@article {pmid41803939,
year = {2026},
author = {Fauszt, P and Mikolas, M and David, P and Szoke, Z and Gashi, N and Szilagyi-Tolnai, E and Szilágyi, E and Szarvas, MM and Fazekas, ME and Kun-Nemes, A and Stagel, A and Gal, F and Czegledi, L and Biro, S and Stundl, L and Remenyik, J and Paholcsek, M},
title = {Longitudinal source-sink dynamics of fecal litter and farm indoor environmental resistomes in broiler chicken and Cherry Valley ducks.},
journal = {Animal microbiome},
volume = {8},
number = {1},
pages = {},
pmid = {41803939},
issn = {2524-4671},
abstract = {BACKGROUND: Antimicrobial resistance is a major One Health threat, and intensive poultry systems function as amplifiers. Although broilers and ducks are reared under similarly controlled conditions, their microecologies diverge. Integrated, longitudinal source-sink analyses quantifying overlap and directional flux between host-associated and environmental resistomes remain scarce. A two-year (2022–2024), longitudinal, commercial-scale comparison was undertaken across 15 stocking cycles under harmonized husbandry in Ross 308 broiler and Cherry Valley duck. Parallel shotgun metagenomics profiled fecal litter and farm indoor environments across standardized production, with daily monitoring in one complete cycle per system; in total, 96 pooled samples were sequenced to quantify cross-compartment overlaps.

RESULTS: Antibiotic resistance gene (ARG) reservoir dominance proved to be system-specific, duck systems were environment-centric, whereas broiler systems were fecal litter-centric. Although overall ARG diversity was similar between systems (broiler 2,542; duck 2,494 types), ducks exhibited greater compartmental divergence, with ~ 2.6-fold more environment-unique ARGs than paired fecal litter and 1.15-fold higher environmental richness than broilers. Compartment coupling also differed: broilers showed tighter host-environment overlap, while ducks were more partitioned. A shared environmental ARG pool (57.5%) indicated substantial cross-system exchange potential. Temporally, shared ARGs accumulated across the grow-out and peaked pre-depopulation. The distribution of significant ARG carrier species revealed asymmetric host-environment coupling: overlap across compartments was 66.67% in broilers versus 45.45% in ducks, notably. The impact of antimicrobial use was nuanced: short, targeted courses were associated with lower aaAMR burden overall Collectively, the recurrent detection of clinically consequential carriers (P. aeruginosa, E. coli, A. baumannii, S. aureus, K. pneumoniae, S. maltophilia, toxigenic Clostridium spp.) underscored One Health risks of zoonotic spillover and food-chain contamination.

CONCLUSION: Reservoir behavior in intensive poultry systems should be treated as system-specific, and matrix-targeted, with biofilm and humidity management prioritized in duck operations, and litter/manure control emphasized in broilers. The finisher-depopulation window emerges as a critical intervention point, warranting intensified mitigation clean-out. Finally, mitigation should extend beyond individual farms to transport crates, vehicles, shared equipment, and supply chains.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42523-026-00544-x.},
}

@article {pmid41827064,
year = {2026},
author = {Yu, S and Yue, X and Yang, Q and Xu, P and Yuan, H and Tang, W and Luan, Y and Wang, Q},
title = {Omics integration reveals how the gut microbiota of Warmblood horses responds to equestrian show jumping-a short-duration, high-intensity technical exercise stress.},
journal = {Animal microbiome},
volume = {8},
number = {1},
pages = {},
pmid = {41827064},
issn = {2524-4671},
abstract = {BACKGROUND: Intestinal microbial homeostasis and metabolic balance play a crucial role in maintaining normal physiological function in horses. Exogenous stress involving abrupt turns and jumps during show jumping significantly impacts intestinal microbial homeostasis and metabolic balance in these animals.

RESULTS: By comparing rectal (faecal) samples from 10 Warmblood horses collected before and immediately after a show jumping competition on the same day, we observed substantial alterations in intestinal microbial homeostasis and metabolic balance post-exercise. Microbial evenness significantly increased following the competition, accompanied by enrichment of specific taxa such as Bacteroides, Ruminococcus, Prevotella, and Fibrobacter. Metabolite analysis revealed a marked decrease in antioxidant-related compounds, including orsellinic acid, 2,3-dimethyl-2-cyclohexen-1-one, and (1 R,6 R)-1,4,5,5a,6,9-hexahydrophenazine-1,6-dicarboxylate. Conversely, glucosan and thiamine pyrophosphate levels increased. Post-competition, membrane lipid metabolism pathways were significantly downregulated, while antioxidant responses and energy metabolism pathways were upregulated. Spearman correlation analysis indicated positive associations between Fibrobacter, Ruminococcus, and Prevotella with energy metabolism-related metabolites, whereas Lysinibacillus correlated positively with metabolites involved in antioxidant activity and intestinal mucosal protection.

CONCLUSION: Collectively, our findings demonstrate that show jumping induces shifts in intestinal microbial homeostasis and metabolic balance in Warmblood horses. These adaptations appear conducive to preserving epithelial integrity and enhancing energy provision to meet the demands of high-intensity exercise. This study provides novel insights into the impact of acute high-intensity exercise on equine gut microbial dynamics and metabolism, offering a theoretical basis for probiotic-based interventions to support intestinal health in sport horses.},
}

@article {pmid41992382,
year = {2026},
author = {Cuteri, V and Preziuso, S and Li, Y and Laus, F},
title = {Fecal virome at the human-animal interface: a one health perspective on an uncharted frontier.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-026-00569-2},
pmid = {41992382},
issn = {2524-4671},
}

@article {pmid41992389,
year = {2026},
author = {Gu, S and Jiang, C and Zhang, P and Luo, S and Gong, Y and Feng, W and Xiong, J and Zhang, J and Chen, K and Ning, K and Miao, W},
title = {Unraveling the colonization process of microeukaryotic communities on artificial micro-ecological islands.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00897-5},
pmid = {41992389},
issn = {2524-6372},
support = {2022FY100400//the Science & Technology Fundamental Resources Investigation Program/ ; 2022xjkk0204//the Third Xinjiang Scientific Expedition Program/ ; U22A20454//the National Natural Science Foundation of China/ ; SNJNP2022008//the Background Resources Survey in Shennongjia National Park/ ; SNJGKL2022008//the Open Project Fund of Hubei Provincial Key Laboratory for Conservation Biology of Shennongjia Snub-nosed Monkeys/ ; },
abstract = {BACKGROUND: Micro-ecological islands provide unique habitats for microbes and play a crucial role in the functioning of aquatic ecosystems. Microbes settle on these micro-ecological islands, forming distinct microbial communities. Previous studies have provided some understanding of the colonization processes and regulatory mechanisms of protozoa in microbial communities. However, these islands are also subject to colonization by a variety of microbes beyond protozoa, and comprehensive cross-kingdom studies and their potential mechanisms remain largely unexplored.

RESULTS: Using polyurethane foam units (PFU) to simulate micro-ecological islands, we studied the colonization dynamics of microbes in two distinct aquatic ecosystems, the Yangtze River and East Lake. Over 10-day colonization survey was conducted, we applied eDNA-PFU technology combined with metagenomic sequencing to comprehensively identify species present in the microbial communities, including bacteria, fungi, flagellates, protozoa, and metazoa. We found that microeukaryotes, rather than prokaryotes, were the primary colonizers in these two aquatic ecosystems. Our study reveals a colonization process of microeukaryotes in PFUs, profoundly influenced by their motility modes. Additionally, we propose a hypothetical food web framework within micro-ecological islands that maintains community stability, representing the most fundamental biological interactions.

CONCLUSIONS: Overall, this study enriches our understanding of micro-ecological islands and provides deeper insights into the colonization processes and regulatory mechanisms of microbial communities. It highlights the practical significance of micro-ecological islands in biological resource management, environmental protection, and biodiversity conservation.},
}

@article {pmid41993122,
year = {2026},
author = {Saez-Torillo, SN and Danielsson, R and Nguyen, TQ and Lima, J and Cleveland, MA and Roehe, R and Martínez-Álvaro, M},
title = {Predicting beef diet nutritional composition and intake from rumen metagenomic profiles.},
journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)},
volume = {25},
number = {},
pages = {297-309},
pmid = {41993122},
issn = {2405-6383},
abstract = {Knowledge of diet composition and intake levels in beef cattle is valuable for post hoc feed traceability and for more accurate modelling of the diet impact on methane emissions and performance traits. However, a direct measure of this information can be costly and labour-intensive and is not always feasible. In this study, rumen metagenomic data combined with machine learning algorithms were used to predict diet type, nutritional composition, and intake levels. An external validation to assess the generalizability of the models was also performed. Rumen samples were collected from 142 animals belonging to two breeds, Luing (n = 70) and Charolais crossbred (n = 72), with 425.6 ± 43.5 d old and 461.9 ± 70.2 kg body weight. The animals participated in a 56-d feeding trial and were assigned to diets differing in forage-to-concentrate ratio, with 72 animals receiving a concentrate-based diet and 70 receiving a forage-based diet. Liquid ruminal contents were collected immediately postmortem and subsequently subjected to metagenomic sequencing. Based on these sequences, the relative abundance of microbial genes (MGs), microbial genera (MTs), and phyla were determined. The log-ratio between the abundances of Verrucomicrobia and Chlorobi discriminated diet type with an average classification accuracy of 0.86 ± 0.05, while using the log-ratio transformed abundances of 4769 MTs and MGs as predictors reached 0.90 ± 0.05. All this microbiome information was used in a random forest model to predict continuous values for nutritional diet components starch, crude protein, neutral and acid detergent fibre, and metabolizable and gross energy with external validation prediction accuracy values between 0.77 and 0.83. Microbiome features important for prediction of diet components such as fibre and starch included Mitsuokella, Selenomonas, and MGs involved in flagellar assembly and aminoacyl-tRNA biosynthesis. Microbiome data were more informative for predicting the feed composition than the amount of feed consumed, which reached a prediction accuracy of 0.27 ± 0.12 for dry matter intake (DMI). However, microbiome data can still be used as a screening tool to classify DMI into low, medium, or high with a classification accuracy of 0.74. Incorporating dietary information into linear phenotypic and genetic models to predict methane production (MP) and DMI reduced root mean square error (RMSE) by 26.9% and 9.6%, respectively, in the phenotypic model. In the genetic model, only MP showed a reduction in RMSE, with a 31% improvement. These findings highlight rumen microbiome data as a valuable tool for the post hoc prediction of feed composition in beef cattle.},
}

@article {pmid41993390,
year = {2026},
author = {Hutchinson, NT and Ye, N and Jennings, M and Fang, C and Qi, N and Li, J},
title = {Engineered Lactate Catabolizing Probiotics Reveal Timescale Dependent Microbiome-Host Metabolic Coupling.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.07.716956},
pmid = {41993390},
issn = {2692-8205},
abstract = {The exchange of lactate, a metabolic substrate and regulator, between the gut lumen and systemic circulation for use in host and microbial processes is well documented, but tools capable of uncovering whether this process influences host metabolic status across acute and chronic contexts are lacking. In our prior work, we engineered probiotic Bacillus subtilis PY79 to produce lactate oxidase (LOX) intracellularly, allowing it to rapidly convert intestinal lactate to pyruvate. Following oral administration, LOX reduced systemic lactate concentrations at rest and under challenge conditions, providing a platform for investigating lactate's influence on host metabolism and microbiota. In the present work, we demonstrate that acute LOX administration effectively rewired microbiota function and host energy balance, as revealed by 16S sequencing and indirect calorimetry. In silico microbial community modeling via MICOM and metagenomic inference via PICRUSt2 suggested that acute shunting of lactate to pyruvate induced microbiota remodeling towards anabolic processes, reflected by increased flux of pyruvate, acetate, and formate, alongside moderate to large increases (Cohen's d = 0.60-1.00) in pathways for fructan degradation, B-vitamin biosynthesis, and lipid synthesis. These anabolic shifts temporally aligned with transient increases in host energy expenditure (β = 1.08, p<0.05) via glucose oxidation (β = 0.01, p<0.05), hinting at functional coupling between microbial biosynthesis and host energy balance via lactate exchange. Of note, acute LOX administration also improved thermoregulation and survival following LPS-induced sepsis, demonstrating functional relevance of these metabolic effects during acute inflammatory challenge. To assess chronic effects, we administered LOX for 6 weeks during diet-induced obesity. LOX treatment persistently reduced blood lactate. However, this chronic lactate reduction did not curtail the progression of diet-induced obesity or induce sustained modulation of host energy expenditure. This disconnect between acute and chronic findings suggests that gut-centric lactate conversion affects energy balance through microbiome and/or host-dependent mechanisms, but cannot override homeostatic forces in the long term to produce clinical benefit during chronic disease. Our results validate LOX probiotics as a tool for acute metabolic augmentation, and highlight a clear homeostatic limit to gut-centric therapies. This platform may enable targeted design of probiotic interventions matched to therapeutic timescale and inform synbiotic formulations that overcome homeostatic compensation.},
}

@article {pmid41993414,
year = {2026},
author = {Liu, S and Mehta, P},
title = {Ecology of metagenomes: incorporating genotype-to-phenotype maps into ecological models.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.07.717079},
pmid = {41993414},
issn = {2692-8205},
abstract = {UNLABELLED: A major theoretical problem in community ecology is to understand how genes, organisms, and environments combine to shape the structure and diversity of ecological communities. However, most classic ecological models work entirely with phenotypic parameters, neglecting the central role played by genes. This limitation is particularly acute in microbial ecology, where the widespread use of sequencing technologies allows researchers to directly measure the genomic and metagenomic properties of communities. Here, we bridge this gap by incorporating genotype-to-phenotype maps into classical ecological models, including the generalized Lotka-Volterra model (GLV) and consumer resource models (CRMs). We focus on the case where genotype-to-phenotype maps are linear, which provides a tractable yet powerful framework for analyzing complex traits. Even in this simple setting, the resulting ecological dynamics give rise to novel gene-level ecological dynamics that can be recast entirely in terms of genes, allowing us to develop an ecology of metagenomes. We find that ecological interactions between genes lead to pervasive "metagenomic hitchhiking" - low-fitness genes can survive in the ecosystem because they are integrated into genomes of high-fitness species. We also show that phylogenetic relationships between species mold the ability of closely related strains to stably coexist in complex communities. This highlights how lineage structure and competitive interactions jointly shape community composition. Our framework provides a principled foundation for interpreting metagenomic data through the lens of ecological theory.

AUTHOR SUMMARY: Recent advances in sequencing technologies have transformed our ability to characterize microbial communities at the genomic level. However, most classic ecological models work entirely with phenotypic parameters, neglecting the central role played by genes. Here, we address this gap by extending classical ecological models to explicitly include genotype-to-phenotype maps. We focus on complex traits where the genotype-to-phenotype map is approximately linear. We show that the resulting ecological dynamics that can be recast entirely in terms of genes, allowing us to develop an ecology of metagenomes. Our framework provides a novel perspective for interpreting metagenomic data through the lens of ecological theory.},
}

@article {pmid41993507,
year = {2026},
author = {Coleman, I and Ma, J and Qian, G and Jiang, Y and Brown Kav, A and Korem, T},
title = {End-to-end evaluation of pipelines for metagenome-assembled genomes reveals hidden performance gaps.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.06.712906},
pmid = {41993507},
issn = {2692-8205},
abstract = {The generation of Metagenome Assembled Genomes (MAGs) has become a standard and basic step in the analysis of metagenomic data. This multi-step process, which includes assembly, binning, refinement, and quality control, has many alternative approaches, algorithms, and parameters. Determining the ideal approach for a given ecosystem and study, or highlighting algorithmic gaps in need of additional research and development, requires rigorous benchmarking. We present MAG-E (MAG pipeline E valuator), a generalizable and expandable framework for end-to-end evaluation of entire MAG pipelines: from assembly, through binning, to quality control and filtering. MAG-E relies on simulations that are built to match an ecosystem of interest and provide a ground truth for accurate evaluation. To demonstrate the capabilities of MAG-E, we benchmark two assemblers, six binning algorithms, three binning modes, and three quality control and refinement methods in the context of the human gut microbiome. Our findings offer multiple insights into optimal MAG generation in this context. We find that metaSPAdes consistently outperforms MEGAHIT in terms of recall (completeness), and that COMEBin overall outperforms alternative binning algorithms, but has lower precision than SemiBin2. While multi-sample binning results in higher precision, as previously shown, single-sample binning has higher recall and leads to better overall performance with modern binners. Binning refinement, which combines bins from multiple different algorithms, leads to reduced performance. We further show that CheckM2 systematically overestimates completeness and underestimates contamination, and that this is partially ameliorated when using GUNC. Finally, we analyze performance at the contig level, and demonstrate that binning algorithms systematically underperform for prophages and fail to bin contigs that are shared between genomes. Overall, MAG-E offers deep insights into successes and gaps in this important analytic process.},
}

@article {pmid41993555,
year = {2026},
author = {Herzog, HM and Fang, C and Lam, L and Jin, K and Zamarioli, A and Dinh, E and Gupta, CL and Sharma, A and Moody, T and Pierce, JL and Hohl, MS and Takimoto, SW and Lyalina, S and Wentworth, KL and Yu, K and Lu, VF and Mamikunian, I and Hunt, NK and Lynch, S and Pollard, KS and Hernandez, CJ and Perrien, DS and Hsiao, EC},
title = {Gut microbiome-dependent IL-1 signaling is a mediator of ACVR1 [R206H] -driven heterotopic ossification.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.05.716562},
pmid = {41993555},
issn = {2692-8205},
abstract = {UNLABELLED: Inflammatory diseases cause significant morbidity and mortality, but their pathobiology is often difficult to dissect due to complex genetic-environmental interactions. Genetic forms of heterotopic ossification, such as fibrodysplasia ossificans progressiva (FOP), reduce genetic variability, allowing careful dissection of non-genetic drivers of inflammation. While >95% of FOP patients harbor the ACVR1 [R206H] mutation, patients exhibit significant variability in disease progression, suggesting a role of environmental drivers. Here, we identify the gut microbiome as a regulator of inflammation-driven HO in FOP. Metagenomic profiling of cohabitating FOP/unaffected sibling pairs revealed a pathogenic gut microbiome profile in FOP patients (Bray-Curtis, p < 0.05). In Pdgfrα-Cre/Acvr1 [R206H] (FOP) mice, gut microbiome ablation by antibiotics reduced spontaneous HO formation (47.4% reduction, p < 0.05) and reduced plasma IL-1 pathway activity. IL-1β blockade in FOP mice suppressed trauma-induced HO formation. These findings identify a gut microbiome-IL-1-HO axis with modifiable targets for developing treatments for HO and related inflammatory conditions.

ONE SENTENCE SUMMARY: Antibiotic disruption of the gut microbiome reduces HO in FOP mice via an IL-1 mediated pathway.},
}

@article {pmid41993727,
year = {2026},
author = {Sun, Y and Qiu, JW and Chen, C and Martín-Durán, JM and Oatley, G and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , },
title = {The chromosomal genome sequence of the tubeworm, Lamellibrachia columna Southward, 1991 (Sabellida: Siboglinidae).},
journal = {Wellcome open research},
volume = {11},
number = {},
pages = {127},
pmid = {41993727},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual Lamellibrachia columna (tubeworm; Annelida; Polychaeta; Sabellida; Siboglinidae). The genome sequence has a total length of 879.73 megabases. Most of the assembly (99.96%) is scaffolded into 15 chromosomal pseudomolecules. The mitochondrial genome has also been assembled, with a length of 16.78 kilobases. Gene annotation of this assembly by Ensembl identified 21 983 protein-coding genes.},
}

@article {pmid41993799,
year = {2026},
author = {Yue, XL and Wu, YH and Zheng, DQ and Sun, C and Xu, L and Cui, L and Xu, XW},
title = {[13]C-labeled single-cell Raman sorting reveals sulfur-driven dark carbon fixation in coastal sediments.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag073},
pmid = {41993799},
issn = {2730-6151},
abstract = {Chemoautotrophs drive carbon fixation in coastal sediments, but most of them remain uncultured with poorly characterized in situ activities. In this study, a cultivation-independent single-cell approach combining Raman spectroscopy with [13]C-stable isotope probing was developed to enable direct identification of active chemoautotrophs in coastal sediments using function-specific spectral biomarkers, targeted metagenomic sequencing and pure culture verification. [13]C-induced shifts in cytochrome c (749, 1129, 1312, 1589 cm[-1]) and phenylalanine (1002 cm[-1]) Raman bands were systematically evaluated and applied as functional biomarkers through investigations of both representative chemoautotrophic strains and environmental samples. The combined analysis of targeted sorting of active chemoautotrophic cells and metagenomic sequencing revealed dominant species and a complete Calvin-Benson-Bassham (CBB) cycle pathway in sulfur-oxidizing guilds. Remarkably, a novel sulfur-oxidizing chemoautotroph, Guyparkeria sp. TX1, which showed ≥99% gene sequence similarity to contigs recovered from sorted-cell metagenomes, was isolated from enrichment cultures. Its significant carbon fixation capacity provided experimental validation for the effectiveness of Raman-based in situ functional screening. This study establishes Raman-based functional biomarkers applicable to chemoautotrophic carbon fixation, enabling in situ mapping of microbial carbon fluxes. By integrating single-cell phenotypic activity with genomic potential, this work advances the mechanistic understanding of sulfur-driven dark carbon fixation, which sustains coastal blue carbon ecosystems as a keystone process.},
}

@article {pmid41993915,
year = {2026},
author = {Hoedt, EC and Burns, GL and Hedley, KE and Waller, S and Sanchez, TC and Chisolm, O and MacCallum, H and Richardson, S and Suthers, B and Pepper, E and Keely, S and Talley, NJ},
title = {Shared functional microbiome signatures in Parkinson's disease and constipation predominate irritable bowel syndrome despite taxonomic divergence.},
journal = {Brain, behavior, & immunity - health},
volume = {53},
number = {},
pages = {101218},
pmid = {41993915},
issn = {2666-3546},
abstract = {BACKGROUND: Gastrointestinal dysfunction, including constipation, is a common non-motor feature of Parkinson's disease (PD) and often precedes motor symptoms. The gut microbiome interacts with the host through neural, hormonal, and immune pathways, yet whether constipation represents a cause or consequence of PD remains unclear. Therefore, we aimed to interrogate the associations between microbiome and immune alterations in relation to constipation to provide novel insight into microbiome-gut-brain axis mechanisms in PD.

METHODS: We analysed peripheral blood mononuclear cells (PBMCs) for circulating gut-homing T cell populations and used shotgun metagenomics to profile the stool microbiome composition and functional capacity in PD patients (n = 18), healthy controls (n = 21), and individuals with constipation-predominant irritable bowel syndrome (IBS-C; n = 8). Associations between immune markers and microbial taxa were assessed, and functional pathway differences were evaluated.

RESULTS: Circulating gut-homing T cell frequencies did not differ significantly between PD and controls, but constipated PD patients showed a trend toward increased circulating gut-homing T cells. Microbiome beta-diversity analyses revealed distinct taxonomic shifts in PD and IBS-C, while functional capacity was largely conserved. Of the differential functional pathways tryptophan biosynthesis, polyamine production, and vitamin B metabolism, processes critical for neurotransmitter synthesis, epithelial integrity, and neuroimmune regulation were reduced in PD compared to IBS-C.

