@article {pmid41225090,
year = {2026},
author = {Ziaei, H and Rezaei, N},
title = {Introduction to Oral Immunity.},
journal = {Advances in experimental medicine and biology},
volume = {1492},
number = {},
pages = {3-21},
pmid = {41225090},
issn = {0065-2598},
abstract = {The oral immune system functions as a primary line of defense, composed of oral epithelial barriers, salivary antimicrobial factors, and various innate and adaptive immune components to prevent pathogen entry. Resident immune cells in oral tissues help maintain tolerance to commensal microorganisms while simultaneously responding to harmful external stimuli and contributing to systemic immune regulation. This chapter provides a comprehensive overview of the immunological components and their functions in the oral cavity, emphasizing the dual role of maintaining tolerance to commensal microbes and dietary antigens while initiating protective responses against pathogens. Any disruptions in this balance, such as oral dysbiosis or immune dysregulation, can lead to the development of local inflammatory conditions; it may also contribute to systemic immune disturbances and related pathologies. Immune mechanisms also regulate craniofacial development and postnatal bone remodeling and regeneration, mainly through cytokine-mediated signaling pathways and interactions between stem cells and immune cells. Several local and systemic immunological pathways are often dysregulated in oral inflammatory conditions, which makes them important therapeutic targets. Therapeutic strategies targeting these pathways include immune checkpoint inhibitors, microbiome-directed interventions, stem cell-based therapies, and salivary diagnostics for real-time and noninvasive immune profiling. These offer promising approaches for restoring oral and systemic immune balance. Finally, this chapter has reviewed recent technological advances, such as single-cell RNA sequencing (scRNA-seq), spatial transcriptomics, metagenomics, and multi-omics integration, in the context of oral immunity. These novel techniques are transforming oral immunology, since they enable high-resolution characterization of cellular, microbial, and molecular interactions, and support the transition toward establishing more precise diagnosis and treatment plans. These findings suggest that oral immunity plays a critical role in linking local mucosal defense and systemic immune responses. Therefore, understanding oral immune mechanisms in health and inflammatory conditions is important for revealing disease pathogenesis and guiding targeted interventions.},
}

@article {pmid41224996,
year = {2025},
author = {Nadel, O and Hanna, R and Rozenberg, A and Shitrit, D and Tahan, R and Pekarsky, I and Béjà, O and Kleifeld, O and Lindell, D},
title = {Viral NblA proteins negatively affect oceanic cyanobacterial photosynthesis.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {41224996},
issn = {1476-4687},
abstract = {Marine picocyanobacteria are abundant photosynthetic organisms of global importance. They coexist in the ocean with cyanophages-viruses that infect cyanobacteria. Cyanophages carry many auxiliary metabolic genes acquired from their hosts that are thought to redirect host metabolism for the phage's benefit[1-5]. One such gene is nblA, which is present in multiple cyanophage families[2,6-8]. Under nutrient deprivation cyanobacterial NblA is responsible for inducing proteolytic degradation of the phycobilisome[9-11], the large cyanobacterial photosynthetic light-harvesting complex. This increases the pool of amino acids available for essential tasks[11], serving as a survival mechanism[12]. Ectopic expression of different cyanophage nblA genes results in host pigment protein degradation[6,8,13]. However, the benefit of the virus-encoded NblA for cyanophages and the broader impact on the host are unclear. Here, using a recently developed genetic manipulation system for marine cyanophages[14], we reveal that viral NblA significantly accelerates the cyanophage infection cycle, directs degradation of the host phycobilisome and other proteins, and reduces host photosynthetic light-harvesting efficiency. Metagenomic analysis revealed that cyanophages carrying nblA are widespread in the oceans and comprise 35% and 65% of oceanic T7-like cyanophages in surface and deep photic zones, respectively. Our results show a large benefit of NblA to the cyanophage, while it exerts a negative effect on the host photosynthetic apparatus and host photosynthesis. These findings suggest that cyanophage NblA has an adverse global impact on light harvesting by oceanic picocyanobacteria.},
}

@article {pmid41224779,
year = {2025},
author = {Secaira-Morocho, H and Jiang, X and Zhu, Q},
title = {Augmenting microbial phylogenomic signal with tailored marker gene sets.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9943},
pmid = {41224779},
issn = {2041-1723},
support = {RFGA2023-008-15//ADHS | Arizona Biomedical Research Commission (ABRC)/ ; },
abstract = {Phylogenetic marker genes are traditionally selected from a fixed collection of whole genomes representing major microbial phyla, covering only a small fraction of gene families. However, most microbial diversity resides in metagenome-assembled genomes, which exhibit taxonomic imbalance and harbor gene families that do not fit the criteria for universal orthologs. To address these limitations, we introduce TMarSel, a software tool for automated, free-from-expert opinion, and tailored marker selection for deep microbial phylogenomics. TMarSel allows users to select a variable number of markers and copies based on KEGG and EggNOG gene family annotations, enabling a systematic evaluation of the phylogenetic signal from the entire gene family pool. We show that an expanded marker selection tailored to the input genomes improves the accuracy of phylogenetic trees across simulated and real-world datasets of whole genomes and metagenome-assembled genomes compared to previous markers, even when metagenome-assembled genomes lack a fraction of open reading frames. The selected markers have functional annotations related to metabolism, cellular processes, and environmental information processing, in addition to replication, translation, and transcription. TMarSel provides flexibility in the number of markers, copies, and annotation databases while remaining robust against taxonomic imbalance and incomplete genomic data.},
}

@article {pmid41224755,
year = {2025},
author = {Gupta, S and Almeida, A},
title = {Integration of metagenome-assembled genomes with clinical isolates expands the genomic landscape of gut-associated Klebsiella pneumoniae.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9959},
pmid = {41224755},
issn = {2041-1723},
support = {MR/W016184/1//RCUK | Medical Research Council (MRC)/ ; },
abstract = {Klebsiella pneumoniae is an opportunistic pathogen causing diseases ranging from gastrointestinal disorders to severe liver abscesses. While clinical isolates of K. pneumoniae have been extensively studied, less is known about asymptomatic variants colonizing the human gut across diverse populations. Developments in genome-resolved metagenomics have offered unprecedented access to metagenome-assembled genomes (MAGs), expanding the known bacterial diversity within the gut microbiome. Here we analysed 656 human gut-derived K. pneumoniae genomes (317 MAGs, 339 isolates) from 29 countries to investigate the population structure and genomic landscape of gut-associated lineages. Over 60% of MAGs were found to belong to new sequence types, highlighting a large uncharacterized diversity of K. pneumoniae missing among sequenced clinical isolates. In particular, integrating MAGs nearly doubled gut-associated K. pneumoniae phylogenetic diversity, and uncovered 86 MAGs with >0.5% genomic distance compared to 20,792 Klebsiella isolate genomes from various sources. Pan-genome analyses identified 214 genes exclusively detected among MAGs, with 107 predicted to encode putative virulence factors. Notably, combining MAGs and isolates revealed genomic signatures linked to health and disease and more accurately classified disease and carriage states compared to isolates alone. These findings showcase the value of metagenomics to understand pathogen evolution and diversity with implications for public health surveillance strategies.},
}

@article {pmid41224035,
year = {2025},
author = {Wu, X and Wang, C and Wang, D and Yu, Z and Meng, F},
title = {Microbiota ecology upon moderate concentrations of total ammoniacal nitrogen enhances methane production of anaerobic membrane bioreactor.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133630},
doi = {10.1016/j.biortech.2025.133630},
pmid = {41224035},
issn = {1873-2976},
abstract = {In this study, the ecological responses of microbial community of anaerobic membrane bioreactor (AnMBR) upon exposure to moderate concentration total ammoniacal nitrogen (TAN) were studied to unveil the underlying mechanisms of reactor performance variation. The 16S rRNA gene and community assembly analysis indicated that the moderate ammonia concentration imposed limited selection pressure on the methanogenic community. Instead, the community assembly was governed by the random birth, death, and reproduction of community members. Network analysis further suggested that the moderate concentration of TAN established strong cooperative linkage between hydrogenotrophic methanogens (HM) and syntrophic acetate oxidizing bacteria (SAOB) in AnMBR. Metagenome sequencing analysis provided convergent evidence that there were enriched genes responsible for the SAOB-HM pathway as well as direct interspecific electron transfer. Moreover, the morphology of anaerobic granular sludge (AnGS) suggested that the decreased particle size enhanced substrate mass transfer efficiency among community members and the methanogens in inner layer of AnGS received more protection from its neighbors in moderate TAN phases. Consequently, the biogas production, methane (CH4) yield and specific methanogenic activity (SMA) of granular sludge in moderate TAN phases were significantly increased compared to the low TAN phase. Together, this study has expanded our understanding of facilitation of moderate concentration TAN-containing wastewater treatment on AnMBR process.},
}

@article {pmid41223797,
year = {2025},
author = {Xu, YY and Tan, X and Dang, CC and Liu, LY and Wang, X and Zhao, ZC and Ren, NQ and Wu, YN and Xie, GJ},
title = {Thermophilic Sulfide-Driven autotrophic Denitrification: High-Rate nitrogen removal and metagenomic insights into microbial cooperation.},
journal = {Environment international},
volume = {205},
number = {},
pages = {109918},
doi = {10.1016/j.envint.2025.109918},
pmid = {41223797},
issn = {1873-6750},
abstract = {Sulfide-driven autotrophic denitrification (SDAD) plays a pivotal role in linking nitrogen and sulfur cycles, particularly in thermophilic environments. However, the performance and metabolic mechanisms of thermophilic SDAD systems remain underexplored. This study successfully enriched thermophilic sulfide-oxidizing denitrifiers from hot spring sediments (60 °C) in an expanded granular sludge bed (EGSB) reactor, achieving a stable nitrate removal rate of 250 mg N L[-][1] d[-][1]. This thermal system demonstrated a higher tolerance threshold for sulfides (250 mg TDS L[-1]) than mesophilic processes. The influent sulfide-to-nitrate (S/N) molar ratio critically influenced nitrogen removal efficiency with nitrite accumulation at low S/N ratios (1:1), whereas higher ratios (2:1) restored complete nitrate reduction. Microbial community analysis demonstrated Thermus (52.89 %) as the predominant genus in the SDAD system, marking the first report of its dominance in thermophilic nitrogen-sulfur coupling, alongside uc_Aquificales (21.78 %). Metagenomic insights further revealed two high-quality genomes: Thermus scotoductus exclusively executed complete sulfide-to-sulfate oxidation via the Sox system and partially catalyzed denitrification (narGHI); while Aquificaeae_UBA11096 adopted Sox-independent enzyme system and complete denitrification. Strikingly, Thermus scotoductus encoded nrfH, and it might be the overlooked " nitrogen retainer" in geothermal ecosystems. This work elucidates the cooperative and competitive interactions between thermophilic denitrifiers, and establishes a multi-level thermal adaptability analysis. These findings advance understanding of their biogeochemical roles in geothermal ecosystems, and provide a sustainable strategy for nitrogen removal in high-temperature wastewater treatment.},
}

@article {pmid41223750,
year = {2025},
author = {Yao, S and Luo, Y and Zhou, Y and Wang, Y and Yang, L and Kong, Q and Zhang, H},
title = {Microbial functional shifts in a paradigmatic petrochemical brownfield: Mechanisms of adaptation in soil and groundwater.},
journal = {Ecotoxicology and environmental safety},
volume = {306},
number = {},
pages = {119380},
doi = {10.1016/j.ecoenv.2025.119380},
pmid = {41223750},
issn = {1090-2414},
abstract = {The long-term presence of pollutants from the petrochemical industry, including benzene, nitro compounds, and amine-based aromatics, poses a significant threat to soil and groundwater, resulting in shifts in microbial community structures. In this study, 48 soil and groundwater samples from contaminated environments were analyzed using metagenomic technology and gas chromatography-mass spectrometry to examine the metabolic strategies employed by microorganisms in response to these pollutants. The results revealed that microbial community composition was significantly influenced by varying contamination levels, primarily determined by the distance from contamination sources and the diffusion characteristics of the environmental media. In highly contaminated areas, specific bacterial genera, including Pseudomonas and Stutzerimonas, became dominant, suggesting an adaptation toward pollutant degradation. Soil and groundwater microorganisms exhibited distinct adaptive mechanisms: in soils, enhanced motility, metabolism, and toxicant transport were associated with the expression of genes such as mcp, tktA, and pleD, while in groundwater, pollutant degradation and the maintenance of cellular function were driven by genes including xylA, dmpB, nfnB, and glnA. These findings emphasise the capacity of microbes to adapt to pollutants from petrochemical industry environments, thus providing valuable insights into microbial remediation strategies for environmental pollution management.},
}

@article {pmid41223625,
year = {2025},
author = {Yang, B and Wang, H and Yan, Y and Bao, P and Feng, Q and Chen, B and Jia, Y and Shu, WS and Lu, H},
title = {Coupling Microalgae-based Biochar with MBGS Enhances Microbial Synergy and Multi-Pollutant Removal from Saline Aquaculture Wastewater.},
journal = {Water research},
volume = {289},
number = {Pt B},
pages = {124881},
doi = {10.1016/j.watres.2025.124881},
pmid = {41223625},
issn = {1879-2448},
abstract = {The microalgal-bacterial granular sludge (MBGS) system has gained attention as an energy-efficient, multifunctional approach for wastewater treatment, yet its stability and pollutant removal under combined salinity and antibiotic stress remain unclear. In this study, we developed an MBGS system integrated with nitrogen-rich microalgae-derived biochar to enhance removal of organic matter, nutrients, and enrofloxacin (ENR) from saline aquaculture wastewater. The biochar-coupled MBGS achieved high removal efficiencies: 94.2±4.8% COD, 87.1±3.6% NH4[+]-N, 60.3±4.6% PO4[3-]-P, and 60.1±3.5% ENR. Microbial community analysis revealed enrichment of ammonia-oxidizing bacteria (Nitrosomonas, 3.3-9.7%), nitrite-oxidizing bacteria (Nitrospira, 2.3-6.4%), denitrifiers (Thauera, 14.9-27.6%), phosphate-accumulating organisms (Acinetobacter, 0.8-7.7%), and photosynthetic microalgae (Chlorophyceae, 1.4-23.6%). Fluorescence in situ hybridization (FISH) confirmed that biochar enhanced the spatial organization of these functional microbes within MBGS. Metagenomics revealed increased abundance of genes associated with carbon (porCD, CS, korD), nitrogen (amoAB, narGHI, norBC), phosphorus (ppk, phaA, acs), and photosynthesis-related (petABCD, psaA) genes, indicating improved metabolic capacity and synergy. Genome-resolved metagenomics further identified Nitrosomonas europaea, Acinetobacter sp002296655, Thauera aminoaromatica, and Chlorobium sp013334435 as core taxa driving carbon, nitrogen, and phosphorus cycling and energy flow, promoting synergistic interactions and enhancing pollutant removal under stress. Coupling MBGS with microalgae-based biochar improves resilience and multi-pollutant removal, offering a robust, sustainable strategy for advanced aquaculture wastewater treatment.},
}

@article {pmid41223471,
year = {2025},
author = {Zhang, Y and Gao, M and Zhang, X and Tang, A and Wang, S and Wang, X},
title = {How microalgae-bacteria consortia adapt sulfamethoxazole pressure: Insights from physiological and genetic responses.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140406},
doi = {10.1016/j.jhazmat.2025.140406},
pmid = {41223471},
issn = {1873-3336},
abstract = {Microalgae-bacteria consortia (MBC) are regarded as an energy-saving alternative for wastewater treatment process, while their reliability is challenged under long-term antibiotic pressure. Unfortunately, the underlying physiological and genetic mechanisms enabling adaptation to such prolonged antibiotic pressure remain largely unknown. This study systematically investigates the adaptive responses of MBC systems to sulfamethoxazole (SMX) pressure during two exposure stages (100 and 200 μg/L). While the system remained stable at 100 μg/L SMX (stage I), its performance declined at 200 μg/L (stage II), with COD and ammonium removal decreasing by 7.5 % and 8.8 %, respectively. This was accompanied by adverse physiological responses, including a 36.3 ± 3.2 % decrease in photosynthetic oxygen production, a 96.2 ± 9.7 % increase in ROS levels, and a 49.0 ± 5.3 % reduction in EPS content. Remarkably, both pollutant removal and physiological state were fully restored following a 100-day recovery period. This resilience may be attributed to the enrichment of microbial communities such as Chlorophyta and Bacillariophyta, whose presence strongly correlated with reduced antibiotic resistance gene (ARG) dissemination. Genetic analysis further indicated that suppressed ATP synthase and electron transfer within the oxidative phosphorylation pathway may represent important adaptive costs. Fortunately, the response regulators within the two-component system functioned as central mediators, coordinating both extracellular EPS secretion and intracellular antioxidant activity. Overall, this study advances current understandings of adaptive mechanism and offers insights for facilitating stable operation under long-term antibiotic pressure.},
}

@article {pmid41222958,
year = {2025},
author = {Yang, Y and Li, Q and Xiao, Y and Shen, Y and Zhang, Y and Zhang, W and Lei, N and Pei, X and Xie, Y},
title = {Elucidating the Mechanism of PFOA Regulation of Biofilms in Aquatic Systems at Gene and Metabolic Levels.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c06467},
pmid = {41222958},
issn = {1520-5851},
abstract = {Perfluorooctanoic acid (PFOA) is prevalent in aquatic ecosystems and exhibits significant toxicity to aquatic organisms. Microorganisms can adhere to the surfaces of submerged plants, forming complex extracellular structures referred to as attached biofilms. However, the mechanisms underlying the regulation of biofilm formation by PFOA remain unclear. This study cultured plant-attached biofilms under PFOA stress to investigate the mechanisms by which PFOA regulates biofilm formation, utilizing metagenomics and metabolomics. Results show that the biofilm structure was significantly altered under PFOA exposure, characterized by an increase in polysaccharide and protein content. Furthermore, PFOA bound to proteins within extracellular polymeric substances contributes to a reduction in PFOA toxicity. PFOA regulates biofilm formation by modifying the content of signaling molecules and the abundance of genes (bapA and ABC.PE.S) associated with quorum sensing, establishing a natural barrier against the toxic effects of PFOA. In addition, PFOA was found to inhibit the metabolism of linoleic and linolenic acids, thus indirectly promoting the formation of biofilms, which allowed microbial aggregation and coresistance to the toxic effects of exogenous pollutants. This study provides a comprehensive understanding on the mechanisms by which PFOA regulates biofilm formation, which is crucial for enhancing our understanding of microbial processes in aquatic ecosystems.},
}

@article {pmid41222645,
year = {2025},
author = {Rana, S and Das, KK and Singh, SK and Bhattacharyya, D},
title = {Deciphering Fungal Communities in Three Species of Phlogacanthus Nees (Acanthaceae) Using Amplicon-Metagenomic Analysis.},
journal = {Current microbiology},
volume = {83},
number = {1},
pages = {16},
pmid = {41222645},
issn = {1432-0991},
abstract = {Fungal communities play vital roles in plant health, nutrient cycling, and ecological balance. Species of Phlogacanthus Nees, valued for their medicinal and ecological importance, harbor diverse fungal microbiomes that may influence growth, resilience, and metabolite production. This study investigated fungal communities associated with three Phlogacanthus species-P. tubiflorus Nees (SKS-1), P. thyrsiformis (Roxb. ex Hardw.) Mabb. (SKS-2), and P. curviflorus (Wall.) Nees (SKS-3)-using high-throughput amplicon-metagenomic sequencing of the ITS2 region on the Illumina MiSeq platform. A total of 153 operational taxonomic units (OTUs) were identified, with SKS-2 showing the highest richness (129 OTUs), followed by SKS-1 (112) and SKS-3 (95). Seventy OTUs were shared across all species, while 10, 22, and 8 were unique to SKS-1, SKS-2, and SKS-3, respectively. Alpha diversity indices (Chao1, ACE, Shannon, Simpson, Inverse Simpson, Fisher's alpha) confirmed SKS-2 as the most species-rich fungal habitat. A high proportion of unclassified taxa in SKS-2, along with dominance of Pleosporales, suggests the presence of novel fungi with ecological and biotechnological significance. Beta diversity analysis using Bray-Curtis dissimilarity and Principal Coordinate Analysis revealed significant differences among the fungal communities of the three species. Overall, SKS-2 emerged as the most diverse habitat, while SKS-3 supported a unique but less diverse assemblage. This is the first report profiling fungal microbiomes of Phlogacanthus species. The results highlight their potential as reservoirs of endophytes with applications in plant growth promotion, stress tolerance, biocontrol, enzyme production, and bioactive metabolite discovery, offering leads for sustainable agriculture and biotechnology.},
}

@article {pmid41222234,
year = {2025},
author = {Sinno, A and Baghdadi, R and Narch, R and El Rayes, S and Tokajian, S and Al Khoury, C},
title = {Charting the virosphere: computational synergies of AI and bioinformatics in viral discovery and evolution.},
journal = {Journal of virology},
volume = {},
number = {},
pages = {e0155425},
doi = {10.1128/jvi.01554-25},
pmid = {41222234},
issn = {1098-5514},
abstract = {The advancement of metagenomic sequencing has revealed a vast viral diversity while simultaneously exposing limitations of homology-based tools such as BLAST and HMMER, which often fail to detect highly divergent viral genomes. The integration of artificial intelligence (AI) into viromics has transformed this landscape, introducing machine learning and deep learning models-including convolutional neural networks (CNNs), recurrent neural networks (RNNs), and transformers-that extend viral discovery beyond sequence similarity constraints. Structure-based frameworks such as AlphaFold, ESMFold, and Foldseek further enable annotation of divergent viral proteins through conserved 3D folds, while graph neural networks (GNNs) model host-virus interaction and explainable AI enhances interpretability of prediction. Despite their high sensitivity and scalability, AI-driven approaches face notable challenges: computational burden, data set bias, limited explainability, and elevated false discovery rates. This review traces the evolution of computational virology from traditional methods to AI-based and hybrid frameworks. We examine landmark AI tools while underscoring the continuing importance of phylogenetics and functional annotation in contextualizing AI predictions. We propose an integrated workflow that combines AI pattern recognition with classical bioinformatics to enhance both scalability and interpretability. By addressing the limitations of solely AI-driven or traditional approaches, this review presents a unified computational strategy to accelerate viral discovery, enhance evolutionary insights, and strengthen global preparedness for emerging infectious diseases.},
}

@article {pmid41222171,
year = {2025},
author = {Lazov, CM and Larsen, LE and Johnston, CM and Rasmussen, TB and Hjulsager, CK},
title = {Announcement of two complete coding genomes of mink coronavirus and one partial coding genome of mink enteric calicivirus from mink in Denmark.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0045925},
doi = {10.1128/mra.00459-25},
pmid = {41222171},
issn = {2576-098X},
abstract = {Two complete coding genomes of mink coronavirus and one partial coding genome of the sapovirus mink enteric calicivirus were assembled from metagenomic sequencing data from mink on different farms with diarrhea outbreaks in 2015 in Denmark.},
}

@article {pmid41222160,
year = {2025},
author = {Liu, W and Nagasaka, K and Wu, J and Ban, H and Mimick, E and Meng, L and Neches, RY and Moniruzzaman, M and Yoshida, T and Nishimura, Y and Endo, H and Okazaki, Y and Ogata, H},
title = {Giant viruses specific to deep oceans show persistent presence and activity.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0093225},
doi = {10.1128/msystems.00932-25},
pmid = {41222160},
issn = {2379-5077},
abstract = {Giant viruses (GVs) of the phyla Nucleocytoviricota and Mirusviricota are large double-stranded DNA viruses that infect diverse eukaryotic hosts and impact biogeochemical cycles. Their diversity and ecological roles have been well studied in the photic layer of the ocean, but less is known about their activity, population dynamics, and adaptive strategies in the aphotic layers. Here, we conducted eight seasonal time-series samplings of the surface and mesopelagic layers at a coastal site in Muroto, Japan, and integrated 18S metabarcoding, metagenomic, and metatranscriptomic data to investigate mesopelagic GVs and their potential hosts. The analysis identified 48 GV genomes including six that were exclusively detected in the mesopelagic layer. Notably, these mesopelagic-specific GVs showed persistent activity across seasons. To further investigate the distribution and phylogenomic features of GVs at a global scale across broader depths, we compiled 4,473 species-level GV genomes from the OceanDNA MAG project and other resources and analyzed 1,890 marine metagenomes. This revealed 101 deep-sea-specific GVs, distributed across the GV phylogenetic tree, indicating that adaptation to deep-sea environments has occurred in multiple lineages. One clade enriched with deep-sea-specific GVs included a GV genome identified in our Muroto data, which displayed a wide geographic distribution. Seventy-six KEGG orthologs and 74 Pfam domains were specifically enriched in deep-sea-specific GVs, encompassing functions related to the ubiquitin system, energy metabolism, and nitrogen acquisition. These findings support the scenario that distinct GV lineages have adapted to hosts in aphotic marine environments by altering their gene repertoire to thrive in this unique habitat.IMPORTANCEGiant viruses are widespread in the ocean surface and are key in shaping marine ecosystems by infecting phytoplankton and other protists. However, little is known about their activity and adaptive strategies in deep-sea environments. In this study, we performed metagenomic and metatranscriptomic analyses of seawater samples collected from a coastal site in Japan and discovered giant virus genomes showing persistent transcriptional activity across seasons in the mesopelagic water. Using a global marine data set, we further uncovered geographically widespread and vertically extensive groups of deep-sea-specific giant viruses and characterized their distinctive gene repertoire, which likely facilitates adaptation to the limited availability of light and organic compounds in the aphotic zone. These findings expand our understanding of giant virus ecology in the dark ocean.},
}

