@article {pmid40600049,
year = {2025},
author = {Xu, H and Zhang, R and Zhang, X and Zhang, Z and Feng, Y and Lin, L},
title = {Pulmonary microbial spectrum of Burkholderia multivorans infection identified by metagenomic sequencing.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1577363},
pmid = {40600049},
issn = {2296-858X},
abstract = {PURPOSE: Burkholderia multivorans, a Gram-negative bacterium, often infect patients with severe immunocompromised and cystic fibrosis. B. multivorans infection is challenging to treat due to its ability to disrupt the action of multiple antimicrobial agents through intrinsic and acquired resistance mechanisms. A better understanding of the pulmonary microbial spectrum of B. multivorans infection is crucial for the prevention and treatment of B. multivorans.

CASE PRESENTATION: This case series reviewed the respiratory microbiome structure and alternations during the treatment of B. multivorans infection through metagenomic next-generation sequencing (mNGS). Analysis of mNGS data of 19 pharyngeal secretion samples collected from the 3 COVID-19 patients at different time points showed that the relative abundance of B. multivorans was fluctuated and eventually increased, indicating the possible development of drug resistance. A total of 40 antibiotic-resistant genes (ARGs) were detected. Significantly, the levels of CEOA, CEOB, and OPCM were consistent with the trends in the relative abundance of B. multivorans. Besides, we described nine previously uncharacterized non-synonymous mutations in PenA of B. multivorans. These mutations lead to amino acid changes Thr32Ala, Ala43Ser, Gln105Arg, Asn202Ser, Gln219Arg, Gly241Ala, Val259Ala, Thr279Ala, and Ser298Ile that may associate with resistance to β-lactam antibiotics.

CONCLUSION: This report shed light on the importance of rapidly diagnosis and treatment of B. multivorans infection. mNGS serve as a powerful microbial detection tool that provides a comprehensive, sensitive, and rapid method for pathogen detection and drug resistance analysis.},
}

@article {pmid40599704,
year = {2025},
author = {Klimczuk, A and Chattoo, S and Izugbara, C and Klimczuk-Kochańska, M and Toczyski, P and Kumar, A and Kanozia, R and Gawron, GP and Ozair, A},
title = {Editorial: Towards 2030: sustainable development goal 3: good health and wellbeing. A sociological perspective.},
journal = {Frontiers in sociology},
volume = {10},
number = {},
pages = {1616878},
pmid = {40599704},
issn = {2297-7775},
}

@article {pmid40599650,
year = {2025},
author = {Zhang, H and Zheng, X and Huang, Y and Zou, Y and Zhang, T and Repo, MA and Yin, M and You, Y and Jie, Z and Xu, WA},
title = {Novel potential biomarkers for predicting childhood caries via metagenomic analysis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1522970},
pmid = {40599650},
issn = {2235-2988},
mesh = {Humans ; *Dental Caries/diagnosis/microbiology ; Child ; *Biomarkers/analysis ; *Metagenomics/methods ; Saliva/microbiology ; Female ; Male ; *Microbiota/genetics ; Bacteria/classification/genetics/isolation & purification ; Metagenome ; },
abstract = {BACKGROUND: Dental caries is a prevalent global health issue, particularly among children, with significant oral and overall health implications. The oral microbiome is considered a critical factor in caries development, with various microbial species implicated in the disease process.

OBJECTIVES: This study aims to explore the changes and interactions of oral microbiota in childhood caries using metagenomic analysis, and identify potential biomarkers for early caries detection and treatment.

METHODS: Saliva samples were collected from 241 children aged 6 to 9 years, categorized into caries-free (CF), low-caries (CL), and caries-severe (CS) groups. Metagenomic sequencing was performed to analyze the oral microbiome, followed by a series of statistical and functional analyses to characterize microbial diversity and function.

RESULTS: The study revealed significant differences in the microbial community composition among the groups, with the CS group exhibiting higher alpha and beta diversity than that of the CF group. Numerous unclassified microorganisms, such as Campylobacter SGB19347 and Catonella SGB4501, are intimately linked to dental caries and display intricate interaction networks, suggesting the potential formation of a distinct ecological network. In functional assessment, we identified a possible link between pectin and caries, suggesting that microorganisms that produce pectinase enzymes might play a role in the advancement of severe dental caries. Additionally, we identified 16 species as the best marker for severe dental caries, achieving an impressive AUC of 0.91.

CONCLUSION: The role of microbiota in dental caries is multifaceted, involving a complex interplay of microbial species and functions. Our findings enhance the understanding of the microbial basis of dental caries and offer potential diagnostic and therapeutic targets. The predictive capacity of the identified biomarkers warrants further investigation for early caries detection and intervention.

CLINICAL SIGNIFICANCE: The identification of novel biomarkers through metagenomic analysis enables early detection and targeted intervention for childhood caries, potentially transforming children dental care and significantly improving long-term oral health outcomes.},
}

Humans
*Dental Caries/diagnosis/microbiology
Child
*Biomarkers/analysis
*Metagenomics/methods
Saliva/microbiology
Female
Male
*Microbiota/genetics
Bacteria/classification/genetics/isolation & purification
Metagenome

@article {pmid40599424,
year = {2025},
author = {Pérez-Valera, E and Elhottová, D},
title = {Dataset of 111 metagenome-assembled genomes from cattle manure, soil and manured soil samples.},
journal = {Data in brief},
volume = {61},
number = {},
pages = {111748},
pmid = {40599424},
issn = {2352-3409},
abstract = {This data report presents 111 metagenome-assembled genomes (MAGs) reconstructed from manure, soil and manured soil samples from microcosms after enriching for non-fermenting Gram-negative bacteria (NFGNB). Two independent microcosm experiments were conducted to investigate the spread of NFGNB from the fresh manure of dairy cows under antibiotic prophylaxis to the pasture soil of two organic farms. After sampling the microcosms on days 2, 14 and 28, the manure and soil samples were plated in duplicate on CHROMagar Acinetobacter medium for NFGNB enrichment and incubated at 28°C for 24 h. DNA was extracted from the cultures and sequenced using the Illumina NovaSeq 6000 platform with 150-bp paired-end reads. Reads were assembled with metaSPAdes both individually and by co-assembly. MAGs were reconstructed using MetaBAT, MaxBin, SemiBin2, COMEbin, and AVAMB, and then de-replicated at >95 % ANI (pairwise comparisons) using dRep. A total of 111 MAGs of at least medium quality (MIMAG standard) were obtained. These included 10 high-quality MAGs (>90 % completeness, <5 % contamination, rRNA genes and tRNA for at least 18 amino acids), 47 putative high-quality MAGs (>90 % completeness, <5 % contamination) and 54 medium-quality MAGs (>50 % completeness, <10 % contamination). The FASTA files of the MAGs as well as their taxonomic identifications, completeness and contamination, origin, genomic statistics and rRNA sequences are publicly available in a Zenodo dataset and the genomes in the NCBI database. The majority of MAGs (99) were assigned to Pseudomonadota, mainly Pseudomonas (28 MAGs), Stenotrophomonas (20 MAGs) and Acinetobacter (18 MAGs), while the remaining 12 MAGs belonged to Bacteroidota. Most MAGs (44) were of manure origin, followed by manured soil (38 MAGs) and soil (29 MAGs). High-quality MAGs were predominantly obtained from manure (6 high-quality, 21 putative high-quality), compared to manured soil (3 high-quality, 12 putative high-quality) and soil (1 high-quality, 14 putative high-quality). By providing their MAGs, this dataset offers a valuable resource for researchers investigating the genomic characteristics associated with the survival, environmental dispersal and ecological role of potentially hazardous NFGNB species in soil, particularly following the application of antibiotic-treated animal manure, and for comparative genomics studies in related environments.},
}

@article {pmid40598913,
year = {2025},
author = {Ni, N and Qiu, J and Ge, W and Guo, X and Zhu, D and Wang, N and Luo, Y},
title = {Fibrous and Fragmented Microplastics Discharged from Sewage Amplify Health Risks Associated with Antibiotic Resistance Genes in Aquatic Environments.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c01335},
pmid = {40598913},
issn = {1520-5851},
abstract = {Wastewater treatment plants (WWTPs) are key sources of antibiotic resistance genes (ARGs) and microplastics (MPs) in aquatic environments. However, field data on ARG-MP copollution remain scarce, hindering environmental risk assessment of ARGs. This study used metagenomic sequencing and high-throughput qPCR to examine the composition and association of ARGs and MPs in sewage discharge-receiving waters. The results indicated that sewage discharge significantly increased the abundance of ARG-MP complexes in receiving waters, with fibrous and fragmented MPs exhibiting enhanced ARG enrichment and thereby serving as selective vectors for pathogens. Effluents promoted plasmid-mediated gene transfer and microbial functional shifts, driving intracellular ARG proliferation in the plastisphere. Fibrous and fragmented MPs showed strong co-occurrence patterns with ARGs, virulence factor genes, and mobile genetic elements, suggesting their role in antimicrobial resistance dissemination. A projection pursuit regression model indicated effluent-induced MP risk escalation at the estuary and downstream areas, which was associated with fragmented and polyamide MPs. Notably, WWTPs released substantial extracellular ARGs, with MPs potentially serving as a protective niche and a proliferative microenvironment. Here, we determined the role of WWTPs in shaping the aquatic resistome via MPs, which provides critical data for risk assessment and control strategies.},
}

@article {pmid40598608,
year = {2025},
author = {Liu, F and McNally, J and Flemming, D and Ingham, AB and Hunt, PW and Li, RW},
title = {Escherichia coli is implicated in the development and manifestation of host susceptibility to the roundworm Trichostrongylus colubriformis infections in sheep.},
journal = {Veterinary research},
volume = {56},
number = {1},
pages = {133},
pmid = {40598608},
issn = {1297-9716},
support = {58-8042-3-022-F//Agricultural Research Service/ ; 242102311161//Henan Provincial Science and Technology Research Project/ ; },
mesh = {Animals ; *Sheep Diseases/parasitology/microbiology/immunology ; Sheep ; *Trichostrongylosis/veterinary/parasitology/immunology ; *Trichostrongylus/physiology ; *Escherichia coli/physiology ; *Gastrointestinal Microbiome ; Disease Susceptibility/veterinary/parasitology/microbiology ; RNA, Ribosomal, 16S/genetics/analysis ; },
abstract = {Applied breeding for host resistance to gastrointestinal nematodes represents a cost-effective strategy for parasitic control. While resistance is under moderate genetic influences, gut microbial components involved in the development of resistance or susceptibility remain largely unknown. Here we characterize the structure and metabolic potential of the proximal colon microbiota in unique ovine populations bred for resistance and susceptibility using a full-length 16S rRNA gene sequencing-based microbiome approach. The resistant lambs produced significantly fewer parasite eggs than susceptible animals grazing on the same pasture. Further, the resistant lambs displayed a significant reduction in worm establishment in response to a Trichostrongylus colubriformis challenge infection (P < 0.0001; N = 20 per group). Among 32 bacterial species or strains displaying a significant difference in relative abundance between the resistant and susceptible group, E. coli was more abundant in susceptible lambs. E. coli was also ranked as the most important species in distinguishing the resistant and susceptible status. Moreover, a microbial signature or balance consisting of E. coli (Numerator) and Parabacteroides distasonis and Bacteroides thetaiotaomicron (Denominator) predicted the resistance status with high accuracy. The metagenome function prediction also revealed that several pathways related to infectious diseases, such as Shigellosis and pathogenic E. coli infection, were significantly altered between the two phenotypes. Our findings demonstrated that microbial signatures with a high predictive power for the resistance status can be developed as biomarkers to facilitate the selection for host resistance in sheep.},
}

Animals
*Sheep Diseases/parasitology/microbiology/immunology
Sheep
*Trichostrongylosis/veterinary/parasitology/immunology
*Trichostrongylus/physiology
*Escherichia coli/physiology
*Gastrointestinal Microbiome
Disease Susceptibility/veterinary/parasitology/microbiology
RNA, Ribosomal, 16S/genetics/analysis

@article {pmid40598447,
year = {2025},
author = {Bulzu, PA and Henriques Vieira, H and Ghai, R},
title = {Lineage-specific expansions of polinton-like viruses in photosynthetic cryptophytes.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {154},
pmid = {40598447},
issn = {2049-2618},
support = {25-15920S//Grantová Agentura České Republiky/ ; 24-11998S//Grantová Agentura České Republiky/ ; 20-12496X//Grantová Agentura České Republiky/ ; },
mesh = {*Cryptophyta/virology/genetics ; Metagenomics ; Phylogeny ; Genome, Viral ; Photosynthesis ; *Giant Viruses/genetics/classification ; *DNA Viruses/genetics/classification ; },
abstract = {BACKGROUND: Polinton-like viruses (PLVs) are diverse eukaryotic DNA viral elements (14-40 kb) that often undergo significant expansion within protist genomes through repeated insertion events. Emerging evidence indicates they function as antiviral defense systems in protists, reducing the progeny yield of their infecting giant viruses (phylum Nucleocytoviricota) and influencing the population dynamics and evolution of both viruses and their hosts. While many PLVs have been identified within the genomes of sequenced protists, most were recovered from metagenomic data. Even with the large number of PLVs identified from metagenomic data, their host-virus linkages remain unknown owing to the scarcity of ecologically relevant protist genomes. Additionally, the extent of PLV diversification within abundant freshwater taxa remains undetermined. In order to tackle these questions, high-quality genomes of abundant and representative taxa that bridge genomic and metagenomic PLVs are necessary. In this regard, cryptophytes, which are among the most widely distributed, abundant organisms in freshwaters and have remained largely out of bounds of genomic and metagenomic approaches, are ideal candidates for investigating the diversification of such viral elements both in cellular and environmental context.

RESULTS: We leveraged long-read sequencing to recover large (200-600 Mb), high-quality, and highly repetitive (> 60%) genomes of representative freshwater and marine photosynthetic cryptophytes. We uncovered over a thousand complete PLVs within these genomes, revealing vast lineage-specific expansions, particularly in the common freshwater cryptophyte Rhodomonas lacustris. By combining deep sequence homology annotation with biological network analyses, we discern well-defined PLV groups defined by characteristic gene-sharing patterns and the use of distinct strategies for replication and integration within host genomes. Finally, the PLVs recovered from these cryptophyte genomes also allow us to assign host-virus linkages in environmental sequencing data.

CONCLUSIONS: Our findings provide a primer for understanding the evolutionary history, gene content, modes of replication and infection strategies of cryptophyte PLVs, with special emphasis on their expansion as endogenous viral elements (EVEs) in freshwater bloom-forming R. lacustris. Video Abstract.},
}

*Cryptophyta/virology/genetics
Metagenomics
Phylogeny
Genome, Viral
Photosynthesis
*Giant Viruses/genetics/classification
*DNA Viruses/genetics/classification

@article {pmid40598440,
year = {2025},
author = {Lin, Z and Zhou, X and Lu, T and An, W and Chen, S and Li, S and Miao, H and Han, X},
title = {Co-cultivation of Lactobacillus acidophilus and Bacillus subtilis mediates the gut-muscle axis affecting pork quality and flavor.},
journal = {Journal of animal science and biotechnology},
volume = {16},
number = {1},
pages = {93},
pmid = {40598440},
issn = {1674-9782},
abstract = {BACKGROUND: Pork quality and flavor are critical determinants of consumer preference, yet the role of gut microbiota in shaping meat characteristics remains underexplored. In this study, we investigated how a probiotic consortium (FAM: Lactobacillus acidophilus and Bacillus subtilis) modulates the gut-muscle axis to enhance pork flavor.

RESULTS: In finishing pigs, FAM supplementation significantly increased flavor-associated nucleotides and umami-enhancing amino acids in longissimus dorsi muscle. Metagenomic analysis revealed FAM-driven enrichment of glycan-degrading Prevotella and short-chain fatty acid-producing Phascolarctobacterium, accompanied by reduced antibiotic resistance genes and virulence factors. Spearman correlation linked Prevotella copri abundance with elevated muscle amino acids, suggesting microbial-encoded CAZymes as key mediators.

CONCLUSIONS: This study provides the first evidence that probiotic-induced gut microbiota remodeling enhances pork flavor through metabolic cross-talk along the gut-muscle axis. The findings suggest a novel strategy for improving pork quality via dietary interventions targeting gut microbiota.},
}

@article {pmid40598319,
year = {2025},
author = {Maeke, MD and Yin, X and Wunder, LC and Vanni, C and Richter-Heitmann, T and Miravet-Verde, S and Ruscheweyh, HJ and Sunagawa, S and Fabian, J and Piontek, J and Friedrich, MW and Hassenrück, C},
title = {Extensive data mining uncovers novel diversity among members of the rare biosphere within the Thermoplasmatota.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {155},
pmid = {40598319},
issn = {2049-2618},
support = {EXC-2077-390741603//Deutsche Forschungsgemeinschaft/ ; EXC-2077-390741603//Deutsche Forschungsgemeinschaft/ ; XJ2300006031//Start-up research fund of Hainan University, China/ ; LT0050/2023-L//Human Frontier Science Program/ ; 205320_215395//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; 03F0814//German Federal Ministry of Education and Research (BMBF)/ ; 03F0848A//German Federal Ministry of Education and Research (BMBF)/ ; },
mesh = {Phylogeny ; *Geologic Sediments/microbiology ; *Archaea/classification/genetics/isolation & purification ; Metagenomics/methods ; *Data Mining/methods ; Metagenome ; Biodiversity ; RNA, Ribosomal, 16S/genetics ; Ecosystem ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Rare species, especially of the marine sedimentary biosphere, have long been overlooked owing to the complexity of sediment microbial communities, their sporadic temporal and patchy spatial abundance, and challenges in cultivating environmental microorganisms. In this study, we combined enrichments, targeted metagenomic sequencing, and extensive data mining to uncover uncultivated members of the archaeal rare biosphere in marine sediments.

RESULTS: In protein-amended enrichments, we detected the ecologically and metabolically uncharacterized class Candidatus Penumbrarchaeia within the phylum Thermoplasmatota. By screening more than 8000 metagenomic runs and 11,479 published genome assemblies, we expanded the phylogeny of Ca. Penumbrarchaeia by 3 novel orders. All six identified families of this class show low abundance in environmental samples characteristic of rare biosphere members. Members of the class Ca. Penumbrarchaeia were predicted to be involved in organic matter degradation in anoxic, carbon-rich habitats. All Ca. Penumbrarchaeia families contain high numbers of taxon-specific orthologous genes, highlighting their environmental adaptations and habitat specificity. Besides, members of this group exhibit the highest proportion of unknown genes within the entire phylum Thermoplasmatota, suggesting a high degree of functional novelty in this class.

CONCLUSIONS: In this study, we emphasize the necessity of targeted, data-integrative approaches to deepen our understanding of the rare biosphere and uncover the functions and metabolic potential hidden within these understudied taxa. Video Abstract.},
}

Phylogeny
*Geologic Sediments/microbiology
*Archaea/classification/genetics/isolation & purification
Metagenomics/methods
*Data Mining/methods
Metagenome
Biodiversity
RNA, Ribosomal, 16S/genetics
Ecosystem
Sequence Analysis, DNA

@article {pmid40597897,
year = {2025},
author = {Wang, X and Xie, Y and Chen, M and Zhu, H and He, G and Yu, W and Qiao, D and Shen, Y and Song, L and Deng, Q},
title = {The complex diagnosis of post-dialysis fever: a case report and literature review of infective endocarditis in a dialysis patient.},
journal = {BMC nephrology},
volume = {26},
number = {1},
pages = {331},
pmid = {40597897},
issn = {1471-2369},
support = {2024-KHRCBZ-B15 and 2024-KHRCBZ-B08//Science and Technology plan project of the First People' s Hospital of Yunnan Province/ ; 82460150//National Natural Science Foundation of China/ ; 202401AU070048//Yunnan Fundamental Research Projects/ ; },
mesh = {Humans ; Male ; Aged ; *Renal Dialysis/adverse effects ; *Kidney Failure, Chronic/therapy ; *Fever/etiology/diagnosis/microbiology ; *Endocarditis, Bacterial/diagnosis/microbiology ; *Endocarditis/diagnosis ; },
abstract = {BACKGROUND: Post-dialysis fever is a common but diagnostically challenging issue in hemodialysis patients, with potential causes including dialysis-related infections, pulmonary infections, and cardiovascular complications.

CASE PRESENTATION: We report a 76-year-old male with end-stage renal disease (ESRD) on maintenance hemodialysis, coronary artery disease, and prior cardiac stent implantation, who presented with recurrent post-dialysis fever. Despite persistently negative conventional cultures, metagenomic next-generation sequencing (NGS) of pre-dialysis blood samples identified Pseudomonas aeruginosa (P. aeruginosa), Cutibacterium acnes (C. acnes; formerly Propionibacterium acnes), Staphylococcus epidermidis (S. epidermidis), and Corynebacterium accolens (C. accolens) and Epstein-Barr virus (EBV), while post-dialysis samples revealed only C. acnes and EBV. Given the temporal association with fever, these two pathogens were considered the primary causative agents. Subsequent transesophageal echocardiography (TEE) confirmed aortic valve vegetations, establishing the diagnosis of infective endocarditis (IE). Following targeted antimicrobial and antiviral adjustments based on NGS findings, the patient exhibited complete resolution of post-dialysis fever and was discharged. However, as the vegetation was not surgically removed, he was hospitalized multiple times over the following five months for recurrent infections and ultimately died of septic shock and multi-organ failure due to carbapenem-resistant Klebsiella pneumoniae.

CONCLUSIONS: This case underscores the complementary role of TEE and NGS in diagnosing IE in high-risk patients, enabling the detection of uncommon pathogens and informing targeted therapy to improve clinical outcomes.

CLINICAL TRIAL NUMBER: Not applicable.},
}

Humans
Male
Aged
*Renal Dialysis/adverse effects
*Kidney Failure, Chronic/therapy
*Fever/etiology/diagnosis/microbiology
*Endocarditis, Bacterial/diagnosis/microbiology
*Endocarditis/diagnosis

@article {pmid40597620,
year = {2025},
author = {Yang, L and Yan, Y and Shen, J and Xia, Y and Lang, F and Chen, C and Zou, W},
title = {Metagenomic insights into microbial community succession and its functional changes during the stage of acetic acid fermentation of shanxi aged vinegar.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {374},
pmid = {40597620},
issn = {1471-2180},
support = {20220401931002//Open Project Program of Shanxi Provincial Key Laboratory for Vinegar Fermentation Science and Engineering/ ; 20220401931002//Open Project Program of Shanxi Provincial Key Laboratory for Vinegar Fermentation Science and Engineering/ ; 20220401931002//Open Project Program of Shanxi Provincial Key Laboratory for Vinegar Fermentation Science and Engineering/ ; 20220401931002//Open Project Program of Shanxi Provincial Key Laboratory for Vinegar Fermentation Science and Engineering/ ; 20220401931002//Open Project Program of Shanxi Provincial Key Laboratory for Vinegar Fermentation Science and Engineering/ ; 20220401931002//Open Project Program of Shanxi Provincial Key Laboratory for Vinegar Fermentation Science and Engineering/ ; 20220401931002//Open Project Program of Shanxi Provincial Key Laboratory for Vinegar Fermentation Science and Engineering/ ; 202202140601018; 202102130501008//Key Research and Development Program Projects in Shanxi Province/ ; 202202140601018; 202102130501008//Key Research and Development Program Projects in Shanxi Province/ ; 202202140601018; 202102130501008//Key Research and Development Program Projects in Shanxi Province/ ; 202202140601018; 202102130501008//Key Research and Development Program Projects in Shanxi Province/ ; 202202140601018; 202102130501008//Key Research and Development Program Projects in Shanxi Province/ ; 202202140601018; 202102130501008//Key Research and Development Program Projects in Shanxi Province/ ; 202202140601018; 202102130501008//Key Research and Development Program Projects in Shanxi Province/ ; 2023NSFSC0184//Sichuan Natural Science Foundation General Project/ ; 2023NSFSC0184//Sichuan Natural Science Foundation General Project/ ; 2023NSFSC0184//Sichuan Natural Science Foundation General Project/ ; 2023NSFSC0184//Sichuan Natural Science Foundation General Project/ ; 2023NSFSC0184//Sichuan Natural Science Foundation General Project/ ; 2023NSFSC0184//Sichuan Natural Science Foundation General Project/ ; 2023NSFSC0184//Sichuan Natural Science Foundation General Project/ ; },
mesh = {*Acetic Acid/metabolism ; Fermentation ; *Metagenomics/methods ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Acetobacter/metabolism/genetics ; Metabolic Networks and Pathways ; *Microbiota/genetics ; Food Microbiology ; Metagenome ; },
abstract = {Traditional fermentation of Shanxi aged vinegar involves complex microbial interactions driving flavor synthesis, but the mechanisms underpinning metabolic adaptation and community succession remain poorly characterized. This study aimed to unravel stage-specific microbial dynamics and their functional contributions to flavor formation during Cupei fermentation. Metagenomic sequencing analyzed microbial communities and metabolic pathways at three fermentation stages (D3, D6, D9). Functional annotation (KEGG, CAZy) and species-level contribution assessments identified key taxa and genes linked to flavor biosynthesis. Microbial succession shifted from Lactobacillus dominance (64.68% at D3) to Acetobacter prevalence (48.04% at D9), with Lactobacillus acetotolerans persisting throughout (17.15-26.23%). Early-stage carbohydrate metabolism (GHs-driven: 60.38% at D3) transitioned to late-stage amino acid (15.62%) and cofactor synthesis (12.17%), activating valine, leucine, and histidine pathways critical for flavor compounds. Acetobacter oryzoeni and Acetobacter pomorum drove acetate (ALDH: 27.07-41.52%), valine (ilvE: 53.21-20.22%), and histidine (hisD: 41.83-33.30%) metabolism at D9. Low abundance species (Weissella confusa, 0.51%) and uncultured Limosilactobacillus sp. contributed via multi-gene networks (e.g., dat, ldh), which revealed an important functional contribution by overlooked low-abundance species. The study uncovers ecological coupling between microbial succession and metabolic adaptation, where dominant taxa and rare species synergistically govern flavor formation. These insights enable targeted microbial community design for flavor optimization in traditional fermented foods.},
}

*Acetic Acid/metabolism
Fermentation
*Metagenomics/methods
*Bacteria/genetics/classification/metabolism/isolation & purification
Acetobacter/metabolism/genetics
Metabolic Networks and Pathways
*Microbiota/genetics
Food Microbiology
Metagenome

@article {pmid40597432,
year = {2025},
author = {Ehau-Taumaunu, H and Bell, TH and Sadeghi, J and Hockett, KL},
title = {Rapid and sustained differentiation of disease-suppressive phyllosphere microbiomes in tomato following experimental microbiome selection.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {77},
pmid = {40597432},
issn = {2524-6372},
support = {492F//PA Vegetable Growers Association/ ; 1016871//National Institute of Food and Agriculture/ ; },
abstract = {BACKGROUND: Microbial-based treatments to protect plants against phytopathogens typically focus on soil-borne disease or the aboveground application of one or a few biocontrol microorganisms. However, diverse microbiomes may provide unique benefits to phytoprotection in the phyllosphere, by restricting pathogen access to niche space and/or through multiple forms of direct antagonism. We previously showed that successive experimental passaging of phyllosphere microbiomes along with the phytopathogen Pseudomonas syringae pv. tomato (Pto), which causes bacterial speck in tomato, led to the development of a disease suppressive microbial community. Here, we used amplicon sequencing to assess bacterial and fungal composition at the end of each passage, as well as shotgun metagenomics at key passages based on observed disease-suppressive phenotypes, to assess differences in functional potential between suppressive and non-suppressive communities.