CONCLUSION: Our findings highlight unique microbial and immune signatures in PD, partially overlapping with IBS-C, and underscore the importance of microbial metabolic pathways in gut-brain axis disorders. Collectively our findings suggest a contribution to dopaminergic dysfunction, neuroinflammation, and impaired gut motility. Future longitudinal studies are needed to clarify causal relationships and inform targeted interventions for PD-related gastrointestinal dysfunction.},
}

@article {pmid41993958,
year = {2026},
author = {Meng, H and Zhao, S and Jin, H and Zhang, H and Li, Q and Zhang, L and Hu, J and Kong, F and Du, X and Li, Q and Ajwad Rahim, M and Xu, L and Xue, Y},
title = {Unveiling the Role of Rumen Microbiome in Modulating Intramuscular Fat Deposition of Pingliang Red Cattle.},
journal = {Food science & nutrition},
volume = {14},
number = {4},
pages = {e71681},
pmid = {41993958},
issn = {2048-7177},
abstract = {Pingliang Red cattle is renowned for its tender meat and symmetrical intramuscular fat (IMF) deposition. Rumen microbiota are crucial for energy metabolism and nutrient acquisition in cattle, significantly influencing IMF deposition. Therefore, this study aimed to explore how rumen microbiota impact IMF deposition in Pingliang Red cattle. 34 castrated Pingliang Red cattle were subjected to the same management for 2 months, followed by centralized and unified slaughtering. Based on the measured IMF content in the longissimus dorsi, 18 cattle were selected and divided into a high-intramuscular-fat group (HIMF, n = 9) and a low-intramuscular-fat group (LIMF, n = 9). Rumen fluid was subsequently collected for metagenomic sequencing. Results showed significant differences in taxonomic abundance at both the genus and species levels, the relative abundance of carbohydrate-active enzyme (CAZy) families, and functional profiles (p < 0.05). Specific rumen microbes, such as Limosilactobacillus panis (AUC = 0.765) and Fibrobacter succinogenes (AUC = 0.753), served as potential biomarkers for HIMF deposition in Pingliang Red cattle. With the exception of Bacillus, Fibrobacter succinogenes, Limosilactobacillus panis, Prevotella intermedia, and Streptomyces exhibited positive correlations with IMF content. Functional analysis based on KEGG orthology (KO) indicated that specific enzymes promote IMF deposition by regulating the metabolism of short-chain fatty acids (SCFAs), long-chain fatty acids (LCFAs), and lipopolysaccharides, as well as insulin signaling. These findings provide a theoretical reference for regulating rumen microbial communities to improve IMF deposition.},
}

@article {pmid41994130,
year = {2026},
author = {Khan, D and Espinoza, JL and Tientcheu, PE and Otchere, ID and Mohammed, NI and Worwui, A and Nicol, MP and Kwambana-Adams, B and Antonio, M and Dupont, CL},
title = {Shotgun metagenomic profiling of bacterial microbiomes, metagenome-assembled genomes and antimicrobial resistance in respiratory and blood samples from Gambian children with pneumonia.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-8724320/v1},
pmid = {41994130},
issn = {2693-5015},
abstract = {Pneumonia is a leading cause of morbidity and mortality in children, with bacterial pathogens being important etiologic agents. Most microbiome studies in pneumonia use technologies with limited taxonomical resolution and few include lung aspirate or blood samples. In this study, we assessed the microbial communities of the nasopharynx, nasopharynx/oropharynx, induced sputum, lung aspirate and blood, and recovered metagenome-assembled genomes from the same sites using shotgun metagenomics sequencing of samples from children with severe and very severe pneumonia in The Gambia. Our data show that Proteobacteria and Firmicutes were the most common phyla across the body sites, and this was largely driven by S. pneumoniae, H. influenzae/aegyptius and M. catarrhalis. Furthermore, we observed species overlap of blood and respiratory samples with average Jaccard similarity index values ranging from 34% to 58%. We recovered 60 medium and 35 high-quality MAGs in these niches including 11 S. pneumoniae , 10 H. influenzae strains and a limosilactobacillus with less than 95% Average Nucleotide Identity to any known species in GTDB-TK. We also showed that the resistomes in our MAGs were highly species specific with more than 70% of the detected AMR genes found exclusively in a single species.},
}

@article {pmid41994193,
year = {2026},
author = {Jiang, T and Yan, F and Liu, B and Li, Q and Wang, K and Ru, X and Hao, Y and Guan, Y and Wang, Y},
title = {Intraventricular hemorrhage, suspected EBV reactivation, and TBA-positive epilepsy after deep cervical lymphovenous anastomosis in Alzheimer's disease: a case report.},
journal = {Frontiers in aging neuroscience},
volume = {18},
number = {},
pages = {1791011},
pmid = {41994193},
issn = {1663-4365},
abstract = {Lymphovenous anastomosis (LVA) is emerging as a potential surgical intervention to ameliorate cervical lymphatic outflow and enhance glymphatic clearance in Alzheimer's disease (AD). However, the spectrum of neurological sequelae associated with this procedure remains poorly characterized. We report the case of a 67-years-old male with amyloid PET-confirmed AD who underwent bilateral deep cervical LVA. Twenty-three days postoperatively, he presented with high-grade fever and altered consciousness. Head CT revealed acute hemorrhage in the posterior horn of the left lateral ventricle (∼2 mL). Cerebrospinal fluid (CSF) analysis demonstrated lymphocytic pleocytosis and significantly elevated protein levels; the fluid was uniformly bloody, confirming intraventricular hemorrhage. Plasma metagenomic next-generation sequencing (mNGS) identified Epstein-Barr virus (EBV), with serology supporting reactivation. Following antiviral and empirical antibiotic therapy, the patient's condition stabilized, and the hemorrhage resolved. Four months postoperatively, he developed new-onset generalized seizures. Despite negative results from a conventional autoimmune encephalitis antibody panel in both serum and CSF, a tissue-based assay (TBA) proved positive in both samples. Seizures were successfully controlled with levetiracetam. This case suggests a potential association between invasive lymphatic procedures and a hemorrhage-infection-immune cascade in highly vulnerable AD patients with preexisting metabolic and neurodegenerative risk factors.},
}

@article {pmid41994268,
year = {2026},
author = {Zhang, F and Chen, J and Yuan, Y and Chen, J and Jiang, W and Xiang, W and Wang, N and Wu, Z and Fan, S and Zhang, K and Ma, Y and Liu, T and Zhang, J and Yu, Q and Zhang, J},
title = {The enhancing therapeutic effect of neonatal jaundice by bifidobacterium through regulating inflammation and gut microbiota in combination with phototherapy-a randomized controlled trial.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1761245},
pmid = {41994268},
issn = {1664-302X},
abstract = {BACKGROUND: Hyperbilirubinemia is among the most common conditions in neonates, and phototherapy is currently the most widely used treatment. However, it can induce side effects such as skin rashes, diarrhea, and gut microbiota dysbiosis, particularly affecting Bifidobacterium levels. This study aimed to investigate whether the supplementation of Bifidobacterium can alleviate dysbiosis and improve clinical outcomes in jaundiced neonates.

METHODS: A total of 79 jaundiced neonates were enrolled and divided into four groups: Phototherapy Control, M-16V, Bb-12, and the combined M-16V+Bb-12 group. Probiotics were administered until 30 days post-discharge, and neurodevelopment was assessed at 1.5-2 years using the Griffith Development Scales. Fecal samples collected before, during, and after treatment were analyzed using metagenomic sequencing and non-targeted metabolomics.

RESULTS: Probiotic supplementation significantly increased daily defecation frequency, accelerated the reduction rate of transcutaneous bilirubin, and shortened hospital stays. Griffith scores indicated that Bb-12 supplementation improved scores in personal-social and performance domains. Metagenomic analysis revealed significant differences in beta diversity between the control and probiotic groups; specifically, M-16V and combined supplementation increased the abundance of Bifidobacterium breve. Pathway enrichment analysis showed up-regulation of pyrimidine-containing compound metabolic processes, intramolecular transferase activity, and DNA conformation change. Metabolomics further demonstrated that combined supplementation elevated levels of 5-methyltetrahydrofolate (linked to DNA synthesis), benzoic acid and indoleacetic acid (linked to growth and development), and the anti-inflammatory metabolite indole-3-lactic acid.

DISCUSSION: For neonates receiving phototherapy, the addition of M-16 V + Bb-12 probiotics can improve the diversity of microflora, reduce the fixed value of harmful bacteria in the intestine, and enhance the excretion of bilirubin from the intestine, to improve the inflammatory damage and microbiota disorder caused by phototherapy, and achieve the effect of clinically improving jaundice, reducing bilirubin, shortening the length of hospitalization, and promoting neurodevelopment. It provides a safer and more effective treatment for neonatal jaundice.},
}

@article {pmid41994275,
year = {2026},
author = {Yu, T and Yu, Y and Zhao, J and Li, H and Lu, H and Li, Y and Peng, Y and Wang, S and Wei, W and Cheng, X},
title = {Qifuyin improves physiological frailty by regulating the intestinal flora in 3xTg-AD mice.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1753643},
pmid = {41994275},
issn = {1664-302X},
abstract = {OBJECTIVE: Alzheimer's disease (AD) is often accompanied by motor dysfunction, impaired limb strength, and gut microbiota disturbances. This study aimed to evaluate the effects of Qifuyin (QFY), a traditional Chinese medicine formula, on motor deficits, limb strength, aging, and gut microbiota composition in 3xTg-AD mice, a widely used model of AD.

METHODS: Male and female 3xTg-AD mice were administered QFY at low, medium, or high doses. Motor function was assessed using grip strength and rotarod tests. Aging was evaluated through aging scores. Gut microbiota composition was analyzed at the phylum, family, genus, and species levels. Functional profiling of microbiota was performed using KEGG, eggNOG, and carbohydrate-active enzyme (CAZyme) databases. Pearson correlation analyses were conducted to explore relationships between microbiota composition and motor performance.

RESULTS: QFY treatment significantly improved both absolute and normalized grip strength in male and female 3xTg-AD mice. Similarly, motor coordination, as assessed by latency to fall on the rotarod, was significantly enhanced in the groups of QFY. Aging scores were significantly reduced after the treatment of QFY. Microbiome analysis revealed that QFY treatment restored species diversity and improved the overall composition of gut microbiota, with significant increases in Muribaculaceae and decreases in Alcaligenaceae, Rhodanobacteraceae, and Spirochaetaceae. Principal component analysis (PCA) indicated that the gut microbiota composition of the QFY group resembled that of the control (Con) group. Functional analyses showed that treatment of QFY restored microbial pathways related to metabolism and genetic information processing, with significant correlations between microbial alterations and improved motor outcomes. Additionally, QFY modulated the abundance of key carbohydrate-active enzymes, including GH43 and GH35, which were positively correlated with grip strength and rotarod performance.

CONCLUSION: Qifuyin improves motor function, reduces aging-related deficits, and restores gut microbiota homeostasis in 3xTg-AD mice. These findings suggest that QFY may offer therapeutic potential for addressing frailty and motor dysfunction in AD, in association with alterations in gut microbiota composition and predicted microbial functions.},
}

@article {pmid41994276,
year = {2026},
author = {Xian, J and Li, Y and Feng, Z and Jin, Y and Cai, T and Cao, M and Cao, Y},
title = {High-fat diet-driven gut microbial sphingolipid metabolic reprogramming is associated with stress susceptibility in CUMS rats.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1802003},
pmid = {41994276},
issn = {1664-302X},
abstract = {The escalating comorbidity between depression and metabolic syndromes induced by a high-fat diet (HFD) poses a substantial social and economic burden on society. However, the precise molecular mechanisms by which a HFD qualitatively alters the basal pathophysiology of chronic unpredictable mild stress (CUMS) remain unclear. In this study, the differential roles of microbial and metabolic pathways in the onset and exacerbation of depression were investigated using CUMS rat models fed a normal diet (ND-CUMS) or HFD (HFD-CUMS). Our findings indicated that HFD intervention showed a trend toward aggravating depressive behaviors and resulted in significantly more severe neuronal injury in the hippocampus relative to the ND-CUMS group. Notably, integrated multi-omics (metagenome and metabolome) analysis revealed a crucial pathway divergence: basal CUMS depression was strongly associated with the dysregulation of glycerophospholipid metabolism, linked to microbiota such as Bacteroides thetaiotaomicron and Terrisporobacter glycolicus, while HFD triggered a predominant disruption of the sphingolipid metabolism pathway. Exploratory mediation analysis suggested that a sphingolipid-related signature that may statistically connect HFD-associated microbial shifts with neural injury and behavioral readouts. Therefore, our findings reveal a distinct mechanistic shift underpinning metabolic-comorbid depression. HFD does not merely exacerbate stress-induced depression but fundamentally transitions the underlying pathology from glycerophospholipid to sphingolipid signaling, highlighting the potential of targeting specific lipid metabolic reprogramming as a promising therapeutic strategy for combating metabolic-comorbid depression.},
}

@article {pmid41994278,
year = {2026},
author = {Dang, M and Tang, Y and Chen, J and Xie, W and Zhong, Y and Yu, B and Zhang, E and Wang, Z},
title = {Rhizospheric soil microbial community structure and metabolic characteristics of wild Cymbidium mastersii at different altitudes.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1720137},
pmid = {41994278},
issn = {1664-302X},
abstract = {INTRODUCTION: Cymbidium mastersii, a perennial orchid of high ornamental value, faces severe survival challenges due to extremely low natural seed germination rates (<15%), habitat degradation, and illegal harvesting. It is listed as a Category II Nationally Protected Plant Species in China.

METHODS: We examined the rhizosphere microbial communities and metabolomes of C. mastersii across elevation gradients. We investigated the rhizospheric soil microbial community composition and metabolic characteristics of C. mastersii across different elevations.

RESULTS: The dominant bacterial phylum was Pseudomonadota, with relative abundances of 38.22% (CmL, low elevation), 36.91% (CmM, mid-elevation), and 62.54% (CmH, high elevation). While the dominant bacterial genera varied significantly with elevation, taxonomic richness exhibited a consistent decline with increasing altitude (p < 0.05, linear regression), indicating altitudinal filtering of microbial diversity. LC-MS/MS metabolomic profiling identified 1,516 metabolites, predominantly enriched in lipid and lipid-like molecules, carbohydrates and derivatives, and aromatic compounds. Functional contribution analysis revealed Bradyrhizobium as the most influential taxon (10% variance explained), displaying a nonlinear elevational response. Correlation analysis of differential metabolites confirmed significant species-metabolite correlations (P < 0.05, R > 0.7). Our findings underscore the critical role of trophic interactions in shaping rhizosphere community assembly in alpine plants, thereby contributing to the broader understanding of microbial biogeography along elevational gradients.

DISCUSSION: This study not only confirms that the altitudinal gradient serves as a key environmental filter shaping the rhizosphere microecology of C. mastersii, but more importantly, by integrating metagenomic and metabolomic approaches, we systematically reveal for the first time that altitude differentially selects for microbial taxa with specific functions, ultimately driving the restructuring of the rhizosphere metabolic environment. Moving beyond mere community description, our work aims to elucidate the underlying pathways responsible for these shifts and their potential functional implications for host plant adaptation.},
}

@article {pmid41994292,
year = {2026},
author = {Sun, M and Lei, Z and Li, B and Gao, SH and Fan, L},
title = {Virus-encoded metabolism may support environmental stress adaptation of microbial hosts in an estuarine hypoxic zone.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1785655},
pmid = {41994292},
issn = {1664-302X},
abstract = {Hypoxic zones in estuaries threaten the ecological balance and the productivity in coastal areas. However, it is poorly understood how viruses regulate metabolic processes of their microbial hosts to adapt to the hypoxic environment, and consequently impact the biogeochemical cycles in hypoxic zones. In this study, the diversity and functional potentials of the bacterial, archaeal and viral communities of a hypoxic zone at the Pearl River Estuary was characterized along with local environmental factors, with a particular focus on viral auxiliary metabolic genes (AMGs). The viral community derived from the virion fraction and the cellular fraction of the seawater were distinctly different, with the cellular fraction generating fewer unique viruses, but more types of AMGs. Overall, more AMGs were identified in samples with higher dissolved oxygen levels. Globally conserved AMGs were infrequently observed in the current samples, suggesting a certain level of adaptation of AMGs to the local environment. There were strong correlations in abundances among cyanobacteria, cyanophages, and photosynthesis AMGs, suggesting potential viral participation in estuarine primary production. Many AMGs involved in nutrient limitation endurance were found, potentially assisting their host with phosphorus, iron and B family vitamin shortages. Although putative hosts were predicted for the viruses, the functionality of their AMGs appears to be a better predictor of their distribution than the hosts they infect. Our study provides a functional insight into the viral community in poorly researched estuarine hypoxic zones, and sheds light on the potential interactions of viruses with their microbial hosts for co-adaptation to this unique environment.},
}

@article {pmid41994309,
year = {2026},
author = {Sarkar, P and Sarkar, S and Unnisa, M and Singh, AP and Inavolu, P and Rughwani, H and Jakkampudi, A and Jaggaiahgari, S and Reddy, DN and Talukdar, R},
title = {The Jejunal Microbiota in Patients With Chronic Pancreatitis: Results From a Pilot Study.},
journal = {Gastro hep advances},
volume = {5},
number = {5},
pages = {100907},
pmid = {41994309},
issn = {2772-5723},
abstract = {BACKGROUND AND AIMS: Chronic pancreatitis (CP) is associated with several systemic metabolic abnormalities including diabetes. While the colonic microbiota and its association with diabetes in CP have been reported, the specific composition of the small intestinal microbiota and its function in CP remains poorly understood. In this pilot study, we primarily aimed to characterize the jejunal microbiota in patients with CP and explore potential associations with diabetes.

METHODS: Jejunal aspirates were collected in a RNAlater-containing sterile container from 29 patients with CP and 10 controls. The samples were then snap lysed followed by metagenomic DNA extraction. Next-generation sequencing was performed for the variable region 3-4 of the 16SrDNA in Illumina MiSeq. After quality control, microbial profiling and functional analysis were conducted using standard bioinformatics pipelines. We also evaluated tight junction integrity in jejunal biopsy samples using immunofluorescence. Furthermore, we assessed for plasma and stool metabolites.

RESULTS: Patients with CP exhibited higher abundances of Prevotella vespertina, Prevotella oris, and Prevotella salivae, while controls demonstrated higher abundances of Prevotella scopos, Veillonella, Rothia, and Lachnospiraceae. Immunofluorescence showed decreased expression of the tight junction protein occludin in the jejunal mucosa of CP diabetic (CPD) patients compared to endoscopic controls (EC) (p.corr. CPD-EC = 0.012). No differences were seen between CP nondiabetic and endoscopic controls, and between the CP subgroups (CPND-EC = 0.29 and CPD-CPND = 1 respectively). Overall, there were significant plasma metabolomic abnormalities in patients with CP and a trend toward reduction of butyrate in the stool samples of the CP patients with diabetes.

CONCLUSION: Our observations suggest alterations in the jejunal microbiota and mucosal barrier function in CP. These were associated with lower fecal butyrate. This may contribute to the pathogenesis of associated metabolic complications in CP. Further large-scale longitudinal and mechanistic studies are needed to validate our findings.},
}

@article {pmid41994369,
year = {2026},
author = {Bao, Q and Zhang, X and Guo, J},
title = {Enterovirus D68 and mycobacterial coinfection: case report.},
journal = {Therapeutic advances in infectious disease},
volume = {13},
number = {},
pages = {20499361261432918},
pmid = {41994369},
issn = {2049-9361},
abstract = {The threat of viral epidemics to long-standing diseases, such as mycobacterial infection, is constantly evolving. Enterovirus D68 (EV-D68) is an emerging cause of respiratory infection and has raised great interest since its first outbreak in 2014. Very few studies have been done to describe the clinical aspects of the coinfection of EV-D68 and mycobacteria, so this study was conducted to help round out the understanding of this coinfection pattern. We observed three adult cases of EV-D68 and mycobacteria, who were admitted to the first affiliated hospital of Zhejiang University in August/September 2024. Only one case had a definite past history of immunodeficient disease and received long-term corticosteroid treatment, and the other two were previously healthy. The diagnoses of EV-D68 and mycobacterial infection were all simultaneously confirmed through the metagenomic Next-Generation Sequencing in bronchoalveolar lavage fluid specimens. All three patients were presented with severe respiratory symptoms, such as fever, cough, dyspnea and tachypnea, without any manifestations of central nervous system involvement. The radiological findings in chest CT scans varied from patchy opacity to massive consolidation. The individualized anti-mycobacterium treatment showed little therapeutic effect, while the improvement of symptoms and pulmonary lesions in chest CT was observed after starting or intensifying the administration of corticosteroid. All patients had a marked clinical improvement when discharged from hospital, and it took about 6-9 months for the lung lesions of mycobacterial infections to nearly resolve. These cases illustrate the potential for EV-D68 coinfection to exacerbate pulmonary inflammation in patients with mycobacterial disease, highlighting the need for vigilance regarding possible viral coinfections in settings with a high tuberculosis burden, such as China.},
}

@article {pmid41994453,
year = {2026},
author = {Zhang, W and Zhang, K and Liao, Y and Yang, Z and Xia, Z and Ke, X and Zhang, D and Chen, J and Wu, H and Hong, Y and Wang, H and Liu, Z and Suo, L and Zhang, Y and Zhang, C},
title = {Characterization of the aqueous humor microbiome in Posner-Schlossman syndrome: an exploratory metagenomic sequencing study.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1780981},
pmid = {41994453},
issn = {2296-858X},
abstract = {OBJECTIVE: This study aims to characterize the aqueous humor (AH) microbiome in Posner-Schlossman syndrome (PSS) patients and evaluate its potential as a diagnostic and therapeutic target.

METHODS: Metagenomic next-generation sequencing (mNGS) was performed on 59 AH samples from patients diagnosed with PSS (n = 28) and myopia patients who underwent intraocular lens (ICL) implantation (n = 31). Taxonomic profiling and diversity analyses were conducted to characterize the microbial communities. Interactions among microbial community members were evaluated using correlation analyses.

RESULTS: Key findings revealed that intraocular microbiomes existed in both normal and diseased eyes; however, PSS patients exhibited lower microbial diversity (Shannon index, p = 0.066; Simpson index, p = 0.065) and distinct community structures (PERMANOVA, p = 0.05). Disease-specific microbial signatures were identified: Paeniglutamicibacter was uniquely enriched in the PSS group, whereas Escherichia coli dominated in the ICL group. Moreover, ecological network analysis demonstrated contrasting interaction patterns. The microbiomes in the PSS group formed stable, tightly connected networks with balanced positive/negative correlations, whereas those in the ICL group exhibited antagonistic relationships, suggesting competitive exclusion. These results challenge the traditional view of ocular sterility and reveal dynamic microbiome shifts associated with PSS pathogenesis. The enrichment of Paeniglutamicibacter in PSS may represent an associated microbial signature that could potentially reflect compensatory responses to chronic inflammation, although experimental validation is needed to confirm this hypothesis.

CONCLUSION: Our study provides preliminary evidence supporting the concept of intraocular microbiome dysbiosis in PSS, which requires validation in future studies. These findings suggest that potential microbial biomarkers warrant further investigation for their diagnostic and therapeutic implications.},
}

@article {pmid41994458,
year = {2026},
author = {Jiang, L and Ye, T and Cai, H and He, F},
title = {Case Report: A rare case of Pneumocystis jirovecii infection with left hydropneumothorax following immunotherapy for stage IVB clear cell renal cell carcinoma.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1784855},
pmid = {41994458},
issn = {2296-858X},
abstract = {BACKGROUND: Pneumocystis jirovecii pneumonia (PJP) is an opportunistic infection that predominantly affects immunocompromised individuals, most commonly HIV-infected patients with significantly reduced CD4+lymphocyte counts, and is associated with high clinical mortality. Currently, there are few reports of pneumothorax secondary to PJP, and most cases occur in HIV-infected populations. However, PJP complicated by hydropneumothorax in cancer patients receiving immunotherapy is exceedingly rare, with limited reports in the literature. To our knowledge, this article reports a rare clinical case of Pneumocystis jirovecii infection complicated by left-sided hydropneumothorax in a patient with stage IVB clear cell renal cell carcinoma after immunotherapy, aiming to provide valuable insights for the early diagnosis and management of PJP and its complications in cancer patients undergoing immunotherapy.

CASE: A 57-year-old male patient had previously undergone surgical treatment for left renal clear cell carcinoma, and developed recurrent metastases to the descending colon, liver, and upper pole of the left kidney after surgery, with a clinical stage of T4NxM1 stage IVB. After receiving targeted combination immunotherapy with sequential PD-1 inhibitors (toripalimab) plus anti-angiogenic agents (sunitinib, axitinib)-a regimen that enhances anti-tumor immunity but may disrupt pulmonary immune homeostasis-the patient gradually developed progressive dyspnea, chest tightness, hypoxemia, and anuria. Multiple auxiliary examinations were performed clinically, including chest X-ray, bronchoalveolar lavage, and metagenomic sequencing of pathogenic microorganisms. Based on the above examination results, the final diagnosis was Pneumocystis jirovecii pneumonia complicated by left-sided hydropneumothorax.