@article {pmid41222147,
year = {2025},
author = {Vogel, H and Weiss, B and Rama, F and Rinklef, A and Engl, T and Kaltenpoth, M and Vilcinskas, A},
title = {A multi-partner symbiotic community inhabits the emerging insect pest Pentastiridius leporinus.},
journal = {mBio},
volume = {},
number = {},
pages = {e0310325},
doi = {10.1128/mbio.03103-25},
pmid = {41222147},
issn = {2150-7511},
abstract = {The planthopper Pentastiridius leporinus has emerged as a severe crop pest, rapidly expanding both its host plant range and the affected areas in central Europe. Originating as a monophagous herbivore of reed grass, P. leporinus recently adopted polyphagous feeding and is now a pest of sugar beet, potato, carrot, and onion, suggesting rapid ecological niche expansion. P. leporinus vectors two bacterial pathogens: the γ-proteobacterium Candidatus Arsenophonus phytopathogenicus (CAP) and the stolbur phytoplasma Candidatus Phytoplasma solani (CPS), which are responsible for a range of disease syndromes, including syndrome basses richesses in sugar beet. We used long-read metagenomic sequencing to characterize the genomes of microbes associated with P. leporinus, resulting in the complete sequences of CAP and CPS, as well as obligate symbionts of the genera Purcelliella, Karelsulcia, and Vidania, and facultative symbionts Rickettsia and Wolbachia. The obligate symbionts are inferred to provide or contribute to the biosynthesis of 10 essential amino acids and to B vitamin. The genomes of CPS and CAP encode numerous pathogenicity factors, enabling the colonization of different hosts. Bacterial fluorescence in situ hybridization revealed the tissue distribution, cellular localization, relative abundance, and transmission patterns of these bacteria. The intracellular presence of all obligate symbionts in bacteriomes, the intracellular presence of Wolbachia, and the intranuclear localization of Rickettsia suggest vertical transmission. CPS was restricted to salivary glands, suggesting strict horizontal, plant-mediated transmission, whereas CAP colonized all tissue types, allowing for horizontal and vertical transmission. Our data suggest that P. leporinus hosts an exceptionally broad range of symbionts, encompassing mutualistic, commensal, and pathogenic interactions.IMPORTANCEThe planthopper Pentastiridius leporinus has recently expanded its host plant range and emerged as a severe pest of sugar beet and potato crops in central Europe, which is exacerbated by its capacity to vector bacterial pathogens to its host plants. Because microbial symbionts may play an important role for both the host plant shifts and the transmission of pathogens, we used metagenomic sequencing and fluorescence in situ hybridization to characterize the microbial community associated with P. leporinus. We detected three bacteriome-localized obligate symbionts that together provision all essential amino acids and several B-vitamins to the host, as well as two intracellular bacteria with a broader tissue distribution. In addition, we infer localization, transmission, and putative pathogenicity factors for the two major phytopathogens that are vectored by P. leporinus. Our results reveal a complex community of symbiotic bacteria that likely shapes the interaction of this emerging pest with its host plants.},
}

@article {pmid41222145,
year = {2025},
author = {Koo, H and Heber, K and Tian, S and Connolly, ST and Hao, F and Zhao, J and Swencki-Underwood, B and Patterson, AD and Townsend, GE and Bisanz, JE},
title = {A synthetic gut microbiota provides an understanding of the maintenance and functional impact of phage.},
journal = {mBio},
volume = {},
number = {},
pages = {e0234125},
doi = {10.1128/mbio.02341-25},
pmid = {41222145},
issn = {2150-7511},
abstract = {UNLABELLED: Phages are under intense study as therapeutics and mediators of microbial community behavior; however, tractable models are needed to study phages in the context of the mammalian gut. To address this gap, we isolated phages against members of a synthetic gut microbial community (sFMT), identifying the Bacteroides uniformis JEB00023 (DSM 6597) phage HKP09. While resistance to HKP09 was observable within hours of infection in monoculture, high titers of HKP09 were maintained in vitro and in gnotobiotic mouse models over extended periods. Sequencing of resistant B. uniformis lines revealed phase variation upstream of a capsular polysaccharide locus driving the generation of resistant and sensitive subpopulations, thus demonstrating a mechanism allowing stable coexistence of both virus and bacterial host. Communities infected in vitro and in vivo with HKP09 showed transiently reduced loads of B. uniformis DSM 6597. Its impact in the gut was distinct from communities constructed without its host B. uniformis strain (sFMT∆JEB00023). Rather than a compensatory increase in closely related Bacteroides strains, the most significant impacts were observed on distantly related strains, demonstrating that phage perturbations more broadly impact community structure in ways not easily predicted by phylogeny or simple strain exclusion. Metabolomic analyses of the feces of HKP09-infected sFMT-colonized gnotobiotic animals demonstrated altered abundances of amino acids and microbial fermentation products compared to uninfected mice and those colonized with sFMT∆JEB00023. Taken together, these data provide a controlled model for studying phages in the context of the mammalian gut, providing mechanistic insights into phage-host dynamics and their consequences on the function of microbial communities.

IMPORTANCE: Phages are key members of the gut microbiome, but the understanding of their biological significance for host health lags behind their bacterial hosts. In this study, we demonstrate the use of a phage-infection model using defined, synthetic microbial communities that colonize the intestinal tract of mice. We uncovered that spontaneous inversions in the genome of Bacteroides uniformis perpetually generate subpopulations, which are either sensitive or resistant to phage infection, allowing for the coexistence of predator and prey in this species. Phage infection demonstrated broad impacts on community structure and metabolism in animals, which are not easily predicted by the exclusion of the viral host. This research demonstrates a tractable approach through which the impacts of phage on both the microbiome and mammalian host can be deciphered.},
}

@article {pmid41222144,
year = {2025},
author = {Ericsson, AC and McAdams, ZL and Dorfmeyer, RA and Hart, ML and O'Neill-Blair, A and Amos-Landgraf, J and Franklin, CL},
title = {Dominant effects of the immediate environment on the gut microbiome of mice used in biomedical research.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0111225},
doi = {10.1128/msystems.01112-25},
pmid = {41222144},
issn = {2379-5077},
abstract = {Studies using genetically engineered mouse (GEM) models are often performed over extended periods. The microbiomes of GEM colonies are expected to retain some of the microbial features present in the founder mice used to generate each GEM model and to acquire new features through dietary and environmental sources. The rate at which these processes occur over time likely varies between institutions. To assess the relative effect size of environment on the microbiome of GEMs used in biomedical research, we performed 16S rRNA metabarcoding of fecal samples from 275 distinct GEM lines (n = 351) maintained by 139 different laboratories at 84 different research institutions in 34 U.S. states or districts and seven other countries, and compared intra-strain, inter-strain, inter-lab, and inter-institution similarities. Reference data from mice harboring supplier-origin (SO) microbiomes (n = 1,171) were used to determine the relative contribution and nature of microbes from known and unknown sources. Paradoxically, the data indicate that the immediate laboratory-level environment is the dominant factor shaping the microbiome of GEM models, but that the microbiome of GEMs develops similarities in beta-diversity, regardless of other factors. Related to this, we detected an unexpectedly high prevalence and abundance of Helicobacter spp. in GEM microbiomes, the abundance of which correlated significantly with the abundance of multiple resident taxa colonizing the mucosa. These findings suggest a higher prevalence of Helicobacter spp. in laboratory mice than previously appreciated, and the possibility of positive and negative interactions with other taxa is found to affect GEM model phenotypes.IMPORTANCEThere are concerns regarding the reproducibility and predictive value of mouse models of human disease. Notwithstanding those legitimate concerns, genetically engineered mouse (GEM) models provide an invaluable platform to investigate gene function or effects of environmental factors in a biological system. The microbiome of GEM models significantly influences model phenotypes and thus represents a possible source of poor reproducibility. While the microbiome is often incorporated in research investigating disease mechanisms using GEMs, limited information is available regarding the similarity of the microbiome of GEM models within and between research labs at the same institution, or across institutions. Moreover, while the microbiome of founder mice from different suppliers is known to differ, the degree to which features present in supplier-origin microbiomes are retained in GEM colonies throughout experimentation is unclear. These data demonstrate the robust effect of lab-level environment and the need for sample collection concurrent with phenotyping.},
}

@article {pmid41222143,
year = {2025},
author = {Liu, P and Zhang, R and Meng, F and Zhang, C and Roberts, AP and Wang, Y and Zhu, K and Cao, Z and Pan, Y and Li, J},
title = {Deep-branching magnetotactic bacteria form intracellular carbonates enriched in trace metals.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0113125},
doi = {10.1128/msystems.01131-25},
pmid = {41222143},
issn = {2379-5077},
abstract = {UNLABELLED: Microbial biomineralization is a fundamental driver of global biogeochemical cycles, yet the ability of prokaryotes to form intracellular carbonates remains rarely documented. Here, we report three ecotypes of magnetotactic bacteria (MTB) affiliated with the Pseudomonadota and the deep-branching Nitrospirota phyla that concurrently synthesize magnetite magnetosomes and intracellular calcium carbonate inclusions enriched in Ba, Mg, and Ni. These carbonate granules are typically spherical and contrast with the highly ordered morphology of magnetite crystals. Comparative genomic analyses reveal that these MTB encode multiple metal-permease systems (e.g., GDT1, CorA, ZnuA2), which suggests both a capacity for selective uptake of divalent cations from their environment and a process likely linked to intracellular carbonate precipitation. By uncovering new examples of bacterial intracellular calcification, our findings expand the known diversity and genetic basis of prokaryotic biomineralization. Moreover, they highlight a potential role of MTB in mediating heavy-metal cycling and provide a refined framework for understanding microbially driven carbonate formation.

IMPORTANCE: Intracellular biomineralization is a hallmark of animals and algae, yet among prokaryotes, it has traditionally been associated with a limited range of lineages and minerals. This study reveals that magnetotactic bacteria (MTB) from both the Pseudomonadota and the deep-branching Nitrospirota phyla are capable of intracellularly forming carbonate granules enriched in diverse divalent cations, including environmentally scarce trace metals Ba²⁺ and Ni²⁺, and biologically essential Mg²⁺. These findings significantly expand the known taxonomic and functional diversity of prokaryotic intracellular calcifiers. By integrating electron microscopy, metagenomics, and structural protein modeling, we propose a potential metal-selective transport system that facilitates trace element accumulation and carbonate precipitation. This work establishes a previously underappreciated role for MTB in trace metal biogeochemical cycling (i.e., Ba²⁺ and Ni²⁺) and suggests that intracellular calcification may be a more widespread bacterial trait than previously assumed.},
}

@article {pmid41221535,
year = {2025},
author = {Xie, K and Zhang, Y and Tan, S and Luo, J and Ou, X and Tan, S},
title = {Gut microbiota involvement in the alteration of inflammatory cell infiltration and gut barrier integrity in liver cirrhosis.},
journal = {Biomedical reports},
volume = {23},
number = {6},
pages = {193},
pmid = {41221535},
issn = {2049-9442},
abstract = {The gut microbiota is essential for the development and regulation of the immune and intestinal homeostasis of the host. The present study aimed to investigate the composition, diversity and functional features of the microbiota in patients with liver cirrhosis. and healthy volunteers using high-throughput sequencing of the 16S rRNA gene, and evaluated inflammatory cell infiltration and the gut barrier in both the colonic mucosa and liver sections using histological analysis. Diversity and metagenome function of the gut microbiota significantly differed between healthy volunteers and patients with liver cirrhosis. Patients with cirrhosis showed decreased microbial richness, evenness, and diversity, with functional prediction indicating enrichment of phosphotransferase and membrane transport pathways, while amino acid and energy metabolism pathways were predominant in healthy controls. Furthermore, gut microbial dysbiosis associated with liver cirrhosis augmented inflammatory cell infiltration in the colonic mucosa and liver sections, impaired gut barrier function and enhanced intestinal permeability and bacterial translocation. The gut microbiota contributes to the pathophysiology of liver cirrhosis, which may impact prevention and treatment strategies for patients with liver cirrhosis.},
}

@article {pmid41221508,
year = {2025},
author = {Siljanen, HMP and Manoharan, L and Hilts, AS and Bagnoud, A and Alves, RJE and Jones, CM and Kerou, M and Sousa, FL and Hallin, S and Biasi, C and Schleper, C},
title = {Targeted metagenomics using probe capture detect a larger diversity of nitrogen and methane cycling genes in complex microbial communities than traditional metagenomics.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf183},
pmid = {41221508},
issn = {2730-6151},
abstract = {Microorganisms are key players in the global cycling of nitrogen and carbon, controlling their availability and fluxes, including the emissions of the powerful greenhouse gases nitrous oxide and methane. Standard sequencing methods often reveal only a limited fraction of their diversity, because of their low relative abundance, the insufficient sequencing depth of traditional metagenomes of complex communities, and limitations in coverage of DNA amplification-based assays. Here, we developed and tested a targeted metagenomics approach based on probe capture and hybridization to simultaneously characterize the diversity of multiple key metabolic genes involved in inorganic nitrogen and methane cycling. We designed comprehensive probe libraries for each of the 14 target marker genes comprising 264 111 unique probes. In validation experiments with mock communities, targeted metagenomics yielded gene profiles similar to the original communities. Only GC content had a small effect on probe efficiency, as low GC targets were less efficiently detected than those with high GC, within the mock communities. Furthermore, the relative abundances of the marker genes obtained using targeted or traditional shotgun metagenomics were significantly correlated. In addition, using archaeal amoA genes as a case-study, targeted metagenomics identified a substantially higher taxonomic diversity and a larger number of sequence reads per sample, yielding diversity estimates 28 or 1.24 times higher than shotgun metagenomics or amplicon sequencing, respectively. Our results show that targeted metagenomics complements current approaches to characterize key microbial populations and functional guilds in biogeochemical cycles in different ecosystems, enabling more detailed, simultaneous characterization of multiple functional genes.},
}

@article {pmid41221507,
year = {2025},
author = {Clinton, CK and Jackson, FLC},
title = {Persistent human-associated microbial signatures in burial soils from the 17th and 18th century New York African burial ground.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf181},
pmid = {41221507},
issn = {2730-6151},
abstract = {Understanding the long-term persistence of human-associated microbial signatures in burial soils offers a untapped insights into historical human health, decomposition, and ecological transformation. This study investigates whether centuries-old burial soils retain distinguishable microbial evidence of human decomposition using 16S rRNA gene sequencing on 81 samples from the New York African Burial Ground (NYABG), a 17th and 18th century cemetery for free and enslaved Africans. Comparative analyses against six control soils from nearby urban parks were conducted using QIIME2, ALDEx2, and ANCOM. Burial soils exhibited significantly greater alpha diversity (Faith's PD, Shannon, observed ASVs; P < .01) and distinct beta diversity patterns (Bray-Curtis, UniFrac; PERMANOVA P = .001). Enrichment of Firmicutes, Actinobacteriota, and gut-associated genera such as Bacillus and Ruminococcus characterized burial soils, whereas oligotrophic taxa dominated controls. Tentative identifications of human-associated pathogenic genera (e.g. Fusobacterium periodonticum, Prevotella pleuritidis) were observed exclusively in burial soils, suggesting their origin from the interred individuals but requiring further validation. These findings demonstrate that soil microbiomes reflect host-associated microbial communities long after decomposition, providing a scalable, nondestructive approach for reconstructing ancient microbial communities and host-associated health signatures. This work establishes the NYABG burial soil microbiome as a valuable model for microbial archaeology and introduces a replicable framework for integrating environmental microbiology, bioarchaeology, and historical epidemiology through the lens of postmortem microbial ecology.},
}

@article {pmid41221399,
year = {2025},
author = {Huang, Y and Zhou, Q and Gui, M and Guo, D and Cheng, J and Ma, W and Shu, P and Liu, X},
title = {Dynamic multi-omics mechanisms underpinning retinol tolerance: stage-specific reconstruction of skin barrier function and host-microbiome metabolic interactions.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1668712},
pmid = {41221399},
issn = {1664-302X},
abstract = {BACKGROUND: Retinol remains an essential component in anti-aging skincare; however, a subset of users develop intolerance, characterized by compromised barrier integrity and inflammation. The temporal dynamics of how skin microbiota and host metabolism co-evolve during retinol tolerance establishment remain poorly understood.

METHODS: We conducted a prospective 28-day longitudinal study with 18 Chinese women (aged 25-40): 9 retinol-intolerant subjects monitored at baseline, adverse reaction phase, and tolerance establishment, while baseline data from 9 retinol-tolerant individuals served as controls. We integrated cutaneous phenotypic measurements, metagenomic sequencing, and untargeted metabolomics.

RESULTS: In the intolerant group, skin phenotype assessment revealed a distinct biphasic response-an acute phase marked by increased stratum corneum hydration, reduced sebum secretion, lower skin pH, and improved wrinkle metrics, followed by a re-equilibration phase characterized by sustained barrier restoration. Metagenomic profiling of 969 microbial species demonstrated that, although overall microbial α-diversity remained stable across time points in both groups, key taxa in the intolerant group exhibited transient "rise-and-fall" dynamics. At baseline, the intolerant group exhibited overrepresentation of Cutibacterium acnes, whereas the tolerant group was enriched in potentially protective species, including Sphingomonas hankookensis and Acinetobacter johnsonii. Untargeted metabolomics showed marked temporal fluctuations with an initial phase of metabolic turbulence, followed by partial recovery. During the early adverse reaction phase in intolerant subjects, lipid and fatty acid metabolic pathways-specifically, glycerophospholipid, linoleic acid, α-linolenic acid, and ether lipid metabolism-were significantly upregulated, concomitant with the suppression of TCA cycle and sphingolipid activity. Conversely, as tolerance was established, enhanced activity in the TCA cycle, sphingolipid, ascorbate, and pentose metabolism pathways-coupled with a reduction in pro-inflammatory arachidonic acid derivatives-indicated metabolic reconstitution and restoration of barrier integrity.

DISCUSSION: Integrated multi-omics correlation analyses further underscored the tightly interconnected regulation of host-microbe energy metabolism, antioxidant defenses, and membrane repair in response to retinol-induced stress. These findings elucidate the temporal interplay between host and microbial processes underpinning retinol tolerance and highlight baseline biomarkers that may facilitate personalized skincare interventions.},
}

@article {pmid41221168,
year = {2025},
author = {Yu, X and Cheng, J and He, J and Wu, X and Wang, W and Chen, M and Zhuo, B and Ge, Y},
title = {First Documented Case of Pneumonia with Nocardia africana and SARS-CoV-2 Co-Detection in Mainland China.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {5721-5730},
pmid = {41221168},
issn = {1178-6973},
abstract = {Nocardia spp. are zoonotic pathogens that can cause infections ranging from localized lesions to systemic dissemination, primarily via pulmonary inhalation or percutaneous inoculation. We report the first confirmed case of Nocardia africana pneumonia with SARS-CoV-2 co-detection in mainland China, diagnosed through bronchoalveolar lavage fluid (BALF) analysis using metagenomic next-generation sequencing (mNGS) and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). A 76-year-old male presented with persistent cough and fever, accompanied by radiographic evidence of progressive pneumonia. Targeted antimicrobial therapy with trimethoprim-sulfamethoxazole and amoxicillin-clavulanate resulted in clinical resolution within 12 days. This case underscores three critical implications for post-COVID-19 pandemic medicine: the requirement for heightened vigilance for opportunistic pathogens (eg, Nocardia species) in pneumonia patients with recurrent fever, the essential role of advanced diagnostics (eg, mNGS and MALDI-TOF MS) in identifying fastidious organisms like actinomycetes, and the potential for antimicrobial resistance in N. africana, which necessitates susceptibility-guided therapy.},
}

@article {pmid41220843,
year = {2025},
author = {Kwon, K and Kim, M and Jung, Y and Yoon, MY and Lee, JY and Yoon, SS and Rho, M and Chung, YW and Ryu, JH},
title = {Intestinal Dysbiosis Caused by Epithelial Fabp6 Gene Disruption Exacerbates Gut Inflammatory Disease.},
journal = {Immune network},
volume = {25},
number = {5},
pages = {e35},
pmid = {41220843},
issn = {1598-2629},
abstract = {Ileal lipid binding protein (Ilbp), encoded by Fabp6 gene, plays a critical role in intracellular transport of bile acids (BAs) from apical to basolateral side of ileal enterocytes, maintaining BA homeostasis within enterohepatic circulation. However, pathophysiological consequences of Ilbp deficiency remain largely unexplored. Here, we demonstrate that disruption of BA balance, caused by intestinal epithelial cell (IEC)-specific Fabp6 gene knockout (Fabp6 [ΔIEC]), exacerbates dextran sulfate sodium (DSS)-induced gut inflammation. Fecal microbiota transplantation from Fabp6 [ΔIEC] mice to germ free recipient mice replicated the adverse effects observed in Fabp6 [ΔIEC] mice, which were mitigated when these mice were co-housed with control (Fabp6 [f/f]) mice. Metagenomic analysis identified Ligilactobacillus murinus as a primarily diminished strain in Fabp6 [ΔIEC] mice. Oral administration of L. murinus isolated from feces of Fabp6 [f/f] mice ameliorated DSS-induced colitis in Fabp6 [ΔIEC] mice by restoring epithelial barrier integrity and lowering pro-inflammatory cytokines IL-1β, IL-6 and TNF-α. Furthermore, daily administration of taurodeoxycholic acid-one of the BAs reduced in Fabp6 [ΔIEC] mice and that promotes the growth of L. murinus in an in vitro growth assay-also exhibited a protective effect against DSS-induced colitis through a similar mechanism. These findings suggest that deficiency of specific BAs due to epithelial Fabp6 deletion leads to gut dysbiosis, predisposing the host to inflammatory disease.},
}

@article {pmid41220286,
year = {2025},
author = {Lee, JY and Yoo, JH and Kim, JE and Bae, JW and Lee, CK},
title = {Translating Gut Microbiota into Diagnostics: A Multidimensional Approach for the Diagnosis of Inflammatory Bowel Disease.},
journal = {Gut and liver},
volume = {},
number = {},
pages = {},
doi = {10.5009/gnl250360},
pmid = {41220286},
issn = {2005-1212},
abstract = {The gut microbiota has emerged as a key factor in the pathophysiology of inflammatory bowel disease (IBD), providing novel opportunities for diagnostic innovation. Traditional biomarkers, such as C-reactive protein and fecal calprotectin, are widely used in clinical practice; however, their ability to reflect disease complexity and microbial dysregulation remains limited. Recent advances in metagenomics and multi-omics integration have enabled high-resolution profiling of microbial communities and their functional capacities and associated metabolites. Differential abundance analysis and machine learning models have been used to identify microbial biomarkers that can distinguish patients with IBD from healthy individuals. Multicohort studies integrating microbiome and metabolomic data have further improved diagnostic accuracy and generalizability. Transcriptomic and proteomic analyses provide complementary insights into host-microbe interactions and disease mechanisms. In this review, we explored the potential of metagenomic biodata as diagnostic markers for IBD, with an emphasis on a multidimensional analytical approach. We highlight the recent developments in sequencing technologies, computational pipelines for microbial feature selection, and machine learning strategies applied to biomarker discovery. The integration of multi-omics data deepens our understanding of host-microbe interactions and facilitates the development of microbiota-informed diagnostic tools. As multidimensional microbial profiling evolves, its clinical utility for the diagnosis and stratification of IBD requires further investigation.},
}

@article {pmid41219964,
year = {2025},
author = {George, NA and Zhou, Z and Anantharaman, K and Hug, LA},
title = {Discarded diversity: novel megaphages, auxiliary metabolic genes, and virally encoded CRISPR-Cas systems in landfills.},
journal = {Virology journal},
volume = {22},
number = {1},
pages = {370},
pmid = {41219964},
issn = {1743-422X},
support = {R35GM143024/GM/NIGMS NIH HHS/United States ; 2016-03686//Natural Sciences and Engineering Research Council of Canada/ ; Tier II chair//Canada Research Chairs/ ; },
abstract = {BACKGROUND: Viruses are the most abundant microbial entities on the planet, impacting microbial community structure and ecosystem services. Despite outnumbering bacteria and archaea by an order of magnitude, viruses have been comparatively underrepresented in reference databases. Metagenomic examinations have illustrated that viruses of bacteria and archaea have been specifically understudied in engineered environments. Here we employed metagenomic and computational biology methods to examine the diversity, host interactions, and genetic systems of viruses predicted from 27 samples taken from three municipal landfills across North America.

