@article {pmid41407999,
year = {2025},
author = {Li, Z and Yang, S and Li, C and Zhang, L and Xi, N and Li, D and Li, L},
title = {Metagenomic next-generation sequencing for the diagnosis of suspected spinal infections from biopsy samples: a novel biopsy toolkit design and real-life diagnostic value.},
journal = {European spine journal : official publication of the European Spine Society, the European Spinal Deformity Society, and the European Section of the Cervical Spine Research Society},
volume = {},
number = {},
pages = {},
pmid = {41407999},
issn = {1432-0932},
}

@article {pmid41407459,
year = {2025},
author = {Lin, QX and Wei, JJ and Lian, TT and Lin, BQ and Ren, JH and Zheng, XY and Wu, XQ and Li, J and Chen, H and Xie, SJ and Yang, T},
title = {[Diagnostic value of intestinal tissue metagenomic next-generation sequencing in severe diarrhea following haploidentical hematopoietic stem cell transplantation].},
journal = {Zhonghua xue ye xue za zhi = Zhonghua xueyexue zazhi},
volume = {46},
number = {11},
pages = {1020-1025},
doi = {10.3760/cma.j.cn121090-20241206-00540},
pmid = {41407459},
issn = {0253-2727},
support = {YJRC4415//Hospital talent scientific research project/ ; },
mesh = {Humans ; *Hematopoietic Stem Cell Transplantation/adverse effects ; Male ; Female ; Adult ; Middle Aged ; *High-Throughput Nucleotide Sequencing ; Child, Preschool ; Adolescent ; *Diarrhea/diagnosis/etiology/microbiology ; Child ; *Metagenomics ; Young Adult ; Transplantation, Haploidentical/adverse effects ; },
abstract = {Objective: To evaluate the diagnostic value of intestinal tissue metagenomic next-generation sequencing (mNGS) in severe diarrhea following haploidentical allogeneic hematopoietic stem cell transplantation (allo-HSCT) . Methods: Sixteen patients who developed severe diarrhea or hematochezia after haploidentical allo-HSCT at the First Affiliated Hospital of Fujian Medical University (June 2023-August 2024) were enrolled. All underwent gastrointestinal endoscopy and mNGS for microbial detection. Clinical, endoscopic, pathological, and microbiological data were analyzed to evaluate the diagnostic value of mNGS and treatment outcomes following targeted therapy. Results: The study included 16 patients (12 males, 4 females; median age 32.5 years, range 3-60 years). Diarrhea occurred a median of 3.93 months post-transplant (range 1.63-10.40 months). Stool cultures were negative except for one case with Candida. One patient tested positive for Clostridium difficile antigen. Endoscopy revealed mucosal congestion, edema, erosion, and bleeding, with focal inflammation on pathology. mNGS detected pathogens in 87.5% (14/16) of cases, including mixed infections in 78.5% (11/14). Common pathogens were Klebsiella pneumoniae, Enterococcus faecium, Escherichia coli, Rhizopus microsporus, EBV, and CMV. Targeted treatment adjustments led to symptom improvement in 87.5% of patients. Conclusion: Allo-HSCT patients are prone to infectious diarrhea due to immunosuppression. Molecular analysis of endoscopic biopsy tissues using mNGS can accurately identify pathogens, guide targeted therapy, and improve clinical outcomes.},
}

Humans
*Hematopoietic Stem Cell Transplantation/adverse effects
Male
Female
Adult
Middle Aged
*High-Throughput Nucleotide Sequencing
Child, Preschool
Adolescent
*Diarrhea/diagnosis/etiology/microbiology
Child
*Metagenomics
Young Adult
Transplantation, Haploidentical/adverse effects

@article {pmid41407286,
year = {2025},
author = {Herbst, R and Ibrahim, A and Hübner, A and Knüpfer, U and Regestein, L and Wiedemann, C and Hellmich, UA and Warinner, C and Stallforth, P},
title = {Actifensin Evolution in the Human Oral Cavity over the Past 100,000 Years.},
journal = {Journal of the American Chemical Society},
volume = {},
number = {},
pages = {},
doi = {10.1021/jacs.5c14335},
pmid = {41407286},
issn = {1520-5126},
abstract = {Bacterially produced antimicrobial peptides (AMPs), or bacteriocins, play key roles in shaping microbial communities via interspecies competition. Unlike the more temporally dynamic gut microbiome, the oral microbiome exhibits long-term stability and is preserved into deep time in dental calculus, enabling evolutionary analysis across time. Here, we combine metagenomics, structural modeling, and experimental validation to investigate AMP diversity in ancient and modern dental biofilms from humans, Neanderthals, and nonhuman primates spanning 100,000 years. Using our newly developed platform, AMPcombi, we uncover evolutionary trajectories of bacteriocins and elucidate their ecological functions. Among these, we identify a conserved family of Actinomyces-derived defensin-like peptides, termed actifensins, present across all time periods. Phylogenetic, structural, and functional analyses revealed shared ancestry and adaptive diversification between ancient (paleo-) and modern actifensins, with evidence of positive selection and maintained antimicrobial activity. Our findings position the oral microbiome as a valuable reservoir for natural product discovery. In the face of rising antimicrobial resistance, evolutionary insights into AMP function open a door to next-generation therapeutics. AMPcombi streamlines this process, linking ancient biomolecules with biotechnology.},
}

@article {pmid41407095,
year = {2025},
author = {Chen, M and Cai, Y and Shi, Q and Xu, A and Tang, T and Qian, J and Yu, S and Zhu, H and Xu, J and Li, J and Shen, B},
title = {Antimicrobial management and infection outcomes of Elizabethkingia spp. co-detection in lower respiratory tract: a real-world mNGS-based observational study.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {},
number = {},
pages = {108316},
doi = {10.1016/j.ijid.2025.108316},
pmid = {41407095},
issn = {1878-3511},
abstract = {OBJECTIVES: Elizabethkingia spp. infections pose a major threat to human health with high mortality. This study aimed to further understand its detection status, co-detection patterns, pathogenicity, and antimicrobial resistance in lower respiratory tract infections (LRTI) through metagenomic high throughput sequencing (mNGS)-based real-world research.

DESIGN AND METHODS: We retrospectively analyzed 105 LRTI patients positive for Elizabethkingia spp. by mNGS from July 2021 to February 2025. Pathogen profiles, antimicrobial management, and outcomes were reviewed via electronic medical records.

RESULTS: mNGS detection rates for Elizabethkingia spp. in respiratory samples were 21.5% in General Intensive Care Unit (GICU) and 11.1% in Emergency Intensive Care Unit (EICU), more sensitive than culture. Polymicrobial co-detection was ubiquitous (99%), indicating a diverse polymicrobial community. Clinical isolates exhibited variable susceptibility (74%-100%) to trimethoprim-sulfamethoxazole, ciprofloxacin, levofloxacin, doxycycline, minocycline, rifampicin, and azithromycin. Patients receiving targeted antimicrobial therapy based on mNGS indicators (Stringent Map Read Number (SMRN) rank ≤2, normalized SMRN (nSMRN) ≥1000, or SMRN percentage ≥25%) had significantly higher effective treatment rates.

CONCLUSIONS: Elizabethkingia spp. detection rates in ICU respiratory samples are high, frequently complicated by polymicrobial co-detection. Lack of targeted therapy is a key factor in treatment failure. mNGS-derived indicators and local susceptibility databases are essential for guiding effective intervention.},
}

@article {pmid41407051,
year = {2025},
author = {Yuan, Z and Zeng, W and Zhan, M and Peng, Y},
title = {Static magnetic field enhances respiratory dissimilatory nitrate reduction to ammonium over denitrification in sulfide-based autotrophic systems.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133796},
doi = {10.1016/j.biortech.2025.133796},
pmid = {41407051},
issn = {1873-2976},
abstract = {Dissimilatory nitrate reduction to ammonium (DNRA) represents a sustainable strategy for nitrogen resource recovery from wastewater, yet selectively enhancing DNRA over denitrification in sulfide-based autotrophic systems remains challenging. This study investigates the impact of static magnetic field (SMF, 0-100mT) on nitrate reduction pathways in sulfide-rich wastewater. SMF elevated DNRA efficiency to 41.8 % with an influent sulfide concentration of 200 mgS/L (S/N ratio of 3:1) under 30 mT, supported by nrfA upregulation (7.6 × 10[10] vs. 4.0 × 10[7] copies/g SS in control). [15]N isotope labeling and enhanced direct extracellular electron transfer via cytochrome c and conductive pili confirmed that SMF preferentially drove nitrate flux toward DNRA. Metagenomics revealed that SMF enriched DNRA taxa (Aeromonas, Shewanella) and enhanced their synergy with Thiobacillus, improving metabolic flexibility. This work unveils microbial competition mechanisms between denitrification and DNRA in sulfide-based systems and proposes an innovative SMF-assisted ammonium recovery approach, advancing the understanding of sulfide-based nitrogen removal technologies.},
}

@article {pmid41406967,
year = {2025},
author = {Liu, J and Glukhov, E and De Clerck, O and Gerwick, WH and Donia, MS},
title = {Environmentally controlled production of pagoamide A in marine macroalgae by an intracellular bacterial symbiont.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2025.11.023},
pmid = {41406967},
issn = {1879-0445},
abstract = {Marine algae are a rich source of diverse molecules, most of which are thought to be produced by the alga itself. We recently reported the discovery of pagoamide A from a cultured marine macroalga collected from American Samoa. Here, we found that the production of pagoamide A is conditional upon environmental temperature. Using comparative metagenomic, metatranscriptomic, and metabolomic analyses of algal cultures, we identified a nonribosomal peptide synthetase biosynthetic gene cluster (NRPS BGC) in the algal microbiome that varies in abundance between producing and non-producing conditions and whose architecture and biosynthetic logic match pagoamide A (named pag). pag belongs to a bacterium that we named "Candidatus Bryopsidiphilus pagoamidifaciens BP1," a new genus in the family Amoebophilaceae and a relative of amoeba, arthropod, and nematode endosymbionts. Ca. B. pagoamidifaciens lives intracellularly in its Bryopsis sp. algal host, harbors a reduced genome (1.7 Mbp), has lost most genes essential for free living, and is enriched in genes containing eukaryotic domains. By quantitatively monitoring longitudinal algal cultures under varying conditions for 9 weeks, we found that the abundance of both Ca. B. pagoamidifaciens and pagoamide A undergoes dramatic fluctuations in response to temperature changes. Finally, we discovered three additional strains of Ca. B. pagoamidifaciens that vary in their NRPS BGCs and eukaryotic domain-containing genes from algal samples of diverse geographical origins. Our findings suggest that symbiont-derived production of algal molecules is more common than previously anticipated and provide a unique case of environmental control of both symbiont and chemical levels in marine algae.},
}

@article {pmid41406735,
year = {2025},
author = {López-Dávalos, PC and Requena, T and Pozo-Bayón, MÁ and Muñoz-González, C},
title = {In vivo metabolism of fruity carboxylic esters in the human oral cavity is partly driven by microbial enzymes.},
journal = {Food chemistry},
volume = {501},
number = {},
pages = {147554},
doi = {10.1016/j.foodchem.2025.147554},
pmid = {41406735},
issn = {1873-7072},
abstract = {Food flavor perception is shaped by biochemical events during oral processing, with oral metabolism remaining poorly understood. This study investigated the oral fate of fruity carboxylic esters and its relationship with salivary and microbiological parameters. Participants (n = 101) rinsed their mouths with either water (control) or an ester-containing solution for 30 s. Esters and their corresponding acids were analyzed by gas chromatography-mass spectrometry before and after rinsing. Results showed a significant decrease in ester and a marked increase in acid levels, indicating rapid metabolic conversion. Ester recovery was associated with the physicochemical properties of the compounds, participants' body mass index, and salivary esterase activity (SEAC). SEAC also correlated with oral microbiota composition and the abundance of microbial genes encoding carboxylic ester hydrolases, as assessed by shotgun metagenomics. These findings provide the first evidence of rapid ester metabolism in the human mouth and its relationship with the salivary microbiome.},
}

@article {pmid41406531,
year = {2025},
author = {Zhao, Y and Mu, H and Hu, BX and Zhi, C and Wang, H and Huang, L and Huang, F and Han, K},
title = {Root exudates drive metabolic remodeling of microbial and resistance to facilitate sulfonamide biodegradation in karst soil-carbonate rock interface.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140829},
doi = {10.1016/j.jhazmat.2025.140829},
pmid = {41406531},
issn = {1873-3336},
abstract = {Sulfonamide antibiotics have become pervasive contaminants in karst systems, where low carbon and rapid infiltration hinder natural attenuation, leading to persistent groundwater pollution and elevated antibiotic resistance risks. Although root exudates shape soil microbial metabolism and resistance, their role at the karst soil-carbonate rock interface remains unclear. This study demonstrates that artificial root exudates (ARE) significantly boost sulfamethazine (SMZ) removal at the soil-carbonate rock interface, achieving up to 92.0 % (35.1 % higher than control). Analyses of 16S rRNA gene sequences and metagenomes reveal that ARE remodels microbial communities by enriching potential degraders and upregulating genes for carbohydrate metabolism and xenobiotic degradation. Co-occurrence networks become more modular and recruit rare taxa as connectors, enhancing resilience through cross-module connectivity. ARE also reduces antibiotic resistance risks by suppressing sul1/sul2 hosts and key integrases. Nine metabolites were identified based on RRLC-MS/MS analysis, and four transformation pathways were proposed, confirming active biodegradation. Scanning electron microscopy further shows that ARE induces mineral dissolution and organic aggregation, creating porous microhabitats that facilitate SMZ degradation. This study offers novel insights into the coupled biotic-abiotic mechanisms of root exudates-mediated sulfonamide degradation at the low-carbon karst interface and provides a framework for plant-assisted antibiotic remediation in karst systems.},
}

@article {pmid41406522,
year = {2025},
author = {Zhang, B and Hu, X and Han, L and Guo, Z and Liu, Y and Li, H and He, Y and Liu, T and Pan, Q and Mu, Y and Qu, J and Yu, H and Shen, A and Zhao, W and Ma, T and Tan, W and Zhang, Y},
title = {Unveiling the black box: Multi-omics reveal how biochar supercharges synthetic biofilms for superior bioremediation.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140816},
doi = {10.1016/j.jhazmat.2025.140816},
pmid = {41406522},
issn = {1873-3336},
abstract = {Biofilms formed by flora can be sustainably applied in a variety of fields such as bioremediation, wastewater treatment, corrosion prevention, and agricultural production. However, highly practical biofilms often result in low microbial activity, due to undesired impacts including environmental stress and microbial competition. Leveraging the advantages of carrier materials, we aimed to enhance the degradation efficiency and resilience of biofilms by integrating biochar. In this study, the biochar with excellent economic benefits and adsorption capacity was prepared and selected as the carrier material. The growth characteristics, pollutant removal performance, and nutrient cycling within biochar-based biofilms were systematically investigated. The result validated the pollutant remediation efficiency of biofilms increased by 14∼18 % after adding biochar, and found a positive nutrient cycling existing within the biochar-based biofilms. Subsequently, the enhanced remediation mechanisms of biochar-based biofilms at the molecular level were explored through metagenomic and metabolomic analyses. Our results indicate superior strengths of biochar-based biofilms in both metabolic activity and beneficial genes compared to monocultured biofilms. This study aims to improve the stability of biofilms formed by functional flora and reveal their potential in bioremediation for contaminants.},
}

@article {pmid41406519,
year = {2025},
author = {Lin, Z and Yan, Z and Kong, W and Zhou, Y and Xu, Y and Xie, J and Gu, W and Gong, B and Li, Y and Zhang, C},
title = {Unveiling the simultaneous organophosphate esters degradation mechanisms in biological wastewater nitrogen removal systems under varying phosphorus source conditions: Microbial insights and ecological interactions.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140835},
doi = {10.1016/j.jhazmat.2025.140835},
pmid = {41406519},
issn = {1873-3336},
abstract = {The discharge of organophosphate esters (OPEs) in wastewater increasingly threatens aquatic ecosystems. Although biological nitrogen removal (BNR) system shows potential OPEs removal and the performance might be influenced by phosphorus sources, the underlying mechanisms remained poorly understood. This study investigated the synchronous OPEs and nitrogen removal under varying phosphorus source conditions, revealing the microbial insights and ecological collaboration that facilitated OPEs degradation in BNR systems. Results demonstrated that the acclimated BNR systems achieved almost complete degradation of 10 mg/L tri-n-butyl phosphate (TnBP) and tris(2-chloroethyl) phosphate (TCEP). OPEs degradation pathways mainly involved hydrolysis, hydroxylation, and dehydrogenation, while phosphorus limitation could enhance the enzymatic activities of phosphotriesterase (PTE) and alkaline phosphatase (ALP). 16S rRNA sequencing and metagenomic analysis revealed that Rhodococcus, Nitrospira, and Phaeodactylibacter were the enriched OPEs degraders, which harbored pivotal functional genes including php, phoD, glpQ, and cpdA. Moreover, molecular ecological networks analysis highlighted synergistic interactions among nitrifying bacteria, denitrifying bacteria, and OPEs degrader, suggesting the collaboration among consortia facilitated complete OPEs degradation. The microbial OPEs degrading functions and ecological interactions in BNR systems were further stimulated by phosphorus-limited condition. This study provides novel insights into the microbial mechanisms of OPEs degradation and offers a promising strategy for upgrading wastewater treatment plants to cope with emerging contaminants.},
}

@article {pmid41406442,
year = {2025},
author = {Li, Y and Li, H and Lv, C and Hu, X and Zhang, B},
title = {Bacterial changes and quality deterioration of freshwater shellfish Hyriopsis cumingii meat under different temperature storage.},
journal = {Canadian journal of microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1139/cjm-2025-0056},
pmid = {41406442},
issn = {1480-3275},
abstract = {Hyriopsis cumingii is an important economic freshwater shellfish in China and there is a need to understand changes in the microbial community structure resulting in multidimensional quality degradation when the fish is stored at different temperatures. This study integrated 16S rRNA full-length sequencing with multidimensional quality indicators to investigate the temperature-regulated bacterial community shifts and quality deterioration mechanisms in stored H. cumingii meat. The results showed that bacterial richness (Chao1 index) decreased progressively with both refrigerated (4°C) and room-temperature (25°C) storage. Community composition underwent significant restructuring, with Bacteroidota decreasing at 25°C while Bacillota increased compared to 4°C storage. Additionally, the refrigerated group showed enrichment of Delftia turuhatensis and Chryseobacterium indologenes compared to the room-temperature storage group. Temperature significantly restructured bacterial communities, with notably higher pathogenic bacteria under refrigeration and spoilage bacteria dominance at room temperature. Metagenomic functional profiling revealed temperature-driven metabolic pathway divergence, indicating distinct spoilage mechanism. Predictable quality changes in H. cumingii correlated with temperature-imposed microbial composition.},
}

@article {pmid41405224,
year = {2025},
author = {Kok, CR and Morrison, MD and Thissen, JB and Mabery, S and Carson, ML and Kimbrel, JA and Bennett, JW and Tribble, DR and Millar, EV and Mende, K and Be, NA},
title = {Microbiome dynamics in the congregate environment of U.S. Army Infantry training.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0047425},
doi = {10.1128/spectrum.00474-25},
pmid = {41405224},
issn = {2165-0497},
abstract = {Within military training and operational environments, individuals from diverse backgrounds share common spaces, follow structured routines and diets, and engage in physically demanding tasks. While there has been interest in leveraging microbiome features to predict and improve military health and performance, the longitudinal convergence of microbiomes in such constrained environments has not been established. To assess the degree of microbiome convergence, we performed shotgun metagenomic sequencing on swab samples from a military trainee cohort. Samples were taken across four different body sites, three timepoints, and two spatially distinct platoons. We observed evidence of convergence in one platoon, whereby similarity in microbiome composition increased over time, with numerous differentially abundant species. We found no indication of strain transfer between individuals, suggesting that convergence was influenced by external environmental factors, diet, and lifestyle. Microbial shifts observed in the convergence process included a decrease in fungal species, such as Malassezia restricta in nasal cavities, and a decrease in Prevotella species at inguinal regions across time. Shifts in multiple Corynebacterium species were also observed with varying magnitudes depending on the body site. Overall, we provide preliminary evidence of convergence of host microbial communities in military-associated environments that were distinguishable using shotgun metagenomic sequencing approaches. The data presented here on microbiome convergence, dynamics, and stability may inform risk-based mitigation in congregate military settings facilitating development of targeted microbial, dietary, or other interventions to optimize health and performance of military populations.IMPORTANCEMicrobiome convergence in deployed environments could impact the health and readiness of the warfighter, with potential implications for susceptibility to biothreats. This study describes a shotgun metagenomic approach used to study the microbiomes of swab samples collected at different body sites in a military trainee cohort. The results presented here provide a foundation for developing future microbiome-based interventions and protocols to enhance operational readiness.},
}

@article {pmid41404904,
year = {2025},
author = {Jensen, EEB and Jespersen, ML and Svendsen, CA and Sonda, T and Otani, S and Aarestrup, FM},
title = {Tanzanian goat gut microbiomes adapt to roadside pollutants and environmental stressors.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0203625},
doi = {10.1128/spectrum.02036-25},
pmid = {41404904},
issn = {2165-0497},
abstract = {The impact of environmental pollution reaching and affecting the gut microbiome is rising. Pollution from vehicle emissions can release compounds harmful to both animal and environmental health, and their effect on the host microbiome is yet to be determined, particularly in understudied locations. Here, we have investigated the potential effect of environmental pollution on the gut microbiome of Tanzanian goats grazing near a heavily trafficked road compared to goats living in a more rural setting. We identified 1,468 metagenome-assembled genomes (MAGs), of which 768 were unidentified species, and created a genomic database to which 52% of the bacterial community could be assigned. We find significant differences in the composition of the bacterial communities and resistomes between rural and road-exposed goats, but not a major difference in antimicrobial resistance (AMR) abundance. Genes involved in pollutant biodegradation were significantly more abundant in the microbiome of goats grazing along the road. This includes genes involved in degradation of naphthalene and toluene (both present in motor vehicle exhaust), as well as the detoxification enzyme, glutathione S-transferase. These findings suggest living near a heavily trafficked road selects for xenobiotic degrading functions within the goat gut microbiome, which might aid the host in detoxification of these compounds.IMPORTANCETo the best of our knowledge, this is the first study on the potential effect of environmental pollution on the gut microbiome of Tanzanian goats. Using shotgun metagenomics, we compare the gut microbiome of goats living near a heavily-trafficked road in Kigoma, Tanzania, with the gut microbiome of goats living in a rural area. We find that genes involved in pollutant biodegradation were significantly more abundant in the gut microbiome of the road-exposed goats, which potentially aids pollutant detoxification in the host. The effect of environmental pollution on the gut microbiome remains poorly understood; however, with this study, we link a potential effect of environmental pollution to changes in the gut microbiome of Tanzanian goats.},
}

