@article {pmid40866974,
year = {2025},
author = {Zhang, J and Tang, F and Ni, B and Zhang, Q and Gong, X and Mao, F and Cao, J and Liu, Y},
title = {PGIP: a web server for the rapid taxonomic identification of parasite genomes.},
journal = {Parasites & vectors},
volume = {18},
number = {1},
pages = {365},
pmid = {40866974},
issn = {1756-3305},
support = {2020YFC1200100//National Key R&D Program of China/ ; ZDXYS202207//Jiangsu Province Capability Improvement Project through Science, Technology, and Education/ ; 82372275//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Parasitic diseases remain a global health challenge, and traditional methods in their diagnosis face limitations in sensitivity and scalability. Genome-based sequencing technologies have improved and are increasingly employed for the identification of parasites; however, their clinical adoption remains hindered by the complexity of bioinformatics analysis, reliance on incomplete reference databases, and accessibility barriers for nonspecialists. Overcoming these challenges necessitates the development of standardized analytical workflows and high-quality genomic resources specifically tailored for parasite identification.

METHODS: We developed a user-friendly web server named the Parasite Genome Identification Platform (PGIP). The reference database was sourced from the National Center for Biotechnology Information (NCBI), WormBase, European Nucleotide Archive (ENA), and VEuPathDB, rigorously filtered for quality, and deduplicated using Cluster Database at High Identity with Tolerance (CD-HIT) to ensure accuracy and nonredundancy. To streamline analysis, we integrated a standardized identification pipeline built on Nextflow, which encompasses host DNA depletion, quality control, parasite species identification via both reads mapping and assembly-based approaches, and automated report generation for comprehensive diagnostic insights.

RESULTS: PGIP integrates a curated database of 280 parasite genomes; which is rigorously filtered for quality and taxonomic accuracy. Validation across diverse datasets demonstrated the precise species-level resolution of PGIP, and its compatibility with clinical samples. The platform features an intuitive graphic interface; and one-click analysis significantly reduces reliance on bioinformatics expertise, thus enabling rapid diagnosis.

CONCLUSIONS: PGIP offers an accurate, efficient, and a user-friendly web server designed to simplify and accelerate the taxonomic identification of parasite genomes using data from metagenomic next-generation sequencing. Its automated framework reduces the need for specialized expertise, enabling rapid application in clinical and public health settings.},
}

@article {pmid40866789,
year = {2025},
author = {Kusakabe, S and Kurashige, R and Fukushima, K and Shimizu, K and Yoshihara, T and Motooka, D and Nakamura, S and Kurashige, M and Nakata, K and Hino, A and Kasahara, H and Ueda, T and Fujita, J and Hosen, N and Takehara, T and Oda, J},
title = {Fecal microbiota transplantation for Crohn's disease-like intestinal lesions arising after allogeneic stem cell transplantation.},
journal = {International journal of hematology},
volume = {},
number = {},
pages = {},
pmid = {40866789},
issn = {1865-3774},
abstract = {Several cases of inflammatory bowel disease (or similar gastrointestinal lesions) arising after allogeneic hematopoietic stem cell transplantation have been reported, but the effect of intestinal dysbiosis on development of these lesions remains unclear. We performed fecal microbiota transplantation (FMT) and 16S rRNA microbiome analysis in a patient who developed Crohn's disease-like lesions after allogeneic transplantation. A 62-year-old woman underwent haploidentical stem cell transplantation from her daughter to treat double-hit lymphoma relapsed after chimeric antigen receptor T-cell therapy, and achieved remission without developing acute graft-versus-host disease. Eight months later, she developed Crohn's disease-like intestinal lesions after cytomegalovirus enteritis. Her condition did not improve with the conventional treatment, so she underwent FMT from her daughter as part of a clinical trial. Diarrhea gradually improved, and follow-up endoscopy 4 months after the FMT showed ulcer healing and scarring. The 16S rRNA analysis revealed a reduction in the relative abundance of the Enterococcus genus after FMT, suggesting that dysbiosis may have contributed to lesion development. The patient is currently on a regular diet, with no symptom recurrence, and the primary disease remains in remission. Although this outcome suggests that FMT is effective, careful patient selection is required to reduce the risk of FMT-associated sepsis.},
}

@article {pmid40866482,
year = {2025},
author = {Martin, C and Emerson, JB and Roux, S and Anantharaman, K},
title = {A call for caution in the biological interpretation of viral auxiliary metabolic genes.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {40866482},
issn = {2058-5276},
support = {R35GM143024//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; DE-SC0021198//DOE | SC | Biological and Environmental Research (BER)/ ; DE-AC02-05CH11231//DOE | SC | Biological and Environmental Research (BER)/ ; },
abstract = {Virus-encoded auxiliary metabolic genes (AMGs) are non-essential genes that increase viral fitness by maintaining or manipulating host metabolism during infection. AMGs are intriguing from an evolutionary perspective, as most viral genomes are highly compact and have limited coding capacity for accessory genes. Advances in viral (meta)genomics have expanded the detection of putative AMGs from viruses in diverse environments. However, this has also led to many instances of misannotation due to the limitations of annotation tools, resulting in misinterpretations about the roles of some viral genes. Here, we highlight studies that support claims about AMGs with more than just function predictions for guidance on best practices. We then propose the adoption of an expanded, inclusive view of all genes auxiliary to core viral functions with the term 'auxiliary viral genes' (AVGs), alongside an associated eco-evolutionary framework for considering the types of analyses that can better support claims made about AVGs.},
}

@article {pmid40865847,
year = {2025},
author = {Dong, BX and Liu, YJ and Liu, SH and Lu, W and Zhu, C and Tian, YJ and Li, G},
title = {Per822: A pH-stable metagenome-derived perhydrolase for dye decolorization, oil stain removal, and benzo[a]pyrene degradation.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {147131},
doi = {10.1016/j.ijbiomac.2025.147131},
pmid = {40865847},
issn = {1879-0003},
abstract = {Per822, a newly discovered metagenomic perhydrolase, merges promiscuous catalysis with exceptional robustness, unlocking versatile solutions for sustainable chemistry. The results revealed that Per822 possesses both esterase and peroxidase activities. Its esterase activity was optimal at pH 8.5 and 40 °C, while its peroxidase activity reached optimal levels at pH 4.5 and 45 °C. Additionally, Per822 demonstrated stability across a broad pH and temperature range. It also retained high activity in various surfactants and organic solvents, highlighting its potential for industrial applications. Application studies showed that Per822 effectively removed chili oil stains from cotton fabric when used as a laundry additive. In dye decolorization experiments, Per822 achieved efficient decolorization of multiple dyes after the addition of Br[-] and Fe[2+]. Notably, in the degradation of benzo(a)pyrene (BaP), the peracetic acid generated by Per822 (at a concentration of 64 mM) achieved a degradation rate of 99.06 % within 72 h. Subsequent plant and microbial toxicity tests indicated a significant reduction in the toxicity of the BaP degradation products. In conclusion, Per822, with its multifunctionality, stability, and outstanding performance in laundry, dye decolorization, and environmental remediation, shows great potential as a candidate enzyme for various applications in industries such as detergents, environmental repair, and organic synthesis.},
}

@article {pmid40865528,
year = {2025},
author = {Shi, Y and Li, Y and Li, H and Haerheng, A and Marcelino, VR and Lu, M and Lemey, P and Tang, J and Bi, Y and Pettersson, JH and Bohlin, J and Klaps, J and Wu, Z and Wan, W and Sun, B and Kang, M and Holmes, EC and He, N and Su, S},
title = {Extensive cross-species transmission of pathogens and antibiotic resistance genes in mammals neglected by public health surveillance.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2025.08.016},
pmid = {40865528},
issn = {1097-4172},
abstract = {Non-traditional farmed and wild mammals are often neglected in pathogen surveillance. Through metagenomic and metatranscriptomic sequencing of fecal and tissue samples from 973 asymptomatic mammals, we identified 128 viruses (30 novel), including a new coronavirus genus, 10,255 bacterial species (over 7,000 undescribed), 201 fungi, and 7 parasites. Farmed and wild mammals shared 13.3% of virus species, including canine coronavirus in Asiatic black bears and Getah virus in rabbits, while the 2.3.4.4b clade of H5N1 avian influenza virus was found in a wild leopard cat. We identified potential bacterial pathogen transmission between farmed and wild mammals and bacterial strains with high genetic similarity to those found in humans. We observed 157 clinically prioritized antibiotic resistance genes (ARGs) in mammalian microbiomes with greater than 99% identity to ARGs from human microbiomes, often co-occurring with mobile genetic elements. Overall, this work highlights cross-species risks at the human-animal interface.},
}

@article {pmid40865345,
year = {2025},
author = {Tao, X and Gao, Y and Jin, Z and Lu, S and Li, Z and Guo, S and Fan, Q and Li, J and Qiao, C and Lei, H and Zhang, Z and Zhao, C and Wu, J},
title = {Co-administration of berberine and evodiamine: Mitigating evodiamine-induced hepatotoxicity and potentiating colitis treatment.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {147},
number = {},
pages = {157185},
doi = {10.1016/j.phymed.2025.157185},
pmid = {40865345},
issn = {1618-095X},
abstract = {BACKGROUND: The combined therapeutic mechanisms of evodiamine (EVO) and berberine (BBR), which are the primary bioactive components contributing to the pharmacological effects of Euodiae Fructus and Rhizoma Coptidis, a classic herb pair used for colitis, have not yet been fully elucidated PURPOSE: This study aimed to investigate the critical mechanisms by which co-administration EVO and BBR mitigated EVO-induced hepatotoxicity while exerting therapeutic effects against colitis.

METHODS: Safety and therapeutic outcomes of EVO alone and combined BBR were validated in normal and colitis models. RNA-seq sequencing was performed on liver and colon tissues from different groups, while metagenomic sequencing was utilized to analysis fecal samples. An integrated bioinformatics analysis of transcriptomic and metagenomic data was conducted to reveal the mechanisms underlying EVO-induced hepatotoxicity and the protective and synergistic effects of BBR against colitis. Molecular biology experiments were employed to validate the regulatory mechanism, with a particular emphasis on the interactions within the gut- liver axis, including those related to lipid metabolism and inflammatory pathways.

RESULTS: BBR attenuated EVO-induced hepatotoxicity in C57 mice by ameliorating pathological injuries and hepatic steatosis as well as inhibiting abnormal AST/ALT elevation, thereby revealing its hepatoprotective effects. In colitis mice, the combination therapy exhibited enhanced efficacy in reducing mucosal damage, restoring goblet cells populations, and suppressing pro-inflammatory cytokines production compared to monotherapy. Integrated analysis of RNA-seq combined with experimental validation revealed that EVO-induced hepatotoxicity was associated with the disrupted fatty acid β-oxidation and cholesterol synthesis homeostasis. Notably, co-administration of BBR effectively rescued metabolic disturbance through modulating core regulatory targets such as ACSL1, CPT1B, SQLE, DHCR7. Additionally, the combination treatment synergistically inhibited IL-17/NF-κB signaling, upregulated tight junction proteins, and rectified gut microbiota dysbiosis, thereby alleviating intestinal injury in colitis mice. Furthermore, ACSL3, a central regulator of fatty acid β-oxidation, was identified as a pivotal target through which the combination of EVO combined BBR suppressed lipid peroxidation-mediated activation of IL-17/NF-κB, leading to alleviate inflammation in LPS-induced NCM460 cell.

CONCLUSION: ACSL3 was identified as the critical therapeutic target through underlying the amelioration of fatty acid metabolism-mediated inflammatory injury in colitis by the combined administration of EVO and BBR, thereby offering a scientific foundation for precise and safe clinical drug administration.},
}

@article {pmid40865323,
year = {2025},
author = {Xu, X and Lin, X and Fang, M and Huo, M and Kou, Z and Ma, W and Li, X and Cheng, Q and Wang, H and Huang, L},
title = {The mobility, host, and co-occurrence of antibiotic resistance genes in multi-type pig manure-soil systems: Metagenome assembly analysis.},
journal = {Journal of environmental management},
volume = {393},
number = {},
pages = {127087},
doi = {10.1016/j.jenvman.2025.127087},
pmid = {40865323},
issn = {1095-8630},
abstract = {Antibiotic resistance genes (ARGs) pose significant threats to public health and environmental safety, yet the mobility and hosts of ARGs in animal manure-soil systems remain poorly understood. Here, we evaluated the environmental risks of tilmicosin (TIL) and investigated ARG profiles, mobility, and drivers in pig manure-soil systems using metagenomic assembly. TIL was effectively degraded during aerobic composting and fertilization via hydroxylation, demethylation, and deglycosylation. Notably, the total abundance of ARGs significantly decreased during aerobic composting and fertilization, and manure types affected the distribution and composition of ARGs in fertilized soils. There was a special correlation between the genetic location and type of ARGs. In addition, the results showed co-localization of some specific ARGs and mobile genetic elements (MGEs) (tetA-tetR- transposase; tetR-floR- Tn3 family). A significant correlation was found between Escherichia coli and multiple ARG types, especially multidrug ARGs. Microbial community was the dominant factor driving the variations of ARGs in pig manure-soil systems, followed by MGEs, environmental factors, and antibiotic concentration. This study advances the understanding on the environmental risk assessment of TIL and elucidates the key drivers of ARG dissemination in pig manure-soil systems, providing critical insights and actionable strategies for sustainable livestock management and environmental risk control.},
}

@article {pmid40865317,
year = {2025},
author = {Liu, Y and Dou, X and Wang, C and Song, M and Liu, D and Liu, X and Zhu, Q},
title = {Long-term nitrogen addition enhanced soil carbon sequestration through coupled physicochemical and microbial mechanisms in a temperate forest.},
journal = {Journal of environmental management},
volume = {393},
number = {},
pages = {127068},
doi = {10.1016/j.jenvman.2025.127068},
pmid = {40865317},
issn = {1095-8630},
abstract = {As critical carbon (C) sinks in terrestrial ecosystems, temperate forests exhibit complex responses to atmospheric nitrogen (N) deposition. Through a 13-year controlled field experiment, we systematically investigated the effects of three N forms (NO3[-]-N, NH4[+]-N, NH4NO3-N) at two deposition levels (50/150 kg N·ha[-1]·yr[-1]) on soil organic C (SOC) dynamics. The experimental data revealed a three-phase SOC accumulation pattern, with aggregate-associated C showing 6.23-43.54 % enhancement. Particularly, silt-clay fractions demonstrated superior C sequestration capacity (13.10 ± 0.45 g kg[-1]), suggesting strengthened physical protection through aggregate stabilization. Nuclear magnetic resonance spectroscopic (NMR) analysis confirmed progressive increases in stable C pools, with aromatic and alkyl C rising by 12.44-42.94 %. Microbial necromass accumulation contributed 11.90-44.31 % to SOC stock, enhancing biochemical resistance to decomposition. Metagenomic evidence revealed N-dependent microbial community restructuring, particularly diminished abundances of ligninolytic genes, which suppressed recalcitrant SOC mineralization. These dual regulation mechanisms - physical protection via aggregate formation and biochemical stabilization through microbial metabolic constraint - synergistically increased SOC stability. Our findings elucidate the C-N coupling mechanisms in forest soils under chronic N enrichment, providing critical insights for predicting terrestrial C sink potential under global change scenarios.},
}

@article {pmid40865218,
year = {2025},
author = {Yang, H and Fu, H and Zhao, Y and Li, R and Cao, M and Liu, Y and Ni, Y and Song, W and Liang, Y and Cai, P and Chang, W and Tao, F and Wang, H and Liu, K},
title = {Antibiotic resistance genes in multi-matrices of Chaohu Lake: Spatiotemporal variation and correlation with pesticides and PPCPs.},
journal = {Journal of hazardous materials},
volume = {497},
number = {},
pages = {139604},
doi = {10.1016/j.jhazmat.2025.139604},
pmid = {40865218},
issn = {1873-3336},
abstract = {This study explored the spatiotemporal distributions of microorganisms and antibiotic resistance genes (ARGs) in the surface water, sediments, and fish intestinal contents (IC) of Chaohu Lake, and further revealed the pharmaceuticals and personal care products (PPCPs), pesticides in lake water and their relationships with ARGs. 53 types of pesticides and 25 types of PPCPs were identified in the river-lake system basin, with the highest concentrations observed for tebuconazole (1142.36 ng/L) and amantadine (851.41 ng/L). Higher concentrations of these target contaminants were detected in the western part of the lake and during the wet season. No significant east-west differences in ARGs and microbiota across the three environmental matrices were found, whereas seasonal variations impacted lake water and IC more profoundly than sediments. Significant correlations between microbiota and ARGs in the lake water and IC, while those in sediments showed weaker associations. Co-occurrence network analysis showed, among three environmental media, β-lactam and multidrug-resistant genes were widespread found, and Proteobacteria were identified as a stable host. Non-antibiotic pollutants, such as amantadine and terbuthylazine, displayed significant positive correlations with ARGs, similar to sulfamethoxazole and clindamycin. Our findings highlight the important roles of seasonal hydrological changes and non-antibiotic pollutants in the dissemination of ARGs.},
}

@article {pmid40864189,
year = {2025},
author = {Salomon, MJ and Burton, RA},
title = {Exploring arbuscular mycorrhizal colonization in Agave tequilana: Insights into mycorrhizal partnerships of an emerging crop.},
journal = {Mycorrhiza},
volume = {35},
number = {5},
pages = {52},
pmid = {40864189},
issn = {1432-1890},
mesh = {*Mycorrhizae/physiology/classification/genetics ; *Agave/microbiology ; Soil Microbiology ; Plant Roots/microbiology ; *Crops, Agricultural/microbiology ; Plantago/microbiology ; South Australia ; },
abstract = {This study explores the arbuscular mycorrhizal (AM) fungi associations of Agave tequilana, an emerging crop with significant commercial potential that is increasingly being grown outside its native distribution in the arid regions of the Americas. A greenhouse experiment was conducted using field-collected soil inoculum from various locations in South Australia to inoculate A. tequilana plus Plantago lanceolata as a comparative model host. Metagenomic sequencing of the colonized roots with AM fungal-specific amplicons assessed the AM fungal community structure. The Shannon alpha diversity was similar between both plant species, and both predominantly associated with the genus Glomus. However, A. tequilana had a narrower AM fungal community compared to P. lanceolata, which was associated with a broader diversity of AM fungi. Beta diversity analysis of the AM fungal community composition revealed that the factor species (agave/plantago) was significant (p = 0.0001), whereas the inoculum location was not (p = 0.29). The association of A. tequilana with AM fungi from the family Acaulosporaceae, as found in Mexican studies, could not be confirmed. These findings suggest a specialized adaptation of A. tequilana to specific AM fungal species, which could have important implications for using AM fungi in sustainable agave production when cultivated outside their native regions.},
}

*Mycorrhizae/physiology/classification/genetics
*Agave/microbiology
Soil Microbiology
Plant Roots/microbiology
*Crops, Agricultural/microbiology
Plantago/microbiology
South Australia

@article {pmid40863630,
year = {2025},
author = {Hu, GA and Sun, HY and Yin, QJ and Wang, H and Liu, SY and Wang, BG and Wang, H and Li, X and Wei, B},
title = {Exploring the Biosynthetic Potential of Microorganisms from the South China Sea Cold Seep Using Culture-Dependent and Culture-Independent Approaches.},
journal = {Marine drugs},
volume = {23},
number = {8},
pages = {},
pmid = {40863630},
issn = {1660-3397},
support = {2022YFC2804700//National Key Research and Development Program/ ; 42276137//National Natural Science Foundation of China/ ; RF-A2022013//Fundamental Research Funds for the Provincial Universities of Zhejiang/ ; },
mesh = {China ; *Geologic Sediments/microbiology ; RNA, Ribosomal, 16S/genetics ; Metagenomics/methods ; Secondary Metabolism/genetics ; *Microbiota/genetics ; *Bacteria/genetics/metabolism ; *Seawater/microbiology ; Ecosystem ; Oceans and Seas ; },
abstract = {Cold seep ecosystems harbor unique microbial communities with potential for producing secondary metabolites. However, the metabolic potential of cold seep microorganisms in the South China Sea remains under-recognized. This study employed both culture-dependent and culture-independent approaches, including 16S rRNA amplicon sequencing and metagenomics, to investigate microbial communities and their potential for secondary metabolite production in the South China Sea cold seep. The results indicate microbial composition varied little between two non-reductive sediments but differed significantly from the reductive sediment, primarily due to Planctomycetes and Actinobacteria. Predicting the Secondary Metabolism Potential using Amplicon (PSMPA) predictions revealed 115 strains encoding more than 10 biosynthetic gene clusters (BGCs), with lower BGC abundance in reductive sediment. Culture-dependent studies showed Firmicutes as the dominant cultivable phylum, with strains from shallow samples encoding fewer BGCs. Metagenomic data confirmed distinct microbial compositions and BGC distributions across sediment types, with cold seep type having a stronger influence than geographic location. Certain BGCs showed strong correlations with sediment depth, reflecting microbial adaptation to nutrient-limited environments. This study provides a comprehensive analysis of the metabolic capabilities of South China Sea cold seep microorganisms and reveals key factors influencing their secondary metabolic potential, offering valuable insights for the efficient exploration of cold seep biological resources.},
}

China
*Geologic Sediments/microbiology
RNA, Ribosomal, 16S/genetics
Metagenomics/methods
Secondary Metabolism/genetics
*Microbiota/genetics
*Bacteria/genetics/metabolism
*Seawater/microbiology
Ecosystem
Oceans and Seas

@article {pmid40863595,
year = {2025},
author = {You, Y and Zhao, S and Xie, B and Li, Z and Gong, W and Zhang, G and Li, Q and Zhao, X and Xin, Z and Wu, J and Gao, Y and Xiang, H},
title = {A Review of Maricultural Wastewater Treatment Using an MBR: Insights into the Mechanism of Membrane Fouling Mitigation Through a Microalgal-Bacterial Symbiotic and Microbial Ecological Network.},
journal = {Membranes},
volume = {15},
number = {8},
pages = {},
pmid = {40863595},
issn = {2077-0375},
support = {No. 52100036, No. 52270027//The National Natural Science Fund of China/ ; No. ZR2021QE119, ZR2023ME212//The Natural Science Foundation of Shandong Province of China/ ; No. QA202140//Open Project of State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology/ ; 2023SYLHY13//the Taishan Industrial Experts Program and the Double First-class Discipline Construction Fund Project of Harbin Institute of Technology at Weihai/ ; },
abstract = {Membrane bioreactors (MBRs) have been utilized for maricultural wastewater treatment, where high-salinity stress results in dramatic membrane fouling in the actual process. A microalgal-bacterial symbiotic system (MBSS) offers advantages for photosynthetic oxygen production, dynamically regulating the structure of extracellular polymeric substances (EPSs) and improving the salinity tolerance of bacteria and algae. This study centered on the mechanisms of membrane fouling mitigation via the microalgal-bacterial interactions in the MBSS, including improving the pollutant removal, optimizing the system parameters, and controlling the gel layer formation. Moreover, the contribution of electrochemistry to decreasing the inhibitory effects of high-salinity stress was investigated in the MBSS. Furthermore, patterns of shifts in microbial communities and the impacts have been explored using metagenomic technology. Finally, this review aims to offer new insights for membrane fouling mitigation in actual maricultural wastewater treatment.},
}

@article {pmid40863548,
year = {2025},
author = {García-Muñoz, A and Pino-Bodas, R},
title = {Evaluating the Assembly Strategy of a Fungal Genome from Metagenomic Data: Solorina crocea (Peltigerales, Ascomycota) as a Case Study.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {11},
number = {8},
pages = {},
pmid = {40863548},
issn = {2309-608X},
support = {CNS2022-135904//Agencia Estatal de Investigación/ ; 2020-T1/AMB-19852//CAM Atracción de Talento program/ ; },
abstract = {The advent of next-generation sequencing technologies has given rise to considerably diverse techniques. However, integrating data from these technologies to generate high-quality genomes remains challenging, particularly when starting from metagenomic data. To provide further insight into this process, the genome of the lichenized fungus Solorina crocea was sequenced using DNA extracted from the thallus, which contains the genome of the mycobiont, along with those of the photobionts (a green alga and a cyanobacterium), and other associated microorganisms. Three different strategies were assessed for the assembly of a de novo genome, employing data obtained from Illumina and PacBio HiFi technologies: (1) hybrid assembly based on metagenomic data; (2) assembly based on metagenomic long reads and scaffolded with filtered mycobiont long and short reads; (3) hybrid assembly based on filtered mycobiont short and long reads. Assemblies were compared according to contiguity and completeness criteria. Strategy 2 achieved the most continuous and complete genome, with a size of 55.5 Mb, an N50 of 148.5 kb, and 519 scaffolds. Genome annotation and functional prediction were performed, including identification of secondary metabolite biosynthetic gene clusters. Genome annotation predicted 6151 genes, revealing a high number of genes associated with transport, carbohydrate metabolism, and stress response.},
}

