes such as POSTN and SPARC. These upregulated genes were significantly enriched in LPS-associated inflammatory cascades, extracellular matrix degradation, and metabolic reprogramming pathways. Crucially, LPS signaling genes including TLR4, MYD88, NFKB1, and RELA were upregulated in chondrocytes with high PV abundance, while short-chain fatty acid receptor genes were minimally expressed with no significant group differences. Finally, CellChat analysis revealed that high PV abundance amplified the communication between chondrocytes and macrophages, fibroblasts, and endothelial cells, which was mediated by the CXCL pathway for immune recruitment, the VEGF and ANGPT pathways for angiogenesis, and the TGF-β pathway for pro-fibrotic remodeling.

CONCLUSION: This study suggests that gut-derived PV may activate the inflammatory response of chondrocytes through the LPS-mediated TLR4-MYD88 signaling axis and reshape the intercellular communication network, thereby potentially contributing to the process of IVDD. These findings provide novel mechanistic insights into the gut-disc axis theory and offer new perspectives on IVDD therapeutic strategies targeting microbe-host interactions.},
}

@article {pmid42036057,
year = {2026},
author = {Stem, AD and Alayyoub, M and Aalizadeh, R and Nikolopoulou, V and Lisgara, A and Shvartsman, A and Anitha, M and Patterson, A and Coble, R and Rushing, B and Sumner, S and Vasiliou, V},
title = {Integrated Multi-Omics Reveals Synergistic Hepatotoxicity of Ethanol and PFOS Co-Exposure.},
journal = {Chemico-biological interactions},
volume = {},
number = {},
pages = {112101},
doi = {10.1016/j.cbi.2026.112101},
pmid = {42036057},
issn = {1872-7786},
abstract = {Alcohol-associated liver disease (ALD) and exposure to per- and polyfluoroalkyl substances (PFAS) share key mechanisms of hepatotoxicity, yet their combined effects remain poorly characterized. We evaluated the impact of concurrent ethanol and perfluorooctanesulfonic acid (PFOS) exposure using a murine Lieber-DeCarli model characterized via multi-omic, spatial lipidomic, and metagenomic analyses. Exposure to PFOS resulted in rapid weight loss, while co-exposure led to decreased survival and pronounced hepatomegaly exceeding the effects of either exposure alone despite reduced cumulative ethanol intake. Histological analysis revealed enhanced hepatocellular injury with combined macrovesicular and microvesicular steatosis, consistent with impaired lipid handling and mitochondrial dysfunction. Transcriptomic and metabolomic profiling demonstrated disruption of xenobiotic metabolism, fatty acid β-oxidation, mitochondrial function, and bile acid transport, with PFOS acting as a dominant driver of metabolic stress and ethanol amplifying injury-related responses. Spatial lipidomics revealed hepatocyte-scale remodeling of membrane phospholipids, characterized by increased phosphatidic acid and depletion of phosphatidylinositol and phosphatidylserine under PFOS-containing conditions. Plasma metabolomics indicated systemic metabolic disturbance, including altered amino acid and redox pathways and depletion of microbiome-derived indole metabolites. Metagenomic analysis revealed reduced bacterial load and severe dysbiosis characterized by loss of commensal anaerobes, expansion of opportunistic taxa, and decreased microbial biosynthetic capacity. These findings indicate that PFOS increases susceptibility to alcohol-induced liver injury potentially through coordinated disruption of hepatic metabolism and gut-liver crosstalk, highlighting environmental PFAS exposure as a potential modifier of ALD severity.},
}

@article {pmid42036452,
year = {2026},
author = {Byun, HR and Ji, SR and Frank, LE and Kipp, EJ and Larsen, PA and Chae, JS},
title = {Application of nanopore adaptive sampling for metagenomic detection of tick-borne RNA viruses.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-50572-5},
pmid = {42036452},
issn = {2045-2322},
support = {550-20250009//Seoul National University/ ; },
abstract = {Nanopore sequencing is a powerful tool for real-time pathogen detection and genomic characterization; however, its application to individual ticks is limited by abundant host-derived nucleic acids and low viral RNA levels. In this study, we applied nanopore adaptive sampling (NAS) to sequence viral RNA from individual Haemaphysalis (H.) ticks collected in the Republic of Korea (ROK). By combining NAS with long-read sequencing, high-resolution genome assembly can be achieved from samples containing low-abundance viral RNA and relatively short complementary DNA (cDNA) fragments generated during library preparation. These results indicate that NAS remains effective under suboptimal fragment-size conditions and improves genome assembly compared to conventional nanopore workflows. Phylogenetic analyses revealed that the detected Dabieshan tick virus (DTV) sequences were clustered with isolates from China and Japan, suggesting regional circulation facilitated by the widespread distribution of H. longicornis. Unlike previous studies relying on pooled samples without selective sequencing, NAS allowed high-resolution viral genome assembly from single ticks. These findings confirm the presence and genotypes of DTV for the first time in the ROK and demonstrate NAS as a practical, scalable approach for tick-borne RNA virus surveillance in single ticks, improving genomic assembly and supporting the monitoring of emerging tick-borne viruses in endemic regions.},
}

@article {pmid42036496,
year = {2026},
author = {Tow, WK and Teh, CSJ and Ooi, CW and Lee, RFS and Krishnasamy, M and Palanisamy, UD and Sundralingam, U},
title = {Metagenomic insights into urolithin formation from rambutan rind extract by rat faecal-derived microbiome.},
journal = {Applied microbiology and biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00253-026-13841-x},
pmid = {42036496},
issn = {1432-0614},
abstract = {Ellagitannins and ellagic acid are microbially converted into urolithins, metabolites associated with antioxidant, anti-inflammatory, and mitochondrial-related activities. Although several human-derived urolithin-producing strains and their associated enzymes have recently been characterised, the diversity of microbial strategies across host systems remains poorly understood. This study investigated urolithin production in the Sprague-Dawley rat faecal-derived microbial communities supplemented with rambutan rind extract, an ellagitannin-rich agricultural by-product containing 35-40% geraniin. Rambutan rind extract supplementation was associated with reduced isobutyric acid levels at study endpoint. Ex vivo anaerobic fermentation of hydrolysed rambutan rind extract (113 µM ellagic acid equivalent) resulted in the formation of urolithin C (9.4 ± 0.6 µM) and Isourolithin A (12.5 ± 0.6 µM) by day 9. Shotgun metagenomics analysis revealed very low relative abundance of Actinobacteria (< 0.009%), despite this phylum encompassing most previously characterised urolithin-producing taxa. Canonical ellagic acid degradation genes and the MetaCyc EA degradation pathway were not detected. Comparative pathway analysis indicated overlap in general metabolic pathways with Ellagibacter isourolithinifaciens DSM 104140[T] reflecting shared metabolic frameworks rather than conserved urolithin biosynthetic pathways, with highly divergent homologues (Eadh1, Eadh2, Eadh3, and Ucdh). Together, these findings demonstrate that rambutan rind extract can support urolithin formation in rat faecal-derived microbial consortia and highlight functional associations consistent with alternative or yet-uncharacterised microbial strategies for ellagitannin biotransformation. These findings support a discovery-driven framework for investigating urolithin biotransformation in non-human gut microbiomes using ellagitannin-rich agricultural substrates. KEY POINTS: • Rambutan rind extract supports urolithin formation in rat-derived gut microbiota. • Substrate concentration influences urolithin production under ex vivo conditions. • Rat gut microbiota shows homologues' divergence in urolithin-associated proteins.},
}

@article {pmid42032888,
year = {2026},
author = {Wu, S and Wang, Y and Li, H and Fang, X and Guo, J and Luo, X and Li, M and Song, F and Tan, Q and Deng, X and Xiao, S and Liu, H and Hu, C and Pan, Z},
title = {Rhizosphere microbiome influences fruit quality in citrus.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.71159},
pmid = {42032888},
issn = {1469-8137},
support = {2023YFD2300603//The National Key Research and Development Program of China/ ; 2017YFD0202001//The National Key Research and Development Program of China/ ; 2019YFD1000103//The National Key Research and Development Program of China/ ; },
abstract = {Fruit quality is shaped by both crop genetics and cultivation environments, with soil conditions driving rhizosphere microbiome assembly. While rhizosphere microbes are known to enhance nutrient utilization and plant metabolism, their direct contribution to fruit quality regulation remains poorly understood. In this study, we demonstrate that the Satsuma mandarin (Citrus unshiu Marc.) and Navel orange (Citrus sinensis L. Osbeck) rhizosphere microbiome influence fruit sugar concentration, a key determinant of fruit quality. The rhizosphere core microbiota and soil mineral nutrients were positively correlated with fruit quality indices. Fruit quality-correlated bacterial operational taxonomic units (OTUs) explained an average of 32.6% of the observed variation in quality parameters. Inoculation with three bacterial strains (affiliated with Burkholderia, Pseudomonas, Rhizobium) and two bacterial consortia significantly increased fruit sugar concentrations. Metagenomic analysis linked sugar-associated microbes to iron (Fe) utilization, revealing genomic enrichment of siderophore biosynthesis gene clusters. Consistently, the selected bacterial strains exhibited siderophore secretion capabilities, increased leaf Fe content by 23.3-47.8% in citrus rootstock. Further field application of chelated-Fe fertilizer also increased fruit sugar concentration. Collectively, our results revealed an influence of the rhizosphere microbiome on fruit quality that is related to Fe acquisition optimization and subsequent sugar accumulation in citrus.},
}

@article {pmid42032992,
year = {2025},
author = {Huang, Z and Wei, J and Luo, J and Pan, X and Wei, C and Zhou, Y and Xiao, S and Xu, N and Zhong, Y and Luo, M},
title = {[Comparison of 16S rRNA gene hypervariable regions V3-V4 and V4 sequencing results of gut microbiota in obese children with non-alcoholic fatty liver disease].},
journal = {Zhong nan da xue xue bao. Yi xue ban = Journal of Central South University. Medical sciences},
volume = {50},
number = {12},
pages = {2312-2324},
doi = {10.11817/j.issn.1672-7347.2025.240565},
pmid = {42032992},
issn = {1672-7347},
support = {2022JJ40668//the Natural Science Foundation of Hunan Province/ ; },
mesh = {Humans ; *Non-alcoholic Fatty Liver Disease/microbiology ; *Gastrointestinal Microbiome/genetics ; *RNA, Ribosomal, 16S/genetics ; Child ; Feces/microbiology ; Male ; Female ; *Pediatric Obesity/microbiology ; *Obesity/microbiology/complications ; Adolescent ; },
abstract = {OBJECTIVES: 16S rRNA gene sequencing is an important method for studying microbial structure in samples. However, whether selecting different hypervariable regions for sequencing in the same sample affects the results remains unclear. This study aims to compare the sequencing results of 16S rRNA gene hypervariable regions V3 to V4 and V4 in children with obesity-related non-alcoholic fatty liver disease (NAFLD), and to provide evidence for scientifically evaluating gut microbiota detection results in obese children with NAFLD.