CONCLUSION: Although PJP complicated by hydropneumothorax after immunotherapy is rare, it should be considered as a possible etiology when cancer patients develop progressive dyspnea with difficulty maintaining oxygen saturation after receiving immune checkpoint inhibitor-based therapy, particularly in the context of immune checkpoint inhibitor use. While biomarkers for predicting immunotherapy efficacy and irAEs are well-studied, the identification of specific biomarkers for predicting opportunistic infections like PJP in this context remains an area of active research.},
}

@article {pmid41994961,
year = {2026},
author = {Sun, QG and Zang, D and Xin, Y and Cui, J and Han, X and Chen, J},
title = {Multi-omics Analysis Reveals the Correlation of Gut Microbiota and Metabolites With Thalidomide Treatment for Chemotherapy-Induced Nausea and Vomiting in Small Cell Lung Cancer.},
journal = {Biotechnology journal},
volume = {21},
number = {4},
pages = {e70228},
doi = {10.1002/biot.70228},
pmid = {41994961},
issn = {1860-7314},
support = {82203056//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/genetics ; *Small Cell Lung Carcinoma/drug therapy ; *Lung Neoplasms/drug therapy ; Male ; Female ; Middle Aged ; *Thalidomide/therapeutic use/adverse effects/pharmacology ; *Vomiting/chemically induced/drug therapy ; *Nausea/chemically induced/drug therapy ; Aged ; *Antineoplastic Agents/adverse effects/therapeutic use ; Metabolomics/methods ; Metabolome/drug effects ; Feces/microbiology ; Multiomics ; },
abstract = {Small cell lung cancer (SCLC) is a highly aggressive malignancy, and chemotherapy frequently causes nausea and vomiting, which can impair treatment tolerance. Because thalidomide (THD) has shown potential clinical benefit in alleviating nausea and anorexia, we investigated whether its effects might be associated with changes in gut microbial composition and metabolite profiles. Fecal samples were collected from patients with SCLC and categorized into THD-treated and control groups. Metagenomic sequencing and nontargeted metabolomic profiling were performed to characterize microbial composition and metabolic signatures. THD treatment was also associated with higher microbial alpha diversity and increased abundance of genera such as Eubacterium and Prevotella. Metabolomic analysis identified several differential metabolites, including hydrogenated MDI, becocalcidiol, β-octylglucoside, and azelaic acid. Collectively, these findings suggest that the gut microbiota-metabolite axis may be associated with the potential effects of THD on CINV and anorexia in patients with SCLC. The identified microbial taxa and metabolites may serve as candidate biomarkers or potential therapeutic targets, although further validation in larger studies is necessary.},
}

Humans
*Gastrointestinal Microbiome/drug effects/genetics
*Small Cell Lung Carcinoma/drug therapy
*Lung Neoplasms/drug therapy
Male
Female
Middle Aged
*Thalidomide/therapeutic use/adverse effects/pharmacology
*Vomiting/chemically induced/drug therapy
*Nausea/chemically induced/drug therapy
Aged
*Antineoplastic Agents/adverse effects/therapeutic use
Metabolomics/methods
Metabolome/drug effects
Feces/microbiology
Multiomics

@article {pmid41995327,
year = {2026},
author = {Chen, Y and Tang, X and Lu, S and Guo, L and Wang, L and Min, L and Niu, T and Zhou, Y},
title = {The diagnostic and prognostic utility of blood metagenomic next-generation sequencing for invasive pulmonary aspergillosis.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0338425},
doi = {10.1128/spectrum.03384-25},
pmid = {41995327},
issn = {2165-0497},
abstract = {UNLABELLED: Differentiating invasive pulmonary aspergillosis (IPA) from colonization in patients with Aspergillus-positive blood metagenomic next-generation sequencing (mNGS) remains a clinical challenge. This study aims to evaluate the diagnostic and prognostic value of blood mNGS-derived fungal load (reads per million [RPM]) and two key serological biomarkers (galactomannan [GM] and 1,3-β-D-glucan [BDG]) in distinguishing these two entities. This retrospective study enrolled 95 patients with Aspergillus detected by blood mNGS, stratified into infection (n = 60) and colonization (n = 35) groups using modified EORTC/MSGERC criteria. We analyzed clinical characteristics, co-infection spectra, and serological biomarkers (GM and BDG). Diagnostic performance was evaluated via receiver operating characteristic (ROC) analysis, and prognostic factors for 28-day mortality were identified using least absolute shrinkage and selection operator-Cox regression. Distinct co-infection patterns were observed between groups: the infection group was dominated by polymicrobial co-infections, including clinically significant pathogens such as Acinetobacter baumannii, Klebsiella pneumoniae, Mucor spp., and Human cytomegalovirus; in contrast, the colonization group primarily featured single viral co-infections. While mNGS effectively detected Aspergillus, RPM alone showed limited ability to discriminate infection from colonization, with area under the curves (AUCs) ranging from 0.406 to 0.657 across patient groups. The optimal RPM cutoff varied substantially by immune status, being highest in immunocompetent patients (RPM cutoff: 1.77). Diagnostic performance significantly improved when RPM was integrated with GM (AUC up to 0.900 at a cutoff of 0.36 optical density index) or BDG (AUC up to 0.881 pg/mL), particularly in immunocompetent individuals. RPM also correlated with albumin, hemoglobin, platelet counts, and lymphocyte counts (all P < 0.05). Multivariate analysis identified reversed halo sign (hazard ratio [HR] = 2.143), decreased ratio of partial pressure of arterial oxygen to fraction of inspired oxygen (PaO2/FiO2; HR = 1.361), and elevated lactate dehydrogenase (HR = 1.055) as independent predictors of 28-day mortality. Blood mNGS demonstrates high sensitivity for detecting Aspergillus but requires integration with serological biomarkers to differentiate IPA from colonization. The RPM can offer prognostic utility. A multimodal strategy is crucial for early diagnosis and improving outcomes in high-risk patients.

IMPORTANCE: First large-scale validation of blood mNGS for invasive pulmonary aspergillosis diagnosis-this study represents the first sizable cohort systematically evaluating blood metagenomic next-generation sequencing (mNGS) for distinguishing invasive pulmonary aspergillosis from colonization, addressing a critical gap in non-invasive diagnostic approaches for critically ill patients. Comprehensive Aspergillus co-infection profiling-we identified distinct co-infection patterns, with the infection group showing significantly higher rates of polymicrobial infections, providing crucial insights into co-infection dynamics in Aspergillosis. Optimized diagnostic integration strategy-our findings demonstrate that while mNGS-derived reads per million alone show limited diagnostic value, their integration with serological biomarkers significantly improves performance, establishing a clinically relevant multimodal diagnostic framework. Robust prognostic stratification model-through least absolute shrinkage and selection operator-Cox regression, we established a validated prognostic model identifying reversed halo sign, decreased PaO2/FiO2, and elevated lactate dehydrogenase as independent predictors of 28-day mortality, providing clinically actionable tools for risk stratification.},
}

@article {pmid41995478,
year = {2026},
author = {Conley, TE and Duncan, A and Modasia, A and Ford, AC and Pritchard, DM and Hildebrand, F and Warren, FJ and Spiller, R and Probert, CS},
title = {The Emerging Short Chain Fatty Acid Enriched Metabotype in Irritable Bowel Syndrome and Its Potential Clinical Relevance.},
journal = {Alimentary pharmacology & therapeutics},
volume = {},
number = {},
pages = {},
doi = {10.1111/apt.70677},
pmid = {41995478},
issn = {1365-2036},
abstract = {BACKGROUND: Metabolomic analysis in irritable bowel syndrome (IBS) has identified metabotypes enriched in faecal short-chain fatty acids (SCFAs), but it remains unclear whether this reflects rapid colonic transit or if these metabolites actively contribute to pathophysiology.

AIMS: We aimed to determine whether an SCFA metabotype could be identified within a cohort of patients with moderate-severe IBS-D and assess whether this metabotype associated with greater clinical severity, alterations in gut transit time and specific microbiome features.

METHODS: This was a post hoc cross-sectional exploratory analysis of baseline data from the multicentre, randomised, placebo-controlled trial of ondansetron in IBS-D (TRITON: ISRCTN17508514). Faecal volatile organic compounds were profiled by GC-MS. The microbiome was characterised by whole-genome shotgun metagenomic sequencing. Unsupervised hierarchical clustering was used to identify an SCFA-enriched metabotype and non-negative matrix factorisation (NMF) enabled the derivation of complementary metabosignatures by assessing continuous gradients in metabolite composition.

RESULTS: A SCFA-enriched metabotype was identified in 20/63 participants (31.7%). This metabotype was associated with more severe abdominal pain, urgency, increased stool frequency and faster whole-gut transit. NMF identified three metabosignatures: S3 was typified by a high proportion of SCFAs and captured the SCFA-enriched metabotype, while S1 and S2 corresponded to the non-SCFA ("Other") metabotype. SCFA relative abundance positively correlated with symptom severity and inversely correlated with transit time. The Other metabotype and S1/S2 signatures were enriched in taxa linked to slower transit, whereas S3 showed no overlapping taxa with the SCFA metabotype.

CONCLUSION: A faecal metabotype enriched in SCFAs associated with an IBS-D phenotype characterised by pain, urgency, rapid transit and higher stool frequency.},
}

@article {pmid41995796,
year = {2026},
author = {Vial, M and Costil, K and Agogué, J and Eustache, S and Heighton, S and Gissat, L and Gueuné, H and Caplat, C},
title = {Spatial and temporal variability of biofouling communities during early development in three French harbors of the English Channel.},
journal = {Environmental monitoring and assessment},
volume = {198},
number = {5},
pages = {},
pmid = {41995796},
issn = {1573-2959},
mesh = {*Biofouling/statistics & numerical data ; *Biofilms/growth & development ; *Environmental Monitoring ; France ; Aquatic Organisms/physiology ; Chlorophyll A/analysis ; Seawater/microbiology ; },
abstract = {Biofouling, the colonization of submerged surfaces by marine organisms, causes major economic losses in maritime activities. Although non-biocidal surface coatings are promoted as environmentally friendly antifouling solutions, the respective roles of surface properties and environmental conditions in shaping biofouling stages remain unclear. We hypothesized that coating surface properties primarily control early biofilm formation, whereas local environmental conditions govern subsequent macrofouling development. To test this hypothesis, we studied biofouling on two non-biocidal coatings - an anticorrosion epoxy and a fluoropolymer foul-release coating (FRC) - immersed under static conditions in three French harbors along the English Channel during the spring bloom. Early biofilm formation was assessed after 2 weeks in April, May, and June 2023 using chlorophyll a and the carbohydrate/protein ratio of extracellular polymeric substances (EPS). Macrofouling development over 3 months was evaluated through biomass, surface coverage rate, taxonomic composition, and microorganism abundances. Metagenomic analyses complemented the visual observations in Cherbourg during April and May 2023. The FRC showed a higher EPS carbohydrate/protein ratio, indicating greater resistance to initial microbial colonization, but exhibited significantly lower macrofouling intensity than the epoxy. This decoupling supports the hypothesis that surface properties and settlement processes operate at different spatial and temporal scales. Spatial variability in biofouling patterns may largely be associated with differences in nutrient availability and anthropogenic pressure. These findings demonstrate that early biofilm metrics alone cannot predict long-term fouling and highlight that antifouling performance depends on both material properties and environmental context. Integrating surface physicochemistry with site-specific ecological drivers can improve both coating design and antifouling evaluation strategies.},
}

*Biofouling/statistics & numerical data
*Biofilms/growth & development
*Environmental Monitoring
France
Aquatic Organisms/physiology
Chlorophyll A/analysis
Seawater/microbiology

@article {pmid41996042,
year = {2026},
author = {Myoung, K and Kim, S and Choi, EJ and Kim, HJ and Baek, HS and Park, WS and Hwang, JS},
title = {Integrated analysis of age-related microbiome and metabolites reveals youth-associated metabolites in young Korean women's skin.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {41996042},
issn = {1618-1905},
abstract = {Alterations in the composition and functional potential of the skin microbiome are closely associated with aging. Nevertheless, integrative analyses that concurrently examine microbial composition, functional gene profiles, and skin surface metabolomics remain limited, particularly among Asian populations. In this study, we performed a comprehensive multi-omics analysis integrating skin microbiome and surface metabolomic data from Korean women to explore metabolites associated with youthful skin state. Twenty-three healthy female participants in their 20s and 60s were recruited. Skin physiological parameters were assessed, and microbiome and metabolite samples were collected from the cheek area. Unsupervised clustering of microbiome functional profiles revealed three microbial community patterns that were not strictly aligned with chronological age. Based on these patterns, samples were grouped into three functional groups. The cluster enriched in participants in their 20s showed higher relative abundance of Cutibacterium and enrichment of microbial pathways related to carbohydrate and energy metabolism. Metabolomic profiling showed that phenyllactic acid (PLA) and hydroxyphenyllactic acid were more abundant in participants in their 20s and in the functionally young cluster. These metabolite patterns were accompanied by higher abundance of genes associated with phenylalanine metabolism. In vitro experiments further showed that PLA increased procollagen production and reduced the secretion of collagen-degrading enzymes in human dermal fibroblasts under inflammatory conditions. Together, these findings suggest links between microbiome functional profiles, phenylalanine-related metabolites, and skin physiology. This study provides an integrated view of microbiome-metabolite relationships in Korean skin and identifies PLA as a candidate metabolite associated with youthful skin environments.},
}

@article {pmid41996045,
year = {2026},
author = {Mohanty, A and Pavan-Kumar, A and Chaudhari, A and Kumari, K and Kumar, P and Maurye, P},
title = {Comparative performance of traditional and commercial DNA extraction methods for fish gut microbiota analysis.},
journal = {Molecular biology reports},
volume = {53},
number = {1},
pages = {},
pmid = {41996045},
issn = {1573-4978},
support = {FBT-PB1-01//Indian Council of Agricultural Research/ ; },
}

@article {pmid41996243,
year = {2026},
author = {Lin, D and Ma, QX and Ye, YQ and Wanek, W and Gregory, AS and Jones, DL and Graham, DW and Zhu, D and Penuelas, J and Zhu, YG},
title = {Nutrient balance regulates soil microbial health under long-term fertilization.},
journal = {Cell reports},
volume = {45},
number = {4},
pages = {117274},
doi = {10.1016/j.celrep.2026.117274},
pmid = {41996243},
issn = {2211-1247},
abstract = {Fertilizer application in intensive agriculture critically influences microbial communities. It is still unclear how long-term input of different nutrients shapes microbial eco-evolutionary strategies and ecological functions. Through 180-year-old field fertilization experiment, alongside microbial culturing, pot experiments, and comprehensive metagenomic data analysis, we show that exclusive fertilization with inorganic chemicals causes carbon-nitrogen imbalances that increase microbial resource competition and antibiotic resistance gene (ARG) levels. Viruses further amplify this expansion through "piggyback the winner" strategy. The imbalanced use of nitrogen in chemical fertilizers disrupt ecological niche connections, leading to an increase in virulent viruses and reducing microbial nutrient cycling capacity. In contrast, more balanced nutrient supplies from organic fertilization reduced microbial competition and promoted microbial growth. However, responsible antibiotic use in livestock is essential to maximizing these benefits. Our research provides insights into enhancing agricultural sustainability through the management of soil nutrient conditions.},
}

@article {pmid41996362,
year = {2026},
author = {Buni, D and Kovács, ÁB and Wehmann, E and Grózner, D and Bányai, K and Nagy, EZ and Bradbury, J and Bottinelli, M and Stefani, E and Catania, S and Lysnyansky, I and Kovács, L and Gyuranecz, M and Kreizinger, Z},
title = {Identification and detection of genetic markers associated with antimicrobial susceptibility and evaluation of efflux pump mechanisms in Mycoplasma iowae.},
journal = {PloS one},
volume = {21},
number = {4},
pages = {e0347345},
doi = {10.1371/journal.pone.0347345},
pmid = {41996362},
issn = {1932-6203},
mesh = {Microbial Sensitivity Tests ; *Anti-Bacterial Agents/pharmacology ; *Mycoplasma/genetics/drug effects/metabolism ; Genetic Markers ; *Drug Resistance, Bacterial/genetics ; *Bacterial Proteins/genetics/metabolism ; Promoter Regions, Genetic ; },
abstract = {Mycoplasma iowae is an economically significant pathogen that causes reduced hatchability, late embryo mortality and leg deformities, chondrodystrophy and skeletal lesions in poults. While prevention is essential in the control of infection, the appropriate administration of antibiotics may reduce economic losses during outbreaks. As a first step in the exploration of antimicrobial resistance mechanisms in M. iowae, target modification and efflux pump activity were examined in the present study. Point mutations were analyzed in previously described antibiotic binding sites in the whole genome sequences of 99 M. iowae strains. Mismatch amplification mutation assays (MAMAs) were designed and validated for the differentiation of mutations corresponding to elevated minimum inhibitory concentration (MIC) values for fluoroquinolones. Broth microdilution assays were performed to evaluate the effect of efflux pump inhibitors. In the presence of orthovanadate (OV), MIC values were significantly lower than in the absence of OV for spiramycin, tilmicosin, tylosin and oxytetracycline, which may indicate the presence of an active efflux system in M. iowae. Putative promoter regions of efflux-related genes were predicted and characterized. Genetic mutations, previously described in other bacteria, were described to be associated with elevated fluoroquinolone, macrolide and lincomycin MICs in M. iowae, although certain resistant phenotypes remained unexplained, promoting future examinations for deeper insights. The developed MAMAs may support rapid identification of M. iowae strains with elevated MIC values for fluoroquinolones. The better understanding of the efflux pump mechanisms enables the development of alternative methods for the support of therapy against this pathogen.},
}

Microbial Sensitivity Tests
*Anti-Bacterial Agents/pharmacology
*Mycoplasma/genetics/drug effects/metabolism
Genetic Markers
*Drug Resistance, Bacterial/genetics
*Bacterial Proteins/genetics/metabolism
Promoter Regions, Genetic

@article {pmid41996550,
year = {2026},
author = {Bechtner, J and Hosek, J and Schwab, C},
title = {Fecal Material of Captive Wild Animals as Source of CAZymes With Application Potential.},
journal = {Chembiochem : a European journal of chemical biology},
volume = {27},
number = {8},
pages = {e70315},
doi = {10.1002/cbic.70315},
pmid = {41996550},
issn = {1439-7633},
support = {grant NNF22OC0079746//Novo Nordisk Fonden/ ; grant AU FF-F-2020-7//Aarhus Universitets Forskningsfond/ ; },
mesh = {Animals ; *Feces/microbiology ; *Animals, Wild/microbiology ; *Glycoside Hydrolases/metabolism ; Gastrointestinal Microbiome ; },
abstract = {Gastrointestinal systems of mammals and birds host taxonomically complex and functionally diverse microbial communities. Microbial activities contribute to community functioning and interaction with the host but can also be exploited as a source of novel enzymes or other industrially relevant microbial traits. With the overall goal to identify new resources for carbohydrate-active enzymes (CAZymes), we bioprospected fecal microbial communities of the little-explored source of captive wild animals. Using dbcan3, we identified a CAZyome dominated by glycosyl hydrolases (GHs) specialized in degrading oligo- and polysaccharides with much lower diversity and abundance of glycosyl transferases, carboxyl esterases, polysaccharide lyases, and redox enzymes with auxiliary activity. CAZyome profiles differed between animals depending on gut physiology and diet. Crude cell extracts conferred hydrolytic activity against compositionally and structurally diverse polysaccharides and nitrophenyl-sugar analogs. We identified five candidate GH68 and GH70 enzymes with the potential to produce oligo- and polysaccharides from sucrose, highlighting that fecal metagenomes are a source of rare CAZymes with industrial relevance. Taken together, we exemplify the functional potential captive wild animal fecal microbiota and suggest such a gene pool as a largely untapped resource for the discovery of novel biotechnological applications.},
}

Animals
*Feces/microbiology
*Animals, Wild/microbiology
*Glycoside Hydrolases/metabolism
Gastrointestinal Microbiome

@article {pmid41996772,
year = {2026},
author = {Haydar, MS and Alzate Zuluaga, MY and Astolfi, S and Del Buono, D and Cesco, S and Pii, Y},
title = {Nanoparticle-rhizosphere crosstalk: Insights into transformation, microbial interaction, plant uptake and translocation.},
journal = {Chemosphere},
volume = {403},
number = {},
pages = {144936},
doi = {10.1016/j.chemosphere.2026.144936},
pmid = {41996772},
issn = {1879-1298},
abstract = {For soil-applied engineered nanomaterials, the rhizosphere is the critical frontline zone where they encounter crop roots, microbes, and soil, determining their agronomic potential and environmental risks. Within this dynamic interface, nanoparticles (NPs), depending on their surface chemistry, particle size, properties, and composition, undergo physicochemical and biological transformations that govern their stability, dissolution, mobility, availability, and ecotoxicological outcomes. This review synthesizes current mechanistic evidence linking root exudation patterns, microbial activity, and soil physico-chemical conditions to NPs aggregation, dissolution, redox conversions, and eco-/bio-corona formation. Microbial extracellular polymeric substances, low-molecular-weight metabolites, siderophores, and biofilms further reshape particle speciation, modulating ion release, immobilization, nutrient availability, and potential toxicity to soil biota and crops. Once inside roots, nanoparticles follow multiple uptake routes, including apoplastic diffusion, endocytosis, plasmodesmata-mediated transport, and vascular translocation, while undergoing in-planta transformations into ionic or ligand-bound forms with distinct physiological and agronomical consequences. These processes are strongly context-dependent, shaped by plant species, development stage, NPs concentration, and soil-climate conditions, and mediated by a tripartite molecular dialogue among NPs, microbes, and plant signalling pathways that regulate root system architecture, rhizosphere microbial recruitment, and nutrient acquisition efficiency. Advances in high-resolution and multi-omics tools-such as synchrotron-based spectroscopy, single-particle ICP-MS, NanoSIMS, stable-isotopic tracers, and metagenomics are offering new insights into these interactions under realistic agricultural scenarios. We propose an integrated agroecological framework linking rhizospheric NPs transformations to plant uptake and responses, emphasizing the need for standardized exposure metrics, realistic concentrations, and long-term field trials for safe and sustainable nanotechnology use in agriculture.},
}

@article {pmid41996801,
year = {2026},
author = {Chen, Y and Sun, Y and Yang, Y and Hu, S and Cui, K and Zhu, C and Fu, XZ and Li, CX and Jiang, P and Huang, Q},
title = {Differential distribution characteristics of heavy metal resistance genes and driving mechanisms of heavy metal speciation in river-lake system sediments.},
journal = {Journal of hazardous materials},
volume = {510},
number = {},
pages = {142080},
doi = {10.1016/j.jhazmat.2026.142080},
pmid = {41996801},
issn = {1873-3336},
abstract = {River-lake systems are critical zones for heavy metal biogeochemical cycling, yet the mechanisms linking heavy metal pollution to heavy metal resistance genes (MRGs) across hydrological gradients remain elusive. This study selected the Chaohu Lake Basin as a representative river-lake system to investigate the distribution characteristics of MRGs and their driving mechanisms on heavy metal speciation. Based on metagenomic sequencing and ICP-MS analysis of 78 sediment samples collected in wet and dry seasons, we found that the resistome was dominated by multi-metal, Cu, and As resistance genes, with the arsenic resistance gene pstA identified as a consistent network hub. MRGs diversity and network complexity exhibited significant seasonal depletion and spatial heterogeneity along the river-lake gradient. Heavy metals were predominantly fractionated into the stable residual phase; however, the river-lake gradient significantly influenced the spatial distribution of bioavailable fractions. Crucially, Structural Equation Modeling (SEM) revealed a seasonal shift in the regulatory mechanisms controlling heavy metal speciation. In the wet season, the river-lake system operated under a "biologically mediated" mode, where MRGs directly facilitated the mobilization of the reducible fraction. In the dry season, it shifted to a "physicochemically driven" mode, governed primarily by basic physicochemical factors. These findings highlighted that seasonal dynamics and the river-lake gradient jointly coordinated heavy metal fate through a complex interplay of biotic and abiotic factors, providing molecular-level insights for pollution management in continuous aquatic systems.},
}

@article {pmid41996860,
year = {2026},
author = {Ji, Z and Fu, Z and Miao, L and Hang, D and Gu, A},
title = {Relationship between pesticide exposure, gut microbiota, and hypertension.},
journal = {Environment international},
volume = {211},
number = {},
pages = {110250},
doi = {10.1016/j.envint.2026.110250},
pmid = {41996860},
issn = {1873-6750},
abstract = {BACKGROUND: Both pesticide exposure and gut dysbiosis have been independently linked to an elevated risk of hypertension. However, the extent of interaction between these two factors remains poorly characterized in human populations.

METHODS: In a population-based study involving 218 adults from Jiangsu Province, China, we quantified pesticides in serum using LC-MS/MS and analyzed the gut microbiome via metagenomic sequencing. An environmental risk score (ERS) was created to represent pesticide exposure. We also used Mendelian randomization (MR) to identify causal gut microbial genera, multivariable regression for associations, and mediation analysis for potential pathways. Machine learning models were applied to differentiate hypertensive from non-hypertensive individuals based on a combined set of features.

RESULTS: Fourteen pesticides, notably bentazone and perfluorohexanesulfonate, were significantly associated with increased hypertension risk, and the ERS based on these pesticides further corroborated this association. Additionally, the overall microbiota composition was significantly associated with both pesticide exposure and hypertension status. Observational and MR analyses consistently identified branches of Clostridium as potentially contributors to hypertension risk. An interaction was observed between pesticide exposure and specific bacterial taxa. Specifically, high ERS combined with high Catenibacterium (both defined using a median split) abundance increased hypertension risk nearly fourfold. A neural network model achieved the best differentiation performance (AUC = 0.897) for hypertension.