@article {pmid41404801,
year = {2025},
author = {Stonkus, J and Rutkienė, R and Meškienė, R and Jasiūnienė, M and Aučynaitė, A and Kalinienė, L and Lazutka, J and Balčiūnas, D and Vilkaitis, G and Meškys, R},
title = {A new role for PHYHD1 and related dioxygenases: demethylation of 2'-O-methylated nucleosides.},
journal = {Nucleic acids research},
volume = {53},
number = {22},
pages = {},
doi = {10.1093/nar/gkaf1379},
pmid = {41404801},
issn = {1362-4962},
support = {S-MIP-24-50//Research Council of Lithuania/ ; },
mesh = {Zebrafish/genetics/metabolism ; Animals ; *Nucleosides/metabolism ; *Dioxygenases/metabolism/genetics ; Demethylation ; Humans ; Methylation ; RNA/metabolism ; Ketoglutaric Acids/metabolism ; },
abstract = {Nucleoside 2'-O-methylation is a widespread RNA modification found across diverse RNA types in all domains of life. Although considerable progress has been made in mapping 2'-O-methylation sites and elucidating their biological roles, the enzymatic pathways responsible for the catabolism of 2'-O-methylated nucleosides remain largely unexplored. Here, we report a previously unidentified 2'-O-methylated nucleoside demethylation reaction catalyzed by a metagenome-derived bacterial dioxygenase named FJS. We further show that FJS-related enzymes, including human phytanoyl-CoA dioxygenase domain-containing protein 1 (PHYHD1), catalyze the 2-oxoglutarate-dependent demethylation of a broad range of ribose-methylated nucleosides, but do not act on modified nucleotides or 3'-terminal 2'-O-methylated RNA substrates. To determine whether the loss of PHYHD1 function affects 2'-O-methylation levels of RNA-incorporated or free nucleosides, we generated a phyhd1 knockout zebrafish line. While RNA modification levels remained unchanged, the amount of free 2'-O-methylated nucleosides was significantly elevated in both phyhd1 knockout embryos and adult zebrafish. These findings indicate that PHYHD1 does not directly demethylate RNA but instead functions in the turnover of free 2'-O-methylated nucleosides. Together, our study identifies a previously unrecognized metabolic pathway for 2'-O-methylated nucleosides and defines PHYHD1 as the key dioxygenase involved in their demethylation, providing new insights into the catabolism of modified nucleosides.},
}

Zebrafish/genetics/metabolism
Animals
*Nucleosides/metabolism
*Dioxygenases/metabolism/genetics
Demethylation
Humans
Methylation
RNA/metabolism
Ketoglutaric Acids/metabolism

@article {pmid41404617,
year = {2025},
author = {Coleman, I and Mametyarova, N and Zaznaev, A and Cai, P and Yu, L and Meydan, Y and Litman, A and Sharma, A and He, L and Simkhovich, A and Seeram, D and Park, H and Nobel, YR and Kav, AB and Pe'er, I and Uhlemann, AC and Korem, T},
title = {Comparative metagenomics using pan-metagenomic graphs.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.24.690211},
pmid = {41404617},
issn = {2692-8205},
abstract = {Identifying microbial genomic factors underlying human phenotypes is a key goal of microbiome research. Sequence graphs are a highly effective tool for genome comparisons because they enable high-resolution de novo analyses that capture and contextualize complex genomic variation. However, applying sequence graphs to complex microbial communities remains challenging due to the scale and complexity of metagenomic data. Existing multi-sample sequence graphs used in these settings are highly complex, computationally expensive, less accurate than single-sample alternatives, and often involve arbitrary coarse-graining. Here, we present copangraph, a multi-sample sequence-graph-based analysis framework for comprehensive comparisons of genomic variation across metagenomes. Copangraph uses a novel homology-based graph, which provides both non-arbitrary, evolutionary-motivated grouping of sequences into the same node as well as flexibility in the scale of variation represented by the graph. Its construction relies on hybrid coassembly, a new coassembly approach in which single-sample graphs are first constructed separately and are then merged to create a multi-sample graph. We also present an algorithm that uses paired-end reads to improve detection of contiguous genomic regions, increasing accuracy. Our results demonstrate that copangraph captures sequence and variant information more accurately than alternative methods, provides graphs that are more suitable for comparative analysis than de Bruijn graphs, and is computationally tractable. We show that copangraph reflects meaningful metagenomic variation across diverse scenarios. Importantly, it enables significantly better performance than other metagenomic representations when predicting the gut colonization trajectories of Vancomycin-resistant Enterococcus. Our results underscore the value of our multi-sample, graph-based framework for comparative metagenomic analyses.},
}

@article {pmid41404370,
year = {2025},
author = {Liu, M and Wu, M and Tang, Y and Lin, Z and Ye, C and Huang, X and Zhou, L and Lin, Q and Zheng, D and Lu, Y},
title = {Correlation between oral microbial characteristics and overall bone density of Postmenopausal women based on macrogenomic analysis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1663645},
pmid = {41404370},
issn = {2235-2988},
mesh = {Humans ; Female ; *Bone Density ; Middle Aged ; Saliva/microbiology ; *Osteoporosis, Postmenopausal/microbiology ; *Postmenopause ; *Microbiota ; Dental Plaque/microbiology ; *Mouth/microbiology ; Metagenomics ; *Bacteria/classification/genetics/isolation & purification ; Absorptiometry, Photon ; },
abstract = {BACKGROUND: Postmenopausal osteoporosis (PMO), a prevalent bone disease triggered by estrogen deficiency - induced bone mass reduction and deterioration of bone tissue microarchitecture, escalates the risk of fragility fractures. Recent research has highlighted the pivotal role of oral and gut microbiota in PMO development, giving rise to the "oral - gut - bone axis" concept.

METHODS: A total of 21 postmenopausal women, aged 50 - 60, were recruited for the study. Based on bone mineral density (BMD) measurements from dual - energy X - ray absorptiometry (DXA), participants were divided into osteopenia, osteoporosis, and healthy groups. Saliva and dental plaque samples were collected for metagenomic sequencing to analyze microbial diversity and community composition, with differences identified via LEfSe analysis. KEGG pathway analysis was used to reveal variations in microbial functions. Based on these analyses, predictive models for bone density status were constructed using LASSO regression and random forest algorithms.

RESULTS: Significant differences in salivary microbial community structures were found between the osteoporosis and healthy groups (P = 0.041). LEfSe analysis revealed higher abundance of Aggregatibacter, Haemophilus haemolyticus, Haemophilus sputorum, Pasteurellaceae, Neisseria elongata, Aggregatibacter segnis, and Aggregatibacter aphrophilus in the osteopenia group, and higher abundance of Streptococcus pneumoniae and Haemophilus paraphrohaemolyticus in the osteoporosis group compared to the healthy group. The random forest models for osteopenia vs. healthy and osteoporosis vs. healthy yielded AUC values of 0.82 and 0.74, respectively, suggesting potential predictive capability, though further validation in larger cohorts is needed to confirm their generalizability. Functional analysis using LEfSe identified differential KEGG pathways, including glycan biosynthesis and metabolism in cancer, choline metabolism in cancer, and the cGMP-PKG signaling pathway.

CONCLUSION: This exploratory study utilized metagenomic sequencing to analyze the relationship between oral microbiota and PMO while controlling for key confounders. We identified significant compositional and functional alterations in the oral microbiome associated with bone mineral density status, including specific bacterial species showing marked intergroup differences. A model based on differential microbial features exhibited preliminary discriminative capacity, and functional analysis suggested involvement of inflammatory and metabolic pathways. These findings provide initial evidence linking oral microbiota to PMO.},
}

Humans
Female
*Bone Density
Middle Aged
Saliva/microbiology
*Osteoporosis, Postmenopausal/microbiology
*Postmenopause
*Microbiota
Dental Plaque/microbiology
*Mouth/microbiology
Metagenomics
*Bacteria/classification/genetics/isolation & purification
Absorptiometry, Photon

@article {pmid41404316,
year = {2025},
author = {, and Papić, B and Fernández, PS and Garcia-Gutierrez, E},
title = {Training in metagenomics-integrated risk assessment for food-borne pathogens in the Slovenian and Spanish meat chain (METAMEAT).},
journal = {EFSA journal. European Food Safety Authority},
volume = {23},
number = {Suppl 1},
pages = {e231115},
pmid = {41404316},
issn = {1831-4732},
abstract = {Next-generation sequencing (NGS) has become an essential tool for antimicrobial resistance (AMR) surveillance, enabling comprehensive detection of AMR determinants in both bacterial isolates and complex microbial communities. Metagenomic sequencing enables culture-independent profiling of antimicrobial resistance genes (ARGs) in different environments, while whole-genome sequencing (WGS) is widely used in AMR surveillance laboratories to predict phenotypic resistance in major food-borne pathogens. AMR risk assessment usually considers factors such as the pathogenicity of the ARG-carrying bacterial host, the abundance of ARGs and their mobility potential inferred from association with plasmids or other mobile genetic elements that facilitate horizontal gene transfer. Clinical relevance of antimicrobials and the severity of clinical outcomes can further be implemented in AMR risk assessment. Exposure assessment contextualises hazards within real-world scenarios by estimating consumer exposure to AMR bacteria or their ARGs through food or other routes. Despite challenges in fully quantitative assessments, the integration of NGS-based surveillance with risk modelling represents a critical step towards proactive AMR risk management. In this study, broiler samples from different stages of a Slovenian and a Spanish slaughterhouse were analysed using conventional microbiology, shotgun metagenomic sequencing and WGS of isolates of selected pathogenic species. A modular, semi-quantitative risk assessment model was developed that combines (meta)genomic data with key risk factors and, where available, exposure assessment. This approach prioritises AMR risks in broiler meat processing and supports evidence-based decision-making in the areas of food safety and public health.},
}

@article {pmid41404301,
year = {2025},
author = {Bucka-Kolendo, J and Fernández, PS and Garcia-Gutierrez, E},
title = {Training in metataxonomics-integrated risk assessment for foodborne pathogens in the Polish and Spanish dairy chain (DAIRYPOL).},
journal = {EFSA journal. European Food Safety Authority},
volume = {23},
number = {Suppl 1},
pages = {e231113},
pmid = {41404301},
issn = {1831-4732},
abstract = {Food safety is a key concern in the European Union, with the harmonisation of risk assessment methodologies being a strategic priority. The EU-FORA programme, coordinated by EFSA, promotes standardised approaches to microbial risk assessment across Europe. Metagenomic sequencing has advanced the understanding of microbial ecosystems in food production, with Illumina (short-reads) and Oxford Nanopore Technologies (ONT) (long-reads) playing significant roles in detecting pathogens and characterising microbial communities. These technologies differ in accuracy, read length and resolution, potentially influencing risk profiles when used in quantitative microbiological risk assessment (QMRA). This fellowship, conducted at UPCT in Spain and IBPRS-PIB in Poland, compares the two platforms in assessing microbial populations in Polish and Spanish dairy chains. It explores how sequencing strategy affects hazard identification and QMRA outcomes, while also demonstrating how metagenomic data can enhance predictive modelling and support practical improvements in food safety management.},
}

@article {pmid41403886,
year = {2025},
author = {Tarracchini, C and Bottacini, F and Mancabelli, L and Lugli, GA and Turroni, F and van Sinderen, D and Ventura, M and Milani, C},
title = {Approaches to dissect the vitamin biosynthetic network of the gut microbiota.},
journal = {Microbiome research reports},
volume = {4},
number = {4},
pages = {37},
pmid = {41403886},
issn = {2771-5965},
abstract = {B-group vitamins and vitamin K are essential micronutrients required for numerous cellular processes in both microbial and human physiology. While traditionally considered to originate predominantly from dietary sources, the biosynthetic capacity of the human gut microbiota has recently been recognized as a valuable, though historically underappreciated, endogenous source of these vitamins. In particular, the microbial contribution to the host vitamin pool is increasingly acknowledged as a functionally relevant aspect of vitamin homeostasis, especially in the colon, where microbiota-derived vitamins may be absorbed via specific transport mechanisms. This review provides a comprehensive overview of our current understanding of the biosynthesis of B-group vitamins and vitamin K by human gut-associated bacteria, with particular emphasis on key methodologies employed to assess if, how and to what extent members of the gut microbiota supply their host with such micronutrients. Through an integrated overview of available evidence, we highlight both the progress made and the outstanding challenges in elucidating the microbial contribution to the host vitamin metabolism.},
}

@article {pmid41403881,
year = {2025},
author = {Sun, Y and Huang, Y and Li, R and Zhang, J and Fan, X and Su, X},
title = {Benchmarking and optimizing microbiome-based bioinformatics workflow for non-invasive detection of intestinal tumors.},
journal = {Microbiome research reports},
volume = {4},
number = {4},
pages = {43},
pmid = {41403881},
issn = {2771-5965},
abstract = {Background: The human gut microbiome is closely linked to disease states, offering substantial potential for novel disease detection tools based on machine learning (ML). However, variations in feature types, data preprocessing strategies, feature selection strategies, and classification algorithms can all influence the model's predictive performance and robustness. Methods: To develop an optimized and systematically evaluated workflow, we conducted a comprehensive evaluation of ML methods for classifying colorectal cancer and adenoma using 4,217 fecal samples from diverse global regions. The area under the receiver operating characteristic curve was used to quantify model performance. We benchmarked 6,468 unique analytical pipelines, defined by distinct tools, parameters, and algorithms, utilizing a dual validation strategy that included both cross-validation and leave-one-dataset-out validation. Results: Our findings revealed that shotgun metagenomic (WGS) data generally outperformed 16S ribosomal RNA gene (16S) sequencing data, with features at the species-level genome bin, species, and genus levels demonstrating the greatest discriminatory power. For 16S data, Amplicon Sequence Variant-based features yielded the best disease classification performance. Furthermore, the application of specific feature selection tools, such as the Wilcoxon rank-sum test method, combined with appropriate data normalization, also optimized model performance. Finally, in the algorithm selection phase, we identified ensemble learning models (eXtreme Gradient Boosting and Random Forest) as the best-performing classifiers. Conclusion: Based on the comprehensive evaluation results, we developed an optimized Microbiome-based Detection Framework (MiDx) and validated its robust generalizability on an independent dataset, offering a systematic and practical framework for future 16S and WGS-based intestinal disease detection.},
}

@article {pmid41403880,
year = {2025},
author = {Gargari, G and Meroño, T and Peron, G and Del Bo', C and Marino, M and Cherubini, A and Andres-Lacueva, C and Kroon, PA and Riso, P and Guglielmetti, S},
title = {Effect of a polyphenol-rich dietary pattern on subjects aged ≥ 60 years with higher levels of inflammatory markers: insights into microbiome and metabolome.},
journal = {Microbiome research reports},
volume = {4},
number = {4},
pages = {38},
pmid = {41403880},
issn = {2771-5965},
abstract = {Background: Aging may be associated with low-grade chronic inflammation ("inflammaging") and gut microbiome alterations. Dietary polyphenols have been proposed as modulators of these processes. This study aimed to explore the effects of a polyphenol-rich diet (PR-diet) on inflammatory markers, gut microbiota, and metabolomic profiles in subjects aged ≥ 60 years stratified by baseline inflammation levels. Methods: In this post-hoc analysis of the MaPLE (Microbiome mAnipulation through Polyphenols for managing Leakiness in the Elderly) randomized crossover trial, 50 subjects aged ≥ 60 years were categorized into two subgroups: high inflammation (cH) and low inflammation (cL). Participants received a PR-diet or a control diet for 8 weeks, with a washout period in between. Fecal, blood, and urine samples were analyzed using shallow shotgun metagenomics and untargeted metabolomics. Results: The PR-diet was associated with a significant reduction in key inflammatory markers [e.g., interleukin-6 (IL-6), C-reactive protein] in the cH group. Distinct microbial shifts were observed, including an increase in Blautia and Dorea and a modest improvement in microbial diversity in cH subjects. Metabolomic analysis revealed group-specific changes, notably in polyphenol-derived metabolites. Conclusion: These findings suggest that PR-diets may beneficially modulate inflammation and the gut microbial ecosystem in subjects aged ≥ 60 years with elevated baseline inflammation. Stratification by inflammatory status may improve the targeting and personalization of dietary interventions to support healthy aging.},
}

@article {pmid41403720,
year = {2025},
author = {Hong, M and Xiang, W and Kong, L and Wang, X and Fu, L and Chen, L and Liu, F},
title = {Corynebacterium Striatum Infective Endocarditis: A Systematic Review.},
journal = {Journal of inflammation research},
volume = {18},
number = {},
pages = {17309-17318},
pmid = {41403720},
issn = {1178-7031},
abstract = {BACKGROUND: Corynebacterium striatum (CS) is an uncommon but potentially fatal pathogen of infective endocarditis (IE). The literature on the patterns and clinical progression of Corynebacterium striatum infective endocarditis (CSIE) is limited. This article aims to provide insights into the clinical presentation and management of CSIE through a retrospective analysis of documented cases.

METHODS: An electronic search was conducted across various databases including PubMed, China National Knowledge Infrastructure (CNKI), China Science and Technology Journal Database, and Wanfang database to identify relevant articles in both English and Chinese literature documenting CSIE. Subsequently, patient-level data were extracted and subjected to analysis.

RESULTS: The systematic search yielded 38 patients from 35 articles. The median age was 68 [IQR 54, 73] years, and 63.2% of patients were men. A history of heart disease was present in 55.3% of cases, while 15.8% had a history of cardiovascular electronic device implantation. The mitral valve was the most commonly affected site, accounting for 52.8%. The misdiagnosis or missed diagnosis rate of CSIE was 28.9%. Microbiological confirmation by 16S ribosomal ribonucleic acid (16S rRNA) or metagenomic next-generation sequencing (mNGS) was present in 13.2% of cases. Vancomycin was the most effective antibiotic, with 41.7% of the CS isolates showing resistance to multiple drugs. Surgical intervention was performed in 55.3% of the CSIE patients, and the overall fatality rate was 37.8%, both of which were higher than those reported in standard IE due to common pathogens such as Staphylococcus aureus (surgical intervention rate 37.8%, fatality rate 22.4%) and viridans streptococci (surgical intervention rate 29.5%, fatality rate 36.6%).

CONCLUSION: CSIE often presents with nonspecific symptoms, making it prone to misdiagnosis or underdiagnosis. Echocardiography and blood cultures remain the primary diagnostic tools, but advanced approaches such as 16S rRNA and mNGS improve accuracy in pathogen identification. Compared to IE caused by common microorganisms (eg, Staphylococcus aureus, viridans streptococci), CSIE is associated with higher rates of surgical intervention and mortality, underscoring the urgent need for increased clinical vigilance and prompt, targeted management.},
}

@article {pmid41403708,
year = {2025},
author = {McKnight, MM and Szabolcs, N and Graham, A and Neufeld, JD},
title = {Microbial community succession of home aquarium biofilters associated with early establishment of comammox Nitrospira.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf212},
pmid = {41403708},
issn = {2730-6151},
abstract = {Nitrification in aquarium biofilters transforms toxic ammonia (NH3/NH4[+]) into less toxic nitrate (NO3[-]) via nitrite (NO2[-]). Known freshwater aquarium nitrifiers include ammonia- and nitrite-oxidizing bacteria, ammonia-oxidizing archaea (AOA), and complete ammonia-oxidizing Nitrospira (CMX), with CMX recently shown to dominate most freshwater aquarium biofilters. However, little is known about nitrifier succession during aquarium establishment in home settings. Based on CMX prevalence in mature aquariums and the rapid growth of ammonia-oxidizing bacteria (AOB), we hypothesized that AOB initially dominate before CMX establish. To test this, we monitored microbial succession and water chemistry in three home aquariums over 12 weeks, collecting weekly samples from aquarium water, biofilter beads, and sponge filters. Biofilter DNA was analyzed via 16S rRNA gene sequencing and quantitative PCR (qPCR) targeting amoA genes. Nitrification reduced ammonia and nitrite to undetectable levels by week 3 in two aquariums and by week 8 in the third. Ammonia oxidizer detection by qPCR coincided with the onset of ammonia oxidation, with AOA preferentially colonizing biofilter beads. Metagenomic profiling of week 12 biofilter samples confirmed AOA and comammox Nitrospira amoA genes in all aquariums, along with nxrB genes from both comammox and canonical Nitrospira nitrite oxidizers. These results provide insight into the establishment of ammonia oxidizers in residential aquariums. Future work should explore factors influencing nitrifier community assembly, including inoculation sources (e.g. live plants, biological supplements), fish load, and water chemistry.},
}

@article {pmid41403704,
year = {2025},
author = {Yu, QY and Liu, X and Yao, H and Lü, PP and Yang, GJ and Lü, XT and Han, XG and Guo, LD and Huang, Y},
title = {The adaptability of grassland soil microbiomes to resource and stress shifts is mainly accomplished by niche conservatism under nitrogen deposition.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf215},
pmid = {41403704},
issn = {2730-6151},
abstract = {Atmospheric nitrogen (N) deposition usually alters the ratio of resources to stress in terrestrial ecosystems and has important impacts on soil microbiomes. To elucidate the adaptability of soil microbiomes under N deposition scenarios, we conducted a 6-year N addition experiment in a temperate grassland in Inner Mongolia, applying different levels of ammonium nitrate (AN) and urea (AU) to form different resource-to-stress ratio. Our results reveal that the inborn high yield (Y)-resource acquisition (A)-stress tolerance (S) life history strategies of soil microbiomes collectively drive their adaptability to resources and stress under N deposition. Enriched taxa under AN treatment mainly belonged to Actinomycetota and Chloroflexota with Y and S strategies, while those under AU mainly belonged to Pseudomonadota with A and S strategies. Functional preference analysis indicated that bacterial phyla maintained consistent Y-A-S life history strategies across AN and AU treatments. Moreover, strong purifying selection restricted the pace of adaptive evolution, and horizontal gene transfer expanded the functional repertoire in a complementary rather than essential manner. Thus, the adaptation of microbiomes to shifting resources and stress under N deposition scenarios is mainly accomplished by niche conservatism ("move") rather than niche evolution ("evolve"). Our results support the point that it may be easier for microbial species to move into a befitting niche than to evolve to acclimate a new environment.},
}

@article {pmid41403505,
year = {2025},
author = {Sanjrambam, B and Sharma, D and Bakshi, RK and Deka, MB and Agarwala, S and Kalita, A},
title = {Gut microbe's consortium in pregnant women influenced by diet of North-east India: A metagenomic study.},
journal = {Journal of family medicine and primary care},
volume = {14},
number = {11},
pages = {4705-4711},
pmid = {41403505},
issn = {2249-4863},
abstract = {INTRODUCTION: Recent research highlights that the gut microbiota of pregnant women undergoes significant changes throughout pregnancy, influenced by factors such as diet, environment, and sociocultural practices. A diverse gut microbiome during pregnancy is linked to improved metabolic health and the lower risk of complications like gestational diabetes and pre-eclampsia.

