@article {pmid41534271,
year = {2026},
author = {Zhou, W and Duan, C and Xue, M and Li, S and Fan, X and Wu, H},
title = {Diversity and potential environmental risks of DNA viruses on international ships' ballast water at Shanghai port, China.},
journal = {Marine pollution bulletin},
volume = {225},
number = {},
pages = {119198},
doi = {10.1016/j.marpolbul.2025.119198},
pmid = {41534271},
issn = {1879-3363},
abstract = {Over 10 billion tons of ballast water is transferred annually globally, transporting many microorganisms such as bacteria and viruses into new environments and harming local ecology, economy and human health. Numerous studies on bacteria in ballast water have shown its remarkable bacterial diversity and potential risks in recent years. However, the diversity of viruses present in ballast water and their potential environmental implications remain extremely limited in our understanding. In this investigation, we utilized viral metagenomic sequencing to evaluate the viral diversity and distribution in ballast water sourced from five distinct shipping routes that docked at Shanghai Port. Additionally, we compared the distribution of antibiotic resistance genes (ARGs) and virulence factors (VFs) harbored by viruses in ballast water from different routes. The viral diversity and community composition exhibited significant differences in the ballast water samples collected along distinct shipping routes. The virus diversity index varies across different routes, and notably, for the Shannon and Pielou indices, the DJ and GG routes were significantly lower than other routes. Although Caudoviricetes was the dominant viral group, the abundances of Megaviricetes and Faserviricetes were also relatively high, albeit showing variations among different routes. 224 ARGs were identified, including 143 single resistance genes (SARGs) and 81 multiple resistance genes (MARGs), and their distribution varied across different shipping routes. Similarly, certain types of VFs also exhibit differences across various routes, including nutritional/metabolic processes, biofilm formation, and exotoxins. Moreover, the comparison of viral environmental risks showed that ballast water from routes through the Indian Ocean and the South China Sea posed a greater environmental risk. In summary, the results of our research have uncovered the virus diversity and potential risks associated with different routes. This underscores the imperative of implementing targeted management strategies for each individual route.},
}

@article {pmid41533915,
year = {2026},
author = {Pang, J and Wei, Z and Zhang, Z and Xu, X and Peng, Y and Chen, Q and Wei, Y and Liu, J and Zhang, Y and Shi, Q and Wang, Z and Zhang, Y and Chen, K and Zhou, M and Lu, X and Liang, Q},
title = {Genomic Landscape Reveals Correlation of Endosymbiont Ralstonia With Acanthamoeba Keratitis Severity.},
journal = {Investigative ophthalmology & visual science},
volume = {67},
number = {1},
pages = {17},
doi = {10.1167/iovs.67.1.17},
pmid = {41533915},
issn = {1552-5783},
mesh = {Animals ; *Acanthamoeba Keratitis/microbiology/parasitology/diagnosis/genetics ; Mice ; *Acanthamoeba/genetics/microbiology ; *Symbiosis ; *Ralstonia/genetics/physiology ; Humans ; Whole Genome Sequencing ; Disease Models, Animal ; Female ; In Situ Hybridization, Fluorescence ; Microscopy, Electron, Transmission ; Cornea/parasitology/pathology ; Male ; Genome, Bacterial ; Severity of Illness Index ; Genomics ; },
abstract = {PURPOSE: To identify the basic genomic profile of Acanthamoeba, obtain information on Acanthamoeba endosymbionts, and analyze the correlation between these endosymbionts and the prognosis of Acanthamoeba keratitis (AK) patients.

METHODS: Whole-genome sequencing was conducted on 30 cornea-derived Acanthamoeba strains. Pan-genome analysis was performed, and endosymbionts were identified by metagenomic analysis. Gimenez staining, fluorescence in situ hybridization, and transmission electron microscopy were used to prove the existence of endosymbionts. Linear discriminant analysis effect size was used to associate endosymbiont species with AK clinical prognosis. The correlation between the endosymbiont Ralstonia and pathogenicity was experimentally validated by assessing the biological characteristics of Acanthamoeba and by performing clinical and histopathological evaluations in AK mouse models.

RESULTS: Whole genome sequencing revealed that the Acanthamoeba genome size was 37.1-105.0 Mb and GC content was 53.9%-60.5%. Pan-genomic analysis indicated an open state of the Acanthamoeba genome. Metagenomic analysis identified the presence of endosymbionts within Acanthamoeba, notably the endosymbiont Ralstonia, which was associated with poor prognosis at the genus level (P = 0.047). Acanthamoeba harboring the endosymbiont Ralstonia exhibited an increased migration area, enhanced adhesion, and had a more pronounced cytopathic effect. The size of clinical scores and corneal ulcers showed a significant increase in mouse models induced by Acanthamoeba with endosymbiont Ralstonia.

CONCLUSIONS: Whole-genome sequencing highlighted the symbiotic relationship between Acanthamoeba and associated microorganisms. The presence of the endosymbiont Ralstonia influenced the biological characteristics of Acanthamoeba and was correlated with clinical poor prognosis in AK, suggesting its potential as a target for clinical intervention.},
}

Animals
*Acanthamoeba Keratitis/microbiology/parasitology/diagnosis/genetics
Mice
*Acanthamoeba/genetics/microbiology
*Symbiosis
*Ralstonia/genetics/physiology
Humans
Whole Genome Sequencing
Disease Models, Animal
Female
In Situ Hybridization, Fluorescence
Microscopy, Electron, Transmission
Cornea/parasitology/pathology
Male
Genome, Bacterial
Severity of Illness Index
Genomics

@article {pmid41533582,
year = {2026},
author = {Ahrendt, SR and Haridas, S and Stong, S and Salamov, A and Steindorff, A and LaButti, K and Riley, R and Shabalov, I and Lukashin, I and Dusheyko, S and Schulz, F and Romero, MF and Villada, JC and Grigoriev, IV and Mondo, SJ},
title = {Comparative mitogenomics of kingdom Fungi - evolutionary insights and metagenomic applications.},
journal = {Nucleic acids research},
volume = {54},
number = {2},
pages = {},
doi = {10.1093/nar/gkaf1419},
pmid = {41533582},
issn = {1362-4962},
support = {//U.S. Department of Energy Joint Genome Institute/ ; DE-AC02-05CH11231//U.S. Department of Energy/ ; },
mesh = {*Genome, Mitochondrial ; *Evolution, Molecular ; *Metagenomics/methods ; *Fungi/genetics/classification ; Genome, Fungal ; Phylogeny ; RNA, Transfer/genetics ; Molecular Sequence Annotation ; },
abstract = {Mitochondria are essential components of eukaryotic cells, responsible for ATP production through oxidative phosphorylation. Despite their biological importance, unique challenges have hindered the adoption of automated mitochondrial genome (mitogenome) annotation methods, obstructing mitochondrial comparative genomics in a broad evolutionary context. Using Fungi as a study system and a Joint Genome Institute (JGI) annotated high-quality reference set, we observed broad patterns of mitochondrial evolution across the kingdom. We found that the median fungal mitogenome size is 58 kb and identified exceptionally large examples over 1 Mb in Pezizomycetes. All 14 expected oxidative phosphorylation protein-coding genes, plus rps3, were generally conserved. We found evidence of major evolutionary transitions within the Ascomycota, including the transfer of mitochondrially encoded atp8 and atp9 to the nuclear genomes across the Pezizomycotina and shifts in mitogenome tRNA patterns across the kingdom. We found substantial concordance between mitochondrial and nuclear evolution, enabling us to document 3131 total fungal mitogenomes from JGI-derived metagenomic datasets. We also identified 6467 total undeclared mitogenomes embedded in Genbank fungal nuclear assemblies. We provide interactive tools for mitogenome analysis through the JGI MycoCosm platform. Collectively, this work generated nearly 10 000 new fungal mitogenome annotations, providing a foundation and resources for future exploration of comparative fungal mitogenomics.},
}

*Genome, Mitochondrial
*Evolution, Molecular
*Metagenomics/methods
*Fungi/genetics/classification
Genome, Fungal
Phylogeny
RNA, Transfer/genetics
Molecular Sequence Annotation