RESULTS: Bacterial composition changed and diversity declined quickly due to passaging and remained low, particularly in treatments with Pto present, whereas fungal diversity did not. Pseudomonas and Xanthomonas populations were particularily enriched in disease-suppressive microbiomes compared to conducive microbiomes. The relative abundance of Pseudomonas syringae group gemonosp. 3 (the clade to which the introduced pathogen belongs) in shotgun metagenomic data was similar to what we observed for Pseudomonas ASVs in the 16S rRNA gene dataset. We also observed an increase in the abundance of genes associated with microbial antagonism at Passage 4, corresponding to the highest observed disease severity.

CONCLUSIONS: Taxonomic richness and evenness were low within samples, with clustering occurring for suppressive or non-suppressive microbiomes. The relative abundance of genes associated with antagonism was higher for disease-suppressive phyllosphere microbiomes. This work is an important step towards understanding the microbe-microbe interactions within disease-suppressive phyllosphere communities.},
}

@article {pmid40597414,
year = {2025},
author = {Kadyan, S and Park, G and Singh, TP and Patoine, C and Singar, S and Heise, T and Domeier, C and Ray, C and Kumar, M and Behare, PV and Chakrabarty, P and Efron, P and Sheffler, J and Nagpal, R},
title = {Microbiome-based therapeutics towards healthier aging and longevity.},
journal = {Genome medicine},
volume = {17},
number = {1},
pages = {75},
pmid = {40597414},
issn = {1756-994X},
mesh = {Humans ; *Longevity ; *Gastrointestinal Microbiome ; *Healthy Aging ; *Aging ; *Microbiota ; Animals ; },
abstract = {The gut microbiome is our lifetime companion, regulating our health from birth throughout the lifespan. The gut microbiome composition changes continually with age, influencing both physiological and immunological development. Emerging evidence highlights the close association, and thus implication, of the microbiome with healthy disease-free aging and longevity. Accordingly, targeting the gut microbiome is emerging as a promising avenue to prevent, alleviate, and ameliorate aging-related disorders. Herein, we provide a prospective and inclusive framework of the close connection of the gut microbiome with human aging, while contemplating how this association is intertwined with age-related diseases. We delve into recently emerging and potential microbiome-based therapeutics that are projected to aid in alleviating myriad aging-related diseases, thereby enhancing the health and well-being of the aging population. Finally, we present a foundation and perspective underlining the prospects of microbiome-based therapeutics developed and tailored precisely for the elderly, with the overarching goal of promoting health and longevity.},
}

Humans
*Longevity
*Gastrointestinal Microbiome
*Healthy Aging
*Aging
*Microbiota
Animals

@article {pmid40597335,
year = {2025},
author = {Drake, MJ and Pierdon, M and DeMers, G and Daniel, SG and Bittinger, K and Redding, LE},
title = {The effect of dietary zinc on the microbiome and resistome of the gestating sow and neonatal piglets.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {71},
pmid = {40597335},
issn = {2524-4671},
abstract = {Zinc is an important trace element for animal health and physiology, and it is routinely provided as a supplement in livestock diets. High levels of dietary zinc have been found to be beneficial for weanling pigs in preventing diarrhea and improving growth. It has also been associated with better reproductive performance in gestating sows and survival of neonatal piglets. However, little is known about zinc's effect on the microbiome of the gestating sow and her neonatal piglets. Even less is known about its effects on the sow and piglet resistome, which is important because dietary zinc can co-select for antimicrobial resistance. The goal of this randomized controlled dietary feeding trial was to assess the effect of high levels of dietary zinc in the last week of gestation on the microbiomes and resistomes of the gestating sow and her neonatal piglets. Seventy-three gestating sows were randomized to receive a diet with standard zinc levels (125 ppm) or high zinc levels (2500 ppm) approximately one week prior to their anticipated farrowing date. Fecal samples were collected from sows at enrollment and at farrowing and from piglets within 3 days of parturition. Fecal samples underwent 16sS rRNA gene sequencing, and a subset of samples underwent shotgun metagenomic sequencing. Statistically significant differences in richness, diversity and taxonomic composition were observed over time, and sows in the treatment group had significantly higher alpha diversity at farrowing (p = 0.04) and significantly altered levels of 3 taxa (Turicibacter, unclassified Clostridiaceae, and unclassified Christensenellaceae). Several antimicrobial resistance genes were significantly more abundant in the zinc group at farrowing compared to the control group, including tetracycline resistance genes [tet(O); tet(W); tet(32); tet(O/W)]; aminoglycoside resistance genes (APH(3')-IIIa), macrolide-lincosamide-streptogramin (MLS) resistance genes (lsaB; macB); and others (kdpE, Pseudomonas aeruginosa CpxR). No significant differences were observed in the piglet microbiomes or resistomes across sow treatment groups. Overall, high levels of dietary zinc had modest effects on the sow microbiome during the feeding trial. Increases in antimicrobial resistance genes in zinc supplemented sows suggest that supranutritional levels of dietary zinc should be avoided in gestating sows.},
}

@article {pmid40597307,
year = {2025},
author = {Wang, Z and Wang, W and Wang, Y and Hu, H and Wang, B and Zhu, W and Li, X and Hou, X and Sun, W and Liu, Z and Lu, S and Chen, X},
title = {Mapping gut microbiota and metabolite alterations in patients with postmenopausal osteoporosis in the Beijing Community of China.},
journal = {European journal of medical research},
volume = {30},
number = {1},
pages = {539},
pmid = {40597307},
issn = {2047-783X},
support = {No.2020YFC2004900//National Key Research and Development Program of China/ ; H0608//National Natural Science Foundation of China/ ; No.81672201, 81871794//Natural Science Foundation of China/ ; No.7242065//Beijing Natural Science Foundation/ ; },
mesh = {Humans ; Female ; *Gastrointestinal Microbiome ; *Osteoporosis, Postmenopausal/microbiology/metabolism/epidemiology ; Middle Aged ; Aged ; Bone Density ; Beijing ; China ; Feces/microbiology ; },
abstract = {INTRODUCTION: Postmenopausal osteoporosis (PMO) is a chronic disease in the elderly women, which has been shown to be related to the gut microbiota (GM) alternation in recent studies. Few studies have investigated which specific bacterial species and metabolites have an impact on postmenopausal osteoporosis patients, especially in urban communities.

METHODS: With the aim of comprehending GM features and metabolite variation in women suffering from PMO in the Beijing Community of China, we divided the 76 eligible participants into osteoporosis (OP) and health control (HC) groups taking into account the bone mineral density (BMD), and adopted 16 S rRNA gene sequencing and metagenomic sequencing to examine the GM compositions in the respective groups. Besides, the study adopted liquid chromatography and mass spectrometry (LC-MS) for the fecal metabolite analysis.

RESULTS: The OP group presented obviously changed bacterial α-diversity and β-diversity versus the HC group. GM at the genus level was differentially enriched in the OP or HC groups. Megamonas genus exhibited the strongest positive relevance to BMD and OC. Bacteroides genus had the strongest negative relevance to BMD and positive relevance to β-CTX. GM at the species level was also differentially enriched in OP or HC groups. After multiple linear regression analysis, Roseburia_intestinalis and Glycoursodeoxycholic acid were positively associated with BMD, hinting their beneficial effect in BMD. Corresponding signaling pathways also exhibited an obvious change, particularly in up-regulation Glycerol Phosphate Shuttle and down-regulation Malate-Aspartate Shuttle pathways.

CONCLUSIONS: According to the results of this study, GM and metabolites in women with PMO in the Beijing Community changed dramatically, which were significantly associated with BMD and bone turnover markers. Roseburia_intestinalis and Glycoursodeoxycholic acid levels were the most positively associated with BMD. All these assist in understanding the development mechanism of PMO from new perspectives and in developing novel therapeutic methods for improving bone health.},
}

Humans
Female
*Gastrointestinal Microbiome
*Osteoporosis, Postmenopausal/microbiology/metabolism/epidemiology
Middle Aged
Aged
Bone Density
Beijing
China
Feces/microbiology

@article {pmid40596882,
year = {2025},
author = {Hekker, MD and Platteel, TN and Venekamp, RP and Top, J and Geerlings, SE and Schultsz, C and de Vos, MGJ and van de Wijgert, JHHM},
title = {Urinary tract infections in postmenopausal women revisited (UTIr): a prospective observational cohort study to explore the urobiomes of postmenopausal women with and without recurrent urinary tract infections.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {822},
pmid = {40596882},
issn = {1471-2334},
support = {OCENW.XL21.XL21.088//The Dutch Research Council (NWO)/ ; OCENW.XL21.XL21.088//The Dutch Research Council (NWO)/ ; OCENW.XL21.XL21.088//The Dutch Research Council (NWO)/ ; OCENW.XL21.XL21.088//The Dutch Research Council (NWO)/ ; OCENW.XL21.XL21.088//The Dutch Research Council (NWO)/ ; OCENW.XL21.XL21.088//The Dutch Research Council (NWO)/ ; OCENW.XL21.XL21.088//The Dutch Research Council (NWO)/ ; OCENW.XL21.XL21.088//The Dutch Research Council (NWO)/ ; },
mesh = {Humans ; Female ; *Urinary Tract Infections/microbiology/epidemiology ; *Postmenopause ; Prospective Studies ; Middle Aged ; Recurrence ; Vagina/microbiology ; *Microbiota ; Aged ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; },
abstract = {BACKGROUND: Recurrent urinary tract infections (RUTI) are prevalent, particularly among postmenopausal women, and place a significant burden on the affected individuals and the healthcare system. While Escherichia coli is the primary cause of most UTIs in premenopausal women, this may not hold true for postmenopausal women. To facilitate development of novel diagnostics, preventive interventions, and clinical management of RUTI in postmenopausal women, it is essential to strengthen the biological evidence base.

METHODS: This observational prospective cohort study will enrol 20 postmenopausal women without RUTI (controls) and approximately 30 with RUTI (cases), aiming to sample at least 50 UTI episodes. Questionnaires are completed, samples (urine, vulvoperineal and vaginal swabs, and faeces) are collected by participants or study staff at five scheduled time points over one year of follow-up, as well as during and after each UTI episode. All samples will undergo 16S rRNA amplicon sequencing, with selected urine samples also subjected to bacterial culturing, metagenomic sequencing, and metabolomics. Various urobiome comparisons will be conducted, such as between women with and without RUTI in the absence of a UTI, and over time during UTIs. Urobiomes will also be compared to vaginal, vulvoperineal, and gut microbiomes in the same women at the same time points. Finally, urine samples will be cultured to obtain bacterial isolates, which will be characterised and used for co-culture and urothelium organoid experiments.

DISCUSSION: The UTIr cohort study is an exploratory, hypothesis-generating study designed to improve understanding of the ecological mechanisms driving UTI onset, response to antibiotic treatment, and UTI recurrence in postmenopausal women. The data collected from each individual woman is longitudinal and comprehensive, which is instrumental for advancing the field. The study population consists of women over the age of 50 and the study procedures are demanding. Flexibility with protocol procedures has proven to be essential to maximise retention and minimise missing data. We recommend employing a sufficiently large recruitment team and/or planning for a sufficiently long recruitment period to accommodate the demanding nature of these types of in-depth studies with vulnerable populations.

TRIAL REGISTRATION: Not applicable.},
}

Humans
Female
*Urinary Tract Infections/microbiology/epidemiology
*Postmenopause
Prospective Studies
Middle Aged
Recurrence
Vagina/microbiology
*Microbiota
Aged
RNA, Ribosomal, 16S/genetics
Feces/microbiology

@article {pmid40596444,
year = {2025},
author = {Li, YC and Liu, YX and Li, L and Wang, H and Zhao, ZR and Yao, ZY},
title = {Metagenomic next-generation sequencing (mNGS) versus tissue culture technique (TCT) in diagnosis of spinal infection: a systematic review and meta-analysis.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {20926},
pmid = {40596444},
issn = {2045-2322},
support = {2022K57//Quzhou Science and Technology Tackling Project/ ; },
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; *Spinal Diseases/diagnosis/microbiology ; Sensitivity and Specificity ; },
abstract = {Spinal infections pose a significant clinical challenge due to the difficulty of early diagnosis. Traditional Tissue Culture Technique (TCT) has limitations, while Metagenomic Next-Generation Sequencing (mNGS) has emerged as a promising diagnostic tool. However, reports on the diagnostic performance of mNGS and TCT for spinal infections are inconsistent, and there has been a lack of systematic analysis of the evidence. This systematic review and meta-analysis included 10 studies involving a total of 770 patients to compare the diagnostic accuracy of mNGS and TCT. A comprehensive literature search was conducted using PubMed, Embase, Web of Science, Cochrane Library, and SinoMed to identify studies evaluating the diagnostic accuracy of mNGS and TCT for spinal infections. Data were analyzed using Review Manager 5.3 and Stata 16.0 to compute the sensitivity, specificity, and Area Under the Summary Receiver Operating Characteristic Curve (AUC). The meta-analysis revealed pooled estimates for mNGS with a sensitivity of 0.81 (95% CI, 0.74-0.87), specificity of 0.75 (95% CI, 0.48-0.91), and an AUC of 0.85 (95% CI, 0.82-0.88). In contrast, pooled estimates for TCT showed a sensitivity of 0.34 (95% CI, 0.27-0.43), specificity of 0.93 (95% CI, 0.79-0.98), and an AUC of 0.59 (95% CI, 0.55-0.63). While mNGS demonstrates higher sensitivity and overall diagnostic accuracy than TCT, its lower specificity suggests that it may be most effective when used alongside conventional methods to enhance diagnostic reliability in spinal infections.},
}

Humans
*High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
*Spinal Diseases/diagnosis/microbiology
Sensitivity and Specificity

@article {pmid40596159,
year = {2025},
author = {Bayatian, M and Pourbabaee, AA and Amoozegar, MA},
title = {Revealing the composition of bacterial communities in various oil-contaminated soils and investigating their intrinsic traits in hydrocarbon degradation.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {22016},
pmid = {40596159},
issn = {2045-2322},
mesh = {*Soil Microbiology ; *Hydrocarbons/metabolism ; Biodegradation, Environmental ; *Bacteria/genetics/classification/metabolism ; *Soil Pollutants/metabolism ; RNA, Ribosomal, 16S/genetics ; *Petroleum/metabolism ; Soil/chemistry ; *Microbiota ; Petroleum Pollution ; Iran ; High-Throughput Nucleotide Sequencing ; Phylogeny ; },
abstract = {This study explores prokaryotic diversity and oil biodegradation potential in soils from three evaporation ponds in the Ahvaz and Maroon oil fields, Iran. Despite prior studies on prokaryotic diversity in contaminated soils, systematic comparisons within the same region remain limited. The analysis identified distinct physicochemical differences across sites. Ahvaz 1 soil, with a loamy silty clay texture, had the highest salinity (15.4%) and total petroleum hydrocarbons (TPH, 3.5%). Ahvaz 4 soil, loamy silty in texture, showed 7.49% salinity and 1% TPH, while Maroon 3 soil exhibited the lowest salinity (5.06%) and TPH (0.5%). Prokaryotic diversity and biodegradation traits were assessed using 16S rRNA next-generation sequencing (NGS) and qPCR, respectively. NGS revealed reduced prokaryotic diversity in all contaminated soils, with Bacillota dominating, whereas Pseudomonadota prevailed in all control samples. Maroon 3 soils had higher diversity, but Cyanobacteria and Actinomycetota, dominant in controls, were replaced by Chloroflexota, Gemmatimonadota, and Acidobacteriota in polluted soils. At the genus level, Bacillus, Lysinibacillus, Virgibacillus, Brevibacillus, and Paenibacillus showed increased abundance in contaminated soils. Real-time PCR of alkB and C23DO genes indicated enhanced hydrocarbon degradation potential. FAPROTAX and PICRUSt2 analyses revealed enhanced microbial capacity for hydrocarbon degradation in polluted soils, with enriched functions related to chemoheterotrophy, aromatic compound degradation, and increased levels of alkane 1-monooxygenase, alcohol dehydrogenase, and protocatechuate 4,5-dioxygenase subunits. The findings highlight crude oil's impact on microbial community structure, reducing archaea and emphasizing bacterial dominance while underscoring shifts in microbial responses and functional gene expression in hydrocarbon degradation.},
}

*Soil Microbiology
*Hydrocarbons/metabolism
Biodegradation, Environmental
*Bacteria/genetics/classification/metabolism
*Soil Pollutants/metabolism
RNA, Ribosomal, 16S/genetics
*Petroleum/metabolism
Soil/chemistry
*Microbiota
Petroleum Pollution
Iran
High-Throughput Nucleotide Sequencing
Phylogeny

@article {pmid40595658,
year = {2025},
author = {Zhang, Z and Liu, Y and Zhao, W and Liu, K and Chen, Y and Wang, F and Mao, G and Ji, M},
title = {Distinct genes and microbial communities involved in nitrogen cycling between monsoon- and westerlies-dominated Tibetan glaciers.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {5926},
pmid = {40595658},
issn = {2041-1723},
support = {42421001//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42330410//National Natural Science Foundation of China (National Science Foundation of China)/ ; U21A20176//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Tibet ; *Nitrogen Cycle/genetics ; *Ice Cover/microbiology ; *Microbiota/genetics ; Nitrogen/metabolism ; Metagenome/genetics ; Climate Change ; Bacteria/genetics/metabolism/classification ; Temperature ; Nitrous Oxide/metabolism ; Nitrogen Fixation/genetics ; Transcriptome ; },
abstract = {The Tibetan Plateau (TP) glaciers are influenced by monsoon and westerlies. They are highly sensitive to climate change, with atmospheric nitrogen deposition significantly impacting microbial communities and functions. However, key uncertainties persist regarding biogeography and drivers of genes and microbial communities involved in nitrogen cycling. Here, we investigate the diversity and transcriptional activity of microbial communities and nitrogen-cycling genes using 85 metagenomes and 28 metatranscriptomes from the ablation zone of 21 TP glaciers. Our results show that over 90% of the glacial taxa possess the potential for nitrogen metabolism, with ~33% exhibiting transcriptional activity. Moreover, monsoon-dominated glaciers present greater microbial diversity and higher prevalence of nitrogen-fixing genes than westerlies-dominated glaciers, linked to higher temperatures. Comparatively, the latter show elevated genomic potential for nitrous oxide emissions, likely due to higher nitrate concentrations. These findings establish temperature-nitrogen co-regulation of microbial nitrogen transformations, critical for predicting climate feedback in the extreme environment.},
}

Tibet
*Nitrogen Cycle/genetics
*Ice Cover/microbiology
*Microbiota/genetics
Nitrogen/metabolism
Metagenome/genetics
Climate Change
Bacteria/genetics/metabolism/classification
Temperature
Nitrous Oxide/metabolism
Nitrogen Fixation/genetics
Transcriptome

@article {pmid40595444,
year = {2025},
author = {Minabou Ndjite, G and Jiang, AK and Ravel, CT and Grant, MR and Jiang, X and Hall, B},
title = {Gut microbial utilization of the alternative sweetener, D-allulose, via AlsE.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {970},
pmid = {40595444},
issn = {2399-3642},
support = {1R35GM155208-01//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; },
mesh = {*Gastrointestinal Microbiome ; Humans ; *Sweetening Agents/metabolism ; *Fructose/metabolism ; Adult ; *Clostridium/genetics/enzymology/metabolism ; },
abstract = {D-allulose, a rare sugar with emerging potential as a low-calorie sweetener, has garnered attention as an alternative to other commercially available alternative sweeteners, such as sugar alcohols, which often cause severe gastrointestinal discomfort. D-allulose-6-phosphate 3-epimerase (AlsE) is a prokaryotic enzyme that converts D-allulose-6-phosphate into D-fructose-6-phosphate, enabling its use as a carbon source. However, the taxonomic breadth of AlsE across gut bacteria remains poorly understood, hindering insights into the utilization of D-allulose by microbial communities. In this study, we provide experimental evidence showing that Clostridium innocuum is capable of D-allulose metabolism via a homologous AlsE. A bioinformatics search of 85,202 bacterial genomes identified 116 bacterial species with AlsE homologs, suggesting a limited distribution of AlsE in bacteria. Additionally, Escherichia coli contains a copy of alsE, but it does not grow on D-allulose as a sole carbon source unless alsE is heterologously expressed. A metagenomic analysis revealed that 15.8% of 3079 adult healthy human metagenomic samples that we analyzed contained alsE, suggesting a limited prevalence of the enzyme in the gut microbiome. These results suggest that the gut microbiome has limited capacity to metabolize D-allulose via alsE, supporting its use as an alternative sweetener with minimal impact on microbial composition and gastrointestinal symptoms. This finding also enables personalized nutrition, allowing diabetic individuals to assess their gut microbiota for alsE, and manage glycemic response while reducing gastrointestinal distress.},
}

*Gastrointestinal Microbiome
Humans
*Sweetening Agents/metabolism
*Fructose/metabolism
Adult
*Clostridium/genetics/enzymology/metabolism

@article {pmid40595289,
year = {2025},
author = {Kador, SM and Islam, KT and Rubaiyat, RN and Bhuiyan, MIU and Chakrovarty, T and Rahman, MS and Islam, OK and Islam, MT},
title = {Abundance and transmission of antibiotic resistance and virulence genes through mobile genetic elements in integrated chicken and fish farming system.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {20953},
pmid = {40595289},
issn = {2045-2322},
support = {22-FoBST 05//Research Cell, Jashore University of Science and Technology/ ; SRG-221252//Special Research Grant, Ministry of Science and Technology, Bangladesh/ ; },
mesh = {Animals ; *Chickens/microbiology ; *Interspersed Repetitive Sequences/genetics ; Aquaculture ; Fishes ; *Virulence Factors/genetics ; *Drug Resistance, Microbial/genetics ; *Bacteria/genetics/pathogenicity/drug effects ; Gene Transfer, Horizontal ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Virulence/genetics ; Bangladesh ; },
abstract = {Integrated chicken and fish farming systems, common in Bangladesh, present significant public health risks due to the spread of antimicrobial resistance genes (ARGs) and virulence factors (VFGs) through mobile genetic elements (MGEs). This study employs metagenomic sequencing to explore the diversity and abundance of ARGs, VFGs, and MGEs in various environmental samples from these farming systems. A total of 384 ARGs were detected, with tetracycline resistance genes such as tetM and tetX being the most abundant, alongside macrolide-lincosamide-streptogramin and aminoglycoside resistance genes. Droppings harbored the highest proportion of ARGs (62.2%), whereas sediment served as a reservoir for multi-metal resistance genes. Virulence factors associated with immune modulation, such as pvdL and tssH, and biofilm formation genes like algC were particularly prevalent in sediment and droppings. Among MGEs, plasmids and transposons like Tn6072 and Tn4001 were the most abundant, playing a critical role in horizontal gene transfer. Bacterial genera including Bacteroides, Clostridium, and Escherichia were strongly associated with MGEs, indicating their role in the dissemination of resistance and virulence traits. Statistical analyses revealed significant differences in the abundance of ARGs, VFGs, and MGEs across sample types, with sediment and droppings identified as hotspots for gene exchange. These findings underscore the urgent need for improved antibiotic stewardship and waste management practices to limit the spread of antimicrobial resistance and pathogenic bacteria within integrated farming environments.},
}

Animals
*Chickens/microbiology
*Interspersed Repetitive Sequences/genetics
Aquaculture
Fishes
*Virulence Factors/genetics
*Drug Resistance, Microbial/genetics
*Bacteria/genetics/pathogenicity/drug effects
Gene Transfer, Horizontal
Anti-Bacterial Agents/pharmacology
*Drug Resistance, Bacterial/genetics
Virulence/genetics
Bangladesh

@article {pmid40595004,
year = {2025},
author = {Raina, TK and Gupta, M and Salgotra, RK},
title = {Metagenomic analysis to identify unique microbes in the rhizosphere of basmati rice (Oryza sativa L.) accessions.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {22864},
pmid = {40595004},
issn = {2045-2322},
mesh = {*Oryza/microbiology/genetics ; *Rhizosphere ; *Metagenomics/methods ; Soil Microbiology ; *Bacteria/genetics/classification/isolation & purification ; Odorants/analysis ; Microbiota ; },
abstract = {The captivating aroma of basmati rice is highly favoured by consumers across the globe. Unfortunately, the aroma of basmati rice has been gradually diminishing over time due to the excessive use of inorganic fertilizers and the impact of climate change. To understand the microbial community that plays a significant role in aroma enhancement in basmati rice accessions, a systematic study is required. A unique rhizobacteria of basmati rice associated with basmati rice were Actinobacteria, Bacillus subtilis, Burkholderia, Enterobacter, Klebsiella, Lactobacillus, Micrococcus, Pseudomonas, and Sinomonas. The biosynthesis of potential precursors (ornithine, putrescine, proline, and polyamines) of aroma in basmati rice involved various enzymes such as acetylornithine aminotransferase, acetylornithine deacetylase, N-acetylornithine carbomyltransferase, acetylornithine/succinyldiaminopimelate aminotransferase, and ornithine cyclodeaminase. These findings significantly contribute to the existing understanding of the rhizobacteria associated with basmati rice that play a crucial role in enhancing the aroma. The introduction of these cultures into the basmati rice growing areas has the potential to augment the plant growth and enhances the aroma. The present study explored the functional potential of the microbial community associated with aroma improvement in basmati rice. This will also enhance the export potential of the basmati rice in the region on sustainable basis.},
}

*Oryza/microbiology/genetics
*Rhizosphere
*Metagenomics/methods
Soil Microbiology
*Bacteria/genetics/classification/isolation & purification
Odorants/analysis
Microbiota

