@article {pmid41812803,
year = {2026},
author = {Bao, Z and Ji, X and Liu, Q and Zhang, L},
title = {Light-driven N-doped carbon quantum dots facilitate microbial chain elongation: Bridging process enhancement to functional metagenomics.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134393},
doi = {10.1016/j.biortech.2026.134393},
pmid = {41812803},
issn = {1873-2976},
abstract = {Microbial chain elongation (CE) converts low-value substrates into medium-chain fatty acids (MCFAs), but its efficiency is often constrained by limited electron availability and incomplete elongation from C4 to C6 products. This study demonstrates that nitrogen-doped carbon quantum dots (NCQDs), under visible light irradiation, significantly improved CE performance and product selectivity. At 1.5 g/L NCQDs, caproate concentration increased to 3.76 g/L, representing a 276% improvement over the control, while butyrate accumulation decreased, indicating enhanced elongation toward longer-chain products. Electrochemical characterization showed that NCQDs exhibited visible light absorption, a 2.31 eV bandgap, measurable photocurrent responses, and reduced charge-transfer resistance, reflecting enhanced redox activity at the system level. Metagenomic analysis revealed increased relative abundance of Bacillus and enrichment of functional genes associated with reverse β-oxidation and fatty acid biosynthesis pathways. In addition, quorum sensing-related genes (LuxI, LuxR, RpfF) and Hnd hydrogenase-associated gene clusters were enriched, indicating enhanced functional potential for microbial coordination and redox-related metabolism. These coordinated shifts in electrochemical behavior, microbial community composition, and functional gene abundance were consistent with improved caproate production and metabolic selectivity. This work provides an effective hybrid photochemical-microbial strategy associated with enhanced MCFAs production and offers a promising approach for waste valorization into value-added biochemicals.},
}

@article {pmid41812751,
year = {2026},
author = {Prabhakar, S and Rajeev, AC and Sankappa, NM and Premanath, R},
title = {HIGH-THROUGHPUT METAGENOMIC PROFILING OF FUNCTIONAL AND RESISTOME FEATURES IN ESTUARINE MICROPLASTIC MICROBIOMES.},
journal = {Environmental research},
volume = {},
number = {},
pages = {124159},
doi = {10.1016/j.envres.2026.124159},
pmid = {41812751},
issn = {1096-0953},
abstract = {Microplastics (MPs) are now recognized as persistent pollutants in aquatic ecosystems, providing unique surfaces for microbial colonization and acting as vectors for the spread of pathogens, antibiotic resistance, and virulence factors. Estuarine systems, due to their dynamic hydrology and proximity to anthropogenic activity, are particularly vulnerable to MP accumulation and associated microbial risks. This study presents the first comprehensive metagenomic investigation of MP-associated microbial communities across five estuaries spanning the northern and southern coastal regions of Karnataka, India. MPs were isolated, characterized, and the extracted total DNA from the MPs was subjected to high-throughput sequencing and comprehensive bioinformatic analyses. Taxonomic, functional, and resistance gene profiling were performed to evaluate microbial diversity, ecological roles, and potential public health implications. The findings revealed distinct regional differences in microbial community structure and functional potential, with evidence of clinically relevant pathogens, antibiotic resistance genes, and virulence determinants within the plastisphere. These results highlight the role of MPs as reservoirs and vectors for microbial risks in estuarine ecosystems. By linking microbial diversity of MPs with environmental and anthropogenic influences, this work provides crucial baseline data for monitoring and managing estuarine health. It also underscores the urgent need for integrated strategies to mitigate plastic pollution and its cascading ecological and public health impacts.},
}

@article {pmid41811805,
year = {2026},
author = {Vilkoite, I and Silamiķelis, I and Kloviņš, J and Tolmanis, I and Lejnieks, A and Runce, E and Cēbere, K and Margole, K and Sjomina, O and Silamiķele, L},
title = {Colorectal adenoma presence is associated with decreased menaquinone pathway functions in the gut microbiome of patients undergoing routine colonoscopy.},
journal = {PloS one},
volume = {21},
number = {3},
pages = {e0344050},
doi = {10.1371/journal.pone.0344050},
pmid = {41811805},
issn = {1932-6203},
abstract = {BACKGROUND: Colorectal adenomas are key precancerous lesions and a major target for colorectal cancer prevention. While gut microbiome alterations are well described in colorectal cancer, microbial composition and functional capacity at the adenoma stage remain poorly understood. Emerging metagenomic data suggest early adenomas are associated with loss of microbial metabolic functions supporting epithelial and immune homeostasis.

OBJECTIVES: To investigate the association between gut microbiome composition and functional pathways and the presence of colorectal adenomas in patients undergoing routine colonoscopy.

MATERIALS AND METHODS: This cross-sectional case-control study included adult patients undergoing routine colonoscopy. Participants were enrolled based on strict inclusion and exclusion criteria to minimize confounding factors such as inflammatory bowel disease, prior colorectal surgery, and recent antibiotic or probiotic use. Fecal samples were collected prior to bowel preparation, and gut microbiome taxonomic composition and functional pathways were analyzed using shotgun metagenomic sequencing.

RESULTS: A total of 136 participants were included, of whom 56 had colorectal adenomas. Alpha diversity indices did not differ significantly between adenoma-positive and adenoma-negative groups. In contrast, beta diversity analysis revealed significant differences in overall microbial community structure. Descriptive genus-level differences suggested features of dysbiosis in adenoma-positive patients, including higher relative abundance of Bacteroides and Prevotella and lower abundance of Faecalibacterium and Anaerostipes. Differential abundance analysis identified a single species-level feature, UBA7597 sp003448195, enriched in the adenoma group. Functional profiling showed reduced microbial pathways related to menaquinone (vitamin K₂) biosynthesis, Stickland fermentation, and short-chain fatty acid (propionate) production in patients with adenomas.

CONCLUSIONS: The presence of colorectal adenomas was associated with reduced microbial metabolic functions linked to vitamin K₂ biosynthesis, amino acid fermentation, and propionate production, alongside compositional shifts toward a less functionally robust gut microbiome. These findings indicate that early colorectal neoplasia is accompanied by functional microbiome alterations that may serve as markers of adenoma-associated dysbiosis and provide insight into early metabolic changes in the colonic microenvironment.},
}

@article {pmid41811526,
year = {2026},
author = {Tammi, R and Maukonen, M and Kaartinen, NE and Koponen, K and Niiranen, T and Méric, G and Albanes, D and Eriksson, JG and Jousilahti, P and Koskinen, S and Pajari, AM and Knight, R and Havulinna, AS and Salomaa, V and Männistö, S},
title = {Interplay between colorectal cancer-related lifestyles and the gut microbiome: an exploratory analysis of metagenomic data.},
journal = {Cancer causes & control : CCC},
volume = {37},
number = {4},
pages = {},
pmid = {41811526},
issn = {1573-7225},
support = {352481//Strategic Research Council/ ; 352483//Strategic Research Council/ ; },
abstract = {PURPOSE: The gut microbiome may modify the associations between lifestyle factors and colorectal cancer (CRC) risk, but their complex interplay, including the interactions between lifestyle factors, remain underexplored. We examined associations between CRC-related lifestyle patterns and gut microbiome diversity and composition in Finnish adults.

METHODS: Our data included 1,228 adults aged 25-64 years from the National FINRISK/FINDIET 2002 Study. Information on lifestyle and background factors was obtained through self-administered questionnaires. Dietary data were gathered using a 48-h dietary recall. CRC-related lifestyles were modelled using a CRC lifestyle index based on nine major risk factors for CRC. Lower index points reflected higher-risk lifestyles. The gut microbiome profiles were analyzed using shallow shotgun metagenome sequencing. Associations between the index and microbial diversity and composition were assessed using, e.g., linear regression and permutational multivariate ANOVA adjusted for relevant confounders.

RESULTS: The index explained 0.2% of the variation in microbial composition between participants (p < 0.05). Higher-risk lifestyles for CRC were associated with lower microbial diversity (β 0.037, p 0.009). Higher-risk lifestyles were also associated with a higher relative abundance of species representing primarily the family Lachnospiraceae and genera such as Dorea and Mediterraneibacter, and lower relative abundance of species within the genus Bifidobacterium (< 0.0001).

CONCLUSIONS: Participants with higher- and lower-risk lifestyles showed clear differences in their gut microbiome diversity and composition, higher-risk lifestyles being associated with potentially adverse microbial traits. These findings contribute to identifying microbial features that may characterize early stages of CRC development in individuals with high-risk lifestyles.},
}

@article {pmid41810553,
year = {2026},
author = {Boscá-Sánchez, I and Rodríguez-Díaz, J and Yebra, MJ},
title = {Sequence-Based and Functional Analysis for the Discovery of N-Glycan Degrading Glycosidases From the Microbial Metagenome of the Infant Gut.},
journal = {MicrobiologyOpen},
volume = {15},
number = {2},
pages = {e70264},
doi = {10.1002/mbo3.70264},
pmid = {41810553},
issn = {2045-8827},
support = {PID2023-148094OB (C21 and C22)//Ministerio de Ciencia e Innovación/ ; },
abstract = {The role of bacterial glycosyl hydrolases (GHs) in degrading free human milk oligosaccharides is well documented. However, their activity on glycoconjugates is less well known. Here, an in silico analysis of the metagenome of the fecal microbiome of breastfed infants was employed to identify GH2 β-galactosidases, GH20 exo-N-acetylglucosaminidases and GH18 endo-N-acetylglucosaminidases active on N-glycans. A total of nine β-galactosidases were recombinantly expressed and two of them, Gal1b and Gal99, were able to remove galactose from the G2 peptide and asialofetuin. Gal1b, Gal25, Gal37c, Gal99 and Gal296 hydrolyzed lactose and N-acetyllactosamine, indicating specificity for galactose β1,4-linked to glucose or GlcNAc. All of the exo-β-N-acetylglucosaminidases studied here (Exo10a, Exo18, Exo38, Exo39b, Exo360 and Exo399) hydrolyzed the disaccharide N-acetylglucosaminyl-β1,2-mannose, which forms part of the N-glycan structures. Exo10a, Exo38 and Exo360 hydrolyzed N-acetylglucosamine (GlcNAc) from the G2 peptide pretreated with Gal1b. Notably, Exo360 hydrolyzed GlcNAc at both the α1,3 and α1,6 branches of the G2 peptide core mannose simultaneously, whereas Exo10a showed a preference for GlcNAc at one branch. Exo38 and Exo360 also release GlcNAc from asialofetuin once galactose has been removed. The whole structures of N-glycans were liberated from glycoproteins by the action of the endo-N-acetylglucosaminidases Endo38 and Endo358. These enzymes hydrolyze the N,N'-diacetylchitobiose core of N-linked glycans of the high-mannose and non-sialylated complex types, respectively. Overall, these results provide insight into the range of glycosyl hydrolases present in the infant gut microbiota that act on glycoconjugates, which may play a role in the establishment and composition of the newborn microbiota.},
}

@article {pmid41810379,
year = {2026},
author = {Anzà, S and Rosa, BA and Herzberg, MP and Lee, G and Herzog, ED and Zhao, P and England, SK and Ndao, IM and Martin, J and Smyser, CD and Rogers, CE and Barch, DM and Hoyniak, C and McCarthy, R and Luby, J and Warner, BB and Mitreva, M},
title = {Simplifying Daily Cortisol Cycle Analysis: Validation and Benchmarking of the Cortisol Sine Score Against Cosinor and JTK_CYCLE models.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.02.23.26346831},
pmid = {41810379},
abstract = {UNLABELLED: The daily cortisol cycle is a critical indicator of hypothalamic-pituitary-adrenal (HPA) axis function. The current analytical approaches produce several outputs difficult to integrate into simple statistical models, clinical workflows, and ML/AI pipelines requiring single-value inputs. We developed the Cortisol Sine Score (CSS), a model-free scalar metric that quantifies daily cortisol exposure by computing a weighted sum of cortisol measurements across the day, using sine-transformed time-of-day weights. The CSS produces positive values for morning-dominant patterns, negative values for evening-shifted profiles, and near-zero values for flattened rhythms characteristic of chronic stress and circadian disruption. We validated the CSS performance in 3,006 samples from 501 pregnant women enrolled in the March of Dimes program, with cortisol values measured at 6 time points per day collected during the second trimester of pregnancy. The CSS showed strong correlations with observed and model-estimated amplitude and acrophase from Cosinor regression and JTK_CYCLE approaches, with excellent classifying performance (AUC=0.89, high versus low). The CSS successfully captured established associations between social disadvantage and cortisol dysregulation, and demonstrated utility in predicting gut microbiome composition in metagenomic analyses. Importantly, the CSS maintains excellent fidelity to the full 6-sample protocol with as few as 3-4 daily measurements. The 4-sample protocol achieves great performance (r = 0.952, MAE = 0.087) while reducing participant burden. The 06:00 time point was identified as essential for accurate CSS quantification. The CSS bridges the gap between circadian analysis and practical implementation by providing a simple, interpretable, and robust assessment of cortisol daily cycle in large-scale epidemiological studies, clinical screening, and biomedical sensors.

HIGHLIGHTS: Current state-of-the-art approaches estimating the daily cortisol exposures produce multi-output information difficult to implement in simple statistical analyses or ML/AI multi-omics approachesCortisol Sine Score is a novel model-free scalar metric expressing cortisol daily exposure and rhythmicity (morning vs evening exposure)Cortisol Sine Score was validated using 3006 salivary samples from clinical data and golden standards in circadian analyses such as Cosinor and JTK_CYCLECortisol Sine Score was the top performer in our benchmarking approach predicting association with social disadvantage and gut microbiome compositionReliable with 3-4 daily samples, reducing participant burdenOpen-source R package CortSineScore democratizes cortisol cycle analysis.},
}

@article {pmid41810372,
year = {2026},
author = {Ding, SC and Yu, J and Liao, T and Ahmann, LS and Yao, YY and Ho, C and Wang, L and Pinsky, BA and Gu, W},
title = {Adapting Clinical Chemistry Plasma as a Source for Liquid Biopsies.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.08.13.25333564},
pmid = {41810372},
abstract = {BACKGROUND: Circulating cell-free DNA (cfDNA) has become a valuable analyte for molecular testing, but requires specialized collection tubes or immediate processing. We investigated the feasibility of using residual plasma from heparin separators, which are routinely used in clinical chemistry, as an accessible and underutilized source for cfDNA biobanking and testing.

METHODS: We analyzed matched plasma samples from healthy volunteers in two experiments: an immediate-processing tube comparison across EDTA, Streck, and heparin separators (n = 5) and a clinical-handling simulation that paired EDTA and heparin separator tubes and delayed processing at room temperature versus 4°C (n = 6). We also analyzed matched EDTA and heparin separator plasma samples from viral PCR-positive patients (Hospital Cohort; n =38). Whole-genome sequencing and genome-wide enriched methylation sequencing were performed to evaluate concordance across multiple benchmarks, including metagenomics, chromosomal copy number, methylome, and fragmentomics.

RESULTS: Under immediate processing, heparin separator plasma showed high concordance with EDTA and Streck plasma for methylation patterns (Pearson's r = 0.92-0.93, Spearman's ρ=0.65-0.70) and fragmentation features (n = 5). In the clinical-handling simulation, cfDNA integrity in heparin separators was comparable to that in EDTA at 4°C (n=6). In the Hospital Cohort, heparin separators showed a strong concordance with matched EDTA tubes for viral detection (n=38, Pearson's r=0.96), copy number alteration profiling (n=6, Pearson's r=0.96-1.00), and methylation patterns (n=12, r=0.83-0.93).

CONCLUSION: Hospital residual plasma from routine clinical chemistry tests that are processed within a short pre-centrifugation window and refrigerated can provide a vast, untapped resource for cfDNA biobanking and potential testing.},
}

@article {pmid41810244,
year = {2026},
author = {Zhou, F and Zhang, Y and Liu, Y and Mou, Y and Chen, J},
title = {Streptococcus suis meningitis in an elderly man: a case report.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1735413},
pmid = {41810244},
issn = {2296-858X},
abstract = {BACKGROUND: Streptococcus suis is a zoonotic pathogen that resides in pigs. It can be transmitted to humans through several routes, including contact with sick or carrier pigs via broken skin or mucous membranes and consumption of undercooked pork products. Streptococcus suis often causes severe clinical symptoms such as meningitis, sepsis, and shock.

CASE PRESENTATION: A 66-years-old male butcher was admitted to the hospital with a sudden high fever and disturbance of consciousness, and he remained in a state of persistent restlessness. The neurological examination findings were as follows: he was poorly cooperative with the examinations of higher cortical functions and cranial nerves, uncooperative with the examination of limb muscle strength, and unable to cooperate with the examinations of sensation and ataxia. He presented with nuchal rigidity, with a distance of four finger breadths between the chin and chest, and Kernig's sign was positive. The patient was diagnosed with Streptococcus suis meningitis based on the results of Metagenomic Capture sequencing, cerebrospinal fluid culture, and blood culture. Considering the patient's critical condition, he had received empirical treatment with cephalosporin in the previous hospital, but the therapeutic effect was not satisfactory. Moreover, in this region, there is a phenomenon of decreased sensitivity in Streptococcus pneumoniae to penicillin and third-generation cephalosporins. Therefore, the patient received antibiotic treatment with vancomycin (1 g) intravenously every 12 h. Concurrently, he was administered mannitol to reduce intracranial pressure and ulinastatin for anti-inflammatory effects and immune enhancement. Subsequently, vancomycin 20 mg was administered by intrathecal injection. The patient's condition improved, and he was discharged from the hospital. There was no special discomfort during follow-up.

CONCLUSION: This case report describes the diagnosis and treatment process of Streptococcus suis meningitis. It proposes an antibiotic treatment plan centered on vancomycin. Intrathecal injection of antibiotics may provide an effective treatment option for severe patients and offer a treatment choice for drug-resistant bacterial infections in the central nervous system. It was also pointed out that Metagenomic Capture sequencing can reduce host gene interference and increase the detection rate of pathogens. This case aims to enhance clinicians' understanding of the disease and provide a reference for early identification and standardized treatment.},
}

@article {pmid41810234,
year = {2026},
author = {Yang, G and He, S and Wang, J and Yu, S and Zhang, S and Fan, W},
title = {Cryptococcus neoformans infection presenting as a mediastinal mass in an immunocompetent child with parrot exposure: a case report and literature review.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1771746},
pmid = {41810234},
issn = {2296-858X},
abstract = {Cryptococcus neoformans typically causes pulmonary or central nervous system (CNS) infections, but mediastinal mass as its primary manifestation is rare-especially in immunocompetent children with pet parrot exposure. This study reports a 7-year-old girl who presented with recurrent fever and a mediastinal mass secondary to Cryptococcus neoformans infection, with a 5-month history of daily contact with parrot feces. Conventional diagnostic tests (e.g., fungal culture, serology) were negative, and the diagnosis was confirmed by targeted metagenomic next-generation sequencing (tNGS) of bronchoalveolar lavage fluid (BALF). The patient received a three-phase antifungal regimen: induction with amphotericin B + flucytosine, consolidation with fluconazole, and maintenance with low-dose fluconazole. After one year of treatment, the mediastinal mass nearly resolved, and no recurrence was observed. A literature review, supplemented with specific cases of parrot-associated Cryptococcus neoformans infection, highlights that parrot exposure is an underrecognized risk factor for pediatric cryptococcosis, and tNGS significantly improves diagnostic efficiency for atypical extrapulmonary manifestations. This case emphasizes the importance of inquiring about pet bird exposure in children with unexplained mediastinal masses and fever, and supports the use of tNGS for early, non-invasive diagnosis.},
}

@article {pmid41810030,
year = {2026},
author = {Karr, AF and Ruane, R},
title = {Effects of Training Data Quality on Classifier Performance.},
journal = {ArXiv},
volume = {},
number = {},
pages = {},
pmid = {41810030},
issn = {2331-8422},
abstract = {We describe extensive numerical experiments assessing and quantifying how classifier performance depends on the quality of the training data, a frequently neglected component of the analysis of classifiers. More specifically, in the scientific context of metagenomic assembly of short DNA reads into "contigs," we examine the effects of degrading the quality of the training data by multiple mechanisms, and for four classifiers -- Bayes classifiers, neural nets, partition models and random forests. We investigate both individual behavior and congruence among the classifiers. We find breakdown-like behavior that holds for all four classifiers, as degradation increases and they move from being mostly correct to only coincidentally correct, because they are wrong in the same way. In the process, a picture of spatial heterogeneity emerges: as the training data move farther from analysis data, classifier decisions degenerate, the boundary becomes less dense, and congruence increases.},
}

@article {pmid41809988,
year = {2026},
author = {Parks, DH and Newell, RJP and Ginn, AN and Bowerman, KL and Alsheikh-Hussain, A and Fang, L and Shah, S and MacDonald, S and Wimpenny, T and Evans, P and Arias Guzman, NE and Pribyl, AL and Tyson, GW and Hugenholtz, P and Krause, L and Newcombe, J and Griffin, P and Wehrhahn, MC and Angel, NZ and Wood, DLA},
title = {Metagenomics enables parallel detection of 176 clinically relevant targets from faecal samples.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1759322},
pmid = {41809988},
issn = {2235-2988},
mesh = {*Feces/microbiology/virology ; *Metagenomics/methods ; Humans ; High-Throughput Nucleotide Sequencing/methods ; Sensitivity and Specificity ; *Bacteria/genetics/isolation & purification/classification ; *Molecular Diagnostic Techniques/methods ; Virulence Factors/genetics ; Viruses/genetics/isolation & purification ; Reproducibility of Results ; },
abstract = {BACKGROUND: Robust identification of pathogens is essential for managing patients with symptomatic infection, yet conventional diagnostic methods focus on a subset of the most prevalent pathogens and genes. Metagenomic next-generation sequencing (mNGS) is a powerful technology that can comprehensively and simultaneously assess a broader range of pathogens and genes in a sample. This study evaluates the clinical (22 targets), analytical (19 targets), and in silico (176 targets) performance of a faecal mNGS assay on clinically relevant bacterial, eukaryotic, viral, virulence factor (VF) and antimicrobial resistance (AMR) genes.

METHODS: Diagnostic performance was evaluated relative to conventional pathology testing using 510 clinical faecal samples from patients presenting with gastrointestinal symptoms. Contrived samples were used to assess analytical performance and establish the assay's limit of detection by adding cells to a faecal matrix. In silico faecal samples containing targets reflecting the limit of detection of the assay were used to evaluate performance across all 176 targets.

RESULTS: Clinical specificity was ≥96% (≥99% for all but Adenovirus F), and median pathogen sensitivity was 91%. VF and AMR gene detection was less sensitive (median 58.7%). The assay was highly reproducible in biological triplicates (27,656/27,808 calls concordant; 99.5%). Importantly, broad mNGS coverage increased diagnostic yield, with 256/510 (50.2%) samples containing one or more additional targets not reported by standard care, and 181/510 (35.5%) containing AMR genes, including carbapenemases. In silico benchmarking showed strong performance for all 176 targets down to analytically defined detection limits.

CONCLUSIONS: The faecal mNGS assay performed competitively with existing diagnostic techniques while substantially expanding actionable detection in a single assay. These results support stool mNGS as a high-yield second-line or syndromic test for gastrointestinal infection, enabling improved recognition of rare pathogens, co-infections, and resistance determinants.},
}

*Feces/microbiology/virology
*Metagenomics/methods
Humans
High-Throughput Nucleotide Sequencing/methods
Sensitivity and Specificity
*Bacteria/genetics/isolation & purification/classification
*Molecular Diagnostic Techniques/methods
Virulence Factors/genetics
Viruses/genetics/isolation & purification
Reproducibility of Results

@article {pmid41809936,
year = {2026},
author = {Su, M and Luo, Y and Huan, X and Xi, C and Yang, L and Zhong, H and Liu, F and Zhang, Q and Liu, Q and Wang, X and Cao, Y and Wang, M and Ta, F and Wang, B and Ai, J and Zhao, C and Zheng, J and Luo, S},
title = {Application of Droplet Digital PCR in Sputum Samples in Myasthenia Gravis Patients with Pneumonia.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {588779},
pmid = {41809936},
issn = {1178-6973},
abstract = {BACKGROUND: Due to the rapid progression of the pneumonia in patients with Myasthenia gravis (MG), faster pathogen detection techniques are needed. The droplet digital polymerase chain reaction (ddPCR) has the ability to detect pathogens in about 3 h. Thus, this study focused on application of ddPCR in sputum samples in the MG patients with pneumonia and analyzed the association between ddPCR and other laboratory results.

METHODS: We prospectively enrolled 22 MG inpatients with pneumonia and collected 24 sputum samples. All samples were analyzed using traditional culture, ddPCR and metagenomic next-generation sequencing (mNGS) in parallel. Clinical outcomes during hospitalization were documented.

RESULTS: Among the 24 sputum samples collected from 22 MG patients, ddPCR achieved a 100% positivity rate with the identification of bacteria in all 24 samples, while mNGS also demonstrated a high detection rate, identifying bacteria in 23 of 24 samples (95.8%), and additionally detecting viral and fungal pathogens across multiple cases. In 4 patients with negative sputum culture results, pathogens were identified by both ddPCR and mNGS.