OBJECTIVE: This study aimed to investigate the relationship between dietary practices of different communities of Assam and Manipur with the composition of gut microbes during pregnancy.

METHODS: A total of 18 pregnant women completed a survey assessing macronutrient consumption during the first and third trimesters. Dietary data, obtained through questionnaires, were subjected to PCoA (Principal Co-ordinate Analysis) to find similarities and dissimilarities in dietary patterns. Metagenomics analysis of stool samples was done to study the consortium of gut bacteria for the participants.

RESULTS: This study has demonstrated that higher intake of carbohydrates and fats during pregnancy results in a decrease in phylum such as Firmicutes and Actinobacteria. Phylum such as Gemmatimonadetes, Crenarchaeote, Fibrobacteres, and Fusobacteria dominated the gut of most participants.

CONCLUSION: The relationship between gut microbiota composition and dietary habits among pregnant women in Northeast India is essential for designing effective nutritional interventions aimed at improving both maternal and infant health. Future studies should prioritize longitudinal research to better understand these connections and their impact on public health in the region, with a particular focus on identifying the specific foods and dietary patterns responsible for the observed similarities.},
}

@article {pmid41403401,
year = {2025},
author = {Lin, H and Zhu, X and Zhu, J and Chen, N and Bao, W and Peng, Z},
title = {High-Throughput Sequencings Revealed That Gut Microbiota Dysbiosis is Implicated in Gouty Arthritis of Red-Crowned Crane (Grus japonensis).},
journal = {Transboundary and emerging diseases},
volume = {2025},
number = {},
pages = {2422900},
pmid = {41403401},
issn = {1865-1682},
mesh = {*Gastrointestinal Microbiome ; Animals ; *Arthritis, Gouty/veterinary/microbiology ; *Dysbiosis/veterinary/microbiology/complications ; High-Throughput Nucleotide Sequencing/veterinary ; *Bird Diseases/microbiology ; Feces/microbiology ; China/epidemiology ; RNA, Ribosomal, 16S ; },
abstract = {The red-crowned crane (Grus japonensis) is one of the rarest cranes with a global population of less than 4000 individuals. The population of red-crowned crane could be influenced by health threats, including metabolic and infectious diseases. In the Wildlife Rescue Center of Suining County of Jiangsu Province, gouty arthritis (GA) was observed in all four red-crowned cranes since March 2024. A pooled fecal supernatant was first submitted to metagenomics sequencing for screening disease-associated pathogens. Enterobacteria phage phiEcoM-GJ1 was detected as the predominant virus while Escherichia coli and Aeromonas hydrophila were the dominated bacteria in the mixed fecal sample from red-crowned cranes. The 16S rRNA gene sequencing was further performed on both the mixed fecal sample and four individual samples, which showed that Escherichia-Shigella, Lactobacillus, and Enterococcus were the most abundant gut flora in both mixed and individual fecal samples. Furthermore, bacteria isolation and identification with matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF/MS) confirmed that Escherichia coli was predominant (19/29 colonies, 65.52%) in the feces. Therefore, anti-uricacid and antibacteria treatments using plantain herb, doxycycline, Vitamin AD3 and multivitamin B were adopted, leading to a full behavioral recovery within 1 month. Overall, this case-based observational study provides first clue on the gut-joint axis in red-crowned cranes, supporting that gut microbiota dysbiosis is closely associated with GA in red-crowned cranes.},
}

*Gastrointestinal Microbiome
Animals
*Arthritis, Gouty/veterinary/microbiology
*Dysbiosis/veterinary/microbiology/complications
High-Throughput Nucleotide Sequencing/veterinary
*Bird Diseases/microbiology
Feces/microbiology
China/epidemiology
RNA, Ribosomal, 16S

@article {pmid41402348,
year = {2025},
author = {Liu, F and Kang, L and Li, Z and Peñuelas, J and Abbott, BW and Xu, W and Zhou, W and Liu, X and Chen, L and Qin, S and Zhang, D and Peng, Y and Yang, Y},
title = {Chemoautotrophic carbon fixation in thermokarst lakes on the Tibetan Plateau.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-67478-x},
pmid = {41402348},
issn = {2041-1723},
support = {32588202, 32425004, and 32571870//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Dissolved organic carbon (DOC) derived from thermokarst lakes is usually considered to be prone to microbial degradation and releases substantial carbon dioxide to the atmosphere, potentially enhancing the positive permafrost carbon (C)-climate feedback. In contrast to this long-term standing view, here we show that dark C fixation exceeds DOC degradation in ~1/3 of the investigated thermokarst lakes on the Tibetan Plateau, based on the combination of large-scale water and sediment sampling across seasons and years, biodegradable DOC experiments and [14]C-labeling bicarbonate (NaH[14]CO3) assimilation incubation experiment. By employing qPCR, amplicon sequencing and metagenomic analyses, we find that microbial C fixation is mainly driven by nitrifying microorganisms via the Calvin-Benson-Bassham cycle carried out by the cbbL gene (encoding form I ribulose-1,5-bisphosphate carboxylase/oxygenase). These findings demonstrate that chemoautotrophic C fixation predominates in part of thermokarst lakes, which could partly offset C emissions upon permafrost thaw and thus weaken the positive permafrost C-climate feedback.},
}

@article {pmid41401858,
year = {2025},
author = {Memon, FU and Xu, J and Xie, X and Shu, C and Li, Y and Li, K and Xiao, Y and Tian, L},
title = {Strain-specific gut microbiota modulation is linked to resistance to BmNPV infection in silkworms.},
journal = {Journal of invertebrate pathology},
volume = {},
number = {},
pages = {108518},
doi = {10.1016/j.jip.2025.108518},
pmid = {41401858},
issn = {1096-0805},
abstract = {Bombyx mori nucleopolyhedrovirus (BmNPV) is a major pathogen threatening sericulture, yet the role of gut microbiota in strain-specific resistance remains poorly understood. This study compared three silkworm strains with high (Xinjiu, XJ), intermediate (AN3, A3), and low (Zhenchixian, ZCX) resistance to BmNPV. Protein assays showed that the resistant XJ strain exhibited the lowest viral EGFP and VP39 expression, minimal weight loss, and highest survival, whereas the susceptible ZCX strain displayed the opposite trend. Shotgun metagenomics revealed strain-specific microbial responses to infection. XJ and A3 maintained significantly higher alpha diversity and more dynamic beta diversity clustering than ZCX, with infection inducing increased microbial gene abundance and emergence of unique taxa in XJ. Taxonomic profiling showed XJ enriched in Firmicutes and beneficial fungal taxa such as Mucoromycota, Ascomycota, Basidiomycota, and Zoopagomycota, alongside reductions in Actinobacteria and Proteobacteria following infection. At finer resolution, resistant strains were enriched in beneficial bacterial classes (Bacilli, Alphaproteobacteria, Opitutae) and fungal classes (Agaricomycetes, Saccharomycetes), with cooperative co-occurrence networks linking these taxa and antagonizing pathogens. In contrast, ZCX was dominated by Gammaproteobacteria, Actinomycetia, and Hydrogenophilalia, consistent with dysbiosis and susceptibility. Functional analysis demonstrated pronounced metabolic reprogramming in resistant strains, especially XJ, with coordinated activation of carbohydrate, amino acid, nucleotide, and lipid metabolism, forming tightly integrated functional networks. Together, these findings reveal that silkworm resistance to BmNPV is associated with microbiome diversity, restructuring toward beneficial taxa, and synergistic metabolic pathways, offering new insights for probiotic-based antiviral strategies.},
}

@article {pmid41401693,
year = {2025},
author = {Chen, J and Li, J and Lin, Z and Zhang, Y and Lin, L and Guo, S and Huang, S and Li, X and Ma, J},
title = {Research note: Virome of Alectoris chukars by metagenomic analysis in Guangdong, southern China.},
journal = {Poultry science},
volume = {105},
number = {2},
pages = {106246},
doi = {10.1016/j.psj.2025.106246},
pmid = {41401693},
issn = {1525-3171},
abstract = {Alectoris Chukar (Chukar) has been introduced to numerous countries for stocking farms or release for hunting purposes. China imported commercial chuckars in the 1980s, and Guangdong Province was the first province in mainland China to feed on this species on stock farms; however, few reports have described the species and amount of virus circulating in it. In this study, meta-transcriptome analysis was conducted to reveal the virome in 34 unexplained dead chukars in Guangdong, southern China, which identified 2 novel viruses and 1 known virus, including the Alectoris chukar Avian leukosis-like virus (ACALLV) in the family Retroviridae, the GD-Alectoris chukar orthobunya virus (GD-ACOBV) in the family Peribunyaviridae, and an infectious bronchitis virus strain GD-Alectoris chukar strain (IBV-GDAC). These findings are the first to reveal the virome of chukars in Guangdong Province, providing more information to identify the virus circulating in chukars.},
}

@article {pmid41401615,
year = {2025},
author = {Wu, JZ and Wang, JH and Chen, Y and Zhang, Y and Wang, L and Zhao, KL},
title = {Deciphering the microbial response and functional potential involving in cadmium-arsenic co-contaminated paddy soil remediation with silicon-magnetic biochar.},
journal = {Journal of environmental management},
volume = {397},
number = {},
pages = {128318},
doi = {10.1016/j.jenvman.2025.128318},
pmid = {41401615},
issn = {1095-8630},
abstract = {To remediate cadmium (Cd)-arsenic (As) co-contaminated paddy soils, a novel silicon-magnetic biochar (SBC) was synthesized. Its microbial remediation mechanisms were investigated through a rice pot experiment combined with metagenomics. Results showed SBC significantly improved soil properties, including increased pH and dissolved organic carbon (DOC). This led to a drastic reduction in the rhizosphere bioavailability of Cd (by 69.9 %) and As (by 29.5 %). Consequently, SBC enhanced rice growth, with mature plant height and dry biomass increasing by 25.0 % and 46.7 %, respectively. Crucially, SBC reduced Cd and As accumulation in grains by 38.4 % and 55.6 %. Metagenomics revealed SBC enhanced microbial diversity, stability, and functional potential in both soil and phyllosphere, particularly in cellular processes and genetic information processing. SBC enriched key soil taxa linked to detoxification, such as Geobacter, Gemmatirosa, and Flaviaesturariibacter, and beneficial phyllosphere microbes like Ensifer adhaerens and Rhizobium rosettiformans. Functionally, SBC up-regulated microbial Cd efflux genes, while strong physicochemical adsorption and precipitation (with OH[-], Fe, and S[2-]) further enhanced Cd immobilization. Concurrently, it up-regulated As reduction genes while down-regulating As efflux genes, promoting microbial As(III) sequestration. These findings demonstrate SBC passivates Cd and As through synergistic physicochemical immobilization and microbial pathway modulation, which underscore its significant environmental value for restoring soil health and mitigating contamination.},
}

@article {pmid41401609,
year = {2025},
author = {Yue, H and Xu, J and Guan, X and Shen, Y},
title = {Redox-active biochar as insoluble electron acceptors for anaerobic oxidation of ammonium.},
journal = {Journal of environmental management},
volume = {397},
number = {},
pages = {128315},
doi = {10.1016/j.jenvman.2025.128315},
pmid = {41401609},
issn = {1095-8630},
abstract = {Anaerobic ammonium oxidation (anammox) is a promising nitrogen removal process, but its reliance on nitrite presents operational challenges. Here, we demonstrated that redox-active pyrogenic biochar could serve as an insoluble electron acceptor for NH4[+] oxidation by anammox consortia. Through batch incubations, over 95 % total nitrogen removal was consistently achieved with biochar as the sole electron acceptor across two consecutive cycles, though at a slower rate (0.77-1.18 mmol-N·d[-1] g[-1] VSS) compared to conventional anammox reaction. Isotopic tracing confirmed the role of biochar as an electron sink, and electrochemical and spectroscopic analyses illustrated that biochar's electron-accepting capability was attributed to surface quinone-like and pyridinic N groups. High-throughput sequencing and metagenomics revealed the dominance of anammox species Candidatus Brocadia in biochar-driven NH4[+] oxidation, with upregulated genes for extracellular electron transfer (EET) associated with c-type cytochromes. Metabolic reconstruction further elucidated the hydroxylamine pathway in biochar-driven anammox, distinctively different from the canonical nitrite-dependent route. These findings underscored biochar geobatteries as an inexpensive, environmentally sustainable electron acceptor, circumventing nitrite supply limitations. This work advances the understanding of EET-mediated anammox, thereby providing the potential for developing energy-efficient nitrogen removal technologies.},
}

@article {pmid41400382,
year = {2025},
author = {Schmidt, BM and Ranjan, P and Erb-Downward, J and Dickson, RP},
title = {Microbial Dominance in Diabetic Foot Osteomyelitis using Nanopore Sequencing Techniques Predicts Positive Response to Surgical Intervention.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiaf617},
pmid = {41400382},
issn = {1537-6613},
abstract = {BACKGROUND: Existing tools to predict successful response to surgery for the treatment of diabetic foot osteomyelitis are lacking. Recent studies in non-bone infections have revealed that nanopore sequencing can provide real-time metagenomic identification of pathogens. In a cohort of patients with diabetic foot osteomyelitis, we tested the feasibility of generating interpretable metagenomic data from surgically-acquired osseous tissue, and compared bacterial community features (pathogen dominance) with clinical outcomes (resolution of infection). We hypothesized that nanopore-generated microbial data can be feasibly generated from surgically-acquired bone, aligns with conventional culture results, and is predictive of clinical response.

METHODS: We performed a pilot feasibility study of ten consecutive patients hospitalized with diabetic foot osteomyelitis who underwent surgery for osteomyelitis. We performed metagenomic sequencing of surgical bone samples using the MinION (Oxford Nanopore). Our primary metagenomic index was community dominance (relative abundance of most abundant species). Our primary clinical endpoint was clinical response to surgery, adjudicated at one year.

RESULTS: We successfully generated interpretable metagenomic data from all (10/10) specimens, including two specimens with negative culture growth. Among culture-positive specimens, the culture-identified pathogen was either the first or second most abundant organism in all cases. Patients with favorable clinical response exhibited greater pathogen dominance than patients with unfavorable response (p=0.002).

CONCLUSIONS: In patients with surgically treated osteomyelitis, nanopore sequencing can generate interpretable metagenomic data from bone specimens that is culture-concordant and associated with clinical response. These findings support the feasibility and plausibility of using real-time metagenomic sequencing to improve the clinical management of osteomyelitis.},
}

@article {pmid41399631,
year = {2025},
author = {Su, J and Hansen, BE and Wang, Z and Sharmenov, A and Xia, X and Broekhuizen, M and Ma, Z and Peppelenbosch, MP},
title = {Yogurt reintroduction and the circulating microbiome in healthy volunteers: protocol for a prospective, longitudinal, species-controlled crossover clinical trial (MAMI).},
journal = {Contemporary clinical trials communications},
volume = {48},
number = {},
pages = {101579},
pmid = {41399631},
issn = {2451-8654},
abstract = {BACKGROUND: Although the gut microbiome plays a crucial role for maintaining overall host homeostasis and metabolism, it is significantly influenced by dietary changes, leading to substantial temporal variations in microbial composition within and between individuals. Despite this, incidental fecal sampling remains the standard method for microbiome assessment. Recently, the blood microbiome, defined by microbial DNA (cmDNA) circulating in the bloodstream, has emerged as a potentially more stable and integrated alternative. Preliminary data suggest that blood microbiome analysis may offer more consistent insights than fecal-based approaches, although the methodological validity of the approach has been questioned.

METHOD/DESIGN: This study aims to establish or rule-out cmDNA as a representative of the gut microbiome. In a prospective, single-arm crossover trial, effects of dairy product withdrawal and reintroduction of a yoghurt with a known consortium of bacteria will be assessed in healthy volunteers aged 18-65. Participants will first abstain from all dairy products, a phase expected to reduce yogurt-associated cmDNA in the bloodstream. Yogurt will then be reintroduced, during which reappearance of cmDNA of specific bacteria (especially LGG, LA-5 and BB-12) is anticipated. Shotgun metagenomic sequencing will be used to track cmDNA dynamics over time. This longitudinal sampling approach will provide experimental evidence supporting the existence and responsiveness of the circulating microbiome, while also revalidating the bioinformatic pipeline used for its analysis.

CONCLUSION: This pilot study will test whether blood-derived microbial DNA can serve as a valid surrogate for gut microbiome composition. If successful, this approach may provide a more stable and integrative alternative to fecal sampling and support future biomarker development and mechanistic research.

CLINICAL TRIAL REGISTRATION: NCT06944002.},
}

@article {pmid41399416,
year = {2025},
author = {Liu, Y and Zou, T and Lu, M and Li, P and Xiang, T},
title = {Delayed psychiatric sequelae following multifocal central nervous system lesions in leptospirosis: A case report.},
journal = {IDCases},
volume = {42},
number = {},
pages = {e02435},
pmid = {41399416},
issn = {2214-2509},
abstract = {Leptospirosis is a zoonotic infectious disease that can involve multiple organ systems. Neurological involvement is uncommon, and long-term neuropsychiatric sequelae have rarely been described. We report the case of a previously healthy adult who developed acute leptospiral infection complicated by multifocal central nervous system (CNS) lesions. The patient presented with fever, convulsions, altered mental status. Chest computed tomography (CT) scan revealed diffuse ground-glass opacities and patchy consolidations in both lungs. Brain magnetic resonance (MRI) demonstrated multifocal CNS lesions. Cerebrospinal fluid Metagenomic Next-generation Sequencing (mNGS) confirmed leptospiral infection. The patient received appropriate antimicrobial therapy and recovered fully, with follow-up imaging showing resolution of cortical lesions. Three years later, the patient developed new-onset psychiatric symptoms, including delusions, hallucinations, or personality changes, without evidence of recurrent infection or other organic causes. This case highlights that leptospiral infection may cause multifocal CNS lesions and lead to delayed psychiatric sequelae years after apparent recovery.},
}

@article {pmid41399344,
year = {2025},
author = {Hillman, EBM and Carson, D and Walters, JRF and Fritzsche, M and Mate, R and Chappell, KE and Chekmeneva, E and Romero, MG and Lewis, SJ and Rijpkema, S and Wellington, EMH and Arasaradnam, R and Amos, GCA},
title = {Ruminococcus gnavus and Biofilm Markers in Feces From Primary Bile Acid Diarrhea Patients Indicate New Disease Mechanisms and Potential for Diagnostic Testing.},
journal = {Gastro hep advances},
volume = {4},
number = {9},
pages = {100712},
pmid = {41399344},
issn = {2772-5723},
abstract = {BACKGROUND AND AIMS: Bile acid diarrhea (BAD) is a common cause of frequent loose stools, urgency, and incontinence, which is under-recognized due to limited diagnostic test availability and unclear pathogenesis. This study aimed to investigate fecal changes in well-defined subjects.

METHODS: Fecal samples were compared in BAD patients (n = 26), diagnosed by SeHCAT testing, and healthy controls (n = 21). Shotgun metagenomic sequencing was used to identify microbiome species and functional genes. An extended set of 38 bile acids was quantified by liquid chromatography mass spectrometry, including various epimers and intermediates, such as iso- (3-beta-OH), oxo (keto), allo (5-alpha), and 3-sulfated forms.

RESULTS: Alpha diversity, reflecting microbial richness, was reduced in BAD patients with severe forms of the disease, while beta diversity demonstrated distinct microbial profiles between groups. Ruminococcus gnavus (R. gnavus) was prevalent in BAD patients but rare in controls (odds ratio = 73), while Firmicutes bacterium CAG110, Eubacterium siraeum and 2 Oscillibacter species were less common in BAD (odds ratios = 25-30). Overall, 99 taxa differed significantly between groups. Bile acidtransforming genes (baiA, baiB, hdhA) were more abundant in BAD samples (P ≤ .0012). Most fecal bile acids, including iso-bile acids and intermediates, were higher in BAD. Elevated ursodeoxycholic acid-3-sulfate and relatively lower lithocholic acid and allo-bile acids, including isoallolithocholic acid, reflect changes in bacterial metabolism. Biofilm-associated genes (bssS, pgaA, pgaB) were markedly elevated in BAD patients (P ≤ .00008). SeHCAT values negatively correlated with R. gnavus (rho -0.53, P = .008) and positively with E ubacterium siraeum (rho 0.41, P = .041).