@article {pmid40863514,
year = {2025},
author = {Alcaíno, J and Veloso, C and Coche, M and Troncoso, D and Baeza, M},
title = {Fungi in the Chilean Altiplano: Analyses of Diversity and Yeasts with Applied Enzymatic Potential.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {11},
number = {8},
pages = {},
pmid = {40863514},
issn = {2309-608X},
support = {Fondecyt 1230427//Agencia Nacional de Investigacion y Desarrollo de Chile/ ; },
abstract = {Fungal communities in high plateau ecosystems remain understudied despite their crucial roles in soil ecosystems, and yeasts inhabiting extreme regions have potential for industrial and biotechnological applications. We studied the fungal diversity in soils across 14 Chilean Altiplano sites using amplicon-based metagenomics and isolation of yeasts to assess their growth under various conditions and hydrolytic enzyme secretion. Using the metagenomic approach, the Ascomycota and Basidiomycota phyla were found to be the most abundant (85% and 8%, respectively). Unclassified families and genera prevailed at six and ten sites, respectively. At the other sites, the most abundant families included Cladosporiaceae, Teratosphaeriaceae, and Sporormiaceae, and the genera Oleoguttula, Coniochaeta, and Peziza. Biodiversity indices did not correlate with the soil's geographic origin, organic matter content, humidity, or pH. Most isolated yeasts belong to the Naganishia, Holtermanniella, and Vishniacozyma genera, growing at temperatures ranging from 4 °C to 26 °C. Most isolates could use glucose, sucrose, and maltose as carbon sources and exhibited amylase, esterase, pectinase, and protease activities at 30 °C and below. Our results indicate that the evaluated soil physicochemical parameters do not explain the fungal distribution in the Altiplano and highlight the region as a reservoir of unknown fungi, including yeasts with industrially relevant enzymes.},
}

@article {pmid40863505,
year = {2025},
author = {Cho, SE and Park, KH and Shin, K and Lee, DH},
title = {Detection of Pestalotiopsis abbreviata sp. nov., the Causal Agent of Pestalotiopsis Leaf Blight on Camellia japonica Based on Metagenomic Analysis.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {11},
number = {8},
pages = {},
pmid = {40863505},
issn = {2309-608X},
support = {FE0703-2023-02-2024//National Institute of Forestry Science/ ; RS-2023-00250589//National Research Foundation of Korea/ ; Research for the next generation of academics//Gyeongsang National University/ ; },
abstract = {Tree diseases affecting Camellia japonica have emerged as a significant threat to the health and longevity of this ornamental tree, particularly in countries where this tree species is widely distributed and cultivated. Among these, Pestalotiopsis spp. have been frequently reported and are considered one of the most impactful fungal pathogens, causing leaf blight or leaf spot, in multiple countries. Understanding the etiology and distribution of these diseases is essential for effective management and conservation of C. japonica populations. The traditional methods based on pathogen isolation and pure culture cultivation for diagnosis of tree diseases are labor intensive and time-consuming. In addition, the frequent coexistence of the major pathogens with other endophytes within a single C. japonica tree, coupled with inconsistent symptom expression and the occurrence of pathogens in asymptomatic hosts, further complicates disease diagnosis. These challenges highlight the urgent need to develop more rapid, accurate, and efficient diagnostic or monitoring tools to improve disease monitoring and management on trees, including C. japonica. To address these challenges, we applied a metagenomic approach to screen fungal communities within C. japonica trees. This method enabled comprehensive detection and characterization of fungal taxa present in symptomatic and asymptomatic tissues. By analyzing the correlation between fungal dominance and symptom expression, we identified key pathogenic taxa associated with disease manifestation. To validate the metagenomic approach, we employed a combined strategy integrating metagenomic screening and traditional fungal isolation to monitor foliar diseases in C. japonica. The correlation between dominant taxa and symptom expression was confirmed. Simultaneously, traditional isolation enabled the identification of a novel species, Pestalotiopsis, as the causal agent of leaf spot disease on C. japonica. In addition to confirming previously known pathogens, our study led to the discovery and preliminary characterization of a novel fungal taxon with pathogenic potential. Our findings provide critical insights into the fungal community of C. japonica and lay the groundwork for developing improved, rapid diagnostic tools for effective disease monitoring and management of tree diseases.},
}

@article {pmid40863340,
year = {2025},
author = {Renganathan, P and Gaysina, LA and García Gutiérrez, C and Rueda Puente, EO and Sainz-Hernández, JC},
title = {Harnessing Engineered Microbial Consortia for Xenobiotic Bioremediation: Integrating Multi-Omics and AI for Next-Generation Wastewater Treatment.},
journal = {Journal of xenobiotics},
volume = {15},
number = {4},
pages = {},
pmid = {40863340},
issn = {2039-4713},
support = {25-24-00481//Russian Science Foundation/ ; },
abstract = {The global increase in municipal and industrial wastewater generation has intensified the need for ecologically resilient and technologically advanced treatment systems. Although traditional biological treatment technologies are effective for organic load reduction, they often fail to remove recalcitrant xenobiotics such as pharmaceuticals, synthetic dyes, endocrine disruptors (EDCs), and microplastics (MPs). Engineered microbial consortia offer a promising and sustainable alternative owing to their metabolic flexibility, ecological resilience, and capacity for syntrophic degradation of complex pollutants. This review critically examines emerging strategies for enhancing microbial bioremediation in wastewater treatment systems (WWTS), focusing on co-digestion, biofilm engineering, targeted bioaugmentation, and incorporation of conductive materials to stimulate direct interspecies electron transfer (DIET). This review highlights how multi-omics platforms, including metagenomics, transcriptomics, and metabolomics, enable high-resolution community profiling and pathway reconstructions. The integration of artificial intelligence (AI) and machine learning (ML) algorithms into bioprocess diagnostics facilitates real-time system optimization, predictive modeling of antibiotic resistance gene (ARG) dynamics, and intelligent bioreactor control. Persistent challenges, such as microbial instability, ARG dissemination, reactor fouling, and the absence of region-specific microbial reference databases, are critically analyzed. This review concludes with a translational pathway for the development of next-generation WWTS that integrate synthetic microbial consortia, AI-mediated biosensors, and modular bioreactors within the One Health and Circular Economy framework.},
}

@article {pmid40863141,
year = {2025},
author = {Faraj, S and Joblin-Mills, A and Sequeira-Bisson, IR and Leiu, KH and Tung, T and Wallbank, JA and Fraser, K and Miles-Chan, JL and Poppitt, SD and Taylor, MW},
title = {Investigating Multi-Omic Signatures of Ethnicity and Dysglycaemia in Asian Chinese and European Caucasian Adults: Cross-Sectional Analysis of the TOFI_Asia Study at 4-Year Follow-Up.},
journal = {Metabolites},
volume = {15},
number = {8},
pages = {},
pmid = {40863141},
issn = {2218-1989},
support = {3710040, 3719728 & 3720614//New Zealand National Science Challenge High-Value Nutrition Programme/ ; },
abstract = {Background: Type 2 diabetes (T2D) is a global health epidemic with rising prevalence within Asian populations, particularly amongst individuals with high visceral adiposity and ectopic organ fat, the so-called Thin-Outside, Fat-Inside phenotype. Metabolomic and microbiome shifts may herald T2D onset, presenting potential biomarkers and mechanistic insight into metabolic dysregulation. However, multi-omics datasets across ethnicities remain limited. Methods: We performed cross-sectional multi-omics analyses on 171 adults (99 Asian Chinese, 72 European Caucasian) from the New Zealand-based TOFI_Asia cohort at 4-years follow-up. Paired plasma and faecal samples were analysed using untargeted metabolomic profiling (polar/lipid fractions) and shotgun metagenomic sequencing, respectively. Sparse multi-block partial least squares regression and discriminant analysis (DIABLO) unveiled signatures associated with ethnicity, glycaemic status, and sex. Results: Ethnicity-based DIABLO modelling achieved a balanced error rate of 0.22, correctly classifying 76.54% of test samples. Polar metabolites had the highest discriminatory power (AUC = 0.96), with trigonelline enriched in European Caucasians and carnitine in Asian Chinese. Lipid profiles highlighted ethnicity-specific signatures: Asian Chinese showed enrichment of polyunsaturated triglycerides (TG.16:0_18:2_22:6, TG.18:1_18:2_22:6) and ether-linked phospholipids, while European Caucasians exhibited higher levels of saturated species (TG.16:0_16:0_14:1, TG.15:0_15:0_17:1). The bacteria Bifidobacterium pseudocatenulatum, Erysipelatoclostridium ramosum, and Enterocloster bolteae characterised Asian Chinese participants, while Oscillibacter sp. and Clostridium innocuum characterised European Caucasians. Cross-omic correlations highlighted negative correlations of Phocaeicola vulgatus with amino acids (r = -0.84 to -0.76), while E. ramosum and C. innocuum positively correlated with long-chain triglycerides (r = 0.55-0.62). Conclusions: Ethnicity drove robust multi-omic differentiation, revealing distinctive metabolic and microbial profiles potentially underlying the differential T2D risk between Asian Chinese and European Caucasians.},
}

@article {pmid40863111,
year = {2025},
author = {Dong, R and Gu, X and Su, L and Wu, Q and Tang, Y and Liang, H and Xue, X and Zhang, T and Zhan, J},
title = {The Impact of Uranium-Induced Pulmonary Fibrosis on Gut Microbiota and Related Metabolites in Rats.},
journal = {Metabolites},
volume = {15},
number = {8},
pages = {},
pmid = {40863111},
issn = {2218-1989},
abstract = {Background/Objectives: This study aimed to evaluate the effects of lung injury induced by insoluble uranium oxide particles on gut microbiota and related metabolites in rats. Methods: The rats were randomly divided into six UO2 dose groups. A rat lung injury model was established through UO2 aerosol. The levels of uranium in lung tissues were detected by ICP-MS. The expression levels of the inflammatory factors and fibrosis indexes were measured by enzyme-linked immunosorbent assay. Paraffin embedding-based hematoxylin & eosin staining for the lung tissue was performed to observe the histopathological imaging features. Metagenomic sequencing technology and HM700-targeted metabolomics were conducted in lung tissues. Results: Uranium levels in the lung tissues increased with dose increase. The expression levels of Tumor Necrosis Factor-α (TNF-α), Interleukin-1β (IL-1β), Collagen I, and Hydroxyproline (Hyp) in rat lung homogenate increased with dose increase. Inflammatory cell infiltration and the deposition of extracellular matrix were observed in rat lung tissue post-exposure. Compared to the control group, the ratio of Firmicutes and Bacteroides in the gut microbiota decreased, the relative abundance of Akkermansia_mucinphila decreased, and the relative abundance of Bacteroides increased. The important differential metabolites mainly include αlpha-linolenic acid, gamma-linolenic acid, 2-Hydroxybutyric acid, Beta-Alanine, Maleic acid, Hyocholic acid, L-Lysine, L-Methionine, L-Leucine, which were mainly concentrated in unsaturated fatty acid biosynthesis, propionic acid metabolism, aminoacyl-tRNA biosynthesis, phenylalanine metabolism, and other pathways in the UO2 group compared to the control group. Conclusions: These findings suggest that uranium-induced lung injury can cause the disturbance of gut microbiota and its metabolites in rats, and these changes are mainly caused by Akkermansia_mucinphila and Bacteroides, focusing on unsaturated fatty acid biosynthesis and the propionic acid metabolism pathway.},
}

@article {pmid40862625,
year = {2025},
author = {Ao, J and Tang, X and Li, Z and Tang, Z},
title = {Shrub encroachment alters microbial community composition and soil carbon and nitrogen cycling functional genes in northern peatlands.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0054225},
doi = {10.1128/spectrum.00542-25},
pmid = {40862625},
issn = {2165-0497},
abstract = {Changes in vegetation, such as shrub encroachment in grassland and wetland ecosystems, significantly influence soil microbial communities and biogeochemical processes. However, the specific impact of shrub encroachment on peatland ecosystems remains poorly understood. This study used a "space-for-time" approach, collecting soil samples from three encroachment stages-uninvaded, shrub invasion, and shrub invasion expansion-at two depths (0-30 cm and 30-60 cm). Metagenomic sequencing was used to assess the microbial community composition and functional gene dynamics. Shrub encroachment significantly alters soil physicochemical properties, nutrient availability, and microbial communities. Alpha diversity of bacteria and fungi was influenced by shrub encroachment and depth, whereas beta diversity varied mainly with depth. Functional carbon fixation genes (korA and pps) increased during shrub encroachment, while methane oxidation (hdrA2) and carbon degradation genes (GH31 and GH51) decreased before increasing. In addition, functional genes linked to nitrogen cycling (nifD, nifH, amoA, and amoC) declined, indicating a reduction in nitrogen fixation and nitrification pathways. Correlation and Mantel tests revealed that the total soil carbon content was the primary driver of these functional changes. These findings highlight the dynamic microbial responses to shrub encroachment and offer insights into the soil carbon and nitrogen-cycling mechanisms in peatlands.IMPORTANCEShrub encroachment is transforming peatlands and altering their ecological and biogeochemical functions. This study provides critical insights into how shrub invasion affects microbial communities and functional genes responsible for carbon and nitrogen cycling in peatland soils. By revealing the underlying genetic mechanisms, this study enhances our understanding of the consequences of vegetation shifts on ecosystem processes. These findings are essential for predicting and managing peatland responses to environmental changes, helping to preserve their role as vital carbon and nutrient reservoirs.},
}

@article {pmid40862360,
year = {2025},
author = {Ochiai, KK and Toyoda, A and Itoh, T and Goshima, G and Uesaka, K},
title = {High-quality metagenome-assembled genomes of bacteria associated with long-term cultivated giant coenocytic green alga Bryopsis.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0072225},
doi = {10.1128/mra.00722-25},
pmid = {40862360},
issn = {2576-098X},
abstract = {Seaweeds often associate with coexisting bacteria to support nutrient cycling and help defend against pathogenic microbes. Here, we report 38 closed circular and 12 fragmented metagenome-assembled genomes (MAGs) from bacteria tightly associated with the long-term cultivated coenocytic macroalga Bryopsis sp. KO-2023 from Sugashima Island, Japan.},
}

@article {pmid40862358,
year = {2025},
author = {Ruth, N and Olsen Martinez, A and Hatch, A and McGowen, J and Pacheco, S and Shakya, M and Sanders, CK},
title = {Bacteriophage and megaviruses from outdoor microalgae ponds in Mesa, Arizona.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0052525},
doi = {10.1128/mra.00525-25},
pmid = {40862358},
issn = {2576-098X},
abstract = {Microalgae are a promising resource for production of industrially relevant compounds, including renewable fuels and nutraceuticals. However, little is known about the presence and impacts of viruses in outdoor cultivation ponds. We present sequences of bacteriophage and potential megavirus genomes from metagenomic sequencing of microalgae ponds in Mesa, Arizona, USA.},
}

@article {pmid40862349,
year = {2025},
author = {Benot, AO and Waldschmidt, G and Tiyapun, C and Okyere, IJ and Goff, JL},
title = {Metagenomic characterization of fire-adapted soil microbiomes in the Albany Pine Bush Preserve.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0066425},
doi = {10.1128/mra.00664-25},
pmid = {40862349},
issn = {2576-098X},
abstract = {The Albany Pine Bush Preserve's documented fire history enables a unique study of fire-dependent ecosystems. We identified 94 unique bacterial and archaeal metagenome-assembled genomes spanning 27 classes, providing genomic insights into microbial nutrient cycling in these systems.},
}

@article {pmid40862153,
year = {2025},
author = {Pacheco-Acosta, S and Castro-Toro, G and Rojas-Villalobos, C and Valenzuela, C and Haristoy, JJ and Zapata-Araya, A and Moya-Beltrán, A and Sepúlveda-Rebolledo, P and Pérez-Rueda, E and Ulloa, R and Giaveno, A and Issotta, F and Díez, B and Beard, S and Quatrini, R},
title = {Exploring the eco-evolutionary role of plasmids and defense systems in 'Fervidacidithiobacillus caldus' extreme acidophile.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1610279},
pmid = {40862153},
issn = {1664-302X},
abstract = {Plasmids are major drivers of microbial evolution, enabling horizontal gene transfer (HGT) and facilitating adaptation through the dissemination of relevant functional genes and traits. However, little is known about plasmid diversity and function in extremophiles. 'Fervidacidithiobacillus caldus', a meso-thermo-acidophilic sulfur oxidizer, is a key player in sulfur cycling in natural and industrially engineered acidic environments. Here, we present a bioinformatic analysis of the plasmidome, and associated anti-mobile genetic element (anti-MGE) defense systems (defensome), across genomes of this species and metagenomes from diverse natural and industrial settings harboring 'F. caldus'. We identified >30 distinct plasmids, representing five consistent replication-mobilization families. Plasmids ranged in size between 2.5-65 kb, with gene content and plasmid modularity scaling with element size and copy numbers inversely correlating with size. Plasmids carried variable numbers of hypothetical proteins and transposases, with annotated cargo genes reflecting functional differentiation by habitat. Defensome profiling revealed over 50 anti-MGE systems in sequenced 'F. caldus' isolates, including diverse restriction-modification systems, CRISPR-Cas types IV-A and V-F, and widespread abortive infection and composite defense systems such as Wadjet, Gabija, and Zorya. In environmental populations, an inverse relationship was observed between defensome complexity and plasmidome abundance and diversity, underscoring a pivotal role of the host defensome in modulating persistence, compatibility, and overall plasmid diversity across 'F. caldus' populations. Yet, other plasmids appeared decoupled from both host abundance and defensome complexity, suggesting potential host shifts, environmental persistence, or differential replication under suboptimal growth conditions for the host. Altogether, these findings point to a modular, functionally diverse adaptive plasmidome shaped by environmental pressures, by the interplay with the host's defensome, and likely also by other eco-evolutionary processes at play in natural environments. While these associations are compelling, causal relationships remain to be experimentally validated. These insights broaden our understanding of mobile genetic elements in extreme environments and provide a foundation for plasmid-based vector design and synthetic biology applications in acidophiles, with direct implications to biomining and environmental remediation.},
}

@article {pmid40862113,
year = {2025},
author = {Wang, W and Wang, L and Chen, J and Yang, X and Guo, Q and Zhang, Z and Liang, J and Gu, P and Shao, J},
title = {The gut microbiome: a vital link to hyperuricemia, gout and acute flares?.},
journal = {Frontiers in endocrinology},
volume = {16},
number = {},
pages = {1643566},
pmid = {40862113},
issn = {1664-2392},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Hyperuricemia/microbiology ; *Gout/microbiology ; Male ; Middle Aged ; Female ; Adult ; Uric Acid/blood ; RNA, Ribosomal, 16S/genetics ; Case-Control Studies ; Aged ; Feces/microbiology ; Bacteria/genetics/classification ; },
abstract = {OBJECTIVES: To explore the associations between the gut microbiome and asymptomatic hyperuricemia, as well as acute gout flares.

METHODS: Forty-three Chinese participants were divided into healthy and hyperuricemic groups according to serum uric acid (SUA) levels. The hyperuricemia group were further separated into asymptomatic hyperuricemia (HUA) and gout patients on the basis of their clinical symptoms. In addition, the gout group was further divided into intercritical gout and acute gout groups on the basis of the claim of joint pain and relevant clinical parameters. 16S rRNA sequencing was used to evaluate the microbiome composition of all the groups.

RESULTS: A dramatic decreasing trend in microbial richness and diversity was observed in hyperuricemic patients compared with healthy controls. The same decreasing trend in microbial relative abundance was also observed. The butyrate-producing genera Faecalibacterium, Coprococcus and Enterococcus were markedly decreased in hyperuricemic patients. Moreover, opportunistic pathogens, such as the phylum Proteobacteria and genus Fusobacterium, were enriched in the hyperuricemia group. Furthermore, the gut microbiota of gout patients also exhibited significantly reduced microbial diversity compared with asymptomatic hyperuricemic patients, characterized by decreased richness of the genera Dialister, Ruminococcus, and Faecalibacterium. Greater differences in microbial richness and diversity can still be observed when gout flares occur. The abundances of Bacteroides and Lachnospira genera decreased in the acute gout stage.

CONCLUSION: Our study revealed that community richness and diversity change during the process of gout or HUA, especially during acute gout flares. Metagenomic species were significantly altered during different stages of hyperuricemia.},
}

Humans
*Gastrointestinal Microbiome
*Hyperuricemia/microbiology
*Gout/microbiology
Male
Middle Aged
Female
Adult
Uric Acid/blood
RNA, Ribosomal, 16S/genetics
Case-Control Studies
Aged
Feces/microbiology
Bacteria/genetics/classification

@article {pmid40861498,
year = {2025},
author = {Cao, XG and Zhu, XF and Yu, Z and Wang, CY and Shao, M and Meng, HD and Huang, CJ},
title = {Diagnostic performance and clinical utility of metagenomic next-generation sequencing in suspected central nervous system infections: a prospective comparative study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1612628},
pmid = {40861498},
issn = {2235-2988},
mesh = {Humans ; Prospective Studies ; Female ; *Central Nervous System Infections/diagnosis/cerebrospinal fluid/microbiology ; Male ; Middle Aged ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Adult ; Aged ; Sensitivity and Specificity ; Young Adult ; Bacteria/genetics/isolation & purification/classification ; Cerebrospinal Fluid/microbiology ; },
abstract = {OBJECTIVE: To assess the diagnostic performance and clinical utility of metagenomic next-generation sequencing (mNGS) in patients with suspected central nervous system (CNS) infections.

METHODS: prospective study was conducted from December 2019 to January 2024, enrolling 110 patients with suspected CNS infections. Cerebrospinal fluid (CSF) samples were subjected to mNGS, conventional biochemistry, and culture. Clinical features and outcomes were compared between patients confirmed with CNS infections and those without.

RESULTS: Of the enrolled patients, 69 were diagnosed with CNS infections. mNGS identified pathogens in 62 cases (77.11%), including 54 clinically confirmed true positives (49.09%), significantly surpassing traditional CSF culture (6.36%). mNGS reported results within 24 hours, considerably shorter than the 72~120 hours required for culture. Compared to the non-infection group, patients with CNS infections had significantly higher ICU admission(ICUA) rates, prolonged hospital stays, increased healthcare costs, and elevated rates of antibiotic adjustment and mNGS positivity (P<0.05). CSF turbidity, cell count, and protein levels were significantly elevated, while glucose and chloride levels were reduced. Logistic regression identified mNGS, CSF protein, and glucose levels as independent predictors of CNS infection. Receiver operating characteristic (ROC) analysis demonstrated superior diagnostic accuracy for continuous CSF variables over binary ones, with mNGS showing robust performance [area under the curve (AUC) = 0.794].

CONCLUSION: mNGS offers rapid and accurate pathogen detection, outperforming conventional methods in sensitivity and turnaround time, and provides valuable guidance for individualized antimicrobial treatment in CNS infections.},
}

Humans
Prospective Studies
Female
*Central Nervous System Infections/diagnosis/cerebrospinal fluid/microbiology
Male
Middle Aged
*High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
Adult
Aged
Sensitivity and Specificity
Young Adult
Bacteria/genetics/isolation & purification/classification
Cerebrospinal Fluid/microbiology

@article {pmid40861485,
year = {2025},
author = {Li, J and Yuan, W and Gao, C and Liu, L and Song, L and Cao, W and Zhu, X and Han, Y and Liang, R and Lan, G and Yu, S and Wang, Y and Tan, L and Dai, H and Xie, X and Peng, L and Peng, F},
title = {Comparison of pathogen detection performance between metagenomic next-generation sequencing and conventional culture in organ preservation fluids and recipient wound drainage fluids.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1563962},
pmid = {40861485},
issn = {2235-2988},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Female ; Male ; Middle Aged ; Adult ; *Bacteria/isolation & purification/genetics/classification ; *Kidney Transplantation/adverse effects ; Fungi/isolation & purification/genetics ; Body Fluids/microbiology ; Aged ; Drainage ; Wound Infection/microbiology ; Tissue Donors ; *Organ Preservation Solutions ; },
abstract = {BACKGROUND: Prompt identification and management of donor-derived infections post-kidney transplantation are critical. This study aims to assess the effectiveness of metagenomic next-generation sequencing (mNGS) in detecting pathogens within donor organ preservation fluids and recipient wound drainage fluids, with a comparison made against conventional culture methods.

METHODS: This study involved 141 kidney transplant patients (May 1st, 2020 to Jan 31st, 2024). Donor organ preservation fluids and recipient wound drainage fluids were collected and analyzed by mNGS and conventional culture. Pathogen detection differences between mNGS and culture were evaluated. The antibiotic adjustment and infectious complications of the recipients were recorded.

RESULTS: For organ preservation fluids, the positive rate of convention culture were lower than that of mNGS (24.8% (35/141) vs 47.5% (67/141), p<0.05). For recipient wound drainage fluids, the positivity rate of convention culture were lower than that of mNGS (2.1% (3/141) vs 27.0% (38/141), p<0.05). Compared to traditional culture-based methods, mNGS demonstrated a significantly higher positive detection rate for the combination of ESKAPE pathogens and/or fungi (28.4% (40/141) vs 16.3% (23/141) p< 0.05). Of the pathogens detected through convention culture, mNGS was capable of detecting 79.2% (19/24) of combinations comprising Enterobacteriaceae and non-fermenting bacteria, yet it detected only 22.2% (2/9) of Gram-positive bacteria, and 55.6% (5/9) of fungi. Certain clinically atypical pathogens, mainly Mycobacterium, Clostridium tetanus, and parasites, can solely be detected via mNGS. The rehospitalization rate due to infections was 13.5% (19/141), while the donor-derived infection rate amounted to 2.8% (4/141). Guided by mNGS and bacterial culture results, adjustments were made to antibiotic administration, with no severe vascular complications arising.