@article {pmid41532487,
year = {2026},
author = {Goh, KM and Nurhazli, NAA and Tan, JH and Liew, KJ and Chan, KG and Pointing, SB and Sani, RK},
title = {Thermophiles in the genomic Era (2015-2025): a review on biodiversity, metagenome-assembled genomes, and future directions.},
journal = {Critical reviews in microbiology},
volume = {},
number = {},
pages = {1-18},
doi = {10.1080/1040841X.2026.2614431},
pmid = {41532487},
issn = {1549-7828},
abstract = {Thermophile research has been transformed over the past decade by advances in genome sequencing. Once centered on culture collections and physiological studies of terrestrial hot springs and deep-sea hydrothermal vents, the field now employs amplicon sequencing, shotgun metagenomics, and long-read platforms to reveal the diversity, ecology, and genomic potential of thermophiles. Metagenome-assembled genomes (MAGs), metatranscriptomes, and metaproteomes have become crucial for linking taxonomy with function, uncovering previously hidden microbial dark matter in heated ecosystems. Bioinformatics, increasingly integrated with machine learning, has expanded insights into microbial biology, biomolecules, and ecological interactions. These advances highlight the broader environmental significance of thermophiles, spanning fundamental roles in ecosystem processes to practical applications. In 2015, we published Thermophiles in the Genomic Era: Biodiversity, Science, and Application to capture early next-generation sequencing milestones. A decade later, with tremendous progress achieved, this review revisits the field by synthesizing recent advances across viruses, planktonic thermophiles, and biofilm communities, emphasizing the power of genome-resolved approaches. We also highlight overlooked areas, opportunities for ecological integration and predictive modeling, and the importance of translating discoveries into biotechnological innovation. Our aim is to provide young researchers with a roadmap of emerging questions and strategies likely to shape the next decade of thermophile research.},
}

@article {pmid41532447,
year = {2026},
author = {Ning, W and Hu, G and Yuan, D and Arick, MA and Hsu, CY and Magbanua, ZV and Pechanova, O and Peterson, DG and Dong, Y and Udall, JA and Grover, CE and Wendel, JF},
title = {Comparative Population Genomics of Relictual Caribbean Island Gossypium hirsutum.},
journal = {Molecular ecology},
volume = {35},
number = {2},
pages = {e70239},
doi = {10.1111/mec.70239},
pmid = {41532447},
issn = {1365-294X},
support = {141589//National Science Foundation Plant Genome Program/ ; 22-605//Cotton Incorporated/ ; 58-6066-0-066//USDA ARS Non-Assistance Cooperative Agreements/ ; 58-6066-0-064//USDA ARS Non-Assistance Cooperative Agreements/ ; //Iowa State University/ ; },
mesh = {*Gossypium/genetics ; *Genetics, Population ; Genetic Variation ; Phylogeny ; Gene Flow ; Genome, Plant ; Puerto Rico ; Guadeloupe ; Metagenomics ; Domestication ; Genomics ; Islands ; },
abstract = {Gossypium hirsutum is the world's most important source of cotton fibre, yet the diversity and population structure of its wild forms remain largely unexplored. The complex domestication history of G. hirsutum combined with reciprocal introgression with a second domesticated species, G. barbadense, has generated a wealth of morphological forms and feral derivatives of both species and their interspecies recombinants, which collectively are scattered across a large geographic range in arid regions of the Caribbean basin. Here we assessed genetic diversity within and among populations from two Caribbean islands, Puerto Rico (n = 43, five sites) and Guadeloupe (n = 25, one site), which contain putative wild or introgressed forms. Using whole-genome resequencing data and a phylogenomic framework derived from a broader genomic survey, we parsed individuals into feral derivatives and truly wild forms. Feral cottons display uneven levels of genetic and morphological resemblance to domesticated cottons, with diverse patterns of genetic variation and heterozygosity. These patterns are inferred to reflect a complex history of interspecific and intraspecific gene flow that is spatially highly variable in its effects. Wild cottons in both Caribbean islands appear to be relatively inbred, especially the Guadeloupe samples. Our results highlight the dynamics of population demographics in relictual wild cottons that experienced profound genetic bottlenecks associated with repeated habitat destruction superimposed on a natural ecogeographical distribution comprising widely scattered populations. These results have implications for conservation and utilisation of wild diversity in G. hirsutum.},
}

*Gossypium/genetics
*Genetics, Population
Genetic Variation
Phylogeny
Gene Flow
Genome, Plant
Puerto Rico
Guadeloupe
Metagenomics
Domestication
Genomics
Islands

@article {pmid41531535,
year = {2025},
author = {Walia, A and Selvarajan, R and Ogola, HJO and Chauhan, R and Bala, J and Verma, SK and Kumar, R},
title = {Genome-resolved analysis of traditional fermented biofertilizers as scalable solutions for soil restoration.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1725475},
doi = {10.3389/fmicb.2025.1725475},
pmid = {41531535},
issn = {1664-302X},
abstract = {Soil degradation threatens global food security by eroding nutrient reserves and biological resilience. Microbial solutions that regenerate soil fertility through ecological processes offer a sustainable alternative to chemical intensification, yet lack mechanistic validation linking genomic potential to field performance. Fermented microbial consortia, naturally assembled through traditional practices worldwide, represent promising but underexplored technologies for biological soil restoration. Here, we integrate shotgun metagenomics, metagenome-assembled genome (MAG) reconstruction, and two-season field trials to evaluate Jeevamrit, a cattle-derived fermented biofertilizer widely used across South Asia, as a model system for understanding microbial-mediated soil restoration. Metagenomic profiling revealed that Jeevamrit fermentation of cattle dung and urine produces a functionally rich microbial consortium dominated by Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes. Thirty high-quality MAGs encoded genes for nitrogen fixation (nifHDK), phosphate solubilization (phoA, pstS), potassium transport (trkA, phoR), siderophore biosynthesis, and phytohormone production (trpA, miaB), alongside enriched CAZymes (GH13, PL1) and biosynthetic clusters (NRPS, PKS, terpenes) supporting nutrient turnover and rhizosphere signaling. Field application in severely degraded Himalayan rice soils substantially improved soil health relative to controls: soil organic carbon increased from 0.53%-0.68% to 0.76%-1.04% (up to 96% increase), microbial biomass carbon rose from ~72 mg C kg[-1] to 186-282 mg C kg[-1] (159% increase), available phosphorus increased 39.5%, and grain yield improved 74%, while pH and electrical conductivity remained stable. Principal component analysis confirmed that SOC, microbial biomass, and nutrient availability drove treatment differentiation, corroborating genomic predictions. This genome-to-field framework establishes fermented microbial consortia as multifunctional solutions that restore soil fertility through ecological intensification rather than chemical supplementation. By demonstrating that traditional farmer innovations can be genomically validated and mechanistically understood, this work provides a replicable model for scaling nature-based, low-cost soil restoration technologies to address global agricultural sustainability challenges.},
}

@article {pmid41531093,
year = {2026},
author = {Liu, SE and Dong, ZF and Zhang, AH and Min, W},
title = {[Effect of Biodegradable Mulching Film on Soil Microbial Community in Cotton Field was Revealed Based on Metagenomics].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {47},
number = {1},
pages = {650-662},
doi = {10.13227/j.hjkx.202411219},
pmid = {41531093},
issn = {0250-3301},
mesh = {*Soil Microbiology ; *Gossypium/growth & development ; Metagenomics ; Soil/chemistry ; Biodegradation, Environmental ; *Agriculture/methods ; Microbiota ; },
abstract = {Biodegradable mulching films （BMPs） have been widely used as an alternative to conventional plastic mulching films （CMPs）. However， the long-term effects of BMPs on soil microbial community structure remain unclear. Therefore， in this study， we set up two treatments， CMPs and BMPs， and conducted a field experiment with 26 a of CMPs and 11 a of BMPs coverage. Using metagenomics technology， the effects of BMPs on soil microbial community structure in cotton fields in arid areas were investigated. The results showed that compared with those under the CMPs treatment， the BMPs treatment significantly reduced soil water content （SWC）， bulk density （BD）， and available phosphorus （AP） by 25.00%， 12.50%， and 12.09%， respectively， but significantly increased soil porosity （SP） by 10.07%. The BMPs treatment （124） significantly reduced the number of unique species compared with that in the CMPs treatment （182）. At the phylum level， the BMPs treatment significantly increased the relative abundance of Proteobacteria and significantly decreased the relative abundance of Actinobacteria. At the genus level， the BMPs treatment significantly increased the relative abundances of Nocardioides， Solirubrobacter， and Nitrospira and significantly decreased the relative abundance of Sphingomonas. Meanwhile， the proportion of positive correlations and the average degree between microbial communities in the BMPs treatment were increased significantly by 16.32% and 8.71% compared with those in the CMPs treatment， respectively， reducing the modularization degree of the microbial community by 1.89% and promoting the symbiotic relationship and stability of the microbial community. The BMPs treatment significantly increased the relative abundance of genes such as xylA， narG/nxrA， and nasA and significantly decreased the relative abundance of genes such as accA， frdA， nirB， nrtA， gcd， and phoR， promoting carbon degradation， denitrification， and assimilative nitrate reduction processes and inhibiting dissimilatory nitrate reduction and inorganic phosphorus solubilization processes. Soil SWC and AP were the key environmental factors affecting microbial community composition. Biodegradable mulching film increased the complexity and stability of soil microbial communities compared with traditional mulching film， and soil SWC and AP were the key environmental factors affecting the composition of microbial communities.},
}

*Soil Microbiology
*Gossypium/growth & development
Metagenomics
Soil/chemistry
Biodegradation, Environmental
*Agriculture/methods
Microbiota