METHODS: Obese children with NAFLD and children with simple obesity who visited Hunan Children's Hospital between January 2019 and September 2021 were selected as study subjects. Fecal samples were collected, and total DNA was extracted. After PCR amplification of the gut microbiota V3 to V4 region and V4 region, sequencing was performed. α-diversity, β-diversity, and microbial community structure differences between the 2 hypervariable regions were compared. Seven samples were selected for metagenomic sequencing as the gold standard to evaluate the performance of V3 to V4 and V4 region sequencing.

RESULTS: A total of 145 participants were included, including 92 in the case group and 53 in the control group. The number of operational taxonomic units (OTUs) obtained by V3 to V4 sequencing (16 977) was higher than that obtained by V4 sequencing (3 362). α-diversity analysis showed that in the overall population, the Shannon index (5.49±1.11) and Chao1 index (1 843.04±580.78) in the V3 to V4 region were higher than the Shannon index (4.98±0.65) and Chao1 index (379.59±47.27) in the V4 region (all P<0.001). β-diversity analysis showed overall differences in microbial community structure between the V3 to V4 and V4 regions, and the intergroup differences were greater than the intragroup differences (P<0.05). Welch's t-test results showed that in the overall population, the numbers of differential taxa detected by V3 to V4 and V4 sequencing at the phylum, class, order, family, and genus levels were 2, 9, 35, 33, and 72, respectively; in the case group, the numbers were 1, 9, 32, 35, and 66; and in the control group, the numbers were 0, 7, 27, 21, and 0. Linear discriminant analysis effect size (LEfSe) analysis showed that V3 to V4 sequencing identified 29 differential taxa between the case group and control group, whereas V4 sequencing identified 7 differential taxa. Sensitivity analysis showed that the Shannon index obtained by V3 to V4 sequencing (5.41±1.62) was not significantly different from that of metagenomic sequencing (6.39±0.42) (P=0.169), while the Chao1 index (1 889.92±781.73) was lower than that of metagenomic sequencing (3 092.71±505.89), with a statistically significant difference (P<0.01). The Shannon index and Chao1 index obtained by V4 sequencing were both lower than those of metagenomic sequencing, with statistically significant differences (4.89±0.94 vs 6.39±0.42, 362.41±35.22 vs 3 092.71±505.89, respectively, both P<0.01).

CONCLUSIONS: Sequencing of the V3 to V4 and V4 regions of the 16S rRNA gene affects the results of gut microbiota structure analysis in obese children. The V3 to V4 region is more likely to detect differential taxa between case and control groups and provides a more accurate estimation of α-diversity. It may therefore be considered a preferred region for gut microbiota sequencing in children with NAFLD. However, there is currently no unified standard for selecting V regions in 16S rRNA gene sequencing, and the detection region and method should be selected comprehensively according to research objectives and sample characteristics.},
}

Humans
*Non-alcoholic Fatty Liver Disease/microbiology
*Gastrointestinal Microbiome/genetics
*RNA, Ribosomal, 16S/genetics
Child
Feces/microbiology
Male
Female
*Pediatric Obesity/microbiology
*Obesity/microbiology/complications
Adolescent

@article {pmid42026803,
year = {2026},
author = {Zhang, F and Hu, K and Sun, C and Chen, R and Ni, G and Liu, X and Wei, L and Su, R},
title = {Gene-level gut microbiome signatures as predictive biomarkers for response to immune checkpoint inhibitors across multiple cancer types.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2662690},
doi = {10.1080/19490976.2026.2662690},
pmid = {42026803},
issn = {1949-0984},
mesh = {Humans ; *Immune Checkpoint Inhibitors/therapeutic use ; *Gastrointestinal Microbiome/genetics/drug effects ; *Neoplasms/drug therapy/microbiology ; Deep Learning ; Biomarkers, Tumor/genetics ; *Bacteria/classification/genetics/isolation & purification ; Female ; Male ; Metagenomics ; },
abstract = {Targeting programmed cell death protein 1 (PD-1) and cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) with immune checkpoint inhibitors (ICIs) has improved survival across multiple cancer types, but the variability in patient response highlights the need for better predictive biomarkers. Existing studies rely on taxonomic abundance derived from reference genome databases, limiting the discovery and functional interpretation of uncharacterized microbes. Here, we integrated metagenomic data from multiple ICI-treated cohorts spanning diverse cancer types and geographic regions and developed a deep learning model, named BioP-VAE, that incorporates biological prior knowledge via protein sequence embeddings and uses gene-level microbial abundance features as input. Gene-level microbial abundance outperformed taxonomy abundance in predicting both ICI response and 12-month progression-free survival (PFS). In patients receiving combination immune checkpoint blockade (CICB), BioP-VAE achieved a mean AUC of 0.89 in intracohort and 0.88 in cross-cohort evaluation. Notably, in the monotherapy-treated intracohorts, BioP-VAE achieved a mean AUC of 0.97. Feature attribution analysis revealed key microbial genes. Additionally, we identified distinct predictive microbial signatures via age-stratified analysis, suggesting that host age may modulate microbiome‒immune interactions. Importantly, this is the first large-scale study to evaluate gene-level microbial abundance features for ICI response prediction across multiple cancer types by deep learning. Our findings demonstrate that incorporating biological prior knowledge into deep learning models can improve the discovery of microbial biomarkers that can be generalized across cancer types and treatment settings, offering a novel strategy for patient stratification in immunotherapy.},
}

Humans
*Immune Checkpoint Inhibitors/therapeutic use
*Gastrointestinal Microbiome/genetics/drug effects
*Neoplasms/drug therapy/microbiology
Deep Learning
Biomarkers, Tumor/genetics
*Bacteria/classification/genetics/isolation & purification
Female
Male
Metagenomics

@article {pmid42027256,
year = {2026},
author = {Lu, S and Xia, Y and Sun, Q and Sun, Y and Chen, R and Jin, H and Zhang, J and Liu, W and Huang, J},
title = {Characterization of the Gut Virome in Patients with Inflammatory Bowel Disease and Non-Alcoholic Fatty Liver Disease.},
journal = {Journal of inflammation research},
volume = {19},
number = {},
pages = {581751},
pmid = {42027256},
issn = {1178-7031},
abstract = {OBJECTIVE: The dysbiosis of the gut microbiota is a well-known correlate in the pathogenesis of inflammatory bowel disease (IBD). However, the microbiome characteristics of patients with IBD who also have non-alcoholic fatty liver disease (NAFLD) are understudied, particularly the potential pathogenic mechanisms of the gut virome.

MATERIALS AND METHODS: In this study, we conducted a comprehensive gut virome correlation study, along with serum metabolomics analysis, by performing virus-like particle (VLP) and metagenomic sequencing on fecal samples from patients with inflammatory bowel disease and non-alcoholic fatty liver disease (IBD-NAFLD) and NAFLD (MASLD) controls without gastrointestinal diseases.

RESULTS: The results showed that changes in the fecal virome were associated with IBD-NAFLD (MASLD), particularly with an increase in the abundance of Caudovirales in IBD-NAFLD (MASLD) patients. Subsequent analysis of the gut virome identified Bacteroides as the top predicted host for the viruses. Additionally, we identified the pathways involved in all differential metabolites through KEGG annotation analysis, with the highest correlation being the galactose metabolism pathway.

CONCLUSION: In conclusion, by using a customized integrated gut virome catalog tailored for IBD, we revealed the fundamental changes in the gut virome of IBD-NAFLD (MASLD) patients. This study is the first to uncover the specificity of the gut virome in IBD-NAFLD (MASLD) patients and predict Bacteroides as a potential host, suggesting a microbial signature primarily influenced by intestinal inflammation.},
}

@article {pmid42027295,
year = {2026},
author = {Sangodkar, N and Gonsalves, MJ and Nazareth, DR},
title = {Methanotrophy dominated symbiosis in novel species Gigantidas niobengalensis from the cold seeps of Krishna-Godavari basin.},
journal = {FEMS microbes},
volume = {7},
number = {},
pages = {xtag014},
pmid = {42027295},
issn = {2633-6685},
abstract = {Bathymodiolus mussels, which are prominent invertebrates at cold seeps and hydrothermal vents, are known for hosting symbiotic microbes within their gills. In this study, the microbial communities associated with the gills of novel bathymodioline mussel Gigantidas niobengalensis from an active cold seep site of Krishna-Godavari (K-G) basin was investigated by 16S rRNA amplicon sequencing. The average abundance of culturable methanotrophs in the gill tissues was 3.4 ± 0.9 × 10[4] CFU g[-1] with average methane oxidation rates of 1.71 ± 0.04 to 1.89 ± 0.02 µM g[-1] d[-1] under aerobic and 1.86 ± 0.001 to 1.98 ± 0.005 µM g[-1] d[-1] under anaerobic conditions. Metagenomic analysis revealed dominance of methanotrophs within the microbial communities comprising of >55% bacterial and >28% archaeal methanotrophs; with phyla Proteobacteria, Firmicutes, Bacteroidetes, Verrucomicrobia, Actinobacteria, Euryarchaeota, and Crenarcheaota being prevalent. Functional classification highlighted methane metabolism (20%) and carbon fixation (22%) as major energy metabolism pathways. This study represents the first metagenomic characterization of gill-associated symbionts in the novel cold seep mussel G. niobengalensis from the Indian Ocean. The findings fill a knowledge gap on chemosynthetic symbioses in Indian cold seep ecosystems and provide insights into metabolic adaptation of G. niobengalensis in the cold seep ecosystem.},
}

@article {pmid42027454,
year = {2026},
author = {Chen, X and Gong, L and Lu, Y and Liu, W and Liu, F and Li, Q and Wang, L and Qiu, L and Zhang, D and Ye, X},
title = {Epidemiological characteristics and environmental surveillance of human psittacosis in Lishui City, Zhejiang Province, China (2021-2024).},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1769696},
pmid = {42027454},
issn = {1664-302X},
abstract = {INTRODUCTION: Psittacosis, caused by Chlamydia psittaci, is an underdiagnosed zoonosis that can lead to severe pneumonia and fatal outcomes. In China, traditional poultry farming poses substantial risks for avian-to-human transmission, yet comprehensive epidemiological evidence is scarce. To address this gap, we aimed to define the local epidemiology, risk factors, and environmental reservoirs of human psittacosis in Lishui City, Zhejiang Province.

METHODS: We conducted a multi-source epidemiological study (2021-2024) integrating surveillance data, clinical records, contact investigations, and environmental sampling. Cases were confirmed by quantitative polymerase chain reaction (qPCR) or metagenomic next-generation sequencing (mNGS).