CONCLUSIONS: By employing mNGS to analyze drainage fluids and organ preservation fluids, highly pathogenic and atypical pathogenic microorganisms can be rapidly identified with high throughput. While limitations exist in detecting fungi and Gram-positive bacteria, mNGS are need to be jointly applied with conventional culture under current conditions.},
}

Humans
*High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
Female
Male
Middle Aged
Adult
*Bacteria/isolation & purification/genetics/classification
*Kidney Transplantation/adverse effects
Fungi/isolation & purification/genetics
Body Fluids/microbiology
Aged
Drainage
Wound Infection/microbiology
Tissue Donors
*Organ Preservation Solutions

@article {pmid40861425,
year = {2025},
author = {Dong, C and Chen, L and Li, D and Zhang, X and Chen, Y},
title = {Effects of swimming training on cecum microorganisms and metabolites in rats with high fat diet.},
journal = {Frontiers in molecular biosciences},
volume = {12},
number = {},
pages = {1569239},
pmid = {40861425},
issn = {2296-889X},
abstract = {Swimming is a whole-body aerobic exercise that has preventive and therapeutic effects on chronic metabolic diseases triggered by a high-fat diet. SPF grade rats (n = 48) were selected. They were divided into 4 groups (GB, GY, ZY and ZB) with 12 rats in each group. The GB and GY groups were fed high-fat chow during the pre-test period, and the ZY and ZB groups were fed normal chow. Swimming training was carried out in ZY and GY groups and no swimming exercise in GB and ZB groups in the later part of the trial. Histopathological staining was performed on the cecum and liver of 48 rats. Physiological and biochemical indices such as ACP, ALP and AST were measured in the blood of the rats in each group, and 6 samples of cecum contents were taken from each group for metagenomics and widely targeted metabolomics. The results showed that AST, ALP, ACP, LDL, IL-6, TNF-α, and IL-1β were significantly lower in the GY group than in the GB group; the structural liver lesions were severe in the GB and GY groups; and the ZY group had higher levels of Prevotellaceae, Muribaculaceae, and Spirochaetes. In comparison with the GB group, the GY group showed significant increases in metabolites associated with metabolic pathways such as ABC transporters and sulfur metabolism. The results show that feeding high-fat diet can cause tissue and organ lesions, cecal microbe and metabolite structure changes in rats. However, swimming training increased the content of beneficial microorganisms and metabolites in rats' cecum. This study provides a theoretical basis for swimming exercise to alleviate metabolic disorders caused by high fat diet.},
}

@article {pmid40861207,
year = {2025},
author = {Chen, P and Li, J and Liu, PX and Gou, H and Yu, M and Li, LL and Huang, L},
title = {Nocardia otitidiscaviarum meningitis in an immunocompetent patient diagnosed by metagenomic next-generation sequencing: a case report.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1588977},
pmid = {40861207},
issn = {2296-858X},
abstract = {Cerebral nocardiosis caused by Nocardia represents a rare and diagnostically challenging infectious disease, predominantly affecting immunocompromised patients. This opportunistic infection may also pose life-threatening risks to immunocompetent individuals. The diagnostic process is frequently complicated by the absence of distinctive clinical manifestations and technical limitations inherent to conventional microbiological detection methods, which collectively impede the acquisition of definitive pathogenic evidence, thereby resulting in diagnostic delays. This case report describes a 67-year-old immunocompetent male bricklayer who presented with recurrent febrile episodes during hospitalization and was ultimately diagnosed with purulent meningitis based on clinical history corroborated by cerebrospinal fluid (CSF) analytical findings. Ceftriaxone was initially employed as an anti-infective agent, however, it was ineffective. Consequently, the treatment was escalated to a combination of meropenem and vancomycin, yet the patient's condition did not significantly improve. Concurrently, repeated cultures of the patient's blood and CSF yielded no identifiable pathogens. Notably, three months ago, the patient accidentally sustained a laceration on the left thigh by an unknown object during work. An abscess gradually developed at the site of the laceration, and incision and drainage were carried out at a local hospital. However, the wound did not heal satisfactorily after the surgery, raising concerns about potential rare pathogenic bacterial infections. Ultimately, the pathogen was successfully identified as Nocardia otitidiscaviarum through metagenomic next-generation sequencing (mNGS). Following this diagnosis, the patient's condition was rapidly controlled after initiating treatment with the targeted drug combination of sulfamethoxazole, meropenem, and amikacin. Given the high misdiagnosis rate and poor sensitivity of cultures for Nocardia otitidiscaviarum in cases of intracranial infections, this case underscores the critical role of mNGS in the diagnosis and selection of effective antibiotics for treating Nocardia intracranial infections.},
}

@article {pmid40861206,
year = {2025},
author = {Li, C and Zhong, X and Guo, S and Liu, F and Song, Y and Zhao, Z and Jiang, G},
title = {A case report of rapid diagnosis of Sporothrix globosa infection using MetaCAP.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1644400},
pmid = {40861206},
issn = {2296-858X},
abstract = {BACKGROUND: Sporothrix globosa (S. globosa) is a significant pathogenic fungus responsible for, causing sporotrichosis. Metagenomics capture (MetaCAP), a high-throughput sequencing technology for pathogen nucleic acid detection based on probe capture, facilitates early diagnosis of S. globosa infections. Herein, we present a case of S. globosa infection diagnosed using MetaCAP.

CASE SUMMARY: A 47 year-old female, initially diagnosed with reactive perforating collagenosis, developed epidermal erosion at the affected site after self-applying a poorly air-permeable topical patch purchased online. She subsequently exhibited progressive redness, edema, severe pruritus, and an increase in papules that coalesced into plaques following exposure to decaying wood. She revisited our hospital for further consultation. The diagnosis of sporotrichosis caused by S. globosa was confirmed through a pathological examination of the affected skin tissue and MetaCAP testing. Then, she was treated with itraconazole and naftifine hydrochloride and ketoconazole cream. After a three-month follow-up, the patient's skin rash showed significant improvement.

CONCLUSION: A case of S. globosa infection was promptly diagnosed through MetaCAP and effectively treated with itraconazole.},
}

@article {pmid40861112,
year = {2025},
author = {Wilson, TM and de Sousa, DER and Macêdo, IL and Machado, M and de Toledo Costa, GR and Fair, P and Ritter, JM and Bullock, HA and DeLeon-Carnes, M and Lee, E and de Oliveira Passos, PH and Ramos, DG and Romano, APM and da Silva, SP and Casseb, LMN and Martins, LC and Maia, LJ and Ribeiro, BM and de Lima, EMM and de Melo, CB and de Castro, MB},
title = {Emergence of a Novel Canine Distemper Virus Variant in Urbanized Free-Ranging Marmosets (Callithrix penicillata).},
journal = {Transboundary and emerging diseases},
volume = {2025},
number = {},
pages = {4818076},
pmid = {40861112},
issn = {1865-1682},
mesh = {Animals ; *Distemper Virus, Canine/genetics/isolation & purification/classification ; *Distemper/virology/epidemiology ; *Callithrix/virology ; Phylogeny ; Brazil/epidemiology ; *Monkey Diseases/virology/epidemiology ; Dogs ; Male ; *Disease Outbreaks/veterinary ; Female ; },
abstract = {The black-tufted marmoset (Callithrix penicillata), commonly found in urban areas of Central Brazil, is vulnerable to pathogen spillover from domestic animals and humans. Here, we report an outbreak of natural canine distemper virus (CDV) infection among urbanized free-ranging black-tufted marmosets. Five fatalities occurred in marmosets living in a neighborhood with unvaccinated dogs. Clinically, affected marmosets had lethargy, ataxia, mucocutaneous ulcerations, and crusting lesions. Postmortem findings included epithelial erosions, interstitial pneumonia, bronchopneumonia, and suppurative myocarditis, frequently associated with secondary bacterial infections. Immunohistochemistry (IHC) confirmed the presence of CDV antigen in multiple organs, and secondary bacterial infections were common, involving species, such as Bordetella, Haemophilus, and Streptococcus. Transmission electron microscopy (TEM) demonstrated paramyxovirus-like inclusion bodies and metagenomic sequencing identified a novel CDV variant. Phylogenetic analyses placed this strain within the Europe 1/South America 1 lineage, closely related to domestic dog-derived strains from the region. Comparative H gene analysis uncovered unique R519I substitutions in the CDV marmoset variant, suggesting potential for cross-species adaptation. This study provides evidence that CDV can naturally infect free-living New World primates, with possible implications for animal health, conservation, and interspecies transmission. These findings highlight the vulnerability of urban wildlife to CDV spillover from domestic dogs and emphasize the importance of monitoring pathogen transmission at the human-animal interface from a One Health perspective.},
}

Animals
*Distemper Virus, Canine/genetics/isolation & purification/classification
*Distemper/virology/epidemiology
*Callithrix/virology
Phylogeny
Brazil/epidemiology
*Monkey Diseases/virology/epidemiology
Dogs
Male
*Disease Outbreaks/veterinary
Female

@article {pmid40860566,
year = {2025},
author = {Arnau, V and Ortiz-Maiques, A and Valero-Tebar, J and Mora-Quilis, L and Kurmauskaite, V and Campos Dopazo, L and Domingo-Calap, P and Džunková, M},
title = {CleanBar: a versatile demultiplexing tool for split-and-pool barcoding in single-cell omics.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf134},
pmid = {40860566},
issn = {2730-6151},
abstract = {Split-and-pool barcoding generates thousands of unique barcode strings through sequential ligations in 96-well plates, making single-cell omics more accessible, thus advancing microbial ecology, particularly in studies of bacterial interactions with plasmids and bacteriophages. While the wet-lab aspects of the split-and-pool barcoding are well-documented, no universally applicable bioinformatic tool exists for demultiplexing single cells barcoded with this approach. We present CleanBar (https://github.com/tbcgit/cleanbar), a flexible tool for demultiplexing reads tagged with sequentially ligated barcodes, accommodating variations in barcode positions and linker lengths while preventing misclassification of natural barcode-like sequences and handling diverse ligation errors. It also provides statistics useful for optimizing laboratory procedures. We demonstrate CleanBar's performance with the Atrandi platform for microbial single-cell genomics, coupled with PacBio sequencing, to reach a cell throughput comparable with traditional bulk metagenomics, but overcoming its limitations in studying phage-bacteria interactions. In four Klebsiella strains infected with their corresponding phages and a control phage, the single-cell genomics revealed infection heterogeneity and enabled phage copy number estimation per cell. By combining efficiency, adaptability, and precision, CleanBar, when applied to the Atrandi split-and-pool barcoding platform and PacBio sequencing, serves as a powerful high-throughput tool for advancing microbial single-cell genomics and understanding microbial ecology and evolution.},
}

@article {pmid40860446,
year = {2025},
author = {Xie, X and Cheng, W and Li, Z and He, R and Yuan, K and Zhang, Q and Yang, R and Ming, L and Yu, K and Luan, T and Chen, B},
title = {Functional metagenomics reveals novel antibiotic resistomes in polar soils.},
journal = {iMeta},
volume = {4},
number = {4},
pages = {e70069},
pmid = {40860446},
issn = {2770-596X},
abstract = {Using a robust functional metagenomics approach, we demonstrated that polar environments are important reservoirs of novel antibiotic resistance genes (ARGs). DNA was initially extracted from cultured bacterial consortia in the polar soils and recombined into plasmid vectors and then transformed into Escherichia coli (E. coli) for the subsequent screening of antibiotic resistance. Consequently, we identified 671 novel polar ARGs with experimentally verified resistance against multiple clinical antibiotics (cefotaxime, folate synthesis inhibitors, and clindamycin). Bioinformatics analysis revealed that novel polar ARGs had limited mobility and dissemination potential and were seldom carried by human bacterial pathogens. Overall, this study offers a comprehensive perspective on previously overlooked novel ARGs in polar regions, advancing our understanding of environmental resistomes.},
}

@article {pmid40860434,
year = {2025},
author = {Liu, S and Zhuang, Y and Chen, T and Gao, D and Xiao, J and Wang, J and Li, J and Zhao, X and Peng, R and Guo, W and Wei, J and Sha, M and Wang, J and Ma, J and Ma, M and Li, M and Wang, W and Wang, YJ and Li, S and Cao, Z},
title = {Spatio-temporal characteristics of the gastrointestinal resistome in a cow-to-calf model and its environmental dissemination in a dairy production system.},
journal = {iMeta},
volume = {4},
number = {4},
pages = {e70047},
pmid = {40860434},
issn = {2770-596X},
abstract = {Microbiome and resistome transmission from mother to child, as well as from animal to environment, has been widely discussed in recent years. Dairy cows mainly provide milk and meat. However, in the dairy production system, the characteristics and transmission trends of resistome assembly and the microbiome in the gastrointestinal tract (GIT) remain unclear. In this study, we sequenced the GIT (rumen fluid and feces) microbiome of dairy cow populations from two provinces in China (136 cows and 36 calves), determined the characteristics of their resistome profiles and the distribution of antibiotics resistance genes (ARGs) across bacteria and further tracked the temporal dynamics of the resistome in offspring during early life using multi-omics technologies (16S ribosomal RNA [rRNA] sequencing, metagenome, and metatranscriptome). We characterized the GIT resistome in cows, distinguished by gut sites and regions. The abundance of ARGs in calves peaked within the first 3 days after birth, with Enterobacteriaceae as the dominant microbial host. As calves aged, resistome composition stabilized, and overall ARG abundance gradually decreased. Both diet and age influenced carbohydrate-active enzymes and ARG profiles. Resistance profiles in ecological niches (meconium, colostrum, soil, and wastewater) were unique, resembling maternal sources. Mobile genetic elements (MGEs), mainly found in soil and wastewater, played an important role in mediating these interactions. Multidrug resistance consistently emerged as the most significant form of resistance at the both the metagenome and metatranscriptome levels. Several antibiotic classes showed higher proportions at the RNA level than at the DNA level, indicating that even low-abundance gene groups can have a considerable influence through high expression. This study broadens our understanding of ARG dissemination in livestock production systems, providing a foundation for developing future preventive and control strategies.},
}

@article {pmid40860431,
year = {2025},
author = {Liu, Y and Yang, L and Meskini, M and Goel, A and Opperman, M and Shyamal, SS and Manaithiya, A and Xiao, M and Ni, R and An, Y and Zhang, M and Tian, Y and Zhou, S and Ye, Z and Zhuang, L and Li, L and Saraswat, I and Kar, A and Ali, SL and Ullah, S and Ali, SY and Kaushik, S and Tian, T and Jiao, M and Wang, S and Ghisleni, G and Armanni, A and Fumagalli, S and Wang, W and Cao, C and Carpena, M and Prieto, MA and Bruno, A and Jin, C and Hu, H and Zhang, Y and du Preez, I and Aspatwar, A and Zhang, L and Gong, W},
title = {Gut microbiota and tuberculosis.},
journal = {iMeta},
volume = {4},
number = {4},
pages = {e70054},
pmid = {40860431},
issn = {2770-596X},
abstract = {Tuberculosis (TB), caused by Mycobacterium tuberculosis (MTB), remains a significant global health challenge. Recent advancements in gut microbiota (GM) research have shed light on the intricate relationship between GM and TB, suggesting that GM alterations may influence host susceptibility, disease progression, and response to antituberculosis drugs. This review systematically synthesizes and analyzes the current research progress on the relationship between GM and TB, focusing on six key aspects: (1) bidirectional effects between GM dynamics and TB progression; (2) the interaction between GM and anti-TB drugs; (3) GM and TB immune response; (4) GM as a potential target for diagnosis and treatment of TB; (5) multi-omics and artificial intelligence (AI) technologies in GM-TB research; (6) current challenges and future directions in GM-TB research. We highlight the bidirectional nature of the GM-TB interaction, where MTB infection can lead to GM dysbiosis, and changes can affect the host's immune response, contributing to TB onset and progression. Advanced molecular techniques, such as next-generation sequencing and metagenomics, along with AI, play pivotal roles in elucidating these complex interactions. Future research directions include investigating the relationship between GM and TB vaccine efficacy, exploring GM's potential in TB prevention, developing microbiome-based diagnostic and prognostic tools, and examining the role of GM in TB recurrence. By addressing these areas, we aim to provide a comprehensive perspective on the latest advancements in GM and TB research and offer insights for future studies and clinical applications. Ultimately, the development of novel microbiome-based strategies may offer new tools and insights for the effective control and management of TB, a disease that continues to pose a significant threat to public health.},
}

@article {pmid40859872,
year = {2025},
author = {Bunka, L and Rozenberga, M and Silamiķelis, I and Saksis, R and Birzniece, L and Megnis, K and Fedulovs, A and Pahirko, L and Zaļizko, P and Krustiņš, E and Kloviņš, J and Sokolovska, J and Elbere, I},
title = {Dual-approach analysis of gut microbiome in patients with type 1 diabetes and diabetic kidney disease.},
journal = {Annals of medicine},
volume = {57},
number = {1},
pages = {2531254},
pmid = {40859872},
issn = {1365-2060},
mesh = {Humans ; *Diabetes Mellitus, Type 1/microbiology/complications ; *Diabetic Nephropathies/microbiology ; *Gastrointestinal Microbiome/genetics ; Male ; Female ; Feces/microbiology ; Adult ; RNA, Ribosomal, 16S/genetics ; Case-Control Studies ; Middle Aged ; Disease Progression ; Metagenomics/methods ; Biopsy ; Young Adult ; Bacteroides/isolation & purification/genetics ; },
abstract = {BACKGROUND: Type 1 diabetes (T1D) is a multifactorial autoimmune disease mediated by genetic, epigenetic, and environmental factors. Diabetic kidney disease (DKD) is a major complication of diabetes mellitus which affects 30-40% of T1D patients. Increasing evidence suggests the significant role of the microbiome in the progression of both T1D and DKD.

MATERIALS AND METHODS: Here we recruited 76 T1D patients and 22 healthy controls and combined data from sigmoid colon biopsy samples analysed with V3-V4 region amplification of 16S rRNA gene and shotgun metagenomics data obtained from faecal samples. Additionally, we compared T1D patients with and without progression of DKD.

RESULTS: We observed significant differences within both sample types at various taxonomic and functional levels. T1D patient microbiota detected using biopsy samples had a lower abundance of the Bacteroides genus when compared to healthy controls. Significantly, despite only a few taxonomic differences patients with and without DKD progression were vastly different at the functional pathway level within the faecal samples - we observed 2 and 61 enriched pathways in these groups. respectively, with several of these pathways linked to the mediation of renal function.

CONCLUSION: Altogether, we present novel data about microbial signatures relevant to T1D and DKD progression, which partly supports previous data and also presents possible tissue type or population-specific elements. DKD progression is characterized with significant differences within the functional level of the gut microbiome.},
}

Humans
*Diabetes Mellitus, Type 1/microbiology/complications
*Diabetic Nephropathies/microbiology
*Gastrointestinal Microbiome/genetics
Male
Female
Feces/microbiology
Adult
RNA, Ribosomal, 16S/genetics
Case-Control Studies
Middle Aged
Disease Progression
Metagenomics/methods
Biopsy
Young Adult
Bacteroides/isolation & purification/genetics

@article {pmid40859560,
year = {2025},
author = {Ma, D and Wang, J and Fan, B and Liang, J and Liu, Q and He, Z},
title = {The clinical characteristics and diagnostic and treatment protocol for 14 acute Vibrio vulnificus infections caused by aquatic products.},
journal = {Medicine},
volume = {104},
number = {34},
pages = {e43942},
pmid = {40859560},
issn = {1536-5964},
mesh = {Humans ; Retrospective Studies ; Male ; *Vibrio Infections/diagnosis/therapy/drug therapy/etiology/microbiology ; Female ; Middle Aged ; *Vibrio vulnificus/isolation & purification ; Adult ; Anti-Bacterial Agents/therapeutic use ; Aged ; },
abstract = {Vibrio vulnificus infections caused by aquatic product-related injuries pose severe clinical challenges due to their rapid progression and high morbidity and mortality. Early diagnosis and timely intervention are critical to improving patient outcomes, yet standardized diagnostic and treatment protocols remain limited. We conducted a retrospective descriptive case series of 14 patients with confirmed V vulnificus infection admitted between 2020 and 2023. Clinical data, including demographic characteristics, injury history, symptoms, laboratory results, diagnostic methods, treatment strategies, and outcomes, were collected and analyzed. Microbial culture and metagenomic next-generation sequencing (mNGS) were compared in terms of diagnostic timing. All 14 patients had a clear history of aquatic product-related trauma, with 85.7% (12/14) presenting within 24 hours of injury. The average time from injury to symptom onset was 13.11 ± 6.61 hours. All patients exhibited limb erythema, swelling, warmth, and pain; 11 patients (78.6%) developed complications such as sepsis (42.9%), compartment syndrome (35.7%), or multiple organ dysfunction syndrome (28.6%). Ten cases were confirmed by microbial culture (average time: 1.68 ± 0.63 days), and 4 by mNGS (average time: 1.00 day). The average time to diagnosis was shorter in patients diagnosed by culture than those requiring mNGS (1.86 ± 0.68 vs 4.82 ± 0.90 days). All patients received empirical combination antibiotic therapy upon admission; the average duration of intravenous antibiotic treatment was approximately 10 days. Six patients (42.9%) underwent amputation, and 2 (14.3%) died. Among the survivors, 50% achieved Brunnstrom stage V to VI hand function recovery at final follow-up. Early identification and aggressive treatment are essential in managing V vulnificus infections related to aquatic product injuries. mNGS plays an important supplementary role in diagnosis, especially in culture-negative cases. The proposed diagnostic and treatment protocol, based on real-world experience, may help improve clinical decision-making and reduce poor outcomes such as amputation and death.},
}

Humans
Retrospective Studies
Male
*Vibrio Infections/diagnosis/therapy/drug therapy/etiology/microbiology
Female
Middle Aged
*Vibrio vulnificus/isolation & purification
Adult
Anti-Bacterial Agents/therapeutic use
Aged

@article {pmid40859350,
year = {2025},
author = {Klaes, S and White, C and Alvarez-Cohen, L and Adrian, L and Ding, C},
title = {De novo peptide databases enable protein-based stable isotope probing of microbial communities with up to species-level resolution.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {111},
pmid = {40859350},
issn = {2524-6372},
abstract = {BACKGROUND: Protein-based stable isotope probing (Protein-SIP) is a powerful approach that can directly link individual taxa to activity and substrate assimilation, elucidating metabolic pathways and trophic relationships within microbial communities. In Protein-SIP, peptides and corresponding taxa are identified by database matching, making database quality crucial for accurate analyses. For samples with unknown community composition, Protein-SIP typically employs either unrestricted reference databases or metagenome-derived databases. While (meta)genome-derived databases represent the gold standard, they may be incomplete and are typically resource-intensive to generate. In contrast, unrestricted reference databases can inflate the search space and require complex post-processing.

RESULTS: Here, we explore the feasibility of using de novo peptide sequencing to construct peptide databases directly from mass spectrometry raw data. We then use the mass spectrometric data from labeled cultures to quantify isotope incorporation into specific peptides. We benchmark our approach against the canonical approach in which a sample-matching (meta)genome-derived protein sequence database is used on three different datasets: (1) a proteome analysis from a defined microbial community containing [13]C-labeled Escherichia coli cells, (2) time-course data of an anammox-dominated continuous reactor after feeding with [13]C-labeled bicarbonate, and (3) a model of the human distal gut simulating a high-protein and high-fiber diet cultivated in either [2]H2O or H2[18]O. Our results show that de novo peptide databases are applicable to different isotopes, detecting similar amounts of labeled peptides compared to sample-matching (meta)genome-derived databases, and also identify labeled peptides missed by this canonical approach. Furthermore, we show that peptide-centric Protein-SIP allows up to species-level resolution and enables the assessment of activity related to individual biological processes. Finally, we provide access to our modular Python pipeline to assist the construction of de novo peptide databases and subsequent peptide-centric Protein-SIP data analysis (https://git.ufz.de/meb/denovo-sip).

CONCLUSIONS: De novo peptide databases enable Protein-SIP of microbial communities without prior knowledge of the composition and can be used complementarily to (meta)genome-derived databases or as a standalone alternative in exploratory or resource-limited settings.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s40793-025-00767-6.},
}

@article {pmid40859318,
year = {2025},
author = {Lin, Z and Jiang, Y and Liu, H and Yang, J and Yang, B and Zhang, K and Tang, P and Xiang, B and Sun, B},
title = {Airway microbiota and immunity associated with chronic obstructive pulmonary disease severity.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {962},
pmid = {40859318},
issn = {1479-5876},
support = {GMUCR2024-02009//Major clinical research project of Guangzhou Medical University/ ; 2023B110008//Guangdong Provincial Key Laboratory of Prevention and Control for Severe Clinical Animal Diseases/ ; },
mesh = {*Pulmonary Disease, Chronic Obstructive/immunology/microbiology/pathology/genetics ; Humans ; *Microbiota ; *Severity of Illness Index ; Male ; Female ; Aged ; Middle Aged ; Bronchoalveolar Lavage Fluid/microbiology ; *Immunity ; Cohort Studies ; Biomarkers/metabolism ; Dysbiosis ; Reproducibility of Results ; *Respiratory System/microbiology ; Metagenomics ; Bacteria ; },
abstract = {BACKGROUND: Chronic Obstructive Pulmonary Disease (COPD) is characterized by progressive airflow limitation and chronic inflammation. Although airway microbes and host immunity are known contributors, the molecular mechanisms underlying disease severity remain unclear. This study explores microbial dysbiosis and host immune responses across varying COPD severities.