CONCLUSION: BAD may result from an overgrowth of R. gnavus, associated with intestinal biofilms and an altered bile acid metabolism.},
}

@article {pmid41399017,
year = {2025},
author = {Song, Y and Kjellander, C and Robinson, W and Öhrmalm, L and Giske, C and Gyarmati, P},
title = {Diagnostic Accuracy of Shotgun Metagenomics for Bloodstream Infections Is Influenced by Bioinformatics Workflow Selection.},
journal = {MicrobiologyOpen},
volume = {14},
number = {6},
pages = {e70158},
doi = {10.1002/mbo3.70158},
pmid = {41399017},
issn = {2045-8827},
support = {//The authors received no specific funding for this work./ ; },
mesh = {Humans ; *Metagenomics/methods ; *Computational Biology/methods ; Workflow ; *Sepsis/diagnosis/microbiology ; Hematologic Neoplasms/complications ; Bacteria/genetics/isolation & purification/classification ; },
abstract = {Bloodstream infection (BSI) is a severe and often fatal condition, and a major cause of mortality in patients with hematological malignancies due to underlying conditions and anticancer therapy-induced immunodeficiency. Rapid identification of the causative pathogens is essential as BSI results in worsened prognosis, extended hospitalization, delays or dose reductions in therapy, and may progress to sepsis and septic shock if untreated. Shotgun metagenomics is a culture-independent technique capable of detecting a wide range of fungal, viral, and bacterial organisms along with their antimicrobial resistance genes. Several studies showed that shotgun metagenomics enables the diagnosis of BSI, specifically in cases where conventional methods/culture-dependent techniques fail to identify the causative pathogens. However, evaluation of the accuracy of the applied bioinformatics pipelines remains incomplete. This study aimed to compare and optimize four commonly used bioinformatics pipelines (BLAST, Kraken, Metaphlan, RTG Core) for shotgun metagenomics by assessing their accuracy in identifying pathogens in blood samples from patients with hematological malignancies and suspected BSI, with blood culture serving as the reference standard. Our work shows that the selection of bioinformatics pipelines for diagnosing BSI strongly affects the precision of the findings, and an optimized BLAST pipeline was superior to the alternatives, as it was the only method that accurately identified the causative pathogens.},
}

Humans
*Metagenomics/methods
*Computational Biology/methods
Workflow
*Sepsis/diagnosis/microbiology
Hematologic Neoplasms/complications
Bacteria/genetics/isolation & purification/classification

@article {pmid41398941,
year = {2025},
author = {Song, Y and Hou, S and Xiang, Y and Zou, D and Gu, S and Pu, X and Liu, Q and Chu, M},
title = {Dietary energy levels modulate rumen metabolites and function in sheep by regulating the rumen microbiome.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-025-04636-7},
pmid = {41398941},
issn = {1471-2180},
support = {XQSWYZQZ-JBKY-4//Project of State Key Laboratory of Animal Biotech Breeding of China/ ; CAAS-ZDRW202502 and ASTIP-IAS13//Agricultural Science and Technology Innovation Program of China/ ; CARS-38-02//Earmarked Fund for China Agriculture Research System of MOF and MARA/ ; },
abstract = {In intensive ruminant production, high-energy diets are commonly used to enhance animal productivity, as dietary formulation significantly influences rumen fermentation and microbial communities. This study investigated the effects of varying dietary energy levels on the rumen microbial community structure, function, and metabolic profiles in Small-tailed Han (STH) sheep. Thirty 6-month-old sheep were randomly assigned to three groups: high-energy (HE), conventional-energy (CE), and low-energy (LE). All groups were fed iso-nitrogenous diets formulated to provide high-, conventional-, and low-energy levels of 10.8, 9.5, and 8.2 MJ/kg of digestible energy (DE), respectively. Rumen content was collected post-slaughter and analyzed via metagenomic sequencing to assess microbial composition and function, alongside non-targeted metabolomics to characterize the rumen fluid metabolome. Results revealed that Bacteroidota and Bacillota were the dominant phyla. High-energy feeding significantly reduced the relative abundance of Bacteroidota while increasing that of Bacillota, leading to a markedly higher Bacillota-to-Bacteroidota ratio. Functional analysis indicated significant enrichment of carbohydrate metabolism pathways in the HE group, whereas the LE group exhibited enrichment in fundamental cellular processes such as ABC transporters and ribosome, indicating a "survival mode". Metabolomic analysis demonstrated that dietary energy levels substantially reshaped the rumen metabolomic profile. Metabolites in the HE group were enriched in pathways including steroid hormone biosynthesis and the prolactin signaling pathway, while the LE group showed enrichment in histidine metabolism and the TCA cycle. Several aromatic amino acid metabolic pathways were commonly enriched across comparisons. These findings indicate that while the composition of the dominant phyla (Bacteroidota and Bacillota) was conserved across diets with different digestible energy levels, this dietary variation altered community diversity, structure, functional potential, and profoundly reshaped the rumen metabolic environment. This study provides scientific evidence regarding the impact of dietary energy on rumen fermentation and production performance in fattening sheep.},
}

@article {pmid41398701,
year = {2025},
author = {Wang, M and Zhang, C and Zhao, L and Yin, Q and Cui, Z and Chen, X and Ren, J and Wang, Y and Xu, M and Cao, Y and Wu, S and Yao, J},
title = {Unraveling the interaction between the phageome and bacteriome in the rumen and its role in influencing metabolome dynamics in dairy cows at different lactation stages.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02260-1},
pmid = {41398701},
issn = {2049-2618},
support = {2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 2022GD-TSLD-46-0501//Shaanxi Livestock and Poultry Breeding Double-chain Fusion Key Project/ ; 2022GD-TSLD-46-0501//Shaanxi Livestock and Poultry Breeding Double-chain Fusion Key Project/ ; 2022GD-TSLD-46-0501//Shaanxi Livestock and Poultry Breeding Double-chain Fusion Key Project/ ; 2022GD-TSLD-46-0501//Shaanxi Livestock and Poultry Breeding Double-chain Fusion Key Project/ ; 2022GD-TSLD-46-0501//Shaanxi Livestock and Poultry Breeding Double-chain Fusion Key Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 2022ZDLNY01-09//Key Research and Development Program of Shaanxi Province/ ; 2022ZDLNY01-09//Key Research and Development Program of Shaanxi Province/ ; 2022ZDLNY01-09//Key Research and Development Program of Shaanxi Province/ ; 2022ZDLNY01-09//Key Research and Development Program of Shaanxi Province/ ; 2022ZDLNY01-09//Key Research and Development Program of Shaanxi Province/ ; 32272829//National Natural Science Foundation of China/ ; 32272829//National Natural Science Foundation of China/ ; 32272829//National Natural Science Foundation of China/ ; 32272829//National Natural Science Foundation of China/ ; 32272829//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Although the roles of rumen microbiome in milk yield and milk protein synthesis have been widely recognized, knowledge on how ruminal microbiome dynamic changes affect these two traits during the whole lactation is lacking. Phages have been shown to affect the microbiota, but little is known about the shift patterns of ruminal phages and if they may modulate rumen microbiome during lactation. Herein, a longitudinal study was performed to identify the potential roles of ruminal phageome and bacteriome interactions, and metabolic function shift in affecting milk yield and protein content using metagenomic and metabolomic profiling of rumen microbiome from the peak, early, and later mid-lactation stages.

RESULTS: A total of 780 ruminal bacterial phages were identified, which exhibited two primary shifting patterns: (1) decreasing then increasing; (2) decreasing then stabilizing through the lactation. Bacteriome also showed first increasing then stabilizing or continuously declining besides exhibiting two similar shifting patterns to those of phages. By associating the differentially abundant phages with their host bacteria, we observed that significantly increased Lactococcus phage BM13, Corynebacterium phage P1201, and Campylobacter phage CJIE4-5 in peak lactation, along with Lactobacillus phage Lv-1 in early and later mid-lactation, were positively correlated with the relative abundance of their hosts. However, significantly increased Bacillus phage BCU4 and the Enterococcus phage phiNASRA1 in early mid-lactation were negatively related to their host abundance. In terms of bacteria, Ruminococcus flavefaciens and Faecalibacterium sp. CAG 74 had the highest abundance in peak lactation, whereas most Prevotella species were more abundant in early and later mid-lactation. Notably, ruminal carbohydrate and amino acid metabolism functions were enhanced in early mid-lactation. Further structural equation model and network analysis revealed that abundant Bacillus phage BCU4 and Enterococcus phage phiNASRA1 in early mid-lactation were associated with increased relative abundance of Prevotella species, possibly due to a reduction in Bacillus cereus and Enterococcus faecalis. Additionally, these Prevotella species exhibited positive relationships with rumen metabolites, such as L-phenylalanine, phenylacetylglycine, N-acetyl-D-phenylalanine, and propionate content, which contributed to the improved milk protein yield.

CONCLUSIONS: This study revealed the bacteriome and phageome interactions at different lactation stages, and the key phages and bacteria regulating the rumen function and metabolism thus contributing to the milk traits of cows. The potential regulatory roles of phages in affecting the rumen bacteriome suggest that they can be powerful targets for future interventions to improve rumen functions. Video Abstract.},
}

@article {pmid41398277,
year = {2025},
author = {Xiao, Y and Liu, H and Wang, P and Zhang, Y and Wang, F and Jing, H},
title = {Microbial population structure along the water columns and sediments in the Diamantina and Kermadec trenches.},
journal = {BMC biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12915-025-02490-7},
pmid = {41398277},
issn = {1741-7007},
support = {424MS115//the Hainan Provincial Natural Science Foundation of China/ ; 424QN341//the Hainan Provincial Natural Science Foundation of China/ ; 2022YFC2805400//the National Key R&D Program of China/ ; 2022YFC2805505//the National Key R&D Program of China/ ; KJRC2023C37//the Innovational Fund for Scientific and Technological Personnel of Hainan Province/ ; },
abstract = {BACKGROUND: Microbes are widespread from the marine surface to the hadal zones and play a significant role in global biogeochemical cycling. Physicochemical properties of hadal zone shift with depth, in turn influencing the distribution profiles, biogeochemical functions, and adaptative mechanisms of microbial communities in hadal trenches. However, the ecological functions and evolutions of microbial communities along the surface water down to the sediments in the Diamantina and Kermadec trenches have been rarely studied.

RESULTS: Here, we provided a detailed metagenomic analysis of samples along the water columns (0-6553 m) and sediments (3060-9232 m) in the Diamantina and Kermadec trenches. The euphotic waters had a significantly higher ɑ-diversity than the deep-sea waters and sediments (p < 0.05, ANOSIM). Clear inter/intra-trench discrepancies of microbial communities along water layers appeared, with remarkable vertical connectivity exhibited in the Diamantina Trench (97.5%) than the Kermadec Trench (88.8%). Positive correlations among Proteobacteria, Bacteroidota, Actinobacteria, and Thaumarchaeota in seawaters and between Proteobacteria and Chloroflexi in sediments were revealed from the co-occurrence network. Niche-specific microbial groups showed distinct dominant metabolic pathways in carbon fixation, nitrogen, and sulfur cycles. Furthermore, we reconstructed 119 metagenome-assembled genomes (MAGs) of Rhodobacterales, and their notably low ratios of non-synonymous substitutions to synonymous substitutions (pN/pS, 0.23) and high carbon atoms per residue side chain (C-ARSC, 2.86) in deep-sea sediments suggested a pronounced selection critical for their survival.

CONCLUSIONS: We found a clear connectivity of microbial communities in vertical profile, and discrepancy existed between the Diamantina and Kermadec trenches; Rhodobacterales' evolutionary adaptation related to genomic features (pN/pS and SNVs/kbp) in the deep-sea trench environments. These findings provided new insights into the community succession and potential adaption mechanism along the water columns to sediments in deep trenches.},
}

@article {pmid41398218,
year = {2025},
author = {Huang, R and Zhang, Y and Arif, M and Song, C and Yang, L},
title = {16S rDNA sequencing of the intestinal metagenome of Wanxi White Goose (Anser cygnoides) with different egg production abilities.},
journal = {BMC genomic data},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12863-025-01401-7},
pmid = {41398218},
issn = {2730-6844},
support = {202423l10050055//Anhui Province Science and Technology Innovation Project/ ; },
}

@article {pmid41398180,
year = {2025},
author = {Song, X and Fu, Y and Xu, H and Wang, H and Chen, J and Huang, S and Chen, Y and Xu, J and Li, W and Zhang, J and Wu, P and Shen, Q and Yang, S and Wang, X and Liu, Y and Ji, L and Li, Y and Yang, H and Tang, J and Zhou, C and Zhang, W},
title = {Maternal health status is associated with paired maternal and cord blood virome and mother-to-infant transmission.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-025-00880-x},
pmid = {41398180},
issn = {2055-5008},
support = {JSYGY-1-2023-03(03)//Jiangsu Provincial Hospital Association/ ; SH2023058//Social Development Projects in Zhenjiang/ ; 2023YFD1801300//National Key Research and Development Programs of China/ ; 82341106//National Natural Science Foundation of China/ ; },
abstract = {The viromes of maternal peripheral blood (MPB) and umbilical cord blood (UCB) provide crucial insights into mother-to-infant transmission and the associations of maternal health with early-life viral colonization. Using viral metagenomic sequencing of 433 MPB and 426 UCB samples, we assembled 57 near-complete genomes from four core viral families (Anelloviridae, Circoviridae, Parvoviridae, Flaviviridae). MPB viromes were primarily composed of bacteriophages and Anelloviridae, while UCB exhibited relatively increased abundances of Parvoviridae and Human Endogenous Retroviruses. Maternal disease correlated with reduced α-diversity in MPB but elevated richness in UCB. β-Diversity varied significantly with both health status and sample type. Differential abundance analysis identified health-specific signatures, including enriched Parvoviridae in diseased UCB. Phylogenetic evidence indicated possible vertical transmission and high genetic diversity among identified viruses. This study systematically characterizes the maternal-fetal blood virome and reveals associations between maternal health status and viral community structure, providing a basis for understanding early-life viral exposure and informing future preventive strategies.},
}

@article {pmid41398168,
year = {2025},
author = {Zhang, Y and Huang, Q and Tunçil, YE and Giriwono, PE and Xie, Z and Zhang, B},
title = {Metagenomic insights into effect of pulse cell wall integrity on gut microbiota, CAZyme gene responses and starch/protein metabolism during in vitro fecal fermentation.},
journal = {NPJ science of food},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41538-025-00660-z},
pmid = {41398168},
issn = {2396-8370},
support = {32272342//Natural Science Foundation of China/ ; NL2024010//National Engineering Research Center of Wheat and Corn Further Processing Open Project/ ; },
abstract = {The physical structure of pulse cotyledon cells modulates gut microbiota by controlling starch and protein availability for colonic fermentation, yet the mechanisms governing the interplay between saccharolytic and proteolytic fermentation remain unclear. Here, enzymatically treated white kidney bean cotyledon cells with weakened cell walls (CWs) underwent in vitro fecal fermentations and shotgun sequencing. Impaired CWs enhanced fermentation, increased acetate and propionate production, and reduced branched-chain fatty acids (BCFAs) and ammonia. Damaged CWs upregulated CAZymes encoding genes GH4, GH15, GH126, CBM20, and CBM26, which are associated with amylase, α-glucosidases, and amyloglucosidase activities involved in starch degradation. Furthermore, amino acid pathway enrichment revealed that IhgO and csiD, involved in lysine degradation, as well as astA-E, PRODH, putA and E1.2.1.88, involved in the conversion of arginine and proline to glutamate, were upregulated. Instead, isolated protein showed the highest ammonia and BCFAs production, accompanied by elevated glutamate dehydrogenase (gudB, GLUD1_2, and E1.4.1.4), soxA and soxB, involved in serine metabolism, and DBT, involved in branched-chain amino acid degradation. These findings provide metagenomic insights into how pulse CW integrity regulates saccharolytic and proteolytic fermentation, deepening our understanding of whole pulse foods in supporting gut health.},
}

@article {pmid41330588,
year = {2025},
author = {Chen, HP and Zhu, B and Wang, XF and Zhou, XJ and Du, Y and Mu, ZL},
title = {[Nasal infection with Mycobacterium avium complex: a case report].},
journal = {Zhonghua er bi yan hou tou jing wai ke za zhi = Chinese journal of otorhinolaryngology head and neck surgery},
volume = {60},
number = {11},
pages = {1439-1440},
doi = {10.3760/cma.j.cn115330-20241219-00698},
pmid = {41330588},
issn = {1673-0860},
support = {82360504//National Natural Science Foundation of China/ ; },
mesh = {Female ; Humans ; Middle Aged ; Biopsy ; Endoscopy ; *Epistaxis/diagnosis/microbiology/therapy ; Metagenomics ; *Mycobacterium avium Complex/genetics/isolation & purification ; *Mycobacterium avium-intracellulare Infection/complications/diagnosis/microbiology/therapy ; Nasal Cavity/diagnostic imaging/microbiology/pathology ; Nasal Mucosa/diagnostic imaging/microbiology/pathology ; Nasal Septum/diagnostic imaging/microbiology/pathology ; *Rhinitis/complications/diagnosis/microbiology/therapy ; },
}

Female
Humans
Middle Aged
Biopsy
Endoscopy
*Epistaxis/diagnosis/microbiology/therapy
Metagenomics
*Mycobacterium avium Complex/genetics/isolation & purification
*Mycobacterium avium-intracellulare Infection/complications/diagnosis/microbiology/therapy
Nasal Cavity/diagnostic imaging/microbiology/pathology
Nasal Mucosa/diagnostic imaging/microbiology/pathology
Nasal Septum/diagnostic imaging/microbiology/pathology
*Rhinitis/complications/diagnosis/microbiology/therapy

@article {pmid41397341,
year = {2025},
author = {Sun, Z and Dong, D and Song, X and Wei, Y and Li, Y and Dai, H and Liu, C and Zhang, M and Li, M},
title = {Halophytes regulate microbial synergy to enhance N removal and mitigate greenhouse gas in low C/N mariculture wastewater: Revealed by isotopic & metagenomics.},
journal = {Water research},
volume = {290},
number = {},
pages = {125154},
doi = {10.1016/j.watres.2025.125154},
pmid = {41397341},
issn = {1879-2448},
abstract = {Constructed wetlands (CWs) are promising for nitrogen removal from mariculture wastewater, but their efficiency under low C/N ratios remains limited by halophytes selection and unclear microbial mechanisms. Here, we investigated three halophytes (Sesuvium, Suaeda and Mangrove) in seawater CWs under C/N ratios of 5, 2.5 and 1, with unplanted controls, using metagenomics and [15]N-isotope tracing. Plants significantly enhanced total nitrogen (TN) removal under low C/N, with Sesuvium performing best (85.5% and 63.3% at C/N = 2.5 and 1), significantly surpassing Suaeda, Mangrove and controls. It also minimized greenhouse gas (GHG) emissions and reduced NH4[+]-N/NO2[-]-N accumulation. Microbial processes dominated TN removal (71.7-78.9%), whereas direct plant uptake contributed only 5.2-7.6%. Novelly, stable isotope tracing with [15]N-labeled CH4N2O confirmed that urea-N and NO3[-]-N are simultaneously removed via anammox. Under low C/N (2.5 and 1), Sesuvium selectively enriched anammox and sulfur autotrophic denitrification (SAD) taxa. Shifts in NO3[-]-N reduction pathways-from heterotrophic denitrification/dissimilatory nitrate reduction to ammonium (DNRA) under high C/N to anammox/SAD under low C/N-explained the superior performance of Sesuvium. This study highlights Sesuvium as an optimal halophyte for efficient nitrogen removal and lowest GHG emissions in low-C/N seawater CWs, providing mechanistic insights into plant-microbe interactions for mariculture wastewater treatment.},
}

@article {pmid41396836,
year = {2025},
author = {Xie, D and Tian, Y and Zheng, F and Wu, L and Xu, G and Liu, Q and Lu, G},
title = {Multi-Omics and Integrative Analytics in Natural Products Discovery.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {225},
pages = {},
doi = {10.3791/69458},
pmid = {41396836},
issn = {1940-087X},
mesh = {*Biological Products/chemistry/metabolism/analysis ; *Genomics/methods ; *Metabolomics/methods ; *Proteomics/methods ; *Drug Discovery/methods ; Computational Biology/methods ; Multiomics ; },
abstract = {Natural products (NPs) have long been an essential source of new bioactive compounds for drug discovery; however, traditional methods for screening and isolating these compounds can be slow and often yield diminishing returns. Fortunately, advanced multi-omics and computational approaches present powerful solutions to these challenges. This review highlights innovative methodologies that integrate metabolomics, genomics, transcriptomics, and proteomics with bioinformatics and analytical chemistry to accelerate NP discovery. For instance, untargeted metabolomics platforms like high-resolution liquid chromatography-tandem mass spectrometry (LC-MS/MS) and Global Natural Products Social (GNPS) molecular networking allow for comprehensive profiling of new compounds, while targeted isotope-labeling strategies enhance this process. Additionally, genome and metagenome mining tools such as antibiotics and secondary metabolite analysis shell (antiSMASH), Deep Biosynthetic Gene Cluster (DeepBGC), and Pipeline for Reconstructing Integrated Syntheses of Metabolites (PRISM) quickly identify biosynthetic gene clusters (BGCs) in both cultured and uncultured organisms, often using heterologous expression to validate products. Transcriptomic analyses, including RNA sequencing (RNA-seq), co-expression networks, and fluxomics, help clarify how pathways are regulated, while quantitative proteomics techniques like tandem mass tags/isobaric tags for relative and absolute quantitation (TMT/iTRAQ) and label-free methods, along with chemoproteomics approaches such as cellular thermal shift assay and thermal proteome profiling (TPP), uncover molecular targets and their mechanisms of action. This review also places significant emphasis on the role of artificial intelligence (AI) and machine learning (ML) in integrating multi-omics data, spanning activities from constructing gene-metabolite correlation networks to leveraging knowledge graphs and graph neural networks for data fusion and functional prediction. Finally, this review concludes by discussing the synergistic benefits of multi-omics for natural-product discovery, addressing current technical challenges, and exploring future directions toward high-throughput, intelligent data integration for next-generation NP research.},
}

*Biological Products/chemistry/metabolism/analysis
*Genomics/methods
*Metabolomics/methods
*Proteomics/methods
*Drug Discovery/methods
Computational Biology/methods
Multiomics

@article {pmid41396495,
year = {2025},
author = {Sari, DWK and Khamid, NL and Ikhrami, MA and Hardaningsih, I and Satriyo, TB and Suparmin, A},
title = {A Metagenomic Analysis of Gut Microbiome and Growth Performance of Giant Gourami (Osphronemus goramy) Fed with Raw Plant-Based Diet.},
journal = {Marine biotechnology (New York, N.Y.)},
volume = {27},
number = {6},
pages = {168},
pmid = {41396495},
issn = {1436-2236},
support = {2938/UN1/PN/PT.01.10/2022//Universitas Gadjah Mada/ ; },
mesh = {*Gastrointestinal Microbiome/genetics ; Animals ; *Animal Feed/analysis ; Plant Leaves/chemistry ; Aquaculture ; Diet/veterinary ; *Perciformes/growth & development/microbiology ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; Bacteria/classification/genetics ; Diet, Plant-Based ; },
abstract = {The increasing demand for global protein and awareness of environmental issues challenge sustainable aquaculture growth. The freshwater fish giant gourami (Osphronemus goramy) has the potential to be farmed sustainably. The gut microbiome approach is key to sustainable aquaculture by supporting fish health and feed utilization. This study evaluated the effect of taro leaves supplementation on giant gourami growth and gut microbiome composition. Four groups of fish (initial weight 378 ± 26.14 g) were fed commercial feed with 0%, 25%, 50%, and 75% taro leaves substitution for 16 weeks. Growth parameters such as absolute weight gain (AWG), specific growth rate (SGR), protein efficiency ratio (PER), survival rate (SR), and condition factor (CF) were measured, and gut microbiota was analyzed using 16 S rRNA gene sequencing via Oxford Nanopore Technology. The 50% taro leaves group showed significantly higher AWG (78.87 ± 11.96 g, p < 0.05) and PER (1.92 ± 0.37, p < 0.05) compared to the 100% commercial feed (53 ± 5.6 g and 0.54 ± 0.18, respectively). The condition factor of fish in all feeding experiments (1.40-1.55) demonstrated optimal growth conditions. The gut microbiome was dominated by Clostridium, with taro leaves substitution increasing Cellulosilyticum, Fusobacterium, and Ilyobacter, which are linked to cellulose breakdown and SCFA production. These findings suggest that giant gourami do not require solely commercial feed and are promising for sustainable aquaculture practice.},
}

*Gastrointestinal Microbiome/genetics
Animals
*Animal Feed/analysis
Plant Leaves/chemistry
Aquaculture
Diet/veterinary
*Perciformes/growth & development/microbiology
RNA, Ribosomal, 16S/genetics
Metagenomics
Bacteria/classification/genetics
Diet, Plant-Based

@article {pmid41396065,
year = {2025},
author = {Herrera, G and Zouiouich, S and Diaz-Mayoral, N and Purandare, V and Trabert, B and Wan, Y and Liu, J and Dagnall, CL and Jones, K and Hicks, BD and Hutchinson, A and Li, S and Shi, J and Abnet, CC and Vogtmann, E},
title = {Comparison of oral collection methods for 16S rRNA gene and shotgun metagenomic sequencing.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0180625},
doi = {10.1128/spectrum.01806-25},
pmid = {41396065},
issn = {2165-0497},
abstract = {UNLABELLED: To understand how sample collection affects oral microbiome studies, we evaluated the comparability of unpreserved saliva, saliva in glycerol, and mouthwash samples, their room temperature stability, and intraindividual stability over 6 months. Saliva and mouthwash samples were collected from 20 healthy participants 6 months apart. Saliva was divided, with half preserved in glycerol. Some aliquots were frozen immediately, while others were stored at room temperature for a week. DNA was extracted using the PowerSoil Pro and 16S rRNA gene, and shotgun metagenomic sequencing was conducted. Intraclass correlation coefficients (ICCs) from taxonomic and functional tables were compared to assess variability. We estimated sample size requirements based on the intraindividual stability over 6 months. Saliva in glycerol appeared more similar to unpreserved saliva than mouthwash, with higher median ICCs at genus (0.88 vs 0.60), species (0.92 vs 0.64), and gene levels (0.84 vs 0.36; all P < 0.01). Room temperature storage affected saliva in glycerol more than mouthwash (median genus-level ICC = 0.65). No significant differences were observed at the gene level. Intraindividual stability over 6 months was moderate. To detect an odds ratio of 1.5 with one sample per individual, estimated sample sizes ranged from 665 (common species) to 219,547 (rare species). Oral microbiome stability varies by collection method; mouthwash provides greater room temperature stability and may be preferable when immediate freezing is not feasible. For epidemiological studies, consistent use of a single collection method and inclusion of longitudinal sampling can improve reproducibility and power to detect associations with health outcomes.