RESULTS: We identified 28 laboratory-confirmed cases, showing annual fluctuations in reported case numbers. Infections, mostly confirmed by mNGS, were predominantly sporadic among elderly agricultural workers (mean age 62.6 years), with 96.4% reporting recent poultry exposure. All patients presented with pneumonia; 64.3% developed severe disease, resulting in three deaths. The median diagnostic delay-from symptom onset to diagnosis-was 12 days. A household cluster of three cases was detected; however, no secondary transmission occurred among 205 close contacts outside the household. C. psittaci DNA was detected in 14.79% (21/142) of environmental samples, with the highest number of cases detected in duck manure samples, with the highest positive rate (26.7%). Phylogenetic analysis of 20 ompA gene sequences revealed a predominantly genotype A and the waterfowl-TW genotype, which are closely related to strains from southern China.

DISCUSSION: Psittacosis in Lishui presents as a sporadic but clinically severe disease in older rural residents. The high frequency of severe pneumonia and prolonged diagnostic delay underscores an urgent need to improve clinical suspicion and access to molecular diagnostics. Detection of C. psittaci nucleic acid in environmental samples suggests possible environmental contamination; however, viability and transmissibility were not assessed.},
}

@article {pmid42027830,
year = {2026},
author = {Chen, L and Ding, Y and Liu, Y and Xie, Q and Hu, J and Wang, M and Zeng, X and Zou, D},
title = {Case Report: Ultrasound guided puncture for type 2 diabetes mellitus combined with psoas abscess-a report of two cases.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1773238},
pmid = {42027830},
issn = {2296-858X},
abstract = {BACKGROUND: Psoas abscess (PA) is a rare infectious disease, with type 2 diabetes mellitus (T2DM) serving as a significant risk factor. The combination of metagenomic next-generation sequencing (mNGS) and ultrasound offers innovative approaches for the rapid and precise treatment of PA.

CASE PRESENTATION: Case 1: A 77-year-old woman presented with lumbar pain was initially misdiagnosed with lumbar disc herniation based on CT scan. Subsequent CT scan and ultrasound-guided puncture confirmed a left lumbar PA. mNGS detected the presence of Streptococcus agalactiae, which was negative on conventional culture. The patient was successfully treated with vancomycin for 5 weeks, with no recurrence at 3-year follow-up. Case 2: A 56-year-old woman with a 10-year history of T2DM presented with poor appetite and fatigue. CT imaging identified a left lumbar PA along with perirenal infection. Pus from ultrasound-guided puncture for conventional culture and mNGS detected the presence of Staphylococcus aureus. Treatment with oxacillin and vancomycin led to clinical resolution. The follow-up CT scan in 2024 indicated complete resorption of the lesion.

CONCLUSION: mNGS combined with ultrasound-guided puncture overcomes conventional culture limitations. This approach suggests clinical feasibility.},
}

@article {pmid42028026,
year = {2026},
author = {Heinzelmann, D and Reuss, F and Zeh, N and Nilson, R and Walker, E and Fieder, J and Lindner, B and Renner, B and Schulz, P and Fischer, S and Schmidt, M},
title = {Discovery of a chimeric transposase-transposon system for advanced genome engineering.},
journal = {iScience},
volume = {29},
number = {5},
pages = {115548},
pmid = {42028026},
issn = {2589-0042},
abstract = {Transposases have transformed genetic engineering, yet functional systems remain scarce. In response, an unknown transposase system from Acyrthosiphon pisum was identified by metagenomic screening. Through systematic optimization, we enhanced nuclear localization, transposon architecture, and created a hyperactive transposase variant to boost efficiency. Intriguingly, the combined application of the newly discovered transposase with inverted terminal repeat sequences from a related pea aphid species, Aphis craccivora, further enhanced transposition activity, resulting in the first chimeric transposase system reported so far. We investigated the genomic integration events following transposition in mammalian cells to understand the underlying mechanisms and optimize the efficiency of transgene integration. This optimized system can expedite the generation of recombinant protein-producing Chinese Hamster Ovary (CHO) cell lines, even surpassing the hyperactive piggyBac system with regard to cell-specific productivity. These findings introduce a significant addition to the field of semi-targeted transgene integration technologies, offering substantial potential for enhancing biologics manufacturing.},
}

@article {pmid42028145,
year = {2026},
author = {Chen, Y and Zhang, L and Wang, T and Pan, X and Chen, D and Liu, J},
title = {Characteristics of CD4[+]T-cell reduction and pulmonary infections in critically ill immunocompromised patients.},
journal = {Journal of intensive medicine},
volume = {6},
number = {2},
pages = {157-165},
pmid = {42028145},
issn = {2667-100X},
abstract = {BACKGROUND: The CD4[+]T-cell count is a key indicator for evaluating immunosuppression. Infections significantly influence the survival and prognosis of critically ill patients. This study aims to systematically evaluate the association between reduced CD4[+] T-cell counts and lung infections in immunosuppressed ICU patients, offering clinical evidence to guide the management of lung infections in this population.

METHODS: This retrospective, single-center study included 40 immunocompromised patients admitted to the ICU from January 1, 2021, to June 30, 2023. All participants underwent metagenomic next-generation sequencing. Patients with suspected lung infections based on their CD4[+]T-cell counts were divided into mild (350/µL
RESULTS: Amang these forty immunosuppressed patients, 8 were assigned to the mild group, 16 to the moderate group, and 16 to the severe group. Streptococcus pneumoniae was almost all distributed in moderate patients (75.0%), while severe patients had a higher proportion of fungi detected (25.7%). Respiratory microbiome analysis identified Acinetobacter baumannii, Human alphaherpesvirus 1, and Klebsiella pneumoniae as the most abundant species. Although no significant difference in the alpha diversity index was found among the groups, index values were lower in the severe group than in the moderate group. Beta diversity analysis showed that the microbial community structure did not significantly differ among the three groups. A total of 27 microbial markers were obtained, with multiple streptococcal species showing enrichment in moderate group and Candida tropicalis in severe group. By day 28, four patients (50.0%) in the mild group had died compared with six (37.5%) in the moderate group and nine (56.3%) in the severe group. There were no significant difference in the duration of ICU or hospital stays.

CONCLUSIONS: This study on ICU-admitted immunocompromised patients identified the prevalent pathogens and microbiome features associated with pulmonary infections, as well as their relationship with CD4[+]T-cell depletion. These findings are valuable for optimizing clinical diagnosis and treatment strategies and may contribute to improving patient outcomes.},
}

@article {pmid42028191,
year = {2026},
author = {Hariharamohan, M and Chindarkar, M and Swain, HS and Rajesh, N and Rajesh, V},
title = {Integrating physicochemical and microbial characterization of red rice broth fermented over an 18-hour period augmented with metagenomic and metabolomic approaches.},
journal = {RSC advances},
volume = {16},
number = {23},
pages = {21129-21141},
pmid = {42028191},
issn = {2046-2069},
abstract = {Fermentation enhances the nutritional properties of foods. Fermented water of Kerala red rice (Oryza sativa L. subsp. indica), traditionally consumed in South India remains underexplored scientifically. This study characterizes the nutritional, microbial, and metabolite profiles of Kerala red rice water (broth) after 18 hours of natural fermentation using biochemical assays, shotgun whole-genome metagenomic sequencing (Illumina NovaSeq X Plus), untargeted gas chromatography-mass spectrometry (GC-MS) metabolomics, and a phytase-mediated mineral release assay. Fermentation enhanced nutritional quality with increase in carbohydrates by 22.7%, protein by 163.52%, and free amino acids by 35.47% compared to unfermented controls. Phytase activity rose from negligible levels to 0.12 U mL[-1]. Metagenomics identified 50 taxa, dominated by Proteobacteria (59.63%) and Firmicutes (40.12%), with ∼34% of the community carrying phytase-encoding genes. Dominant genera included Pantoea, Saccharibacillus, and Bacillus. Fermentation also enhanced mineral release, with calcium, iron, and zinc in the fermented rice water showing increases of approximately 1190%, 566%, and 93%, respectively, relative to unfermented controls over a 360 min in vitro digestion period. These findings provide the first integrated insight bridging traditional dietary practice with modern analytical science.},
}

@article {pmid42028978,
year = {2026},
author = {Xiao, L and Liu, J and Noyce, GL and Lee, J and Duarte, CM and Zhou, M and Luo, M and Sun, R and Dang, R and Zhou, L and Zhang, L and Fu, C and Tan, Y and Yu, J and Han, G},
title = {Microbial Responses to Warming Reduce Deep Blue Carbon Storage.},
journal = {Global change biology},
volume = {32},
number = {4},
pages = {e70883},
doi = {10.1111/gcb.70883},
pmid = {42028978},
issn = {1365-2486},
support = {U2106209//National Natural Science Foundation of China/ ; 42077025//National Natural Science Foundation of China/ ; 42277236//National Natural Science Foundation of China/ ; 42071126//National Natural Science Foundation of China/ ; 2021213//Youth Innovation Promotion Association of the Chinese Academy of Sciences/ ; XDA23050202//Strategic Priority Research Program of Chinese Academy/ ; YICE3510303//Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences/ ; },
mesh = {*Soil Microbiology ; *Carbon Cycle ; *Carbon/metabolism ; *Global Warming ; Soil/chemistry ; *Carbon Sequestration ; Wetlands ; *Climate Change ; Plants/metabolism ; },
abstract = {Coastal wetlands are critical blue carbon reservoirs, yet the depth-resolved impacts of warming on belowground carbon dynamics remain poorly understood. Over the course of an 8-year in situ experiment, we investigated plant-derived carbon inputs, soil carbon losses via respiration, and microbially mediated carbon fixation across a 60 cm soil profile under a projected 2°C atmospheric warming scenario. Plant carbon fixation (above- and belowground net primary productivity) and soil respiration exhibited synchronized responses to warming, with an initial increase, followed by a decline in the mid-term, and no significant response in the later stages. Soil and microbial respiration stabilized after prolonged exposure to elevated temperatures, as these processes were constrained by substrate availability. In contrast, phospholipid fatty acid profiling, amino sugar biomarkers, and metagenome-assembled genomes consistently indicated a greater than one-third reduction in microbial carbon fixation within subsoils (40-60 cm). Our fully factorial, depth-stratified warming design reveals the particular vulnerability of deep soil microbial carbon retention to long-term climate warming, independent of shifts in plant input or respiratory carbon loss. This work highlights underappreciated pathways influencing soil blue carbon dynamics in a changing world.},
}

*Soil Microbiology
*Carbon Cycle
*Carbon/metabolism
*Global Warming
Soil/chemistry
*Carbon Sequestration
Wetlands
*Climate Change
Plants/metabolism