CONCLUSION: The ddPCR demonstrated rapid and sensitive identification of predefined bacterial targets and drug-resistance genes, making it suitable for initial diagnostic screening and timely clinical decision-making in MG patients with pneumonia. The speed of ddPCR detection is faster than mNGS and traditional culture, and the results are similar to mNGS and culture, with good consistency.},
}

@article {pmid41809703,
year = {2026},
author = {Suvvari, TK and Kodakandla, R and Kandi, V},
title = {Redefining the diagnostic pathway for pulmonary nocardiosis: The imperative for early metagenomic sequencing.},
journal = {World journal of radiology},
volume = {18},
number = {2},
pages = {119080},
pmid = {41809703},
issn = {1949-8470},
abstract = {In this article, we comment on the pivotal article by Wang et al. We focus on the critical intersection of advanced imaging and molecular diagnostics highlighted by their findings. The study delineates specific high-risk computed tomography patterns, notably consolidation with nodules/cavities, particularly in immunocompromised hosts or patients with bronchiectasis, that should serve as immediate red flags for pulmonary nocardiosis. Traditionally, diagnosis has relied on slow-growing cultures, leading to dangerous therapeutic delays. This editorial argues that the presence of these defined radiologic signatures may represent an important step toward refining the diagnostic pathway for pulmonary nocardiosis. Rather than a confirmatory last resort, metagenomic next-generation sequencing should be deployed as a first-line investigative tool following high-suspicion imaging. We propose a concrete, integrated diagnostic algorithm where imaging triage triggers parallel processing with metagenomic next-generation sequencing and conventional microbiology. This synergy of morphology and metagenomics promises to expedite species-specific diagnosis, guide timely targeted therapy, and ultimately improve outcomes for patients with this challenging and often elusive infection.},
}

@article {pmid41809656,
year = {2026},
author = {Burakova, I and Smirnova, Y and Morozova, P and Pogorelova, S and Kryukova, O and Kislova, T and Korneeva, O and Syromyatnikov, M},
title = {The effect of short-term consumption of Bifidobacterium bifidum on the gut microbiome of obese individuals.},
journal = {Experimental biology and medicine (Maywood, N.J.)},
volume = {251},
number = {},
pages = {10894},
pmid = {41809656},
issn = {1535-3699},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Obesity/microbiology ; *Probiotics/administration & dosage/therapeutic use ; *Bifidobacterium bifidum/physiology ; Male ; Female ; Adult ; Middle Aged ; Dysbiosis/microbiology ; Feces/microbiology ; High-Throughput Nucleotide Sequencing ; },
abstract = {It is known that gut microbiota dysbiosis can lead to obesity by disrupting energy consumption and metabolism. Probiotic supplements are a potential therapeutic option for improving intestinal homeostasis. The aim of this study was to investigate the effect of a probiotic supplement containing Bifidobacterium bifidum on the intestinal microbiome of people with obesity using high-throughput sequencing on the DNBSEQ-G50 platform. The study demonstrated a positive effect of the supplement on bacterial species such as Bacteroides uniformis, Alistipes putredinis, Alistipes shahii, Dysosmobacter welbionis, and Gemmiger formicilis. Therefore, we suggest the potential use of this bacterial species in the treatment of gut microbiota dysbiosis of obese individuals.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Obesity/microbiology
*Probiotics/administration & dosage/therapeutic use
*Bifidobacterium bifidum/physiology
Male
Female
Adult
Middle Aged
Dysbiosis/microbiology
Feces/microbiology
High-Throughput Nucleotide Sequencing

@article {pmid41809628,
year = {2026},
author = {Zhang, W and Tang, Y and Luo, R and He, J and Yan, J and Long, F and Li, L},
title = {Altitudinal changes induce responses in Coptis chinensis Franch. rhizomes: endophytic communities, metabolite types, and alkaloid contents.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1777206},
pmid = {41809628},
issn = {1664-462X},
abstract = {Coptis chinensis Franch. is a perennial medicinal plant with huge economic and social benefits, but how altitude affects the accumulation of bioactive compounds through microbial ecosystems remains unexplored. This study examined how microbial communities at different altitudes influence the bioactive components of Coptis chinensis, to help identify beneficial microorganisms for application to its rhizomes. Samples of Coptis chinensis were cultivated at four different altitudes in Shizhu, Chongqing. To characterize the phytochemical profile of Coptis chinensis, nine specific alkaloids were quantified by High Performance Liquid Chromatography (HPLC) and Ultraviolet-Visible Spectrophotometry (UV-Vis), with Liquid Chromatography-Mass Spectrometry (LC-MS) subsequently employed to characterize differential metabolite accumulation at each altitude. Microbial community structure in the rhizomes was analyzed by metagenomic sequencing. Results indicated that the contents of groenlandicine, coptisine, berberine, and total alkaloids increased with altitude, with the total alkaloid content rising from 15.97% at 907 m to 17.82% at 1698 m (P < 0.01). Analysis revealed 912 differential metabolites, with distinct accumulation patterns at different altitudes. Microbial diversity in the rhizomes also varied by altitude, with significant shifts in Mucoromycota, Pseudomonadota, Rhizophagus, and Mesorhizobium populations. Moreover, the relative abundance of these microorganisms was intricately linked to alkaloid content. High altitude significantly enhances alkaloid accumulation in C. chinensis, and this effect is primarily mediated by the enrichment of beneficial endophytes, which promote the biosynthesis of target alkaloids via optimizing nitrogen utilization and inducing the expression of key enzymes.},
}

@article {pmid41809269,
year = {2026},
author = {Pei, J and Chen, L and Pushparaj, R and Huang, P and Pan, G and Sun, C and Gao, X and Zhang, L and Manirujjaman, M and Huang, CK and Ting, PS and Deng, Z and Chen, S and Zhang, X and Vatsalya, V and McClain, CJ and Feng, W},
title = {High-dose taurine supplementation exacerbates alcohol-associated liver disease by inducing gut microbiota dysbiosis and bile acid dysregulation in mice.},
journal = {eGastroenterology},
volume = {4},
number = {1},
pages = {e100321},
pmid = {41809269},
issn = {2976-7296},
abstract = {BACKGROUND: β-aminoethanesulfonic acid (taurine) is a conditionally essential amino acid that plays critical roles in bile acid (BA) conjugation, antioxidative defence and metabolic regulation. Previous studies showed that faecal taurine level was reduced in patients with alcohol-associated liver disease (ALD), suggesting that taurine supplementation may have beneficial effects. This study aimed to determine whether oral taurine supplementation prevents the development of ALD in mice and to elucidate the underlying mechanisms.

METHODS: A total of 8-week-old male mice were subjected to a chronic-plus-binge ALD model. Taurine was administered orally via the diet for ten days before and during ethanol exposure. Faecal 16S ribosomal RNA metagenomic analysis, liver RNA sequencing and BA profiling were performed.

RESULTS: High-dose taurine supplementation (3 g/kg body weight/day) was associated with worsened ethanol-induced liver injury, as indicated by increased serum alanine aminotransferase (ALT) and aspartate aminotransferase (AST) levels, hepatic steatosis, apoptosis and inflammation. At the molecular level, high-dose taurine treatment was associated with reduced Cpt1a expression, altered expression of genes involved in fatty acid β-oxidation and lipogenic gene Fasn, and decreased expression of Baat, accompanied by changes in taurine-conjugated BA profiles. These alterations were accompanied by changes in BA composition and intestinal FXR-associated gene expression. Taurine supplementation was also associated with shifts in gut microbial composition, including enrichment of hydrogen sulfide-producing bacteria, increased microbial H2S production, impaired intestinal barrier-related parameters and increased bacterial translocation to the liver, paralleling enhanced hepatic inflammatory responses. In contrast, low-dose taurine supplementation (0.2 g/kg body weight/day) was associated with improved liver phenotypes, including reduced steatosis, lower serum ALT and AST levels, decreased Fasn expression and enhanced BA conjugation. Collectively, these results indicate a dose-dependent association between taurine supplementation and ALD-related outcomes.

CONCLUSIONS: Our findings suggest that high-dose taurine supplementation is associated with unfavourable alterations in gut microbiota composition, intestinal barrier integrity, BA metabolism and hepatic taurine-related pathways in ALD, coinciding with exacerbated liver injury. In contrast, low-dose taurine supplementation was associated with improved hepatic outcomes. These results highlight the importance of dose considerations in taurine supplementation and support the concept that taurine may exert divergent effects on ALD depending on the administered dose.},
}

@article {pmid41809220,
year = {2026},
author = {Wishahi, M},
title = {Gut microbiotas attributed to disorders and diseases of the gastrointestinal tract, colorectal cancer, bladder cancer: Geographical factors, inflammation, metabolic toxic.},
journal = {World journal of gastrointestinal pharmacology and therapeutics},
volume = {17},
number = {1},
pages = {115573},
pmid = {41809220},
issn = {2150-5349},
abstract = {Recently, there were several publications that attributed gut microbiota (GM) to various gastrointestinal tract functional disorders and diseases, including inflammatory bowel diseases, colon cancer, pancreatic cancer, and diverticulosis. GM is attributed to the initiation of urinary tract diseases and bladder carcinoma (BCa). The concern is whether GM is dysbiotic or protective. We explored the studies on GM contribution to colorectal cancer and BCa. Selected studies from different geographical regions on tissue samples or faecal samples from patients with colorectal cancer and controls. The results showed diverging results of microbiota abundance, genus, class, and phylum. These data indicated that other factors of environmental, diet, ethnic, and personal factors are contributors to GM in the initiation of inflammation and tumors. GM are not inhabitants in the urinary tract; it is postulated that GM attributes to BCa via the circulating metabolic toxins in the initiation of tumorigenesis and BCa.},
}

@article {pmid41808765,
year = {2026},
author = {Rivera-Sánchez, ES and Salinas-García, M and Viviano, E and Villaró-Cos, S and Lafarga, T},
title = {Effect of salinity on growth and microbial diversity in cultures of Scenedesmus almeriensis produced at a pilot scale.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {14},
number = {},
pages = {1753183},
pmid = {41808765},
issn = {2296-4185},
abstract = {Introduction: Freshwater scarcity represents a major constraint for the sustainable industrial-scale cultivation of microalgae. This study investigates the feasibility of producing Scenedesmus almeriensis using seawater in 3.1 m[3] tubular photobioreactors under winter-spring conditions. The appearance of algal predators represents a significant challenge in industrial facilities, and this research also explores whether seawater can serve as a strategic water source for more resilient and efficient production systems. Methods: Biomass productivity and microbial diversity were compared between freshwater and seawater-based cultures under batch and semi-continuous regimes at dilution rates of 0.1, 0.2, and 0.3 day[-1]. The production was carried out in duplicate using identical tubular photobioreactors. Analytical determinations included measuring biomass concentration, chlorophyll fluorescence, and oxygen production via photorespirometry. Microbial diversity was assessed through microscopy and metagenomic analysis (18S and 16S rDNA) to identify taxonomic classifications and potential biotic contaminants. Results and Discussion: Maximum biomass concentrations reached 0.60 and 2.15 g·L[-1] in freshwater and seawater, respectively. Production using seawater led to a higher biomass productivity (0.18 g·L[-1]·day[-1]) compared to freshwater (0.06 g·L[-1]·day[-1]) at a fixed dilution rate of 0.1 day[-1]. Seawater cultures exhibited greater stability and higher photosynthetic efficiency, with Scenedesmus dominating up to 70% of the microalgal community due to reduced contamination by zooplankton, fungi, and ciliates. In contrast, freshwater cultures were rapidly degraded by rotifers and anaerobic fungi, leading to a culture crash when dilution rates were increased. These findings highlight the potential of seawater to act as a biological barrier against contaminants while significantly reducing freshwater requirements in industrial microalgae production.},
}

@article {pmid41808728,
year = {2026},
author = {Pereira, MH and Tyagi, S and Mohanty, A and Garg, S and Kumar, A},
title = {Metagenomic studies reveal diverse microbial community in the developmental stages of highly adaptable malarial vector Anopheles stephensi liston.},
journal = {3 Biotech},
volume = {16},
number = {4},
pages = {124},
pmid = {41808728},
issn = {2190-572X},
abstract = {UNLABELLED: Anopheles stephensi, a highly adaptable malaria vector species, continues to expand its range from South Asia to Sub-Saharan Africa, posing a serious global public health concern. In India, it serves as the principal urban vector of both Plasmodium falciparum and P. vivax. Conventional control measures reliant on chemical insecticides have raised issues of resistance, highlighting the need for alternative strategies such as microbiota-mediated vector control. This study aimed to test the hypothesis that a subset of bacterial taxa persist across developmental stages of An. stephensi, representing potential candidates for transstadial transmission and future paratransgenic manipulation. Using both culture-based data and next-generation sequencing (NGS) approaches targeting the 16 S rRNA gene (V3-V4 region), we characterized bacterial communities from breeding water, larvae, pupae, and adult mosquitoes (male and female) collected in Goa, India. Across all developmental stages, Proteobacteria and Firmicutes were the dominant phyla, while 15 bacterial genera formed the putative core microbiome shared by ≥ 80% of stages at ≥ 0.1% abundance. Among these, Pseudomonas (adult males: 11.5%, pupae: 3.2%), Exiguobacterium, Acinetobacter, Psychrobacter, and Asticcacaulis were consistently detected, together contributing approximately 30% of total microbial composition. Alpha diversity indices indicated higher richness and evenness in pupae and adults than in larvae, suggesting microbial enrichment during metamorphosis. Beta diversity and PCoA analyses clustered pupal and adult stages distinctly from larvae and breeding water, confirming selective microbial retention through development. These findings reveal that An. stephensi harbors a stable, stage-spanning core microbiome dominated by metabolically versatile genera with potential for transstadial persistence. The dominance of Pseudomonas across life stages supports its candidacy for paratransgenic applications aimed at disrupting malaria transmission. This work provides the first integrated culture-NGS baseline of An. stephensi microbiota from India, offering essential insight for microbiome-based vector control strategies.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-026-04739-6.},
}

@article {pmid41808525,
year = {2026},
author = {Jiménez, DJ and Rosado, AS},
title = {Discovering PETases: An Interlink Between Engineering Enzymes and Microbiomes.},
journal = {Environmental microbiology},
volume = {28},
number = {3},
pages = {e70272},
doi = {10.1111/1462-2920.70272},
pmid = {41808525},
issn = {1462-2920},
support = {BAS/1/1096-01-01//King Abdullah University of Science and Technology/ ; },
mesh = {*Microbiota ; *Polyethylene Terephthalates/metabolism ; *Hydrolases/metabolism/genetics ; Metagenomics ; Biocatalysis ; *Bacteria/enzymology/genetics ; },
abstract = {Polyethylene terephthalate (PET), an abundant synthetic polyester, is the only plastic that has been enzymatically recycled at an industrial scale. Over the last decades, research efforts have focused on screening and engineering PET-degrading hydrolases (PETases), aiming to identify variants that can operate efficiently in both environmental and industrial settings. The detection of potential PETases from marine and terrestrial ecosystems has primarily been conducted via metagenomics using homology strategies. However, the use of benchmark PETases as references has limited the searches, narrowing the sequence landscape. Currently, there remains a need to identify efficient thermophilic, halotolerant and pH-robust PETases for the industrial biocatalysis of PET. In line with this, in this article, we discuss recent findings related to the following topics: (i) the identification of suitable ecosystems for mining PETases; (ii) the discovery of PETases via the restructuring of microbiomes; (iii) advancements in metagenomics and artificial intelligence (AI)-based approaches for the detection and ranking of PETases and (iv) the future of PET biocatalysis. Overall, we suggest that disrupting microbiomes with polyester-rich substrates, combined with innovative computational and AI-based strategies, can be an effective pathway for the discovery of PETases that can be used as scaffolds for protein engineering and biotechnological applications.},
}

*Microbiota
*Polyethylene Terephthalates/metabolism
*Hydrolases/metabolism/genetics
Metagenomics
Biocatalysis
*Bacteria/enzymology/genetics

@article {pmid41808169,
year = {2026},
author = {Cui, T and Yang, Y and Lange, D and Wang, X and Ruan, J and Ji, J and Dang, K and Zhou, Y and Xiao, J},
title = {Gut microbiome and metabolome signatures in calcium oxalate stone recurrence: a multi-omics study.},
journal = {Microbial cell factories},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12934-026-02977-0},
pmid = {41808169},
issn = {1475-2859},
support = {20240930//Beijing Key Clinical Specialty Project/ ; BJPSTP-2024-30//Beijing Physician Scientist Training Project/ ; 82000717//National Natural Science Foundation of China/ ; QML20190106//Beijing Hospitals Authority Youth Programme/ ; },
}

@article {pmid41807455,
year = {2026},
author = {Bi, D and Wu, Y and Ji, G and Zhu, X and Li, H and Xie, R and Gao, Y and Deng, Z and Han, D and Qin, H and Wei, Q},
title = {Integrating ANI and phylogenies for re-evaluation of Fusobacterium taxonomy and disease associations.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-70540-x},
pmid = {41807455},
issn = {2041-1723},
support = {82572576//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82072236//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82072634//National Natural Science Foundation of China (National Science Foundation of China)/ ; SHDC2020CR2069B//Shanghai Hospital Development Center (SHDC)/ ; },
abstract = {The genus Fusobacterium encompasses significant pathogens implicated in diseases spanning from infections to cancer. However, taxonomic ambiguities persist within the genus, particularly concerning Fusobacterium nucleatum (sensu lato). Through genus-wide average nucleotide identity (ANI) and phylogenetic analyses of 540 Fusobacterium genomes, we identify an ANI gap (93.38%-93.89%) for species delineation, leading to comprehensive taxonomic revisions that resolve these ambiguities. We further establish gyrB and rpoB as high-resolution taxonomic markers with phylogenies consistently supporting the revised taxonomy. Leveraging these markers, we develop B&B, a general strategy for precise species identification without whole-genome sequencing, and validate its accuracy in clinically relevant strains. Integrating the revised taxonomy with genomic/metagenomic toolkits demonstrate broad utilities, reinterpreting key colorectal cancer-associated species. This work establishes a unified taxonomic framework and enables standardised species classification for Fusobacterium isolates and microbiomes, highlighting the genetic divergence among Fusobacterium species and providing the taxonomic precision essential for advancing Fusobacterium-related research.},
}

@article {pmid41806991,
year = {2026},
author = {Martinez-Tellez, B and Schönke, M and Kovynev, A and Garcia-Dominguez, E and Ortiz-Alvarez, L and Verhoeven, A and Gacesa, R and Vich Vila, A and Ducarmon, QR and Jimenez-Pavon, D and Gomez-Cabrera, MDC and Weersma, RK and Smits, WK and Giera, M and Ruiz, JR and Rensen, PC},
title = {Roseburia inulinivorans increases muscle strength.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-336980},
pmid = {41806991},
issn = {1468-3288},
abstract = {BACKGROUND: Gut bacteria have been implicated in a wide range of health conditions, yet their potential role in preventing and treating muscle-wasting disorders remains largely unexplored.

OBJECTIVE: We aimed to investigate whether specific gut microbial species are associated with muscle strength and to explore underlying mechanisms linking the gut microbiota to muscle health.

DESIGN: We conducted metagenomic analyses in cohorts of younger and older adults extensively phenotyped for muscle strength. Associations were tested between bacterial taxa and performance measures. Causality was assessed by oral supplementation of candidate species in antibiotic-treated mice. Metabolomic profiling and muscle phenotyping were performed to elucidate mechanisms.

RESULTS: The relative abundance of Roseburia inulinivorans, but not other Roseburia species, was positively associated with multiple strength measures including handgrip, leg press and bench press in humans. Supplementation of R. inulinivorans in mice significantly enhanced forelimb grip strength, whereas other Roseburia species had no effect. Metabolomic analyses revealed that R. inulinivorans reduced amino acid concentrations in the caecum and plasma, while activating the purine and pentose phosphate pathway in muscle. These changes coincided with increased muscle fibre size and a shift from type I to type II fibres. Accordingly, we observed that the relative abundance of R. inulinivorans is lower in older adults compared with young adults.

CONCLUSION: R. inulinivorans emerges as a species-specific modulator of muscle strength, linking gut microbiota to muscle metabolism and function. These findings support its potential as a probiotic candidate for nutraceutical interventions targeting age-related muscle-wasting diseases.

TRIAL REGISTRATION NUMBER: NCT02365129.},
}

@article {pmid41612181,
year = {2026},
author = {Zhang, J and Deng, J and He, B and Wang, H and Lin, D and Li, J and Zhong, Q and Chen, Y and Liao, S and Wang, J and Wang, Y and Su, M and Guo, X},
title = {The study on the identification of cross-boundary microbiome enterotypes between high-altitude and coastal populations and their predictive value.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41612181},
issn = {1471-2180},
support = {2024B03J0562//the Science and Technology Program of Guangzhou/ ; },
abstract = {OBJECTIVE: To investigate the differences in gut microbiome composition among multi-center populations from coastal and high-altitude regions of China and their association with colorectal adenoma (CRA).

METHODS AND ANALYSIS: Metagenomic sequencing was performed on stool samples collected from 295 participants. Diversity, principal component, and linear discriminant analyses were conducted to assess microbial composition and functional differences related to geography and disease status.

RESULTS: In high-altitude populations, bacterial enterotypes were predominantly Prevotella, fungal enterotypes Saccharomyces, and archaeal enterotypes Methanobrevibacter, differing from those in coastal populations. Combining bacterial, fungal, and archaeal features improved classification accuracy between high-altitude and coastal populations (AUC = 0.84) and between high-altitude and coastal adenoma patients (AUC = 0.85). Specific enterotypes were observed to correlate significantly with metabolic pathways in high-altitude populations.