@article {pmid40594802,
year = {2025},
author = {Deka, NC and Kumari, G and Nath, T},
title = {Microbial dynamics in rice ecosystem under supplementation of organic sources of nitrogen with inorganics and their concomitant impact on yield.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {20473},
pmid = {40594802},
issn = {2045-2322},
abstract = {Microorganisms play crucial role in the ecosystem building. Their presence or absence in a particular environment are indicative of the web of interactions they undergo to impact the life of other components of the system. The current experiment was undertaken in rice-rice cropping sequence, for two years, to understand the changes in composition of microorganism as a result of interaction of herbicide and different nutrient sources added to soil under lowland area and a resultant grain yield obtained in rice. The experiment was divided into two simultaneous studies, i.e., field experiment and metagenomic study, to obtain the rice yield and soil microbial dynamics, respectively. Pooled soil samples were collected from rice field with constant herbicide application, i.e. Pyraszosulfuron (pre-emergent) @25 g/ha + 2, 4-D (post-emergent @0.5 kg/ha), but with 5 different sources of nutrients, viz., T0—absolute control, T1—100% N-P2O5-K2O through inorganic fertilizers (recommended dose of 40-20-20 kg/ha)), T2—75% N through inorganic + 25% N through FYM (P2O5 and K2O recommended doses), T3—75% N through inorganic + 25% N through vermicompost (P2O5 and K2O recommended doses) and T4—75% N through inorganic + 25% N through crop residues and bio-fertilizer (P2O5 and K2O recommended doses). Based on the amplicon DNA sequencing approach, it was observed that though there was an overall increase in bacterial phyla, viz., Chloroflexi, Actinomycetes, Euryarchaeota, Firmicutes in all the treatments from 0 days after transplanting (DAT) to physiological maturity of plant, however, soil treated with vermicompost (TH3) showed a dramatic increase in the population of one particular microbe viz., Firmicutes. Amongst fungal populations, Actinomycetes increased in soils of all the treatments from 0 DAS to physiological maturity, however, the increase was lowest in soil treated with vermicompost while it was highest in soil having crop residues (T4). The result obtained in microbial dynamics in case of vermicompost supplementation are concomitant to the biological yield of rice that was observed to be the highest in the same. The findings highlighted that the soil with vermicompost supplementation outperformed in terms of beneficial microbial changes and highest grain yield which, again, could be attributed to the favourable niche provided by vermicompost. Hence, supplementing vermicompost along with inorganic N sources can surpass the other organic sources in preventing deleterious effects of the chemical build-up in soil, due to herbicides and inorganic fertilizers, while synthesizing and releasing plant hormones, metabolites and antibiotics to suitably allow the growth and dominance of beneficial bacterial population.},
}

@article {pmid40594590,
year = {2025},
author = {Lan, N and Mao, C and Chen, M and Wang, X and Bai, S and Ren, J},
title = {Metagenomic insights into resistance trends related to microbial VB12 synthesis in eutrophic urban lakes.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {20599},
pmid = {40594590},
issn = {2045-2322},
support = {2023-YBSF-666//Scientific and Technological Research Foundation of Shaan'xi Province, Key Research and Development Project/ ; 2021A011//Shaanxi Provincial Key Research and Development Plan Project/ ; YXJLRH2022006//Basic and Clinical Integration Innovation Project of Xi' an Jiao tong University/ ; TQ202205//Nanjing Tianqing Scientific Research Fund of First Affliated Hospital of Xi'an Jiaotong University/ ; },
mesh = {*Lakes/microbiology ; *Metagenomics/methods ; *Metagenome ; *Vitamin B 12/biosynthesis/genetics ; Eutrophication ; Humans ; *Bacteria/genetics/metabolism ; *Drug Resistance, Microbial/genetics ; *Drug Resistance, Bacterial/genetics ; },
abstract = {Vitamin B12 (VB12) is essential for human health, and its deficiency can lead to various health issues, including anemia and neurological problems. Additionally, the presence of antibiotic resistance genes in various environments raises concerns about the spread of antibiotic resistance. This study aims to explore potential connections between these two functional gene categories in freshwater environments, which are closely intertwined with human health. We conducted a comprehensive metagenomic sequencing analysis across 23 sampling points from five different eutrophic urban lakes. The results highlight the dominance of the precorrin-2 synthesis pathway in the microbial synthesis of VB12 within urban lakes. Eutrophication may potentially enhance the precorrin-2 synthesis pathway while inhibiting others. The risk of antibiotic resistance is reduced in the anaerobic pathway of VB12 synthesis, while the abundance of metal resistance genes is increased. Binning analysis reveals that 26 metagenome-assembled genomes (MAGs) actively participate in VB12 synthesis, with at least 4 MAGs showing resistance during the VB12 synthesis process and demonstrating pathogenicity. These findings provide critical insights into the VB12 synthesis process and its implications for human health in terms of resistance risks.},
}

*Lakes/microbiology
*Metagenomics/methods
*Metagenome
*Vitamin B 12/biosynthesis/genetics
Eutrophication
Humans
*Bacteria/genetics/metabolism
*Drug Resistance, Microbial/genetics
*Drug Resistance, Bacterial/genetics

@article {pmid40594354,
year = {2025},
author = {Flores, SS and Cordovez, V and Arias Giraldo, LM and Leon-Reyes, A and van 't Hof, P and Raaijmakers, JM and Oyserman, BO},
title = {Unveiling diversity and adaptations of the wild tomato Microbiome in their center of origin in the Ecuadorian Andes.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {22448},
pmid = {40594354},
issn = {2045-2322},
support = {CZ07-000440-2018//SENESCYT scholarship/ ; 10093//Chancellor Grant and COCIBA-USFQ/ ; 10093//Chancellor Grant and COCIBA-USFQ/ ; 024.004.014/NWO_/Dutch Research Council/Netherlands ; 024.004.014/NWO_/Dutch Research Council/Netherlands ; },
mesh = {*Solanum lycopersicum/microbiology/genetics ; *Microbiota/genetics ; Soil Microbiology ; Rhizosphere ; Ecuador ; Plant Roots/microbiology ; Biodiversity ; *Adaptation, Physiological ; Phylogeny ; },
abstract = {Microbiome assembly has been studied for many plant species and is recognized as a key driver of plant growth and plant tolerance to (a)biotic stresses. To date, assembly of the tomato rhizosphere microbiome has been investigated primarily for commercial varieties and field soils subjected to agricultural management practices, whereas the microbiome of wild tomato genotypes in their native habitats remains largely unexplored. This research focused on distinct populations of Solanum pimpinellifolium in three natural habitats in the Ecuadorian Andes to identify the taxonomic and functional diversity of their rhizosphere microbiome. The results showed that, despite genotypic differences among the wild tomato populations, different soil types and soil microbiome compositions, the rhizosphere microbiome showed strikingly compositional similarity across the three habitats. Proteobacteria, in particular taxa classified as Enterobacteriaceae, and specific unclassified fungal taxa were highly represented in the rhizosphere of S. pimpinellifolum. Metagenomic analyses suggested that the prevalence of Enterobacteriaceae on wild tomato roots may be explained by several traits, in particular nutrient competition, motility, iron acquisition, membrane transport, stress response, and plant hormone biosynthesis. These results reveal a conserved microbiome signature associated with wild tomato rhizosphere in their center of origin. Just as the genomes of wild crop ancestors provide a valuable source of beneficial traits for breeding cultivated varieties, exploring their microbiome in native environments could uncover microbial taxa and traits that similarly contribute to crop growth and health.},
}

*Solanum lycopersicum/microbiology/genetics
*Microbiota/genetics
Soil Microbiology
Rhizosphere
Ecuador
Plant Roots/microbiology
Biodiversity
*Adaptation, Physiological
Phylogeny

@article {pmid40594317,
year = {2025},
author = {Song, X and Li, JN and Wang, D and Han, ZY and Yan, XX and Yang, ZH and Xu, J and Wang, Q and Wu, D},
title = {Metagenomics reveals functional profiles of gut microbiota during the recovery phase of acute pancreatitis.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {20549},
pmid = {40594317},
issn = {2045-2322},
support = {32170788//National Natural Science Foundation of China/ ; 2022-PUMCH-B-023//National High Level Hospital Clinical Research Funding/ ; ZK108000//National Key Clinical Specialty Construction Project/ ; 7232123//Natural Science Foundation of Beijing/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; *Pancreatitis/microbiology ; Male ; Female ; Middle Aged ; Adult ; Aged ; Acute Disease ; Bacteria/genetics/classification ; },
abstract = {Gut microbiota play a critical pathogenic role in acute pancreatitis (AP). This study aimed to investigate the composition and function of gut microbiota during the recovery phase of AP. Rectal swab samples obtained from 12 AP patients of varying severity during both the acute and recovery phases were sequenced using shotgun metagenomic sequencing. We analysed α-diversity, enterotypes, and the dominant microbiome composition, and performed differential analysis of gut microbiota composition and functional enrichment. During the recovery phase of AP, microbial diversity remained decreased, and minimal difference were observed in the structural diversity of the microbiome. There was an increasing tendency of beneficial bacteria (Bacteroidales) and a decreasing tendency of harmful bacteria (Firmicutes) in the recovery phase of mild AP (MAP). However, in the recovery phase of moderately severe AP (MSAP) and severe AP, Enterococcus abundance increased compared with that in the acute phase. Some signalling pathways showed opposite trends in the recovery phase of MAP and MSAP compared to the acute phase. These results suggested that gut microbiome composition and function are associated with AP recovery, which may inform strategies for the treatment and prognosis of AP.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Metagenomics/methods
*Pancreatitis/microbiology
Male
Female
Middle Aged
Adult
Aged
Acute Disease
Bacteria/genetics/classification

@article {pmid40594045,
year = {2025},
author = {Bhamidipati, SV and Surathu, A and Chao, H and Agustinho, DP and Xiang, Q and Kottapalli, K and Santhanam, A and Momin, Z and Walker, K and Menon, VK and Weissenberger, G and Emerick, N and Mahjabeen, F and Meng, Q and Hu, J and Sucgang, R and Henke, D and Sedlazeck, FJ and Khan, ZM and Metcalf, GA and Avadhanula, V and Piedra, PA and Ramani, S and Atmar, RL and Estes, MK and Petrosino, JF and Gibbs, RA and Muzny, DM and Javornik, SC and Doddapaneni, H},
title = {Complete genomic characterization of global pathogens respiratory syntical virus and human norovirus using probe based capture enrichment.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {20526},
pmid = {40594045},
issn = {2045-2322},
mesh = {Humans ; *Norovirus/genetics/isolation & purification ; *Genome, Viral ; *Respiratory Syncytial Virus, Human/genetics ; *Caliciviridae Infections/virology ; Genomics/methods ; *Respiratory Syncytial Virus Infections/virology ; Genotype ; Phylogeny ; Gastroenteritis/virology ; Oligonucleotide Probes/genetics ; },
abstract = {Respiratory syncytial virus (RSV) is the leading cause of lower respiratory tract infections in children worldwide, while human noroviruses (HuNoV) are a leading cause of epidemic and sporadic acute gastroenteritis. Generating full-length genome sequences for these viruses is crucial for understanding viral diversity and tracking emerging variants. However, obtaining high-quality sequencing data is often challenging due to viral strain variability, quality, and low titers. Here, we present a set of comprehensive oligonucleotide probe sets designed from 1,570 RSV and 1,376 HuNoV isolate sequences in GenBank. Using these probe sets and a capture enrichment sequencing workflow, 85 RSV positive nasal swab samples and 55 (49 stool and six human intestinal enteroids) HuNoV positive samples encompassing major subtypes and genotypes were characterized. Samples with Ct values 17.0-29.9 for RSV, and 20.2-34.8 for HuNoV, with some HuNoV below the detection limit were sequenced. The percentage of reads mapped to viral genomes was 85.1% for RSV and 40.8% for HuNoV post-capture, compared to 0.08% and 1.15% in pre-capture libraries. Full-length genomes were obtained for all RSV positive samples and in 47/55 HuNoV positive samples-a significant improvement over genome recovery from pre-capture libraries. RSV transcriptome (subgenomic mRNAs) sequences were also characterized from this data.},
}

Humans
*Norovirus/genetics/isolation & purification
*Genome, Viral
*Respiratory Syncytial Virus, Human/genetics
*Caliciviridae Infections/virology
Genomics/methods
*Respiratory Syncytial Virus Infections/virology
Genotype
Phylogeny
Gastroenteritis/virology
Oligonucleotide Probes/genetics

@article {pmid40593979,
year = {2025},
author = {Chen, L and Chen, H and Lv, T and Guo, X and Wu, W and Zhao, D and Liu, F},
title = {Differences of the respiratory microbiota between children suffering from community acquired pneumonia with presence or absence of asthma.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {20458},
pmid = {40593979},
issn = {2045-2322},
mesh = {Humans ; *Asthma/microbiology/complications ; *Community-Acquired Infections/microbiology/complications ; *Microbiota ; Male ; Female ; Child ; Child, Preschool ; *Pneumonia/microbiology/complications ; Infant ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Adolescent ; Community-Acquired Pneumonia ; },
abstract = {Recent advancements in respiratory microbiota research have progressively elucidated their pivotal role in pediatric respiratory pathologies. Alterations in airway microbial communities are intricately associated with diverse respiratory conditions and distinct disease states. This study conducted a comparative analysis of respiratory microecological profiles in pediatric cohorts diagnosed with community-acquired pneumonia (CAP), stratified by the presence or absence of comorbid bronchial asthma, from whom nasopharyngeal aspirates were obtained for metagenomic next-generation sequencing (mNGS). Analyses revealed comparable alpha-diversity indices between groups; however, beta-diversity metrics demonstrated marked compositional divergence. In the asthma-CAP cohort, Streptococcus pneumoniae and Rothia mucilaginosa emerged as predominant taxa, whereas Mycoplasmoides pneumoniae and Trichoderma citrinoviride dominated microbial profiles in uncomplicated CAP patients.},
}

Humans
*Asthma/microbiology/complications
*Community-Acquired Infections/microbiology/complications
*Microbiota
Male
Female
Child
Child, Preschool
*Pneumonia/microbiology/complications
Infant
High-Throughput Nucleotide Sequencing
Metagenomics
Adolescent
Community-Acquired Pneumonia

@article {pmid40593735,
year = {2025},
author = {Flores Ventura, E and Esteban-Torres, M and Gueimonde, M and van Sinderen, D and Koren, O and Hall, LJ and Segata, N and Valles-Colomer, M and Collado, MC},
title = {Mother-to-infant vertical transmission in early life: a systematic review and proportional meta-analysis of Bifidobacterium strain transmissibility.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {121},
pmid = {40593735},
issn = {2055-5008},
support = {CEX2021-001189-S-20-1//Ministerio de Ciencia e Innovación/ ; CEX2021-001189-S/ MCIN/AEI / 10.13039/501100011033//Ministerio de Ciencia e Innovación/ ; PID2022-139328OA-I00//Ministerio de Ciencia e Innovación/ ; CEX2021-001189-S/ MCIN/AEI / 10.13039/501100011033//Ministerio de Ciencia e Innovación/ ; 898088//European Union's Horizon 2020/ ; SFI/12/RC/2273-P1 and SFI/12/RC/2273-P2/SFI_/Science Foundation Ireland/Ireland ; 220876/Z/20/Z//Wellcome Trust Investigator/ ; Beatriz Galindo Junior Fellowship BG22/00172//Ministerio de Universidades/ ; 639226/ERC_/European Research Council/International ; },
mesh = {Female ; Humans ; Infant ; Infant, Newborn ; Pregnancy ; *Bifidobacteriales Infections/transmission/microbiology ; *Bifidobacterium/classification/genetics/isolation & purification ; Gastrointestinal Microbiome ; *Infectious Disease Transmission, Vertical ; Metagenomics ; Mothers ; Vagina/microbiology ; },
abstract = {Early-life colonization is a critical developmental process influencing infant biological programming, with bifidobacteria playing a key role. This systematic review examines the transmissibility of Bifidobacterium strains from mothers to infants. Adhering to Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) guidelines, 31 articles from 2009 to 2024 were selected from 2825 screened titles and abstracts. Using a narrative synthesis and meta-analysis, the review focuses on studies employing strain-level metagenomic approaches (Protocol registry CRD: CRD42023490507). Ten studies using shotgun metagenomic sequencing identified specific strains of B. adolescentis, B. angulatum, B. bifidum, B. breve, B. pseudocatenulatum, B. catenulatum, and B. longum shared between mothers and infants. A meta-analysis of 810 mother-infant pairs revealed an overall species transmissibility estimate of 30% (95% CI: 0.17; 0.44), with B. longum strains persisting in infants' guts for up to 6 months. Strain transmissibility was higher in vaginally delivered infants compared to those delivered by caesarean section. This review highlights the high transmission rates of maternal Bifidobacterium strains in early-life gut seeding, particularly B. bifidum and B. longum. Despite ongoing research, uncertainties remain regarding the precise characteristics, transmission routes, and mechanisms of transmitted strains. Comprehensive approaches, including metagenomic sequencing and longitudinal studies, are needed to understand the role of vertical transmission in infant gut microbiome engraftment and its functional implications.},
}

Female
Humans
Infant
Infant, Newborn
Pregnancy
*Bifidobacteriales Infections/transmission/microbiology
*Bifidobacterium/classification/genetics/isolation & purification
Gastrointestinal Microbiome
*Infectious Disease Transmission, Vertical
Metagenomics
Mothers
Vagina/microbiology

@article {pmid40593605,
year = {2025},
author = {Butcher, J and Villette, C and Zumsteg, J and Maurer, L and Barchietto, T and Rigo, R and Floch, K and Cseh, A and Buchet, S and Stintzi, A and Heintz, D},
title = {Microbial bioremediation of persistent organic pollutants in plant tissues provides crop growth promoting liquid fertilizer.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {5768},
pmid = {40593605},
issn = {2041-1723},
support = {251174 and 199015//Agence de l'Eau Seine-Normandie/ ; 251174 and 199015//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; OGI-149//Genome Canada (Génome Canada)/ ; OGI-149//Ontario Genomics Institute (OGI)/ ; },
mesh = {*Fertilizers ; Biodegradation, Environmental ; Wetlands ; *Persistent Organic Pollutants/metabolism ; Bacteria/metabolism/genetics ; Fungi/metabolism/genetics ; *Crops, Agricultural/growth & development/microbiology ; Wastewater ; Metagenomics ; },
abstract = {Constructed wetlands are used to clean domestic wastewater via phytoremediation, commonly involving the use of reeds. The process results in the production of large amounts of polluted plant tissues, which are then considered unusable waste products. In this study, the reusability of reeds and nettle-polluted tissues is investigated. Fermenting contaminated plant tissues to produce liquid fertilizer is a sustainable means to remove 87-95% of persistent organic pollutants. A multiomics approach combining metabolomics and amplicon metagenomics is used to analyze the mechanisms that occur during fertilizer production from polluted plant tissues and identify the microbes that are likely key for this transformation. A consortium of bacteria and fungi with cellulolytic activity is identified. In addition, the obtained liquid fertilizer positively impacts plant growth in the presence of pathogens and therefore exhibits potential application in farming. This approach may be a simple, commercially attractive solution for the management of contaminated plant tissues originating from constructed wetlands, which are currently considered problematic, useless waste products.},
}

*Fertilizers
Biodegradation, Environmental
Wetlands
*Persistent Organic Pollutants/metabolism
Bacteria/metabolism/genetics
Fungi/metabolism/genetics
*Crops, Agricultural/growth & development/microbiology
Wastewater
Metagenomics

@article {pmid40593262,
year = {2025},
author = {Liu, L and Li, M and Qin, Y and Liu, Y and Li, M and Lian, B and Guo, R and Xiao, Y and Yin, C},
title = {Childhood obesity and insulin resistance is correlated with gut microbiome serum protein: an integrated metagenomic and proteomic analysis.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {21436},
pmid = {40593262},
issn = {2045-2322},
support = {81903340//National Natural Science Foundation of China/ ; },
mesh = {Child ; Female ; Humans ; Male ; *Blood Proteins/metabolism ; Feces/microbiology ; *Gastrointestinal Microbiome ; *Insulin Resistance ; Metagenomics/methods ; *Pediatric Obesity/microbiology/blood/metabolism ; Proteomics/methods ; },
abstract = {The aim of this study was to investigate the changes in the gut microbiota and proteins related to metabolism and immunity caused by childhood obesity and insulin resistance (IR) and to assess the underlying relationship between the gut microbiota and IR in children. Nineteen children with obesity and sixteen healthy children were recruited. Children with obesity were divided into two groups: obese with IR and obese without IR. All of the obese children participated in a 1-month lifestyle-based weight loss program. Faecal metagenomics and serum Olink proteomics combined with clinical parameters were used to identify the metabolic alterations associated with childhood obesity and IR. The gut microbiota and serum protein were significantly altered in obese children with IR. The relative abundances of Akkermansia muciniphila, IGFBP1 and GP6 were decreased in obese children with IR. Butyricicoccus sp. AM29-23AC, DLK1, CD163, CCL16 and CTSD levels were recovered after IR improved. TNFR1 had a significant indirect effect on the interaction between s-Citrobacter.freundii and fasting insulin. In conclusion, obese children with IR have abnormal gut microbiota and serum proteins related to metabolism and immunity, which can be improved after weight loss. The gut microbiome of children with obesity may contribute to the development of IR by triggering metabolic inflammation.Clinical Trial Registration: This study was registered with the Chinese Clinical Trial Registry (Registration number: ChiCTR2300072179).},
}

Child
Female
Humans
Male
*Blood Proteins/metabolism
Feces/microbiology
*Gastrointestinal Microbiome
*Insulin Resistance
Metagenomics/methods
*Pediatric Obesity/microbiology/blood/metabolism
Proteomics/methods

@article {pmid40593191,
year = {2025},
author = {Park, K and Lee, J and Kim, J and Kim, SG and Song, DH and Gu, SH and Lee, SH and Lee, D and Kim, WK and Song, JW},
title = {Discovery and genomic characterization of Ulleung virus harbored by Crocidura utsuryoensis on Ulleung Island in Republic of Korea.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {21748},
pmid = {40593191},
issn = {2045-2322},
support = {UE242006TD and 411FF5-912A01201//Agency for Defense Development/ ; },
mesh = {Animals ; Phylogeny ; *Shrews/virology ; Republic of Korea ; *Genome, Viral ; *Orthohantavirus/genetics/classification ; Genomics ; Haplotypes ; Islands ; },
abstract = {Hantaviruses are zoonotic RNA viruses that cause hemorrhagic fever with renal syndrome and hantavirus cardiopulmonary syndrome, posing significant public health risks. This study reports the identification and genomic characterization of Ulleung virus (ULLEV), a newly discovered genetic lineage of Orthohantavirus jejuense harbored by Crocidura utsuryoensis, a shrew species endemic to Ulleung Island, Republic of Korea. In 2009, a surveillance effort involving 62 shrews revealed a molecular prevalence of 64.5%. Metagenomic next-generation sequencing identified four viral variants, with ULLEV Cu09-33 fully characterized. Comparative genomic and phylogenetic analyses confirmed ULLEV as a distinct subtype within O. jejuense and suggested that ULLEV and Jeju virus (JJUV) share a common ancestor, with divergence shaped by long-term co-evolution with their hosts and geographic isolation. Haplotype network analysis of mitochondrial DNA detected eight unique haplotypes in C. utsuryoensis, distinct from C. shantungensis populations, indicating genetic isolation. While incongruences among the tripartite genomes of ULLEV and JJUV suggested independent evolutionary trajectories, evidence for reassortment remains insufficient. These findings highlight the ecological significance of geographically isolated environments as reservoirs for unique hantavirus lineages and underscore the need for expanded genomic surveillance and phylogenetic studies to assess the zoonotic potential and public health implications of ULLEV.},
}

Animals
Phylogeny
*Shrews/virology
Republic of Korea
*Genome, Viral
*Orthohantavirus/genetics/classification
Genomics
Haplotypes
Islands

@article {pmid40593012,
year = {2025},
author = {Sitko, K and Piotrowska, E and Podlacha, M and Zagórska, N and Starke, MD and Trzeciak, M and Tukaj, S},
title = {Topical application of the HSP90 inhibitor 17-AAG reduces skin inflammation and partially restores microbial balance: implications for atopic dermatitis therapy.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {21245},
pmid = {40593012},
issn = {2045-2322},
support = {2020/39/B/NZ6/00357//Polish National Science Centre (NCN)/ ; 2020/39/B/NZ6/00357//Polish National Science Centre (NCN)/ ; 2020/39/B/NZ6/00357//Polish National Science Centre (NCN)/ ; 2020/39/B/NZ6/00357//Polish National Science Centre (NCN)/ ; 2020/39/B/NZ6/00357//Polish National Science Centre (NCN)/ ; },
mesh = {*Benzoquinones/administration & dosage/pharmacology ; *Lactams, Macrocyclic/administration & dosage/pharmacology ; Animals ; *Dermatitis, Atopic/drug therapy/pathology/chemically induced/microbiology/metabolism ; *HSP90 Heat-Shock Proteins/antagonists & inhibitors/metabolism ; Mice ; Humans ; Disease Models, Animal ; Administration, Topical ; *Skin/drug effects/pathology/microbiology ; Female ; Cytokines/metabolism ; Eosinophils/drug effects/metabolism ; Gastrointestinal Microbiome/drug effects ; Staphylococcus aureus/drug effects ; Inflammation/drug therapy ; Keratinocytes/drug effects/metabolism ; },
abstract = {Heat shock proteins belonging to the HSP90 family promote inflammation and are potential therapeutic targets in inflammatory and autoimmune diseases. Here the effects of the HSP90 inhibitor 17-AAG applied topically were evaluated in a DNCB-induced murine model of atopic dermatitis (AD). The use of 17-AAG improved clinical disease activity without causing toxicity in the animals. Topical application of 17-AAG resulted in reduced epidermal hyperplasia, decreased expression of TSLP, IL-5, and IL-6, as well as reduced activation of NF-κB in the skin. In addition, the eosinophil proportion in the blood and eosinophil peroxidase (EPX) activity in the skin were significantly reduced in 17-AAG-treated AD mice. The inhibitory effects of 17-AAG on the production of epidermal alarmins, T-helper cell-associated cytokines, and ROS release were demonstrated in cultures of activated human keratinocytes, CD4[+] T lymphocytes, and eosinophils, respectively. Finally, next-generation sequencing metagenomic approaches revealed that topical application of 17-AAG partially restored the normal gut microbiome in AD mice. Moreover, 17-AAG inhibited Staphylococcus aureus biofilm formation in vitro. The findings of this study, combined with the observed increase in HSP90 and EPX activity in the leukocytes of the analyzed cohort of AD patients, support the potential therapeutic use of HSP90 inhibitors in individuals with AD.},
}

*Benzoquinones/administration & dosage/pharmacology
*Lactams, Macrocyclic/administration & dosage/pharmacology
Animals
*Dermatitis, Atopic/drug therapy/pathology/chemically induced/microbiology/metabolism
*HSP90 Heat-Shock Proteins/antagonists & inhibitors/metabolism
Mice
Humans
Disease Models, Animal
Administration, Topical
*Skin/drug effects/pathology/microbiology
Female
Cytokines/metabolism
Eosinophils/drug effects/metabolism
Gastrointestinal Microbiome/drug effects
Staphylococcus aureus/drug effects
Inflammation/drug therapy
Keratinocytes/drug effects/metabolism