@article {pmid41531057,
year = {2026},
author = {Fan, YT and Chang, S and Wang, ER and Zhu, YY and Wang, SJ and Yin, XY},
title = {[Distribution， Diffusion Regularity， and Influencing Factors of Antibiotic Resistance Genes in the Water Transfer Chain from Luanhe River to Tianjin Based on Metagenomics].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {47},
number = {1},
pages = {256-268},
doi = {10.13227/j.hjkx.202410104},
pmid = {41531057},
issn = {0250-3301},
mesh = {Rivers/microbiology ; China ; *Drug Resistance, Microbial/genetics ; *Metagenomics ; *Water Microbiology ; Environmental Monitoring ; Water Supply ; },
abstract = {Yuqiao Reservoir is an important drinking water source for Tianjin. As the source of the "Water Diversion Project from Luanhe River to Tianjin"， there are more than one hundred types of contamination of antibiotic resistance genes （ARGs） in the Panjiakou and Daheiting Reservoirs. However， the level of ARGs in the upstream water transfer chain of Yuqiao Reservoir （Linhe River， Shahe River， and Lihe River） has not yet been studied. It is necessary to characterize the dynamic mechanism of ARGs in this basin to gain a deeper understanding of water ecosystem security. In this study， metagenomic methods were used to investigate the distribution characteristics of ARGs and mobile genetic elements （MGEs） in the surface water of the water transfer chain from Luanhe River to Tianjin during different periods， combined with the correlation mechanisms among microbial community structure and environmental factors. The results showed that the water transfer chain of the Luan River to Tianjin contained 21 types of ARGs with 1 161 subtypes. The main types of ARGs were multidrug， macrolide-lincosamide-streptogramin b （MLSB）， and tetracycline， with macB and tetA58 being the dominant ARGs. The predominant types of MGEs were integration/excision （IE） and replication/recombination/repair （RRR）. Compared to that during the flood period， there was a significant positive correlation between ARGs and MGEs during the dry period. Correlation analysis indicated that temperature， dissolved oxygen， and nitrate showed significant correlation with various ARGs （P < 0.05）. The abundance of ARGs was more easily affected by multiple environmental factors， but the composition of ARGs showed correlations only with total phosphorus and dissolved total phosphorus. Proteobacteria was the most dominant phylum， and several dominant microbial genera， such as Acidovorax and Rhodoferax， also showed significant correlation with ARGs， especially during the dry period. The co-occurrence network analysis revealed the most significant co-occurrence relationship between ARGs and MGEs， and some microbial genera related to nutrient elements and photosynthesis also showed co-occurrence relationships with major ARGs. This project aims to profoundly understand the biogeochemical cycle mechanisms of ARGs in the upstream water transfer chain of the reservoir， and it can provide a scientific basis for decision-making to control the transmission of resistance genes within the regional basin.},
}

Rivers/microbiology
China
*Drug Resistance, Microbial/genetics
*Metagenomics
*Water Microbiology
Environmental Monitoring
Water Supply

@article {pmid41530917,
year = {2026},
author = {Lee, HG and Song, JY and Yoon, J and Chung, Y and Kwon, SK and Kim, JF},
title = {metaFun: An analysis pipeline for metagenomic big data with fast and unified functional searches.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2611544},
doi = {10.1080/19490976.2025.2611544},
pmid = {41530917},
issn = {1949-0984},
mesh = {*Metagenomics/methods ; Humans ; *Metagenome ; *Big Data ; *Software ; Colorectal Neoplasms/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Computational Biology/methods ; Gastrointestinal Microbiome ; Reproducibility of Results ; },
abstract = {Metagenomic approaches offer unprecedented opportunities to characterize microbial community structure and function, yet several challenges remain unresolved. Inconsistent genome quality impairs reliability of metagenome-assembled genomes, lack of unified taxonomic criteria limits cross-study comparability, and multi-step workflows involving numerous programs and parameters hinder reproducibility and accessibility. We benchmarked existing programs and parameters using simulated metagenomic data to identify optimal configurations. metaFun is an open-source, end-to-end pipeline that integrates quality control, taxonomic profiling, functional profiling, de novo assembly, binning, genome assessment, comparative genomic analysis, pangenome annotation, network analysis, and strain-level microdiversity analysis into a unified framework. Interactive modules support standardized data interpretation and exploratory visualization. The pipeline is implemented with Nextflow and containerized with Apptainer, ensuring environment reproducibility and scalability. Comprehensive documentation is available at https://metafun-doc.readthedocs.io/en/main. The pipeline was validated using a colorectal cancer cohort dataset. By addressing key methodological gaps, metaFun facilitates accessible and reproducible metagenomic analysis for the broader research community.},
}

*Metagenomics/methods
Humans
*Metagenome
*Big Data
*Software
Colorectal Neoplasms/microbiology
*Bacteria/classification/genetics/isolation & purification
*Computational Biology/methods
Gastrointestinal Microbiome
Reproducibility of Results

@article {pmid41530889,
year = {2026},
author = {Bonacolta, AM and Keeling, PJ},
title = {Modern microbialites harbor an undescribed diversity of chromerid algae.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00852-4},
pmid = {41530889},
issn = {2524-6372},
support = {GBMF9201//Gordon and Betty Moore Foundation/ ; },
abstract = {BACKGROUND: Chromerid algae are the closest photosynthetic relatives of apicomplexan parasites. While chromerids have been central to understanding the evolutionary transition from free-living algae to parasitism within Apicomplexa, their ecology remains poorly understood. Although often considered coral-associated symbionts, emerging evidence suggests this link is incidental and that chromerids may be more broadly associated with calcium carbonate environments, including microbialites. These microbial structures represent modern analogues of ancient reef-like ecosystems but are difficult to study due to their rarity and protected status as world heritage sites. Prokaryotic members of the microbialite microbiome have been studied at length, while the microeukaryotes associated with these environments have gone mostly ignored. To further investigate the link between microbialites and chromerid algae, we re-analyzed previously published microbialite sequencing data with the aim of investigating chromerid diversity and distribution.

RESULTS: Through a novel plastid-focused metagenomic binning workflow combined with re-analysis of rRNA metabarcoding data, we reveal that chromerid algae are consistent associates of microbialites across diverse marine and freshwater environments worldwide. Most notably, we report the first recovery of plastid genomes from microbialite-associated chromerids: a complete Vitrella brassicaformis plastid genome and a second, partial plastid genome from a previously undescribed Chromera-related lineage in Highborne Cay thrombolites. This partial plastid genome contained photosystem genes, confirming this novel Chromera-related lineage as a photosynthetic chromerid. These findings not only expand the known ecological and biogeographic range of chromerids but also provide evidence for their overlooked diversity.

CONCLUSIONS: Our analyses prove that this overlooked algal lineage is not found exclusively associated with corals, but instead occurs across a wide range of microbialite habitats, including those found in freshwater. By extending their known distribution beyond coral hosts and the marine environment, our results not only highlight the diversity and ecological range of the most recently discovered algal lineage but also broaden our understanding of the ancestral lifestyles that may have preceded apicomplexan evolution. This research underscores the value of targeted mining of public sequencing datasets to address specific ecological questions, particularly in rare or hard-to-access environments such as microbialites.},
}

@article {pmid41530817,
year = {2026},
author = {Li, R and Liao, X and Fu, X and Li, X and Liao, X and Cen, S and Zeng, J and Huang, L and Chi, H and Zou, Y},
title = {Microbiota-driven tryptophan metabolism and AhR triggered intestinal stem cell differentiation: mechanisms of huangqin decoction in ulcerative colitis repair.},
journal = {Chinese medicine},
volume = {21},
number = {1},
pages = {33},
pmid = {41530817},
issn = {1749-8546},
support = {2022A1515140011//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 2023A1515010012//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 20231800936162//Dongguan Science and Technology of Social Development Program/ ; 20221800905632//Dongguan Science and Technology of Social Development Program/ ; },
abstract = {BACKGROUND: Promoting intestinal barrier repair and epithelial regeneration is a core therapeutic objective in managing ulcerative colitis (UC). Intestinal stem cell (ISC) differentiation is pivotal in sustaining epithelial renewal and mucosal homeostasis. Huangqin decoction (HQD), a classical herbal formulation comprising Scutellaria baicalensis, Ziziphus jujuba, Paeonia lactiflora, and Glycyrrhiza uralensis, is clinically used for inflammatory bowel disease. Nevertheless, how HQD precisely regulates ISC differentiation to promote UC repair remains unclear.

PURPOSE: This research sought to assess whether HQD ameliorates UC by concurrently modulating the gut microbiome, tryptophan metabolism, aryl hydrocarbon receptor (AhR) activation, and ISC differentiation.