CONCLUSION: Significant differences in gut microbiome enterotypes exist across geographic populations, with specific enterotypes in high-altitude populations potentially associated with a lower prevalence of CRA. These findings provide new insights into the gut microbiome–geography relationship and support microbiome-based diagnostic and therapeutic strategies.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-025-04578-0.},
}

@article {pmid41806901,
year = {2026},
author = {Yin, Z and Ping, H and Li, C},
title = {Associations between Antibiotic and Metal Resistance Genes in Geothermal Springs.},
journal = {Environmental research},
volume = {},
number = {},
pages = {124235},
doi = {10.1016/j.envres.2026.124235},
pmid = {41806901},
issn = {1096-0953},
abstract = {Metals, particularly toxic heavy metal(loid) pollutants, have been widely reported to facilitate the co-selection of antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) in contaminated environments. However, in natural geogenically metal-rich systems such as geothermal springs-often considered pristine environments analogous to early Earth-the occurrence of ARGs and their associations with MRGs remain poorly understood. Here, we investigated ARGs and MRGs distribution patterns in China's largest geothermal field using metagenomic and metatranscriptomic analyses. ARGs were detected in all studied geothermal springs, with total abundances ranging from 52.80 to 668.12 TPM. Macrolide-lincosamide-streptogramin (MLS), bacitracin, and rifamycin resistance genes were the most abundant ARGs. Significant associations between ARGs and MRGs were observed across the geothermal springs, as evidenced by Mantel tests and Procrustes analysis. For instance, bacitracin (R = 0.96, P = 1.06E-05) and rifamycin (R = 0.95, P = 3.41E-05) resistance genes exhibited strong positive correlations with arsenic (As) resistance genes. Metagenome-assembled genomes (MAGs) analyses further identified putative key drivers mediating the linkage between ARGs and MRGs (e.g., Thiomonas and Tepidimonas). Metatranscriptomic data confirmed the active transcription of ARGs, MRGs, and mobile genetic elements (MGEs). Collectively, this study provides a systematic understanding of the distribution patterns of ARGs in pristine geothermal springs and highlights their associations with MRGs.},
}

@article {pmid41806753,
year = {2026},
author = {Wang, R and Liu, Z and Zhang, Q and Lian, J and Meng, H},
title = {Performance of oxic/anoxic process for treating aniline wastewater and gaseous N2O emission characteristics under low dissolved oxygen conditions.},
journal = {Journal of environmental management},
volume = {403},
number = {},
pages = {129250},
doi = {10.1016/j.jenvman.2026.129250},
pmid = {41806753},
issn = {1095-8630},
abstract = {In the biological treatment of aniline wastewater, the influence mechanism of dissolved oxygen (DO) concentration on the degradation of pollutants and N2O emission remains unclear. In this study, three A/O reactors were constructed to treat aniline wastewater, with the aerobic stage was operated under distinct low DO conditions: R1 (0.2-1.0 mg/L, ultralow oxygen), R2 (0.3-1.5 mg/L, lower oxygen), and R3 (0.4-2.0 mg/L, low oxygen). The results showed that as DO concentration increased, the removal rates of aniline, COD and NH4[+]-N improved slightly, whereas TN removal rate decreased significantly. During one operating cycle, cumulative gaseous N2O emissions were lowest in R2 and highest in R3. Therefore, considering pollutants removal, N2O emission and energy conservation, the lower oxygen control strategy (0.3-1.5 mg/L) was recommended. The metagenomic data revealed the enrichment of the aniline-degrading bacteria CAADHD01, and denitrifying bacteria JABWCM01, UBA12294, and Thauera in all reactors. The metabolic pathways of aniline and nitrogen were inferred. Aniline degradation primarily occurred via the meta-cleavage pathway, and nitrogen transformation involved assimilation, nitrification, and denitrification, while nitrification was inhibited by aniline. At the lower oxygen level (R2), the abundance of hao (hydroxylamine oxidoreductase gene) was lowest, and that of nosZ (nitrous oxide reductase gene) was highest, leading to lowest N2O emission. This study provides valuable strategies for N2O reduction during the biological treatment of aniline wastewater.},
}

@article {pmid41806446,
year = {2026},
author = {Lo Giudice, A and Papale, M and Bertolino, M and Reboa, A and Rizzo, C},
title = {Diversity and ecology of the prokaryotic microbiome associated with marine sponges across Antarctica.},
journal = {The Science of the total environment},
volume = {1025},
number = {},
pages = {181655},
doi = {10.1016/j.scitotenv.2026.181655},
pmid = {41806446},
issn = {1879-1026},
abstract = {Antarctic sponges host diverse and functionally relevant microbial communities that play central roles in the structure and resilience of polar benthic ecosystems. This review provides a focused analysis of the prokaryotic microbiomes associated with Antarctic sponges, with an emphasis on three ecologically significant species: Mycale (Oxymycale) acerata, Dendrilla antarctica, and Hymeniacidon torquata. Drawing from recent molecular studies, we examine the composition, predicted functional potential, and environmental responsiveness of these bacterial and archaeal communities. Comparative analyses with surrounding seawater and sediments reveal both overlaps and distinct host-specific microbial signatures, suggesting that sponge-associated microbiomes are shaped by selective pressures at the host and habitat levels. A conserved microbial core appears to coexist with more variable taxa influenced by host physiology and environmental gradients. We also discuss the impact of environmental stressors on microbiome structure and stability. Functional insights from metagenomic data highlight key microbial contributions to nutrient cycling, symbiotic lifestyles, secondary metabolite and vitamin production, quorum sensing, and the biodegradation of aromatic compounds. This review critically assesses current knowledge on Antarctic sponge-associated prokaryotic microbiomes, identifying recurrent taxonomic and functional patterns and evaluating evidence for core microbial functions across species and regions. We hypothesize that, despite taxonomic variability and geographical sampling bias, Antarctic sponge microbiomes share conserved functional traits shaped by host- and environment-driven selective pressures. Although foundational knowledge has expanded, particularly for shallow-water species, significant gaps persist-especially in underexplored habitats and in linking predicted functions to ecological dynamics. We conclude by outlining research priorities, including standardized protocols, broader spatial and temporal sampling, and multi-omics integration to better understand microbiome resilience under climate-driven change.},
}

@article {pmid41806005,
year = {2026},
author = {Dong, X and Zhang, T and Tang, B and Zeng, Q and Hu, Z and Huang, P and Xiong, X and Wang, X and Dong, W and Cai, Y},
title = {Microbial and metabolic profiles in autism spectrum disorder with atopic dermatitis in children.},
journal = {AMB Express},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13568-026-02037-1},
pmid = {41806005},
issn = {2191-0855},
}

@article {pmid41805951,
year = {2026},
author = {López-Puentes, D and Ojeda-Pérez, ZZ and Arias-Moreno, DM},
title = {Metagenomic Insights into the Microbial Composition and Functional Potential of Cocoa (Theobroma Cacao L.) During Fermentation and Drying in Colombia.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02704-7},
pmid = {41805951},
issn = {1432-184X},
}

@article {pmid41805398,
year = {2026},
author = {Bouderka, F and López-García, P and Deschamps, P and Zhou, Y and Krupovic, M and Gutiérrez-Preciado, A and Ciobanu, M and Bertolino, P and David, G and Moreira, D and Jardillier, L},
title = {Parasitic connections: a patescibacterial epibiont, its methylotrophic gammaproteobacterial host, and their phages.},
journal = {mBio},
volume = {},
number = {},
pages = {e0002526},
doi = {10.1128/mbio.00025-26},
pmid = {41805398},
issn = {2150-7511},
abstract = {Patescibacteriota form a very diverse and widely distributed phylum of small bacteria inferred to have an episymbiotic lifestyle. However, the prevalence of this lifestyle within the phylum and its host specificity remain poorly known due to the scarcity of cultured representatives. Here, we describe a complex system consisting of a patescibacterium, its gammaproteobacterial hosts, and their respective phages based on enrichment cultures and metagenomic data from two shallow, geographically close, freshwater ecosystems. The patescibacterium Strigamonas methylophilicida sp. nov. defines a new genus within the family Absconditicoccaceae. It grows as an epibiont on cells of methanotrophic species of the gammaproteobacterial family Methylophilaceae. Strigamonas cells grow tightly attached to the host, sometimes forming stacks that connect two host cells. Despite a surprisingly large genome (1.9 Mb) compared to many other Patescibacteriota, S. methylophilicida lacks many essential biosynthetic pathways, including the complete biosynthesis of phospholipids, amino acids, and nucleic acids, implying a dependence on the host to obtain these molecules. We also identified and assembled the complete genomes of one patescibacterial phage that might represent a new virus family within the class Caudoviricetes, and two Methylophilaceae phages predicted to have head-tailed and filamentous virions, respectively. The patesciphage uses a modified genetic code similar to that of its host and encodes four tRNA genes, including the suppressor tRNA gene for the UGA stop codon, which is reassigned to glycine in many Patescibacteriota. Our results confirm a prevalent episymbiotic lifestyle in Absconditicoccaceae and further suggest a clade-specific adaptation of this patescibacterial family for gammaproteobacterial hosts.IMPORTANCEPatescibacteriota are ultra-small bacteria with reduced genomes that rely on symbiotic interactions with other prokaryotes; however, their host specificity and associated viral parasites remain poorly characterized due to limited cultured representatives. By combining targeted cultivation with genomic and microscopy analyses, we reveal previously unrecognized host lineages and expand the known viral diversity infecting this major, but still poorly known, bacterial phylum. We describe Strigamonas methylophilicida, a new patescibacterial species of the family Absconditicoccaceae that grows as an epibiont on various methylotrophic Gammaproteobacteria. This expands the host range for this family, previously found to infect only photosynthetic partners. Using enrichment cultures and metagenomics, we retrieved complete genomes of novel phages infecting S. methylophilicida and its methylotrophic hosts, including one phage that uses a modified genetic code matching that of the patescibacterium, which shows a specific viral adaptation to infect Absconditicoccaceae hosts. Our findings reveal a previously unrecognized patescibacteria-methylotrophs-phages tripartite interaction in freshwater environments, highlight the adaptations of patescibacterial phages, and shed light on the complex ecology and evolution of host-parasite-phage dynamics in understudied bacterial lineages.},
}

@article {pmid41805177,
year = {2026},
author = {Pereira, AC and Cortez, F and Chaves, G and Nanetti, E and Leite, RB and Mendes, MC and Oliveira, I and Abreu, H and Martins, M and Keller-Costa, T and Costa, R},
title = {Thirteen metagenome-assembled genomes of Paraglaciecola chathamensis associated with the farmed red seaweeds Porphyra dioica and Porphyra umbilicalis.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0149625},
doi = {10.1128/mra.01496-25},
pmid = {41805177},
issn = {2576-098X},
abstract = {We report 13 metagenome-assembled genomes (MAGs) of Paraglaciecola chathamensis (Gammaproteobacteria) retrieved from farmed Atlantic Nori (Porphyra spp.) across several developmental stages. MAGs encode proteins involved in host-microbe interactions, nutrient acquisition, nitrogen and cofactor metabolism, stress resilience, and genome plasticity, illuminating the possible roles of Paraglaciecola in the Porphyra holobiont.},
}

@article {pmid41805117,
year = {2026},
author = {Chen, S and Li, C and Wang, Z and Teng, Y and Ren, W and Wang, H and Ma, J and Ma, W and Luo, Y and Kuramae, EE},
title = {Specific Metabolites Modulate Core Microbes and Microbial Interactions to Drive Fomesafen Dissipation in the Soybean Rhizosphere.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c15254},
pmid = {41805117},
issn = {1520-5118},
abstract = {Rhizosphere metabolites regulate organic pollutant dissipation through microbiome modulation, yet dynamic interrelationships among metabolite shifts, microbial assembly, and pollutant removal remain unclear. Using multiomics (16S rRNA sequencing, metabolomics, and metagenomics), this study deciphered the temporal dynamics of rhizosphere metabolites and microbiome during the dissipation of fomesafen in soybean pots. Fomesafen dissipation exhibited biphasic kinetics during soybean growth, with an initial rapid phase followed by prolonged stabilization, which was synchronized with time-dependent microbiome perturbations of initial enrichment and subsequent attenuation. Metabolomics revealed fomesafen-induced shifts in rhizosphere metabolites, with 2-naphthalenesulfonic acid (↓20.84%) and 2-hydroxyoctadecanoic acid (↑13.30%) exhibiting opposing effects on microbial assembly, which ultimately affect fomesafen dissipation, as outlined in our conceptual model. Microcosm experiments further demonstrated 2-naphthalenesulfonic acid enhanced while 2-hydroxyoctadecanoic acid inhibited fomesafen dissipation. Our findings highlight the significance of rhizosphere metabolite-mediated interactions between core microbes and potential fomesafen-degraders in governing fomesafen dissipation.},
}

@article {pmid41804674,
year = {2026},
author = {Liu, D and Luo, M and Li, M and Chen, C and Chen, S and Wu, Y and Zhang, G and Gao, Y and Hong, Y and Zhou, Q and Li, X and Zhou, S and Wu, Y and Zhao, Y and Zhang, Y and Yin, J},
title = {Dynamic interaction between Escherichia coli enterotoxins and bacteriocins.},
journal = {The FEBS journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/febs.70488},
pmid = {41804674},
issn = {1742-4658},
support = {2023YFD1401400//the National Key R&D Program of China/ ; 32471200//the National Natural Science Foundation of China/ ; kq2208167//the Natural Science Foundation of Changsha/ ; xjt [2021] 346//the postgraduate joint training base project in Hunan Province/ ; 2023JJ10029//the Natural Science Foundation for Distinguished Young Scholars of Hunan Province/ ; },
abstract = {The intestinal microbiota constitutes a crucial defense barrier against pathogenic invasion; however, the molecular mechanisms enabling pathogens to evade or modulate this defense remain poorly understood. Here, we established a coculture model combining the commensal Escherichia coli Y18J, isolated from the piglet gut, and the enterotoxigenic E. coli (ETEC) strain W25K to investigate microbe-pathogen interactions. Our findings reveal a bidirectional regulatory mechanism between Y18J and W25K mediated by bacteriocin and toxin signaling. Colicin B/M produced by Y18J upregulates the expression of heat-stable enterotoxin (ST) in W25K during the early phase of coculture, while ST suppresses colicin B/M synthesis in Y18J. At later stages, colicin B/M stimulates heat-labile enterotoxin (LT) expression, which in turn enhances colicin B/M production. Notably, LT markedly reduces intestinal colonization of W25K(ST[-]LT[+]) in murine hosts. Leveraging metagenomic and bioinformatic analyses, we further identified a Ligilactobacillus strain within the murine gut microbiota capable of producing multiple bacteriocins that effectively inhibit W25K colonization. Transcriptomic profiling of Y18J revealed glutamine synthetase as a pivotal regulator of colicin B/M-mediated antagonism. Mechanistic investigations demonstrated that ST suppresses colicin B/M expression through the cGMP signaling pathway, whereas LT enhances it via the cAMP signaling pathway. Collectively, these findings uncover a dual regulatory mechanism through which bacterial enterotoxins modulate probiotic antimicrobial activity, providing new insights into the molecular dialog between commensal and pathogenic bacteria. This study establishes a conceptual framework for developing microbiota-based strategies to prevent and control enteric infections.},
}

@article {pmid41804664,
year = {2026},
author = {Bai, Y and Xu, Y and Wu, D and Su, Y and Zhan, M and Xie, B},
title = {The Polymer-Plastisphere-Function Nexus Links to Divergent Biodegradation of Microplastics During Composting.},
journal = {Environmental microbiology},
volume = {28},
number = {3},
pages = {e70278},
doi = {10.1111/1462-2920.70278},
pmid = {41804664},
issn = {1462-2920},
support = {22276059//National Natural Science Foundation of China/ ; 2018YFC1901000//National Key Research and Development Program of China/ ; },
mesh = {Biodegradation, Environmental ; *Composting ; *Microplastics/metabolism ; *Bacteria/metabolism/genetics/classification/isolation & purification ; *Polymers/metabolism/chemistry ; *Soil Microbiology ; Microbiota ; Polyesters/metabolism ; *Soil Pollutants/metabolism ; Soil/chemistry ; },
abstract = {Microplastic (MP) biodegradation is critical for mitigating plastic pollution, yet the ecological mechanisms linking polymer properties to plastisphere microbiome assembly and catalytic function remain unclear. Using thermophilic composting as an accelerated model, we reveal a fundamental dichotomy in which biodegradable MPs (BMPs: polylactic acid [PLA] > polybutylene succinate [PBS] > poly (butylene adipate-co-terephthalate) [PBAT]) undergo rapid thermophilic degradation shaped by stronger environmental filtering of diverse degraders, whereas conventional MPs (CMPs: low-density polyethylene [LDPE]) exhibit delayed degradation with greater stochastic influence. Metagenomics uncovered 489 degradative genes predominantly distributed across uncultured taxa, enabling reconstruction of polymer-specific multi-enzyme pathways, supported by isolating 32 potential degraders (31 candidate novel). PLA/PBS degradation primarily relied on thermophilic-phase PLA depolymerase and cutinase, PBAT on late-stage polyesterase and PETase, and LDPE on alkane monooxygenase and laccase. Statistical modelling showed BMP degradation strongly associated with plastisphere-physicochemical interactions (> 90% variance), whereas CMP appeared primarily constrained by material properties (e.g., degrader succession in PLA, enrichment in PBS/PBAT, and high molecular weight in LDPE). Functionally dominant degraders (1.9% of total microbes) were estimated to contribute 52.4%-80.6% of biodegradation efficiency. This work elucidates the core polymer-plastisphere-functional nexus underlying MP biodegradation during composting, providing a predictive framework and microbial resource for targeted remediation.},
}

Biodegradation, Environmental
*Composting
*Microplastics/metabolism
*Bacteria/metabolism/genetics/classification/isolation & purification
*Polymers/metabolism/chemistry
*Soil Microbiology
Microbiota
Polyesters/metabolism
*Soil Pollutants/metabolism
Soil/chemistry

@article {pmid41804366,
year = {2026},
author = {Jiang, W and Luo, M and Jiang, M and Yang, J and Qin, L and Yang, Z and Xue, F and Long, Z and Zhao, L and Long, H},
title = {Clinical Features and Risk Factors for Severe Disease in 57 Cases of Chlamydia psittaci Pneumonia: A Retrospective Study.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {584050},
pmid = {41804366},
issn = {1178-6973},
abstract = {BACKGROUND: This study aimed to analyze the clinical features of Chlamydia psittaci (C. psittaci) pneumonia and identify risk factors for severe patients to facilitate early diagnosis and treatment.

METHODS: In this retrospective analysis, we collected and summarized the clinical data of 57 patients with C. psittaci pneumonia confirmed by metagenomic next-generation sequencing (mNGS) or targeted next-generation sequencing (tNGS), who were admitted to the First Affiliated Hospital of Guilin Medical University between July 2020 and August 2025. Patients were further divided into a severe group (n=23) and a non-severe group (n=34) for comparative analysis of their clinical characteristics.

RESULTS: The mean age of the patients was 58.68 ± 12.36 years. Common symptoms included fever, cough/sputum, fatigue, dyspnea, and neurological and gastrointestinal symptoms. The severe group had a significantly higher incidence of fatigue, dyspnea, and neurological and gastrointestinal manifestations. Laboratory findings revealed that most patients had normal or mildly elevated white blood cell counts with lymphopenia, alongside significantly elevated levels of C-reactive protein (CRP), procalcitonin (PCT), and erythrocyte sedimentation rate (ESR). Anemia, hypoalbuminemia, and abnormalities in liver enzymes, myocardial enzymes, and electrolytes were also commonly observed. The predominant chest computed tomography finding was consolidation, with pleural effusion present in 59.6% of all patients and occurring more frequently in the severe group. Multivariate analysis identified CRP as an independent risk factor for severe C. psittaci pneumonia, while albumin and platelet count were protective factors.

CONCLUSION: Pneumonia patients presenting with non-specific influenza-like symptoms should raise clinical suspicion for C. psittaci pneumonia. Particular vigilance for potential progression to severe disease is warranted in male patients, the elderly, those with underlying comorbidities, and individuals presenting with neurological or gastrointestinal symptoms. Elevated CRP, hypoalbuminemia, and thrombocytopenia serve as significant predictors of severe C. psittaci pneumonia.},
}

@article {pmid41803907,
year = {2026},
author = {Fernández-de-Bobadilla, MD and Pérez-Cobas, AE and Andremont, A and Martínez, JL and Baquero, F and Lanza, VF and Coque, TM},
title = {The antimicrobial gut resistome of the Wayampi reveals a shared background of antibiotic and metal resistance genes with industrialized populations, underscoring the "robust-yet-fragile" architecture of human gut microbiomes.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02345-5},
pmid = {41803907},
issn = {2049-2618},
support = {pFIS F19/00366//Instituto de Salud Carlos III/ ; CB21/13/00084//Instituto de Salud Carlos III/ ; CC23140547//Fundación Francisco Soria Melguizo/ ; MISTAR AC21_2/00041//Joint Programming Initiative on Antimicrobial Resistance/ ; "Ayudas de atracción de talento investigador César Nombela" 2023-T1/SAL-GL28953//Comunidad de Madrid/ ; FP7#282004//European Union/ ; },
abstract = {BACKGROUND: Metagenomics enables detailed profiling of genes encoding antimicrobial resistance. However, most studies focus exclusively on antibiotic resistance genes (ARGs), excluding those associated with non-antibiotic antimicrobials (metals, biocides), and often rely on methods with low-sensitivity and low-specificity. Furthermore, they rarely examine populations exposed to minimal anthropogenic pollution. We analyzed fecal resistomes of 95 Wayampi individuals, an Indigenous community in remote French Guiana, using a targeted metagenomic capture platform covering 8667 genes, including ARGs, metal resistance genes (MRGs) and biocide resistance genes (BRGs) (PMID: 29335005). Resistome profiles were compared with those of Europeans to assess population-level differences.

RESULTS: ARG richness was similar between groups (259 in Wayampi vs. 264 in Europeans, 159 shared), but MRGs + BRGs gene richness was significantly higher in Wayampi (11,930 vs. 7419). Most genes appeared in a minority of individuals (mean 5% for ARGs, 2% for MRGs + BRGs), but several ARGs for tetracyclines [tet(32), tet(40), tet(O), tet(Q), tet(W), tet(X), tetAB(P)], aminoglycosides (ant6'-I, aph3-III), macrolides (ermB, ermF, mefA), and sulfonamides (sul2) were present in all individuals. Tetracycline resistance genes predominated overall, while beta-lactam resistance genes were more common in Wayampi, and genes conferring resistance to aminoglycosides, amphenicols, and folate inhibitors were more frequent in Europeans. Among MRGs, copper and arsenic resistance genes prevailed in both groups, followed by those for zinc, iron, cobalt, and nickel. Up to 76% of Wayampiis carried acquired MRGs for copper (pcoABCDRS and tcrB), silver (silACFPRS), arsenic (ars), and mercury (mer) detoxification. Shannon diversity indices were similar for ARGs, MRGs, and BRGs, but composition and evenness differed significantly. UMAP and ADONIS analyses distinguished cohorts based on ARG profiles (p < 0.001), but not on MRGs or BRGs. Correlation analysis revealed conserved gene-sharing networks and introgression of acquired ARGs and MRGs within both gut microbiomes.

CONCLUSIONS: The diverse and balanced Wayampi resistome reflects a less perturbed microbiome compared to industrialized populations, and reveals a background of "core" and "shell" acquired ARGs and MRGs, consistent with the "robust-yet-fragile" architecture of scale-free networks. The patchy yet resilient gene distribution suggests varying levels of conserved gene sharing highways among populations, likely shaped by long-term microbial-human evolution, and supports a broader view on acquired antimicrobial resistance. Video Abstract.},
}

@article {pmid41803767,
year = {2026},
author = {Maeda, K and Tamura, Y and Nagai, Y and Kariya, Y and Katsuta, H and Ajiro, N and Yoshida, H and Han, Y and Hashimoto, S and Chikamatsu, K and Takaki, A and Matsumoto, Y and Fatimah, RM and Tanaka, M and Nakamura, S and Iida, T and Mitarai, S and Nagai, T},
title = {Non-tuberculous Mycobacterial pulmonary disease due to novel mycobacterium: Mycobacterium habikinoensis: a case report.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-026-12857-y},
pmid = {41803767},
issn = {1471-2334},
}

@article {pmid41803729,
year = {2026},
author = {Tian, J and Jiang, Y and Ye, N and Zhang, Y},
title = {A case of uveitis and retinal vasculitis induced by varicella-zoster virus: vitrectomy treatment and literature review.},
journal = {BMC ophthalmology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12886-026-04710-2},
pmid = {41803729},
issn = {1471-2415},
support = {20260814//Medical Science Research Project of Hebei/ ; 20260814//Medical Science Research Project of Hebei/ ; 20260814//Medical Science Research Project of Hebei/ ; },
}

@article {pmid41803682,
year = {2026},
author = {Shen, Z and Zhang, Z and Gao, J and Chen, J and Xu, Q and Li, D and Zeng, L and Cheng, D and Wang, K and Zhang, J and Wong, JWC},
title = {Microbial succession accompanies increased antibiotic resistance risk during grass carp (Ctenopharyngodon idella) spoilage under ambient household conditions.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-04924-w},
pmid = {41803682},
issn = {1471-2180},
support = {2024A1515140076//Guangdong Basic and Applied Basic Research Foundation/ ; 22206107//National Natural Science Foundation of China/ ; 2023ZT10L060//Program for Guangdong Introducing Innovative and Entrepreneurial Teams of China/ ; 221110133//Dongguan University of Technology Top Talent Professor Start Up Fund/ ; },
abstract = {Understanding fish spoilage mechanisms under household storage conditions is critical for food safety in regions with limited cold chain infrastructure, where ambient storage remains common practice. This study investigated the spoilage dynamics, microbial succession, and antibiotic resistance gene (ARG) proliferation in grass carp stored under simulated household conditions at 13.0 ± 3.4 °C using three packaging scenarios. The biogenic amine index (BAI) of fish exceeded 50 mg/kg within 16 h, marking early spoilage onset. After 64 h, K-values surpassed 60%, TVB-N exceeded the safety limit of 20 mg/100 g, and BAI reached over 220 mg/kg, indicating advanced spoilage. 16S rRNA amplicon sequencing demonstrated dramatic microbial community shifts from Cyanobacteriota-dominated fresh samples to Pseudomonadota-dominated spoilage communities, with Aeromonas emerging as the primary specific spoilage organism (SSO), increasing from 0.001% to 67.2% at 64 h. Pathogen abundance escalated from 0.06% to 72.2% in muscle tissues, posing substantial food safety risks. Distinct microbial community structures were observed across tissue types (muscle vs. gut) and packaging treatments, with storage time exerting the strongest selective pressure on community composition. Metagenomic analysis revealed progressive ARG enrichment, with surface samples exhibiting 2.6-fold higher total ARG abundance and 3.8-fold greater ARG type richness compared to the fresh gut baseline by 24 ~ 64 h. Rapid ARG enrichment was detected during early spoilage (24 h), representing a critical food safety concern. Notably, carbapenem resistance genes (e.g., OXA-12, cphA6) were substantially enriched, underscoring the high risk posed by these clinically relevant resistance genes. These findings demonstrate that grass carp stored under ambient household conditions maintain acceptable quality for < 16 h, necessitating immediate consumption or cold chain implementation to ensure food safety and minimize ARG dissemination.},
}

@article {pmid41803498,
year = {2026},
author = {Zhou, H and Sun, R and Nie, X and Xia, L and Dong, H and Liu, Y and Hou, S and Dong, W and Zhu, X and Yao, Y and Zhao, GP and Lu, S and Wang, Y and Yang, C},
title = {A clinic-responder-derived defined microbial consortium enhances anti-PD-1 immunotherapy efficacy in mice.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41803498},
issn = {2058-5276},
support = {82241228//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32230060//National Natural Science Foundation of China (National Science Foundation of China)/ ; 31925001//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82073152//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82241227//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82030045//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82241228//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Targeting the gut microbiota is a promising strategy to enhance the efficiency of cancer immunotherapy; however, success has been limited. Here we combined metagenomic analysis and in silico prediction to identify bacterial species associated with immunotherapy response in patients with non-small-cell lung cancer. We constructed a defined consortium (RCom) of 15 bacterial species, most of which were isolated from responder patient faeces, associated with improved clinical response to anti-programmed cell death protein 1 (PD-1) treatment. Metabolic models and in vitro experiments revealed that RCom is a stable and cooperative community, and in vivo experiments showed that RCom engrafts and produces immunomodulatory metabolites. Oral administration of RCom improved the anti-tumour activity of anti-PD-1 by increasing the intratumoural infiltration and cytotoxic function of CD8[+] T cells in syngeneic tumour models and across mice with heterogeneity in baseline gut microbiota composition. RCom supplementation also limited anti-PD-1 resistance in mice conferred by faecal microbiota transplantation from individual non-responsive patients. These findings suggest that RCom is a potential adjuvant to improve responsiveness to anti-PD-1 therapy in cancer.},
}