METHODS: We conducted integrated metagenomic and transcriptomic analyses on bronchoalveolar lavage fluid from two cohorts: a discovery cohort and a validation cohort. We investigated microbial diversity, pathogenic bacterial enrichment, and host gene expression patterns. Functional metagenomics was used to assess antibiotic resistance genes. Host-microbe network analyses explored correlations between pathogens and immune-metabolic pathways. Diagnostic models utilizing microbial-immune biomarkers were developed, trained on a subset of the discovery cohort, tested on remaining discovery samples, and validated by quantitative polymerase chain reaction (qPCR) in the validation cohort to distinguish COPD from controls and stratify disease severity.

RESULTS: Severe COPD exhibited reduced microbial diversity and an increased presence of pathogenic bacteria, including Moraxella osloensis and Streptococcus species. These pathogens were associated with dysregulated inflammatory signaling, and significant neutrophil activity, evidenced by the formation of Neutrophil Extracellular Traps (NETs), and oxidative stress, which correlated with airway remodeling and a decline in lung function. Functional metagenomics showed a significant increase in antibiotic resistance genes in severe cases, linked to chronic treatment pressures. Host-microbe network analyses revealed strong correlations between these pathogens and disrupted immune-metabolic pathways, such as altered energy metabolism and inflammatory cascades, consistent across both cohorts. Diagnostic models based on microbial-immune biomarkers demonstrated high accuracy in differentiating COPD patients from controls and in stratifying disease severity.

CONCLUSIONS: This study identifies microbial and immune signatures associated with COPD severity, providing mechanistic insights into its pathophysiology. The findings may inform precision medicine strategies by targeting airway dysbiosis and immune dysregulation. While causal relationships could not be established in this cross-sectional study, the findings provide a foundation for future mechanistic investigations using advanced in vitro and in vivo models.},
}

*Pulmonary Disease, Chronic Obstructive/immunology/microbiology/pathology/genetics
Humans
*Microbiota
*Severity of Illness Index
Male
Female
Aged
Middle Aged
Bronchoalveolar Lavage Fluid/microbiology
*Immunity
Cohort Studies
Biomarkers/metabolism
Dysbiosis
Reproducibility of Results
*Respiratory System/microbiology
Metagenomics
Bacteria

@article {pmid40859157,
year = {2025},
author = {Gao, ZQ and Su, JW and Qin, Y and Ye, T and Cao, H and Yang, LH and Elsheikha, HM},
title = {Metagenomic analysis of vitamins B and K2 biosynthesis in chicken gut microbiota across laying periods.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {553},
pmid = {40859157},
issn = {1471-2180},
}

@article {pmid40858551,
year = {2025},
author = {Salcher, MM and Layoun, P and Fernandes, C and Chiriac, MC and Bulzu, PA and Ghai, R and Shabarova, T and Lanta, V and Callieri, C and Sonntag, B and Posch, T and Lepori, F and Znachor, P and Haber, M},
title = {Bringing the uncultivated microbial majority of freshwater ecosystems into culture.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {7971},
pmid = {40858551},
issn = {2041-1723},
support = {19-23469S//Grantová Agentura České Republiky (Grant Agency of the Czech Republic)/ ; 22-03662S//Grantová Agentura České Republiky (Grant Agency of the Czech Republic)/ ; 25-15813S//Grantová Agentura České Republiky (Grant Agency of the Czech Republic)/ ; 20-12496X//Grantová Agentura České Republiky (Grant Agency of the Czech Republic)/ ; 21-21990S//Grantová Agentura České Republiky (Grant Agency of the Czech Republic)/ ; 022/2019/P//Jihočeská Univerzita v Českých Budějovicích (University of South Bohemia in České Budějovice)/ ; 017/2022/P//Jihočeská Univerzita v Českých Budějovicích (University of South Bohemia in České Budějovice)/ ; },
abstract = {Axenic cultures are essential for studying microbial ecology, evolution, and genomics. Despite the importance of pure cultures, public culture collections are biased towards fast-growing copiotrophs, while many abundant aquatic prokaryotes remain uncultured due to uncharacterized growth requirements and oligotrophic lifestyles. Here, we applied high-throughput dilution-to-extinction cultivation using defined media that mimic natural conditions to samples from 14 Central European lakes, yielding 627 axenic strains. These cultures include 15 genera among the 30 most abundant freshwater bacteria identified via metagenomics, collectively representing up to 72% of genera detected in the original samples (average 40%) and are widespread in freshwater systems globally. Genome-sequenced strains are closely related to metagenome-assembled genomes (MAGs) from the same samples, many of which remain undescribed. We propose a classification of several novel families, genera, and species, including many slowly growing, genome-streamlined oligotrophs that are notoriously underrepresented in public repositories. Our large-scale initiative to cultivate the "uncultivated microbial majority" has yielded a valuable collection of abundant freshwater microbes, characterized by diverse metabolic pathways and lifestyles. This culture collection includes promising candidates for oligotrophic model organisms, suitable for a wide array of ecological studies aimed at advancing our ecological and functional understanding of dominant, yet previously uncultured, taxa.},
}

@article {pmid40858544,
year = {2025},
author = {Zou, X and Cao, H and Hong, L and Suo, L and Wang, C and Chang, K and Ni, Y and Liu, B and Cao, B},
title = {Enrichment of Streptococcus oralis in respiratory microbiome enhance innate immunity and protects against influenza infection.},
journal = {Signal transduction and targeted therapy},
volume = {10},
number = {1},
pages = {272},
pmid = {40858544},
issn = {2059-3635},
abstract = {Respiratory microbial dysbiosis has been implicated in the occurrence and progression of community-acquired pneumonia (CAP). However, the dynamic variation in the respiratory microbiota and its interaction with the host response remain poorly understood. Here, we performed metagenomic analysis of respiratory and gut microbiota, along with blood transcriptomics, using longitudinally collected samples from 38 CAP patients. CAP patients presented disrupted sputum microbiota at the early, middle, and late stages of hospitalization. Microbial pathways involved in peptidoglycan biosynthesis and immune evasion, particularly contributed by the Streptococcus genus, were enriched in CAP patients. Additionally, several Streptococcus strains demonstrated correlation between respiratory and gut microbiota in CAP patients. By incorporating host response data, we revealed that Streptococcus oralis (SOR) was associated with host pathways involved in the innate immune response to infection, and this microbe‒host interaction was reproduced in a newly enrolled CAP cohort consisting of 22 patients with influenza infection. The host-SOR interaction was validated in a mouse model, where SOR demonstrated protective efficacy against influenza virus infection comparable to that of the well-established respiratory probiotic Lactobacillus rhamnosus GG. Preaspiration of SOR in mice significantly mitigated body weight loss, reduced lung inflammation, and lowered viral loads following influenza virus challenge. Host response profiling indicated that SOR priming activated a greater innate immune response at the early stage of infection and that this response resolved timely as the host began to recover. These findings suggest that respiratory commensals play an immune-protective role by inducing a timely innate immune response to prevent CAP progression.},
}

@article {pmid40858074,
year = {2025},
author = {Ruiz-Castilla, FJ and Barbudo-Lunar, M and Gutiérrez, MC and Michán, C and Martín, MÁ and Alhama, J},
title = {Storage of Alperujo influences composting performance: Insights into gaseous emissions and functional metagenomics.},
journal = {Journal of environmental management},
volume = {393},
number = {},
pages = {127015},
doi = {10.1016/j.jenvman.2025.127015},
pmid = {40858074},
issn = {1095-8630},
abstract = {Alperujo (AL), the primary by-product of olive oil extraction, poses a significant environmental challenge in the Mediterranean region. Understanding the AL composting process is essential for controlled aerobic revalorisation to obtain a stable and good quality organic amendment with the minimum environmental impact. Our approach assumes that full-scale pond storage duration modifies the degree of hydrolytic fermentation of AL, affecting the subsequent stages of the composting process. In this work, AL raw materials for composting were stored for 3 or 6 months. Subsequently, during pilot-scale composting, the loss of organic matter (OM) not only induced key changes in the solid mass but also in gaseous emissions, which decreased along with the storage time. Consequently, the initial C/N ratio decreased from 25.76 to 22.24, and composting yields relative to the AL initially mixed with a bulking agent (3/1, wt./wt.) were 76.4 % and 41.7 %, respectively. Phenolic compounds were effectively degraded throughout the composting process under both initial conditions, enhancing the potential value of the final products. Metagenomic analysis revealed differences in the raw material bacteriome, variations that also became evident throughout composting. The thermophilic stage fostered the selection of a range of thermotolerant microorganisms, many of them with lignocellulosic activity, which is essential for the decomposition of OM. Then, at the final mesophilic phase, a significant increase in bacterial diversity and metabolic activity was observed. This study contributes to better understand the functional role of the microbiome in AL composting, particularly regarding the bacterial community dynamics and gaseous emissions to the atmosphere.},
}

@article {pmid40858027,
year = {2025},
author = {Miao, Y and Liu, X and Liu, M and Huang, Y and Hu, Q and Zhang, Q and Xie, Z and Li, Q},
title = {Vertical migration of antibiotics, ARGs, and pathogens in industrial multi-pollutant soils: Implications for environmental and public health.},
journal = {Ecotoxicology and environmental safety},
volume = {303},
number = {},
pages = {118912},
doi = {10.1016/j.ecoenv.2025.118912},
pmid = {40858027},
issn = {1090-2414},
abstract = {Urban soils accumulating multiple pollutants act as critical reservoirs for antibiotic resistance genes (ARGs) and pathogens, yet their vertical migration in industrial soils remains poorly understood. Here, we investigated antibiotics, ARGs, and pathogenic hosts in soil profiles (0-310 cm) from Shanghai's Taopu Industrial Park (China) using ultra-performance liquid chromatography tandem mass spectrometry and metagenomic sequencing. Nineteen antibiotics (0.7-113.6 ng g[-1]) decreased exponentially with depth, influenced by polycyclic aromatic hydrocarbons (PAHs). Among 1183 ARG subtypes, 437 persisted across depths, with relative abundance increasing with soil depth, primarily driven by microbial community shifts, where metabolic pathways (e.g., carbohydrate and nitrogen metabolism as network hubs) contributed substantially to ARG dissemination. Random forest modelling identified clay (38 %) and fluoranthene (21 %) as primary drivers for bacterial communities, while pathogens responded divergently: antibiotics explained 48 % of Acinetobacter abundance variation, whereas clay governed 36 % of Pseudomonas abundance. The top 30 ARG-host genera included seven pathogens enriched in middle-deep layers (20-310 cm), indicating elevated groundwater contamination risks. Our findings reveal synergistic pollutant-microbial metabolic interactions promoting deep-soil resistance propagation, advocating urgent co-pollutant mitigation to safeguard urban soil systems.},
}

@article {pmid40858016,
year = {2025},
author = {Ji, F and Yang, X and Quan, H and Liu, J and Li, R and Lu, H},
title = {Enhanced performance of algal-bacterial granular sludge in treating wastewater under PFOA stress: Synergistic effects and mechanisms.},
journal = {Journal of hazardous materials},
volume = {497},
number = {},
pages = {139631},
doi = {10.1016/j.jhazmat.2025.139631},
pmid = {40858016},
issn = {1873-3336},
abstract = {The ubiquitous distribution of perfluorooctanoic acid (PFOA) in wastewater poses significant challenges for wastewater treatment systems, yet its impact on granular sludge systems remains poorly understood. This study investigated the performance of aerobic granular sludge (AGS) and algal-bacterial granular sludge (ABGS) systems in terms of stability, nutrient and PFOA removal, enzyme activity, and microbial communities under PFOA stress. Both systems demonstrated tolerance and adsorptive removal of PFOA with enhanced total nitrogen (TN) and slightly decreased total phosphorus (TP) removals. Notably, ABGS showed superior performance with approximately 19 % and 80 % improved removal for TN and PFOA compared to AGS under 1 mg/L PFOA stress. Microbial community and metagenomic analyses revealed that the proliferation of nitrogen-removal bacteria (e.g., Nitrospirae increased by around 360 %) and the increased abundance of denitrification-related genes (including genes associated with electron donor pathways) boosted TN removal. Under PFOA stimulation, the synergistic interaction between bacteria and algae in the ABGS system secreted about 12 % more extracellular polymeric substances (EPS). The higher concentration and diverse composition of EPS offered abundant adsorption sites for PFOA while serving as a protective barrier that restricted its penetration into cells. This protective mechanism was further supported by the enhanced antioxidant defenses in ABGS as evidenced by the lower increase in reactive oxygen species and lactate dehydrogenase levels compared to AGS. These findings deepen our understanding of the stress responses and adaptive mechanisms of granular sludge systems under long-term per- and polyfluoroalkyl substance exposure and highlight the potential of ABGS in treating PFOA-laden wastewater.},
}

@article {pmid40858011,
year = {2025},
author = {Ji, Q and Zhu, J and Hou, G and Liang, G and Yan, P and Liu, X and Yu, Z and Xue, K and Wang, Z and Liu, R},
title = {Antibiotic stress alters lysogeny-lysis dynamics and drives phage-mediated transfer of antibiotic resistance genes in the activated sludge process.},
journal = {Journal of hazardous materials},
volume = {497},
number = {},
pages = {139659},
doi = {10.1016/j.jhazmat.2025.139659},
pmid = {40858011},
issn = {1873-3336},
abstract = {The spread of antibiotic resistance genes (ARGs) in wastewater treatment systems poses a significant public health concern, yet the role of bacteriophages (phages), particularly temperate phages, in mediating horizontal gene transfer (HGT) of ARGs under antibiotic stress remains poorly understood. This study investigated the effects of escalating ciprofloxacin (CIP; 0-200 μg/L)-selected as a representative antibiotic due to its frequent occurrence and persistence in wastewater-on phage lysogeny-lysis dynamics and phage-mediated ARG transfer in a laboratory-scale activated sludge reactor. Integrating metaviromic and metagenomic analysis revealed that the phage-mediated ARG-HGT events mainly occurred at the highest CIP concentration stage (200 μg/L), indicating that high-level antibiotic stress is essential for triggering significant ARG transfer. Notably, all these HGT events were associated with temperate phages. The HGT-associated ARGs may confer host resistance to antibiotics, as supported by the ARG expression and antibiotic resistance activity experiment. Although temperate dynamics generally shifted toward lysogeny under escalating stress, most of the temperate phages involved in ARG-HGT became more active at higher CIP concentration stages, which may facilitate host survival under stress conditions.},
}

@article {pmid40857949,
year = {2025},
author = {Jin, L and Yuan, L and Bürgmann, H and Ju, F},
title = {Wastewater treatment plant effluent drives coupled changes of viral and bacterial community structure and function in impacted rivers.},
journal = {Environment international},
volume = {203},
number = {},
pages = {109737},
doi = {10.1016/j.envint.2025.109737},
pmid = {40857949},
issn = {1873-6750},
abstract = {The discharge of wastewater treatment plant (WWTP) effluent containing bacteria and viruses has significant ecological and public health implications for aquatic ecosystems. While viruses infecting bacterial hosts are abundant and diverse in wastewater, their environmental fate, host association, and functional impact in affected river ecosystems remain poorly understood. Using a metagenomic approach, we characterized double-stranded DNA viral communities across nine WWTPs and impacted riverine habitats, including water, suspended particles, sediment, and epilithic biofilm. River water was the most affected habitat by WWTP effluent, with viral diversity increasing by 22 % (±15 %) downstream. In contrast, no significant differences were observed in either viral or bacterial community structures across locations in biofilm or sediment. Among 38,826 viral operational taxonomic units (vOTUs) recovered from 148 metagenomes, 18 % were shared exclusively between effluent and downstream habitats, primarily with river water (99 % of the vOTUs). These wastewater-associated vOTUs were predicted to infect key bacterial taxa involved in carbon and nitrogen cycling (e.g., Nitrosomonas and Methylomonadaceae) and potential human pathogens (e.g., Vibrio and Ralstonia). Additionally, WWTP effluent increased the diversity of virus-encoded auxiliary metabolic genes, especially those involved in carbon, nutrient, and drug metabolism, suggesting potential roles in shaping host fitness and environmental adaptation. Overall, our findings demonstrate that WWTP effluent drives coupled changes in viral and bacterial communities in river water, highlighting the potential ecological consequences of virus-host interactions in wastewater-impacted aquatic environments.},
}

@article {pmid40857926,
year = {2025},
author = {Zou, Y and Chen, W and Wang, L and Li, Y and Wang, Z and Tao, R},
title = {Microbial metabolic functions, rather than taxonomic composition, predominantly shape the distribution of antibiotic resistance genes in an effluent-impacted hyporheic zone.},
journal = {Water research},
volume = {287},
number = {Pt B},
pages = {124455},
doi = {10.1016/j.watres.2025.124455},
pmid = {40857926},
issn = {1879-2448},
abstract = {Discharge of wastewater treatment plant effluent into rivers introduces substantial loads of emerging pollutants; however, the distribution and drivers of antibiotic resistance genes (ARGs) in subsurface areas such as the hyporheic zone (HZ) remain poorly understood. Using metagenomic and bioinformatic approaches, this study examined ARG profiles and identified the dominant factors shaping their distribution in the HZ of a river where treated sewage serves as the primary water source. ARG abundances were higher in winter and in surface sediment samples (0-10 cm). On average, 53.5 % of detected ARGs conferred resistance to more than one antibiotic, reflecting disturbance caused by effluent discharge. Microbial communities were characterized in terms of both taxonomic diversity and metabolic functions related to elemental cycling. The results showed that Bray-Curtis dissimilarities based on functional profiles were lower than those based on taxonomic compositions. Moreover, physicochemical properties of the HZ exerted opposite effects on microbial metabolic functions (path coefficient:0.41) and taxonomic structure (0.75), indicating a clear decoupling between metabolic function and taxonomy. Compared with microbial composition, ARG composition exhibited stronger correlations with the profiles of carbon and phosphorus cycle genes. Furthermore, 46.1 % of the recovered metagenome-assembled genomes (MAGs) carried ARGs, with detection frequencies exceeding 60.0 % in MAGs associated with elemental cycling. Notably, both network analysis and co-localization patterns on contigs demonstrated positive and physical linkages between ARGs and functional genes for carbohydrate metabolism and organic phosphorus release. These findings revealed that in effluent-dominated rivers with minimal base flow, microbial metabolic functions dominate ARG distribution dynamics in the HZ.},
}

@article {pmid40857774,
year = {2025},
author = {Liang, A and Wu, X and Zhu, Y and Pan, L and Wang, A and Wu, C and Xia, J},
title = {Targeted next-generation sequencing (tNGS): An upcoming application for pathogen identification in clinical diagnosis.},
journal = {Journal of infection and public health},
volume = {18},
number = {10},
pages = {102936},
doi = {10.1016/j.jiph.2025.102936},
pmid = {40857774},
issn = {1876-035X},
abstract = {Rapid and efficient detection of pathogens is a goal for clinical laboratories. Traditional methods such as post-culture identification, smear microscopy, antigen-antibody detection, and polymerase chain reaction cannot perform hundreds of high-throughput tests simultaneously. With the development of genetic engineering, next-generation sequencing technology has gradually been introduced into clinical testing. The new technology of targeted next-generation sequencing (tNGS) has the advantages of high sensitivity, high efficiency, and relatively low cost. This review of articles on tNGS published in the past two decades summarizes tNGS workflow and clinical applications, compares it with traditional culture and metagenomic next-generation sequencing (mNGS), and highlights its role in detecting multiple pathogens in mixed infections and drug-resistance genes. It also elaborates on the latest guidelines and the quality control process. By highlighting the practical clinical use of tNGS, it offers insights for optimizing the detection of multiple pathogens in polymicrobial infections to enhance diagnostic accuracy and efficiency.},
}

@article {pmid40857503,
year = {2025},
author = {Yue, Y and Mao, Y and Read, TD and Fedirko, V and Satten, GA and Chen, X and Zhan, X and Hu, YJ},
title = {Integrative analysis of microbial 16S gene and shotgun metagenomic sequencing data improves statistical efficiency in testing differential abundance.},
journal = {Journal of the American Statistical Association},
volume = {},
number = {},
pages = {},
doi = {10.1080/01621459.2025.2516205},
pmid = {40857503},
issn = {0162-1459},
abstract = {The most widely used technologies for profiling microbial communities are 16S marker-gene sequencing and shotgun metagenomic sequencing. Surprisingly, many microbiome studies have performed both experiments on the same cohort of samples. The two sequencing datasets often reveal consistent patterns of microbial signatures, suggesting that an integrative analysis of both datasets could enhance the testing power for these signatures. However, differential experimental biases, partially overlapping samples, and uneven library sizes pose tremendous challenges when combining the two datasets. In this article, we introduce the first method of this kind, named Com-2seq, that combines the two datasets for testing differential abundance at the genus level as well as the community level while overcoming these difficulties. Our simulation studies demonstrate that Com-2seq substantially enhances statistical efficiency over analysis of a single dataset and outperforms two ad hoc approaches to integrative analysis. In analysis of real microbiome data, Com-2seq uncovered scientifically plausible findings, namely, the association of Butyrivibrio, Gemella and Ignavigranum with prediabetes status, which would have been missed by analyzing a single dataset. Butyrivibrio failed to reach the significance level in the analysis of each dataset despite showing a consistent trend; Gemella and Ignavigranum failed to produce adequate data in the 16S experiment.},
}

@article {pmid40857268,
year = {2025},
author = {Umair, M and Yasir, M and Jamal, Z and Hakim, R and Saeed, SY and Salman, M and Iqbal, A and Khan, MQ and Khanzada, F and Javed, Y},
title = {Whole-Genome sequencing of Chikungunya Virus (CHIKV) from Pakistan: Detection of the East/Central/South African (ECSA) genotype during the 2024 outbreak in Mansehra.},
journal = {PloS one},
volume = {20},
number = {8},
pages = {e0329856},
doi = {10.1371/journal.pone.0329856},
pmid = {40857268},
issn = {1932-6203},
mesh = {Pakistan/epidemiology ; *Chikungunya virus/genetics/isolation & purification ; *Chikungunya Fever/epidemiology/virology ; Humans ; *Disease Outbreaks ; Whole Genome Sequencing ; Phylogeny ; Genotype ; *Genome, Viral ; Male ; Female ; Adult ; Mutation ; High-Throughput Nucleotide Sequencing ; },
abstract = {The 2024 chikungunya virus (CHIKV) outbreak in Mansehra, Khyber Pakhtunkhwa, Pakistan, marked a significant public health event, providing a unique opportunity to investigate the genomic diversity and evolutionary dynamics of circulating strains. Using metagenomic next-generation sequencing (mNGS), we analyzed serum samples from patients presenting with acute febrile illness and joint pain, identifying 16 CHIKV-positive cases, six of which yielded near-complete genomes. Phylogenetic analysis revealed that all isolates belonged to the East/Central/South African (ECSA) genotype, closely related to strains from India (2020-2024) and China (2017). Notably, this study represents the first comprehensive whole-genome sequencing of CHIKV in Pakistan, uncovering unique mutations in structural (E1: I28V, V290I; E2: Y39H, D54E) and non-structural proteins (NSP1: I167V, M376T; NSP4: G27R, P52S, I403V), suggesting potential viral adaptations to local environmental and vector conditions. The absence of the E1-A226V mutation, associated with enhanced transmission by Aedes albopictus, highlights the need for continued genomic surveillance to monitor emerging variants. Additionally, the detection of a GB virus-C co-infection in one case underscores the utility of mNGS in identifying co-circulating pathogens. This study provides critical insights into the genomic landscape of CHIKV in Pakistan, emphasizing the importance of enhanced surveillance, diagnostics, and vector control strategies to mitigate future outbreaks. The findings underscore the necessity of regional collaboration and genomic monitoring to address the evolving threat of CHIKV in South Asia.},
}

Pakistan/epidemiology
*Chikungunya virus/genetics/isolation & purification
*Chikungunya Fever/epidemiology/virology
Humans
*Disease Outbreaks
Whole Genome Sequencing
Phylogeny
Genotype
*Genome, Viral
Male
Female
Adult
Mutation
High-Throughput Nucleotide Sequencing

@article {pmid40856799,
year = {2025},
author = {Pushkareva, E and Keilholz, L and Böse, J and von Berg, KL},
title = {Genetic Diversity and Potential of Cyanobacteria and Fungi Living on Arctic Liverworts.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {90},
pmid = {40856799},
issn = {1432-184X},
support = {PU867/1-1//Deutsche Forschungsgemeinschaft/ ; },
mesh = {Arctic Regions ; *Hepatophyta/microbiology ; *Cyanobacteria/genetics/classification/isolation & purification/physiology ; *Fungi/genetics/classification/isolation & purification ; *Genetic Variation ; Symbiosis ; Soil Microbiology ; Phylogeny ; Nitrogen Fixation ; },
abstract = {Liverworts often form symbiotic associations with fungi and cyanobacteria, yet the distribution and specificity of these relationships remain largely unexplored, particularly in Arctic environments. This study used metagenomic sequencing to investigate fungal and cyanobacterial communities associated with Arctic liverworts, analyzing photosynthetic parts of gametophytes and their rhizoids with attached soil separately. The results revealed that Ascomycota dominated the fungal community. The cyanobacterial community was primarily composed of heterocytous Nostoc and non-heterocytous filamentous Leptolyngbya, with Nostoc showing evidence of nitrogen fixation, especially in gametophytes, suggesting a potential role in enhancing nitrogen availability for the host. These findings underscore the ecological significance of liverwort-associated microorganisms in Arctic ecosystems, with microbial composition differing between upper and lower parts of plants, as well as between leafy and thalloid liverworts, indicating possible functional specialization.},
}