@article {pmid40592825,
year = {2025},
author = {Mali, N and Mali, S and Zhang, L and Fu, P},
title = {Interplay between gut microbiota and acute kidney injury: a review of their mutual influence and causation.},
journal = {Renal failure},
volume = {47},
number = {1},
pages = {2522976},
pmid = {40592825},
issn = {1525-6049},
mesh = {Humans ; *Acute Kidney Injury/microbiology/immunology/physiopathology ; *Gastrointestinal Microbiome/immunology/physiology ; Kidney/physiopathology/microbiology ; Animals ; },
abstract = {It is unclear, therefore, exactly how gut microbes and renal processes communicate. Recent developments in the field of microbiome research present chances to enhance our comprehension and management of acute kidney injury (AKI). This review highlights important ideas and suggests more research while giving a general summary of the microbiome's influence on kidney function and AKI. AKI is a complex condition that develops through a variety of pathways. Recent experimental research has highlighted the important role that the gut microbiota plays in the course of AKI. Our understanding of human biology has been completely transformed by the current increase in gut microbiota research. Amazing progress in DNA sequencing analysis, especially in the areas of metagenomics and metatranscriptomics, has greatly increased our ability to measure and track complex microbial populations. As such, we are now in a better position to look at how these communities affect human health and illness. As a result, the relationships between renal physiology and pathophysiology and the gut microbiota are now better understood. Both experimental AKI and chronic renal illness have been linked to changes in the intestinal microbiome. This succinct review attempts to examine our present knowledge of the immune-modulatory effects of the gut microbiota, how kidney disorders are influenced by it, and the possible reciprocal interaction between kidney diseases and the microbiota. Subsequent investigations ought to concentrate on delving deeper into the function of the gut microbiota in renal disorders and finding possible therapeutic strategies for adjusting it.},
}

Humans
*Acute Kidney Injury/microbiology/immunology/physiopathology
*Gastrointestinal Microbiome/immunology/physiology
Kidney/physiopathology/microbiology
Animals

@article {pmid40592271,
year = {2025},
author = {Fan, Q and Bai, J and Jiao, T and Zhao, Z and Hou, F},
title = {Circular transmission network and reverse contribution pattern of antibiotic resistance genes in the Qinghai-Tibet Plateau ecosystem.},
journal = {Journal of hazardous materials},
volume = {495},
number = {},
pages = {139054},
doi = {10.1016/j.jhazmat.2025.139054},
pmid = {40592271},
issn = {1873-3336},
abstract = {The dissemination of antibiotic resistance genes (ARGs) poses a major global public health challenge, yet transmission mechanisms within extreme ecosystems are poorly understood. Using metagenomics and metagenome-assembled genome (MAG) analysis, we investigated ARG composition, risk, and pathways across a complete Qinghai-Tibet Plateau food chain (soil, earthworm, herbage, yak, pika, snowfinch, herdsman). Contrary to conventional theory, ARG assemblages correlated negatively with microbial diversity. Our MAG-centric approach provided direct evidence that Horizontal Gene Transfer (HGT), including striking bacteria-archaea cross-domain transfer of 18 ARGs, predominates ARG dissemination, with specialized 'ARG reservoir' host phyla (e.g., Pseudomonadota) decoupling ARG functional diversity from overall microbial community structure. Earthworms function as 'ARG bioamplifiers', enriching 79.81 % of soil ARGs and contributing 49.43 % to herbage. Crucially, apex consumers (snowfinches, herdsmen) are not merely recipients; their feces drive a significant 'reverse contribution' of high-risk ARGs back into the ecosystem, establishing a complete circular ARG feedback network. Herdsman feces contained all Rank I-IV high-risk ARGs, while snowfinch feces held Rank II/IV, highlighting human activities' impact on escalating ARG risks in this extreme setting. These findings, particularly the novel HGT mechanisms and host specialization insights, challenge the traditional unidirectional transmission model, presenting a new paradigm for managing antibiotic resistance risks in extreme ecosystems within the One Health framework.},
}

@article {pmid40592243,
year = {2025},
author = {Gao, Z and Liu, X and Yu, J and Li, Z and Shi, H and Zhang, G and Ling, J},
title = {Structural basis of immunomodulation by edible fungal polysaccharides: From molecular characteristics to action mechanisms.},
journal = {Carbohydrate research},
volume = {555},
number = {},
pages = {109591},
doi = {10.1016/j.carres.2025.109591},
pmid = {40592243},
issn = {1873-426X},
abstract = {Edible Fungal polysaccharides as Immunomodulators: A Systematic Review at the Crossroads of Immunology, Natural Products Chemistry, and Microbiology. The chemical structure-specifically molecular weight, branching degree, and functional group modifications-directly dictates immunological activity. For instance, high-molecular-weight β-glucans activate macrophage surface receptors through triple-helix conformations, whereas sulfation enhances electrostatic interactions with immune cells. Mechanistically, polysaccharides regulate macrophage polarization, dendritic cell maturation, and T/B cell activation, therebyengaging core signaling pathways such as TLR4/MyD88/NF-κB, NLRP3 inflammasome, and MAPK, This orchestrates synergistic enhancement of innate and adaptive immunity. Recent research further demonstrate that polysaccharides can also reshape the gut microbiota-immune metabolic axis by promoting the production of short-chain fatty acids (SCFAs) and activating receptors (e.g., GPR43), indirectly modulating systemic immune responses. Clinically, polysaccharides from Ganoderma lucidum and Lentinus edodes demonstrate efficacy in cancer adjuvant therapy by enhancing immune function and reducing radiotherapy/chemotherapy side effects. However, species-specific receptor recognition heterogeneity and lack of standardized preparation protocols impede clinical translation. Therefore,the implementing an integrated strategy of "polysaccharide structure-immunometabolic reprogramming-precision delivery" to overcome the existing bottlenecks. Combining multi-omics approaches (e.g., gut metagenomics and metabolomics) will advance therapeutics targeting microbiota-immune crosstalk. Such strategies aim to address chronic inflammatory inflammation", malignancies, and related pathologies with enhanced mechanistic specificity.},
}

@article {pmid40592211,
year = {2025},
author = {Zhioua, S and Khan, I and Gonzalez, D and Junier, P and Sieber, S},
title = {Genomic and chemical characterization of cytotoxic Ahp-cyclodepsipeptides from Phormidium using Thamnocephalus platyurus bioassay.},
journal = {The Science of the total environment},
volume = {993},
number = {},
pages = {179750},
doi = {10.1016/j.scitotenv.2025.179750},
pmid = {40592211},
issn = {1879-1026},
abstract = {Toxic benthic cyanobacterial mats have been identified globally as a potential health hazard since they can produce potent cyanotoxins. Such mats have been connected to the death of mammals worldwide, with a significant fraction of recent cases associated to benthic cyanobacterial blooms producing anatoxin-a or its derivatives. A recent event involving the death of a dog led to monitoring of mats in the area and to the discovery of the first cyanopeptolin producer among the genus Phormidium. Using metagenomics, the genome of the dominant species in the cyanobacterial mats collected was reconstructed, but no evidence for the production of anatoxin-a or other congeners was obtained. In contrast, the biosynthetic gene cluster for cyanopeptolin was detected in the genome. Further chemical analysis of metabolites extracted from the same mats enabled the isolation and characterization of two novel cyanopeptolins with their truncated products. Toxicity was confirmed using the cytotoxic reporting organism Thamnocephalus platyurus. The untruncated cyanopeptolins had an LC50 as low as 6.4 μM while the truncated products did not exhibit cytotoxicity in the same assay. The presence of truncated analogues lacking cytotoxicity might suggest that other mat-associated microorganisms could degrade those compounds. While Phormidium may not be the direct cause of dog's death, our study provides the first evidence that Phormidium can produce cyanopeptolins. This highlights the underexplored variety of neglected cyanotoxin classes. These findings not only expand the known chemical diversity of cyanotoxins but also raise concerns regarding the potential ecological impact of toxic Ahp-cyclodepsipeptides in freshwater environments.},
}

@article {pmid40591894,
year = {2025},
author = {Fu, S and Du, X and Xu, Z and Li, H and Yao, H and Tang, S and Zhao, W and Hao, M and Qiu, Z and Wang, Z},
title = {The potential of wastewater monitoring as a novel surveillance tool for early warning of Bordetella pertussis outbreaks.},
journal = {Emerging microbes & infections},
volume = {},
number = {},
pages = {2528537},
doi = {10.1080/22221751.2025.2528537},
pmid = {40591894},
issn = {2222-1751},
abstract = {The prolonged latency period and delayed reporting of clinical surveillance data have led to a sluggish response to Bordetella pertussis outbreaks in China. Wastewater-based surveillance (WBS) provides real-time, cost-effective monitoring of various viruses. To confirm whether this approach can be applied to B. pertussis, 271 patients infected with B. pertussis were enrolled to evaluate the fecal shedding patterns of the bacterium. Concurrently, we collected wastewater samples in a typical northern (Xi'an) and southern city (Nanchang) in China, from September 2023 to July 2024. The concentrations of B. pertussis in the sewage were detected using quantitative polymerase chain reaction (qPCR). Additionally, metagenomic sequencing with pre-enrichment was employed to trace genotypes of B. pertussis. We report that 40.2% of cases tested positive for B. pertussis in fecal samples. Sewage surveillance identified two waves of B. pertussis infection in Xi'an and one wave of B. pertussis outbreak in Nanchang. The concentration of B. pertussis in sewage showed a strong correlation with the dynamics of diagnosed cases. Notably, each peak of sewage B. pertussis concentration occurred 10 days prior to clinical surveillance, underscoring the value of WBS in early warning. Additionally, both clinical and wastewater surveillance demonstrated consistency in the prevalence estimation of B. pertussis infection cases. Finally, relative to clinical surveillance, wastewater sequencing also revealed the same genotypes of B. pertussis. This study presents the first comprehensive analysis of the fecal shedding of B. pertussis, thereby establishing the potential for early detection of B. pertussis outbreaks through WBS.},
}

@article {pmid40591379,
year = {2025},
author = {Orenburkina, OI and Rezbaeva, GN and Dudurich, VV and Babushkin, AE and Sogomonian, KS and Danilova, AA and Danilov, LG},
title = {[Microbiota of the ocular surface in children with myopia].},
journal = {Vestnik oftalmologii},
volume = {141},
number = {3},
pages = {5-12},
doi = {10.17116/oftalma20251410315},
pmid = {40591379},
issn = {0042-465X},
mesh = {Humans ; Child ; *Myopia/diagnosis/microbiology/physiopathology ; Male ; Female ; Adolescent ; *Microbiota ; *Conjunctiva/microbiology ; *Bacteria/genetics/isolation & purification/classification ; RNA, Ribosomal, 16S/genetics ; Disease Progression ; },
abstract = {UNLABELLED: A healthy ocular surface is characterized by relatively stable and comparatively low microbial diversity. However, pathological conditions can provoke shifts in the composition of bacterial taxa, which may be associated, among other factors, with the progression of myopia.

PURPOSE: This study compared the taxonomic diversity of the conjunctival microbiota in children with varying degrees of myopia and those without clinically confirmed myopia.

MATERIAL AND METHODS: Ocular surface samples were obtained from 29 children aged 6-17 years with myopia (58 eyes) and from 12 children of the control group aged 9-17 years (24 eyes). The taxonomic composition of the conjunctival microbiota was analyzed using 16S ribosomal RNA gene (rRNA) sequencing, followed by microbiome profiling through bioinformatics and statistical tools.

RESULTS: The ocular surface microbiota in children with myopia demonstrated higher alpha diversity compared to the control group. This was confirmed by values of the Chao (reflecting low-abundance taxa) and Shannon (reflecting overall bacterial diversity - higher diversity means higher index; optimal value; 3.1-4.2) indices. The results revealed a clear trend toward differentiation in bacterial composition between myopic and control groups. These differences were associated with changes in the relative abundance of opportunistic bacteria depending on the degree of myopia.

CONCLUSION: The taxonomic diversity of the ocular microbiota at the genus level in patients with varying degrees of myopia was characterized by a higher number of taxonomic units compared to the control group. The general trend is an increase in the biodiversity of the bacterial composition due to an increase in the relative representation of opportunistic microorganisms. Further research on the influence of the ocular microbiota on the progression of myopia is needed.},
}

Humans
Child
*Myopia/diagnosis/microbiology/physiopathology
Male
Female
Adolescent
*Microbiota
*Conjunctiva/microbiology
*Bacteria/genetics/isolation & purification/classification
RNA, Ribosomal, 16S/genetics
Disease Progression

@article {pmid40590722,
year = {2025},
author = {Jin, H and Li, X and Wang, J and Cui, Y and Huang, S and Shi, K and Zhou, T and Yan, J},
title = {Draft genomes of Dehalococcoides mccartyi strain J1 and Trichlorobacter lovleyi strain J2 from a tetrachloroethene-dechlorinating consortium.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0048525},
doi = {10.1128/mra.00485-25},
pmid = {40590722},
issn = {2576-098X},
abstract = {Two metagenome-assembled genomes were recovered from an anaerobic consortium capable of complete reductive dechlorination of tetrachloroethene to ethene. The draft genomes, assigned to Dehalococcoides mccartyi strain J1 and Trichlorobacter lovleyi strain J2, are 1.37 and 3.84 Mb in size and encode 1,448 and 3,630 genes, respectively.},
}

@article {pmid40590427,
year = {2025},
author = {Nalla, S and Ganta, S and Bukke, SPN and Bandaru, N and Onohuean, H and Alagbonsi, AI},
title = {Kaempferide and Norbergenin avert aluminium chloride-induced amyloid β accumulation and neurocognitive shutdown via oxidative and apoptotic mechanisms.},
journal = {International journal of immunopathology and pharmacology},
volume = {39},
number = {},
pages = {3946320251343687},
pmid = {40590427},
issn = {2058-7384},
mesh = {Animals ; Aluminum Chloride ; Male ; *Apoptosis/drug effects ; Rats, Wistar ; *Oxidative Stress/drug effects ; *Neuroprotective Agents/pharmacology ; *Amyloid beta-Peptides/metabolism ; Rats ; *Cognition/drug effects ; Antioxidants/pharmacology ; Chlorides/toxicity ; Disease Models, Animal ; Aluminum Compounds ; },
abstract = {OBJECTIVE: To investigate the involvement of oxidative and apoptotic mechanisms in the possible neuroprotective effect of Kaempferide (KPD) and Norbergenin (NRG) against AlCl3-induced cognitive shutdown in rats.

INTRODUCTION: Aluminium chloride (AlCl3) is widely known as a neurotoxic agent that induces memory and cognitive shutdown via induction of oxidative stress and apoptosis. KPD is an O-methylated flavonol that possesses anti-oxidant, anti-inflammatory, anti-dementia and anti-depression properties, whereas NRG, a demethylated compound derived from bergenin, possesses an anti-oxidant property and has neuroprotective effects. Both alleviate D-galactose-induced neurotoxicity in rats.

METHODS: Eighty-four male Wistar rats were randomly divided into two experimental models: prophylactic (pre-treatment with donepezil, KPD or NRG; n = 42) and curative (post-treatment with donepezil, KPD, or NRG; n = 42). In each of these models, the animals were divided into seven groups (n = 6 per group): group 1 (normal saline), group 2 (200 mg/kg AlCl3), group 3 (donepezil + AlCl3), group 4 (5 mg/kg KPD + AlCl3), group 5 (10 mg/kg KPD + AlCl3), group 6 (5 mg/kg NRG + AlCl3) and group 7 (10 mg/kg NRG + AlCl3)Results:Kaempferide and Norbergenin averted the increase in TBARS, NO and AChE, and decrease in the number of crossings, time spent and distance moved in the target quadrant, latency of fall, speed, paw withdrawal threshold (PWT), SOD, CAT, GPx, GR and GSH induced by AlCl3. These agents also averted the upregulation of Aβ1-41, p-Tau, caspase-3, Bax and downregulation of Akt, p-CREB, SOD1 and BCl-2 induced by AlCl3Conclusion:The neuroprotective effects of KPD and NRG against AlCl3-induced Aβ accumulation and cognitive shutdown are mediated via suppression of oxidative stress and apoptosis.},
}

Animals
Aluminum Chloride
Male
*Apoptosis/drug effects
Rats, Wistar
*Oxidative Stress/drug effects
*Neuroprotective Agents/pharmacology
*Amyloid beta-Peptides/metabolism
Rats
*Cognition/drug effects
Antioxidants/pharmacology
Chlorides/toxicity
Disease Models, Animal
Aluminum Compounds

@article {pmid40590044,
year = {2025},
author = {Zhang, L and Rao, Y and Li, Z and Fan, M and Xiang, Z and Wang, J},
title = {The Advance and Clinical Practice on Lung Disease Caused by Mycobacterium abscessus.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {3103-3115},
pmid = {40590044},
issn = {1178-6973},
abstract = {Mycobacterium abscessus (M. abscessus) lung disease has gradually become a common clinical condition, with its incidence rate continuously rising, especially among patients with weakened immune function or those with chronic lung diseases. Given the high resistance of M. abscessus to antibiotics, the options for antibiotics are very limited. Additionally, long treatment times and poor patient compliance lead to low cure rates and high recurrence rates, making it one of the significant public health challenges threatening global health. This article presents two cases of patients diagnosed with M. abscessus lung disease using next-generation metagenomic sequencing technology. It reviews and analyzes the current research on M. abscessus along with details from these cases. Furthermore, this article emphasizes the necessity of timely, regular, and comprehensive treatment for M. abscessus lung disease. Meanwhile, we call for the formulation of robust prevention strategies, the optimization and innovation of treatment regimens, and the enhancement of follow-up management after cure to improve the understanding and handling capabilities of M. abscessus lung disease, thereby addressing the increasing clinical challenges.},
}

@article {pmid40589867,
year = {2025},
author = {Xu, W and Han, D and Chen, T and Wang, Q},
title = {Infected pericardial effusion caused by Prevotella intermedia: a rare diagnosis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1612282},
pmid = {40589867},
issn = {2235-2988},
mesh = {Humans ; *Pericardial Effusion/microbiology/diagnosis ; *Prevotella intermedia/isolation & purification/genetics ; *Bacteroidaceae Infections/diagnosis/microbiology ; High-Throughput Nucleotide Sequencing ; China ; Male ; Metagenomics ; Anti-Bacterial Agents/therapeutic use ; Female ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Prevotella intermedia is a Gram-negative bacterium that thrives in anaerobic environments. It presents challenges in detection through routine laboratory assays, and hitherto, there has been no documented instance of detecting this bacterium in pericardial effusion in China. Metagenomic Next-Generation Sequencing (mNGS) can boost the detection rate of this pathogen and furnish early guidance for clinical management.},
}

Humans
*Pericardial Effusion/microbiology/diagnosis
*Prevotella intermedia/isolation & purification/genetics
*Bacteroidaceae Infections/diagnosis/microbiology
High-Throughput Nucleotide Sequencing
China
Male
Metagenomics
Anti-Bacterial Agents/therapeutic use
Female
RNA, Ribosomal, 16S/genetics

@article {pmid40589860,
year = {2025},
author = {Nimnoi, P and Pongsilp, N},
title = {Insights into the metagenomic and metabolomic compositions of the bacterial communities in Thai traditional fermented foods as well as the relationships between food nutrition and food microbiomes.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19606},
pmid = {40589860},
issn = {2167-8359},
mesh = {*Fermented Foods/microbiology ; Thailand ; *Food Microbiology ; *Bacteria/genetics/classification/metabolism ; *Microbiota ; Metagenomics ; Metabolomics ; Fermentation ; },
abstract = {Five Thai traditional fermented foods, including khao-mak (sweet fermented sticky rice), pak-kard-dong (sour salt-fermented mustard greens), nor-mai-dong (sour salt-fermented bamboo sprouts), moo-som (sour salt-fermented pork), and pla-som (sour salt-fermented fish), were analyzed for their food nutrition and bacterial community structures. Sour salt-fermented bamboo sprouts possessed the highest unique amplicon sequence variables (ASVs), which were 3,476, as well as the highest bacterial diversity and richness, while in contrast, sweet fermented sticky rice possessed the lowest such indices. The phylum Firmicutes accounted for the largest proportions in both sour salt-fermented meats and sweet fermented sticky rice whereas the Proteobacteria occupied the largest proportions in both sour salt-fermented vegetables. The bacterial community structures of both sour salt-fermented meats were similar in terms of composition at class level, while the dominant genera compositions were totally different among all foods. Gene functions, enzymes, and metabolic pathways annotated from the bacterial communities in all foods were those involved in growth metabolisms, genetic information processing, environmental information processing, and cellular signaling. Sour salt-fermented bamboo sprouts had the highest numbers of unique annotated genes, enzymes, and metabolic pathways.},
}

*Fermented Foods/microbiology
Thailand
*Food Microbiology
*Bacteria/genetics/classification/metabolism
*Microbiota
Metagenomics
Metabolomics
Fermentation

@article {pmid40589579,
year = {2025},
author = {Zhang, YH and Hu, YQ and Zeng, YX and Hu, T and Han, W and Du, Y and Hu, Z and Meng, SS},
title = {Bacterial community composition and function in different habitats in Antarctic Fildes region revealed by high-throughput sequencing.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1524681},
pmid = {40589579},
issn = {1664-302X},
abstract = {INTRODUCTION: Pristine soil, ornithogenic soil, intertidal sediment, and marine sediment represent four of typical habitats in the Fildes region, maritime Antarctica. However, information on bacterial community composition and function in these Antarctic habitats remain limited.

METHODS: In this study, using a combination of 16S rRNA gene amplicon sequencing and shotgun metagenomic sequencing, 12 samples collected from various habitats in the region were analyzed.

RESULTS AND DISCUSSION: Bacterial community compositions in terrestrial habitats (i.e., pristine and ornithogenic soils) were found to be distinct (p < 0.01) from those in marine habitats (i.e., marine and intertidal sediments). Organic carbon (p < 0.01) and pH (p < 0.01) were two major environmental factors affecting the bacterial community composition in the diverse habitats. Proteobacteria (represented by Gamma-, Alpha-, and Betaproteobacteria; > 30%), Actinobacteria (represented by Actinobacteria; > 20%), and Bacteroidetes (represented by Flavobacteriia; > 10%) were dominant in bacteria related to carbon, nitrogen, and sulfur metabolism across all samples. Though most metabolic pathways were common in both terrestrial and marine habitats, terrestrial samples showed more diverse metabolic pathways than marine samples. However, among the top 15 abundant metabolic pathways, genes related to 11 metabolic pathways were relatively more abundant in marine habitats than in terrestrial habitats (p < 0.05). More abundant genes related to methane metabolism (e.g., pmoA), nitrification (e.g., amoA and hao), reductive citrate cycle pathway (e.g., frdA), repair of DNA damage (e.g., lexA and uvrB), salt and osmotic stress tolerance (e.g., betB, gltB, and treS), and aromatic hydrocarbon degradation (e.g., bcrC and bssA) were detected in pristine and/or ornithogenic soils, whereas genes related to sulfur metabolism (e.g., soxY, fccB, dsrAB, and sat), nitrogen fixation (e.g., nifH), acetyl-CoA metabolism (e.g., acsB, cdhD, and cdhE), carbohydrate degradation (e.g., amyA and chiA), and cold adaptation (e.g., cspA, deaD and recQ) were in higher abundance in marine and/or intertidal sediments. The influence of penguin feces on soil bacterial community composition and ecological function was observed in this study. The study findings will improve our understanding of bacterial community composition and function in various habitats in maritime Antarctica under the background of global climate change.},
}

@article {pmid40589577,
year = {2025},
author = {Dong, W and Lun, Y and Sun, J and Liu, B},
title = {Lactobacillus plantarum SAL delays aging-associated oxidative stress and gut microbiota dysbiosis in mice.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1607824},
pmid = {40589577},
issn = {1664-302X},
abstract = {INTRODUCTION: Lactobacillus plantarum SAL, isolated from multidrug-resistant patients' feces, exhibits superior in vitro probiotic traits including bile salt resistance, gastric acid tolerance, and potent antioxidant capacity. While Lactobacillus plantarum generally enhances gut microbiota structure/function, improving health and lifespan in model organisms, the in vivo effects, mechanisms, and potential anti-aging properties of the SAL strain remain unexplored. This study addresses this critical research gap.

METHODS: Twenty-four SPF KM male mice were divided into a control group (CON), model group (MOD), and a SAL strain intervention group (SAL). MOD and SAL groups received d-gal-induced aging models. SAL group was orally administered SAL strain suspension daily, while MOD and CON groups received saline for 10 weeks. After the intervention, serum and liver tissues were collected to detect aging biomarkers (β-galactosidase) and oxidative stress markers.Colon tissue histopathological examination was performed, and fresh fecal samples were subjected to metagenomic sequencing and analysis. Additionally, Spearman correlation analysis was conducted to evaluate the relationships between genuslevel differential gut microbiota and oxidative stress markers in serum and liver tissues.

RESULTS: Compared with the MOD group, the SAL group exhibited significantly reduced MDA levels in serum and liver tissues (all p < 0.05), elevated activities of SOD and T-AOC (all p < 0.05), and increased serum GSH-Px and CAT activities (all p < 0.05). Colon histology showed structural improvements, including increased crypt numbers, restored architecture, reduced submucosal space, and upregulated expression of ZO-1, Occludin, and Muc2 (all p < 0.05). Gut microbiota analysis revealed increased abundances of Firmicutes and Verrucomicrobia, decreased Bacteroidetes, and elevated Firmicutes/Bacteroidetes (F/B) ratio (p < 0.05). Differential genera Lactobacillus and Mucispirillum showed significant negative correlations with MDA levels (all p < 0.05), while Lactobacillus positively correlated with SOD, GSH-Px, and T-AOC activities.

DISCUSSION: The SAL strain intervention significantly improved redox homeostasis, restored intestinal barrier integrity, and reversed gut dysbiosis, highlighting its dual regulatory role in anti-aging mechanisms. These findings demonstrate the potential of L. plantarum SAL as an anti-aging probiotic and establish a theoretical framework for microbiota - targeted interventions to alleviate age-related pathologies.},
}

@article {pmid40588758,
year = {2025},
author = {Wang, Y and Lu, Z and Hu, J and Yuan, X and Chen, W and Lu, S and Pan, Y and Chen, Q and Hu, S and Zhang, W and Xiong, C},
title = {The silent spread: uncovering the diversity and evolution of poxviruses in ticks across Western China's host landscapes.},
journal = {Virology journal},
volume = {22},
number = {1},
pages = {214},
pmid = {40588758},
issn = {1743-422X},
support = {Grant No. GWVI-11.1-03//the Shanghai New Three-year Action Plan for Public Health/ ; },
abstract = {BACKGROUND: Poxviruses are a diverse group of pathogens with significant implications for both human and animal health. Ticks, as hematophagous arthropods, are capable of switching hosts during their life cycle. Although previous research has suggested the potential for parapoxviral transmission via ticks, the poxviral transmission dynamics remain poorly understood, particularly regarding the role of ticks as vectors.