METHODS: Mice developed colitis after drinking water with a 3.5% (w/v) concentration of dextran sulfate sodium. We evaluated HQD effects on colon length, weight trajectory, disease activity index score, histological damage, and colonic inflammatory mediator abundance. Metagenomic sequencing resolved microbiota restructuring, while UPLC-MS/MS quantified fecal tryptophan metabolites such as indole derivatives. AhR pathway activity (AhR, CYP1A1), its downstream cytokine IL-22, and ISC fate were mapped by combining immunofluorescence, ELISA, Western blot, and RT-qPCR, probing Lgr5 for stem-cell identity and MUC2, LYZ, and ChgA for lineage-specific differentiation. The involvement of AhR and gut microbiota was investigated using AhR inhibitors and broad-spectrum antibiotics.

RESULTS: High-dose HQD significantly alleviated colitis symptoms, reduced colon damage, and corrected gut dysbiosis. HQD increased the abundance of related bacteria that elevated colonic levels of indole-3-propionic acid, indole-3-acetamide, and tryptamine, acting as AhR ligands that upregulate AhR and its downstream targets CYP1A1 and IL-22. Crucially, HQD promoted a shift in expression from the ISC marker Lgr5 toward differentiation markers MUC2, LYZ, and ChgA, indicating enhanced ISC differentiation and improved barrier function. These effects were effectively blocked by AhR inhibition or antibiotic treatment.

CONCLUSION: HQD restores intestinal mucosal integrity and attenuates colonic inflammation by modulating gut microbiota composition, increasing microbial tryptophan metabolites with AhR-agonist activity, activating the AhR signaling pathway, and promoting ISC differentiation into functional epithelial cells. This work reveals a novel "microbiota-tryptophan metabolism-AhR-ISC differentiation" axis underlying HQD's therapeutic efficacy in UC.},
}

@article {pmid41530663,
year = {2026},
author = {Yu, HL and Elsheikha, HM and Liang, HR and Qin, SY and Peng, P and Liu, J and Tang, Y and Guo, L and Ni, HB and Xie, LH and Lei, CC and Su, JW and Yu, MY and Qin, Y and Jiang, J and Liu, J and Xu, Y and Zhang, XX},
title = {Blastocystis infection enhances vitamins B and K2 biosynthesis in the Tibetan antelope (Pantholops hodgsonii) gut microbiota.},
journal = {BMC genomics},
volume = {27},
number = {1},
pages = {40},
pmid = {41530663},
issn = {1471-2164},
support = {2023YFF1305403//the National Key Research and Development Program of China/ ; 2022KJ169//the Shandong Province Higher Education Institutions "Youth Innovation Team Plan"/ ; },
}

@article {pmid41530170,
year = {2026},
author = {Maeke, MD and Hassenrück, C and Aguilar-Muñoz, P and Aravena, C and Burmeister, C and Crispi, O and Diallo, POD and Fernández, C and Gouriou, M and Jamont, A and Laymand, E and Marie, B and Molina, V and Ortega-Retuerta, E and Rabouille, S and Sajeeb, MI and Sierks, M and Stevens, M and Turon, R and Valdés-Castro, V and Beier, S},
title = {Metabarcoding and metagenomic data across aquatic environmental gradients along the coasts of France and Chile.},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {29},
pmid = {41530170},
issn = {2052-4463},
support = {Laboratoire international associé program//Centre National de la Recherche Scientifique (National Center for Scientific Research)/ ; 1211977//Fondo Nacional de Desarrollo Científico y Tecnológico (National Fund for Scientific and Technological Development)/ ; BE 5937/2-3//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {Chile ; France ; Metagenomics ; Ecosystem ; *DNA Barcoding, Taxonomic ; *Metagenome ; Seawater/microbiology ; Salinity ; Microbiota ; },
abstract = {Coastal marine environments, such as lagoons, fjords or estuaries, experience pronounced environmental variability, with fluctuations in salinity, temperature and nutrient levels shaping microbial community structure and function. These gradients result in diverse habitats, which may harbour taxonomic and genetic novelty with biogeochemical and biotechnological relevance. To explore microbial diversity and functional potential across these dynamic ecosystems, we sampled 26 sites along the coasts of France and Chile, including lagoons, estuaries, fjords, harbours, as well as coastal and offshore marine sites. Surface waters were collected from all sites, with deeper layers included at three sites. Monthly sampling at six sites in France enabled the assessment of seasonal dynamics. In total, 116 samples were processed for both metabarcoding and metagenomic sequencing yielding over 53,000 amplicon sequence variants (ASVs) and 1,372 metagenome-assembled genomes (MAGs). This dataset further includes a comprehensive gene catalogue and environmental variables such as salinity, temperature, nutrient concentrations, productivity, as well as oxygen consumption metrics collected across the different ecosystems.},
}

Chile
France
Metagenomics
Ecosystem
*DNA Barcoding, Taxonomic
*Metagenome
Seawater/microbiology
Salinity
Microbiota

@article {pmid41530166,
year = {2026},
author = {Zhang, Q and Chen, B and Zhang, Z and Yu, Y and Jin, M and Lu, T and Zhang, Z and Pang, Q and Xu, N and Sun, J and Chen, J and Wang, J and Zhu, D and Qian, H and Penuelas, J and Zhu, YG},
title = {Cobamide-producing microbes as a model for understanding general nutritional interdependencies in soil food webs.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-68255-6},
pmid = {41530166},
issn = {2041-1723},
support = {2022C02029//Natural Science Foundation of Zhejiang Province (Zhejiang Provincial Natural Science Foundation)/ ; 42307158//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Nutrient crossfeeding critically governs microbiome-host interactions and ecosystem stability. Cobamides, synthesized only by prokaryotes, offer a powerful and tractable model for studying nutrient-mediated interdependencies in soil food webs; however, their ecological role in sustaining soil health remains unclear. Here, we construct the Soil Cobamide Producer database (SCP v.1.0) by integrating over 48,000 metagenomic and genomic datasets from 1,123 sampling sites. This database catalogs phylogenetically diverse prokaryotes (19 phyla, 302 genera) with cobamide biosynthetic potential. Using this resource, we identify host-specific colonization patterns of cobamide-producing microbes in fauna. These microbes also carry diverse functional traits that may contribute to trophic cascades and microbial community stability. In an Enchytraeid model, these colonizers support host development, modulate gene expression, and promote gut stability through transkingdom interactions, with cobamide biosynthesis serving as one representative trait among multiple microbial functions. At macroecological scales, cobamide-producing microbes occur across relatively high trophic levels, reflecting a broader principle of nutrient transfer that may also apply to other essential metabolites. This framework provides a general basis for studying nutritional microbes in soil food webs and advances One Health research.},
}

@article {pmid41530018,
year = {2026},
author = {FitzGerald, JA and Lester, KL and O' Sullivan, N and Crispie, F and Lawton, EM and Cotter, PD and McNally, P and Cox, DW},
title = {Parallel metagenomic- and culture-based approaches show nasal swabs are a good proxy for broncho-alveolar lavage in children with cystic fibrosis.},
journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jcf.2025.12.011},
pmid = {41530018},
issn = {1873-5010},
abstract = {BACKGROUND: Broncho-Alveolar Lavage (BAL) is the reference standard for airway surveillance in clinical management of cystic fibrosis (CF), but is invasive and requires general anaesthesia in children. Non-invasive alternatives can lack specificity (Oropharyngeal swabs; OPS), or evaluation in paediatric CF (Middle meatus sampling; MMS). We sought to determine if MMS via nasal-swabs performed better than OPS at representing the microbiological attributes of BAL.

METHODS: In a stable preschool CF cohort attending a single specialist centre, we evaluated the microbiological yield of BAL, MMS, and OPS sampling using both standard clinical culturing, and shotgun metagenomic sequencing (Illumina NextSeq 500).

RESULTS: Matched BAL, MMS, and OPS from 30 preschool children provided 88 samples. While both culture and metagenomic surveillance performed well at detecting S. pneumoniae in BAL, MMS performed better at detecting S. aureus, M. catarrhalis and Escherichia coli, while OPS performed better at detecting H. Influenzae. Metagenomics revealed a significantly more diverse microbiome in OPS than BAL or MMS. While agreement on pathogen profiles varied widely between metagenomics and culture methods, MMS more accurately represented BAL, particularly for Streptococcus, M. catarrhalis, and Escherichia.