Arctic Regions
*Hepatophyta/microbiology
*Cyanobacteria/genetics/classification/isolation & purification/physiology
*Fungi/genetics/classification/isolation & purification
*Genetic Variation
Symbiosis
Soil Microbiology
Phylogeny
Nitrogen Fixation

@article {pmid40856764,
year = {2025},
author = {Sharma, P and Iqbal, MZ and Chandra, R},
title = {Bacterial allies in chromium hyperaccumulation: native rhizobacterial dynamics of profusely growing Dactyloctenium aegyptium in highly tainted tannery sludge.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {9},
pages = {314},
pmid = {40856764},
issn = {1573-0972},
support = {IF210284//Department of Science and Technology, Ministry of Science and Technology, India/ ; },
mesh = {*Chromium/metabolism ; Biodegradation, Environmental ; *Sewage/microbiology/chemistry ; *Bacteria/metabolism/classification/genetics/isolation & purification ; Plant Roots/microbiology/metabolism ; Soil Pollutants/metabolism ; Tanning ; Soil Microbiology ; Microbiota ; Rhizosphere ; Industrial Waste ; },
abstract = {Tannery sludge has highly toxic heavy metals like chromium (Cr), posing environmental and health risks. This research investigates the potential of Dactyloctenium aegyptium (L.) Willd. and the associated rhizobacterial communities for bacterial-assisted phytoremediation of tannery sludge, having 6403.16 ± 0.71 mg/kg Cr. The analyses of culturable bacterial communities resulted in the exploration of two highly potent plant growth-promoting strains (CRB2 and CRB5), out of the six culturable strains obtained. SEM imaging depicted robust bacterial colonization on the plant root surface, confirming active plant-microbe interaction. D. aegyptium showed significant Cr accumulation (4936 ± 1.34 mg/kg) within the tissues, followed by substantial translocation to shoots and leaves (TF = 1.01). With a BCF of 1.66 for Cr, D. aegyptium bespeaks evident hyperaccumulation potential. TEM imaging revealed the granular metal deposition in the plant tissues. Post-plant growth, the sludge exhibited an 80.3% reduction in Cr concentration, alongside enhanced physicochemical properties (reduced pH, increased organic matter, reduced metal content). Furthermore, metagenomics analyses showed that the growth of D. aegyptium drastically changed rhizobacterial communities, decreasing species richness and increasing functional pathways associated with stress responses and metal tolerance. Important genes (copA, czcA, nirA), enzymes (dioxygenases, trimethylamine-N-oxide reductase), and proteins (CsgE, DsbG), essential for the nitrogen cycle, chromium detoxification, and plant-microbe associations, were found to be involved in metabolic pathways. The study amalgamates morphophysiological and advanced metagenomic approaches to put forth an understanding of species-specific plant-microbe interactions for the development of scalable and sustainable remediation and engineering of rhizospheric microbiomes for eco-restoration of heavy metal-polluted industrial sites.},
}

*Chromium/metabolism
Biodegradation, Environmental
*Sewage/microbiology/chemistry
*Bacteria/metabolism/classification/genetics/isolation & purification
Plant Roots/microbiology/metabolism
Soil Pollutants/metabolism
Tanning
Soil Microbiology
Microbiota
Rhizosphere
Industrial Waste

@article {pmid40856172,
year = {2025},
author = {de-Dios, T and Bonucci, B and Barbieri, R and Kushniarevich, A and D'Atanasio, E and Dittmar, JM and Cessford, C and Solnik, A and Robb, JE and Warinner, C and Oras, E and Scheib, CL},
title = {Bone adhered sediments as a source of target and environmental DNA and proteins.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msaf202},
pmid = {40856172},
issn = {1537-1719},
abstract = {In recent years, sediments from cave environments have provided invaluable insights into ancient hominids, as well as past fauna and flora. Unfortunately, locations with favourable conditions for ancient DNA (aDNA) preservation in sediments are scarce. In this study we analysed a set of samples obtained from sediments adhered to different human skeletal elements, originating from Neolithic to Medieval sites in England, and performed metagenomics and metaproteomics analysis. From them, we were able to reconstruct a partial human genome. The genetic profile of those human sequences matches the one recovered from the original skeletal element. Additionally, aDNA sequences matching the genomes of endogenous gut microbiome bacteria were identified. We also found the presence of genetic sequences corresponding to animals and plants. In particular we managed to retrieve the partial genome and proteome of a Black Rat (Rattus rattus), sharing close genetic affinities to other medieval Rattus rattus. Our results demonstrate that material usually discarded, as it is sediments adhering to human remains, can be used to get a glimpse of the environmental conditions at the time of the death of an individual.},
}

@article {pmid40855911,
year = {2025},
author = {Wei, L and Wu, H and Wen, L and Chen, M and Cui, B and Wang, X and Wu, T and Cheng, Y},
title = {Rice protein peptides alleviate lipid accumulation via modulating liver metabolism and remodeling the gut microbiota in HFD-induced mice.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo01536g},
pmid = {40855911},
issn = {2042-650X},
abstract = {Hyperlipidemia is a significant risk factor for lipid metabolism disorder and gut health impairment. Rice protein peptides (RPs) have emerged as promising interventions for hyperlipidemia management, owing to their safety profile, bioavailability, and cost-effectiveness. However, comprehensive investigations into their anti-hyperlipidemic effects and underlying mechanisms remain insufficiently explored. This study aimed to investigate the efficacy of RPs in alleviating hyperlipidemia and hepatic lipid accumulation by lipidomic and microbiome analyses. Results revealed that RP administration significantly ameliorated lipid metabolism disorders by reducing fat accumulation, normalizing blood lipid levels, and inhibiting lipase activity. Additionally, RPs exhibited hepatoprotective effects by increasing antioxidant enzyme activity and decreasing pro-inflammatory cytokines. Lipidomic analysis further revealed that RPs altered lipid metabolic patterns, identifying 10 differentially regulated lipid species that may serve as potential biomarkers for hyperlipidemia. Furthermore, RP supplements significantly regulated the mRNA levels of gene expression (HMGR, SREBP2, CYP7A1, LDLR, PPARα, PPARγ, FAS, and ACS) involved in hepatic lipid metabolism. Metagenomic analysis demonstrated that RPs reversed gut microbiota dysbiosis by reducing the Firmicutes/Bacteroidetes ratio and increasing the abundance of beneficial genera such as Akkermansia, Muribaculaceae, Clostridia_UCG-014, and Blautia. Furthermore, RP intervention significantly elevated fecal short-chain fatty acid (SCFA) content, particularly butyrate, isobutyrate, and isovalerate, suggesting a link between microbial modulation and metabolic improvement. These findings suggested RPs as an effective strategy for improving lipid metabolism and the gut microbiota composition, offering a promising dietary intervention for hyperlipidemia management.},
}

@article {pmid40855532,
year = {2025},
author = {Babalola, OO and Ogundeji, FO and Akanmu, AO},
title = {Dataset of 16S rRNA and ITS gene amplicon sequencing of celery and parsley rhizosphere soils.},
journal = {BMC genomic data},
volume = {26},
number = {1},
pages = {60},
pmid = {40855532},
issn = {2730-6844},
support = {UID123634 and UID132595//National Research Foundation/ ; },
mesh = {*Rhizosphere ; *RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; Bacteria/genetics/classification ; Fungi/genetics/classification ; *Apium/microbiology ; Metagenomics ; Microbiota ; Phylogeny ; },
abstract = {OBJECTIVES: This amplicon metagenomic study examines the relative abundance, taxonomic profiles and community structure of bacterial and fungal communities associated with the roots of parsley (Petroselinum crispum) and celery (Apium graveolens) under monocropping and intercropping systems. The study aims to provide a baseline understanding of how intercropping influences rhizosphere microbial dynamics.

DATA DESCRIPTION: The dataset provides insight into the effects of parsley-celery intercropping system on soil microbial richness, diversity and community structure. Amplicon metagenomic sequencing was performed on the DNA samples, targeting the 16S rRNA gene (V3-V4 region) and the ITS region for bacterial and fungal communities, respectively. The quantified libraries were pooled and sequenced using Illumina platforms, and the raw sequences were analyzed using the Quantitative Insights Into Microbial Ecology (QIIME 2 version 2019.1.) pipeline. The resulting Amplicon Sequence Variant (ASV) profiles revealed Actinobacteria and Protobacteria as the most predominant bacteria phyla, followed by Bacteroidota, Gemmatimonadota and Acidobacteriaota. The most predominant taxonomic distribution of fungi at the phylum level includes Ascomycota and Mortierellomycota. The dataset includes raw sequence reads in FASTQ format (.fastq.gz), which have been deposited in the Sequence Read Archive (SRA) of the National Center for Biotechnology Information (NCBI) under the Bioproject Accession numbers; SRP540554 (16S rRNA) and SRP540675 (ITS).},
}

*Rhizosphere
*RNA, Ribosomal, 16S/genetics
*Soil Microbiology
Bacteria/genetics/classification
Fungi/genetics/classification
*Apium/microbiology
Metagenomics
Microbiota
Phylogeny

@article {pmid40855409,
year = {2025},
author = {Graeber, E and Tysha, A and Nisar, A and Wind, D and Mendling, W and Finzer, P and Dilthey, A},
title = {Shallow shotgun metagenomic sequencing of vaginal microbiomes with the Oxford Nanopore technology enables the reliable determination of vaginal community state types and broad community structures.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {544},
pmid = {40855409},
issn = {1471-2180},
mesh = {Female ; Humans ; *Vagina/microbiology ; *Microbiota/genetics ; *Metagenomics/methods ; Vaginosis, Bacterial/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Adult ; RNA, Ribosomal, 16S/genetics ; High-Throughput Nucleotide Sequencing/methods ; *Nanopore Sequencing/methods ; Sequence Analysis, DNA/methods ; Young Adult ; DNA, Bacterial/genetics ; Cohort Studies ; Nanopores ; },
abstract = {BACKGROUND: The vaginal microbiome plays an important role in female health; it is associated with reproductive success, susceptibility to sexually transmitted infections, and, importantly, the most prevalent vaginal condition in reproduction-age women, bacterial vaginosis (BV). Traditionally, 16S rRNA gene sequencing-based approaches have been used to characterize the composition of vaginal microbiomes, but shallow shotgun metagenomic sequencing (SMS) approaches, in particular when implemented with the Oxford Nanopore Technologies, have important potential advantages with respect to cost effectiveness, speed of data generation, and the availability of flexible multiplexing schemes.

RESULTS: Based on a study cohort of n = 52 women, of which 23 were diagnosed with BV, we evaluated the applicability of Nanopore-based SMS for the characterization of vaginal microbiomes in direct comparison to Illumina 16S-based sequencing. We observed perfect agreement between the two approaches with respect to detecting the dominance of individual samples by either Lactobacilli, vaginosis-associated, or other taxa; very high concordance (92%) with respect to community state type (CST) classification; and a high degree of concordance with respect to the overall clustering structures of the sequenced microbiomes. Comparing the inferred abundances of individual species in individual samples, we observed significant differences (Wilcoxon signed-rank test p < 0.05) between the two approaches for 12 of the 20 species most abundant in our cohort, indicating differences in the fine-scale characterization of vaginal microbiomes. Higher overall abundance of Gardnerella vaginalis, associated with an increased number of CST IV detections, in the Nanopore shallow SMS data indicated potentially increased sensitivity of this approach to dysbiotic states of the vaginal microbiome. Nanopore shallow SMS also enabled the methylation-based quantification of different human cell types in the characterized samples as well as the detection of non-prokaryotic species, including Lactobacillus phage and Candida albicans in study participants with microscopically detected Candida. One important potential limitation of the evaluated Nanopore-based SMS approach was marked variation in sequencing yields.

CONCLUSION: Our study demonstrated the successful application and potential advantages of Nanopore-based shallow SMS for the characterization of vaginal microbiomes and paves the way for its application in larger-scale research or diagnostic settings.},
}

Female
Humans
*Vagina/microbiology
*Microbiota/genetics
*Metagenomics/methods
Vaginosis, Bacterial/microbiology
*Bacteria/classification/genetics/isolation & purification
Adult
RNA, Ribosomal, 16S/genetics
High-Throughput Nucleotide Sequencing/methods
*Nanopore Sequencing/methods
Sequence Analysis, DNA/methods
Young Adult
DNA, Bacterial/genetics
Cohort Studies
Nanopores

@article {pmid40855353,
year = {2025},
author = {Mousa, AA and Zhang, H and Duan, H and Zhang, J and Mao, S},
title = {Correction: Metagenomic analysis reveals rumen microbiome enrichment and functional genes adjustment in carbohydrate metabolism induced by different sorting behavior in mid-lactation dairy cows.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {90},
pmid = {40855353},
issn = {2524-4671},
}

@article {pmid40828281,
year = {2025},
author = {Enciso Garcia, JS and Chignola, M and Ragionieri, L and Rey, F and Fluch, M and Borruso, L and Corretto, E and Schuler, H},
title = {High-Throughput Amplicon Sequencing for Analyzing Microbial Communities of Insects.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2935},
number = {},
pages = {237-258},
pmid = {40828281},
issn = {1940-6029},
mesh = {Animals ; *Insecta/microbiology ; *High-Throughput Nucleotide Sequencing/methods ; *Microbiota/genetics ; *Bacteria/genetics/classification/isolation & purification ; Symbiosis ; RNA, Ribosomal, 16S/genetics ; Metagenomics/methods ; DNA, Bacterial/genetics ; Sequence Analysis, DNA/methods ; },
abstract = {Insects represent more than 80% of all described species on the planet. This diversity is a result of millions of years of evolution, during which insects have colonized nearly every habitat. Their success is partly due to their ability to form symbiotic relationships with a wide variety of other organisms, especially microorganisms. Identifying and characterizing associated microorganisms are crucial to understanding the complexity and dynamics of these symbiotic relationships. To date, advancements in sequencing technologies that provide large sequence data sets have become ideal tools for characterizing insect microbiomes, including information about non-cultivable microorganisms commonly found in insects. Despite the growing number of studies focused on insect microbiome characterization, there are few protocols detailing methodological procedures for fieldwork, DNA extraction, and data processing. Here, we present an overview of the characterization of insect-associated bacterial communities. We cover best practices for data interpretation and visualization, including alpha and beta diversity analyses, community composition profiling, and statistical testing to identify microbial associations of insects.},
}

Animals
*Insecta/microbiology
*High-Throughput Nucleotide Sequencing/methods
*Microbiota/genetics
*Bacteria/genetics/classification/isolation & purification
Symbiosis
RNA, Ribosomal, 16S/genetics
Metagenomics/methods
DNA, Bacterial/genetics
Sequence Analysis, DNA/methods

@article {pmid40855336,
year = {2025},
author = {Haro-Moreno, JM and Roda-Garcia, JJ and Molina-Pardines, C and López-Pérez, M},
title = {The hidden genetic reservoir: structural variants as drivers of marine microbial and viral microdiversity.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {110},
pmid = {40855336},
issn = {2524-6372},
support = {PRE2021-098122//Ministerio de Ciencia e Innovación/ ; PID2023-150293NB-I00//Ministerio de Economía y Competitividad/ ; },
}

@article {pmid40854874,
year = {2025},
author = {Kaelin, EA and Mitchell, C and Soria, J and La Rosa, A and Ticona, E and Coombs, RW and Frenkel, LM and Bull, ME and Lim, ES},
title = {Longitudinal cervicovaginal bacteriome and virome alterations associate with discordant shedding and ART duration in women living with HIV in Peru.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {7904},
pmid = {40854874},
issn = {2041-1723},
support = {R00DK107923//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; },
abstract = {Despite successful suppression of plasma HIV replication by antiretroviral therapy (ART), some women living with HIV (WLHIV) can still experience genital HIV shedding (discordant shedding). Female genital tract (FGT) bacterial and viral microbiome (bacteriome and virome) community dynamics during long-term ART in WLHIV are poorly understood but might contribute to discordant HIV shedding, as the bacteriome and virome are known to influence FGT health. Here, using metagenomic next-generation sequencing, we characterize the bacteriome and virome in 125 cervicovaginal specimens collected over two years from 31 WLHIV in Lima, Peru, and show that FGT bacteriome instability is associated with discordant HIV shedding, while longitudinal changes in FGT virome composition are associated with ART duration. Intrapersonal bacteriome variation is higher in discordant HIV shedders compared to non-shedders. Cervicovaginal virome composition changes over time, particularly in non-shedders. Specifically, anellovirus relative abundance is inversely associated with ART duration and CD4 counts. Our results suggest that discordant HIV shedding is linked with FGT bacteriome instability, and immune recovery during ART influences FGT virome composition.},
}

@article {pmid40854687,
year = {2025},
author = {Ahmed, OY and Boucher, C and Langmead, B},
title = {Robust 16S rRNA classification based on a compressed LCA index.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.279846.124},
pmid = {40854687},
issn = {1549-5469},
abstract = {Taxonomic sequence classification is a computational problem central to the study of metagenomics and evolution Advances in compressed indexing with the r-index enable full-text pattern matching against large sequence collections. But the data structures that link pattern sequences to their clades of origin still do not scale well to large collections. Previous work proposed the document array profiles, which use O(rd) words of space where r is the number of maximal-equal letter runs in the Burrows-Wheeler transform and d is the number of distinct genomes. The linear dependence on d is limiting, since real taxonomies can easily contain 10,000s of leaves or more. We propose a method called cliff compression that reduces this size by a large factor, over 250× when indexing the SILVA 16S rRNA gene database. This method uses Θ(r log d) words of space in expectation under a random model we propose here. We implemented these ideas in an open source tool called Cliffy that performs efficient taxonomic classification of sequencing reads with respect to a compressed taxonomic index. When applied to simulated 16S rRNA reads, Cliffy's read-level accuracy is higher than Kraken2's by 11-18%. Clade abundances are also more accurately predicted by Cliffy compared to Kraken2 and Bracken. Overall, Cliffy is a fast and space-economical extension to compressed full-text indexes, enabling them to perform fast and accurate taxonomic classification queries. Cliffy's accuracy underscores the advantages of full-text indexes, which offer a more precise solution compared to k-mer indexes designed for a specific k value.},
}

@article {pmid40854639,
year = {2025},
author = {Silvederio, GXL and Javellana, TF and Genciana, ABN and Fontanilla, MAG and Traifalgar, RFM and Huervana, FH and Del Castillo, CS},
title = {Gut microbiome composition and diversity of wild-caught and hatchery-bred milkfish (Chanos chanos) fry.},
journal = {Journal, genetic engineering & biotechnology},
volume = {23},
number = {3},
pages = {100520},
doi = {10.1016/j.jgeb.2025.100520},
pmid = {40854639},
issn = {2090-5920},
abstract = {Milkfish is the most produced finfish in the Philippines, with approximately 75 % of its fry sourced from hatcheries. Despite numerous studies on gut microbiota of wild and cultured fish species, the diversity and functional roles of the milkfish fry gut microbiome remain poorly understood. This study presents the first gut microbiome profiles of wild and hatchery-bred milkfish fry using 16S rRNA amplicon analysis. A total of 437 OTUs were recovered and significant differences in gut bacterial communities among fry from different sources was observed, indicating that habitat is a key determinant of gut microbiome diversity. The core gut microbiota analysis identified Vibrionaceae and Roseobacteraceae as the most common and abundant bacterial families across fry sources. However, Paenibacillaceae and Bacillaceae under Phylum Bacillota were dominant in wild fry sources, particularly Hamtic and Kirayan, whereas families belonging to Phyla Cyanobacteriota, and Thermodesulfobacteria were more prevalent in Dumagas and Kirayan hatchery fry sources. Functional predictions of the gut bacterial microbiome revealed 26 differentially abundant pathways between wild-caught and hatchery-bred fry, including those related to metabolism, organismal systems, cellular processes, environmental and genetic information processing. These findings highlight significant variations in gut microbiome composition, diversity, and functional potential across different sources of wild-caught and hatchery-bred fry. Understanding these source-specific microbial communities could provide insight into the development of interventions that can improve gut health and enhance milkfish hatchery practices. It can also generate information on ideal fry selection across local milkfish sources that will enhance larval productivity and survival in the succeeding nursery and grow-out culture stages.},
}

@article {pmid40854459,
year = {2025},
author = {Zhang, B and Yin, R and Quan, X and Gao, Z and Zhou, K and Wang, X},
title = {Synergistic sulfur-iron redox in novel composite biofilm carriers drives efficient mixotrophic denitrification and phosphate removal: Metagenomic insights into nitrogen/sulfur metabolic networks and microbial interactions.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133194},
doi = {10.1016/j.biortech.2025.133194},
pmid = {40854459},
issn = {1873-2976},
abstract = {Multifunctional biofilm carriers were developed through encapsulating acetate starch or FeCl3 using paraffin and sulfur (Paraffin-Sulfur-Acetate Starch and Paraffin-Sulfur-FeCl3), aimed at enhancing nitrate removal via mixotrophic denitrification and phosphate removal via controlling Fe[3+] release. A sequencing batch biofilm reactor with these composite carriers attained efficient nitrogen removal (99.9 % for NO3[-]-N, 98.7 ± 2.2 % for total nitrogen, 24 h cycle) and phosphate removal (98.5 %) over 60 days. The composite carriers provided multiple electron donors (S[0], acetate starch, and paraffin) to sustain mixotrophic denitrification, with sulfur autotrophic denitrification contributing 65.5 %-83.7 % of total nitrogen removal. Metagenomic analysis revealed diverse nitrogen metabolism pathways, including sulfur (S[0]/S[2-]/Sn[2-]) and Fe[2+]-based autotrophic denitrification, acetate starch/paraffin-based heterotrophic denitrification, and ammonium oxidation via Fe[3+] (Feammox). Synergistic sulfur-iron redox cycling was established through coupled biotic-abiotic reactions. This study presents a novel and sustainable strategy for nitrogen and phosphate removal from low carbon/nitrogen ratio wastewater.},
}

@article {pmid40854360,
year = {2025},
author = {Liu, L and Wang, C and Zhang, SJ and Zhang, L and Peng, Y and Qi, WK},
title = {Underlying Mechanisms of Pollutant Removal Enhancement through the Formation of Low Levels of Granular Sludge in an Innovative Continuous-flow Reactor.},
journal = {Environmental research},
volume = {},
number = {},
pages = {122678},
doi = {10.1016/j.envres.2025.122678},
pmid = {40854360},
issn = {1096-0953},
abstract = {In situ cultivation and long-term stabilization of continuous-flow aerobic granular sludge (AGS) pose significant challenges for the sustainable advancement of wastewater technology. Herein, we demonstrated the successful 330-day operation of a novel continuous-flow self-circulating AcOA-Zier reactor. Aeration-driven liquid recirculation achieved recirculation-to-influent (R/I) ratios of 26-70, optimizing dissolved oxygen gradients and enabling exceptional contaminant removal of 96% for chemical oxygen demand (COD) and 95% for total inorganic nitrogen (TIN). High hydrodynamic shear promoted granulation, yielding an average particle size of 369.7 μm, with >83% of the granules in the optimal 200-600 μm range being used to ensure operational stability. Microbial community profiling revealed Proteobacteria (80%), Chloroflexi (7.1%) and Bacteroidota (10.2%) as keystone taxa underpinning granule formation, structural integrity, and pollutant degradation. Metagenomics identified narG, nirK, norBC, nosZ and nxrB as core nitrogen cycling genes, with Methylotenera and unclassified_c_Betaproteobacteria serving as the dominant functional microorganisms. In this work, we established granulation dynamics and particle stability as pivotal factors for scalable AGS systems, providing a framework for optimizing energy-efficient, high-performance wastewater treatment processes.},
}

@article {pmid40853285,
year = {2025},
author = {Nieves-Morales, R and Paez-Diaz, JA and Rivera-Lopez, EO and Rodríguez-Ramos, J and Rios-Velazquez, C},
title = {Prokaryotic communities profile from metagenomic libraries of the brown rock sea cucumber (Holothuria glaberrima) intestinal system.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0073125},
doi = {10.1128/mra.00731-25},
pmid = {40853285},
issn = {2576-098X},
abstract = {Environmental rDNA profiling enables the identification of unculturable microbial communities. To access prokaryotic diversity in the metagenomic libraries of sea cucumber's intestinal environment, 16S rDNA sequencing was performed to provide insight into the libraries' taxonomic composition, unraveling microbial groups potentially associated with biomedical, environmental, and biotechnological applications.},
}

