@article {pmid41526579,
year = {2026},
author = {Fang, H and Pu, M and Jiang, A and Haiti, F and Liu, Y and Ailijiang, N and Mamat, A and Tu, X},
title = {Prevalence of antibiotic resistance gene in different wastewater treatment systems and effluent-irrigated soils through metagenomic analysis.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-35758-1},
pmid = {41526579},
issn = {2045-2322},
support = {XJJT2KX-FWCG-202411-0736//Research and Demonstration Application of Technology for the Construction of Near Zero Carbon Smart Service Areas with Self Consistent Water Resources and Energy in Desert Areas/ ; XJJT2KX-FWCG-202411-0736//Research and Demonstration Application of Technology for the Construction of Near Zero Carbon Smart Service Areas with Self Consistent Water Resources and Energy in Desert Areas/ ; XJJT2KX-FWCG-202411-0736//Research and Demonstration Application of Technology for the Construction of Near Zero Carbon Smart Service Areas with Self Consistent Water Resources and Energy in Desert Areas/ ; XJJT2KX-FWCG-202411-0736//Research and Demonstration Application of Technology for the Construction of Near Zero Carbon Smart Service Areas with Self Consistent Water Resources and Energy in Desert Areas/ ; 51968067//National Natural Science Foundation of China/ ; 2024TSYCCX0014//the "Tianshan Yingcai" Cultivation Program/ ; },
abstract = {Wastewater treatment systems (WWTS) are considered to be the main source of antibiotic resistance genes (ARGs) spreading into the environment. In this study, samples were collected from WWTS influent, biological treatment tank effluent, and recycled water treatment plant (RTP) effluent during summer and winter, followed by metagenomic sequencing. The study investigated the differences in antibiotic resistance gene transfer between two typical wastewater treatment plants (WWTPs) processes and the impact of recycled water irrigation on ARG dissemination in soil. The WWTS (HD and MD) adopting two combined processes of "Adsorption-Biodegradation Process(AB)+ Anaerobic-Anoxic-Oxic Process(AAO)" and "AAO + Membrane Bioreactor(MBR)" as the research objects for the first time.The primary ARGs types identified were multidrug resistance, tetracycline, macrolide, and aminoglycoside resistance genes. The top three ARGs subtypes by relative abundance in the influent, biological treatment tank effluent, and total effluent were msrE, mphE, and ANT(6)-Ia, respectively. Seasonal variations did not significantly influence the distribution of ARGs in the two WWTSs. The AAO and AB processes increase the relative abundance and diversity of ARGs, while ARGs relative abundance decreases after RTP treatment but may proliferate new ARGs subtypes. Additionally, the efficiency of reducing the relative abundance of ARGs in summer is higher than that in winter. The two WWTSs were able to efficiently remove msrE and mphE. The abundance and diversity of ARGs and microorganisms were maximum in soil samples from the RTP. The microbial genera significantly related to ARGs may become its potential host, such as Rhodanobacter had significant correlations with ropB2, carA, and oleB. These results provide new insights into the control of ARGs contamination and focus on the risks associated with irrigated wastewater.},
}

@article {pmid41526362,
year = {2026},
author = {Ascandari, A and Aminu, S and Benhida, R and Daoud, R},
title = {Cross-cohort resistome and virulome gradients structure the colorectal cancer microbiome.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-025-00905-5},
pmid = {41526362},
issn = {2055-5008},
abstract = {The gut microbiome is increasingly implicated in colorectal cancer (CRC), yet the functional signatures associated with disease progression remain poorly resolved across populations. We performed an assembly-based metagenomic analysis of more than 500 samples from three geographically distinct cohorts to characterize resistome and virulome patterns associated with CRC. Using a cross-validated modeling framework based on Partial Least Squares (PLS) regression, we identified two reproducible latent functional gradients that structured variation in antimicrobial-resistance and virulence-factor profiles. One gradient was enriched for adhesion, efflux, and biofilm-associated functions, while the second reflected immunomodulatory and barrier-related pathways. These components were statistically robust, directionally stable across cohorts, and consistent with functional themes frequently reported in CRC microbiome studies. To summarize variation along these gradients, we derived an exploratory Dual-Axis Index (DAI) based on the two stable PLS components. Although its discriminative performance was moderate, the DAI provided an interpretable low-dimensional representation of how resistome-virulome patterns differed across healthy, adenoma, and carcinoma states. These results suggest that functional gene profiles in CRC are organized along reproducible statistical axes, and highlight functional modules, such as adhesion-, iron-associated, and immune-interaction pathways that may complement taxonomic or metabolic biomarkers in future multimodal approaches. Our work provides a reproducible, assembly-based framework for examining the functional organization of CRC-associated microbiomes across diverse populations.},
}

@article {pmid41526357,
year = {2026},
author = {Cronin, P and Siegers, JY and Heang, V and Tok, S and Sin, S and Sievers, B and Omondi, V and Nuon, S and Chhel, K and Nouhin, J and Chim, V and Seng, B and Hak, M and San, S and Tum, S and Claes, FF and Firth, C and Su, YCF and Smith, GJD and Karlsson, EA},
title = {Environmental metagenomics enhances detection of circulating viruses from live poultry markets in Cambodia.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-68245-8},
pmid = {41526357},
issn = {2041-1723},
abstract = {Environmental surveillance has emerged as a pivotal strategy for early detection of pathogens that pose a threat to humans. In Asia, live-bird markets (LBMs) are key human-animal interfaces for zoonotic virus transmission. Traditional sampling strategies are time-consuming, expensive and carry significant biosafety risks. Here, we assess the performance of metagenomics on environmental samples (ES) versus traditional poultry swabs for detecting viral pathogens in two Cambodian LBMs between January 2022 and April 2023. ES, including air (n = 35), cage swabs (n = 17), carcass wash water (n = 17) and drinking water (n = 9) are collected alongside oropharyngeal and cloacal swabs from chickens (n = 30) and ducks (n = 29). ES is sensitive in detecting 40 viruses from pathogen families including Orthomyxoviridae and Coronaviridae. Air samples capture the greatest diversity of poultry viruses. Viral contigs from ES show high sequence identity to poultry swab contigs when aligned to the same gene. We show ES outperforms poultry samples in detecting the highly pathogenic influenza A/H5N1, including clades 2.3.4.4b and 2.3.2.1c, which are found in the environment but are missed by poultry swabs. Our findings show metagenomics on ES replicates traditional surveillance, offering broader coverage and improved pathogen detection. This approach could be pivotal for mitigating zoonotic spillover and enhancing pandemic preparedness.},
}

@article {pmid41525981,
year = {2026},
author = {Yan, Y and Gao, Y and Gao, M and Chen, J and Cui, L and Ma, Y},
title = {Decipherment of dissolved organic matter compositions on waste activated sludge under in situ multi-enzyme pretreatment: novel bioavailability-oriented evaluation framework.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133995},
doi = {10.1016/j.biortech.2026.133995},
pmid = {41525981},
issn = {1873-2976},
abstract = {This study systematically elucidated the dissolved organic matters (DOM) molecular conversion and biological response mechanisms during anaerobic digestion (AD) of waste activated sludge (WAS) under different multi-enzyme pretreatment durations. Fourier transform ion cyclotron resonance mass spectrometry analysis revealed that the biodegradable protein-like and amino sugar-like substances were converted into recalcitrant aromatic nitrogen-containing compounds via hydrolysis, condensation, and cyclization processes as extended pretreatment duration, significantly reducing DOM bioavailability. Metagenomic sequencing further indicated that the DOM deterioration inhibited the enrichment of hydrolytic and acidogenic bacteria, thereby suppressed the acetotrophic methanogenesis and methane production. Based on these insights, a novel DOM bioavailability-oriented evaluation framework was proposed for WAS pretreatment optimization, focusing on three key metrics, including the relative abundance of biodegradable substrates, key microorganisms and functions, and methanogenic pathways. Expectantly this study may provide theoretical and data support for future precise design of enzymatic pretreatment process and high-efficiency AD of WAS.},
}

@article {pmid41525926,
year = {2026},
author = {Sbampato, V and De Marco, G and Tsoupras, A and Khan, A and Beaugé, A and Dayer, R and Tabard-Fougère, A and Ceroni, D},
title = {Next Generation Sequencing for Diagnosing Primary Osteoarticular Infections Compared to Conventional Culture: A Systematic Review and Meta-Analysis.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {108380},
doi = {10.1016/j.ijid.2026.108380},
pmid = {41525926},
issn = {1878-3511},
abstract = {BACKGROUND: Osteoarticular infections (OAIs) in children is a significant diagnostic challenge for healthcare professionals. Traditional culture techniques are often time consuming and demonstrated low sensitivity. This systematic review aims to evaluate the diagnostic yield of metagenomic Next Generation Sequencing (mNGS) compared to standard culture for detecting pathogens in OAIs.

METHODS: A systematic review (PROSPERO CRD420251131272) of three databases (2000-2025) was performed. Study quality was assessed using the QUADAS-2 tool. A meta-analysis was performed using a random-effects model to calculate pooled positive detection rate with 95% confidence intervals (95%CI). Heterogeneity was quantified (I[2]), and sensitivity analysis with leave-one-out and subgroups were performed.

FINDINGS: From 35 included studies (>3000 patients), mNGS demonstrated a significantly higher pooled positive detection rate (81%; 95%CI:75 to 85%) than traditional culture (35%; 95%CI:29 to 41%) with high heterogeneity (>80%). mNGS performed consistently in pediatric (79%) and adult (81%) subgroups and was particularly effective for spinal infections (82%).

INTERPRETATION: The mNGS demonstrates a significantly higher diagnostic yield than standard culture for pathogen detection in osteoarticular infections. Its simplicity of execution, its fast-processing methods and high sensitivity, are promising factors that could lead to a more reliable detection of the causative microorganism responsible for an osteoarticular infection.},
}

@article {pmid41525910,
year = {2026},
author = {Fourgeaud, J and Veyrenche, N and Laloum, I and Jais, JP and Roger, C and Rabant, M and Mallet, V and Beaufrère, A and Fontaine, H and Leruez-Ville, M and Durand, F and Anglicheau, D},
title = {Occult rat Hepatitis E Virus Infection as a Cause of Cirrhosis and Post-Transplant Recurrence: Insights into the Role of Metagenomics.},
journal = {American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajt.2026.01.005},
pmid = {41525910},
issn = {1600-6143},
abstract = {We report the case of a kidney transplant recipient (2011) who developed persistent elevation of liver enzymes beginning in 2015. Extensive investigations including standard Hepatitis E virus PCR failed to identify a cause. In 2019, she developed decompensated cirrhosis and underwent liver-kidney transplantation in 2021. Post-transplant, liver function tests remained abnormal. Given suspicion of an unidentified pathogen, metagenomic next-generation sequencing was performed on the graft and identified rat hepatitis E virus. Retrospective testing of native liver and serum samples confirmed infection since 2015. Ribavirin therapy resulted in normalization of liver enzymes and viral clearance.},
}

@article {pmid41525322,
year = {2026},
author = {Karagiannis, TT and Chen, Y and Bald, S and Tai, A and Reed, ER and Milman, S and Andersen, SL and Perls, TT and Segrè, D and Sebastiani, P and Short, MI},
title = {Integrative analysis across metagenomic taxonomic classifiers: A case study of the gut microbiome in aging and longevity in the Integrative Longevity Omics Study.},
journal = {PLoS computational biology},
volume = {22},
number = {1},
pages = {e1013883},
doi = {10.1371/journal.pcbi.1013883},
pmid = {41525322},
issn = {1553-7358},
abstract = {There are various well-validated taxonomic classifiers for profiling shotgun metagenomics data, with two popular methods, MetaPhlAn (marker-gene-based) and Kraken (k-mer-based), at the forefront of many studies. Despite differences between classification approaches and calls for the development of consensus methods, most analyses of shotgun metagenomics data for microbiome studies use a single taxonomic classifier. In this study, we compare inferences from two broadly used classifiers, MetaPhlAn4 and Kraken2, applied to stool metagenomic samples from participants in the Integrative Longevity Omics study to measure associations of taxonomic diversity and relative abundance with age, replicating analyses in an independent cohort. We also introduce consensus and meta-analytic approaches to compare and integrate results from multiple classifiers. While many results are consistent across the two classifiers, we find classifier-specific inferences that would be lost when using one classifier alone. Both classifiers captured similar age-associated changes in diversity across cohorts, with variability in species alpha diversity driven by differences by classifier. When using a correlated meta-analysis approach (AdjMaxP) across classifiers, differential abundance analysis captures more age-associated taxa, including 17 taxa robustly age-associated across cohorts. This study emphasizes the value of employing multiple classifiers and recommends novel approaches that facilitate the integration of results from multiple methodologies.},
}

@article {pmid41525137,
year = {2026},
author = {Jackson, SA and Hrab, P and Zdouc, MM and Clarke, DJ and Dobson, ADW},
title = {New insights into the microbiome of the deep-sea sponge Inflatella pellicula and the secondary metabolic potential of metagenome-assembled genomes and the wider microbiome.},
journal = {Microbial genomics},
volume = {12},
number = {1},
pages = {},
pmid = {41525137},
issn = {2057-5858},
mesh = {*Porifera/microbiology ; Animals ; *Metagenome ; *Microbiota/genetics ; Secondary Metabolism/genetics ; Phylogeny ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Multigene Family ; Genome, Bacterial ; Sequence Analysis, DNA ; },
abstract = {Marine sponges are found in all of the world's oceans, from the surface waters to the deepest abyssal zones. The marine sponge holobiont is a rich source of microbial and chemical diversity. Up to 63 bacterial phyla have been observed to be associated with sponges, and thousands of unique natural products have been extracted from sponges or their microbial symbionts. However, sponges from the deep sea and their associated microbial communities are relatively understudied, largely due to sampling-associated difficulties. Secondary metabolism biosynthetic gene clusters are phylogenetically distinct and hold the potential to produce novel chemistry with potential pharmacological or industrial utility. In order to gain further insights into the microbiome of the deep-sea sponge Inflatella pellicula, the metagenome of this sponge, sampled from a depth of 2,900 m, was sequenced. A large fraction of the sequence reads appeared to be 'biological dark matter' and could not be taxonomically classified. Further, unlike similar studies from different marine ecosystems, relatively few metagenome-assembled genomes (MAGs) could be assembled, and relatively few secondary metabolism biosynthetic gene clusters were identified. The identified clusters were, however, very dissimilar to known characterized clusters, but some shared similarities with clusters annotated in MAGs assembled from sponge metagenomes from disparate geographic locations. Therefore, renewed efforts to cultivate the hosts of these gene clusters may yield valuable small-molecule natural products.},
}

*Porifera/microbiology
Animals
*Metagenome
*Microbiota/genetics
Secondary Metabolism/genetics
Phylogeny
*Bacteria/genetics/classification/metabolism/isolation & purification
Multigene Family
Genome, Bacterial
Sequence Analysis, DNA

@article {pmid41524947,
year = {2026},
author = {Shafi, Z and Shahid, M and Singh, R},
title = {Food-borne bacterial pathogens: emerging approaches in detection and prevention.},
journal = {Archives of microbiology},
volume = {208},
number = {2},
pages = {109},
pmid = {41524947},
issn = {1432-072X},
mesh = {*Food Microbiology/methods ; *Foodborne Diseases/prevention & control/microbiology/diagnosis ; *Bacteria/isolation & purification/genetics/classification/pathogenicity ; Humans ; Food Safety ; Computational Biology/methods ; },
abstract = {Food-borne bacterial pathogens remain a major public health concern, causing extensive illness and economic losses worldwide. Conventional detection methods are often slow and insufficient for identifying viable but non-culturable pathogens. Recent microbiological, biotechnological and bioinformatic advances have markedly improved food safety monitoring. Rapid molecular assays (PCR, qPCR, microarrays), next-generation sequencing, metagenomics, and emerging CRISPR-based diagnostics enable faster and more accurate pathogen detection and outbreak tracing. Bioinformatic tools-including genomic databases, phylogenetics, and machine-learning models-support predictive risk assessment and real-time surveillance. Preventive innovations such as bacteriophages, probiotics, antimicrobial peptides, nanotechnology-based interventions, and engineered microbes provide sustainable alternatives to chemical preservatives. Key challenges include variability across food matrices, biosafety considerations, and limited integration of multi-omics approaches into routine workflows. Overall, these emerging strategies offer improved precision and responsiveness for detecting and preventing food-borne bacterial pathogens.},
}

*Food Microbiology/methods
*Foodborne Diseases/prevention & control/microbiology/diagnosis
*Bacteria/isolation & purification/genetics/classification/pathogenicity
Humans
Food Safety
Computational Biology/methods

@article {pmid41524921,
year = {2026},
author = {Nayab, GE and Ur Rahman, R and Hanan, F and Khan, I and Fahim, M},
title = {Metagenomic Exploration of the Bacteriome Reveals Natural Wolbachia Infections in Yellow Fever Mosquito Aedes aegypti and Asian Tiger Mosquito Aedes albopictus.},
journal = {Current microbiology},
volume = {83},
number = {2},
pages = {133},
pmid = {41524921},
issn = {1432-0991},
mesh = {Animals ; *Aedes/microbiology/classification ; *Wolbachia/genetics/classification/isolation & purification ; Phylogeny ; Pakistan ; Metagenomics ; *Mosquito Vectors/microbiology ; RNA, Ribosomal, 16S/genetics ; Female ; *Microbiota ; *Metagenome ; Electron Transport Complex IV/genetics ; DNA, Bacterial/genetics ; },
abstract = {Dengue and associated complications are spreading to non-endemic regions of Pakistan. Vector control, the foremost and widely adopted strategy for managing dengue has been implemented through various measures in Pakistan. Biological control through the use of Wolbachia, a bacterium naturally present in various insect genera, including Aedes, has demonstrated promising results globally. In this study we collected Aedes species and investigated its microbiomes with a particular focus on identifying the endosymbiont Wolbachia. Mosquitoes were collected via Gravitraps in the Peshawar region of Pakhtunkhwa province in the northwest of Pakistan. The identity of the mosquitoes was initially confirmed through morphological characters followed by molecular identification using species-specific Cytochrome oxidase I (COI) primers. The DNA from female Ae. aegypti and Ae. albopictus was further subjected to 16 S rRNA sequencing. The hypervariable regions V3/V4 of 16 S rRNA were used for sequencing using the paired-end Illumina MiSeq platform. The phylogenetic analysis of the COI gene in our samples demonstrated similarity to Aedes species previously documented in Pakistan. In comparative analysis of the microbiomes, Ae. albopictus was found to harbor 921 bacterial species, while Ae. aegypti only had 239 species. The metagenomic analysis revealed single-strain Wolbachia pipientis infection in Ae. aegypti, while Ae. albopictus harbored a double-strain infection involving a supergroup A strain (referred to as Wolbachia pipientis in 16 S EzBioCloud database) and a supergroup B strain (referred to as Wolbachia bourtzisii in16S EzBioCloud database).},
}

Animals
*Aedes/microbiology/classification
*Wolbachia/genetics/classification/isolation & purification
Phylogeny
Pakistan
Metagenomics
*Mosquito Vectors/microbiology
RNA, Ribosomal, 16S/genetics
Female
*Microbiota
*Metagenome
Electron Transport Complex IV/genetics
DNA, Bacterial/genetics

@article {pmid41524878,
year = {2026},
author = {Ohsawa, M and Nishi, H and Hamai, Y and Emi, M and Ibuki, Y and Komatsuzawa, H and Kawaguchi, H and Okada, M},
title = {Relationship Between the Oral Microbiome and Treatment Efficacy in Esophageal Squamous Cell Carcinoma.},
journal = {Annals of surgical oncology},
volume = {},
number = {},
pages = {},
pmid = {41524878},
issn = {1534-4681},
abstract = {BACKGROUND: As the relationship between oral microbiota and treatment efficacy in esophageal cancer remains unexplored, we aimed to clarify it using metagenomic analysis.

PATIENTS AND METHODS: Of the 140 consecutive patients with esophageal squamous cell carcinoma (ESCC) who underwent esophagectomy with R0 resection at Hiroshima University Hospital between April 2020 and May 2024, 74 who received neoadjuvant therapy were included in this study. 16S rRNA gene from oral tongue coating samples was amplified using polymerase chain reaction and subjected to next-generation sequencing. The oral microbiome data were analyzed using QIIME2 and linear discriminant analysis effect size, and the relationship between the oral microbiota and treatment efficacy and prognosis was assessed.

RESULTS: Alpha diversity of the oral microbiota was significantly correlated with the pathological response. Univariate and multivariate analyses showed that the alpha diversity of the oral microbiome (high versus low) was a significant predictor of a good pathological response. Patients with high alpha diversity had significantly improved recurrence-free survival and overall survival compared with those with low alpha diversity. Furthermore, eight bacterial groups (Lactobacillales, Peptostreptococcales-Tissierellales, Bifidobacteriaceae, Erysipelotrichaceae, Lactobacillaceae, Anaerovoracaceae, Staphylococcaceae, and Aerococcaceae) were significantly more abundant in individuals who responded well to neoadjuvant therapy and two bacterial groups (Streptococcaceae and Corynebacteriaceae) were significantly more abundant in poor responders.

CONCLUSIONS: Our results demonstrate a correlation between the oral microbiome and ESCC treatment efficacy, suggesting that it is a significant prognostic factor. Our findings may also help predict the efficacy of esophageal cancer treatment.},
}

@article {pmid41524860,
year = {2026},
author = {Parab, C and Yadav, KD and Prajapati, V},
title = {Metagenomic Insights into Microbial Community Succession and its Functional Changes during Natural Fermentation of Food Waste.},
journal = {Applied biochemistry and biotechnology},
volume = {},
number = {},
pages = {},
pmid = {41524860},
issn = {1559-0291},
abstract = {Food waste is a global concern, necessitating sustainable management strategies. While fermentation offers a promising approach to valorizing food waste, studies about microbial dynamics and functionality assessment of semi-controlled naturally fermented food waste are still seldom. This study employed whole-genome metagenomic sequencing to investigate the microbial succession and functional pathways during natural fermentation of food waste over 15 days. Physicochemical analysis revealed that pH decreased from 5.20 to 4.32 on day 3 and then neutralized. Protein, lipids, and carbohydrate were in the range of 4.03-4.90%, 9.99-17.78%, and 85.44-77.84%, respectively. Taxonomic profiling revealed clear community restructuring from an initially diverse consortium dominated by Enterobacter, Klebsiella, Pseudomonas, and Acinetobacter (collectively > 45% relative abundance at day 0) to a highly specialized lactic acid bacteria (LAB) community (> 80% by day 15). Lactobacillus helveticus and Limosilactobacillus panis emerged as the late-stage co-dominant species, together accounting for 60-75% of the total reads. Functional annotation based on the PFAM, eggNOG, GO, and EC databases revealed a progressive reduction in gene family richness and metabolic breadth, with early samples being enriched in carbohydrate-active enzymes, membrane transporters, and amino acid metabolism pathways. By contrast, late-stage communities were dominated by LAB-associated fermentative functions, including lactate and acetate production, stress-response modules, and transport systems supporting acid tolerance, driven mainly by Lactobacillus, Weissella, Streptococcus, Gluconobacter, Aeromonas, Saccharomyces, Klebsiella, and Cronobacter. These findings provide insights into the microbial dynamics and functional adaptations during natural fermentation of food waste, contributing to the development of optimized waste valorization strategies.},
}

@article {pmid41524778,
year = {2026},
author = {Sundaray, JK and Roy, D and Mohapatra, M and Mohanty, D and Das, II and Parida, CK},
title = {Metagenomic profiling of fish-associated microbiota: ecological perspectives from freshwater to marine environment-a review.},
journal = {Archives of microbiology},
volume = {208},
number = {2},
pages = {105},
pmid = {41524778},
issn = {1432-072X},
support = {Project Code: 1006449//Centre for Agricultural Bioinformatics (CABin) Project/ ; },
}

@article {pmid41524715,
year = {2026},
author = {Pasqualini, J and Maritan, A and Rinaldo, A and Facchin, S and Savarino, EV and Altieri, A and Suweis, S},
title = {Linking complex microbial interactions and dysbiosis through a disordered Lotka-Volterra model.},
journal = {eLife},
volume = {14},
number = {},
pages = {},
pmid = {41524715},
issn = {2050-084X},
support = {ANR-23-CE30-0012-01//Agence Nationale de la Recherche/ ; CUP 2022WPHMXK//National Recovery and Resilience Plan/ ; PNC0000002-DARE//DigitalLifelong Prevention/ ; },
mesh = {*Dysbiosis/microbiology ; *Microbial Interactions ; Humans ; *Microbiota ; Metagenomics ; Models, Biological ; },
abstract = {The rapid advancement of environmental sequencing technologies, such as metagenomics, has significantly enhanced our ability to study microbial communities. The eubiotic composition of these communities is crucial for maintaining ecological functions and host health. Species diversity is only one facet of a healthy community's organization; together with abundance distributions and interaction structures, it shapes reproducible macroecological states, that is, joint statistical fingerprints that summarize whole-community behavior. Despite recent developments, a theoretical framework connecting empirical data with ecosystem modeling is still in its infancy, particularly in the context of disordered systems. Here, we present a novel framework that couples statistical physics tools for disordered systems with metagenomic data, explicitly linking diversity, interactions, and stability to define and compare these macroecological states. By employing the generalized Lotka-Volterra model with random interactions, we reveal two different emergent patterns of species interaction networks and species abundance distributions for healthy and diseased microbiomes. On the one hand, healthy microbiomes have similar community structures across individuals, characterized by strong species interactions and abundance diversity consistent with neutral stochastic fluctuations. On the other hand, diseased microbiomes show greater variability driven by deterministic factors, thus resulting in less ecologically stable and more divergent communities. Our findings suggest the potential of disordered system theory to characterize microbiomes and to capture the role of ecological interactions on stability and functioning.},
}