@article {pmid42028995,
year = {2026},
author = {Liu, M and Du, M and Xi, Z and Tastambek, KT and Bao, Y and Song, X and Zhou, A and Wang, Y},
title = {Bacillus aerius synergizes with coal gangue to enhance Medicago sativa growth via soil microbiome and gene regulation.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0026826},
doi = {10.1128/aem.00268-26},
pmid = {42028995},
issn = {1098-5336},
abstract = {UNLABELLED: The extensive accumulation of coal gangue poses significant environmental threats through water contamination, soil degradation, and atmospheric pollution, necessitating the urgent development of ecological utilization strategies. This study elucidates the mechanistic basis by which the thermophilic bacterium Bacillus aerius (B. aerius) enhances plant growth in coal gangue-amended sandy soils. Through integrated analysis of nutrient dynamics, phytohormonal activities, soil enzymatic profiles, and metagenomic functional profiling, we demonstrate significant synergy between coal gangue and B. aerius. When applied together in sandy soils, the germination rate, plant height, root length, and fresh biomass of Medicago sativa (alfalfa) increased by 1.18-2.06 times. The levels of soil nitrogen, phosphorus, and potassium also significantly increased, resulting in notable improvements in soil fertility. The bacterial treatment enhanced the activities of indole-3-acetic acid, 1-aminocyclopropane-1-carboxylate (ACC) deaminase, and various soil enzyme activities while also optimizing the microbial community structure and increasing the abundance of beneficial bacteria, including Bacillus. Metagenomic analysis revealed the upregulation of growth-promoting genes such as acdS, nifK, and phnG, which collectively drive plant growth through multiple pathways, including enhanced soil nutrient availability, hormone regulation, soil enzyme activities, and nutrient cycling. Collectively, this work deciphers molecular-scale bacteria-gangue synergism, providing a theoretical foundation for sustainable coal gangue utilization and ecological restoration of degraded soils.

IMPORTANCE: The accumulation of coal gangue poses significant environmental challenges, necessitating the development of eco-friendly utilization strategies. This study demonstrates that the thermophilic bacterium Bacillus aerius acts synergistically with coal gangue to promote alfalfa growth in sandy soils while improving soil fertility. The combined treatment enhanced plant morphological traits, soil nutrient availability, beneficial microbial communities, and associated biological activities, with these effects supported by molecular evidence. As the first study to verify this growth-promoting mechanism, our findings address a critical knowledge gap and provide a theoretical foundation for the sustainable utilization of coal gangue in the ecological restoration of degraded soils.},
}

@article {pmid42029028,
year = {2026},
author = {Valdez-Nuñez, LF and Chávez, IJ and Sekerci, F and Ayala-Muñoz, D and Straub, D and Kappler, A and Fischer, S and Mansor, M},
title = {Desulfosporosinus and Acididesulfobacillus dominate an acidophilic sulfate-reducing bacteria consortium during acid mine drainage bioremediation.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0030826},
doi = {10.1128/aem.00308-26},
pmid = {42029028},
issn = {1098-5336},
abstract = {Acid mine drainage (AMD) is an environmental threat due to its low pH and high metal content. Biological treatment of AMD using acidophilic sulfate-reducing bacteria (aSRB) represents a potential solution for this problem, but their substrate specificity and low tolerance to extreme acidity (pH ≤3.0) and toxic metals limit their application. Here, we used an indigenous aSRB-containing consortium to remove metals and neutralize a synthetic AMD (sAMD) system starting at pH 2.9. The consortium was enriched from acidic sediments of an abandoned mine tunnel in Peru. A bioremediation experiment (pH 2.9) was set up with Fe[2+] (40.25 mM), Al[3+] (5.39 mM), and Zn[2+] (3.97 mM) as the main dissolved metals. Glycerol and yeast extract were used as carbon sources. Physicochemical parameters, mineral formation, microbial communities, and dissolved metals were monitored for 160-200 days. At the end of the incubation, the final pH reached 6.1 and 100% of Zn[2+], >99% of Fe[2+], and >94% of Al[3+] were removed by the aSRB consortium as X-ray diffraction-amorphous minerals. The aSRB Desulfosporosinus and Acididesulfobacillus dominated the bioremediation experiment. Two high-quality metagenome-assembled genomes taxonomically affiliated to the aforementioned aSRB showed metabolic potential related to sulfur compounds reduction as well as to organic carbon degradation (e.g., glycerol and acetate). Differences related to carbon degradation during AMD bioremediation suggest a synergy between Acididesulfobacillus and Desulfosporosinus, thus avoiding toxic waste product accumulation. Overall, we obtained a novel aSRB-containing microbial consortium that can be used for acidity neutralization and metal removal, suitable for more robust AMD treatment technologies.IMPORTANCEAcid mine drainage (AMD) remains one of the biggest environmental challenges of the mining industry. Treatment technologies based on the application of microbial consortia are gaining popularity, taking advantage of synergistic interactions between different species to widen substrate specificity and to limit toxicity. Our research work here shows two acidophilic sulfate-reducing bacteria, Desulfosporosinus and Acididesulfobacillus, working together in AMD bioremediation. Desulfosporosinus initiated sulfate reduction at pH ~3.0 with glycerol as the carbon source and acetate as the waste product. Once pH rose to ~4.0, Acididesulfobacillus continued with sulfate reduction with acetate as a carbon source, thus avoiding acetate accumulation and cell toxicity. In the end, this synergistic interaction neutralized acidic pH and removed metals to a great extent, making it suitable for biological treatment of AMD.},
}

@article {pmid42029155,
year = {2026},
author = {Perlas, A and Reska, T and Sánchez-Cano, A and Mejías-Molina, C and Gygax, D and Martínez-Puchol, S and Rusiñol, M and Eger, E and Schaufler, K and Höfle, U and Croville, G and Le Loc'h, G and Guérin, J-L and Urban, L},
title = {Real-time genomic pathogen, resistance, and host range characterization from passive water sampling of wetland ecosystems.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0254325},
doi = {10.1128/aem.02543-25},
pmid = {42029155},
issn = {1098-5336},
abstract = {UNLABELLED: Wetland ecosystems provide interfaces for the transmission of microbial pathogens and antimicrobial resistances (AMR) between migratory birds, wild and domestic animals, and human populations. The efficient surveillance of wetlands is, however, challenging, since the typically low concentration of pathogens requires the sampling of large volumes of water and subsequent targeted detection, which is inherently limited to a few pathogens or AMR genes of interest. Here, we present a holistic, accessible, and cost-efficient framework to characterize the pathogen and resistance load of water sources together with their potential associated hosts by combining passive water sampling through torpedo-shaped devices with nanopore sequencing technology. We used this framework to characterize anthropogenically influenced and natural wetland ecosystems along the East Atlantic Flyway, where we obtained robust assessments of the microbial communities from long-read metagenomic and RNA virome data and showed that anthropogenically impacted wetland ecosystems consistently exhibited higher relative abundances of pathogens and AMR genes. By focusing on avian influenza viruses (AIV), we finally highlight the additional need for targeted screening and whole-genome sequencing of pathogens of interest; we detected and characterized AIV at a third of the monitored sites and used environmental DNA to explore potential animal hosts to better understand the role of wetland ecosystems as One Health interfaces, where the health of animals, humans, and the environment are interconnected and pathogen transmission can occur across these domains.

IMPORTANCE: Wetlands connect wildlife, livestock, and people, making them key places to watch for pathogens and antibiotic resistance. Yet potentially harmful microbes are easy to miss in water because they represent only a small fraction of the abundant microbial life in water, making them hard to detect. We paired 3D-printed passive torpedo-shaped samplers with a portable genetic sequencer to analyze all microbes captured. We deployed this approach at 12 wetlands in Germany, France, and Spain. It revealed local microbial communities, identified disease-causing bacteria, and linked many antibiotic resistance genes to likely bacterial hosts. By comparing locations, we observed that sites near cities, farms, or wastewater had higher levels of pathogens and resistance than protected natural sites. Our analysis also recovered all viruses present, including those from mammals, birds, fish, insects, and plants. We also specifically looked for the virus that causes avian flu, found it at several sites, and classified it as low pathogenicity. Because our method is non-invasive to wildlife, affordable, and practical to deploy, it can provide early warnings to conservation and public health agencies and guide action where risks are present.},
}

@article {pmid42029954,
year = {2026},
author = {Gao, J and Li, HL and Li, MS and Shao, ZJ and Yang, ZF and Li, CJ and Zhang, ZX and Zhu, D and Lv, ZH and Song, RH and Li, JL and Hu, W and Yin, YR},
title = {Cloning, heterologous expression, and characterization of a metagenome-derived GH10 xylanase with salt and alkali tolerance from Xinjiang saline-alkali soil.},
journal = {Antonie van Leeuwenhoek},
volume = {119},
number = {5},
pages = {},
pmid = {42029954},
issn = {1572-9699},
support = {YWLCYXZX2023300075//the Yunnan Provincial Clinical Medical Center for Emergency Traumatic Diseases/ ; 32560004//the National Natural Science Foundation of China Regional Program/ ; },
mesh = {*Metagenome ; Cloning, Molecular ; *Endo-1,4-beta Xylanases/genetics/metabolism/chemistry ; *Soil Microbiology ; *Alkalies ; Hydrogen-Ion Concentration ; *Soil/chemistry ; Enzyme Stability ; Salt Tolerance ; Escherichia coli/genetics ; Xylans/metabolism ; Recombinant Proteins/genetics/metabolism/isolation & purification ; Temperature ; Amino Acid Sequence ; China ; Sodium Chloride ; Phylogeny ; },
abstract = {Xylanases are widely used in baking, seafood processing, and paper production, but their performance is often compromised under high-salt, acidic, or alkaline conditions, limiting broader industrial deployment. Identifying robust xylanases from saline-alkali environments is therefore of practical importance. Here, we report a GH10 xylanase gene, XynE102, mined from a saline-alkali soil metagenome from Karamay, Xinjiang. The deduced amino acid sequence shares 69.17% identity with a xylanase from Cellvibrionaceae bacterium (GenBank accession HEY7885703.1). XynE102 was cloned and heterologously expressed in Escherichia coli, and the recombinant enzyme was purified by Ni-NTA affinity chromatography. Using beechwood xylan as substrate, XynE102 exhibited optimal activity at 50 °C and pH 7.0. It retained ≥ 50% relative activity between 30 and 55 °C and pH 5.6-8.6, and ≥ 75% activity in 2.0 M NaCl. Notably, after preincubation at 40 °C for 60 and 120 min, its activity increased to 130% and 165% of the initial value, respectively. Following 24 h preincubation at pH 7-10, residual activity remained ≥ 80%, indicating pronounced alkaline stability. At 1 mM, Mn[2+], Co[2+], and Fe[3+] activated the enzyme, whereas Mg[2+], Cu[2+], and Cd[2+] inhibited it; 1% SDS had no measurable effect. XynE102 primarily hydrolyzed xylan to xylobiose and xylotetraose. It also hydrolyzed alkali-treated corn stalk and hot-water-pretreated wheat bran, yielding reducing sugar concentrations of 5.44 mM and 4.18 mM, respectively, after 24 h. Taken together, these results indicate that XynE102 is a neutral-pH xylanase with notable salt and alkali tolerance, supporting its potential for prebiotic XOS production and food-processing applications under moderate temperature conditions.},
}