@article {pmid40852940,
year = {2025},
author = {Philip, M and Nilsen, T and Majaneva, S and Pettersen, R and Stokkan, M and Ray, JL and Keeley, N and Rudi, K and Snipen, LG},
title = {A Targeted Reference Database for Improved Analysis of Environmental 16S rRNA Oxford Nanopore Sequencing Data.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e70036},
doi = {10.1111/1755-0998.70036},
pmid = {40852940},
issn = {1755-0998},
support = {320076//Norges Forskningsråd/ ; },
abstract = {The Oxford Nanopore Technologies (ONT) sequencing platform is compact and efficient, making it suitable for rapid biodiversity assessments in remote areas. Despite its long reads, ONT has a higher error rate compared to other platforms; necessitating high-quality reference databases for accurate taxonomic assignments. However, the absence of targeted databases for underexplored habitats, such as the seafloor, limits ONT's broader applicability for exploratory analysis. To address this, we propose an approach for building environmentally targeted databases to improve 16S rRNA gene (16S) analysis using Oxford Nanopore Technologies (ONT), using seafloor sediment samples from the Norwegian coast as an example. We started by using Illumina short-read data to create a database of full-length or near full-length 16S sequences from seafloor samples. Initially, amplicons are mapped to the SILVA database, with matches added to our database. Unmatched amplicons are reconstructed using METASEED and Barrnap methodologies with amplicon and metagenome data. Finally, if the previous strategies did not succeed, we included the short-read sequences in the database. This resulted in AQUAeD-DB, which contains 14,545 16S sequences clustered at 95% identity. Comparative database analysis reveals that AQUAeD-DB provides consistent results for both Illumina and Nanopore read assignments (median correlation coefficient: 0.50), whereas a standard database showed a substantially weaker correlation. These findings also emphasise its potential to recognise both high and low abundance taxa, which could be key indicators in environmental studies. This work highlights the necessity of targeted databases for environmental analysis, especially for ONT-based studies, and lays the foundations for future extension of the database.},
}

@article {pmid40852627,
year = {2025},
author = {O'Kane, C and Johnson, NS and Scribner, KT and Kanefsky, J and Li, W and Robinson, JD},
title = {Development of PCR Blocking Primers Enabling DNA Metabarcoding Analysis of Dietary Composition in Hematophagous Sea Lamprey.},
journal = {Ecology and evolution},
volume = {15},
number = {8},
pages = {e71999},
pmid = {40852627},
issn = {2045-7758},
abstract = {Conventional dietary assessments are challenging in hematophagous species, particularly in sea lamprey (Petromyzon marinus). However, recent technological developments and molecular approaches have provided an attractive alternative through the use of DNA metabarcoding. While DNA metabarcoding has been used for dietary analyses in numerous species, including lampreys, applications of universal primers that detect a diverse set of prey items can be limited by the amplification of predator DNA. In this study, we designed and tested eight blocking primers designed to suppress the amplification of sea lamprey DNA with vertebrate-universal primers targeting the mitochondrial 12S rRNA gene. This approach allowed for the use of a single marker to amplify a taxonomically diverse suite of host species, in contrast to previous studies that used multiple taxon-specific primer pairs (e.g., Salmonidae, Cyprinidae, and Catostomidae). Candidate blocking primers evaluated in this study differed in base pair length, end sequence modification, and purification method. Samples with different sea lamprey-to-host DNA ratios were subjected to multiple detection methods including gel electrophoresis, quantitative PCR, and DNA metabarcoding to assess the ability of each blocking primer to selectively suppress amplification of the sea lamprey 12S gene region. All blocking primers tested performed well and demonstrated high effectiveness, suppressing sea lamprey reads by > 99.9% in mock communities and improving host DNA sequence recovery across various sample types, including wild-caught lamprey. Results show that the blocking primers evaluated can facilitate molecular diet analysis in sea lamprey, allowing the amplification of a taxonomically diverse range of host fish species with universal primers.},
}

@article {pmid40852466,
year = {2025},
author = {Yan, B and Wang, Y and Wang, Z and Huang, A and Jin, X and Jiang, T and Xue, H and Shen, Z and Wang, S and Xu, H and Zhu, R},
title = {Potential role of gut bacteria in the development of hepatocellular carcinoma.},
journal = {Access microbiology},
volume = {7},
number = {8},
pages = {},
pmid = {40852466},
issn = {2516-8290},
abstract = {Liver cancer is the fourth most deadly cancer, and early detection and timely treatment apparently play a crucial role in it. Intestinal bacteria affect the development of liver cancer through various pathways. In this study, the gut bacteria of liver cancer patients are analysed in detail by using metagenomic sequencing technology, and some of the bacterial species and metabolic pathways that may affect the development of liver cancer have been identified. Additionally, we identified bacterial factors that may impact key clinical indicators of the tumour. The findings of this study provide a scientific foundation for understanding the mechanisms underlying liver cancer development. This study freshened insights into clinical treatment strategies for liver cancer.},
}

@article {pmid40852206,
year = {2025},
author = {Wang, D and Wang, H and Zhang, D and Yan, X},
title = {Early diagnosis of streptococcus cristatus in blood culture-negative infective endocarditis by capture-based metagenomic next-generation sequencing: a case report.},
journal = {Frontiers in cardiovascular medicine},
volume = {12},
number = {},
pages = {1604687},
pmid = {40852206},
issn = {2297-055X},
abstract = {BACKGROUND: Infective endocarditis (IE) is a life-threatening infectious cardiac condition characterized by therapeutic complexity and high mortality rates, for which precise pathogen identification is critical to guide accurate treatment. Although this disease is frequently caused by commensal microorganisms of the oral flora, including Streptococcus cristatus (S. cristatus); however, S. cristatus is not a common pathogen associated with IE.

CASE PRESENTATION: A 59-year-old male patient was admitted to our intensive care unit due to chest tightness and shortness of breath persisting for 10 days, with symptoms worsening over the last 6 h, including dyspnea and an inability to lie down. After the patient was admitted to the hospital for comprehensive examinations, a preliminary clinical diagnosis of IE, aortic valve vegetation formation, acute non-ST-segment elevation myocardial infarction, and heart failure was established. The patient had negative preoperative blood culture results and received empiric therapy with moxifloxacin combined with piperacillin-tazobactam for infection control, subsequently undergoing cardiac surgery. Intraoperatively obtained valve vegetations were sent for pathological testing, tissue bacterial culture, and capture-based mNGS (metagenomic next-generation sequencing) testing. The capture-based mNGS results for the vegetation was returned as S. cristatus within 24 h, with 250,119 sequences detected and 54.56% coverage, which facilitated the rapid identification of the pathogenic microorganism of IE in the early stage. The tissue culture result of the vegetation was returned on the 5th day of delivery, confirming the presence of S. cristatus. The patient was successfully discharged after comprehensive treatment and returned to the hospital 3 weeks post-discharge for a follow-up examination, which suggested a good recovery.

CONCLUSIONS: This case highlights a rare instance of S. cristatus endocarditis, which was ultimately confirmed at an early stage through capture-based mNGS performed on valvular vegetation. This suggests that for postoperative patients with persistent infection and blood culture-negative IE, valvular capture-based mNGS serves as a rapid and efficient diagnostic tool to expedite pathogen identification and guide targeted antimicrobial therapy.},
}

@article {pmid40852121,
year = {2025},
author = {Goh, YQ and Cheam, G and Yeong, M and Bhayana, N and Thomson, A and Zhang, J and Xu, J and Conway, P and Shrestha, S and Wang, Y},
title = {Ex vivo study on prebiotic & choline combination to modulate gut bacteria, enhance choline bioavailability, and reduce TMA production.},
journal = {Microbiome research reports},
volume = {4},
number = {2},
pages = {21},
pmid = {40852121},
issn = {2771-5965},
abstract = {Aim: Choline is a universal methyl group donor, playing an essential role in DNA methylation, signaling pathways, and the transport and metabolism of lipids. The primary source of choline intake is diet, and chronic deficiency has been associated with dementia, cardiovascular disease, and liver disease. Choline bioavailability can be diminished by gut microbes that express choline trimethylamine-lyase (cutC), an enzyme that converts choline into trimethylamine (TMA), a precursor for TMA N-oxide (TMAO), which is associated with an increased risk of cardiovascular diseases. Gut microbiota modulation can be achieved by prebiotics such as galactooligosaccharides, inulin, and fructooligosaccharides. The aim of our study is to use choline with prebiotics to modulate the gut microbiota to enhance choline bioavailability and minimize TMA production. Methods: We employed an ex vivo microcosm system consisting of healthy human stool samples with choline and different prebiotics and measured TMA and choline levels by targeted metabolomics. Shotgun metagenomic profiling was also performed to investigate alternation in gut microbiota composition during choline and prebiotic interventions. Results: Our study showed that choline to TMA conversion is dependent on a choline derivative and supplementing galactooligosaccharides (GOS) reduces this conversion. Choline to TMA conversion was associated with enriched microbiota from the genus Dialister, whereas GOS supplementation led to an increase in Blautia and a reduction in Clostridia populations. Loss of Clostridia also reduced a subset of Clostridium species, Clostridium citroniae, known to encode the cutC gene. The abundance of Dialister enhanced the chorismate biosynthesis pathway, while a reduction in Clostridium supported tryptophan and methionine pathways. Conclusion: This study is the first to identify the combination of choline and GOS supplementation as a potential strategy to modulate gut microbiota and its metabolites in order to improve disease etiology.},
}

@article {pmid40851860,
year = {2025},
author = {Shen, J and Kong, J and Xu, Y and Hu, Y and Feng, L},
title = {Virus in infectious uveitis: bibliometric analysis and a clinical study.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1588195},
pmid = {40851860},
issn = {1664-302X},
abstract = {INTRODUCTION: In recent years, advancements in detection technology have led to increased research interest in viral uveitis.

METHODS: This study conducted a comprehensive analysis, comprising a bibliometric examination of literature on virus and infectious uveitis and a retrospective study focusing on infectious uveitis. The bibliometric analysis aimed to elucidate past and emerging trends in this field over several decades. In the retrospective study, intraocular fluid samples were collected from 73 patients suspected of having infectious uveitis for metagenomic next-generation sequencing (mNGS), with 29 samples also subjected to microbiological culture.

RESULTS: Analysis of the literature revealed a steady rise in annual publications on virus and infectious uveitis from 1990 to 2021, reaching a peak in 2021. The United States emerged as the most prolific contributor, with significant collaborative relationships with other nations. Keywords were clustered into five categories, covering diagnostic criteria, diagnostic tools, clinical manifestations, epidemiology, and etiology of viral uveitis. Interestingly, research focus shifted from predominant viral types and serodiagnosis towards intraocular fluid testing. mNGS demonstrated a notably higher positivity rate (73.97%) compared to culture (3.45%), identifying various pathogens including viruses, bacteria, fungi, Toxoplasma gondii, and Rickettsia felis. Varicella-Zoster Virus, Epstein-Barr Virus, Klebsiella pneumoniae, and Torque Teno Virus were among the most common pathogens detected. Additionally, coexisting microorganisms such as Torque Teno Virus and Epstein-Barr Virus were identified.

CONCLUSION: Viral uveitis has consistently garnered research attention, with future directions likely focusing on virus types and diagnostic tools. Viruses are the main causative microorganisms of infectious uveitis. The high efficacy of mNGS in identifying diverse pathogens from minute volumes of intraocular fluid samples highlights its pivotal role in diagnosing infectious uveitis.},
}

@article {pmid40851855,
year = {2025},
author = {Zou, C and Dai, T and Liang, Z and Li, M and Meng, L and Zhao, X and Li, N and Wei, Q and Abd Elhamid, MA and Atif, AM and Soaud, SA and Wen, M and Yan, K and El-Sappah, AH},
title = {Loquat-tea intercropping enhances rhizosphere microbial diversity and functional profiles in tea soil ecosystems.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1651997},
pmid = {40851855},
issn = {1664-302X},
abstract = {INTRODUCTION: Intercropping systems can significantly influence soil microbial communities, affecting plant health and soil nutrient cycling, which has better economic and ecological benefits than monoculture of tea.

METHODS: This study investigated the impact of loquat-tea intercropping on the microbial community structure and functional gene composition in the rhizosphere soil of tea (Camellia sinensis). Using metagenomic sequencing, we analyzed rhizosphere soils from loquat-tea intercropping (PP_CS), tea monoculture (CS), and loquat monoculture (PP).

RESULTS AND DISCUSSION: A total of 161 phyla, 269 classes, 485 orders, 1,000 families, 3,838 genera, and 27,624 species were annotated across samples. Dominant phyla included Actinobacteria, Proteobacteria, Acidobacteria, and Chloroflexi. The genera Bradyrhizobium (4.20%) and Trebonia (3.78%) were notably enriched in the intercropping system. The analysis of community differences showed that unclassified_c_acidobacteria was in pp_cs group, demonstrating the highest LDA score (4.4 score). Functional annotation via the Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed that metabolic pathways were predominant across all treatments, with 36,111,608 reads assigned to metabolism. The comparative analysis at KEGG level 3 revealed that Metabolic pathways 289 constituted the most abundantly annotated functional category across all three groups. Redundancy analysis (RDA) showed strong correlations between key microbial genera (Trebonia, Bradyrhizobium) and soil properties, including organic matter (OM), alkali hydrolyzed nitrogen (AN), available phosphorus (AP), and available potassium (AK). These findings suggest that loquat-tea intercropping promotes microbial diversity and enhances functional potential, improving soil health and nutrient availability in tea cultivation systems.},
}

@article {pmid40851072,
year = {2025},
author = {Zhang, L and Wang, S and Wong, MCS and Mok, CKP and Ching, JYL and Mak, JWY and Chen, C and Huo, B and Yan, S and Cheung, CP and Chiu, EOL and Fung, EYT and Cheong, PK and Chan, FKL and Ng, SC},
title = {The resident gut microbiome modulates the effect of synbiotics on the immunogenicity after SARS-COV-2 vaccination in elderly and diabetes patients.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {171},
pmid = {40851072},
issn = {2055-5008},
support = {COVID19F07//Health Bureau, The Government of the Hong Kong Special Administrative Region/ ; COVID19F07//Health Bureau, The Government of the Hong Kong Special Administrative Region/ ; COVID19F07//Health Bureau, The Government of the Hong Kong Special Administrative Region/ ; COVID19F07//Health Bureau, The Government of the Hong Kong Special Administrative Region/ ; NCI202346//New Cornerstone Science Foundation/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; Aged ; *Synbiotics/administration & dosage ; SARS-CoV-2/immunology ; Female ; Male ; *COVID-19/prevention & control/immunology ; *COVID-19 Vaccines/immunology/administration & dosage ; Feces/microbiology ; Bifidobacterium ; *Immunogenicity, Vaccine ; *Diabetes Mellitus/immunology/microbiology ; Vaccination ; BNT162 Vaccine/immunology ; Middle Aged ; Antibodies, Viral/blood ; },
abstract = {The study aims to tackle the seed and soil microbiome and mechanisms that contribute to the effect of synbiotics in enhancing immunogenicity after SARS-CoV-2 vaccination in elderly and diabetic patients. Among 369 subjects who received 3 months of SIM01, a gut microbiota-derived synbiotic formula of three Bifidobacterium strains (B. adolescentis, B. bididum, and B. longum) or a placebo after the SARS-CoV-2 vaccines (mRNA vaccine BNT162b2 (Pfizer-BioNTech) or the inactivated vaccine Sinovac-CoronaVac), we performed metagenomic sequencing in stool samples of 280 vaccinees collected at baseline and 3-month postvaccination and metabonomic sequencing in 276 vaccinees collected at baseline and 1-month postvaccination. The open niche of autochthonous gut microbiota (lower levels of Bifidobacterium and decreased functional potential for carbohydrate metabolism) was associated with enhancing SIM01-contained species. The enrichment of three bifidobacterial species after 3 months of SIM01 intervention (BABBBL_fc) was positively correlated with the level of neutralizing antibodies to the BNT162b2 vaccine at 6-month postvaccination. The fold change of benzoic acid was positively correlated with BABBBL_fc in the BNT162b2 vaccinees, which was also implicated with SARS-CoV-2 surrogate virus neutralization test (sVNT)% levels at 1-month postvaccination. Importantly, SIM01 strain engraftment assessed by StrainPhlAn (A metagenomic strain-level population genomics tool) was associated with a higher fold change of three bifidobacterial species and could be predicted based on the baseline gut microbiome. Therefore, the resident gut microbiome affected the SIM01 engraftment, which was associated with the immunogenicity of SARS-CoV-2 BNT162b2 vaccines.},
}

Humans
*Gastrointestinal Microbiome/immunology
Aged
*Synbiotics/administration & dosage
SARS-CoV-2/immunology
Female
Male
*COVID-19/prevention & control/immunology
*COVID-19 Vaccines/immunology/administration & dosage
Feces/microbiology
Bifidobacterium
*Immunogenicity, Vaccine
*Diabetes Mellitus/immunology/microbiology
Vaccination
BNT162 Vaccine/immunology
Middle Aged
Antibodies, Viral/blood

@article {pmid40841983,
year = {2025},
author = {Grant, ML and Petri, RM and Baecklund, TM and Wilson, GA and Kyle, CJ},
title = {Subspecific variation in gut microbiota of North American bison in a sympatric setting reveals differentially abundant taxa.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {89},
pmid = {40841983},
issn = {2524-4671},
support = {RGPIN-2023-04503//Natural Sciences and Engineering Research Council of Canada/ ; },
abstract = {UNLABELLED: Gut microbiomes play critical roles in host-environment interactions, reflecting habitat and foraging niches. North American bison (Bison bison) subspecies—plains bison (B. bison bison) and wood bison (B. bison athabascae)—exhibit limited genetic variation from historic population bottleneck events, potentially undermining their evolutionary potential. Understanding variation in gut microbiota composition between subspecies may shed light on genetic, phenotypic, and ecological divergence relevant to their adaptive capacities. Using 16S rRNA metabarcoding of fecal samples, we characterized the gut microbiota of both subspecies in the sympatric environment of Elk Island National Park, providing insight into potential phylogenetic gut microbiome divergence. Like other ruminants, the gut microbial community of both subspecies consists primarily of the bacterial phyla Firmicutes and Bacteroidetes. Subspecific classification explained no significant differences in alpha diversity (p > 0.05) in the overall dataset, but has a potentially significant effect on beta diversity (p < 0.05, R[2] = 0.04). Gut microbiota divergence between subspecies may be driven by differential abundance of specific taxa and associated functional pathways, likely influenced by dietary preferences, ancestral phenotypes, and historical ranges. Our findings support further investigation into diet-microbiome relationships between subspecies in sympatric environments and metagenomic approaches to explore functional differences in the gut microbiome.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42523-025-00451-7.},
}

@article {pmid40851063,
year = {2025},
author = {Suppiah, J and Zulkifli, MMS and Adiee, AH and Zainudin, NAZ and Dukut Soeharto, ME and Ramli, N and Wan, MK and Sulong, MR and Suli, Z and Mohd Zain, R},
title = {Genomic evidence links human dengue cases with undetermined serotypes to sylvatic lineages.},
journal = {Tropical medicine and health},
volume = {53},
number = {1},
pages = {114},
pmid = {40851063},
issn = {1348-8945},
abstract = {BACKGROUND: Sylvatic dengue viruses, typically maintained in non-human primate and forest mosquito cycles, have rarely been associated with human infections. However, sporadic spillovers have been reported in Southeast Asia, including Malaysia. These events are often under-detected due to the genetic divergence of sylvatic strains from endemic urban dengue viruses. During routine surveillance in Malaysia (2024-2025), a subset of clinically confirmed dengue cases yielded undetectable serotype results by commercial real-time reverse transcription polymerase chain reaction (RT-PCR) assays, prompting investigation into a possible sylvatic origin.

METHODS: We investigated 22 such cases through clinical, serological, molecular, and phylogenetic analyses. NS1 antigen and broad-range RT-PCR confirmed acute dengue infection. Selected samples underwent sequencing and lineage determination.

RESULTS: Most patients presented with severe dengue during early illness (mean day 3), with 95.5% NS1 positivity and predominantly primary infection profiles. Despite serotyping failure, sequencing revealed that eight of nine analyzed samples belonged to sylvatic DENV2, while one represented a divergent DENV3. Comparative amino acid analysis uncovered a unique signature in recent Malaysian sylvatic DENV2 strains, differentiating them from both urban and historical sylvatic lineages. This includes the V270 mutation in the M gene; R844, V884, and I898 in the NS1 gene; T1207 in the NS2A gene; A1597 in the NS3 gene; and D3048 and I3373 in the NS5 gene. Phylogenetic analysis clustered these strains into a distinct Malaysian clade, separate from the African sylvatic lineage.

CONCLUSIONS: This study provides the first genomic evidence of a recent sylvatic DENV2 spillover into humans in Malaysia, likely undetected by standard diagnostics due to genetic divergence. These findings underscore the urgent need to enhance surveillance tools and explore the sylvatic transmission cycle's role in dengue epidemiology.},
}

@article {pmid40850953,
year = {2025},
author = {Tang, M and Li, C and Ge, X and Kuang, Y and Qiu, L and Chan, KC and Chen, Z and Guo, L and Zhao, Z and Zhang, B and Liu, S and Zhou, X},
title = {Honeybee-Gilliamella synergy in carbohydrate metabolism enhances host thermogenesis in cold acclimation.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {172},
pmid = {40850953},
issn = {2055-5008},
support = {RDF-23-01-067//Research Development Fund of Xi'an Jiaotong-Liverpool University/ ; 2023YFD2201804//Program of the Ministry of Science and Technology of China/ ; 2023YFD2201804//Program of the Ministry of Science and Technology of China/ ; 32470455//National Natural Science Foundation of China/ ; 2023IOZ0104//program from Institute of Zoology, Chinese Academy of Sciences/ ; No.SYND-2021-30//Program from the Sanya Institute of China Agricultural University/ ; },
mesh = {Animals ; Bees/microbiology/physiology ; *Carbohydrate Metabolism ; Cold Temperature ; *Acclimatization ; *Thermogenesis ; Gastrointestinal Microbiome ; Glucose/metabolism ; Symbiosis ; Metagenomics ; Metabolomics ; Pyruvic Acid/metabolism ; },
abstract = {How gut symbionts contribute to host adaptation remains largely elusive. Studying co-diversified honeybees and gut bacteria across climates, we found cold-adapted species (Apis mellifera, A. cerana) exhibit enhanced genomic capacity for glucose, pyruvate, lipid and glucuronate production versus tropical species. Metagenomics revealed Gilliamella as the most enriched gut bacterium in cold-adapted bees. Germ-free honeybees inoculated with the Gilliamella from A. cerana showed increased activity, body temperature and fat storage upon cold exposure. Saccharide metabolomics demonstrated higher hindgut glucose levels in Gilliamella-colonized A. mellifera versus germ-free bees, and in A. cerana versus three sympatric tropical species. Although Gilliamella can hydrolyze β-glucan into glucose, cultural experiments suggest it preferentially degrades glucuronate to pyruvate. In turn, monocolonized bees upregulated hindgut glucose/pyruvate utilization while increasing glucuronate provision, suggesting nutritional complementarity. Gilliamella's transporter genes predominantly target ascorbate (a glucuronate derivative), which is elevated in inoculated hindguts. Accordingly, Gilliamella converts ascorbate to D-xylulose-5P (promoting lipogenesis), while showing reduced growth on glucuronate/ascorbate versus glucose, potentially minimizing glucose competition with hosts. We revealed a highly coordinated host-symbiont metabolic synergy enhancing host energy acquisition for cold adaptation.},
}

Animals
Bees/microbiology/physiology
*Carbohydrate Metabolism
Cold Temperature
*Acclimatization
*Thermogenesis
Gastrointestinal Microbiome
Glucose/metabolism
Symbiosis
Metagenomics
Metabolomics
Pyruvic Acid/metabolism

@article {pmid40850684,
year = {2025},
author = {Lei, G and Han, Z and Wang, X and Malacrinò, A and Kang, T and Zhang, D and Zhang, J and Zhang, Z and Wu, H},
title = {Synthetic microbial communities rescues strawberry from soil-borne disease by enhancing soil functional microbial abundance and multifunctionality.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2025.08.040},
pmid = {40850684},
issn = {2090-1224},
abstract = {INTRODUCTION: Synthetic microbial communities (SynCom) contribute to mitigating soil-borne crop diseases while enhancing both crop quality and yield. However, relatively little research has been done on the intricate regulatory mechanisms of SynCom on the suppression of soil-borne diseases.

OBJECTIVES: We aimed to elucidate the dynamic regulatory mechanisms and legacy effects of a SynCom on the composition of soil functional microorganisms, soil multifunctionality and crucial functions, and the suppression of soil-borne diseases.

METHODS: We conducted an extensive series of experiments to assess the effect of a SynCom on the changes in the rhizosphere functional microorganisms and soil functions (e.g., multifunctionality, functionality of C, N, and P cycling) across six successive generations of strawberry in consecutive monoculture soils by employing amplicon metagenomics and transcriptome sequencing.

RESULTS: Our results showed that the SynCom increased the aboveground fresh biomass of strawberry by 31-70.3% and the fruit biomass by 171.39-280.71%, and decreased the Fusarium oxysporum abundance by 17.91-49.51% compared to the consecutive monoculture. The SynCom significantly enhanced the soil C cycling and P cycling function, and soil multifunctionality (SMF). SynCom treatment significantly increased the Shannon diversity index and relative abundances of potentially beneficial bacteria and consumer protistan communities, while exerted a significant inhibitory effect on the Shannon diversity index and relative abundances of fungal pathogen. SEM result showed that SynCom significantly affected SMF by influencing soil nutrients, the abundance and diversity of functional microbial community. Our result also showed that the SynCom established the positive legacy effects on the abundance of rhizosphere soil beneficial bacteria, strawberry biomass and plant disease resistance-associated pathways (phenylpropanoid biosynthesis pathway, alpha-linolenic acid metabolism pathway), and negative effect on the abundance of pathogenic F. oxysporum under the 7th generation of strawberry cropping.