*Dysbiosis/microbiology
*Microbial Interactions
Humans
*Microbiota
Metagenomics
Models, Biological

@article {pmid41523444,
year = {2025},
author = {Hofmann, SP and Bieri, U and von Stauffenberg, F and Schneider, S and Singer, G and Greiner, M and Hefermehl, LJ},
title = {Atypical Polypoid Bladder Lesion Mimicking Urothelial Carcinoma in a Young Male: A Case Report About a Possible Autoimmune-Triggered Granulomatous Inflammation With Secondary Colonization.},
journal = {Cureus},
volume = {17},
number = {12},
pages = {e98879},
pmid = {41523444},
issn = {2168-8184},
abstract = {Gross hematuria is a critical clinical symptom requiring thorough diagnostic evaluation, particularly due to its association with urothelial carcinoma. However, other differential diagnoses must also be considered, including renal carcinoma, infection, urolithiasis, and autoimmune disease. We report the case of a 28-year-old male presenting with gross hematuria, flank pain, and dysuria. Imaging revealed bladder wall thickening and bilateral narrowing of the renal pelvis. Cystoscopy showed a large, polypoid lesion suggestive of urothelial carcinoma. Transurethral resection (TUR-B) was performed; however, histological analysis revealed granulation tissue with inflammatory infiltrates, multinucleated giant cells, and necrosis but no evidence of malignancy. Metagenomic sequencing identified Peptoniphilus sp. SAHP1, Anaerococcus mediterraneensis, and Trichomonas vaginalis, though their pathogenic role remained uncertain. Shortly after, the patient developed systemic inflammatory symptoms, including exanthema and gingivostomatitis. Biopsy of skin lesions showed leukocytoclastic vasculitis, and serologic testing yielded borderline myeloperoxidase-specific antineutrophil cytoplasmic antibody (MPO-ANCA) positivity. Under corticosteroid therapy, all symptoms, including the bladder lesion, regressed completely. This case highlights a rare constellation of findings mimicking urothelial carcinoma, ultimately pointing to a probable autoimmune vasculitic process with possible secondary microbial colonization. It underscores the diagnostic challenges posed by atypical presentations and the need for integrative interpretation of clinical, histological, and molecular findings in complex cases.},
}

@article {pmid41523323,
year = {2026},
author = {Chen, J and Wu, Y and Tang, J and Guo, J and Zhai, Y},
title = {Pertussis is identified among common respiratory diseases: A case report.},
journal = {SAGE open medical case reports},
volume = {14},
number = {},
pages = {2050313X251411124},
pmid = {41523323},
issn = {2050-313X},
abstract = {Pertussis, caused by Bordetella pertussis, is increasingly recognized in adults who often present with atypical symptoms, leading to underdiagnosis. We report a case of a 64-year-old woman with a persistent cough and sore throat initially treated as refractory community-acquired pneumonia. Despite empirical antibiotic therapy, her symptoms persisted. Conventional diagnostic tests, including sputum and bronchoalveolar lavage fluid cultures, were negative. Metagenomic next-generation sequencing of bronchoalveolar lavage fluid identified Bordetella pertussis with high sequence coverage (7497 reads). The patient showed no clinical improvement with azithromycin, prompting a switch to trimethoprim-sulfamethoxazole, after which she improved and was discharged to complete a 14-day course. At 1-month follow-up, she was asymptomatic with resolved radiographic findings. This case highlights that pertussis can mimic refractory pneumonia in adults without typical features such as whooping cough, and underscores the diagnostic value of metagenomic next-generation sequencing when conventional methods fail. Clinicians should consider pertussis in adults with prolonged cough unresponsive to standard community-acquired pneumonia therapy and be aware of potential macrolide resistance, which may necessitate alternative antibiotics like trimethoprim-sulfamethoxazole.},
}

@article {pmid41523242,
year = {2025},
author = {Qi, W and Tian, L and Li, Z and Xu, J and Wang, T},
title = {Pathogen spectrum and management strategies for opportunistic infections in lung cancer in the immunotherapy era: recent advances from fungi to mycobacteria.},
journal = {American journal of cancer research},
volume = {15},
number = {12},
pages = {5140-5167},
pmid = {41523242},
issn = {2156-6976},
abstract = {Lung cancer is one of the most common cancers and the leading cause of cancer death worldwide. Opportunistic infections (OI) are increasingly recognized in this population due to disease-related immune dysfunction and treatment-induced immunosuppression. Compared with the chemotherapy era, the use of immune checkpoint inhibitors and targeted agents has shifted the OI profile. Pneumocystis jirovecii pneumonia (PJP) and invasive pulmonary aspergillosis (IPA) are reported more often in older adults and patients with lymphopenia, while tuberculosis (TB) and nontuberculous mycobacteria (NTM) cluster in those with structural lung disease (e.g., bronchiectasis, cavities) and prolonged immunosuppression. High-risk features include absolute lymphocyte count <500/µL, corticosteroids ≥20 mg prednisone-equivalent for ≥4 weeks, airway obstruction, prior TB, chronic obstructive pulmonary disease/interstitial lung disease (ILD), and recent broad-spectrum antibiotics. Diagnosis should integrate high-resolution computed tomography (HRCT) patterns (e.g., diffuse ground-glass for PJP; nodules with halo sign for IPA), microbiology [bronchoalveolar lavage fluid (BALF) culture/microscopy, galactomannan (GM)/β-D-glucan (BDG)], and metagenomic next-generation sequencing, interpreted against host factors and treatment timeline, while carefully distinguishing immune-related pneumonitis and TKI-associated ILD. Prophylaxis with TMP-SMX is recommended for high-risk patients; voriconazole (or isavuconazole) is first-line for IPA with attention to drug-drug interactions; TB/NTM regimens require coordination with anticancer therapy, especially where rifamycins interact with TKIs. Vaccination (influenza, pneumococcus, zoster) and antimicrobial stewardship are essential. Future work should validate risk scores prospectively and clarify microbiome-immunotherapy-infection relationships.},
}

@article {pmid41523161,
year = {2025},
author = {Sanchez, G and Simakov, O and Nyholm, S and Nishiguchi, M and McFall-Ngai, M and Lami, R and Heath-Heckman, E 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 bigfin reef squid, Sepioteuthis lessoniana d'Orbigny, 1826 and its associated microbial metagenome sequences.},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {351},
pmid = {41523161},
issn = {2398-502X},
abstract = {We present a genome assembly from a specimen of Sepioteuthis lessoniana (bigfin reef squid; Mollusca; Cephalopoda; Myopsida; Loliginidae). The genome sequence has a total length of 5,056.23 megabases. Most of the assembly (86.4%) is scaffolded into 44 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 16.64 kilobases in length. Gene annotation of this assembly on Ensembl identified 28,970 protein-coding genes.},
}

@article {pmid41522572,
year = {2025},
author = {Pfliegler, WP and Németh, B and Bodnár, V and Pusztahelyi, T and Carbone, I and Pócsi, I},
title = {Global population genomics redefines domestication and clinical diversity in the Aspergillus flavus-oryzae complex.},
journal = {IMA fungus},
volume = {16},
number = {},
pages = {e172343},
pmid = {41522572},
issn = {2210-6340},
abstract = {Aspergillus flavus is a globally important human pathogen and agricultural contaminant, while its domesticated relative A. oryzae is widely used in food fermentation and biotechnology. Despite their importance, the evolutionary relationship, population structure and domestication history of these fungi remain unresolved. Here, we present the first global population genomic analysis of 639 A. flavus and A. oryzae isolates from clinical, environmental and food-fermentation sources across multiple continents. Our analyses reveal a complex evolutionary landscape comprising well-separated clades interspersed with highly admixed mosaic groups and potential evidence for multiple independent domestication events giving rise to A. oryzae. Clinical A. flavus isolates are distributed across several clades and mosaic groups, some overlapping with fermentation strains, highlighting an apparent role of domestication and admixture in shaping pathogen diversity. These results challenge current species boundaries and provide a framework for understanding evolutionary history, taxonomy and pangenomic architecture in these fungi, with broad implications for pathogenicity, food safety, biocontrol and metagenomic surveillance.},
}

@article {pmid41522496,
year = {2026},
author = {Gedam, PA and Khandagale, K and Barvkar, VT and Bhandari, S and Patil, S and Wayal, S and Bhangare, I and Bhagat, KP and Landage, K and Kale, R and Bhoite, V and More, S and Mahajan, V and Gawande, S},
title = {Microbial allies: shaping growth, physiology, and rhizosphere dynamics of onion (Allium cepa L.).},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e20566},
pmid = {41522496},
issn = {2167-8359},
mesh = {*Rhizosphere ; *Onions/microbiology/growth & development/physiology ; *Soil Microbiology ; Fertilizers ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification ; },
abstract = {The present study investigates the dual impact of microbial biofertilizers on the phenotypic performance and rhizosphere microbiome composition in an onion crop. A pot experiment was conducted with seven treatments of microbial inoculants, such as Azotobacter, Azospirillum, Piriformospora indica, phosphate solubilizing bacteria (PSB), and control treatments with and without chemical fertilizers. The growth, physiological, and biochemical traits of onion were assessed alongside rhizospheric soil microbiome profiling using 16S rRNA metagenomic sequencing. Significant enhancement in plant height, leaf number, leaf area, chlorophyll content, photosynthetic rate, and antioxidant enzyme activity with low leaf temperature was observed in plants inoculated with Azotobacter and Azospirillum. Notably, the Azotobacter treatment yielded a significant enhancement in the bulb phenol content. Rhizosphere metagenomic analysis revealed 17 dominant phyla, with Actinobacteria (25.3%), Proteobacteria (22.2%), Firmicutes (12.8%), and Chloroflexi (11.02%) comprising over 70% of the total microbiome. Alpha and beta diversity metrics indicated that microbial inoculation, especially with Azospirillum and PSB, enriched the soil microbial community structure. Distinct clustering and correlations with specific microbial taxa such as Candidatus Nitrososphaera and Pseudomonas were observed in response to individual biofertilizer treatments. This study highlights the potential of biofertilizers not only in enhancing onion growth and development but also in modulating beneficial rhizosphere microbial communities. Integrating biofertilizers into onion production systems could reduce the dependency on chemical fertilizers and promote sustainable crop management.},
}

*Rhizosphere
*Onions/microbiology/growth & development/physiology
*Soil Microbiology
Fertilizers
*Microbiota
RNA, Ribosomal, 16S/genetics
Bacteria/genetics/classification

@article {pmid41522492,
year = {2026},
author = {Arredondo, A and Àlvarez, G and Isabal, S and Teughels, W and Laleman, I and Contreras, MJ and Isbej, L and Huapaya, E and Mendoza, G and Mor, C and Nart, J and Blanc, V and León, R},
title = {Cross-sectional comparative shotgun metagenomic analysis of the subgingival resistome in healthy subjects and patients with periodontitis from four countries.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2610588},
pmid = {41522492},
issn = {2000-2297},
abstract = {BACKGROUND: The oral cavity is a known reservoir of antibiotic resistance genes (ARGs), but little is known about their subgingival distribution across health states and regions.

OBJECTIVE: This study aimed to characterize and compare the subgingival resistome and mobile genetic elements (MGEs) in healthy subjects (HS) and periodontitis patients (PP) from Belgium, Chile, Peru and Spain.

DESIGN: Subgingival samples pooled from the deepest site of each quadrant of 40 HS and 40 PP were analyzed via shotgun metagenomic sequencing. After human DNA depletion, the microbial composition was assessed with MetaPhlAn 4.0; ARGs were identified using MEGAHIT and AMRFinderPlus; and MGEs with MGEfinder.

RESULTS: ARG richness was significantly higher in PP (mean 3.98) than in HS (2.15). PP from Peru showed more ARGs than HS from Chile and Spain. In total, 28 ARGs were found, conferring resistance to eight antibiotic classes. β-lactam, tetracycline and aminoglycoside resistance were more abundant in PP. Macrolide resistance was lower in Chilean samples than in Peruvian and Spanish ones. Additionally, 99 MGE-associated genes were detected, with 16 differing by diagnosis and 78 by country.

CONCLUSIONS: Subgingival resistome profiles vary significantly by periodontal status and geography, underscoring the influence of clinical and regional factors on antimicrobial resistance in the oral microbiome.},
}

@article {pmid41521629,
year = {2026},
author = {Shelton, BR and Larrere, J and Yusta Belsham, D and Omacini, M and Argüelles-Moyao, A and Buscardo, E and Alves da Silva, DK and Zhao, X and Nakamura, N and Ángeles-Argáiz, R and Paz, C and Matías-Ferrer, N and Hart, MM},
title = {Fungal ecology in the age of 'omics.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70900},
pmid = {41521629},
issn = {1469-8137},
abstract = {The advancement of technology in recent decades has given us an unprecedented ability to observe the natural world. With modern sequencing and bioinformatics technologies, we can obtain more information about the microscopic world, and its interactions with the macroscopic world, than ever before. However, fungal studies that use meta'omic technologies have been sparse compared with bacterial and plant-focused studies. In this review, we highlight the ways that meta'omics can help to address pressing questions in belowground plant-fungal ecology, show consistencies that are emerging - and discrepancies that still exist - among analysis pipelines, and advocate for reporting standards that will allow meta'omic research to more fully benefit fungal ecology.},
}

@article {pmid41521588,
year = {2026},
author = {Alolod, GAL and Guzman, JPMD and Bermeo-Capunong, MRA and Konishi, K and Koiwai, K and Kondo, H and Hirono, I},
title = {Metagenomic Insights on the Progression of White Muscle Disease in Kuruma Shrimp (Penaeus japonicus) Caused by Photobacterium damselae subsp. damselae.},
journal = {Journal of fish diseases},
volume = {},
number = {},
pages = {e70117},
doi = {10.1111/jfd.70117},
pmid = {41521588},
issn = {1365-2761},
support = {22H00379//Japan Society for the Promotion of Science/ ; JPMJSA1806//Japan Science and Technology Agency/ ; },
abstract = {Kuruma shrimp (Penaeus japonicus) is an economically important shrimp perennially affected by diseases. In 2022, White Muscle Disease (WMD) was first characterised in this Penaeid species, caused by Photobacterium damselae subsp. damselae (Pdd). In this study, muscular and gut microbiome dynamics and their function in the disease progression are investigated by 16S rRNA metagenome sequencing using Illumina sequencing technologies. Alpha diversity indices showed that Pdd infection in the muscle, stomach, and intestine did not significantly change bacterial diversity between control and infected groups at all time points observed (Days 0, 1, 3, 5, 7 and 10). In the infected samples, the Shannon and Simpson indices increased starting Day 5 (D5), in congruence with the first observation of muscle whitening. Bacterial composition for the infected group at the genus level revealed that Photobacterium and Vibrio have increased their relative abundance in the muscle at Day 5 (D5) until Day 7 (D7), but declined at Day 10 (D10). As for stomach samples, Photobacterium declined in abundance and later increased significantly at Day 7 (D7). Photobacterium in the intestinal samples from the infected group increased at Day 5 (D5) but later decreased at Day 7 (D7). Meanwhile, linear discriminant analysis Effect Size (LEfSe) identified that most taxa belong to phylum Pseudomonadota, which can be potential markers for WMD. Moreover, the temporal dynamics of the amplicon sequencing variant ASV2, confirmed to be 100% homologous to the WMD-P3 strain used in this study, were characterised. For all tissues, the logarithmic relative abundance is considered high and very apparent in infected samples collected at Day 7 (D7). Overall, our study provides an understanding of the muscle and gut microbial community, specifically at the genus level, distinguished between WMD-infected and healthy Kuruma shrimps.},
}

@article {pmid41521100,
year = {2026},
author = {Zhu, NQ and Zhang, QB and Wang, ZX and Li, RD},
title = {Bacteroides in Bile Detected by Metagenomic Next-Generation Sequencing: Potential Novel Indicator for Early Allograft Dysfunction After Liver Transplantation.},
journal = {Transplantation proceedings},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.transproceed.2025.11.001},
pmid = {41521100},
issn = {1873-2623},
abstract = {OBJECTIVE: Metagenomic next-generation sequencing (mNGS) is an effective method for the detection of microorganisms. Early allograft dysfunction (EAD) is a common complication after liver transplantation. The association between early postoperative microorganisms in bile and EAD is unclear, so we evaluated the association of microorganisms and other potential risk factors with EAD.

METHODS: A total of 100 patients who underwent orthotopic liver transplantation with biliary T tube placement in Huashan Hospital Fudan University from March 2021 to July 2022 were studied. Clinical data, the occurrence of EAD, and bile microorganisms' information detected by mNGS were collected.

RESULTS: EAD occurred in 22 recipients (22%). Patients with EAD had a longer length of postoperative hospital stay. Bacteroides spp. detected by mNGS in bile was identified as an independent risk factor for EAD. Also, operation time, the MELD score of the recipient, and donor AST level were also independent risk factors for EAD.

CONCLUSION: Bacteroides spp. detected by mNGS in bile after liver transplantation was identified as an independent risk factor for EAD, which may reflect the translocation of intestinal flora into the biliary tract and may serve as a potential early warning indicator of poor quality of the donor liver. Recipients with EAD had longer LOS, which may indicate a poor short-term prognosis.},
}

@article {pmid41519985,
year = {2026},
author = {Bodhe, I and Gokuladoss, V},
title = {Sustainable CO2 valorization for PHB production towards circular economy: metagenomic insights on enriched indigenous microbial cultures.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-26791-7},
pmid = {41519985},
issn = {2045-2322},
}

@article {pmid41519950,
year = {2026},
author = {Ye, X and Zhang, T and Zhou, J and Zhao, C and Wu, J},
title = {The gut microbial profile and circulating metabolism are associated with functional constipation in children.},
journal = {Pediatric research},
volume = {},
number = {},
pages = {},
pmid = {41519950},
issn = {1530-0447},
abstract = {BACKGROUND: A growing body of evidence highlights the link between gut microbiome imbalances and constipation. However, the role of gut microbiota and its metabolic interactions in pediatric functional constipation (FC) remains incompletely understood.

METHODS: We recruited a total of 40 children with FC and 40 healthy children (CONT). 16SrRNA and metagenomic sequencing were used to evaluate the changes in the gut microbiota structure and gene function in FC patients. Differences in serum metabolite levels were analyzed via targeted metabolomic sequencing.

RESULTS: The FC group exhibited a decrease in gut microbiota diversity, an increase in Bacteroides and Prevotella abundances, depletion of genera such as Lactobacillus and Bifidobacterium and an imbalance of related metabolic activities. Metabolomic analysis revealed that the levels of several metabolites, including taurine and glycochenodeoxycholic acid, which are involved in bile acid (BA) metabolic pathways, differed between the FC and CONT groups. Differences in metabolite levels were associated with changes in the abundances of specific bacteria and with intestinal dysfunction in FC patients.

CONCLUSION: FC in children is associated with distinct gut microbiota alterations and dysregulated BA metabolism. These findings provide potential therapeutic targets for modulating the gut microbiome and metabolic pathways in FC management.

IMPACT: This study offers a comprehensive perspective on the intricate relationship between microbial composition and metabolic pathways in the context of functional constipation in children. This study focuses on children, highlighting how disruptions in bile acid metabolism due to gut microbiota disorders are linked to the occurrence of functional constipation. These findings suggest that disturbances in bile acid metabolism may play a role in the mechanisms underlying functional constipation by impairing intestinal secretion and transport functions. This study offers a new way to study the effects of the gut microbiota, bile acid metabolism, and the gut‒brain axis.},
}

@article {pmid41519314,
year = {2026},
author = {Su, J and Jiang, S and Chu, M and Dong, X and Zhang, C and Li, X and He, K},
title = {Time-course with multi-omics reveals hyperlipidemia dysregulates diurnal rhythms in gut-liver axis.},
journal = {Genomics},
volume = {},
number = {},
pages = {111198},
doi = {10.1016/j.ygeno.2026.111198},
pmid = {41519314},
issn = {1089-8646},
abstract = {BACKGROUND: Chronic overconsumption of high-fat diets contributes to obesity, with hyperlipidemia being a common comorbidity. The cardiovascular system is strongly influenced by circadian rhythms, which regulate key functions such as endothelial activity, thrombosis, and blood pressure. Circadian rhythms are central regulators of metabolic and physiological processes, and dietary pattern shifts can disrupt the synchronization of the internal clock within metabolic systems.

RESULTS: Using a hyperlipidemic mouse model, we investigated diurnal rhythm-related effects on the liver and intestine through transcriptomic, metagenomic, and metabolomic profiling. We identified several key genes-including CD36, Hmgcs1, Ehhadh, Cyp4a12b, Ifi27l2b, Ugt2b1, Ces2a, Cyp3a11, Selenbp2, and Gal3st1-that are regulated by the hepatic circadian clock and modulate metabolites via the gut-liver axis. The gut microbiota exhibited diurnal rhythmicity that coordinates intestinal digestion and metabolism, forming a synergistic circadian metabolic network. Hyperlipidemia disrupted normal circadian regulation in the liver and intestine, affecting lipid synthesis, transport, accumulation, and catabolism.

DISCUSSION: Our hepatic transcriptomic analysis revealed that a high-fat diet induces aberrant expression of lipid metabolism genes during the night. This diet also perturbs the circadian rhythm of the gut microbiota, leading to intestinal metabolic dysregulation. Metabolites entering the portal circulation act as signaling molecules that bind hepatic receptors and directly regulate the transcription of lipid metabolism genes. The loss of rhythmic metabolite secretion consequently disrupts circadian gene expression, contributing to hepatic lipid dysregulation via the gut-liver axis-a key mechanism in hyperlipidemia pathogenesis.