RESULTS: We identified numerous viruses that are not represented in reference databases, including the third largest bacteriophage genome identified to date (~ 678 kbp), and noted a large diversity of viruses in landfills that has limited overlap across landfills and is distinct from viromes in other systems. Host-virus interactions were examined via host CRISPR spacer to viral protospacer mapping which captured hyper-targeted viral populations and six viral populations predicted to infect hosts across multiple phyla. Auxiliary metabolic genes (AMGs) were identified with the potential to augment hosts' methane, sulfur, and contaminant degradation metabolisms, including AMGs not previously reported in the literature. CRISPR arrays and CRISPR-Cas systems were identified from predicted viral genomes, including the two largest bacteriophage genomes to contain these genetic features. Some virally encoded Cas effector-like proteins appear distinct relative to previously reported Cas effectors and are interesting targets for potential genome editing tools.

CONCLUSIONS: Our observations indicate landfills, as heterogeneous contaminated sites with unique selective pressures, are key locations for diverse viruses and atypical virus-host dynamics.},
}

@article {pmid41219190,
year = {2025},
author = {Chung, D and Brask, N and Matar, S and Gallot-Lavallée, L and Pringle, ES and Duguay, BA and Blais, C and Latimer, J and Haro, R and Slamovits, CH and Leyland, B and Rest, JS and Collier, JL and McCormick, C and Archibald, JM},
title = {Persistent mirusvirus infection in the marine protist Aurantiochytrium.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9922},
pmid = {41219190},
issn = {2041-1723},
support = {GBMF5782//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; },
abstract = {Mirusviruses are abundant and broadly distributed double-stranded (ds) DNA viruses recently discovered in marine metagenomic data. Their host range and ecological impact are unclear. The protist Aurantiochytrium limacinum possesses two mirusvirus-like genomic elements, one a circular episome (AurliV-1) and the other (AurliV-2) a chromosomal integrant. Here we show that genes in both genomes are expressed and viral particles containing mainly AurliV-1 DNA are produced under starvation conditions and when cells are cultured in standard growth medium. We detected viral particles of ~140 nm in the nucleus, in cytoplasmic vesicles, between the plasma membrane and cell wall, and in the extracellular environment. Of 67 AurliV-1-encoded proteins detected using proteomics, 45 are enriched under starvation conditions, including the structurally important major capsid and triplex proteins. Our results establish Aurantiochytrium as a model system for elucidating mirusvirus-host interactions and demonstrate persistent viral infection in a microbial eukaryote.},
}

@article {pmid41218604,
year = {2025},
author = {Lyu, L and Fan, Y and Bryrup, T and Clos-Garcia, M and Brix, S and Eiken, M and Stankevic, E and Lund, AB and Knop, FK and Jørgensen, NR and Vestergaard, H and Hansen, T and Hansen, T and Nielsen, T and Pedersen, O},
title = {Glucocorticoid-induced changes of the gut microbiota and metabolic markers in healthy young men: Outcome of a randomized controlled trial.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {102426},
doi = {10.1016/j.xcrm.2025.102426},
pmid = {41218604},
issn = {2666-3791},
abstract = {Glucocorticoids induce insulin resistance and suppress immunity, but their impact on gut microbiota, which may modulate metabolism and immunity remains under explored. In this 7-day trial, we assess glucocorticoid-induced changes in gut microbiota and metabolic markers in 56 healthy men, randomly assigned to three interventions: oral prednisolone (PO group), intramuscular methylprednisolone acetate (IM group), or saline (CTL group). Shotgun metagenomics reveal that PO glucocorticoid causes shifts in bacterial abundance, increasing Blautia and Collinsella, while decreasing Dysosmobacter welbionis and Anaerotignum faecicola, linked with insulin resistance and immunosuppression markers. Additionally, PO treatment alters microbial pathways and enzymes related to glycolysis and lipid metabolism, with changes in predicted metabolites such as hypoxanthine and phenylacetate. IM treatment results in minimal microbiota changes. These findings underscore the route-dependent effects of glucocorticoids on gut microbiota and their potential impact on host metabolism and immunity. The trial was approved by the Danish Medicine Agency (EudraCT protocol number: 2016-001850-16).},
}

@article {pmid41214576,
year = {2025},
author = {Feng, Y and Zhang, R and Wen, G and Xie, L and Chen, T and Liu, W},
title = {The role of gut microbiota tyrosine decarboxylases in levodopa pharmacokinetics: insights from a levodopa challenge test.},
journal = {BMC neurology},
volume = {25},
number = {1},
pages = {460},
pmid = {41214576},
issn = {1471-2377},
support = {822QN459//Youth Project of Hainan Natural Science Foundation/ ; 82371268//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: The gut microbiota is known to influence levodopa metabolism in the intestinal tract, primarily through the action of tyrosine decarboxylase, an enzyme encoded by the tyrosine decarboxylase gene (tyrDC). However, the effect of the abundance of the tyrDC gene on levodopa pharmacokinetics remains unclear.

METHODS: The aim of this study was to investigate this relationship in Parkinson’s disease (PD) patients undergoing a levodopa challenge test. Our study enrolled 12 PD patients with a good response to levodopa. Plasma levodopa pharmacokinetics were determined via liquid chromatography‒tandem mass spectrometry, while tyrDC gene abundance in faecal samples was assessed via metagenomic shotgun sequencing.

RESULTS: A total of 12 PD patients (age: 58.00 ± 8.80 years) with an Hoehn and Yahr stage of 2.25 (2.0–3.0) and a disease duration of 8.46 ± 4.94 years were enrolled. After levodopa administration, the MDS-UPDRS-III score decreased 71.28%±17.09%. We found no significant association between tyrDC gene abundance and levodopa pharmacokinetics.

CONCLUSION: These findings indicate that the influence of the intestinal microbiota on PD patients with a good response to levodopa during the levodopa challenge test may be minimal, which may provide new insight into levodopa therapy.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12883-025-04428-6.},
}

@article {pmid41206538,
year = {2025},
author = {Hall, MB and Zhou, C and Coin, LJM},
title = {Genome size estimation from long read overlaps.},
journal = {Bioinformatics (Oxford, England)},
volume = {41},
number = {11},
pages = {},
doi = {10.1093/bioinformatics/btaf593},
pmid = {41206538},
issn = {1367-4811},
support = {FSPGN000045//Australian Government Medical Research Future Fund (MRFF) Genomics Health Futures Mission (GHFM) Flagships-Pathogen Genomics/ ; //META-GP/ ; //DELIVERING A CLINICAL METAGENOMICS PLATFORM FOR AUSTRALIA/ ; },
abstract = {MOTIVATION: Accurate genome size estimation is an important component of genomic analyses such as assembly and coverage calculation, though existing tools are primarily optimized for short-read data.

RESULTS: We present LRGE, a novel tool that uses read-to-read overlap information to estimate genome size in a reference-free manner. LRGE calculates per-read genome size estimates by analysing the expected number of overlaps for each read, considering read lengths and a minimum overlap threshold. The final size is taken as the median of these estimates, ensuring robustness to outliers such as reads with no overlaps. Additionally, LRGE provides an expected confidence range for the estimate. We validate LRGE on a large, diverse bacterial dataset and confirm it generalizes to eukaryotic datasets. On bacterial genomes, LRGE outperforms k-mer-based methods in both accuracy and computational efficiency and produces genome size estimates comparable to those from assembly-based approaches, like Raven, while using significantly less computational resources.

Our method, LRGE (Long Read-based Genome size Estimation from overlaps), is implemented in Rust and is available as a precompiled binary for most architectures, a Bioconda package, a prebuilt container image, and a crates.io package as a binary (lrge) or library (liblrge). The source code is available at https://github.com/mbhall88/lrge and an archive at https://doi.org/10.5281/zenodo.17183812 under an MIT license.},
}

@article {pmid41218490,
year = {2025},
author = {Qingrui, L and Hongyang, L and Guijun, W and Yiqiao, Z and Yue, C and Changqun, D and Chang'e, L},
title = {Synergistic ecotoxicity of nanoscale zero-valent iron and cadmium in soil: Insights from Eisenia fetida.},
journal = {Ecotoxicology and environmental safety},
volume = {306},
number = {},
pages = {119381},
doi = {10.1016/j.ecoenv.2025.119381},
pmid = {41218490},
issn = {1090-2414},
abstract = {Nano-zero-valent iron (nZVI) has been extensively applied as a soil conditioner in remediation practices. However, studies have suggested that excessive doses of nZVI can adversely affect soil organisms and even exacerbate the toxicity of contaminants such as cadmium (Cd) in earthworms. This study investigated whether nZVI induces stress and exacerbates Cd toxicity in Eisenia fetida under controlled laboratory conditions. Four treatments were established: control (no nZVI or Cd), nZVI (10 g∙kg[-1]), Cd (30 mg∙kg[-1]), and Cd-nZVI (30 mg∙kg[-1] Cd + 10 g∙kg[-1] nZVI). Survival rate, biomass, Cd bioaccumulation, enzyme activity, and other indicators were measured. On day 7 of exposure, reactive oxygen species (ROS) levels in the nZVI, Cd, and Cd-nZVI groups were 1.4-, 1.5-, and 1.6-fold higher than those in the control group, respectively (P < 0.05). Over time, both survival rate and biomass declined, with the lowest survival rate and greatest biomass loss observed in the Cd-nZVI group on day 28. Histological staining revealed that under Cd or nZVI stress, the circular muscle layer of the earthworms was loosened, intestinal tissue was partially detached, and the number of villi decreased. Metagenomic sequencing indicated significant alterations in the community structure of the earthworm intestinal microbiota under different treatments. Both 30 mg∙kg[-1] Cd and 10 g∙kg[-1] nZVI disrupted gut microbial balance, which was further exacerbated by combined exposure.},
}

@article {pmid41218435,
year = {2025},
author = {Ren, J and Wang, J and Dong, Y and Xiao, L and Wang, L and Ji, J and Liu, Y},
title = {Microbial community dynamics and its relationship with biogeochemical processes under geochemical perturbations.},
journal = {Water research},
volume = {289},
number = {Pt B},
pages = {124889},
doi = {10.1016/j.watres.2025.124889},
pmid = {41218435},
issn = {1879-2448},
abstract = {Environmental microbial communities are crucial in regulating ecosystem functions and are increasingly affected by human-induced geochemical perturbations. While microbial communities are known to shift under such perturbations, the explicit link between these shifts and corresponding biogeochemical processes remains unclear. Here, we conducted time-series sediment incubation experiments under elevated nitrate conditions, combining 16S rRNA gene sequencing, qPCR, and metagenomics to track microbial taxonomic and functional dynamics. We further developed a gene-centric, process-based biogeochemical model to quantitatively connect microbial community structure to geochemical reaction kinetics. Our results revealed that functional metagenomics provided a broader view of functional diversity than qPCR and enabled detailed analysis of gene co-occurrence. Through modeling, we uncover a quantitative coupling between functional gene abundance and reaction rates under geochemical perturbations. However, this relationship can be obscured by redox-driven abiotic processes affected by perturbations and the nonlinear nature of enzyme-mediated reactions, making it difficult to resolve using standard statistical approaches. Together, these findings improve our understanding of the linkage between microbial function and biogeochemical processes, and underscore the value of gene-centric, process-based models for predicting ecosystem behavior under geochemical stress.},
}

@article {pmid41218045,
year = {2025},
author = {Kitsanayanyong, L and Chongprachavat, N and Rairat, T and Keetanon, A and Wimanhaemin, P and Chuchird, N},
title = {Exploring the gut microbiota of Pacific white shrimp (Litopenaeus vannamei) suffering pale shrimp disease.},
journal = {PloS one},
volume = {20},
number = {11},
pages = {e0336700},
doi = {10.1371/journal.pone.0336700},
pmid = {41218045},
issn = {1932-6203},
abstract = {Pale shrimp disease is an emerging threat in Thailand, characterized by pale body coloration in Pacific white shrimp (Litopenaeus vannamei). Although the etiology had been identified as Photobacterium damselae subsp. damselae, the disease effects on gut microbiome remain poorly understood. This study investigated changes in the gut microbiota of Pacific white shrimp suffering from pale shrimp disease (diseased group) compared to disease-free shrimp (healthy group) collected from Surat Thani Province, Thailand. DNA extracted from the intestinal samples was subjected to 16S rRNA metagenomic sequencing, followed by taxonomic identification, diversity analyses, and functional prediction of the metabolic pathways. Despite a limited number of biological replicates, the occurrence of pale shrimp disease was able to reveal alterations in intestinal microbial composition, diversities, and functional features compared to the healthy shrimp. In most cases, the intestinal microbiota of the diseased shrimp were dominated by only 2 genera of bacteria, i.e., Photobacterium (54.63-70.53%) and Vibrio (24.94-26.12%), which together accounted for 79.58-95.47% of the total bacterial community. α-diversity, as indicated by the observed features, Shannon, and Simpson indices, was significantly decreased, and dominance was significantly increased in the diseased shrimp compared to healthy shrimp. Likewise, β-diversity was significantly different between groups; PCoA of un-weighted and weighted UniFrac clearly distinguished intestinal microbiota of the shrimp into 2 clusters, and ANOSIM of these data revealed statistical differences between groups, suggesting different microbiota communities between healthy and diseased shrimp. Moreover, diseased shrimp had significantly higher predicted functional features associated with bacterial virulence factors and antibacterial resistance. These exploratory findings suggest an association among pale shrimp disease, gut microbiota dysbiosis, and the proliferation of opportunistic taxa, particularly Photobacterium.},
}

@article {pmid41217732,
year = {2025},
author = {Boutin, S and Klein, S and Untergasser, G and Loka, TP and Jakob, S and Caf, Y and Khatamzas, E and Knabl, L and Wrettos, G and Knobloch, H and Nurjadi, D},
title = {Evaluating Seqstant LiveGene Analysis in real-time assessment of metagenomic next-generation sequencing (mNGS) data from respiratory samples.},
journal = {Infection},
volume = {},
number = {},
pages = {},
pmid = {41217732},
issn = {1439-0973},
abstract = {BACKGROUND: The detection of pathogens causing infections by conventional diagnostic methods can be challenging and next-generation sequencing (NGS) technology offers a promising alternative method. In this study, we evaluated the performance of real-time metagenomic next-generation sequencing (rt-mNGS) for the detection of pathogens in respiratory samples.

METHOD: We used rt-mNGS, using the Seqstant LiveGene Analysis platform, on 335 respiratory samples in comparison to conventional culture results.

RESULTS: We observed an overall good concordance in 71.64% (240/335) of the methods. The rt-mNGS outperformed the gold standard culture in 16.12% (54/335) of the samples, while the culture was superior in detecting the clinically relevant pathogen in 12.24% (41/335) of the samples. The non-inferiority of rt-mNGS was statistically significant (δ = 10, α = 0.05, 1 - β = 0.8). We also observed that the real-time analysis of NGS data is beneficial in obtaining reliable, timely results, as the initial report at cycle 46 exhibits a Positive Predictive Value (PPV) of 93.75% at the species-level with a sensitivity of 32.09%.

CONCLUSION: Overall, our study showed the non-inferiority of rt-mNGS compared to the standard-of-care microbiology for respiratory samples with statistical significance. Moreover, the rt-mNGS method exhibited superior sensitivity and superior overall performance. It also uniquely detected certain organisms that are typically hard to culture. However, rt-mNGS reported a higher number of false positives and faced limitations in detecting Aspergillus spp. In conclusion, the study highlights the potential of rt-mNGS as a powerful tool in clinical diagnostics of respiratory infections and beyond.},
}

@article {pmid41217690,
year = {2025},
author = {Nguyen, HN and Kim, OTP and Tran, TT},
title = {Metagenomic analysis of microbial communities and associated resistance genes, virulence genes, and mobile genetic elements in natural honey from Mu Cang Chai, Vietnam.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {11},
pages = {445},
pmid = {41217690},
issn = {1573-0972},
support = {B2023-SPH17; VINIF.2021.TS.127//The Ministry of Education and Training, Vietnam; PhD Scholarship Programme of Vingroup Innovation Foundation (VINIF)/ ; B2023-SPH17; VINIF.2021.TS.127//The Ministry of Education and Training, Vietnam; PhD Scholarship Programme of Vingroup Innovation Foundation (VINIF)/ ; },
abstract = {Natural honey is preferred over honey from farmed bees in Vietnam, often commanding higher prices; therefore, it needs proper guidance. Environmental DNA from natural honey can be used to monitor its safety and authenticate its quality, as it contains DNA traces from various organisms. In this study, shotgun metagenomic sequencing was employed to identify risk factors in three natural honey samples from Mu Cang Chai, one of the central honey-producing regions in Northwest Vietnam. Our data revealed that more than 95% of the identified DNA belonged to bacteria in all three samples. Some opportunistic pathogenic bacteria, such as Klebsiella pneumoniae, Burkholderia contaminans, and Ralstonia picketti, were found dominant in the examined samples. Moreover, the bacteria in these honey samples carried numerous antibiotic resistance genes (ARGs), as well as virulence genes (VGs). The resistome profiles revealed the detection of 491 ARG sequences across three honey samples, belonging to 43 gene families that encode various resistance proteins. The most frequently encountered drug classes associated with these ARGs were cephalosporins, fluoroquinolones, and tetracyclines. On the other hand, the virulome profiles showed a rich composition of VGs: a total of 94 unique VGs linked to 25 virulence factors. They included nutritional factors, secretion systems, biofilm formation, exotoxins, and immunomodulation; the nutritional factors were the most prevalent function of these VGs. Mobilome profiles showed that only a small fraction of ARGs (0.6%) and VGs (15%) were located on mobile genetic elements (MGEs) such as plasmids and proviruses, suggesting most were chromosomally encoded; however, the presence of MGEs carrying these determinants (ARGs and VGs) still indicates a latent potential for horizontal gene transfer. Although these results are based on a case study of only three samples of natural honey collected in Mu Cang Chai, they highlight the need for a broader examination and the importance of monitoring the risk of pathogenicity in unprocessed foods, such as natural honey.},
}

@article {pmid41217278,
year = {2025},
author = {Zhang, C and Chang, N and Yin, G and Shen, W and Lu, L and Bao, M and Guan, D and Zhang, S and Wang, R and Zhang, H},
title = {Drivers of Metal Resistance-Virulence Co-Selection in Landfill Leachates.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf275},
pmid = {41217278},
issn = {1365-2672},
abstract = {AIMS: Metal resistance genes (MRGs) and virulence factor genes (VFGs) are driven by environmental factors and host immunity, respectively, and they are traditionally considered to evolve independently. However, their co-selection dynamics in landfill leachates remain poorly characterized. In this study, a multi-regional metagenomic assessment integrating environmental gradients was first presented to reveal how heavy metals shape MRG-VFG interactions and associated ecological risks in landfill leachates.

METHODS AND RESULTS: Landfill leachates were collected from 13 landfills spanning six regions in China. Multi-regional metagenomic sequencing combined with co-occurrence network analysis was applied to examine pathogen-gene relationships. The results revealed pronounced regional disparities in pathogen, MRG, and VFG distribution, alongside shared features. Staphylococcus aureus and Pseudomonas aeruginosa were identified as dominant pathogens. tufA and gyrA emerged as conserved VFGs, whereas arsB and copA represented dominant MRGs. Network analysis revealed Escherichia coli, Salmonella enterica, and Acinetobacter baumannii as central nodes carrying overlapping functional genes, forming a "metal resistance-virulence" synergy module. Redundancy analysis revealed that specific heavy metals (Cu, Zn, Cr, and As) were crucial for the formation and stability of "pathogen-MRG-VFG" functional assemblies.

CONCLUSIONS: This study addresses a critical knowledge gap by integrating multi-regional metagenomic evidence with environmental selection pressures. MRGs conferred survival advantages and synergized with VFGs to enhance pathogen infectivity. These findings provide insight into MRG-VFG co-selection mechanisms in landfill leachates and guide targeted monitoring to mitigate environmental and health risks.},
}

@article {pmid41217198,
year = {2025},
author = {Valade, M and Le Bideau, M and Grimaldier, C and Boschi, C and Colson, P and La Scola, B},
title = {Development of cell combos micromethod to isolate respiratory viruses not detected by molecular techniques.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0257125},
doi = {10.1128/spectrum.02571-25},
pmid = {41217198},
issn = {2165-0497},
abstract = {Virological diagnosis of respiratory infections relies mainly on molecular methods but can be overlooked in cases of unexpected or unknown emerging viruses. In this case, modern approaches use mainly metagenomics without a priori. The other approach to detecting new viruses is based on their isolation in cell culture using virus-specific cells and culture conditions. Unfortunately, inoculation on several lines and metagenomics requires a large volume of clinical sample, while the initial sample has already been largely used to carry out multiplexed RT-PCR. Herein, we aimed to develop micro-methods to inoculate combos of cell lines to isolate respiratory viruses missed by molecular techniques. Ten cell lines were selected, and then five cell combos of two cell lines each were developed. Strains of 15 respiratory virus species were inoculated, and viral growth was assessed by cytopathic effect detection and RT-PCR assays. Among these, all grew on at least one combo. The Caco-2/MRC5 combo was the most promising. As proof-of-concept, 859 human respiratory samples found negative by multiplex RT-PCR panels were inoculated into these five cell combos and monitored for the appearance of cytopathic effects. The efficiency of this approach was evidenced by isolating 12 herpes simplex or varicella-zoster viruses not detected by respiratory multiplex PCR assays. In conclusion, this updated approach can detect known but, most importantly, likely emerging respiratory viruses. It could be used to investigate undiagnosed respiratory infection outbreaks especially if optimized with an approach allowing for the detection of viral multiplications with minor or no cytopathic effects.IMPORTANCEThe detection of respiratory viruses relies on a range of laboratory methods each of which has distinct advantages in terms of speed, practicality, and sensitivity. Current molecular methods for respiratory virus detection, such as multiplex PCR, may fail to identify unexpected, genetically divergent, or emerging viruses. This study presents an innovative approach using micromethods inoculating combinations of cell lines (cell combos) to enhance the isolation of a broad panel of respiratory viruses, including those undetected by standard molecular techniques. This strategy revives and modernizes classical virology techniques for use in contemporary diagnostics, particularly during unexplained respiratory outbreaks. It opens up new possibilities for detecting both known and unknown viruses across different sample types.},
}

@article {pmid41217051,
year = {2025},
author = {Alam, SS and Mehdi, A and Zafar, A and Ali, S and Rehman, AU and Liaqat, I and Peng, L and Kanwal, F and Afzal, S and Haq, IU and Aftab, MN},
title = {Advances in microbial biofuel production by metabolic and enzyme engineering, synthetic biology, metagenomics, and genome editing applications.},
journal = {Emerging topics in life sciences},
volume = {},
number = {},
pages = {},
doi = {10.1042/ETLS20240002},
pmid = {41217051},
issn = {2397-8554},
abstract = {Microorganisms are the primary source of genetic diversity on earth due to their unparalleled metabolic and functional variability. With the depletion of fossil fuels, a sustainable alternative approach is the use of biofuels, where plant biomass as feedstock is essentially degraded to sugars with the aid of microbe-derived enzymes, followed by the conversion of those sugars to biofuels. Several cellulolytic and non-cellulolytic enzymes are involved in biofuel synthesis. Molecular cloning, along with the advancements in genetic and metabolic engineering in microbial cells, plays a significant contribution to biofuel overproduction. Advanced molecular technologies such as metagenomics and synthetic biology approaches are also being used to construct effective microorganisms for biofuel manufacturing. Obtaining novel enzymes from undiscovered microbial consortia and functional gene analysis is possible through a metagenomics approach. While synthetic biology provides engineered biological systems to generate required biofuel productivity, the CRISPR-Cas genome editing tool is another revolutionary tool being utilized for efficient biofuel production. This article provides a brief overview of different methods of biofuel production using microorganisms.},
}

@article {pmid41216332,
year = {2025},
author = {Facciotti, F and Di Stefano, G and Maragno, P and Ferraro, C and Dridi, D and Somigliana, E and Viganò, P and Vercellini, P and Casalechi, M},
title = {Microbiome dysbiosis and endometriosis: a systematic scoping review of current literature and knowledge gaps.},
journal = {Human reproduction open},
volume = {2025},
number = {4},
pages = {hoaf061},
pmid = {41216332},
issn = {2399-3529},
abstract = {STUDY QUESTION: What is the evidence available concerning gut and reproductive tract microbiomes in patients with endometriosis and what are the methodological approaches employed in microbiome studies on endometriosis?

SUMMARY ANSWER: The taxonomic profiles exhibited pronounced heterogeneity within women with and also within women without endometriosis across reviewed studies for all the anatomical districts evaluated.