METHODS: Tick samples were collected from western China, followed by metagenomic sequencing. The diversity of potential blood-feeding hosts and the prevalence of poxviruses were assessed using BWA. Poxviral sequences were assembled using MetaSPAdes and TGICL, and phylogenetic analysis was conducted to examine the origin of prevalent poxviruses and the unblasted poxviral fragments in ticks.

RESULTS: A total of 61 poxvirus species across 22 genera were identified, with 387 distinct poxviral sequences assembled. Of these, viral and host abundance were relatively higher in Tibet than in samples from Shaanxi and Gansu. Notably, unblasted gene fragments were identified within the assembled poxviral genomes, originating from a broad range of hosts, including mammals (e.g., rodents), fish, and arthropods. Phylogenetic analysis of the parapoxviruses revealed ongoing mutations, particularly in the Parapoxvirus orf, suggesting an increase in adaptability and potential pathogenicity. The results indicate that environmental factors such as altitude, host availability and host sensitivity may significantly shape viral diversity and transmission dynamics.

CONCLUSIONS: Ticks may contribute to the ecological circulation of poxviruses by switching hosts during their life cycle, potentially influencing viral genetic diversity. It underscores the risks of zoonotic spillover, particularly in regions with frequent human-animal interactions.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12985-025-02844-1.},
}

@article {pmid40588733,
year = {2025},
author = {Zhang, H and Fu, Y and Cao, C and Jiang, H and Tang, R and Dai, Z and Zhang, W},
title = {Identification and characterization of novel CRESS-DNA viruses in the human respiratory tract.},
journal = {Virology journal},
volume = {22},
number = {1},
pages = {211},
pmid = {40588733},
issn = {1743-422X},
support = {82341106//National Natural Science Foundation of China/ ; 2023YFD1801301 and 2022YFC2603801//National Key Research and Development Programs of China/ ; JLY2021151//Clinical Medicine Science and Technology Development Foundation of Jiangsu University/ ; },
mesh = {Humans ; Phylogeny ; *DNA Viruses/classification/genetics/isolation & purification ; Metagenomics ; Genome, Viral ; High-Throughput Nucleotide Sequencing ; *Respiratory System/virology ; Computational Biology ; *Nasopharynx/virology ; DNA, Viral/genetics ; Female ; Male ; Adult ; },
abstract = {CRESS-DNA viruses are small, circular, single-stranded DNA viruses that have been identified in diverse environments and hosts, including vertebrates, invertebrates, and environmental samples. However, their diversity and role in the human respiratory tract remain poorly understood. In this study, we employed viral metagenomics to analyze 140 nasopharyngeal swab samples from asymptomatic individuals. High-throughput sequencing and bioinformatics analyses were used to identify and characterize novel CRESS-DNA viruses. Phylogenetic relationships were inferred based on Rep protein sequences using maximum likelihood analysis. We identified and characterized eight novel CRESS-DNA viruses, which were classified into the families Endolinaviridae and Naryaviridae, with one potentially representing a novel viral family. These viruses exhibited typical circular genomic structures encoding Rep and Cap proteins, with conserved motifs associated with rolling circle replication. Phylogenetic analysis showed that some viruses were closely related to sequences from vertebrate hosts or environmental samples, suggesting a diverse ecological distribution. Our findings expand the known diversity of CRESS-DNA viruses in the human respiratory tract and highlight their potential ecological and evolutionary significance. Further studies are needed to explore their host specificity, replication mechanisms, and potential roles in human health and disease.},
}

Humans
Phylogeny
*DNA Viruses/classification/genetics/isolation & purification
Metagenomics
Genome, Viral
High-Throughput Nucleotide Sequencing
*Respiratory System/virology
Computational Biology
*Nasopharynx/virology
DNA, Viral/genetics
Female
Male
Adult

@article {pmid40588688,
year = {2025},
author = {Svetina, M and Kunej, T and Korošec, P and Rijavec, M},
title = {Towards a Multi-omics Understanding of Anaphylaxis: Insights into Pathogenesis and Biomarker Identification.},
journal = {Clinical reviews in allergy & immunology},
volume = {68},
number = {1},
pages = {61},
pmid = {40588688},
issn = {1559-0267},
support = {P3-0360//The Slovenian Research and Innovation Agency/ ; J3-50114//The Slovenian Research and Innovation Agency/ ; P3-0360//The Slovenian Research and Innovation Agency/ ; P3-0360//The Slovenian Research and Innovation Agency/ ; },
mesh = {Humans ; *Anaphylaxis/etiology/diagnosis/metabolism/genetics ; *Biomarkers/metabolism ; Metabolomics/methods ; Genomics/methods ; Proteomics ; Epigenomics ; Transcriptome ; Animals ; Genetic Predisposition to Disease ; Multiomics ; },
abstract = {Anaphylaxis is a severe, life-threatening hypersensitivity reaction that presents significant challenges in both clinical practice and scientific research. While individual omics studies have provided valuable insights into the genetic predisposition, immune dysregulation, and metabolic alterations associated with anaphylaxis, a comprehensive understanding of its full pathophysiology remains elusive. Multi-omics integration, which combines genomics, epigenomics, transcriptomics, proteomics, and metabolomics, has the potential to uncover novel mechanisms, biomarkers, and therapeutic targets. However, studies employing comprehensive multi-omics approaches in anaphylaxis are still limited. This review of 107 studies published between 2000 and 2024-including genomics (43), metagenomics (2), epigenomics (2), transcriptomics (20), proteomics (26), and metabolomics (14)-synthesizes findings from existing single-omics studies on human anaphylaxis, identifies key interconnections across omics layers, and underscores the critical need for large-scale, integrative research. Advancing this type of research is essential to advance our understanding of anaphylaxis, improve risk prediction, and enhance both diagnosis and treatment strategies.},
}

Humans
*Anaphylaxis/etiology/diagnosis/metabolism/genetics
*Biomarkers/metabolism
Metabolomics/methods
Genomics/methods
Proteomics
Epigenomics
Transcriptome
Animals
Genetic Predisposition to Disease
Multiomics

@article {pmid40588027,
year = {2025},
author = {Zhang, J and Yu, Z and Gao, Y and Li, Y and Hu, X and Gu, H and Tang, C and Liu, J and Liu, J and Zhang, S and Sima, X and Wang, G and Liu, P and Rui, Y and Franks, A and Liu, X and Jin, J},
title = {Warming-induced unstable microbial community metabolically lowers straw-carbon sequestration in paddy soils.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2025.06.075},
pmid = {40588027},
issn = {2090-1224},
abstract = {INTRODUCTION: Growing academic attention has been given to the crucial role of soil microorganisms in the net loss of soil organic carbon (SOC) under climate warming and the effectiveness of straw-C sequestration to replenish the SOC stock. However, the lack of empirical investigations in anaerobic paddy soils hinders accurate estimation of the global soil C-climate feedback and development of countermeasures.

OBJECTIVES: This study aimed to unravel the impact of warming on the complexity of the microbial community network of the paddy soil in response to warming, and correspondent changes of microbial metabolic functions relevant to the transformation of straw-C in SOC pools.

METHODS: We amended [13]C/[15]N-labeled rice straw into a long-term paddy soil and incubated under three temperature treatments (25, 35 and 45 °C) for 140 days to quantify straw-C sequestration in various SOC fractions, and further deployed metagenomic sequencing and solid-state [13]C NMR analyses to explore relevant biochemical mechanisms.

RESULTS: Warming (35 °C and 45 °C vs. 25 °C) enhanced SOC decomposition, but straw amendment did not replenish the loss C in mineral-associate C, a major SOC fraction of this soil, especially at 45 °C. Compared to 25 °C, temperature increases to 35 °C and 45 °C led to decreases in microbial diversity indices by an average of 19 % and 43 %, respectively. Warming also destabilized the microbial community network with less connectivity and keystone nodes in the paddy soil. Furthermore, warming decreased the abundances of organic C- and N-mineralization genes. Those genes encode enzymes involved in the degradation of both labile and recalcitrant organic compounds, including starch, cellulose, hemicellulose, chitin, pectin and aromatics, as well as in N mineralization, such as glutamate dehydrogenase and glutamate synthase. A subsequent deficiency in the synthesis of those enzymes appeared to suppress the transformation of straw-C and N, thereby reducing their sequestration efficiency in the mineral-associate C fraction in the paddy soil.

CONCLUSION: The detrimental impact of warming on the microbial metabolic profiles lowered the role of straw amendment in sustaining SOC stability under warming. An improved understanding of the warming-induced loss of microbial community diversity and correspondent weakening metabolic functions for the turnover of exogenous C should be accounted for global mitigation practices in paddy fields under climate warming.},
}

@article {pmid40587929,
year = {2025},
author = {Chen, J and Guo, Y and Lin, Y and Zhang, Y and Qian, Q and Zhang, X and Lin, P and Chen, C and Xie, S},
title = {Fate, mobility and pathogenicity of antibiotic resistome in a full-scale drinking water treatment plant: Highlighting the chlorination risks.},
journal = {Journal of environmental management},
volume = {390},
number = {},
pages = {126425},
doi = {10.1016/j.jenvman.2025.126425},
pmid = {40587929},
issn = {1095-8630},
abstract = {Drinking water treatment plants (DWTPs) serve as the last barrier in preventing the spread of antibiotic resistance genes (ARGs) into tap water, yet the distribution and dissemination mechanisms of ARGs in DWTPs remain unclear. In this study, the antibiotic resistome of a full-scale DWTP using Nansi Lake (an important node of the South-to-North Water Diversion Project's eastern route, China) as water source was investigated based on metagenomic analysis. The results showed that coagulation and chlorination were the two crucial processes increasing the relative abundance of ARGs in the DWTP, and the former predominantly enhanced that of sulfonamide RGs, while the latter increased that of bacitracin, aminoglycoside and multidrug RGs. ARG hosts and mobile genetic elements (MGEs) both played significant roles in ARG compositions. The persistence of Sphingorhabdus during the conventional treatment stages and the dissemination potential of plasmids accounted for the relative abundance of sulfonamide RGs, while the chlorine and multidrug resistance of Acinetobacter, Acidovorax, and Pseudomonas, along with the coexistence of various MGEs, suggested the persistence and transmission risk of ARGs after chlorination. Ozonation and activated carbon filtration could eliminate some human-pathogenic bacteria (HPB), but the chlorination process significantly increased the relative abundance of HPB. The multidrug-resistant HPB such as Acinetobacter calcoaceticus and Acinetobacter haemolyticus were the key targets for risk control in the DWTP. Our findings provide new insights into the fate, mobility, and pathogenicity of ARGs in a typical DWTP, offering beneficial guidance for decision-making in the risk control of ARGs in DWTPs.},
}

@article {pmid40586794,
year = {2025},
author = {Chadd, EF and Ergunay, K and Kumsa, B and Bourke, BP and Broomfield, BS and Long, LS and Linton, YM},
title = {Nanopore sequencing reveals a diversity of microorganisms in ticks from Ethiopia.},
journal = {Parasitology research},
volume = {124},
number = {7},
pages = {73},
pmid = {40586794},
issn = {1432-1955},
support = {FY23 Award # 23-101//Deployed Warfighter Protection (DWFP) Program/ ; Award # P0031_21_WR//Armed Forces Health Surveillance Division/ ; },
mesh = {Animals ; Ethiopia ; *Nanopore Sequencing ; Metagenomics ; *Bacteria/genetics/classification/isolation & purification ; *Ticks/microbiology ; Rickettsia/genetics/isolation & purification ; *Viruses/classification/genetics/isolation & purification ; Metagenome ; Phylogeny ; *Biodiversity ; },
abstract = {Ethiopia is home to a diverse group of ixodid ticks that are known to transmit disease to both animals and humans. Recent advances in metagenome sequencing show there is more microorganism diversity found in ticks than previously known. Compared to amplicon-based gene identification methods, agnostic metagenomic sequencing provides broader insights into the diversity of microorganisms in ticks, providing knowledge that will better enable public health measures in preventing the spread of zoonotic disease. In the present study, metagenomic sequencing was used to look at the microbial diversity of ticks collected from livestock in Ethiopia. This study identified six bacterial genera (Coxiella, Francisella, spotted-fever group (SFG) Rickettsia, Spiroplasma, Ehrlichia, and Borrelia), one genus of eukaryotic parasite (Babesia sp.), and one virus species (Parapoxvirus bovinestomatitis) from 154 tick pools representing 22 species of ticks among four genera (Amblyomma, Haemaphysalis, Hyalomma, and Rhipicephalus). We were able to differentiate between pathogenic and nonpathogenic microorganisms, highlighting concerns among traditional gene-targeted screening methods. Among all pooled samples, the predominant microorganisms included Coxiella-like endosymbionts (55.2%), SFG Rickettsia (38.3%), and nonpathogenic Francisella spp. (26.0%). Rickettsia africae was the predominant pathogenic agent detected, and phylogenetic analysis of two samples from A. gemma and A. variegatum confirmed the presence of R. africae. This study highlights the power of metagenomics applied to potential vectors of zoonotic disease, and it expands the knowledge on tick-pathogen associations in Ethiopia.},
}

Animals
Ethiopia
*Nanopore Sequencing
Metagenomics
*Bacteria/genetics/classification/isolation & purification
*Ticks/microbiology
Rickettsia/genetics/isolation & purification
*Viruses/classification/genetics/isolation & purification
Metagenome
Phylogeny
*Biodiversity

@article {pmid40586686,
year = {2025},
author = {Goens, M and Mouton, W and Oriol, G and Cheynet, V and Restier, L and Bal, A and Brengel-Pesce, K and Rozières, A and Viret, C and Nancey, S and Faure, M and Trouillet-Assant, S and Duclaux-Loras, R},
title = {Deep Characterisation of Circulating Torque Teno Virus DNA Load in Crohn's Disease Patients.},
journal = {Journal of medical virology},
volume = {97},
number = {7},
pages = {e70473},
doi = {10.1002/jmv.70473},
pmid = {40586686},
issn = {1096-9071},
support = {//This study was suported by an Appel d'offre jeune chercheur des Hospices Civils de Lyon and bioMérieux./ ; },
mesh = {Humans ; *Torque teno virus/genetics/isolation & purification ; *Crohn Disease/virology ; Male ; *DNA, Viral/blood/genetics ; *Viral Load ; Female ; Adult ; Middle Aged ; *DNA Virus Infections/virology ; Real-Time Polymerase Chain Reaction ; Young Adult ; Metagenomics ; Aged ; Recurrence ; },
abstract = {Torque teno virus (TTV) DNA load in plasma is suggested as a marker for immunosuppression post-transplantation. Crohn's disease (CD) arises from genetic susceptibility, environmental factors, and dysbiosis, causing immune responses. This study examines TTV DNA load in CD patients in remission and its correlation with relapse. Using quantitative real-time polymerase chain reaction (PCR) and metagenomic analysis, the dynamic of plasma TTV DNA load was analyzed from a cohort of CD patients (n = 39) over 1 year and compared with controls (n = 49). At inclusion, TTV DNA was significantly higher in CD patients compare to control (Median [IQR]: 3.27 [2.43-3.67] and 2.05 [1.28-2.80] Log copies/mL, p = 0.0004). Plasma TTV DNA load failed to predict disease relapse in CD patients. Augmented plasma TTV DNA levels in CD patients correlated with diminished circulating CD3 + T cells and especially CD4 + T cells. No preferential representation of TTV subspecies or Anelloviridae genera was detected in CD patients' plasma. This study revealed elevated TTV DNA levels in CD patients' plasma compared to healthy controls, underscoring the intriguing potential of TTV blood sampling as a biomarker in CD.},
}

Humans
*Torque teno virus/genetics/isolation & purification
*Crohn Disease/virology
Male
*DNA, Viral/blood/genetics
*Viral Load
Female
Adult
Middle Aged
*DNA Virus Infections/virology
Real-Time Polymerase Chain Reaction
Young Adult
Metagenomics
Aged
Recurrence

@article {pmid40586597,
year = {2025},
author = {Khatib, L and Song, SJ and Dilmore, AH and Sanders, JG and Brennan, C and Hernandez, AR and Myers, T and Oles, R and Farmer, S and Cowart, C and Birmingham, A and Diaz, EA and Nizet, O and Gilbert, K and Litwin, N and Das, P and Nowinski, B and Bryant, M and Tribelhorn, C and Sanders-Bodai, K and Chaumont, S and Knol, J and Roeselers, G and Laiola, M and Shetty, SA and Veiga, P and Tap, J and Derrien, M and Koutnikova, H and Cotillard, A and Lay, C and Tovar, AR and Torres, N and Arteaga, L and González, A and McDonald, D and Bartko, A and Knight, R},
title = {A three-country analysis of the gut microbiome indicates taxon associations with diet vary by taxon resolution and population.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0054425},
doi = {10.1128/msystems.00544-25},
pmid = {40586597},
issn = {2379-5077},
abstract = {UNLABELLED: Emerging research suggests that diet plays a vital role in shaping the composition and function of the gut microbiota. Although substantial efforts have been made to identify general patterns linking diet to the gut microbiome, much of this research has been concentrated on a small number of countries. Additionally, both diet and the gut microbiome have highly complex and individualized configurations, and there is growing evidence that tailoring diets to individual gut microbiota profiles may optimize the path toward improving or maintaining health and preventing disease. Using fecal metagenomic data from 1,177 individuals across three countries, we examine the relationship between diet and bacterial genera, focusing on Prevotella and Faecalibacterium, which have gained significant attention for their potential roles in human health and strong associations with dietary patterns. We find that these two genera in particular show significant associations with many aspects of diet but these associations vary in scale and direction, depending on the level of metagenomic resolution (i.e., genus level by reads and strain level by metagenome-assembled genomes) and the contextual population. These results highlight the growing importance of building metagenomic data sets that are standardized, comprehensive, and representative of diverse populations to increase our ability to tease apart the complex relationship between diet and the microbiome.

IMPORTANCE: An analysis of fecal microbiome data from individuals in the United States, United Kingdom, and Mexico shows that associations with dietary components vary both by country and by level of resolution (i.e., genus and strain). Our work sheds light on why there may be conflicting reports regarding microbial associations with diet, disease, and health.},
}

@article {pmid40586571,
year = {2025},
author = {Jiang, Y and An, Z and Li, W and Xia, S and Ding, Q and Zhong, J and Wang, H and Xu, Y and Chen, K and Shen, Y},
title = {Integrated multi-omics reveals the impact of ruminal keystone bacteria and microbial metabolites on average daily gain in Xuzhou cattle.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0076925},
doi = {10.1128/spectrum.00769-25},
pmid = {40586571},
issn = {2165-0497},
abstract = {UNLABELLED: The rumen microbiome plays a crucial role in determining the metabolic and digestive efficiency of livestock. Despite its crucial role, the impact of the rumen microbiome on average daily gain (ADG) in Xuzhou cattle remains underexplored. Xuzhou cattle is a well-known breed in China, renowned for rapid growth and superior meat quality. We selected 10 individuals from the Xuzhou cattle population and categorized Xuzhou cattle into High-ADG and Low-ADG groups and analyzed their rumen microbiota. Through comprehensive metagenomic and metabolomic analyses, we characterized the microbial diversity and functional composition of the rumen microbiome, uncovering distinct taxonomic and functional alterations associated with ADG. Thirteen kingdoms, 224 phyla, and over 16,000 species were identified, and principal coordinates analysis (PCoA) indicated significant microbial differentiation between the two groups on phylum, genus, and species levels (P < 0.05). Notably, Lentisphaerae, along with several other genera and species, presented a higher abundance in High, suggesting a potential connection with enhanced growth performance. Further functional annotation revealed that the High group displayed enriched carbohydrate and amino acid metabolism pathways, with a greater abundance of carbohydrate-active enzymes (CAZymes), particularly those involved in the degradation of complex carbohydrates. The Low-ADG group exhibited reduced metabolic activity in these pathways. Metabolomic analysis revealed 10 significantly altered metabolites, including gamma-glutamyltyrosine and N-acetylaspartic acid, which were upregulated in the High-ADG group, indicating their potential role in growth promotion. Spearman's rank correlation analysis further uncovered significant interactions between key microbiomes and metabolites, which correlated with ADG. Random forest analysis identified Victivallales and Lentisphaerae as key taxa, with gamma-glutamyltyrosine and Asp-Phe emerging as predictive biomarkers for ADG.

IMPORTANCE: This study identifies key microbiota (Victivallales and Lentisphaerae) and metabolites (gamma-glutamyltyrosine, Asp-Phe, N-acetylaspartic acid, Gly-Phe) that positively regulate average daily gain (ADG) in Xuzhou cattle through amino acid metabolism. This fundamental information is vital for the development of potential manipulation strategies to improve the daily gain level through precision feeding.},
}

@article {pmid40586543,
year = {2025},
author = {Begmatov, S and Beletsky, AV and Mardanov, AV and Lukina, AP and Glukhova, LB and Karnachuk, OV and Ravin, NV},
title = {Novel lineages of bacteria with reduced genomes from the gut of farm animals.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0029425},
doi = {10.1128/msphere.00294-25},
pmid = {40586543},
issn = {2379-5042},
abstract = {Genome reduction and associated metabolic deficiencies have been described in various lineages of parasitic and symbiotic microorganisms that obtain essential nutrients from their partners, and in some free-living microorganisms that inhabit stable environments. The animal gut is a relatively stable ecosystem, characterized by an abundance of organic substances and a high concentration of microorganisms, which provides favorable conditions for the survival of microorganisms with reduced genomes. Metagenomic analysis of 49 samples of feces of farm animals (cows, sheep, yaks, and horses) revealed uncultured lineages of bacteria with reduced genomes (<1 Mbp): family UBA1242 (Christensenellales, Firmicutes), order Rs-D84 (Alphaproteobacteria), and family UBA9783 (Opitutales, Verrucomicrobiota), defined in genome-taxonomy database. Analysis of the genomes showed that these bacteria lacked pathways for the biosynthesis of amino acids, nucleotides, lipids, and many other essential metabolites. The UBA9783 genomes encoded a near-complete Embden-Meyerhof glycolytic pathway and the non-oxidative phase of the pentose phosphate pathway, while in UBA1242 and Rs-D84, these pathways are incomplete. All bacteria are limited to fermentative metabolism and lack aerobic and anaerobic respiratory pathways. All UBA9783 and some Rs-D84 genomes encoded F0F1-type ATP synthase and pyrophosphate-energized proton pump; they also can import and utilize peptides and some amino acids. While UBA9783 bacteria could thrive as specialized free-living organisms in the organic-rich gut environment, the UBA1242 and Rs-D84 lineages appear to have adopted the lifestyle of an obligate symbiont/parasite, obtaining metabolites from other cells.IMPORTANCEThe microbiota of the animal gastrointestinal tracts is a complex community of microorganisms which interact in a synergistic or antagonistic relationship and play key nutritional and metabolic roles. However, despite its importance, the gut microbiota of farm animals, especially its uncultured majority, remains largely unexplored. We performed a metagenomic analysis of the gut microbiome of farm animals and characterized three uncultured lineages of bacteria with reduced genomes (<1 Mbp) from the phyla Firmicutes, Proteobacteria, and Verrucomicrobiota. These bacteria were predicted to possess key metabolic deficiencies such as the inability to synthesize essential cell metabolites, suggesting their adaptation to the lifestyle of a symbiont/parasite, or a scavenger obtaining nutrients from the organic-rich gut environment. This study shows that genome reduction with metabolic specialization and adaptation to a partner-dependent lifestyle occurred through convergent evolution in several phylogenetically distant lineages of gut microbiota.},
}

@article {pmid40586542,
year = {2025},
author = {Bruno, JS and Heidrich, V and Restini, FCF and Alves, TMMT and Miranda-Silva, W and Knebel, FH and Cóser, EM and Inoue, LT and Asprino, PF and Camargo, AA and Fregnani, ER},
title = {Dental biofilm serves as an ecological reservoir of acidogenic pathobionts in head and neck cancer patients with radiotherapy-related caries.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0025725},
doi = {10.1128/msphere.00257-25},
pmid = {40586542},
issn = {2379-5042},
abstract = {UNLABELLED: Radiotherapy-related caries (RRC) is an aggressive and debilitating oral toxicity that affects half of the patients who undergo radiotherapy for head and neck cancer. However, the etiology of RRC is not fully established, and there are no clinically validated methods for preventing it. To gain a better understanding of the risk factors and the microbiome's role in causing RRC, we compared clinicopathological characteristics, oncological treatment regimens, oral health condition, and the oral microbiota at three different oral sites of radiotherapy-treated patients with (RRC+) and without radiotherapy-related caries (RRC-). We observed no significant differences between these groups in the clinicopathological characteristics and treatment regimens. However, RRC+ patients were older and had poorer oral health conditions at the start of the radiotherapy treatment, with a lower number of teeth and a higher proportion of rehabilitated teeth. RRC+ patients had lower microbiota diversity and the dental biofilm of RRC+ patients displayed striking alterations in microbiome composition compared to RRC- patients, including enrichment of acidogenic species and altered metabolic potential, with a higher abundance of genes linked to energy-related pathways associated with the synthesis of amino acids and sugars. We also compared the microbiota of RRC+ tissue with conventional caries tissue, revealing lower bacterial diversity and enrichment of Lactobacillaceae members in RRC+. The insights into the irradiated oral microbiota enhance the understanding of RRC etiology and highlight the potential for microbial-targeted therapies in its prevention and treatment.