CONCLUSIONS: Exposure to specific pesticides, particularly bentazone, is associated with increased hypertension risk. This relationship is influenced by interactions with gut bacteria and partially mediated through alterations in the gut microbiota. These findings highlight the role of environmental chemicals and the gut microbiome in the development of hypertension.},
}

@article {pmid41997101,
year = {2026},
author = {Liu, W and Yang, Y and Bian, J and Li, X and Lu, Z},
title = {Niche adaptation of marine heterotrophic nitrification-aerobic denitrification bacterium in mariculture wastewater treatment: Synergistic mechanism of nitrogen removal and sulfamethoxazole biotransformation.},
journal = {Water research},
volume = {300},
number = {},
pages = {125914},
doi = {10.1016/j.watres.2026.125914},
pmid = {41997101},
issn = {1879-2448},
abstract = {Efficient removal of nitrogen from mariculture wastewater (MW) by marine heterotrophic nitrification-aerobic denitrification (MHNAD) bacteria is an innovative approach to overcoming salt inhibition. However, their performance and survival strategies under long-term antibiotics exposure in real wastewater conditions remain elusive, limiting practical implementation. Here, a bench-scale biofloc-biological aerated filter (BF-BAF) system treating real MW was operated for 100 days. Under long-term exposure to sulfamethoxazole (SMX) (1.3 ± 0.4 mg/L), the stabilized nitrogen removal system achieved removal efficiencies of 97.2 ± 2.5 % and 91.6 ± 4.1 % for NH4[+]-N and SMX, respectively. MHNAD bacteria, dominated by Marinobacter and Celeribacter, were enriched (2.3-67.7 %) and identified as habitat-specific genera, while the growth of Nitrosomonas (0.02-0.04 %)-the sole ammonia-oxidizing bacteria (AOB) detected-was severely inhibited. Metagenomic analysis revealed upregulation of nitrogen assimilation (glnA and nasA) and denitrification genes (nirK and norC), driving niche differentiation. A novel MHNAD strain, Marinobacter sp. LAN01, was isolated from the settleable bioflocs. Multi-omics analysis indicated that LAN01 adapts to SMX stress by reallocating intracellular resources via NH4[+]-N assimilation (glnA-driven) and facilitates SMX degradation via N-acetylation, S-N bond cleavage, and hydrolysis. Nucleotide metabolism was downregulated to suppress DNA synthesis, thereby reducing the accumulation and transfer of sulfonamide resistance genes (sul1 and sul2). Overall, this works revealed the mechanism of synergistic nitrogen removal and antibiotic degradation, and highlighted the long-term application potential of BFT, paving the way for sustainable MW treatment.},
}

@article {pmid41997104,
year = {2026},
author = {Zhang, X and Weng, S and Zhen, Z and Tang, Z and Huang, X},
title = {Phage predation mitigates the spread of antibiotic resistance in anaerobic digestion under shortened solid retention times.},
journal = {Water research},
volume = {300},
number = {},
pages = {125921},
doi = {10.1016/j.watres.2026.125921},
pmid = {41997104},
issn = {1879-2448},
abstract = {Optimizing anaerobic digestion (AD) via shortening solid retention time (SRT) enhances methane recovery, yet the mechanistic impact of SRT reduction on antimicrobial resistance (AMR) dissemination remains underexplored. Herein, we employed metagenomics to investigate how reduced SRTs (from 60 to 5 days) regulated the dynamics of antibiotic resistance genes (ARGs) mediated by pathogenic hosts, plasmids, and phages in mesophilic and thermophilic AD systems. Shortened SRTs elevated ARG abundance by 5.9-388% under mesophilic conditions, driven by the SRT-elicited niche expansion of antibiotic-resistant bacteria (ARB) and the persistent dominance of ESKAPE pathogen Enterobacter hormaechei, the latter intrinsically harbored and transmitted high-risk ARGs (aadA, sul1, and qacEdelta1) via multi-resistant plasmids. Notably, plasmid-mediated and cross-phylum transmission substantially enhanced ARG mobility. Contrastingly, thermophilic conditions eliminated ARGs by 17.0-57.1% under shortened SRTs, driven by thermophilic ARB niche differentiation. Crucially, both homology search and phage-host prediction indicated the lack of ARGs matching between phages and hosts under reduced SRTs, denoting a negligible contribution of transduction to horizontal ARG transfer. The dominance of lytic phages (85.3%), intensified lytic phage-host interactions, and heightened abundance of lytic phages lysing ARB collectively imposed potent phage top-down control over ARG hosts, with the lytic phage predation on ARB being validated by laboratory assays. We also identified 9 high-risk digestate ARG biomarkers (ANT(6)-Ia, aadA, ermA, mel, qacEdelta1, sul1, tet44, tetM, tetQ) by integrating criteria of prevalence, gene mobility, clinical relevance, and host pathogenicity to inform monitoring. Overall, this study underlined the significance of phage predation in mitigating ARG propagation under shortened SRTs, informing the development of novel AMR control strategies in AD practices.},
}

@article {pmid41997155,
year = {2026},
author = {Yang, W and Lee, YJ and Silva, RMB and DeLiberto, A and Yancey, CE and McCallum, D and Buss, JA and Moncion, R and Ong, JL and Mabuchi, M and Hough, DM and Weigele, PR and Ettwiller, LM},
title = {The discovery of 5mC-selective deaminases and their application to ultra-sensitive direct sequencing of methylated sites at base resolution.},
journal = {Molecular cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.molcel.2026.03.027},
pmid = {41997155},
issn = {1097-4164},
abstract = {Mining phages for new enzymatic activities continues to be important for the development of new tools for biotechnology. In this study, we used MetaGPA-a method linking genotype to phenotype in metagenomic data-to identify deoxycytidine deaminases, a protein family highly associated with cytosine modifications in metaviromes. Unexpectedly, a subset of these deaminases exhibited a preference for 5-methylcytosine (5mC) over cytosine (C) in both mononucleotide and single-stranded DNA substrates. In a methylome-sequencing workflow, deamination of 5mC by these enzymes enabled direct conversion of methylated cytosine while completely eliminating any background deamination of unmodified cytosine. This direct conversion allows for precise identification of methylated sites at single-base resolution with unmatched sensitivity enabling broad applications for the simultaneous sequencing of genome and methylome.},
}

@article {pmid41997245,
year = {2026},
author = {Wang, X and Wang, X and Ai, S and Wu, F and Xi, J and Li, J and Liu, Z},
title = {Harnessing native microbes: Intermittent aeration for bioremediation of phenolic compounds contaminated freshwater.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134641},
doi = {10.1016/j.biortech.2026.134641},
pmid = {41997245},
issn = {1873-2976},
abstract = {Phenolic pollutants pose persistent risks to freshwater ecosystems due to their toxicity, structural diversity, and resistance to biodegradation. This study investigated microbial community dynamics, gene-level adaptation, and biostimulation strategies for phenolic removal using native microbial community. Metagenome analyses revealed marked taxonomic shifts under phenolic stress, with engineered systems favoring modular cooperative degradation, whereas the natural community relied on dominance of stress-resistant taxa and inter-phylum horizontal gene transfer (HGT). Functional profiling identified 28 candidate KEGG Orthologs (KOs), including oxidative, ring-cleaving, and energy-support genes, enriched across core degraders such as Pseudomonas, Sphingobium, and Bordetella. Biostimulation assays demonstrated oxygen availability as the primary limiting factor: intermittent aeration (IA) enhanced phenolic degradation by 29%, while IA combined with activated carbon (IA + AC) achieved up to 75% improvement, especially for complex compounds like bisphenol A (BPA) and nitrophenol. Predictive modeling based on KO abundance and stimulation methods (R[2] = 0.75-0.88) successfully predicted degradation performance across 50 natural samples. While IA + AC provided the most consistent improvement, 15 communities achieved comparable efficiencies under IA alone, highlighting context-dependent biodegradation capacities linked to HGT and metabolic pathway diversity. These findings establish a scalable predictive framework and emphasize the importance of tailoring biostimulation strategies to native microbial capacities, offering a practical route for in situ bioremediation of phenol-contaminated freshwater systems.},
}

@article {pmid41998153,
year = {2026},
author = {Li, S and Zhu, D and Saha, K and Kundu, BB and Sonkusale, S and Britton, RA and Ajo-Franklin, CM},
title = {Synthetic microbial co-cultures for modular bioelectronic sensing in diverse environments.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {41998153},
issn = {1546-1696},
support = {W911NF-22-1-0239//United States Department of Defense | United States Army | U.S. Army Research, Development and Engineering Command | Army Research Office (ARO)/ ; W911NF-22-1-0239//United States Department of Defense | United States Army | U.S. Army Research, Development and Engineering Command | Army Research Office (ARO)/ ; W911NF-22-1-0239//United States Department of Defense | United States Army | U.S. Army Research, Development and Engineering Command | Army Research Office (ARO)/ ; RR190063//Cancer Prevention and Research Institute of Texas (Cancer Prevention Research Institute of Texas)/ ; RR190063//Cancer Prevention and Research Institute of Texas (Cancer Prevention Research Institute of Texas)/ ; RR190063//Cancer Prevention and Research Institute of Texas (Cancer Prevention Research Institute of Texas)/ ; R01 AI173318/AI/NIAID NIH HHS/United States ; R01 AI173318/AI/NIAID NIH HHS/United States ; },
abstract = {Whole-cell bioelectronic sensors are particularly well-suited for environmental and health monitoring as they can be integrated into compact electronic devices for field deployment over extended periods. However, current engineering strategies lack modularity, are limited to a few microbial chassis and depend on specialized instruments for signal detection. We present the electroactive co-culture sensing system (e[-]COSENS), a plug-and-play system for whole-cell bioelectronic sensor development. Here a 'sender' bacterium produces electron mediators in response to analytes and a 'receiver' bacterium utilizes the electron mediators to generate electrical signals via extracellular electron transfer. Modularly swapping the sender bacterium and its associated genetic sensing elements achieved bioelectronic sensing of metals, small molecules and peptides in distinct environments, such as urban waterways, milk, saliva and microbial communities. We designed a centimeter-sized bioelectronic device for portable signal readout using a household digital multimeter. The e[-]COSENS system simplifies the whole-cell bioelectronic sensor design and expands the potential of bioelectronic sensor applications.},
}

@article {pmid41998361,
year = {2026},
author = {Thiyagarasaiyar, K and Paul, D and Kerttula, J and Keski-Karhu, M and Soosaar, K and Mander, Ü and Hallin, S and Machacova, K and Pumpanen, J and Siljanen, HMP},
title = {Genetic Potential for N2O Metabolism in Tree Tissues: Insights From Nitrogen Cycling Gene Prevalence and nosZ Diversity Across Tree Species.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02773-8},
pmid = {41998361},
issn = {1432-184X},
}

@article {pmid41998362,
year = {2026},
author = {Parida, D and Dhali, SL and Bala, K and Nogueira, R},
title = {Early microbial colonization study of daily-use plastics exposed to river water.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {5},
pages = {},
pmid = {41998362},
issn = {1573-0972},
}

@article {pmid41792614,
year = {2026},
author = {Zhou, J and Gu, T and Zhou, J and Zeng, X and Liu, Y and Chen, F and Hu, Y and Li, S},
title = {Clostridium zhoujianii sp. nov., a novel gram-negative species isolated from bat feces and its genetic characteristics.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41792614},
issn = {1471-2180},
support = {Qiankehe Platform Talent-ZDSYS [2023] 004//Key Laboratory of Microbiol and Infectious Disease prevention &Control in Guizhou Province/ ; Guo Jikong Zong Ren Han [2024] 122//Project for Public Health Talent Cultivation of China/ ; Qiankehe [2025] 024//The local science foundation of Guizhou Province guided by the Central Committee of China/ ; },
abstract = {UNLABELLED: A strictly anaerobic, rod-shaped bacterial strain, designated LP20ᵀ, was isolated from the intestinal contents of bats collected in Qiandongnan, China. Phylogenetic analysis of the 16 S rRNA gene revealed that strain LP20ᵀ shared its highest similarity with Clostridium paraputrificum ATCC 25780ᵀ (98.10%), a value below the accepted threshold for species delineation. Whole-genome sequencing further supported its taxonomic novelty, with ANI, dDDH, and AAI values to the closest relatives all falling well below species-level cutoffs. Strain LP20ᵀ exhibited unusual Gram-stain-negative morphology, grew optimally at 30–37℃ and pH 7.0–8.0, and possessed distinctive fatty acid and polar lipid profiles, including the presence of an unidentified aminophospholipid. Phenotypic assays revealed several metabolic and enzymatic traits that differentiated LP20ᵀ from its closest phylogenetic neighbors. 16 S rRNA amplicon sequencing and metagenomic screening confirmed the presence of this species in multiple bat hosts, suggesting a wider distribution within bat gut microbiomes. Functional genomic analysis indicated enrichment of genes involved in carbohydrate metabolism and a limited antibiotic resistance profile. Based on polyphasic evidence, strain LP20ᵀ represents a novel species within the genus Clostridium, for which the name Clostridium zhoujianii sp. nov. is proposed. The type strain is LP20ᵀ (= JCM 37970ᵀ = GDMCC 1.5627ᵀ).

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04884-1.},
}

@article {pmid41796297,
year = {2026},
author = {Shi, K and He, Q and Wang, S and Guo, J},
title = {An adaptive weight self-distillation deep learning framework for phenotype prediction from longitudinal gut microbiome data.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41796297},
issn = {1471-2180},
support = {62562022//National Natural Science Foundation of China/ ; Guike ZY22096025//Special Funds for Guiding Local Scientific and Technological Development by the Central Government/ ; 2025JJA170175//Guangxi Natural Science Foundation/ ; Z-C20241570//Guangxi Health Commission Self-Funded Research Project/ ; },
abstract = {BACKGROUND: The gut microbiota plays a vital role in maintaining human health. In recent years, extensive researches has focused on phenotype prediction in relation to various diseases, with the gut microbiota as a key predictor. Nevertheless, most existing studies rely on single-time-point analyses, which are insufficient to capture the dynamic patterns of host states and temporal variations inherent in longitudinal data.

RESULTS: In this study, we propose a deep learning framework, AWSD-CNN-LSTM, designed to classify host phenotypes using longitudinal metagenomic data. Unlike conventional approaches that treat each time point as an independent sample, our method models the sequential samples of each individual as a whole, integrating convolutional neural network (CNN) and long short-term memory network (LSTM) to effectively capture temporal dependencies in longitudinal microbiome sequencing data. In addition, the model incorporates an adaptive point-wise self-distillation mechanism to more accurately characterize host-specific patterns. Compared with state-of-the-art methods, AWSD-CNN-LSTM demonstrates superior performance on the PROTECT, DIABIMMUNE, and Infants datasets, achieving area under the receiver operating characteristic curve (AUC) values of 0.896, 0.813, and 0.894, respectively.

CONCLUSIONS: For the task of disease phenotype classification based on temporal data, we propose a novel framework that effectively captures the characteristics of time-series data and achieves high accuracy across multiple datasets. Our approach holds promise as a potential new tool for microbial knowledge discovery.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04922-y.},
}

@article {pmid41987827,
year = {2026},
author = {Bornbusch, SL and Thacher, PR and Francisque, M and DeCandia, AL and Bortner, R and Garelle, D and Kendrick, EL and Maslanka, MT and Muletz-Wolz, CR},
title = {How "pro" are probiotics for wildlife species? Novel data, lack of evidence, and future directions.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag036},
pmid = {41987827},
issn = {2730-6151},
abstract = {Treatments that aim to purposefully manipulate host-associated microbiomes are now prevalent in human and animal medicine. Probiotics that contain live bacteria are purported to improve microbiome function and host health. Although research is advancing, commercial probiotic development has outpaced empirical study of probiotic efficacy. Probiotics are widely used in ex-situ wildlife care despite a lack of empirical study or support. We interrogate the relevance of commercial probiotics in ex-situ wildlife by (a) sequencing the composition of commercial probiotics used to treat wildlife, (b) comparing the probiotic sequences to data on the microbiomes of >900 animal species, and (c) characterizing the effects of a commercial probiotic on probiotic colonization, prevalence of a potential enteric pathogen (Clostridium perfringens), and metagenomic function in endangered black-footed ferrets (Mustela nigripes). We found mislabeling and potential contaminants in probiotics marketed for a range of species. The probiotic bacteria were rare or absent in published animal microbiomes. In black-footed ferrets, probiotic treatment induced minimal probiotic colonization, negligible functional change, and limited influence on the potential enteric pathogen. Given our findings, which reiterate concerns about the efficacy of commercial probiotics across human and animal sectors, greater effort must be put towards identifying species-specific probiotic candidates and studying alternative microbial therapies for wildlife under human care.},
}

@article {pmid41987902,
year = {2026},
author = {De, R and Kanungo, S and Mukhopadhyay, AK and Dutta, S},
title = {Comparative metagenomic analysis of diarrheal and non-diarrheal gut microbiome delineating the identification of prospective prognostic markers and probiotics to protect from diarrhea: a brief report.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1729497},
pmid = {41987902},
issn = {2235-2988},
mesh = {*Diarrhea/microbiology/prevention & control ; *Gastrointestinal Microbiome/genetics ; Humans ; RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; Cross-Sectional Studies ; *Probiotics/therapeutic use ; Feces/microbiology ; Pilot Projects ; Female ; Prognosis ; Male ; High-Throughput Nucleotide Sequencing ; Adult ; *Bacteria/classification/genetics/isolation & purification ; Middle Aged ; Prospective Studies ; Biomarkers/analysis ; DNA, Bacterial/genetics ; },
abstract = {INTRODUCTION: Diarrhea is a leading contributor of mortality globally. To mitigate its disease burden, improved prognosis and alternative therapeutic approaches must be deployed. A cross-sectional gut microbiome analysis of 23 non-diarrheal and 5 diarrheal fecal samples was conducted with the aim of meeting the WHO's GAPPD (Global Action Plan for Pneumonia and Diarrhea) goals.

HYPOTHESIS: Next-generation sequencing is a potent tool being increasingly used for epidemiological surveillance. It can help in the comparison of the structural diversity of the gut microbiome between diarrheal and non-diarrheal samples, thereby aiding in the identification of prospective prognostic and therapeutic candidates.

AIM: The pilot study was designed to identify prospective taxa that were comparatively enriched in non-diarrheal samples and to predict gut microbial community interactions.

METHODOLOGY: 16S rRNA amplicon sequencing and subsequent analysis were undertaken for taxonomic profiling and abundance interpretation of OTUs.

RESULTS: Significant differences between the two groups with respect to structural composition was revealed. Firmicutes was the most abundant phylum in the majority of the samples. The B/F ratio was consistently <1 in all diarrheal samples. A significant difference in the mean B/F ratio of the two groups was found. Proteobacteria was significantly more abundant in the diarrheal group. On the other hand, Prevotellaceae was the most abundant family in non-diarrheal samples and was suppressed significantly in diarrheal samples. Streptococcaceae was the most abundant family in 60% of diarrheal samples; where Streptococcaceae was suppressed, Bacteroideaceae and Nocardiaceae were the most abundant. In non-diarrheal samples, where Streptococcaceae was almost completely suppressed, Bifidobacteriaceae was the most abundant and significantly suppressed other families. A negative correlation was observed between Prevotellaceae and Bacteroideaceae in the non-diarrheal group. Prevotella copri was the most abundant species in 70% of non-diarrheal samples and was significantly suppressed in diarrheal samples. Proteus mirabilis was identified in all the non-diarrheal samples, while they were absent in diarrheal samples.

CONCLUSION: The OTUs associated with diarrheal dysbiosis can serve as prognostic markers. To our knowledge, this is the first report on the comparative analysis of diarrheal and non-diarrheal microbiome, distinctly addressing the gut microbiome dysbiosis from the context that can lead to the development of prognostic markers and probiotics to protect the endemic population from diarrhea and help in achieving Sustainable Development Goals 2 and 3.},
}

*Diarrhea/microbiology/prevention & control
*Gastrointestinal Microbiome/genetics
Humans
RNA, Ribosomal, 16S/genetics
*Metagenomics/methods
Cross-Sectional Studies
*Probiotics/therapeutic use
Feces/microbiology
Pilot Projects
Female
Prognosis
Male
High-Throughput Nucleotide Sequencing
Adult
*Bacteria/classification/genetics/isolation & purification
Middle Aged
Prospective Studies
Biomarkers/analysis
DNA, Bacterial/genetics

@article {pmid41988145,
year = {2026},
author = {Liu, L and Wang, L and Zhang, P and Gan, M and Liujiang, R and Cheng, G and Ge, M},
title = {Neonatal herpes simplex virus encephalitis: a single-center retrospective study of 14 cases.},
journal = {Frontiers in pediatrics},
volume = {14},
number = {},
pages = {1740937},
pmid = {41988145},
issn = {2296-2360},
abstract = {BACKGROUND: This single-center retrospective study aims to analyze the clinical characteristics, treatment strategies, and outcome at discharge of neonatal-onset herpes simplex virus encephalitis (NHSE).

METHODS: We conducted a single-center retrospective case review of infants diagnosed with NHSE at the Children's Hospital of Fudan University between February 1, 2016, and February 1, 2024. Clinical data, including demographics, clinical symptoms, laboratory findings, neuroimaging results, treatment regimens, and outcomes at discharge, were collected and analyzed.

RESULTS: A total of 14 infants with NHSE (7 males, 7 females) were identified at our center, with a median age at diagnosis of 26 days (range: 7-51 days). Initial symptoms predominantly included fever and seizures, with neurological involvement (e.g., seizures, lethargy, irritability or altered mental states) in 13 cases. Physical examinations, such as bulging anterior fontanel, were noted. Herpes simplex virus (HSV)-DNA was detected in 13 cases (6 HSV-1, 7 HSV-2) through cerebrospinal fluid (CSF) polymerase chain reaction (PCR) or metagenomic testing. Among these, 9 cases were identified via CSF-PCR, with 7 testing positive on the initial examination and 2 on repeated testing. Notably, 6 cases were diagnosed using metagenomic next-generation sequencing (mNGS), all of which yielded positive results on the first test. Ten out of the 12 children often exhibited temporal lobe spikes on video electroencephalograms (VEEGs). Early magnetic resonance imaging (MRI) revealed cytotoxic edema, progressing to multicystic encephalomalacia. All received acyclovir antiviral treatment. Seven discontinued treatments, one was referred for ocular lesions, and six improved and were discharged.