WHAT IS KNOWN ALREADY: Both human and animal studies support differences in the microbiome composition of individuals with and without endometriosis. Endometriosis onset occurs with variable symptoms and manifestations. The microbiome composition at different sites may contribute to this variability.

STUDY DESIGN SIZE DURATION: We used the scoping review methodology. Systematic searches of studies from the PubMed, EMBASE, and Web of Science databases published between 1 January 2016 and 1 November 2024 addressing endometriosis microbiome characterization in: (i) gut, (ii) vaginal fluid, (iii) cervical fluid, (iv) peritoneal fluid, (v) uterine fluid, (vi) ovarian cyst fluid, (vii) oropharyngeal fluid, and (viii) eutopic and (ix) ectopic tissues were performed using a combination of MeSH terms. References from relevant publications were systematically screened.

Results were reported in accordance with the PRISMA-ScR guidelines. Studies that did not report original data, not written in English or providing a review of the field were excluded. From the 2182 publications retrieved, 36 papers were selected and analyzed, focusing on sample characterization (patients, controls, tissues, and fluids) and methodologies used.

Sound evidence is lacking to support a specific gut dysbiosis profile in women with endometriosis. The largest metagenome study performed using shotgun sequencing and controlling for multiple hypotheses testing did not detect significant differences between women with and without the disease. For eutopic and ectopic tissue microbiomes, the literature is too scant to draw any conclusion. Some data suggest a possible enrichment of Streptococcus sp. in cervical fluid and of Pseudomonas sp. in peritoneal fluid and a depletion of Lachnospira sp. in stool/anal fluid of endometriosis patients. However, these findings may be explained by confounders or by intrinsic patient or population characteristics. We appraised the limitations of the studies and proposed suggestions for optimizing sequencing techniques and experimental designs.

The number of participants per study greatly varied and, with few exceptions, was typically low. Incomplete information on methodological approaches was broadly observed. The impact of participants' menstrual cycle phase, diet, and drug assumption was frequently not considered.

Standardization of research protocols to allow reproducibility is required, as well as collaborations to harmonize data analysis, interpretation, and, more importantly, health outcome prediction or improvement.

The review was funded by the Italian Ministry of Health: RF-2019-12369460, and Current Research IRCCS. P.Vi. serves as co-editor in Chief of Journal of Endometriosis and Uterine Disorders. E.S. serves as Editor in Chief of Human Reproduction Open and discloses research grants from Ferring, Ibsa, Gedeon Richter, and Theramex, and honoraria from Ibsa and Gedeon Richter. P.Ve. serves as Associate Editor for Human Reproduction Open; is a member of the Editorial Board of the Journal of Obstetrics and Gynaecology Canada, of the Italian Journal of Obstetrics and Gynaecology, and of the International Editorial Board of Acta Obstetricia et Gynecologica Scandinavica; has received royalties from Wolters Kluwer for chapters on endometriosis management in the clinical decision support resource UpToDate; and maintains both a public and private gynecological practice. All other authors declare they have no conflict of interest.

REGISTRATION NUMBER: 10.17605/OSF.IO/X6HBT at https://osf.io/registries.},
}

@article {pmid41216322,
year = {2025},
author = {Li, C and Hou, J and Datry, T and Adyel, TM and Zhou, W and Wu, J and You, G and Jin, T and Deng, Y and Miao, L},
title = {How river drying influences greenhouse gas emissions: insights from species and gene shifts.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf187},
pmid = {41216322},
issn = {2730-6151},
abstract = {Drying is threatening global river ecosystems due to climate change, altering community composition and function even upon flow resumption. This mesocosm study investigated the greenhouse gas emissions fluxes and underlying mechanisms from benthic habitats prone to 20-100 days of drying. Results show that CO2 and N2O emissions from biofilms did not increase when drying increased, due to the changes in functional communities and genes. Notable is the transformation of biofilm from carbon source to sink following prolonged drying (mean emission fluxes ranged from 804.78 to -305.55 mg m[2] h[2]). This was mainly due to strong increases in the abundance of genes involved in the Calvin-Benson-Bassham cycle (2.82 × 10[-5] to 7.12 × 10[-5]), and functional taxa such as gemmatimonadota and pseudomonadota. These findings reveal a potential mitigation effect of drying on greenhouse gas emissions from rivers and streams, which could be relevant in the face of climate change.},
}

@article {pmid41216321,
year = {2025},
author = {Hawthorne, SEG and Tsola, SL and Carrión, O and Todd, JD and Eyice, Ö},
title = {Active microorganisms and potential metabolic pathways mediating anaerobic degradation of DMSP in anoxic saltmarsh sediment.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf180},
pmid = {41216321},
issn = {2730-6151},
abstract = {Dimethylsulfoniopropionate (DMSP) is a globally abundant organosulfur compound produced by marine organisms, where it plays key physiological roles in stress protection and serves as a major source of carbon, sulfur, and energy for microbial communities. Importantly, DMSP degradation contributes to the formation of the climate-active gas dimethyl sulfide (DMS), which can drive the production of potent greenhouse gases, methane and carbon dioxide, in anoxic environments. While aerobic DMSP degradation is well studied, its fate under anoxic conditions remains poorly understood, and the microbial populations and metabolic pathways underlying these biotransformations are virtually unknown. Here, we present the first detailed investigation of microbial DMSP cycling in anoxic saltmarsh sediments. Our sediment samples had high in situ DMSP concentrations (up to 7.7 μmol/g) and the conversion efficiencies of DMSP to DMS under anoxic conditions (~68%) were comparable to those in oxic environments. Furthermore, using [13]C-labelled DMSP in stable isotope probing (SIP) experiments, combined with 16S rRNA gene sequencing and metagenomics, we identified Amphritea (Oceanospirillales) as a key active DMSP degrader, likely operating via the dddD-encoded lysis pathway. Additional taxa, including Geopsychrobacter, were implicated as potential secondary consumers, while Arcobacteraceae may contribute to sulfur cycling rather than direct DMSP catabolism. This study uncovers a previously overlooked route for DMSP transformation via anaerobic metabolism, expands the known metabolic roles of saltmarsh microorganisms and highlights the potential for DMSP to drive climate-active gas production in anoxic coastal ecosystems.},
}

@article {pmid41216320,
year = {2025},
author = {González-Rosales, C and Rezaei Somee, M and Buck, M and Bertilsson, S and Mehrshad, M and Dopson, M},
title = {A global deep terrestrial biosphere core microbiome.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf176},
pmid = {41216320},
issn = {2730-6151},
abstract = {The deep biosphere encompasses life beneath the Earth's surface and constitutes a substantial portion of the planet's microbial biomass. This study analyzed nucleic acid datasets from low-carbon and low-energy deep terrestrial subsurface groundwaters across four continents and revealed four core global populations. These populations exhibited metabolic strategies and adaptations reflecting depth and environmental constraints. Erythrobacter featured heterotrophic metabolism; Thiobacillus demonstrated sulfur oxidation coupled to denitrification along with carbon and nitrogen fixation; Methanobacteriaceae were methanogenic autotrophs using the Wood-Ljungdahl pathway (WL); and Candidatus Desulforudis audaxviator functioned as a sulfate-reducer also encoding the WL pathway. Depth-related adaptations suggested heterotrophic dominance at shallower depths with increasing contributions from autotrophy with depth. Finally, comparative genomics revealed minimal evolutionary changes among these populations, suggesting functional conservation since diverging from their ancestral lineages. These findings underscore a global deep biosphere core community.},
}

@article {pmid41216181,
year = {2025},
author = {Song, Z and Huang, T and Jiang, X and Hu, M and Wu, H and Wang, J},
title = {A case report of Staphylococcus saccharolyticus bloodstream infection in a non-implanted host diagnosed by mNGS: Mechanism and pathogenesis analysis.},
journal = {IDCases},
volume = {42},
number = {},
pages = {e02408},
pmid = {41216181},
issn = {2214-2509},
abstract = {BACKGROUND: Staphylococcus saccharolyticus is an obligate anaerobic skin commensal that is rarely implicated in bloodstream infections, particularly in immunocompetent individuals without implanted medical devices. Due to its low virulence and fastidious growth requirements, it is often overlooked or dismissed as a contaminant. This report describes a rare case of S. saccharolyticus bacteremia and explores the underlying pathogenic mechanism.

CASE PRESENTATION: A 50-year-old immunocompetent female presented with recurrent low-grade fever and oral mucosal ulceration. Pathogen detection was performed using plasma-based metagenomic next-generation sequencing (mNGS), which identified S. saccharolyticus at a relative abundance of 15 % (seven species-specific reads). The result was corroborated by anaerobic blood culture. Laboratory assessment revealed severe vitamin D deficiency (25-hydroxyvitamin D: 11.6 ng/mL). Initial treatment with ceftriaxone was ineffective. Following the initiation of intravenous moxifloxacin and oral vitamin D supplementation (cholecalciferol 2000 IU/day), the patient's fever resolved within five days, and high-sensitivity C-reactive protein (hsCRP) levels decreased markedly from 88.3 mg/L to 12.0 mg/L. Mechanistically, the combination of mucosal barrier disruption due to oral ulceration and vitamin D deficiency may have facilitated translocation of the anaerobic pathogen into the bloodstream.

CONCLUSIONS: This case underscores the diagnostic value of mNGS in detecting low-biomass anaerobic infections and proposes a synergistic "mucosal barrier disruption-pathogen translocation" model. It also highlights the potential role of host-directed adjunctive therapy in managing bloodstream infections not associated with prosthetic material.},
}

@article {pmid41215794,
year = {2025},
author = {Onile-Ere, O and Name, PE and Tibiri, EB and Tiendrébéogo, F and Pita, J and Mohammed, IU and Nkere, CK and Oranusi, S and Eni, A},
title = {Dataset of rolling circle amplification (RCA) enriched metagenome of Cassava obtained through nanopore sequencing.},
journal = {Data in brief},
volume = {63},
number = {},
pages = {112204},
pmid = {41215794},
issn = {2352-3409},
abstract = {The dataset presented here was obtained by sequencing selected historic herbarium cassava samples collected across Nigeria. Total DNA was extracted from the samples using the CTAB method, after which the samples were enriched by Rolling Circle Amplification (RCA) and then sequenced on the MinION. The dataset consists of raw sequencing data in FASTQ format reflecting microbial diversity in cassava leaf samples. Taxonomic classification of the samples using the Kraken2 PlusPFP-16 database revealed 12 kingdoms, 36 phyla, 67 classes, 154 orders, 273 families, 524 genera, and 895 species across the dataset, with a substantial proportion (77.9%) of reads remaining unclassified following host removal. The data is beneficial for exploring the microbiome diversity of cassava leaves across Nigeria, as well as serving as a reference for future microbial discovery, given the large number of unidentified reads in the dataset.},
}

@article {pmid41214992,
year = {2025},
author = {Li, C and Yang, F and Han, Y and Yang, C and Qin, X and Zheng, H and Chen, L and Lu, J and Zhang, C and Lu, F and Wang, L},
title = {Aldehyde metabolism in Maotai-flavor Baijiu: insights from integrated metagenomic and metaproteomic analyses.},
journal = {Food research international (Ottawa, Ont.)},
volume = {221},
number = {Pt 3},
pages = {117518},
doi = {10.1016/j.foodres.2025.117518},
pmid = {41214992},
issn = {1873-7145},
abstract = {Acetaldehyde and acetal are crucial to the flavor of Maotai-flavor Baijiu, affecting aroma release and sauce-aroma traits. Targeted control of acetaldehyde metabolic flux is critical for stabilizing base liquor quality. However, the diversity of acetaldehyde-metabolizing enzymes and their microbial drivers remain uncharacterized, critically impeding precision control. This study selected the third production round to systematically investigate acetaldehyde accumulation dynamics and metabolic mechanisms. Time-resolved profiling showed that acetaldehyde and acetal concentrations display an initial rise, followed by a decline and stabilization. By integrated metagenomic and metaproteomic analyses, we confirmed that the metabolic network comprised two biosynthetic and three conversion pathways. The dominant biosynthetic pathway featured pyruvate decarboxylase (PDC)-catalyzed decarboxylation, while ethanolamine ammonia-lyase contributed minimally. Among conversion pathways, NADH-dependent alcohol dehydrogenase (NADH-ADH) reduction to ethanol predominated, with lower-flux oxidation to acetate and acetyl-CoA. Dynamic enzyme profiling revealed that PDC activity preceded the activation of NADH-ADH during stacking fermentation, resulting in a temporal mismatch between aldehyde production and consumption, which led to metabolic retention. During pit fermentation, acetaldehyde was more efficiently converted to ethanol through upregulation of NADH-ADH and NADH/NAD[+] ratio. As main contributors of PDC and NADH-ADH, Schizosaccharomyces pombe and Saccharomyces cerevisiae exhibited dual regulatory roles in acetaldehyde metabolism, with their metabolic mode shifts governed by dissolved oxygen and the NADH/NAD[+] ratio. Microbial interaction analysis and simulated fermentation confirmed that Pichia kudriavzevii synergized with Saccharomyces cerevisiae and Schizosaccharomyces pombe, driving rapid acetaldehyde accumulation during the stacking fermentation. These findings establish a theoretical framework for optimizing brewing processes and enhancing base liquor quality.},
}

@article {pmid41214941,
year = {2025},
author = {Kahraman Ilıkkan, Ö and Cerit, ZG and Baloglu, MC and Yılmaz, R},
title = {Microbial monitoring and Resistome analysis in white cheese production at a dairy plant: MALDI-TOF MS and shotgun metagenomics approaches.},
journal = {Food research international (Ottawa, Ont.)},
volume = {221},
number = {Pt 3},
pages = {117432},
doi = {10.1016/j.foodres.2025.117432},
pmid = {41214941},
issn = {1873-7145},
abstract = {This study presents a comprehensive microbiological evaluation of white cheese production in a small-scale dairy facility in northern Türkiye, integrating culture-dependent and culture-independent methods. Ten samples, including raw milk, milk with starter culture added, curd, clot, final cheese product, and environmental samples such as milk truck, cheese vessel, stirrer, cutting wire, and cheesecloth, were analyzed. Pathogenic bacteria were identified using MALDI-TOF MS, while shotgun metagenomics enabled a detailed investigation of microbial communities, antibiotic resistance genes (ARGs), and functional properties. The analysis using MALDI-TOF MS revealed ten pathogenic species, among which Staphylococcus aureus and Escherichia coli were the most dominant. Shotgun metagenomics corroborated the prevalence of S. aureus in dairy samples and Salmonella spp. on equipment surfaces, particularly the cheese vessel, stirrer, and cutting wire. The highest E. coli contamination was detected on cheesecloth, underscoring a critical point of concern. Across 15 antibiotic classes, 974 ARGs were identified, with equipment samples harboring significantly higher ARG loads than dairy products. Resistance mechanisms included β-lactamase enzymes, RND efflux pumps, and ribosomal protection proteins. Equipment samples showed an enrichment of carbohydrate-active enzymes (CAZymes), notably glycoside hydrolases and glycosyl transferases, suggesting microbial biofilm development and increased spoilage potential. Functional gene profiling revealed distinct metabolic signatures between dairy and equipment samples, with enriched pathways related to virulence and antimicrobial resistance in environmental samples. These findings underscore the limitations of conventional thermal treatment and the necessity of stringent sanitation practices, particularly for reusable equipment such as cheesecloth. The combined use of MALDI-TOF MS and shotgun metagenomics offers an effective strategy for microbial risk assessment in traditional cheese production systems.},
}

@article {pmid41214546,
year = {2025},
author = {Su, YS and Tsai, WH and Wu, HC and Chiu, YT and Jiang, NR and Lee, CY and Cheng, SH and Huang, CT and Chi, CY and Lin, EJ and Kuo, YP and Tsai, WT and Tien, CF and Liao, YC and Lee, KL and Chen, FJ and Yu, GY},
title = {Multiplex metagenomic sequencing for rapid viral pathogen identification and surveillance in clinical specimens.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {1531},
pmid = {41214546},
issn = {1471-2334},
abstract = {BACKGROUND: Rapid and accurate viral detection is essential for clinical diagnosis and effective outbreak surveillance. Traditional methods, including culture-based isolation and antigen tests, are time-consuming and limited by tissue tropism. Multiplex PCR panels, although faster, are constrained by predefined targets, limiting their ability to detect novel or unexpected viral strains.

METHODS: We applied Oxford Nanopore Technology sequencing (ONT-Seq), a long-read, real-time, and multiplex metagenomic platform, to 85 clinical specimens using a sequence-independent, single-primer amplification (SISPA) workflow. Sequencing results were compared with routine clinical diagnostics for concordance and for identification of co-infections RESULTS: ONT-Seq achieved 80% concordance with clinical diagnostics and identified co-infections in 7% of cases missed by routine testing, including influenza C virus (ICV), and Sapporovirus. Among 58 adenovirus-positive cases, 31 samples with over 80% genome coverage at 20× depth were used for phylogenetic analysis, revealing adenovirus B3 as the predominant circulating strain.

CONCLUSIONS: ONT-based metagenomic sequencing enhances the detection of both known and emerging viruses in clinical specimens. Its ability to provide real-time, unbiased data supports its utility in improving diagnostic accuracy and viral surveillance.

CLINICAL TRIAL: Not applicable.},
}

@article {pmid41212644,
year = {2025},
author = {Acosta, DJ and Barth, DR and Bondy, J and Appler, KE and De Anda, V and Ngo, PHT and Alper, HS and Baker, BJ and Marcotte, EM and Ellington, AD},
title = {Plastic degradation by enzymes from uncultured deep sea microorganisms.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
pmid = {41212644},
issn = {1751-7370},
abstract = {Polyethylene terephthalate (PET)-hydrolyzing enzymes (PETases) are a recently discovered enzyme class capable of plastic degradation. PETases are commonly identified in bacteria; however, pipelines for discovery are often biased to recover highly similar enzymes. Here, we searched metagenomic data from hydrothermally impacted deep sea sediments in the Guaymas Basin (Gulf of California) for PETases. A broad diversity of potential proteins were identified and 22 were selected based on their potential thermal stability and phylogenetic novelty. Heterologous expression and functional analysis of these candidate PETases revealed three candidates capable of depolymerizing PET or its byproducts. One is a PETase from a Bathyarchaeia archaeon (dubbed GuaPA, for Guaymas PETase Archaeal) and two bishydroxyethylene terephthalate-hydrolyzing enzymes (BHETases) from uncultured bacteria, Poribacteria, and Thermotogota. GuaPA is the first archaeal PETase discovered that is able to depolymerize PET films and originates from a specific enzyme class which has endowed it with predicted novel structural features. Within 48 h, GuaPA released ~3-5 mM of terephthalic acid and mono-(2-hydroxyethyl) terephthalate from low crystallinity PET. PET co-hydrolysis containing GuaPA and one of the newly discovered BHETases further improves the hydrolysis of untreated PET film by 68%. Genomic analysis of the PETase- and BHETase-encoding microorganisms reveals that they likely metabolize the products of enzymatic PET depolymerization, suggesting an ecological role in utilizing anthropogenic carbon sources. Our analysis reveals a previously uncharacterized ability of these uncultured microorganisms to catabolize PET, suggesting that the deep ocean is a potential reservoir of biocatalysts for the depolymerization of plastic waste.},
}

@article {pmid41212311,
year = {2025},
author = {Slobodkin, AI and Rusanov, II and Slobodkina, GB and Chernyh, NA and Stroeva, AR and Merkel, AY},
title = {A culture-independent study of the structure, functions and methane oxidation activity of microbial communities of geothermal springs in Dagestan.},
journal = {Extremophiles : life under extreme conditions},
volume = {29},
number = {3},
pages = {42},
pmid = {41212311},
issn = {1433-4909},
abstract = {Microbial communities inhabiting geothermal springs in the Republic of Dagestan, Russia, have not been studied by culture-independent methods. We have investigated the taxonomic composition, metabolic potential and rates of methane oxidation of microbial communities in two geothermal springs with methane emission (Artuzen and Miatli) located in Dagestan. Methane oxidation rates measured by the radiotracer technique varied from 3.7 to 96.5 nmol CH4 cm[- 3] day[- 1]. 16S rRNA gene amplicon sequencing indicates that in the Artuzen hot springs (54 °C), with a salinity of 2.5%, the primary production of organic matter is performed by mesophilic cyanobacteria, while in the freshwater Miatli hot springs (58 °C) primary producers are thermophilic cyanobacterium Thermosynechococcus and photosynthetic members of Chloroflexi. Analysis of metabolic capabilities of the metagenome assembled genomes in one of Artuzen samples shows that anaerobic bacteria belonging to Anaerolineae and Marinisomatota are the key decomposers of complex organic substances. The main terminal electron-accepting process in the sediment is acetoclastic methanogenesis carried out by the genus Methanocrinis. The presence of "Candidatus Methanospirareceae" (ANME-1) suggests the involvement of anaerobic archaea in methane oxidation. Thus, our study extends the current knowledge of the phylogenetic and metabolic diversity and activity of the prokaryotes inhabiting terrestrial hydrothermal environments.},
}

@article {pmid41211992,
year = {2025},
author = {Wang, Y and Tian, F and Zhang, J and Xu, S and Li, M and Tong, Y},
title = {Identification and characterization of a novel plaque-invisible lytic single-stranded RNA phage.},
journal = {Journal of virology},
volume = {},
number = {},
pages = {e0163724},
doi = {10.1128/jvi.01637-24},
pmid = {41211992},
issn = {1098-5514},
abstract = {The RNA phages offer promising applications in biotechnology, including vaccine development and drug delivery. However, their potential remains underexplored due to the limited number of known RNA phages, partly because conventional methods fail to identify plaque-invisible lytic phages that do not form plaques. Here, we introduced a novel method that combines RNA-inclusive metagenomic studies and quantitative reverse transcription-PCR (RMS-RT-qPCR) to identify and characterize active RNA phages from environmental samples. This study led to the discovery of a new active Qbeta-like phage, named Cute. Genomic analysis revealed that Cute is a new member of the Qubevirus genus. Although Cute does not form plaques, it can be observed to continuously release into the supernatant when co-cultured with the host by RT-qPCR detection. This discovery underscores the potential diversity of RNA phages in nature and the limitations of traditional culture-dependent techniques. Our findings suggest that RMS-RT-qPCR could aid in the discovery of active RNA phages with significant biotechnological applications.IMPORTANCEThe discovery and characterization of RNA phages might be historically constrained by traditional culture-based methods. Our study provides a powerful tool for identifying active RNA phages by combining RNA-inclusive metagenomic analysis with RT-qPCR. This method expands our understanding of the diversity and ecological roles of RNA phages, which are often overlooked in microbiome studies. This research highlights the importance of RNA phages in natural ecosystems and their potential applications in biotechnology and medicine, such as antimicrobial therapies and vaccine development. By expanding our understanding of RNA phage diversity, this study opens new avenues for their utilization in various fields, emphasizing the need for continued exploration of these versatile biological entities.},
}

@article {pmid41211985,
year = {2025},
author = {Hypša, V and Martinů, J and Mahmood, S and Gupta, S and Nováková, E and Roth, S and Balvín, O},
title = {Dynamic but constrained: repeated acquisitions of nutritional symbionts in bed bugs (Heteroptera: Cimicidae) from a narrow taxonomic pool.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0124725},
doi = {10.1128/msystems.01247-25},
pmid = {41211985},
issn = {2379-5077},
abstract = {Bed bugs (Heteroptera: Cimicidae) harbor obligate bacterial symbionts that supplement their blood diet with missing nutrients, especially B vitamins. The primary symbiont, transovarially transmitted Wolbachia, is notable for a horizontally acquired biotin operon. Additional maternally inherited bacteria, including Symbiopectobacterium and Tisiphia, have been detected but are considered facultative and nonessential. However, nearly all current knowledge is derived from the human-associated Cimex lectularius, leaving symbiont diversity across more than 100 bed bug species largely unknown. Using amplicon and metagenomic data, we identified Wolbachia, Symbiopectobacterium, Sodalis, Serratia, and Tisiphia as candidate symbionts, with at least 16 independent acquisition events across the cimicid species, sometimes involving multiple strains per host. Phylogenetic comparisons indicated that some of these origins were followed by cospeciation. Wolbachia was present in most hosts except Cacodminae, where Symbiopectobacterium occurred as the sole symbiont, suggesting its obligate role. Analysis of 23 draft genomes revealed heterogeneity in size and gene content, consistent with varying stages of symbiotic reduction. Most lineages lost many biosynthetic pathways; only riboflavin and lipoic acid synthesis remained universally conserved. Our survey reveals a dynamic evolution of bed bug symbioses, with repeated symbiont acquisitions, cospeciation, and frequent coinfections. Despite independent origins, most symbionts belong to Wolbachia, Symbiopectobacterium, or Sodalis, implying unknown mechanisms shaping host specificity. Two points merit further study. First, Symbiopectobacterium as the sole obligate symbiont in Cacodminae suggests broader sampling may uncover greater symbiotic diversity. Second, uncertainties in biotin synthesis function call for deeper investigation into the evolution of this pathway in symbiotic bacteria.IMPORTANCEBed bugs are obligate blood-feeding insects that depend on bacterial partners to supply nutrients missing from their diet. Most previous research has focused on the human-associated species Cimex lectularius, leaving little known about symbiont diversity across other species. By surveying a broad phylogenetic range, we found that bed bugs have repeatedly acquired different bacteria as symbionts, including lineages not previously recognized as essential. Notably, finding Symbiopectobacterium as the sole symbiont in one subfamily shows that the nutritional partnerships in bed bugs are more dynamic than previously thought. At the same time, the majority of the 16 independent acquisitions involve only four bacterial genera, suggesting efficient mechanisms that constrain and shape bed bug-symbiont specificity.},
}