CONCLUSION: Collectively, our study demonstrated the effectiveness of employing SynCom in mitigating soil-borne Fusarium oxysporum diseases by enhancing soil functional microbial abundance and soil multifunctionality.},
}

@article {pmid40850647,
year = {2025},
author = {Rieber, H},
title = {Re: 'Diagnostic accuracy of 16S rDNA PCR, Multiplex PCR and Metagenomic Next-Generation Sequencing in Periprosthetic Joint Infections' by Olearo et al.},
journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cmi.2025.08.021},
pmid = {40850647},
issn = {1469-0691},
}

@article {pmid40850580,
year = {2025},
author = {Chalwatzis, L and Cruyssen, CV and Mazzini, I and Morandini, A and Mautner, A and Vielnascher, R and Guebitz, GM and Ribitsch, D},
title = {Depolymerisation of waste- and bio-based polyesters by an activated sludge hydrolase.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133186},
doi = {10.1016/j.biortech.2025.133186},
pmid = {40850580},
issn = {1873-2976},
abstract = {This study investigates enzymatic hydrolysis of four novel polyesters (REPolymers) with different structures based on terephthalic acid, ethylene glycol, glutaric acid, and decanediol. These polyesters were synthesized from PET building blocks and bio-based monomers. A hydrolase from Rhizobacter sp. (Rhb), identified from a wastewater treatment sludge metagenome, was used to predict biodegradation and to assess enzymatic recycling potential of the REPolymers. Rhb shows homology to Ideonella sakaiensis PETase but exhibits superior thermostability and activity due to specific amino acids previously identified in PETase engineering. Using mass spectrometry and HPLC-DAD analysis, hydrolysis of REPolymers (5 - 34 kDa) was mechanistically studied. Mono-(2-hydroxyethyl) terephthalic acid (MHET) was the primary product, with longer PET oligomers and aliphatic dimers also detected, indicating endo-wise cleavage of aromatic and aliphatic ester bonds. Consistent degradation patterns showed dimer accumulation across different REPolymers. These findings illuminate how the polyester structure affects enzymatic hydrolysis, supporting the development of novel waste/bio-based polymers and recycling strategies.},
}

@article {pmid40850300,
year = {2025},
author = {Gupta, S and Chauhan, R and Pandey, S},
title = {Biopriming with halotolerant microbes enhances growth performance, resilience and rhizospheric microbial diversity of Solanum melongena under saline conditions.},
journal = {Plant physiology and biochemistry : PPB},
volume = {229},
number = {Pt A},
pages = {110400},
doi = {10.1016/j.plaphy.2025.110400},
pmid = {40850300},
issn = {1873-2690},
abstract = {The study demonstrated the beneficial effects of halotolerant Bacillus licheniformis O1 and Brevibacterium sp. O5 from the Aloe vera rhizosphere on aubergine growth performance in a saline environment (200 mM NaCl). qRT-PCR confirmed the upregulation of IAA biosynthesis genes (trpA and trpB), salt tolerance (kdpA, kdpB, nhaA), osmoprotectants (proA and proB), and antioxidants (sodA, sodB, and HPII) under saline conditions. This supports the intrinsic bacterial resilience of both the strains, which maintains cellular homeostasis under saline conditions (10 % NaCl). The strains exhibited multipartite PGP traits, including phosphate solubilization and the production of IAA, ammonia, siderophores, HCN, ACC deaminase, EPS, and biofilms. Furthermore, seed biopriming with a bacterial consortium synergistically improved the physiological and biochemical responses, including germination rate (87 %), total chlorophyll (by ∼1.10-fold), carotenoids (by∼1.55-fold), proline (by 4.56-fold), total soluble sugar (by 2.76-fold), and vegetative parameters, including shoot and root biomass (by 1.12- and 3.23-fold, respectively) of eggplants under saline stress. They mitigated salt-induced oxidative stress by reducing the H2O2 and O2[.] levels and MDA levels (by > 50 %) in plants, as confirmed by histochemical and quantitative assays. The key mechanisms involved in the enhancement of antioxidant activity (SOD, PPO, POD, APX, and CAT) by 1.71-13.21 times and non-enzymatic activity (phenolic and flavonoid content) by 2.39 and 4.07 times, respectively, in eggplants. The inoculants also improved soil resilience by increasing enzymatic activity (dehydrogenase, urease, amylase, and phosphatase) 0.74- to 12.7-fold under saline stress. Taxonomic analysis revealed that consortium inoculation increased species richness and relative abundance of beneficial bacteria in the eggplant rhizosphere, supporting enhanced soil and plant resilience to salinity stress.},
}

@article {pmid40849730,
year = {2025},
author = {Zhou, SY and Lie, Z and Lei, C and Zhang, Q and Liu, X and Wu, G and Neilson, R and Huang, FY and Chu, G and Meng, Z and Zhu, D and Tissue, DT and Peñuelas, J and Liu, J},
title = {Multi-Scale Evidence for Declining Microbial Carbon Fixation Along Forest Succession Gradients.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf191},
pmid = {40849730},
issn = {1751-7370},
abstract = {Although soil carbon accumulates during subtropical forest succession, changes in microbial communities and their carbon fixation capacity remain unclear. Using an integrative approach that combines field experimentation, extensive global metagenomic data, and isotope labelling, we analyzed 84 soil microbiomes from a long-term successional site and 755 global metagenomes to investigate microbial community dynamics and their role in carbon fixation. Based on field data, bacteria, fungi, and protists had synchronous succession with vegetation; however, the relative abundance of carbon fixation genes declined significantly in later successional stages. To further investigate this outcome, we analyzed global data from planted and mature natural forests and found significantly higher carbon fixation potential in planted forests, predominantly driven by Pseudomonadota and Actinomycota members. Field-based 13C labelling results further confirmed a significant decline in microbial CO2 fixation rates with forest succession. These findings underscore the ecological importance of microbial carbon fixation in early forest succession, emphasizing its foundational role in initiating soil carbon accumulation and shaping long-term carbon cycling trajectories.},
}

@article {pmid40849632,
year = {2025},
author = {Jang, S and Lee, EJ and Park, S and Lim, H and Ahn, B and Huh, Y and Koh, H and Park, YR},
title = {Spatial host-microbiome profiling demonstrates bacterial-associated host transcriptional alterations in pediatric ileal Crohn's disease.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {189},
pmid = {40849632},
issn = {2049-2618},
mesh = {Humans ; *Crohn Disease/microbiology/genetics/pathology ; *Gastrointestinal Microbiome/genetics ; Case-Control Studies ; Child ; Male ; *Bacteria/classification/genetics/isolation & purification ; Female ; *Ileum/microbiology/pathology ; Prospective Studies ; Adolescent ; Transcriptome ; Gene Expression Profiling ; Metagenome ; Computational Biology/methods ; *Host Microbial Interactions/genetics ; },
abstract = {BACKGROUND: Crohn's disease (CD) is a chronic inflammatory bowel disease involving complex relationships between the gut microbiome and host immune system. However, the spatial relationships between tissue-resident bacteria and host cells in CD pathogenesis remain poorly understood. We developed a spatial host-microbiome profiling approach to simultaneously detect host transcriptomics and bacterial species at high taxonomic resolution in pediatric ileal CD tissues.

RESULTS: In this prospective case-control study, we analyzed 14 terminal ileal tissue samples from six pediatric patients with ileal CD and two controls. Spatial host-microbiome sequencing, combined spatial transcriptomics and in-situ polyadenylation, and bulk shotgun metagenome sequencing were performed. We developed a comprehensive bioinformatics pipeline to identify bacterial species and analyze host-microbiome interactions at cellular resolution, resulting in 13,876 analyzed cells. Our approach revealed increased bacterial abundance in CD tissues compared with controls. The extent of bacterial infiltration at diagnosis correlated with disease prognosis and severity of endoscopic findings. We identified 16 potentially beneficial and nine pathogenic microbiome members in ileal CD, including several newly discovered risk-modulating bacterial species. Cell-type-specific host gene expression analysis revealed transcriptome alterations related to bacterial defense mechanisms in the presence of various bacterial species.

CONCLUSIONS: Our spatial host-microbiome profiling approach enables simultaneous species-level identification of bacteria and host transcriptomics. It reveals the intricate interactions between host cells and bacteria, providing cellular-level insights into CD pathogenesis. Our approach offers a powerful tool for investigating host-microbiome interactions in various microbiome-associated diseases to direct new strategies for microbiome-based therapeutics and prognostic markers. Video Abstract.},
}

Humans
*Crohn Disease/microbiology/genetics/pathology
*Gastrointestinal Microbiome/genetics
Case-Control Studies
Child
Male
*Bacteria/classification/genetics/isolation & purification
Female
*Ileum/microbiology/pathology
Prospective Studies
Adolescent
Transcriptome
Gene Expression Profiling
Metagenome
Computational Biology/methods
*Host Microbial Interactions/genetics

@article {pmid40849498,
year = {2025},
author = {Feng, Y and Shi, J and Li, Z and Li, Y and Yang, J and Huang, S and Zheng, J and Han, W and Qiao, Y and Zhang, J and Liu, Q and Yang, Y and Hu, C and Wu, L and Zhang, X and Tang, J and Huang, X and Ma, P},
title = {Discovery of CRISPR-Cas12a clades using a large language model.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {7877},
pmid = {40849498},
issn = {2041-1723},
support = {23HC1400700//Science and Technology Commission of Shanghai Municipality (Shanghai Municipal Science and Technology Commission)/ ; 32161133022//National Natural Science Foundation of China (National Science Foundation of China)/ ; 22177073//National Natural Science Foundation of China (National Science Foundation of China)/ ; 24141901302//Shanghai Science and Technology Development Foundation (Shanghai Science and Technology Development Fund)/ ; },
mesh = {*CRISPR-Cas Systems/genetics ; *CRISPR-Associated Proteins/genetics/metabolism/chemistry/classification ; *Bacterial Proteins/genetics/metabolism/chemistry ; Machine Learning ; *Endodeoxyribonucleases/genetics/metabolism/chemistry ; Polymorphism, Single Nucleotide ; Cryoelectron Microscopy ; Large Language Models ; },
abstract = {CRISPR-Cas systems revolutionize life science. Metagenomes contain millions of unknown Cas proteins. Traditional mining relies on protein sequence alignments. In this work, we employ an evolutionary scale language model (ESM) to learn the information beyond sequences. Trained with CRISPR-Cas data, ESM accurately identifies Cas proteins without alignment. Limited experimental data restricts feature prediction, but integrating with machine learning enables trans-cleavage activity prediction of uncharacterized Cas12a. We discover 7 undocumented Cas12a subtypes with unique CRISPR loci. Structural analyses reveal 8 subtypes of Cas1, Cas2, and Cas4. Cas12a subtypes display distinct 3D-folds. CryoEM analyses unveil unique RNA interactions with the uncharacterized Cas12a. These proteins show distinct double-strand and single-strand DNA cleavage preferences and broad PAM recognition. Finally, we establish a specific detection strategy for the oncogene SNP without traditional Cas12a PAM. This study highlights the potential of language models in exploring undocumented Cas protein function via gene cluster classification.},
}

*CRISPR-Cas Systems/genetics
*CRISPR-Associated Proteins/genetics/metabolism/chemistry/classification
*Bacterial Proteins/genetics/metabolism/chemistry
Machine Learning
*Endodeoxyribonucleases/genetics/metabolism/chemistry
Polymorphism, Single Nucleotide
Cryoelectron Microscopy
Large Language Models

@article {pmid40849482,
year = {2025},
author = {Zhang, Y and Liao, YT and Liu, F and Li, RW and Wu, VCH},
title = {Impact of diet in shaping gut virome of grain-fed and grass-fed beef cattle revealed by a comparative metagenomic study.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {190},
pmid = {40849482},
issn = {2049-2618},
support = {2030-42000-0055-000-D//USDA-ARS CRIS projects/ ; 2030-42000-0055-000-D//USDA-ARS CRIS projects/ ; 2030-42000-0055-000-D//USDA-ARS CRIS projects/ ; 2030-42000-0055-000-D//USDA-ARS CRIS projects/ ; 2030-42000-0055-000-D//USDA-ARS CRIS projects/ ; },
mesh = {Animals ; Cattle ; *Virome/genetics ; Metagenomics/methods ; *Animal Feed/analysis ; *Gastrointestinal Microbiome/genetics ; Feces/virology ; *Viruses/classification/genetics/isolation & purification ; *Poaceae ; *Diet/veterinary ; *Edible Grain ; },
abstract = {BACKGROUND: In the United States beef industry, grain-feeding and grass-feeding are the two most common types of cattle feeding. Different feeding methods are likely to affect gut microbiota compositions and subsequently change microbial adaptation and cattle metabolism. However, there is limited information regarding the impact of diet on cattle gastrointestinal virome. This study examined the composition of fecal virome from grain-fed and grass-fed beef cattle and identified unique virome features to understand the relationship between these two feeding types.

RESULTS: Six grain-fed and six grass-fed Angus beef cattle were weighed, and their fecal samples were collected for further viral metagenomic sequencing. The difference in animal growth revealed a significantly higher post-weaning weight in grain-fed cattle than in grass-fed cattle after day 56. Furthermore, the analysis of the fecal viral population showed that approximately 795 and 1266 predicted viral sequences were obtained in the grain-fed and grass-fed samples, respectively. Among those, 54.3% of the grain-fed and 26.3% of the grass-fed viral sequences were identified as known viruses. The taxonomic classification showed that viruses belonging to the order Caudovirales, mostly bacteriophages, dominated the cattle virome in both sample groups, followed by the order Cremeviriles and Petitvirales. At the family level, 13 and 16 different viral families were detected in the grain and grass-fed groups, respectively. The comparison of virome features from the two groups indicated that the viral population from the kingdom Bamfordvirae had a significantly higher abundance in the grain-fed group than in the grass-fed cattle virome. In contrast, the kingdom Heunggongvirae had a significantly higher abundance in the grass-fed group than in the grain-fed cattle virome. Moreover, the viruses, belonging to the order Caudovirales and the family Podoviridae, had significantly higher abundances in the grass-fed virome than in the grain-fed virome.

CONCLUSIONS: The findings indicate the influence of animal feeds on the changes in gastrointestinal viral compositions and their potential association with cattle weight gain. The current outcome can contribute to further understanding of phage-bacterial interactions and their underlying mechanisms in regulating the animal host's metabolism and feed efficiency. Video Abstract.},
}

Animals
Cattle
*Virome/genetics
Metagenomics/methods
*Animal Feed/analysis
*Gastrointestinal Microbiome/genetics
Feces/virology
*Viruses/classification/genetics/isolation & purification
*Poaceae
*Diet/veterinary
*Edible Grain

@article {pmid40848995,
year = {2025},
author = {Wang, J and Xue, L and Zhang, M and Shen, P and Zhao, W and Tong, Q and Wu, S and Dai, W and Yang, X and Wang, H},
title = {Colonoscopic fecal microbiota transplantation for Mild-to-Moderate Parkinson's Disease: A randomized controlled trial.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {106086},
doi = {10.1016/j.bbi.2025.106086},
pmid = {40848995},
issn = {1090-2139},
abstract = {OBJECTIVE: Growing evidence supports the efficacy and safety of fecal microbiota transplantation (FMT) in treating Parkinson's disease (PD). Fecal microbiota are commonly transplanted via oral capsules, a nasojejunal tube, or colonoscopy, but freezing often decreases the diversity and viability of transplanted microbiota. This single-center, double-blind, randomized, placebo-controlled trial aims to explore the efficacy and safety of fresh FMT via colonoscopy in dealing with PD.

METHODS: Thirty patients with mild-to-moderate PD (Hoehn-Yahr stage I-III) were randomly assigned into the FMT group (fresh FMT via colonoscopy) and placebo group (saline injection via colonoscopy) in a 1:1 ratio. Motor and non-motor symptoms, constipation, quality of life, cognitive function, emotional state and sleep quality were assessed using relevant scales. Fecal samples were harvested before and at 4, 8 and 12 weeks after treatment for metagenomic and metabolomics analyses.

RESULTS: A total of 30 patients with mild-to-moderate PD were enrolled in the present study, involving 18 males and 12 females with a median age of 68 years, a median age of onset of 63.5 years, and a median disease duration of 3 years. At 12 weeks, scores of the UPDRS Ⅲ (group × time effect, B =  - 8.80 [-13.79, -3.81]), PAC-QOL (group × time effect, B =  - 29.67 [-45.35, -13.98]), UPDRS Ⅱ (group × time effect, B =  - 5.07 [-8.85, -1.28]), NMSS (group × time effect, B =  - 35.60 [-53.59, -17.61]), PDQ-39 (group × time effect, B =  - 17.80 [-28.21, -7.39]), HAMA (group × time effect, B =  - 1.66 [-2.92, -0.40]), and HAMD (group × time effect, B =  - 1.33 [-2.49, -0.16]) were significantly reduced in the FMT group, while CSBM per week (group × time effect, B = 3.03 [1.42, 4.63]) and the Bristol Stool Scale score (group × time effect, B = 1.95 [0.12, 3.79]) significantly increased (all P < 0.05). Significant alterations were seen in the gut microbiota and fecal metabolites in the FMT group. No adverse events were observed during the follow-up period.

CONCLUSION: Fresh FMT via colonoscopy is a safe and well-tolerated procedure for treating mild-to-moderate PD. It effectively alleviates motor and non-motor symptoms, thus facilitating defecation and improving the quality of life. These effects can be maintained for a minimum of 12 weeks and may be attributed to the optimization of gut microbiota and fecal metabolites.},
}

@article {pmid40848874,
year = {2025},
author = {Fonnes, S and Mollerup, S and Paulsen, SJ and Petersen, AM and Holzknecht, BJ and Westh, H and Rosenberg, J},
title = {A prospective cohort study of the rectal microbiome in patients with suspected appendicitis.},
journal = {Clinics and research in hepatology and gastroenterology},
volume = {},
number = {},
pages = {102675},
doi = {10.1016/j.clinre.2025.102675},
pmid = {40848874},
issn = {2210-741X},
abstract = {PURPOSE: Diagnosing appendicitis is difficult. An infectious origin has been proposed, therefore signals from the microbiome could be a potential diagnostic measure. The aim was to evaluate the diagnostic potential of the rectal microbiome in patients with suspected appendicitis.

METHODS: We included adult Danish patients with suspected appendicitis undergoing appendectomy in a prospective, observational cohort study. Patients were first grouped as patients with and without appendicitis according to histopathological findings, and second, as having uncomplicated or complicated appendicitis according to the surgical report. Rectal swabs were analysed with shotgun metagenomics. The outcomes were alpha diversity, beta diversity, and differential abundance of bacteria.

RESULTS: Rectal swabs from 220 patients were analysed: 49 patients without appendicitis, 111 patients with uncomplicated and 60 patients with complicated appendicitis, respectively. Across all groups, both the alpha and beta diversity were similar. The relative abundance of bacterial genera and species was also similar across all groups. Thus, the three groups of patients had similar rectal microbiomes.

CONCLUSION: The rectal microbiome in adult patients with suspected appendicitis was similar and does not seem to have the potential to be used to diagnose neither appendicitis nor the severity of appendicitis preoperatively.

TRIAL REGISTRATION: NCT03349814 (clinicaltrials.gov).},
}

@article {pmid40848630,
year = {2025},
author = {Zhang, L and Zhang, Y and Huang, J and Zhou, R and Wu, C},
title = {Temperature-driven functional microbial interactions in soy sauce fermentation: Effects of Zygosaccharomyces rouxii and Wickerhamiella versatilis on flavor enrichment and biogenic amine reduction.},
journal = {International journal of food microbiology},
volume = {442},
number = {},
pages = {111399},
doi = {10.1016/j.ijfoodmicro.2025.111399},
pmid = {40848630},
issn = {1879-3460},
abstract = {This study elucidates the temperature-dependent interactions between halotolerant yeasts and microbial communities during secondary fortified soy sauce fermentation (SFFSS) and their implications for flavor enhancement and safety. A dual-mode fermentation system compared natural temperature fermentation (NTF) and controlled temperature fermentation (CTF, 30 °C), each with and without co-inoculation of Zygosaccharomyces rouxii and Wickerhamiella versatilis (ZC). Multi-omics analyses integrating amplicon sequencing, metagenomics, and metabolomics revealed that CTF control elevated amino acid nitrogen and aroma compounds, while increasing biogenic amines (BA) by 47.88 %. In both NTF and CTF modes, the ZC pattern significantly reduced lactic acid while enhancing succinic acid, umami/sweet free amino acids, and key aroma compounds (e.g., 4-ethylguaiacol, 5-ethyl-4-hydroxy-2-methyl-3(2H)-furanone), alongside enriching functional bacteria (Staphylococcus, Weissella), stabilizing fungal communities, and suppressing Tetragenococcus and Ligilactobacillus pobuzihii. Mechanistically, ZC pattern promoted tricarboxylic acid cycle flux and amino acid metabolism, synergistically enhancing volatile phenolics, esters, and alcohols, and reduced BA by >87 % via dual modulation of decarboxylase inhibition and oxidase activation. Network analyses linked microbial composition shifts to targeted flavor metabolite synthesis, providing a mechanistic framework for microbial community engineering. These findings highlight yeast-mediated, temperature-driven modulation of microbiota-metabolite networks as a viable strategy for producing high-quality, safe soy sauce with optimized flavor complexity.},
}

@article {pmid40848515,
year = {2025},
author = {Ni, J and Fu, L and Xiao, J and Li, C and Wu, X and Yuan, Z and Wang, J and Tang, S and Deng, F and Shen, S},
title = {Metagenomic evidence of viral secretion from tick salivary glands to saliva: implications for potential horizontal transmission.},
journal = {Ticks and tick-borne diseases},
volume = {16},
number = {5},
pages = {102540},
doi = {10.1016/j.ttbdis.2025.102540},
pmid = {40848515},
issn = {1877-9603},
abstract = {Ticks transmit diverse viral pathogens to hosts during blood-feeding via saliva secretion. This study characterized viral compositions in salivary glands and saliva from adults of four tick species (Ixodes persulcatus, Rhipicephalus microplus, Haemaphysalis longicornis, and Haemaphysalis concinna) collected in China. Meta-transcriptomic analysis revealed distinct viromes across species, with Flaviviridae dominant in R. microplus, Nairoviridae in H. concinna and I. persulcatus, and Phenuiviridae in H. longicornis and I. persulcatus. Among 27 viruses detected in salivary glands, 14 were identified in saliva, indicating horizontal transmission potential. Viruses with higher abundance (transcripts per thousand bases per million, TPM) in salivary glands were more likely to be secreted in saliva. Genomic sequences of eight viruses, including severe fever with thrombocytopenia syndrome virus (SFTSV), tick-borne encephalitis virus (TBEV), Jingmen tick virus (JMTV), Songling virus (SGLV), Wetland virus (WELV), Beiji nairovirus (BJNV), Mukawa virus (MKWV), and Wuhan tick virus 2 (WHTV2), which are associated with human diseases or possess spillover potentials, were fully assembled from salivary glands and confirmed in saliva. Notably, SFTSV in H. longicornis; MKWV, Sichuan tick hepe-like virus, and Jilin luteo-like virus 2 in I. persulcatus; and JMTV in R. microplus showed significantly increased abundance in saliva, indicating an enhanced secretion of these viruses into saliva. Conversely, TBEV, BJNV, and Sara tick phlebovirus in I. persulcatus, SGLV and WELV in H. concinna, and WHTV2 in R. microplus exhibited reduced salivary abundance despite glandular presence. These findings demonstrate differential secretion capabilities of tick-borne viruses (TBVs) from glands to saliva, advancing understanding of horizontal transmission risks for pathogens affecting human health.},
}

@article {pmid40848105,
year = {2025},
author = {Proskynitopoulos, PJ and Woltemate, S and Rhein, M and Böke, I and Molks, J and Schröder, S and Schneider, HU and Bleich, S and Frieling, H and Geffers, R and Glahn, A and Vital, M},
title = {The effect of alcohol withdrawal therapy on gut microbiota in alcohol use disorder and its link to inflammation and craving.},
journal = {Alcohol, clinical & experimental research},
volume = {},
number = {},
pages = {},
doi = {10.1111/acer.70128},
pmid = {40848105},
issn = {2993-7175},
support = {//Hetzler Foundation for Addiction Research and Prevention/ ; },
abstract = {BACKGROUND: Alcohol use disorder (AUD) is linked to changes in the function and composition of the human gut microbiome (GM). The GM affects inflammation by producing anti-inflammatory molecules such as short-chain fatty acids (SCFA), in particular butyrate, which are linked to appetite regulation, a mechanism involved in alcohol craving. This study investigates changes in GM composition and functional capacity to produce SCFA during alcohol withdrawal and their link to inflammation and craving.