CONCLUSIONS: MMS and OPS cultures performed well as proxies for BAL in relation to certain pathogens. Metagenomics detected pathogens in many samples that were unobserved in culture, and showed the oropharynx microbiome to be much more diverse. Lung and nares microbiomes were more similar in composition and diversity. Our data suggest that nasal sampling of the middle meatus may be a more accurate surrogate for lower airway samples.},
}

@article {pmid41529797,
year = {2026},
author = {Cao, X and Zhang, L and Tu, H and Li, T and Wang, G and Xiao, L and Zhang, Y and Liu, P and Li, Y and Li, J and Li, X and Hu, B and Zhang, S and Li, B},
title = {Membrane aerated biofilm reactor for largely enhanced nitrogen removal in low carbon/nitrogen ratio municipal wastewater: integrating nitrification, partial denitrification, and anammox.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133994},
doi = {10.1016/j.biortech.2026.133994},
pmid = {41529797},
issn = {1873-2976},
abstract = {This study first established an integrated nitrification-partial denitrification-anammox (INPDA) process in a single-stage membrane aerated biofilm reactor (MABR) under low dissolved oxygen concentrations (0.12-0.27 mg/L) and low carbon/nitrogen ratios (1.0-3.0), without the need for anaerobic ammonia-oxidizing bacteria (AnAOB) inoculation. The optimal effluent total nitrogen (TN) concentration reached below 5 mg/L, achieving a 92.7% TN removal efficiency. Nitrifiers (including Ellin6067 and Nitrospira) oxidized a portion of ammonium to nitrate, which was subsequently reduced to nitrite by partial denitrifier Thauera utilizing influent organic carbon. Subsequently, AnAOB Candidatus Brocadia converted remaining ammonium and available nitrite into nitrogen. Metagenomics further confirmed a 32.96-fold increase in anammox-associated gene (hdh) abundance during INPDA establishment. Notably, this elevated hdh abundance remained stable even as carbon/nitrogen ratio increased, demonstrating process robustness. This study established a promising single-stage MABR strategy to advance mainstream anammox application.},
}

@article {pmid41529636,
year = {2026},
author = {Díaz-Moreno, N and Lebrero, R and Cantera, S},
title = {Toluene bioconversion into ectoines by halophile mixed microbial cultures.},
journal = {Journal of hazardous materials},
volume = {503},
number = {},
pages = {141045},
doi = {10.1016/j.jhazmat.2026.141045},
pmid = {41529636},
issn = {1873-3336},
abstract = {Toluene, which has been listed in the Pollutant Release and Transfer Register (PRTR) of many countries, is one of the most emitted pollutants to the atmosphere. This study demonstrates for the first time a new perspective in toluene treatment based on its continuous bioconversion into high-value chemicals, specifically ectoine and hydroxyectoine, which hold considerable commercial relevance in the cosmetic industry with market prices reaching 1000 € kg[-1]. Specific ectoine and hydroxyectoine contents of 27.3 mg gTSS[-1] were achieved together with toluene elimination capacities of 7.2 ± 1.9 g m[-3] h[-1] and a maximum biomass concentration of 1.8 g L[-1]. Ectoine synthesis predominated initially, later shifting toward hydroxyectoine, reaching a combined amount of 71.2 mg L[-1] (ectoine:hydroxyectoine 32:68) by the end of the assay. Metagenomic analysis revealed key pathways and taxa involved in toluene degradation and ectoine and hydroxyectoine synthesis. Members of Paenibacillus, Rhodococcus and Microbacterium were identified as possessing the enzymes required for toluene degradation via the TOL pathway, while Gordonia, the most abundant genus, was primarily associated with the degradation of intermediates such as benzoate, muconate, or oxoadipate derivatives and their bioconversion into ectoine. These findings revealed a potential metabolically diverse consortium with functional complementarities, where metabolic synergies overcome species-specific limitations and promote the elimination and subsequent valorization of toluene into high-value products fostering sustainable industrial innovation.},
}

@article {pmid41529631,
year = {2026},
author = {Wang, Y and Qian, Y and Shi, C and Bi, J and Dong, P and Zou, Y and Yang, Y and Tao, Y and Li, H},
title = {Seasonal dynamics and stability of gut antibiotic resistance genes in plateau pika (Ochotona curzoniae) and plateau zokor (Eospalax baileyi).},
journal = {Journal of hazardous materials},
volume = {503},
number = {},
pages = {141112},
doi = {10.1016/j.jhazmat.2026.141112},
pmid = {41529631},
issn = {1873-3336},
abstract = {The extreme ecosystems of the Tibetan Plateau harbor an alarming reservoir of antibiotic resistance genes (ARGs) within wildlife gut microbiomes-an emerging contaminant with significant implications for One Health. However, seasonal dynamics and pathogenic risks of these ARGs remain poorly understood. Through a 2.5-year study comparing the subterranean plateau zokor (Eospalax baileyi) and the surface-dwelling plateau pika (Ochotona curzoniae), we demonstrate how species-specific ecological strategies shape distinct ARG transmission patterns. Our results demonstrated striking eco-evolutionary trade-offs: surface pikas showed 1.3 times higher ARG diversity with strong seasonal variation, influenced by temperature-modulated bacterial community turnover and mobile genetic elements (MGEs). Conversely, subterranean zokors maintained stable, were enriched with high-risk ARGs dominated by mepA and tetO, reflecting their isolated niche. Both species consistently carried pathogenic-ARG complexes (Clostridium-bacA, Staphylococcus-Ermb) across seasons, genders, and ages, indicating established resistance reservoirs in plateau food webs. Metagenomic binning revealed co-transfer potential between ARGs and MGEs. This pioneering longitudinal study exposes a dual pattern: seasonal changes cause temporary turnover of ARGs, which harbor lower resistance risk in surface-dwelling animals, while subterranean hosts retain stable, higher-risk resistance. These findings establish critical baselines for monitoring antimicrobial resistance in vulnerable ecosystems and underscore the need for integrated One Health strategies.},
}

@article {pmid41529629,
year = {2026},
author = {Chen, Z and Zhao, Y and Jin, L and Ma, R and Zhao, H and Ren, H and Huang, H},
title = {Insights into the molecular mechanism driving transformation and detoxification of erythromycin in anoxic biofilters.},
journal = {Journal of hazardous materials},
volume = {503},
number = {},
pages = {141116},
doi = {10.1016/j.jhazmat.2026.141116},
pmid = {41529629},
issn = {1873-3336},
abstract = {Erythromycin (ERY), the most prevalent macrolide antibiotic detected in aquatic environments worldwide, has attracted considerable scientific interest. This concern stems from its persistent environmental presence, largely due to the limited removal efficiency of conventional wastewater treatment processes. Anoxic biofilters were established with two nutritional modes (heterotrophic/autotrophic) and two filter media (bio-ceramic/poly-urethane particle) to reveal the migration and transformation patterns of ERY. Through non-targeted and targeted analysis, 18 transformation products (TPs) were identified, including 11 previously unreported TPs. By integrating metagenomic analysis with molecular docking, key genes, enzymes, and pathways were identified. Linking the molecular mechanism of ERY transformation with toxicity prediction can categorize the toxicity of TPs from high to low into four levels. It is worth noting that the hydrolysis, phosphorylation, and oxidation of hydroxy process is most conducive to reducing the environmental toxicity of ERY. This study elucidated the fate characteristics of ERY in anoxic biofilter at the molecular level. This work provides a theoretical basis for optimizing biofilter operation to mitigate ERY. It also offers insights for developing green, advanced wastewater treatment technologies aimed at ensuring water quality health.},
}

@article {pmid41529435,
year = {2026},
author = {Xiao, Y and Sheng, ZM and Taubenberger, JK},
title = {Precursors to the 1918 pandemic: Finding Rickettsia felis and Mucor co-infection associated with a death in 1912.},
journal = {International journal of paleopathology},
volume = {52},
number = {},
pages = {69-75},
doi = {10.1016/j.ijpp.2026.01.001},
pmid = {41529435},
issn = {1879-9825},
abstract = {OBJECTIVE: To investigate potential molecular evidence of the presence of infuenza A in a patient who died in 1912.

MATERIALS: Two to three paraffin curls from a formalin-fixed paraffin-embedded (FFPE) lung sample from an autopsy case of a one-and-a-half-year-old girl who reportedly died of acute pneumonia at the Royal London Hospital on February 1, 1912.

METHODS: RNA was extracted from the sample. Real-time reverse transcription PCR (RT-PCR) was performed to screen for influenza A virus, followed by total RNA library preparation and high-throughput sequencing on the Illumina NextSeq platform. Bioinformatic analysis was conducted on the obtained reads, which included metagenomic classification and sequence alignment to reference genomes.

RESULTS: Real-time RT-PCR and next-generation sequencing both revealed no evidence of influenza A virus infection. However, metagenomic analysis identified a significant number of reads matching Rickettsia felis, with 233 unique reads specifically aligning to its OmpB gene, and over 4 million fungal reads classified within the Mucor genus, although the exact species could not be determined. These findings provide suggestive molecular evidence of co-infection with R. felis and a Mucor species.

CONCLUSIONS: This study demonstrates the utility of modern molecular techniques in evaluating early diagnoses. Despite records attributing the cause of death to acute pneumonia, no influenza A virus RNA was detected. The identification of R. felis and Mucor sequences suggests that this rare co-infection may have contributed to the infant's death.