CONCLUSIONS: This study identifies critical temporal windows and core microbial taxa involved in microbiota-metabolite-gene crosstalk via the gut-liver axis, offering a theoretical foundation for circadian rhythm-targeted interventions in metabolic diseases.},
}

@article {pmid41519162,
year = {2026},
author = {Olmstead, M and Van Nest, K and Swistek, S and Cohnstaedt, LW and Oppert, B and Shults, P},
title = {Microbial communities in filth flies collected from dairy and poultry farms for supplemental animal feed.},
journal = {Journal of economic entomology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jee/toaf283},
pmid = {41519162},
issn = {1938-291X},
support = {NP104- 3020-32000-20-00D//USDA/ ; },
abstract = {Alternative protein sources are needed due to the rising demand and increasing cost of protein ingredients in livestock diets. Mass collection of wild-caught flies from locations with high insect pressure may be an economical and environmentally sustainable approach to supplement livestock feed, but there may be feed safety issues from microbes found in field-caught insects. Therefore, we evaluated a sequencing-based approach to accurately identify potential pathogens in wild-caught flies captured on 2 different livestock farms. In this study, we combined whole-genome shotgun metagenomic sequencing with total RNA-seq to identify a broad range of microbial taxa present in and on wild-caught flies. We describe several databases tailored to the host insect, host animals, and pathogens associated with livestock and humans. Sequences were identified from potentially pathogenic bacteria including Escherichia coli, Gallibacterium anatis, Helicobacterium pullorum, Morganella morganii, Proteus mirabilis, and Providencia alcalifaciens. In addition, sequences from the pathogenic fungi Aspergillus fumigatus and viruses such as the fly pathogen Musca hytrosavirus were found. Despite the limitations of current database curation, a combination of metagenomics and total RNA-seq approaches to taxa identification can provide insight into a broad spectrum of potential pathogens in insects used as supplemental livestock feed.},
}

@article {pmid41518832,
year = {2025},
author = {Hellwig, P and Seick, I and Meinusch, N and Benndorf, D and Wiese, J and Reichl, U and Heyer, R},
title = {Molecular community data meets anaerobic digestion Model 1 (ADM1) - a study about the correlation between metagenome-centric metaproteomics data of a two-step full-scale anaerobic digester and its corresponding mathematical model.},
journal = {Water research},
volume = {292},
number = {},
pages = {125272},
doi = {10.1016/j.watres.2025.125272},
pmid = {41518832},
issn = {1879-2448},
abstract = {Advanced models, such as the Anaerobic Digestion Model No 1 (ADM1), are essential for operating, planning, and optimizing renewable energy production in anaerobic digester plants (AD-P)s. In this study, the ADM1da model was employed to simulate a two-step AD-P in an industrial setting. The ADM1da model is an extended ADM1 model for mixed substrates, accounting for substrate-specific disintegration, temperature effects, biogas-related mass reduction, and mineral solids content. ADM1 models can represent the anaerobic digestion processes, although the biological assumptions are coarse and reflect the knowledge and available tools for microbial communities at the time of development. Meanwhile, metagenome-centric metaproteomics provides deeper insight into the metabolic activities of microbial communities in AD-Ps. Until now, this data has not been integrated with ADM1 models. The objective of this study is to assess the feasibility of incorporating metagenome-centric metaproteome data into the ADM1 model. In a novel approach, 49 high-quality metagenome-assembled genomes (MAGs) with associated protein abundances were systematically classified into the trophic groups defined by the ADM1 model using specifically developed grouping rules. Abundances of MAGs were more variable than the process parameter-dependent dynamics of ADM1. Depending on the grouping rules, 32%-78% of all high-quality MAGs were successfully categorized into ADM1 trophic groups. However, some MAGs, e.g., Methanotrix, were multifunctional (acetoclastic and hydrogenotrophic methanogenesis) and required assignment to multiple groups. Unfortunately, more precise grouping rules resulted in greater discrepancies between metaproteomics data and the model. Additionally, 22% of the MAGs could not be assigned. The metagenome-centric metaproteome data imply that ADM1 probably needs extension to cover the observed microbial function of syntrophic acetate oxidizers, hydrolytic bacteria, lactate- and ethanol-fermenting bacteria, and mortality by phages. It was also observed that changes in process parameters, such as those caused by seasonal feeding, led to significant changes in the protein abundance Integrating metagenome-centric metaproteomic data into ADM1 trophic groups was shown to be feasible.Some trophic groups detected in protein data but not implemented in ADM1 imply the need for data-driven model enhancement and approval. In the future, more accurate models considering molecular data could support a deeper understanding of microbial community dynamics in AD-Ps.},
}

@article {pmid41518812,
year = {2026},
author = {Wang, M and Masoudi, A and Wang, C and Wu, C and Yu, Z and Liu, J},
title = {Urban habitat types modulate soil contamination and bacterial functional traits through antibiotic resistance genes and metal(loid) interactions.},
journal = {Journal of hazardous materials},
volume = {503},
number = {},
pages = {141092},
doi = {10.1016/j.jhazmat.2026.141092},
pmid = {41518812},
issn = {1873-3336},
abstract = {Urban soils are important reservoirs for contaminants, including metal(loid)s and antibiotic resistance genes (ARGs), posing threats to ecosystem function and public health. However, the variation in these contaminants across urban habitat types remains poorly understood. This study integrated shotgun metagenomics, 16S rRNA sequencing, quantitative PCR, and multivariate modeling to investigate the co-distribution of ARGs, metal(loid)s, and bacterial functional traits across six urban habitat types: afforestation areas, croplands, orchards, parks, ruderals, and semi-natural remnants. Our findings revealed habitat-specific contamination patterns, with croplands and orchards showing the highest ARG risks and strong co-selection signals mediated by mobile genetic elements (MGEs) and biocide/metal resistance genes (BMRGs). In contrast, ruderals and remnants exhibited significantly lower ARG abundances (<1.2 × 10[4] copies/g) and metal(loid) concentrations (Cd < 0.05 mg/kg and Pb < 10 mg/kg), as well as nearly 50 % fewer plasmid-associated ARGs, indicating reduced horizontal gene transfer potential. Integrative modeling identified functional genes and BMRGs as the most consistent drivers of MGE dynamics, while MGEs showed limited direct influence on ARGs, suggesting that mobility alone may not explain the spread of resistance in urban soils. Metagenomic analyses linked ARG profiles to disruptions in bacterial functions essential for nutrient cycling and ecosystem services, indicating that resistance risks in urban soils are closely tied to declines in functional capacity. A substantial overlap in ARGs between orchard soils and fruits underscored the potential for soil-to-human transmission. These results provide a cross-habitat framework that links contaminant profiles, resistance mobilization, and functional consequences in urban soils.},
}

@article {pmid41518802,
year = {2026},
author = {Yang, X and Ji, XH and Li, C and Lai, JL and Luo, XG},
title = {Multi-omics assessment of synthetic microbiome-mediated remediation of cyclotetramethylene tetranitroamine (HMX) contaminated water.},
journal = {Journal of hazardous materials},
volume = {503},
number = {},
pages = {141026},
doi = {10.1016/j.jhazmat.2026.141026},
pmid = {41518802},
issn = {1873-3336},
abstract = {Cyclotetramethylene tetranitroamine (HMX) is a typical high-energy nitramine pollutant with an environmental persistence and toxic effects that pose serious ecological risks. In this study, a synthetic microbiome with complementary functions is built that enables the integration of multigroup technology to conduct a systematic analysis of the mechanism of remediation of HMX-contaminated water bodies. Four core bacterial strains (Bacillus altitudinis, B. cereus, B. subtilis, and Pseudomonas stutzeri) were directionally domesticated and screened from HMX-contaminated water. Through functional verification, they were confirmed to express key enzymes NfsA, YdhA, FdhA, and NirS, respectively, to form a complete HMX deep degradation-level connection path. The synthetic microbiome achieved 100 % removal of HMX and its intermediates within 60 days, and isotope tracing (δ[15]N enrichment +2.7 ‰) confirmed its complete mineralization ability. Multiomic analysis showed that the restoration process is accompanied by a systematic reshaping of the water microecology and chemical environment, so that the microbial community structure is optimized and the synthetic microbiome is successfully colonized and becomes the core node. Meanwhile, the energy metabolic network (glycolysis, TCA cycle, oxidative phosphorylation) is significantly enhanced; metagenomic data also revealed reduced viral abundance. Ionomics revealed that key nutrient elements, such as P and S, are efficiently assimilated and utilized. These findings identify an efficient HMX bioremediation strategy that utilizes the multiple dimensions of "community structure-metabolic function-environmental effects" through a multigroup integration framework. More importantly, this study provides a theoretical basis and practical paradigm for the rational design of functional microbial communities.},
}

@article {pmid41518728,
year = {2026},
author = {Sun, J and Lyons, R and Weigh, KV and Lieske, S and Newsham, KK and Hopkins, DW and Dennis, PG},
title = {Putative drivers of maritime Antarctic soil resistomes in the early 21st century: A baseline for monitoring environmental change and human influence.},
journal = {The Science of the total environment},
volume = {1014},
number = {},
pages = {181361},
doi = {10.1016/j.scitotenv.2026.181361},
pmid = {41518728},
issn = {1879-1026},
abstract = {Antibiotic resistance genes (ARGs) are present in all ecosystems and encode the defences that microorganisms have naturally evolved to defend themselves against antimicrobial agents. The use and synthesis of antibiotics by humans, however, has led to a proliferation of ARGs, resulting in their consideration as emerging environmental pollutants, even in some of the most pristine terrestrial ecosystems on Earth. Here we used shotgun metagenomics to characterise the abundance and diversity of ARGs in 29 maritime Antarctic soils collected in the 2007-2008 austral summer that varied in edaphic conditions and levels of human visitation. In total, 1831 ARGs were identified, spanning 29 naturally occurring ARGs that confer resistance to either single or multiple drug classes, such as glycopeptide, fluoroquinolone and tetracycline. The ARG profiles were not significantly associated with predicted levels of human visitation and harboured novel and potentially ancient ARGs, suggesting that these soils were relatively pristine. Furthermore, we observed that the abundance and diversity of ARGs was strongly associated with soil pH and mean annual surface air temperature (MASAT), as well as moisture content, C:N ratio, DOC and Mg concentration, albeit to a lesser extent. Our study provides a useful baseline for future studies, greatly expands the geographical coverage of Antarctic soil resistomes, and highlights putative environmental drivers of ARGs for the early 21st century including pH and MASAT, the latter of which is predicted to rise towards the end of this century.},
}

@article {pmid41518205,
year = {2026},
author = {Ren, H and Jiao, X and Wang, R and Liu, J and Wu, D and Liu, J and Wang, M and Shangguan, W and Cao, S and Chen, P},
title = {DSN-based Host DNA Depletion for Simultaneous Detection of DNA and RNA Pathogens in next-generation sequencing.},
journal = {Letters in applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/lambio/ovaf145},
pmid = {41518205},
issn = {1472-765X},
abstract = {In recent years, nucleic acid sequencing has been increasingly used in clinical pathogen detection. Typically, 20-100 million metagenomic reads are generated per sample, but 90-99% originate from host nucleic acids, leaving only 1-2 million for microbial identification-potentially compromising detection sensitivity. Here, we present a novel duplex-specific nuclease (DSN)-based method to reduce host nucleic acid content in next-generation sequencing. Validated using mock communities and clinical samples, it yielded a 2- to 3-fold increase in pathogen RPM (reads per million) in metagenomic NGS (mNGS) and a more pronounced 3- to 10-fold improvement in probe-based targeted NGS (tNGS). Optimal performance was achieved with: 65°C annealing temperature; 2 μg Cot-1 DNA and 50 μmol rProbe as driver DNA; and 150 mmol·L-1 tetramethylammonium chloride (TMAC)-using 25 ng input nucleic acid for library preparation. The DSN workflow adds less than 30 minutes to library preparation and enables rapid, low-loss microbial enrichment, enhancing pathogen detection in clinical NGS. While effective, its host depletion efficiency could be further improved by expanding driver DNA coverage to additional abundant human genomic regions, such as LINE and LTR repeats.},
}

@article {pmid41518158,
year = {2026},
author = {Barberá, A and Ortolá, R and Sotos-Prieto, M and Rodríguez-Artalejo, F and Moya, A and Ruiz-Ruiz, S},
title = {The Role of the Gut Microbiome in the Complex Network of Frailty Syndrome and Associated Comorbidities in Aging.},
journal = {Aging cell},
volume = {25},
number = {2},
pages = {e70365},
pmid = {41518158},
issn = {1474-9726},
support = {PID2019-105969GB-I00//Spanish Ministry of Science, Innovation and Universities/ ; PMPTA22/00107//Carlos III Health Institute (ISCIII)/ ; PMPTA22/00037//Carlos III Health Institute (ISCIII)/ ; PMPTA23/00001//Carlos III Health Institute (ISCIII)/ ; INVEST/2022/309//Next Generation-EU/ ; 22/1111//ISCIII/ ; //The Secretary of R + D + I/ ; //ERDF/ESF/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Frailty/microbiology ; Male ; Female ; Aged ; *Aging ; Comorbidity ; Aged, 80 and over ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; },
abstract = {The gut microbiota changes throughout life, potentially influencing health and triggering physiological disorders. Frailty syndrome (FS) is an age-related condition that reduces quality of life and increases hospitalization and mortality risks, making early detection and prevention essential in older populations. This study analyzed 16S rRNA gene and metagenomics sequencing of fecal samples from 203 older adults (FS: n = 64, non-FS (NFS): n = 139) to assess the role of gut microbiota in FS and related comorbidities, such as sarcopenia and impaired lower extremity function (ILEF) or anthropometric variables. Consistent taxonomic patterns were observed: Eggerthella, Parabacteroides, and Erysipelatoclostridium were significantly abundant in FS, while Christensenellaceae R-7 group, Erysipelotrichaceae UCG-003, and Hungatella were enriched in NFS. Christensenellaceae R-7 group was also associated with better mobility. Metagenomics analysis identified 680 KEGG functions differing between groups, categorized into 28 metabolic pathways. FS individuals had overrepresented biotin metabolism, antimicrobial resistance, and energy production, but underrepresented ribosomal and protein synthesis and sporulation pathways. Resistome analysis found the tetM/tetO (K18220) gene most abundant, alongside tetracycline, β-lactam, and macrolide resistance, primarily mediated by antibiotic efflux and transporters. These findings highlight distinct microbial and functional signatures associated with FS, underscoring the complex interplay between the gut microbiota and host physiology in aging. Adjusting for covariates, age and diabetes acted as confounding factors in FS for both 16S gene and metagenomics sequencing. This study offers new insights into fundamental questions in the biology of aging and opens avenues for microbiota-targeted strategies to improve the quality of life in older adults.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Frailty/microbiology
Male
Female
Aged
*Aging
Comorbidity
Aged, 80 and over
RNA, Ribosomal, 16S/genetics
Metagenomics

@article {pmid41517763,
year = {2026},
author = {Zhu, Q and Liu, Q},
title = {Early diagnosis of Lemierre syndrome using targeted next-generation sequencing combined with metagenomics capture: A case report and literature review.},
journal = {Medicine},
volume = {105},
number = {2},
pages = {e46988},
doi = {10.1097/MD.0000000000046988},
pmid = {41517763},
issn = {1536-5964},
support = {2022KC22269//Project of Xuzhou Key Research and Development Program/ ; },
mesh = {Humans ; Female ; *Lemierre Syndrome/diagnosis/microbiology/therapy ; Adolescent ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; *Fusobacterium necrophorum/isolation & purification/genetics ; Early Diagnosis ; Anti-Bacterial Agents/therapeutic use ; },
abstract = {RATIONALE: Lemierre syndrome (LS) is a rare but life-threatening complication of acute oropharyngeal infections. It is characterized by septic thrombophlebitis of the internal jugular vein and subsequent metastatic abscess formation. The most common causative pathogen of LS is Fusobacterium necrophorum (FN). This paper presents the case of a 17-year-old female patient with LS, in whom FN was rapidly detected and LS was diagnosed using targeted next-generation sequencing (tNGS) combined with metagenomics capture (MetaCAP). This approach enabled timely detection of FN and guided appropriate treatment.

PATIENT CONCERNS: The patient, a female 17-year-old student, experienced a fever after catching a cold, with a peak temperature of 39.8 °C on May 22, 2024, accompanied by chills and shivering, sore throat, right chest pain, back pain, cough, and hemoptysis.

DIAGNOSES: The patient was initially diagnosed with non-severe community-acquired pneumonia at admission on May 26, 2024. She was finally diagnosed with LS after FN was detected using bronchoalveolar lavage fluid tNGS combined with serum MetaCAP.

INTERVENTIONS: The patient received targeted antimicrobial therapy and thorough thoracic drainage in the shortest time after being definitely diagnosed with LS using tNGS and MetaCAP technologies.

OUTCOMES: The clinical symptoms of the patient were significantly improved. A chest computed tomography scan on July 15, 2024 indicated complete resolution of exudates and solid lesions in both lungs.

LESSONS: This case underscores the significant role of tNGS combined with MetaCAP in the early detection of FN and timely diagnosis of LS, systematically explores the epidemiology, clinical features, diagnosis and treatment of LS, thus providing a reference for clinicians to rapidly diagnose and treat LS.},
}

Humans
Female
*Lemierre Syndrome/diagnosis/microbiology/therapy
Adolescent
*High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
*Fusobacterium necrophorum/isolation & purification/genetics
Early Diagnosis
Anti-Bacterial Agents/therapeutic use

@article {pmid41517713,
year = {2026},
author = {Sun, Z and Xu, K and Huo, L and Zhang, X and Chen, B},
title = {Family psittacosis cluster diagnosed by metagenomic next-generation sequencing in Hangzhou City, Eastern China: A case series.},
journal = {Medicine},
volume = {105},
number = {2},
pages = {e47139},
doi = {10.1097/MD.0000000000047139},
pmid = {41517713},
issn = {1536-5964},
mesh = {Humans ; *Psittacosis/diagnosis/drug therapy/microbiology ; *Chlamydophila psittaci/genetics/isolation & purification ; China ; Male ; *High-Throughput Nucleotide Sequencing/methods ; Middle Aged ; Female ; Metagenomics/methods ; Adult ; Anti-Bacterial Agents/therapeutic use ; Doxycycline/therapeutic use ; Animals ; Moxifloxacin/therapeutic use ; },
abstract = {RATIONALE: Psittacosis, a human infection caused by Chlamydia psittaci (C psittaci), is often underdiagnosed due to its nonspecific presentation and the limitations of conventional diagnostic methods. This diagnostic challenge can lead to missed outbreaks and delays in appropriate treatment. This report aims to highlight the critical role of metagenomic next-generation sequencing (mNGS) in rapidly identifying C psittaci and facilitating the investigation of a family cluster, thereby providing a clearer rationale for its application in similar scenarios.

PATIENT CONCERNS: In this study, we report a family cluster of psittacosis cases. All affected individuals had a history of direct or indirect contact with backyard poultry during a visit to a rural village before symptom onset. The index case (Case 1) presented with fever and chills and was subsequently hospitalized. The 2 secondary cases (Cases 2 and 3) exhibited similar clinical manifestations and were treated at the same hospital, where doctors promptly collected specimens for testing based on their shared medical history.

DIAGNOSES: The diagnosis of C psittaci pneumonia was confirmed by mNGS analysis of bronchoalveolar lavage fluid obtained from 3 patients through bronchoscopy.

INTERVENTIONS: Combination therapy involving intravenous moxifloxacin and doxycycline was administered for the treatment of infectious pneumonia.

OUTCOMES: Following timely diagnosis and targeted antimicrobial therapy, all 3 patients attained full clinical recovery.

LESSONS: C psittaci pneumonia presents with nonspecific clinical and radiographic features that are indistinguishable from other causes of community-acquired pneumonia. mNGS markedly enhances diagnostic accuracy and shortens the time to diagnosis, proving to be an invaluable tool for early identification and management of outbreaks, particularly in patients with avian or poultry exposure.},
}

Humans
*Psittacosis/diagnosis/drug therapy/microbiology
*Chlamydophila psittaci/genetics/isolation & purification
China
Male
*High-Throughput Nucleotide Sequencing/methods
Middle Aged
Female
Metagenomics/methods
Adult
Anti-Bacterial Agents/therapeutic use
Doxycycline/therapeutic use
Animals
Moxifloxacin/therapeutic use

@article {pmid41517247,
year = {2026},
author = {Shah, SMH and Volpe, S and Colonna, F and Valentino, V and De Filippis, F and Torrieri, E and Cavella, S},
title = {Combined Effect of Plasma-Activated Water, Edible Coating, and Active Packaging on Cherry Tomato Shelf-Life: Kinetics and Microbiome Approach.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {1},
pages = {},
pmid = {41517247},
issn = {2304-8158},
support = {817936//European Commission/ ; },
abstract = {Cherry tomatoes are highly appreciated for their nutritional value but remain highly perishable due to rapid respiration and senescence. This study evaluated a multi-hurdle strategy combining plasma-activated water (PAW), sodium caseinate-based edible coating, and antioxidant active packaging to preserve minimally processed (MP) cherry tomatoes stored at 1 °C, 4 °C, and 8 °C for 15 days. Quality evolution was monitored through physical, chemical, nutritional, and microbiological parameters and described using pseudo-zero- and first-order kinetic models, with temperature dependence expressed by the Arrhenius equation. The combined treatment (prototype) slowed the degradation rates of pH, titratable acidity, total polyphenols, and antioxidant capacity, as reflected by consistently lower kinetic rate constants across all temperatures. Prototype samples showed better retention of polyphenols and antioxidant capacity, particularly at 1 °C and 4 °C, without detrimental effects on visual appearance. Metagenomic analysis revealed that the multi-hurdle treatment reshaped the microbial community, reducing the relative abundance of potentially problematic taxa such as Acinetobacter johnsonii and limiting the occurrence of antimicrobial resistance (AMR) genes at the end of storage. This study provides the first integrated assessment of PAW, edible coating, and antioxidant active packaging as a synergistic multi-hurdle strategy, demonstrating their combined ability to extend shelf life while modulating the microbiome and resistome of minimally processed cherry tomatoes.},
}

@article {pmid41516169,
year = {2025},
author = {Uvarova, YE and Khlebodarova, TM and Vasilieva, AR and Shipova, AA and Babenko, VN and Zadorozhny, AV and Slynko, NM and Bogacheva, NV and Bukatich, EY and Shlyakhtun, VN and Korzhuk, AV and Pavlova, EY and Chesnokov, DO and Peltek, SE},
title = {Genetic Characterisation of Closely Related Lactococcus lactis Strains Used in Dairy Starter Cultures.},
journal = {International journal of molecular sciences},
volume = {27},
number = {1},
pages = {},
pmid = {41516169},
issn = {1422-0067},
support = {075-15-2025-516//Ministry of Science and Higher Education of the Russian Federation (the Federal Scientific-technical program for genetic technologies development for 2019-2030)/ ; FWNR- 2022-0022//Ministry of Science and Higher Education project "Study of metabolic control networks in living systems under environmental interaction, including in genetically modified organisms."/ ; },
mesh = {*Lactococcus lactis/genetics/classification/isolation & purification/metabolism ; *Cheese/microbiology ; Food Microbiology ; Phylogeny ; Genome, Bacterial ; Fermentation ; Microbiota/genetics ; },
abstract = {The complex microbiota of cheese starters plays a key role in determining the structure and flavour of the final product, primarily through their acid-forming capacity, protease activity, and exopolysaccharide synthesis. However, the specific microbial communities underlying the unique qualities of artisanal cheeses remain poorly understood. This study presents the microbiological and molecular genetic characterisation of the microbiome isolated from an artisanal cheese starter in Kosh-Agach, Altai, Russia. Metagenomic analysis of this starter revealed the presence of three bacterial genomes corresponding to those of Lactococcus lactis. Pure cultures from this starter were obtained by sequential subculture, and seventeen colonies displaying distinct characteristics on differential media were selected. Genome sequencing was performed for each colony. Bioinformatic analysis based on the rpoB gene grouped the isolates into three clusters, each corresponding to a distinct strain of Lactococcus lactis subsp. diacetilactis. This classification was further confirmed by microbiological and microscopic analyses. A notable finding was that none of the strains produced the characteristic aroma compounds of L. l. subsp. diacetilactis, namely, diacetyl and CO2. The functional properties and metabolic characteristics of this starter consortium are discussed.},
}

*Lactococcus lactis/genetics/classification/isolation & purification/metabolism
*Cheese/microbiology
Food Microbiology
Phylogeny
Genome, Bacterial
Fermentation
Microbiota/genetics

@article {pmid41516078,
year = {2025},
author = {Lupusoru, R and Moleriu, LC and Mare, R and Sporea, I and Popescu, A and Sirli, R and Goldis, A and Nica, C and Moga, TV and Miutescu, B and Ratiu, I and Belei, O and Olariu, L and Dumitrascu, V and Dragomir, RD},
title = {AI-Guided Multi-Omic Microbiome Modulation Improves Clinical and Inflammatory Outcomes in Refractory IBD: A Real-World Study.},
journal = {International journal of molecular sciences},
volume = {27},
number = {1},
pages = {},
pmid = {41516078},
issn = {1422-0067},
support = {without a Grant Number.//"Victor Babes" University of Medicine and Pharmacy, Eftimie Murgu Square, No. 2, 300041 Timisoara, Romania;/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Adult ; Female ; Male ; *Inflammatory Bowel Diseases/microbiology/therapy ; Middle Aged ; Biomarkers/blood ; *Artificial Intelligence ; Feces/microbiology ; Inflammation/microbiology ; Metagenomics/methods ; Treatment Outcome ; Young Adult ; Multiomics ; },
abstract = {Inflammatory bowel disease (IBD) remains difficult to manage in patients who fail multiple therapeutic lines, and growing evidence suggests that alterations in the gut microbiome contribute to persistent symptoms and inflammatory activity. This study evaluated a three-month, AI-guided, multi-omic personalized microbiome modulation program in adults with treatment-refractory IBD. Baseline stool metagenomic sequencing, blood biomarkers, micronutrient panels, and clinical data were integrated through an artificial intelligence platform to generate individualized plans combining dietary adjustments, targeted synbiotics, selective antimicrobials, and micronutrient correction. Clinical outcomes, inflammatory markers, and microbial signatures were reassessed after three months. Across 358 participants, stool frequency decreased substantially, urgency and rectal bleeding resolved in most patients, and over 70% reported a "much improved" overall condition. Inflammatory biomarkers showed marked normalization, with reductions in hs-CRP and fecal calprotectin observed in over 85% of cases. Micronutrient deficiencies, particularly iron and zinc, also improved, and beneficial microbial taxa such as Faecalibacterium prausnitzii, Bifidobacterium longum, and Akkermansia muciniphila increased significantly. These findings suggest that personalized, multi-omic microbiome modulation may support clinically meaningful improvements by targeting microbial, metabolic, and immune imbalances rather than symptoms alone. While encouraging, these results require confirmation in randomized controlled studies.},
}

Humans
*Gastrointestinal Microbiome
Adult
Female
Male
*Inflammatory Bowel Diseases/microbiology/therapy
Middle Aged
Biomarkers/blood
*Artificial Intelligence
Feces/microbiology
Inflammation/microbiology
Metagenomics/methods
Treatment Outcome
Young Adult
Multiomics