*Metagenome
Cloning, Molecular
*Endo-1,4-beta Xylanases/genetics/metabolism/chemistry
*Soil Microbiology
*Alkalies
Hydrogen-Ion Concentration
*Soil/chemistry
Enzyme Stability
Salt Tolerance
Escherichia coli/genetics
Xylans/metabolism
Recombinant Proteins/genetics/metabolism/isolation & purification
Temperature
Amino Acid Sequence
China
Sodium Chloride
Phylogeny

@article {pmid42030718,
year = {2026},
author = {Chen, L and Zhong, J and Deng, N and Lin, H and Zhang, L},
title = {Spatiotemporal patterns of arsenic and its microbial arsenic transformation in the Pearl River Estuary.},
journal = {Journal of hazardous materials},
volume = {510},
number = {},
pages = {142145},
doi = {10.1016/j.jhazmat.2026.142145},
pmid = {42030718},
issn = {1873-3336},
abstract = {Estuarine ecosystems are critical zones for arsenic (As) biogeochemical cycling, yet the spatiotemporal distribution and microbial transformation mechanisms of As in these dynamic environments remain poorly understood. This study integrated geochemical analyses with metagenomic and metatranscriptomic approaches to investigate As distribution and microbial transformation mechanisms in Pearl River Estuary (PRE). Our results revealed distinct spatiotemporal patterns of As in the PRE. As in sediment were significantly higher in the western region and exhibited a clear decreasing gradient from upstream to downstream. As(V) was the dominant species in both sediments and water, while organic As remained below detection limits. Seasonally, As concentrations peaked in winter and spring. Microbial community analysis showed that highly diverse microbial taxa capable of transforming As were detected, with Proteobacteria identified as the dominant phylum. Among key functional genes, arsM exhibited the highest abundance and transcription level, indicating substantial methylation potential throughout the estuary. Notably, metagenome-assembled genome (MAG) analysis uncovered a previously undocumented metabolic transition along the estuarine gradient, shifting from As(V) reduction coupled with methylation and efflux in upstream to As(III) oxidation with a more diversified strategy in mid-downstream. This systematic study clarified the distribution and microbial transformation mechanisms of As in the PRE, advancing our understanding of As biogeochemical cycling in estuarine ecosystems.},
}

@article {pmid42030844,
year = {2026},
author = {Zhao, H and Che, W and Tan, X and Shen, Y and Xu, Y and Man, Y},
title = {Distribution characteristics and potential microbial degradation mechanisms of microplastics in oyster aquaculture areas of southern China.},
journal = {Journal of hazardous materials},
volume = {511},
number = {},
pages = {142136},
doi = {10.1016/j.jhazmat.2026.142136},
pmid = {42030844},
issn = {1873-3336},
abstract = {Microplastic (MP) pollution in coastal aquaculture is a growing environmental and public health concern. Despite increasing reports, the cross-regional and cross-media pollution patterns, ecological risks, and microbial degradation potentials in aquaculture ecosystems remain poorly understood. We investigated oyster farming systems in South China: Zhanjiang Bay (ZJB, semi-enclosed) and Xuwen (XW, open coast). MP abundances ranged from 20 to 54 items/L in seawater and 950-6483 items/kg in sediment, with particles < 50 μm and granular shapes dominant in both media, as determined by Laser Direct Infrared Imaging. MP spatial patterns differed markedly between regions; XW exhibited higher seawater MP levels attributed to larger farming scales, whereas ZJB showed greater sediment MP accumulation owing to weaker water exchange and a longer farming history. Source apportionment identified aquaculture facilities as the primary source (44.86%). Notably, while the overall pollution load was relatively low, the potential ecological risk index reached 866.51 (classified as "dangerous"), driven predominantly by highly toxic polymers such as polyurethane (PU) and polyvinyl chloride (PVC). The distribution of plastic-degrading genes (PDGs) and their host microbial communities was primarily determined by these aquaculture facilities and the environmental medium (sediment vs. seawater), rather than by localized water-quality conditions. Metagenomic analysis identified sediments as key metabolic hotspots, harboring diverse functional genes involved in polyethylene β-oxidation, polystyrene aromatic ring cleavage, and PU hydrolysis. These findings bridge the gap in understanding MP dynamics between diverse aquaculture habitats and highlight the potential of indigenous microbes in natural attenuation, providing critical insights for MP risk management.},
}

@article {pmid42030878,
year = {2026},
author = {Saini, K and Prajapati, A and Kumar, SS and Kumar, V and Bajar, S},
title = {Performance assessment of sulfate-reducing bacterial consortium for the treatment of real landfill leachate under anaerobic conditions.},
journal = {Journal of environmental management},
volume = {405},
number = {},
pages = {129743},
doi = {10.1016/j.jenvman.2026.129743},
pmid = {42030878},
issn = {1095-8630},
abstract = {Landfill leachate contains complex organic pollutants, ammonia, sulfate, and toxic metals, posing major environmental challenges. This study evaluated a sulfate-reducing bacterial (SRB) consortium isolated from electroplating wastewater for the treatment of real landfill leachate under anaerobic conditions. Physicochemical characterization revealed a Leachate Pollution Index (LPI) of 63.16, confirming the high hazardous nature of the leachate. The acclimatized SRB consortium exhibited strong metabolic activity and rapidly degraded pollutants. Within 10 days of treatment, the system achieved 82.84% removal of chemical oxygen demand (COD) and 97.83% removal of biochemical oxygen demand (BOD5), demonstrating efficient biodegradation of both biodegradable and persistent organic compounds. The concentrations of heavy metals were reduced to below the detection limit (BDL), primarily due to sulfide-mediated precipitation. Thus, SRB provide dual benefits of organic degradation and metal detoxification. Metagenomic profiling (16S rRNA sequencing) revealed dominant sulfate-reducing species, including Desulfovibrio vulgaris, Desulfotomaculum nigrificans, Desulfobulbus propionicus, and Desulfosporosinus orientis. Kyoto Encyclopedia of Genes and Genomes (KEGG) based functional annotation was performed to elucidate the metabolic potential of the SRB consortium. Scanning electron microscopy (SEM) analysis before and after treatment confirmed microbial colonization and sulfide-mediated metal precipitation. Overall, SRB-based anaerobic processes demonstrate significant potential as a sustainable and efficient treatment for high-strength landfill leachate with strong potential for scale-up and integration into waste management systems. Although the treated effluent did not meet CPCB (India) and EPA COD discharge standards, this bioremediation approach provides a cost-effective alternative to conventional physicochemical treatments. Further optimization of operational parameters and microbial activity could enhance treatment efficiency and facilitate regulatory compliance.},
}

@article {pmid42030912,
year = {2026},
author = {Hua, Y and Xu, X and Chen, Y and Li, Y and Dai, X},
title = {Making waves: Wastewater sludge holds untapped antimicrobial potential.},
journal = {Water research},
volume = {300},
number = {},
pages = {125989},
doi = {10.1016/j.watres.2026.125989},
pmid = {42030912},
issn = {1879-2448},
abstract = {Wastewater treatment plants are widely recognized as critical nodes in the environmental dissemination and control of antimicrobial resistance (AMR). This risk-focused view is warranted, but incomplete. Wastewater sludge is one of the largest engineered and repeatedly accessible microbiomes on Earth, continuously shaped by diverse microbial inputs and exposure to antimicrobial compounds and other stressors. These conditions may also harbor underexplored antimicrobial functions. Here we propose framing sludge as a dual-function node within AMR stewardship: a resource for routine surveillance and risk management, and a source material for an offline, containment-first workflow to identify antimicrobial candidates, particularly antimicrobial peptides. We summarize recent advances in metagenomics and machine-learning-enabled peptide prioritization and outline an evidence ladder that links sequence signals to functional validation. A central principle is to decouple discovery from plant operations and to apply explicit decision gates early in the pipeline, including cross-resistance screening and resistance-evolution assays, to prevent inadvertently increasing selection pressure or AMR risks. Finally, we call for shared benchmarks to improve comparability across studies, including curated datasets, standardized validation panels, and routine reporting of negative findings and resistance-related outcomes. Together, these steps can help translate sludge-enabled discovery into environmentally responsible innovation aligned with AMR stewardship.},
}

@article {pmid42030968,
year = {2026},
author = {Brown, JR and Chiu, CY and López-Labrador, FX and de Vries, JJC},
title = {The impact of clinical metagenomic testing on patient management: facts versus fantasy.},
journal = {The Lancet. Infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1016/S1473-3099(26)00106-4},
pmid = {42030968},
issn = {1474-4457},
abstract = {Clinical metagenomic testing by agnostic, unbiased next-generation sequencing is a diagnostic approach with the broad-based capacity to detect all known and novel pathogens in a single assay. After the discovery of this potentially transformative method decades ago, the availability of clinical metagenomic testing in the daily practice of the infectious disease specialist is accelerating. Prospective metagenomic studies have supplemented the substantial existing body of retrospective, exploratory literature, and these reports offer us a glimpse into the real-world use of clinical metagenomic testing for the diagnosis of infections in patients. In this Review, we examine the evidence collected from the prospective reports published to date, focusing on their impact on patient management, treatment, and outcomes.},
}

@article {pmid42031746,
year = {2026},
author = {Yang, Y and Zhang, H and Herbold, CW and Huang, Y and Wang, R and Liu, J and Zhang, D and Ou, J and Zheng, F and Mao, C and Huang, J and Yu, Y and He, J and He, Z and Yan, Q},
title = {Trophic status strongly regulates nitrous oxide but not methane production in global freshwater lake sediments.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42031746},
issn = {2041-1723},
support = {92051120//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32030015//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32470097//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32100086//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Nitrous Oxide/metabolism/analysis ; *Methane/metabolism/analysis ; *Lakes/chemistry/microbiology ; *Geologic Sediments/chemistry/microbiology ; Denitrification ; Nitrification ; Eutrophication ; Greenhouse Gases/metabolism/analysis ; Metagenomics ; },
abstract = {Freshwater lakes are globally significant sources of potent greenhouse gases (GHGs), but how their GHGs emissions respond to changing nutrient levels remains unclear. Here, we demonstrated that nitrous oxide (N2O) production pathways in lake sediments are tightly linked to trophic state, whereas methane (CH4) production appears to be multifactorial Through global metagenomics and controlled batch experiments. In eutrophic sediments, N2O is efficiently removed through complete denitrification, with nitrification serving as the main production pathway, whereas oligotrophic sediments produce N2O primarily via incomplete denitrification. By simulating nutrient transitions using an innovative cross-inoculation experiment, we further revealed that lake sediments systematically shift between these N2O production pathways as their trophic state changes, from denitrification-driven to nitrification-dominated during eutrophication, with the inverse pattern during oligotrophication. Consequently, N2O emissions can be effectively mitigated by inhibiting nitrification in eutrophic lakes and restricting incomplete denitrification in oligotrophic ones. Our findings establish trophic status as a key driver of N2O production sources in lake sediments.},
}