CONCLUSIONS: In this single-center cohort, NHSE often presents with nonspecific fever and seizures, with late onset and absent indicative rashes, complicating early diagnosis. For newborns suspected of having NHSE, early CSF HSV-DNA testing and prompt antiviral treatment are essential to improve outcomes. Metagenomic sequencing is especially valuable for accurate, rapid diagnosis when conventional methods fail.},
}

@article {pmid41989131,
year = {2026},
author = {Schön, ME and Schvarcz, CR and Malkewitz, SV and Hinner, FC and Koslová, A and Mersdorf, U and Schimm, F and Rickert, S and Pozhydaieva, N and McBeain, K and Hackl, T and Schneider, AC and Barenhoff, K and Höfer, K and Edwards, KF and Steward, GF and Fischer, MG},
title = {Strain-level diversity of giant viruses infecting chlorarachniophyte algae in the subtropical North Pacific.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag093},
pmid = {41989131},
issn = {1751-7370},
abstract = {Giant DNA viruses are ubiquitous among unicellular eukaryotes and occur in marine, freshwater, and terrestrial environments. Despite intense metagenomic data mining, their strain-level diversity remains largely unexplored. Here we introduce a model system comprising four isolates of a giant virus called ChlorV, which infects marine microalgae of the class Chlorarachniophyceae (Rhizaria) from station ALOHA, Hawai'i. The ChlorV genomes are 469 kbp to 493 kbp long and encode approximately 400 proteins, at least 106 of which are present in purified virions. Although the four viral genomes are highly syntenic, they differ by several insertions and deletions that often encode methyltransferases. We found that some of these methyltransferase genes correlated with specific DNA methylation patterns in the same ChlorV strain. Our study describes the first giant viruses infecting the eukaryotic supergroup Rhizaria and demonstrates how viral strain-level variation in gene content and epigenetic features may affect eco-evolutionary processes in marine microalgae.},
}

@article {pmid41989380,
year = {2026},
author = {Hontelez, S and Guthrie, M and Stobernack, T and van Baarlen, P and Rousseau, C and Boks, MP and Pereira, RR and Boekhorst, J and Kleerebezem, M},
title = {Microbiome signatures correlate with diet-mediated ADHD symptom reduction.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2659400},
doi = {10.1080/19490976.2026.2659400},
pmid = {41989380},
issn = {1949-0984},
mesh = {Humans ; *Attention Deficit Disorder with Hyperactivity/diet therapy/microbiology ; Child ; Male ; *Gastrointestinal Microbiome ; Female ; Feces/microbiology ; *Diet ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {Attention-deficit hyperactivity disorder (ADHD) is one of the most common childhood neuropsychiatric conditions. Both (epi)genetic and environmental factors are suggested to contribute to the etiology of ADHD. In the last decade, nutrition has received considerable attention as a potential environmental factor triggering ADHD behavior, particularly applying a few-foods diet (FFD) has been shown to elicit considerable behavioral improvements. These studies are observational rather than investigating underlying molecular mechanisms. The present study included 79 children (boys aged 8-10) with ADHD following a progressive, i.e., increasingly restrictive, FFD diet for 5 weeks. Minimally invasive samples (feces, urine, blood, and buccal swabs) were collected before and after the intervention to obtain a multi-omics perspective of the dietary responses in the participating children. For 63% of the participating children, a more than 40% behavior score improvement was observed, with an average improvement of 73%. The strength of diet-induced changes in ADHD symptoms among children was significantly associated with the gut microbiome composition, particularly when analyzing species-stratified abundance profiles of previously characterized gut-brain modules in the fecal metagenomic data. While integrative multi-omics analysis did not identify composite signatures linked to symptom changes, the strongest multi-omics signal confirmed compliance with the dietary intervention. Our findings implicate a role of the gut microbiome and its metabolic capacity to communicate with the central nervous system in children with food-associated ADHD.},
}

Humans
*Attention Deficit Disorder with Hyperactivity/diet therapy/microbiology
Child
Male
*Gastrointestinal Microbiome
Female
Feces/microbiology
*Diet
Bacteria/classification/genetics/isolation & purification

@article {pmid41989870,
year = {2026},
author = {Zhu, YC and Deng, Y and Zeng, JQ},
title = {Effects of concurrent Helicobacter pylori infection and small intestinal bacterial overgrowth on the gut microbiota and metabolic profiles: A multi-omics study.},
journal = {Acta microbiologica et immunologica Hungarica},
volume = {},
number = {},
pages = {},
doi = {10.1556/030.2026.02894},
pmid = {41989870},
issn = {1588-2640},
abstract = {This study investigated the synergistic effects of Helicobacter pylori (Hp) infection and small intestinal bacterial overgrowth (SIBO) on the gut microbiota structure and metabolic profiles and elucidate the underlying pathophysiological mechanisms. Forty-two patients with gastrointestinal symptoms were recruited and assigned to group A (Hp+ SIBO+), B (Hp+ SIBO-), C (Hp- SIBO+), or D (Hp- SIBO-) based on their Hp infection and SIBO status. Fecal samples were collected for metagenomic sequencing and untargeted metabolomic analysis. The associations between microbiota and metabolites were evaluated using alpha/beta diversity analysis, differential species screening, metabolite identification, and Procrustes/Spearman correlation analysis. Neither Hp infection nor SIBO significantly altered the alpha or beta diversity of the gut microbiota (both P > 0.05). However, specific shifts in microbial abundance were observed. Specifically, the abundance of short-chain fatty acid-producing bacteria such as Megamonas was significantly decreased in the SIBO+ groups. Metabolomic analysis revealed significant enrichment of inflammatory metabolites (e.g., prostaglandin derivatives) in group A, disordered bile acid conjugates (e.g., chenodeoxycholylisoleucine) and nucleotide metabolism in SIBO+ groups, and abnormal lipid/carbohydrate metabolism pathways in Hp+ groups. Multi-omics integration analysis indicated a strong coupling between the microbial structure and metabolic profiles (Procrustes analysis, P < 0.05). In group A, the abundance of Faecalibacterium and Hominenteromicrobium was negatively correlated with bile acid levels, suggesting impaired bile acid transformation. Hp infection and SIBO might synergistically exacerbate gut ecological and metabolic disorders by reshaping specific microbiota and metabolic networks (enhanced inflammatory response, disrupted bile acid circulation). Their co-occurrence produces additive effects, which could explain the aggravated clinical symptoms. This study provides a theoretical basis for interventions targeting microbiota-metabolite interactions, such as probiotics and bile acid modulators.},
}

@article {pmid41990029,
year = {2026},
author = {Sun, Y and Zhang, M and Wang, X and Huang, X and Yu, Y and Pan, H and Li, H and Shi, L and Yang, W and Zhang, C and Ding, B and Liu, X and Li, J and Qian, C and Cheng, B and Zhang, C and Ran, J and Li, M},
title = {Gut Microbiota of Gray Snub-Nosed Monkeys: Adaptation to Seasonal Variations Through Energy Compensation and Thermogenesis.},
journal = {Integrative zoology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1749-4877.70092},
pmid = {41990029},
issn = {1749-4877},
support = {32330015//National Natural Science Foundation of China/ ; 32070404//National Natural Science Foundation of China/ ; QLKH [2023] 11//Guizhou Forestry Administration Scientific Research Project/ ; QLKH [2025] 11//Guizhou Forestry Administration Scientific Research Project/ ; //Investigation of Nationally Protected Wildlife Species in Tongren Region/ ; GZKPC-2025-01//Guizhou Province/ ; QCZH [2023]82//Protection and Restoration of Forests and Grasslands in 2024 from the Central Finance/ ; [2023]188//Guizhou Science and Technology Support Plan Project/ ; QKHFQ [2023]009//Construction of Capacity for Ecosystem Optimization and Innovation in Key Ecological Zones of Guizhou Province/ ; YWZ[2024]005//Construction of Capacity for Ecosystem Optimization and Innovation in Key Ecological Zones of Guizhou Province/ ; QKHPT[2021]5625//Guizhou Outstanding Young Scientist Program/ ; QJJ[2024]337//Natural Science Research Projects of the Education Department of Guizhou Province/ ; [2022]031//Guizhou Provincial Department of Education/ ; 2024BS011//Doctoral Program of the Science Research Foundation of Guizhou Education University/ ; 2024BS006//Doctoral Program of the Science Research Foundation of Guizhou Education University/ ; },
abstract = {As an extremely endangered species, the gray snub-nosed monkey (Rhinopithecus brelichi) relies on its gut microbiota for adaptation to environmental changes, particularly in coping with fluctuations in energy and nutrient availability. In this study, we employed metagenomic, metatranscriptomic, and widely targeted metabolomic analyses to characterize the gut microbiota of gray snub-nosed monkeys. Based on metagenome-assembled genomes (MAGs), we recovered 1229 non-redundant MAGs. Among them, a total of 103 MAGs exhibited significant seasonal variation, primarily belonging to the phyla Bacillota_A, Bacteroidota, and Bacillota_I. During winter, metagenomic results indicated that the gut microbiota exhibited an enhanced capacity to produce energy substrates such as amino acids, short-chain fatty acids, pyruvate, and acetyl-CoA, with increased conversion of these substrates. Metatranscriptomic analysis further confirmed that key carbon cycle-related genes and metabolic pathways were significantly upregulated in winter. Additionally, metabolite analysis indicated significantly lower levels of amino acids in winter fecal samples, suggesting that gray snub-nosed monkeys efficiently absorb and utilize metabolites, with the gut microbiota likely contributing to energy compensation. Notably, the gut microbiota may also synergistically support the host's non-shivering thermogenesis, helping maintain physiological functions in extreme cold conditions. This study elucidates the cooperative role of the gut microbiota in helping gray snub-nosed monkeys adapt to seasonal environmental fluctuations, providing new insights into how gut microbiota optimize winter energy utilization-an understanding with important implications for the conservation of endangered wildlife.},
}

@article {pmid41990134,
year = {2026},
author = {Chen, X and Wang, Y and Feng, J and Chen, H and Yao, B and Li, F and Yang, Q and Qu, J},
title = {Hypobaric hypoxia affects gut microbiota of rats through affected community assembly, reduced network resilience, and metabolic reprogramming.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiag039},
pmid = {41990134},
issn = {1574-6941},
abstract = {In host-microbe interactions, host diet and environmental stress are key driving factors shaping the gut microbiota. Although previous studies have shown that hypoxia affects the structure and function of the gut microbiota in rodents, most have relied on 16S rRNA gene sequencing and lacked analysis of community assembly mechanisms, co-occurrence networks, and functional pathways. Here, we used metagenomic next-generation sequencing (mNGS) to examine the gut microbiota of rats exposed to hypobaric hypoxia (WH, simulated 6000 m altitude) compared to WL group (2100 m altitude). Hypoxia significantly altered β-diversity of gut microbiota, but did not affect its α-diversity. Community assembly was primarily governed by stochastic processes, with hypoxia stress reducing their impact. Microbial co-occurrence networks were dominated by positive correlations, although network resilience and stability declined under hypoxia. Helicobacter and Eubacterium were identified as high-abundance differentiating genera, and Akkermansia muciniphila was significantly enriched in WH group. Functional analysis revealed alterations in pathways related to protein synthesis and carbohydrate metabolism, suggesting that hypoxia may affect nutrient utilization by the host. Overall, these findings provide a comprehensive view of how hypoxic stress reshapes the gut microbiota of rats, offering new insights into microbial dynamics under environmental stress.},
}

@article {pmid41990403,
year = {2026},
author = {Zhao, J and Li, T and Huang, H and Servellita, V and Sotomayor-Gonzalez, A and Yakovleva, O and Wang, X and Ragupathy, V and Biswas, S and Barilko, P and Sun, E and Huynh, S and Hunsicker, M and DeQuach, J and Morales, JD and Highbarger, H and Dewar, RL and Porth, C and Denny, TN and McGivern, DR and Chiu, CY and Hewlett, I},
title = {Development and genomic characterization of a diverse HIV-1 variant reference panel for nucleic acid-based testing.},
journal = {Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology},
volume = {184},
number = {},
pages = {105941},
doi = {10.1016/j.jcv.2026.105941},
pmid = {41990403},
issn = {1873-5967},
abstract = {BACKGROUND: The high worldwide genetic diversity of HIV poses significant challenges for its detection and diagnosis by nucleic acid testing (NAT). Well-characterized reference panels are important for evaluating the analytical performance of HIV tests.

OBJECTIVE: To develop a reference panel for HIV NAT that reflects the genetic diversity of circulating strains.

STUDY DESIGN: HIV was cultured from blood specimens collected from blood donor and clinical sites in Cameroon. Metagenomic next-generation sequencing in combination with spiked primer enrichment along with Sanger sequencing were used to sequence 101 cultured HIV-1 samples representing 59 strains. To establish an HIV-1 variant reference panel, a diverse subset of cultured viruses was analyzed in multiple laboratories with different assays to determine consensus viral loads.

RESULTS: Near full-length HIV-1 genomes, with an average of 9589 base pairs (bp), were recovered from 37 (62.7%) of the 59 strains. The whole genome sequences of 28 strains exhibited more than 95% similarity to our previously reported genomes obtained by Sanger sequencing. An HIV variant reference panel for NAT comprising 18 diverse HIV-1 strains was developed. The panel included four subtypes, four circulating recombinant forms, and eight unique recombinant forms. Strains were prepared at low (n = 18, 2.53 log10 copies/mL), medium (n = 18, 3.61 log10 copies/mL), and high viral loads (n = 15, 4.66 log10 copies/mL), yielding 51 panel members in total.

CONCLUSION: This diverse HIV reference panel can be used to evaluate the performance of HIV NAT and is available upon request to developers and manufacturers of HIV tests.},
}

@article {pmid41990622,
year = {2026},
author = {Liu, L and Wang, C and Qi, WK and Zhang, SJ and Li, YY and Peng, Y},
title = {Mechanisms of aerobic simultaneous nitrogen removal under low COD/N conditions: Diffusion-reaction coupling and particle size effects via self-recirculating microgranular system.},
journal = {Water research},
volume = {300},
number = {},
pages = {125937},
doi = {10.1016/j.watres.2026.125937},
pmid = {41990622},
issn = {1879-2448},
abstract = {Nitrogen removal from ammonium-rich, carbon-limited wastewater remains constrained in continuous-flow microgranular sludge systems. In this study, a three-stage up-flow self-recirculating microgranular sludge reactor was developed to investigate nitrogen removal mechanisms under low chemical oxygen demand to nitrogen ratios (COD/N < 2.5) and high influent total nitrogen (TN > 400 mg/L). During long-term operation, the system achieved stable removal efficiencies of ammonium (98%), TN (94%), and COD (95%). Under ammonium stress, particle size decreased to a mean diameter of 249.2 μm, forming stable, non-flocculent microaggregates. Microgranules < 0.2 mm exhibited pronounced simultaneous partial nitrification-denitrification (SPND) and simultaneous nitrification-denitrification (SND) activities under aerobic conditions. Simultaneous nitrogen removal (SNR) activity peaked at 0.52 g TN/(g VSS·d) at a DO of 2 mg/L. In contrast, microgranules > 0.2 mm primarily followed SND-dominated pathways. Their SNR activity increased with DO and reached a maximum of 0.46 g TN/(g VSS·d). Microbial community and metagenomic analyses revealed a redox-stratified functional structural organization. Rubrivivax (11.5%) dominated the surface layer, likely linking organic matter degradation with nitrogen oxide reduction. Hyphomicrobium (11.9%) was enriched in intermediate layers and was associated with SND. In the core, the co-enrichment of Hyphomicrobium (7.2%) and Methylotenera (6.1%) supported the coupling of SND and SPND processes. These findings provide a basis for improving nitrogen removal from ammonium-rich, carbon-limited wastewater.},
}

@article {pmid41990624,
year = {2026},
author = {Wang, G and Yang, F and Xu, S and Lin, D and Yang, R and Yan, P and Chen, Y and Fang, F and Guo, J},
title = {Microbial niches and metabolism drive spatial heterogeneity of hydroxyapatite precipitation in aerobic granular sludge.},
journal = {Water research},
volume = {300},
number = {},
pages = {125923},
doi = {10.1016/j.watres.2026.125923},
pmid = {41990624},
issn = {1879-2448},
abstract = {Biologically induced phosphate precipitation (BIPP) in aerobic granular sludge (AGS) provides a promising approach to address phosphorus removal instability and granule structural fragility in practical applications. However, the roles of microbial communities, ecological niches, and metabolic activities in driving phosphate precipitation and shaping its spatial distribution within AGS remain underexplored. This study systematically investigates AGS physicochemical properties, reactor performance, phosphorus speciation, precipitation composition and distribution, microbial community structure, and metabolic activity using sodium propionate (RP) and sodium acetate (RA) as sole carbon sources. The findings reveal for the first time the mechanisms by which microbial communities, ecological niches, and metabolic functions regulate phosphate precipitation and determine its spatial heterogeneity. BIPP contributes 22.6% and 60.1% of total phosphorus removal in RP and RA, respectively, thereby enhancing phosphorus removal efficiency and granule structural stability. Multi-scale analyses-including Standards, Measurements and Testing, Raman spectroscopy, X-ray diffraction, scanning electron microscopy-energy dispersive X-ray spectroscopy, and micro-computed tomography-reveal that hydroxyapatite (HAP) predominantly accumulates in the outer region of RP granules but in the inner region of RA granules. Periodic water quality variations, fluorescence in situ hybridization, granule-stratified sequencing, and metagenomic analyses indicate that the spatial heterogeneity of HAP is driven by the ecological niche separation and metabolic activities of polyphosphate-accumulating organisms (PAOs) and glycogen-accumulating organisms (GAOs). In RP granules, PAO‑driven anaerobic phosphate release creates a high‑phosphate microenvironment, which promotes HAP formation in the granule outer region. In RA, GAO‑mediated endogenous denitrification increases local pH, thereby inducing HAP precipitation in the granule interior. Overall, this study elucidates the mechanisms underlying the spatial heterogeneity of phosphate precipitation in AGS from the perspectives of microbial community structure, ecological niches, and metabolic pathways. These findings provide guidance for optimizing AGS systems to achieve efficient phosphorus removal and stable operation.},
}

@article {pmid41990657,
year = {2026},
author = {Ye, YQ and Lin, D and Shen, LQ and Wu, D and Li, Y and Wang, YF and Zhu, D},
title = {Viral communities as mirrors and vectors: Tracing antibiotic resistome distribution and dissemination across diverse habitats in Macao.},
journal = {Journal of hazardous materials},
volume = {509},
number = {},
pages = {142056},
doi = {10.1016/j.jhazmat.2026.142056},
pmid = {41990657},
issn = {1873-3336},
abstract = {Virus-mediated transmission of antibiotic resistance genes (ARGs) is increasingly recognized as a significant threat to global human health. However, the role of viral communities in ARGs dissemination across highly urbanized coastal regions containing with diverse habitats remains poorly understood. Here, we conducted shotgun metagenomic analyses on 49 samples collected from four habitats (urban sewage, soil, sediment, and coastal water) in Macao China, to characterize their viral communities and resistome profiles. We identified 23,579 viral operational taxonomic units (vOTUs) and 965 ARGs subtypes across these habitats. Viral community composition and total ARGs profiles exhibited system-scale spatial concordance, with a distance-decay trend, together with a positive association between viral ARGs and total ARGs abundance. Approximately 62.80% of ARGs subtypes were shared among habitats, suggesting a high degree of compositional overlap in resistome profiles among habitats. Urban sewage and coastal waters showed enriched viral abundance and ARGs diversity, with high-risk ARGs in sewage being 10.3- and 24.7-fold greater than in soils and sediments. High-risk ARGs (e.g., macB, udg) showed co-occurrence with virulence factor genes (VFGs) on viral contigs, and prophages were identified within Pseudomonadota and Bacteroidota, the dominant groups for phages and ARGs. The co-occurrence of ARGs and auxiliary metabolic genes (AMGs) within these hosts suggests that phages may facilitate the propagation of ARGs while enhancing host adaptability, thereby promoting their enrichment. By integrating multi-habitat analyses in human-impacted coastal regions, this study highlights the potential role of viruses in ARGs dissemination and informs resistome surveillance.},
}

@article {pmid41991090,
year = {2026},
author = {Lee, JS and Jeon, YJ and Kim, TH and Khan, W and Yun, YM},
title = {Multiscale destabilization of anaerobic digestion by chloramphenicol: Divergence between methanogen detectability and methane recovery.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134635},
doi = {10.1016/j.biortech.2026.134635},
pmid = {41991090},
issn = {1873-2976},
abstract = {Antibiotic residues in livestock waste streams can affect anaerobic digestion (AD), yet their functional impact on microbial viability and metabolic pathways remains unclear. This study evaluated concentration-dependent effects of chloramphenicol (CAP) by integrating process kinetics, cellular integrity, dissolved-phase responses, and functional gene profiles. Methane yield was maintained at ≤ 50 mg/L CAP but declined sharply at higher concentrations, reaching near-complete inhibition at 1,000 mg/L. Estimated inhibition thresholds were derived as IC30 = 285 mg/L, IC60 = 535 mg/L, and IC90 = 852 mg/L from the fitted concentration-response relationship. Severe inhibition coincided with residual organic acid accumulation, pH decline, and enrichment of propionate and butyrate fractions with undetectable acetate. Flow cytometry revealed a marked CAP-dependent decline in intact biomass, with live-cell (P2) counts decreasing from 4.8 × 10[6] cells/mL in the control to 1.0 × 10[5] cells/mL at 1,000 mg/L, accompanied by increased forward- (FSC-A) and side-scatter (SSC-A) area indicative of structural stress. Fluorescence excitation-emission matrix (FEEM) analysis showed concentration-dependent enrichment of soluble microbial products (SMPs) fluorescence, and inoculum-only incubation confirmed biomass-associated solubilization under CAP exposure. Although methanogens remained numerically detectable (76.0% vs. 81.1%), key genes related to cofactor synthesis and electron transfer (comD, frhB, fwdA/fwdC, mcr) declined substantially at 1,000 mg/L. These convergent signals were consistent with multiscale destabilization. Given that microbial activity was not directly measured, the observed discrepancy between methanogen detectability and methane recovery should be interpreted as indicative of a potential functional imbalance rather than definitive evidence of functional decoupling.},
}

@article {pmid41991504,
year = {2026},
author = {Elhani, I and Bredon, M and Enea, D and Desmons, A and Arrive, L and Bazille, C and Lefevre, A and Aouba, A and Bigot, A and de Moreuil, C and Alonso, I and Blasco, H and Creusot, L and Dupuy, C and Emond, P and Krasniqi, P and Lamaziere, A and Oeuvray, C and Rainteau, D and Svrcek, M and Rolhion, N and Sokol, H and Georgin-Lavialle, S},
title = {Functional changes in the gut microbiota are associated with the intestinal phenotype in A20 haploinsufficiency.},
journal = {Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology},
volume = {37},
number = {4},
pages = {e70343},
doi = {10.1111/pai.70343},
pmid = {41991504},
issn = {1399-3038},
support = {//snfmi-remi/ ; //fai2r/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Haploinsufficiency ; Female ; Male ; *Tumor Necrosis Factor alpha-Induced Protein 3/genetics ; Child ; Phenotype ; Feces/microbiology ; Adolescent ; *Inflammatory Bowel Diseases/genetics ; Child, Preschool ; Bile Acids and Salts/metabolism ; },
abstract = {BACKGROUND: A20 haploinsufficiency (HA20) is an autoinflammatory disease driven by pathogenic variants in TNFAIP3, which plays a crucial role in regulating immune responses. The clinical manifestations of HA20 resemble those of inflammatory bowel disease (IBD), with prominent gastrointestinal (GI) involvement. Given the well-established association between gut microbiota alterations and IBD, this study aimed to describe the GI involvement of HA20 patients and to investigate their fecal microbiota using shotgun sequencing and metabolomics.

METHODS: This study included 16 HA20 patients and 22 healthy age and sex-matched controls. GI clinical phenotype, liver imaging, and liver and GI tissue histology were assessed. Shotgun metagenomic sequencing was performed on fecal DNA. Fecal metabolomic profiling of bile acids, short-chain fatty acids (SCFAs), and tryptophan metabolites was performed.

RESULTS: Liver imaging revealed chronic liver disease in 3/5 patients, showing as liver dysmorphia and portal hypertension. Histological analysis showed lymphoplasmocytic infiltrate of the GI tract and the liver. The fecal microbiota of HA20 patients was characterized by marked alterations, including a reduction in microbial diversity and an increase in the pro-inflammatory bacterium Ruminococcus gnavus. Microbial bile acid deconjugation and desulfation were impaired. Additionally, tryptophan metabolism was altered, with a shift towards the kynurenine pathway.

CONCLUSION: Our results show that HA20 is associated with gut microbiota alterations and significant disruptions in metabolic pathways, particularly involving bile acids. These alterations could contribute to the chronic inflammation observed in HA20. These findings highlight the role of the gut-liver axis and of mucosal barrier dysfunction in HA20.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Haploinsufficiency
Female
Male
*Tumor Necrosis Factor alpha-Induced Protein 3/genetics
Child
Phenotype
Feces/microbiology
Adolescent
*Inflammatory Bowel Diseases/genetics
Child, Preschool
Bile Acids and Salts/metabolism

@article {pmid41991911,
year = {2026},
author = {Liu, Y and Huang, P and Zhang, C and Dong, Q and Wang, X and Tian, F and Zhao, J and Sun, Z and Chen, L and Chen, W and Zhai, Q},
title = {A microbiome catalog of Chinese traditional artisanal cheeses provides insights into functional and microbial diversity.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-71929-4},
pmid = {41991911},
issn = {2041-1723},
support = {32425044//China National Funds for Distinguished Young Scientists/ ; 2022YFD2100703//Ministry of Science and Technology of the People's Republic of China (Chinese Ministry of Science and Technology)/ ; },
abstract = {Cheese has been consumed globally over millennia and serves as a natural reservoir of diverse microorganisms. Chinese traditional cheeses rely on natural fermentation and have unique physiochemical and microbial characteristics compared to European cheeses. However, there is a major knowledge gap in the understanding of Chinese cheese microbiome. Here, we present a curated Cheese microbiome catalog (cCMC) consisting of 3327 high-quality metagenome-assembled genomes, recovered from metagenomic sequencing of 235 Chinese cheese samples covering all traditional artisanal cheese-producing regions in China, together with 198 publicly available non-Chinese cheese metagenomic datasets. This catalog represents 395 nonredundant species spanning 50 families, including 85 putative novel species. We identified six lactic acid bacteria species enriched in Chinese cheeses, and confirmed that the unique presence of Acetobacteraceae contributes to improving the nutritional quality of Chinese cheese. A total of 8851 biosynthetic gene clusters were detected from cCMC, with over 57% classified as novel. We demonstrated that SNP-level variations among different Lactobacillus helveticus strains are associated with differences in β-galactosidase thermostability. Using the cCMC database, we developed a synthetic microbial community as the starter culture for Qula, a yak milk-based Chinese cheese produced by the Tibetans. Overall, the cCMC provides a comprehensive resource of cheese to enable future attempts on large-scale industrial production of naturally fermented cheeses with distinctive ethnic features.},
}

@article {pmid41965542,
year = {2026},
author = {Priya, S and Sridhar, SB and Shareef, J and Wadhwa, T and Balusamy, B and Meenakshi, DU and Sundram, S and Malviya, R},
title = {Epidemiology, diagnosis and emerging therapies for Lyme disease of the Northern Hemisphere.},
journal = {International journal of emergency medicine},
volume = {19},
number = {1},
pages = {},
pmid = {41965542},
issn = {1865-1372},
abstract = {BACKGROUND: Lyme disease is the most widespread tick-borne infection in the Northern Hemisphere and is challenging to diagnose and treat due to its changing clinical presentation, antigenic variation, tissue tropism, and the expanding distribution of vectors. This review includes ecology, pathogenesis, diagnostics, treatment, post-treatment, prevention, and novel translational approaches.