IMPORTANCE: The oral microbiome plays a key role in health and disease, yet methodological inconsistencies in sample collection and processing can introduce variability and limit comparability across studies. This study investigates the impact of different oral sample collection methods on microbiome profiling and their stability over time. We demonstrate that sample type significantly influences taxonomic and functional microbiome profiles, with mouthwash showing greater stability during delayed processing and saliva in glycerol more closely resembling fresh saliva. Importantly, intraindividual microbial communities were only moderately stable over 6 months, emphasizing the need for consistent sampling protocols and consideration of temporal variation. These findings have direct implications for microbiome study design, highlighting that methodological choices can affect reproducibility, statistical power, and biological interpretation. Our results support the use of mouthwash as a practical alternative when freezing is delayed and underscore the value of longitudinal sampling for detecting biologically meaningful changes.},
}

@article {pmid41396034,
year = {2025},
author = {Xu, F and Yang, B and Cui, S and Yang, Z and Dai, N and Stanton, C and Ross, RP and Zhao, J and Lai, J and Chen, W and Wang, Y},
title = {Influence of gestational diabetes mellitus on the breast milk microbiota and oligosaccharides and their effects on the infant gut microbiota.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo04527d},
pmid = {41396034},
issn = {2042-650X},
abstract = {While the interplay between gestational diabetes mellitus (GDM) and the maternal-infant microbial axis is increasingly recognized, the specific pathways of influence remain unclear. This study comprehensively investigated the impact of GDM on the breast milk microbiota, human milk oligosaccharides (HMOs), and the subsequent development of the infant gut microbiota. We analyzed breast milk and paired infant fecal samples collected from healthy and GDM-affected mothers at two time points (0-7 and 42 days postpartum). The microbiota of both sample types was profiled by metagenomic sequencing, and HMOs in breast milk were quantified via liquid chromatography-tandem mass spectrometry (LC-MS/MS). Our findings revealed that GDM had a strong influence on the infant gut microbiota via reducing HMO concentrations than via direct alterations to the breast milk microbiota. These GDM-associated HMO alterations induced stage-specific shifts in the offspring's gut microbiota. Notably, the correlation between specific HMOs and gut bacteria reversed from the colostrum stage to the mature milk stage. This suggests that HMOs influence microbial colonization not only through direct utilization but also, and perhaps more importantly, via indirect ecological mechanisms such as cross-feeding. Collectively, our results identify maternal HMOs as a critical link between maternal metabolism and infant gut health, highlighting their potential as a promising nutritional target to improve long-term metabolic outcomes in GDM-exposed infants.},
}

@article {pmid41395987,
year = {2025},
author = {Sun, Z and Zhang, P and Li, Y and Zhang, C and Liu, Y and Ma, B and Lan, Q and Qi, H},
title = {Microsporidia keratoconjunctivitis identified as an emerging zoonotic threat from pet parrots: Clinical and metagenomic next-generation sequencing evidence.},
journal = {Virulence},
volume = {},
number = {},
pages = {2605385},
doi = {10.1080/21505594.2025.2605385},
pmid = {41395987},
issn = {2150-5608},
abstract = {Microsporidia are opportunistic, obligate intracellular fungi capable of causing keratoconjunctivitis. Because the clinical manifestations of microsporidia keratoconjunctivitis are indistinguishable from those of other etiologies, and the organism is difficult to culture, its diagnosis is challenging. The transmission routes of microsporidia keratoconjunctivitis remain poorly defined, and zoonotic sources have long been suspected but rarely confirmed. Between September 2024 and October 2025, a total of 15 confirmed cases of microsporidia keratoconjunctivitis were identified at Peking University Third Hospital. The diagnosis was established based on Giemsa-stained corneal scrapings and/or metagenomic next-generation sequencing (mNGS) of conjunctival lavage samples. Among these 15 patients, microsporidia spores were observed in corneal scrapings from nine individuals, while 13 tested positive for Encephalitozoon hellem (E. hellem) by mNGS. Notably, all affected patients reported a history of parrot exposure. Self-reported parrot exposures included direct ocular contact (n = 3) and indirect contact (n = 12). Six patients reported that their parrots had exhibited ocular abnormalities and diarrhea before the onset of the patients' symptoms, and two patients stated that their parrots had died prior to their clinical presentation. Ocular and fecal samples from three parrots associated with four patients were collected, and all the parrots tested positive for E. hellem by mNGS. These findings provide both clinical and molecular evidence supporting pet parrots as a zoonotic source of microsporidia keratoconjunctivitis. This emerging zoonotic threat calls for greater clinical awareness and attention to animal exposure history during diagnosis.},
}

@article {pmid41395968,
year = {2025},
author = {Almuhaideb, E and Hasan, NA and Grim, C and Rashed, SM and Parveen, S},
title = {Effects of aquaculture practices on Vibrio population dynamics and oyster microbiome.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0198525},
doi = {10.1128/aem.01985-25},
pmid = {41395968},
issn = {1098-5336},
abstract = {Oyster aquaculture is essential for ensuring a sustainable food source. Despite stringent controls, cases of oyster-related illnesses linked to pathogenic Vibrio parahaemolyticus (Vp) and Vibrio vulnificus (Vv) persist. This study investigated the impact of aquaculture practices on the oyster microbiome and pathogen levels, focusing on two common systems: on-bottom and floating cages. From June to November 2019, monthly samples were collected from the Chesapeake Bay, including oysters and water from each aquaculture system. Oyster samples included both fresh and temperature-abused oysters. The study utilized the most probable number and real-time PCR (MPN-qPCR) method to quantify total and pathogenic Vp and Vv in water and oyster samples. DNA was extracted from oyster homogenates and filtered water samples for shotgun metagenomic sequencing. The results revealed significant impacts of aquaculture practices on the diversity of the oyster microbiome, particularly affecting the distribution of phages, antibiotic resistance, and virulence factor genes. Shotgun metagenomic sequencing consistently showed higher genetic representation of Vibrio in floating cages for both fresh and temperature-abused oyster samples. MPN-qPCR results differed between practices, showing higher Vibrio levels in bottom cages for fresh oysters and higher levels in floating cages under temperature abuse. These discrepancies are likely explained by the stable conditions in bottom cages, the effects of temperature abuse, and the growth bias inherent to the MPN method. These results underscore the need for a holistic, time-sensitive approach, taking into account microbial states and the dynamic aspects of the oyster environment to understand the complex relationship between aquaculture practices and the oyster microbiome.IMPORTANCEThis study holds great importance for food safety, antibiotic resistance surveillance, aquaculture management, and environmental health. Unraveling the population dynamics of microbial communities in oysters and their responses to different aquaculture practices enhances our ability to ensure safer seafood, monitor antibiotic resistance, optimize aquaculture methods, and mitigate potential public health challenges. Moreover, it demonstrates the applicability of advanced metagenomic tools for future research. Furthermore, this research addresses critical aspects of food safety, food security, public health, and sustainable aquaculture practices, making it highly relevant in today's context.},
}

@article {pmid41395946,
year = {2025},
author = {Jansen, D and Bens, L and Wagemans, J and Green, SI and Hillary, T and Vanhoutvin, T and Van Laethem, A and Vermeire, S and Sabino, J and Lavigne, R and Matthijnssens, J},
title = {Hidradenitis suppurativa patients exhibit a distinctive and highly individualized skin virome.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0129025},
doi = {10.1128/msystems.01290-25},
pmid = {41395946},
issn = {2379-5077},
abstract = {Hidradenitis suppurativa (HS) is a chronic inflammatory disease characterized by recurring skin lesions. Despite ongoing research, the exact cause underlying initiation and progression of disease remains unknown. While prior research has linked the skin microbiota to HS pathology, the role of viruses has remained unexplored. To investigate the skin virome, metagenomic sequencing of viral particles was performed on 144 skin samples from 57 individuals (39 HS patients and 18 controls). It was found that the virome is not only linked to BMI, but also to the presence and severity of HS, marking a diverging viral profile in the progression of disease. Despite no differences in alpha-diversity, HS patients exhibited a significantly higher beta-diversity compared to healthy controls, indicating a more personalized virome with reduced viral sharing among patients. We identified distinct groups of commonly shared phages, referred to as the core phageome, associated with either healthy controls or patients. Healthy controls displayed a higher abundance of two core Caudoviricetes phages predicted to infect Corynebacterium and Staphylococcus, comprising normal skin commensals. In contrast, HS patients carried previously uncharacterized phages that were more prevalent in advanced stages of the disease, which likely infect Peptoniphilus and Finegoldia, known HS-associated pathogens. Interestingly, genes involved in superinfection exclusion and antibiotic resistance could be found in phage genomes of healthy controls and HS patients, respectively. In conclusion, we report the existence of distinct core phages that may have clinical relevance in HS pathology by influencing skin bacteria through mechanisms such as superinfection exclusion and antibiotic resistance.IMPORTANCEAn increasing body of research showed that the microbiome has an important role in complex human disease. In line with this, here, we analyzed a longitudinal HS cohort and found a relationship between the skin virome and HS pathology. This relationship was defined by distinct groups of phages associated with either healthy controls or HS patients, yet, in both instances, capable of enhancing bacterial fitness. In healthy individuals, these phages were widely shared, fostering symbiosis by ensuring stability of the commensal skin microbiota. Conversely, in HS patients, these phages revealed a more individualistic nature and could contribute to dysbiosis by providing antibiotic resistance genes to bacterial pathogens. Overall, these findings point to a potential clinical significance of the virome in understanding and addressing HS pathology.},
}

@article {pmid41395940,
year = {2025},
author = {Karamycheva, S and Wolf, YI and Koonin, EV and Makarova, KS},
title = {Spatial-temporal genome analysis and its application for the prediction of functional systems in bacteria and archaea.},
journal = {mBio},
volume = {},
number = {},
pages = {e0312725},
doi = {10.1128/mbio.03127-25},
pmid = {41395940},
issn = {2150-7511},
abstract = {Evolution of prokaryotic genomes is highly dynamic, including extensive gene gain via horizontal gene transfer and gene loss, as well as different types of genome rearrangements. Most quantitative analyses of prokaryotic genome evolution are based on single-gene events, although the distribution of genes is known to be non-random at the scales of operons and various genomic islands. Here, we present a spatial-temporal phylogenomic approach for detecting arrays of genes that are likely to have been acquired as a single block. It is shown that the acquisition of multi-gene blocks makes a major contribution to prokaryotic genome evolution and that these blocks consist primarily of co-directed, functionally coherent genes. A detailed analysis of the spatial-temporal data for the genomes of multiple groups of bacteria and archaea shows that the larger blocks of co-acquired genes represent primarily mobile genetic elements (MGEs), in many cases not identified previously. For example, this includes a new group of pleolipoviruses in Haloarchaea and a group of MGEs specific for Bacteroidota with hypervariable gene content and carrying a unique RNA polymerase enzyme. We also show that some ancestral phage-related large islands correspond to previously unnoticed R-type pyocins in Proteus and Morganella genomes. Many of the smaller gene blocks prone to high genome flux are expected to comprise antivirus defense systems and toxins-antitoxins. In a pilot analysis, eight novel toxin-antitoxin and seven novel defense systems were predicted in archaea of the phylum Thermococcaceae.IMPORTANCEWith many thousands of diverse bacterial and archaeal genomes made available by the fast advancing genomic and metagenomic sequencing, methods for in-depth analysis of genome organization and evolution are essential for extracting the maximum amount of information from this wealth of genomic data. We present a spatial-temporal approach for genome analysis that detects blocks of genes that were simultaneously acquired during genome evolution and shows that genes in such blocks are mostly transcribed in the same direction and have related functions, allowing for the prediction of previously unknown functional systems. The predictive power of the approach is demonstrated by detecting multiple novel mobile genetic elements and antivirus defense systems. Unlike most other functional prediction methods, the spatial-temporal approach does not require prior knowledge of the functions of any genes and has the potential to predict hundreds of novel functional systems amenable to further in-depth study, especially for poorly characterized groups of bacteria and archaea.},
}

@article {pmid41395693,
year = {2025},
author = {Stone, J and Tripyla, A and Scalise, MC and Balmer, ML and Bally, L and Meinel, DM},
title = {Taxonomic and functional shifts in the microbiome of severely obese, prediabetic patients: Ketogenic diet versus energy-matched standard diet.},
journal = {Diabetes, obesity & metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1111/dom.70364},
pmid = {41395693},
issn = {1463-1326},
support = {PCEFP3_194618/1//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; PCEGP3_186978//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; //Stiftung FHNW/ ; //Nestlé Health Science/ ; //Pierre Mercier Foundation/ ; },
abstract = {AIMS: Obesity and type 2 diabetes mellitus (T2DM) are among the leading global health challenges of the 21st century. While caloric restriction remains the cornerstone of weight loss interventions, ketogenic diets (KD), characterised by low carbohydrate and high fat intake, have been shown to improve metabolic health partly by modulating the gut microbiome. This study investigated the effects of a short-term KD on gut microbiome composition and function in severely obese, prediabetic patients, compared to an energy-matched standard diet (SD).

METHODS: In a randomised trial, patients with BMI >35 kg/m[2] and prediabetes underwent either a 2-week KD or isocaloric SD, both inducing a 30% energy deficit. Faecal samples collected before and after the intervention, alongside samples from healthy controls, were analysed by whole-genome metagenomic sequencing.

RESULTS: At baseline, prediabetic patients exhibited greater interindividual variability and lower alpha diversity than healthy controls. KD resulted in a significant reduction of alpha diversity, largely driven by a selective loss of Lachnospiraceae, with a concomitant increase in Bacteroidaceae. Functional profiling revealed that KD, but not SD, altered genes coding for enzymes involved in energy metabolism, amino acid synthesis, nucleic acid activity, RNA modification, and vitamin biosynthesis. Additionally, serum acetate levels increased significantly following KD.

CONCLUSIONS: These findings underscore that KD, independent of caloric intake, acutely remodels the gut microbiome's taxonomic and functional landscape, highlighting the microbiome as a potential mediator of KD's metabolic effects.},
}

@article {pmid41395487,
year = {2025},
author = {Bai, Z and Wang, Y and Li, Y and Xu, J and Lai, Z},
title = {The gut microbiota in liver transplantation recipients during the perioperative and postoperative recovery period.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1684303},
pmid = {41395487},
issn = {1664-302X},
abstract = {BACKGROUND: Chronic Liver Disease (CLD) is one of the frequent causes of death, especially in the developing world. Liver transplantation (LT) is an effective modality to treat end-stage liver disease. Perioperative management of liver transplantation patients and prevention of postoperative complications are the key to improving patient prognosis and quality of life, and the intestinal flora of these patients can affect postoperative complications and overall prognosis.

METHOD: We collected a total of 151 fecal samples from 59 liver transplantation patients at different stages from the First Hospital of Shanxi Medical University. Using 16S rRNA sequencing technology, we compared the characteristics and changes of their microbiota. We selected 42 samples for metagenomic sequencing using the microPITA method to further analyze the composition and functional differences of the microbiota during the perioperative period of liver transplantation across various time points.

RESULTS: After liver transplantation (LT), the diversity of gut microbiota initially decreased and then increased. Firmicutes, Proteobacteria, and Bacteroidota were the main bacterial groups during the perioperative period. Firmicutes and Proteobacteria initially decreased and then increased, while Bacteroidota exhibited the opposite process. Alpha diversity and beta diversity analyses indicated that 1 month post-transplantation was a turning point for microbiota recovery (P < 0.01). Metagenomic sequencing, analyzed using the LEfSe method, identified a total of 50 genera that played significant roles in this process. The changes in microbiota exhibited the same trend as the 16S rRNA results. KEGG pathway analysis also indicated that 1 month was a critical time point, with Ko02010 potentially being a key pathway for recovery in LT patients, and it showed a negative correlation with Bacteroidota (P < 0.05).

CONCLUSION: The diversity of intestinal flora in the perioperative period of LT patients decreased first and then increased, and the turning point of intestinal flora recovery was 1 month after LT surgery.},
}

@article {pmid41395483,
year = {2025},
author = {Lawal, OU and Parreira, VR and Rizvi, F and Precious, M and Anderson, REV and Overton, AK and Knapp, JJ and Maxwell, B and Thomas, S and Zambrano, M and Landgraff, C and Fleury, MD and Knox, NC and Charles, TC and Goodridge, L},
title = {Evaluation of sampling methods for genomic surveillance of SARS-CoV-2 variants in aircraft wastewater: advancing global early-warning systems for future pandemics.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1717424},
pmid = {41395483},
issn = {1664-302X},
abstract = {BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an ongoing threat to global health. Wastewater-based surveillance (WBS) has proven to be an important tool for tracking the dissemination of SARS-CoV-2 variants of concern (VOCs) in the community. In Canada, metagenomic analysis of aircraft wastewater was adopted at an early stage of the pandemic to track importation of emerging variants into the country. However, the acute need to determine the presence of emerging SARS-CoV-2 sublineages meant that the sampling methods utilized were not adequately validated. Here, we compared two different sampling methods for genomic surveillance of SARS-CoV-2 VOCs in aircraft sewage samples.

METHODS: Eighty-eight composite wastewater samples were collected over 9 weeks using both autosampler and passive torpedo samplers at the same location. SARS-CoV-2 nucleic acid in the samples was quantified using RT-qPCR. RNA samples were extracted and sequenced with the MiniSeq system using the tiled-amplicon sequencing approach with ARTIC V4.1 primer sets. Raw reads were preprocessed and SARS-CoV-2 mutations, variants lineages, and other sequence metrics from the two sampling methods were compared.

RESULTS: The two sampling methods yielded comparable viral load by RT-qPCR, but the autosampler produced higher genome coverage relative to the passive samplers. The Omicron lineages identified differed by sampling method. BQ.1* and BA.5.2*, which were the predominant lineages in wastewater and clinical samples at the time, were identified as dominant in the autosampler and passive sampler, respectively. Additionally, the autosampler captured higher diversity and relative abundance of VOCs, including emerging variants (XBB* and CH.1* lineages), as well as more clinically relevant mutations (S:K444T, T22942A, S:R346T) relative to passive sampler. Overall, the passive samplers produced concordant results with the autosampler for measuring SARS-CoV-2 load with RT-qPCR in aircraft wastewater.

CONCLUSION: Taken together, our results suggest underestimation of the diversity and abundance of SARS-CoV-2 VOCs and mutations in aircraft sewage using passive torpedo samplers. These data can be used to optimize genomic surveillance approaches for SARS-CoV-2 VOCs in aircraft wastewater samples.},
}

@article {pmid41395471,
year = {2025},
author = {Cheng, YN and Chen, GT and Huang, WC and Chiu, YP and Tang, Y and Fu, PK and Lee, TY},
title = {Lung microbiome signatures and explainable predictive modeling of glucocorticoid response in severe community acquired pneumonia.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1706432},
pmid = {41395471},
issn = {1664-302X},
abstract = {INTRODUCTION: Systemic glucocorticoids (SG) are administered to quell hyper-inflammation in severe community acquired pneumonia (SCAP), yet trials report inconsistent efficacy and no mechanistic explanation.

METHODS: We enrolled 200 ventilated SCAP patients, whom received hydrocortisone within 48 h of ICU admission, and generated longitudinal lower-airway microbiome profiles by 16S rRNA amplicon and metagenomic sequencing on ICU Days 1, 3 and 7. Compositional data were integrated with clinical variables through a fully reproducible bioinformatics analysis workflow.

RESULTS: Baseline community structures did not differ between SG and control cohorts, but by Day 7 survivors exhibited enrichment of Actinobacteria and Gammaproteobacteria whereas non-survivors accumulated Alphaproteobacteria and Campylobacteria. A random-forest model restricted to Bacilli and Alphaproteobacteria achieved AUROC = 0.89 (sensitivity 0.83, specificity 0.81) on a patient-held-out test set, significantly outperforming conventional severity indices like APACHE II, SOFA and mNUTRIC scores.