*Nitrous Oxide/metabolism/analysis
*Methane/metabolism/analysis
*Lakes/chemistry/microbiology
*Geologic Sediments/chemistry/microbiology
Denitrification
Nitrification
Eutrophication
Greenhouse Gases/metabolism/analysis
Metagenomics

@article {pmid42031750,
year = {2026},
author = {Hallgren, J and Dharamshi, JE and Rodríguez-Gijón, A and Nuy, J and Garcia, SL and Jonas, K},
title = {Addendum: Widespread potential for phototrophy and convergent reduction of lifecycle complexity in the dimorphic order Caulobacterales.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42031750},
issn = {2041-1723},
}

@article {pmid42032005,
year = {2026},
author = {Gladkikh, AS and Naydenov, DD and Sharova, AA and Popova, MR and Arbuzova, TV and Klyuchnikova, EO and Sbarzaglia, VA and Gibitova, EA and Forghani, M and Tokarevich, NK and Lunina, GA and Ramsay, ES and Dedkov, VG},
title = {Metaviromic analysis of Ixodes ticks in Northwestern Russia reveals high viral diversity and novel RNA virus lineages.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-50087-z},
pmid = {42032005},
issn = {2045-2322},
support = {N. 24-45-20005//RSF grant/ ; },
abstract = {Ticks of the genus Ixodes are recognized as important vectors of a wide range of viral pathogens with potential implications for public and veterinary health. Recent advances in metagenomic sequencing have uncovered an unprecedented diversity within tick-associated viromes, yet much of the global tick metavirome remains unexplored, particularly in vast and ecologically diverse regions such as Northwestern Russia. In this study, we present a comprehensive metaviromic and phylogenetic characterization of viruses detected in Ixodes persulcatus and Ixodes ricinus ticks collected from five regions in Northwestern Russia between 2021 and 2023. Using high-throughput RNA sequencing, we identified viral sequences representing families Nairoviridae, Partitiviridae, Phenuiviridae, Flaviviridae, Chuviridae, and Narnaviridae, Orthototiviridae. Putative novel viral lineages were identified. Phylogenetic analyses revealed strong geographic structuring of some viral lineages. This suggests either the presence of local genotypes, or underrepresentation of Eurasian tick-associated viromes, in current databases. In addition to TBEV, other viruses previously associated with human illness were detected in ticks in Northwestern Russia (Beiji nairovirus, Mukawa virus). Our findings provide the first high-resolution snapshot of the tick virome in Northwestern Russia. They emphasize the importance of continued viral surveillance in underrepresented biogeographic zones. These data contribute to the growing global virome map and may inform the development of region-specific vector-borne disease countermeasures.},
}

@article {pmid42032049,
year = {2026},
author = {Zhang, X and Li, W and Wu, H and Cai, T and Chen, H and Zeng, S},
title = {Enhanced pathogen identification in fungal endophthalmitis by metagenomic next-generation sequencing: a retrospective clinical evaluation.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-50225-7},
pmid = {42032049},
issn = {2045-2322},
support = {LHGJ20220091//Henan Province Medical Science and Technology Key Project/ ; 2023A1515012220//Guangdong Basic and Applied Basic Research Foundation/ ; 2024ZDJS120//Guangdong Province Research Capability Improvement Project for Key Construction Disciplines/ ; 2025XSJ013；2024XK003；2021BQ011//Nanfang College Guangzhou/ ; },
abstract = {Fungal endophthalmitis (FE) is a vision-threatening emergency that requires rapid pathogen identification. Conventional microbial culture demonstrates limited sensitivity in FE, warranting improved diagnostic approaches. We evaluated the detection performance of unbiased metagenomic next-generation sequencing (mNGS) in 31 clinically diagnosed FE cases, including 16 vitreous humor (VH) and 15 aqueous humor (AH) specimens. mNGS showed a positivity rate of 90.3% (28/31, 95% CI: 74.2%-98%), outperforming culture (9.1%, 2/22, 95% CI: 1.1%-29.2%). The positivity rates were 100% for endogenous FE and 85% for exogenous FE, while VH and AH specimens achieved 100% and 80% positivity, respectively. mNGS identified polymicrobial infections in 5 exogenous cases, and a total of 15 fungal species across 9 genera, dominated by Aspergillus flavus, Candida albicans, and Aspergillus niger. Candida albicans and Aspergillus flavus were the predominant pathogens in endogenous and exogenous FE, respectively. Notably, mNGS enabled detection of rare fungal species including Aspergillus niger, Aspergillus welwitschiae, Fusarium oxysporum, Memnoniella echinata, Rhizopus oryzae, Rhizopus microsporus, Chaetomium globosum, and Debaryomyces fabryi. Sequencing results were supported or supplemented by culture, beta-D-glucan, and galactomannan testing in selected cases. Among mNGS-positive cases, 82.1% (23/28) experienced clinical management changes guided by fungal identification. We further propose a laboratory workflow integrating mNGS with conventional assays, tailored to the obtained specimen volume of intraocular fluids.},
}

@article {pmid42032279,
year = {2026},
author = {Ducarmon, QR and Karcher, N and Giri, S and Tytgat, HLP and Delannoy-Bruno, O and Pekel, S and Springer, F and Wörz, P and Schudoma, C and Typas, A and Zeller, G},
title = {Cayman enables large-scale analysis of gut microbiome carbohydrate-active enzyme repertoires.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {42032279},
issn = {2058-5276},
support = {LUMC Fellowship//Leids Universitair Medisch Centrum (Leiden University Medical Center)/ ; 395357507//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 01KD2102A//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; ALTF 1030-2022//European Molecular Biology Organization (EMBO)/ ; },
abstract = {Carbohydrate-active enzymes (CAZymes) are crucial for digesting glycans, but tools for CAZyme profiling and interpretation of substrate preferences in microbiome data are lacking. Here we develop a CAZyme profiler called Cayman (Carbohydrate Active Enzymes Profiling of Metagenomes) and a hierarchical substrate annotation scheme for use with genomic or shotgun metagenomic datasets. Using these tools, we systematically surveyed CAZymes in human gut microorganisms (n = 107,683 genomes) and identified several putative mucin-foraging bacteria, including Hungatella and Eisenbergiella species, which were confirmed experimentally. We compared CAZymes in gut metagenomes (n = 3,960) from high-income settings versus low- and middle-income settings and found that low- and middle-income setting metagenomes are enriched in fibre-degrading CAZymes, while CAZyme richness is generally higher in high-income setting metagenomes. Additional analysis (n = 1,998) indicated that metagenomes of individuals with colorectal cancer are depleted in fibre-targeting and enriched in glycosaminoglycan-targeting CAZymes. Finally, we inferred CAZyme substrates from genomic co-localization of CAZyme domains. Cayman is broadly applicable and freely available from https://github.com/zellerlab/cayman .},
}

@article {pmid42032281,
year = {2026},
author = {Tonkin-Hill, G and Shao, Y and Zarebski, AE and Mallawaarachchi, S and Xie, O and Mäklin, T and Thorpe, HA and Davies, MR and Bentley, SD and Lawley, TD and Corander, J},
title = {Strain-level transmission inference across multi-kingdom metagenomic data using TRACS.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {42032281},
issn = {2058-5276},
support = {2025515//Department of Health | National Health and Medical Research Council (NHMRC)/ ; DE240100316//Department of Education and Training | Australian Research Council (ARC)/ ; 220540/Z/20/A//Wellcome Trust (Wellcome)/ ; 220540/Z/20/A//Wellcome Trust (Wellcome)/ ; 220540/Z/20/A//Wellcome Trust (Wellcome)/ ; 220540/Z/20/A//Wellcome Trust (Wellcome)/ ; },
abstract = {Coexisting strains of the same species within metagenomic data pose a substantial challenge to inferring transmission of pathogenic and commensal microbes. Here we present TRAnsmision Clustering of Strains (TRACS), a highly accurate algorithm for estimating genetic distances between strains at the level of individual single nucleotide polymorphisms, which is robust to intra-species diversity within the host. Analysis of faecal microbiota transplantation datasets and extensive simulations demonstrates that TRACS outperforms existing methods. We use TRACS to infer transmission networks in patients colonized with multiple strains, including severe acute respiratory syndrome coronavirus 2 amplicon sequencing data, deep population sequencing data of Streptococcus pneumoniae and single-cell genome sequencing data from patients infected with Plasmodium falciparum. Applying TRACS to gut metagenomic samples from a mother-infant cohort revealed species-specific transmission rates and identified increased the persistence of Bifidobacterium breve in infants, a finding previously missed owing to the presence of multiple strains. Our study shows that TRACS can be used across microbial kingdoms to uncover strain dynamics.},
}

@article {pmid42032282,
year = {2026},
author = {},
title = {Benchmarking shotgun metagenomics.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {42032282},
issn = {2058-5276},
}

@article {pmid42012708,
year = {2026},
author = {Kværner, AS and Birkeland, E and Avershina, E and Botteri, E and Bucher-Johannessen, C and Knudsen, MD and Hjartåker, A and Page, CM and Hov, JR and Song, M and Randel, KR and Hoff, G and Rounge, TB and Berstad, P},
title = {Alcohol consumption and colorectal carcinogenesis: an exploration of the gut microbial pathway as a potential mediator.},
journal = {European journal of nutrition},
volume = {65},
number = {4},
pages = {},
pmid = {42012708},
issn = {1436-6215},
abstract = {BACKGROUND: Alcohol consumption is one of the major risk factors of colorectal cancer (CRC), yet the mechanisms underlying this relationship, particularly the role of gut microbes, are not fully understood.

OBJECTIVE: To study associations of alcohol intake with the gut microbiome and colorectal lesions among CRC screening participants. Of particular interest was the potential role of gut microbes in mediating the association between alcohol intake and colorectal lesions.

METHODS: Screening participants with a positive faecal immunochemical test at ages 55–77 were eligible for the CRCbiome study. Alcohol intake was assessed using a validated, semi-quantitative food frequency questionnaire and linked with shotgun metagenome based gut microbial profiles to study associations with screen-detected colorectal lesions. The potential role of alcohol-associated gut microbes in mediating the association between alcohol intake and colorectal lesions was examined using causal mediation analysis.