SIGNIFICANCE: Retrospective diagnosis is enhanced by the use of modern molecular and bioinformatic techniques. This case study provides important paleopathological insight into the etiology of recorded "acute pneumonia", indicating the presence of pathogens other than influenza A leading up to the 1918 pandemic.

LIMITATIONS: Contamination during autopsy, tissue processing, or storage cannot be ruled out. Due to the lack of remaining material, histopathological confirmation of Mucor or Rickettsia infection was not possible.

Molecular and bioinformatic research into other cases of suspected influenza A.},
}

@article {pmid41529381,
year = {2026},
author = {Haars, J and Cumlin, T and Ladenvall, C and Lennerstrand, J and Kaden, R},
title = {Twist-ONT: Combining nanopore sequencing with the twist comprehensive viral research panel.},
journal = {Virology},
volume = {616},
number = {},
pages = {110789},
doi = {10.1016/j.virol.2026.110789},
pmid = {41529381},
issn = {1096-0341},
abstract = {The Twist Comprehensive Viral Research Panel (Twist CVRP) is a probe-based hybridization capture enrichment method for whole-genome sequencing, designed to target all known pathogenic viruses. Unlike shotgun metagenomics, where human DNA dominates, this method enriches for viral sequences within samples. This study presents a novel protocol called Twist-ONT, integrating Twist CVRP with Oxford Nanopore Technologies (ONT) long-read sequencing. Using clinical nasopharyngeal/throat swab and plasma samples PCR-positive for a variety of different viruses, the protocol's capability for viral species classification was demonstrated. It is also shown how high-quality whole-genome assemblies and consensus sequences can be generated from the sequencing reads of this protocol. This protocol facilitates further studies into the viromes of clinical samples and viral genomics in general using ONT sequencing.},
}

@article {pmid41529347,
year = {2026},
author = {Singh, S and Bajaj, A and Manickam, N},
title = {Microbiome of soil waste dumpsite and adjacent river habitat harbors dynamic plastic degrading bacterial diversity and abundant functional enzymes.},
journal = {The Science of the total environment},
volume = {1014},
number = {},
pages = {181331},
doi = {10.1016/j.scitotenv.2025.181331},
pmid = {41529347},
issn = {1879-1026},
abstract = {Landfill leachates and adjacent riverine ecosystems are usually the reservoirs of plastic-derived contaminants and other xenobiotics. Yet these sites are still less explored for their degradation potential. This study employed a whole metagenome analysis to characterize microbial communities and functional genes from the Ghaila municipal dumpsite and the Gomti river, Lucknow, India. Physicochemical analyses revealed neutral to slightly alkaline pH and elevated BOD and COD in downstream river sites, indicating high organic and plastic-associated pollutant loads. Taxonomic profiling identified 57 phyla, dominated by Proteobacteria, Bacteroidetes, Chloroflexi, and Firmicutes, with occurrence of key genera such as Pseudomonas, Acinetobacter, Flavobacterium, and Sphingomonas in abundance. Functional annotation of the metagenomic sequences detected 31 enzymes targeting 24 polymeric substances, including PETase, MHETase, urethanases, laccases, and nylon hydrolases in both dumpsite leachate and sludge (p < 0.05) samples. Antibiotic resistance genes (ARGs) and metal resistance genes (MRGs) were widely distributed, particularly in leachate and sludge, underscoring their role as resistance reservoirs. These findings demonstrate that municipal dumpsite ecosystems are hotspots for plastic and xenobiotic degradation, highlighting their potential as genetic resources for bioremediation and advancing understanding of contaminant-driven microbial adaptation at landfill-river interfaces. NUCLEOTIDE SEQUENCE ACCESSION NUMBER: The complete metagenome sequence has been deposited at NCBI GenBank having accession no: SAMN42678420 to SAMN42678429 (BioProject).},
}

@article {pmid41528680,
year = {2026},
author = {Wu, C and Zeng, B and Ning, Z and Wang, W and Wang, Y and Zhang, Q and Lu, D},
title = {Cloning and Characterization of a PL6 Alginate Lyase Aly94 from the Marine Bacteria.},
journal = {Molecular biotechnology},
volume = {},
number = {},
pages = {},
pmid = {41528680},
issn = {1559-0305},
support = {32201039//National Natural Science Foundation of China/ ; ZR2022QC247//Natural Science Foundation of Shandong Province/ ; 2023YX040//Weifang Science and Technology Development Plan Project (Medical Category)/ ; },
abstract = {Microbial alginate lyases are essential biocatalysts for analyzing alginate structure and sustainably producing bioactive alginate oligosaccharides (AOS). In this study, we characterized Aly94, a novel alginate lyase from the polysaccharide lyase family 6 (PL6) family, identified from a marine sediment metagenomic library. Biochemical analyses showed Aly94 exhibits optimal activity at 40 ℃ in 50 mM NaH2PO4-Na2HPO4 buffer (pH 7.0). Adding 20 mM NaCl significantly increases its catalytic efficiency. The enzyme exhibits a strong preference for polyguluronate (polyG) over polymannuronate (polyM), with specific activities of 4.19 U/mg (polyG), 0.25 U/mg (polyM), and 2.45 U/mg (alginate). When degrading substrates-particularly polyG-Aly94 primarily generates trisaccharides. Although Aly94 acts as an endolytic alginate lyase, it also could digest the monosaccharides from small oligosaccharide chains (∆G3, ∆G4). These catalytic properties, combined with its polyG-specific depolymerization, made Aly94 a promising candidate for biotechnological applications requiring controlled alginate saccharification and high-value AOS production.},
}

@article {pmid41528333,
year = {2026},
author = {Velioglu, EM and Arslan, U and Kayis, SA and Maçin, S and Kamada, N and Hakki, SS},
title = {Corrigendum: Correlation in the change of gut microbiota with clinical periodontal parameters in grade C periodontitis patients after non-surgical periodontal therapy.},
journal = {Journal of medical microbiology},
volume = {75},
number = {1},
pages = {},
doi = {10.1099/jmm.0.002120},
pmid = {41528333},
issn = {1473-5644},
}

@article {pmid41528142,
year = {2026},
author = {Boey, JS and Tee, HS and Waite, DW and Handley, KM},
title = {Genetic mechanisms for estuarine carbohydrate degradation and linked transcriptional activity.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0185225},
doi = {10.1128/aem.01852-25},
pmid = {41528142},
issn = {1098-5336},
abstract = {The current understanding of carbohydrate substrate degradation is largely derived from incubation experiments involving specific substrates. In estuaries, carbohydrates are often grouped together with other sources of carbon, for analytical purposes, and measured as total and fractional organic matter. Here, we describe putative carbohydrate degradation at the polysaccharide level by the prokaryotic community in an estuary. Samples were collected along a freshwater-to-marine salinity gradient from both the water column and underlying benthic sediments. Metagenomic and metatranscriptomic data were used to determine carbohydrate-active enzyme (CAZyme)-encoding metagenome-assembled genomes and associated transcriptional activity across the gradient. Previous work demonstrated assimilation of xylan (a component of hemicellulose) in estuaries. We show the genetic mechanisms associated with the degradation of xylan, as well as arabinogalactan (also from hemicellulose), and various other glycans were widespread among estuarine taxa and actively expressed. In addition, results show different carbohydrate degradation strategies between planktonic and benthic organisms. For example, results indicate that sediment communities harbored a greater variety and density of CAZyme-encoding genes and capacity to degrade complex plant biomass (cellulose and hemicellulose) and dedicated more gene transcription overall to CAZymes than planktonic communities. In contrast, planktonic prokaryotes tended to express a greater fraction of their CAZyme-encoding gene repertoires. The transcription of gene clusters associated with degrading beta-1,3-glucans such as laminarin was prevalent in the water column. Microbial activity to degrade alpha-glucans such as glycogen was predicted to be ubiquitous but was greatest in planktonic communities. Taken together, results highlight differences in the capacity of planktonic and benthic communities to degrade carbohydrates, which reflect differences in substrate availability and complexity.IMPORTANCEEstuaries are productive ecosystems that combine various forms of organic carbon from autochthonous (e.g., algal primary producers and mangroves) and allochthonous (e.g., terrestrial plant) sources. The degradation and recycling of this organic carbon is driven by heterotrophic bacteria that are expected to harbor diverse genetic mechanisms for carbohydrate degradation to match the diversity and complexity of organic carbon encountered in the environment. Results here illustrate the diversity of carbohydrate-active enzymes (notably glycosyl hydrolases) encoded by estuarine communities and the different substrate prioritizations of planktonic and benthic communities.},
}