IMPORTANCE: This study focuses on a dedicated collection of diverse oral sites to comprehensively investigate microbial differences between patients who develop RRC and those who do not. RRC is a severe oral disease that profoundly impacts on the oral health and overall quality of life of cancer survivors. Leveraging shotgun metagenomics, we characterize the unique microbial variations in in vivo irradiated dental biofilms, unveiling novel insights into the microbial ecology of radiotherapy-treated patients. Furthermore, this research integrates extensive data on oral health and oncological profiles, providing a comprehensive understanding of the intricate relationship between oral microbial communities and the outcomes of radiotherapy-induced toxicity.},
}

@article {pmid40586540,
year = {2025},
author = {Bulka, O and Edwards, EA},
title = {Complete metagenome-assembled genome sequence of Solidesulfovibrio sp. DCME from a dichloromethane dechlorinating microbial community.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0051525},
doi = {10.1128/mra.00515-25},
pmid = {40586540},
issn = {2576-098X},
abstract = {Here, we announce the closed genome of Solidesulfovibrio sp. DCME, assembled from metagenomic sequencing of an anaerobic dichloromethane mineralizing enrichment culture. The Solidesulfovibrio genus is known to cycle hydrogen, a key process for facilitating dichloromethane mineralization, which nominates this microbe as an important player in its microbial community.},
}

@article {pmid40586419,
year = {2025},
author = {Dason, MS and Corà, D and Re, A},
title = {Sequence modeling tools to decode the biosynthetic diversity of the human microbiome.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0033325},
doi = {10.1128/msystems.00333-25},
pmid = {40586419},
issn = {2379-5077},
abstract = {Understanding the biosynthetic potential of the human microbiome remains a significant challenge with far-reaching scientific and translational implications. Analyses of human-associated (meta)genomic sequencing data undeniably show that the biosynthetic diversity encoded in these genomes is largely underexplored. A crucial step in studying specialized metabolites involves the sequence-based identification of genes encoding biosynthetic pathways, typically organized into biosynthetic gene clusters (BGCs). In this review, we provide a concise and updated overview of the widening range of computational approaches that have effectively addressed the sequence-based identification of BGCs across both isolated genomes and complex microbial communities. These advancements are set to deepen our understanding of the biosynthetic potential and diversity of microorganisms residing in different human body sites.},
}

@article {pmid40586263,
year = {2025},
author = {Bonham, KS and Margolis, ET and Fahur Bottino, G and Sobrino, AC and Patel, F and McCann, S and Zieff, MR and Miles, M and Herr, D and Davel, L and Bosco, C and , and Huttenhower, C and Pini, N and Alexander, DC and Jones, DK and Williams, SCR and Amso, D and Gladstone, M and Fifer, WP and Donald, KA and Gabard-Durnam, LJ and Klepac-Ceraj, V},
title = {Codevelopment of gut microbial metabolism and visual neural circuitry over human infancy.},
journal = {mBio},
volume = {},
number = {},
pages = {e0083525},
doi = {10.1128/mbio.00835-25},
pmid = {40586263},
issn = {2150-7511},
abstract = {Infancy is a time of elevated neuroplasticity supporting rapid brain and sensory development. The gut microbiome, also undergoing extensive developmental changes in early life, may influence brain development through the metabolism of neuroactive compounds. Here, we leverage longitudinal data from 194 South African infants across the first 18 months of life to show that microbial genes encoding enzymes that metabolize molecules playing a key role in modulating early neuroplasticity are associated with visual cortical neurodevelopment, measured by the Visual-Evoked Potential (VEP). Neuroactive compounds included neurotransmitters GABA and glutamate, the amino acid tryptophan, and short-chain fatty acids involved in myelination, including acetate and butyrate. Microbial gene sets around 4 months of age were strongly associated with the VEP from around 9-14 months of age and showed more associations than concurrently measured gene sets, suggesting that microbial metabolism in early life may affect subsequent neural plasticity and development.IMPORTANCEOver the past decade, extensive research has revealed strong links between the gut microbiome and the brain, at least in adults or those with neuropsychiatric disorders. This study explores how these associations emerge in early development using a longitudinal sample of 194 infants with repeated microbiome metabolism and electroencephalography (EEG) measures during the critical early period of visual cortex neuroplasticity. We examined microbial genes encoding enzymes for neuroactive compounds (e.g., GABA, glutamate, tryptophan, and short-chain fatty acids) and their association with the visual-evoked potential (VEP). Genes from 4-month stool samples strongly correlated with VEP features between 9 and 14 months, suggesting that early microbial metabolism influences later visual neurodevelopment. These prospective associations were more numerous than the concurrent ones. Our findings suggest that early gut microbiome metabolic potential plays a crucial role in shaping neural plasticity and visual neurodevelopment.},
}

@article {pmid40585302,
year = {2025},
author = {Louca, S},
title = {Machine learning models for delineating marine microbial taxa.},
journal = {NAR genomics and bioinformatics},
volume = {7},
number = {2},
pages = {lqaf090},
pmid = {40585302},
issn = {2631-9268},
mesh = {*Machine Learning ; *Archaea/genetics/classification ; *Bacteria/genetics/classification ; Metagenome ; Phylogeny ; Genome, Bacterial ; *Aquatic Organisms/genetics/classification ; },
abstract = {The relationship between gene content differences and microbial taxonomic divergence remains poorly understood, and algorithms for delineating novel microbial taxa above genus level based on multiple genome similarity metrics are lacking. Addressing these gaps is important for macroevolutionary theory, biodiversity assessments, and discovery of novel taxa in metagenomes. Here, I develop machine learning classifier models, based on multiple genome similarity metrics, to determine whether any two marine bacterial and archaeal (prokaryotic) metagenome-assembled genomes (MAGs) belong to the same taxon, from the genus up to the phylum levels. Metrics include average amino acid and nucleotide identities, and fractions of shared genes within various categories, applied to 14 390 previously published non-redundant MAGs. At all taxonomic levels, the balanced accuracy (average of the true-positive and true-negative rate) of classifiers exceeded 92%, suggesting that simple genome similarity metrics serve as good taxon differentiators. Predictor selection and sensitivity analyses revealed gene categories, e.g. those involved in metabolism of cofactors and vitamins, particularly correlated to taxon divergence. Predicted taxon delineations were further used to de novo enumerate marine prokaryotic taxa. Statistical analyses of those enumerations suggest that over half of extant marine prokaryotic phyla, classes, and orders have already been recovered by genome-resolved metagenomic surveys.},
}

*Machine Learning
*Archaea/genetics/classification
*Bacteria/genetics/classification
Metagenome
Phylogeny
Genome, Bacterial
*Aquatic Organisms/genetics/classification

@article {pmid40584717,
year = {2025},
author = {Shao, J and Xu, X and Xie, X and Fan, Y and Zhang, D and Tang, W},
title = {A case report of septic shock caused by opportunistic infections associated with anti-interferon-γ autoantibody positivity: diagnostic and therapeutic challenges.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1592152},
pmid = {40584717},
issn = {2296-858X},
abstract = {BACKGROUND: Since 2004, there has been an increasing number of reports on severe, persistent, or recurrent Salmonella infections in adults with adult immunodeficiency associated with anti-gamma interferon antibody positivity (AIGA). AIGA patients experience rapid disease progression upon infection with opportunistic pathogens, high mortality rates, and strong disease latency, posing significant challenges for diagnosis and treatment. This article discusses the diagnosis and treatment strategies for AIGA with opportunistic pathogen infection through the diagnosis and treatment process of a 61-year-old male patient.

METHODS: The patient presented with diarrhea and fever for 2 weeks and was diagnosed with non-typhoidal Salmonella infection at an external hospital. The condition progressed to shock and the patient was transferred to our EICU. After admission, the pathogens were confirmed through chest CT, blood culture, blood metagenomic next-generation sequencing (mNGS), and bronchoalveolar lavage fluid (BALF) mNGS, and cell immune function screening and anti-gamma interferon antibody testing were completed. The anti-infective treatment regimen was adjusted based on the test results, and immunoglobulin therapy was administered.

RESULTS: The patient's blood culture was positive for non-typhoidal Salmonella, and blood mNGS confirmed non-typhoidal Salmonella and Legionella pneumophila; BALF mNGS showed Enterococcus faecium, Legionella pneumophila, Candida tropicalis, Candida glabrata, HSV1, and CMV mixed infection. Immune function screening indicated a significant decrease in CD4 + T cells (303 cells/μL) and a significant increase in anti-gamma interferon antibody (163.78 ng/mL), confirming the diagnosis of AIGA. After treatment with meropenem, linezolid, doxycycline, ganciclovir, and caspofungin combined with anti-infective and immunoglobulin therapy, the patient's condition significantly improved and was discharged.

CONCLUSION: AIGA patients experience rapid disease progression after infection with opportunistic pathogens. Early identification of anti-gamma interferon antibody and mixed infection pathogens is crucial for treatment.},
}

@article {pmid40584560,
year = {2025},
author = {Billard, H and Fuster, M and Enault, F and Carrias, JF and Fargette, L and Carrouée, M and Desmares, P and Delmont, TO and Nogaret, P and Bigeard, E and Tanguy, G and Baudoux, AC and Christaki, U and Sime-Ngando, T and Colombet, J},
title = {Unexpected diversity and ecological significance of uncultivable large virus-like particles in aquatic environments.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf098},
pmid = {40584560},
issn = {2730-6151},
abstract = {The discovery of jumbo phages and giant viruses of microeukaryotes has transformed our perception of the virosphere. Metagenomic and metatranscriptomic data further highlight their diversity and ecological impact. Nevertheless, sequence-based approaches fail to take into account the morphological diversity of non-cultivated viruses, resulting in our fragmented understanding of their nature and role in the environment. Here, we combined flow cytometry and electron microscopy to uncover both previously unsuspected morphological diversity and significant abundances of large virus-like particles in aquatic environments. We discovered new viral morphotypes, all likely to be associated with microeukaryotes. We also obtained insights into the multi-year dynamics of the abundances of both giant microeukaryotic virus-like particles and jumbo phage-like particles. This work deepens our understanding of large virus and reveals their key role as regulators of microbial communities.},
}

@article {pmid40584555,
year = {2025},
author = {Li, W and Fan, Q and Yang, Y and Xiao, X and Li, J and Zhang, Y},
title = {Benchmarking and optimizing qualitative and quantitative pipelines in environmental metatranscriptomics using mixture controlling experiments.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf090},
pmid = {40584555},
issn = {2730-6151},
abstract = {Metatranscriptomic analysis is increasingly performed in environments to provide dynamic gene expression information on ecosystems, responding to their changing conditions. Many computational methods have undergone remarkable development in the past years, but a comprehensive benchmark study is still lacking. There are concerns regarding the accuracies of the qualitative and quantitative profilers obtained from metatranscriptomic analysis, especially for the microbiota in extreme environments, most of them are unculturable and lack well-annotated reference genomes. Here, we presented a benchmark experiment that included 10 single-species and their cell or RNA-admixtures with the predefined species compositions and varying evenness, simulating the low annotation rate and high heterogeneity. In total, 1 metagenome sample and 24 metatranscriptome were sequenced for the comparisons of 36 combination of analysis methods for tasks ranging from sample preparation, quality control, rRNA removal, alignment strategies, taxonomic profiling, and transcript quantification. For each part of the workflow mentioned above, corresponding metrics have been established to serve as standards for assessment and comparison. Evaluation revealed the performances and proposed an optimized pipeline named MT-Enviro (MetaTranscriptomic analysis for ENVIROnmental microbiome). Our data and analysis provide a comprehensive framework for benchmarking computational methods with metatranscriptomic analysis. MT-Enviro is implemented in Nextflow and is freely available from https://github.com/Li-Lab-SJTU/MT-Enviro.},
}

@article {pmid40584035,
year = {2025},
author = {Li, X and Li, D and Wang, C and Li, Q and Nie, Y and Zhang, L and Xu, J and Ma, Y},
title = {Metagenomic insights into the effects of Chive seed flavonoid on intestinal fermentation, morphology, and microbiota composition in sheep.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1590400},
pmid = {40584035},
issn = {1664-302X},
abstract = {Chive seed flavonoid (CSF) exhibits antioxidant, digestive, and immunomodulatory properties, yet their effects on ruminant intestinal development and microbial ecosystems remain underexplored. This study systematically evaluated CSF supplementation (0.25% of concentrate) on intestinal morphology, volatile fatty acids (VFAs) dynamics, and microbiota composition in 16 weaned Hu lambs (3 months; 19.57 ± 1.56 kg initial weight) using histomorphometry, VFA quantification, and full-length 16S rRNA sequencing. Animals were randomly allocated to a control (basal diet) or CSF-supplemented group (T), following a 7-day adaptation and 90-day experimental protocol. Key findings revealed: (1) The T group demonstrated increased jejunal and ileal villus length (p < 0.05), elevated villus height-to-crypt depth ratio (V/C; p < 0.05), thickened muscular layers (p < 0.05), and reduced crypt depth (p < 0.05). (2) CSF supplementation significantly elevated acetate, propionate, butyrate, and total VFAs (p < 0.05) in ileum, cecum, colon, and rectum, with notable jejunal propionate and total VFAs increases (p < 0.05). (3) Upregulated expression of ileal and cecal genes (IGF1, CD81, CTNNBL1, SLC39A8) linked to tissue morphogenesis and VFAs absorption was observed in the T group (p < 0.01). (4) Full-length 16S analysis demonstrated CSF-enhanced microbial diversity and selective enrichment of Cyanobacteriota, Bacillus, Acetobacterium, and Streptomyces [Linear Discriminant Analysis Effect Size (LEfSe) analysis]. Regional microbial shifts included Bacteroidota proliferation in the small intestine and rectum, Actinomycetota dominance in duodenum/cecum/colon, and ileal enrichment of Bacillota, Clostridium, and Streptomyces. KEGG pathway analysis confirmed CSF-driven enhancements in carbohydrate/energy metabolism, immune regulation, and intestinal barrier pathways (p < 0.05). In conclusion, dietary supplementation with 0.25% CSF improved intestinal morphology, increased the production of VFAs, and optimized microbial composition, thereby promoting intestinal health in sheep. This study provides a theoretical basis for the application of CSF in promoting healthy production in sheep.},
}

@article {pmid40584012,
year = {2025},
author = {Li, Y and Zhu, J and Li, Q and Hong, H and Li, T and Jia, H and Hou, B and Lu, H and Li, Y and Xie, J and Wang, F and Ye, H and Liu, K and Lu, A and Zhao, J},
title = {Non-linear frequency-doubling up-conversion in sulfide minerals enables deep-sea oxygenic photosynthesis.},
journal = {National science review},
volume = {12},
number = {6},
pages = {nwaf219},
pmid = {40584012},
issn = {2053-714X},
abstract = {Visible light emission exceeding purely thermal radiation has been imaged at deep-sea hydrothermal vents, yet the underlying mechanisms remain unexplained. Here, we show that visible light can be produced from geothermal infrared radiation via nonlinear frequency-doubling up-conversion in sulfide minerals that are abundant in hydrothermal vents. Chalcopyrite exhibits significant second harmonic generation, which is further amplified under high pressure, yielding a 400-700 nm photon flux three orders of magnitude greater than blackbody emission. When exposed to 1064 nm of irradiation, chalcopyrite induces fluorescence responses in the cyanobacterium Synechococcus sp. PCC 7002 at 656 and 685 nm, suggesting that the up-converted 532 nm light is absorbed by phycobilisomes and transferred to photosystem II. Metagenomic analysis reveals a strong correlation between cyanobacteria and high-temperature, chalcopyrite-rich vents. Similar up-conversion processes have also been observed in other sulfide minerals, emitting wavelengths covering the entire visible spectrum. These findings unveil a novel mineral-mediated photonic mechanism that generates biologically relevant visible light at hydrothermal vents, which can be harnessed by oxygenic photosynthetic cyanobacteria in Earth's deep biosphere and possibly beyond.},
}

@article {pmid40583454,
year = {2025},
author = {Aldrian, D and Pollio, A and Mayerhofer, C and Diederen, K and Jacobs, JP and Pai, N and Szamosi, JC and Hart, L and Turner, D and Del Chierico, F and Cardile, S and Grigoryan, Z and Chen, LA and Hurych, J and Cinek, O and Taddei, CR and Schwerd, T and Wine, E and Griffiths, AM and Müller, T and Vogel, GF},
title = {Fecal Microbial Community Profiling Allows Discrimination of Phenweotype and Treatment Response in Pediatric Crohn's Disease and Ulcerative Colitis-An International Meta-Analysis.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izaf135},
pmid = {40583454},
issn = {1536-4844},
abstract = {BACKGROUND AND AIMS: The pathophysiology of pediatric inflammatory bowel disease (PIBD), encompassing Crohn's disease (CD) and ulcerative colitis (UC), is not entirely understood. Dysregulation of the intestinal microbiome is recognized as both a disease-driving and a potential therapeutic target. This study aimed to systematically analyze gut microbiome compositions and its applicability as a biomarker for disease progress and treatment response.

METHODS: Bibliographic and nucleotide databases were searched. Raw 16S-rRNA sequencing reads were subjected to a uniform downstream dada2/phyloseq pipeline to extract taxonomy, community structure, and abundance information. Patient metadata were extracted from publications, and study authors were contacted for further details if required.

RESULTS: Twenty-six studies comprising 3956 stool samples (CD 41%, UC 36%, 23% healthy) were included in the analyses. Median age of individuals was 12 (interquartile range 4). Sex distribution was comparable. Alpha diversity was reduced between the healthy and both UC and CD treatment-naïve groups (P < .001) and further reduced with increasing clinical disease activity. Beta diversity revealed altered community structure in treatment-naïve children with PIBD (P < .001). This alteration remained in patients in clinical remission (P < .001). Machine learning models discriminated between treatment-naïve patients with CD or UC with an area under the receiver operating characteristics curve (AUROC) of 98%. Microbial communities differed between patient responders versus nonresponders to treatment (P < .001). Further, microbial community profiling distinguished treatment response (eg, steroid, nutrition, or TNFα) with AUROCs of 82%-90%.

CONCLUSIONS: Gut microbial community structure is substantially altered in active and inactive PIBD and may be utilized as a biomarker for differentiating PIBD subtype and predicting treatment response.},
}

@article {pmid40582827,
year = {2025},
author = {Han, RQ and Shi, Y and Song, YC and Song, RX and Xue, NN},
title = {[Distribution Characteristics of Soil Resistance Genes in Cotton Fields with Different Continuous Cropping Years].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {46},
number = {6},
pages = {3934-3941},
doi = {10.13227/j.hjkx.202405127},
pmid = {40582827},
issn = {0250-3301},
mesh = {*Gossypium/growth & development/genetics ; Soil/chemistry ; *Soil Microbiology ; *Drug Resistance, Microbial/genetics ; Agriculture/methods ; China ; },
abstract = {With the continuous development of intensive agriculture， the crop rotation index has increased. Continuous planting of a single type of crop introduces specific environmental selective pressures that may lead to changes in the soil resistome. Therefore， investigating the composition and characteristics of antibiotic resistance genes （ARGs） and metal resistance genes （MRGs） in soil with different degrees of continuous cropping is of great significance for promoting the green development of agriculture. In this study， we employed metagenomics techniques to examine the profile of ARGs in cotton field soils across different levels of continuous cropping years in the Xinjiang Arid Region. Our findings revealed that the types and abundance of ARGs and MRGs in cotton field soils differed with the length of continuous cropping periods. A total of 1 181 ARGs and 506 MRGs were found in the present study. Continuous cropping led to the emergence of some new ARGs and MRGs. Network and Procrustes analysis indicated a significant correlation between the composition of ARGs and MRGs. Additionally， the actP gene was the key node connecting ARGs and MRGs. Mantel tests demonstrated that ARGs and MRGs were not correlated with soil pH， alkali-hydrolyzable nitrogen， total nitrogen， or total potassium levels. However， a strong positive correlation was observed between these genes and soil electrical conductivity （Mantels' P=0.001） and a significant but weak correlation with the continuous cropping years （Mantels' P < 0.05）.},
}

*Gossypium/growth & development/genetics
Soil/chemistry
*Soil Microbiology
*Drug Resistance, Microbial/genetics
Agriculture/methods
China

@article {pmid40582607,
year = {2025},
author = {Páez-Triana, L and Luna, N and Cruz-Saavedra, L and Ramírez, AL and Medina, JE and Castañeda, S and Gómez, M and Garcia-Corredor, DJ and Medellín, MOP and Patiño, LH and Muñoz, M and Ramirez, JD},
title = {Characterizing the diversity of Rhipicephalus sanguineus sensu lato (s.l) virome in Colombia.},
journal = {Acta tropica},
volume = {},
number = {},
pages = {107715},
doi = {10.1016/j.actatropica.2025.107715},
pmid = {40582607},
issn = {1873-6254},
abstract = {Ticks within the species complex Rhipicephalus sanguineus sensu lato are carriers for various pathogens worldwide. Among them are some RNA viruses, who have gained increased attention due to their potential for interaction between pathogenic and non-pathogenic organism, shifts in tick distribution, and the emergence of diseases transmitted by ticks to human populations. Our study aimed to investigate the RNA virus composition in R. sanguineus s.l. (also known as R. linnaei) ticks collected from the Santander and Casanare regions in eastern Colombia. We employed Oxford Nanopore sequencing technology coupled with viral enrichment procedures. Thirty-nine adult ticks, removed from dogs, were sequenced with Oxford Nanopore sequencing. These reads underwent two distinct analyses: one focused on sequencing reads utilizing Centrifuge/BLAST for direct assignment, and one involved assembly of viral metagenomic assembled genomes (vMAGs) using the Genome Detective Tool program. Our investigation showed the presence of six distinct viruses within the tick virome: Trinbago virus, Mivirus sp., Bole tick virus 4, Brown dog tick phlebovirus 2, Totiviridae sp., Ixodes scapularis totilike virus, and Brown dog tick phlebovirus 1. Notably, we successfully assembled the genomes for the latter two species, enabling phylogenetic and comparative analyses with genomes from various global regions. Only the category of sex yield significant differences in alpha diversity. We described viruses with potential pathogenicity but also with endosymbiotic potential. The latter group holds promise for developing biotechnological tools to aid future tick vector control strategies. Furthermore, our research offered valuable insights into the predominant viruses found in R. sanguineus s.l. ticks in two previously unexplored regions within Colombia.},
}

@article {pmid40582470,
year = {2025},
author = {Bolloré, K and Tinto, B and Charriat, F and Pisoni, A and Exbrayat, A and Gutierrez, S and Simonin, Y and Tuaillon, E},
title = {Investigation of the viral causes of febrile jaundice in Burkina Faso through metagenomic sequencing.},
journal = {The Journal of infection},
volume = {},
number = {},
pages = {106541},
doi = {10.1016/j.jinf.2025.106541},
pmid = {40582470},
issn = {1532-2742},
abstract = {OBJECTIVES: Yellow fever virus (YFV) is a key concern in West Africa, often associated with febrile jaundice. However, many patients with this syndrome test negative for YFV, raising questions about other potential viral etiologies. This study aimed to characterize the viral landscape in YFV-negative febrile jaundice cases using metagenomic next-generation sequencing (mNGS).

METHODS: Serum samples were collected in 2019 from 152 febrile jaundice patients in Burkina Faso who tested negative for both YFV and malaria. A random subset of 100 samples was analyzed by mNGS to identify viral sequences. Bioinformatic pipelines were applied to classify viral reads, and findings were validated by quantitative PCR (qPCR) and serological assays. Additional specimens from the same cohort, as well as from febrile patients without jaundice, were tested to assess the prevalence of the key viral findings.

RESULTS: mNGS revealed 58 viral species, including four human pathogens: HIV-1 (n=1), YFV (n=1), hepatitis A virus (HAV, n=16), and hepatitis B virus (HBV, n=18). qPCR confirmed 75% of HAV and 67% of HBV cases. Serological testing on additional samples confirmed comparable HAV and HBV prevalence among jaundiced patients, but significantly lower rates among those without jaundice.