METHODS: A literature review was conducted to include literature published between January 2000 and March 2026 in PubMed/MEDLINE, Scopus, and Web of Science, with landmark studies used where applicable. Original research, clinical trials, systematic reviews, and major public health reports were prioritised.

RESULTS: Two-tier serology is the most common diagnostic technique, but it has limited sensitivity in early infection and does not distinguish between active and past infection. Culture and PCR are only useful in a few instances. The use of new technologies such as multiomics biomarkers, metagenomics, T-cell assays, and AI-enhanced diagnostics is promising but has not yet been tested in a prospective multicentre study. Most of the early and disseminated disease can be treated with standard antibiotics, whereas the long-term therapy of PTLD is not justified and can cause more adverse effects. These preventive and curative advancements involve VLA15 vaccination, anti-tick and reservoir-specific approaches, microbiome-engineered vectors, and anti-persister/ biofilm.

CONCLUSION: Lyme disease requires combined prevention, improved diagnostics, enhanced biomarker research, and well-designed PTLD trials. The short-term benefits will be based on the optimisation of existing diagnostics and vector control, and the long-term benefits will be based on rigorous validation of vaccines, biomarkers, and specific therapies.},
}

@article {pmid41973308,
year = {2026},
author = {Aydin, F and Çek, Ş},
title = {Mineral-microbiota interactions in aquaculture: implications for fish gut health and nutrition.},
journal = {Veterinary research communications},
volume = {50},
number = {4},
pages = {},
pmid = {41973308},
issn = {1573-7446},
abstract = {Dietary minerals and gut microbiota engage in a dynamic, bidirectional relationship that shapes the health, immune competence, and productive performance of farmed fish and shrimp. This review explores the bidirectional interactions between mineral supplementation and microbial communities within the gastrointestinal tract of farmed fish and examines the effects of individual and combined mineral supplementation including iron, zinc, magnesium, selenium, manganese, and copper in inorganic, organic, and nanoparticle forms on the intestinal microbiota and histomorphology of farmed aquatic species. Minerals serve essential physiological roles while simultaneously modulating microbial diversity, composition, and metabolic activity; conversely, the gut microbiota influences mineral bioavailability and absorption through enzymatic transformations and competitive uptake. Studies conducted on yellow catfish, largemouth bass, golden pompano, grouper, Nile tilapia, Chinese tongue sole, Pacific white shrimp, channel catfish, zebrafish, and Oriental river prawn were comprehensively examined. Findings indicate that organic and nanoparticle mineral forms generally exhibit higher bioavailability and more favorable effects on intestinal health compared to conventional inorganic sources, with partial substitution strategies (e.g., ~ 50% organic mineral replacement) yielding optimal outcomes in combined formulations. Optimized mineral supplementation was further associated with enrichment of beneficial microbiota, enhanced mucosal barrier integrity through goblet cell proliferation, and reinforcement of innate immune responses, collectively supporting nutrient assimilation, growth performance, and disease resistance. However, the reviewed studies share critical limitations: species diversity was narrow, experimental durations were short (8–80 days), no trial encompassed a full reproductive cycle, and the mechanisms underlying mineral–microbiota crosstalk remain incompletely understood. Synergistic or antagonistic interactions among Zn, Cu, Mn, Fe, and Se are inadequately characterized, and dose optimization specific to species, age, and physiological status has not been achieved. Future research should incorporate long-term and multigenerational designs, metagenomic and metabolomic analyses, comparative multi-mineral trials, and the integration of microbiome-based diagnostics to tailor mineral interventions, alongside validation under commercial aquaculture conditions and ecotoxicological assessment of nanoparticles in aquatic environments.},
}

@article {pmid41981860,
year = {2026},
author = {Liu, B and Yang, J and Wang, J and Zhang, J and Wang, L and Qu, B and Guo, L and Zhang, X and Yang, X and Jiang, Y},
title = {Application of Whole-Genome Sequencing and Metagenomic Sequencing in Microbial Analysis of Milk Powder and Its Processing Environment: Current Findings and Challenges.},
journal = {Comprehensive reviews in food science and food safety},
volume = {25},
number = {3},
pages = {e70478},
doi = {10.1111/1541-4337.70478},
pmid = {41981860},
issn = {1541-4337},
support = {//Danone Asia-Pacific Management Co. Ltd./ ; },
mesh = {*Whole Genome Sequencing ; *Milk/microbiology ; Animals ; *Metagenomics ; *Food Microbiology ; Food Handling ; Powders ; Food Contamination/analysis ; },
abstract = {As dairy enterprises increasingly focus on microbial contamination, traditional detection technologies are gradually showing limitations in terms of detection capability, accurate source tracking, and rapid response, especially when dealing with microbial communities in complex processing environments. Fortunately, whole-genome sequencing (WGS) and metagenomic sequencing provide innovative alternative solutions. These technologies significantly improve the detection of harmful microbes by offering strain-level resolution, detecting low-abundance organisms, and uncovering previously undetectable microbes. This review discusses the application of WGS and metagenomic sequencing in microbial monitoring, contamination source tracking, and quality control across the entire milk powder production chain. In particular, it highlights the progress made in microbial typing and source tracking, as well as in the detection of antibiotic resistance genes (ARGs) and virulence factor genes (VFGs). This review also compares microbial control standards for milk powder and its processing environment across different countries and international organizations, providing a regulatory perspective. Furthermore, the integration of emerging technologies is also discussed, particularly machine learning (ML) and deep learning (DL). Artificial intelligence (AI) enables more efficient, predictive, and accurate microbial monitoring, improving contamination control and contributing to safer and higher-quality milk powder production processes. This review provides critical insights that contribute to improving microbial safety management and control strategies in milk powder production.},
}

*Whole Genome Sequencing
*Milk/microbiology
Animals
*Metagenomics
*Food Microbiology
Food Handling
Powders
Food Contamination/analysis

@article {pmid41982876,
year = {2026},
author = {Ren, J and Lan, Z and Wang, C and Zhu, J and Li, M and Xu, J and Lu, Y and Tu, J and Zhang, X and Boskovic, L and Huang, J and Hu, X},
title = {Metagenomic next-generation sequencing and conventional microbiology for microbial profiling in biliary tract infections: a comparative study with clinical stratification.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1799474},
pmid = {41982876},
issn = {1664-302X},
}

@article {pmid41982885,
year = {2026},
author = {Santiago-Rodriguez, TM and Toranzos, GA},
title = {Editorial: Advances in phage applications: deciphering phage biological and ecological mechanisms through metagenomics.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1822387},
doi = {10.3389/fmicb.2026.1822387},
pmid = {41982885},
issn = {1664-302X},
}

@article {pmid41982959,
year = {2026},
author = {Zhang, K and Zheng, J and Wei, A and Qin, M and Zhu, G},
title = {Pulmonary infection caused by Tropheryma whipplei in a child before hematopoietic stem cell transplantation: a case report.},
journal = {Translational pediatrics},
volume = {15},
number = {3},
pages = {91},
pmid = {41982959},
issn = {2224-4344},
abstract = {BACKGROUND: Tropheryma whipplei (TW) triggers Whipple's disease (WD), a rare, chronic multisystemic infection with heterogeneous clinical presentations that can be easily overlooked, particularly Whipple's pneumonia. The advent of metagenomic next-generation sequencing (mNGS) technology applied to bronchoalveolar lavage fluid (BALF) analysis has enabled the identification of an increasing number of patients with acute pneumonia due to TW. Most reports describe symptomatic middle-aged males with cough, while asymptomatic pediatric cases remain exceptionally rare. Without adequate antibiotic therapy, WD is invariably fatal, especially in patients undergoing hematopoietic stem cell transplantation (HSCT). There is no established consensus on the optimal treatment regimen or duration, particularly for pediatric patients.

CASE DESCRIPTION: An 8-year-old boy with primary immunodeficiency due to a genetic mutation presented without respiratory symptoms. Yet, high-resolution computed tomography (HRCT) revealed nodular lesions. Initially misdiagnosed as a fungal infection, subsequent mNGS analysis of BALF identified TW as the sole pathogen, leading to a diagnosis of TW-associated pneumonia. Following a combined anti-infective therapy regimen, the patient successfully underwent the myeloablative conditioning (MAC) regimen. Neutrophil and platelet engraftment occurred promptly, with no severe transplant-related complications.

CONCLUSIONS: This retrospective analysis describes a clinical scenario involving a pediatric patient who exhibited no respiratory symptoms prior to transplantation but showed characteristic nodular lesions on imaging studies, ultimately confirming acute pneumonia caused by TW. Under a combination anti-infection regimen consisting of intravenous ceftriaxone, oral doxycycline, and oral hydroxychloroquine, the child tolerated the MAC regimen well. Neutrophil and platelet engraftment proceeded without delay, and follow-up imaging confirmed complete resolution of the pulmonary lesions.},
}

@article {pmid41983569,
year = {2026},
author = {Vogel, MA and Machairas, F and Ferchiou, S and Osvatic, J and Alzubaidy, H and Séneca, J and Hausmann, B and Klun, K and Petersen, JM},
title = {Symbiont diversity within Loripes orbiculatus and the case for multiple hosts.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag094},
pmid = {41983569},
issn = {1751-7370},
abstract = {Seagrasses support immense biodiversity and are critical for maintaining coastal ecosystem health. These foundation species benefit from a 'three-way' facultative relationship with one of the common inhabitants of seagrass meadows, lucinid bivalves, which host specific bacterial Ca. Thiodiazotropha symbionts. Relatives of the bivalve symbionts have been detected on seagrass roots raising the possibility that these symbionts may colonize both animals and plants; however, no study has yet compared bivalve- and seagrass-associated symbionts at the same site and time. Our combination of 16S rRNA gene amplicon and metagenome sequencing revealed a greater diversity than was previously observed within both lucinid bivalves and on seagrass roots from the Adriatic Sea and resulted in the closed genome of one prominent symbiont species. We show that two of the Ca. Thiodiazotropha ASVs found on seagrass roots are identical to those found in bivalve hosts at the same site. This suggests that symbiont sharing may occur in the seagrass habitat between these two host species, which has important evolutionary and ecological implications for both hosts and symbionts.},
}

@article {pmid41983714,
year = {2026},
author = {Viguier, C and Mansuy, JM and Martin-Blondel, G},
title = {Recent advances in flavivirus encephalitis.},
journal = {Current opinion in infectious diseases},
volume = {},
number = {},
pages = {},
pmid = {41983714},
issn = {1473-6527},
abstract = {PURPOSE OF REVIEW: Flaviviruses are an increasing public health concern, responsible for a broad spectrum of human disease ranging from asymptomatic or mild febrile illness to severe neuroinvasive infections such as encephalitis. Flavivirus encephalitis is associated with substantial mortality and long-term neurological sequelae, yet no specific antiviral therapy is currently available. Diagnosis remains challenging because of transient viremia and serological cross-reactivity, and preventive strategies are unevenly implemented. This review summarizes recent advances in the diagnosis, prognostic assessment, treatment, and prevention of flavivirus-associated encephalitis.

RECENT FINDINGS: Recent studies have reshaped diagnostic strategies through improved viral detection, including multimatrix molecular testing and metagenomic approaches, alongside better characterization of host-response markers in cerebrospinal fluid. Recent work has substantially refined understanding of host susceptibility, highlighting preexisting antitype I interferon autoantibodies as a major driver of severe disease across neurotropic flaviviruses, and identifying several biomarkers with potential prognostic value. Neuroimaging work has refined MRI pattern recognition across flaviviral encephalitis, with limited but evolving prognostic implications. While management remains largely supportive, the therapeutic pipeline is increasingly diverse, with growing interest in host-directed strategies.

SUMMARY: Flavivirus encephalitis represents a major clinical challenge driven by host vulnerability, diagnostic complexity, and the absence of validated therapies. Integrating recent advances in diagnostics, risk stratification, and prevention is essential, while ongoing therapeutic development offers cautious optimism for future management.},
}

@article {pmid41983840,
year = {2026},
author = {Ibadullayeva, A and Khamzina, A and Smagulov, D and Khamzin, K},
title = {An overview of the livestock microbiome: sheep, horses, cattle, camels, and chickens.},
journal = {Brazilian journal of biology = Revista brasleira de biologia},
volume = {86},
number = {},
pages = {e299936},
doi = {10.1590/1519-6984.299936},
pmid = {41983840},
issn = {1678-4375},
mesh = {Animals ; Cattle/microbiology ; *Livestock/microbiology ; Camelus/microbiology ; Sheep/microbiology ; *Microbiota/genetics/physiology ; Chickens/microbiology ; Horses/microbiology ; },
abstract = {The animal microbiome plays a crucial role in determining the health, productivity, and welfare of livestock species, including sheep, horses, cattle, camel, and chicken. These animal species were selected due to the high consumption of their products in Kazakhstan. Enhancing their productivity, while maintaining the safety and quality of meat and milk derived from them, represents a pressing research priority. This review article includes current research on the composition, diversity, and purposes of the microbiota found within different organ systems of these species. This study focuses on recent advancements in sequencing technology, including metagenomics, 16S rRNA sequencing, and multiomic methods, to combine data on microbial diversity, composition, and functionality within the gastrointestinal tract and other organs. The key findings show differences in microbial communities associated with breed, age, and diet, the impact of microbiota on methane emissions and feed efficiency in ruminants, and the possibility of using microbiome management techniques (e.g., probiotics, prebiotics, and feed additives) to enhance livestock production. The microbiome influences various species, extending its effects beyond digestion and immunity to reproductive health and behavior. Despite advancements, translating microbiome data into actionable interventions is interfered by variability resulting from genetic, environmental, and management factors. Integrating microbiome research more closely with animal genetics and livestock production methods could lead to innovative approaches for improving the health, efficiency, and welfare of farm animals, ultimately supporting sustainable livestock farming practices.},
}

Animals
Cattle/microbiology
*Livestock/microbiology
Camelus/microbiology
Sheep/microbiology
*Microbiota/genetics/physiology
Chickens/microbiology
Horses/microbiology

@article {pmid41983925,
year = {2026},
author = {El Zibaoui, R and Venkatesan, A},
title = {An update on infectious encephalitis: from epidemiology to management.},
journal = {Current opinion in infectious diseases},
volume = {},
number = {},
pages = {},
pmid = {41983925},
issn = {1473-6527},
abstract = {PURPOSE OF REVIEW: Infectious encephalitis (IE) is a serious neurological condition that poses a major global health threat. This review summarizes emerging pathogens, particularly arboviruses, updated diagnostic strategies, and evolving treatment approaches, emphasizing ongoing gaps in diagnosis and management.

RECENT FINDINGS: Established arboviruses such as West Nile virus, Japanese encephalitis virus, Powassan virus, and Eastern Equine virus have regained attention due to their geographic expansion and the appearance of distinct genotypes. In parallel, increasing reports of encephalitis by newly emerging pathogens such as Oropouche virus and scrub typhus speak to the evolving nature of the epidemiology of IE. Advances in diagnostics, including multiplex PCR and metagenomic next-generation sequencing, have enhanced the breadth and accuracy of pathogen identification. As treatment options remain scarce, the role of immunomodulatory agents and novel antiviral molecules in the management of IE is actively being investigated.

SUMMARY: The emergence of novel and reemerging pathogens highlights the need for rapid, accurate diagnostics. Advanced molecular techniques and the identification of novel therapeutic targets have the potential to change the landscape of IE. However, strengthening surveillance and vaccination strategies, along with ongoing efforts in vaccine development, remain crucial for optimizing patient outcomes, increasing public health preparedness, and mitigating future outbreaks.},
}

@article {pmid41984378,
year = {2026},
author = {Tao, X and Du, Z and Wang, X and Lv, L and Zhang, G and Liang, J and Zou, W},
title = {Volatile Fatty Acid Production from Baijiu Distillers' Grains Via Anaerobic Fermentation with Rumen Microbes: Performance and Mechanism.},
journal = {Applied biochemistry and biotechnology},
volume = {},
number = {},
pages = {},
pmid = {41984378},
issn = {1559-0291},
support = {52400160//National Natural Science Foundation of China/ ; 52360020//National Natural Science Foundation of China/ ; E2024202030//Natural Science Foundation of Hebei Province/ ; RKJH[2025]26//Renhuai Municipal Science and Technology Program/ ; Qiankehe Jichu QN [2025] 292//Youth Science and Technology Talent Project of the Guizhou Provincial Basic Research Program/ ; },
}

@article {pmid41984912,
year = {2026},
author = {Fri, J and Njanje, I and Mahopo, TC and Mavhandu-Ramarumo, LG and Bessong, PO and , },
title = {The Gut Bacterial Resistome in the First Two Years of Life: Protocol for a Longitudinal Observational Birth Cohort Study.},
journal = {JMIR research protocols},
volume = {15},
number = {},
pages = {e86058},
doi = {10.2196/86058},
pmid = {41984912},
issn = {1929-0748},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Infant, Newborn ; Female ; Infant ; Longitudinal Studies ; Prospective Studies ; Birth Cohort ; South Africa ; *Drug Resistance, Bacterial ; Anti-Bacterial Agents/pharmacology ; Observational Studies as Topic ; Rural Population ; Milk, Human/microbiology/chemistry ; Male ; Risk Factors ; },
abstract = {BACKGROUND: Antimicrobial resistance (AMR) is a global health threat that increases the burden of infectious diseases and disproportionately affects communities of low socioeconomic status. Despite the call for community-level AMR data, prospective studies from rural sub-Saharan African communities to inform appropriate targeted interventions remain scarce. Given the role of enteric bacteria in AMR transmission dynamics, there is a need to understand the timing, risk factors, and ecological drivers of gut resistome acquisition and development during infancy.

OBJECTIVE: This study aimed to characterize the temporal dynamics of enteric bacterial resistomes during the first 2 years of life and to identify drivers of AMR acquisition and development in a community-based, prospective, observational birth cohort study in a rural South African community.

METHODS: The study aims to enroll 200 newborns and their mothers within 17 days post partum. Data on key exposures and variables include sociodemographics; perinatal and anthropometrics; feeding practices and dietary exposures; illness, medication, and vaccination history; breast milk metabolomic profiles; household socioeconomic status; maternal psychosocial and behavioral factors; hygiene and sanitation practices; and environmental exposures including hydro-meteorological variables, in-house livestock and pets, and drinking water quality. Biological samples include stools from monthly collections and diarrhea episodes for metagenomic analysis and breast milk for metabolomics. Planned analyses include assessing the infant microbiome and resistome structure (diversity, abundance, and composition) across time points and modeling associations between risk factors and AMR outcomes. Additionally, a cross-sectional community survey on knowledge, attitudes, and practices regarding antimicrobial use is conducted to inform knowledge translation through responsive dialogues, thereby developing ethnographically relevant packages for community-level AMR stewardship.

RESULTS: Participant identification and enrollment began in August 2023. By October 2025, 167 newborns had been enrolled, with 20 having completed the 24-month follow-up. The characteristics of the enrolled participants are presented in this protocol.

CONCLUSIONS: This study will offer a unique opportunity to generate longitudinal resistome data from a rural sub-Saharan African setting. The study is expected to contribute knowledge on the microbiome and resistome structure dynamics and trajectories associated with key risk factors of acquisition and development. In addition, co-produced ethnographically tailored educational packages, informed by knowledge, attitudes, and practices and bacterial resistome data, will drive sustainable community-centered AMR awareness interventions.},
}

Humans
*Gastrointestinal Microbiome/drug effects
Infant, Newborn
Female
Infant
Longitudinal Studies
Prospective Studies
Birth Cohort
South Africa
*Drug Resistance, Bacterial
Anti-Bacterial Agents/pharmacology
Observational Studies as Topic
Rural Population
Milk, Human/microbiology/chemistry
Male
Risk Factors

@article {pmid41985067,
year = {2026},
author = {Sarmah, MP and Zoramthara, K and Manngaihsiam, R and Boro, HH and Baraka, AGA and Saeed, AL and Gurusubramanian, G and Kharat, KR},
title = {Microbiome Simplification During Metamorphosis in Larva and Adults of Armigeres subalbatus (Coquillett, 1898) (Culicidae) Revealed by Shotgun Metagenomics.},
journal = {Archives of insect biochemistry and physiology},
volume = {121},
number = {4},
pages = {e70159},
doi = {10.1002/arch.70159},
pmid = {41985067},
issn = {1520-6327},
support = {EM/Dev/11/SG/01993/2024//Indian Council of Medical Research/ ; DST/INSPIRE Fellowship/[IF240039]//Department of Science & Technology, New Delhi, India (INSPIRE-JRF)/ ; },
mesh = {Animals ; Larva/microbiology/growth & development ; *Microbiota ; Metagenomics ; *Culicidae/microbiology/growth & development ; *Metamorphosis, Biological ; Bacteria/genetics/classification ; Metagenome ; },
abstract = {Armigeres subalbatus is medically significant vector for filarial worms and the Japanese encephalitis virus. Shotgun metagenomic sequencing was employed to investigate the bacterial communities in A. subalbatus mosquitoes. The diversity metrics (Shannon H', Simpson 1-D, Berger-Parker) were calculated for larval and adult stages. De novo assembly and binning were used to recover metagenome-assembled genomes (MAGs) with > 82% completeness and < 4% contamination. Functional profiling assessed gene expression via transcripts per million (TPM) and clusters of orthologous groups (COG) categories. Larval microbiomes showed high alpha diversity (Shannon H' ≈ 1.336 ± 0.163, Simpson 1-D = 0.684 ± 0.046), dominated by Gammaproteobacteria (Aeromonas, Morganella, and Yersinia) and Bacteroidota, with persistent Shewanella and Acinetobacter. Adult microbiomes exhibited low diversity (Shannon H' = 0.637 ± 0.100, Berger-Parker = 0.682 ± 0.026), near-monoculture dominated by Aeromonas hydrophila, alongside low-abundance Stenotrophomonas, Pseudomonas, and Microbacterium. Six high-quality MAGs were recovered: larval (Bacteroidota, Shewanella, and Acinetobacter); adult (Acinetobacter, Stenotrophomonas, and Shewanella), confirming persistence of Shewanella and Acinetobacter, absence of Bacteroidota, and emergence of Stenotrophomonas in adults. Adult microbiomes displayed metabolic hyperactivity, with 1.5-4 times higher transcriptional output across COG categories compared to larvae. Chemotaxis [Methyl-accepting chemotaxis protein (MCP), K03406: ~6000 TPM in adults vs. < 1000 TPM in larvae] and ABC transporters (PF00005: > 10,000 TPM in adults) dominated adults, while larval expression was balanced among housekeeping functions. The microbiome undergoes significant restructuring during mosquito development, shifting from diverse larval communities to metabolically active, low-diversity adult assemblages. Recovered MAGs provide a genomic basis for future studies on mosquito microbiota dynamics and functions.},
}

Animals
Larva/microbiology/growth & development
*Microbiota
Metagenomics
*Culicidae/microbiology/growth & development
*Metamorphosis, Biological
Bacteria/genetics/classification
Metagenome

@article {pmid41985316,
year = {2026},
author = {Ariaee, A and Hunter, A and Wignall, A and Bremmell, K and Prestidge, C and Joyce, P},
title = {Spray dried inulin-montmorillonite hybrids alleviate high-fat diet-induced inflammatory and metabolic dysregulation in rats.},
journal = {Biomaterials advances},
volume = {185},
number = {},
pages = {214878},
doi = {10.1016/j.bioadv.2026.214878},
pmid = {41985316},
issn = {2772-9508},
abstract = {Metabolic dysregulation is strongly associated with excessive dietary lipid absorption and gut microbiota imbalances under high-fat diet (HFD) conditions. This study evaluates a spray-dried inulin-montmorillonite (INU-MMT) hybrid designed to simultaneously restrict intestinal lipid digestion and modulate gut microbiota composition. In simulated intestinal digestion, INU-MMT maintained the strong lipid-inhibitory effect of montmorillonite, reducing free fatty acid release by 2.8-fold compared to HFD conditions, while exhibiting improved dispersion stability attributed to INU's ability to reduce clay platelet aggregation. In a 21-day HFD-fed rat model, INU-MMT supplementation (1 g/kg/day) attenuated cumulative weight gain by 4.7% compared to the HFD control, exceeding reductions with INU (2.0%) and MMT (1.5%) alone. 16S rRNA gene sequencing of fecal samples revealed improved gut microbial diversity (Simpson's index, p = 0.0161) and uniquely enriched health-associated taxa including Akkermansiaceae (2.5-fold), Eggerthellaceae (7.7-fold), Ruminococcaceae (3.5-fold), and Peptostreptococcaceae (8-fold). Beta diversity analysis highlighted that INU-MMT induced a distinct microbial composition from INU, suggesting the complimentary effects of the hybrid promote a more widespread microbial change than prebiotic alone. Predictive metagenomic analysis using the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States 2 (PICRUSt2) software demonstrated a 98% reduction in microbial triacylglycerol lipase abundance, consistent with the observed in vitro lipolysis suppression. These findings demonstrate that the INU-MMT hybrid preserves MMT's restriction of lipid digestion while delivering INU's prebiotic benefits, producing additive effects in diet-induced weight gain and microbiota modulation. The multifunctional nature of this spray-dried hybrid highlights its potential as a dietary strategy for metabolic dysregulation.},
}

@article {pmid41985330,
year = {2026},
author = {Kwiendacz, H and Cembrowska-Lech, D and Skonieczna-Żydecka, K and Klimontowicz, K and Podsiadło, K and Wierzbicka-Woś, A and Styburski, D and Kaczmarczyk, M and Gumprecht, J and Łoniewski, I and Nabrdalik, K},
title = {Multi-strain probiotic enhances metformin tolerance by modulating gut microbiome and bile acid pathways: Insight from multi-omics post-hoc analysis (ProGasMet trial).},
journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie},
volume = {198},
number = {},
pages = {119370},
doi = {10.1016/j.biopha.2026.119370},
pmid = {41985330},
issn = {1950-6007},
abstract = {BACKGROUND: Metformin is the cornerstone therapy for type 2 diabetes, but gastrointestinal intolerance commonly limits dose escalation and long-term adherence. In the ProGasMet trial, multi-strain probiotic supplementation improved metformin tolerability. However, the underlying microbiome-metabolome mechanisms remain unclear.