@article {pmid41211947,
year = {2025},
author = {Calvez, E and Quétel, I and Saint-Alban, L and Gutiérrez-Bugallo, G and Dollin, C and Ramdini, C and Vega-Rúa, A},
title = {Contrasted impacts of commercial diets and rearing water on Aedes aegypti fitness and microbiota.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0054325},
doi = {10.1128/msphere.00543-25},
pmid = {41211947},
issn = {2379-5042},
abstract = {Mosquito rearing optimization in laboratory conditions is crucial for both vector research and control. Although the addition of nutrients is important for Aedes aegypti development from immature stages to adult mosquitoes, little is known about the nutrient composition of commercial diets used for mosquito rearing and their influence on Ae. aegypti life traits. Here, we evaluated the influence of four commercial diets commonly used to rear Ae. aegypti in the laboratory on its fitness, lifespan, and microbiota. We also compared the effect of these diets on this mosquito when combined with two different rearing waters (laboratory versus field-collected waters). Our investigations demonstrated that higher levels of protein and lipid in commercial diets promote better Ae. aegypti development, lifespan, and size in both water. Metagenomic analysis revealed specific modulations of adult microbiota composition according to both diet and rearing water. Chryseobacterium dominated the microbiota of female mosquitoes reared in laboratory water, except for yeast condition, where a more diverse microbiota was observed. When reared in larval site water, the microbiota diversity was overall higher despite diet addition, except for fish food, which promoted Sphingobacterium dominance. Given the pivotal influence of diet addition during the larval stage on Ae. aegypti microbiota and life traits, rearing conditions should be carefully chosen according to the goals of the research (i.e., vectorial capacity estimations) or vector control intervention.IMPORTANCEAedes aegypti is the main vector of arbovirus, such as dengue, yellow fever, and chikungunya viruses. Vector research and control are primarily carried out in laboratories, with larval stage rearing conducted using commercial diet. If many nutrients are essential for Ae. aegypti development, gaining insight into the influence of these diets and their nutrient levels is important to promote optimized rearing worldwide. In this study, our results indicated a significant impact of commercial diet on Ae. aegypti development, lifespan, size, and microbiota related to contrasted protein, lipid, and carbohydrate levels in these diets. This study will help people working with Ae. aegypti raise awareness in staff working with Ae. aegypti to select optimized diets for their specific purpose.},
}

@article {pmid41211940,
year = {2025},
author = {Roberts, WR and Parks, M and Ashner, M and Ashworth, MP and Denne, N and Ruck, EC and Spiliotopoulos, E and Wang, A and Amin, SA and Schaack, S and Wickett, NJ and Alverson, AJ},
title = {Reference genome for the benthic marine diatom Psammoneis japonica: Bacterial associations and repeat-driven genome size evolution in diatoms.},
journal = {Journal of phycology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpy.70101},
pmid = {41211940},
issn = {1529-8817},
support = {1150213//Division of Molecular and Cellular Biosciences/ ; 1353131//Division of Environmental Biology/ ; 1353152//Division of Environmental Biology/ ; 2331644//Division of Environmental Biology/ ; 2336342//Division of Environmental Biology/ ; },
abstract = {We sequenced the genome, transcriptome, and bacterial metagenome of Psammoneis japonica, a benthic, chain-forming, and araphid marine diatom. This combination of traits fills several gaps in genome sequencing coverage across diatoms. The nuclear genome (QPGO00000000) is an estimated 91.4 Mb in length, with 11,047 genes that comprise 18% of the total genome. Repetitive elements account for 33% of the genome, and other noncoding sequences comprise the remaining 49% of the genome. A global analysis of diatom genomes showed that repetitive elements are the principal driver of genome size variation in diatoms. Four complete genomes of Planctomycetota, ɑ-proteobacteria, and Bacteroidota were also recovered, and each had only moderate similarity to previously sequenced bacterial genomes. This finding supports the idea that bacterial species richness in the phycosphere is under-described and far exceeds the number of diatom host species, which themselves number in the tens to hundreds of thousands of species.},
}

@article {pmid41211921,
year = {2025},
author = {Wang, Q and Bao, H},
title = {Integrated metagenomics and metabolomics reveal the dynamic mechanism in the rhizosphere soil of Morus alba L. and Fraxinus mandshurica Rupr. with Inonotus hispidus.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0125125},
doi = {10.1128/aem.01251-25},
pmid = {41211921},
issn = {1098-5336},
abstract = {Inonotus hispidus is a medicinal fungus that grows on Morus alba L., Fraxinus mandshurica Rupr., and Ziziphus jujuba Mill. However, there have been no reports on the comparative study of microbial diversity and metabolites in the rhizosphere soil of different tree species, specifically M. alba and F. mandshurica, growing with I. hispidus. Therefore, this study conducts a multi-omics joint analysis utilizing metagenomics and metabolomics to explore the differences in the synergistic mechanisms between different hosts of I. hispidus. Using metagenomics technology, a total of 177 phyla and 2,651 genera were identified as significantly different. At both the phylum and genus levels, Actinomycetota and Pseudomonadota as well as Solirubrobacter and Bradyrhizobium emerged as the predominant phyla and genera, respectively. In the Kyoto Encyclopedia of Genes and Genomes database, carbohydrate and amino acid metabolisms were identified as the primary metabolic pathways. Differential analysis of these metabolic pathways revealed that glucokinase and pyruvate kinase were downregulated. Additionally, metabolomics analysis identified 558 differential metabolites, with tyrosine metabolism being the foremost metabolic pathway involved. This pathway included five differential metabolites, among which salidroside, 3,4-dihydroxyphenylpropanoate, rosmarinate, and homovanillate were significantly upregulated in M. alba in association with I. hispidus. Furthermore, correlation analysis indicated that Enhydrobacter was positively correlated with 10 differential metabolites, while Gaiella, Haladaptatus, Jiangella, and Prauserella showed negative correlations. This study lays a solid foundation for elucidating the interactions between I. hispidus and its hosts, as well as for the effective utilization of I. hispidus resources across different tree species.IMPORTANCEInonotus hispidus, which is traditionally recognized as the authentic source of the medicinal fungus, primarily grows on Morus alba L. It is commonly found in ancient regions along the Yellow River, including Linqing, Xiajin, and Wudi in Shandong, as well as Chengde in Hebei Province and Aksu in Xinjiang. In traditional Chinese medicine, it is known as "Sanghuang" and has a long history of medicinal use. In addition to M. alba, I. hispidus also grows on other broad-leaved species, such as Ulmus macrocarpa, Acer truncatum, and Fraxinus mandshurica. The lack of fundamental research on its multi-host and -source diversity has hindered its industrial development and medicinal value. Consequently, this study employs metagenomics and metabolomics to investigate the rhizosphere soil microbial diversity and differential metabolites associated with the different host plants of I. hispidus, specifically M. alba and F. mandshurica, with the aim of providing a reference for its resource conservation and development.},
}

@article {pmid41211880,
year = {2025},
author = {Duan, C and Zang, Z and Xu, Y and He, H and Li, S and Liu, Z and Lei, Z and Zheng, JS and Li, SZ},
title = {FGeneBERT: function-driven pre-trained gene language model for metagenomics.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {6},
pages = {},
doi = {10.1093/bib/bbaf592},
pmid = {41211880},
issn = {1477-4054},
support = {2022ZD0115101//National Science and Technology Major Project/ ; U21A20427//National Natural Science Foundation of China/ ; WU2022A009//National Natural Science Foundation of China/ ; WU2023C019//Center of Synthetic Biology and Integrated Bioengineering of Westlake University/ ; //InnoHK program and Ant Group through CAAI-Ant Research Fund/ ; },
abstract = {Metagenomic data, comprising mixed multi-species genomes, are prevalent in diverse environments like oceans and soils, significantly impacting human health and ecological functions. However, current research relies on K-mer, which limits the capture of structurally and functionally relevant gene contexts. Moreover, these approaches struggle with encoding biologically meaningful genes and fail to address the one-to-many and many-to-one relationships inherent in metagenomic data. To overcome these challenges, we introduce FGeneBERT, a novel metagenomic pre-trained model that employs a protein-based gene representation as a context-aware and structure-relevant tokenizer. FGeneBERT incorporates masked gene modeling to enhance the understanding of inter-gene contextual relationships and triplet enhanced metagenomic contrastive learning to elucidate gene sequence-function relationships. Pre-trained on over 100 million metagenomic sequences, FGeneBERT demonstrates superior performance on metagenomic datasets at four levels, spanning gene, functional, bacterial, and environmental levels and ranging from 1 to 213 k input sequences. Case studies of ATP synthase and gene operons highlight FGeneBERT's capability for functional recognition and its biological relevance in metagenomic research.},
}

@article {pmid41211879,
year = {2025},
author = {},
title = {Retraction and replacement of: FGeneBERT: function-driven pre-trained gene language model for metagenomics.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {6},
pages = {},
doi = {10.1093/bib/bbaf591},
pmid = {41211879},
issn = {1477-4054},
}

@article {pmid41210936,
year = {2025},
author = {Xu, Y and Miao, J and Chen, J and Ye, L and Yang, K and Wang, H},
title = {Metagenomic next-generation sequencing facilitates precision treatment and prognostic improvement in pulmonary cryptococcosis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1638215},
pmid = {41210936},
issn = {2235-2988},
abstract = {BACKGROUND: The early diagnosis of pulmonary cryptococcosis (PC) remains challenging due to the low sensitivity and prolonged turnaround time of conventional diagnostic methods. Despite the broad-spectrum pathogen detection capability of metagenomic next-generation sequencing (mNGS), its clinical utility in the diagnosis and therapeutic management of pulmonary cryptococcosis remains underexplored.

METHODS: In this retrospective study, 31 patients diagnosed with Cryptococcus infection through mNGS at The First Affiliated Hospital of Zhengzhou University between July 2023 to March 2025 were included. data on clinical characteristics, treatment regimens, and patient prognosis were systematically collected.

RESULTS: Compared to conventional pathogen detection methods, mNGS demonstrated superior sensitivity, shorter turnaround time (1.00 d vs. 4.50 d, p = 0.002), and significantly reduced interval from admission to clinical decision-making (3.50 d vs. 9.00 d, p = 0.002). Among 31 patients with mNGS-identified cryptococcal infection, only 12 underwent fungal culture, with merely 1 case yielding positive results (positivity rate: 8.33%). Antimicrobial therapy was optimized for all patients based on mNGS findings. During post-discharge follow-up of 27 cases, 1 patient experienced disease recurrence, 1 died from tumor metastasis, and 1 was lost to follow-up.

CONCLUSION: Our retrospective analysis revealed that mNGS facilitated treatment optimization, improved clinical outcomes, and provided crucial evidence supporting the precision management of pulmonary cryptococcosis.},
}

@article {pmid41210414,
year = {2025},
author = {Hu, L and Li, S and Gao, F and Diao, S and Liu, X and Qiu, J},
title = {Silent Threat: Multi-Organ Failure in Neonatal Scrub Typhus Without Traditional Markers.},
journal = {Clinical case reports},
volume = {13},
number = {11},
pages = {e71352},
pmid = {41210414},
issn = {2050-0904},
abstract = {Scrub typhus, an acute zoonotic disease from Orientia tsutsugamushi, is uncommon in newborns and presents atypical symptoms. Untimely diagnosis and treatment can lead to a prolonged and potentially fatal course. Early diagnosis and treatment are essential for better patient outcomes. Metagenomic next-generation sequencing can rapidly and accurately diagnose pathogens, aiding precise treatment.},
}

@article {pmid41210074,
year = {2025},
author = {Lin, L and You, W and Liao, Y and Wu, B and Lin, H and Huang, Z and Zeng, J and Zhang, Z and Huang, C and Li, W and Fang, X},
title = {Impact of Antibiotic Exposure Duration on Pathogen Detection in Periprosthetic Joint Infection.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {5661-5670},
pmid = {41210074},
issn = {1178-6973},
abstract = {OBJECTIVE: Antibiotic exposure affects pathogen detection in periprosthetic joint infection (PJI). This study evaluated the impact of antibiotic duration before sampling on the diagnostic performance of microbiological cultures and metagenomic next-generation sequencing (mNGS).

METHODS: We conducted a retrospective analysis of 153 patients with PJI treated at our center between January 2013 and March 2024. Patients who had discontinued antibiotics for at least 7 days before sampling and those with no history of antibiotic use were classified into the antibiotic-withdrawal group (AWD group). Based on the duration of antibiotic exposure, those who received antibiotics for ≤7 days before sampling was assigned to the short-term antibiotic group (STA group), while those with >7 days of continuous antibiotic use were included in the long-term antibiotic group (LTA group). By comparing microbiological culture and mNGS results across these groups, we analyzed how antibiotic duration before sampling affects etiological diagnosis in PJI patients.

RESULTS: In the AWD group, microbial culture positivity (86.3%, 44/51) was comparable to mNGS (92.2%, 47/51; P=0.338). However, mNGS demonstrated superior positivity rates in both the STA (86.7% vs 70.0%, P=0.027) and LTA groups (76.2% vs 54.8%, P=0.039). Prolonged antibiotic use (>7 days) markedly reduced culture positivity (86.3% to 54.8%, P=0.001), whereas the decline in mNGS sensitivity was smaller (92.2% to 76.2%, P=0.032), indicating its greater resistance to antibiotic effects. Among culture-negative PJI cases, mNGS maintained robust diagnostic performance across all groups (CN-AWD: 57.1%; CN-STA: 66.7%; CN-LTA: 57.9%), with no significant differences observed.

CONCLUSION: Antibiotic use before sampling significantly impacts PJI pathogen detection. We recommend either: (1) sampling after ≥7 days without antibiotics, or (2) for patients on prolonged antibiotics (>7 days), combining microbial culture with routine mNGS to improve diagnostic accuracy.},
}

@article {pmid41209715,
year = {2025},
author = {Yadav, P and Kumar, A and Ram, K and Kumar, A and Gupta, RK and Dufossé, L},
title = {Microbial degradation of microplastics: Effectiveness, challenges, and sustainable solutions.},
journal = {Current research in microbial sciences},
volume = {9},
number = {},
pages = {100495},
pmid = {41209715},
issn = {2666-5174},
abstract = {Microplastics (MPs), defined as plastic particles ranging from 1 µm to 5 mm, have emerged as pervasive contaminants in both terrestrial and aquatic environments, posing significant ecological and human health risks. Their sources are broadly categorized as primary, such as microbeads, microfibres, paints and pharmaceutical additives, and secondary, which result from the degradation of larger plastic products. This growing concern of MPs led to development of different mitigation techniques but the recent advancements in microbial biodegradation present a promising approach to mitigating MPs pollution. Thus, microbial biodegradation could play a crucial role in developing sustainable solutions to tackle global MPs pollution. This review explores the potential of various microorganisms, including bacteria, fungi, and algae, in degrading MPs through enzymatic processes, thereby shortening the half-life of these pollutants. A detailed examination of the degradation mechanisms of commonly used polymers such as polyethylene, polystyrene, and polyvinyl chloride highlights the efficacy and limitations of microbial biodegradation. Despite the promising capabilities of certain strains, the overall weight loss rate of MPs remains quite low, typically ranging from 0 to 15%, necessitating further investigation into optimizing enzymatic activity and environmental conditions. Advancements in metagenomics and enzyme engineering offer pathways to enhance degradation efficiency, potentially achieving up to 90% degradation within 10 hrs under optimized conditions. This review underscores the need for comprehensive research to identify key microbial strains and enzymes involved, understand their degradation pathways, and investigate the influence of different environmental matrices on biodegradation processes.},
}

@article {pmid41208101,
year = {2025},
author = {Paul, JK and Akter, A and Jewel, NA and Rolin, MH and Karim, D and Niloy, RK and Mondal, SI},
title = {Exploration of Human Skin Phageome to Reveal Endolysins and Novel Antimicrobial Peptides for Therapeutic Applications.},
journal = {MicrobiologyOpen},
volume = {14},
number = {6},
pages = {e70115},
doi = {10.1002/mbo3.70115},
pmid = {41208101},
issn = {2045-8827},
support = {//The study was supported by the SUST Research Center (Grant number: LS/2023/1/05)./ ; },
abstract = {The global rise of antibiotic-resistant pathogens has intensified the search for alternative therapeutics. Bacteriophage-derived endolysins are emerging as promising candidates. They exhibit strong potential due to their target specificity, rapid bactericidal action, and low tendency to induce bacterial resistance. This study presents a comprehensive metagenomic analysis of the human skin phageome using 1564 samples from 10 metagenomic projects. Our analysis led to the classification of 696 phage genomes into clusters and singletons. These genomes displayed considerable variation in size, GC content (average 56%), and coding efficiency (72%). A total of 968 endolysins were identified, including 75 SAR variants, with diverse domain architectures such as CHAP, Amidase, and SH3, suggesting host-specific adaptations. Notably, we identified 37 previously unreported endolysin-derived antimicrobial peptides (AMPs), several of which exhibited nontoxic, antifungal, and antiviral properties. Molecular dynamics and docking studies revealed strong binding affinity and stability of peptides EP-464 and EP-519 to key virulence factors, including Staphylococcus epidermidis autolysin (PDB: 4EPC), beta-lactamase VIM-2 (PDB: 5O7N), and AHL synthase LasI (PDB: 1RO5). These interactions suggest potential for disrupting bacterial virulence, resistance mechanisms, and quorum sensing. This study provides the first large-scale functional characterization of the human skin phageome focused on therapeutic endolysins and their novel AMP derivatives, offering promising candidates for the development of next-generation antimicrobial agents. However, further experimental validation is essential to assess their clinical efficacy in treating skin-related infections.},
}

@article {pmid41207803,
year = {2025},
author = {You, TY and Chen, YW and Chen, SY and Jan, HE and Lee, NY and Ko, WC},
title = {Etiological identification of Rickettsia typhi and Coxiella burnetii by metagenomic next-generation sequencing among adults with acute febrile illness in southern Taiwan.},
journal = {Journal of the Formosan Medical Association = Taiwan yi zhi},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jfma.2025.11.012},
pmid = {41207803},
issn = {0929-6646},
}

@article {pmid41207298,
year = {2025},
author = {Zhai, Z and Che, X and Shen, W and Zhang, Z and Li, Y and Pan, J},
title = {HLRMDB: a comprehensive database of the human microbiome with metagenomic assembly, taxonomic classification, and functional annotation by analysis of long-read and hybrid sequencing data.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkaf1152},
pmid = {41207298},
issn = {1362-4962},
support = {32470699//National Natural Science Foundation of China/ ; //Chongqing Medical University/ ; },
abstract = {The human microbiome harbours an immense diversity of uncultivated microbes; short-read metagenomic sequencing has elucidated much of this diversity, but fragment repeats and mobile elements constrain strain-level resolution. Fortunately, long-read metagenomic sequencing can generate reads spanning tens of kilobases with single-molecule accuracies exceeding 99%, enabling near-complete genome and gene cluster recovery in a cultivation-independent manner. However, systematic resources that aggregate and standardise long-read outputs remain limited. Here, we present HLRMDB (http://www.inbirg.com/hlrmdb/), a comprehensive database of human microbiome datasets derived from long-read and hybrid metagenomic sequencing. We curated 1672 publicly available metagenomes (1291 long reads; 381 hybrids) spanning 38 studies, 39 sampling contexts and 42 host health states. A uniform assembly and binning pipeline reconstructed >98 Gb of contigs and yielded 18 721 metagenome-assembled genomes (MAGs). These MAGs span 21 phyla and 1323 bacterial species, with 6339 classified as near-complete and 5609 as medium-quality. HLRMDB integrates these genome-resolved data with extensive gene-centric functional profiles and antimicrobial resistance annotations. An interactive web interface supports flexible access to both sample-level and genome-level results, with multiple visualisations linking raw reads to assembled genomes. Overall, HLRMDB offers a harmonised, long-read-oriented repository that supports reproducible, strain-resolved comparative genomics and context-sensitive ecological investigations of the human microbiome.},
}

@article {pmid41207243,
year = {2025},
author = {Kumalo, PC and Amoah, ID and Pierneef, RE and Ismail, A and Bux, F and Kumari, S},
title = {Unveiling the role of aeration systems in the bioaerosol emission rate, particle size and microbial composition from wastewater treatment plants.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140394},
doi = {10.1016/j.jhazmat.2025.140394},
pmid = {41207243},
issn = {1873-3336},
abstract = {Wastewater treatment plants (WWTPs) are important sources of bioaerosols; however, the influence of aeration on emission characteristics, particle size distribution, and microbial composition remains poorly studied. This study investigates how surface aeration (SA) and diffused aeration (DA) systems affect bioaerosol emission rates, particle size distribution, and microbial diversity using an 8-stage Andersen cascade impactor and shotgun metagenomics. Bioaerosol emission rates were estimated by combining measured particle concentrations with system-specific airflow rates. Abiotic factors were analysed through redundancy analysis to determine their influence on community structure. SA consistently generated higher emission rates, particularly in respirable particles (0.43-2.1 µm), which are capable of deep respiratory deposition. Dominant taxa included Rhodococcus, Pseudomonas, Bacillus, Meyerozyma, and Siphoviridae, with SA showing higher relative abundance of opportunistic pathogens even in smaller particle sizes. In contrast, DA systems exhibited a lower emission rate but broader microbial diversity, reflecting more stable aeration conditions. The study indicated that activated sludge was the main source of microbial populations, with a larger bioaerosol -activated sludge overlap in SA than DA. Redundancy analysis revealed that wind speed (WS) and relative humidity (RH) significantly influenced bacterial and viral populations, while WS and air temperature (AT) affected eukaryotes. Notably, SA emissions decreased with distance (100 m), while DA emissions increased. By quantifying emission rates rather than concentrations and integrating high-throughput metagenomics, this study provides a comprehensive framework for characterising bioaerosol hazards in WWTPs. These findings highlight the need for mitigation strategies in WWTPs, especially near SA systems.},
}

@article {pmid41207031,
year = {2025},
author = {Ren, Y and Li, Y and Lei, Y and He, R and Fu, J and Ma, D and Zhong, G},
title = {Deciphering microbial and metabolite dynamics in rice noodle fermentation: A metagenomic and untargeted metabolomic approach.},
journal = {Food chemistry},
volume = {497},
number = {},
pages = {147011},
doi = {10.1016/j.foodchem.2025.147011},
pmid = {41207031},
issn = {1873-7072},
abstract = {Inoculated fermentation accelerates rice noodle production and improves quality, but the underlying microbe-metabolite dynamics remain unclear. This study employed metagenomic and non-targeted metabolomic profiling to investigate microbial succession and metabolic transformations during fermentation. Lacticaseibacillus rhamnosus, Lactococcus cremoris, and Saccharomyces cerevisiae were identified as dominant strains, with Lacticaseibacillus rhamnosus rapidly outcompeting other microbes and suppressing Klebsiella pneumoniae and Salmonella enterica by over 70 %. At 6 h, rice noodle hardness and springiness improved markedly, driven by microbial shifts and metabolic outputs. Metabolomic analysis identified 1405 metabolites, of which 57 showed significant changes: aspartic and citric acid levels declined by 14.99 % and 33.16 %, while citrulline, γ-aminobutyric acid, lactate, and Cinnamic acid increased by 16.38 %, 8.96 %, 70.69 %, and 63.90 %, respectively. Enzyme annotation indicated α-amylase and glycogen synthase regulate starch degradation and amylose synthesis. These findings provide insights into the microbial and metabolic mechanisms that enhance the quality of fermented rice noodles.},
}

@article {pmid41206939,
year = {2025},
author = {Yu, H and Xu, Y and Chen, D and Gong, M and Sun, W and Liu, M and Zhang, T and Xue, J},
title = {The application of mNGS of bronchoalveolar lavage fluid in dissecting pulmonary infections in patients with CTD-ILD.},
journal = {Rheumatology (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/rheumatology/keaf571},
pmid = {41206939},
issn = {1462-0332},
abstract = {OBJECTIVES: To evaluate the application of metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) in the diagnosis of pulmonary infection in patients with connective tissue disease-associated interstitial lung disease (CTD-ILD).