@article {pmid41528122,
year = {2026},
author = {McMurray-Jones, A and Spann, K and Yarlagadda, PKDV and Fernando, J and Roberts, LW},
title = {Environmental surveillance of bacteria in a new intensive care unit using plate sweeps.},
journal = {Microbial genomics},
volume = {12},
number = {1},
pages = {},
pmid = {41528122},
issn = {2057-5858},
mesh = {*Intensive Care Units ; *Bacteria/genetics/isolation & purification/classification/drug effects ; Humans ; Queensland ; *Environmental Monitoring/methods ; Drug Resistance, Bacterial/genetics ; Microbiota/genetics ; Metagenomics/methods ; Cross Infection/microbiology ; },
abstract = {The hospital environment plays a critical role in the transmission of infectious diseases. Surveillance methods often rely on selective enrichment or deep metagenomic sequencing, which both have significant drawbacks in terms of community resolution and cost. Plate sweeps provide a practical moderate approach to cultivate a wide range of bacteria, capturing more diversity than a single colony pick without high sequencing costs. Here, we use this approach to characterize a newly built hospital intensive care unit (ICU) in Queensland, Australia. Between November 2023 and February 2024, we sampled 78 sites within an 8-bed private hospital ICU pre- and post-patient introduction to the environment. Samples were enriched on non-selective media before DNA was extracted from whole plate sweeps and sequenced using Illumina. We assessed species, antimicrobial resistance (AMR) genes, virulence genes and transmission across all samples and between the pre- and post-patient samples using Kraken2, AbritAMR and Tracs. While the rate of positive microbial growth within the ICU environment did not change significantly pre- and post-patient introduction, the post-patient microbiome consisted of largely different bacterial species; of 22 genera identified, only 3 genera were represented at both timepoints. Post-patient samples were enriched in AMR genes, including resistance to fosfomycin, quinolones and beta-lactams. Common genera identified post-patient were Pseudomonas, Delftia and Stenotrophomonas, often associated with areas of plumbing. Cluster analysis identified 17 possible transmission links from a single timepoint, highlighting several areas in the ICU (e.g. communal bathrooms) as key areas for transmission. We demonstrate the utility of plate sweeps as a means of economical non-selective environmental surveillance and highlight their ability to identify hotspots of transmission within a hospital ward that could be targeted by infection control prior to an outbreak of a more serious pathogen.},
}

*Intensive Care Units
*Bacteria/genetics/isolation & purification/classification/drug effects
Humans
Queensland
*Environmental Monitoring/methods
Drug Resistance, Bacterial/genetics
Microbiota/genetics
Metagenomics/methods
Cross Infection/microbiology

@article {pmid41527828,
year = {2026},
author = {Kaur, I and Shaw, B and Multani, A and Malhotra, S and Dong, HV and Lukose, C and Prabaker, K and Saleh, T and Sim, YB and Tymchuk, CN and Uslan, DZ and Zhou, H and Brewer, TF and Yang, S},
title = {Clinical utility of serial plasma cell-free DNA metagenomic next-generation sequencing assays.},
journal = {Infection control and hospital epidemiology},
volume = {},
number = {},
pages = {1-3},
doi = {10.1017/ice.2025.10390},
pmid = {41527828},
issn = {1559-6834},
abstract = {This single center retrospective observational study of serial plasma metagenomic next-generation sequencing testing shows that >95% of serial testing was without meaningful clinical impact. Only 5/173 cases were adjudicated as having significant clinical impact.},
}

@article {pmid41527291,
year = {2026},
author = {Chen, W and Guo, R and Zhang, W and Wang, X and Chen, R and Hu, X and Liang, J and Xing, G and Xu, D and Ma, X and Chen, Q and Sha, S and Tao, E and Cheng, L and Fan, S and Liu, H and Lu, T and Yu, H and Su, J and Xu, J and Qin, Y and Liu, J and Zhong, X and Hu, X and Hu, X and Zheng, W and Hu, Z and Yan, Q and Kang, J and Yang, J},
title = {Alterations of the gut virome in patients with Parkinson's disease.},
journal = {The journals of gerontology. Series A, Biological sciences and medical sciences},
volume = {},
number = {},
pages = {},
doi = {10.1093/gerona/glag001},
pmid = {41527291},
issn = {1758-535X},
abstract = {Gut microbiota plays a pivotal role in Parkinson's disease (PD) pathogenesis. However, the role of enteric viruses remains underexplored. Here, we reanalyzed publicly available metagenomic datasets from two independent cohorts, including 79 PD patients and 79 controls, to characterize gut virome profiles and explore the potential role of enteric viruses in PD pathogenesis and early diagnosis. Our findings indicate increased richness and diversity of the gut virome in PD, with 640 vOTUs differing in abundance between groups. Notably, Siphoviridae and Myoviridae were more abundant in PD patients. A variety of viruses enriched in PD or healthy subjects (HS) preferentially infect bacterial hosts that produce short-chain fatty acids. Furthermore, specific viral functional orthologs, such as thymidylate synthase (K00560) and integrases (K14059), displayed notable differences in prevalence between PD-enriched and HS-enriched vOTUs. Finally, we constructed a random forest model using the top 22 most significant vOTUs, which achieved an AUC of 0.822, demonstrating strong performance in distinguishing PD patients from healthy controls. This is the first study to characterize the gut virome profile in PD, laying a robust foundation for future investigations into the underlying mechanisms and early diagnosis strategies for PD as well as other neurodegenerative disorders.},
}

@article {pmid41527156,
year = {2026},
author = {Buffoni, M and Kerkvliet, JJ and Enting, H and Kers, JG and Rogers, M and Visser, JAGM and Paganelli, FL and Willems, RJL and Schürch, AC},
title = {Coccidiosis prevention strategies shape the microbiome, resistome and mobilome composition in the broiler gut.},
journal = {Animal microbiome},
volume = {8},
number = {1},
pages = {3},
pmid = {41527156},
issn = {2524-4671},
abstract = {BACKGROUND: Coccidiosis is a parasitic infection in the gut of livestock that poses a significant health challenge in poultry farming, underscoring the important role of intervention and prevention strategies in the poultry industry. The use of anticoccidial drugs raises concerns about antimicrobial resistance (AMR) due to their antimicrobial properties and the ability of bacteria to evolve resistance to these drugs. Whether anticoccidial drug resistance could extend beyond coccidiostats, leading to cross-resistance and co-selection against other antimicrobial resistance genes (ARGs), is currently under discussion. Also, it is not well understood to what extent coccidiosis reduction strategies may enable the emergence of ARGs in farm environments and transmission of ARGs to other environments through bacterial clonal transfer or horizontal transmission via mobile genetic elements (MGEs) like plasmids or transposons.

RESULTS: In this study, we used metagenomic sequencing of caecal and faecal dropping samples from broiler chickens to investigate how two anticoccidial prevention strategies (vaccination and coccidiostat drugs) influence bacterial taxonomic composition and ARG profiles. We also explored the mobile resistome, ARGs located on mobile genetic elements (MGEs) such as plasmids, which are capable of disseminating, investigating ARGs identifying with the potential to disseminate within and beyond farm settings. Our exploratory findings in bacterial composition, as well as resistome composition with 21 differentially abundant ARGs, illustrating the potential impact of anticoccidial strategies on the chicken gut microbiome and resistome. We also identified 14 plasmid fragments containing ARGs in faecal dropping samples, highlighting mobile ARGs potentially able to disseminate to other environments, including humans.

CONCLUSIONS: Our findings demonstrate the impact of anticoccidial strategies on the chicken gut microbiome and resistome with potential consequences for the dissemination of ARGs.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42523-025-00497-7.},
}

@article {pmid41527141,
year = {2026},
author = {Liu, YY and Xia, F and Yimuran, R and Nuermamaiti, A and Yang, Y and Zhou, JT},
title = {Assessing whether rectal swabs reflect appendiceal microbiota profiles in acute appendicitis: a 16S rRNA-based comparative study.},
journal = {Gut pathogens},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13099-025-00794-1},
pmid = {41527141},
issn = {1757-4749},
support = {2023D01A93//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; },
abstract = {BACKGROUND: Acute appendicitis is associated with characteristic changes in the intestinal microbiota, but direct sampling of appendiceal contents is invasive and cannot be performed in healthy controls. We therefore evaluated whether rectal swabs could partially capture appendiceal microbiome signatures in adults with acute appendicitis.

METHODS: In a prospective cross-sectional study, we enrolled adults with acute appendicitis and healthy volunteers between October 2023 and December 2024. Four types of samples were collected: feces from healthy controls (HC), appendiceal luminal contents from patients with acute appendicitis (AC), intraoperative rectal swabs from patients with acute appendicitis (RS), and initial postoperative feces from patients with acute appendicitis (IF; first stool within 24 h after surgery). 16 S rRNA gene (V3-V4) sequencing was performed, and reads were processed with QIIME2. Alpha and beta diversity, differential taxonomic composition, and PICRUSt2-based functional predictions were compared across matrices. Genus-level and functional concordance between paired AC-RS samples was assessed.