@article {pmid41803098,
year = {2026},
author = {Zhu, Y and Sun, M and Chen, B and Liu, X and Yang, G and Li, X},
title = {Diagnostic Value of Cerebrospinal Fluid Metagenomics Next-generation Sequencing in Neurobrucellosis in Children: Erratum.},
journal = {The Pediatric infectious disease journal},
volume = {45},
number = {4},
pages = {384},
pmid = {41803098},
issn = {1532-0987},
}

@article {pmid41803086,
year = {2026},
author = {Faure, E and Pommellec, J and Noel, C and Cormier, A and Delpech, LM and Eren, AM and Fernandez-Guerra, A and Vanni, C and Fourquez, M and Houssais, MN and Guyet, U and Da Silva, C and Gavory, F and Perdereau, A and Labadie, K and Wincker, P and Poulain, J and Hassler, C and Lin, Y and Cassar, N and Maignien, L},
title = {Water mass specific genes dominate the Southern Ocean microbiome.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {41803086},
issn = {2041-1723},
support = {18-CE02-0024//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-10-INBS-09-08//Agence Nationale de la Recherche (French National Research Agency)/ ; },
mesh = {*Microbiota/genetics ; *Seawater/microbiology ; Oceans and Seas ; Metagenome/genetics ; Antarctic Regions ; *Bacteria/genetics/classification ; Sulfonium Compounds/metabolism ; Arctic Regions ; Plankton/genetics ; Phylogeny ; },
abstract = {The Southern Ocean (SO) plays a key role in regulating global biogeochemical cycles and climate, yet microbial genes sustaining its biological activity remain poorly characterized. We introduce a microbial genes collection from 218 metagenomes sampled during the Antarctic Circumnavigation Expedition, the majority of which are missing from functional databases. 38% even lack homologs in current reference marine gene catalogs, defining a singular genetic seascape. We show that SO gene assemblages exhibit a common polar signature with the Arctic Ocean while being structured by water masses at the SO-scale. We analyze genomic markers of diverse SO biomes, focusing on dimethylsulphoniopropionate (DMSP) cleavage by polar-adapted bacteria, organic matter consumption in the blooming Mertz polynya and adaptation to polar conditions in the ubiquitous bacteria Pelagibacter. Our work takes a step towards a comprehensive understanding of SO's plankton ecology and evolution, capturing the current state of the unique microbial diversity in this rapidly changing Ocean.},
}

*Microbiota/genetics
*Seawater/microbiology
Oceans and Seas
Metagenome/genetics
Antarctic Regions
*Bacteria/genetics/classification
Sulfonium Compounds/metabolism
Arctic Regions
Plankton/genetics
Phylogeny

@article {pmid41802657,
year = {2026},
author = {Ma, R and Jia, B and Zhang, X and Zhao, Z and Zhao, F and Liong, MT and Ali, A and Abd Hamid, IJ and Hasan, TH and Taib, F and Sun, Z},
title = {Bifidobacterium longum subsp. infantis B8762 Modulates the Infant Gut-Lung Axis via Microbial and Metabolic Reprogramming.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {108431},
doi = {10.1016/j.micpath.2026.108431},
pmid = {41802657},
issn = {1096-1208},
abstract = {Respiratory and gastrointestinal infections are leading causes of morbidity in children. Increasing evidence highlights the gut-lung axis as a key regulatory interface influencing infection susceptibility. Bifidobacterium longum subsp. infantis B8762 (B8762) has shown clinical efficacy in reducing such infections, but its mechanistic basis remains unclear. In a randomized, double-blind, placebo-controlled study involving 115 infants (probiotic group: n = 57, placebo group: n = 58; aged 6-12 months), fecal metagenomic sequencing was performed to assess microbial and functional changes after four weeks of B8762 supplementation (0.5 × 10[10] CFU/day).B8762 significantly altered the gut microbial structure (β-diversity, P < 0.05) without affecting α-diversity. The intervention enriched beneficial taxa including Bifidobacterium longum, Eubacterium limosum, and Roseburia hominis, while reducing potential pathogens such as Staphylococcus aureus and Candida parapsilosis (P < 0.05). Functionally, B8762 upregulated metabolic pathways involved in coenzyme A and L-tryptophan biosynthesis and enhanced predicted production of immunoregulatory metabolites including butyrate, inosine, and chenodeoxycholic acid. In summary, this study suggests that B8762 modulates the pediatric gut microbiota toward a composition and metabolic profile that supports mucosal barrier integrity and systemic immune regulation. These findings provide mechanistic insight into its protective role against respiratory and gastrointestinal infections in children, supporting its use as a targeted gut-lung axis probiotic intervention.},
}

@article {pmid37647722,
year = {2023},
author = {Le Lay, C and Stott, MB and Shi, M and Sadiq, S and Holmes, EC},
title = {A metatranscriptomic analysis of geothermal hot springs reveals diverse RNA viruses including the phylum Lenarviricota.},
journal = {Virology},
volume = {587},
number = {},
pages = {109873},
doi = {10.1016/j.virol.2023.109873},
pmid = {37647722},
issn = {1096-0341},
mesh = {*Hot Springs/virology/microbiology ; *RNA Viruses/genetics/classification/isolation & purification ; Phylogeny ; New Zealand ; Archaea/virology/genetics ; Bacteria/virology/classification ; *Transcriptome ; Genome, Viral ; Metagenomics ; },
abstract = {Little is known about the diversity of RNA viruses in geothermal systems. We generated total RNA sequencing data from two hot springs in Kuirau Park, Rotorua, New Zealand. In one data set, from a 71.8 °C pool, we observed a microbial community that was 98.5% archaea. The second data set, representing a cooler 36.8 °C geothermal hot spring, had a more diverse microbial profile: 58% bacteria, 34.5% eukaryotes and 7.5% archaea. Within this latter pool, we detected sequences likely representing 23 RNA viruses from the families Astroviridae, Tombusviridae, Polycipiviridae, Discistroviridae, Partitiviridae, and Mitoviridae, as well as from unclassified clades of the orders Tolivirales, Picornavirales, and Ghabrivirales. Most viruses had uncertain host associations. Of particular note, we identified four novel RNA viruses from the phylum Lenarviricota, commonly associated with bacteria and fungi, that occupied a divergent phylogenetic position within unclassified clades and may represent an ancient order-level taxon of unknown host association.},
}

*Hot Springs/virology/microbiology
*RNA Viruses/genetics/classification/isolation & purification
Phylogeny
New Zealand
Archaea/virology/genetics
Bacteria/virology/classification
*Transcriptome
Genome, Viral
Metagenomics

@article {pmid41802644,
year = {2026},
author = {Wang, X and Feng, X and Zhou, Z and Li, M and Zhang, R},
title = {A pre-LECA origin of giant viruses as revealed by polymerase-based time tree.},
journal = {Molecular phylogenetics and evolution},
volume = {},
number = {},
pages = {108602},
doi = {10.1016/j.ympev.2026.108602},
pmid = {41802644},
issn = {1095-9513},
abstract = {The viral phylum Nucleocytoviricota (NCLDV) infects a wide range of eukaryotic hosts and exhibits genome complexities and virion sizes comparable to prokaryotes, blurring the boundaries between cellular life and viral entities. Despite significant advances from large-scale metagenomic surveys and identification of endogenous viral elements that expand our understanding of NCLDV's genomic diversity and host range, their evolutionary origin remains contentious. Here, we utilize DNA-directed DNA polymerase (DNAP) and RNA polymerase (RNAP), conserved markers across eukaryotes, prokaryotes, and NCLDVs, to leverage abundant eukaryotic fossils for dating the origins of NCLDVs. Phylogenetic analyses showed that NCLDV's DNAP and RNAP consistently form deep branches separate from their eukaryotic homologs. Molecular dating analyses further indicated that both DNAP and RNAP in NCLDV originated before the emergence of last eukaryotic common ancestor (LECA), findings which are robust across various dating settings. Notably, the estimated origin based on RNAP was older compared to DNAP, underscoring the need to identify additional orthologues shared with eukaryotes. Collectively, our findings represent the first attempt, to the best of our knowledge, to establish a reliable temporal framework for NCLDV evolution, supporting a pre-LECA origin of ancestral NCLDVs and suggesting a prolonged co-evolutionary history with their (proto-)eukaryotic hosts during eukaryogenesis.},
}

@article {pmid41802510,
year = {2026},
author = {Gou, X and Shen, Y and Liu, F and Wang, Y and Zong, Y and Dequ, and Zeng, CR and Nhamdriel, T and Kuang, T and Fan, G},
title = {Swertia chirayita ameliorates MAFLD by improving intestinal microenvironment and hepatic lipogenesis.},
journal = {Journal of ethnopharmacology},
volume = {},
number = {},
pages = {121471},
doi = {10.1016/j.jep.2026.121471},
pmid = {41802510},
issn = {1872-7573},
abstract = {Metabolic-associated fatty liver disease (MAFLD) is emerging as a very serious threat to human health. The search for effective remedies for MAFLD from natural herbs is gaining increasing attention. Swertia chirayita (SC) is a famous herb in China, India, and Nepal. It has long been employed within the traditional Tibetan medical system for managing hepatic disorders. Nevertheless, the therapeutic impacts and possible mechanisms of SC in the context of MAFLD are unclear.

AIM OF THE STUDY: This present investigation was designed to research the pharmacological influence and potential mechanisms of SC in MAFLD rats. We conducted a particular examination of its effects on the intestinal microenvironment and hepatic lipogenesis.

MATERIALS AND METHODS: The pharmacological effects of SC were evaluated in MAFLD rats established through a 12-week high-fat diet (HFD) feeding. After 8 weeks of SC administration, biochemical assessments were conducted for body fat, liver function, glucose metabolism, lipid parameters, and inflammatory factors. The main chemical constituents of SC and three short-chain fatty acids (SCFAs) in rat feces were quantitatively analyzed by HPLC. Furthermore, targeted metabolomics, transcriptomics, metagenomics, and Western blotting were employed to investigate possible mechanisms by which SC improves MAFLD.

RESULTS: Treatment with SC significantly ameliorated excessive fat accumulation and insulin resistance in MAFLD rats. It also improved hepatic enzyme activities (AST and ALT), several lipid metrics (TG, TC, and LDL-C), and liver histopathological changes. Moreover, SC attenuated systemic inflammation, as shown by decreased circulating IL-1β, TNF-α, LPS, and IL-6. Metagenomic profiling revealed that SC administration helped reestablish the dysregulation of multiple types of gut microbiota (bacteria, fungi, archaea, and viruses) in MAFLD rats. It improved microbial diversity, community composition, and transkingdom correlations. In addition, SC enhanced gut barrier function by raising the amount of butyric acid, acetic acid, and propionic acid and upregulating the expression of several ZO-1, occludin, and claudin-1. Liver transcriptomic analysis suggested that SC could regulate the metabolism of bile acids (BAs). Importantly, targeted metabolite analysis and western blotting demonstrated that SC improved bile acid dysfunction in MAFLD rats. In particular, SC increased TCDCA, TCA, and DCA, thereby activating the FXR/FGF15 signaling axis. This activation then controlled the production of SHP and SREBP-1c proteins in the hepatic, thereby inhibiting hepatic lipogenesis to improve MAFLD.

CONCLUSIONS: SC has shown a good therapeutic effect on MAFLD by improving intestinal microenvironment and hepatic lipogenesis. Specifically, it improves the imbalance of multiple types of gut microbiota, restores disrupted transkingdom interactions, promotes creation of beneficial SCFAs and bile acid, protects the intestinal barrier, and inhibits hepatic lipogenesis by regulating the BAs/FXR/FGF15 and SHP/SREBP-1c signaling pathways.},
}

@article {pmid41801404,
year = {2026},
author = {Petouhoff, A and Hicks, R and Husain, M and Hoyd, R and Xu, M and Dravillas, C and Patel, SH and Johns, A and Grogan, M and Li, M and Lopez, G and Miah, A and Liu, Y and Muniak, M and Schmidt, M and Das, A and Lathrop, H and Das, P and Secor, A and Haddad, T and Tinoco, G and Carbone, D and Kendra, K and Otterson, GA and Presley, CJ and Mace, T and Spakowicz, D and Owen, DH},
title = {Impact of proton pump inhibitors on immunotherapy is modulated by prior chemotherapy and linked to gut microbiome-immune cell signatures.},
journal = {Cancer immunology, immunotherapy : CII},
volume = {75},
number = {4},
pages = {},
pmid = {41801404},
issn = {1432-0851},
support = {P30CA016058/NH/NIH HHS/United States ; UL1TR002733/TR/NCATS NIH HHS/United States ; Innovator Award 1046611//American Lung Association/ ; Research Scholar Award RSG-23-1023205//American Cancer Society/ ; },
mesh = {Humans ; *Proton Pump Inhibitors/therapeutic use/pharmacology ; *Gastrointestinal Microbiome/drug effects/immunology ; Male ; Female ; Middle Aged ; Aged ; *Immunotherapy/methods ; Retrospective Studies ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; Prospective Studies ; *Neoplasms/drug therapy/immunology/mortality ; Melanoma/drug therapy/immunology ; Carcinoma, Non-Small-Cell Lung/drug therapy/immunology ; },
abstract = {Proton pump inhibitors (PPIs) are one of the most widely used medications in the world. They have been associated with an altered microbiome, which is demonstrated to be important for immune checkpoint inhibitor (ICI) response. We sought to determine whether PPI use was associated with shorter overall survival (OS) in patients treated with ICIs, and whether these changes were associated with altered microbiomes and immune cell composition. Our retrospective study of patients with advanced cancer (n = 1078) evaluated the impact of PPI use on OS. We also analyzed stool samples from melanoma patients treated with ICIs (n = 42) and stool and blood samples from patients with non-small cell lung cancer (NSCLC) and renal cell carcinoma treated with ICIs (n = 8). With the data from our prospective study, we assessed microbiome composition from stool samples using metagenomic whole-genome shotgun; immune cell populations from blood samples were determined using CyTOF. Associations between PPI use, clinical outcomes, the microbiome, and immune cell populations were evaluated using survival analyses, diversity metrics, and multivariable models. PPI use was associated with shorter OS in patients with advanced cancers treated with ICIs, with the strongest effects seen in melanoma. PPI use was associated with worse clinical outcomes and microbiome alterations in patients with advanced cancers treated with ICIs, suggesting that its use may influence the efficacy of immunotherapy; prospective studies implicate its effect on the microbiome. These findings underscore the importance of considering the microbiome and concomitant medications when to enhance treatment response and efficacy.},
}

Humans
*Proton Pump Inhibitors/therapeutic use/pharmacology
*Gastrointestinal Microbiome/drug effects/immunology
Male
Female
Middle Aged
Aged
*Immunotherapy/methods
Retrospective Studies
*Immune Checkpoint Inhibitors/therapeutic use/pharmacology
Prospective Studies
*Neoplasms/drug therapy/immunology/mortality
Melanoma/drug therapy/immunology
Carcinoma, Non-Small-Cell Lung/drug therapy/immunology

@article {pmid41801284,
year = {2026},
author = {Wang, J and Ge, H and Liu, Y and Huang, C and Zhang, L and Yu, Y and Xu, L and Fang, H},
title = {Earthworm gut microbiome promotes biodegradation of albendazole in soil.},
journal = {Crop health},
volume = {4},
number = {1},
pages = {},
pmid = {41801284},
issn = {2948-1945},
support = {2023YFD1902903//National Key Research and Development Program of China/ ; 42177252//National Natural Science Foundation of China/ ; 2023C02039-01//Leading Goose" R&D program of Zhejiang Province of China/ ; },
abstract = {The excretion of the anthelmintic drug albendazole (ALB) from treated animals into the soil, as well as its widespread application as a fungicide, poses a serious ecological risk to the soil environment. In this study, we investigated the degradation of ALB in soil and its bioaccumulation in earthworms, changes in the microbiome and degradation genes, and the effect of zinc oxide nanoparticles on the degradation and enrichment behaviors of ALB and microbial community structure and function. Our findings showed that ALB selectively enriched specific albendazole degradation genes (i.e., hmr and ami) in the earthworm, preferentially activating the pathways associated with sulfur reduction, amination of ALB sulfone, and hydroxylation of ALB. Metagenomic analysis revealed that the relative abundances of ppo, xylA, cutC, and nfsl in the earthworm gut were 0.19-52.64-fold higher in the ALB treatment than in the control, indicating their potential dominance in ALB biodegradation. Network analysis further identified potential bacterial hosts carrying biodegradation genes and albendazole degradation genes. Notably, Sphaerobacter, Saccharothrix, Actinomadura, and Nocardia were recognized as potential dual hosts of biodegradation genes and albendazole degradation genes, displaying a 0.05-1.32-fold elevation in relative abundance in ALB-treated earthworm guts compared to the control. Additionally, ZnO nanoparticles were found to reduce ALB bioaccumulation in earthworms and accelerate its dissipation in soil. These findings provide novel insights into the bioremediation mechanisms of pesticides in soil-earthworm ecosystems.},
}

@article {pmid41800893,
year = {2026},
author = {Ge, T and Zhao, T and Ruan, Y and Ye, L and Xiao, Y and Xiao, F and Li, Y and Li, X and Wang, R and Hu, H and Lu, C and Sun, H and Zhang, C and Yu, G and Zhang, T},
title = {Dysbiosis of fecal virome in pediatric Crohn's disease and its dynamic changes during infliximab therapy.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0148925},
doi = {10.1128/msystems.01489-25},
pmid = {41800893},
issn = {2379-5077},
abstract = {UNLABELLED: The gut virome is an emerging but underexplored component of the human microbiota, especially in pediatric Crohn's disease (CD). This study aimed to characterize the fecal virome in children with CD and evaluate its association with clinical response to infliximab (IFX) therapy. A total of 85 participants, including 60 pediatric CD patients and 25 healthy controls (HC), were recruited. Among the CD patients, 53 received ≥3 IFX infusions, 41 achieved remission (IFX-R), and 12 did not (IFX-NR). Viral-like particles in fecal samples were enriched and profiled by metagenomic sequencing, while bacterial communities were assessed via 16S rRNA gene sequencing. Pediatric CD patients exhibited significantly reduced viral richness and altered viral community compared to HCs. Functional analyses revealed that CD patients exhibit a shift in fecal virome function from DNA repair to viral replication and assembly. Trans-kingdom correlations were disrupted in CD, particularly between Torque teno viruses and beneficial bacteria, such as Blautia. An integrated machine learning model combining viral and bacterial markers achieved a certain level of diagnostic accuracy for pediatric CD (area under the curve [AUC] = 89.3%). IFX treatment influences the gut virome, with remission associated with higher abundances of Microviridae and Siphoviridae, while Anelloviridae, Myoviridae, and Podoviridae were enriched in IFX-NR at baseline. These findings suggest the virome as a potential biomarker for predicting clinical outcome in pediatric CD, offering a novel avenue for disease diagnosis and personalized treatment strategies.

IMPORTANCE: Crohn's disease (CD) in children poses a growing clinical challenge, with increasing incidence and variable response to biologic therapies such as infliximab (IFX). While gut bacterial dysbiosis has been extensively studied, the role of the gut virome in pediatric CD remains largely unexplored. This study provides the first longitudinal characterization of the fecal virome in children with CD undergoing IFX therapy. We reveal distinct viral community patterns, functional alterations, and virus-bacteria interactions in pediatric CD patients. Notably, integration of virome and bacteriome profiles enhances diagnostic accuracy, offering a promising avenue for predictive biomarker development. Furthermore, virome changes may be associated with the IFX treatment outcomes in children with CD. These findings highlight the gut virome as a critical but overlooked dimension of host-microbiome interactions in pediatric CD, with potential implications for personalized therapy and mechanistic understanding of treatment resistance.},
}

@article {pmid41800589,
year = {2026},
author = {Juan, DR and Dilanaz, A and Camila, RV and Fernando, DG and Pedro, SR and Ana, MB and Ricardo, U and Barrie, JD and Mario, V and Díez, B and Matías, C and Pedro, T and Alejandra, G and Francisco, I and Raquel, Q},
title = {Microbial succession and assembly shaped by sulfur, spatial partitioning, and water flow in a volcanic acidic river of northern Patagonia.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag048},
pmid = {41800589},
issn = {1751-7370},
abstract = {Extreme acidic environments represent natural laboratories for investigating the mechanisms of microbial community assembly, yet the ecological processes structuring these communities remain incompletely understood. Here, we investigate how spatial partitioning, hydrodynamics, and colonization history shape microbial succession in a unique sulfur-rich, acidic river of volcanic origin in northern Patagonia. We combined 16S rRNA gene profiling and shotgun metagenomics with a multi-scale experimental framework encompassing water column fractionation and colonization assays under native and controlled conditions. Microbial diversity was strongly influenced by spatial fractionation, with free-living communities exhibiting higher richness and temporal variability than particle-associated assemblages. Water flow modulated community structure, increasing evenness in free-living fractions under high-flow conditions, but had limited impact on particle-attached communities. Colonization of sulfur-beads followed a structured successional trajectory, with autotrophic sulfur oxidizers dominating early stages and heterotrophs adapted to biofilm lifestyles increasing over time. Ex situ recolonization assays revealed strong priority effects, with initial colonizers determining successional trajectories. Turnover analyses revealed that the balance among stochastic and deterministic assembly processes shifted across communities with pronounced stochasticity in the water column and flow-dependent effects in free-living communities, while biofilm associated communities on sulfur-beads exhibited stronger contribution of deterministic selection. These ecological patterns were mirrored by functional differentiation, with gene enrichment analyses revealing adaptive signatures of substrate attachment and resource acquisition. By integrating fine-scale environmental variation with colonization dynamics, this study reveals how microscale habitat structure and temporal fluxes jointly modulate microbial community assembly rules, offering a nuanced framework to dissect ecological processes in extreme systems.},
}

@article {pmid41800425,
year = {2026},
author = {Huangfu, H and Pu, J and Jiao, M and Zhou, H and Fan, Q and Deng, H and Ling, Q and Luo, X and Xu, J},
title = {Unveiling the RNA viral diversity in three organs of the Asian house shrew (Suncus murinus) from Tropical Hainan, China: a previously underappreciated key zoonotic reservoir.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1738936},
pmid = {41800425},
issn = {1664-302X},
abstract = {Shrews represent an important reservoir of diverse human-pathogen viruses with implications for human infectious diseases. As the most populous shrew species, the Asian house shrew-Suncus murinus (Su. murinus) is widely distributed across South and Southeast Asia-particularly tropical and subtropical regions-yet its virome remains poorly studied. In this study, we collected 249 Su. murinus from 18 cities/counties (excluding Sansha) across Hainan Island and conducted RNA sequencing on gut, spleen, and lung tissues. We identified 192 RNA viruses, comprising 120 known viral species and 72 novel viruses, including key zoonotic viral families: Arenaviridae, Hantaviridae, Paramyxoviridae etc. We assembled 102 complete and nearly complete genomes. Notably, 64 known viruses exhibited cross-species transmission potential, including 57 with spillover risk and 7 human-pathogenic viruses: Mammarenavirus choriomeningitidis (LCMV), Henipavirus (HeV), Wenzhou virus (WENV), Langat virus (LGTV), Amur virus (AMRV), Influenza A virus (H1N1), and Rotavirus A (RVA). Additionally, AMRV, LGTV, and LCMV were reported here for the first time in Su. murinus based on metagenomic detection. Our phylogenetic and RT-PCR results indicate Su. murinus is a candidate reservoir for Langya-like henipavirus. Collectively, our study reveals tropical populations of Su. murinus are a previously underappreciated reservoir of viral diversity, underscoring their key role in zoonotic emergence and necessitating surveillance in tropical regions.},
}

@article {pmid41800416,
year = {2026},
author = {Bustos, ML and Song, K and Brochu, HN and Zhang, Q and Iyer, LK and Icenhour, CR},
title = {Impact of non-standardized reporting on reproducibility, usability, and integration in nasopharyngeal metagenomic research: a systematic review.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1707004},
pmid = {41800416},
issn = {1664-302X},
abstract = {INTRODUCTION: The nasopharyngeal microbiome plays a critical role in respiratory health and disease and is a major focus of metagenomic research. However, inconsistent reporting practices across studies limit reproducibility, dataset usability, and cross-study integration, thereby reducing the overall scientific value of publicly available nasopharyn.