METHODS: Patients with CTD-ILD who had been evaluated for suspected pulmonary infection by mNGS of BALF were identified, and were then categorized either as pulmonary infection or non-infectious disease progression of CTD-ILD based on clinical composite assessment. The performance of mNGS in the diagnosis of pulmonary infection was compared with that of conventional microbiological tests (CMTs).

RESULTS: In the 48 patients with CTD-ILD who had been evaluated for pulmonary infection by mNGS of BALF, the majority (66.67%) were patients with idopathic inflammatory myopathy-associated ILD (IIM-ILD). According to the clinical composite assessment, 36 patients were classified as pulmonary infection and 12 as non-infectious disease progression. Cytomegalovirus (CMV), pneumocystis jirovecii, and aspergillus were among the most common causative pathogens. While mNGS was superior in identifying bacteria, viruses, and pneumocystis jirovecii, CMTs identified more aspergillus and cryptococcus. Decreased albumin, reduced immunoglobulin M, and increased lactate dehydrogenase (LDH) were predictors for pulmonary infections in CTD-ILD. Short disease duration, decreased lymphocytes, and reduced immunoglobulins were predictive of infection with pneumocystis jirovecii. Older age and increased serum ferritin were more common in patients with aspergillus infection.

CONCLUSION: Pulmonary infections are common in patients with CTD-ILD. mNGS has the advantages of rapidly detecting more bacteria, viruses, and pneumocystis jirovecii. However, infection with aspergillus should be more rigorously evaluated in combination with CMTs.},
}

@article {pmid41206936,
year = {2025},
author = {Borman, T and Sannikov, A and Finn, RD and Limborg, MT and Rogers, AB and Kale, V and Hanhineva, K and Lahti, L},
title = {HoloFoodR: a statistical programming framework for holo-omics data integration workflows.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaf605},
pmid = {41206936},
issn = {1367-4811},
abstract = {SUMMARY: Holo-omics is an emerging research area that integrates multi-omic datasets from the host organism and its microbiome to study their interactions. Recently, curated and openly accessible holo-omic databases have been developed. The HoloFood database, for instance, provides nearly 10,000 holo-omic profiles for salmon and chicken under controlled treatments. However, bridging the gap between holo-omic data resources and algorithmic frameworks remains a challenge. Combining the latest advances in statistical programming with curated holo-omic data sets can facilitate the design of open and reproducible research workflows in the emerging field of holo-omics.

HoloFoodR R/Bioconductor package and the source code are available under the open-source Artistic License 2.0 at the package homepage https://doi.org/10.18129/B9.bioc.HoloFoodR.

SUPPLEMENTARY INFORMATION: Available in the package vignette https://ebi-metagenomics.github.io/HoloFoodR/articles/case_study.html.},
}

@article {pmid41206740,
year = {2025},
author = {Lage, OM and Godinho, O and García-Domínguez, R and Øvreås, L and Devos, DP},
title = {A century of research on Planctomycetota bacterial phylum, previously known as Planctomycetes.},
journal = {FEMS microbiology reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsre/fuaf056},
pmid = {41206740},
issn = {1574-6976},
abstract = {100 years after Planctomycetes were discovered and fifty years since the first isolate was successfully cultured, this bacterial phylum remains enigmatic in many ways. In the last few decades, a significant effort to characterize new isolates has resulted in over 150 described species, allowing a more comprehensive analysis of their features. However, metagenomic studies reveal that a diverse group of Planctomycetes has yet to be cultured and characterized, and that many biological surprises are yet to bee revealed. This is the case for the recently discovered phagotrophic Candidatus Uabimicrobium, which challenges our understanding of the distinction between prokaryotes and eukaryotes. The unique biology of Planctomycete cells, such as their ability to divide without the FtsZ protein, their complex structure and characteristic morphology, their relatively large genomes containing many genes with unknown function, and their variable metabolic capabilities, imposes significant barriers for researchers. Although ubiquitous, the precise ecological roles of Planctomycetes in various environments are still not fully understood. However, their distinctive metabolism opens the door to a great potential of biotechnological applications, which are beginning to be unveiled. In this article, we first review the historical milestones in Planctomycetes research and describe the pioneers of the field. We then describe the controversies and their resolutions, we highlight the past discoveries and current interrogations related to Planctomycetes and discuss the ongoing challenges that hinder a comprehensive understanding of their biology. We end up with directions for exploring the biology and ecological roles of these fascinating organisms.},
}

@article {pmid41206659,
year = {2025},
author = {Siddiqui, R and Maciver, SK and Khan, NA},
title = {Beyond Predation: Potential Metabolic Roles of Intracellular Bacteria in Acanthamoeba Ecology.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnaf124},
pmid = {41206659},
issn = {1574-6968},
abstract = {Although Acanthamoeba is well known as a reservoir and "Trojan horse" for other microbes, its relationship with intracellular organisms may extend beyond protection. Here, we discuss that certain bacteria contribute metabolically to the host, breaking down complex substrates and providing nutrients that expand its ecological adaptability. The proposed model reframes amoebae not only as predators and shelters, but also as metabolic consortia, with implications for environmental microbiology, protist ecology, and the evolution of opportunistic pathogens. Further studies using integrated multi-omics and co-culture approaches, combining metagenomic and metabolomic profiling of Acanthamoeba-bacteria interactions and transcriptomic analyses will help identify bidirectional metabolic exchange and functional gene expression within the symbiosis.},
}

@article {pmid41206461,
year = {2025},
author = {Kifushi, M and Nishikawa, Y and Hosokawa, M and Anai, T and Takeyama, H},
title = {Strain-level dissection of complex rhizoplane and soil bacterial communities using single-cell genomics and metagenomics.},
journal = {DNA research : an international journal for rapid publication of reports on genes and genomes},
volume = {},
number = {},
pages = {},
doi = {10.1093/dnares/dsaf032},
pmid = {41206461},
issn = {1756-1663},
abstract = {Root exudates shape root-associated microbial communities that differ from those in soil. Notably, specific microorganisms colonize the root surface (rhizoplane) and strongly associate with plants. Although retrieving microbial genomes from soil and root-associated environments remains challenging, single amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) are essential for studying these microbiomes. This study compared SAGs and MAGs constructed from short-read metagenomes of the same soil samples to clarify their advantages and limitations in soil and root-associated microbiomes, and to deepen insights into microbial dynamics in rhizoplane. We demonstrated that SAGs are better suited than MAGs for expanding the microbial tree of life in soil and rhizoplane environments, due to their greater gene content, broader taxonomic coverage, and higher sequence resolution of quality genomes. Metagenomic analysis provided sufficient coverage in the rhizoplane but was limited in soil. Additionally, integrating SAGs with metagenomic reads enabled strain-level analysis of microbial dynamics in the rhizoplane. Furthermore, SAGs provided insights into plasmid-host associations and dynamics, which MAGs failed to capture. Our study highlights the effectiveness of single-cell genomics in expanding microbial genome catalogs in soil and rhizosphere environments. Integrating high-resolution SAGs with comprehensive rhizoplane metagenomes offers a robust approach to elucidating microbial dynamics around plant roots.},
}

@article {pmid41205488,
year = {2025},
author = {Lv, AP and Ying-Han, and Fang, BZ and Wang, GZ and Liu, MC and Bian, BR and Zheng, ZH and Li, K and Li, BY and Jiao, JY and Liu, L and Dong, L and Chen, LQ and Yang, F and Li, WJ},
title = {Metagenome-assembled genomes reveal Pseudogracilibacillus amylolyticus sp. nov., a functional uncultured microorganism in high-temperature Daqu.},
journal = {Systematic and applied microbiology},
volume = {48},
number = {6},
pages = {126667},
doi = {10.1016/j.syapm.2025.126667},
pmid = {41205488},
issn = {1618-0984},
abstract = {Daqu, a traditional fermentation starter for Chinese liquor production, harbors a complex microbial community that plays a pivotal role in shaping the flavor and quality of the final product of Baijiu. This study characterized three metagenome-assembled genomes (MAGs) from high-temperature Daqu of Jiang-flavor Baijiu, revealing a novel taxon within the genus Pseudogracilibacillus. Phylogenomic analysis demonstrated that three MAGs (A3-12A_bin_9[TS], M2-6-2A_bin_27 and M2-7-9A_bin_18) formed a distinct monophyletic clade, supported by the threshold value of ANI recommended for bacterial species, while showing significant divergence from other related type species within the genus Pseudogracilibacillus. Functional annotation revealed the metabolic versatility of this taxon, including starch and aromatic compound degradation (potentially contributing to flavor formation), biosynthetic capacity and adaptive traits such as oxidative phosphorylation flexibility and ABC transporter diversity, underscoring its ecological role in Daqu fermentation. Based on genomic and phylogenetic characteristics, these MAGs should be classified as representing a new taxon of this genus, for which the name Pseudogracilibacillus amylolyticus sp. nov. is proposed following the rules of the published Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode). This discovery expands the diversity of the family Bacillaceae in Baijiu fermentation and provides insights into the functional potential of uncultured microbes in traditional food ecosystems.},
}

@article {pmid41205408,
year = {2025},
author = {Bao, C and Ma, Y and Li, M and Li, Y and Zhang, C and Liu, X and Fan, R and Cui, W and Fan, X and Zheng, F and Duan, F and Liu, J},
title = {Assessment of glymphatic dysfunction in ulcerative colitis using DKI-ALPS: An innovative imaging biomarker.},
journal = {Journal of neuroradiology = Journal de neuroradiologie},
volume = {53},
number = {1},
pages = {101402},
doi = {10.1016/j.neurad.2025.101402},
pmid = {41205408},
issn = {0150-9861},
abstract = {PURPOSE: Ulcerative colitis (UC) is associated with higher anxiety, depression, and cognitive disorders linked to brain glymphatic dysfunction. In this study, we used along-the-perivascular-space (ALPS) index (based on DTI and DKI) to determine if UC relates to glymphatic dysfunction and explore how microbiota dysbiosis and inflammation affect brain glymphatic function.

MATERIALS AND METHODS: In this study, 63 patients with UC and 68 healthy controls underwent 3-Tesla MRI scans to evaluate DTI-ALPS and DKI-ALPS index. The protocol included diffusion-weighted imaging (DWI) and diffusion kurtosis imaging (DKI) sequences to calculate the ALPS index, which quantifies glymphatic system function. All participants completed cognitive (MMSE) and depression (SAS/SDS) assessments (SAS/SDS). Patients with UC also underwent assessment for inflammation and gut microbiota (based on metagenomic analysis). Data analysis was performed using correlation analysis and linear regression.

RESULTS: Patients with UC showed lower DTI-ALPS index (1.25) and DKI-ALPS index (1.40) compared to controls (1.40 vs. 1.69; P < 0.001). In multi-adjusted linear regression models, UC was associated with lower DTI-ALPS index and DKI-ALPS index (β =-0.142 vs.-0.284), with DKI-ALPS showing higher sensitivity. The results remained significant even after stratification by age and sex. The Mayo score correlated negatively with DTI and DKI-ALPS index. The ALPS index correlates with gut microbiota, particularly those involved in butyrate and short-chain fatty acid (SCFA) production. DTI-ALPS index was significantly correlated with ESR (β =-0.003), CRP (β =-0.035), SII (β =-0.062), INFLA (β =-0.010), and SIRI (β =-0.058). We also observed significant correlations between DKI ALPS index and ESR (β =-0.006), CRP (β =-0.051), SII (β =-0.130), INFLA (β =-0.017), SIRI (β =-0.095), IL-6 (β =-0.081) and NLR (β =-0.108).

CONCLUSIONS: UC is associated with brain glymphatic dysfunction, correlating with inflammation level. DKI-ALPS serves as a more sensitive method than DTI-ALPS, offering a new approach for managing ulcerative colitis through glymphatic dysfunction.},
}

@article {pmid41205292,
year = {2025},
author = {Smallbone, JA and Gregson, BH and McGenity, TJ and Holland, RD and Whitby, C and Cameron, TC and Chamberlain, J and Clift, LG and Hynes, C and McKew, BA},
title = {Effects of the 2023 Poole Harbour oil spill on sediment bacterial communities and ecosystem functioning.},
journal = {Marine pollution bulletin},
volume = {222},
number = {Pt 3},
pages = {118904},
doi = {10.1016/j.marpolbul.2025.118904},
pmid = {41205292},
issn = {1879-3363},
abstract = {In March 2023, approximately 27 t of fluid from an oil and gas reservoir (containing approximately 85 % water and 15 % crude oil spilt from a fractured pipeline beneath Ower Bay creek, entering Poole Harbour (Dorset, UK). This event provided a unique opportunity to investigate the impacts of hydrocarbon contamination on microbial communities in-situ in a temperate coastal, shallow, fine sediment environment. Our aims were to quantify hydrocarbon concentrations (via gas chromatography mass spectrometry (GC-MS)) and effects on microbial community structure and functional potential (via metagenomic sequencing) to understand the capacity for microbial biodegradation across the impacted region. Hydrocarbon contamination was localised to the Spill Site (approximately an area of 1500 m[2]) at the head of the creek, with minimal impact at the Mid Point (164 m from the Spill Site) and End Point (387 m from the Spill Site) and with no indication of contamination at Brownsea Island located in the heart of the harbour. By October 2023, n-alkane and 4-5 ring PAH concentrations had declined to background levels, highlighting the combined effects of the remediation response and natural hydrocarbon biodegradation at the Spill Site. Clear changes in bacterial community structure were observed in the seven months following the spill, with notable hydrocarbon-degrading bacteria i.e. Anaerolinea, Thiobacillus and Dechloromonas favouring the Spill Site, suggesting a significant increase in anaerobic biodegradation occurred as a result of significant increase in assA (anaerobic alkylsuccinate synthase), abcA (anaerobic benzene carboxylase) and ahyA (anaerobic alkane hydroxylase) genes. Overall, 24 alkane and aromatic hydrocarbon degradation genes, from both aerobic and anaerobic degradation pathways, were identified from contigs throughout the study site, being present within 48 out of 221 Metagenome-Assembled Genomes (MAGs), highlighting the sites capacity for hydrocarbon biodegradation under both aerobic and anaerobic conditions.},
}

@article {pmid41205042,
year = {2025},
author = {Zolkefli, N and Shui, X and Ma, K and Mustapha, NA and Maeda, T},
title = {Unveiling the Impact of Indole Derivatives on Methanogenic Archaea and Microbial Functions in Anaerobic Digestion of Waste Sewage Sludge.},
journal = {Applied biochemistry and biotechnology},
volume = {},
number = {},
pages = {},
pmid = {41205042},
issn = {1559-0291},
abstract = {As an interspecies-signaling molecule, indole that is also regulating the microbial community quorum sensing (QS) can be an indispensable factor in influencing the performance of an anaerobic digestion process. Mainly released by Gram-negative bacteria, the impact of indole regulation on methane production in such a system is hardly exposed. This research intends to analyze the methane production affected by the microbial community fluctuations in the waste sewage sludge (WSS) in response to QS repression by indole and its analogs: 4-fluoroindole (4-FI), 5-fluoroindole (5-FI), 6-fluoroindole (6-FI), 3-indoleacetic acid (3-IAA), and 3-indoleacrylic acid (3-IARA). Illumina MiSeq platform was utilized to delve into the active microbes, with ribonucleic acid (RNA) used as the template to generate the 16S metagenomic library. As results, all of them inhibit methane generation even with substrates (acetic acid) availability, and this phenomenon can be led by the slight imbalance of Gram-positive/negative bacterial composition and the inactivation of the viable core fermenters: Firmicutes, Proteobacteria, and Chloroflexi. Plus, the following compounds, indole, 3-IAA, and 6-FI directly disrupted methane production by both acetoclastic and hydrogenotrophic methanogenic archaea. Methanosarcina acetivorans C2A, as a prominent methane synthesizer, was also characterized in terms of its viability and methane synthesis activity against them. Notably, Methanosarcina acetivorans C2A was non-viable in the presence of indole and 6-FI, thus lowering methane production. From here, the affirmation of the direct and indirect inhibitions of methanogenic archaea by indole and its derivatives will pave the way for a valuable future exploration of QS mechanism mapping in archaea during methanogenesis.},
}

@article {pmid41204634,
year = {2025},
author = {Yuan, L and Li, Y and Wang, Z and Xie, X and Wu, Q},
title = {Gut Microbiota-Mediated Antihypertensive Effects of Probiotic Fermented Milk: A Multi-Omics Study.},
journal = {Journal of food science},
volume = {90},
number = {11},
pages = {e70654},
doi = {10.1111/1750-3841.70654},
pmid = {41204634},
issn = {1750-3841},
support = {21977020//National Natural Science Foundation of China/ ; 2022B1111070006//the Key-Area Research and Development Program of Guangdong Province/ ; 2020GDASYL-20200102003//GDAS' Project of Science and Technology Development/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Probiotics/pharmacology ; Rats, Inbred SHR ; *Antihypertensive Agents/pharmacology ; Rats ; *Hypertension/diet therapy ; Male ; Blood Pressure/drug effects ; *Cultured Milk Products/microbiology ; Fermentation ; Lactobacillus plantarum/metabolism ; Renin-Angiotensin System/drug effects ; Metabolomics ; Multiomics ; },
abstract = {The precise molecular mechanisms through which gut microbiota mediate the antihypertensive effects of probiotic fermented milk (PFM) remain largely unexplored. This study aimed to elucidate these mechanisms by employing a multi-omics approach, combined with metagenomic deep sequencing technology, non-targeted metabolomics technology, and antibody chip protein detection technology to elucidate the potential mechanisms behind the antihypertensive effects of milk fermented by Lactiplantibacillus plantarum SR37-3 (PFM-SR37-3) in spontaneously hypertensive rats (SHR). Our findings demonstrate that PFM-SR37-3 intervention significantly reduces blood pressure in SHR and is associated with partial inactivation of the renin-angiotensin system (RAS). Notably, long-term administration of PFM-SR37-3 inhibited the progressive rise in systolic blood pressure (SBP), with final measurements of 187.17 ± 3.61 mmHg in the model group versus 172.21 ± 11.81 mmHg in the PFM-SR37-3-treated group after 4 weeks (p < 0.01). PFM-SR37-3 modulates key host metabolic pathways (especially arachidonic acid metabolism) by reshaping the gut microbiota (such as enrichment of Lactobacillaceae), with concomitant reductions in the levels of proinflammatory cytokines (such as ICAM-1 and Fractalkine). This "gut-immune" pathway is an important complement to its partial inhibition of the RAS. Collectively, these data highlight strong associations between PFM-induced gut microbial shifts and antihypertensive effects, providing a multi-faceted view of the potential mechanisms and underscoring the therapeutic potential of PFM in managing hypertension.},
}

Animals
*Gastrointestinal Microbiome
*Probiotics/pharmacology
Rats, Inbred SHR
*Antihypertensive Agents/pharmacology
Rats
*Hypertension/diet therapy
Male
Blood Pressure/drug effects
*Cultured Milk Products/microbiology
Fermentation
Lactobacillus plantarum/metabolism
Renin-Angiotensin System/drug effects
Metabolomics
Multiomics

@article {pmid41204581,
year = {2025},
author = {Zhuang, Q and Xu, R and Sun, X and Pan, X and Wan, L and Li, S and Chen, H and Yu, X and Zheng, L and Yu, Y and Deng, Z and Zheng, X and Chen, Z},
title = {Performance of metagenomic next-generation sequencing in bronchoalveolar lavage fluid for pathogen detection in patients with acute exacerbations of bronchiectasis.},
journal = {Medicine},
volume = {104},
number = {45},
pages = {e45606},
doi = {10.1097/MD.0000000000045606},
pmid = {41204581},
issn = {1536-5964},
support = {FYQM-LC-202003//The Affiliated Hospital of Medical School of Ningbo University Youth Talent Cultivation Program/ ; 2021Y13//Ningbo Medical Science and Technology Program/ ; 2015C50012//Ningbo Social and Scientific Development Fund/ ; 2020SWSQNGG-05//Ningbo Health Youth Technical Key Talents Training Special Project/ ; 2018A610271ã€2017A610250//the Natural Science Foundation of Ningbo/ ; 2022ZYC-Z31//Clinical Medicine Special Fund Project of Zhejiang Medical Association/ ; Normal project No.6//Special Project on Scientific and Technological Research of COVID-19 Infection Diseases/ ; 2016KYB268//Medical Health Science and Technology Project of Zhejiang Provincial Health Commission/ ; },
mesh = {Humans ; *Bronchiectasis/microbiology ; *Bronchoalveolar Lavage Fluid/microbiology ; Male ; Retrospective Studies ; Female ; Middle Aged ; *High-Throughput Nucleotide Sequencing/methods ; Aged ; *Metagenomics/methods ; Pseudomonas aeruginosa/isolation & purification ; Sensitivity and Specificity ; },
abstract = {This study aimed to evaluate the diagnostic value of metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) in detecting pathogens among bronchiectasis patients with acute exacerbations. A retrospective analysis was conducted on 89 bronchiectasis patients who were treated for acute exacerbations at the First Affiliated Hospital of Ningbo University from April 1, 2021, to September 30, 2023. Among the 89 patients, 88 were diagnosed with pulmonary infection, of which 15.9% (14/88) were cases of mixed infections. The sensitivity of BALF-mNGS for detecting pathogens in bronchiectasis patients during acute exacerbations was significantly higher than that of BALF culture (93.2% vs 28.4%; P < .001). All cases of mixed infection were fully identified by BALF-mNGS. The most common pathogens in patients with bronchiectasis were Pseudomonas aeruginosa, nontuberculous mycobacteria, Haemophilus influenzae, and Aspergillus. In conclusion, compared with the traditional microbial culture method, BALF-mNGS significantly improves the accuracy of diagnosis for detecting pathogens associated with bronchiectasis infections.},
}

Humans
*Bronchiectasis/microbiology
*Bronchoalveolar Lavage Fluid/microbiology
Male
Retrospective Studies
Female
Middle Aged
*High-Throughput Nucleotide Sequencing/methods
Aged
*Metagenomics/methods
Pseudomonas aeruginosa/isolation & purification
Sensitivity and Specificity

@article {pmid41204496,
year = {2025},
author = {Tian, J and Dong, J and Yu, G and Guan, W},
title = {Bronchoscopy-associated dissemination of pulmonary nocardiosis caused by Nocardia terpenica in an immunocompetent patient with bronchiectasis: A case report.},
journal = {Medicine},
volume = {104},
number = {45},
pages = {e45875},
doi = {10.1097/MD.0000000000045875},
pmid = {41204496},
issn = {1536-5964},
mesh = {Humans ; Female ; *Nocardia Infections/drug therapy/diagnosis/etiology/microbiology ; Middle Aged ; *Bronchoscopy/adverse effects ; *Bronchiectasis/complications ; *Nocardia/isolation & purification ; Anti-Bacterial Agents/therapeutic use/administration & dosage ; Bronchoalveolar Lavage/adverse effects ; Trimethoprim, Sulfamethoxazole Drug Combination/therapeutic use/administration & dosage ; Bronchoalveolar Lavage Fluid/microbiology ; Immunocompetence ; },
abstract = {RATIONALE: Bronchoscopy with bronchoalveolar lavage (BAL) is essential for diagnosing pulmonary infections; however, its potential to iatrogenically disseminate a localized Nocardia infection represents a severe and unreported risk. This case aims to alert clinicians to this danger and underscore essential therapeutic lessons for disseminated disease.

PATIENT CONCERNS: A 51-year-old immunocompetent woman with longstanding bronchiectasis presented with 1-day of hemoptysis and a 40-year history of chronic cough and sputum production. These symptoms had worsened over the preceding 2 months despite broad-spectrum antibiotic therapy.

DIAGNOSES: Bronchiectasis was diagnosed based on chronic respiratory symptoms and characteristic computed tomography findings. Nocardia terpenica infection was confirmed by BAL fluid culture and metagenomic next-generation sequencing. Within 24 hours post-BAL, the patient developed fever, respiratory failure, and new bilateral consolidations on computed tomography, indicating procedure-related disseminated nocardiosis.

INTERVENTIONS: Diagnostic bronchoscopy with BAL was performed. Therapeutically, the patient received a total of 24 days of intensive combination therapy with intravenous imipenem/cilastatin and oral trimethoprim-sulfamethoxazole (TMP-SMX), followed by sequential long-term oral TMP-SMX monotherapy.

OUTCOMES: The initial 10-day course of combination therapy led to rapid clinical improvement, with resolution of fever and respiratory failure within 3 days, and normalization of C-reactive protein levels by day 10. Radiographic improvement was also evident. However, relapse (recurrent fever and malaise) occurred promptly within 3 days after de-escalation to TMP-SMX monotherapy. After reinstitution of imipenem/cilastatin plus TMP-SMX for an additional 14 days (totaling 24 days of intensive therapy), the patient achieved sustained clinical and radiographic remission. She was successfully discharged on long-term TMP-SMX monotherapy and remained well at the 2-month follow-up.