METHODS: Sixty-three patients (mean age 48, SD = 12) with AUD were enrolled. We collected stool (n = 63) and blood (n = 48) during the first 48 h (timepoint A) of withdrawal therapy and between Days 10-14 (timepoint B). Microbiota were analyzed using shotgun metagenomics along with bacterial load determinations. TNF-α, IL-6, IL-8, and IL-10 were measured in plasma.

RESULTS: Bacterial diversity (species richness, Shannon Index) did not change significantly throughout withdrawal, while overall bacterial load increased. Abundances of several taxa changed, and the overall community composition during withdrawal was approaching those of healthy controls; the potential to synthesize butyrate, a key SCFA, increased. However, it remained at lower levels compared with controls. Both diversity parameters correlated with cell concentrations and the butyrate pathway at baseline. The latter was negatively associated with IL-6 at baseline. IL-8 and IL-10 levels decreased significantly during withdrawal, as did craving, which was linked to abundance alterations of six species and IL-8.

CONCLUSIONS: Alcohol withdrawal affected GM composition and increased concentration of the butyrate pathway along with overall bacterial load. Changes in bacterial composition and the butyrate production capacity demonstrate a shift toward healthier microbiota during withdrawal therapy. Changes in some species and IL-8 were linked to alcohol craving, replicating findings of previous studies. Our study adds new findings helping to understand the microbiome-gut-brain axis.},
}

@article {pmid40848091,
year = {2025},
author = {Dong, Y and Fan, S and He, S and Zhao, W and Lancuo, Z and Sharshov, K and Li, Y and Wang, W},
title = {RNA-viromics unveils diverse RNA viral communities in Large-billed crows and Northern Ravens.},
journal = {Virus genes},
volume = {},
number = {},
pages = {},
pmid = {40848091},
issn = {1572-994X},
support = {grant No. 32111530018//the National Natural Science Foundation of China and Russian Foundation for Basic Research Cooperative Exchange Project/ ; grant No. 2022-HZ-812//program of science and technology international cooperation project of Qinghai province/ ; },
abstract = {Birds have historically served as key vectors for viruses causing significant diseases. Corvid birds, often living in close proximity to livestock, poultry, and humans, provide substantial opportunities for cross-species viral transmission. Such transmission can occur through their feces or via ectoparasites (such as ticks, mites, and fleas) on their bodies, thereby releasing viruses into the environment. Despite the development of viral metagenomics, an increasing number of RNA viruses are being characterized across different species. RNA viruses in birds' gut microbial communities remain poorly studied. Here we report an extensive analysis of an RNA virome in fecal samples from Large-billed crows (Corvus macrorhynchos) and Northern Ravens (Corvus corax), both of which are common Corvus species found in the high-altitude forest and grassland regions of the Qinghai-Tibetan Plateau. This study aims to assess the RNA viruses present in the intestines of these corvids and provides the first comprehensive characterization of the diversity of gut-colonizing viruses in these two crow species.},
}

@article {pmid40847462,
year = {2025},
author = {Ma, H and Wang, M and Feng, Y and Zhang, W and Wang, W and Xie, Y and Kong, G and Feng, J and Wang, P and Wang, Q and Huang, X},
title = {Microbial profile of the appendix niche in acute appendicitis: a novel sampling approach.},
journal = {FEBS open bio},
volume = {},
number = {},
pages = {},
doi = {10.1002/2211-5463.70105},
pmid = {40847462},
issn = {2211-5463},
support = {GSWSKY2020-50//Gansu Provincial Health Commission, Provincial Health Industry Research Project/ ; 20240050058//Lanzhou University Student Innovation and Entrepreneurship Action Plan Project/ ; CY2023-QN-B17//Cuiying Scientific and Technological Innovation Program of the Second Hospital of Lanzhou University in 2023/ ; },
abstract = {Relatively little is known about the microbial variations within the human appendix niche. To overcome this knowledge gap, we employed endoscopic retrograde appendicitis treatment (ERAT) technology to collect microbial samples from the appendix lumen, followed by shotgun metagenomic sequencing on participants with acute appendicitis without antibiotic treatment. Compared to the cecum and terminal ileum, the appendix had a higher abundance at the genus level of Sphingobium, Leptotrichia and Oribacterium, as well as a significant increase in species-level abundance of oral bacteria, including Streptococcus sanguinis, Streptococcus australis, Streptococcus sp. A12, Leptotrichia sp. oral taxon 215, Veillonella dispar, Veillonella infantium and Oribacterium sinus. Pearson correlation analysis showed that bacterial species abundant in the appendix, such as Acinetobacter johnsonii, Sphingobium yanoikuyae and Agrobacterium tumefaciens, had negative correlations with the top five most abundant Gene Ontology (GO) categories (molecular function, biological process and cellular component). Conversely, species underrepresented in the appendix, including Mogibacterium diversum, Streptococcus sanguinis, Megasphaera micronuciformis and Actinomyces graevenitzii, had significant positive correlations with these GO categories. Our results show that ERAT technology can be used to improve sampling and microbiome profiling in the appendix. Furthermore, this in-depth microbial characterization could inform clinicians during antibiotic prescription. However, further large sample size studies are required to validate these results.},
}

@article {pmid40847380,
year = {2025},
author = {Wang, X and Liu, J and Chai, B and Wu, T},
title = {Protozoa-driven micro-food webs shaping carbon and nitrogen cycling in reservoir ecosystems.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {109},
pmid = {40847380},
issn = {2524-6372},
support = {YDZJSX2022B001//Shanxi Provincial Central Guidance Special Project/ ; 202304041101020//Science and Technology Cooperation and Exchange Special Project of Shanxi Province/ ; U23A20157//Key Project of the National Natural Science Foundation of China Joint Fund for Regional Innovation and Development/ ; },
abstract = {Protozoa-driven micro-food webs are pivotal regulators of microbial community structure and carbon-nitrogen cycling. By mediating trophic cascades that regulate bacterial and algal populations, protozoa influence nutrient remineralization and energy flow. Their regulation is crucial for stabilizing biogeochemical processes and preventing harmful algal blooms. However, little is known about the detailed relationship between the traits of micro-food webs and carbon/nitrogen cycling processes. Using metagenomic data, we investigated the complexity and stability of micro-food webs in three distinct zones of the Fenhe Reservoir-the inflow river zone, shallow wetland, and deep-water zone-to assess their impacts on carbon and nitrogen cycling. Our findings revealed distinct spatial patterns in micro-food web complexity and stability, with the highest diversity and interaction density in inflowing river zones and a gradual simplification towards deep-water zones. Functional gene analysis shows significant differences in carbon degradation, fixation pathways, and nitrogen transformation processes, with shallow waters exhibiting strong microbial-mediated nitrification and denitrification, while deep waters rely on anaerobic nitrogen reduction pathways. Partial least squares path modeling (PLS-PM) indicated that protozoan-driven micro-food web structures regulate microbial functional differentiation, thereby influencing carbon and nitrogen cycle. Additionally, environmental parameters such as organic carbon concentration and nitrogen availability significantly shape microbial interactions and biogeochemical transformations. These findings highlight the intricate relationship between microbial community composition, food web stability, and elemental cycling, providing critical insights for reservoir ecosystem management and water quality optimization.},
}

@article {pmid40847349,
year = {2025},
author = {Li, X and Liu, J},
title = {Molecular diagnostic technology: beyond analytical accuracy.},
journal = {Critical care (London, England)},
volume = {29},
number = {1},
pages = {382},
pmid = {40847349},
issn = {1466-609X},
mesh = {Humans ; *Molecular Diagnostic Techniques/methods/standards/trends ; Multiplex Polymerase Chain Reaction/methods/standards ; High-Throughput Nucleotide Sequencing/methods ; Sensitivity and Specificity ; },
abstract = {Infectious diseases cause high morbidity and mortality, and early, effective antimicrobial therapy improves outcomes. However, conventional microbiology methods like culture are slow and insensitive. Emerging molecular diagnostics-such as multiplex PCR (mPCR), droplet digital PCR (ddPCR), and metagenomic next-generation sequencing (mNGS)-offer rapid, accurate pathogen identification. Challenges persist in result interpretation (e.g., setting positivity thresholds, low positive predictive value) and clinician trust. While molecular diagnostics excel in sensitivity, their real-world impact on specificity and patient prognosis - clinical accuracy -remains limited. Key hurdles include patient selection, timing, result interpretation, and pathogen relevance. Addressing these gaps is critical for standardizing these technologies and maximizing their clinical benefit.},
}

Humans
*Molecular Diagnostic Techniques/methods/standards/trends
Multiplex Polymerase Chain Reaction/methods/standards
High-Throughput Nucleotide Sequencing/methods
Sensitivity and Specificity

@article {pmid40847308,
year = {2025},
author = {Wan, S and Li, M and Li, W and Ren, Y and Wu, Y and Luo, Q and Gong, W},
title = {Development and validation of a multimodal model integrating gut microbiota and metabolite for identifying sarcopenia in patients with MASLD: a study from two centers in China.},
journal = {Nutrition journal},
volume = {24},
number = {1},
pages = {129},
pmid = {40847308},
issn = {1475-2891},
support = {82401448//National Natural Science Foundation of China/ ; 2021A1515110799//Basic and Applied Basic Research Foundation of Guangdong Province/ ; JCYJ20240813145414019//Shenzhen Science and Technology Program/ ; NSZD2024015//Shenzhen Nanshan District Science and Technology Plan Funding Program/ ; },
}

@article {pmid40847279,
year = {2025},
author = {Azmi, MAI and William-Dee, J and Morni, MA and Azhar, NAA and Sabarudin, NA and Jinggong, ER and Zolkapley, S and Baharom, NIM and Haqeem, MD and Sien, VL and Mohamad Azmi, AH and Adrus, M and Tan, CS and Khan, FAA},
title = {Metagenomic insights into host-specific gastroenteritis bacteria in forest rodents of Sarawak, Borneo: implications for one health surveillance of rodent-borne pathogens.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {531},
pmid = {40847279},
issn = {1471-2180},
support = {GL/F07/SRDC/05/2021; RDCRG02/CAT/2020/_33//Sarawak Research and Development Council/ ; GL/F07/SRDC/05/2021; RDCRG02/CAT/2020/_33//Sarawak Research and Development Council/ ; GL/F07/SRDC/05/2021; RDCRG02/CAT/2020/_33//Sarawak Research and Development Council/ ; GL/F07/SRDC/05/2021; RDCRG02/CAT/2020/_33//Sarawak Research and Development Council/ ; GL/F07/SRDC/05/2021; RDCRG02/CAT/2020/_33//Sarawak Research and Development Council/ ; F07/PGRG/2046/2020//Postgraduate Research Grant, UNIMAS/ ; },
mesh = {Animals ; *Gastroenteritis/microbiology/veterinary ; Borneo/epidemiology ; Feces/microbiology ; *Bacteria/genetics/classification/isolation & purification ; Forests ; *Rodentia/microbiology ; Humans ; RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; One Health ; Host Specificity ; Phylogeny ; Zoonoses/microbiology ; DNA, Bacterial/genetics ; Disease Reservoirs/microbiology ; *Rodent Diseases/microbiology ; },
abstract = {Rodents are known to act as reservoirs for zoonotic diseases due to their widespread distribution and synanthropic nature. Among these, foodborne pathogens capable of causing gastroenteritis in humans are of particular concern, as rodents can facilitate their transmission through contamination of food sources. Forest-dwelling rodents may harbour bacterial taxa native to their habitat, posing a risk of zoonotic spillover to nearby human settlements. This risk is further heightened by the growing prevalence of ecotourism activities, particularly in tropical countries like Malaysia. In this study, rodent trapping was conducted in selected forested areas adjacent to human settlements across Sarawak. Nanopore sequencing of the full-length 16 S rRNA gene was conducted on faecal DNA from 46 rodent individuals representing seven different species (Maxomys surifer, M. tajuddinii, M. whiteheadi, Niviventer cremoriventer, Rattus tanezumi, R. tiomanicus and Sundamys muelleri). A total of ten bacterial species associated with gastroenteritis were successfully detected. Notable findings in this study include Campylobacter, Salmonella and Shigella species, which are known to cause bacterial gastroenteritis in humans. Also, the presence of certain bacterial taxa in specific rodent genera suggests potential host specificity of foodborne pathogens. This study highlights the potential public health risks caused by rodent-borne bacterial transmission and the importance of monitoring forest rodents as potential reservoirs of zoonotic pathogens.},
}

Animals
*Gastroenteritis/microbiology/veterinary
Borneo/epidemiology
Feces/microbiology
*Bacteria/genetics/classification/isolation & purification
Forests
*Rodentia/microbiology
Humans
RNA, Ribosomal, 16S/genetics
*Metagenomics/methods
One Health
Host Specificity
Phylogeny
Zoonoses/microbiology
DNA, Bacterial/genetics
Disease Reservoirs/microbiology
*Rodent Diseases/microbiology

@article {pmid40847264,
year = {2025},
author = {Shinge, SAU and Zhang, B and Zheng, B and Qiang, Y and Ali, HM and Melchiade, YTV and Zhang, L and Gao, M and Feng, G and Zeng, K and Yang, Y},
title = {Unveiling the Future of Infective Endocarditis Diagnosis: The Transformative Role of Metagenomic Next-Generation Sequencing in Culture-Negative Cases.},
journal = {Journal of epidemiology and global health},
volume = {15},
number = {1},
pages = {108},
pmid = {40847264},
issn = {2210-6014},
support = {GCCRCYJ065//Sun Yat-sen University Eighth Hospital Cohort Construction Project/ ; GCCRCYJ065//Sun Yat-sen University Eighth Hospital Cohort Construction Project/ ; GCCRCYJ065//Sun Yat-sen University Eighth Hospital Cohort Construction Project/ ; GCCRCYJ065//Sun Yat-sen University Eighth Hospital Cohort Construction Project/ ; GCCRCYJ065//Sun Yat-sen University Eighth Hospital Cohort Construction Project/ ; GCCRCYJ065//Sun Yat-sen University Eighth Hospital Cohort Construction Project/ ; GCCRCYJ065//Sun Yat-sen University Eighth Hospital Cohort Construction Project/ ; GCCRCYJ065//Sun Yat-sen University Eighth Hospital Cohort Construction Project/ ; GCCRCYJ065//Sun Yat-sen University Eighth Hospital Cohort Construction Project/ ; GCCRCYJ065//Sun Yat-sen University Eighth Hospital Cohort Construction Project/ ; },
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; *Endocarditis/diagnosis/microbiology ; },
abstract = {Culture-negative infective endocarditis (CNE) remains a significant diagnostic challenge in cardiology and infectious disease, often leading to delayed or empirical treatment. Metagenomic next-generation sequencing (mNGS) has emerged as a complementary diagnostic tool capable of identifying fastidious, unexpected, or novel pathogens without prior assumptions. This narrative review synthesizes evidence from 152 studies (2015-2024), evaluating mNGS within existing diagnostic frameworks for culture-negative IE. Compared to conventional diagnostics (blood cultures, PCR, 16 S rRNA sequencing), mNGS demonstrates enhanced detection capabilities for polymicrobial infections and rare pathogens, though methodological heterogeneity across studies precludes definitive performance comparisons. Performance varies substantially based on sample type, sequencing platform, and bioinformatic pipelines. Real-world applications reveal persistent challenges, including cost barriers, interpretive complexities in low-biomass samples, and contamination risks. Integration with host-response biomarkers and AI-driven interpretation platforms shows promise for advancing clinical utility. For mNGS to be effectively integrated into routine CNE care, standardization, regulatory clarity, and equitable implementation will be essential.},
}

Humans
*High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
*Endocarditis/diagnosis/microbiology

@article {pmid40841623,
year = {2025},
author = {Zhang, Y and Ma, Y and Yue, R and Meng, Y and Jin, Y and Yin, C and Zhou, Q and Shi, R},
title = {Meningitis caused by Aspergillus fumigatus: a case report.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {1051},
pmid = {40841623},
issn = {1471-2334},
abstract = {BACKGROUND: Aspergillus fumigatus is a common pathogen that causes intracranial aspergillosis. A. fumigatus intracranial infection mainly occurs in the brain parenchyma. Head CT or MRI examination showed aspergillous abscess, which is extremely rare to caused meningitis alone. We report a case of aspergillosis meningitis with short-term death.

METHOD: We utilized the DNBSEQ™ sequencing platform, which employs DNA nanoballs (DNBs) technology. Briefly, DNBs are arrayed on a patterned flow cell, where DNA polymerase catalyzes the incorporation of fluorescently labeled nucleotides during sequencing-by-synthesis. The emitted fluorescence signals are digitally captured and computationally processed to generate high-accuracy base sequence data.

CASE PRESENTATION: A 51-year-old woman with a medical history of post-hepatitis B cirrhosis, type 2 diabetes mellitus, and thyroid carcinoma presented with acute-onset altered mental status. Physical examination revealed positive meningeal signs. Initial neuroimaging studies, including two serial head CT scans and two MRI examinations, showed no evidence of fungal abscess formation in the brain parenchyma. The diagnosis of A. fumigatus meningitis was confirmed through cerebrospinal fluid (CSF) analysis, including metagenomic next-generation sequencing (mNGS) and galactomannan (GM) testing. Despite prompt initiation of voriconazole therapy, the patient’s condition deteriorated, resulting in death after 10 days of treatment.

CONCLUSION: A. fumigatus meningitis represents a rare but life-threatening infection characterized by diagnostic challenges and alarmingly high mortality rates. Stringent diagnostic vigilance is essential to avoid diagnostic errors in these cases. The PMseq-DR platform, a high-throughput metagenomic sequencing technology for cerebrospinal fluid (CSF) analysis, provides a valuable diagnostic tool for rapid pathogen identification. For patients presenting with meningitis of unknown etiology following conventional diagnostic workup (including microbial culture, galactomannan assay, and 1-3-β-D-glucan testing), comprehensive CSF pathogen analysis becomes critical. In such scenarios, prompt implementation of high-throughput sequencing is recommended to enable accurate diagnosis and timely therapeutic intervention.},
}

@article {pmid40846880,
year = {2025},
author = {Kotrbová, L and Grabicová, K and Švecová, H and Staňová, AV and Petrlíková, M and Grabic, R and Kodešová, R and Chroňáková, A},
title = {The effect of WWTP products amendments on Phaseolus vulgaris rhizosphere and its ability to inactivate clarithromycin.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {30950},
pmid = {40846880},
issn = {2045-2322},
support = {QK21020080//Ministerstvo Zemědělství/ ; QK21020080//Ministerstvo Zemědělství/ ; QK21020080//Ministerstvo Zemědělství/ ; QK21020080//Ministerstvo Zemědělství/ ; QK21020080//Ministerstvo Zemědělství/ ; QK21020080//Ministerstvo Zemědělství/ ; QK21020080//Ministerstvo Zemědělství/ ; 063/2023/P//Grantová agentura Jihočeské univerzity v Českých Budějovicích/ ; },
mesh = {*Rhizosphere ; *Phaseolus/microbiology/drug effects/growth & development ; *Clarithromycin/pharmacology/metabolism ; Soil Microbiology ; *Anti-Bacterial Agents/pharmacology ; RNA, Ribosomal, 16S/genetics ; *Wastewater/chemistry ; Phylogeny ; Microbiota/drug effects ; },
abstract = {With increasing efforts to reuse wastewater treatment plant (WWTP) products in agriculture, assessing their impact on soil-plant systems is crucial, while the effects of accompanying antibiotic residues on soil microbial communities have not yet been adequately studied. This study focuses on clarithromycin (CLR), highly present in wastewater, and investigates the CLR-degradation potential of plant-associated microorganisms. Phaseolus vulgaris plants were grown in raised beds filled with Haplic Cambisol and amended with or without WWTP products (treated wastewater, biosolid, or composted biosolid), as a source of CLR residues. The rhizosphere microbiomes after biosolid amendments was significantly enriched by Pseudomonadaceae as assessed by 16S rRNA metagenomics and cultures enriched by CLR revealed dominance of Proteobacteria. However, no degradation of CLR by microbial consortia or enrichment cultures was observed, suggesting the multiplication of CLR-resistant bacteria with other resistance mechanisms. Cultivation-based approach combined with antibiotic modulation assays and subsequent LC-MS analysis confirmed the complete CLR removal by seven phylogenetic groups of actinomycetes in vitro. The proportion of isolates indicated that the rhizosphere is a natural reservoir for CLR-inactivating microorganisms; however, the amendment of soils with WWTP products can significantly increase their abundance and diversity.},
}

*Rhizosphere
*Phaseolus/microbiology/drug effects/growth & development
*Clarithromycin/pharmacology/metabolism
Soil Microbiology
*Anti-Bacterial Agents/pharmacology
RNA, Ribosomal, 16S/genetics
*Wastewater/chemistry
Phylogeny
Microbiota/drug effects

@article {pmid40846855,
year = {2025},
author = {Zhang, M and Wang, X and Yao, H and Shen, Y and Teng, Y and Garber, PA and Pan, H and Li, M},
title = {Plasticity of the gut microbiome of golden snub-nosed monkeys (Rhinopithecus roxellana) in response to seasonal variation in diet.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {169},
pmid = {40846855},
issn = {2055-5008},
support = {32330015, 31821001//National Natural Science Foundation of China/ ; 32070404//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Seasons ; *Gastrointestinal Microbiome ; *Diet ; *Colobinae/microbiology ; Metagenomics ; *Bacteria/classification/genetics/isolation & purification ; Metagenome ; Feces/microbiology ; },
abstract = {The effects of seasonal fluctuations in food availability on gut microbiome composition, diversity, and function present significant challenges to animals with hard-to-digest diets. Here, we investigate seasonal variation the gut microbiome of wild golden snub-nosed monkeys (Rhinopithecus roxellana), a foregut fermenting primate, using metagenomics and metatranscriptomics data. We reconstructed 578 metagenome-assembled genomes (MAGs), 76.5% of which did not have exact matches in reference databases, highlighting the novelty of their gut microbiota. The gut microbiome of wild golden snub-nosed monkeys exhibited high diversity and enrichment in plant secondary compound metabolism during summer, while in winter it was enriched with enzymes that function in lichen polysaccharide degradation and Lachnospiraceae, which is important for energy balance. Captive monkeys on a consistent diet showed minimal seasonal variation in gut microbiome composition. Habitat changes also affected golden snub-nosed monkey microbiota community assembly and carbon cycling pathways. These findings underscore the gut microbiome's plasticity in meeting host dietary needs under varying environmental conditions.},
}

Animals
*Seasons
*Gastrointestinal Microbiome
*Diet
*Colobinae/microbiology
Metagenomics
*Bacteria/classification/genetics/isolation & purification
Metagenome
Feces/microbiology

@article {pmid40846661,
year = {2025},
author = {Qin, Q and Zhu, Y and Yang, L and Guo, R and Song, L and Wang, D and Li, W},
title = {Oral microbiome between patients with non-obstructive and obstructive hypertrophic cardiomyopathy.},
journal = {Chinese medical journal},
volume = {},
number = {},
pages = {},
pmid = {40846661},
issn = {2542-5641},
abstract = {BACKGROUND: The profile and clinical significance of the oral microbiome in patients with non-obstructive hypertrophic cardiomyopathy (noHCM) and obstructive hypertrophic cardiomyopathy (oHCM) remain unexplored. The objective of this study was to evaluate the difference of oral microbiome between noHCM and oHCM patients.

METHODS: This cross-sectional study enrolled 18 noHCM patients and 26 oHCM patients from Fuwai Hospital, Chinese Academy of Medical Sciences between 2020 and 2021. Clinical and periodontal evaluations were conducted, and subgingival plaque samples were collected. Metagenomic sequencing and subsequent microbial composition and functional analyses were performed.

RESULTS: Compared to oHCM patients, those with noHCM had higher systolic blood pressure (138.1 ± 18.8 mmHg vs. 124.2 ± 13.8 mmHg, P = 0.007), a larger body circumference (neck circumference: 39.2 ± 4.0 cm vs. 35.1 ± 3.7 cm, P = 0.001; waist circumference: 99.7 ± 10.5 cm vs. 92.2 ± 10.8 cm, P = 0.027; hip circumference: 102.5 ± 5.6 cm vs. 97.5 ± 9.1 cm, P = 0.030), a greater left ventricular end-diastolic diameter (46.6 ± 4.9 mm vs. 43.1 ± 4.9 mm, P = 0.026), and a lower left ventricular ejection fraction (64.1 ± 5.7 % vs. 68.5 ± 7.8%, P = 0.048). While overall biodiversity and general microbial composition were similar between the noHCM and oHCM groups, ten taxa displayed significant differences at the genus and species levels, with Porphyromonas gingivalis showing the highest abundance and greater enrichment in noHCM (relative abundance: 7.79535 vs. 4.87697, P = 0.043). Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis identified ten distinct pathways, with pathways related to energy and amino acid metabolism being enriched in oHCM patients, and those associated with genetic information processing less abundant in the oHCM group. Metabolic potential analysis revealed ten significantly altered metabolites primarily associated with amino sugar and nucleotide sugar metabolism, porphyrin metabolism, pentose and glucuronate interconversion, and lysine degradation.

CONCLUSIONS: The higher abundance of Porphyromonas gingivalis, which is known to impact cardiovascular health, in noHCM patients may partially account for clinical differences between the groups. Pathway enrichment and metabolic potential analyses suggest microbial functional shifts between noHCM and oHCM patients, potentially reflecting inherent metabolic changes in HCM.},
}