RESULTS: Of 1468 participants with dietary data, 414 were diagnosed with advanced lesions. Alcohol intake was positively associated with advanced lesions in a dose-dependent manner (ptrend = 0.008), with odds ratio of 1.09 (95% confidence interval, 1.00, 1.19) per 10 g/day increase. Compared to non-consumers, those consuming alcohol were characterized by a distinct microbial profile, manifested as modest, but consistent, shifts in α- and β-diversity, and differentially abundant bacteria. A causal mediation analysis showed that 12% of the association between alcohol intake and advanced lesions was mediated by alcohol-associated gut bacteria.

CONCLUSION: Alcohol consumption was associated with a distinct microbial profile, which partly explained the association between alcohol intake and advanced colorectal lesions. Trial registration: The BCSN is registered at clinicaltrials.gov (National clinical trial (NCT) no. 01538550).

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00394-026-03960-6.},
}

@article {pmid42020953,
year = {2026},
author = {Flatau, R and Bickley, CD and Altamia, MA and Gasser, MT and Distel, DL},
title = {Metabolic potential structures gill symbiont communities in two common shipworm species.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag089},
pmid = {42020953},
issn = {1751-7370},
abstract = {Shipworms (Bivalvia: Teredinidae) are the most prolific wood consumers in marine environments. These wormlike marine bivalves digest wood using carbohydrate-active enzymes (CAZymes) produced by intracellular bacterial endosymbionts housed within their gills. Although several shipworm species are known to host multiple co-occurring symbiont species, the factors that influence symbiont community assembly, including the phylogenetic identity and metabolic capabilities of the symbionts, remain poorly understood. We sequenced gill symbiont metagenomes from multiple specimens of two shipworm species, Teredo bartschi (22 specimens) and Lyrodus pedicellatus (14 specimens), which have sympatric distribution in the wild, and which were reared together in laboratory co-culture. From these metagenomes, we assembled 90 metagenome-assembled genomes (MAGs) representing seven distinct symbiont species. The metagenome of each host specimen contained between 1 and 5 symbiont species, with each including at least one nitrogen-fixing symbiont. Six of the seven identified symbiont species were found in both host species, demonstrating a lack of host species specificity in these symbioses. We identified patterns of symbiont occurrence and co-occurrence in these two hosts and used these patterns to constrain the core set of CAZyme and nitrogen-fixation gene classes necessary to support host survival. Our results indicate that, in these two host species, symbiont community composition reflects the symbionts' capabilities for carbohydrate degradation and nitrogen fixation, rather than strict species-specific mechanisms of host and symbiont sorting.},
}

@article {pmid42021075,
year = {2026},
author = {Ishikawa, R and Nakamura, M and Sakurai, A and Nakayama-Imaohji, H and Kuwahara, T and Ichimura-Shimizu, M and Shishibori, M and Kataoka, K},
title = {Influences of ampicillin exposure in early life on the murine gut microbiota and steatotic liver disease associated with western diet.},
journal = {The journal of medical investigation : JMI},
volume = {73},
number = {1.2},
pages = {186-207},
doi = {10.2152/jmi.73.186},
pmid = {42021075},
issn = {1349-6867},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Ampicillin/adverse effects/pharmacology ; Mice, Inbred C57BL ; Mice ; *Fatty Liver/etiology/microbiology ; *Diet, Western/adverse effects ; Female ; *Anti-Bacterial Agents/adverse effects ; Male ; Dysbiosis/chemically induced ; },
abstract = {Dysbiosis of gut microbiota is one of the important factors associated with metabolic dysfunction-associated steatotic liver disease (MASLD). Antibiotic use, especially in early life, could profoundly disrupt an establishing process of stable gut microbiota, and the influence on gut environment may persist throughout life. In this study, we examined effects of ampicillin exposure (AMP) in early life on the temporal changes of fecal microbiota and severity of MASLD in western diet-fed C57BL/6J mice. Histological evaluation of MASLD showed that steatosis in female mice and lobular inflammation was significantly influenced with AMP, and that NAS (MASLD activity score constituting from score of steatosis, lobular inflammation, and ballooning degeneration) tended to be high in female of AMP-treated group. 16S metagenome analyses of fecal microbiota showed significant decrease of α-diversity and remarkable shift to normally minor bacterial species at 4 weeks of age in AMP-treated mice, and the influence was continuously observed even after finishing the western diet feeding period. α-Diversity at 4weeks of age negatively correlated with combined scores of steatohepatitis and fibrosis. These results suggest that AMP in early life induced dysbiosis of gut microbiota and could promote the development of western diet-associated steatotic liver disease. J. Med. Invest. 73 : 186-207, February, 2026.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Ampicillin/adverse effects/pharmacology
Mice, Inbred C57BL
Mice
*Fatty Liver/etiology/microbiology
*Diet, Western/adverse effects
Female
*Anti-Bacterial Agents/adverse effects
Male
Dysbiosis/chemically induced

@article {pmid42021418,
year = {2026},
author = {Ravi, A and Shestivska, V and Thiago Dobbler, P and Sechovcová, H and Maixnerová, M and Semerád, J and Nehasilová, A and Vadroňová, M and Odriozola, I and Šubrtová Salmonová, H and Větrovský, T and Musilová, Š and Cajthaml, T and Pěchoučková, E and Nemec, A and Kyselková, M},
title = {Cattle feces are a reservoir of diverse Acinetobacter species with potential to spread antibiotic resistance genes.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-026-00568-3},
pmid = {42021418},
issn = {2524-4671},
}

@article {pmid42021724,
year = {2026},
author = {Batra, N and Rout, PR and Dey, P},
title = {Modulation and adaptation of gut microbial metabolic functions under probiotic and postbiotic treatment using a novel in vitro anaerobic pseudo-colon system.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo04976h},
pmid = {42021724},
issn = {2042-650X},
abstract = {Probiotic and postbiotic compounds found in food influence gut microbiota to attenuate chronic metabolic diseases; however, the underlying mechanisms are not yet fully understood. This study employed a customized in vitro anaerobic pseudo-colon system (AMMR) to evaluate the impacts of Lactiplantibacillus plantarum (probiotic) and butyrate (postbiotic) on gut microbial composition and functionality, using human fecal samples. Metagenomic (16S rRNA) profiling and untargeted metabolomic (GC-MS) analysis were conducted after 48 h treatments. The results showed that butyrate supplementation markedly enhanced microbial diversity, inhibited opportunistic pathobionts (e.g., Enterococcus and Klebsiella), and selectively enriched butyrate producers (e.g., Lachnoclostridium), while diminishing the Firmicutes : Bacteroidetes ratio. It increased indole levels metabolically and redirected pathways towards amino acid synthesis and energy metabolism, while suppressing fatty acid formation. In contrast, L. plantarum exhibited modest alterations in microbial diversity while enhancing Bacteroides and Klebsiella and preserving elevated Enterococcus levels. It elevated saturated fatty acids (octanoic/capric acid) and enhanced amino acid catabolic pathways (valine/leucine) and redox regulators (taurine metabolism). Correlation analysis revealed that butyrate was associated with fiber-degrading microbes, whereas L. plantarum was associated with lactic acid bacteria, suggesting distinct ecological niches and interaction patterns. These findings collectively indicate that butyrate and L. plantarum elicit complementary microbial alterations, i.e., butyrate directly transforms the microbial structure and metabolism towards an anti-inflammatory phenotype, while L. plantarum largely influences via metabolic byproducts and niche adjustment. The complementary actions highlight the therapeutic potential of integrated probiotic-postbiotic approaches for the enhancement of gut health.},
}

@article {pmid42021875,
year = {2026},
author = {Li, H and Song, Z and Zhao, Y and Li, M},
title = {[Advances in the Application of Artificial Intelligence in Clinical Microbiological Testing].},
journal = {Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition},
volume = {57},
number = {2},
pages = {313-318},
pmid = {42021875},
issn = {1672-173X},
mesh = {*Artificial Intelligence ; Humans ; Deep Learning ; *Microbiological Techniques/methods ; Algorithms ; Microbial Sensitivity Tests ; },
abstract = {Traditional microbiological detection methods have inherent limitations in detection speed, sensitivity, and specificity, making them increasingly unable to meet growing clinical demands. In recent years, artificial intelligence (AI) has been rapidly integrated into clinical microbiological testing, with numerous studies demonstrating its significant potential to enhance pathogen identification, predict antimicrobial susceptibility testing, and advance laboratory automation. This article systematically reviews classical AI algorithms and their latest advancements in this field. For visual data applications, deep learning-based models are used to automatically analyze microscopy images or colony morphology, significantly improving recognition efficiency and diagnostic accuracy. For non-visual data, AI has achieved breakthroughs in analyzing multi-omics data such as genomics, transcriptomics, and metagenomics, and is widely used for rapid pathogen identification and prediction of antimicrobial resistance. Despite its promising prospects, the application of AI in clinical microbiological testing remains in the early stages of transitioning from scientific research to clinical practice. This paper further discusses the key challenges and opportunities encountered during this technological translation, aiming to help clinical professionals comprehensively understand the current status, future trends, and potential impact of AI in this field, thereby promoting its development into reliable and scalable routine diagnostic methods.},
}

*Artificial Intelligence
Humans
Deep Learning
*Microbiological Techniques/methods
Algorithms
Microbial Sensitivity Tests

@article {pmid42021890,
year = {2026},
author = {Zhang, W and Zhong, S and Lu, S and Xiao, X and Xie, Y},
title = {[Diagnostic Performance of Metagenomic Next-Generation Sequencing for Mucormycosis: A Retrospective Cohort Study].},
journal = {Sichuan da xue xue bao. Yi xue ban = Journal of Sichuan University. Medical science edition},
volume = {57},
number = {2},
pages = {411-418},
pmid = {42021890},
issn = {1672-173X},
mesh = {Humans ; *Mucormycosis/diagnosis/microbiology ; Retrospective Studies ; Female ; *High-Throughput Nucleotide Sequencing/methods ; Male ; Middle Aged ; Mucorales/genetics/isolation & purification ; *Metagenomics/methods ; Adult ; Aged ; ROC Curve ; Sensitivity and Specificity ; },
abstract = {OBJECTIVE: Mucormycosis is a life-threatening invasive fungal infection with high mortality, yet traditional diagnostic methods are limited by low positivity rates. This study aims to evaluate the diagnostic performance and clinical utility of metagenomic next-generation sequencing (mNGS) in mucormycosis.

METHODS: A retrospective analysis was conducted on 135 patients with mNGS results positive for Mucorales fungi at West China Hospital of Sichuan University from November 1, 2022, to October 31, 2024. Based on comprehensive clinical diagnostic criteria (including proven and probable cases), patients were classified into a confirmed mucormycosis group and a non-mucormycosis group. Receiver operating characteristic (ROC) curve analysis was used to evaluate the diagnostic performance of normalized read counts (lgRPM) from different specimen types. Fungal species distribution and laboratory parameters were compared between the two groups.