CONCLUSION: mNGS uncovered undiagnosed viral infections, demonstrating its value for differential diagnosis and surveillance in resource-limited settings.},
}

@article {pmid40582136,
year = {2025},
author = {Song, L and Hu, C and Zhang, X and Liu, Y and Song, G and Wu, J and Wang, Z and Sun, M},
title = {Effects of feeding on microbial community structure and pathogen abundance in marine aquaculture ponds.},
journal = {Marine environmental research},
volume = {210},
number = {},
pages = {107319},
doi = {10.1016/j.marenvres.2025.107319},
pmid = {40582136},
issn = {1879-0291},
abstract = {Microbial communities in aquaculture ponds play a vital role in regulating water quality, driving nutrient cycling, and maintaining ecological balance. In 2023, we conducted a study to evaluate how feeding affects microbial communities by comparing the microbial composition and water quality in both fed and unfed aquaculture ponds. Metagenomic sequencing indicated that feeding significantly elevated the relative abundance of bacteria within the microbial community. Ecological similarity analysis showed that bacterial community in the ponds predominantly originated from internal pond sources, rather than from adjacent coastal waters. Furthermore, the relative abundance of pathogenic bacteria was significantly higher in fed ponds, with Vibrio parahaemolyticus levels reaching 1.6 times those in unfed ponds. In addition, water quality assessments further showed that feeding elevated nutrient concentrations, leading to eutrophication. Analyses of redundancy and correlation showed a notable positive link (p < 0.05) between the levels of pathogenic bacteria and the concentration of organic nutrients. These results suggest that excessive feeding contributes to eutrophication, which promotes the growth of bacteria, including pathogenic strains, thereby increasing the risk of disease outbreaks in aquaculture systems.},
}

@article {pmid40581627,
year = {2025},
author = {Nørgaard, JC and Marandi, RZ and Ilett, EE and Gulay, A and Paredes, R and Lundgren, JD and Jørgensen, M and Sengeløv, H},
title = {The gut microbiome and its resistome as predictors of clinical infections and phenotypic antibiotic resistance in hematopoietic stem cell transplant recipients.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiaf330},
pmid = {40581627},
issn = {1537-6613},
abstract = {A relationship between the gut microbiome composition, its resistome, and risk of clinical infections may exist and was explored here using 663 shotgun-sequenced fecal samples from 276 stem cell transplant patients. E. faecium, E. coli, and E. faecalis were the three most prevalent causes of clinical infection, with vancomycin resistance in E. faecium as the most common antibiotic resistance feature. Associations between the gut microbiome, resistome, and clinical infections were tested, with significant findings (FDR<0.05) evaluated in multivariable analysis. A 10% increase in gut abundance of E. faecium was positively associated with subsequent clinical infection with E. faecium (OR=1.14, p=0.02). Additionally, a 1% increase in vanA gene abundance was positively associated with vancomycin-resistant E. faecium infection (OR=1.27, p<0.01). Here we used metagenomics to enhance the understanding of infectious sources and to identify patients at risk of clinical infection with antibiotic-resistant bacterial strains.},
}

@article {pmid40581162,
year = {2025},
author = {Haider, SA and Jamal, Z and Ammar, M and Hakim, R and Afrough, B and Kreku, A and Inamdar, L and Salman, M and Umair, M},
title = {Genomic characterization of the Coxsackievirus A24 variant in the Acute Hemorrhagic Conjunctivitis outbreak (2023) in Islamabad, Pakistan through metagenomic next generation sequencing.},
journal = {Journal of virological methods},
volume = {338},
number = {},
pages = {115213},
doi = {10.1016/j.jviromet.2025.115213},
pmid = {40581162},
issn = {1879-0984},
abstract = {Pakistan experienced a significant outbreak of Acute Hemorrhagic Conjunctivitis (AHC) in 2023. To identify the cause, in the absence of targeted diagnostic tests, the National Institute of Health, Islamabad, studied 15 conjunctivitis patients from Islamabad in September 2023. Metagenomic Next Generation Sequencing (mNGS) was performed on 10 samples collected within 48 h of symptom onset. The human Coxsackievirus A24 variant (CV-A24v), genotype IV, was detected in three samples. Phylogenetic analysis showed ∼99 % similarity with recent strains from China and 94 % similarity with the 2015 France outbreak. Mutation analysis revealed mostly non-synonymous substitutions, particularly in the VP1 region (n = 14), and differences in 2 C and 3D regions of nonstructural proteins. Comparison with 2005 Pakistan outbreak sequences showed divergence in the VP1 region, with two distinct mutations ("L16I" and "L25H"), with L16I being a rare mutation observed only in strain from China and India in 2023. Structural modeling of VP1 proteins indicated conformational differences between the 2023 and 2005 strains, suggesting potential impacts on viral infectivity and immune escape. These findings indicate the reemergence of CV-A24v in Pakistan and highlight the importance of adaptable diagnostic strategies to respond to emerging infectious threats.},
}

@article {pmid40581059,
year = {2025},
author = {Shi, Y and Zuo, S and Zhang, Z and Li, A and Ji, B},
title = {Mechanistic insights into nitrogen source influence on microalgal-bacterial granular sludge: Community dynamics and metabolic functions.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132895},
doi = {10.1016/j.biortech.2025.132895},
pmid = {40581059},
issn = {1873-2976},
abstract = {This study investigated the effects of nitrogen source (different ammonia to urea ratios) on pollutant removal, microbial community evolution and function in the MBGS system. Results showed that a higher ammonia proportion significantly enhanced total nitrogen removal during the initial 7-day operation compared to urea (p < 0.05). However, this nitrogen source-dependent effect adapted and diminished during the subsequent 14 days (p > 0.05). Microbial analysis revealed that urea enriched Proteobacteria (specifically Alphaproteobacteria including Roseomonas), while ammonia stimulated Firmicutes (specifically Clostridia including Acetoanaerobium), Betaproteobacteria, and Cyanophyceae. Metagenomic analysis identified that Alphaproteobacteria played a dominant role in key genes (ureA/B/C, GLUD, gltB) involved in nitrogen metabolism. Robust correlations between nitrogen source composition and microbial population dynamics underscores the self-regulating capacity of the MBGS system. These comprehensive findings demonstrate the excellent adaptability of the MBGS to varying nitrogen compositions through microbial community regulation.},
}

@article {pmid40580838,
year = {2025},
author = {Mirzaei, S and Gorczyca, B and Uyaguari-Diaz, M and Sparling, R and Maksimova, E},
title = {Microbial consortia in full-scale pre-ozonated biologically active filters treating a high-DOC water: Effects of seasonal and operational variations.},
journal = {Water research},
volume = {285},
number = {},
pages = {124065},
doi = {10.1016/j.watres.2025.124065},
pmid = {40580838},
issn = {1879-2448},
abstract = {This study investigated the microbial dynamics in full-scale biologically active anthracite/silica sand (BAS) and granular activated carbon (BAC) filters used to treat high-DOC coagulated softened water. By analyzing these filter types across two seasons (winter and summer), we examined the impact of operational conditions-including temperature (1 °C vs. 25 °C), backwashing cycle (72 h vs. two weeks), and empty bed contact time (10 vs. 24 min in BAC and 4 vs. 10 min in BAS)-on organic matter removal, biological activity, and bacterial taxonomy and functionality. The highest DOC (19.1 %) and BDOC (34.8 %) removal rates were observed in BAC during summer and post-backwashing, whereas BAS in both seasons and BAC in the winter showed minimal effects on the organic matter concentration. No direct correlation was found between ATP levels, bacterial 16S rRNA bacterial gene copy numbers, and DOC/BDOC removal in BAC. However, an optimal condition of 13 × 10[-6] ATP per bacterial gene copy number in BAC during summer post-backwashing coincided with the highest DOC and BDOC removal. Bacterial taxa with established associations to DOC degradation accounted for over 60 % of the total bacterial orders identified in both BAS and BAC across seasons. The BAC environment appeared to selectively enrich consortia capable of transforming complex DOC fractions, likely facilitated by its greater surface area, extended EBCT, and less frequent backwashing. These conditions supported the persistence and activity of specific bacterial orders, including Actinomycetales, Myxococcales, Planctomycetales, and Rhizobiales. Subsystem-level metagenomic analysis indicated a significant enrichment of genes associated with metabolic functions linked to enzymes such as decarboxylase, N-methylhydantoinase A, cyclic beta-1,2-glucan synthase, carbon monoxide dehydrogenase, cell division protein FtsH, N-methylhydantoinase B, and UDP-glucose 4-epimerase in BAC samples. This study deepens our understanding of the BAF microbiome's role in natural organic matter removal and its relationship with operational parameters, addressing critical gaps in drinking water biological treatment.},
}

@article {pmid40580736,
year = {2025},
author = {Peng, C and Li, M and Wang, J and Zhang, J and Liu, X and Wang, L},
title = {Metagenomic and metabolomic insight into microplastic-derived inhibition of tetracycline degradation in sediments.},
journal = {Journal of hazardous materials},
volume = {495},
number = {},
pages = {139045},
doi = {10.1016/j.jhazmat.2025.139045},
pmid = {40580736},
issn = {1873-3336},
abstract = {Microplastics (MPs) have been extensively reported to affect organic compound metabolism and nutrient cycling in the ecosystem, particularly in aquatic sediments. However, the specific microbial pathways and underlying mechanisms governing these impacts remain incompletely understood. Herein, this study integrates field investigations and simulation experiments to demonstrate the inhibitory effects of MP contamination on tetracycline (TC) biodegradation in sediments. Our findings reveal three distinct TC biotransformation pathways in sediments, with monooxygenase-mediated hydroxylation emerging as the predominant pathway. Comparative analysis revealed significant reductions in monooxygenase abundance (56.6 %), host bacterial populations (38.5 %), and TC biodegradation efficiency (23.8 %) in MP-amended sediments compared with the control after 28 days (p < 0.05). MPs reduce microbial metabolic activity and cooperative relationships among microorganisms, which inhibit cooperative metabolism of complex organic compounds (including tetracycline). Ultimately, MPs occupy interstitial spaces within sediment matrices, thereby altering redox conditions and promoting microbial succession toward taxa less efficient in TC metabolism. Moreover, the plastisphere exhibits significantly reduced metabolic capacity for TC transformation compared with inorganic mineral-associated biofilms, thereby impeding TC biotransformation within sediments. This finding further implies that continuous MP accumulation may exacerbate interference with biogeochemical cycles.},
}

@article {pmid40580733,
year = {2025},
author = {Du, S and Tang, H and Wang, Z and Chen, H and Fang, X and Sun, J and Niu, Z and Liu, Y and Hu, Y and Su, W and Zhang, Z and Prapamontol, T and Nakayama, SF and Huang, J and Norback, D and Wu, Q and Tan, Y and Zhao, Z},
title = {Children's home environments as reservoirs of antimicrobial resistance: Divergent urban-rural risks from antibiotic resistance genes and pathogens.},
journal = {Journal of hazardous materials},
volume = {495},
number = {},
pages = {139053},
doi = {10.1016/j.jhazmat.2025.139053},
pmid = {40580733},
issn = {1873-3336},
abstract = {Antibiotic resistance genes(ARGs) and pathogens pose a global health challenge, particularly for vulnerable children. However, limited knowledge is on their existence in home environments where children spend majority of time, even less on urban-rural differences. We collected settled dust from children's homes in urban(n = 31) and rural (n = 34) areas of Shanghai, China, and analyzed microbiomes, ARGs and pathogens through metagenomic sequencing. Home dust microbial compositions differed significantly between urban and rural environment. ARGs were widely detected in home environment (rural:758 subtypes; urban:733). Significant urban-rural differences were also observed in ARGs and pathogens composition, diversity, co-occurrence patterns, assembly processes and drivers. Specifically, rural dust was enriched with more differentially abundant ARG subtypes. Urban dust was enriched with clinically critical multidrug-resistant pathogens (e.g. Acinetobacter baumannii), contrasting with rural areas enriched in plant-associated pathogens. Stochastic processes dominated the assembly of ARGs and pathogens, while environmental factors partially explained their variations. Temperature was positively associated with total ARG abundance in both areas. Residential greenness had a positive relationship with ARG abundance in rural but negative in urban settings. Our findings indicated children's homes as reservoirs of antimicrobial resistance, urging vigilance against rural ARG enrichment and urban multidrug-resistant pathogen risks for pediatric health.},
}

@article {pmid40580323,
year = {2025},
author = {Callejas, C and Guerrero, L and Erijman, L and López, I and Borzacconi, L},
title = {Microbiota and methanogenic activities in an anaerobic internal circulation reactor: insights into biogas production from brewery wastewater.},
journal = {Biodegradation},
volume = {36},
number = {4},
pages = {56},
pmid = {40580323},
issn = {1572-9729},
support = {2019//Comisión Sectorial de Investigación Científica/ ; 2019//Comisión Sectorial de Investigación Científica/ ; 2019//Comisión Sectorial de Investigación Científica/ ; },
mesh = {*Bioreactors/microbiology ; *Methane/metabolism ; *Microbiota ; *Biofuels/microbiology ; *Wastewater/microbiology ; Anaerobiosis ; Archaea/metabolism/genetics/classification ; Bacteria/metabolism/genetics/classification ; RNA, Ribosomal, 16S/genetics ; Sewage/microbiology ; },
abstract = {In this study, we analyzed the prokaryotic community and methanogenic activities in sludge samples collected from a full-scale internal circulation (IC) reactor used to treat brewery wastewater. The reactor performance was monitored over 15 months, and specific methanogenic activities were periodically measured in fresh sludge samples using CO2/H2 or acetate as substrates. The maximum hydrogenotrophic activities were consistently higher than maximum acetoclastic activities, suggesting the relevance of hydrogenotrophic methanogens in the sludge. Over six months, the prokaryotic community present in four sludge samples was analyzed using amplicon libraries and metagenomics. V4-16S rRNA amplicon libraries revealed the presence of a diverse microbial community dominated by Firmicutes and Bacteroidetes among bacterial phyla, and Halobacterota and Euryarchaeota among archaea. Furthermore, the 16S libraries constructed with cDNA were consistent with the methanogenic activity assays. A genome-centric metagenomics approach was used to assemble 42 high-quality metagenome-assembled genomes (MAGs), among which Methanothrix and Methanobacterium were the dominant archaeal members, and Acidobacteriota, Synergistota, Krumholzibacteriota, and Nitrospirota phyla were among the bacteria. Potential acetogenic members were explored via the fths gene; 15 MAGs contained this marker gene. A combination of methanogenic activity tests, amplicon libraries, and MAG analysis was used to gain insights into the prokaryotic structure and functional potential of the microbial community driving methane production in the reactor.},
}

*Bioreactors/microbiology
*Methane/metabolism
*Microbiota
*Biofuels/microbiology
*Wastewater/microbiology
Anaerobiosis
Archaea/metabolism/genetics/classification
Bacteria/metabolism/genetics/classification
RNA, Ribosomal, 16S/genetics
Sewage/microbiology

@article {pmid40580246,
year = {2025},
author = {Mauduit, O and Kumar, P and Scholand, KK and Aksan, E and Schaefer, L and Abu-Romman, A and Delcroix, V and Yu, Z and Sindikubwabo, AI and Korstanje, R and Makarenkova, HP and de Paiva, CS},
title = {Exploring the transformative effects of calorie restriction on the lacrimal gland in adult mice.},
journal = {GeroScience},
volume = {},
number = {},
pages = {},
pmid = {40580246},
issn = {2509-2723},
support = {EY035333/EY/NEI NIH HHS/United States ; EY026202/EY/NEI NIH HHS/United States ; EY002520/EY/NEI NIH HHS/United States ; T32 EY007001/EY/NEI NIH HHS/United States ; AG038070//National Institute of Aging/ ; },
abstract = {Advanced age is one of the most recognizable risk factors for dry eye. Dry eye disease affects millions worldwide and can result from age-related lacrimal gland dysfunction, which correlates with a decline in lacrimal gland secretory cell function and chronic inflammation. This study investigated the potential of calorie restriction to maintain lacrimal gland and ocular surface health. Adult female C57BL/6 J mice were subjected to a 40% calorie restriction for 4 months, starting at 6-7 months and continuing until 10-11 months. These mice were compared to controls fed ad libitum. Bulk RNA sequencing of lacrimal glands, conjunctiva, and cornea subjected to calorie restriction compared to ad libitum revealed significant differentially expressed genes (DEGs). Pathways enriched in the upregulated DEGs indicate enhanced circadian rhythm, secretory functions, and lipid metabolism. These findings were confirmed using individual qRT-PCR and western blotting. In contrast, pathways enriched in the downregulated DEGs were associated with immune cell activation, adaptive immune responses, extracellular matrix remodeling, and metalloproteinase activity. Histological sections of calorie-restricted lacrimal glands revealed reduced mononuclear cell infiltration and fewer positive cells for CD4, CD19, and MHC II than in ad libitum lacrimal glands. Calorie restriction also prevented age-related corneal barrier dysfunction and mitigated age-related conjunctival goblet cell loss, hallmarks of dry eye disease. These findings suggest that calorie restriction supports lacrimal gland and ocular surface health by reducing inflammation and extracellular matrix remodeling and by enhancing the lacrimal gland's secretory function.},
}

@article {pmid40580234,
year = {2025},
author = {Biessy, L and Sissons, J and Kihika, JK and Wood, SA and Pearman, JK},
title = {Microbial adaptations to acidic, nutrient- and metal-rich lakes in Aotearoa New Zealand.},
journal = {Extremophiles : life under extreme conditions},
volume = {29},
number = {2},
pages = {24},
pmid = {40580234},
issn = {1433-4909},
mesh = {*Lakes/microbiology/chemistry ; New Zealand ; *Microbiota ; *Adaptation, Physiological ; Geologic Sediments/microbiology ; *Metals/analysis ; Nutrients/analysis ; Bacteria/genetics/metabolism ; },
abstract = {Four lakes in the same region of Aotearoa New Zealand were investigated to characterize sediment microbial communities and functions under contrasting environmental conditions. Two lakes, an acidic lake (Rototai) and a lake with elevated metals and nutrients (Killarney) were impacted by extreme stressors, while the lowland mesotrophic lake (Kaihoka East) and an alpine lake (Peel) were used as reference lakes. Using metabarcoding and metagenomics analysis, we profiled community composition, functional pathways, and resistance mechanisms in the lake sediments. Rototai contained high abundances of genes involved in sulfur cycling (assimilatory and dissimilatory sulfate reduction, sulfur oxidation) and acid tolerance (kdp potassium-transport system, ClcA antiporters). In contrast, Killarney had elevated abundances of genes involved in methanogenesis, however despite high metal concentrations, no enrichment of metal-resistance genes was detected. Kaihoka East contained the highest prokaryotic diversity and an elevated abundance of genes involved in nitrification. Although community taxonomic differences were modest across lakes, functional analyses revealed distinct metabolic adaptations. These findings highlight the utility of using metagenomic approaches to identify biogeochemical processes and stress-response strategies in lakes. Improved understanding of microbial functional diversity in surface sediments has implications for lake management, particularly in systems impacted by acidification, high nutrient loading, and metal contamination.},
}

*Lakes/microbiology/chemistry
New Zealand
*Microbiota
*Adaptation, Physiological
Geologic Sediments/microbiology
*Metals/analysis
Nutrients/analysis
Bacteria/genetics/metabolism

@article {pmid40580061,
year = {2025},
author = {Rathour, R and Ma, Y and Xiong, J and Wang, XW and Petersen, J and Zhang, X},
title = {Hemolymph microbiota and host immunity of crustaceans and mollusks.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf133},
pmid = {40580061},
issn = {1751-7370},
abstract = {None declared.Conflicts of interestCrustaceans and mollusks have major economic importance and are also key players in aquatic biogeochemical cycles. However, disease outbreaks, temperature fluctuations, pollutants, and other stressors have severely threatened their global production. Invertebrates generally rely on their innate immune system as the primary defence mechanism, operating at cellular and humoral levels to protect against pathogens. The hemolymph plays a vital role in immune responses, containing microbial communities that interact with the host's immune processes. Significant advances in molecular methods such as metagenomics, metatranscriptomics, metaproteomics, and metabolomics have revealed the presence of a resident hemolymph microbiome and delineated its potentially vital role in immune homeostasis and overall host health. Accordingly, understanding the composition and role of the hemolymph microbiota, alongside innate immune responses, has become a key focus in recent research aimed at unravelling disease resistance mechanisms and supporting sustainable aquaculture practices. Here, we summarize the latest advancements in understanding the host and environmental factors that shape hemolymph microbiota diversity in various crustaceans and mollusks species. We also consider the innate immune responses of the hosts, as these modulate interactions between hosts, microbes, and environments. Interactions within the hemolymph microbiome significantly affect host health, providing critical insights for advancing sustainable aquaculture.},
}

@article {pmid40579799,
year = {2025},
author = {Zamparo, S and Brocca, G and Marroni, F and Radovic, S and Castellano, C and Torge, D and Bianchi, S and Groman, D and Macchiarelli, G and Muscatello, LV and Volpatti, D and Orioles, M},
title = {Metabarcoding Reveals a Potentially Undescribed Columnaris-Causing Bacterium in Peracute Skin Disease of Rainbow Trout (Oncorhynchus mykiss, Walbaum).},
journal = {Journal of fish diseases},
volume = {},
number = {},
pages = {e70004},
doi = {10.1111/jfd.70004},
pmid = {40579799},
issn = {1365-2761},
abstract = {Columnaris-causing bacteria (CCB) represent a group of four Flavobacterium species, previously classified under Flavobacterium columnaris, causing a threatening condition in salmonid farming characterised by cutaneous and gill lesions, commonly referred to as 'saddleback disease'. A peracute skin disease outbreak with high mortality in rainbow trout (Oncorhynchus mykiss) farms in Northern Italy was investigated. The disease presented with skin discoloration and scale lifting without internal organ abnormalities, leading to a weekly cumulative mortality of up to 80%. The disease was successfully managed with Oxytetracycline treatment, with no relapses observed. Conventional investigation methods produced inconsistent results, prompting additional analyses. Metagenomic sequencing of the 16S rRNA identified Flavobacterium species differing from the classical CCB based on the alignment of the V3 and V4 regions, with best matches to Flavobacterium bernardetii, Flavobacterium aquicola, and Flavobacterium hiemivividum. Histopathology and SEM confirmed epidermal necrosis and bacterial infiltration in the dermis, with filamentous bacteria resembling Flavobacterium morphology yet differing from classical CCB lesions. These findings point to a previously undescribed Flavobacterium-related skin disease with significant economic implications, supporting the value of metagenomic in investigating microbial dynamics in aquaculture diseases, especially in sites exposed to external environments. Further research is required to clarify the pathogenic mechanisms and guide effective management strategies for future outbreaks.},
}

@article {pmid40578342,
year = {2025},
author = {Wong, KK and Wu, BG and Chung, M and Li, Q and Darawshy, F and Tsay, JJ and Holub, M and Barnett, CR and Kwok, B and Kugler, MC and Chung, C and Natalini, JG and Singh, S and Li, Y and Schluger, R and Ficaro, L and Carpenito, J and Collazo, D and Perez, L and Kyeremateng, Y and Chang, M and Czachor, A and Singh, R and Mccormick, C and Campbell, CD and Keane, R and Askenazi, M and Hansbro, PM and Weiden, MD and Huang, YJ and Stringer, KA and Clemente, JC and Li, H and Jones, D and Ghedin, E and Segal, LN and Sulaiman, I},
title = {Microbial contribution to metabolic niche formation varies across the respiratory tract.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2025.06.002},
pmid = {40578342},
issn = {1934-6069},
abstract = {Variations in the airway microbiome are associated with inflammatory responses in the lung and pulmonary disease outcomes. Regional changes in microbiome composition could have spatial effects on the metabolic environment, contributing to differences in the host response. Here, we profiled the respiratory microbiome (metagenome/metatranscriptome) and metabolome of a patient cohort, uncovering topographical differences in microbial function, which were further delineated using isotope probing in mice. In humans, the functional activity of taxa varied across the respiratory tract and correlated with immunomodulatory metabolites such as glutamic acid/glutamate and methionine. Common oral commensals, such as Prevotella, Streptococcus, and Veillonella, were more functionally active in the lower airways. Inoculating mice with these commensals led to regional increases in several metabolites, notably methionine and tyrosine. Isotope labeling validated the contribution of Prevotella melaninogenica in generating specific metabolites. This functional characterization of microbial communities reveals topographical changes in the lung metabolome and potential impacts on host responses.},
}

@article {pmid40578105,
year = {2025},
author = {Wang, C and Luan, X and Zhang, J and Zhang, H and Zhang, Y and Yang, M and Tian, Z},
title = {Responses of viral communities in aerobic biofilms under antibiotic stress.},
journal = {Water research},
volume = {285},
number = {},
pages = {124099},
doi = {10.1016/j.watres.2025.124099},
pmid = {40578105},
issn = {1879-2448},
abstract = {Bacteriophages are pivotal in shaping microbial communities, but their structural and functional responses to antibiotic stress in aerobic biofilms remain underexplored. This study aims to fill this void by providing a comprehensive understanding of how viral communities in aerobic biofilms adapt to increasing antibiotic pressures through interactions with their bacterial hosts. Three lab-scale aerobic biofilm systems were established and operated for 577 days, two of those were exposed to increasing influent concentrations of oxytetracycline (OTC) and streptomycin (STM), respectively. The dynamics of the biofilm virome under antibiotic stress was revealed by metagenomic sequencing. Results showed that the virome in aerobic biofilms displayed a high percentage (98.7 %) of unknown bacteriophages, indicating considerable viral diversity. As for the hosts of phages, a total of 1741 bacteriophage contigs were associated with 660 distinct bacterial hosts. In antibiotic-treated systems, broad-host-range generalist bacteriophages accounted for over 17.95 % (STM) and 17.90 % (OTC), compared to 14.32 % in the control. Furthermore, viral community did not carry diverse antibiotic resistance genes, which only accounted for 0.34 % of the resistome. Additionally, it did not regulate the number of resistant bacteria by activating the lytic and lysogenic cycles in this study. This indicated that the contribution of transduction to the horizontal spread of resistant determinants is very limited in the aerobic biofilm. Under antibiotic stress, viral auxiliary metabolic genes compensated for incomplete metabolic pathways in host cells, particularly those related to carbohydrate, amino acid, and cofactor metabolism. These genes likely offer dual benefits to bacterial hosts by repairing antibiotic-induced cellular damage and supporting energy generation, thereby providing adaptive advantages for bacterial survival and proliferation under antibiotic selection pressure. This study uncovers the complex interactions between bacteriophages, their hosts, and environmental pressures. It suggests that viral communities in these environments compensate for functional metabolism rather than promote resistance development under antibiotic stress, providing new insights into the potential roles of bacteriophages in the regulation of microbial-driven processes.},
}

@article {pmid40578104,
year = {2025},
author = {Li, X and Wang, H and Abdelrahman, HA and Kelly, AM and Roy, LA and Soto, E and Wang, L},
title = {Resistome and microbiome shifts in catfish rearing water: the influence of temperature and antibiotic treatments.},
journal = {Water research},
volume = {285},
number = {},
pages = {124074},
doi = {10.1016/j.watres.2025.124074},
pmid = {40578104},
issn = {1879-2448},
abstract = {The increasing reliance on aquaculture for sustainable protein production highlights the need for responsible antibiotic use to manage bacterial infections, particularly in intensive farming systems. This study investigated the effects of three FDA-approved antibiotics (Aquaflor®, Romet®, Terramycin®) at common fish bacterial disease outbreak temperatures (20 °C, 25 °C, and 30 °C) on the microbiome and resistome of aquaculture water using a catfish model system. Metagenomic analyses evaluated the abundance, diversity, and mobility of antimicrobial resistance genes (ARGs) and antibiotic-resistant bacteria (ARB). The impact of temperature on Aquaflor- and Romet-induced changes in ARG abundance, richness, and resistome composition followed a U-shaped trend, with the least effect observed at 25 °C. Of the three antibiotics tested, Terramycin exerted the most significant influence on the water microbiome and resistome, enriching tetracycline resistance genes and co-selecting for floR, sul, and dfrA genes. Temperature also induced notable shifts in the ARB population, with Mantel tests revealing strong correlations between ARG profiles and changes in the overall bacterial community and ARB populations. While certain ARG classes consistently remained associated with specific host phyla, others shifted, highlighting the potential for horizontal gene transfer (HGT) as a critical mechanism for disseminating resistance genes like tet(C), particularly after antibiotic treatment. This is further supported by the observed reduction in plasmid numbers following treatment, which coincided with increased HGT events. Our findings highlight the pivotal role of temperature in influencing resistome dynamics, emphasizing the importance of accounting for environmental factors when applying antibiotics to effectively mitigate antimicrobial resistance in aquaculture systems.},
}

@article {pmid40578039,
year = {2025},
author = {Wen, Y and Li, M and Hao, Y and Peng, J and Wei, X and Zhang, Z and Liu, B and Wang, Y and Peng, T and Ma, Y},
title = {HDAC/NF-κB signaling pathway mediates gut microbiota dysbiosis in rheumatoid arthritis: Intervention mechanisms of Fengshining decoction.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {145},
number = {},
pages = {156976},
doi = {10.1016/j.phymed.2025.156976},
pmid = {40578039},
issn = {1618-095X},
abstract = {BACKGROUND: Gut microbiota dysbiosis has been associated with the development of rheumatoid arthritis (RA). Fengshining (FSN) is a traditional Chinese medicine decoction that can effectively alleviate RA. However, how FSN modulates the gut microbiota to mitigate RA has not been comprehensively studied. This study evaluated the gut microecological mechanisms underlying FSN's effects on RA, focusing on the impact of gut-derived short-chain fatty acids (SCFAs), specifically butyrate, in RA treatment.

METHODS: The pharmacological effects of FSN on type II collagen-induced arthritis (CIA) in mice were assessed via pathological indicators, metagenomics, and metabolomics analyses. Furthermore, the impact of FSN on gut microbiota and metabolic profiles was also evaluated. Moreover, a pseudo-germ-free CIA model was established to validate whether exogenous butyrate alleviates RA. This study also elucidated whether fecal microbiota transplantation (FMT) from FSN-treated mice could mitigate RA symptoms.

RESULTS: The data showed that FSN markedly alleviated CIA symptoms and reduced serum inflammatory cytokine levels. Metagenomic and metabolomic analyses revealed that FSN-enriched SCFA-producing bacteria, including Butyrivibrio, Faecalicatena, and Lacrimispora. Furthermore, FSN increased the activity of carbohydrate metabolism-related enzymes and upregulated the expression patterns of homologous protein families. Moreover, exogenous butyrate supplementation suppressed pro-inflammatory factors, modulating immune responses, and enhanced intestinal barrier function. Further, Western blot analysis validated that FSN inhibited the HDAC/NF-κB pathway.