DISCUSSION: Collectively, our results demonstrate that SG therapy imposes reproducible ecological pressures on the lung microbiome and that a two-feature microbial fingerprint can forecast treatment success with single-sample resolution. These findings show that SG therapy actively reshapes the respiratory ecosystem and that lightweight microbiome-aware machine learning can stratify treatment response, offering a tractable path toward precision corticosteroid stewardship.},
}

@article {pmid41395467,
year = {2025},
author = {Hagarová, L and Kupka, D},
title = {Insights into the microbiome of mine drainage from the Mária mine in Rožňava, Slovakia: a metagenomic approach.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1675058},
pmid = {41395467},
issn = {1664-302X},
abstract = {The Mária mine, particularly the Strieborná vein, in Rožňava, is one of the most important mines in Slovakia, containing Ag-bearing tetrahedrite (40-46 wt% Cu, 26 wt% Sb, ~1 wt% Ag), making it an important source of strategic and critical raw materials. This mine discharges a unique neutral-pH (6.9), metal-rich mine water drainage (402 mg L[-1] SO4 [2-], 4.65 mg L[-1] Fe) that has remained microbiologically uncharacterized. This study presents the first comprehensive shotgun metagenomic survey of this mine effluent, generating ~227 million high-quality reads that assembled into 157,676 contigs and 378,023 non-redundant genes. Taxonomic analysis revealed a community dominated by Betaproteobacteria (> 66%), with abundant lithotrophic genera Sulfuritalea (6.93%), Ferrigenium (5.45%), Gallionella (3.79%), and Sideroxydans (3.65%), alongside the heterotrophic genus Pseudomonas (5.2%). Among the most prevalent neutrophilic iron-oxidizing bacterial strains were Sulfuritalea hydrogenivorans (6.93%), Ferrigenium kumadai (5.45%) and Gallionella capsiferriformas (3.79%). Acidophilic genera (e.g., Thiobacillus sp. at 0.43%, Ferrovum myxofaciens, Acidithiobacillus ferrivorans, Leptospirillum ferrooxidans) collectively accounted for <1% of the community. Functional annotation against KEGG, CAZy, COG, eggNOG, Swiss-Prot, CARD and BacMet databases demonstrated pronounced enrichment of iron cycling (e.g., the iron complex outer-membrane receptor protein TC.FEV.OM), sulfur oxidation (e.g., SoxA, SoxX, SoxB), carbon turnover (glycosyltransferase and glycoside hydrolase families) and nitrogen cycling (e.g., NifH, NifD, NirK, glnA). The antibiotic-resistance profile was dominated (> 95%) by tetracycline and fluoroquinolone determinants, while metal-resistance systems for Ni, Ag, As, Cu and Zn (including CzcD, CzcA, CznA, ArsD and AioX/AoxX) were likewise pervasive. This integrated taxonomic-functional portrait highlights a microbiome finely adapted to this unique geochemistry, combining lithotrophic metabolisms with multi-metal resistance. Our findings establish a critical baseline for long-term monitoring and highlight a high abundance of neutrophilic Fe(II)-oxidizers, suggesting they may represent promising candidates for targeted cultivation and subsequent evaluation in biotechnology applications.},
}

@article {pmid41394950,
year = {2026},
author = {Krishnan, LRA and Nair, S and Girija, D and Vishnu, BR},
title = {Unravelling the complex bacterial diversity in the rice rhizosphere of Kole lands of Thrissur through the metagenomics approach.},
journal = {3 Biotech},
volume = {16},
number = {1},
pages = {27},
pmid = {41394950},
issn = {2190-572X},
abstract = {UNLABELLED: The Kole wetlands of Kerala are highly productive rice ecosystems that lie below mean sea level and alternate between flooded and dry phases, shaping their ecological structure. This study focused on assessing bacterial diversity in the rice rhizosphere of Thrissur Kole lands. Rhizosphere soil was sampled from three Kole wetland locations, Puzhakkal (Pzk), Mullassery (Mls), and Cherpu (Chr). Bacterial communities were profiled by constructing metagenomic libraries and sequencing the 16S rRNA V3-V4 regions using the Illumina MiSeq platform. The sequences of the samples Pzk, Mls, and Chr were submitted in the SRA portal under the bioaccession numbers SAMN17776076, SAMN17776077, and SAMN17776078, respectively. High-quality, chimera-free sequences were clustered into OTUs using the QIIME pipeline. Taxonomic assignment was performed in MEGAN by matching reads to sequence databases and allocating NCBI-based taxon IDs. Phylum-level bacterial and archaeal diversity was further analyzed using the MG-RAST pipeline. The predominant bacterial phyla identified were Proteobacteria, Chloroflexi, Acidobacteria, Actinobacteria, Bacteroidetes, and Nitrospirae, with bacterial relative abundance being highest in the Pzk sample and comparatively lower in the Chr sample. The major archaeal phyla included Euryarchaeota, Crenarchaeota, and Thaumarchaeota. Many members of these bacterial and archaeal groups are known to thrive in waterlogged, oxygen-limited, or anoxic conditions, characteristic of Kole lands. Plant Growth Promoting Rhizobacteria (PGPR) such as Azospirillum, Paenibacillus, and Cellulosimicrobium were detected and could potentially be exploited as acid-tolerant biofertilizers. Biocontrol agents belonging to the genera Bacillus and Pseudomonas were also present. Further investigation is required for the characterization of the 'Unclassified' genera at taxonomic and functional levels to elucidate their ecological functions.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-025-04630-w.},
}

@article {pmid41394910,
year = {2025},
author = {Barton, KA and Finnerty, PB and Rupasinghe, R and González-Crespo, C and Mahar, JE and Eden, JS and Meisuria, NY and Martínez-López, B and Newsome, TM and Peel, AJ and Smith, JA and Brookes, VJ},
title = {The final frontier: using carcasses for one health surveillance at the ecosystem interface.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1683110},
pmid = {41394910},
issn = {2297-1769},
abstract = {Anthropogenic activities such as agricultural intensification, urbanisation, globalisation, and climate change are accelerating disease emergence globally, yet surveillance systems have largely overlooked the critical role of vertebrate carcasses in pathogen transmission. This omission is concerning because animal mass mortality events (MMEs) are increasing in frequency and magnitude, while populations of key vertebrate scavengers, especially obligate scavengers like vultures, are declining, resulting in longer carcass persistence and altered disease risks. Carcasses serve as essential resources in food webs but also act as complex microbe transmission hubs through direct consumption, environmental contamination, vector-mediated dispersal, and increased host aggregation, facilitating cross-species and trophic spillover events. Scavengers can amplify or mitigate microbe transmission: their consumption of carcasses can remove infectious material, but their mobility and sociality may also disperse potential pathogens across large areas. Technological advances, including remote sensing, camera traps, GPS telemetry, and machine learning, now enable detailed tracking of scavenger-carcass interactions and identification of transmission hotspots. Simultaneously, metagenomic sequencing allows untargeted detection of known and novel pathogens in carcass-associated microbial communities ("necrobiome"), with portable platforms supporting field-based surveillance. Integrating carcass-based surveillance into One Health frameworks through interdisciplinary collaboration among ecologists, epidemiologists, and data scientists offers a proactive approach to early outbreak detection, improved pandemic preparedness, and ecosystem health monitoring. Given the projected increase in climate-driven mortality events, incorporating carcass-scavenger networks into disease surveillance strategies is a valuable and under-utilised complement to existing approaches, enhancing our ability to monitor and mitigate emerging infectious diseases.},
}

@article {pmid41394788,
year = {2025},
author = {Zhang, B and Wang, J and Li, Q and Ge, J and Zhang, C and Zhou, T and Guo, H and Yang, B and Jiang, H},
title = {Clinical Efficacy and Diagnostic Value of Metagenomic Next-Generation Sequencing (mNGS) in Hospital-Acquired Pneumonia: A Stratified Retrospective Study of Responders and Non-Responders.},
journal = {Risk management and healthcare policy},
volume = {18},
number = {},
pages = {3803-3818},
pmid = {41394788},
issn = {1179-1594},
abstract = {INTRODUCTION: Hospital-acquired pneumonia (HAP) remains a major challenge in clinical practice, particularly due to polymicrobial infections and antimicrobial resistance. Traditional diagnostic methods, such as culture and PCR, are limited by low sensitivity, slow turnaround time, and inability to detect fastidious or novel pathogens. Metagenomic next-generation sequencing (mNGS) offers an unbiased approach to pathogen detection and may improve diagnostic accuracy and clinical decision-making.

METHODS: We conducted a retrospective study of 300 adult HAP patients admitted to Beijing Rehabilitation Hospital, China. Bronchoalveolar lavage fluid samples were analyzed using the Illumina sequencing platform for mNGS. Detection rates, pathogen spectrum, resistance gene identification, and treatment modifications were compared with conventional culture methods.

RESULTS: mNGS achieved a pathogen detection rate of 92%, significantly higher than the 72% achieved by culture. It identified a broader spectrum of bacteria, fungi, and viruses, including Pseudomonas, Klebsiella, and Aspergillus, which were often missed by culture. Polymicrobial infections were detected in 28% of cases, and antibiotic resistance genes were identified in 30% of samples. The median turnaround time for mNGS results was 48 hours after BAL sampling. Based on mNGS findings, treatment regimens were adjusted in 26% of patients.

CONCLUSION: mNGS demonstrated superior diagnostic performance compared with culture by increasing pathogen detection rates, identifying resistance genes, and guiding treatment adjustments in HAP patients. Despite its promise for precision medicine, further studies are needed to assess cost-effectiveness and generalizability, given the retrospective and single-center design of this study.},
}

@article {pmid41394752,
year = {2025},
author = {Hillary, LS and Knotts, TA and Adams, SH and Ali, MR and Olm, MR and Emerson, JB},
title = {DNA extraction and virome processing methods strongly influence recovered human gut viral community characteristics.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.25.690293},
pmid = {41394752},
issn = {2692-8205},
abstract = {Accurately characterising the human gut virome is critical to understanding virus-microbiome-host interactions. However, widely used methods introduce biases that complicate data interpretation and limit cross-study comparability. For instance, multiple-displacement amplification (MDA) preferentially amplifies single-stranded DNA viruses, while total metagenomes are dominated by non-viral sequences, reducing viral signal. These traditional methods have not been systematically compared to viral size-fraction metagenomes (viromes) prepared without MDA. To address this, we applied four common methods for characterising human gut viral community composition (total metagenomes, viromes with/ without DNase treatment (to remove free DNA), and MDA viromes) to a human stool sample, with technical triplicates for each approach. MDA biased viral community composition to a shocking degree: Microviridae formed ∼90% of MDA viromes compared to just 2% of non-MDA viromes. Removing ssDNA viruses from data analyses substantially reduced, but did not eliminate, MDA bias. Metagenomes were enriched for putative temperate phages and predicted Bacillota-phages , whereas predicted Bacteroidetes -phages dominated all viromes, suggesting that metagenomes and viromes select for different populations within the total viral community. DNase treatment had little-to-no effect on virome richness or community composition. This proof-of-principle experiment demonstrates that preparatory methods for viral community analysis can lead to substantially different conclusions from the same faecal sample, and we provide a comprehensive omic data analysis framework for comparing laboratory methodologies for viral ecology. With sufficient DNA yields now easily achievable from human gut viromes without the use of MDA, our results suggest that this biased amplification method should be avoided in human gut virome studies.},
}

@article {pmid41394329,
year = {2025},
author = {Yao, X and Sang, H and Gao, S and Hu, X and Yan, J and Liu, T and Chang, H and Pang, G and Dong, H and Meng, X and Jiang, L and Kong, M},
title = {Diagnostic Utility of Bronchoalveolar Lavage Metagenomic Next-Generation Sequencing for Pulmonary Mucormycosis: A Single-Center Retrospective Cohort Study.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {6469-6480},
pmid = {41394329},
issn = {1178-6973},
abstract = {BACKGROUND: Although pulmonary mucormycosis is rare, it is highly invasive and carries a significant mortality rate. Due to its nonspecific clinical manifestations, it is often misdiagnosed as other invasive fungal diseases. Bronchoalveolar lavage fluid metagenomic next-generation sequencing is a rapid, precise, and comprehensive method for pathogen detection, showing great potential in the early diagnosis of pulmonary mucormycosis in a single-center retrospective series. It provides clinicians with faster and more accurate etiological information, thereby improving patient outcomes and reducing mortality rates.

METHODS: This study conducted a retrospective analysis of the clinical data from 14 patients diagnosed with pulmonary mucormycosis between 1/6/2021 and 30/6/2024. Peripheral blood samples were collected to perform a complete blood count, measure C-reactive protein levels, and conduct 1,3-β-D-glucan and Galactomannan tests. Lung tissue samples were sent to the pathology laboratory for histological examination. Bronchoalveolar lavage fluid was subjected to fungal culture and metagenomic next-generation sequencing. Additionally, a three-month follow-up on the patients' survival status was carried out via telephone.

RESULTS: Males accounted for 57.14% of the cases. Diabetes mellitus was present in 12 patients (85.71%, 12/14), and fever was observed in 12 patients (85.71%, 12/14). The 14 patients were categorized as proven cases (4 cases), probable cases (4 cases), and possible cases (6 cases). Two patients (14.29%, 2/14) were diagnosed with disseminated mucormycosis. Chest Computed Tomography scans revealed cavities in half of the patients (50.00%, 7/14). Fungal hyphae were identified in all the histopathological examinations (100%, 4/4). Metagenomic next-generation sequencing detected Mucorales pathogens in all the (100%, 14/14) cases, which is higher positivity than the positive rates of the 1,3-β-D-glucan test (35.71%, 5/14), Galactomannan test (42.86%, 6/14) and fungal culture (7.14%, 1/14). The turnaround time for metagenomic next-generation sequencing reports is 1-3 days, which is much shorter than the time required to obtain results from fungal culture (2-5 days). Additionally, metagenomic next-generation sequencing identified bacterial and viral co-infections, with 11 patients diagnosed as having mixed infections. All patients were treated with antifungal agents targeting Aspergillus species, such as voriconazole, posaconazole, isavuconazole, or amphotericin B, resulting in 9 patients improving, 2 patients being transferred to higher-level hospitals, and 3 patients discontinuing treatment. The 90-day follow-up revealed a mortality rate of 28.57%.

CONCLUSION: Metagenomic next-generation sequencing can serve as an important complement to traditional diagnostic methods, enabling rapid and accurate differentiation of Mucorales from other fungi. This allows patients to receive timely and targeted antifungal therapy, playing a critical role in early intervention and improving prognosis.},
}

@article {pmid41394107,
year = {2025},
author = {Yang, Y and Jia, XF and Cui, GH and Huang, QY and Lin, MM and Shi, ZM and Ye, H and Zhang, XZ},
title = {Jinghuaweikang capsule alleviates Helicobacter pylori-infected gastric mucosal inflammation and drug resistance by regulating intestinal microbiota and MAPK pathway.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1628594},
pmid = {41394107},
issn = {2235-2988},
mesh = {Animals ; *Helicobacter Infections/drug therapy/microbiology/pathology ; *Helicobacter pylori/drug effects ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Drugs, Chinese Herbal/administration & dosage/pharmacology ; Disease Models, Animal ; *Gastric Mucosa/pathology/drug effects/microbiology ; *MAP Kinase Signaling System/drug effects ; *Drug Resistance, Bacterial/drug effects ; Anti-Bacterial Agents/pharmacology ; Male ; Inflammation/drug therapy ; *Gastritis/drug therapy/microbiology ; Capsules ; },
abstract = {BACKGROUND: Helicobacter pylori (H. pylori) infection represents a prevalent global health burden. Current eradication strategies are complicated by increasing antibiotic resistance and detrimental alterations to the gut microbiome. Jinghuaweikang capsule (JWC), a traditional Chinese medicine, has demonstrated efficacy against H. pylori, yet its mechanisms involving microbiota-inflammation interactions remain incompletely elucidated.

AIM: This study aimed to investigate the effects of the JWC on gastric mucosal inflammation and the expression of drug-resistance genes in H. pylori-infected mice.

METHODS: Sixty Kunming mice were randomly allocated into six groups, including normal control group (Control), model group (Model), Western medicine triple group (AC), low-dose JWC group (JWCL), medium-dose JWC group (JWCM), and high-dose JWC group (JWCH). A mouse model of H. pylori infection was established by intragastric administration of an H. pylori SS1 solution for two weeks. The efficacy of this model was evaluated using rapid urease test (RUT) and Warthin-Starry (WS) silver stain. Subsequently, the experimental cohort of mice underwent pharmacological intervention. Hematoxylin and eosin (HE) staining, enzyme-linked immunosorbent assay (ELISA), and quantitative real-time polymerase chain reaction (qRT-PCR) were used to assess the impact of JWC on inflammation within the gastric mucosa of mice infected with H. pylori. Metagenomic sequencing technology was used to identify alterations in the intestinal microbiota and antibiotic resistance genes in the murine models. Western blotting was used to assess the expression levels of proteins involved in the mitogen-activated protein kinase (MAPK) signaling pathway.

RESULTS: JWC mitigated gastric mucosal inflammation induced by H. pylori infection and reduced the concentrations of interleukin- (IL-) 6, IL-1β, and tumor necrosis factor-α (TNF-α) while inhibiting gene expression level. Metagenomic sequencing revealed that triple therapy in Western medicine markedly diminished the diversity of the intestinal microbiota while elevating the abundance of antibiotic-resistance genes, including macB, arlR, evgS, tetA(58), and mtrA. The diversity and richness of the intestinal microbiota in the JWC group were comparable to those in the control group, with an increase in the abundance of beneficial bacteria such as Muribaculaceae_bacterium. Furthermore, the expression levels of the antibiotic resistance genes macB, tetA(58), bcrA, oleC, and arlS were downregulated. Moreover, the activation of MAPK signaling pathway components phospho-ERK and phospho-p38 was inhibited.

CONCLUSION: JWC preserves microbial diversity and promotes a beneficial compositional shift, mitigates the risk of antibiotic resistance, modulates the MAPK signaling pathway, and alleviates gastric mucosal inflammation in mice infected with H. pylori.},
}

Animals
*Helicobacter Infections/drug therapy/microbiology/pathology
*Helicobacter pylori/drug effects
*Gastrointestinal Microbiome/drug effects
Mice
*Drugs, Chinese Herbal/administration & dosage/pharmacology
Disease Models, Animal
*Gastric Mucosa/pathology/drug effects/microbiology
*MAP Kinase Signaling System/drug effects
*Drug Resistance, Bacterial/drug effects
Anti-Bacterial Agents/pharmacology
Male
Inflammation/drug therapy
*Gastritis/drug therapy/microbiology
Capsules

@article {pmid41394104,
year = {2025},
author = {Xuan, F and Li, C and Zhao, H and Liu, N and Zhao, X and Zhang, B and Wu, X},
title = {Diagnosis, treatment, and monitoring of cytomegalovirus pneumonia in a hematopoietic stem cell transplantation child.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1665477},
pmid = {41394104},
issn = {2235-2988},
mesh = {Humans ; *Hematopoietic Stem Cell Transplantation/adverse effects ; Child ; Female ; *Cytomegalovirus Infections/diagnosis/drug therapy ; Antiviral Agents/therapeutic use ; *Cytomegalovirus/isolation & purification/genetics ; *Pneumonia, Viral/diagnosis/drug therapy/virology ; Leukemia, Myelogenous, Chronic, BCR-ABL Positive/therapy/complications ; Bronchoalveolar Lavage Fluid/virology ; Acetates/therapeutic use ; Quinazolines/therapeutic use ; },
abstract = {BACKGROUND: Cytomegalovirus (CMV), an opportunistic pathogen, can cause severe pneumonia in Chronic myeloid leukemia (CML) children undergoing hematopoietic stem cell transplantation (HSCT), resulting in a high mortality rate.

CASE PRESENTATION: An 11-year-old girl was hospitalized with a 3-day history of fever and vomiting, presenting with anemia and massive splenomegaly. A series of diagnostic tests, including blood cell count, bone marrow analysis, flow cytometry, chromosomal examination, and genetic testing, confirmed a diagnosis of CML at blast-phase. Following a one-year course of tyrosine kinase inhibitor-based chemotherapy, the patient entered the chronic phase and underwent a 6/12 human leukocyte antigen (HLA)-matched HSCT from her father. Two weeks after HSCT, the patient developed grade III skin graft-versus-host disease and hemorrhagic cystitis, which were effectively treated and symptoms were alleviated. One month after transplantation, the patient presented with serious pneumonia and pancytopenia. Although five blood cultures and two sputum cultures were all negative, metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) indicated a high abundance of CMV (16635 reads), leading to a diagnosis of CMV pneumonia. Notably, no typical resistant mutations were identified in the CMV genome. Targeted treatment with sodium phosphonoformate and letermovir was administered. As a result, the patient's condition improved remarkably with the abundance of CMV decreasing to only 12 reads. After one-year of monitoring, the primary disease was well-controlled, and no CMV reactivation was observed.