LESSONS: This is the first report suggesting that bronchoscopy, particularly BAL, can disseminate a localized airway Nocardia infection, causing acute disseminated pulmonary nocardiosis. Extreme caution is warranted when performing bronchoscopy in bronchiectasis patients with suspected or confirmed nocardiosis. For disseminated pulmonary nocardiosis, intensive combination therapy for at least 3 weeks is mandatory to prevent relapse, regardless of a rapid initial response.},
}

Humans
Female
*Nocardia Infections/drug therapy/diagnosis/etiology/microbiology
Middle Aged
*Bronchoscopy/adverse effects
*Bronchiectasis/complications
*Nocardia/isolation & purification
Anti-Bacterial Agents/therapeutic use/administration & dosage
Bronchoalveolar Lavage/adverse effects
Trimethoprim, Sulfamethoxazole Drug Combination/therapeutic use/administration & dosage
Bronchoalveolar Lavage Fluid/microbiology
Immunocompetence

@article {pmid41203618,
year = {2025},
author = {Moriel, N and Jones, L and Harpenas, E and Rakow, N and Shmorak, S and Eventov Friedman, S and Ofek Shlomai, N and Yassour, M},
title = {Development of the preterm infant gut and gastric residuals microbiome.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9848},
pmid = {41203618},
issn = {2041-1723},
mesh = {Humans ; *Infant, Premature ; Infant, Newborn ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Female ; Male ; Intensive Care Units, Neonatal ; Metagenomics ; Bacteria/classification/genetics/isolation & purification ; *Stomach/microbiology ; Gestational Age ; Enteral Nutrition ; },
abstract = {Prematurity, defined as birth before 37 weeks of gestation, is the leading cause of mortality in children under five, affecting ~11% of live births worldwide (≈15 million annually). Despite advances in neonatal care, preterm infants remain at high risk of complications. In neonatal intensive care units, gastric residuals (GRs) are routinely monitored to guide enteral feeding, yet their microbial composition remains poorly understood. We performed metagenomic sequencing of 199 stool and 69 GR samples from 39 preterm infants during hospitalization to characterize stomach and gut microbiomes. To our knowledge, this is the first metagenomic sequencing of the GR in premature infants. We identified 11 GR microbial clusters, commonly dominated by Staphylococcus, Streptococcus, and Klebsiella, with microbial diversity correlating with aspiration frequency. Colonization was dynamic: early GR samples were enriched with Staphylococcus epidermidis and Bradyrhizobium, while later samples featured Escherichia coli, Staphylococcus hominis, and Streptococcus thermophilus. Stool samples formed eight microbial clusters, frequently enriched with Enterobacteriaceae. S. epidermidis was linked to higher gestational age and lower richness, whereas Bifidobacterium breve, a beneficial commensal, appeared later. Comparative analysis showed overlap between gut and gastric microbiota, with GR samples more dynamic and less subject-specific. Strain-level analysis revealed both individual-specific and widely shared taxa, including a pathogenic Klebsiella aerogenes strain associated with bacteremia, detectable a week before clinical isolation. These findings provide new insights into microbial colonization dynamics of preterm infants.},
}

Humans
*Infant, Premature
Infant, Newborn
*Gastrointestinal Microbiome/genetics
Feces/microbiology
Female
Male
Intensive Care Units, Neonatal
Metagenomics
Bacteria/classification/genetics/isolation & purification
*Stomach/microbiology
Gestational Age
Enteral Nutrition

@article {pmid41203352,
year = {2025},
author = {Tonoli, A and Dalby, PA and Hailes, HC and Jeffries, JWE},
title = {Transketolase enzyme discovery and engineering.},
journal = {Methods in enzymology},
volume = {722},
number = {},
pages = {343-368},
doi = {10.1016/bs.mie.2025.07.002},
pmid = {41203352},
issn = {1557-7988},
mesh = {*Transketolase/genetics/metabolism/chemistry/isolation & purification ; Substrate Specificity ; *Protein Engineering/methods ; Directed Molecular Evolution/methods ; Ribosemonophosphates/metabolism ; Metagenomics/methods ; Pyruvates ; },
abstract = {Transketolases (TKs) are important C-C bond forming enzymes that in vivo transfer a two carbon ketol unit to the acceptors d-ribose-5-phosphate or d-erythrose-4-phosphate. There is significant interest in biocatalytic applications where frequently the donor β-hydroxypyruvic acid is used. In recent years there has been interest in the discovery of new TKs with unique or robust properties that are an excellent starting point for mutagenesis, or that are able to accept new acceptors or donors. Similarly, TK mutagenesis has led to TKs with alternative substrate profiles. In this chapter, firstly an overview of the substrates accepted by TKs is briefly summarized. Then, metagenomic strategies for the discovery of unique TKs and how this approach has developed with an early example, and a more recent study on the discovery of 'split'-TKs, are described with methods. Finally, enzyme evolution methods and approaches to develop a wide range of TKs with modified substrate acceptance and improved stabilities are detailed.},
}

*Transketolase/genetics/metabolism/chemistry/isolation & purification
Substrate Specificity
*Protein Engineering/methods
Directed Molecular Evolution/methods
Ribosemonophosphates/metabolism
Metagenomics/methods
Pyruvates

@article {pmid41203168,
year = {2025},
author = {Vangah, SJ and Kermani, AA and Vali, H and Noghabi, KA and Zahiri, HS},
title = {Engineering Saccharomyces cerevisiae for the secretion of an acidic, halotolerant, and cold-adapted xylanase derived from the camel rumen metagenome: Enzyme characterization and strain assessment.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {148805},
doi = {10.1016/j.ijbiomac.2025.148805},
pmid = {41203168},
issn = {1879-0003},
abstract = {This study reports the development of a recombinant Saccharomyces cerevisiae strain engineered to produce and secrete a novel xylanase (rXylM) derived from the camel rumen metagenome. The recombinant enzyme exhibited optimal activity at 35 °C, pH 5.0, and retained 58 % of its activity even at 5 °C. The enzyme activity was not significantly affected by high sodium chloride (NaCl) concentrations up to 5 M. These properties characterize rXylM as an acidic, halotolerant, and cold-adapted xylanase. The combination of these adaptive traits in a single enzyme offers substantial advantages for industrial applications. Enzyme kinetic analysis was performed at 35 °C and pH 5.0 using beechwood xylan, wheat bran, and high-extraction wheat flour as substrates, yielding specific activities of 1190 U/mg, 1029 U/mg, and 383 U/mg respectively. Scanning electron microscopy (SEM) revealed noticeable morphological alterations indicating substantial degradation of the substrates following treatment with rXylM. The engineered strain, CEN.PK-Xyl, was assessed as a leavening agent for baking applications. Rheological analysis of the dough demonstrated a significant reduction in elasticity and viscous resistance, improving dough handling and kneading properties. Correspondingly, the resulting bread exhibited a significant decrease in hardness, gumminess, and chewiness, indicating an improvement in texture and overall quality. Cytotoxicity evaluation using the MTT assay showed that rXylM did not affect the viability of L929 mouse fibroblast cells under the tested conditions. The favorable biochemical properties and non-toxicity of rXylM, together with the established safety of S. cerevisiae, highlight CEN.PK-Xyl as a promising platform for applications in food, feed, bioprocessing, and fermentation.},
}

@article {pmid41203007,
year = {2025},
author = {Li, H and Wang, X and Zhang, X and Mu, H and Hao, R and Li, Y and Liu, Q and Chi, R and Zhai, D},
title = {Disrupted Microbiome-Metabolome Networks Underlie Gut Barrier and Immune Imbalance in Severe Fever with Thrombocytopenia Syndrome.},
journal = {Microbes and infection},
volume = {},
number = {},
pages = {105586},
doi = {10.1016/j.micinf.2025.105586},
pmid = {41203007},
issn = {1769-714X},
abstract = {Severe fever with thrombocytopenia syndrome (SFTS) is a life-threatening tick-borne viral infection with a high mortality rate and limited treatment options. While gastrointestinal symptoms are common, the contribution of gut microbiome disruption to disease progression remains unclear. Previous studies have noted taxonomic shifts in SFTS-associated microbiota, but their functional and metabolic consequences have not been systematically characterized. We conducted an integrated metagenomic and metabolomic analysis of fecal samples from 20 SFTS patients and 20 healthy controls. At the time of admission, patients with SFTS exhibited acute-stage infection, characterized by symptoms such as fever, thrombocytopenia, and gastrointestinal disturbances. Metagenomic sequencing was used to assess the microbial gene content, taxonomic composition, and functional potential. Untargeted metabolomics analysis using liquid chromatography-tandem mass spectrometry (LC-MS/MS) was performed to profile fecal metabolites. The SFTS patients showed a significantly reduced microbial gene richness, alpha diversity, and compositional stability. Short-chain fatty acid (SCFA)-producing genera (e.g., Faecalibacterium and Roseburia) were depleted, while mucin-degrading and opportunistic taxa (e.g., Pseudomonas and Akkermansia) were enriched. Functionally, biosynthetic and homeostatic pathways were suppressed; while stress-adaptive, biofilm-forming, and virulence-associated pathways were elevated. Metabolomic profiling revealed depletion of anti-inflammatory metabolites (e.g., bile acids and curcumin sulfate) and enrichment of proinflammatory compounds (e.g., porphyrins and beta-tyvelose). Multi-omic correlation highlighted strong links between microbial disruption and altered metabolite production. In conclusion, SFTS is associated with significant alterations in the gut microbiome and its metabolic profile, which is characterized by the loss of beneficial microbial taxa and functions, alongside the emergence of virulence factors and stress-related signatures. These findings underscore the role of microbiome dysfunction in SFTS and suggest that microbiota-targeted strategies may offer supportive benefits, particularly in alleviating SFTS-associated gastrointestinal disturbances and secondary microbial imbalance.},
}

@article {pmid41202935,
year = {2025},
author = {Wu, B and Cheng, Y and Gu, J and Yuan, H and Murphy, JD},
title = {Toward sustained and efficient n-caproate production: Insights into magnetite-encapsulated biochar mediated microbial chain elongation.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133617},
doi = {10.1016/j.biortech.2025.133617},
pmid = {41202935},
issn = {1873-2976},
abstract = {Decarbonization of the chemical sector may be facilitated by microbial chain elongation, through conversion of organic waste into chemical products. Challenges in efficient interspecies electron transfer is a barrier to this technology. Here we introduce a magnetite-encapsulated biochar (Fe@biochar) amendment strategically integrated with chain elongation to facilitate sustained and efficient n-caproate production. This strategy increased n-caproate yields to 13.92 g COD/L, 199 % and 71 % higher than the control (4.66 g COD/L) and biochar (8.13 g COD/L) groups, respectively. Most importantly, Fe@biochar consistently enhanced n-caproate production after recycle, a continuity not observed with biochar. This difference may be attributed to the inhibitory effects of high concentrations of undissociated n-caproic acid (up to 9.06 mM or 2.32 g COD/L) on functional microbes in the biochar group. Microbial community analysis identified Clostridium_sensu_stricto as the key genus involved in n-caproate production. Comparative metagenomic and microbial activity analyses revealed the energy metabolism, where Fe@biochar promoted extracellular iron-based electron transfer, and further accelerated intracellular electron sinks. This is substantiated by a 3.6 fold increase in electron transfer system activity and evaluated relative abundances of key genes encoding acetyl-CoA synthetase (15.0 % increase), cytochrome c biosynthesis (28.7 % increase) and NADH dehydrogenase (48.0 % increase). This study offers a new paradigm for sustained n-caproate production.},
}

@article {pmid41202544,
year = {2025},
author = {Zhang, H and Sun, H and Pan, X and Wu, D and Liang, H and Tang, J and Fang, H and Wu, X},
title = {Sediment archives urban-rural divergence in antibiotic resistance gene contamination within a freshwater lake.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140322},
doi = {10.1016/j.jhazmat.2025.140322},
pmid = {41202544},
issn = {1873-3336},
abstract = {Freshwater lakes are critical ecosystems for sustaining biodiversity and human well-being, yet increasing anthropogenic activities threaten their ecological safety through pollution such as antibiotic resistance genes (ARGs). Previous studies on ARG pollution in aquatic systems have largely overlooked the distinct impacts of urban versus rural landscapes, limiting targeted mitigation strategies. Here, we investigate the urban-rural heterogeneity of ARG pollution in Chaohu lake, a major urban-rural junction lake in China, using shotgun metagenomic sequencing and Bayesian source-tracking approaches. Our findings reveal significant spatiotemporal variations in ARG abundance, with urban-adjacent regions (western lake) exhibiting 1.22- to 1.25-fold higher ARG levels than rural-adjacent areas (eastern lake) in water and sediments, respectively. Notably, a significant distance-decay relationship of ARG profiles was observed in sediments, highlighting that sediments act as a stable environmental archive recording the urban-rural divergence. Agricultural activities were identified as the dominant source lake-wide, contributing over 60 % of the total ARG load, thereby surpassing urban sewage inputs. Meanwhile, the abundance of mobile genetic elements (MGEs), particularly transposases, was significantly higher in the western lake, indicating a greater potential for horizontal gene transfer. The presence of multidrug-resistant, ARG-carrying pathogens, such as Stenotrophomonas maltophilia and Pseudomonas putida, was significantly enriched in these areas, correlating with higher ecological and health risks as quantified by the antibiotic resistome risk index. These results underscore the urgent need for landscape-specific management strategies to curb ARG dissemination, prioritizing agricultural non-point source control in urban-rural transitional zones to safeguard freshwater ecosystems and human health.},
}

@article {pmid41202381,
year = {2025},
author = {Jiang, CH and Zhang, SJ and Li, P and Miao, H and Zhao, YY},
title = {Natural products targeting TGF-β/Smad signaling in renal fibrosis: Multiomics-based novel molecular mechanisms and therapeutic strategies.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {148},
number = {},
pages = {157496},
doi = {10.1016/j.phymed.2025.157496},
pmid = {41202381},
issn = {1618-095X},
abstract = {BACKGROUND: Renal diseases including acute kidney injury (AKI) and chronic kidney disease (CKD) have become one of the major global public health challenges. Regardless of the underlying aetiology, renal fibrosis is a common pathological endpoint in the progression of diverse kidney diseases to end-stage renal disease. Increasing studies have highlighted that emerging multi-omics techniques (metagenomics, transcriptomics, proteomics and metabolomics) have been used for elucidating the pathogenesis of kidney disease and underlying molecular mechanism of renal fibrosis. However, few reviews provide a comprehensive and systematic presentation of multi-omics signaling-mediated TGF-β/Smad pathway in both AKI and CKD as well as therapeutic strategies for targeting signaling cascades by natural products.

PURPOSE AND STUDY DESIGN: This review summarizes multi-omics signaling-mediated TGF-β/Smad pathway and therapeutic strategies of natural products by targeting this signaling axis in patients and animal models with kidney disease.

METHODS: All the available information is searched by several electronic database such as Web of Science, Pubmed, ScienceDirect, Splinker, Google Scholar, etc., that covered approximately 1000 publications from 2015 to 2025.

RESULTS: Ample evidence has indicated that transforming growth factor-β (TGF-β)/suppressor of mothers against decapentaplegic (Smad) signaling pathway plays a central role in renal fibrosis. Based on the multi-omics techniques, a variety of novel mediators are identified and affects kidney diseases by regulating TGF-β/Smad pathway. Therefore, targeting TGF-β/Smad pathway is an important and promising antifibrotic therapy. This review summarizes TGF-β/Smad pathway in both AKI and CKD, elaborate on the multidimensional regulatory mechanisms in renal fibrosis by crosstalk between TGF-β/Smad pathway and novel multi-omics signaling-associated mechanisms including microbial dysbiosis, dysregulating non-coding ribonucleic acids including long non-coding RNAs and microRNAs and metabolite disorder and shed light on the latest therapeutic effects of natural products such as terpenoids, anthraquinones, xanthones and flavonoids as well as natural polysaccharides by targeting multi-omics signaling-mediated TGF-β/Smad pathway.

CONCLUSION: This review presents a multiomics-driven therapeutic strategy for the development of effective and precise antifibrotic therapies.},
}

@article {pmid41201920,
year = {2025},
author = {Soni, S and Mittal, P and Lo, JH and Yang, Y and Smbatyan, G and Lee, K and Wan, J and Kumagai, H and Yen, K and Mehta, HH and Miller, B and Torres-Gonzalez, L and Battaglin, F and Shah, UH and Bartolini, M and Zhang, W and Craig, DW and Millstein, J and Cohen, P and Lenz, HJ},
title = {Age-diet interactions significantly influence intratumoral gene expression, gut microbiome signature and tumor microenvironment in colorectal cancer.},
journal = {Neoplasia (New York, N.Y.)},
volume = {70},
number = {},
pages = {101245},
doi = {10.1016/j.neo.2025.101245},
pmid = {41201920},
issn = {1476-5586},
mesh = {*Colorectal Neoplasms/pathology/etiology/genetics/metabolism/microbiology ; Animals ; *Gastrointestinal Microbiome ; Mice ; *Tumor Microenvironment/genetics ; Humans ; *Diet ; *Gene Expression Regulation, Neoplastic ; Disease Models, Animal ; Age Factors ; Male ; *Aging ; },
abstract = {Colorectal Cancer (CRC) is the third most prevalent malignancy, leading to significant morbidity and mortality globally. Epidemiological studies suggest that chronological age and diet are among the major contributing factors correlated with the incidence of CRC. Our study aimed to provide insights into the association between age, diet, and gut microbiome in CRC using molecular techniques including RNA sequencing, cytokine analysis, and metagenomic analysis. We used syngeneic MC38 mice model divided into two age groups (old and young) and three diet groups (standard chow, calorie-restricted and high-fat). The major findings of this study are that age and diet impact intratumoral gene signaling (nuclear and mitochondrial), and hub genes we identified are associated with prognosis in CRC. Fecal microbiome analysis showed that old microbiomes have higher alpha diversity compared to young mice. Our results demonstrate that interactions between host (age) and external (diet) factors regulate tumor growth mediated by cytokines, mitochondrial derived proteins, and the gut microbiome. Collectively, our findings advance current understanding of the mechanisms by which aging, diet and gut microbiota impact CRC onset and progression though further investigation is warranted.},
}

*Colorectal Neoplasms/pathology/etiology/genetics/metabolism/microbiology
Animals
*Gastrointestinal Microbiome
Mice
*Tumor Microenvironment/genetics
Humans
*Diet
*Gene Expression Regulation, Neoplastic
Disease Models, Animal
Age Factors
Male
*Aging

@article {pmid41201839,
year = {2025},
author = {da Silva Fong, D and Abrantes, J and Moura, T and Serra-Pereira, B and Xavier, R and Veríssimo, A and Varsani, A and Neves, F},
title = {Identification and characterization of a novel papillomavirus in thornback skate (Raja clavata).},
journal = {Microbial genomics},
volume = {11},
number = {11},
pages = {},
doi = {10.1099/mgen.0.001541},
pmid = {41201839},
issn = {2057-5858},
mesh = {Animals ; Phylogeny ; Genome, Viral ; *Skates, Fish/virology ; *Papillomaviridae/genetics/isolation & purification/classification ; *Papillomavirus Infections/virology/veterinary ; Sequence Analysis, DNA ; DNA, Viral/genetics ; },
abstract = {Papillomaviruses are non-enveloped, double-stranded DNA viruses capable of infecting a wide range of vertebrates, from chondrichthyans to mammals. In this study, we report for the first time the identification and complete genome of a papillomavirus in the thornback skate (Raja clavata), named Raja clavata papillomavirus 1 (RclaPV1). The genomic sequence was determined using a metagenomic approach and subsequently confirmed by PCR. The RclaPV1 genome is 5,539 bp in length and displays the typical organization of papillomaviruses, encoding 4 core proteins on a single DNA strand: two early genes (E1 and E2) and two late genes (L1 and L2). Maximum likelihood phylogenetic analyses of the L1 and E1 genes indicate that RclaPV1 belongs to the Secondpapillomavirinae subfamily, clustering with fish and amphibian papillomaviruses and showing closer evolutionary relationships to amphibians than to fish.},
}

Animals
Phylogeny
Genome, Viral
*Skates, Fish/virology
*Papillomaviridae/genetics/isolation & purification/classification
*Papillomavirus Infections/virology/veterinary
Sequence Analysis, DNA
DNA, Viral/genetics

@article {pmid41201733,
year = {2025},
author = {Saleh, RM and Hassan, OM},
title = {The infectome framework: linking polymicrobial ecology and biofilm dynamics to precision diagnostic approaches.},
journal = {Infection},
volume = {},
number = {},
pages = {},
pmid = {41201733},
issn = {1439-0973},
abstract = {Chronic infections are a persistent global health problem and are frequently sustained by polymicrobial communities rather than by a single pathogen. This review brings together current evidence for the infectome concept, defined as the dynamic set of pathogenic or pathobiont taxa in the host, their shared functional capacities, and the interactions that connect them. We analyze how community-level processes promote persistence, cause diagnostic failure, and drive therapeutic resistance, with emphasis on multispecies biofilms, quorum sensing, horizontal gene transfer, metabolic cooperation, and immune modulation. We also highlight advances in multi-omics and computational integration that now permit high-resolution infectome profiling and reveal taxa and interspecies networks that are not captured by routine culture. Clinical examples such as periodontitis, bacterial vaginosis, chronic rhinosinusitis, device-associated infections, and recurrent urinary tract infections show the translational value of this shift. On the therapeutic side, we discuss infectome-informed options including antivirulence agents, biofilm-disrupting enzymes, bacteriophages and lysins, community-wide susceptibility-guided regimens, and microbiome-restoration strategies. Finally, we identify the main requirements for the field: standardized sampling and analytic workflows, reproducible infectome signatures linked to clinical outcomes, and trial designs able to capture ecological dynamics and meet regulatory expectations for community-targeted interventions. Adopting an infectome perspective can enable precision infectiology and reshape the management of chronic and recurrent infections.},
}

@article {pmid41201496,
year = {2025},
author = {Ren, QD and Li, MR and Farag, MA and Qiu, LL and Wang, YA and Liu, D and Liu, HR and Sun, JY and Li, NY and Liu, C},
title = {Pomegranate peel extract alleviates diabetic retinopathy by suppressing the PI3K/AKT/HIF-1α/VEGF pathway and gut microbiota modulation.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2025.10.048},
pmid = {41201496},
issn = {2090-1224},
abstract = {INTRODUCTION: Diabetic retinopathy (DR) is a severe microvascular complication of diabetes mellitus. Pomegranate peel extract (PPE) has shown potential in mitigating various diabetic complications, yet its role in DR remains unexplored.

OBJECTIVE: To investigate the beneficial effects and underlying action mechanisms of PPE in managing DR.

METHODS: PPE was extracted using 50 % ethanol. The effects and underlying mechanisms of PPE on DR were evaluated in streptozotocin (STZ)-induced DR rats and high-glucose-incubated adult retinal pigment epithelial cell line (ARPE-19) cells. Phenotypic parameters, network pharmacology (NP), and gut microbiota metagenomic analysis were employed to elucidate the impact and mechanisms of PPE in DR.

RESULTS: In DR rats, oral administration of PPE significantly mitigated retinal damage. NP analysis indicated potential mechanisms, involving the hypoxia-inducible factor-1/vascular endothelial growth factor (HIF-1/VEGF), phosphoinositide 3-kinase/protein kinase B (PI3K/AKT), and reactive oxygen species (ROS) pathways. PPE suppressed oxidative stress and inhibited the activation of PI3K/AKT/HIF-1α/VEGF pathway in the retina of DR rats and high-glucose-incubated ARPE-19 cells. Moreover, PPE improved gut microbiota dysbiosis in DR rats, particularly increasing Akkermansia muciniphila, which likely contributed to reduced inflammation and oxidative stress.

CONCLUSION: PPE exhibited therapeutic effects in DR by directly alleviating retinal damage via the suppression of oxidative stress and inhibition of PI3K/AKT/HIF-1α/VEGF pathway, as well as indirectly modulating gut microbiota. These findings suggested that PPE may serve as a promising nutraceutical for DR management.},
}

@article {pmid41201223,
year = {2025},
author = {Zha, Y and Xiang, M and Zuo, Y and Liu, D and Wang, Q},
title = {High-dose Dietary Fibre Supplementation Enhances the Gut Microbiome, Health, and Athletic Performance of College Basketball Players.},
journal = {International journal for vitamin and nutrition research. Internationale Zeitschrift fur Vitamin- und Ernahrungsforschung. Journal international de vitaminologie et de nutrition},
volume = {95},
number = {5},
pages = {37069},
doi = {10.31083/IJVNR37069},
pmid = {41201223},
issn = {0300-9831},
support = {2019YFF0301702//National Key R&D Program of China/ ; XJ2022000601//Doctoral Research Fund/ ; },
mesh = {Humans ; Male ; *Gastrointestinal Microbiome/drug effects ; *Basketball/physiology ; *Athletic Performance/physiology ; Young Adult ; *Dietary Fiber/administration & dosage ; Adolescent ; *Dietary Supplements ; Adult ; Body Composition ; Athletes ; Universities ; },
abstract = {BACKGROUND: Prolonged or intense exercise can disrupt gastrointestinal (GI) function and gut microbiota, impairing athletic performance. Dietary fibre supplementation may enhance gut microbiota diversity, improve body composition, and promote recovery in athletes. This study aimed to explore the effects of dietary fibre supplementation at two doses for 8 weeks on these aspects in college basketball players.