METHODS AND ANALYSIS: We performed an exploratory multi-omics analysis using Period 1 of a randomized, double-blind, placebo-controlled trial. Participants with metformin intolerance received a multi-strain probiotic or placebo for 12 weeks. Paired stool samples collected at baseline and end of treatment were available from 34 participants (68 samples). We integrated shotgun metagenomic species profiles, predicted gut metabolic modules, and untargeted faecal LC-MS metabolomics using multi-block sparse PLS (DIABLO), complemented by longitudinal covariate-adjusted feature-level analyses and associations with gastrointestinal symptom burden (QACSMI and a simplified GI score).

RESULTS: In multi-omics integration at 12 weeks, bile acid-related metabolites were among the strongest contributors to group separation, with hyodeoxycholic acid and related compounds enriched in the probiotic arm. Global biodiversity and community-wide turnover did not differ between groups. Feature-level analyses suggested modest, directionally coherent changes in selected taxa, functional modules, and metabolites. Higher hyodeoxycholic acid concentrations were associated with lower gastrointestinal symptom burden in probiotic-treated participants, a pattern not observed under placebo.

CONCLUSION: Probiotic supplementation may be associated with coordinated microbiome-metabolome shifts in metformin-intolerant type 2 diabetes, highlighting bile acid remodelling, particularly hyodeoxycholic acid, as a plausible candidate for improved tolerability. These results support prioritising secondary bile acid-microbiome pathways for confirmation in larger trials incorporating targeted bile acid quantification and causal modelling.},
}

@article {pmid41985671,
year = {2026},
author = {Wang, Y and Liu, X and Li, Z and Kang, A and Bai, Y and Wang, Y and Liu, Y and Zhang, C and Yang, J and Cai, Q and Feng, Y and Yi, H and Zhang, M and Zhang, F and Liu, H and Xu, C},
title = {Oligofructose alleviates hyperandrogenism in polycystic ovary syndrome through gut microbiota-derived bile acids.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2026.04.036},
pmid = {41985671},
issn = {2090-1224},
abstract = {INTRODUCTION: Polycystic ovary syndrome (PCOS) is a common endocrine disorder in reproductive-age women, characterized by hyperandrogenism and metabolic dysfunction. Dietary interventions are recommended as one of the first-line therapies. Oligofructose (OFS), a prebiotic fiber, has demonstrated clinical benefits in PCOS; however, its underlying mechanism remains unclear.

OBJECTIVES: To determine whether OFS alleviates PCOS-like phenotypes through bile acid-dependent mechanisms and to identify downstream ovarian steroidogenic responses.

METHODS: Letrozole-induced PCOS-like mice received OFS supplementation. Microbiota dependence was assessed using antibiotic depletion and fecal microbiota transplantation (FMT). Bile acid involvement was evaluated using cholestyramine. Gut microbial composition and function were profiled by 16S rRNA and metagenomic sequencing, and bile acids were quantified by UHPLC-MS/MS. Ovarian transcriptomics, ex vivo ovarian explants, and primary granulosa cells were used to examine steroidogenic changes, with pharmacological inhibition applied to assess TGR5-related signaling.

RESULTS: OFS improved reproductive and metabolic abnormalities in PCOS-like mice. These benefits were abolished by microbiota depletion and bile acid sequestration, indicating microbiota- and bile acid-dependent effects. OFS was associated with increased circulating hyodeoxycholic acid (HDCA), which negatively correlated with serum testosterone. HDCA supplementation partially reproduced endocrine improvements under microbiota-depleted conditions. Ovarian transcriptomic and functional analyses demonstrated enhanced aromatization following OFS treatment. In ex vivo ovarian explants and primary granulosa cells, HDCA increased estradiol production, reduced testosterone, and upregulated CYP19A1 (encoding aromatase). Under androgen stimulation, pharmacological inhibition of TGR5 attenuated HDCA-associated increases in estradiol and aromatase activity, supporting involvement of TGR5-related signaling.

CONCLUSION: OFS alleviates PCOS-like phenotypes in a microbiota- and bile acid-dependent manner and enhances ovarian aromatization. These findings move beyond descriptive bile acid alterations in PCOS by providing functional evidence that dietary fiber-induced bile acid remodeling is associated with modulation of ovarian steroidogenic regulation.},
}

@article {pmid41986005,
year = {2026},
author = {Ansari, A and Shete, O and Ghosh, TS},
title = {Artificial intelligence in microbial metagenomics.},
journal = {Progress in molecular biology and translational science},
volume = {221},
number = {},
pages = {255-276},
doi = {10.1016/bs.pmbts.2026.01.009},
pmid = {41986005},
issn = {1878-0814},
mesh = {*Metagenomics/methods ; *Artificial Intelligence ; Humans ; Microbiota/genetics ; Machine Learning ; },
abstract = {Rapid advancements in genomic sequencing technologies and similar technological advancements in the area of accessing, isolating, extracting and functional probing of microbes residing in diverse environments has resulted in a deluge of microbiome sequencing and microbial genomic sequencing data. Concomitant developments in the area of data science, specifically in the domains of advanced statistics, and artificial intelligence (AI) can facilitate mining this data to answer complex biological questions and developing translational applications in diverse areas, ranging from health-care to industrial microbiology. For most researchers, information on which AI tools address specific biological questions is scattered across disparate sources. In this chapter, we explore the various applications of AI-based methodologies (using case-studies) in answering different biological questions using microbial genomics and metagenomic data. We also discuss different AI and machine-learning (ML) based approaches to integrate metagenomic data with other "omics" data. Finally, we highlight both challenges and possibilities with this rapidly progressing field.},
}

*Metagenomics/methods
*Artificial Intelligence
Humans
Microbiota/genetics
Machine Learning

@article {pmid41986051,
year = {2026},
author = {},
title = {Correction to 'Clinical Value of Metagenomic Next-Generation Sequencing in Early Diagnosis of Peritoneal Dialysis-Associated Peritonitis: A Randomised Controlled Observational Trial'.},
journal = {Nephrology (Carlton, Vic.)},
volume = {31},
number = {4},
pages = {e70203},
doi = {10.1111/nep.70203},
pmid = {41986051},
issn = {1440-1797},
}

@article {pmid41986605,
year = {2026},
author = {Sumithra, TG and Gayathri, S and Mannur, VS and Neethu, N and Ratheesh Kumar, R and Nair, AV and Ratheesh, L and Zainul Abid, PM and Sundari, BKR and Dharani, G and Krupesha Sharma, SR},
title = {Bathymetry and environmental features govern the microbial communities in mesopelagic sediments of the Lakshadweep Islands of India.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-48651-8},
pmid = {41986605},
issn = {2045-2322},
support = {Deep-sea Metagenomics for enhanced next-generation bioethanol production' under Deep Ocean Mission (DOM) [MoES/PAMC/DOM/176/2023 (E-14624)]//Ministry of Earth Sciences/ ; },
}

@article {pmid41986657,
year = {2026},
author = {Luchen, CC and Piedade, GJ and Chibuye, M and Simuyandi, M and Chisenga, CC and Chilengi, R and Bosomprah, S and Schultsz, C and Mende, DR and Harris, VC},
title = {Distinct infant resistome trajectories shaped by country income and geography revealed through global metagenomics reanalysis.},
journal = {npj antimicrobials and resistance},
volume = {4},
number = {1},
pages = {},
pmid = {41986657},
issn = {2731-8745},
support = {2023159//Amsterdam University Medical Center Amsterdam Public Health Research Institute/ ; LSHM23007//Track-AMR/ ; LSHM23007//Track-AMR/ ; 09150161810022//Netherlands Organisation for Health Research and Development (ZonMw) VENI/ ; 219775/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; LSHM21033//Co-funding by PPP Allowance awarded by Health~Holland, Top Sector Life Sciences & Health GLORIA/ ; AI173360/NH/NIH HHS/United States ; },
abstract = {Antimicrobial resistance (AMR) costs lives, diminishes antimicrobial effectiveness and increases health care costs. We conducted a re-analysis of pooled fecal metagenomes from individual participants to characterise AMR gene (ARG) distributions in 0-2 year-old healthy infants across income and geography. From 2275 screened studies, we included nine datasets and 1944 fecal metagenomes. Resistome gene identifier (RGI) was used to identify ARGs, and gut microbiomes were profiled using Sylph. We assessed associations between ARGs, Escherichia coli abundance, and national-level indicators. In the first 3 months of life, ARG abundance patterns were not significantly different across income groups; however, by 6 months of age, infants in LICs had higher ARG abundance, associated with increased E. coli carriage. Caesarean section rates, antibiotic use, and income inequality positively correlated with ARG abundance in younger infants; physician density negatively correlated with ARG abundance in older children. These descriptive age- and context-specific associations may inform interventions to mitigate the carriage and spread of ARGs and the rise of AMR in vulnerable pediatric populations.},
}

@article {pmid41986663,
year = {2026},
author = {Luiken, REC and Prinsen, H and Dasari, SN and Zweerus, H and Timmerman, AJ and Speksnijder, DC and Dohmen, W and Wagenaar, JA and Heederik, DJJ and Zomer, AL},
title = {Changes in antimicrobial resistance profiles of Escherichia coli and the metagenome on Dutch pig farms after antimicrobial usage interventions.},
journal = {npj antimicrobials and resistance},
volume = {4},
number = {1},
pages = {},
pmid = {41986663},
issn = {2731-8745},
abstract = {The use of antimicrobials in livestock farming drives selection and dissemination of antimicrobial resistance (AMR), prompting implementation of veterinary stewardship programs to reduce antimicrobial usage (AMU). We evaluated changes in AMR on 45 Dutch pig farms before and after tailored, coaching-based interventions using phenotypic testing of Escherichia coli and metagenomic profiling of pooled faeces. Post-weaning pig farms, including nursery and fattening units, entered the intervention in a stepped-wedge design, with intervention periods ranging from 10 to 27 months. Across farms, AMU and abundances of several antimicrobial resistance gene classes declined over time, alongside reductions in overall resistome levels. Proportions of phenotypic AMR in E. coli were more variable, although decreased AMU was associated with lower resistance for specific antimicrobial classes, such as tetracyclines and beta-lactams. While longer follow-up is required to fully assess long-term impacts, these findings indicate that veterinary antimicrobial stewardship programs can yield measurable short-term reductions in AMR at farm level.},
}

@article {pmid41986664,
year = {2026},
author = {Frey, B and Varliero, G and Rüthi, J and Alekseev, I and Qi, W and Povazhnyi, V and Zemlianskii, V and Stierli, B and Ermokhina, K and Schaepman-Strub, G and Cuartero, J},
title = {Metagenomic insights into viral and microbial genes of Russian High-Arctic soil microbiomes.},
journal = {Communications biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42003-026-10050-0},
pmid = {41986664},
issn = {2399-3642},
abstract = {High-Arctic soils are extreme ecosystems where microbial and viral roles remain poorly studied. Climate-driven vegetation expansion may alter these environments, but its impact is unknown. We generate a shotgun metagenomic database from four High-Arctic islands, comparing vegetated and unvegetated sites at two depths (0-2 cm and 30-50 cm). We analyse the functional gene potential, including biosynthetic gene clusters (BGCs) and antibiotic resistance genes (ARGs) in metagenome-assembled genomes (MAGs), and assess viral diversity. Vegetated soils at 30-50 cm were enriched in genes for carbon/nitrogen cycling, energy production, and carbohydrate metabolism, indicating enhanced nutrient inputs. Conversely, unvegetated soils show higher BGC and ARG richness, reflecting microbial competition under nutrient limitation. Viral richness decreases in surface vegetated soils, while diversity and giant virus (Nucleocytoviricota) abundance increase with depth. These findings reveal how vegetation and soil depth modulate microbiomes and viromes, critical for predicting ecosystem trajectories in a warming world.},
}

@article {pmid41986859,
year = {2026},
author = {Iñiguez-Luna, MI and Gómez-Godínez, LJ and Cadena-Zamudio, JD and Cadena-Zamudio, DA and Aguirre-Noyola, JL and Barrera-Guzmán, LA},
title = {Omics Sciences: Driving the Conservation and Characterization of Plant Genetic Resources.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3011},
number = {},
pages = {345-364},
pmid = {41986859},
issn = {1940-6029},
abstract = {Omics sciences have revolutionized the conservation and characterization of plant genetic resources by enabling a comprehensive understanding of genetic diversity, molecular mechanisms, and adaptive traits. Advances in genomics, transcriptomics, proteomics, metabolomics, and metagenomics have facilitated the identification of genes and metabolic pathways associated with stress tolerance, nutritional value, and agronomic performance. These technologies have enhanced the efficiency of germplasm banks by improving genetic resource characterization, optimizing conservation strategies, and accelerating breeding programs for climate-resilient crops. Additionally, omics approaches contribute to biodiversity conservation by revealing evolutionary relationships, ecosystem dynamics, and the functional roles of microbial communities in plant health. The integration of multi-omics data with bioinformatics and artificial intelligence further enhances predictive capabilities, enabling targeted conservation and breeding efforts. This review highlights the pivotal role of omics sciences in securing plant genetic resources for sustainable agriculture and global food security.},
}

@article {pmid41975427,
year = {2026},
author = {Zhang, Z and Bai, J and Liu, Y and Wang, J and Lv, Z and Tang, L and Wang, R and Gao, L and Liu, C and Lu, S and Fu, X and Ni, J and Wan, P},
title = {Effects of synthetic breast milk on the gut metagenome and whole blood transcriptome in lambs.},
journal = {BMC veterinary research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12917-026-05460-5},
pmid = {41975427},
issn = {1746-6148},
support = {NYHXGG.2023AA206-3//Agricultural GG Project of Xinjiang Production and Construction Corps/ ; 2025AB5012//Tacheng Talents Project/ ; 2025AA01504//Project of Major Science and Technology Project of the Corps/ ; 2022TSYCCX0124//Young Science and Technology Top Talent Program of Tianshan Talent Training Program in Xinjiang Province/ ; XJARS-09-26//Xinjiang Agriculture Research System/ ; CARS-39-07//China Agriculture Research System/ ; },
}

@article {pmid41975703,
year = {2026},
author = {Rong, R and Long, Y and Li, Y and Lin, L and Yang, J and Hu, Z and Liu, D and Chen, P},
title = {Metagenomic and Targeted Next-Generation Sequencing in Infectious Disease Diagnostics: Current Applications, Challenges, and Future Perspectives.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {16},
number = {7},
pages = {},
pmid = {41975703},
issn = {2075-4418},
support = {2024ZD0533100//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; 2024ZD0533106//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; P12220011-230148//Undergraduate teachingquality and teaching reform licensing project SYSU/ ; },
abstract = {Metagenomic and targeted next-generation sequencing (NGS) technologies are rapidly transforming diagnosis and management for infectious diseases. This review comprehensively examines the current applications of metagenomic NGS (mNGS) and targeted NGS (tNGS) in clinical microbiology, highlighting their roles in pathogen detection, antimicrobial resistance profiling, virulence characterization, and outbreak investigation-particularly in complex cases such as pneumonia, critical illness with pulmonary infections, and pediatric acute respiratory illnesses. We discuss the diagnostic performance, advantages, and limitations of these approaches, including challenges related to sensitivity, specificity, standardization, bioinformatic complexity, and cost-effectiveness. Furthermore, we explore emerging opportunities for integrating NGS-based surveillance with public health strategies, such as wastewater epidemiology, to monitor healthcare-associated infections (HAIs) and antimicrobial resistance (AMR) at the population level. Finally, we outline key steps needed to translate these powerful genomic tools from research settings into routine clinical and public health practice.},
}

@article {pmid41975975,
year = {2026},
author = {Szala, Ł and Staninska-Pięta, J and Piotrowska-Cyplik, A},
title = {Microbiome of Bovine Milk and Factors Influencing Its Composition.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {7},
pages = {},
pmid = {41975975},
issn = {2076-2615},
support = {MEiN/2023/DPI/2870//Ministry of Science and Higher Education/ ; },
abstract = {The bovine milk microbiome is a complex and dynamic microbial ecosystem, comprising both commensal and pathogenic bacteria. Its composition is shaped by endogenous factors, including udder physiology, lactation stage, and health status, particularly mastitis, as well as by exogenous factors, such as housing conditions, farm infrastructure, milking practices, and post-milking processing. Mastitis not only alters milk quality but also induces persistent dysbiosis that may persist even after clinical recovery, highlighting the need for continuous microbiome monitoring to ensure milk safety. Advances in molecular and metagenomic techniques have enabled the detection of microbial taxa that are difficult to identify using traditional culture-based methods. However, challenges remain due to low microbial biomass, reagent contamination, and the inability to distinguish live from dead bacteria, all of which complicate accurate characterization. Environmental contamination from skin, air, and equipment, along with microbial shifts during transport, storage, pasteurization, and product separation, further modulate microbial communities. While mastitis-related changes in milk microbiota have been extensively studied, the effects of other bovine diseases and systemic health conditions remain largely unexplored, constituting a critical knowledge gap. Understanding the factors that shape milk microbial communities is essential for ensuring dairy product safety, optimizing herd management, and developing microbiome-based innovations in milk production.},
}

@article {pmid41976452,
year = {2026},
author = {Li, X and Li, Y and Li, Q and Jin, Y and Chen, Y},
title = {Rumen Metagenomic and Muscle Metabolomic Characterization of Meat Quality in Duolang Sheep at Different Ages.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {7},
pages = {},
pmid = {41976452},
issn = {2304-8158},
support = {2022TSYCLJ0014//Program for Science and Technology Innovation Talents/ ; 2023B02015//Key Research and Development Program Project of Xinjiang Uygur Autonomous Region/ ; },
abstract = {This study aimed to investigate the changes in the meat quality characteristics of Duolang sheep using rumen metagenomic and muscle metabolomic analyses across different age groups. A total of 24 three-month-old male Duolang sheep were selected and reared, and samples of longissimus thoracis muscle and rumen contents were collected at 4, 6, and 8 months of age to evaluate meat quality, metabolites, rumen metagenome, and volatile fatty acids (VFAs). The results indicated that the lightness (L*45min) and yellowness (b*45min) of the longissimus thoracis muscle at 45 min post-slaughter were significantly higher at 4 and 6 months than at 8 months of age (p < 0.05). In terms of ruminal VFAs, butyrate concentration was significantly higher at 6 months than at 4 months (p < 0.05), and valerate concentration exhibited a quadratic relationship with age (p = 0.02). With increasing age, the relative abundances of Prevotella and Fibrobacter increased, whereas those of Methanobrevibacter and Bacteroides decreased (p < 0.05), leading to shifts in functional pathways related to amino acid, lipid, and carbohydrate and energy metabolism. Untargeted metabolomics revealed that muscle betaine and inosine peaked at 4 months of age, whereas L-arginine, L-proline, and inosinic acid were most abundant at 6 months of age (p < 0.05). Correlation analysis revealed that the b*45min was positively associated with ruminal concentrations of propionate, butyrate, and valerate, as well as with the relative abundances of key Selenomonadales taxa (p < 0.05). Inosinic acid exhibited a positive correlation with the abundance of the genus Sodaliphilus and ruminal butyrate concentration (p < 0.05), while Sodaliphilus abundance was negatively correlated with inosine (p < 0.05). In summary, this study demonstrates that age-related variations in the meat quality of Duolang sheep are closely associated with rumen microbial ecology and muscle metabolites, offering novel insights into the molecular mechanisms underlying meat quality formation and identifying potential biomarkers.},
}

@article {pmid41976454,
year = {2026},
author = {Olupot, CK and Sheehan, O and Kampff, Z and McDonnell, B and Woods, DF and Lugli, GA and Ventura, M and Reen, FJ and Sinderen, DV and Mahony, J},
title = {Raw Milk Cheese Microbiomes: A Paradigm for Interactions of Lactic Acid Bacteria in Food Ecosystems.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {7},
pages = {},
pmid = {41976454},
issn = {2304-8158},
abstract = {While industrial-scale dairy fermentations often employ pasteurized milk as the substrate, many farmhouse and traditional production practices apply raw milk derived from a variety of mammals. Certain artisanal production systems rely on the autochthonous microbiota of the milk, fermentation vessels, equipment and/or environment to initiate milk coagulation. While the technological properties of lactic acid bacteria associated with dairy fermentations are well described, their interactions with other organisms during fermentation and cheese ripening are poorly investigated. This study presents an overview of the microbial ecology of raw and pasteurized milk used in the production of Irish farmhouse cheeses using metagenomic and culture-based approaches. Metagenomic analysis of four raw milk-derived cheeses established the dominant presence of either lactococci or Streptococcus spp. and with a secondary population of various lactobacilli. Interestingly, the Brie sample was also demonstrated to possess significant proportion of Hafnia spp. This was corroborated in culture-based analysis where Hafnia isolates were also identified. Furthermore, we report on the motility phenotype, lactose utilization ability and metabolic products of isolates of Hafnia paralvei and Hafnia alvei, and determine that these strains could grow in a non-antagonistic manner on plates with strains of Lactococcus lactis and Streptococcus thermophilus. As artisanal and farmhouse production systems are often associated with protected or regionally significant products, it is essential to develop a clear understanding of the microbial communities within and the complex relationships between the community members.},
}

@article {pmid41976504,
year = {2026},
author = {Buranavanitvong, N and Thanthithum, C and Kanyakam, K and Azzout-Marniche, D and Jouan-Rimbaud Bouveresse, D and Chotechuang, N and Prakitchaiwattana, C},
title = {Diet-Associated Gut Bacterial Microbiota and Metabolome Signatures Linked to Fermented Food Intake in Healthy Postmenopausal Women.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {7},
pages = {},
pmid = {41976504},
issn = {2304-8158},
support = {FOOD_FF_68_290_2300_073//Thailand Science Research and Innovation Fund Chulalongkorn University/ ; GCUGR1125671022D//the 90th Anniversary of Chulalongkorn University Scholarship under the Ratchadapisek Somphot Endowment Fund/ ; NA//the Second Century Fund (C2F), Chulalongkorn University/ ; },
abstract = {Long-term adherence to plant-based diets can modify gut bacterial microbiota composition and metabolite profiles, which may be particularly relevant for postmenopausal women who frequently adopt such diets and experience age-related changes in nutrient absorption and metabolism. Fermented foods, commonly consumed in vegetarian diets, enhance dietary diversity and nutritional quality. This study compared gut bacterial microbiota and fecal metabolomes between vegetarians (VGs) and omnivores (OMs) and evaluated the contribution of fermented food intake. Thirty-two healthy postmenopausal Thai women (>55 years; 16 VGs, 16 OMs) were enrolled. Gut bacterial microbiota and fecal metabolites were analyzed using 16S rRNA metagenomic and untargeted [1]H-NMR metabolomics. The five most frequently consumed fermented foods were microbiologically characterized. Fermented food consumption was found to be significantly different between groups. OM participants reported infrequent consumption (<10% per week), whereas VG participants consumed fermented foods daily, often in multiple forms (>60% of weekly meals). VG participants exhibited enrichment of Prevotella, Faecalibacterium, and Blautia, while OM participants showed higher abundances of Bacteroides and Escherichia-Shigella. LEfSe identified Weissella as a bacterial taxon associated with the VG group. Functional prediction and metabolomic analyses indicated enhanced carbohydrate fermentation and increased short-chain fatty acid (SCFA) production in VGs, whereas OM profiles reflected greater protein catabolism. Fermented foods consumed by VGs shared microbial biomarkers with the VG gut bacterial microbiota and were rich in SCFAs and essential amino acids, supporting their potential role as microbial and metabolic contributors within the gut ecosystem and nutritional adequacy in postmenopausal vegetarians.},
}