@article {pmid41515236,
year = {2025},
author = {Zhang, Z and Wang, S and Sun, G and Pan, D},
title = {Intermittent Fasting and Probiotics for Gut Microbiota Modulation in Type 2 Diabetes Mellitus: A Narrative Review.},
journal = {Nutrients},
volume = {18},
number = {1},
pages = {},
pmid = {41515236},
issn = {2072-6643},
support = {82204030//National Natural Science Foundation of China/ ; 2025M770748//China Postdoctoral Science Foundation/ ; 2024T170134//China Postdoctoral Science Foundation/ ; },
mesh = {*Probiotics/therapeutic use/administration & dosage ; *Diabetes Mellitus, Type 2/microbiology/therapy ; Humans ; *Gastrointestinal Microbiome/physiology ; *Fasting ; Blood Glucose/metabolism ; Animals ; Dysbiosis ; Intermittent Fasting ; },
abstract = {Background: Type 2 diabetes mellitus (T2DM) is a global epidemic in which gut microbiota dysbiosis contributes to impaired glucose homeostasis and chronic inflammation. Intermittent fasting (IF) and probiotic supplementation have independently demonstrated glycemic benefits in T2DM, largely through microbiota remodeling. This narrative review synthesizes evidence up to October 2025 to clarify the microbiota-dependent mechanisms of IF and probiotics, and to evaluate the biological plausibility and preliminary clinical data for their combined application in T2DM management. Methods: We conducted a comprehensive literature review of preclinical and clinical studies (PubMed, Embase, Web of Science, and Cochrane Library) examining IF regimens (primarily time-restricted feeding and 5:2 protocols) and multi-strain probiotics containing Lactobacillus and Bifidobacterium species in T2DM or relevant models. Mechanistic pathways, microbial compositional shifts, and metabolic outcomes were qualitatively synthesized, with emphasis on overlapping signaling (short-chain fatty acids, bile acids, GLP-1, and barrier function). Results: IF consistently increases Akkermansia muciniphila and, variably, Faecalibacterium prausnitzii abundance, restores microbial circadian rhythmicity, and enhances SCFA and secondary bile acid production. Multi-strain probiotics modestly reduce HbA1c (-0.3% to -0.6%) and fasting glucose, outperforming single-strain preparations. Both interventions converge on reduced endotoxaemia and improved intestinal integrity. Preclinical models indicate potential synergy, whereas the only direct human trial to date showed neutral results. Conclusions: IF and probiotics engage overlapping microbiota-mediated pathways, supporting their combined use as an adjunctive strategy in T2DM. Adequately powered randomized trials incorporating deep metagenomics, metabolomics, and hard clinical endpoints are now required to confirm additive or synergistic efficacy.},
}

*Probiotics/therapeutic use/administration & dosage
*Diabetes Mellitus, Type 2/microbiology/therapy
Humans
*Gastrointestinal Microbiome/physiology
*Fasting
Blood Glucose/metabolism
Animals
Dysbiosis
Intermittent Fasting

@article {pmid41515159,
year = {2025},
author = {Robert, M and Saha, S and Dizman, N and Rohlfs, M and Sirmans, E and Simon, J and Amaria, RN and Glitza Oliva, IC and Tawbi, HA and Davies, MA and Ikeguchi, A and Basen-Engquist, K and Schadler, K and Roth, ME and Song, W and Zhang, X and Ajami, NJ and Cohen, L and Wargo, JA and Peterson, CB and McQuade, JL and Daniel, CR},
title = {Investigating Chronic Toxicity, Diet, Patient-Reported Outcomes and the Microbiome in Immunotherapy-Treated Metastatic Melanoma Survivors: A New Frontier.},
journal = {Nutrients},
volume = {18},
number = {1},
pages = {},
pmid = {41515159},
issn = {2072-6643},
support = {na/MRA/Melanoma Research Alliance/United States ; na//Andrew Sabin Family Fellowship/ ; na//MD Anderson Melanoma Moon Shot/ ; 1P30CA016672/NH/NIH HHS/United States ; 1R01CA291965/NH/NIH HHS/United States ; 1P50CA221703/NH/NIH HHS/United States ; 1R01HL158796/NH/NIH HHS/United States ; },
mesh = {Humans ; *Melanoma/therapy/drug therapy/psychology ; Male ; Female ; Middle Aged ; *Gastrointestinal Microbiome ; *Patient Reported Outcome Measures ; *Cancer Survivors/psychology ; *Diet ; Aged ; Adult ; *Immunotherapy/adverse effects ; Quality of Life ; *Immune Checkpoint Inhibitors/adverse effects/therapeutic use ; Depression ; Anxiety ; Prospective Studies ; Exercise ; },
abstract = {Background/Objectives: Immune checkpoint blockade (ICB) therapies have significantly improved outcomes in metastatic melanoma. However, immune-related adverse events (irAEs) and persistent chronic toxicities (CTs) among this emerging survivor population likely influence different facets of quality of life. This study characterized CT, patient-reported outcomes (PROs), diet, physical activity and gut microbiome features in a cohort of long-term survivors with a history of ICB-treated metastatic melanoma. Methods: Forty-eight patients with a history of metastatic melanoma who initiated ICB treatment at least 3 years earlier and were not currently on treatment were prospectively enrolled from a melanoma survivorship clinic. Participants completed screening questionnaires for depression, anxiety, diet and physical activity. The gut microbiome was characterized via metagenomic sequencing in a subsample (n = 39). Patients' clinicopathological characteristics and experience of irAEs (during treatment) and CT (persisting >6 months after completion of therapy) were extracted retrospectively from the medical record. Results: In the overall cohort, 60% were experiencing CT, while 16% and 20% reported clinically relevant levels of depression and anxiety symptoms, respectively. We observed significant differences in overall gut microbiome composition between survivors with and without CT (p = 0.02). Consumption of fruit and vegetables was inversely associated with anxiety (ρ = 0.3, p = 0.038). Added sugar consumption was correlated with the severity of experienced symptoms (ρ = 0.4, p = 0.003), with pronounced associations across the spectrum of symptoms, including pain, fatigue and shortness of breath (p < 0.05). Conclusions: These results suggest that CT is experienced by a substantial proportion of ICB-treated metastatic melanoma survivors. Patients experiencing CT also showed distinct microbiome features. However, additional research in prospective settings is needed to confirm these hypotheses.},
}

Humans
*Melanoma/therapy/drug therapy/psychology
Male
Female
Middle Aged
*Gastrointestinal Microbiome
*Patient Reported Outcome Measures
*Cancer Survivors/psychology
*Diet
Aged
Adult
*Immunotherapy/adverse effects
Quality of Life
*Immune Checkpoint Inhibitors/adverse effects/therapeutic use
Depression
Anxiety
Prospective Studies
Exercise

@article {pmid41514837,
year = {2026},
author = {Li, L and Zhang, H and Zhan, L and Guan, W and Hu, J and Wei, Z and Wu, W and Wu, Y and Xing, Q and Wu, J and Li, Z and Liu, Q and Chen, J and Yuan, A and Guo, D and Ouyang, K and Yang, J and Hu, W and Zhao, X},
title = {Synergistic Regulation of Bile Acid-Driven Nitrogen Metabolism by Swollenin in Ruminants: A Microbiota-Targeted Strategy to Improve Nitrogen Use Efficiency.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {1},
pages = {},
pmid = {41514837},
issn = {2076-2615},
support = {32160804//National Natural Science Foundation of China/ ; 32202762//National Natural Science Foundation of China/ ; 32360855//National Natural Science Foundation of China/ ; 32460886//National Natural Science Foundation of China/ ; 20224BAB215037//Jiangxi Provincial Natural Science Foundation/ ; 20252BAC240611//Jiangxi Provincial Natural Science Foundation/ ; 20224ACB205007//Jiangxi Provincial Natural Science Foundation/ ; 20232BBF60009//Key Project Under the Key R&D Program of Jiangxi Provincial Department of Science and Technology/ ; },
abstract = {The annual nitrogen loss from the livestock production sector poses a significant threat to the global natural environment. Therefore, it is urgent to focus on improving the nutrient utilization efficiency of ruminants and promoting the sustainable development of livestock production. Twelve 60-day-old Ganxi goats with similar body weights were selected and randomly assigned to two dietary treatment groups. The control group was fed only a basal diet, while the treatment group was supplemented with 32 mg/d of Swollenin. The experiment lasted for 30 days. At the end of the experimental period, the goats were euthanized, and their intestinal contents were collected, rapidly frozen, and stored at -80 °C for subsequent metagenomic and metabolomic analyses. In the Swollenin group, we observed changes in gut microbiota structure and significantly enhanced feed conversion efficiency compared to the control group. Notably, genera such as Bacteroides, Ruminococcus, and Bifidobacterium exhibited significantly higher abundance. Following Swollenin supplementation, the gene abundance associated with the secondary bile acid biosynthesis pathway in the intestinal tract of young goats was significantly higher. The levels of primary bile acids (BAs), including taurocholic acid, glycocholic acid, taurochenodeoxycholic acid, and glycochenodeoxycholic acid, were significantly lower, while the concentrations of secondary BAs such as ursodeoxycholic acid and deoxycholic acid were significantly higher. The abundance of nitrogen-fixing and nitrogen-assimilating genes in the gut of young goats in the Swollenin group was significantly higher. Furthermore, co-occurrence network analysis revealed a strong correlation between bile acid metabolism and nitrogen metabolism pathways. These results suggest that nutritional regulation may serve as a preventive strategy to optimize the symbiotic development of animals and their gut microbiota, ultimately improving nitrogen utilization.},
}

@article {pmid41514742,
year = {2025},
author = {Song, Y and Hu, Z and Yang, X and An, Y and Lu, Y},
title = {Duckweed as a Sustainable Aquafeed: Effects on Growth, Muscle Composition, Antioxidant and Immune Markers in Grass Carp.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {1},
pages = {},
pmid = {41514742},
issn = {2076-2615},
support = {2020B1111530002//Guangdong Foundation for Program of Science and Technology Research/ ; },
abstract = {Duckweed (Spirodela polyrhiza), a fast-growing aquatic plant rich in protein and bioactive compounds, offers a sustainable alternative to conventional aquafeed protein sources. This study evaluated the effects of incorporating 25-75% duckweed meal into a commercial feed on grass carp (Ctenopharyngodon idella) over a 6-week trial. Fish meal, wheat starch, and vegetable oil was added in amounts to obtain isonitrogenous and isoenergetic diets. Additionally, another grass carps were used for extended feeding until they reached approximately 1000 g, using the feed with the optimal duckweed inclusion rate (25%). Fish fed a diet consisting of 75% commercial feed and 25% duckweed meal (F75D25) exhibited significantly higher weight gain. Muscle analysis revealed increased protein content (up 15%, p < 0.05) and improved amino acid and fatty acid profiles. Liver, muscle, and blood assays showed elevated antioxidant enzyme activities (SOD up 20%, LYS up 18%; p < 0.05) and immune markers (CRP, GOT; p < 0.05), indicating enhanced health status. Transcriptomic and metagenomic analyses confirmed the upregulation of immune-related genes (e.g., SOD1, IL-6; fold change > 2, p < 0.01) and beneficial shifts in gut microbiota (e.g., increased Firmicutes). These findings highlight duckweed's potential as a nutrient-rich, health-promoting ingredient for sustainable aquaculture diets.},
}

@article {pmid41514654,
year = {2025},
author = {Liu, KYP and Huang, A and Pepin, C and Shen, Y and Tsang, P and Poh, CF},
title = {Oral Microbiome in Oral Cancer Research from Sampling to Analysis: Strategies, Challenges, and Recommendations.},
journal = {Cancers},
volume = {18},
number = {1},
pages = {},
pmid = {41514654},
issn = {2072-6694},
abstract = {The oral microbiome has become an emerging focus of oral cancer research, with growing evidence linking microbial communities to disease development, progression, and prognosis. However, there is limited consensus on optimal sampling strategies, storage methods, and analytical approaches. This narrative review critically evaluates current strategies for sampling, preservation, DNA extraction, sequencing, and data analysis in oral microbiome research related to oral cancer. We compared commonly used sampling methods, including saliva, oral rinse, swab, brush, and tissue biopsy, and reviewed preservation conditions, extraction kits, sequencing platforms, and analytical pipelines reported in recent oral microbiome studies. Sampling approaches affect microbial yield and site specificity. Saliva and oral rinse samples are convenient and noninvasive but may dilute lesion-specific microbial signals, whereas lesion-directed swabbing or brushing yields greater microbial biomass and biological relevance. Preservation media and storage temperature significantly influence microbial stability, and DNA extraction methods vary in their ability to remove host DNA. Although 16S rRNA gene sequencing remains the most common approach, shotgun metagenomics offers higher resolution and function insights but is still limited by clinical applicability. Differences in data pre- and post-processing models and normalization strategies further contribute to inconsistent microbial profiles. Given that oral mucosal sites differ markedly in structure and microenvironment, careful consideration is required to ensure that collected samples accurately represent the biological question being addressed. Methodological consistency across all workflow stages-from collection to analysis-is essential to generate reproducible, high-quality data and to enable reliable translation of oral microbiome research into clinical applications for cancer detection and risk assessment. Together, these insights provide a framework to guide future study design and support the development of clinically applicable microbiome-based biomarkers.},
}

@article {pmid41514452,
year = {2026},
author = {Weiss, A and Elena, AX and Klümper, U and Dumack, K},
title = {Viral and eukaryotic drivers of prokaryotic and antibiotic resistance gene diversity in wastewater microbiomes.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02307-3},
pmid = {41514452},
issn = {2049-2618},
support = {544004729//Deutsche Forschungsgemeinschaft/ ; 01DO2200//Bundesministerium für Forschung, Technologie & Raumfahrt/ ; },
abstract = {BACKGROUND: Antibiotic resistance genes (ARGs) are proliferating in wastewater microbiomes, yet the biotic forces shaping their diversity remain poorly understood. Here, we integrate 14 months of metagenomic and metatranscriptomic data from a wastewater treatment plant to reveal that viruses and microeukaryotes, long-overlooked trophic actors, may play an important role in shaping bacterial and ARG diversity.

RESULTS: We show that viral and microeukaryotic communities exhibit strong seasonal dynamics that cascade through the microbial food web, significantly structuring prokaryotic communities and subsequently ARG profiles. Crucially, we find that viral and microeukaryotic diversity are positively associated with bacterial diversity, which in turn shapes ARG diversity, underscoring the regulatory potential of ecological interactions.

CONCLUSIONS: Our findings challenge the abiotic-centric paradigm and establish the central role of multi-trophic interactions in shaping ARG dynamics in wastewater ecosystems. Video Abstract.},
}

@article {pmid41381025,
year = {2026},
author = {Zabaleta, WDB and Gomez, JDR and Santofimio Villa, LF and Angarita, NB and Alzate, JF and Garzón, YEG and Cantillo-Barraza, O and Triana-Chavez, O and Vargas, PAO and Urrea, DA},
title = {Metatranscriptomic insights into feeding preferences, bacterial diversity, and insect-specific viruses genomics in Aedes aegypti populations from Ibagué, Colombia.},
journal = {Acta tropica},
volume = {273},
number = {},
pages = {107941},
doi = {10.1016/j.actatropica.2025.107941},
pmid = {41381025},
issn = {1873-6254},
mesh = {Animals ; *Aedes/virology/microbiology/physiology ; Colombia ; Female ; *Mosquito Vectors/virology/microbiology ; *Feeding Behavior ; *Bacteria/classification/genetics/isolation & purification ; *Insect Viruses/genetics/classification/isolation & purification ; Microbiota ; Metagenomics ; Genome, Viral ; },
abstract = {Aedes aegypti is not only the primary vector of medically important arboviruses worldwide, but also a host of a wide range of arthropod-specific viruses (ISVs), whose genomic and biological diversity remains largely unknown across most regions of Colombia. Investigating its associated microbiota including viruses and bacteria is essential, as these interactions can influence vector competence. Metatranscriptomic analysis of this vector provides quantitative insights into the presence of such microorganisms and their potential links to blood meal sources. In this study, we analyzed 320 blood-fed female A. aegypti mosquitoes collected from urban areas of Ibagué, Colombia, using RNA-Seq to identify eukaryotic, prokaryotic, and viral sequences, with particular emphasis on insect-specific viruses (ISVs). This approach allowed us to assess the diversity and relative abundance of microorganisms across four mosquito populations, infer potential feeding sources, identify and recover complete viral genomes, and detect parasite families. Despite inherent limitations related to taxonomic classification based on databases, our findings contribute to a better understanding of the ecological and epidemiological characteristics of A. aegypti populations circulating in Ibagué, Colombia, and their vector-pathogen-host interactions.},
}

Animals
*Aedes/virology/microbiology/physiology
Colombia
Female
*Mosquito Vectors/virology/microbiology
*Feeding Behavior
*Bacteria/classification/genetics/isolation & purification
*Insect Viruses/genetics/classification/isolation & purification
Microbiota
Metagenomics
Genome, Viral

@article {pmid41514445,
year = {2026},
author = {Li, M and Zhu, S and Sun, H and Huo, Y and Cao, Q and Deng, Z and Li, K and He, Y and Lu, X and Gao, J and Xu, C},
title = {Rumen microbiota modulates metabolic stress in high-yield dairy cows: insights from early to peak lactation.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02318-0},
pmid = {41514445},
issn = {2049-2618},
support = {32402957//National Natural Science Foundation of China/ ; 32125038//National Natural Science Foundation of China/ ; BX20240417//China National Postdoctoral Program for Innovative Talents/ ; 2024M753563//China Postdoctoral Science Foundation funded project/ ; 2023YFD1801100//National Key Research and Development Program of China/ ; },
abstract = {BACKGROUND: Early lactation (EL) in high-yield dairy cows represents a critical lactation phase marked by significant metabolic stress, which often provokes health disorders and production losses. The rumen microbiome is instrumental in regulating host health and metabolism. However, its contribution to metabolic stress experienced by EL cows has been largely unexplored.

RESULTS: Metabolic stress was prominently observed during EL in the form of elevated oxidative stress (OS), inflammation, and lipolysis. This stress gradually decreased with the progression of lactation from day in milk (DIM) 21 to 90. To identify the underlying mechanisms, this study analyzed EL cows (DIM 32) and peak lactation (PL, DIM 72) using an integrative approach including rumen metagenomics, rumen metabolomics, host metabolomics, and their interactions. Metagenomic analysis revealed a higher abundance of methanogenic archaea (Methanobrevibacter and Methanosphaera) in EL cows, driving increased methane production and subsequent energy loss. This energy waste likely worsened the negative energy balance and caused excessive lipolysis in EL cows. In contrast, the rumen microbiota of PL cows was enriched with Prevotella species and anti-inflammatory bacterial genera (Bacteroides, Parabacteroides, and Alistipes), which are associated with the alleviation of host metabolic stress. Functional analysis of the rumen microbiota uncovered increased tryptophan biosynthesis in EL cows, driving kynurenine production. Conversely, PL cows exhibited a greater abundance of enzymes involved in tryptophan metabolism, thus facilitating the production of indole-3-acetic acid (IAA). Metabolomics analysis also identified the tryptophan metabolism pathway as a shared link between the rumen and serum. Specifically, the kynurenine pathway, associated with OS and inflammation, was upregulated in EL cows, while the indole pathway, particularly the production of IAA, was markedly elevated in PL cows, which attenuated OS and inflammation.

CONCLUSIONS: The study results indicate that the rumen microbiota is pivotal in mitigating metabolic stress in EL cows by modulating tryptophan metabolism. Specifically, the transition from EL to PL was characterized by an enhanced tryptophan-indole pathway and a suppressed tryptophan-kynurenine pathway. The results offer meaningful insights into the microbial mechanisms underlying metabolic stress and identify potential strategies for improving cow health and productivity during lactation. Video Abstract.},
}

@article {pmid41514433,
year = {2026},
author = {Yang, J and Feng, Y and Guo, T and Guo, S and Yang, M and Zhou, D and Lin, P and Wang, A and Jin, Y},
title = {The impact of rumen and hindgut microbiomes on the persistent productivity of long-lived dairy cows.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02309-1},
pmid = {41514433},
issn = {2049-2618},
support = {2023YFD1801100//National Key R&D Program of China/ ; 2022GD-TSLD-46//Shaanxi Livestock and Poultry Breeding Double-chain Fusion Key Project/ ; 2018BBF33001//The Key R&D Program of Ningxia Hui Autonomous Region/ ; },
abstract = {BACKGROUND: In high-producing dairy systems, the average productive lifespan of cows is around 2.5-4 years. Persistent productivity and longevity are key determinants of dairy cow production performance and herd profitability. Although gastrointestinal microbiota influences dairy cow productivity, the mechanisms by which host-microbiome interactions support sustained productivity in long-lived dairy cows remain unclear. Therefore, this study integrated the metagenomics and metabolomics of the rumen and rectum, along with serum and milk metabolomics, to elucidate the potential impact of the rumen and rectum microbiota on the productivity of long-lived dairy cows.

RESULTS: Serum alanine aminotransferase (ALT), alkaline phosphatase (ALP), total cholesterol (TC), and high-density and low-density lipoprotein cholesterol (HDL-C and LDL-C) levels in long-lived dairy cows were positively correlated with milk yield (MY) and elevated in long-lived high-yielding (LH) dairy cows, whereas insulin (INS) and glucagon (GCG) were negatively correlated with MY and higher in long-lived low-yielding (LL) dairy cows. Rumen propionate level was elevated in LH group and positively correlated with MY. The rumen microbiome, in LH cows upregulated pathways involved in amino acid, cofactor, and vitamin metabolism. LH cows' rumen and rectum microbial networks had cohesion and vulnerability levels similar to those of LL cows and exhibited dependence on key nodes. The rumen and rectum MY-associated purine metabolites, guanosine and D-ribose-1-phosphate, mediated 65.56% and 67.55% of the significant positive effects of Acidaminococcaceae bacterium and Parabacteroides sp. on MY, respectively. Furthermore, the specific lipid metabolism-associated rumen microbiota module enhanced serum eicosapentaenoic acid (EPA) levels by modulating rumen α-linolenic acid metabolism, thereby promoting the synthesis of Pe(20:5/0:0) in milk, which positively contributed to MY.