METHODS: A systematic review was conducted to evaluate the impact of non-standardized reporting on reproducibility, usability, and integration of nasopharyngeal metagenomic datasets. A total of 988 studies were screened, and 227 manuscripts met predefined inclusion and exclusion criteria for full-text review. Methodological reproducibility, metadata completeness, and compatibility between reported laboratory methods and deposited datasets were assessed. Reproducible datasets were further analyzed to evaluate the interchangeability of nasopharyngeal aspirates and nasopharyngeal swabs.

RESULTS: Only 78 studies (34%) contained methods sections sufficient for reproducibility, and of these, 33 studies (15%) provided analytically sufficient metadata to support secondary analysis. Mismatches between reported laboratory methods and deposited datasets were identified in 4% of studies. These deficiencies were primarily attributed to incomplete methodological reporting, inaccessible or insufficient metadata, and incompatible file formats. Comparative analysis of reproducible datasets demonstrated significant differences in microbial profiles between nasopharyngeal aspirates and nasopharyngeal swabs, confirming that these specimen types are not interchangeable within a study.

DISCUSSION: The findings demonstrate that inadequate reporting standards substantially impair the reproducibility, reuse, and integration of nasopharyngeal metagenomic data. The observed methodological and metadata inconsistencies limit the reliability of downstream analyses and cross-study comparisons. Standardized reporting guidelines are urgently needed to improve transparency, ensure reproducibility, and enhance the integrative potential of nasopharyngeal microbiome research. Adoption of comprehensive and consistent reporting practices would significantly strengthen the scientific rigor and utility of metagenomic studies in this field.},
}

@article {pmid41800387,
year = {2026},
author = {Gupta, S and Quarato, V and Lai, W and Kobel, CM and Aho, VTE and Vera-Ponce de León, A and La Rosa, SL and Sandve, SR and Pope, PB and Hvidsten, TR},
title = {OmniCorr: an R-package for visualizing putative host-microbiome interactions using multi-omics data.},
journal = {Bioinformatics advances},
volume = {6},
number = {1},
pages = {vbag057},
pmid = {41800387},
issn = {2635-0041},
abstract = {Holo-omics leverages omics datasets to explore the interactions between hosts and their associated microbiomes. Although the generation of omics data from matching host and microbiome samples is steadily increasing, there remains a scarcity of computational tools capable of integrating and visualizing this data to facilitate the prediction and interpretation of host-microbiome interactions. We present OmniCorr, an R package designed to: (i) manage the complexity of omics data by clustering co-varying features (e.g. genes, proteins, and metabolites) into modules, (ii) visualize correlations of these modules across different omics layers, host-microbiome interfaces, and metadata, and (iii) identify statistically significant associations indicative of putative host-microbiome interactions. OmniCorr's utility is demonstrated using datasets from two systems: (i) Atlantic salmon, integrating host transcriptomics with metagenomics and metatranscriptomics to explore dietary impacts, and (ii) cattle, combining host proteomics with metaproteomics to investigate methane emission variability. Availability and implementation: OmniCorr is freely available at https://github.com/shashank-KU/OmniCorr.},
}

@article {pmid41800013,
year = {2026},
author = {Walia, T and Srivastava, N and Shetty, RM and Rana, V},
title = {Metagenomics as an Effective Diagnostic Approach for Exploring Oral Microbial Diversity and Dental Diseases: A Narrative Review.},
journal = {International journal of clinical pediatric dentistry},
volume = {19},
number = {2},
pages = {278-284},
pmid = {41800013},
issn = {0974-7052},
abstract = {AIM AND BACKGROUND: The oral cavity harbors a diverse microbiota that significantly influences oral health and disease. Conventional microbiological techniques have limitations in detecting the full range of microbial species, particularly those that are uncultivable. Metagenomics, through culture-independent, high-throughput sequencing methods, offers a comprehensive approach to studying oral microbial diversity. This narrative review aims to evaluate the role of metagenomics in exploring the oral microbiome and its association with dental diseases.

METHODS: This review systematically synthesized current literature and research on metagenomic technologies, including 16S ribosomal RNA (rRNA) sequencing, shotgun metagenomics, metatranscriptomics, metaproteomics, and metabolomics. It highlighted their principles, diagnostic capabilities, and limitations in analyzing microbial communities in caries, endodontic infections, and periodontitis. It also reviewed auxiliary tools such as quantitative polymerase chain reaction (qPCR), microarrays, fluorescence in situ hybridization (FISH), and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), and discussed the integration of artificial intelligence (AI) in metagenomic data interpretation.

RESULTS: Metagenomic studies have expanded the scope of known microbial species involved in dental caries beyond Streptococcus mutans, highlighting the contributions of Lactobacillus, Veillonella, Actinomyces, and Candida albicans. In endodontics, resistant species such as Enterococcus faecalis, Porphyromonas endodontalis, and Fusobacterium nucleatum are implicated in persistent infections. In periodontitis, a dysbiotic microbial shift has been associated with the presence of complex microbial consortia, including red and orange complex bacteria.

CONCLUSION: Metagenomics is a powerful diagnostic tool that provides an in-depth characterization of the complex microbial ecosystem of the oral cavity. It offers diagnostic potential through early and accurate detection of pathogenic shifts, promotes personalized treatment planning, and opens avenues for the development of potential biomarkers of disease progression.

CLINICAL SIGNIFICANCE: The integration of metagenomics into dental practice can revolutionize caries risk assessment, treatment precision, and disease prevention strategies. Although challenges such as high cost, data complexity, and lack of standardization remain, ongoing advancements in sequencing technologies and bioinformatics are expected to enhance its accessibility and clinical relevance.

HOW TO CITE THIS ARTICLE: Walia T, Srivastava N, Shetty RM, et al. Metagenomics as an Effective Diagnostic Approach for Exploring Oral Microbial Diversity and Dental Diseases: A Narrative Review. Int J Clin Pediatr Dent 2026;19(2):278-284.},
}

@article {pmid41799966,
year = {2026},
author = {Habuding, X and Chen, J and Zhu, J and Wang, G and Ma, L and Abulikemu, T},
title = {Integrated metagenomic and culturomic strategies to mine and validate beneficial rhizosphere Actinobacteria from lavender.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1745076},
pmid = {41799966},
issn = {1664-462X},
abstract = {INTRODUCTION: The lavender industry faces significant constraints from soil salinization and continuous cropping obstacles. However, systematic exploration and functional analysis of beneficial rhizosphere microbial resources, particularly Actinobacteria, remain inadequate.

METHODS: To address this, we integrated metagenomic and culturomic strategies to investigate the rhizosphere and endophytic microbiomes in saline-alkaline lavender cultivation areas in Huocheng, China (soil pH ~8.04, salt ~0.074%). Metagenomic functional annotation and soil factor correlation analysis guided a subsequent culturomics approach to isolate strains. Isolates were screened for plant growth-promoting (PGP) traits, and selected strains were evaluated in pot inoculation experiments with Arabidopsis thaliana.

RESULTS: High-throughput sequencing revealed that Actinomycetota dominated the microbial communities, with Streptomyces and Nocardioides as key genera. Metagenomic analysis showed the community was enriched with functional genes related to saline-alkaline stress response, secondary metabolite synthesis, and nutrient cycling, whose distribution correlated significantly with soil pH and salinity. From this resource, 10 actinobacterial strains with multiple PGP traits (e.g., P-solubilization, siderophore production, IAA, ACC deaminase, and nitrogenase activity) were obtained. Pot experiments confirmed that these saline-alkaline-derived actinobacteria, both as single strains and as a bacterial consortium (C4 + A1), significantly promoted the growth of A. thaliana.

DISCUSSION: This study achieves a closed-loop verification from in silico functional prediction to empirical validation of beneficial strains. It provides the first systematic elucidation of the functional adaptation mechanisms of the lavender rhizosphere actinobacterial community under saline-alkaline stress and identifies elite microbial resources with both stress tolerance and PGP functions. The findings offer novel microbial agents and a theoretical foundation for developing specialized inoculants to mitigate saline-alkaline obstacles in lavender cultivation.},
}

@article {pmid41799605,
year = {2026},
author = {Suzuki, Y and Osumi, W and Taniguchi, K and Kato-Kogoe, N and Sakaguchi, S and Nakamura, S and Imai, Y and Nakano, T and Ueno, T and Lee, SW},
title = {Comparison of Pre- and Postoperative Gut Microbiota Diversity in Patients With Rectal Cancer Undergoing Stoma Creation and Closure.},
journal = {Annals of gastroenterological surgery},
volume = {10},
number = {2},
pages = {492-501},
pmid = {41799605},
issn = {2475-0328},
abstract = {AIM: To investigate the impact of temporary stoma creation and its subsequent closure on gut microbiota composition and diversity in patients undergoing rectal cancer surgery.

METHODS: Nineteen patients with primary rectal cancer who underwent curative surgery were enrolled and divided into two groups: stoma (n = 10, all underwent temporary ileostomy) and non-stoma (n = 9). Fecal samples were collected preoperatively and 6 months postoperatively. Gut microbiota composition was analyzed using 16S rRNA gene sequencing. Alpha diversity (observed operational taxonomic units and Shannon index) and beta diversity (UniFrac distances) were compared between time points. Taxonomic shift was identified using Linear discriminant analysis Effect Size (LEfSe).

RESULTS: In the stoma group, alpha diversity significantly decreased after surgery (p = 0.049), and beta diversity analyses revealed significant changes in microbial composition (PERMANOVA; unweighted p = 0.026; weighted p = 0.046). LEfSe analysis identified an increased abundance of potentially pathogenic genera (e.g., Enterococcus and Eggerthella) and a decreased abundance of short-chain fatty acid-producing genera (e.g., Megamonas and Anaerostipes). These changes persisted for at least 6 months after stoma closure. In contrast, the non-stoma group showed no significant alterations in microbial diversity or composition over time.

CONCLUSION: Temporary stoma creation in rectal cancer surgery induces persistent alterations in gut microbiota; these alterations are characterized by reduced diversity and a shift toward a dysbiotic profile with increased pathogenic and decreased beneficial taxa. These findings highlight the potential need for microbiota-targeted strategies to mitigate long-term dysbiosis in patients undergoing stoma-related procedures.},
}

@article {pmid41799583,
year = {2026},
author = {Ofuchi, T and Hu, Q and Omachi, K and Kanemitsu, K and Otsu, H and Yonemura, Y and Tobo, T and Baba, Y and Iwatsuki, M and Mimori, K},
title = {Intratumoral Fusobacterium nucleatum Drives Cancer-Associated Fibroblasts Enrichment and Immune Exclusion in Esophageal Squamous Cell Carcinoma.},
journal = {Annals of gastroenterological surgery},
volume = {10},
number = {2},
pages = {611-620},
pmid = {41799583},
issn = {2475-0328},
abstract = {BACKGROUND: Fusobacterium nucleatum, an oral commensal bacterium, has been increasingly recognized for its oncogenic role in gastrointestinal malignancies. In esophageal squamous cell carcinoma (ESCC), F. nucleatum has been implicated in promoting tumor progression and facilitating immune evasion. However, its relationship with stromal remodeling and the tumor microenvironment (TME) remains unclear.

METHODS: We performed integrative analyses using metagenomic profiling and transcriptomic deconvolution, and histopathological assessment of 93 The Cancer Genome Atlas (TCGA)-ESCC cases and an independent cohort of 126 resected tumors. F. nucleatum status was determined by microbial abundance and quantitative Polymerase Chain Reaction (q-PCR).

RESULTS: F. nucleatum-positive tumors showed significant enrichment of TNFα/NF-κB signaling and reduced CD8[+] T cell infiltration. Stromal analysis revealed a marked increase in cancer-associated fibroblasts (CAFs) in F. nucleatum-positive tumors, confirmed by transcriptomic deconvolution and α-SMA immunohistochemistry. Notably, immunohistochemical analysis demonstrated increased nuclear localization of NF-κB p65, indicating F. nucleatum-induced NF-κB activation in tumor cells. Clinically, among elderly patients with poor performance status, the prevalence of F. nucleatum positivity was significantly higher.

CONCLUSION: F. nucleatum may contribute to the progression of ESCC by inducing NF-κB-mediated inflammatory signaling in tumor cells and promoting CAFs activation. Its presence may facilitate immune exclusion and tumor invasion through stromal remodeling. Furthermore, F. nucleatum positivity may reflect broader host vulnerability, particularly in frail elderly individuals. These findings highlight F. nucleatum as a potential biomarker of tumor immune dynamics and suggest the importance of maintaining good oral hygiene to reduce F. nucleatum colonization.},
}

@article {pmid41798955,
year = {2026},
author = {Xiao, Y and Zhang, T and Chen, Q and Zhang, Y and Chen, B and Wang, M and Zhang, Y and Huang, M and Su, Y and Guo, J},
title = {Multi-omics analysis reveals the mechanism of verbenalin in treating gout via modulating purine metabolism, gut microbiota, and inflammatory pathways.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1761558},
pmid = {41798955},
issn = {1664-3224},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Rats ; Male ; *Purines/metabolism ; Disease Models, Animal ; *Gout/drug therapy/metabolism ; Inflammation/drug therapy/metabolism ; Signal Transduction/drug effects ; *Anti-Inflammatory Agents/pharmacology ; Hyperuricemia/drug therapy ; Rats, Sprague-Dawley ; Metabolomics/methods ; Arthritis, Gouty/drug therapy/metabolism ; Multiomics ; },
abstract = {BACKGROUND: Gout is a prevalent metabolic disorder characterized by hyperuricemia and inflammation. Verbenalin, an iridoid glycoside from Verbena officinalis, possesses anti-inflammatory properties; however, its therapeutic potential and underlying mechanisms in gout remain underexplored.

OBJECTIVE: This study aimed to evaluate the pharmacological effects and elucidate the molecular mechanisms of verbenalin in a rat model of gout.

METHODS: Hyperuricemia and acute gouty arthritis were induced in rats using potassium oxonate/hypoxanthine and monosodium urate, respectively. Verbenalin was administered orally for 7 days. Therapeutic efficacy was assessed via physical symptom scores (inflammation, gait, swelling), renal/hepatic function indices, and histopathology. Furthermore, a multi-omics strategy integrating transcriptomics, metagenomics, and metabolomics, combined with Western blotting, was employed to investigate the pharmacological mechanisms.

RESULTS: Verbenalin treatment significantly alleviated joint inflammation and swelling while improving gait scores. It effectively lowered serum uric acid (UA), creatinine, and BUN levels, inhibited hepatic xanthine oxidase (XOD) activity, and promoted urinary UA excretion. Histopathological damage in the joints, kidneys, and liver was markedly mitigated. Mechanistically, verbenalin downregulated the expression of urate transporters (URAT1, GLUT9) and inflammatory mediators (NLRP3, IL-1β) by inhibiting the PI3K-AKT and MAPK signaling pathways. Multi-omics analysis further revealed that verbenalin restored gut microbiota diversity and modulated purine metabolism, correlating with reduced UA levels.

CONCLUSION: These findings demonstrate that verbenalin may exert anti-gout effects through the potential synergy of modulating purine metabolism, shifting gut microbiota composition, and suppressing PI3K-AKT and MAPK inflammatory signaling pathways. This study provides a preliminary scientific basis for further investigation into verbenalin as a prospective multi-target therapeutic candidate.},
}

Animals
*Gastrointestinal Microbiome/drug effects
Rats
Male
*Purines/metabolism
Disease Models, Animal
*Gout/drug therapy/metabolism
Inflammation/drug therapy/metabolism
Signal Transduction/drug effects
*Anti-Inflammatory Agents/pharmacology
Hyperuricemia/drug therapy
Rats, Sprague-Dawley
Metabolomics/methods
Arthritis, Gouty/drug therapy/metabolism
Multiomics

@article {pmid41797781,
year = {2026},
author = {Zhang, X and Li, W and Zhao, S and Han, Y and Ma, W and Jiang, Z and Ma, Y and Zhang, G and Wang, J and Jia, H and Guo, S and Cui, N},
title = {Fulminant amebic colitis complicated by appendiceal perforation and massive abdominal hemorrhage: a case report and literature review.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1760895},
pmid = {41797781},
issn = {2296-858X},
abstract = {INTRODUCTION: Fulminant amebic colitis complicated by intestinal perforation or massive intra-abdominal hemorrhage is uncommon but associated with extremely high mortality. In non-endemic regions, diagnosis is frequently delayed because early manifestations resemble bacterial appendicitis or perforated peritonitis.

CASE PRESENTATION: We report a fatal case of Entamoeba histolytica infection presenting with appendiceal perforation, septic shock, and recurrent intra-abdominal bleeding. Surgery revealed extensive transmural necrosis, deep ulcers, and exposure of submucosal vessels. Metagenomic next-generation sequencing (mNGS) of blood and peritoneal drainage fluid was performed, followed by histopathological confirmation. Despite emergent appendectomy, bowel resection, and prompt initiation of anti-amebic therapy, the patient developed refractory septic shock and recurrent intra-abdominal hemorrhage, resulting in death.

CONCLUSION: mNGS can facilitate early recognition of severe amebiasis when conventional diagnostic modalities are uncertain, particularly in non-endemic settings. Fulminant amebic colitis complicated by perforation or hemorrhage carries a poor prognosis. Timely clinical suspicion and early anti-amebic therapy are essential to improve outcomes.},
}

@article {pmid41797768,
year = {2026},
author = {Dai, M and Pang, L and Hu, M and Meng, J and Ji, C and Sheng, L and Zhang, W},
title = {Case report: Be alert to parvovirus infection in patients with unexplained anemia after cerebral hemorrhage surgery.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1700344},
pmid = {41797768},
issn = {2296-858X},
abstract = {BACKGROUND: Human parvovirus B19 (PVB19) is a highly prevalent single-stranded DNA virus that infects a large proportion of the global population. It can involve multiple organ systems, leading to a broad spectrum of clinical manifestations. While most infections in immunocompetent individuals are mild and self-limiting, PVB19 can occasionally cause severe and diverse complications.

CASE PRESENTATION: We report a rare case of an immunocompetent patient who experienced unexplained clinical deterioration following surgical evacuation of an intracerebral hemorrhage. The patient presented with refractory anemia, impaired consciousness, fever, seizures, and progressive dysfunction of the cardiac, hepatic, and renal systems. Metagenomic next-generation sequencing revealed high levels of PVB19 DNA in the cerebrospinal fluid, blood, and pleural effusion. The patient was treated with intravenous immunoglobulin (IVIG) therapy and supportive care. Following treatment, improvements were observed in consciousness, mobility, and anemia. However, renal function failed to recover and ultimately progressed to renal failure, necessitating renal replacement therapy.

CONCLUSION: This case underscores the potential severity of PVB19 infection following cerebral hemorrhage surgery, particularly when accompanied by unexplained anemia. Accurate diagnosis requires a high index of suspicion and the use of advanced diagnostic tools. Management primarily involves IVIG therapy and supportive care. This case highlights the importance of expanding the differential diagnosis in postoperative patients presenting with unexplained anemia and multi-organ dysfunction, as early recognition of atypical infections may improve clinical outcomes.},
}

@article {pmid41797508,
year = {2026},
author = {Huang, C and Xiao, W and Zhao, J and Zhong, R and Gao, L and Ma, H and Tian, L and Yue, P and Lin, Y and He, Q and Xia, B and Yuan, J and Yang, M and Meng, W},
title = {Gut Microbiome Dysbiosis Promotes Gallstone Formation via Bile Acid Metabolic Disorder: A Multiomics Study.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {40},
number = {6},
pages = {e71656},
doi = {10.1096/fj.202503254RRRRRR},
pmid = {41797508},
issn = {1530-6860},
support = {82204123//MOST | National Natural Science Foundation of China (NSFC)/ ; 82473707//MOST | National Natural Science Foundation of China (NSFC)/ ; LCYSSQ20220823091203008//Funding of Shenzhen Clinical Research Center for Gastroenterlogy (Gastrointestinal Surgery)/ ; 2022YFC2407405//MOST | National Key Research and Development Program of China (NKPs)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Bile Acids and Salts/metabolism ; *Dysbiosis/microbiology/metabolism/complications ; *Gallstones/microbiology/metabolism/etiology ; Male ; Female ; Middle Aged ; Feces/microbiology ; Adult ; Aged ; Multiomics ; Amidohydrolases ; },
abstract = {Gallstone disease is a common global digestive disorder. This study intends to analyze gut microbiota-gallstone disease interactions, to inform disease mechanism and microbiota-targeted prevention and treatment strategies. Participants were recruited from health check-up populations, outpatients, and inpatients. Basic information and biological samples were collected: fecal samples for metagenomic sequencing, and serum samples for bile acid metabolism detection. A total of 62 gallstone patients and 62 healthy controls were enrolled in this study. Compared with the control group, gallstone patients exhibited increased level of bile salt hydrolase (BSH)-producing bacteria, including the genera Bacteroides, Enterococcus, Bifidobacterium, and the family Lactobacillaceae. Further KEGG analysis revealed that the significantly enriched signaling pathways in the gallstone patients were mainly related to bile acid biosynthesis, lipid and bile acid precursor metabolism. Subsequently, we found that in gallstone patients, the levels of hydrophobic bile acids, (e.g., lithocholic acid, LCA), was increased, while the levels of hydrophilic bile acids taurolithocholic acid (TLCA) were decreased. In the correlation analysis between differential bile acids and differential bacterial species, Bacteroides intestinalis was positively correlated with LCA, while Bacteroides fragilis was negatively correlated with TLCA. These results further confirm the role of BSH-active bacteria in bile acid dysregulation. This study proposes the "intestinal microbiota imbalance-bile acid metabolic disorder-gallbladder stone formation" axis, and confirms that gallstone patients exhibit intestinal dysbiosis, which leads to bile acid dysregulation. Furthermore, the accumulation of hydrophobic bile acids is identified as a key factor in gallbladder stone formation.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Bile Acids and Salts/metabolism
*Dysbiosis/microbiology/metabolism/complications
*Gallstones/microbiology/metabolism/etiology
Male
Female
Middle Aged
Feces/microbiology
Adult
Aged
Multiomics
Amidohydrolases

@article {pmid41797187,
year = {2026},
author = {Tang, Z and Liu, X and Yang, J and Zhang, F and Shan, X and Liu, Y and Li, F and Lu, S and Xi, B},
title = {Unraveling the redox-driven mechanisms of viral-bacterial interactions in modulating the fate of antibiotic resistance genes.},
journal = {Bioresource technology},
volume = {449},
number = {},
pages = {134358},
doi = {10.1016/j.biortech.2026.134358},
pmid = {41797187},
issn = {1873-2976},
abstract = {Antibiotic resistance genes (ARGs) are emerging contaminants in wastewater systems, where heterogeneous redox conditions regulate microbial community assembly and ARG dissemination. However, how within-system redox gradients generated by electrochemical configurations structure bacterial and viral processes and ultimately control ARG dynamics remains unclear. Here, we established a vertical-flow wetland (VW), a direct-current powered VW (DW), and a microbial fuel cell-coupled VW (MW), and performed metagenomic analyses of substrates adjacent to anodes and cathodes to resolve spatial ARG patterns and mechanisms. Across all systems, 478 ARG subtypes from 26 classes were detected, dominated by sulfonamide, multidrug, and tetracycline resistance genes. Electrochemical operation substantially reduced total ARG abundance, with inhibition efficiencies of 49% in DW and 73% in MW and suppressed high-risk genes such as sul1, sul2, tetG, and bacA. Pronounced divergence occurred between anodic and cathodic microenvironments, with ARG levels averaging 0.419 and 0.229 copies per cell, respectively. Redox differentiation reshaped ARG host composition, microbial diversity, ecological networks, virus-host interactions, and metabolic strategies. Cathodic reductive zones were enriched in viral auxiliary metabolic genes linked to folate pathways, potentially alleviating sulfamethoxazole-driven selection, whereas anodic oxidative environments favored outer-membrane porins and mobile genetic elements, coinciding with elevated ARG abundance and greater horizontal transfer potential. Collectively, these results highlight redox-driven microbial metabolism, viral auxiliary functions, and MGE-mediated mobility as key regulators of ARG fate in electrochemical wetlands and provide guidance for engineering redox-optimized systems to mitigate ARG dissemination.},
}

@article {pmid41797140,
year = {2026},
author = {You, G and Jin, H and Wu, M and Li, Y and You, X and Huang, C and Xu, Y and Hou, J},
title = {Insights into antibiotic resistance gene dynamics during Tanfloc-induced flocculation-storage process for cyanobacteria removal in an algae-laden drinking water source.},
journal = {Journal of environmental management},
volume = {403},
number = {},
pages = {129223},
doi = {10.1016/j.jenvman.2026.129223},
pmid = {41797140},
issn = {1095-8630},
abstract = {Tannin-based flocculants (TA) are increasingly promoted as green polymeric alternatives for cyanobacteria removal in algae-laden drinking water sources, yet their potential to influence antibiotic resistance gene (ARG) dissemination during subsequent flocculation-storage remains unclear. This study compared TA with polyaluminum chloride (PACl) to assess ARG fate in both supernatant and cyanobacteria-laden drinking water sludge throughout flocculation and 8-day storage. Results showed that TA achieved over 97% removal efficiency for both cyanobacteria and ARGs at a low dosage of 20 mg/L, outperforming PACl. Moreover, TA treatment led to markedly reduced release of microcystin-LR and dissolved organic matter (DOM) after storage. Nevertheless, elevated biomass within TA-induced flocs promoted ARG proliferation, primarily due to enhanced production of triplet-state DOM and suppression of carotenoid synthesis. Metagenomic evidence indicated elevated abundances of CAZyme genes (e.g., GH43, CE4, CE1, GH9, CE11), highlighting an increased functional potential for TA-associated polymer breakdown and consequent weakening of the floc coating after 8 days, which in turn promoted ARG escape from flocs. Meanwhile, increased motility of phycosphere-associated antibiotic-resistant bacteria (e.g., Pseudomonas) promoted ARG transfer into the supernatant, accompanied by enrichment of mobile genetic elements and virulence factor genes, which collectively amplified ecological risks. These findings underscore that ARG release and dissemination should be explicitly integrated into safety assessments of TA-based cyanobacteria control, and they provide mechanistic guidance for mitigating ARG hazards in algal-affected drinking water supplies.},
}