@article {pmid41977149,
year = {2026},
author = {Liszkowska-Walisiak, W and Motyl, I and Płacheta-Kwiatkowska, B and Wlaźlak, M and Ruman, T and Nizioł, J and Wilkowska, A and Maher, A and Berłowska, J},
title = {Apple Pomace Fermented with Non-Saccharomyces Yeast as a Factor Modulating Gut Microbiota.},
journal = {International journal of molecular sciences},
volume = {27},
number = {7},
pages = {},
doi = {10.3390/ijms27072960},
pmid = {41977149},
issn = {1422-0067},
mesh = {*Malus/metabolism/chemistry ; *Gastrointestinal Microbiome ; *Fermentation ; Humans ; *Yeasts/metabolism ; Fatty Acids, Volatile/metabolism ; Bacteria/classification/genetics ; },
abstract = {The valorisation of agro-industrial by-products through fermentation offers an opportunity to develop functional ingredients with targeted effects on gut microbiota. This study evaluates the impact of apple pomace fermented at a low temperature (15 °C) by cold-adapted yeast on the structure and metabolic activity of human gut microbiota, simulated using the Simulator of the Human Intestinal Microbial Ecosystem (SHIME[®]). The fermented apple pomace preparation was characterised by high stability under gastrointestinal conditions, supporting its potential applicability as a functional food ingredient. Supplementation with fermented apple pomace induced distinct changes in the composition and activity of gut microbiota compared to the non-fermented substrate, including increased abundance of the genera Akkermansia, Coriobacteriaceae, and Parabacteroides, and reduced abundance of Bifidobacterium, Klebsiella, Serratia, and Raoultella. The fermented preparation was associated with reduced accumulation of metabolites typically linked to proteolytic fermentation and a more stable metabolic profile throughout the supplementation and washout phases. Short-chain fatty acid analysis indicated that fermentation influenced both the quantity and proportional balance of microbial fermentation products, promoting profiles closer to physiological reference ranges. Overall, fermentation of apple pomace at 15 °C enhanced its functional properties and modulated gut microbiota metabolism in a manner consistent with improved ecosystem stability. These findings highlight the potential of fermented fruit by-products as sustainable ingredients for dietary strategies aiming to support gut microbial functionality.},
}

*Malus/metabolism/chemistry
*Gastrointestinal Microbiome
*Fermentation
Humans
*Yeasts/metabolism
Fatty Acids, Volatile/metabolism
Bacteria/classification/genetics

@article {pmid41977414,
year = {2026},
author = {Wang, C and Hou, L and Wang, Y and Gao, G and Geng, Y and Pan, J},
title = {Preliminary Study on the Synergistic Degradation Mechanism of the Microbial Community on the Wood of the Dingtao M2 Tomb.},
journal = {International journal of molecular sciences},
volume = {27},
number = {7},
pages = {},
doi = {10.3390/ijms27073233},
pmid = {41977414},
issn = {1422-0067},
support = {2024YFF0907700//National Key R&D Program of China/ ; N/A//Fundamental Research Funds for the Central Universities/ ; N/A//Preservation Research Center of the Mausoleum of the Dingtao King/ ; },
mesh = {*Wood/microbiology/metabolism ; *Microbiota ; Lignin/metabolism ; *Penicillium/metabolism/genetics ; Metagenomics/methods ; },
abstract = {According to our investigation carried out in July 2023, the wood of the Western Han Dynasty Dingtao M2 Tomb, stored in the preservation room, exhibited signs of microbial degradation. Our metagenomic analysis first revealed Penicillium as the dominant genus on the end of the wrapped wood. Furthermore, functional annotations demonstrated that the resident microbial community possessed cellulolytic and ligninolytic capabilities. Targeted metabolomic analysis evaluated the degradation capacity of Penicillium charlesii DTP_1, a strain isolated from the wrapped wood. We hypothesize that DTP_1 provides an acidic microenvironment via the production of organic acids; the functional microbial community then decomposes lignin into small metabolites via enzymatic action, and these products are then utilized by the microbial community, including DTP_1. Finally, we verified that liquid cinnamaldehyde and volatile gaseous allicin and carvacrol exhibit better inhibitory efficacy. Nevertheless, further optimization of plant-derived agents and application methods are still required. This study proposes a putative mechanism underlying the degradation of the Dingtao M2 Tomb wood by the microbial community, thereby providing theoretical support for the conservation of wooden cultural heritage and relics.},
}

*Wood/microbiology/metabolism
*Microbiota
Lignin/metabolism
*Penicillium/metabolism/genetics
Metagenomics/methods

@article {pmid41978025,
year = {2026},
author = {De Nat, M and Boscolo, S and Gallo, SP and Nanni, L and Fusaro, D},
title = {Ensemble Deep Learning Models on Raw DNA Sequences for Viral Genome Identification in Human Samples.},
journal = {Sensors (Basel, Switzerland)},
volume = {26},
number = {7},
pages = {},
doi = {10.3390/s26072238},
pmid = {41978025},
issn = {1424-8220},
mesh = {*Deep Learning ; Humans ; *Genome, Viral/genetics ; Neural Networks, Computer ; *Sequence Analysis, DNA/methods ; Metagenomics/methods ; Base Sequence ; *Viruses/genetics ; },
abstract = {Detecting highly divergent or previously unknown viruses is a critical bottleneck in clinical diagnostics and pathogen surveillance. While alignment-based methods often fail to classify sequences lacking homology to known references, deep learning offers a powerful alternative for signal extraction from 'viral dark matter.' In this work, we present a high-performance ensemble of deep convolutional neural networks specifically designed to identify viral contigs in complex human metagenomic datasets. Our framework processes sequences acquired from high-throughput biological sensors and integrates complementary architectures to capture both local motifs and global genomic signatures. The proposed ensemble achieves state-of-the-art performance, reaching an AUROC of 0.939 on 300 bp contigs and significantly outperforming existing models such as transformer-based approaches, ViraMiner, and DeepVirFinder. Crucially, our results demonstrate high robustness to data degradation, maintaining stable predictive power even with a 10% random nucleotide substitution rate, a common challenge in degraded clinical samples. Furthermore, the model generalizes to 'unseen' viral families not present during training, demonstrating its utility for emerging threat detection. To ensure full reproducibility and facilitate further research in clinical sensing, the complete code and datasets are publicly available on Github.},
}

*Deep Learning
Humans
*Genome, Viral/genetics
Neural Networks, Computer
*Sequence Analysis, DNA/methods
Metagenomics/methods
Base Sequence
*Viruses/genetics

@article {pmid41979145,
year = {2026},
author = {Alderete, TL and Holzhausen, EA and Liang, D and Jones, RB and Lurmann, F and Goran, MI and Chang, HH and Sarnat, JA},
title = {Early-Life Air Pollution Exposure Is Associated with the Infant Gut Microbiome and Fecal Metabolome in the First Two Years of Life.},
journal = {Research report (Health Effects Institute)},
volume = {},
number = {237},
pages = {1-58},
pmid = {41979145},
issn = {1041-5505},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Feces/chemistry/microbiology ; Female ; *Metabolome/drug effects ; Infant ; Male ; *Air Pollution/adverse effects/analysis ; *Air Pollutants/adverse effects/analysis ; Pregnancy ; Particulate Matter/adverse effects/analysis ; *Environmental Exposure/adverse effects ; California ; Prenatal Exposure Delayed Effects ; Infant, Newborn ; },
abstract = {INTRODUCTION: Obesity is a major public health concern because it increases the risk of numerous diseases, including cardiovascular disease and type 2 diabetes. Ambient and near-roadway air pollution has been associated with childhood obesity risk, independent of diet and physical activity. However, the biological mechanisms underlying these relationships remain unclear. Based on our previous work and existing literature, we hypothesized that exposure to air pollutants alters the developing infant gut microbiome and fecal metabolome, with implications for childhood obesity risk. In this study, we aimed to determine whether prenatal or early-life exposure to ambient air pollution and near-roadway air pollution is associated with the gut microbiome and fecal metabolome during the first 2 years of life.

METHODS: Our analysis had two components, both of which examined participants from the Southern California Mother's Milk Study, a Latino cohort in which we collected detailed information regarding maternal and child health during the first 24 months of life. Residential-based estimates of exposure to ambient particulate matter (particulate matter ≤2.5 µm and ≤10 µm in aerodynamic diameter: PM2.5 and PM10, respectively), nitrogen dioxide (NO2), and ozone (O3), as well as near-roadway air pollution (NOx), were modeled using residential address histories. High-throughput metagenomics and metabolomics were performed on stool samples collected at 1, 6, 12, 18, and 24 months of age. Overall, our sample included 207 unique individuals with gut microbiome data and 127 unique individuals with fecal metabolomics data. In the first analysis component, we examined the cross-sectional associations of pre- and postnatal exposure to ambient and near-roadway pollutants with the infant gut microbiome and fecal metabolome at 1, 6, 12, 18, and 24 months of age. In the second analysis component, we examined the longitudinal associations of pre- and postnatal exposure to air pollutants with the trajectory of the developing infant gut microbiome and fecal metabolome.

RESULTS: Our findings indicate that exposure to air pollutants during prenatal and postnatal periods is associated with significant changes in the developing gut microbiome and its metabolic output, as evidenced by perturbations in the fecal metabolome. These molecular alterations were evident in both cross-sectional and longitudinal analyses. The results suggest that early-life exposure to air pollution can disrupt the developmental trajectory of the gut microbiome, potentially leading to changes with substantial health implications. These findings underscore the importance of mitigating air pollution exposure during critical developmental periods to protect and promote gut health and overall well-being in infants.

CONCLUSIONS: We identified gut microbes and fecal metabolites associated with early-life exposure to air pollution. Many of these markers of gut bacterial composition and function have been linked to childhood obesity. These findings contribute to our understanding of mechanisms underlying the obesogenic effects of air pollutants in early life. Future work in this cohort will include integrated mixture and multi-omics analyses to explore the joint impact of air pollution exposure on the gut microbiome and fecal metabolome.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Feces/chemistry/microbiology
Female
*Metabolome/drug effects
Infant
Male
*Air Pollution/adverse effects/analysis
*Air Pollutants/adverse effects/analysis
Pregnancy
Particulate Matter/adverse effects/analysis
*Environmental Exposure/adverse effects
California
Prenatal Exposure Delayed Effects
Infant, Newborn

@article {pmid41979617,
year = {2026},
author = {Li, G and Dan, N and Lu, T},
title = {Two Cases of Severe Chlamydia psittaci Pneumonia with Respiratory Failure and Literature Review.},
journal = {Clinical laboratory},
volume = {72},
number = {4},
pages = {},
doi = {10.7754/Clin.Lab.2025.250675},
pmid = {41979617},
issn = {1433-6510},
mesh = {Humans ; *Chlamydophila psittaci/genetics/isolation & purification ; *Respiratory Insufficiency/microbiology/diagnosis/etiology ; *Psittacosis/diagnosis/drug therapy/microbiology/complications ; Male ; Anti-Bacterial Agents/therapeutic use ; Middle Aged ; High-Throughput Nucleotide Sequencing ; Female ; Treatment Outcome ; },
abstract = {BACKGROUND: Chlamydia psittaci pneumonia is a zoonotic disease with non-specific clinical manifestations, often leading to delayed diagnosis. Metagenomic next-generation sequencing (mNGS) can help us identify pathogens in a timely manner and quickly adjust treatment strategies.

METHODS: We reported two cases of severe Chlamydia psittaci pneumonia with respiratory failure and reviewed relevant literature.

RESULTS: Both patients were diagnosed with Chlamydia psittaci infection through mNGS after routine pathogen testing failed. After using Omadacycline based treatment, the patients' clinical and radiological characteristics improved significantly and were successfully cured.

CONCLUSIONS: For patients infected with Chlamydia psittaci pneumonia, timely identification of the pathogen is crucial. mNGS can quickly detect Chlamydia psittaci in critically ill patients, guide clinical timely targeted treatment, and improve patient symptoms.},
}

Humans
*Chlamydophila psittaci/genetics/isolation & purification
*Respiratory Insufficiency/microbiology/diagnosis/etiology
*Psittacosis/diagnosis/drug therapy/microbiology/complications
Male
Anti-Bacterial Agents/therapeutic use
Middle Aged
High-Throughput Nucleotide Sequencing
Female
Treatment Outcome

@article {pmid41979623,
year = {2026},
author = {Xie, BX and Chen, Y and Tan, YR and Jiang, T and Huang, MH and Zhu, YM and Chen, S},
title = {Challenges in the Diagnosis of Hematogenous Disseminated Pulmonary Tuberculosis with Multiple Organ Involvement.},
journal = {Clinical laboratory},
volume = {72},
number = {4},
pages = {},
doi = {10.7754/Clin.Lab.2025.250640},
pmid = {41979623},
issn = {1433-6510},
mesh = {Humans ; *Mycobacterium tuberculosis/genetics/isolation & purification ; *Tuberculosis, Pulmonary/diagnosis/microbiology ; Pericardial Effusion/microbiology ; Male ; Tomography, X-Ray Computed ; High-Throughput Nucleotide Sequencing ; Middle Aged ; *Tuberculosis, Miliary/diagnosis/microbiology ; Antitubercular Agents/therapeutic use ; },
abstract = {BACKGROUND: Tuberculosis is a public health problem worldwide, and China is a high-burden country. Hematogenous disseminated pulmonary tuberculosis is one of the most serious forms of tuberculosis, and diagnosing hematogenous pulmonary tuberculosis is a challenge, even for the most experienced clinicians, who may also feel perplexed. We report a case of hematogenous disseminated tuberculosis involving multiple organs that was initially misdiagnosed as metastatic malignancy. The diagnosis was finally confirmed by metagenomic Next-Generation Sequencing (m-NGS) of peritoneal and pericardial effusions, which detected Mycobacterium tuberculosis complex.

METHODS: Appropriate laboratory tests, m-NGS, Chest and abdominal CT, Pericardiocentesis, and Peritoneal puncture.

RESULTS: Chest and abdominal CT showed diffuse nodules in both lungs, pericardial effusion, bilateral pleural effusion, and abdominal pelvic effusion. Tuberculosis bacillus antibody was negative, erythrocyte sedimentation rate increased to 42 mm/H, and the carcinoembryonic antigen (CEA) increased to 7.1 ng/mL, peritoneal effusion adenosine deaminase increased to 65.17 U/L, pericardial effusion adenosine deaminase increased to 142.39 U/L. m-NGS of pericardial effusion and peritoneal effusion detected 886,963 M. tuberculosis complex.

CONCLUSIONS: Miliary tuberculosis is a severe and rare form of tuberculosis. Delayed diagnosis may be the most important factor leading to death from miliary tuberculosis. We report a case where Mycobacterium tuberculosis was identified through mNGS of pericardial and peritoneal effusions, enabling rapid diagnosis of disseminated tuberculosis. This case provides a new approach for the rapid diagnosis of disseminated tuberculosis.},
}

Humans
*Mycobacterium tuberculosis/genetics/isolation & purification
*Tuberculosis, Pulmonary/diagnosis/microbiology
Pericardial Effusion/microbiology
Male
Tomography, X-Ray Computed
High-Throughput Nucleotide Sequencing
Middle Aged
*Tuberculosis, Miliary/diagnosis/microbiology
Antitubercular Agents/therapeutic use

@article {pmid41980062,
year = {2026},
author = {Zhan, J and Yang, W and Guo, J and Yu, Y and Lai, S and Liu, X and Zhou, S},
title = {Iron plaques as terminal electron acceptors optimize clostridial fermentation and nitrogen fixation in rice rhizospheres.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag088},
pmid = {41980062},
issn = {1751-7370},
abstract = {Fermentative Clostridium species associated with rice roots can contribute substantially to biological nitrogen fixation in anoxic paddy soils, yet whether their biological nitrogen fixation is regulated by the redox chemistry of rhizosphere remains unclear. Here we show that iron plaques on rice roots function as terminal electron acceptors that reprogram Clostridium fermentation and thereby enhance biological nitrogen fixation. In nitrogen-fixation microcosms, Clostridium sensu stricto I was selectively enriched under plaque-associated Fe(III)-reducing conditions, coinciding with elevated nitrogen fixation. Metabolomic profiling coupled with metabolic flux analysis revealed that Fe(III) reduction redirects a portion of carbon and electron flow from low-energy-yield solventogenesis toward high-energy-yield acidogenesis. This shift increases cellular ATP generation and expands the reductant pool, thereby benefiting the energetic and reductant demands of nitrogenase. Integrated transcriptomic and metagenomic analyses further identified NosR, a flavin mononucleotide-binding protein that is upregulated during Fe(III) reduction and may facilitate electron delivery to plaque-associated Fe(III). Our findings establish a mechanism in which iron plaque reduction optimizes fermentation for biological nitrogen fixation, providing fundamental insights into coupled Fe-N cycling in rice rhizospheres and suggesting potential strategies for sustainable nitrogen management in flooded agroecosystems.},
}

@article {pmid41980294,
year = {2026},
author = {Paulí, S and Rosell-Díaz, M and Moreno-Navarrete, JM and Pons Tamarit, J and Pérez-Brocal, V and Moya, A and Puig, J and Garre-Olmo, J and Ramos, R and Fernández-Real, JM and Mayneris-Perxachs, J},
title = {Glucose metabolism's impact on Blastocystis presence in the human gut.},
journal = {Clinical nutrition (Edinburgh, Scotland)},
volume = {61},
number = {},
pages = {106647},
doi = {10.1016/j.clnu.2026.106647},
pmid = {41980294},
issn = {1532-1983},
abstract = {BACKGROUND AND AIMS: The role of Blastocystis spp. parasite in human health remains debated. Recent literature associates it with a healthy gut and lifestyle. Evidence suggests that Blastocystis spp. could enhance glucose homeostasis, although Blastocystis spp. is considered to be epiphenomena for a lifestyle. Moreover, some subtypes seem to have a beneficial impact while others would hinder the host's health. Here, we explore the complex link between Blastocystis spp. and glucose metabolism parameters.

METHODS: We explored shotgun metagenomic profiles of the gut microbiota from fecal samples associated with glucose metabolism parameters in 4 independent cohorts (CGM, n = 65; IMAGEOMICS, n = 1030; PECT, n = 841 and MEIFLO, n = 22), using microbiome compositional analysis methodology. We leverage data from MEIFLO, a recent clinical trial conducted in patients recently diagnosed with type 2 diabetes (T2D), to investigate how metformin-induced improvement in glucose metabolism influences gut microbiota composition, using Linear Models for Differential Abundance. We studied possible associations of Blastocystis spp. with leukocyte telomere length.

RESULTS: We confirmed and extended the relationship between glucose homeostasis and Blastocystis spp. and subtypes ST1 and ST4, showing its association with glucose and insulin levels in all cohorts. Importantly, we observed that glucose homeostasis may shape Blastocystis spp. abundance in the gut, rather than the reverse, based on clinical trial data showing that metformin (not placebo) increased Blastocystis spp. in recently diagnosed T2D patients. We identify Blastocystis as one of the microbial genera most strongly and directly associated with telomere length in the IMAGEOMICS cohort.

CONCLUSIONS: The direct relation between Blastocystis and telomere length aligns with the observed inverse associations of glucose levels with telomere length, and glucose levels with Blastocystis. We propose that Blastocystis may be associated with healthy glucose metabolism as an outcome and potentially serve as an indicator of improved metabolic health.},
}

@article {pmid41980639,
year = {2026},
author = {Li, R and Li, S and Yan, Y and Xie, Y and Liu, L and Zhao, J and Zhang, J and Cai, Z and Huang, X},
title = {Reductive soil disinfestation and hydrothermal biochar regulate antibiotic resistance mechanisms by reshaping soil bacterial functional traits and interaction patterns.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134622},
doi = {10.1016/j.biortech.2026.134622},
pmid = {41980639},
issn = {1873-2976},
abstract = {The health risk posed by antibiotic resistance genes (ARGs) in agricultural soils has become a growing concern. However, a systematic understanding of how microbial life history strategies, functional traits, and community interactions jointly shape ARG dynamics remains lacking. This knowledge gap not only constrains our ability to elucidate the evolutionary mechanisms underlying microbial resistance but also hampers the precise prediction and effective management of soil ARG risks. Here, we established distinct soil habitats through diverse soil managements, including control (CK), reductive soil disinfestation (RSD), and RSD combined with hydrothermal biochar application (HCR), to investigate how microbial traits and interactions shape ARG resistance mechanisms using metagenomic analyses. Our results showed that RSD and HCR treatments significantly reduced the overall abundance and ecological risk of ARGs compared to CK. In CK soils, microbial communities characterized by intensive interactions, high metabolic activity, and rapid growth efficiency promoted the enrichment of ARGs conferring resistance via antibiotic target alteration, protection, or replacement. In contrast, RSD/HCR treatments favored slow-growing, functionally complex, and competition-dominated communities, which were enriched in ARGs associated with antibiotic efflux mechanisms. Moreover, ARGs exhibited pronounced co-occurrence patterns with antimicrobial biosynthetic gene clusters in highly competitive environments. Collectively, this study reveals the selective responses of ARG resistance mechanisms to distinct microbial ecological strategies and provides new insights for the precise management of environmental antibiotic resistance risks.},
}

@article {pmid41980640,
year = {2026},
author = {Yang, H and Peng, N and Fan, Y and Huang, J and Zhang, J and Li, L and Ding, J and Tang, Z and Song, J and Liu, D and Hu, R and He, Z and Wang, C},
title = {Genome-Resolved insights into significance of DNRA Microbes in N2O production during manure composting.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134617},
doi = {10.1016/j.biortech.2026.134617},
pmid = {41980640},
issn = {1873-2976},
abstract = {Nitrous oxide (N2O) production during manure composting has traditionally been attributed primarily to heterotrophic denitrification (HD), while the roles of alternative pathways remain poorly resolved. Using time-resolved multi-omics across 37 samples from various manure sources, our study investigated the transcriptional landscape of N2O-producing pathways during composting. Microorganisms associated with dissimilatory nitrate reduction to ammonium (DNRA), including Fermentimonas and JAHWKS01 lineages, accounted for 21.2-33.1% of N2O-producing gene expression-comparable to HD-revealing DNRA as a previously underappreciated source. DNRA-associated gene expression was regulated by viral factors, predominantly through lytic Caudoviricetes phages. Expanding our analysis to 174 public metagenomic datasets revealed that DNRA-derived N2O-producing gene abundance peaked under static and hyperthermophilic conditions, highlighting aeration and temperature as critical mitigation controls. Furthermore, our study identified a substantial proportion of microorganisms harboring both DNRA and HD pathways. These findings refine mechanistic understanding of composting N2O emissions and inform multi-pathway mitigation strategies.},
}

@article {pmid41980647,
year = {2026},
author = {Song, M and Jiang, L and Lin, Z and Li, J and Luo, C and Qiu, R},
title = {Size-dependent effect of microplastics on sulfamethoxazole degraders in soil as revealed by integration of SIP and metagenomics.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134620},
doi = {10.1016/j.biortech.2026.134620},
pmid = {41980647},
issn = {1873-2976},
abstract = {Microbes related to antibiotic degradation in situ in agricultural soil with MPs and their response to different sizes of MPs are ambiguity. This study investigated the microbes participating in antibiotic degradation in soils with 4.5 mm and 0.1 mm MPs by using DNA-SIP with metagenomics, Raman-activated cell sorting (RACS) with sulfamethoxazole (SMX) and polyethylene as the model compound and MPs. The 4.5 mm MPs enhanced SMX degradation by promoting diversity and abundance of degraders benefiting from improved soil properties, relation between degraders and SMX, and bacteria with positive co-occurrence relationship with degraders. The 0.1 mm MPs inhibited SMX degradation by decreasing diversity, abundance of degraders, and intensifying bacteria mutually exclusive with degraders due to harsher soil conditions. Furthermore, DNA-SIP-RACS successfully acquired cells of SIP-identified putative degraders, and directly linked SMX degradation potential with metC1, metF1and luxS1, proving possibility of applying this approach in antibiotic-degrading microbes in soil.},
}