CONCLUSION: This study indicated that the gut microecological mechanism of FSN might be associated with its herbal components, which regulate gut microbiota diversity, restore the intestinal barrier, and boost microbial metabolite production. Furthermore, butyrate was observed to modulate intestinal mucosa, inhibit inflammatory responses, repair the intestinal barrier, and mitigate joint damage, thus alleviating RA symptoms.},
}

@article {pmid40577874,
year = {2025},
author = {Li, Y and Zhu, Z and Li, S and Tan, Y and Xu, H and Sheng, X and Qi, B and Wu, J and Li, L and Zhao, Z},
title = {Phase-specific microbial relay strategy enhances lipid degradation and humification in aerobic composting of lipid-rich food waste.},
journal = {Journal of environmental management},
volume = {390},
number = {},
pages = {126342},
doi = {10.1016/j.jenvman.2025.126342},
pmid = {40577874},
issn = {1095-8630},
abstract = {Lipid-rich food waste poses significant challenges in aerobic composting owing to oil-induced physicochemical barriers (>10 % oil content reduces porosity by 32-45 % and suppresses microbial activity). To bridge this gap, we designed a phase-specific microbial relay strategy integrating Pseudomonas aeruginosa DO1 with thermophilic consortia derived from agricultural soils (CK3). The results demonstrated that DO1 achieved 25 % lipid degradation within 96 h (mesophilic phase, <45 °C) through lipase secretion (121.18-131.45 U/mL) and enzymatic emulsification of lipids, after which its abundance decreased (from 26.99 % to 8.41 %). Subsequently, CK3-derived thermophilic bacteria (Bacillus, 38.54 %; Thermoactinomyces, 2.53 %) and fungi (Wallemia, 21.12 %) dominated the thermophilic phase (>50 °C for >5 d), driving β-oxidation-mediated lipid degradation to 91.91 % and enhancing humification with 92.74 % humic substances. Metagenomic analysis confirmed the enrichment of lipolytic pathways (ko00071, p < 0.01) and the upregulation of ammonia-assimilation genes (glsA/gdhB), reducing nitrogen loss to 25.1 %. This temperature-phased relay strategy enables the efficient in situ degradation of high-lipid waste (>15 % oil), offering a scalable solution for industrial composting.},
}

@article {pmid40577531,
year = {2025},
author = {Duxbury, SJN and Raguideau, S and Cremin, K and Richards, L and Medvecky, M and Rosko, J and Coates, M and Randall, K and Chen, J and Quince, C and Soyer, OS},
title = {Niche formation and metabolic interactions contribute to stable diversity in a spatially structured cyanobacterial community.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf126},
pmid = {40577531},
issn = {1751-7370},
abstract = {Understanding how microbial communities maintain stable compositional diversity is a key question in microbial ecology. Studies from pairwise interactions and synthetic communities indicate that metabolic interactions and spatial organisation can influence diversity, but the relevance of these factors in more complex communities is unclear. Here we used a cyanobacterial enrichment community that consistently forms millimetre-scale granular structures, to investigate compositional diversity and its stability. Over a year of passaging in media without significant carbon source, we found stable co-existence of 17 species belonging to diverse bacterial phyla. Metagenomic analysis revealed polysaccharide breakdown genes and complementary vitamin biosynthesis pathways in these species. Supporting these findings, we show growth of several isolated species on cyanobacterial slime components and experimentally verify vitamin exchanges between two members of the community. Several species had genes for (an)oxygenic photosynthesis and sulfur cycling, the expression of which we verified via meta transcriptomics. Consistent with this, we found that the granular structures displayed oxygen gradients with anoxic interiors. Cyanobacteria and other bacteria were distributed on the periphery and insides of these structures, respectively. Perturbation of the community via glucose addition resulted in fold increases of the heterotrophs, whereas disturbing the community by continual shaking led to fold reductions in several heterotrophs, including anoxygenic phototrophs. In contrast, removal of vitamins supplementation did not consistently alter species coverages, due to predicted vitamin sharing amongst community members. Taken together, these findings indicate that spatial organisation, microenvironment niche formation and metabolic interactions contribute to community compositional diversity and stability.},
}

@article {pmid40577477,
year = {2025},
author = {Li, B and Jiang, L and Johnson, T and Wang, G and Sun, W and Wei, G and Jiao, S and Gu, J and Tiedje, J and Qian, X},
title = {Global health risks lurking in livestock resistome.},
journal = {Science advances},
volume = {11},
number = {26},
pages = {eadt8073},
pmid = {40577477},
issn = {2375-2548},
mesh = {*Livestock/microbiology ; Animals ; *Global Health ; Humans ; Manure/microbiology ; Anti-Bacterial Agents/pharmacology ; Risk Assessment ; *Metagenome ; *Drug Resistance, Microbial/genetics ; *Drug Resistance, Bacterial/genetics ; },
abstract = {Livestock farming consumes more than 70% of global antibiotics annually, making livestock manures an important vector of anthropogenically influenced antibiotic resistance genes (ARGs). The global pattern of the livestock resistome, its driving mechanisms, and transmission potential to the clinic are not well assessed. We analyzed 4017 livestock manure metagenomes from 26 countries and constructed a comprehensive catalog of livestock ARGs and metagenome-assembled genomes. Livestock resistome is a substantial reservoir of known (2291 subtypes) and latent ARGs (3166 subtypes) and is highly connectable to human resistomes. We depicted the global pattern of livestock resistome and prevalence of clinically critical ARGs, highlighting the role of farm and human antibiotic stewardship in shaping livestock resistome. We developed a risk-assessment framework by integrating mobility potential, clinical significance, and host pathogenic relevance, and prioritized higher risk livestock ARGs, producing a predictive global map of livestock resistome risks that can help guide research and policy.},
}

*Livestock/microbiology
Animals
*Global Health
Humans
Manure/microbiology
Anti-Bacterial Agents/pharmacology
Risk Assessment
*Metagenome
*Drug Resistance, Microbial/genetics
*Drug Resistance, Bacterial/genetics

@article {pmid40576662,
year = {2025},
author = {Goldschmidt, I and Kramer, M and Junge, N and Ouro-Djobo, N and Poets, A and Rathert, M and Geffers, R and Baumann, U and Hartleben, B and Schulze, KD and Woltemate, S and Vital, M},
title = {Short- and long-term development of gut microbiota in children after liver transplantation - a prospective observational trial.},
journal = {Liver transplantation : official publication of the American Association for the Study of Liver Diseases and the International Liver Transplantation Society},
volume = {},
number = {},
pages = {},
doi = {10.1097/LVT.0000000000000659},
pmid = {40576662},
issn = {1527-6473},
abstract = {In children, little is known on gut microbiota (GM) in end-stage liver disease and its association with graft function after pediatric liver transplantation (pLT). We analyzed GM composition and function in children before pLT, longitudinally post-pLT and in long-term survivors (LT-pLT) in order to assess the impact of disease severity, treatment and pLT on GM and delineate associations with graft and patient health. Fecal samples (FS) of 29 children (17f, age 2.6 [0.2-15.7] years) awaiting pLT were included with longitudinal follow-ups until 12M post-transplant in 18, and compared with 38 LT-pLT (21f, age 11 [2.7-17.7] years, 7.8 [1.0-17.0] years post-pLT) and 94 healthy controls (HC). Samples were analyzed using quantitative 16S rRNA gene analyses combined with shotgun metagenomics (subset of samples). Pre-pLT patients showed reduced alpha-diversities and altered GM composition compared with LT-pLT and HC, associated with disease severity and anti-pruritic treatment with Rifampicin. Dysbiosis increased after pLT and started to recover after 3M. Although bacterial concentrations, alpha diversity and gene richness increased post-pLT, levels remained below those of HC. Abundances of key functions, e.g. the capacity to synthesize butyrate, also remained reduced. Quantitative analyses revealed true extent of differences between patients and HC that were underestimated using relative abundance data. GM diversity and functional capacities correlated negatively with transaminase levels mid- and long-term after pLT. Random Forest analyses based on GM were able to predict hepatocellular damage at high accuracy (AUC: 0.89). We provide comprehensive, quantitative insights into GM composition and function before and after pLT. A link between GM alterations with (long-term) graft health was uncovered providing possible targets to modulate GM function in order to increase graft and patient health.},
}

@article {pmid40576316,
year = {2025},
author = {Lui, LM and Nielsen, TN and Smith, HJ and Chandonia, J-M and Kuehl, JV and Song, F and Sczesnak, A and Hendrickson, A and Hazen, TC and Fields, MW and Arkin, AP},
title = {Sediment and groundwater metagenomes from subsurface microbial communities from the Oak Ridge National Laboratory Oak Ridge Reservation, Oak Ridge, Tennessee, USA.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0001425},
doi = {10.1128/mra.00014-25},
pmid = {40576316},
issn = {2576-098X},
abstract = {We report 26 subsurface sediment and 9 groundwater metagenomes from the Oak Ridge Reservation at Oak Ridge, TN, USA. Samples were collected from various depths and phases (attached vs planktonic) to study subsurface microbial metabolism, the effect of contamination on microbial communities, and differences across groundwater and sediment microbial communities.},
}

@article {pmid40575481,
year = {2025},
author = {Chen, L and Li, Z and Yuan, D and Chen, Y and Xu, Y and Tang, W and Liu, C},
title = {Microorganism changes in the gut of Apis mellifera surviving for the long term in Camellia oleifera forests.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1608835},
pmid = {40575481},
issn = {2235-2988},
mesh = {Animals ; Bees/microbiology ; *Camellia ; *Gastrointestinal Microbiome ; Oligosaccharides/metabolism ; Forests ; Metabolomics ; Metagenomics ; *Gastrointestinal Tract/microbiology ; *Bacteria/classification/genetics/isolation & purification/metabolism ; },
abstract = {Alpha-galactosides (oligosaccharides) in C. oleifera nectar and pollen cause honey bee larval rot and worker bloats. Honey bee colonies surviving in C. oleifera forests for a long period have low rates of larval rot and worker bloats; however, the mechanism of oligosaccharide metabolism is unclear. In this study, we used metagenomics and metabolomics to investigate the structure and function of the gut flora and the digestion characteristics of oligosaccharides in the gut of A. mellifera foragers (CN group) that had been in the C. oleifera forest for a long period (continuously for 14 years), and those that had not been pollinated with C. oleifera (N group) after 24 h of consumption of C. oleifera honey. The results revealed that the abundance of Gilliamella apicola up to 24.08%, which can metabolize α-galactoside (α-Gal), was significantly higher (P < 0.05) in the gut of foragers in the CN group than in the N group. Additionally, the gut flora of foragers in the CN group carried a significantly higher (P < 0.05) abundance of genes encoding α-galactosidase (Glycoside hydrolase family 4, GH4) than the N group. Similarly, metabolomic results indicated that the three toxic oligosaccharides in C. oleifera honey were lower in the gut of CN group foragers. These results suggest that the gut flora of A. mellifera, which inhabits oil tea forests for long periods of time, changes and adapts to the predominant ecological niche, enhancing the host's ability to metabolize toxic oligosaccharides. This important discovery provides positive guidance for the subsequent directions for breeding of A. mellifera (G. apicola enrichment and GH4 upregulation), specialized in pollinating C. oleifera.},
}

Animals
Bees/microbiology
*Camellia
*Gastrointestinal Microbiome
Oligosaccharides/metabolism
Forests
Metabolomics
Metagenomics
*Gastrointestinal Tract/microbiology
*Bacteria/classification/genetics/isolation & purification/metabolism

@article {pmid40575480,
year = {2025},
author = {Tang, Y and Tang, S and Zhang, Y and Lin, Z and Shan, S},
title = {The significance of metagenomic next-generation sequencing and targeted next-generation sequencing in the diagnostic evaluation of patients with suspected pulmonary infections.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1552236},
pmid = {40575480},
issn = {2235-2988},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; Retrospective Studies ; Bronchoalveolar Lavage Fluid/microbiology/virology ; *Metagenomics/methods ; Male ; Female ; Middle Aged ; Aged ; Sensitivity and Specificity ; *Respiratory Tract Infections/diagnosis/microbiology ; Adult ; Bacteria/genetics/isolation & purification/classification ; Aged, 80 and over ; },
abstract = {OBJECTIVE: To investigate the diagnostic value of metagenomic next-generation sequencing (mNGS) and targeted next-generation sequencing (tNGS) in identifying pathogens in patients with pulmonary infections.

METHODS: A retrospective analysis was conducted on 155 patients with suspected lung infections who underwent alveolar lavage and were admitted to the Department of Respiratory and Critical Care Medicine at Baodi Hospital, Tianjin Medical University, from July 2023 to December 2023. The bronchoalveolar lavage fluid (BALF) samples obtained were subjected to mNGS, tNGS and culture methods to compare their diagnostic efficacy in identifying lung infection pathogens.

RESULTS: The results indicated that both tNGS and mNGS methods exhibit comparable detection efficiencies in identifying pathogens in patients with pulmonary infections, significantly outperforming BALF culture approach. In terms of diagnostic accuracy, tNGS exhibited a higher sensitivity than mNGS, with rates of 96.1% and 75.7% respectively (P>0.05). However, the specificity of tNGS was slightly lower than that of mNGS, with rates of 59.1% and 68.2% respectively (P>0.05). It is noteworthy that this difference in specificity was not statistically significant.

CONCLUSION: tNGS exhibits a diagnostic efficacy comparable to mNGS, particularly in its sensitivity for identifying lung infections, as evidenced by expert insights and clinical applications. Furthermore, tNGS offers advantages in convenience, time efficiency, and cost-effectiveness, hinting at its potential to serve as an alternative to mNGS in clinical settings.},
}

Humans
*High-Throughput Nucleotide Sequencing/methods
Retrospective Studies
Bronchoalveolar Lavage Fluid/microbiology/virology
*Metagenomics/methods
Male
Female
Middle Aged
Aged
Sensitivity and Specificity
*Respiratory Tract Infections/diagnosis/microbiology
Adult
Bacteria/genetics/isolation & purification/classification
Aged, 80 and over

@article {pmid40575430,
year = {2025},
author = {Brar, AS and Vemula, SL and Yanamaladoddi, V and Sodhi, S and Hatwal, J and Sohal, A and Batta, A},
title = {Impact of gut microbiome on atrial fibrillation: Mechanistic insights and future directions in individualized medicine.},
journal = {World journal of cardiology},
volume = {17},
number = {6},
pages = {107386},
pmid = {40575430},
issn = {1949-8462},
abstract = {Atrial fibrillation (AF) is a growing global health burden, with a prevalence of over 52.55 million cases. Rising disability-adjusted life-years, increasing age, and disparities in care have contributed to the worsening severity and mortality of AF. Modifiable risk factors, such as hypertension, obesity, and diabetes mellitus, are associated with alterations in gut microbiota, making the gut-heart axis a potential therapeutic target. Gut dysbiosis influences AF pathogenesis through inflammation, metabolic disruption, and autonomic dysfunction. Key mechanisms include gut barrier dysfunction, short-chain fatty acid (SCFA) depletion, lipopolysaccharides (LPS)-induced inflammation, and ferroptosis-mediated atrial remodeling. Trimethylamine N-oxide, bile acids, and tryptophan metabolites contribute to arrhythmogenic remodeling. Emerging evidence suggests that dietary interventions, including prebiotics and probiotics, as well as gut surveillance, may help mitigate AF progression. Clinical implications of gut modulation in AF include personalized dietary strategies, microbiome assessment through metagenomic sequencing, and targeted interventions such as SCFA-based therapies and ferroptosis inhibition. Metabolite surveillance, including LPS and indoxyl sulfate monitoring, may influence the effectiveness of anticoagulant and antiarrhythmic therapy. Despite growing mechanistic evidence linking gut dysbiosis to AF, clinical applications remain unexplored. This review summarizes the current understanding of the gut microbiome's role in AF.},
}

@article {pmid40575134,
year = {2025},
author = {Foulkes, DM and Cooper, DM and Westland, C and Byrne, DP},
title = {Regulation of bacterial phosphorelay systems.},
journal = {RSC chemical biology},
volume = {},
number = {},
pages = {},
pmid = {40575134},
issn = {2633-0679},
abstract = {In terms of biomass, bacteria are the most successful organisms on earth. This is partly attributed to their tremendous adaptive capabilities, which allows them to sense and rapidly organise responses to changing environmental stimuli. Using complex signalling mechanisms, bacteria can relay cellular information to fine-tune their metabolism, maintain homeostasis, and trigger virulence processes during infection. Across all life, protein phosphorylation represents the most abundant signalling mechanism, which is controlled by a versatile class of enzymes called protein kinases and their cognate phosphatases. For many years, histidine kinase (HK)-containing two-component systems (TCSs) were considered the canonical instruments of bacterial sensing. However, advances in metagenomics has since proven that bacterial phosphorelay is in fact orchestrated by a functionally diverse array of integrated protein kinase types, including Ser, Thr, Tyr and Arg-targeting enzymes. In this review, we provide an up-to-date appraisal of bacterial kinase signalling, with an emphasis on how these sensing pathways are regulated to modulate kinase output. Finally, we explore how selective kinase inhibitors may be exploited to control infections and combat the looming health emergency of multidrug resistant bacteria.},
}

@article {pmid40574876,
year = {2025},
author = {Odenwald, MA and Ramaswamy, R and Lin, H and Lehmann, C and Moran, A and Mullowney, MW and Sidebottom, AM and Hernandez, A and McMillin, M and Rose, A and Moran, D and Little, J and Sulakhe, D and D'Souza, M and Woodson, C and Tanveer, T and de Porto, A and Dylla, N and Sundararajan, A and Burgo, V and Cantoral, J and Jadczak, C and Adler, E and Aronsohn, A and Pamer, EG and Rinella, ME},
title = {Fecal Butyrate and Deoxycholic Acid Concentrations Correlate With Mortality in Patients With Liver Disease.},
journal = {Gastro hep advances},
volume = {4},
number = {8},
pages = {100695},
pmid = {40574876},
issn = {2772-5723},
abstract = {BACKGROUND AND AIMS: The intestinal microbiome produces metabolites, including short chain fatty acids (SCFAs) and secondary bile acids (BAs), that impact host physiology. Loss of intestinal microbiome diversity is associated with cirrhosis progression, but the impact of microbiome-associated metabolites on liver disease remains largely undefined. We aimed to correlate fecal metabolite concentrations with the severity and progression of liver disease.

METHODS: In this cross-sectional study, fecal samples from patients hospitalized with liver disease were analyzed by shotgun metagenomic sequencing to determine microbiome compositions and targeted mass spectrometry to quantify SCFAs and BAs. Random survival forest and logistic regression models identified clinical, metagenomic, and metabolomic features associated with rehospitalization and survival.

RESULTS: This cross-sectional study included 24 chronic liver disease, 18 compensated cirrhosis, 225 decompensated cirrhosis and 40 acute-on-chronic liver failure patients and 27 control fecal donors. Microbiome sequencing and metabolite profiling correlated microbial diversity and SCFA and BA concentrations with liver disease severity. Butyrate and deoxycholic acid (DCA) were more important features than individual microbial species in random survival forest models predicting 30-day transplant-free survival, and low butyrate and DCA were associated with 30-day mortality (P < .0001). After controlling for model for end stage liver disease (MELD)-sodium score, disease stage, age and gender, low fecal concentrations of butyrate and DCA remained significant risk factors for death (Cox 1.38, P = .027). Bacterial species associated with butyrate and DCA concentrations included Bifidobacterium spp. and F. prausnitzii.

CONCLUSION: Mass spectrometry rapidly identifies patients with low fecal butyrate and DCA concentrations who are at increased risk of 30-day mortality. These findings set the stage for clinical trials of microbiome reconstitution with butyrate and DCA-producing bacterial species.},
}

@article {pmid40574752,
year = {2025},
author = {Zhang, X and Li, R and Lu, R and Wu, C and Liang, Z and Zhang, Z and Huang, B and Yang, Y and Qi, Z and Zhang, D and Zhai, D and Wang, Q and Tan, W},
title = {Transition of D3c branch and novel recombination events contribute to the diversity of Coxsackievirus A6 in Beijing, China, from 2019 to 2023.},
journal = {Virus evolution},
volume = {11},
number = {1},
pages = {veaf036},
pmid = {40574752},
issn = {2057-1577},
abstract = {Coxsackievirus A6 (CVA6) is a major pathogen responsible for numerous outbreaks of hand, foot, and mouth disease (HFMD) worldwide. This study investigates the molecular evolution and recombination of CVA6 in Beijing, China. Full-length sequences of 54 CVA6 from Beijing (2019-2023) were obtained through metagenomic next-generation sequencing and Sanger sequencing. These sequences were compared with representative sequences from GenBank to analyse their phylogenetic characteristics, recombination diversity, and evolutionary dynamics. The 54 CVA6 strains co-circulated with those from multiple provinces in China, as well as from South Korea and Japan. Phylogenetic analysis revealed a novel D3c branch, with the VP1 T283A amino acid mutation identified as a key change in its formation. One sequence belonged to the D3a branch, while 53 sequences belonged to the D3c branch. Recombination analysis identified RF-A (46, 85.1%) and three novel recombinant forms (RFs): RF-Z (1, 1.9%), RF-AA (1, 1.9%), and RF-AB (6, 11.1%). Bayesian phylogenetic analysis estimated that the most recent common ancestor of D3c emerged in August 2013 (95% highest probability density (HPD): May 2012 to September 2014), with recombination events occurring in RF-Z (2017-2019), RF-AA (2019-2023), and RF-AB (2021-2023). In conclusion, we revealed a globally circulating CVA6 D3c branch and identified three novel RFs, providing valuable insights for the intervention and control of HFMD.},
}

@article {pmid40574064,
year = {2025},
author = {Varut, RM and Ciolofan, MS and Veronica, ME and Radivojević, K and Trasca, DM and Popescu, C and Diaconu, O and Singer, CE},
title = {Cyclodextrins as Modulators of Gut Microbiota: Pharmaceutical Applications and Impact on Intestinal Health.},
journal = {Pharmaceutics},
volume = {17},
number = {6},
pages = {},
pmid = {40574064},
issn = {1999-4923},
abstract = {Background/Objectives: Cyclodextrins (CDs) have garnered increasing attention in pharmaceutical research due to their ability to enhance drug solubility, bioavailability, and therapeutic efficacy. Meanwhile, the gut microbiota, a key regulator of human health, has emerged as an important target in evaluating the safety and broader implications of pharmaceutical excipients. This review aims to synthesize current knowledge regarding the effects of CDs on the composition and function of the gut microbiota. Methods: A literature search following PRISMA guidelines was conducted in PubMed, ScienceDirect, and Google Scholar to identify studies on cyclodextrins and their interactions with gut microbiota. Results: Cyclodextrins, particularly α-, β-, and γ-CDs, demonstrated the capacity to modulate gut microbiota composition, promoting the growth of beneficial bacteria such as Bifidobacterium and Akkermansia. Supplementation with CDs was also associated with an increased production of short-chain fatty acids (SCFAs), which are essential for maintaining intestinal homeostasis and metabolic health. Moreover, CDs exhibited potential in lowering lipid levels and improving postprandial glycemic control without enhancing insulin secretion. Although generally recognized as safe, the toxicological profile of CDs varies depending on their type, dosage, and route of administration. Conclusions: Cyclodextrins hold considerable promise not only as pharmaceutical excipients but also as modulators of gut microbial communities, suggesting a dual therapeutic and prebiotic role. Future studies integrating metagenomic and metabolomic approaches are necessary to further elucidate the molecular mechanisms underlying CD-microbiota interactions and to optimize their application in enhancing drug delivery efficiency and promoting intestinal health.},
}

@article {pmid40573878,
year = {2025},
author = {Ullah, F and Ali, S and Siraj, M and Akhtar, MS and Zaman, W},
title = {Plant Microbiomes Alleviate Abiotic Stress-Associated Damage in Crops and Enhance Climate-Resilient Agriculture.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {12},
pages = {},
pmid = {40573878},
issn = {2223-7747},
abstract = {Plant microbiomes, composed of a diverse array of microorganisms such as bacteria, fungi, archaea, and microalgae, are critical to plant health and resilience, playing key roles in nutrient cycling, stress mitigation, and disease resistance. Climate change is expected to intensify various abiotic stressors, such as drought, salinity, temperature extremes, nutrient deficiencies, and heavy metal toxicity. Plant-associated microbiomes have emerged as a promising natural solution to help mitigate these stresses and enhance agricultural resilience. However, translating laboratory findings into real-world agricultural benefits remains a significant challenge due to the complexity of plant-microbe interactions under field conditions. We explore the roles of plant microbiomes in combating abiotic stress and discuss advances in microbiome engineering strategies, including synthetic biology, microbial consortia design, metagenomics, and CRISPR-Cas, with a focus on enhancing their practical application in agriculture. Integrating microbiome-based solutions into climate-smart agricultural practices may contribute to long-term sustainability. Finally, we underscore the importance of interdisciplinary collaboration in overcoming existing challenges. Microbiome-based solutions hold promise for improving global food security and promoting sustainable agricultural practices in the face of climate change.},
}

@article {pmid40573780,
year = {2025},
author = {Zhang, S and Luo, Z and Peng, J and Wu, X and Meng, X and Qin, Y and Zhu, F},
title = {Analysis of Cadmium Accumulation Characteristics Affected by Rhizosphere Bacterial Community of Two High-Quality Rice Varieties.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {12},
pages = {},
pmid = {40573780},
issn = {2223-7747},
support = {2024YFD2301400//the National Key Research and Development Program of China/ ; 2024CX09//the Agricultural Science and Technology Innovation Project of Hunan Province, China/ ; },
abstract = {Cadmium-contaminated rice poses serious health risks through the bioaccumulation of Cd (cadmium) from soil to edible grains. Cd contamination disrupts soil microbial ecology and alters microbial diversity. However, the role of cultivar-specific rhizosphere microbial communities in modulating Cd uptake remains unclear. In this study, we aimed to elucidate the mechanism underlying variety-dependent rhizosphere microecological remodeling and Cd accumulation in two independently selected late rice varieties, Yuzhenxiang (YZX) and Xiangwanxian 12 (XWX12). Combining physiological and metagenomic analyses, we revealed variety-specific correlations between root Cd accumulation and dynamic changes in soil pH, soil available phosphorus, and rhizosphere bacteria. The key bacterial genera (Variibacter, Nitrospira) showed differential enrichment patterns under Cd stress. In contrast, Galella and Anaeromyxobacter likely reduce Cd bioavailability by modulating phosphorus availability. Overall, this study elucidates that rice cultivars indirectly shape Cd accumulation patterns via rhizosphere microbial remodeling, providing novel insights for microbial remediation strategies in Cd-contaminated farmland.},
}