@article {pmid41797015,
year = {2026},
author = {Jeon, J and Lee, DH and Kim, JH and Choi, Y and Jin, YK and Hong, JK and Lee, YM},
title = {Methanotrophic community structure and metabolic potential in the sulfate-methane transition zone of the ARAON mounds, Arctic Chukchi Sea.},
journal = {Marine environmental research},
volume = {217},
number = {},
pages = {107959},
doi = {10.1016/j.marenvres.2026.107959},
pmid = {41797015},
issn = {1879-0291},
abstract = {Anaerobic oxidation of methane (AOM) mediated by archaea is a pivotal process for methane consumption in gas seepage-associated sediments. Despite its importance in regulating methane flux, the ecological roles and metabolic potential of microbial communities involved in AOM remain poorly understood in Arctic regions. In this study, we investigated the microbial community structures and methanotrophic signatures in sediments from gas hydrate-bearing and non-gas hydrate-bearing sites in ARAON Mounds (AMs) and reference sites. Microbial communities in AMs were distinct from those in reference sites, with high relative abundances of Euryarchaeota (45.5 ± 11%), Lokiarcheota (35 ± 6.1%), and Atribacterota (50.1 ± 23.3%). Anaerobic methanotrophic archaea (ANME) showed site- and depth-specific distributions, with ANME-1a, ANME-1b, and ANME-2c predominating the sulfate-methane transition zone (SMTZ) of the gas hydrate-bearing sites, and ANME-1a prevailing at non-gas hydrate-bearing sites. Sulfate-reducing bacteria (SRB) affiliated with Seep-SRB1 co-occurred with ANME-1a and ANME-1b within the AMs. Metagenome-assembled genomes (MAGs) of ANME-1b and ANME-2c recovered from the SMTZ of the gas hydrate-bearing site (AM6) harbored key AOM-related genes, and their putative syntrophic bacterial partner, ETH-SRB1, possessed essential genes for sulfate reduction. Additionally, Lokiarchaeota and Atribacterota MAGs encoded genes involved in protein degradation, fermentation, and hydrogen metabolism, indicating their possible roles in methane cycling. Collectively, these results reveal distinct microbial assemblages and their functional genomic traits, suggesting niche specialization associated with methane oxidation potential at the SMTZ of the gas hydrate-bearing site.},
}

@article {pmid41796809,
year = {2026},
author = {He, J and Zhang, A and Wang, L and Ping, Q and Gao, P and Liu, Y},
title = {Aging attenuates threat: how moderate aging of microplastics suppresses antibiotic resistance gene proliferation during sludge anaerobic digestion.},
journal = {Bioresource technology},
volume = {449},
number = {},
pages = {134342},
doi = {10.1016/j.biortech.2026.134342},
pmid = {41796809},
issn = {1873-2976},
abstract = {Microplastics (MPs) are known to promote antibiotic resistance gene (ARG) dissemination in waste activated sludge; however, most existing evidence is based on unaged MPs, and the influence of aging degree remains poorly understood. This study systematically investigated how varying aging degrees of polyethylene (PE) and polypropylene (PP) MPs modulate ARG profiles and transfer mechanisms during anaerobic digestion. The results demonstrated a non-monotonic effect of aging degree on ARG proliferation, with moderate aging of MPs showing the strongest attenuation of ARG promotion. Under moderate carbonyl indices (CI) of 0.104 for PE-MPs and 0.219 for PP-MPs, the average reduction of the most affected ARGs reached 40% and 50%, respectively, compared with the unaged MPs. Metagenomic analysis further revealed that moderate aging of MPs reduced both the abundance and diversity of ARGs stimulated by unaged MPs. Mechanistically, unaged MPs induced multiple biological responses. These included enrichment of dominant ARG-hosting genera within Proteobacteria and Chloroflexi, elevated oxidative stress, increased membrane permeability, and activation of horizontal gene transfer (HGT) pathways, including the type IV secretion system (T4SS), quorum sensing (QS), and two-component systems (TCS). Conversely, aging weakened these microbial signaling and stress responses at moderate aging degrees but led to a rebound at higher aging degrees, thereby modulating HGT potential in a non-monotonic manner. These findings indicate that aging of sludge-relevant MPs (PE and PP) fundamentally alters their ecological impact on the sludge resistome, highlighting the necessity of incorporating aging dynamics into the risk assessment of MPs in engineered ecosystems.},
}

@article {pmid41796197,
year = {2026},
author = {Sujeeth, NK and Dharani Bommi, KB and Manojkumar, S and Angayarkanni, J and Gnanadesigan, M},
title = {Microbiome signatures of mangroves and salt marsh halophyte rhizosphere soil sediments: a metagenomic approach.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-42270-z},
pmid = {41796197},
issn = {2045-2322},
}

@article {pmid41727025,
year = {2026},
author = {Chittimalli, K and Rozario, HE and Martinez, V and McAdams, ZL and Adkins, SA and Ericsson, AC and Jarajapu, YP},
title = {Alamandine/MrgD Pathway Modulates Gut-Bone Marrow Axis in Aging.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41727025},
issn = {2692-8205},
abstract = {Aging is associated with colon epithelial barrier integrity and upregulation of myelopoiesis in the bone marrow (BM). Alamandine (Ala) and MrgD are novel members of the renin angiotensin system (RAS). This study tested the hypothesis that Ala restores the colon epithelial barrier integrity in aging via modulating gut-BM axis. Mice of age 2-3 (Young) or 22-24 months (Old) were treated with saline or Ala by using Osmotic pumps. The intestinal permeability was evaluated by using FITC-dextran. Lgr5[+]Olfm4[+] intestinal stem cells (ISCs), Wnt3a and β-catenin were evaluated by immunohistochemistry or western blotting. Fecal microbiome was analyzed by 16S rRNA sequencing. Monocyte-macrophages were characterized by flow cytometry. Cecal or serum bacterial metabolites were analyzed. The pro-myelopoietic potential of cecal supernatants (CS) was tested in the Young-BM cells. MrgD was expressed in ISCs, which was decreased in the Old. Increased intestinal permeability in aging was reversed by Ala. In the colon organoids, Ala increased Wnt3a levels that were antagonized by the NF449, SQ22536 or 666-15. Ala restored phospho-CREB and active β-catenin levels that were decreased in the Old colon-organoids. Ala increased the richness and β-diversity of the aging microbiome and decreased Bacillota/Bacteroidota. Ala decreased the CD80[+] and increased CX3CR[+] cells in the Old colons. Old-CS induced myelopoiesis in vitro in BM cells with higher number of monocytes and pro-inflammatory macrophages which was not observed in the CS derived from Ala-treated Old mice. Ala is a promising pharmacological agent for reversing the leaky gut of aging by restoring homeostasis in the gut-BM axis.},
}

@article {pmid41795600,
year = {2026},
author = {Fu, Z and Wang, T and Zhang, J and Wang, W and Zhang, X and Wei, K and Tahir, M and Zhong, J},
title = {Multi-Omics Reveals Phenethyl Acetate and Its Producer Lactiplantibacillus plantarum as Key Drivers of Enhanced Palatability in Alfalfa Silage.},
journal = {Microbial biotechnology},
volume = {19},
number = {3},
pages = {e70332},
doi = {10.1111/1751-7915.70332},
pmid = {41795600},
issn = {1751-7915},
support = {32201467//National Natural Science Foundation of China/ ; XDA26040201//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 2025KJHZ0041//Science and Technology Program of the Inner Mongolia Autonomous Region/ ; },
mesh = {*Medicago sativa/microbiology/chemistry/metabolism ; *Silage/microbiology/analysis ; Fermentation ; *Flavoring Agents/metabolism ; Taste ; *Acetates/metabolism ; Amino Acids/analysis/metabolism ; *Lactiplantibacillus plantarum/metabolism ; *Lactobacillaceae/metabolism ; Multiomics ; },
abstract = {High-quality silage enhances palatability and feed intake; however, the effects of co-fermentation with flavouring agents and lactic acid bacteria (LAB) on its flavour quality, core microbiota, and taste-active amino acids remain unclear. This study investigated the effects of fermentation using Lactiplantibacillus plantarum (LP) alone or in combination with phenethyl acetate (LPP) on the flavour profile of alfalfa silage and its subsequent influence on feed intake. Both LP and LPP significantly improved fermentation quality versus control (CK), with markedly higher feed intake-LP > CK and LPP > LP. Key flavour compounds, including dimethyl trisulfide, 4-ethylphenol and β-damascenone, were significantly increased in the LP alone group. Contrarily, essential taste-related amino acids including aspartic acid, alanine, proline, histidine, isoleucine, and valine were decreased, except for arginine. These metabolic shifts collectively contributed to enhanced feed intake. The addition of LPP increased phenylethyl alcohol, benzyl alcohol and hexanal, and decreased arginine, contributing to enhanced palatability. Aryl alcohol dehydrogenase, proline aminopeptidase, histidine dehydrogenase, and branched-chain amino acid transaminase from LP played a crucial role in the formation of phenylethyl alcohol, proline, histidine and isoleucine during fermentation. These results provide insights into how LAB and flavouring agents jointly regulate flavour development in high-quality alfalfa silage.},
}

*Medicago sativa/microbiology/chemistry/metabolism
*Silage/microbiology/analysis
Fermentation
*Flavoring Agents/metabolism
Taste
*Acetates/metabolism
Amino Acids/analysis/metabolism
*Lactiplantibacillus plantarum/metabolism
*Lactobacillaceae/metabolism
Multiomics

@article {pmid41795563,
year = {2026},
author = {Chen, J and Zhou, Z and Liu, D and Yao, Y},
title = {Kaolinite-mediated dual enhancement of tetracycline degradation and methane recovery in anaerobic digestion of contaminated sludge: Microbial community reshaping and metabolic pathway regulation.},
journal = {Journal of hazardous materials},
volume = {507},
number = {},
pages = {141659},
doi = {10.1016/j.jhazmat.2026.141659},
pmid = {41795563},
issn = {1873-3336},
abstract = {Tetracycline (TC) residues in waste-activated sludge (WAS) inhibit key microbial guilds, destabilizing anaerobic digestion (AD). Conventional AD systems rarely achieve both effective antibiotic detoxification and energy recovery. This study investigates the use of kaolinite, a low-cost mineral with superior stability and surface adsorption properties compared to montmorillonite, as an additive for TC-spiked WAS treatment. At an optimal dosage of 0.2 g·L[-1] , kaolinite increased specific methane yield to 44.4 L·kg VS[-1] , a 4.0-fold enhancement over the control, while improving TC removal by 55%. LC-HRMS identified eleven TC transformation products through three main degradation pathways: hydroxylation, N-dealkylation, and ring cleavage. Metagenomic sequencing showed kaolinite selectively enriched syntrophic taxa (Anaerolinea, Hydrogenispora) and the methanogen Methanosarcina, while upregulating genes involved in extracellular electron transfer (e.g., mhcA), methanogenesis (mcrA), and antibiotic resistance/detoxification (tetW, tetX). Network analysis revealed a shift from competitive to mutualistic interactions, enhancing community resilience under TC stress. Mechanistically, kaolinite acts as a "physicochemical buffer and microbial-activity regulator", stabilizing the microenvironment and promoting efficient methanogenesis through direct interspecies electron transfer. These combined effects improve both pollutant removal and methane production, demonstrating a promising approach for optimizing AD in antibiotic-laden sludge management.},
}

@article {pmid41795412,
year = {2026},
author = {Zhang, T and Yang, L and Xie, F and Xing, M and Zhang, H and Song, X and Ai, L},
title = {Docynia delavayi (Franch.) Schneid polyphenols: Optimization of ultrasound-assisted extraction and bioactivity study.},
journal = {Ultrasonics sonochemistry},
volume = {128},
number = {},
pages = {107804},
doi = {10.1016/j.ultsonch.2026.107804},
pmid = {41795412},
issn = {1873-2828},
abstract = {Docynia delavayi is a polyphenol-rich indigenous plant from China, known for its medicinal and edible properties. However, its bioactivities have been scarcely studied. This study aimed to establish an efficient ultrasound-assisted extraction (UAE) process for isolating D. delavayi polyphenols (DDP) and to systematically assess their bioactivities. Single-factor assays combined with response surface methodology were employed to determine optimal UAE conditions for DDP: 43% ethanol, 460 W ultrasonic power, 21 mL/g liquid-to-solid ratio, and 41 min extraction. In vitro evaluation showed that DDP exhibited excellent antioxidant (DPPH radical scavenging IC50 = 3.75 μg/mL) and carbohydrate digestion enzyme (α-Glucosidase and α-Amylase) inhibitory activity. Moreover, DDP also exhibited inhibitory effects on Escherichia coli, Bacillus subtilis, Staphylococcus aureus, and Salmonella. Metagenomic analysis revealed that DDP promoted species associated with short-chain fatty acid synthesis, such as Flavonifractor plautii and Eubacterium sp., while reducing pathogenic bacteria, including Shigella sonnei and Klebsiella pneumoniae. Untargeted metabolomics analysis showed that DDP modulated the intestinal metabolic profile and enriched pathways involved in Fatty acid biosynthesis, Fatty acid metabolism, and Fatty acid elongation in mitochondria. We believe that DDP, owing to its remarkable biological activity, may exhibit significant prebiotic effects, thereby modulating the gut microbiota and metabolic network, ultimately improving host health. This study elucidated an efficient UAE process and the diverse biological activities of DDP, providing an experimental foundation for its development as a natural functional ingredient and supporting high-value utilization of medicinal and edible plant resources.},
}

@article {pmid41795395,
year = {2026},
author = {Chen, Z and Kerfahi, D and He, X and Zhang, X and Zhang, P and Gao, G and Gao, K and Hall-Spencer, JM and Adams, JM and Lin, X},
title = {Ocean acidification reduces diatom and photosynthetic gene abundance on plastic in an coastal bay mesocosm experiment.},
journal = {Marine environmental research},
volume = {217},
number = {},
pages = {107917},
doi = {10.1016/j.marenvres.2026.107917},
pmid = {41795395},
issn = {1879-0291},
abstract = {Discarded plastics are accumulating in the global ocean and posing threats to marine life. The plastisphere - the community colonizing plastic surfaces - profoundly influences the environmental behavior of plastic, affecting its degradation and entry into marine food webs. Ocean acidification (OA) due to anthropogenic CO2 emissions, is also threatening marine ecosystems, but the effect of OA on the structure and ecological functions of plastisphere communities remain poorly understood. Here, using a mesocosm experiment, we investigated the effects of OA on the plastisphere colonizing floating PET plastic bottles. The study was conducted using subtropical eutrophic coastal water from Southern China under two CO2 conditions: increased CO2 to 1000 μatm (HC) and ambient CO2 410 μatm (LC). Metagenomic sequencing of the plastic samples, after exposure for 32 days, showed striking changes in relative abundance of eukaryotes and bacteria caused by HC. There was a 75.3 % decrease in eukaryote read abundances at high CO2, most strikingly a 95.6% decrease in the relative abundance of diatoms. In addition, the relative abundance of genes involved in photosystem II light reactions and pigment synthesis decreased under high CO2 conditions. This suggests that OA could reduce the photosynthetic potential of the plastisphere. Shifts in plastisphere community structure and potentially diminished photosynthesis under OA could influence food chains within plastisphere, plastic degradation, transportation, and carbon cycling involving plastics. Overall, our results suggest that OA can alter the functional ecology of the plastisphere, with potential implications for marine biogeochemical processes and food web dynamics in subtropical eutrophic coastal water.},
}

@article {pmid41795336,
year = {2026},
author = {Hao, J and Zhang, YT and Li, X and Dai, X and Xu, Y},
title = {Water-evaporation-induced efficient high-temperature aerobic fermentation of food waste.},
journal = {Bioresource technology},
volume = {449},
number = {},
pages = {134368},
doi = {10.1016/j.biortech.2026.134368},
pmid = {41795336},
issn = {1873-2976},
abstract = {Aerobic fermentation is an effective approach for reducing, stabilising, and recovering resources from food waste. However, its performance is often constrained by poor oxygen transfer within the fermentation substrate. In this study, we investigated the inductive mechanism of water evaporation enhancing aerobic fermentation of food waste. It was observed that water evaporation, as the primary driving force, promoted microscale moisture redistribution and pore structure optimization, leading to an 84.8% (p < 0.01) increase in the average pore diameter and an 8.7% (p < 0.01) increase in porosity. As a result, a significant increase in the oxygen mass transfer coefficient (+250.1%) was achieved within the food waste. This improved microenvironment steered microbial community succession toward thermophilic functional groups dominated by Bacillus and Diutina, prolonging the thermophilic phase by 167% (p < 0.05) and facilitating the degradation of major organic components. Among them, the degradation rate of lipids was significantly increased by 57.1% (p < 0.01). Consequently, the humic substance content in the fermentation product increased by 18.8% (p < 0.05) and the corresponding germination index increased by 41.4% (p < 0.05). These results were further confirmed by the metagenomic analysis, which indicated that water evaporation induced the significant enrichment of functional genes associated with the tricarboxylic acid cycle and electron transport chain in the aerobic fermentation. These findings offer new mechanistic insights into leveraging microscale moisture regulation to optimize aerobic bioconversion.},
}

@article {pmid41794977,
year = {2026},
author = {Yaikhan, T and Wongsurawat, T and Jenjaroenpan, P and Thaipisuttikul, I and Chayakulkeeree, M and Tribhuddarat, C and Nitayanon, P and Peizner, MT and Tansirichaiya, S and Kamolvit, W and Surachat, K},
title = {Evaluating long-read metagenomics for bloodstream infection diagnostics: a pilot study from a Thai Tertiary Hospital.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-41247-2},
pmid = {41794977},
issn = {2045-2322},
support = {B13F660074//the NSRF through the Program Management Unit for Human Resources & Institutional Development, Research and Innovation/ ; MED6801076S//the National Science Research and Innovation Fund (NSRF) and Prince of Songkla University, Thailand/ ; },
}

@article {pmid41794791,
year = {2026},
author = {Song, Z and Li, R and Liang, L and Zhang, M and Wang, H and Bu, H and Zhang, Y},
title = {Varicella zoster virus-related myelitis: a case series and literature review.},
journal = {Virology journal},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12985-026-03123-3},
pmid = {41794791},
issn = {1743-422X},
support = {No. H2023206903//the National Science Foundation of Hebei Province/ ; },
abstract = {INTRODUCTION: Varicella zoster virus (VZV) is a human neurotropic herpesvirus that remains latent in the dorsal root ganglia and can reactivate to cause herpes zoster. In immunocompromised patients, reactivation may lead to severe neurological complications such as encephalitis, meningitis, myelitis, and neuropathy. However, varicella zoster virus-related myelitis (VZVM) is relatively rare, particularly in immunocompetent adults. The pathogenesis may involve direct viral invasion of the spinal cord parenchyma during the acute phase or a postinfectious immune-mediated inflammatory response.

CASE PRESENTATIONS: This report describes three patients with VZVM(one woman ages 49 years and two men age 60 and 56 years), none of whom presented with a typical rash. Two patients (cases 1 and 2) developed encephalomyelitis at disease onset, characterized by fever, impaired consciousness, and long-segment spinal cord lesions. Metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF) detected VZV nucleic acid in both cases. In case 3, the patient initially developed VZVM complicated by cerebral venous sinus thrombosis. After an interval of approximately 40 days, delayed thoracic myelitis developed, and repeated CSF mNGS testing yielded negative results. All three patients received intravenous antiviral therapy; two additionally received low-dose corticosteroids combined with intravenous immunoglobulin, and one received intravenous methylprednisolone. During follow-up, one patient achieved full recovery of lower-limb motor function, whereas two patients remained paraplegic.

CONCLUSIONS: VZVM presents with diverse clinical manifestations and may occur without the typical vesicular rash. It can develop either during the initial phase of VZV infection or as a delayed complication. Early magnetic resonance imaging and CSF molecular testing support timely diagnosis. Prompt and adequate antiviral therapy combined with immunomodulatory treatment may improve neurological outcomes.},
}

@article {pmid41794462,
year = {2026},
author = {Di Gianvito, P and Sáez, V and Dimopoulou, M and Papandreou, C and Francesca, N and Vrhovsek, U and Rantsiou, K and Cocolin, L and Arapitsas, P and Englezos, V},
title = {The role of mycobiome in terroir and during Muscat grapes fermentation unveiled by multi-omic analysis.},
journal = {Food research international (Ottawa, Ont.)},
volume = {230},
number = {},
pages = {118577},
doi = {10.1016/j.foodres.2026.118577},
pmid = {41794462},
issn = {1873-7145},
abstract = {The wine microbiome is a key determinant in shaping wine terroir. To date, a comprehensive understanding of how microbial signatures influence wine metabolic profile remains poorly understood. To address this, in the present study an integrated shotgun metagenomics and untargeted metabolomic approach was employed to investigate the wine metabolome and connect the composition and functions of microbiomes involved in wine fermentation of Muscat grapes harvested in Italy and Greece. Beta diversity highlighted the dissimilarity between Italian and Greek fungal terroirs. A marked reduction in diversity during fermentation underscored the dominance of the inoculated Saccharomyces cerevisiae starter culture. The LEfSe analysis revealed an enrichment of Torulaspora delbrueckii in Greek samples, while Kluyveromyces marxianus and lactis were more abundant in Italian samples. Functional analysis revealed geographic differences in nucleotide, fatty acids and lysine metabolisms. Significant shifts were observed in energy, carbohydrate, and amino acid metabolisms, reflecting terroir-specific microbial activity. The metabolomics data highlighted regional differences in oligosaccharides, glycosylated phenolics, peptide and amino acid turnover, and central redox metabolites, suggesting divergent microbial responses and metabolic trajectories shaped by terroir and fermentation conditions. Obtained results highlight the effectiveness of this multi-omics approach in identifying product-specific fungal communities and wine metabolite signatures, providing new tools that could be used to ensure wine authenticity and quality control.},
}

@article {pmid41794459,
year = {2026},
author = {Cai, J and Huang, A and You, L and Wang, Z and Huang, C and Huang, R and Li, Y and Liang, T and Zhang, F and Wu, Q and Wang, J and Zhu, Z and Ding, Y},
title = {Neomycin-sensitive gut bacteria-derived brassicasterol mediates the anti-obesity effects of Cordyceps militaris polysaccharide.},
journal = {Food research international (Ottawa, Ont.)},
volume = {230},
number = {},
pages = {118574},
doi = {10.1016/j.foodres.2026.118574},
pmid = {41794459},
issn = {1873-7145},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Obesity/prevention & control/drug therapy ; Diet, High-Fat/adverse effects ; Mice ; *Neomycin/pharmacology ; Mice, Inbred C57BL ; *Cordyceps/chemistry ; Male ; *Anti-Obesity Agents/pharmacology ; Anti-Bacterial Agents/pharmacology ; Liver/metabolism ; *Fungal Polysaccharides/pharmacology ; Lipid Metabolism/drug effects ; },
abstract = {Diet-based modulation of the gut microbiota has emerged as a promising strategy to alleviate obesity and its related complications. Our previous study demonstrated that polysaccharide derived from Cordyceps militaris (CMP) exerts anti-obesity effects, yet the specific mechanism linking gut microbiota to its metabolic impact remains unclear. Herein, we utilized murine models with distinct gut microbial profiles created via antibiotic cocktails to investigate these mechanisms. The protective effects of CMP against high-fat diet (HFD)-induced obesity and associated metabolic disturbances were substantially impaired in mice depleted of neomycin-sensitive gut bacteria. Metagenomic analyses further established that CMP required these bacteria to restore gut microbial homeostasis. Notably, we observed that CMP elevated hepatic levels of brassicasterol in a manner dependent on neomycin-sensitive gut bacteria. Brassicasterol treatment alone replicated the anti-obesity effects of CMP, as indicated by reduced body weight gain, improved lipid and glucose metabolism, and decreased inflammation. Through transcriptomic and functional analyses, we identified hepatic Apoa4 as a key downstream effector of brassicasterol. Our results indicated that brassicasterol upregulated Apoa4, facilitating lipid transport and suppressing inflammation both in vitro and in vivo. Collectively, our findings indicate that CMP exerts its anti-obesity effects through a neomycin-sensitive gut bacteria-brassicasterol-Apoa4 pathway. This work expands the mechanistic understanding of CMP and highlights a novel microbiota-metabolite-host regulatory axis for dietary intervention in metabolic disorders.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Obesity/prevention & control/drug therapy
Diet, High-Fat/adverse effects
Mice
*Neomycin/pharmacology
Mice, Inbred C57BL
*Cordyceps/chemistry
Male
*Anti-Obesity Agents/pharmacology
Anti-Bacterial Agents/pharmacology
Liver/metabolism
*Fungal Polysaccharides/pharmacology
Lipid Metabolism/drug effects

@article {pmid41794383,
year = {2026},
author = {Wannaiampikul, S and Lee, B and Chen, J and Prentice, KJ and Ayansola, R and Xu, A and Santosa, S and Pantopoulos, K and Sweeney, G},
title = {Integrated metabolomics and metagenomics analysis identifies a unique signature characterizing metabolic syndrome.},
journal = {The Journal of nutritional biochemistry},
volume = {},
number = {},
pages = {110327},
doi = {10.1016/j.jnutbio.2026.110327},
pmid = {41794383},
issn = {1873-4847},
abstract = {BACKGROUND: Metabolic Syndrome (MetS) presents a global health challenge, characterized by obesity, hypertension, dyslipidemia, and insulin resistance. Despite recognition of the gut microbiome's role in metabolic health, there remains scope for defining association of unique microbes with clinical status. Unique genetic, dietary, and lifestyle factors may influence gut microbial composition and circulating metabolites, and consequently susceptibility to MetS. By identifying specific microbial and metabolomic signatures associated with MetS, we aim to uncover potential targets for reducing the disease burden.