CONCLUSIONS: This study revealed the potential contributions of the rumen and rectum microbiota to the productivity of long-lived dairy cows via purine metabolites, as well as the potential role of the rumen microbial network module in influencing productivity through α-linolenic acid metabolism, providing new insights for nutritional management strategies aimed at improving the persistent production capacity of dairy cows. Video Abstract.},
}

@article {pmid41514203,
year = {2026},
author = {You, S and Zou, Y and Xiao, Y and He, L and Liu, L and Sun, Y and Jia, Y and Ge, G and Du, S},
title = {Animal performance and gut microbiota of cattle as affected by the unfermented or fermented total mixed ration.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-025-04678-x},
pmid = {41514203},
issn = {1471-2180},
abstract = {Diet regulates the gut microbiota, which in turn affects animal performance, but how diet shapes the animal performance and gut microbiota remains largely unknown. To fill this gap, the author conducted a comprehensive study of the influence of total mixed ration (TMR) or fermented TMR (FTMR) on the animal performance and gut microbiome. Sixteen Simmental male cattle were randomly allocated to two treatments (one cattle per pen). The animals were fed with the TMR and FTMR diets respectively. The results showed that the contents of ADF, NDF, cellulose and total cellulose in the FTMR were significantly decreased (p < 0.05), the average daily weight gain of the Simmental male cattle shows an increasing trend (TMR: 0.31 vs. FTMR: 0.62), while no significant (p = 0.2382) difference was found between the two treatments. The metagenomics analysis showed significant (p < 0.05) difference in the α-diversity and β-diversity, and the dominant bacterial genera were Weissella, Lactiplantibacillus, Levilactobacillus and Companilactobacillus. The 16S rRNA sequencing indicated that a significant (p = 0.018) difference in the bacterial communities between the cattle fed with TMR or FTMR diet, while no significant (p < 0.05) differences were detected on the primary genus. It can be found that the FTMR diet increased the average daily gain of cattle by improving the chemical composition and microbial functional profile of the FTMR diet, and affected the growth performance of cattle.},
}

@article {pmid41514032,
year = {2026},
author = {Roncero-Ramos, B and Romano-Rodríguez, E and Mateos-Naranjo, E and Valle-Romero, P and Redondo-Gómez, S},
title = {Hydro- and Xerohalophyte Species Drive Compositional and Functional Divergence in Bacterial Leaf Endosphere.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02679-x},
pmid = {41514032},
issn = {1432-184X},
support = {PAIDI-DOCTOR 21_00571//Junta de Andalucía/ ; FPU21/04133//Ministerio de Universidades/ ; FPU22/02078//Ministerio de Universidades/ ; PID2021-124750NB-I00//Ministerio de Ciencia e Innovación/ ; },
abstract = {Hydro- and xerohalophytes withstand stress thanks to the resistance traits they have, complemented with the functions of their associated microbiota. Besides, given a higher exposition of the phyllosphere to environmental conditions compared to roots, their endospheric bacteria should be more resistant to stress. In this study, we analysed the composition and functional traits of the bacterial leaf endosphere of six xero- and hydrohalophytes species in two seasons. We sequenced their endospheric metagenomes by shotgun and annotated genes related with Plant-Growth-Promoting (PGP) properties. We showed that the composition, structure and functions of the bacterial endosphere are mainly influenced by host plant species, followed by functional type. Moreover, plant species and functional type promoted a different relative abundance of, respectively, 62 and 6 PGP properties. This study shows that not only the composition but also the functionality of the bacterial leaf endosphere of halophytes is more influenced by host species than functional type. Moreover, the leaf endosphere of the different plant species and functional type could be an important source of bacteria with diverse PGP properties.},
}

@article {pmid41513932,
year = {2026},
author = {Ruiz-Ruiz, S and Piquer-Esteban, S and Pérez-Rocher, B and Pérez-Brocal, V and Arnau, V and Artacho, A and Diaz, W and Jiménez-Hernández, N and Pons, J and Castro, JA and Moya, A},
title = {Lifetime existence of a core of mutualistic symbionts and functionally uncoupled taxa in the gut of a Mediterranean cohort.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-35033-3},
pmid = {41513932},
issn = {2045-2322},
support = {grant number CD15/00067//the Carlos III Health Institute (ISCIII)/ ; project number PMPTA23/00001//the Carlos III Health Institute (ISCIII)/ ; grant Conselleria d´Educació, Cultura, Universitats i Ocupació, cofinançat per la Unió Europea FSE+ 2021-2027, ACIF/2021/341//ACIF fellowship from the Generalitat Valenciana/ ; grant number FPU20/05756//Spanish Ministry of Universities, Vocational Training ans Sports/ ; project number PID2019-105969GB-I00 funding by MICIU/AEI/10.13039/501100011033//the Spanish Ministry of Science and Innovation and Universities/ ; project number SAF2015-65878-R funding by MICIU/AEI/10.13039/501100011033/ and by FEDER Una manera de hacer Europa//the Ministry of Science, Innovation and Universities/ ; project number CIPROM/2021/042//Conselleria d´Educació, Cultura, Universitats i Ocupació/ ; },
}

@article {pmid41513032,
year = {2026},
author = {Liu, S and Liu, Z and Xia, X},
title = {Primary cutaneous blastomycosis in a Chinese-Canadian girl following an insect bite.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {108374},
doi = {10.1016/j.ijid.2026.108374},
pmid = {41513032},
issn = {1878-3511},
abstract = {BACKGROUND: Blastomycosis is a disease caused by the dimorphic fungus Blastomyces species. This infection occurs most frequently among individuals residing in the midwestern, southeastern, and south-central United States, as well as in Canadian provinces bordering the Great Lakes and the St. Lawrence Seaway. Sporadic cases have been reported in China, the diagnosis of imported cases remains a significant challenge.

CASE PRESENTATION: We report a diagnostically challenging case of primary cutaneous blastomycosis in a Chinese-Canadian girl, presenting as two nodules of different sizes on her left lower leg and left arm. The patient was initially diagnosed with insect bite dermatitis in Canada, which showed poor response to treatment. Direct microscopic examination revealed large spherical yeast cells, some with broad-based budding, initially interpreted as protothecosis or coccidioidomycosis. However, metagenomic next-generation sequencing (mNGS) indicated B. dermatitidis, which was subsequently confirmed by fungal culture and ITS sequencing. The patient was prescribed oral itraconazole at 50 mg/day and has since returned to Canada to continue treatment.

CONCLUSIONS: For diagnosing infections caused by highly pathogenic pathogens such as imported blastomycosis, the combination of mNGS and direct microscopic examination represents a valuable diagnostic approach.},
}

@article {pmid41512899,
year = {2026},
author = {Chu, VT and Spottiswoode, N and Ward, R and Yokoe, DS and Ramirez-Avila, L and Phelps, MS and Glascock, A and Crawford, ED and Kamm, J and Hao, S and Li, L and Dynerman, D and Waltari, E and Nafees, S and Kalantar, KL and Caldera, S and Madera, S and Guerrero, ES and Ivashin, D and Serpa, PH and Love, C and Mwakibete, LL and Doernberg, SB and Kistler, A and Alvino, R and Engel, J and Chiu, CY and Pak, C and Cunningham, G and Reyes, H and Buie, B and Messacar, K and Leroue, M and Prince, BC and Detweiler, AM and Stanley, K and Caughell, C and McNeil, N and Neff, N and Nichols, A and Miller, S and DeRisi, JL and Tato, CM and Langelier, CR},
title = {Implementation and outcomes of a rapid response genomic hospital epidemiology programme at an academic medical centre over 7 years.},
journal = {The Lancet. Microbe},
volume = {},
number = {},
pages = {101277},
doi = {10.1016/j.lanmic.2025.101277},
pmid = {41512899},
issn = {2666-5247},
abstract = {Advances in genomic technologies have revolutionised practices for hospital infection prevention and control programmes. In this Personal View, we describe a genomic epidemiology service called the Rapid Response (RR) programme at University of California, San Francisco, a large academic medical centre. In collaboration with the hospital infection-prevention team, the RR programme uses whole-genome sequencing and metagenomic next-generation sequencing for outbreak investigations, special interest analyses of emerging pathogens, and surveillance of high-priority microbes. Over 7 years (2017-24), the RR programme conducted a diversity of outbreak investigations and other analyses; most investigations ruled out transmission, and the rapid turnaround of genomic results averted further resource-intensive work. Longitudinal surveillance enabled early detection of changing incidence trends and guided timely infection-prevention responses. Our experiences with the RR programme build upon growing evidence that genomic epidemiology programmes enhance hospital infection prevention and control, augment priority pathogen surveillance, and improve patient safety.},
}

@article {pmid41512763,
year = {2026},
author = {Liu, X and Li, J and Ma, C},
title = {Sublethal aflatoxin B1 exposure triggers multidimensional damage in honeybee (Apis mellifera) midgut: Integrative evidence from histomorphology, transcriptomics, and metagenomics.},
journal = {Journal of hazardous materials},
volume = {503},
number = {},
pages = {141076},
doi = {10.1016/j.jhazmat.2026.141076},
pmid = {41512763},
issn = {1873-3336},
abstract = {Aflatoxin B1 (AFB1), a highly carcinogenic mycotoxin produced by Aspergillus fungi, has been increasingly identified as a global contaminant in bee pollen. Chronic exposure of honeybees (Apis mellifera) to AFB1-contaminated pollen poses substantial threats to colony health, yet its toxicological impacts remain poorly characterized despite the critical ecological role of these pollinators. In this study, we employed a multidimensional approach to investigate the toxicological effects of sublethal AFB1 exposure on honeybee midgut by integrated morphological, transcriptomic, and metagenomic analyses. Histopathological examination revealed severe midgut epithelium damage, including nuclear disintegration and enhanced apoptosis. Transcriptomic profiling coupled with enzyme activity assays unveiled significant dysregulation in immune response and oxidative stress-related pathways. Furthermore, metagenomic sequencing indicated substantial midgut microbiota alterations, characterized by a pronounced reduction in microbial diversity and beneficial microbe levels. These findings elucidate sublethal AFB1-induced honeybee health deterioration at cellular, molecular, and microbial levels, advancing our understanding of mycotoxin impacts on pollinators.},
}

@article {pmid41512751,
year = {2025},
author = {Zhao, Z and Wei, Y and Pan, X and Zhang, G and Luo, M and Wang, Y and Yi, G and Lei, Y and Sun, G and Li, R},
title = {Fishing boats as underestimated vectors for the transmission of high-risk genetic elements in nearshore ecosystems.},
journal = {Journal of hazardous materials},
volume = {503},
number = {},
pages = {140812},
doi = {10.1016/j.jhazmat.2025.140812},
pmid = {41512751},
issn = {1873-3336},
abstract = {Aquatic biofilms on anthropogenic surfaces have been increasingly recognized as key vectors for the cross-boundary transmission of microorganisms and genetic determinants between distinct ecosystems. Current research remains disproportionately centered on ballast water and large vessels, overlooking small fishing boats. This is despite the fact that these boats are common vectors moving between mariculture and nearshore zones, with hull biofilms that can form potential reservoirs for pathogenic and resistant bacteria. Here, we employ a range of genomics approaches to systematically evaluate how hull material (wood, iron, and foam) influences biofilm composition, function, and risk. The biofilm communities exhibit a high abundance of pioneer microorganisms, strong ecological competitiveness, and low metabolic overlap with native assemblages. Further analysis of antibiotic resistance genes (ARGs), virulence factors (VFs), and mobile genetic elements (MGEs) in biofilms, assembling 379 ARG-VF-MGE-carrying contigs into 50 metagenomic bins, highlighting a substantial potential for horizontal gene transfer (HGT) and pathogen dissemination mediated by fishing boats. Finally, considering their enhanced biofilm colonization potential and the abundance of high-risk genetic elements, iron-hulled boats are likely to serve as significant vectors for the dispersal of resistant and virulent microorganisms into sensitive coastal environments, thereby posing elevated ecological and health risks. Our findings underscore the critical role of hull material in shaping biofilm community assembly and function and identify fishing boats as a key vector for the dispersal of high-risk genetic elements in nearshore environments.},
}

@article {pmid41512717,
year = {2026},
author = {Li, L and Shang, G and Guo, Y and Zhang, J and Qi, Y and Wang, H and Flores, M and Belloch, C and Liu, Y and Jing, W and Li, X and Woldemariam, KY},
title = {Unlocking the genomic landscape of Staphylococcus equorum and understanding the functional role and technological application in dry-cured fermented meat products: A review.},
journal = {International journal of food microbiology},
volume = {449},
number = {},
pages = {111618},
doi = {10.1016/j.ijfoodmicro.2025.111618},
pmid = {41512717},
issn = {1879-3460},
abstract = {In Dry-cured fermented meat products, the role of Staphylococcus equorum has been given less attention. S. equorum enhances the flavour, colour, texture, and nutritional quality, and produces antimicrobial compounds that inhibit pathogens in dry-cured fermented meat products. This review aims to provide a comprehensive evaluation of S. equorum as a potential starter culture in dry-cured fermented meat products, examines the main genomic and metabolic characteristics, and highlights the regulatory mechanisms. S. equorum is a gram-positive, catalase-positive coccus with high salt tolerance and optimal growth at 4-10 °C and pH 5-5.6. Modern PCR-based sequencing and metagenomics allow accurate identification of S. equorum using the major genes, including superoxide dismutase (sodA) and recombinase A (recA). Identification of this species has been made from different dry-cured fermented meat products, including Spanish dry-cured ham and "Chorizo" sausages from Spain, artisanal "Soppressata" fermented sausage from Italy. The functional role of S. equorum in protein and lipid hydrolysis contributes to key flavour and aroma compounds. Moreover, it has potential in the prevention of secondary lipid oxidation (superoxide dismutase (SOD)), contributes to nitrate reductase activity (NOS pathway), and biosynthesis of antibacterial peptide (micrococcin P1), which improves the quality and safety of dry-cured fermented meat products. Keeping this into account, the studies conducted on the S. equorum application as a starter culture in dry-cured fermented meat products are in their early stages and require further investigation and analysis.},
}

@article {pmid41512665,
year = {2026},
author = {Wu, CE and Wang, SY and Chen, JW and Yang, WY},
title = {Effects of Ligilactobacillus salivarius on the control of pullorum disease and cecal microbiota in red-feathered native chickens.},
journal = {Poultry science},
volume = {105},
number = {3},
pages = {106384},
doi = {10.1016/j.psj.2026.106384},
pmid = {41512665},
issn = {1525-3171},
abstract = {Pullorum disease (PD), caused by Salmonella Pullorum (SP), remains a persistent challenge in native chicken production in Asia. Recurrent outbreaks and reliance on antibiotics have raised concerns about antimicrobial resistance. This study established a reproducible clinical PD model in red-feathered native chickens (RFCs) and evaluated Ligilactobacillus salivarius (LS) as a potential alternative to antibiotic. Oral administration of a field SP isolate (SPB6) at 1 × 10[8] CFU per chick for four consecutive days induced typical PD signs and persistent bacterial colonization, whereas a single-dose challenge failed to produce consistent disease. Using this model, 100 SP-free RFCs were randomly assigned to five groups of 20 RFCs each: SP challenge only (A), SP + amoxicillin treatment (B), LS prophylaxis + SP (C), SP + nine-day LS treatment (D), and an unchallenged control group (E). Both amoxicillin and LS treatments reduced SP shedding and tissue colonization; notably, nine-day LS regimen achieved sustained suppression of SP isolation rates and bacterial loads comparable to those observed with amoxicillin on days 7, 10, and 17 after infection. Metagenomic analysis in cecal microbiota revealed that nine-day LS treatment enriched the abundance of short-chain fatty acid-producing species, such as Faecalicatena contorta and Lacrimispora saccharolytica, which are associated with intestinal integrity and immune resilience. In conclusion, LS reduced SP shedding and intestinal colonization, with greater efficacy following prolonged administration. LS also modulated the cecal microbiota in PD-affected RFCs by increasing the relative abundance of beneficial taxa. These findings provide experimental support for the evaluation of LS as a potential alternative to antibiotics for PD control. Further studies that extend the duration of LS administration are warranted and are likely to enhance its protective effects.},
}

@article {pmid41511111,
year = {2026},
author = {Chen, X and Chen, C and Lan, X and Zhang, X and Li, T and Zhang, P and Cheng, G and Zhou, W and Wang, Z and Xie, Y and Zeng, S and Zhou, W and Wang, M},
title = {Machine learning and causal inference applied to the gut metagenome-metabolome axis reveals a link between neonatal jaundice and autism spectrum disorder.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0140525},
doi = {10.1128/msystems.01405-25},
pmid = {41511111},
issn = {2379-5077},
abstract = {UNLABELLED: Neonatal jaundice (NJ) might increase the risk of autism spectrum disorder (ASD) in children. This study examined whether alterations in the gut microbiota could explain the link between NJ and ASD. We analyzed three cohorts: NJ cohort 1 comprised 68 neonates with NJ and 68 healthy controls (HCs); NJ cohort 2 included 56 infants with NJ and 14 HCs; and the ASD cohort consisted of 43 children with ASD and 31 typically developing children. Fecal samples were collected aseptically. We performed 16S rRNA sequencing (NJ cohort 1), liquid chromatography with tandem mass spectrometry metabolomics (NJ cohort 1 and ASD cohort), and shotgun metagenomics (NJ cohort 2 and ASD cohort). We characterized the gut DNA virome, quantified bile acid metabolism genes, and integrated multi-omics data using causal mediation and machine learning causal inference. Both NJ and ASD were associated with increased diversity of bile acid metabolism genes, suggesting biomarker potential. The gut DNA virome was also identified as a potential biomarker. Causal mediation analysis showed that the gut DNA virome influences bile acid metabolism genes in both conditions. Using machine learning-based causal modeling, we further found that gut human betaherpesviruses and human mastadenoviruses contribute to NJ and ASD, respectively, mediated by gut bile acid-metabolizing bacteria. These findings suggest that perturbations in the virome and bile acid-metabolizing bacteria may explain the link between NJ and ASD. Our results indicate that NJ and ASD are associated with bile acid metabolism alterations, which are also influenced by the gut DNA virome. Dysbiosis of the gut DNA virome and bile acid-metabolizing bacteria may mechanistically link NJ and ASD.

IMPORTANCE: Human epidemiological studies have established an association between perinatal pathogenic infections and autism spectrum disorder (ASD), and the gut microbiota plays an extremely important role in this relationship. Neonatal jaundice (NJ) may increase the risk of ASD in children. However, it remains unclear whether alterations in the gut microbiota affect the association between NJ and ASD. Both NJ and ASD are linked to altered gut bile acid metabolism and significantly elevated gene diversity among bile acid metabolism enzymes, and these relationships are influenced by the gut virome. Gut human betaherpesviruses and human mastadenoviruses influence the development of NJ and ASD, respectively, by influencing the abundance of gut bile acid-metabolizing microbes. Alterations of the gut virome and bile acid-metabolizing bacteria appear to explain the link between NJ and ASD. There is a lack of effective treatment options for ASD. We found that both NJ and ASD are linked to altered bile acid metabolism. Gaining a comprehensive understanding of the role of the bile acid-gut microbiota axis in the pathogenesis of NJ and ASD, as well as regulating this axis, may be crucial for developing novel preventive and therapeutic strategies for ASD.},
}

@article {pmid41511092,
year = {2026},
author = {Jabir, T and Venkatachalam, S and Surya Prakash, L},
title = {Metagenome-assembled genomes of bacterial communities in the eastern Southwest Indian Ridge, Indian Ocean.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0087025},
doi = {10.1128/mra.00870-25},
pmid = {41511092},
issn = {2576-098X},
abstract = {This paper presents high-quality metagenome-assembled genomes (MAGs) recovered from hydrothermal plume at the 67.67°E vent field along the eastern Southwest Indian Ridge. A total of 24 high-quality MAGs were obtained having 21 different genera. These MAGs, associated with chemosynthetic pathways including methane, metal, and sulfur metabolism, offer crucial insights into microbial transformation in deep-sea hydrothermal vents.},
}

@article {pmid41511078,
year = {2026},
author = {Bowerman, KL and Soo, RM and Chaumeil, PA and Blyton, MDJ and Sørensen, M and Gunbilig, D and Malig, M and Islam, M and Zaugg, J and Wood, DLA and Liachko, I and Auch, B and Morrison, M and Krause, L and Lindberg Møller, B and Neilson, EHJ and Hugenholtz, P},
title = {A molecular inventory of the faecal microbiomes of 23 marsupial species.},
journal = {Microbial genomics},
volume = {12},
number = {1},
pages = {},
pmid = {41511078},
issn = {2057-5858},
mesh = {*Feces/microbiology/virology ; Animals ; *Marsupialia/microbiology/virology/classification ; Phylogeny ; *Bacteria/genetics/classification/isolation & purification ; Metagenomics/methods ; Metagenome ; *Microbiota/genetics ; *Gastrointestinal Microbiome/genetics ; Viruses/genetics/classification ; },
abstract = {Despite the recent expansion of culture-independent analyses of animal faecal microbiomes, many lineages remain understudied. Marsupials represent one such group, where, despite their iconic status, direct sequencing-based analyses remain limited. Here, we present a metagenomic and metabolomic exploration of the faecal microbiomes of 23 Diprotodontia marsupials, producing a reference set of 3,868 prokaryotic and 12,142 viral metagenome-assembled genomes, the majority (>80 %) of which represent novel species. As with other animals, host phylogeny is the primary driver of microbiome composition, including distinct profiles for two eucalypt folivore specialists (koalas and southern greater gliders), suggesting independent solutions to this challenging diet. Expansion of several bacterial and viral lineages was observed in these and other marsupial hosts that may provide adaptive benefits. Antimicrobial resistance genes were significantly more prevalent in captive than wild animals, likely reflecting human interaction. This molecular dataset contributes to our ongoing understanding of animal faecal microbiomes.},
}

*Feces/microbiology/virology
Animals
*Marsupialia/microbiology/virology/classification
Phylogeny
*Bacteria/genetics/classification/isolation & purification
Metagenomics/methods
Metagenome
*Microbiota/genetics
*Gastrointestinal Microbiome/genetics
Viruses/genetics/classification

@article {pmid41510663,
year = {2026},
author = {Gong, K and Wang, N and Chen, Y and Yu, J and Kuang, C and Xiong, X and Wan, R and Xing, F and Suzuki, M and Peng, L and Chun, C and Zuo, Y},
title = {Enhancing Iron Nutrition in Citrus: Synergistic Roles of Proline-2'-deoxymugineic Acid in Root Physiology and Microbiome.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c09250},
pmid = {41510663},
issn = {1520-5118},
abstract = {Iron (Fe) deficiency severely impairs plant growth and development in calcareous soils. Proline-2'-deoxymugineic acid (PDMA), a phytosiderophore analog that enhances Fe availability, alleviates Fe deficiency in field and vegetable crops but remains untested in perennial woody crops. Herein, we conducted pot and field trials on citrus, integrating physiological assays, RNA sequencing, 16S rRNA profiling, and metagenomics to evaluate PDMA/PDMA-Fe(III) effects on Fe nutrition, yield, root gene expression, and rhizosphere microbial dynamics. Results showed that PDMA/PDMA-Fe(III) significantly improved citrus Fe nutrition-outperforming traditional EDTA-Fe(III)- by increasing rhizosphere Fe availability, thereby increasing yield and downregulating Fe uptake- and stress response-related genes,with PDMA-Fe(III) had stronger suppression. PDMA-Fe(III) minimally disrupted the rhizosphere microbiome, while PDMA recruited plant growth-promoting rhizobacteria (e.g., Pseudomonas, Nitrospira); both treatments enriched microbial carbon fixation pathways. Collectively, PDMA/PDMA-Fe(III) represent eco-efficient Fe fertilizers for citrus orchards, providing sustainable remediation of Fe deficiency in calcareous soils.},
}

@article {pmid41510448,
year = {2025},
author = {Tohya, M and Murase, K and Minagawa, M and Saiura, A and Nakagawa, I and Kirikae, T and Watanabe, S},
title = {Single-Cell Sequencing of a Bile Sample From an Acute Cholecystitis Patient.},
journal = {Cureus},
volume = {17},
number = {12},
pages = {e98748},
pmid = {41510448},
issn = {2168-8184},
abstract = {Single-cell sequencing is a novel approach to genome sequencing of clinical samples. However, there are only few studies using single-cell sequencing of genomes for bacterial infections. A 71-year-old woman presented to the emergency department with epigastric pain, 38.5°C fever, and a history of hypertension and hyperuricemia. From blood test results, acute cholecystitis was suspected. The surgery went well and bilirubin calcium stones were found in the gallbladder. Single-cell sequencing was used to investigate a bile sample from a patient with acute cholecystitis. The sample, cultured on a MacConkey agar plate, produced four colonies, all identified as Escherichia coli by bacteriological and biochemical properties. Whole genome sequences of the four strains were determined using the single-cell amplified genome (SAG) sequencing technique. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values of all four were 99.98-100% and 100%, respectively, indicating that they were the same bacterial species. Compared with type strains, these four strains were closest to Shigella sonnei (ANI 98.65-98.66%; dDDH 88.5%) than E. coli (ANI 96.79-96.80%; dDDH 74.2%), despite lacking stx1, stx2 and ipaH, which Shigella species harbor. 16S metagenome analysis identified E. coli as the predominant bacterial genome in the sample, comprising 93.15%. SAG raw data had a relatively high level of quality, with 98.4-98.7% of the read numbers used after quality trimming. However, the genome sequencing coverage was only 9.45-42.88% when compared to a complete genome of an isolate with a mapping quality set above 99%, resulting in gaps compared to conventional whole genome sequence data of these isolates. The procedures of the SAG sequencing technique should be revised to improve the sequencing coverage and reduce gaps in the sequence data. Nonetheless, single-cell genome sequencing can provide novel information for bacterial infections.},
}

@article {pmid41510411,
year = {2025},
author = {Zhao, J and Wang, Y and Zhang, H and Feng, J},
title = {A Case of Severe Fever With Thrombocytopenia Syndrome Co-infected With Pseudomonas aeruginosa and Aspergillus fumigatus.},
journal = {Cureus},
volume = {17},
number = {12},
pages = {e98752},
pmid = {41510411},
issn = {2168-8184},
abstract = {Severe fever with thrombocytopenia syndrome (SFTS) is a tick-borne infectious disease with a high mortality rate. Co-infections with SFTS virus (SFTSV) and other pathogens can exacerbate the condition, leading to rapidly progressive multiple organ failure. We reported a case of SFTS complicated by Pseudomonas aeruginosa and Aspergillus fumigatus. Despite active symptomatic supportive treatment (including anti-virus, anti-infection, anti-antifungal treatment, liver protection, and other advanced life supports), the patient's condition deteriorated rapidly, leading to multiple organ failure. The patient was discharged home and died on the same day. The next day, her blood test results reported that SFTSV, Pseudomonas aeruginosa and Aspergillus fumigatus were detected through metagenomic next-generation sequencing (mNGS). It suggests that early pathogen screening and targeted anti-infective treatment are crucial for improving the prognosis.},
}

@article {pmid41510275,
year = {2025},
author = {De Vlaminck, I and Mzava, O and Djomnang, LA and Cheng, A and Gomez-Escobar, L and Lenz, J and Belcher, E and Schenck, E},
title = {Metagenomic Cell-free DNA Sequencing for Treatment Monitoring in Sepsis.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-8148988/v1},
pmid = {41510275},
issn = {2693-5015},
abstract = {Sepsis is a life-threatening organ dysfunction caused by a dysregulated response to infection. Early identification of pathogens and accurate assessment of organ injury are critical for improving outcomes, but current methods are often inadequate, especially after initiation of antibiotic treatment. Metagenomic sequencing of cell-free DNA (cfDNA) offers a promising alternative, enabling simultaneous pathogen detection and tissue-of-origin profiling. Contamination, however, can limit its accuracy in low-biomass samples. Here, we apply the Sample-Intrinsic Microbial DNA Found by Tagging and Sequencing (SIFT-seq) assay, which reduces contamination and allows detection of pathogens and organ injury simultaneously. We analyzed 142 plasma specimens: 105 from sepsis patients, 103 collected after initiation of antibiotic treatment, 24 from non-sepsis ICU controls, and 13 from healthy controls. SIFT-seq identified sepsis-causing pathogens in good agreement with pre-antibiotic blood cultures, revealed elevated immune activity and organ injury in sepsis patients, and, when combined with the SOFA score in a multivariate model, improved diagnostic performance (AUC = 0.874). These findings highlight the potential of integrated cfDNA profiling to enhance sepsis diagnosis.},
}

@article {pmid41509546,
year = {2026},
author = {Steriade, C},
title = {The Gut Feeling Behind Autoimmune Encephalitis.},
journal = {Epilepsy currents},
volume = {},
number = {},
pages = {15357597251412104},
pmid = {41509546},
issn = {1535-7597},
abstract = {OBJECTIVE: Autoimmune encephalitis is a cause of brain inflammation characterized by auto-antibodies, which target cell surface neuronal proteins and lead to neuronal dysfunction. The most common form is associated with auto-antibodies to leucine-rich glioma-inactivated 1 (LGI1) protein, the presentation of which includes frequent focal seizures. The exact cause of these auto-antibodies remains unknown, but established predispositions include overrepresented human leukocyte antigen (HLA) alleles. Yet, these HLA alleles are themselves common in the healthy ancestry-matched population. One potential etiological hypothesis is that an environmental trigger, such as the gut microbiome, interacts with a genetically predisposed individual.