RESULTS: After quality control, 64 AC, 34 RS, 24 IF, and 29 HC samples were included. Phylogenetic diversity (PD whole-tree) was higher in AC and RS than HC, with AC also higher than RS; IF showed lower PD than AC. Bray-Curtis principal coordinate analysis showed AC forming a distinct cluster separated from HC and RS along PC1, whereas IF overlapped with HC and RS. AC, RS, and IF were enriched for Escherichia/Shigella and Fusobacterium and depleted in butyrate-producing genera such as Faecalibacterium compared with HC. In the 21 paired AC-RS cases, genus-level relative abundances and several predicted functional pathways showed concordance, indicating that RS captured many but not all appendiceal dysbiosis features.

CONCLUSIONS: Our findings suggest that intraoperative rectal swabs may partially reflect appendiceal microbiome alterations at the genus and pathway levels and may serve as a minimally invasive adjunct for microbiome profiling in acute appendicitis. However, these associations are inferred from 16 S amplicon data in a modestly sized, antibiotic-exposed cohort and should be validated using shotgun metagenomics in larger, clinically stratified populations.},
}

@article {pmid41527052,
year = {2026},
author = {Zhou, L and Xu, Y and Wang, L and Li, X},
title = {Trichoderma harzianum fungemia following COVID-19-related immune dysregulation in an immunocompetent patient: a case diagnosed by mNGS.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-026-12568-4},
pmid = {41527052},
issn = {1471-2334},
support = {No.2020SCZT062//Jilin Provincial Department of Finance,China/ ; },
}

@article {pmid41527012,
year = {2026},
author = {Weber, C and Wind, D and Petzsch, P and Supprian, T and Dilthey, A and Christl, J and Finzer, P},
title = {Dysbiotic shift in the oral microbiota of patients with Alzheimer's disease compared to their healthy life partners-a combinatorial approach and a paired study design.},
journal = {Alzheimer's research & therapy},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13195-025-01941-1},
pmid = {41527012},
issn = {1758-9193},
abstract = {BACKGROUND: The oral microbiota has been associated with Alzheimer's disease (AD). However, earlier studies provided conflicting results using varying sampling methods, sequencing techniques, and statistics, as well as independent subjects.

METHODS: To robustly identify disease-associated microbial features, we recruited patients and their healthy life partners from the same households sharing a more similar microbiota compared to independent individuals increasing statistical power via paired design and combined three different sequencing methods - including metagenomics-and several bioinformatic pipelines. We recruited 26 AD-patients and their life partners. Salivary and supragingival samples were collected and a clinical examination of the mouth was performed.

RESULTS: Both groups showed comparable oral health. By focusing primarily on recurrently identified species across the different datasets we were able to identify a Core dysbiosis. This Core dysbiosis surprisingly spares the most central of oral diseases pathogens, namely Porphyromonas gingivalis. However, it includes numerous other species commonly associated with oral pathologies such as Prevotella nigrescens, Streptococcus anginosus, Dialister invisus, Anaeroglobus geminatus, Olsenella uli and Mogibacterium timidum. In contrast, more host-compatible species such as Prevotella melaninogenica or Streptococcus parasanguinis are identified in controls.

CONCLUSIONS: This is the first study using a combined sequencing approach and a paired study design to identify robust features of the oral microbiota of AD-patients. Although promising, the results should nevertheless be interpreted with caution, as the cross-sectional study design limits the possibilities of interpretation, and larger, longitudinal data are necessary for causal conclusions. However, this combined approach on multiple processing levels to identify intra-partnership differences still offers the possibility to better identify disease-associated microbial features potentially involved in AD-pathogenesis.

TRIAL REGISTRATION: This study was prospectively registered at the German Clinical Trials Register (DRKS00023456) at the 30th of November 2020.},
}

@article {pmid41526953,
year = {2026},
author = {Quijia-Pillajo, J and Naik, S and Chapin, LJ and Owen, JS and Jones, ML},
title = {Calcium phosphate-solubilizing bacteria promote growth and alleviate phosphorus deficiency in French marigold with minimal impact on the rhizosphere microbiome.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-025-00844-w},
pmid = {41526953},
issn = {2524-6372},
support = {2021-09976//NIFA Agriculture and Food Research Initiative - Foundational Knowledge of Agricultural Production Systems/ ; },
abstract = {BACKGROUND: Plant roots are surrounded by communities of microbes that influence plant growth, development, and disease resistance. In soilless culture, microbial diversity in root-associated communities primarily originates from the substrate, irrigation water, and applied microbial inoculants. Phosphate solubilizing bacteria (PSB) capable of mobilizing phosphate from insoluble Ca3(PO4)2 were identified from a greenhouse rhizobacteria collection. Plant growth promoting efficacy was investigated at different substrate pH. The influence of the inoculum composition on plant growth responses to the bacteria was also evaluated. Finally, we analyzed the impact of PSB inoculation on microbiome composition and function.

RESULTS: From 1044 isolates in the rhizobacteria collection, 14 solubilized more than 25% of the phosphorus provided in vitro. Only eight bacterial strains resulted in growth promotion benefits in planta when inoculated as a substrate drench onto marigolds grown in a peat-based substrate (pH 7.0) and fertilized with insoluble Ca3(PO4)2. In a follow up experiment, two newly identified (Pantoea sp. C2G6 and Enterobacter soli C4A1) and three previously identified PSB (Pantoea trifolii C2B11, Pantoea formicae C8D10, and Bacillus velezensis) that have demonstrated superior phosphate-mineral solubilization were evaluated. The PSB were tested at a substrate pH of 6.0 and 6.5 using water, 1% glucose, 2% Micromate, or 0.1X Luria-Bertani (LB) broth as inoculant supplements. All five bacteria promoted growth and improved plant health at both pH levels. A greater benefit to marigold growth and health was observed in plants growing at pH 6.5. C2B11, C8D10, C2G6, and B. velezensis treatment resulted in a significant increase in shoot P content. Microbiome diversity and community structure exhibited no significant alterations in response to PSB treatment. Genes enriched in PSB treated rhizospheres were mostly related to colonization, competition, and biofertilization traits.

CONCLUSIONS: PSB isolated from the rhizosphere of floriculture crops grown in soilless substrates promoted growth and enhanced health of marigolds grown under P limitation. They also enhanced growth under optimal or slightly basic pH, but their efficacy was not improved by the inoculant supplements evaluated in this experiment. The native microbial community in peat-based soilless substrate was resilient to PSB inoculation.},
}

@article {pmid41526915,
year = {2026},
author = {Shao, D and Li, Y and Chen, S and Ma, S and Liu, Y and Huang, W and Liu, D and Lyu, Y and Xia, Z and Wang, Y},
title = {Improved RNA-based metagenomic sequencing for rapid pathogen detection in pets.},
journal = {BMC veterinary research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12917-025-05174-0},
pmid = {41526915},
issn = {1746-6148},
support = {2022YFD18000400//National Key Research and Development Program of China/ ; PC2023A01002//Pinduoduo-China Agricultural University Research Fund/ ; },
}

@article {pmid41519702,
year = {2026},
author = {Zhang, Y and Tian, J and Xu, Y},
title = {Endogenous endophthalmitis secondary to neisseria meningitidis: a case report.},
journal = {BMC ophthalmology},
volume = {26},
number = {1},
pages = {16},
pmid = {41519702},
issn = {1471-2415},
support = {No.20241205//Medical Science Research Project of Hebei/ ; },
abstract = {BACKGROUND: Bacterial endogenous endophthalmitis (BEE) represents a rare but severe ophthalmological emergency which caused by hematogenous spread of bacterial infection. As its characteristics of insidious onset and rapid progression, BEE may lead to vision loss or even enucleation without immediate treatments. In recent years, with increasing numbers of immunosuppression and prevalence of resistant strains, incidence of BEE has risen, and its diagnosis and treatment face new challenges.

CASE PRESENTATION: A 15-year-old female patient was admitted to department of ophthalmology due to blurred vision and photophobia and lacrimation in the left eye for two days, and was first diagnosed as endophthalmitis and secondary glaucoma. During the diagnosis and treatment process, after smear culture of left chamber and vitreous aspirates, as well as the metagenomic next-generation sequencing (mNGS), final diagnosis of infectious endophthalmitis secondary to Neisseria meningitidis (N. meningitidis) was decided and a targeted treatment plan was developed. After intraocular injection and systemic antibiotic therapy, the patients was discharged after full control of the infection and improved endophthalmitis. Combined with literature review, this study discussed the application value of mNGS in diagnosing endogenous endophthalmitis.

CONCLUSION: mNGS shows significant value in the diagnosis of endogenous endophthalmitis in terms of improving positive rate of pathogen detection in intraocular fluid of infectious endophthalmitis and providing strong support for clinical treatments. The successful treatment of this case further confirms the promise of mNGS in ophthalmic infectious diseases. With the continuous progress of technology, mNGS is expected to be popularized and applied in more medical institutions to benefit more patients.},
}

@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.},
}