RESULTS: Among the 135 patients with positive mNGS results for Mucorales, 100 (74.1%) were ultimately diagnosed with mucormycosis. ROC curve analysis revealed that the diagnostic performance of mNGS varied by specimen type. For blood specimens, the area under the curve (AUC) was 0.772, with a specificity of 87.5% at the optimal cutoff value of 0.11 RPM. For bronchoalveolar lavage fluid specimens, the AUC was 0.717, with a sensitivity of 76.5% at the optimal cutoff value of 0.02 RPM. Combined analysis of all specimens showed that at the optimal cutoff value of 0.08 RPM (approximately 8 reads/100M), the sensitivity and specificity were 62.0% and 71.4%, respectively. Species distribution analysis showed that the proportions of Cunninghamella elegans (11.0% vs. 2.9%) and Rhizomucor pusillus (9.0% vs. 2.9%) were significantly higher in the confirmed group than in the non-mucormycosis group (P < 0.05). Levels of C-reactive protein and interleukin-6 were also significantly higher in the confirmed group (P < 0.05). Notably, all seven renal perfusion fluid samples yielded false-positive mNGS results.

CONCLUSION: mNGS technology can effectively improve the diagnostic yield for mucormycosis. However, results should be interpreted in conjunction with specimen type, read count, and clinical characteristics. BALF specimens offer high sensitivity, making them suitable for screening, while blood specimens demonstrate high specificity, making them valuable for confirmation. Positive results from low-biomass samples such as renal perfusion fluid warrant caution against false positivity. Fungal species identification and inflammatory markers may serve as adjunctive evidence for clinical diagnosis.},
}

Humans
*Mucormycosis/diagnosis/microbiology
Retrospective Studies
Female
*High-Throughput Nucleotide Sequencing/methods
Male
Middle Aged
Mucorales/genetics/isolation & purification
*Metagenomics/methods
Adult
Aged
ROC Curve
Sensitivity and Specificity

@article {pmid42022012,
year = {2026},
author = {Conrad, RE and Rodriguez-R, LM and Lindner, BG and Gerhardt, K and Konstantinidis, KT},
title = {An ANIr-based methodology to determine if two sequence-discrete populations are identical and identify cosmopolitan prokaryotic populations.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag068},
pmid = {42022012},
issn = {2730-6151},
abstract = {Although sequence-discrete species appear to dominate microbial communities, readily distinguishing between distinct populations of a species recovered from different short-read metagenomic samples is challenging due to technical limitations associated with read length. To close this gap, we developed a novel algorithm to evaluate which reads in a metagenome belong to a target population based on the distribution of sequence identities of reads aligned to a reference sequence, which are filtered using a Kernel density estimation (KDE) as a flexible alternative to the commonly used static 95% nucleotide identity cutoff. Subsequently, we employed the average nucleotide identity of reads (ANIr) aligning above the KDE threshold, and resampling techniques for estimating the confidence intervals of ANIr values, to quantify intrapopulation sequence diversity and compare populations across globally representative marine samples. Most populations showed high ANIr in only a few samples at similar depths and decreased ANIr and increased gene-content difference between samples where a closely related population is detected (e.g. same 95% ANI-based species). Accordingly, ANIr correlated with the physical distance between the samples, and only a few truly cosmopolitan populations were identified. Among the latter, Alteromonas macleodii [97% average amino-acid identity (AAI) to the type genome] and Prochlorococcus marinus (79% AAI) showed high relative abundance in both surface (0-200 m) and deep (>1000 m) samples. These results suggest that microbial communities under different environmental conditions share very few identical and abundant populations and provide a highly needed methodology to track such populations over space and time, in marine or other habitats.},
}

@article {pmid42022013,
year = {2026},
author = {Franco, MEE and Singer, E and Roux, S and Meredith, LK and U'Ren, JM},
title = {Genomic and metagenomic survey of microbial carbonic anhydrase genes reveals novel clades, high diversity, and biome specificity.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag054},
pmid = {42022013},
issn = {2730-6151},
abstract = {Carbonic anhydrase (CA) enzymes catalyze the interconversion of carbon dioxide and bicarbonate with an efficiency exceeded only by superoxide dismutase. CA enzymes have evolved convergently in phylogenetically distant organisms, forming eight structurally unrelated classes that share physiological functions involved in photosynthesis, respiration, pH homeostasis, CO2 transport, and carbonyl sulfide hydrolysis that play central roles in medicine and the environment. Here, we leverage the recent surge in publicly available genomes and metagenomes to re-examine our understanding of the abundance, diversity, and phylogenetic relationships of the three major CA classes in Bacteria/Archaea and microbial Eukaryotes (Fungi, algae). We recovered a total of 57 218 α-, β-, and γ-CA sequences from 24 184 metagenomes and genomes, including the first putative α-CA from an archaeal species. CA sequences formed 3859 protein clusters (1188 with three or more sequences). Sequences within a cluster were typically taxonomically conserved only at higher levels (i.e. Superkingdom, Phylum). When viewed within a phylogenetic framework, the majority of subclades for each CA class contained CAs representing multiple Superkingdoms, although numerous novel β-CA clades appear unique to Fungi. Queries of CA Hidden Markov models against all public metagenome and metatranscriptome datasets revealed that CA is a ubiquitous enzyme present in virtually all sampled environments. However, CA clusters that were taxonomically conserved also appeared more environment-specific, which may explain high CA diversity. This work represents an important contribution to our understanding of the evolution, diversity, and environmental distribution of an enzyme that is key to life and has broad environmental and industrial applications.},
}

@article {pmid42022196,
year = {2026},
author = {Yan, Z and Xie, J and Jin, L and He, T and Zhang, X and Li, X},
title = {Steam Cooking Methods Promote the Transfer of Viable Antibiotic-Resistant Pathogens from Water into Air.},
journal = {Environment & health (Washington, D.C.)},
volume = {4},
number = {4},
pages = {730-741},
pmid = {42022196},
issn = {2833-8278},
abstract = {Steam cooking is an ancient and widely used method for sterilizing water and food globally. However, its effectiveness may be compromised by the ubiquitous presence of antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) in these media. Here, we combined metagenomic sequencing, quantitative PCR analysis, plate culture, and Sanger sequencing to examine the effects of steam cooking on the profiles of antibiotic resistance in cooked fish, tap water, and indoor air in real cooking environments (i.e., a canteen and a home kitchen) and a laboratory chamber. We found that while steam cooking eliminated over 92.0% of bacteria and ARGs in both tap water and fish, it significantly increased the absolute abundance of bacteria and ARGs in indoor fine particulate matter (PM2.5) across all settings. Tap water was identified as the primary contributor to the increase, transferring 14.6% of bacteria and 33.2% of ARGs into indoor PM2.5 during steam cooking. This process also elevated the relative abundance of certain putative human pathogens in indoor PM2.5, containing ARGs and heat shock proteins and mainly originating from tap water. To test if these transferred ARGs hosts were viable, we conducted plate culture experiments and identified a viable heat-resistant ARB, Bacillus cereus, transferred from water to indoor PM2.5 via water vapor. Our results highlight the cross-medium transport of ARB and ARGs via steam cooking and underscore the potential microbial safety issues to cooking personnel through inhalational exposure.},
}

@article {pmid42022320,
year = {2026},
author = {Zhang, W and Huang, R and Yuan, J},
title = {Case Report: HHV8-positive multicentric Castleman disease in an HIV-positive patient :diagnostic challenges arising from atypical histology and the role of metagenomic sequencing.},
journal = {Frontiers in oncology},
volume = {16},
number = {},
pages = {1779973},
pmid = {42022320},
issn = {2234-943X},
abstract = {BACKGROUND: Multicentric Castleman disease (MCD), especially the HHV8-positive subtype, is a rare lymphoproliferative disorder that presents considerable diagnostic and therapeutic difficulties, particularly among HIV-positive patients. The co-occurrence of other infections, such as syphilis, may further complicate its clinical picture and management.

CASE DESCRIPTION: A 65-year-old man with well-controlled HIV presented with persistent fever, fatigue, and disseminated lymphadenopathy,. Through histopathological examination, molecular testing (including mNGS for HHV8), and PET-CT imaging, HHV8-positive MCD was diagnosed, along with latent syphilis. The patient was successfully treated with R-VP16 (rituximab and etoposide) for MCD and benzathine penicillin for syphilis, showing a positive clinical response. Throughout 36 months of continuous monitoring, the patient has maintained sustained complete remission with no evidence of disease recurrence.

CONCLUSION: This case underscores the importance of considering HHV8-driven lymphoproliferative disorders in HIV patients with unexplained lymphadenopathy and systemic symptoms, particularly in HHV8-endemic regions. It also highlights the essential roles of advanced diagnostics and multidisciplinary management in such complex presentations. The favorable outcome demonstrates the effectiveness of timely and targeted treatment, though long-term follow-up remains necessary due to the potential for relapse or progression.},
}

@article {pmid42022392,
year = {2026},
author = {Abedien, ZU and Lean, IJ and Djordjevic, SP and Hick, PM and Westman, ME and Mckay-Demeler, J and Webster, J and Brito, BP},
title = {Next-generation detection in bovine respiratory and enteric diseases: metagenomic and amplicon sequencing insights into microbial diversity.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1788101},
pmid = {42022392},
issn = {2297-1769},
abstract = {Respiratory and enteric diseases are major contributors to morbidity, mortality, and economic loss in cattle production, with significant implications for animal welfare, particularly in calves. Traditional diagnostic approaches have laid the foundation for pathogen detection in cattle, providing essential tools for disease surveillance and control. However, their targeted nature limits the capacity to identify unexpected, novel, or polymicrobial infections that often underlie complex respiratory and enteric syndromes. Recent advances in molecular technologies, particularly amplicon sequencing (metataxonomics), metagenomics, and metatranscriptomics, enable untargeted, high-resolution profiling of microbial communities directly from clinical samples, offering transformative potential for research and diagnostics. This review synthesises current applications of these approaches in bovine respiratory and enteric disease research, highlighting key findings across virology, bacteriology, and parasitology. Collectively, these studies have expanded the catalogue of the microbial diversity, yet their interpretation remains challenged by the still-evolving understanding of microbial contributions to pathogenesis. Progress toward clinical integration is further hindered by the need for methodological standardisation, validation, and improved interpretive frameworks. Looking ahead, advancing these technologies will require harmonised protocols, integration of multi-omics datasets, and robust experimental and epidemiological studies to establish causal links between microbial signatures and disease outcomes. By bridging discovery and application, these approaches hold the potential to enhance diagnostic accuracy, strengthen surveillance, and support sustainable cattle production systems. As these technologies continue to evolve, they are likely to play an increasingly central role in bovine disease research and diagnostics.},
}