CONCLUSION: The diagnosis, treatment, and monitoring of pneumonia is crucial in post-HSCT patients. This case highlights the utility of mNGS in diagnosing and monitoring CMV pneumonia in post - HSCT patient and the effectiveness of targeted therapy in managing such infections.},
}

Humans
*Hematopoietic Stem Cell Transplantation/adverse effects
Child
Female
*Cytomegalovirus Infections/diagnosis/drug therapy
Antiviral Agents/therapeutic use
*Cytomegalovirus/isolation & purification/genetics
*Pneumonia, Viral/diagnosis/drug therapy/virology
Leukemia, Myelogenous, Chronic, BCR-ABL Positive/therapy/complications
Bronchoalveolar Lavage Fluid/virology
Acetates/therapeutic use
Quinazolines/therapeutic use

@article {pmid41393784,
year = {2025},
author = {Longhi, G and Tarracchini, C and Angelini, L and Anzalone, R and Viappiani, A and Ventura, M and Milani, C and Turroni, F},
title = {Exploring diversity and functional contribution of the microbiome of traditional Italian dry-cured hams.},
journal = {Current research in microbial sciences},
volume = {9},
number = {},
pages = {100516},
pmid = {41393784},
issn = {2666-5174},
abstract = {Traditional dry-cured hams host diverse microbial communities; however, their taxonomic composition, functional capacity, and potential interactions with the human gut remain poorly understood. This study aimed to provide a comprehensive characterization of the microbiota associated with Italian Protected Designation of Origin (PDO) dry-cured hams and to investigate their functional relevance in the food matrix and under simulated intestinal conditions. A total of 96 samples, representing different geographical origins and maturation stages, were analyzed using metagenomics approaches. A conserved microbial core dominated by Staphylococcus equorum (prevalence 80 %) was identified, accompanied by accessory taxa such as Tetragenococcus halophilus (62 %) and Leuconostoc carnosum (10 %). Cluster analyses revealed substantial variability across samples, with community structures influenced more by producer-specific factors than by product type or ripening stage. Functional metagenomics investigation highlighted the presence of metabolic pathways associated with amino acid degradation, carbohydrate metabolism, and lipid transformation, supporting a role for ham-associated microbes in flavor and texture development. Furthermore, cultivation in a simulated gut environment showed a marked reshaping of the microbial community, with low-abundance taxa, including Bacillus spp. and Lactococcus lactis, proliferating under intestinal-like conditions, while the dominance of S. equorum was reduced. Our findings showed that the microbiota of dry-cured ham not only drives key sensory qualities of the product but also comprises a reservoir of live microorganisms capable of tolerating the gut-like conditions. These results highlight the dual role of foodborne microbiota in shaping both food properties and potential interactions with the human host, underscoring the need for further in vivo investigations.},
}

@article {pmid41393342,
year = {2025},
author = {Nishimura, Y and Omae, K and Tominaga, K and Iwasaki, W},
title = {CORGIAS: identifying correlated gene pairs by considering evolutionary history in a large-scale prokaryotic genome dataset.},
journal = {NAR genomics and bioinformatics},
volume = {7},
number = {4},
pages = {lqaf182},
pmid = {41393342},
issn = {2631-9268},
mesh = {Phylogeny ; *Evolution, Molecular ; *Genome, Bacterial ; Databases, Genetic ; },
abstract = {The recent expansion of prokaryotic genomes reveals many ortholog groups (OGs) whose function cannot be inferred from conventional, sequence similarity-based annotation methods, especially in metagenome-assembled genomes. Phylogenetic profiling is one of the promising methods to annotate these OGs, by identifying functional relationships of OGs using co- or anti-occurrence of OG distributions, not sequence similarity. Here, we proposed two new phylogenetic methods for large-scale data, Ancestral State Adjustment (ASA) and Simultaneous EVolution test (SEV), which consider the ancestral state of OG presence/absence. In evaluations using three distinct prokaryotic datasets, ASA and SEV showed better or comparable performance to both established and recently proposed methods for large-scale data. We compared the functionally related OGs detected by each method and found that SEV and its predecessor can identify slowly evolving OGs, such as housekeeping genes. In contrast, ASA and its predecessors can detect functionally related OGs that tend to be gained or lost in a fixed order, indicating a strong evolutionary constraint that provides clues for functional prediction. Using matrix multiplication, we also showed that SEV is scalable in the latest genome databases.},
}

Phylogeny
*Evolution, Molecular
*Genome, Bacterial
Databases, Genetic

@article {pmid41393220,
year = {2026},
author = {Brown, NK and Depuydt, L and Zakeri, M and Alhadi, A and Allam, N and Begleiter, D and Kabilan Karpagavalli, NB and Khajjayam, SS and Wahed, H and Gagie, T and Langmead, B},
title = {KeBaB: k-mer based breaking for finding long MEMs.},
journal = {International Symposium on String Processing and Information Retrieval : SPIRE ... : proceedings. SPIRE (Symposium)},
volume = {16073},
number = {},
pages = {10-17},
pmid = {41393220},
abstract = {Long maximal exact matches (MEMs) are used in many genomics applications such as read classification and sequence alignment. Li's ropebwt3 finds long MEMs quickly because it can often ignore much of its input, skipping matching steps which are redundant to the final output. In this paper we propose KeBaB, a fast and space efficient k-mer filtration step using a Bloom filter. This approach speeds up MEM-finders such as ropebwt3 even further by letting them ignore even more, breaking the input into substrings called "pseudo-MEMs" which are guaranteed to contain all long MEMs. We also show experimentally that KeBaB can accelerate metagenomic classification without significantly reducing accuracy, either by finding all long MEMs or by leveraging the filter to find only the long MEMs present in the t longest pseudo-MEMs.},
}

@article {pmid41392764,
year = {2025},
author = {Wu, Q and Gao, G and Kwok, LY and Qiao, J and Wei, Z and He, Q and Sun, Z},
title = {Bifidobacterium animalis subsp. lactis Bbm-19 ameliorates insomnia by remodeling the gut microbiota and restoring γ-aminobutyric acid and serotonin signaling.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo04374c},
pmid = {41392764},
issn = {2042-650X},
abstract = {Insomnia is associated with dysregulation of the gut-brain axis, yet microbiome-targeted interventions remain underexplored. In this study, we investigated the effects of Bifidobacterium animalis subsp. lactis Bbm-19 (Bbm-19), a strain isolated from human breast milk, in a 4-chloro-DL-phenylalanine-induced mouse model of insomnia. Using integrated behavioral, neurochemical, immunological, and multi-omics approaches, this study demonstrates that insomnia is characterized by shortened sleep duration, prolonged sleep latency, anxiety-like behaviors, and reduced levels of serotonin and gamma-aminobutyric acid in the gut, serum, and brain. Administration of Bbm-19 significantly improved sleep parameters, reduced anxiety-like behaviors, and increased survival. Metagenomic and metabolomic analyses revealed that Bbm-19 restored gut microbiota balance, enriched beneficial taxa, including Muribaculaceae bacterium and Stercoribacter sp., and reprogrammed microbial metabolic modules, particularly those involved in amino acid metabolism (including alanine, aspartate, glutamate, arginine, proline, and tryptophan pathways). Targeted metabolomics confirmed increased levels of gamma-aminobutyric acid and serotonin in fecal and brain tissues, along with normalization of inflammatory cytokine profiles. Spearman correlation analysis linked Bbm-19-enriched taxa to improved neurotransmitter levels and sleep outcomes. Notably, Bbm-19 outperformed lorazepam in modulating gut-specific metabolic functions and synergistically enhanced its effects when co-administered. These findings demonstrate that Bbm-19 ameliorates insomnia through coordinated regulation of the gut microbiota, host metabolism, and neuroimmune signaling, highlighting its potential as a targeted psychobiotic intervention for sleep disorders.},
}

@article {pmid41392335,
year = {2025},
author = {Zheng, X and Luo, X and Zhang, Y and Zou, Z and Yang, J and Liu, H and Lu, Z and Cao, F and Wang, X and Ge, X and Li, X and Wang, J},
title = {Inflammation in Diabetic Kidney Disease Is Linked to Gut Dysbiosis and Metabolite Imbalance.},
journal = {Journal of diabetes},
volume = {17},
number = {12},
pages = {e70175},
doi = {10.1111/1753-0407.70175},
pmid = {41392335},
issn = {1753-0407},
support = {XHZDZK019//Mianyang Central Hospital/ ; 2020FH09//Mianyang Central Hospital/ ; 2022HYX005//Mianyang Central Hospital/ ; 2023YFS0470//Science and Technology Department of Sichuan Province/ ; 2023ZYDF073//Mianyang Science and Technology Bureau/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Dysbiosis/microbiology/metabolism/immunology ; *Diabetic Nephropathies/microbiology/metabolism/immunology ; Male ; Middle Aged ; Female ; *Inflammation/metabolism/microbiology ; Cytokines/blood ; Case-Control Studies ; Aged ; Adult ; Feces/microbiology ; },
abstract = {BACKGROUND: Diabetic kidney disease (DKD) is characterized by a sustained pro-inflammatory response of the immune system, which leads to renal failure progression and related complications. Emerging evidence suggests that gut microbiota dysregulation may be a pathogenic mediator in DKD, while mechanisms remain unclear. This study aimed to identify differences in the gut microbiota of the DKD group and healthy controls (HC).

METHODS: Gut microbiota composition was determined using shotgun metagenomic sequencing on fecal samples; serum cytokines were measured via ELISA, immune phenotypes were detected using flow cytometry.

RESULTS: Significant differences in gut microbiota diversity and richness were observed between patients with DKD and HC, with higher abundances of Enterobacteriaceae, Serratia, and Shigella in the DKD group than in the HC group. Additionally, CD3+ (especially CD4+) T cells were significantly higher in the renal tissue of the DKD group than the HC group. Flow cytometry identified significantly higher circulating levels of NKT cells and CD8+ T cells and lymphocyte ratio in HC than in DKD. CD4+ cells, CD4+ TCM cells, CD8+ TCM cells, and the CD4+/CD8+ cell ratio were significantly higher in the DKD group than in the HC group, as were levels of pro-inflammatory mediators, including IL-6, TNF-α, and sCD14, and expression of the gut barrier dysfunction marker ZO-1.

CONCLUSIONS: Gut barrier dysfunction and gut microbiota imbalance may mediate the pro-inflammatory immune phenotype observed in patients with DKD and thereby contribute to DKD progression. These findings underscore the important role of the microbiota-immune axis in the development of DKD.},
}

Humans
*Gastrointestinal Microbiome
*Dysbiosis/microbiology/metabolism/immunology
*Diabetic Nephropathies/microbiology/metabolism/immunology
Male
Middle Aged
Female
*Inflammation/metabolism/microbiology
Cytokines/blood
Case-Control Studies
Aged
Adult
Feces/microbiology

@article {pmid41392160,
year = {2025},
author = {Jamy, M and Huber, T and Antoine, T and Ruscheweyh, HJ and Paoli, L and Pelletier, E and O Delmont, T and Burki, F},
title = {Identification of a deep-branching lineage of algae using environmental plastid genomes.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-67401-4},
pmid = {41392160},
issn = {2041-1723},
support = {2022-00351//Vetenskapsrådet (Swedish Research Council)/ ; 2021-04055//Vetenskapsrådet (Swedish Research Council)/ ; ERC consolidator grant 101044505//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; },
abstract = {Marine algae underpin entire ocean ecosystems. Yet algae in culture poorly represent their large environmental diversity, and we have a limited understanding of their convoluted evolution by endosymbiosis. Here, we perform a phylogeny-guided plastid genome-resolved metagenomic survey of Tara Oceans expeditions. We present a curated resource of 660 new non-redundant plastid genomes of environmental marine algae, vastly expanding plastid genome diversity within major algal groups, including many without closely related reference genomes. Notably, we recover four plastid genomes, including one near-complete, forming a deep-branching plastid lineage of nano-size algae that we informally name leptophytes. This group is globally distributed and generally rare, although it can reach relatively high abundance in the Arctic. A near-complete mitochondrial genome showing strong co-occurrence with leptophyte plastids is also recovered and assigned to this group. Leptophytes encompass the enigmatic plastid group DPL2, one of the very few known plastid groups not clearly belonging to major algal groups and previously known only from 16S rDNA sequences. Comparative organellar genomics and phylogenomics indicate that leptophytes are sister to haptophytes, and raise the intriguing possibility that cryptophytes acquired their plastids from haptophytes. Collectively, our study demonstrates that metagenomics can reveal hidden organellar diversity, and improve models of plastid evolution.},
}

@article {pmid41392116,
year = {2025},
author = {Li, C and Jiang, P and Fan, C and Chen, J and Liang, S and Chen, S and Mi, H},
title = {Characteristics of gut microbiota and metabolites in rats with ketamine-induced cystitis.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-31280-y},
pmid = {41392116},
issn = {2045-2322},
support = {81860142//National Natural Science Foundation of China/ ; },
abstract = {Ketamine-induced cystitis (KC) manifests as lower urinary tract symptoms stemming from prolonged ketamine abuse, yet its precise pathogenesis remains unclear. It is widely recognized that gut microbiota dysregulation can trigger metabolic aberrations in many diseases. This study aimed to address the dearth of knowledge regarding the functional characteristics of gut microbiota and their metabolites in KC, and to explore the underlying mechanisms of KC from the perspective of the gut-bladder axis. Metagenomic and untargeted metabolomic analyses were employed to elucidate critical features of gut microbiota and metabolism in KC rats. Metagenomic sequencing revealed significant gut microbiota dysregulation, characterized by discrepancies in 46 bacterial taxa at the species level, including Bifidobacterium pseudolongum, Erysipelotrichaceae bacterium OPF54, Firmicutes bacterium CAG: 424, and Phocaeicola sartorii. Untargeted metabolomics identified 13 dysregulated metabolites, encompassing Stachydrine, Quinoline, Sedanolide, and others. Correlation analyses among differential gut microbiota, metabolites, and bladder inflammatory factors in KC rats suggested a potential interconnectivity between these factors. Furthermore, the anti-inflammatory property of Stachydrine was experimentally validated using an in vitro model. These findings collectively indicate that KC rats exhibit alterations in gut microbiota composition and metabolites profiles, establishing a preliminary association among gut microbiota, metabolites, and KC pathogenesis. Finally, validation of the anti-inflammatory effects of Stachydrine provides insight into a potential pathogenic pathway involving gut-bladder axis crosstalk, in which dysregulation of gut microbiota and metabolites contributes to the development of KC.},
}

@article {pmid41392048,
year = {2025},
author = {Liu, X and Chen, Y and Shi, Z and Shi, Z and Pu, T and Zhang, Y and He, F and Li, X and Wang, Y and Jia, J and He, B and Yang, P},
title = {Macrogenomic analysis of the previous crops effects on tobacco soil microbiomes.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-08640-9},
pmid = {41392048},
issn = {2045-2322},
support = {2024530700242003, 2023530700242002//the special funds for the Scientific Research Program of Yunnan Tobacco Company/ ; 2024530700242003, 2023530700242002//the special funds for the Scientific Research Program of Yunnan Tobacco Company/ ; (XDYC CYCX-2022-0071)//the "Xingdian Talent" Industry Innovation Talent Program in Yunnan Province/ ; },
abstract = {Crop rotation serves as a valuable agronomic practice for addressing succession barriers in crops, particularly in tobacco growing. The effect of different previous crops on the microbiology of soils planted with tobacco is an area that deserves further study.This study investigated the chemical properties, microbial community composition, and functional genes related to nutrient cycling in tobacco-planted soils with no preceding crop (CK), garlic (T1), or faba bean (T2) as preceding crops. The results indicated that the T1 treatment significantly decreased the contents of soil organic matter (SOM, 11.32%), total phosphorus (TP, 29.41%), total potassium (TK, 3.33%), and available potassium (AK, 46.88%), whereas the T2 treatment notably increased the content of hydrolyzable nitrogen (HN, 34.88%). Furthermore, the T2 treatment significantly enhanced the diversity of soil bacteria and fungi, particularly the bacterial Shannon index (1.49%) and fungal Chao1 (24.11%) and Shannon (7.73%) indices. In terms of microbial composition, compared to the CK, the T2 treatment enriched the relative abundance of beneficial bacterial genera (e.g., Sphingomonas, Methyloceanibacter, Rhizophagus) and reduced the relative abundance of pathogenic fungi (e.g., Fusarium). Additionally, T2 treatment increased the abundance of functional genes associated with nitrogen, phosphorus, and potassium, thereby promoting the cycling of soil nutrients. Overall, faba bean as a preceding crop was more beneficial for subsequent tobacco cultivation than fallow periods or garlic.},
}

@article {pmid41292709,
year = {2025},
author = {Quiñones-Sanchez, CL and Bilbao-Del Valle, JL and Urdaneta-Colon, MA and Santiago-Rodriguez, TM and Rodriguez-Fernandez, IA},
title = {Optimizing Tissue Lysis and DNA Extraction Protocols to Enhance Bacterial Diversity Profiling in the Drosophila melanogaster Gut Microbiome.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41292709},
issn = {2692-8205},
support = {P20 GM103642/GM/NIGMS NIH HHS/United States ; P30 GM149367/GM/NIGMS NIH HHS/United States ; R25 HG012702/HG/NHGRI NIH HHS/United States ; },
abstract = {The gut microbiota is a dynamic community that influences host metabolism, immunity, and overall health. Accurate characterization of this community requires robust and reproducible DNA extraction methods; however, technical biases introduced during tissue lysis and DNA isolation remain major challenges in microbiome research, particularly in animal model systems. In this study, we compared two commercial DNA extraction kits (Qiagen and Zymo) and two lysis methods (manual pestle homogenization and bead-beating) to evaluate their impact on microbiota profiling in a microbial community standard (MCS) and Drosophila melanogaster gut samples, a tractable model for host-microbe interactions. Full-length 16S rRNA sequencing was performed using Oxford Nanopore Technologies, followed by bioinformatic analysis using EPI2ME for taxonomic classification and standard diversity pipelines. Our data revealed that extraction and lysis methods significantly influence microbial composition, with some protocols resulting in inflated richness in MCS samples. Pestle homogenization with the Qiagen kit yielded the highest bacterial species richness while maintaining consistent representation of both Gram-positive and Gram-negative taxa. These findings demonstrate that extraction methodology strongly affects microbial diversity estimates and emphasize the need for standardized protocols to ensure reproducibility across microbiome studies, particularly those using model systems.},
}

@article {pmid41248092,
year = {2025},
author = {Richie, T and Lee, STM},
title = {Decoding the Gut Microbiota: Mechanisms of Host-Microbe Interactions and Inflammatory Pathologies.},
journal = {Digestion},
volume = {},
number = {},
pages = {1-18},
doi = {10.1159/000549457},
pmid = {41248092},
issn = {1421-9867},
abstract = {BACKGROUND: Microbes residing in the gastrointestinal tract are intertwined with the immune development and overall health of the host throughout stages of life. It is well established that these microbes can have both positive and negative impacts on host health. Having foundational knowledge of these interactions with the host is critical in understanding gastrointestinal health.

SUMMARY: This review discusses the importance of high-resolution study of the gut microbiota, which includes potential modern approaches for analyzing the gut microbiota and considers the challenges and aspects necessary for robust investigation of the gut microbiota. Here, we highlight the complex and highly individualized relationship of microbes interacting within the host results in an ever-changing landscape in the gastrointestinal tract, whether due to host conditions or microbial conditions including microbe-microbe and microbe-host interactions. The vastness and complexity of the gut microbiota contribute to the challenge of quantifying not only a community of microbes in the gut environment, but also maintaining resolution to investigate individual microbes, capturing the network of interactions coinciding in the gastrointestinal tract. Furthermore, the review emphasizes the importance of microbial functions and products to host health outcomes in the context of inflammatory diseases.

KEY MESSAGES: Consideration for microbial functions and interactions with the gut immune system is critical for developing effective treatment strategies of inflammatory disorders. Employing high-resolution microbial techniques to investigate microbes with environmental relevance and community functions are a major challenge in the microbiome field. With new techniques and improvements on existing methodologies, investigating microbes at various community levels is feasible and becoming critical in understanding the community interactions with the host influencing the immune status and overall health outcomes.},
}

@article {pmid41391873,
year = {2025},
author = {Shen, Q and Mao, L and Shi, W and Wang, J and Ndjekadom, A and Bao, Y and Wang, X and Liu, Y and Yang, S and Ji, L and Shan, T and Zhang, W},
title = {Viral communities and identification of a parvovirus and two picornaviruses in geese with gout.},
journal = {The Journal of veterinary medical science},
volume = {},
number = {},
pages = {},
doi = {10.1292/jvms.25-0456},
pmid = {41391873},
issn = {1347-7439},
abstract = {In recent years, an emerging infectious disease characterized by urate deposition in viscera and joints has outbreak in the goose farms of China, causing substantial economic losses. Although goose astrovirus (GoAstV) was believed to be the main causative pathogen, several studies have shown that co-infection with other viruses, such as goose parvovirus, alongside astrovirus, may exacerbate the disease condition. In our previous research, we isolated a goose astrovirus with a novel type of recombination that causes fatal gout in geese in Shanghai, China. By analyzing the viral community using viral metagenomics data of fecal, kidney and liver samples of geese with gout, we found that parvoviruses and picornaviruses occupied a substantial proportion, suggesting their potential involvement in the etiology of goose gout. To determine if there were other causative viruses present in these geese, fecal, kidney, and liver samples were deeply sequenced using viral metagenomics. The results indicated that goose parvovirus and picornavirus constituted the predominant part of all or partial viral communities. Subsequently, the genomes and genomic structures of two picornaviruses, as well as a parvovirus, were determined. Phylogenetic analysis revealed that this parvovirus, named dependoparvovirus_CH_SH01, belongs to the Parvovirinae subfamily within the family Parvoviridae, while the two picornaviruses were classified within the Megrivirus (megrivirus_CH_SH01) or Ludopivirus (ludopivirus_CH_SH01) genus within the Kodimesavirinae subfamily, respectively. Recombination analysis suggested that megrivirus_CH_SH01 was a potential recombinant virus between two megriviruses. Our study suggested that infections with viruses other than astrovirus may be associated with the occurrence of goose gout. Additionally, this work has enriched the virus sequence information for Megrivirus and picornaviruses.},
}

@article {pmid41391818,
year = {2025},
author = {Zhou, H and Gao, and Wu, B and Xu, G and Tian, L and Sun, Y and Yang, F and Ni, K},
title = {Phyllosphere microbiomes in grassland plants harbor a vast reservoir of novel antimicrobial peptides and biosynthetic diversity.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2025.12.017},
pmid = {41391818},
issn = {2090-1224},
abstract = {INTRODUCTION: The phyllosphere microorganisms colonizing plant surface harbor capacities to synthesize diverse specialized metabolites that mediate communication and interactions with environment and host. However, most known metabolites are derived from a few culturable microorganisms, and the genomic diversity and biosynthetic potential of the vast majority of bacteria associated with plants remain largely unexplored.

OBJECTIVES: Here, we aim to explore the genome architecture, biosynthetic ability, and host specific adaptability of grassland ecosystems, uncovering new perspectives on grassland phyllosphere microbial resources.

METHODS: We employed ultra-deep metagenomic sequencing, functional analysis, host-associated characterization, and bioactivity assays to explore the phyllosphere microbiome across 221 grassland plant samples representing 45 families. This approach revealed host preference in biosynthetic gene clusters (BGCs) and validated the antimicrobial efficacy of phyllosphere-derived antimicrobial peptides (AMPs).

RESULTS: Grassland plant phyllosphere microbiomes encode diverse BGCs. We identified 885,396 potential AMPs from over 68 million non-redundant gene sequences. Then, we reconstructed hundreds of near-complete genomes from phyllosphere metagenomes, and 32.61 % of reconstructed genomes were identified as unclassified genomes, primarily within Pseudomonadota, Actinomycetota, Bacillota and Bacteroidota phyla. Of the near-complete genomes, 91.97 % of the BGCs and 99.76 % of the identified AMPs were previously uncharacterized. Host phylogenetic analysis revealed functional divergence. Poaceae-associated Pseudomonas genomes contain an average of 28 BGCs, significantly higher than those in Asteraceae-associated genomes (mean = 14.76, P = 0.033). Similarly, Poaceae-associated Pantoea genomes carried an average of 9 BGCs, exhibiting significant enrichment compared to genomes from Asteraceae (mean = 7.13, P = 6.1e-05), Lamiaceae (mean = 7, P = 0.015), Ranunculaceae (mean = 8.22, P = 0.0053), and Rosaceae (mean = 7.75, P = 0.00069). ParaFit analyses further confirmed that host phylogeny significantly structures microbial functional repertoires, with intra-family hosts sharing more KEGG pathways than inter-family hosts. These results suggest that host evolutionary relationships are associated with metabolic specialization in phyllosphere microbiomes. All 13 AMPs synthesized via solid-phase peptide synthesis demonstrated antimicrobial activity, inhibiting the growth of at least one tested bacterial strain.

CONCLUSION: This study demonstrates the promise of grassland plant phyllosphere microbiome as a rich source for novel antimicrobial agents.},
}

@article {pmid41391639,
year = {2025},
author = {Yuan, F and Wang, L and Nguyen, SM and Shu, XO and Shrubsole, MJ and Wen, W and Cai, Q and Yu, D and Zheng, W},
title = {Plant-based diets, gut microbiota, blood metabolome, and risk of colorectal, liver and pancreatic cancers: results from a large prospective cohort study of predominantly low-income Americans.},
journal = {The American journal of clinical nutrition},
volume = {},
number = {},
pages = {101135},
doi = {10.1016/j.ajcnut.2025.101135},
pmid = {41391639},
issn = {1938-3207},
abstract = {BACKGROUND: Plant-based diets have been advertised for environmental and health benefits. Their effects on cancer risk, gut microbial and blood metabolomic profiles remain unclear.

OBJECTIVE: We investigated plant-based diets in relation to cancer incidence as well as gut microbial composition and blood metabolites in the Southern Community Cohort Study.