METHODS: We correlate comprehensive clinical parameters with fecal metagenomics and untargeted serum metabolomics to delineate population-specific characteristics from 142 individuals with MetS (N=97) or control (CTRL; N=45).

RESULTS: Microbiome species-level alpha diversity was reduced in MetS compared to CTRL. After adjustment for sex, age, BMI, and intensity of statin usage, we identified 20 MetS-related species. A co-abundant network analysis revealed Eubacterium eligens, enriched in the CTRL population, with the highest node degree. Serum metabolomics identified 106 significantly differentially regulated metabolites. N-arachidonoyl dopamine (NADA), an endocannabinoid implicated in GABAergic signaling, was the most significantly altered, enriched in CTRL and correlated with E. Eligens. sPLS-DA modeling revealed that E. eligens and D. formicigenerans species cluster together with metabolites NADA and tetrahydrocorticosterone (THB), representing defining characteristics distinguishing MetS in this population.

CONCLUSIONS: Our data reveal a distinct multi-omic signature of MetS, characterized by a significant reduction in E. eligens and D. formicigenerans abundance, and in circulating NADA and THB levels.},
}

@article {pmid41793958,
year = {2026},
author = {Li, X and Sun, Z and Lin, L and Deng, T and Xu, M},
title = {Attenuation of sulfamethoxazole and associated antimicrobial resistome by enriched electroactive microbial consortia.},
journal = {Environment international},
volume = {209},
number = {},
pages = {110182},
doi = {10.1016/j.envint.2026.110182},
pmid = {41793958},
issn = {1873-6750},
abstract = {Electroactive biofilms with the capacity of extracellular electron transfer (EET) have shown great promise for mitigating antibiotics and antibiotic resistance genes (ARGs). However, detailed interactions between antibiotics and electroactive microorganisms, along with ARGs dissemination dynamics within the electroactive consortia, remained poorly understood. In this study, stable electroactive microbial consortia were enriched, and their influences on the fates of sulfamethoxazole (SMX) and associated ARGs were systematically investigated. The results showed the enriched consortia could degrade SMX effectively within a wide concentration range through co-metabolism which was stimulated by their electrogenic respiration. Moreover, with accelerated SMX removal, the abundances of associated ARGs including sul1 and sul2 in the consortia decreased significantly due to alleviated SMX-induced selective pressure and probably weakened horizontal gene transfer mediated by mobile genetic elements (e.g., IS91 and tnpA). Degrader isolation and metagenomic analysis identified the core EET-proficient genera (e.g., Geobacter and Alcaligenes) as essential for the accelerated co-metabolism biodegradation of SMX, whereas the proliferation of other bacteria with limited or no EET capacity (e.g., Hydrogenophaga, Burkholderia, Comamonas, Desulfovibrio and Pseudomonas) was closely linked to the ARGs dissemination. This work provides a mechanistic elucidation of how electroactive microbial consortia stimulate antibiotic degradation and attenuate ARGs proliferation, offering strategic insights for risk control of the resistome during wastewater treatment.},
}

@article {pmid41793890,
year = {2026},
author = {Dong, M and Zhang, Q and Wang, Y and Wang, S and Feng, G and Qi, H},
title = {Restructuring tilth layers suppresses cotton Verticillium wilt through the niacinamide-mediated enrichment of beneficial Pseudomonas.},
journal = {Microbiological research},
volume = {307},
number = {},
pages = {128491},
doi = {10.1016/j.micres.2026.128491},
pmid = {41793890},
issn = {1618-0623},
abstract = {Restructuring tilth layers (RTL) is an innovative tillage practice that involves the vertical exchange of topsoil and subsoil while the deeper layer is loosened, and this practice has been verified to significantly reduce the incidence of cotton Verticillium wilt. However, the ecological mechanisms underlying disease suppression remain unclear. In this study, we integrated field experiments, metagenomic sequencing, untargeted metabolomics, and functional validation to elucidate the effects of RTL on the rhizosphere ecosystem from the perspectives of microbe and metabolite interactions. RTL significantly altered the diversity and composition of the rhizosphere microbial communities and increased their network complexity and stability. Linear discriminant analysis effect size (LEfSe) revealed that RTL promoted the enrichment of beneficial taxa such as Pseudomonas, Lysobacter, and Mesorhizobium. Metabolomic profiling revealed that the abundance of niacinamide was 19.11-fold higher (P < 0.05) in the RTL rhizosphere than in the control rhizosphere. Exogenous supplementation and antagonistic assays demonstrated that niacinamide stimulated Pseudomonas enrichment and activation in the rhizosphere. Although niacinamide did not have direct antifungal activity, its coapplication with Pseudomonas reduced the disease index of Verticillium wilt by 81.89%. Overall, RTL suppresses Verticillium wilt through two pathways, by establishing a more stable and complex microbial network and regulating rhizosphere metabolite composition, particularly niacinamide accumulation, which drives the colonization and activation of defense mediated by beneficial microbes, forming an ecological defense mechanism that links metabolite signaling, microbial response, and pathogen suppression.},
}

@article {pmid41793868,
year = {2026},
author = {Wang, M and Yu, G and Zhang, Y and Ren, J and Chen, W and Li, Q and Cong, P},
title = {Seasonal dynamics and environmental regulation of pathogenic bacteria in the Weihe River Basin.},
journal = {Journal of hazardous materials},
volume = {506},
number = {},
pages = {141646},
doi = {10.1016/j.jhazmat.2026.141646},
pmid = {41793868},
issn = {1873-3336},
abstract = {Waterborne pathogen transmission poses a significant global environmental health risk. This study employs metagenomic sequencing combined with co-occurrence network analysis, redundancy analysis (RDA), and partial least squares path modeling (PLS-PM) to investigate the distribution and transmission risk of pathogens in the Weihe River Basin. The study identified 232 pathogenic species in the Weihe River's main and tributary waters, with core pathogens (such as Pseudomonas aeruginosa and Salmonella enterica) consistently present across all hydrological periods. RDA analysis indicated temperature, salinity, nitrate-nitrogen, and chlorophyll-a are key environmental factors driving pathogen community structure. The PLS-PM model reveals significant seasonal variations in the association patterns between mobile genetic elements (MGEs) and pathogens. During the high-water period, MGEs showed the strongest correlation with pathogens, suggesting that pathogens are the primary hosts of MGEs. MGEs-mediated horizontal gene transfer may drive pathogen dissemination during this period. During the normal-water period, MGEs primarily facilitated the transfer of virulence factors (VFs), enhancing the potential pathogenicity of pathogens. During the low-water period, environmental factors promoted the spread of MGEs while inhibiting the expression of virulence genes, leading to a reduction in pathogen virulence. Co-occurrence networks further demonstrate that during the high-water period, MGEs closely linked key VFs, such as Capsule, with enteric pathogens; network connectivity decreased significantly during the normal-water period, maintaining only limited associations; during the low-water period, functional VFs were frequently co-occurring with opportunistic pathogens. This study provides scientific evidence and management references for pathogen risk assessment and control in river basins.},
}

@article {pmid41793859,
year = {2026},
author = {Brito, B and Frost, M and Webster, J and To, J and Kirkland, P},
title = {Quantifying the impact of sequencing depth and reference genome choice on metatranscriptomic detection of four bovine RNA viruses.},
journal = {Research in veterinary science},
volume = {204},
number = {},
pages = {106125},
doi = {10.1016/j.rvsc.2026.106125},
pmid = {41793859},
issn = {1532-2661},
abstract = {Metatranscriptomic sequencing enables untargeted detection of RNA viruses across clinical and environmental contexts. Evaluating this approach through metrics such as limits of detection and genome coverage, in direct comparison with established molecular tools like qRT-PCR, is essential for understanding its potential diagnostic utility. In the present study, we assessed the detection performance of metatranscriptomic sequencing for four bovine respiratory RNA viruses: Bovine coronavirus (BCoV), Bovine nidovirus (BNV), Influenza D virus (IDV), and Bovine viral diarrhea virus-1 (BVDV-1) in nasal swabs, using reference-based mapping. Sequencing depth (1, 10, and 20 million (M) reads) and reference genome choice (NCBI RefSeq and study-assembled) were systematically varied to quantify their effects on viral read recovery and genome coverage. For BNV and BCoV, sequencing at ≥10 M reads was sufficient for metatranscriptomic detection of samples that were qRT-PCR positive at high Ct values (up to 40), but recovering high genome completeness was only achieved for samples with Ct < 30. IDV detection was less sensitive: several qRT-PCR-positive samples (Ct 29.6-34.5) yielded no mapped reads even at 20 M. BVDV-1 recovery was strongly reference-dependent; mapping to study-assembled genomes markedly increased read counts and coverage compared with NCBI RefSeq, reflecting divergence between field strains and the standard reference sequence. A low number of mapped reads was observed in several qRT-PCR-negative BVDV-1 pools when using the NCBI RefSeq, consistent with potential misclassification of host-derived sequences. By quantitatively linking qRT-PCR Ct values, sequencing depth, and reference divergence, the present study outlines methodological considerations that may guide future applications of metatranscriptomics into veterinary diagnostics.},
}

@article {pmid41793822,
year = {2026},
author = {Li, P and Wang, Y and Bao, Z and He, X and Wang, S and Su, X and Nie, W and Xu, F and Zhou, H and Li, H and Xu, B},
title = {Metagenomics-based insights into the microbial community composition and quality characteristics development potentiality in traditional dry-cured ham.},
journal = {International journal of food microbiology},
volume = {453},
number = {},
pages = {111705},
doi = {10.1016/j.ijfoodmicro.2026.111705},
pmid = {41793822},
issn = {1879-3460},
abstract = {The objective of this study was to elucidate the formation mechanisms of quality characteristics in traditional dry-cured ham. The microbial community composition in three types of dry-cured ham was analyzed using metagenomics technology. Volatile flavor profiles were characterized via gas chromatography-mass spectrometry (GC-MS) and gas chromatography-ion mobility spectrometry (GC-IMS), while peptide profiles were determined using liquid chromatography-mass spectrometry (LC-MS). Based on metagenomic data, biosynthetic pathways of volatile flavor compounds and bioactive peptides in dry-cured hams were reconstructed. Key microorganisms identified include Staphylococcus equorum, Staphylococcus saprophyticus, Aspergillus glaucus, Aspergillus ruber, Debaryomyces hansenii, and Debaryomyces fabryi. Using GC-MS and GC-IMS, 25 volatile compounds were identified in dry-cured ham, with branched-chain compounds exhibiting higher odor activity values (OAVs). LC-MS analysis identified 203 microbial-derived peptide fragments, predominantly possessing angiotensin-converting enzyme (ACE) inhibitory, dipeptidyl peptidase-IV (DPP-IV) inhibitory, and antioxidant activities. Further investigation into the contribution of microbial communities to the characteristic quality attributes revealed that Staphylococcus species promote the formation of 3-methyl-butanal via branched-chain amino acid transaminase (BCAT) and 3-hydroxy-2-butanone via acetolactate synthase (ALS). With regard to functional bioactive peptides, Staphylococcus indirectly contributes to the synthesis of NPPKFD, DLEE, and KRQKYD via glutamyl endopeptidase activity. Additionally, proteins derived from Aspergillus glaucus (actin-related protein 5) and Staphylococcus equorum (chromosome segregation protein) serve as direct precursors for bioactive peptides, yielding potential sequences such as KNSKDPVSI and LEDDI. This study provides evidence indicating the role of microbial communities in shaping the quality characteristics of dry-cured ham.},
}

@article {pmid41793806,
year = {2026},
author = {Qi, J and Song, Y and Luo, S and Zhu, M and Fu, F and Feng, Y and Mei, W and Feng, H and Li, X and Song, C},
title = {Soil water and inorganic nitrogen contents drive soil microbial carbon fixation during wetland reclamation and restoration.},
journal = {Water research},
volume = {297},
number = {},
pages = {125666},
doi = {10.1016/j.watres.2026.125666},
pmid = {41793806},
issn = {1879-2448},
abstract = {Wetlands are critical terrestrial carbon sinks, playing a vital role in mitigating global warming by fixing substantial atmospheric carbon dioxide. To explore how wetland reclamation and restoration affect soil microbial carbon fixation, we sampled soils from five land-use types in western Jilin Province, China: undisturbed natural reed wetland, reclaimed rice paddy and upland field, restored agricultural drainage wetland and naturally restored wetland after farmland abandonment. We analyzed the effects of wetland reclamation and restoration on microbial communities, metabolic pathways, and carbon fixation potential. Results showed Proteobacteria (31.81 %), Actinobacteria (27.08 %), and Acidobacteria (15.12 %) dominated carbon-fixing microbes, with the reductive tricarboxylic acid cycle and dicarboxylate/4-hydroxybutyrate cycle as major carbon-fixing pathways. The natural wetland had the highest carbon fixation potential, with a mean value of 1.58 mg·kg[-1] across the 0-15 cm topsoil layer and 15-30 cm subsoil layer, which was 1.30 to 4.02 times that of the reclaimed wetlands and restored wetlands. Among reclaimed sites, the rice paddy retained soil microbial community similarity to the natural wetland with complex, stable microbial networks. Compared to the naturally restored wetland, the agricultural drainage-restored wetland showed superior restoration outcomes, including microbial communities more similar to the natural wetland, higher network stability, and greater carbon fixation potential. Soil water and inorganic nitrogen contents were core drivers regulating carbon fixation via RubisCO activity and microbial metabolic pathways. This result highlights that the key to wetland restoration lies in prioritising hydrological regulation and nitrogen management, thereby enhancing microbial carbon fixation potential.},
}

@article {pmid41792922,
year = {2026},
author = {Mertz, CM and Mancuso, CJ and Robinson, DM and Yeboah, LD and Fogel, ML and Takacs-Vesbach, C and Newsome, SD},
title = {Microbially Derived Essential Amino Acids Compensate for Dietary Deficiencies in an Ecologically Relevant Mammalian Host.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag044},
pmid = {41792922},
issn = {1751-7370},
abstract = {Protein is the main structural and functional component of cells, making it crucial for the survival of all living organisms. Yet mammalian herbivores and omnivores often consume diets deficient in the amount of protein required for growth, homeostasis, and reproduction. To compensate, mammals likely rely on their gut microbiota to synthesize essential amino acids (AAESS), particularly during periods of dietary protein limitation. We quantified the contribution of microbially synthesized AAESS to skeletal muscle in captive, wild-derived deer mice (Peromyscus maniculatus) fed diets varying in macromolecular quantity and quality. Using amino acid carbon isotope (δ13C) analysis combined with genetic sequencing, we assessed the origin of AAESS incorporated into host muscle and identified gut microbial taxa with the genetic potential for AAESS biosynthesis. We estimate that up to 25% of host muscle AAESS were microbially derived, with greater microbial contributions in mice fed diets containing low protein or more complex macronutrients. Gut microbial populations with the genetic potential for AAESS biosynthesis were more abundant in mice with larger contributions of microbially-derived AAESS in their tissues. These results demonstrate the crucial and likely pervasive role the gut microbiome plays in host protein metabolism, especially in mammals facing seasonal or persistent dietary protein limitation.},
}

@article {pmid41645132,
year = {2026},
author = {Ma, D and Xu, S and Yu, D and Peng, A and Yang, L and Yang, H and Yuan, Q and Li, Y},
title = {Cytomegalovirus-induced severe enterocolitis associated with ANCA-associated vasculitis and diffuse alveolar haemorrhage in a child: a diagnostic and therapeutic dilemma.},
journal = {BMC pediatrics},
volume = {26},
number = {1},
pages = {},
pmid = {41645132},
issn = {1471-2431},
abstract = {BACKGROUND: ANCA-associated vasculitis (AAV) is rare in children and may be triggered by infections. Cytomegalovirus (CMV), a common pathogen, can rarely cause severe gastrointestinal complications like stricture, obstruction, and perforation. While adult cases suggest a potential association between CMV and AAV, reports of severe intestinal complications leading to AAV in immunocompetent children are scarce.

CASE PRESENTATION: A previously healthy 12-year-old boy presented with fever, abdominal pain, and vomiting. Abdominal CT revealed intestinal obstruction and perforation. Emergency surgery confirmed acute hemorrhagic necrotizing enterocolitis, and metagenomic next-generation sequencing (mNGS) diagnosed CMV viremia. His condition deteriorated rapidly, culminating in acute respiratory failure and acute kidney injury requiring continuous renal replacement therapy. Serological testing using indirect immunofluorescence was positive for cytoplasmic-ANCA (C-ANCA). Confirmatory ELISA testing confirmed positivity for anti-proteinase 3 (PR3) antibodies at a titer of 1:51; anti-myeloperoxidase (MPO) antibodies were negative. Chest CT and bronchoscopy confirmed diffuse alveolar haemorrhage. AAV was diagnosed per the 2022 ACR/EULAR criteria. The central management challenge was the co-occurrence of active CMV infection and fulminant vasculitis. Immunosuppressive therapy was withheld until sepsis parameters normalized. A life-threatening bleeding event on day 13 prompted initiation of high-dose methylprednisolone and cyclophosphamide, leading to rapid clinical improvement. A subsequent renal biopsy showed subacute tubulointerstitial injury without crescents.

CONCLUSION: Severe CMV enterocolitis may be temporally associated with fulminant AAV in children. In pediatric cases of severe CMV infection with multi-organ dysfunction, a high index of suspicion for AAV and ANCA serology testing is warranted. Furthermore, multidisciplinary team input is crucial for guiding optimal timing of immunosuppression in the context of concurrent active infection, which is pivotal for improving patient outcomes.},
}

@article {pmid41792508,
year = {2026},
author = {Li, M and Li, Y and Li, C and Liu, A and Liu, Y and Li, Y and Xiao, J and Zhang, D and Jin, Y and Wang, G and Pang, X and Jiang, K and Yin, Y},
title = {Dynamic reorganisation of intratumoural bacterial florae during colorectal cancer progression.},
journal = {British journal of cancer},
volume = {},
number = {},
pages = {},
pmid = {41792508},
issn = {1532-1827},
support = {81874235/82030081//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {BACKGROUND: Colorectal cancer (CRC) exhibits distinct bacterial community compositions compared to healthy mucosae, which intimately correlate with CRC clinical outcomes. There is a lack of explanation for the inducements of microbiota remodelling.

METHODS: FISH experiments and 16S rRNA sequencing were conducted to determine the inducements of various bacterial colonisation within tissues. Community cultivation was conducted to estimate the capacity of tumours to remodel bacterial communities. Metagenomic analyses were utilised to determine the remodelled communities of CRC with distant metastasis. Scratch tests and three-dimensional (3D) cultivation were employed to investigate the influence of specific taxa on tumour cell behaviours.

RESULTS: Colorectal tumours exhibit heterogeneous and individualised preferences in constantly remodelling intratumoural bacterial florae. Various degrees of colorectal gland differentiation within tumours cause heterogeneous intratumoural bacterial colonisation. CRC progression further alters bacterial community composition. Particularly, Prevotella is significantly enriched in the newly established communities colonising the primary foci of metastatic CRC. Furthermore, Prevotella intermedia (P. intermedia) promotes the invasion, migration, and ectopic tumorigenesis of CRC cells.

CONCLUSIONS: Individual evaluation of the preference of tumours in microbiota may pave the way to the development of CRC therapeutic strategies, and Prevotella is an emerging genus worthy of clinical attention.},
}

@article {pmid41792155,
year = {2026},
author = {Benoit, G and James, R and Raguideau, S and Alabone, G and Goodall, T and Chikhi, R and Quince, C},
title = {High-quality metagenome assembly from nanopore reads with nanoMDBG.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-69760-y},
pmid = {41792155},
issn = {2041-1723},
support = {BBX011089/1,BBS/E/ER/230002C,BB/CSP1720/1,BB/X011054/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; 872539, 956229, 101047160 and 101088572//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; },
abstract = {Third-generation long-read sequencing technologies, significantly improve metagenome assemblies. Highly accurate PacBio HiFi reads can yield hundreds of near-complete metagenome-assembled genomes (MAGs) from a single sample. Recently, the accuracy of the more cost-effective Oxford Nanopore Technologies (ONT) platform has increased to a per-base error rate of 1-2%. However, current metagenome assemblers are optimized for HiFi and do not scale to the large data sets that ONT enables. We present nanoMDBG, an evolution of metaMDBG, which supports the latest ONT reads through an error correction pre-processing step in minimizer-space. Across a range of ONT datasets, including a large 400 Gbp soil sample, nanoMDBG reconstructs up to twice as many high-quality MAGs as the next best ONT assembler, metaFlye, while requiring a third of the CPU time and memory. Critically, the latest ONT technology can now produce comparable MAG construction results as those obtained using PacBio HiFi at the same sequencing depth.},
}

@article {pmid41791848,
year = {2026},
author = {Louca, P and Manning, S and Hackney, E and Sharp, L and Hull, MA and Koo, S and Young, GR and Taylor, GS and Dunneram, Y and Mitra, S and Hampton, JS and Dobson, C and Neilson, LJ and Addison, C and El-Omar, EM and , and Stewart, CJ and Rees, CJ},
title = {Gut microbiome signatures in colorectal neoplasia: a cross-sectional study across neoplasia stages and subtypes.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-337478},
pmid = {41791848},
issn = {1468-3288},
abstract = {BACKGROUND: While colorectal cancer (CRC) has been linked to the gut microbiome, it remains unclear whether specific microbial signatures are detectable in precursor lesions such as adenomatous polyps, serrated lesions or sessile serrated lesions.

OBJECTIVE: To assess gut microbiome taxonomic and functional associations with colorectal neoplasia presence, severity (non-advanced, advanced and CRC) and subtype and evaluate predictive potential in high-risk neoplasia.

DESIGN: Analysed cross-sectional stool metagenomes (pre-colonoscopy) from 1762 participants (97% White British) undergoing colonoscopy in the multicentre COLO-COHORT study. Neoplasia was classified per British Society of Gastroenterology surveillance guidelines. Linear mixed-effects models and random forest classifiers assessed taxonomic and functional associations, adjusting for dietary, clinical and lifestyle covariates.

RESULTS: Gut microbiome composition differences between individuals with and without neoplasia were statistically significant but minimal (R[2]=0.0008, p=0.03). A small number of species, including Mediterraneibacter faecis and Pseudoruminococcus massiliensis, and microbial pathways, including amino acid biosynthesis and β-lactam resistance, were modestly linked to neoplasia, particularly early lesions (q value <0.05). Associations were generally weak and attenuated after covariate adjustment. Predictive models combining the microbiome with clinical/demographic features modestly improved high-risk neoplasia classification (area under the curve=0.64 vs 0.58 for clinical/demographic features alone).