METHODS: To investigate this, we studied 42 patients with LGI1-antibody encephalitis (LGI1-Ab-E) and 27 familial/environmentally matched controls and performed metagenomic shotgun sequencing, to describe the compositional and functional differences in the gut microbiome.

RESULTS: We observed that LGI1-Ab-E gut microbiomes exhibited a significant reduction in the ratio of Firmicutes (or Bacillota) and Bacteroidetes phyla, which is associated with the dosage of HLA susceptibility allele count in patients with LGI1-Ab-E. Furthermore, we identified differences in functional gene profiles in the gut microbiome that led to a reduction of neuroinflammatory protective short-chain fatty acids (SCFAs) in LGI1-Ab-E patients.

SIGNIFICANCE: Taken together, our results suggest that a compositional shift in the gut microbiome of LGI1-Ab-E associates with a neuroinflammatory state, possibly through the reduction of SCFA production. Our study highlights the potential of the gut microbiome to explain some of the complex condition and unravel etiological questions. Validation studies with greater sample sizes are recommended.},
}

@article {pmid41509497,
year = {2025},
author = {Shen, Z and Eckert, J and Saffery, R and Allen, KJ and Walsh, A and , and Deming, C and Chen, Q and Laky, K and Li, JM and Chatman, L and , and Kong, HH and Perrett, KP and Segre, JA and Frischmeyer-Guerrerio, PA},
title = {Skin microbiome composition and function in the development of atopic diseases during infancy.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2025.12.22.696050},
pmid = {41509497},
issn = {2692-8205},
abstract = {BACKGROUND: Atopic dermatitis (AD), food sensitization (FS), and food allergy (FA) frequently co-occur in infancy, but the factors driving distinct atopic phenotypes remain unclear. While FLG null mutations are major genetic risk factors for AD, they explain only a fraction of disease heritability, suggesting a potential role for the skin microbiome.

OBJECTIVE: To determine how early-life skin microbiome composition and its interaction with host genetics contribute to distinct atopic phenotypes in infancy.

METHODS: We analyzed >1,000 skin swabs from 429 infants in the VITALITY cohort using deep shotgun metagenomic sequencing at 2-3 months (pre-diagnosis) and 12 months (post-diagnosis). Differential abundance, strain-level, and microbial genome-wide association analyses were performed to identify taxonomic and functional features associated with AD, FS, FA, and their co-occurrence, as well as with FLG mutation status.

RESULTS: Within AD, microbial signatures differed by co-occurring FA or FS. At 12 months, Staphylococcus epidermidis was enriched in infants with AD alone, whereas infants with AD and FA exhibited decreased Staphylococcus hominis and Lactococcus species, along with increased Dermacoccus nishinomiyaensis and Malassezia slooffiae . At 2-3 months, early skin dysbiosis characterized by enrichment of Staphylococcus species was associated with subsequent development of AD with FS or FA, but not AD alone. Among infants with AD, FLG mutation carriers exhibited additional microbial shifts, including reduced Streptococcus species and increased Malassezia slooffiae . Strain-level analyses revealed mother-infant sharing of skin microbial taxa associated with AD, and microbial genome-wide association analyses identified species-specific genes linked to AD severity.

CONCLUSIONS: Infant atopic phenotypes are associated with distinct, phenotype-specific features of the skin microbiome that emerge both before and after clinical disease onset. By resolving microbial differences within AD according to allergic co-occurrence, host genetics, and early-life timing, this study highlights the infant skin microbiome as a potential target for early risk stratification.},
}

@article {pmid41509203,
year = {2025},
author = {Papalitsas, C and Mouratidis, I and Patsakis, M and Stogiannos, E and Georgakopoulos-Soares, I and Koulouras, G},
title = {Quantum implementation of multi-pattern string matching for k-mer detection.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2025.12.21.695808},
pmid = {41509203},
issn = {2692-8205},
abstract = {MOTIVATION: The exponential growth of publicly available genomic data has created unprecedented opportunities for sequence-based discovery. Locating specific k-mers is fundamental to diverse applications, including metagenomic classification, pathogen and cancer detection, and variant calling yet efficient identification of multiple k-mer patterns across large sequencing data and massive databases remains a significant computational challenge.

METHOD: We implement two quantum algorithms for DNA multi pattern string matching for k-mer detection based on Grover's amplitude amplification with quantum random access memory (QRAM). The first algorithm uses an enumerate-m oracle that sequentially checks a loaded text substring against all m patterns achieving O(√S) query complexity for S text positions but requiring O(m·L) work per oracle call. The second algorithm employs nested Grover search with an outer loop over text positions and an inner loop over pattern space, reducing oracle complexity to O(L) while performing O(√S · √m) in total.

RESULTS: We present two quantum implementations of multi-pattern string matching tailored for k-mer detection. Leveraging quantum parallelism and Grover-inspired search primitives, our methods accelerate dictionary-based pattern matching, particularly in contexts involving large sequences, such as genomic data, and extensive pattern sets.

CONCLUSIONS: While implementation challenges such as QRAM overhead remain, this study demonstrates both the promise and current limitations of quantum-enhanced string matching, establishing a foundational step toward quantum readiness in bioinformatics.

To maximize accessibility and practical use, we provide our methodology at: https://github.com/Georgakopoulos-Soares-lab/quantum-multi-motif-finder.},
}

@article {pmid41508741,
year = {2026},
author = {Zhao, Y and Feng, M and Chi, H and Liu, K and Wen, R and Zhang, W and Liu, P},
title = {Diversity, Function and Activity of DNA Viruses in the Qiangyong Proglacial Lake Sediment, the Tibetan Plateau.},
journal = {Environmental microbiology reports},
volume = {18},
number = {1},
pages = {e70262},
pmid = {41508741},
issn = {1758-2229},
support = {24YFFA006//Key Research and Development Program of Gansu Province/ ; XZ202301ZY0008G//Key Research and Development Plan of Tibet Autonomous Region/ ; 42222105//National Natural Science Foundation of China for Excellent Young Scientists Fund Program/ ; 42171144//National Natural Science Foundation of China General Program/ ; 42201056//Young Scientists Fund of the National Natural Science Foundation of China/ ; //Global Ocean Negative Carbon Emissions (ONCE) Program/ ; },
mesh = {*Lakes/virology ; *DNA Viruses/genetics/classification/isolation & purification ; *Geologic Sediments/virology ; Tibet ; Metagenomics ; Phylogeny ; *Biodiversity ; Metagenome ; },
abstract = {Viruses are the most abundant biological entities on Earth and play crucial roles in regulating ecosystem processes and biogeochemical cycling. Proglacial lakes-key components of cryosphere aquatic systems-host diverse microbial communities despite extreme environmental conditions. However, the composition and ecological roles of DNA viral communities in proglacial lake sediments remain poorly understood. In this study, we applied metagenomic and metatranscriptomic approaches to investigate the diversity, function, activity and host interactions of DNA viruses in sediments from Qiangyong proglacial lake on the Tibetan Plateau. We recovered 4039 viral operational taxonomic units (vOTUs), with 76.6% unclassified at the family level, highlighting a vast reservoir of uncharacterized viral lineages. Host prediction linked 1.8% of vOTUs to key microbial taxa involved in carbon, nitrogen and sulphur cycling. We identified a broad array of virus-encoded auxiliary metabolic genes (AMGs) involved in host resource utilization and metabolic transformation. Moreover, 63 AMGs not previously reported in the literature were discovered, significantly expanding the known viral functional gene repertoire. These findings offer new insights into the diversity and ecological potential of sediment-associated DNA viruses in proglacial lakes, and emphasize their possible roles in shaping microbial communities and influencing biogeochemical processes in cold-region ecosystems.},
}

*Lakes/virology
*DNA Viruses/genetics/classification/isolation & purification
*Geologic Sediments/virology
Tibet
Metagenomics
Phylogeny
*Biodiversity
Metagenome

@article {pmid41508656,
year = {2026},
author = {Cheah, S and Burke, J and Bruinsma, FJ and Evans, M and Tsimiklis, H and Hodge, AM and Lynch, BM and Giles, GG and Sinha, R and Southey, MC and Milne, RL},
title = {Fecal Sample Collection for Gut Microbiome Research in a Prospective Cohort: A Pilot Study within the Australian Breakthrough Cancer Study.},
journal = {Cancer research communications},
volume = {6},
number = {1},
pages = {70-76},
doi = {10.1158/2767-9764.CRC-25-0445},
pmid = {41508656},
issn = {2767-9764},
support = {//Cancer Council Victoria/ ; //Gandel Foundation/ ; //Perpetual (Perpetual Ltd)/ ; //State Trustees Australia Foundation (STAF)/ ; //Winifred and John Webster Charitable Trust Fund/ ; //Pf - Alan (AGL)/ ; //Shaw Family Foundation (SFF)/ ; //Broomhead Family Foundation/ ; },
mesh = {Humans ; Pilot Projects ; *Gastrointestinal Microbiome/genetics ; *Feces/microbiology ; Prospective Studies ; Male ; Female ; *Specimen Handling/methods ; Middle Aged ; Australia ; Aged ; Occult Blood ; Adult ; *Neoplasms/microbiology ; Surveys and Questionnaires ; Metagenomics/methods ; },
abstract = {UNLABELLED: Large prospective analyses of human gut microbiome profiles are needed to elucidate the role of microbiome variation in the development of disease. We conducted a pilot study to assess the feasibility of home fecal sample collection within a cohort study. A subset of cohort study participants was randomly selected and randomized into four groups defined by fecal sample collection method and questionnaire components. Of 1,093 invited participants, 610 (56%) opted-in, and of those, 88% returned a sample. Of those asked to provide a fecal sample via fecal occult blood test (FOBT) card and complete a short "day-of-sample" questionnaire, 49% returned a sample. Sample return was comparable for participants additionally asked to provide a sample via ethanol tube (51%), complete a food frequency questionnaire (48%), or complete both additional activities (49%). Whole-genome sequencing and metagenomic analysis on paired FOBT and ethanol samples showed that both collection methods provided sufficient quality and quantity of DNA for downstream metagenomic analyses and displayed highly concordant microbiome profiles. Home fecal sample collection for microbiome analysis is feasible in a large prospective cohort. Including additional components did not reduce the likelihood of participants completing all requested items.

SIGNIFICANCE: The expansion of this successful pilot to the larger Australian Breakthrough Cancer Study will facilitate future metagenomic and other host- and microbiome-related analyses in this large prospective cohort and potentially as part of an extended international pooling project.},
}

Humans
Pilot Projects
*Gastrointestinal Microbiome/genetics
*Feces/microbiology
Prospective Studies
Male
Female
*Specimen Handling/methods
Middle Aged
Australia
Aged
Occult Blood
Adult
*Neoplasms/microbiology
Surveys and Questionnaires
Metagenomics/methods

@article {pmid41421789,
year = {2025},
author = {Wang, X and Wu, J and Huang, J and Zeng, Y and Xu, Z and Li, C},
title = {Ectopic paragonimiasis presenting as massive pericardial effusion in a child: A rare diagnostic challenge.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {164},
number = {},
pages = {108326},
doi = {10.1016/j.ijid.2025.108326},
pmid = {41421789},
issn = {1878-3511},
abstract = {OBJECTIVES: To report a rare pediatric case of ectopic paragonimiasis presenting as isolated massive pericardial effusion and to emphasize key diagnostic clues for early recognition in endemic regions.

DESIGN OR METHODS: We describe a 10-year-old boy from an endemic area in China who presented with acute gastrointestinal symptoms and recurrent massive pericardial effusion without respiratory manifestations. Diagnostic evaluation included pericardial fluid analysis, microbiological testing, echocardiography, cardiac magnetic resonance imaging(MRI), serological testing for Paragonimus IgG, therapeutic response assessment, and histopathological examination following surgery.

RESULTS: Despite repeated pericardiocenteses and empirical anti-infective therapy, the effusion persisted. Laboratory testing revealed exudative pericardial fluid with negative cytology, acid-fast staining, and metagenomic next-generation sequencing(mNGS), while peripheral eosinophilia and stool ova were absent. Echocardiography showed a characteristic "cocoon-like" pericardial pattern, and serology was positive for Paragonimus IgG.The patient improved after praziquantel and corticosteroids, but progressive pericardial thickening required pericardiectomy, which confirmed necrotizing granulomatous inflammation. The patient recovered with no recurrence during follow-up.

CONCLUSION: Paragonimiasis should be considered in children from endemic areas with unexplained or recurrent pericardial effusion, even in the absence of pulmonary involvement or eosinophilia. Epidemiological exposure, characteristic echocardiographic findings, and serology are critical for diagnosis, and timely anti-parasitic therapy with surgical intervention when necessary may prevent constrictive pericarditis.},
}

@article {pmid41388147,
year = {2026},
author = {Osipova, E and Balakrishnan, CN and Spottiswoode, CN and Lund, J and DaCosta, JM and Hauber, ME and Warren, WC and Sorenson, MD and Sackton, TB},
title = {Comparative population genomics reveals convergent adaptation across independent origins of avian obligate brood parasitism.},
journal = {Nature ecology & evolution},
volume = {10},
number = {1},
pages = {128-139},
pmid = {41388147},
issn = {2397-334X},
support = {DEB-1754397//National Science Foundation (NSF)/ ; IOS-1456524//National Science Foundation (NSF)/ ; DEB-1754406//National Science Foundation (NSF)/ ; DEB-1754311//National Science Foundation (NSF)/ ; DEB-1754643//National Science Foundation (NSF)/ ; },
mesh = {Animals ; *Nesting Behavior ; Male ; *Adaptation, Physiological/genetics ; *Biological Evolution ; *Finches/genetics/physiology ; Female ; *Adaptation, Biological ; Metagenomics ; },
abstract = {Parental care evolved as a strategy to enhance offspring survival at the cost of reduced adult survival and fecundity. While 99% of bird species provide parental care, obligate brood parasites circumvent this trade-off by exploiting the parental behaviours of other species. This radical life-history shift occurred independently seven times in birds, offering an outstanding opportunity to test for convergent adaptation. To investigate genomic adaptations underlying this transition, we analyse population resequencing data from five brood-parasitic species across three independent origins of brood parasitism-three parasitic finches, a honeyguide and a cowbird-alongside related non-parasitic outgroups. Using the McDonald-Kreitman framework, we find evidence for adaptation in genes involved in sperm function in multiple parasitic clades, but not in the matched, non-parasitic outgroups, consistent with evidence for increased male-male competition in parasitic lineages following the loss of parental care. We also detect selective sweeps near genes associated with nervous system development in parasitic lineages, perhaps associated with improved spatial cognition that aids brood parasites in locating and monitoring host nests. Finally, we detect more selective sweeps in the genomes of host specialist brood parasites as compared to non-parasitic outgroups, perhaps reflecting ongoing host-parasite coevolutionary arms races.},
}

Animals
*Nesting Behavior
Male
*Adaptation, Physiological/genetics
*Biological Evolution
*Finches/genetics/physiology
Female
*Adaptation, Biological
Metagenomics

@article {pmid41508467,
year = {2026},
author = {Chang, H and Zhang, Q and Soro, PL and Zhang, W and Ma, L and Feng, Z and Gu, C},
title = {Integrative metagenomic, metabolomic, and transcriptomic analyses unravel flavor development driven by a defined starter cocktail in cocoa fermentation.},
journal = {Food research international (Ottawa, Ont.)},
volume = {225},
number = {},
pages = {118042},
doi = {10.1016/j.foodres.2025.118042},
pmid = {41508467},
issn = {1873-7145},
mesh = {*Fermentation ; *Cacao/microbiology/metabolism ; *Metabolomics/methods ; *Metagenomics/methods ; Saccharomyces cerevisiae/metabolism/genetics ; Gene Expression Profiling ; Odorants/analysis ; Transcriptome ; Food Microbiology ; Hanseniaspora/metabolism ; Gas Chromatography-Mass Spectrometry ; },
abstract = {This study investigated the impact of a defined starter cocktail (Hanseniaspora uvarum XY23.1, Saccharomyces cerevisiae XY23.2, Lactiplantibacillus plantarum XY23.1, and Gluconobacter oxydans XY23.2) on Trinitario cocoa fermentation in Hainan, China. A multi-omic approach integrating shotgun metagenomics, metabolomics (LC-MS and GC-MS), and transcriptomics was employed to comprehensively assess microbial succession, metabolite dynamics, and functional gene expression. Starter inoculation accelerated cocoa fermentation and stabilized microbial succession, and the four introduced strains remained dominance during the process. Metabolomic analysis revealed that the inoculated group had a remarkable increase in the content of the aromatic volatiles phenylethyl alcohol, 3-methylbutyl acetate, and delta-decalactone, which contributes to fruity and floral aroma characteristics. Shotgun metagenomics revealed enrichment of genes involved in carbohydrate utilization, amino acid catabolism, and acetate ester biosynthesis. Transcriptomics also indicated that S. cerevisiae upregulated Ehrlich pathway and glyoxylate cycle under co-culture conditions, demonstrating its central role in aroma formation and redox balance, while H. uvarum upregulated sugar transporters and stress-response genes, demonstrating a putative regulatory role in nutrient competition and interspecies interaction. Overall, our findings elucidate that defined starter cultures can shape cocoa fermentation toward improved consistency and aroma outcomes, providing a foundation for designing function-driven microbial consortia for controlled fermentation applications.},
}

*Fermentation
*Cacao/microbiology/metabolism
*Metabolomics/methods
*Metagenomics/methods
Saccharomyces cerevisiae/metabolism/genetics
Gene Expression Profiling
Odorants/analysis
Transcriptome
Food Microbiology
Hanseniaspora/metabolism
Gas Chromatography-Mass Spectrometry

@article {pmid41508436,
year = {2026},
author = {Li, C and Yang, F and Han, Y and Yang, C and Qin, X and Zheng, H and Chen, L and Lu, J and Zhang, C and Lu, F and Wang, L},
title = {Corrigendum to "Aldehyde metabolism in Maotai-flavor baijiu: insights from integrated metagenomic and metaproteomic analyses" [Food Res. Int. 221(Part 3) (2025) 117518].},
journal = {Food research international (Ottawa, Ont.)},
volume = {225},
number = {},
pages = {117954},
doi = {10.1016/j.foodres.2025.117954},
pmid = {41508436},
issn = {1873-7145},
}

@article {pmid41508161,
year = {2026},
author = {Villafuerte, AB and Comeau, AM and Soria, R and Ortega, R and Wright, RJ and Miralles, I},
title = {Linking microbial taxonomy and function in N and P metabolism: a study of organic amendments in semiarid restored soils.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-025-00845-9},
pmid = {41508161},
issn = {2524-6372},
support = {FIRESOIL CNS2023-14150//Ministerio de Ciencia e Innovación (Spain), Agencia Estatal de Investigación (Spain) and European Union/ ; BIOQUALIRES-PID2021-1275910B-100//Ministerio de Ciencia e Innovación (Spain), Agencia Estatal de Investigación (Spain) and European Union/ ; P_FORT_GRUPOS_2023/69//Research Plan of the University of Almeria/ ; TECHBIOSOL-PID2024-156189OB- I00//Ministerio de Ciencia, Innovación y Universidades/ ; },
abstract = {BACKGROUND: Arid and semi-arid regions cover approximately 41% of Earth's surface and their soils are highly vulnerable to degradation due to harsh climatic conditions and extractive activities, such as opencast mining. Organic amendments are widely used to restore degraded soils because they improve physical, chemical, and biological properties. However, little is known about how these amendments alter microbial communities and the relationship between microbial taxonomy and function, particularly in nitrogen and phosphorus cycling. To address this knowledge gap, the effects of different organic amendments (gardening compost, greenhouse horticultural compost, sewage sludge and two blends of the above) on soil properties, microbial communities and their contributions to nitrogen metabolism and phosphorus turnover in degraded soils from a limestone quarry in the Gádor Range (Almería, SE-Spain) six months after their application were investigated.

RESULTS: Organic amendments increased nutrient content (total organic carbon, total nitrogen and available phosphorus), microbiological activity, and bacterial biomass compared to unamended soils, with the largest increases in sewage-sludge-treated soils. Shotgun metagenomic assays revealed that organic amendments modified bacterial community composition and differentially influenced potential function pathways, contributing more strongly to nitrogen metabolism than phosphorus turnover, particularly within the phosphonate pathway. Across soils, Pseudomonadota and Actinomycetota were the dominant phyla. Sludge-amended soil showed higher relative abundance of Pseudomonas, associated with denitrification processes (nirK, nosZ, norB) and phosphonate degradation via C-P lyase (phnJ). Genera such as Streptomyces were linked to ammonium assimilation (glnAd, gltBD) and phosphonate synthesis (pmmS), and were more abundant in soil with vegetable-compost and unamended soils. Both nitrogen and phosphorus metabolisms exhibited phylogenetically unrestricted functional patterns, indicating high functional redundancy at phylum and genus levels.

CONCLUSIONS: This research establishes key relationships between taxonomy and function in restored soils and demonstrates how organic amendments rephase microbial communities and their potential roles in nutrient cycling. Although dominant taxa and functions were identified, many microorganisms involved in nitrogen and phosphorus turnover remain insufficiently characterized. Further research across restoration contexts is needed to compare nutrient-cycling responses and to deepen understanding of taxonomy-function linkages in soils amended with organic residues.},
}

@article {pmid41508143,
year = {2026},
author = {Gong, Y and Shen, S and Cao, Z and Zou, X and Zhou, S and Jiang, R and Kang, X and Liu, S and Tian, Y},
title = {Prophylactic impact of cecal fermentation broth against gut microbiota dysbiosis of broiler chickens challenged with Escherichia coli.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-025-00514-9},
pmid = {41508143},
issn = {2524-4671},
support = {2024CXZX009//The Science and Technology Innovation Fund of Henan Agricultural University/ ; 30601985//The Scientific Studio of Zhongyuan Scholars/ ; },
}

@article {pmid41508107,
year = {2026},
author = {Bay, P and Cappy, P and Rodriguez, C and Mongardon, N and Petit, M and Voiriot, G and Sonneville, R and Pineton de Chambrun, M and Urbina, T and Pham, T and Decavèle, M and Benghanem, S and Contou, D and Lepeule, R and Melica, G and de Prost, N and Angebault, C and Mekontso Dessap, A and Woerther, PL and Razazi, K},
title = {Real-life impact of clinical metagenomics in the intensive care unit: a multicenter retrospective study in greater paris area hospitals.},
journal = {Critical care (London, England)},
volume = {30},
number = {1},
pages = {18},
pmid = {41508107},
issn = {1466-609X},
}

@article {pmid41507798,
year = {2026},
author = {Zhao, J and Cai, W and Zhang, X and Fang, H and Zhuge, J and Zhang, L and Wang, J and Sun, L and Hua, Z and Fu, J},
title = {Exploring lung microbiota and clinical application of BALF-mNGS in patients with pulmonary mycobacterial diseases: a multicenter retrospective study.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-025-04707-9},
pmid = {41507798},
issn = {1471-2180},
support = {2020ZZ002,2021ZZ003//Project of Zhejiang Administration of Traditional Chinese Medicine/ ; LZ22H150001//Natural Science Foundation of Zhejiang Province/ ; 82072161//National Natural Science Foundation of China/ ; 2024KY1761//2024 Science and Technology Program for Medicine and Health in Zhejiang Province/ ; 2023K112//Quzhou Science and Technology Program/ ; },
abstract = {BACKGROUND: Pulmonary mycobacterial diseases (PMDs) remain a leading cause of infectious disease-related mortality worldwide, with the majority of cases attributed to the Mycobacterium tuberculosis complex (MTBC). However, non-tuberculous mycobacteria (NTM) can also cause PMDs, and the incidence of non-tuberculous mycobacterial pulmonary disease (NTM-PD) has been increasing in recent years.