METHODS: Twenty male college basketball players (aged 17-25 years) were randomly assigned to a high-dose group (HDG; 10 participants; 6.84 g/day dietary fibre) or a low-dose group (LDG; 10 participants; 3.24 g/day dietary fibre). The participants consumed fibre-enriched meals daily while maintaining their regular training schedules. The outcome measures included gut microbiota diversity (metagenomic sequencing), body composition, fatigue recovery markers, glucose and lipid metabolism, and athletic performance. Statistical analyses included paired and independent t tests for within- and between-group comparisons and Spearman's correlation analysis to assess the relationships between gut microbiota and biochemical markers.

RESULTS: One participant in the high-dose group withdrew, and nineteen ultimately completed the study. Both groups showed significant within-group improvements (p < 0.05) in body weight (HDG: -2.77 ± 0.76 kg; LDG: -2.40 ± 0.67 kg), body fat percentage (HDG: -1.87 ± 0.69; LDG: -1.49 ± 0.45), cortisol (HDG: -6.79 ± 4.26 μg/dL; LDG: -4.5 ± 4.84 μg/dL), maximum power (HDG: 27.16 ± 9.77 W; LDG: 14.50 ± 9.43 W), maximal oxygen uptake (HDG: 8.78 ± 0.97; LDG: 6.90 ± 1.37), and half-court triangle run times (HDG: -0.48 ± 0.36 s; LDG: -0.25 ± 0.20 s). Meanwhile, fasting blood glucose significantly decreased (0.91 ± 0.55 mmol/L; p = 0.001), and the gut microbiome changes were more stable in the HDG, whereas the LDG presented greater shifts in microbial diversity. No significant between-group differences were observed.

CONCLUSIONS: Dietary fibre supplementation improved the gut microbiome composition, body composition, fatigue recovery, and athletic performance of college basketball players, regardless of dosage. Further studies are needed to evaluate higher doses and specific fibre types.},
}

Humans
Male
*Gastrointestinal Microbiome/drug effects
*Basketball/physiology
*Athletic Performance/physiology
Young Adult
*Dietary Fiber/administration & dosage
Adolescent
*Dietary Supplements
Adult
Body Composition
Athletes
Universities

@article {pmid41200800,
year = {2025},
author = {Quarton, S and Livesey, A and Jeff, C and Hatton, C and Chen, CH and Scott, A and Parekh, D and Thickett, D and McNally, A and Sapey, E},
title = {Metagenomics in the diagnosis of pneumonia: a systematic review.},
journal = {Infectious diseases (London, England)},
volume = {},
number = {},
pages = {1-25},
doi = {10.1080/23744235.2025.2580954},
pmid = {41200800},
issn = {2374-4243},
abstract = {BACKGROUND: Pneumonia is a major cause of morbidity and mortality, yet causative organisms are rarely identified. Metagenomic next-generation sequencing (mNGS) may improve this, however the impact on outcomes is uncertain and the relative utility in pneumonia subtypes or different clinical samples is unclear.

METHODS: This systematic review compared mNGS with conventional microbiology, assessing pathogen identification, turnaround time and clinical impact. It also reviewed difference related to the pneumonia subtype, or sample used. We searched EMBASE, MEDLINE, Scopus, and the Cochrane Central Register of Controlled Trials (CENTRAL) for studies comparing mNGS with conventional microbiology, in patients with pneumonia. All study types were included (excluding case reports of <10 people). Eligibility assessment and data extraction was performed by two independent reviewers, and risk of bias assessed using the QUADAS-2.

RESULTS: We identified 74 studies including 10,566 people, with all studies having high risk of bias or applicability concerns in at least one domain. Conventional tests identified a pathogen in 43.2% of cases (3559/8229) compared to 78.9% for mNGS (6242/7980). mNGS had faster turnaround times than conventional microbiology (MD -73.6h, CI-111.36 - -35.73 hrs) but meta-analysis was not possible for other outcomes. Most studies did not specify the pneumonia subtype. 92%of studies used exclusively or predominantly bronchoalveolar lavage fluid (BALF), and the utility of other sample types could not be established.

CONCLUSIONS: mNGS may identify possible pathogens with greater frequency than standard techniques although bias in study design limits definite conclusions, and the clinical relevance of this remains unresolved. There is a need for studies assessing clinical outcomes, and the differential impact in pneumonia subtypes and in samples other than BALF.},
}

@article {pmid41200470,
year = {2025},
author = {Maldonado, M and Pita, L and Erpenbeck, D and Hentschel, U 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 sponge, Corticium candelabrum Schmidt, 1862 and its associated microbial metagenome sequences.},
journal = {Wellcome open research},
volume = {10},
number = {},
pages = {535},
pmid = {41200470},
issn = {2398-502X},
abstract = {We present a genome assembly from a specimen of Corticium candelabrum (sponge; Porifera; Homoscleromorpha; Homosclerophorida; Plakinidae). The genome sequence has a total length of 185.49 megabases. Most of the assembly (99.4%) is scaffolded into 22 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 18.19 kilobases in length. Gene annotation of this assembly on Ensembl identified 26,198 protein-coding genes. The metagenome of the specimen was also assembled, and 53 binned bacterial genomes were identified, including 44 high-quality MAGs that were typical of high microbial abundance sponge and included, besides the phyla Chloroflexota (class Dehalococcoidia), Acidobacteriota (order Acidomicrobiales), Alpha- and Gammaproteobacteria, also representatives of several candidatus phyla (Candidatus Latescibacterota, Binatota, Poribacteria).},
}

@article {pmid41200317,
year = {2025},
author = {Kazemzadeh, S and Korneeva, O and Shabunin, S and Syromyatnikov, M},
title = {Antibiotic resistance in mastitis-causing bacteria: Exploring antibiotic-resistance genes, underlying mechanisms, and their implications for dairy animal and public health.},
journal = {Open veterinary journal},
volume = {15},
number = {9},
pages = {3980-4006},
pmid = {41200317},
issn = {2218-6050},
mesh = {Animals ; *Mastitis, Bovine/microbiology/drug therapy ; Female ; Cattle ; *Drug Resistance, Bacterial/genetics ; *Anti-Bacterial Agents/pharmacology ; Public Health ; *Bacteria/drug effects/genetics ; Dairying ; Humans ; Milk/microbiology ; },
abstract = {The development and spread of superbugs, which are bacterial strains resistant to several types of antibiotics, threatening the lives of myriad people and animals worldwide, is one of the most concerning issues facing both global and animal health. Dairy animals are considered to be key reservoirs of antibiotic-resistant bacteria, which are closely correlated with the widespread and inappropriate application of antibiotics in agriculture and veterinary medicine, particularly for mastitis treatment. Although antimicrobial agents are administered in dairy farming for various conditions beyond mastitis, such as respiratory infections and digestive disorders, as well as prophylaxis and growth promotion, the most common reason for antimicrobial use in this industry is mastitis treatment. Since raw milk can be contaminated with opportunistic pathogens carrying antimicrobial resistance genes, these pathogens increase the gene pool from which pathogenic bacteria can acquire resistance traits. Indeed, these resistance genes may be horizontally transferred from livestock to human pathogens through mobile genetic elements through the consumption of raw milk. This phenomenon poses a global health threat, emphasizing the necessity of applying the "One Health" approach in global health and medicine to safeguard animal health and public health. Given the high prevalence and economic impact of mastitis and the evidence supporting mastitis as a major driver of antimicrobial use in dairy farming, this review summarizes recent genomic and metagenomic studies on major mastitis-causing pathogens (Staphylococcus aureus, Escherichia coli, Streptococcus spp., and Pseudomonas spp.) in dairy animals, detailing their primary resistance mechanisms. We highlight advanced surveillance tools, such as metagenomics, whole-genome sequencing, and quantitative polymerase chain reaction, for the rapid detection of resistance genes and mobile elements in the dairy chain.},
}

Animals
*Mastitis, Bovine/microbiology/drug therapy
Female
Cattle
*Drug Resistance, Bacterial/genetics
*Anti-Bacterial Agents/pharmacology
Public Health
*Bacteria/drug effects/genetics
Dairying
Humans
Milk/microbiology

@article {pmid41199950,
year = {2025},
author = {Sang, Z and Zhang, Y and Kao, E and Zhu, T and Yang, J and Xu, ZZ and Huang, S and Teng, F and Wang, W},
title = {Decoding oral leukoplakia: microbiome dysbiosis and inflammatory dynamics unveiled in a rat model.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1613165},
pmid = {41199950},
issn = {1664-302X},
abstract = {INTRODUCTION: Oral leukoplakia (OLK) is an oral precancerous lesion associated with oral microbiome dysbiosis and systemic inflammation. However, the longitudinal changes of the microbiome and its causal relationship with inflammation remain unclear, and traditional sequencing struggles to detect low-biomass samples.

METHODS: A 4-nitroquinoline-1-oxide (4-NQO)-induced rat OLK model was used. The oral microbiome was analyzed via 2bRAD-M sequencing; serum levels of tumor necrosis factor-α (TNF-α) and interleukin-6 (IL-6) were measured. Additionally, functional pathway analysis of the microbiome and its correlation with inflammation were conducted.

RESULTS: In OLK, we observed significant shifts in the oral microbial diversity, marked by elevated abundances of Streptococcus, Glaesserella, and Pseudomonas aeruginosa. Moreover, shifts in the microbiota precede the manifestation of clinical symptoms of OLK. Functional pathway analysis highlighted enrichment in metabolism, quorum sensing, and cancer-associated microRNA pathways. Serum levels of inflammatory markers (TNF-α and IL-6) were significantly elevated in OLK and significantly correlated with specific bacterial taxa.

DISCUSSION: This study demonstrates the utility of 2bRAD-M sequencing in overcoming traditional metagenomic limitations, offering a high-resolution view of microbiome dynamics in low-biomass environments such as the oral mucosa. These findings establish the oral microbiota as candidate early biomarkers for OLK screening and prevention, opening avenues for precision diagnostics and targeted therapies to mitigate cancer risk associated with OLK.},
}

@article {pmid41199948,
year = {2025},
author = {Vasanthrao, R and Nidhin, IK and Taj, Z and Chattopadhyay, I},
title = {Comprehensive whole metagenomics analysis uncovers microbial community and resistome variability across anthropogenically contaminated soils in urban and suburban areas of Tamil Nadu, India.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1649872},
pmid = {41199948},
issn = {1664-302X},
abstract = {INTRODUCTION: Environmental contamination by heavy metals and hydrocarbons significantly impacts microbial diversity and soil functionality.

METHODS: This study employs whole-genome metagenome sequencing to analyse microbial compositions, antibiotic resistance genes (ARGs), heavy metal resistance genes (HMRs), and virulence genes (VGs) in soil samples from diverse locations, including gardens, poultry farms, cattle sheds, markets, hospitals, thermal power plants, paper industries, and waste disposal sites.

RESULTS: The findings indicate that heavy metal concentrations (Pb, Cr, Cd, and Cu) and hydrocarbons (heptadecane, triacontane, docosane, and heneicosane) were positively correlated with several microbial phyla with relatively high abundances in these contaminated sites, such as Actinobacteria, Proteobacteria, Basidiomycota, Ascomycota, Euryarchaeota, and Apicomplexa. The prevalence of multidrug resistance genes, including MexD, MexC, MexE, MexF, MexT, CmeB, MdtB, MdtC, and OprN, was significant, facilitating antibiotic resistance primarily via efflux pump mechanisms (42%), followed by antibiotic inactivation (23%) and changes in antibiotic targets (18%). Virulence genes such as espR, regX3, sigA/rpoV, bap, and sugB were significantly prevalent in contaminated locations, indicating microbial pathogenic potential in polluted ecosystems. The functional gene analysis revealed significant metabolic pathways related to protein metabolism, carbohydrates, amino acids and their derivatives, metabolism, and DNA metabolism, highlighting the microbial adaptation processes engaged in pollution degradation and resource utilisation.

DISCUSSION: This study establishes a clear link between environmental pollution, microbial adaptations, and functional resilience, emphasizing the ecological significance of microbial bio-remediation in shaping targeted remediation strategies and long-term ecological recovery. Understanding these microbial interactions is essential for developing targeted remediation techniques and assessing long-term ecological recovery in contaminated regions.},
}

@article {pmid41199944,
year = {2025},
author = {Dai, L and Guo, XR and Chen, XR and Ma, MH and Liu, ZH and Lai, J and Lu, J and Feng, M and Liu, XX and Yang, SH},
title = {A review of the mechanism, diagnosis, and treatment of Naegleria fowleri infection.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1686695},
pmid = {41199944},
issn = {1664-302X},
abstract = {Naegleria fowleri is a rare pathogen responsible for primary amoebic meningoencephalitis (PAM), a fatal central nervous system infection characterized by rapid clinical progression and an extremely high mortality rate. The existing diagnostic methods are insufficiently sensitive, and therapeutic options are minimal, making early recognition and intervention extremely challenging. This review systematically examines the biological characteristics and pathogenic mechanisms of this pathogen, as well as current diagnostic and treatment strategies, with a particular focus on the groundbreaking applications of emerging technologies such as metagenomic next-generation sequencing (mNGS) in the diagnosis of difficult-to-treat infections. The aim is to provide theoretical support and practical guidance for rapid identification, accurate diagnosis, and timely intervention in clinical practice, serving as a reference for the prevention and treatment of N. fowleri infections.},
}

@article {pmid41199943,
year = {2025},
author = {Zhang, M and Di, H and Wang, S and Ning, Z},
title = {Column experiment reveals high natural attenuation potential for toluene in iron-rich aquifers but significant concomitant secondary Fe pollution risk.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1687219},
pmid = {41199943},
issn = {1664-302X},
abstract = {INTRODUCTION: Iron mineral reduction mediated by indigenous microbes represents a crucial natural attenuation mechanism for organic contaminants like toluene in anaerobic aquifers, yet the partitioning of generated Fe(II) species and associated secondary pollution risks remain poorly constrained.

METHODS: This study employed controlled column experiments simulating an iron-rich aquifer (ferrihydrite-amended quartz sand) to track the biogeochemical dynamics of toluene degradation coupled with iron transformation. Over 43 days, we quantified spatiotemporal changes in toluene concentrations, dissolved/solid-phase iron species, and microbial community structure through high-frequency hydrochemical monitoring and metagenomic sequencing.

RESULTS AND DISCUSSION: Results demonstrated that iron-reducing consortia (notably Thiobacillus and Pseudomonas) drove > 99% toluene degradation within 10 cm flow distance, effectively containing plume migration. However, Fe(III) reduction generated Fe(II) predominantly (98%) as immobile solid-phase minerals, with only 1%-2% manifesting as dissolved Fe[2+]. This dissolved fraction accumulated progressively across space and time, exceeding China's groundwater quality threshold (0.3 mg/L) at 90% of monitoring points by experiment termination despite near-complete toluene removal. The study confirms that iron-rich aquifers provide significant natural attenuation capacity for petroleum hydrocarbons but concurrently pose substantial secondary contamination risks through highly mobile Fe[2+] generation. Therefore, it is recommended to include solidphase ferrous iron [Fe(II)] as an indicator in natural attenuation assessments and to take into account biogeochemical by-products such as Fe[2+] in risk assessment efforts.},
}

@article {pmid41199942,
year = {2025},
author = {Zeng, W and Yang, L and Cui, L and Liang, C and Zhu, D and Fang, Y and Zhang, Y and Liu, H},
title = {Virome analysis and detection of ticks and tick-borne viruses in Shanghai, China.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1699705},
pmid = {41199942},
issn = {1664-302X},
abstract = {INTRODUCTION: Ticks are well-known ectoparasites and vectors responsible for transmitting a diverse range of pathogens, including viruses, bacteria, and protozoa, many of which pose substantial risks to public health and livestock. In recent decades, the incidence and diversity of tick-borne diseases have increased globally, with several novel tick-borne viruses (TBVs) being discovered.

METHODS: This study aimed to characterize the virome of ticks collected from various locations in Shanghai, China, using next-generation sequencing (NGS). A total of 2,568 ticks belonging to three dominant species-Haemaphysalis flava, Haemaphysalis longicornis, and Rhipicephalus sanguineus sensu lato-were collected and analyzed through metagenomic sequencing.

RESULTS: The sequencing analysis identified 214 viral contigs classified into 32 viral families, including Chrysoviridae, Phenuiviridae, Partitiviridae, Nairoviridae, Dicistroviridae, Reoviridae, Botourmiaviridae, and Flaviviridae. Several TBVs with potential relevance to human and animal health, such as Cheeloo Jingmen-like virus (CJLV), Songling virus (SGLV), brown dog tick phlebovirus 1 (BDTPV1), brown dog tick phlebovirus 2 (BDTPV2), and Wuhan mosquito virus 1 (WMV1), were detected. Significant differences in virome composition among tick species based on geographical locations were also observed.

DISCUSSION: These findings highlight the influence of environmental factors on viral diversity in ticks and underscore the need for ongoing surveillance of TBVs. Implementation of longitudinal virome monitoring across tick developmental stages in Shanghai will provide critical insights for early warning systems, disease prevention strategies, and public health interventions.},
}

@article {pmid41199613,
year = {2025},
author = {Kagemasa, S and Kuroda, K and Nakai, R and Sato, M and Li, YY and Kubota, K},
title = {Metabolic Potential of Candidatus Saccharimonadia Including Rare Lineages in Activated Sludge.},
journal = {Environmental microbiology reports},
volume = {17},
number = {6},
pages = {e70231},
doi = {10.1111/1758-2229.70231},
pmid = {41199613},
issn = {1758-2229},
support = {JP18H01564//Japan Society for the Promotion of Science/ ; JP21H01460//Japan Society for the Promotion of Science/ ; JP23H02545//Japan Society for the Promotion of Science/ ; JP23K27236//Japan Society for the Promotion of Science/ ; JP23K19153//Japan Society for the Promotion of Science/ ; JP24H00328//Japan Society for the Promotion of Science/ ; JP21J11654//Japan Society for the Promotion of Science/ ; //Tohou University - AIST matching fund/ ; //MEXT WISE Program for Sustainability in Dynamic Earth (SyDE), Japan/ ; },
mesh = {*Sewage/microbiology ; Phylogeny ; Genome, Bacterial ; Metagenomics ; *Bacteria/metabolism/genetics/classification/isolation & purification ; Wastewater/microbiology ; },
abstract = {Candidatus Saccharimonadia is a class-level lineage of ultrasmall bacteria within the phylum Minisyncoccota (formerly Candidate Phyla Radiation or Ca. Patescibacteria), commonly found in activated sludge processes treating municipal wastewater. In this study, we aimed to elucidate the metabolic potential of Ca. Saccharimonadia by using shotgun metagenomic sequencing combined with a filtration-based size-fractionation approach for activated sludge from five wastewater treatment plants. A total of 65 high-quality metagenomic bins were recovered, belonging to four orders and 19 families of Ca. Saccharimonadia, including previously unreported lineages in activated sludge. These bins had small genomes (approximately 0.46-1.73 Mbp) with limited metabolic capabilities, indicating dependency on other microorganisms. Notably, the order Ca. Saccharimonadales retained a type IV secretion system and effector gene cluster for parasitic interactions with the hosts, suggesting that Ca. Saccharimonadales bacteria may exhibit a parasitic lifestyle. Co-occurrence network analysis showed that members of the order Ca. Saccharimonadales were significantly correlated with multiple lineages, including Actinobacteriota, for which a parasitic relationship has been previously demonstrated. Our results shed light on the potential ecophysiology of the diverse members of Ca. Saccharimonadia, providing a comprehensive understanding of Ca. Saccharimonadia in activated sludge.},
}

*Sewage/microbiology
Phylogeny
Genome, Bacterial
Metagenomics
*Bacteria/metabolism/genetics/classification/isolation & purification
Wastewater/microbiology

@article {pmid41199348,
year = {2025},
author = {Ghozlane, A and Thirion, F and Plaza Oñate, F and Gauthier, F and Le Chatelier, E and Annamalé, A and Almeida, M and Ehrlich, SD and Pons, N},
title = {Accurate profiling of microbial communities for shotgun metagenomic sequencing with Meteor2.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {227},
pmid = {41199348},
issn = {2049-2618},
support = {ANR-11-DPBS-0001//Metagenopolis/ ; },
mesh = {*Metagenomics/methods ; Animals ; Mice ; Humans ; *Microbiota/genetics ; *Bacteria/genetics/classification ; *Metagenome ; *Gastrointestinal Microbiome/genetics ; *Software ; Computational Biology/methods ; },
abstract = {BACKGROUND: The characterization of complex microbial communities is a critical challenge in microbiome research, as it is essential for understanding the intricate relationships between microorganisms and their environments. Metagenomic profiling has advanced into a multifaceted approach, combining taxonomic, functional, and strain-level profiling (TFSP) of microbial communities. Here, we present Meteor2, a tool that leverages compact, environment-specific microbial gene catalogues to deliver comprehensive TFSP insights from metagenomic samples.

RESULTS: Meteor2 currently supports 10 ecosystems, gathering 63,494,365 microbial genes clustered into 11,653 metagenomic species pangenomes (MSPs). These genes are extensively annotated for KEGG orthology, carbohydrate-active enzymes (CAZymes) and antibiotic-resistant genes (ARGs). In benchmark tests, Meteor2 demonstrated strong performance in TFSP, particularly excelling in detecting low-abundance species. When applied to shallow-sequenced datasets, Meteor2 improved species detection sensitivity by at least 45% for both human and mouse gut microbiota simulations compared to MetaPhlAn4 or sylph. For functional profiling, Meteor2 improved abundance estimation accuracy by at least 35% compared to HUMAnN3 (based on Bray-Curtis dissimilarity). Additionally, Meteor2 tracked more strain pairs than StrainPhlAn, capturing an additional 9.8% on the human dataset and 19.4% on the mouse dataset. Furthermore, in its fast configuration, Meteor2 emerges as one of the fastest available tools for profiling, requiring only 2.3 min for taxonomic analysis and 10 min for strain-level analysis against the human microbial gene catalogue when processing 10 M paired reads - operating within a modest 5 GB RAM footprint. We further validated Meteor2 using a published faecal microbiota transplantation (FMT) dataset, demonstrating its ability to deliver an extensive and actionable metagenomic analysis. The unified database design also simplifies the integration of TFSP outputs, making it straightforward for researchers to interpret and compare results.

CONCLUSIONS: These results highlight Meteor2 as a robust and versatile tool for advancing microbiome research and applications. As an open-source, easy-to-install, and accurate analysis platform, Meteor2 is highly accessible to researchers, facilitating the exploration of complex microbial ecosystems.},
}

*Metagenomics/methods
Animals
Mice
Humans
*Microbiota/genetics
*Bacteria/genetics/classification
*Metagenome
*Gastrointestinal Microbiome/genetics
*Software
Computational Biology/methods

@article {pmid41198952,
year = {2025},
author = {Makarova, KS and Shmakov, SA and Wolf, YI and Mutz, P and Altae-Tran, H and Beisel, CL and Brouns, SJJ and Charpentier, E and Cheng, D and Doudna, J and Haft, DH and Horvath, P and Moineau, S and Mojica, FJM and Pausch, P and Pinilla-Redondo, R and Shah, SA and Siksnys, V and Terns, MP and Tordoff, J and Venclovas, Č and White, MF and Yakunin, AF and Zhang, F and Garrett, RA and Backofen, R and van der Oost, J and Barrangou, R and Koonin, EV},
title = {An updated evolutionary classification of CRISPR-Cas systems including rare variants.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41198952},
issn = {2058-5276},
support = {Intramural funds//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; },
abstract = {The known diversity of CRISPR-Cas systems continues to expand. To encompass new discoveries, here we present an updated evolutionary classification of CRISPR-Cas systems. The updated CRISPR-Cas classification includes 2 classes, 7 types and 46 subtypes, compared with the 6 types and 33 subtypes in our previous survey 5 years ago. In addition, a classification of the cyclic oligoadenylate-dependent signalling pathway in type III systems is presented. We also discuss recently characterized alternative CRISPR-Cas functionalities, notably, type IV variants that cleave the target DNA and type V variants that inhibit the target replication without cleavage. Analysis of the abundance of CRISPR-Cas variants in genomes and metagenomes shows that the previously defined systems are relatively common, whereas the more recently characterized variants are comparatively rare. These low abundance variants comprise the long tail of the CRISPR-Cas distribution in prokaryotes and their viruses, and remain to be characterized experimentally.},
}