CONCLUSION: This large prospective cross-sectional study found weak and inconsistent associations between the gut microbiome and premalignant colorectal neoplasia, with no robust microbial signatures. Findings suggest that previously reported microbial shifts may emerge later in disease progression, potentially as a consequence rather than a cause of CRC. Longitudinal, multiomic studies disentangling temporal and causal pathways between the gut microbiome and neoplasia are required.},
}

@article {pmid41791723,
year = {2026},
author = {Raj, A and Pant, A and Kumar, A and Kumar, A and Kalamdhad, AS and Khwairakpam, M},
title = {Systems-Level Insights Into Microbial Naphthalene Biodegradation: An Integrated In Silico and Omics Perspective.},
journal = {Environmental microbiology},
volume = {28},
number = {3},
pages = {e70264},
doi = {10.1111/1462-2920.70264},
pmid = {41791723},
issn = {1462-2920},
support = {IITG/R&D/IPDF/2024-25/20240815P852//Indian Institute of Technology Guwahati/ ; },
abstract = {Naphthalene, a widely detected polycyclic aromatic hydrocarbon (PAH), is among the 16 priority PAHs identified as major environmental hazards due to its persistence, ubiquity, and toxicity to ecosystems and human health. Its occurrence in crude oil, combustion residues, vehicle emissions, and household products highlights the urgent need for sustainable remediation strategies. Microbial-based bioremediation stands out as an eco-friendly and cost-effective approach that harnesses the metabolic versatility of diverse microorganisms, their genes, and enzymes responsible for naphthalene degradation. Recent advances in omics technologies and high-throughput sequencing have expanded our understanding of novel microbial taxa, metabolic pathways, and stress responses under naphthalene exposure. Complementarily, computational modelling, in silico tools, machine learning, and systems biology have enabled the prediction of degradation dynamics and the design of synthetic microbial consortia optimised for field use. Despite these advances, challenges such as environmental fluctuations, co-contaminant effects, and the gap between laboratory and field outcomes remain. Overcoming these requires an integrative framework that connects microbial ecology, omics insights, and computational modelling. This review consolidates current knowledge on microbial degradation of naphthalene, emphasising key taxa, genes, and pathways, and highlights how omics, in silico tools and systems biology can drive sustainable remediation in the Anthropocene.},
}

@article {pmid41791469,
year = {2026},
author = {Ma, J and Liu, J and Guo, Z and Zhu, M and Chai, Z and Jiang, F and Li, Z and Liang, Z and Jiang, Z},
title = {Characteristics of the microbial carbon pump in kelp farming areas and the impact of artificial reefs: A metagenomic and ecological perspective.},
journal = {Environmental research},
volume = {},
number = {},
pages = {124166},
doi = {10.1016/j.envres.2026.124166},
pmid = {41791469},
issn = {1096-0953},
abstract = {The microbial carbon pump (MCP) can transform labile dissolved organic carbon (LDOC) into recalcitrant dissolved organic carbon (RDOC), yet how sedimentary MCP efficiency is regulated by natural gradients of organic carbon input remains unclear. In this study, we investigated sediments in a kelp farming environment, leveraging the contrast between artificial reef (AR) areas and adjacent non-reef (NR) areas. We combined full-length 16S rRNA sequencing, metagenomics, and fluorescent dissolved organic matter (FDOM) characterization to compare microbial processing under these contrasting depositional regimes. Elevated LDOC inputs in the AR zones were associated with reshaped community metabolic profiles and with enhanced turnover and potential formation of RDOC. High substrate availability was linked to coordinated metabolic functional potential, in which increased genetic potential for upstream catabolism covaried with genomic features indicative of expanded acetyl-CoA supply potential. This putative metabolic overflow was more strongly associated with the mevalonate (MVA) pathway than with the alternative methylerythritol phosphate pathway, consistent with a potential routing toward isoprenoid and terpenoid backbone biosynthesis and the formation of carboxyl-rich alicyclic molecule (CRAM) precursors. Genome-resolved reconstructions further suggested metabolic complementarity among taxa, with predicted cross-feeding interactions that could help sustain carbon processing in MVA-enriched copiotrophs. Overall, humic-like FDOM signals co-vary with organic loading driven by artificial reefs, indicating that these engineering interventions serve as controllable levers, providing a scientific basis for optimizing the carbon sink function of marine ranching through strategic artificial reef deployment.},
}

@article {pmid41791253,
year = {2026},
author = {Fu, CX and Cai, JJ and Liu, JL and Qiu, GY and Chen, XD and Zhang, JB and Qiao, M and Tong, WB and Guo, B},
title = {Mechanistic investigation of the associations between bacterial community composition and cadmium distribution in Zizania latifolia.},
journal = {Ecotoxicology and environmental safety},
volume = {312},
number = {},
pages = {119972},
doi = {10.1016/j.ecoenv.2026.119972},
pmid = {41791253},
issn = {1090-2414},
abstract = {The role of bacteria in external niches regulating cadmium (Cd(II)) in plant tissues remains unclear. We explored Cd(II) profiles and identified bacterial contributors among phyllosphere, rhizoplane, and rhizosphere of four Zizania latifolia varieties through integrated metagenomic and chemical analyses. Zizania latifolia accumulated Cd(II) in leaves (0.06-0.77 mg/kg), roots (0.73-1.57 mg/kg), and rhizosphere (0.43-3.15 mg/kg), respectively. The highest enrichment coefficient (leaf-Cd(II)/soil-Cd(II)) was observed in Genotype 3 (0.6). Among top 10 genus-level bacteria, Enterococcus in phyllosphere, Streptomyces and Dechloromonas in rhizoplane, and Bradyrhizobium, Pseudolabrys, Mycobacterium, and Dechloromonas in rhizosphere were significantly related to Cd(II). Enterococcus adsorbed Cd(II) by extracellular polysaccharides and precipitated Cd(II) sulfide. Rhizoplane and rhizosphere bacteria absorbed Cd(II) by cell-surface functional groups, and fixed Cd(II) through synthesizing polyphosphate and driving Fe (II) oxidation. Additionally, 64.4%-80% of bacteria were shared between rhizoplane and rhizosphere, 5.5%-6.9% between rhizoplane and phyllosphere, and 4.4%-6.1% between rhizosphere and phyllosphere. Metagenomic analysis indicated that Cd(II) disturbed bacterial secretion system and amino acid metabolic pathways. These findings provided comprehensive insights into interrelationships between Cd(II) and bacteria in leaves, roots, and rhizosphere of Zizania latifolia, offering valuable foundations for developing targeted strategies to mitigate Cd(II) accumulation in aquatic vegetables.},
}

@article {pmid41790921,
year = {2026},
author = {Wang, J and Jiang, B},
title = {Utilizing metagenomic next-generation sequencing to diagnose central nervous system infections after craniotomy.},
journal = {Journal of infection in developing countries},
volume = {20},
number = {2},
pages = {263-270},
doi = {10.3855/jidc.21771},
pmid = {41790921},
issn = {1972-2680},
mesh = {Humans ; *Craniotomy/adverse effects ; *High-Throughput Nucleotide Sequencing/methods ; Male ; Female ; Prospective Studies ; Middle Aged ; *Central Nervous System Infections/diagnosis/microbiology ; Adult ; *Metagenomics/methods ; Aged ; Sensitivity and Specificity ; Bacteria/genetics/isolation & purification/classification ; Young Adult ; *Postoperative Complications/diagnosis/microbiology ; Adolescent ; },
abstract = {INTRODUCTION: Postoperative central nervous system (CNS) infections in craniotomy patients diagnosed through clinical signs and cerebrospinal fluid (CSF) bacterial culture, pose a challenge due to the morbidity and mortality of bacterial meningitis. The objective of this study was to evaluate the clinical value of metagenomic next-generation sequencing (mNGS) in diagnosing CNS infections post craniotomy.

METHODOLOGY: A prospective study compared mNGS with traditional diagnostics from January 2021 to October 2023. Patients with suspected post-craniotomy intracranial infections were enrolled, following guidelines and regulations.

RESULTS: mNGS and traditional culture diagnosed 111 patients with suspected intracranial infections. mNGS showed higher sensitivity (62.5% vs. 25%). Traditional culture excelled in specificity and positive predictive value. Of the 18 mNGS-positive samples, 12 were culture-negative. mNGS detected pathogens such as Candida albicans (2 cases), Enterobacter cloacae (1 case), Enterococcus faecalis (1 case), Klebsiella pneumoniae (2 cases), Pseudomonas aeruginosa (1 case), Staphylococcus aureus (2 cases), Staphylococcus epidermidis (2 cases), and Streptococcus haemolyticus (1 case). Some pathogens were likely missed due to prior antibiotic use and fastidious growth requirements. Physicians adjusted treatments based on mNGS pathogen detection for culture-negative patients. Empirical therapy continued for patients with negative results until more diagnostic information was available.

CONCLUSIONS: mNGS detects post-neurosurgery CNS infections, especially hard-to-cultivate microorganisms. While mNGS has advantages, traditional culture's higher positive predictive value confirms infections and remains indispensable. Combining mNGS with traditional methods provides a comprehensive diagnostic strategy, aiding physicians in accurately identifying infections, reducing misdiagnosis, and offering personalized treatment plans to improve outcomes and quality of life.},
}

Humans
*Craniotomy/adverse effects
*High-Throughput Nucleotide Sequencing/methods
Male
Female
Prospective Studies
Middle Aged
*Central Nervous System Infections/diagnosis/microbiology
Adult
*Metagenomics/methods
Aged
Sensitivity and Specificity
Bacteria/genetics/isolation & purification/classification
Young Adult
*Postoperative Complications/diagnosis/microbiology
Adolescent

@article {pmid41790828,
year = {2026},
author = {Carrillo, A and Hageman, E and Chittick, L and Mackey, AI and Ndlovu, KS and Tian, F and Gilbert, NE and Muratore, D and Vik, D and LeCleir, GR and Sun, C and Jang, HB and Pavan, RR and Weitz, JS and Wilhelm, SW and Sullivan, MB},
title = {Sub-daily virus sampling at the Bermuda Atlantic Time Series reveals diel and depth-structured population dynamics without community-level shifts.},
journal = {PLoS biology},
volume = {24},
number = {3},
pages = {e3003474},
doi = {10.1371/journal.pbio.3003474},
pmid = {41790828},
issn = {1545-7885},
abstract = {Ocean microbes contribute to biogeochemical cycles and ecosystem function, but they do so under top-down pressure imposed by viruses. While viruses are increasingly understood spatially and beginning to be incorporated into predictive modeling, high-frequency ocean virus dynamics remain understudied due to methodological challenges. Here we sampled stratified Bermuda Atlantic Time Series (BATS) waters for 112 hours at sub-daily 4- (surface) or 12- (deep chlorophyll maximum) hour intervals, purified viral particles from these samples, sequenced their metagenomes, and used the resulting data to characterize high-frequency virus community dynamics. Aggregated community diversity metrics changed with depth, but were not statistically significant temporally at a fixed location. However, finer-scale population-level analyses revealed both depth and temporal change, including physicochemical depth-driven differences and, in surface waters, thousands of viral populations that exhibited statistically significant diel rhythms. Statistical analyses revealed three main archetypes of temporal dynamics that themselves differed in abundance patterns, host predictions, viral taxonomy, and gene functions. Among these, highlights include viruses resembling an archetype with a night peaking pattern in activity that include an over-representation of viruses that putatively infect Prochlorococcus, a phototrophic cyanobacteria. Together, these efforts provide baseline community- and population-scale short-time-frame observations relevant to future climate state modeling.},
}

@article {pmid41790792,
year = {2026},
author = {Hoque, MN and Rana, ML and Gilman, MAA and Pramanik, PK and Islam, MS and Punom, SA and Rahman, R and Hassan, J and Islam, T and Ramasamy, S and Schreinemachers, P and Oliva, R and Rahman, MT},
title = {Shotgun metagenomic profiling reveals Bacillus-dominated bacterial communities in urban rooftop and surface garden soils of Bangladesh.},
journal = {PloS one},
volume = {21},
number = {3},
pages = {e0344114},
doi = {10.1371/journal.pone.0344114},
pmid = {41790792},
issn = {1932-6203},
mesh = {*Soil Microbiology ; Bangladesh ; *Bacillus/genetics/classification/isolation & purification ; *Metagenomics/methods ; *Microbiota/genetics ; Gardens ; Soil/chemistry ; Biodiversity ; },
abstract = {Urban rooftop and surface garden systems play a critical role in food security in densely populated regions, yet their soil microbiomes remain understudied. To date, no baseline data exists on rooftop and surface garden soil microbiomes in Bangladesh. Understanding these communities is vital for enhancing soil health, nutrient cycling, and resilience for sustainable, climate-adapted urban agriculture. This study therefore investigated the bacterial diversity and community structure of rooftop and surface garden soils across Dhaka and Gazipur, Bangladesh. The goal was to uncover location- and garden-type-specific patterns that influence soil functionality. Using shotgun metagenomics of 27 garden soil samples (seven Dhaka rooftop [DRG], six Dhaka surface [DSG], eight Gazipur rooftop [GRG], and six Gazipur surface [GSG]), we identified 755 bacterial species dominated by Firmicutes (65-83%) and Proteobacteria (3-25%). While alpha diversity was consistent across sites (p > 0.05), beta diversity revealed distinct community structuring (p = 0.017), with surface gardens harboring greater bacterial richness (DSG:717, GSG:750 species) and elevated Bacteroidota (DSG:11.5%, GSG:2.7%) compared to rooftop soils. Strikingly, Bacillus species dominated all soils (>53% relative abundance) but exhibited location-specific distributions. DRG soils were notably enriched with B. paralicheniformis (28.3%) and B. licheniformis (25.2%). In contrast, DSG was characterized by B. cereus sensu lato (16.0%), Brevibacillus agri (12.1%), and Flavobacterium thermophilum (11.4%). GRG soils were dominated by B. cereus sensu lato (42.4%) and B. agri (11.5%). GSG soils showed diverse Bacillus species, including B. stratosphericus (14.6%), B. licheniformis (12.7%), B. safensis (9.7%), and B. altitudinis (8.8%). Of 41 detected Bacillus species, more than 58.0% were shared across gardens, yet their abundances varied with microhabitat. Moreover, KEGG profiling revealed marked functional divergence among urban garden soils. Carbohydrate metabolism dominated all sites (9.30-11.07%). DRG was uniquely enriched in photosynthesis (8.40%) and methane metabolism (8.62%), whereas DSG, GRG, and GSG showed higher oxidative phosphorylation (3.75-4.08%), two-component systems (3.24-3.73%), and biosynthetic pathways. This study unveils the ecological dominance of Bacillus species in urban agricultural soils, with location-driven compositional and functional shift. These findings are pivotal for optimizing sustainable urban agriculture in rapidly developing regions, where soil bacteriomes can be harnessed to improve crop resilience and food security.},
}

*Soil Microbiology
Bangladesh
*Bacillus/genetics/classification/isolation & purification
*Metagenomics/methods
*Microbiota/genetics
Gardens
Soil/chemistry
Biodiversity

@article {pmid41790499,
year = {2026},
author = {Liu, G and Bai, P and Ren, M and Li, Q and Li, T},
title = {Vitamin B12-associated interactions between Mesorhizobium sp. TaiHu and Synechococcus sp. PCC 7002 revealed by multi-omics analysis.},
journal = {Microbial genomics},
volume = {12},
number = {3},
pages = {},
doi = {10.1099/mgen.0.001665},
pmid = {41790499},
issn = {2057-5858},
abstract = {The marine cyanobacterium Synechococcus sp. PCC 7002 (Syn7002) is a model organism that lacks the gene cluster required for vitamin B12 biosynthesis, necessitating cooperative interactions with other microbes. In this study, we established a synthetic microbial consortium by co-culturing Syn7002 with a bloom-forming Microcystis community, followed by purification, and subsequently investigated the interactions between Syn7002 and the associated microbial community. Electron microscopy revealed numerous rod-shaped bacteria clustered around Syn7002 cells, indicating close spatial associations between species. Metagenomic analysis showed that the early-stage community consisted mainly of Syn7002, Mesorhizobium sp. TaiHu (MesTH) and Pseudomonas sp. TaiHu (PseTH), although the abundance of PseTH declined after community stabilization. Investigation of vitamin B12 regulation between MesTH and Syn7002 through metatranscriptomic analysis revealed upregulation of nitrogen metabolism-related genes in the microbial community. Transcriptomic data further indicated that vitamin B12 biosynthesis and transport genes were significantly upregulated in MesTH. Combined with vitamin B12-positive control experiments, these results confirm potential vitamin B12 complementarity between the two strains. The results further suggest that MesTH promotes the growth of Syn7002 in the community by providing the small amount of vitamin B12 needed for its growth. These findings provide new insights into vitamin-mediated microbial interactions and reveal additional transcriptional features of the synthetic community.},
}

@article {pmid41790111,
year = {2026},
author = {Kumar, K},
title = {Cultivation of Yet-to-be Cultured Microorganisms: Advances, Strategies, and Prospects.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxag066},
pmid = {41790111},
issn = {1365-2672},
abstract = {More than 99% of microorganisms in the natural environment are not readily culturable using standard laboratory techniques. These microbes can be reservoirs of novel metabolites and biomolecules having pharmaceutical applications against bacterial infections, chronic diseases, and antibiotic resistance. Given this, our work is a comprehensive synthesis of recent advances in understanding, detection, and cultivation of "yet-to-be cultured" (YTBC) microbes. We highlight physiological traits that restrict their domestication under standard laboratory conditions. Some of the factors that may influence are their metabolic dormancy, specialized nutrient demands, siderophore-mediated iron acquisition, microbial signaling, and interspecies interactions. The review discusses various strategies, such as simulated natural environments, co-culture, and advanced bioreactor systems, which can be implemented to cultivate them. We reviewed recent metagenomic approaches and single-cell isolation methods, including label-based techniques (e.g., fluorescence in situ hybridization), label-free approaches such as Raman-activated cell sorting, and high-throughput tools like flow cytometry. We also examined culture-dependent approaches, including co-cultivation with helper strains with a special emphasis on bioreactor-based systems, diffusion chamber, hollow-fiber membrane chamber, high-throughput isolation chip (ichip), and encapsulation. Overall, this review provides a roadmap to unlock the biotechnological potential of YTBC microbes by outlining new technologies, methodological trends, and important knowledge gaps.},
}

@article {pmid41790075,
year = {2026},
author = {Kong, C and Jin, Y and Guo, F and Yang, Y and Liu, G and Chen, Z and Li, J and Wang, Q and Ma, Y},
title = {Revealing the Antagonistic Interactions of Faecalibacterium prausnitzii and Bacteroides fragilis in Colorectal Cancer.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2025.12.030},
pmid = {41790075},
issn = {1528-0012},
abstract = {BACKGROUND & AIMS: Maladaptation of host-microbe metabolic interactions plays a crucial role in development of colorectal cancer (CRC). However, remains a lack of comprehensive studies using multi-omics analysis to illustrate host-microbe metabolic interactions in CRC.

METHODS: We collected and analyzed 440 stool samples from a discovery cohort in Shanghai China (255 patients with CRC and 185 healthy controls). Each sample was subjected to metagenomic sequencing and nontargeted liquid chromatography mass spectrometry. Fresh-frozen specimens of tumors and matched adjacent normal mucosae were extracted from 62 patients with CRC, and whole exome sequencing and RNA sequencing were performed to explore host genomic patterns and host-microbe metabolic interactions. Finally, relationships detected in the discovery cohort were validated against independent cohorts, organoid models, and mice experiments.

RESULTS: The relationship between disrupted microbial homeostasis and CRC progression is characterized by Bacteroides fragilis enrichment and reduction of Faecalibacterium prausnitzii. F prausnitzii metabolizes tryptophan into picolinic acid (PIA) via the enzyme 2-amino-3-carboxymuconate semialdehyde decarboxylase, with PIA exerting an antagonistic effect on enterotoxigenic B fragilis-mediated tumor progression. Mechanistically, enterotoxigenic B fragilis up-regulates the expression of genes associated with poor differentiation and recurrence, namely TCERG1 and CKAP2, and PIA induces tumor cell apoptosis by down-regulating these 2 genes. Independent validation cohorts and murine models corroborated that a tryptophan-rich diet effectively elevates circulating PIA levels, suggesting its potential as an anticancer dietary intervention.

CONCLUSIONS: Our research characterized a representative microbe-metabolite-host regulatory pathway occurring in CRC, namely the F prausnitzii-PIA-TCERG1/CKAP2 axis antagonizing enterotoxigenic B fragilis-induced CRC progression. As a treatment option, we highlight the therapeutic potential inherent in a tryptophan-rich diet and in manipulating microbial composition targeting the F prausnitzii-PIA axis to prevent CRC.},
}

@article {pmid41789948,
year = {2026},
author = {Yadav, S and Yang, T and MacLean, MA and El-Naggar, MY},
title = {Metagenome-assembled genome sequence of Candidatus Electrothrix sp. NPCB-01 from Southern California marine sediments.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0002526},
doi = {10.1128/mra.00025-26},
pmid = {41789948},
issn = {2576-098X},
abstract = {Cable bacteria conduct long-distance electron transport in sediments but are not yet isolated in pure culture. We report the metagenome-assembled genome of Candidatus Electrothrix sp. NPCB-01 from Newport Bay, California. This 3.46-Mb genome encodes sulfur oxidation, nitrogen and carbon metabolism, and nickel homeostasis genes, expanding resources for these electroactive microbes.},
}

@article {pmid41789923,
year = {2026},
author = {Yao, J and Yang, C and Wang, H and Zhang, C and Meng, J},
title = {Metagenomic analysis of gut bacteria in different developmental instars of Spodoptera litura.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0208125},
doi = {10.1128/spectrum.02081-25},
pmid = {41789923},
issn = {2165-0497},
abstract = {Spodoptera litura is a globally distributed agricultural pest across Asia and Australia (EPPO database, https://gd.eppo.int/taxon/PRODLI/distribution), whose gut microbiota significantly influences host feeding, digestion, immunity, and development. We used whole metagenomic sequencing to analyze the diversity and functional roles of gut bacteria at different developmental stages (eggs, first to sixth instar larvae, pupae, and adults). Findings revealed that Pseudomonadota predominated at the phylum level, with notable differences across instars: Bacillota was dominant in young larvae, whereas Verrucomicrobiota was added in older larvae, eggs, pupae, and adults. At the genus level, Pseudomonas dominated, Enterococcus was prevalent in larvae, and Piscirickettsia was prevalent in eggs, pupae, and adults. Metagenomic analysis identified numerous carbohydrate-active enzymes (CAZy database) aiding in plant cell wall polysaccharide digestion. Kyoto Encyclopedia of Genes and Genomes pathway analysis indicated differential gene expression in metabolism and xenobiotic degradation across instars, with metabolic gene annotation levels declining as development progressed. Detoxification-related enzyme genes were predominantly expressed in early instar larvae and adults, uncovering microbial origins of these enzymes.IMPORTANCEOur study provides evidence that the gut microbiota significantly modulates the physiology of Spodoptera litura, with profound effects on its dietary habits, metabolic processes, and host fitness. Using whole metagenomic sequencing, we analyzed gut bacteria across different life stages. At the phylum level, Pseudomonadota and Bacillota were dominant, while at the genus level, Pseudomonas was the most abundant taxon. Metagenomic analysis identified enzymes aiding in plant cell wall digestion. Kyoto Encyclopedia of Genes and Genomes analysis showed varying gene expression in metabolism and detoxification, with higher expression in early instar larvae and adults. This research enhances understanding of S. litura gut microbiota-host interactions and supports novel pest control strategies targeting gut microbiota.},
}

@article {pmid41789917,
year = {2026},
author = {Chen, D and Zhang, Z and Wang, S and Li, W and He, Y and Zhang, W and Sun, W and Chen, M and Zou, S and Qian, X},
title = {Differential assembly and functional roles of bacterial communities in coniferous and mixed conifer-broadleaf forest soils.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0062725},
doi = {10.1128/msphere.00627-25},
pmid = {41789917},
issn = {2379-5042},
abstract = {Forest soils harbor a diverse array of bacteria that play a crucial role in nutrient cycling. However, the differential effects of coniferous versus mixed conifer-broadleaf forests on the distribution of both abundant and rare bacterial taxa remain poorly understood. In this study, we integrated 16S rRNA gene amplicon sequencing with metagenomic shotgun sequencing to conduct a comparative analysis of soil bacterial communities in a conifer plantation and an adjacent mixed conifer-broadleaf forest, specifically examining their community structure, assembly mechanisms, co-occurrence networks, and functional potential. Both abundant and rare taxa showed significant differences in community composition between the two forest types. Soil pH and organic matter content significantly influenced the total and abundant bacterial communities, while available phosphorus and potassium were key determinants of rare community composition. Co-occurrence network analysis revealed that abundant communities formed highly clustered, simplified networks, contrasting with more fragmented and keystone-rich networks in rare communities. Null model analyses indicated that community assembly was largely driven by stochastic processes, with ecological drift accounting for about 80% of the variation in total and rare communities, and dispersal limitation explaining nearly 72% of the variation in abundant communities. Functional predictions indicated that bacterial communities in mixed forests were enriched in pathways linked to glycosylation, carbohydrate degradation, and nitrogen fixation, while coniferous forests favored pathways related to autophagy, signaling, and stress responses. This study highlights the complementary roles of abundant and rare bacterial taxa in forest soil ecosystems and underscores the importance of preserving mixed forests to sustain microbial functional diversity.IMPORTANCEForest soils host a complex web of common and rare bacteria that quietly regulate nutrient cycles. By comparing pure conifer stands with mixed conifer-broadleaf forests, we found that abundant species underpin essential functions while rarer microbes fill specialized niches. Acidity and nutrients strongly influence which bacteria thrive; mixed stands favored microbes that break down carbohydrates and fix nitrogen, whereas conifer soils supported organisms adapted to stress and nutrient-poor conditions. These findings emphasize the importance of preserving diverse forest ecosystems for soil health, carbon storage, and effective forest management strategies in climate change adaptation.},
}