OBJECTIVES: This study aimed to explore the lung microbiota and assess the clinical application of bronchoalveolar lavage fluid metagenomic next-generation sequencing (BALF-mNGS) in patients with PMDs caused by MTBC or NTM.

METHODS: This multicenter, retrospective study included patients with suspected PMDs between July 2021 to June 2025. mNGS and conventional diagnostic methods (CDTs), including GeneXpert, BALF culture, acid-fast bacillus (AFB) staining, and T-SPOT, were performed. Based on the microbiological diagnosis, patients were classified into TB and NTM-PD groups. We further analyzed the clinical impact of different MTBC/NTM abundance levels. The relative abundance of MTBC/NTM was represented by reads ten per million (RTPM). Patient clinical characteristics, length of hospital stay (LOHS), laboratory results, and treatment effectiveness were collected from the electronic medical record system.

RESULTS: Compared with the TB group, patients with NTM-PD exhibited a higher prevalence of immunosuppression (34.96% vs. 53.85%, P = 0.013), particularly prolonged corticosteroid or immunosuppressant therapy (8.94% vs. 21.54%, P = 0.016). In the TB group, higher MTBC abundance was associated with increased positivity of CDTs and alterations in pulmonary microbiota, including enrichment of Candida albicans and other opportunistic pathogens. In the NTM-PD group, although CDTs positivity did not significantly differ between high- and low-abundance subgroups (21.21% vs. 20.00%, P = 0.906), higher NTM abundance was linked to distinct microbial community patterns and a markedly higher ineffective treatment rate (66.67% vs. 39.39%, P = 0.043). Notably, in both TB and NTM-PD groups, elevated MTBC or NTM abundance was associated with longer hospital stays and lower treatment effectiveness, indicating that pathogen abundance is significantly associated with clinical outcomes in pulmonary mycobacterial diseases.

CONCLUSION: BALF-mNGS not only provides superior pathogen detection in patients with PMDs but also shows that lower MTBC/NTM abundance is associated with better clinical prognosis, including shorter hospital stay and better treatment effectiveness, highlighting its potential role as a prognostic indicator.},
}

@article {pmid41507780,
year = {2026},
author = {Gaonkar, PP and Santana-Pereira, ALR and Golden, R and Lambert, A and Higgins, C and Adhikari, Y and Bailey, M and Macklin, K and Huber, L},
title = {Microbiome and resistome dynamics in different stages of commercial broiler production with restricted antimicrobial use.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-025-04664-3},
pmid = {41507780},
issn = {1471-2180},
support = {G00017930//United States Department of Agriculture (USDA)/ ; Intramural funding//Alabama Agricultural Experiment Station/ ; },
abstract = {BACKGROUND: Antimicrobial use (AMU) in poultry production is central to curb the Antimicrobial Resistance (AMR) crisis. Institutional and market pressure led many commercial poultry operations to practice distinct levels of AMU restriction. On-farm data remains one of the main bottlenecks in understanding the impacts of AMU restriction at the farm level and across production systems. However, AMR dynamics in company-wide production chains remain largely unexplored, precluding improvement of AMU policies and stewardship.

STUDY AIM: Here, we shotgun sequenced soil and litter samples from 26 poultry farms and carcass rinses from a processing plant to reconstruct the microbiome and resistome of two vertically integrated commercial poultry operations to explore their dynamics under AMU restriction.

RESULTS: Shotgun sequencing revealed that litter microbiome and resistome changed significantly by production stage and company, reflecting management practices and possible effects of historical AMU. Meanwhile, broiler farms had increased detection of potential pathogens and AMR diversity. We found no evidence of farm-to-fork transmission. Effective biosecurity protocols largely maintained the separation between the internal and external environments of the poultry houses, except on two farms where breaches might have led to external spread of pathogens and AMR.

CONCLUSION: Our study highlights that AMR in commercial poultry system reflects the combined effect of production-stage, company practices, and environmental boundaries. Future studies should integrate quantitative AMR data and culture-based techniques with metagenomic findings to strengthen tracking and surveillance of AMR in poultry farm environments.},
}

@article {pmid41507619,
year = {2026},
author = {Mohamad, M and Sergaki, C and Patel, VC},
title = {Enhancing infection diagnostics in advanced chronic liver disease: harnessing clinical metagenomics for rapid pathogen and antimicrobial resistance detection.},
journal = {npj antimicrobials and resistance},
volume = {4},
number = {1},
pages = {3},
pmid = {41507619},
issn = {2731-8745},
abstract = {Patients with advanced chronic liver disease who have underlying cirrhosis are highly susceptible to bacterial infections, which significantly increase the risk of complications and mortality, compounded by escalating antimicrobial resistance. The current gold standard for infection detection and antimicrobial resistance (AMR) profiling remains dependant on traditional microbiological methods. These conventional approaches are slow, labour-intensive, and often fail to deliver timely and accurate results, delaying critical antimicrobial treatment decisions. Clinical metagenomics (CMg) is emerging as a transformative molecular-based tool in infection diagnostics. By enabling the direct sequencing of pathogens from patient-derived samples, CMg offers rapid and comprehensive identification of pathogens and their resistance profiles. Incorporating this technology into the clinical management of patients with cirrhosis has potential to address diagnostic challenges, reduce reliance on broad-spectrum antibiotics and improve outcomes. To effectively incorporate CMg into infection diagnostics, it will be essential to embed of point-of-care sequencing, standardisation of AMR databases, and accessibility to bioinformatics workflows.},
}

@article {pmid41507585,
year = {2026},
author = {Hsu, CL and Shukla, S and Freund, L and Chou, AC and Yang, Y and Bruellman, R and Raya Tonetti, F and Cabré, N and Mayo, S and Lim, HG and Magallan, V and Cordell, BJ and Lang, S and Demir, M and Stärkel, P and Llorente, C and Palsson, BO and Mandyam, C and Boland, BS and Hohmann, E and Schnabl, B},
title = {Gut microbial ethanol metabolism contributes to auto-brewery syndrome in an observational cohort.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41507585},
issn = {2058-5276},
support = {BX004594//Biomedical Laboratory Research and Development, VA Office of Research and Development (VA Biomedical Laboratory Research and Development)/ ; CTORA23-208366//American Association for the Study of Liver Diseases (AASLD)/ ; CTORA23-208366//American Association for the Study of Liver Diseases (AASLD)/ ; K99 AA031328/AA/NIAAA NIH HHS/United States ; R01 AA029106, R21 AA030654, P30 AR073761//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; },
abstract = {Auto-brewery syndrome (ABS) is a rarely diagnosed disorder of alcohol intoxication due to gut microbial ethanol production. Despite case reports and a small cohort study, the microbiological profiles of patients remain poorly understood. Here we conducted an observational study of 22 patients with ABS and 21 unaffected household partners. Faecal samples from individuals with ABS during a flare produced more ethanol in vitro, which could be reduced by antibiotic treatment. Gut microbiome analysis using metagenomics revealed an enrichment of Proteobacteria, including Escherichia coli and Klebsiella pneumoniae. Genes in metabolic pathways associated with ethanol production were enriched, including the mixed-acid fermentation pathway, heterolactic fermentation pathway and ethanolamine utilization pathway. Faecal metabolomics revealed increased acetate levels associated with ABS, which correlated with blood alcohol concentrations. Finally, one patient was treated with faecal microbiota transplantation, with positive correlations between gut microbiota composition and function, and symptoms. These findings can inform future clinical interventions for ABS.},
}

@article {pmid41507173,
year = {2026},
author = {Han, Y and Liao, J and Li, C and Xing, F and Peng, J and Liu, X and Xie, W and Wu, F and Jian, H and Cheng, R and Dong, X},
title = {Co-occurrence of diverse defense systems shapes complex microbe-virus relationships in deep-sea cold seeps.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-68174-6},
pmid = {41507173},
issn = {2041-1723},
abstract = {Cold seeps host diverse microbes and viruses with numerous unexplored defense and anti-defense systems. Analysis of 3813 microbial and 13,336 viral genomes from 191 metagenomes across 17 cold seep sites reveals extensive microbial defense repertoires, with over 60% representing candidate systems. Experimental validation confirms that several candidates protect against viral infection. These defense systems frequently co-occur, suggesting potential synergistic interactions, and are broadly distributed across sediments. In response, viruses have evolved diverse anti-defense genes, and the concurrent presence of multiple viral and microbial systems highlights intricate coevolution. Functionally critical lineages, such as anaerobic methanotrophic archaea, sulfate-reducing bacteria, and diazotrophs, appear to modify their defensive strategies under ecological and environmental pressures; for example, sulfate-reducing bacteria harbor multiple Gabija systems while corresponding viruses carry anti-Gabija genes, illustrating specific coevolutionary adaptations. Overall, these findings underscore the critical role of virus-microbe interactions in shaping microbial metabolic functions and environmental adaptation in deep-sea ecosystems.},
}

@article {pmid41506580,
year = {2026},
author = {Nichols, S and Estandía, A and Young, CM and Knowles, LS and Palinauskas, V and Okamura, B and Clegg, SM},
title = {Host whole genome sequence data represent an untapped resource for characterising affiliated parasite diversity.},
journal = {International journal for parasitology},
volume = {},
number = {},
pages = {104768},
doi = {10.1016/j.ijpara.2025.104768},
pmid = {41506580},
issn = {1879-0135},
abstract = {Parasites are ubiquitous and exert varied ecological and evolutionary pressures on their hosts. Yet, characterising parasite diversity and distributions can be challenging and costly. Leveraging existing data to identify parasites is thus an attractive alternative. High-throughput sequencing (HTS) can generate whole genome sequence (WGS) data which are increasingly freely available in public repositories and represent an untapped resource for characterising parasites affiliated with hosts. In this study, we examine WGS data generated for the silvereye (Zosterops lateralis), to identify endogenous eukaryotic parasites that were inadvertently captured during host sequencing. We compared detection of parasite genera by this approach with detection via 18S metabarcoding. Mining WGS data for parasite DNA revealed the broadest range of genera. Results were verified by traditional microscopy of blood slides and conducting a targeted multiplex Polymerase Chain Reaction (PCR) for haemosporidian parasites. Detection of haemosporidians was largely consistent across microscopy, multiplex PCR and WGS data while 18S metabarcoding entirely failed to detect this group of parasites. Our results demonstrate that existing WGS datasets can be used to estimate endoparasite diversity and provide greater insights on diversity than metabarcoding whilst also avoiding the costs and challenges of direct sampling. We provide a framework outlining opportunities and constraints to consider when mining WGS data to identify parasite sequences. The framework particularly stresses the influences of sequencing depth, database completeness, and methodological biases. Our findings demonstrate how repurposing existing WGS data can provide a cost-effective and informative means of unravelling complex host-parasite interactions in future disease ecology studies.},
}

@article {pmid41506577,
year = {2026},
author = {Sagar, K and Priti, K and Chandra, H},
title = {Artificial intelligence in metagenome-assembled genome reconstruction: Tools, pipelines, and future directions.},
journal = {Journal of microbiological methods},
volume = {},
number = {},
pages = {107390},
doi = {10.1016/j.mimet.2026.107390},
pmid = {41506577},
issn = {1872-8359},
abstract = {Metagenomic sequencing has revolutionised the field of microbial ecology, as it has led to cultivation-independent exploration of complicated microbial communities. The assembly of metagenome-assembled genomes has provided genome-scale information about uncultivated microorganisms, but issues such as sequencing errors, fragmented assemblies, residual redundancy, uneven coverage, recovery of low-abundance taxa, and highly diversified taxa continue to impair the quality of these genomes. The latest achievements in artificial intelligence, particularly in machine learning and deep learning, have played a significant role in overcoming these limitations by enhancing quality control, error correction, assembly, binning, refinement, and annotation procedures. It is demonstrated that representation learning and graph-based binning methods have high strain-level resolution and can reduce contamination in complex microbial communities, whereas artificial intelligence-based assemblers and polishing tools improve base-level precision and assembly contiguity. This review synthesises traditional and artificial intelligence-based workflows involved in the reconstruction of metagenome-assembled genomes, encompassing quality control, assembly, binning, refinement, and annotation, as well as quantitative benchmarking of significant artificial intelligence-based pipelines. As future directions, the focus on emerging trends, such as explainable artificial intelligence, federated learning, cloud-native scalable pipelines, multimodal and multi-omics integration, and large language model-based annotation, is covered. In general, the incorporation of artificial intelligence represents a paradigm shift in the reconstruction of metagenome-assembled genomes, allowing for a more relevant, scalable, and biologically informative search of the microbial dark matter in various ecosystems.},
}

@article {pmid41506454,
year = {2026},
author = {Shi, T and Xu, S and Lin, Y and Zheng, X and Ruan, H and Shi, W and Zhang, R and Chen, H and Chen, T and Chen, H and Wang, H},
title = {The Clinical Application of Metagenomic Next-Generation Sequencing in Pathogen Identification of Postoperative Spinal Implant Infection.},
journal = {The spine journal : official journal of the North American Spine Society},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.spinee.2026.01.004},
pmid = {41506454},
issn = {1878-1632},
abstract = {BACKGROUND CONTEXT: Postoperative spinal implant infection (PSII) poses significant diagnostic challenges and can lead to serious clinical outcomes. Traditional microbial culture methods are limited by prolonged turnaround times and low sensitivity, which have long hindered a comprehensive understanding of the pathogen spectrum in PSII. Metagenomic next-generation sequencing (mNGS) offers rapid, broad-spectrum, and highly sensitive pathogen detection, providing a promising solution to the diagnostic difficulties associated with PSII.

PURPOSE: This study aimed to evaluate the clinical utility of mNGS for the pathogenic diagnosis of PSII.

STUDY DESIGN/SETTING: Retrospective cohort study.

PATIENT SAMPLE: A retrospective analysis was conducted on clinical data from 122 patients with suspected surgical site infection following spinal implant-related surgery between January 2020 and July 2025.

OUTCOME MEASURES: Identification of pathogenic bacteria in patients.

METHODS: According to the National Healthcare Safety Network (NHSN) criteria, patients were classified into the PSII group (n = 89) and the non-PSII group (n = 33). Pathogen spectrum characteristics of PSII detected by mNGS were analyzed, and the diagnostic performance of mNGS was compared with that of traditional microbial culture, laboratory tests, and imaging studies.

RESULTS: The pathogen detection rate of mNGS was significantly higher than that of traditional culture (79.78% vs. 38.20%, P < 0.001). mNGS successfully detected pathogens in 42.70% (38/89) of culture-negative PSII cases. The main pathogens identified by mNGS included Staphylococcus aureus and coagulase-negative staphylococci (20.00% each, 15/75), Mycobacterium tuberculosis (18.67%, 14/75), and anaerobic bacteria (14.67%, 11/75). Among the 33 patients positive by both mNGS and culture, species-level concordance was 69.70%. No significant difference in the distribution of major pathogens was observed between early-onset (≤3 months) and late-onset (>3 months) infection groups. Antibiotic appropriateness evaluation revealed that only 32.58% (29/89) of patients had initial antibiotic regimens that provided complete coverage against the detected pathogens. The overall diagnostic performance of mNGS for PSII was superior to that of culture, with significantly higher sensitivity (79.78% vs. 38.20%), specificity (100.00% vs. 93.94%), positive predictive value (100.00% vs. 94.44%), negative predictive value (64.71% vs. 36.05%), accuracy (85.25% vs. 53.28%), and AUC (0.8989 vs. 0.6607).

CONCLUSION: mNGS significantly improves the detection of difficult-to-culture pathogens such as M. tuberculosis and anaerobic bacteria in PSII. It is recommended to combine mNGS with conventional methods, thereby improving diagnostic accuracy, guiding rational antibiotic use, and enhancing treatment outcomes.},
}

@article {pmid41506449,
year = {2026},
author = {Zhang, S and Li, Q and Peng, Y and Huo, J and Ran, T and Zhang, X and Wang, R and Jiao, J and Jiang, A and Luo, G and Zhang, Z and Qiu, Q and Li, Z and Mao, S and Yu, Z and Tan, Z and Dong, X and Wang, M},
title = {Spatial heterogeneity of viral communities across the gastrointestinal tracts of ruminants.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2026.01.013},
pmid = {41506449},
issn = {2090-1224},
abstract = {INTRODUCTION: Viruses are abundant biological entities within the gastrointestinal tract (GIT) of ruminants. Current understanding is extensive for bacterial and archaeal communities, but limited for viral communities.

OBJECTIVES: The study aimed to investigate viral diversity, virus-host interactions and ecological functions of viruses across GIT regions and ruminant species.

METHODS: We collected 373 short-read and long-read metagenomes from 10 GIT regions of seven ruminant species, combining Illumina, PacBio HiFi, and Nanopore sequencing. Viral contigs were identified using sequence homology, viral hallmark gene and machine learning, and employed to uncover community assembly of spatial heterogeneity by analyzing virus-host linkage, lifestyle, and auxiliary metabolic genes (AMGs).

RESULTS: We constructed a Ruminant Gastrointestinal Virome Catalog (RGVC) comprising 43,981 vOTUs, revealing that viral communities were remarkably diverse and mainly driven by the GIT regions rather than by the ruminant species. Virus-host linkage analysis identified 4603 putative prokaryotic hosts across 34 classes for 5954 host-linked viruses, along with robust correlation (R[2] = 0.91) observed between abundances of prokaryotic hosts and host-linked viruses across GIT regions. The lysogenic lifestyle was a dominant feature, with integrases being the predominant lysogenic-specific genes. We identified 864 high-confidence AMGs in lysogenic viruses that are annotated as key genes for polysaccharide degradation, glycolysis, and the Wood-Ljungdahl pathway, indicating a putative role for the viruses in supporting these host metabolic functions. The metabolic features of host-linked viruses were further verified by genomic context of selected AMGs of GH10, GPI and FHS with target function.

CONCLUSION: These findings suggest that the GIT viral communities exhibit spatial heterogeneity with distinct virus-host interactions, and offer new perspectives on maintenance of complex ecological and nutritional functions in ruminant GIT.},
}

@article {pmid41506424,
year = {2026},
author = {Shi, R and Han, T and Zhang, H and Huang, H and Xiong, L and Liu, Y and Qi, Z},
title = {Response of Sediment Microbial Community Composition and Function to Mangrove Restoration from an Aquaculture Pond in Southern China.},
journal = {Environmental research},
volume = {},
number = {},
pages = {123718},
doi = {10.1016/j.envres.2026.123718},
pmid = {41506424},
issn = {1096-0953},
abstract = {Mangrove ecosystems, as highly sensitive and productive habitats, host diverse microbial communities essential to biogeochemical cycling. In recent years, large-scale mangrove restoration in former aquaculture ponds has expanded rapidly in China. This represents a typical land-use shift that likely reshapes microbial communities. However, despite its increasing implementation, the accompanying changes in microbial composition and function remain insufficiently understood. Therefore, we compared sediment microbial community composition, diversity, and functional potential between mangrove-planted and reference areas. By absolute-quantification sequencing and metagenomics, we aimed to assess how mangrove restoration regulates the microbial dynamics and their metabolic potentials for carbon, sulfur, and nitrogen cycling after two years of restoration. Mangrove restoration induced a marked phylum shift from Chloroflexota to Pseudomonadota and significantly increased microbial β-diversity (p < 0.05), reflecting enhanced phylogenetic niche differentiation. Specialist species in restored sediments were predominantly Pseudomonadota (e.g., Gammaproteobacteria), contrasting with the Chloroflexota- and Actinobacteriota-dominated reference sites. Functional analysis revealed significant up-regulation of genes involved in polysaccharide metabolism (celB/chbC, sacB, treC, fruB; p < 0.05), assimilatory sulfate reduction, sulfur oxidation (soxZ; p < 0.05), nitrogen fixation (nifH; p < 0.05), and assimilatory nitrate reduction. Furthermore, most high-abundance metagenome-assembled genomes (MAGs) from mangrove sediments encoded sulfate reduction genes. Notably, microbial carbon cycling potential correlated with particulate organic nitrogen, while nitrate concentration linked to nitrogen and sulfur cycling genes, highlighting cross-element synergies. These findings demonstrated that two years of mangrove restoration alters sediment microbiomes and their biogeochemical functions potential, thereby may influence carbon sequestration and nutrient cycling in coastal ecosystems.},
}

@article {pmid41505815,
year = {2026},
author = {Liu, F and Sun, S and Zhang, Y and Wang, F and Yang, X and Zhang, B and Fan, S and Jia, H},
title = {Possible tuberculous meningitis presenting with predominant voiding dysfunction in an elderly patient: A case report.},
journal = {Journal of infection and public health},
volume = {19},
number = {3},
pages = {103128},
doi = {10.1016/j.jiph.2025.103128},
pmid = {41505815},
issn = {1876-035X},
abstract = {Tuberculous meningitis (TBM) typically presents with neurological symptoms. Voiding dysfunction in TBM is usually attributed to spinal cord involvement. We report a rare case of possible TBM co-existing with possible prostatic tuberculosis, presenting primarily with urinary symptoms in the absence of spinal pathology. A 69-year-old male presented with a two-year history of progressive urinary retention, urgency, and frequency. Initial management for benign prostatic hyperplasia was ineffective. He subsequently developed fever, headache, and dizziness. Cerebrospinal fluid (CSF) analysis revealed lymphocytic pleocytosis and elevated protein. Despite extensive testing, including CSF culture, Xpert MTB/RIF, and metagenomic next-generation sequencing (mNGS), no pathogen was identified. However, a history of untreated testicular tuberculosis, pulmonary nodules on CT, and a prostatic nodule on MRI raised suspicion of disseminated tuberculosis. A clinical diagnosis of possible TBM was made based on a Marais score of 11. An intensive anti-tuberculosis regimen including moxifloxacin and linezolid led to complete resolution of neurological and urinary symptoms. This case suggests that voiding dysfunction in TBM patients may stem from concurrent genitourinary tuberculosis rather than spinal cord involvement. It highlights the importance of considering hematogenous dissemination from latent genitourinary foci in elderly patients and the utility of the Marais criteria for the diagnosis of TBM when microbiological evidence is elusive.},
}

@article {pmid41505640,
year = {2026},
author = {Du, S and He, L and Sun, L and Shi, X and Xiao, Y and Jia, Y and Ge, G},
title = {Strategy Development for Improving Ensiling Performance of Ceratoides arborescens (Krascheninnikovia arborescens (Losinsk.) Czerep.) Silage Based on Integrated Omics.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c13269},
pmid = {41505640},
issn = {1520-5118},
abstract = {This study investigated the effects of Lactiplantibacillus plantarum (L. plantarum) on the constituent characteristics, in vitro ruminal fermentation properties, bacterial community structure, metagenome profiles, and metabolite compositions of Ceratoides arborescens silage. Fourier transform infrared spectroscopy analysis demonstrated that L. plantarum inoculation significantly altered the chemical composition, fermentation quality, and in vitro digestibility of the silage. The fermentation process was predominantly driven by Lentilactobacillus and Lactiplantibacillus. Metagenomic profiling and metabolic analyses revealed functional shifts and metabolic alterations, with significant differences observed in the absolute abundance of the carbohydrate-active enzymes. In conclusion, L. plantarum fermentation improved the nutritional value and fermentation properties of Ceratoides arborescens silage by modulating the bacterial community structure, functional gene expression, and metabolic activity. These findings provide mechanistic insights into the beneficial effects of L. plantarum during silage fermentation and offer potential strategies for enhancing the silage quality and ruminal fermentation efficiency.},
}

@article {pmid41505541,
year = {2026},
author = {Leung, PM and Jeffrey, LC and Bay, SK and Gomez-Alvarez, P and Hall, M and Johnston, SG and Dittmann, J and Deschaseaux, E and Hopkins, B and Haskell, J and Jirapanjawat, T and Hutchinson, TF and Coleman, NV and Dong, X and Maher, DT and Greening, C},
title = {Bark microbiota modulate climate-active gas fluxes in Australian forests.},
journal = {Science (New York, N.Y.)},
volume = {391},
number = {6781},
pages = {eadu2182},
doi = {10.1126/science.adu2182},
pmid = {41505541},
issn = {1095-9203},
mesh = {*Methane/metabolism ; *Plant Bark/microbiology ; Australia ; *Microbiota ; *Forests ; *Hydrogen/metabolism ; Carbon Monoxide/metabolism ; Metagenomics ; *Trees/microbiology ; *Bacteria/metabolism/genetics/classification ; Anaerobiosis ; },
abstract = {Recent studies suggest that microbes inhabit tree bark, yet little is known about their identities, functions, and environmental roles. Here we reveal, through gene-centric and genome-resolved metagenomics, that the bark of eight common Australian tree species hosts abundant and specialized microbial communities. The predominant bacteria are hydrogen-cycling facultative anaerobes adapted to dynamic redox and substrate conditions. Furthermore, bark-associated methanotrophs are abundant and can coexist with hydrogenotrophic methanogens. Microcosm experiments showed that bark microorganisms aerobically consume methane, hydrogen, and carbon monoxide at in planta concentrations and produce these gases under anoxia. Combined with in situ field measurements, we show that tree-dwelling microbiota metabolize multiple climate-active gases at marked rates within tree stems, highlighting a potentially substantial role in global atmospheric cycles.},
}

*Methane/metabolism
*Plant Bark/microbiology
Australia
*Microbiota
*Forests
*Hydrogen/metabolism
Carbon Monoxide/metabolism
Metagenomics
*Trees/microbiology
*Bacteria/metabolism/genetics/classification
Anaerobiosis

@article {pmid41504847,
year = {2026},
author = {Wang, W and Li, Y and Sun, J and Jiang, C and Hao, J},
title = {Semi-Rational Design of a Deep-Sea Metagenomic Sucrose Phosphorylase for Enhanced α-Arbutin Biosynthesis.},
journal = {Applied biochemistry and biotechnology},
volume = {},
number = {},
pages = {},
pmid = {41504847},
issn = {1559-0291},
support = {2022YFC2805101//National Key Research and Development Program of China/ ; 2022QNLM030003-2//Qingdao Marine Science and Technology Center/ ; 2023TD71//Central Public-interest Scientific Institution Basal Research Fund, Chinese Academy of Fishery Sciences/ ; },
}

@article {pmid41504449,
year = {2026},
author = {Xu, J and Ma, J and Lin, H and Yan, S and Niu, H},
title = {Metagenomic and metabolomic analyses of rumen fiber digestion in Mongolian cattle fed fresh grass versus hay.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0305125},
doi = {10.1128/spectrum.03051-25},
pmid = {41504449},
issn = {2165-0497},
abstract = {Mongolian cattle exhibit exceptional roughage tolerance due to their rumen microbiome's robust fiber-degrading capacity, enabling efficient utilization of low-quality forage under the Mongolian Plateau's seasonal fluctuations. This study compared rumen microbial composition, CAZyme profiles, fermentation parameters, and metabolic pathways in cattle fed fresh grass (FG) versus hay to elucidate microbe-metabolite interactions underlying fiber digestion. Thirty non-pregnant female Mongolian cattle (460 ± 35 kg, 3-4 years old) were randomly divided into two groups (n = 15/group): one grazed on FG, the other housed and fed autumn-harvested hay (HG). Six animals per group were subsampled for rumen fluid collection and multi-omics analyses (n = 6/group, total n = 12). Compared with the FG group, the HG group showed an increased molar proportion of acetate and a higher acetate-to-propionate ratio, along with reduced molar proportions of propionate and butyrate in rumen fermentation parameters. Metagenomic analysis revealed a higher abundance of Bacteroidalesbacteria and anaerobic fungi (including Neocallimastix sp.JGI-2020a and Piromyces sp.E2) in the HG group. Functional annotation further indicated enriched carbohydrate metabolism pathways in the HG group, along with a greater diversity of CAZymes, particularly those involved in hemicellulose and pectin degradation. Metabolomics identified 13 differentially abundant carbohydrate metabolites, with gluconolactone upregulated in the HG group. Additionally, carbohydrate metabolism pathways identified in the metabolome corroborated the reliability of the metagenomic functional annotations. Correlation network analysis revealed positive associations of Bacteroidaceaebacteria, Neocallimastix sp.JGI-2020a, and Piromyces sp.E2 with acetate, hemicellulose-degrading GHs, and carbohydrate metabolic pathways. In conclusion, hay feeding enhanced ruminal fiber degradation in Mongolian cattle through increased Bacteroidales and anaerobic fungi, diversified CAZymes (especially hemicellulases/pectinases), and upregulated carbohydrate metabolism, reflecting microbial adaptation to low-quality forage.IMPORTANCEMongolian cattle's superior roughage tolerance depends on a specialized rumen microbiome that degrades fibrous substrates via diverse CAZymes. However, microbe-metabolite interactions driving fiber digestion in this breed remain poorly understood. This study revealed an increased abundance of bacteria and fungi involved in rumen fiber degradation, which may be responsible for secreting enzymes associated with hemicellulose and pectin breakdown. Furthermore, the upregulation of key metabolites, including gluconolactone, indirectly promotes acetate production through pathways such as glycolysis and the pentose phosphate pathway. These findings reveal microbial adaptations enhancing low-quality forage utilization, offering new strategies for improving ruminant efficiency in seasonal or resource-limited grazing systems.},
}

@article {pmid41504158,
year = {2025},
author = {Chen, T and Guo, Y and Liang, D and Li, D and Xing, S and Li, D and Zhang, C and Wang, F},
title = {Discriminative Gut Microbial Signatures in Hyperuricemia and Overweight Populations Revealed by Metagenomic Sequencing.},
journal = {International journal for vitamin and nutrition research. Internationale Zeitschrift fur Vitamin- und Ernahrungsforschung. Journal international de vitaminologie et de nutrition},
volume = {95},
number = {6},
pages = {42590},
doi = {10.31083/IJVNR42590},
pmid = {41504158},
issn = {0300-9831},
support = {S2023KFKT-12//Ministry of Agriculture and Rural Affairs/ ; 2024YFF1107000//National Key Research and Development Program of China/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Hyperuricemia/microbiology ; Male ; Female ; *Overweight/microbiology ; Middle Aged ; Cross-Sectional Studies ; Feces/microbiology ; Adult ; Metagenomics ; Metagenome ; },
abstract = {BACKGROUND: This cross-sectional study aimed to investigate the relationships between gut microbiota compositional alterations and chronic metabolic disorders by analyzing taxonomic diversity, community structure, and species-level differences in individuals with hyperuricemia (HUA) and a history of being overweight. Our findings offer novel insights into microbiota-targeted therapeutic strategies for managing metabolic diseases. A total of 144 participants were recruited and divided into three diagnostic categories: healthy controls (HL, n = 29), hyperuricemia group (HU, n = 24), and overweight (OW, n = 91).

METHODS: Comprehensive phenotypic profiles and metagenomes were analyzed for fecal samples from the three groups.

RESULTS: Significant differences were observed in psychological states and microbial ecology between the metabolic disorder groups (HU and OW) and the control group (HL) (p < 0.05). Both the overweight individuals and those with HUA presented significant changes in gut microbial composition, with reduced α-diversity indices (Shannon index: HU vs HL Mann-Whitney U = 306; p = 0.462; OW vs HL Mann-Whitney U = 1008; p = 0.040; richness index: HU vs HL Mann-Whitney U = 307; p = 0.469; OW vs HL Mann-Whitney U = 1072; p = 0.092) compared to healthy individuals. Moreover, analysis of the linear discriminant analysis effect size (LEfSe) identified four discriminatory species in the HU group (Alistipes putredinis, Mediterraneibacter faecis, Streptococcus oralis, and Gemella sanguinis), and five in the OW group (Pantoea endophytica, Pantoea vagans, Phocaeicola coprophilus, Ruminococcus SGB4421, and Klebsiella oxytoca), representing potential biomarkers for the progression of chronic metabolic diseases.

CONCLUSION: This study elucidates the characteristics of overweight individuals and those with HUA in terms of phenotypic features and gut microbiota, providing a theoretical reference for gut microbiota-targeted therapies and lifestyle interventions in chronic metabolic diseases.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Hyperuricemia/microbiology
Male
Female
*Overweight/microbiology
Middle Aged
Cross-Sectional Studies
Feces/microbiology
Adult
Metagenomics
Metagenome

@article {pmid41503923,
year = {2026},
author = {Sun, YF and Yang, KY and Li, H and Liang, YS and Cai, LQ and Xie, JY and Zhang, YW and Liang, JY and Mou, Q and Wang, YM and Chen, D and Qi, MX and Aguila, LCR and Hassan, MA and Li, HS and Pang, H},
title = {LadybirdBase: A comprehensive biology, ecology, and omics resource for ladybird beetles (Coccinellidae).},
journal = {Insect science},
volume = {},
number = {},
pages = {},
doi = {10.1111/1744-7917.70231},
pmid = {41503923},
issn = {1744-7917},
support = {32172472//National Natural Science Foundation of China/ ; //Open Fund of Guangdong Key Laboratory of Animal Protection and Resource Utilization/ ; 2023YFD1400600//National Key Research and Development Program of China/ ; },
abstract = {Ladybird beetles (Coleoptera: Coccinellidae) comprise over 6000 species and have been extensively studied in terms of their biology, ecology, omics, and applications in biological control. However, this knowledge is scattered across diverse publications and databases, limiting accessibility and integration. To address this gap, we developed LadybirdBase (http://www.ladybirdbase.com), a comprehensive database that compiles primarily published resources on 6872 ladybird species. It integrates five modules: Biology (taxonomy and species traits), Ecology (diet ranges and geographic distributions), Genomics (genomes, transcriptomes, and related datasets), Microbiomics (microbial amplicon and metagenome sequencing), and Lab Test (laboratory-derived biological parameters). LadybirdBase also provides analytical tools for species identification via morphology or DNA barcodes, gene and primer searches, and transcriptome-based differential expression analysis. Using Cryptolaemus montrouzieri-a representative biological control ladybird-as an example, we show that by centralizing ecological, laboratory, and multi-omics data, LadybirdBase supports efficacy evaluation, rearing and release optimization, and risk assessment, thereby advancing research and applications in evolutionary biology, ecology, and sustainable pest management.},
}

@article {pmid41503791,
year = {2026},
author = {Jin, J and Yao, G and Zhang, X and Zhang, T and Ye, H and Zhou, X and Yu, Y and Zhao, Y and Qin, Z and Chen, H and Bi, Y and Wang, X and Ren, X and Zhang, Y and Wang, Z and Zhang, Q},
title = {Gut virome dysbiosis contributes to premature ovarian insufficiency by modulating gut bacteriome.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2611645},
doi = {10.1080/19490976.2025.2611645},
pmid = {41503791},
issn = {1949-0984},
mesh = {Female ; Animals ; *Dysbiosis/microbiology/virology ; *Primary Ovarian Insufficiency/microbiology/virology/therapy ; *Gastrointestinal Microbiome ; Rats ; Humans ; Adult ; *Virome ; Fecal Microbiota Transplantation ; *Bacteria/genetics/classification/isolation & purification/virology ; Young Adult ; Feces/virology ; Ovary ; Rats, Sprague-Dawley ; },
abstract = {BACKGROUND: Premature ovarian insufficiency (POI) significantly impairs female fertility and poses substantial health risks; however, its pathogenesis is incompletely understood, and effective therapeutic interventions are limited. Although gut bacteriome has been closely associated with ovarian dysfunction, the role and therapeutic potential of gut viruses, which far outnumber bacteria, remain largely unexplored.

RESULTS: Therefore, we recruited 60 healthy reproductive-aged women and recently diagnosed POI patients and investigated these concerns using various techniques, including whole-genome shotgun sequencing of virus-like particle (VLP) and fecal virome transplantation (FVT) in CTX-induced POI rats. We found considerable interindividual variability in the gut virome. The virome of POI patients exhibited significant dysbiosis, characterized by a marked reduction in virulent phage, significant changes in predominant phages, and a notable increase in horizontal gene transfer of resistance genes and virulence factors. Furthermore, gut VLPs from the healthy reproductive-aged women significantly improved the condition of POI rats. Conversely, gut VLPs from POI patients markedly impaired the ovarian function and reproductive capacity of healthy rats. The above regulatory effect is primarily due to modulations of gut bacteriome, specifically the estrobolome, and intestinal barrier integrity, which subsequently affect hypothalamic-pituitary-ovarian axis hormone levels and regulate ovarian oxidative stress and inflammation, thereby influencing ovarian function.

CONCLUSIONS: Our findings demonstrate the critical roles of the gut virome in regulating ovarian function and provide new insights into the pathogenesis of POI. This study also underscores the therapeutic potential of the gut virome in improving ovarian dysfunction and female infertility including POI.},
}

Female
Animals
*Dysbiosis/microbiology/virology
*Primary Ovarian Insufficiency/microbiology/virology/therapy
*Gastrointestinal Microbiome
Rats
Humans
Adult
*Virome
Fecal Microbiota Transplantation
*Bacteria/genetics/classification/isolation & purification/virology
Young Adult
Feces/virology
Ovary
Rats, Sprague-Dawley

@article {pmid41503787,
year = {2026},
author = {Wang, Y and Yu, Y and Xu, N and Zhang, Z and Chen, B and Song, M and Zhang, Q and Wang, T and Ma, Y and Lu, T and Sun, L and Qian, H},
title = {Genes for Vitamin B Synthesis and Their Distribution in Microbial Producers.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c11883},
pmid = {41503787},
issn = {1520-5118},
abstract = {B vitamins (VBs) are essential micronutrients, yet their microbial production across natural habitats remains poorly understood. We analyzed 126,931 metagenome-assembled genomes to map the distribution of VB producers and constructed a database of 87 VB synthesis genes, identifying VB-independent producers and their environmental drivers. Soil and freshwater habitats harbored the greatest diversity of VB1, VB2, VB7, VB9, and VB12 producers, whereas marine systems contained fewer. Biosynthetic capacity was rare for VB5 and was limited for VB3 and VB6. Gammaproteobacteria are prolific producers, synthesizing up to eight VB types. Soil sulfur content and conductivity significantly enhanced VB production potential, linking beneficial microbes to improved soil health. We further validated VB3 and VB7 synthesis in Acinetobacter kookii, supporting our predictive framework. Because the identified producers include both beneficial and pathogenic taxa, careful evaluation is required. This work provides a robust gene database and a foundation for optimizing microbial VB production in agriculture and biotechnology.},
}

@article {pmid41503705,
year = {2026},
author = {Liu, W and Du, Y and Ning, J and Zheng, S and Qiu, W and Wang, Y},
title = {Geogenic Ammonium Enrichment in Alluvial-Lacustrine Aquifer Systems: Coupled Controls of Microbial Pathways and Organic Matter Composition.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c11156},
pmid = {41503705},
issn = {1520-5851},
abstract = {Elevated geogenic ammonium (NH4[+]) reported globally in alluvial-lacustrine aquifer systems is generally attributed to the mineralization of natural organic matter (OM). However, the contribution of microbial nitrogen (N) metabolism remains unclear. This study integrated hydrogeochemical profiling, metagenomic sequencing, and molecular-level OM characterization to elucidate how microbial nitrogen transformation and organic N mineralization could drive geogenic NH4[+] accumulation in groundwater. A distinct shift in microbial N metabolism pathways was identified along the NH4[+] enrichment gradient. Under N-limited and strongly reducing conditions, N fixation and dissimilatory reduction of nitrate to ammonium provided additional NH4[+] sources, whereas nitrification served as the primary sink by oxidizing NH4[+] to nitrate. At low NH4[+] levels, NH4[+] was mainly produced via deamination of simple mono-N compounds (CHO+1N) found in highly unsaturated low-oxygen (O) compounds and low-O polyphenols. In contrast, at high NH4[+] levels, urease-mediated hydrolysis of multi-N compounds (CHO+nN) in highly unsaturated high-O compounds became dominant. Co-occurrence network analysis revealed tight, pathway-specific linkages between functional genes and NH4[+]-associated OM compounds, highlighting the substrate-dependent nature of geogenic NH4[+] production. These findings could advance our understanding of microbially mediated NH4[+] enrichment mechanisms and offer implications for the management of NH4[+] and other geogenic contaminants in organic-rich aquifers.},
}

@article {pmid41503571,
year = {2026},
author = {Bajaj, JS and Fagan, A and Sterling, RK and Sikaroodi, M and Gallagher, ML and Lee, H and Matherly, SC and Bartels, A and Mousel, T and Davis, BC and Puri, P and Fuchs, M and Thacker, LR and McGinley, JP and Khoruts, A and Gillevet, PM},
title = {The multi-omic basis for hepatic encephalopathy recurrence: Analysis of the THEMATIC trial.},
journal = {JHEP reports : innovation in hepatology},
volume = {8},
number = {1},
pages = {101634},
pmid = {41503571},
issn = {2589-5559},
abstract = {BACKGROUND & AIMS: The THEMATIC trial demonstrated that fecal microbiota transplantation (FMT) reduces recurrence of hepatic encephalopathy (HE) in patients already receiving lactulose and rifaximin. The aim of this analysis was to identify multi-omic predictors of HE recurrence among THEMATIC trial participants.

METHODS: The THEMATIC trial enrolled patients with cirrhosis and HE who received oral or enema FMT vs. placebo (1-3 administrations) and were followed for 6 months. Outcomes included safety and HE recurrence. Serum, urine, and stool samples were collected at baseline and post-FMT for all participants. Stool metagenomics, serum and urine metabolomics, inflammatory cytokines, and clinical data were analyzed. Differences between patients with and without HE recurrence were assessed using pathway, random forest, and latent factor analyses.

RESULTS: HE recurred in 10 of 60 patients (17%), with significantly higher recurrence in the placebo vs. the FMT groups (40% vs. 8%; p = 0.005). Due to the low recurrence rate in the FMT arms, all patients with recurrence were combined and compared with those without recurrence. Stool metagenomics showed that the abundance of short-chain fatty acid (SCFA) producers (Faecalibacterium, Eubacterium, Bacteroides, Blautia spp.) was lower, while that of GABA-producing taxa (Lactobacillus, Bifidobacterium spp.) was higher, in patients with recurrence. Urine and serum metabolomes separated HE recurrence groups on PLS-DA, with serum butyrate and isobutyrate being most significantly associated (p = 0.008). Pathway analyses revealed upregulation of GABA and neurotransmitter pathways in patients with HE recurrence. Random forest and latent factor analysis indicated that SCFA producers and secondary bile acids were protective, whereas IL-6, GABA producers, nicotine metabolites, and primary bile acids were associated with HE recurrence.

CONCLUSIONS: Secondary analysis of the THEMATIC randomized controlled trial indicates that HE recurrence in patients on lactulose and rifaximin is associated with distinct microbiome and metabolomic profiles, particularly involving SCFAs, GABA metabolism, bile acids, and IL-6.

IMPACT AND IMPLICATIONS: Fecal microbiota transplantation (FMT) reduced hepatic encephalopathy (HE) recurrence in patients receiving lactulose and rifaximin in the THEMATIC trial, but the multi-omic mechanisms underlying this effect were unclear. In this secondary analysis, we found that HE recurrence - regardless of FMT or placebo assignment - was associated with distinct multi-omic signatures, including reduced short-chain fatty acid-producing and increased pathobiont taxa, lower urinary and serum short-chain fatty acids, secondary bile acids, and acetaminophen derivatives, and higher GABA-related and nicotine metabolites, along with elevated IL-6 levels. Notably, patients with greater donor microbiota engraftment had lower rates of HE recurrence. These findings suggest that HE recurrence after FMT reflects a multifactorial process involving alterations in gut metagenomics, systemic metabolomics, inflammation, and donor engraftment.

TRIAL REGISTRATION: www.clinicaltrials.gov: NCT03796598.},
}

@article {pmid41503531,
year = {2026},
author = {Burd, EM},
title = {Metagenomic next-generation sequencing reveals cross-reactivity of lateral flow cryptococcal antigen assay with Trichosporon inkin.},
journal = {ASM case reports},
volume = {1},
number = {2},
pages = {},
pmid = {41503531},
issn = {2996-2684},
abstract = {Metagenomic next-generation sequencing (mNGS) in plasma, cerebrospinal fluid (CSF), and bronchoalveolar lavage fluid is a relatively new technology that offers a means to potentially provide a diagnosis in cases where infection is suspected, but conventional diagnostic testing has not revealed a pathogen. There have been many publications of individual cases and overall appraisals of its utility in detecting bacteria, fungi, and DNA viruses associated with otherwise undiagnosed systemic infections. A recent article by Phillips et al. published in ASM Case Reports (2:e00053-25, 2025, https://doi.org/10.1128/asmcr.00053-25) presents a case of meningitis in an immunosuppressed child that was ultimately determined to be caused by Trichosporon inkin using mNGS. Elevated ß-1,3-D-glucan (BDG) levels in CSF and serum projected a diagnosis of fungal meningitis. Bacterial, fungal, and mycobacterial cultures were negative. Positive lateral flow cryptococcal antigen titers in serum and CSF complicated the anticipated diagnosis since Cryptococcus spp. are thought to not have sufficient cell wall BDG to produce positive test results. Given the ultimate diagnosis of T. inkin meningitis and the known cross-reactivity with Trichosporon asahii per package insert, the unexpected cryptococcal antigen results raised the possibility of additional cross-reactivity. The authors uncovered this possibility by testing three known clinical isolates of T. inkin which generated positive results. This case adds to the growing literature that highlights the utility of mNGS in providing a diagnosis in otherwise unresolved cases and shows that mNGS can be further instructive in elucidating limitations in commonly used diagnostic tests.},
}

@article {pmid41503526,
year = {2026},
author = {Phillips, K and Acker, KP and Han, JY and Salvatore, CM and Permar, SR and Rolón, RM and Marino, J and Dysart, C and Berman, DM and Chiu, CY and Kidd, SE and Westblade, LF and Dubois, MM},
title = {Trichosporon inkin meningitis in a pediatric patient diagnosed via metagenomic sequencing.},
journal = {ASM case reports},
volume = {1},
number = {2},
pages = {},
pmid = {41503526},
issn = {2996-2684},
abstract = {BACKGROUND: Trichosporon has emerged as an important cause of invasive fungal infections in immunocompromised patients. There are limited data on invasive Trichosporon infections in children.

CASE SUMMARY: We report a case of culture-negative Trichosporon inkin meningitis diagnosed via metagenomic next-generation sequencing of plasma and cerebrospinal fluid in an infant with retinoblastoma. In addition, we highlight the role of β-1,3-D-glucan in the diagnosis and therapeutic monitoring of trichosporonosis, and cross-reactivity of the cryptococcal antigen lateral flow assay with T. inkin.

CONCLUSION: This diagnosis, which was challenging to make in the absence of a positive culture, highlights the utility of metagenomic sequencing methods and fungal biomarkers in identifying infectious agents and ensuring timely diagnosis and management of patients with rare fungal infections of the central nervous system.},
}

@article {pmid41503489,
year = {2026},
author = {Goddard, TR and Carlson-Jones, JA and Morton, J and Ooi, CY and Tai, A and Warner, MS and Wong, J and Evans, IE and Hopkins, E and Iredell, JR and Jersmann, HP and Whiteson, KL and Bouras, G and Doane, MP and Falk, NW and Green, R and Grigson, SR and Mallawaarachchi, V and Martin, B and Roach, MJ and Ryan, FJ and Tarasenko, A and Papudeshi, B and Drigo, B and Giles, SK and Harker, CM and Hesse, RD and Hodgson, RJ and Hussnain, A and Hutton, A and Inglis, LK and Keneally, C and Kerr, EN and Liddicoat, C and Peddle, SD and Watson, CD and Yang, Q and Decewicz, P and Speck, PG and Mitchell, JG and Dinsdale, EA and Edwards, RA},
title = {Microbial Ecological Signatures Predict Pathogen Emergence and Multidrug Resistance in Cystic Fibrosis Airways up to a Year in Advance.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2025.12.28.25342520},
pmid = {41503489},
abstract = {Chronic infections in cystic fibrosis (CF) emerge from gradual ecological transitions in the airway microbiome, yet early predictive markers remain poorly defined. We developed a new autoencoder-based framework that outperforms read-based or metagenome-assembled genome-based analyses at capturing the continuum from health-associated commensals to pathogen-dominated, antibiotic-tolerant communities. This improvement is achieved by integrating taxonomic and functional data from 127 sputum and bronchoalveolar lavage metagenomes from 64 people with CF into latent "Clusters of Phylogeny and Functions" (COPFs). Coupled with gradient-boosted random forests, COPFs predicted Pseudomonas aeruginosa colonisation, multidrug resistance, and impending infection up to a year before clinical detection. The multidrug-resistant P. aeruginosa signature showed the same resistance-mechanism evolution as found in laboratory experiments. The inclusion of eukaryotic markers revealed persistent Aspergillus fumigatus signatures even during culture-negative intervals. Applying our South Australian-trained model to over 1,000 global metagenomes from 22 independent CF datasets, we achieved 94% accuracy in predicting P. aeruginosa status across platforms and geographies, validating the model's universal utility. Our results demonstrate that combining datasets with deep learning reveals conserved ecological and metabolic mechanisms in disease progression, transforming metagenomics into a predictive framework for managing chronic infections.},
}