METHODS: Included in the analysis were 71,533 participants. Habitual dietary intake assessed at baseline (2002-2009) was used to derive overall plant-based diet index (PDI), healthy plant-based diet index (hPDI), and unhealthy plant-based diet index (uPDI). Incident cancer cases were ascertained via linkage to state cancer registries and the National Death Index. Hazard ratios (HRs) and 95% confidence intervals (CIs) were estimated from Cox proportional hazards models after adjusting for potential confounders. We examined associations of the three indices with gut microbiota and blood metabolites using fecal metagenomic and blood metabolomic data from two subsets of 417 and 1,581 participants, respectively.

RESULTS: During a median follow-up time of 11.6 years, 783, 316, and 295 incident colorectal, liver, and pancreatic cancer cases were identified. High hPDI was related to a lower liver cancer risk (HR=0.67, 95% CI=0.45, 0.99 comparing extreme quartiles, Ptrend=0.03). No apparent association was observed for colorectal cancer (CRC) in the whole cohort. However, among 49,132 CRC screening-naïve participants at baseline, PDI was inversely associated (HR=0.74, 95% CI=0.58, 0.96, Ptrend=0.01), while uPDI was positively associated (HR=1.39, 95% CI=1.06, 1.82, Ptrend=0.02) with CRC risk. No index was associated with pancreatic cancer. These diet indices were associated with microbial taxa and blood metabolites that have been implicated in the tumorigenesis of colorectum and liver.

CONCLUSIONS: A diet high in healthy plant foods and low in animal foods was inversely associated with liver cancer risk and with CRC risk among screening-naïve participants. These associations may be partly mediated through gut microbiota and systemic metabolism.},
}

@article {pmid41391314,
year = {2025},
author = {Yuan, X and Gao, N and Ma, J and Qian, W and Yang, L and Zhu, L and Feng, J},
title = {Warming alters temporal patterns of microbial-mediated nitrogen cycling under microplastics stress in intertidal sediment ecosystems.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140802},
doi = {10.1016/j.jhazmat.2025.140802},
pmid = {41391314},
issn = {1873-3336},
abstract = {Intertidal sediments-hotspots of coastal nitrogen cycling-are preferential sinks for microplastics (MPs) influenced by terrestrial and marine inputs. How warming alters sedimentary microbial nitrogen-cycling functions under MPs stress remains unclear. We incubated sediment microcosms with polyethylene (PE) MPs (0, 0.3, 2.0 % w/w) at 25℃ and 30℃ for 31 days. Microbial community dynamics were tracked by 16S rRNA and metagenomics. While α-diversity was largely unaffected, PE-MPs (especially at 2.0 %) markedly altered microbial community composition from day 16 onward at both temperatures, especially at 2.0 %. At 25℃, the 2.0 % PE-MPs increased microbial interactions and network complexity, with interactions shifting from competition toward cooperation over time. Warming further intensified early competitive interactions in 2.0 % PE-MPs group, driving compositional shifts. Functionally, PE-MPs at 2.0 % modulated the expression of dissimilatory nitrate reduction (DNRA) reductases (nrfA and nrfH), attenuating the increase in sediment NH4[+] over time. Concurrently, upregulation of assimilatory nitrate pathway genes lowered NO3[-]. Expression of nitrification and DNRA genes was generally enhanced at 2.0 % MPs, accompanied by downregulation of glnA (NH4[+] assimilation) and nasB (assimilatory nitrate reduction). Thereby, warming at 30℃ reshaped MPs-driven community dynamics and nitrogen-cycling pathways, slowing the time-dependent declines of NH4[+] and NO3[-] relative to 25℃ and reducing the risk of nitrogen loss from intertidal sediments. These findings highlight the need to incorporate temperature and temporal dynamics into ecological risk assessments of MPs under global climate change.},
}

@article {pmid41391220,
year = {2025},
author = {Xu, QY and Habib, T and Gao, L and Wu, D and Li, XY and Khieu, TN and Chen, YH and Zhang, Y and Liu, YH and She, TT and Fang, BZ and Li, WJ},
title = {Wenzhouxiangella psychrophila sp. nov., Wenzhouxiangella indolica sp. nov., and Halotectona sediminis gen. nov., sp.nov., three novel taxa with ability of IAA production from saline lake sediment.},
journal = {Systematic and applied microbiology},
volume = {49},
number = {1},
pages = {126683},
doi = {10.1016/j.syapm.2025.126683},
pmid = {41391220},
issn = {1618-0984},
abstract = {Indoleacetic acid synthesis (IAA), a crucial plant hormone, can be produced by many microorganisms through different metabolic pathways. While much research has focused on rhizosphere microorganisms, studies on IAA production functional strains in extreme environments are limited. In this study, two IAA-producing strains of the genus Wenzhouxiangella are isolated from saline lake sediment of Xinjiang, designated strains EGI_FJ10305[T] and EGI_FJ10409[T], which show low 16S rRNA gene sequence identities to other validly published Wenzhouxiangella species (< 98.65 %). A series of phylogenetic analysis concludes that two isolated strains represent two novel species within the genus Wenzhouxiangella. Two halotolerant strains are grown at 0-10.0 % (w/v) NaCl (optimum, 4.0 %, EGI_FJ10305[T]) and 0-8.0 % (w/v) NaCl (optimum, 4.0 %, EGI_FJ10409[T]), respectively. Result of functional test confirms that both isolated strains possess the capability to synthesize indole-3-acetic acid (IAA) with substrate tryptophan. Genomic analysis suggests that this capability likely operates through the tryptamine pathway (TAM) and has been inherited from their ancestors rather than acquired through horizontal gene transfer. The proposed names of strains EGI_FJ10305[T] and EGI_FJ10409[T] are Wenzhouxiangella psychrophile sp. nov. and Wenzhouxiangella indolica sp. nov., respectively. Concurrently, metagenomic analysis of the same samples yielded three high-quality MAGs. Phylogenetic analysis subsequently indicated that these three MAGs potentially represent a new genus within the family Wenzhouxiangellaceae, for which we propose the name Halotectona sediminis gen. Nov. sp. nov., in accordance with the published Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode).},
}

@article {pmid41391055,
year = {2025},
author = {An, X and Niu, S and Al, MA and Su, E and Chen, L and He, H and Wang, Y and Zhang, S and Yang, Y and Wang, S and Wen, Z and Xu, B and Ming, Y and Zhu, W and Zhao, Z and Wu, K and Yang, Y and Xie, W and He, Z and Yan, Q},
title = {Dietary macroalgae enhances amino acid metabolism via intestinal Shewanella in grass carp (Ctenopharyngodon idella).},
journal = {Advanced biotechnology},
volume = {3},
number = {4},
pages = {36},
pmid = {41391055},
issn = {2948-2801},
support = {2320004002504//Zhuhai Industry-University-Research Cooperation Project/ ; SML2021SP203//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; SML2024SP002//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; SML2024SP022//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; },
abstract = {The gut microbiome plays pivotal roles in the host's metabolic response to dietary interventions. Dietary macroalgae supplementation represents a promising strategy for enhancing animal growth and health via microbiome modulation. However, the underlying mechanism of how macroalgae supplementation regulates microbiome-host interactions in aquatic species remains unclear. This study investigated the effects of three dietary macroalgae-Sargassum hemiphyllum (S), Asparagopsis taxiformis (A), and Gracilaria lemaneiformis (G)-each supplemented at 5% in feed, on the gut microbiome and metabolism of grass carp (Ctenopharyngodon idella), using integrated approaches of 16S rRNA sequencing, metagenomics, and metabolomics. While all three macroalgae influenced host growth, supplementation of S provided the most comprehensive benefits, with significant enhancement of body weight and hepatic superoxide dismutase activity. Integrated multi-omics analysis revealed that dietary macroalgae supplementation increased the relative abundance of the key gut bacterial genus Shewanella, with the most notable effect observed in the supplementation of S. Subsequent analysis of a metagenome-assembled genome (MAG) of Shewanella (MAG C3_bin52) demonstrated its considerable potential for amino acid biosynthesis and metabolism. This genomic potential was further supported by metabolomic profiling, which indicated significant upregulation of amino acid-related metabolites, particularly in the supplementation S. Pathway analysis confirmed enrichment in processes associated with protein digestion and absorption, amino acid biosynthesis, and related metabolic pathways. These findings highlight the modulation of a macroalgae-microbiome-metabolite axis in grass carp, primarily mediated by the enrichment of Shewanella in gut ecosystem for enhancing host amino acid metabolism. This study advances understanding of dietary modulation of the gut microbiome and provides insights for the sustainable development of aquaculture.},
}

@article {pmid41390863,
year = {2025},
author = {Tran, L and Deckers, TB and Ho, J and Lansing, L and Cunningham, M and Morfin, N and Pepinelli, M and De la Mora, A and Conflitti, IM and Gregoris, A and Wu, L and Trepanier-Leroux, D and Muntz, L and Newman, T and Vishwakarma, S and Bixby, M and Jabbari, H and Guzman-Novoa, E and Hoover, SE and Currie, RW and Pernal, SF and Giovenazzo, P and Foster, LJ and Zayed, A and Ortega Polo, R and Guarna, MM},
title = {Neonicotinoid-induced signature dysbiosis identified via metagenomic sequencing of the honey bee gut microbiome.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-30907-4},
pmid = {41390863},
issn = {2045-2322},
support = {Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Genomics Research and Development Initiative (GRDI)//Agriculture and Agri-Food Canada/ ; Large Scale Applied Research Program//Genome Canada/ ; Large Scale Applied Research Program//Genome Canada/ ; Large Scale Applied Research Program//Genome Canada/ ; Large Scale Applied Research Program//Genome Canada/ ; Large Scale Applied Research Program//Genome Canada/ ; Large Scale Applied Research Program//Genome Canada/ ; Large Scale Applied Research Program//Genome Canada/ ; Large Scale Applied Research Program//Genome Canada/ ; Large Scale Applied Research Program//Genome Canada/ ; Large Scale Applied Research Program//Genome Canada/ ; Large Scale Applied Research Program//Genome Canada/ ; },
}

@article {pmid41390780,
year = {2025},
author = {Bommana, S and Olagoke, O and Hu, YJ and Wang, R and Kama, M and Dehdashti, M and Kodimerla, R and Read, TD and Dean, D},
title = {Azithromycin alters the microbiome composition, function and resistome in women with Chlamydia trachomatis infections.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-025-00858-9},
pmid = {41390780},
issn = {2055-5008},
support = {R01 AI151075/AI/NIAID NIH HHS/United States ; R01 AI151075/AI/NIAID NIH HHS/United States ; },
abstract = {Antibiotics disrupt mucosal microbial communities, yet the effects on microbiomes infected with Chlamydia trachomatis (Ct) remain poorly understood. Some data exist on vaginal microbiomes, but none exist for the endocervix or rectum that are primary sites of infection. We applied metagenomic shotgun sequencing to vaginal, endocervical and rectal samples collected longitudinally from women who cleared their infection post-treatment (n = 10), had persistent infection (n = 11), or remained uninfected (n = 18) to evaluate azithromycin-induced changes in microbial composition, function, and the resistome over time. Our results show shifts in composition and function post-treatment that support persistent Ct, nonsynonymous Ct L22 amino acid substitutions that may be linked to azithromycin resistance, and significant endocervical increases in azithromycin resistance genes in Lactobacillus iners and Gardnerella vaginalis strains with moderate/high biofilm formation potential. These findings highlight the unintended ecological consequences of azithromycin treatment, including likely resistance gene propagation, emphasizing the need for novel treatment and microbiome-preserving strategies.},
}

@article {pmid41390665,
year = {2025},
author = {Cotto, I and Albán, V and Durán-Viseras, A and Jesser, KJ and Zhou, NA and Hemlock, C and Ballard, AM and Fagnant-Sperati, CS and Lee, GO and Hatt, JK and Royer, CJ and Eisenberg, JNS and Trueba, G and Konstantinidis, KT and Levy, K and Fuhrmeister, ER and , },
title = {Environmental exposures associated with the gut microbiome and resistome of pregnant women and children in Northwest Ecuador.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-66567-1},
pmid = {41390665},
issn = {2041-1723},
support = {P30 ES007033/ES/NIEHS NIH HHS/United States ; R01AI162867//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; 2127509//American Society for Engineering Education (ASEE)/ ; },
abstract = {Inadequate water, sanitation, and hygiene (WASH) infrastructure may increase exposure to antimicrobial resistance (AMR). In addition, close human-animal interactions and unregulated antibiotic use in livestock facilitate the spread of resistant bacteria. We use metagenomic sequence data and multivariate models to assess how animal exposure and WASH conditions affect the gut resistome and microbiome in 53 pregnant women and 84 children in Ecuador. Here we show improving WASH infrastructure and managing animal exposure may be important in reducing AMR but could also reduce taxonomic diversity in the gut. Escherichia coli, Klebsiella pneumoniae, and clinically relevant antimicrobial resistance genes (ARGs) are detected across all age groups, but the highest abundance is found in children compared to mothers. In mothers, higher animal exposure trends towards a higher number of unique ARGs compared to low animal exposure and is significantly associated with greater taxonomic diversity. In addition, mothers with sewer systems or septic tanks and piped drinking water have fewer unique ARGs compared to those without, and mothers with longer duration of drinking water access have lower total ARG abundance. In contrast, few associations are observed in children, likely due to the dynamic nature of the gut microbiome during early childhood.},
}

@article {pmid41390664,
year = {2025},
author = {Cao, Q and Deng, Z and Li, M and Zhu, S and Huo, Y and Dong, H and Aernouts, B and Psifidi, A and Xu, C},
title = {Integrated metagenomic and metabolomic analyses reveal tenacissoside G as a potential non-antimicrobial treatment for bovine endometritis.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02264-x},
pmid = {41390664},
issn = {2049-2618},
support = {No. 2024B02016//the Key Research and Development Program of the Xinjiang Uygur Autonomous Region/ ; 32125038//the National Natural Science Foundation of China/ ; 2023YFD1801100//National Key Research and Development Program of China/ ; CARS-36//China Agriculture Research System/ ; },
abstract = {BACKGROUND: Bovine endometritis is a prevalent uterine disease that directly curtails reproductive performance and indirectly reduces milk production by increasing calving intervals. Postpartum uterine bacterial infection is the primary cause of bovine endometritis, which is typically treated with prostaglandin F2α and antimicrobials. However, abuse of antimicrobials has led to the emergence of multidrug-resistant bacteria, threatening both human and animal health. To explore alternatives to antimicrobial therapy for bovine endometritis, we integrated uterine metagenomic and metabolomic analyses and identified a novel bioactive metabolite with therapeutic potential. The potential antibacterial and anti-inflammatory effects of this metabolite against bovine endometritis were evaluated by assessing its inhibitory effect on the growth of F. necrophorum in vitro, and by quantifying histopathological scores and inflammatory cytokine expression levels in an in vivo mouse model of endometritis, respectively.

RESULTS: A total of 40 Holstein dairy cows at 21 days to 30 days postpartum were assigned into heathy cows (n = 15), subclinical endometritis cows (n = 12) and clinical endometritis cows (n = 13) according to clinical signs and laboratory tests for bovine endometritis. The uterine fluid was collected aseptically for metagenomics and metabolomics sequencing to identify bacterial species associated with bovine endometritis and metabolites that could potentially be used for treatment of bovine endometritis. A total of 17 bacterial species were significantly associated with bovine endometritis, with Fusobacterium necrophorum as the most significantly enriched in cows with clinical endometritis compared to healthy counterparts. In total, 391 metabolites were significantly differentially abundant between healthy and clinical endometritis cows. Among these, a plant-derived compound, tenacissoside G was significantly enriched in healthy cows. Notably, the abundance of F. necrophorum was significantly negatively associated with the concentration of tenacissoside G in clinical endometritis cows. Moreover, tenacissoside G significantly inhibited the growth of F. necrophorum in vitro and ameliorated inflammation in endometritis caused by F. necrophorum in a mice model.

CONCLUSION: This study provides new insights into the relationship between uterine microbiome and metabolites in bovine endometritis, potentially leading to novel strategies for treating bovine endometritis. Furthermore, tenacissoside G exhibits therapeutic effects against endometritis induced by F. necrophorum, and could serve as a potential alternative to antimicrobials for treating endometritis. Video Abstract.},
}

@article {pmid41390654,
year = {2025},
author = {Manzoor, H and Jabeen, I and Saeed, MT and Kayani, MUR and Huang, L},
title = {Metagenomic analyses reveal E. coli-derived siderophores as potential signatures for breast cancer.},
journal = {Journal of translational medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12967-025-07513-z},
pmid = {41390654},
issn = {1479-5876},
}

@article {pmid41387797,
year = {2025},
author = {Fu, W and Deng, ZW and Wang, P and Zhu, ZW and Xie, ZB and Li, YZ and Zhang, HQ and Yu, HY},
title = {HIV infection complicated with talaromyces marneffei, tuberculosis, hemophagocytic lymphohistiocytosis and non-Hodgkin lymphoma: a complex case report.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {1714},
pmid = {41387797},
issn = {1471-2334},
support = {2023JJ50447//the Natural Science Foundation of Hunan Province, CN/ ; 2024JJ7349//the Natural Science Foundation of Hunan Province, CN/ ; 2022YLT002//Hunan Provincial People's Hospital Medical Association Special Scientific Research Fund Project, CN/ ; QNJJ202503//Hunan University of Medicine General Hospital Youth Scientific Research Fund/ ; },
abstract = {BACKGROUND: Due to severe immunosuppression, human immunodeficiency virus (HIV) infected individuals are prone to multiple opportunistic infections and malignancies. This report presents a complex case of a 62-year-old male HIV patient who was diagnosed with co-infections of Talaromyces marneffei, tuberculosis, hemophagocytic lymphohistiocytosis (HLH), and ultimately non-Hodgkin B-cell lymphoma. This case provides valuable insights for clinical diagnosis and treatment.

CASE SUMMARY: The patient was admitted with complaints of “poor appetite, weight loss, and diarrhea for two weeks, accompanied by fever for four days.” Upon admission, the patient was diagnosed with HIV infection, with a CD4 + T-cell count of only 25/µL. Pathological examination of cervical lymph node aspiration and metagenomic next-generation sequencing (mNGS) confirmed infections with Talaromyces marneffei, Mycobacterium tuberculosis, and Aspergillus species. During treatment, the patient developed persistent high fever, pancytopenia, decreased fibrinogen, and significantly elevated ferritin levels. Abdominal computed tomography (CT) revealed splenomegaly. Further bone marrow examination confirmed HLH, and symptoms improved after treatment with glucocorticoids and immunoglobulin. However, the patient’s condition further deteriorated, and positron emission tomography computed tomography (PET-CT) along with repeat lymph node biopsy confirmed the diagnosis of non-Hodgkin B-cell lymphoma. Under combined antifungal, anti-tuberculosis, antiretroviral therapy (ART), and chemotherapy, the patient showed clinical improvement.

CONCLUSION: This case highlights the complexity and challenges in diagnosing and managing multiple opportunistic infections and malignancies in advanced HIV patients. It underscores the importance of multidisciplinary collaboration and provides valuable experience for the clinical management of HIV-related opportunistic infections and malignancies.},
}

@article {pmid41390498,
year = {2025},
author = {Freel, KC and Tucker, SJ and Freel, EB and Stingl, U and Giovannoni, SJ and Eren, AM and Rappé, MS},
title = {New SAR11 isolate genomes and global marine metagenomes resolve ecologically relevant units within the Pelagibacterales.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-67043-6},
pmid = {41390498},
issn = {2041-1723},
abstract = {The bacterial order Pelagibacterales (SAR11) is widely distributed across the global surface ocean, where its activities are integral to the marine carbon cycle. High-quality genomes from isolates that can be propagated and phenotyped are needed to unify perspectives on the ecology and evolution of this complex group. Here, we increase the number of complete SAR11 isolate genomes threefold by describing 81 new SAR11 strains from coastal and offshore surface seawater of the tropical Pacific Ocean. Our analyses of the genomes and their spatiotemporal distributions support the existence of 29 monophyletic, discrete Pelagibacterales ecotypes that we define as genera. The spatiotemporal distributions of genomes within genera were correlated at fine scales with variation in ecologically-relevant gene content, supporting generic assignments and providing indications of speciation. We provide a hierarchical system of classification for SAR11 populations that is meaningfully correlated with evolution and ecology, providing a valid and utilitarian systematic nomenclature for this clade.},
}

@article {pmid41390384,
year = {2025},
author = {Shetty, P and Bhat, R and Padavu, S and Rai, P and B, KK and Shetty, S},
title = {Profiling of microbes associated with chronic irreversible pulpitis using metagenomic next-generation sequencing.},
journal = {BMC oral health},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12903-025-07175-9},
pmid = {41390384},
issn = {1472-6831},
support = {N(DU)/RD/NUFR 1Grant/ABSMIDS/2021-22/01-1//NITTE University/ ; },
abstract = {BACKGROUND: Contemporary molecular analytical methodologies have yielded insufficient characterization of the microbial etiology underlying chronic irreversible pulpitis; a pathological condition characterized by irreversible inflammatory alterations of the dental pulp complex necessitating endodontic intervention. This investigation employed shotgun metagenomic sequencing to comprehensively elucidate the microbiome present in affected pulpal tissues, thereby augmenting our understanding of pulpal pathogenesis.

METHODS: The investigation incorporated six subjects (age range 18-35 years) presenting with clinically diagnosed chronic irreversible pulpitis according to the American Association of Endodontists diagnostic criteria. Pulpal tissue specimens were procured under rubber dam isolation utilizing stringent aseptic protocols following coronal access preparation. Genomic DNA extraction was performed via QIAamp DNA Mini Kit methodology followed by high-throughput sequencing on the Illumina Hiseq platform. Subsequent bioinformatic analysis implemented the WGSA2 pipeline for taxonomic classification, generating approximately 79.906 million paired-end reads per specimen.

RESULTS: Metagenomic analysis of the pulpal microbiome revealed taxonomic predominance of Bacteroidetes (45.095%), Firmicutes (17.424%), Proteobacteria (12.731%), and Actinobacteria (9.071%) at the phylum level. Notably, the investigation identified previously undocumented phyla in pulpal infections, including Euryarchaeota, Thermoproteobacteria, Uroviricota,and Apicomplexa. Propionibacterium acidifaciens emerged as the most consistently detected and ecologically significant species, whereas the conventionally recognized odontopathogen Streptococcus mutans exhibited negligible presence. Shannon diversity indices and taxonomic richness parameters demonstrated substantial inter-subject variability, with species abundance ranging from 574 to 5,468 distinct taxonomic units per pulp sample.

CONCLUSION: This investigation elucidated unprecedented microbial diversity within chronic irreversible pulpitis, fundamentally challenging established understanding of endodontic pathogenesis and clinical therapeutic approaches. The substantial inter-subject taxonomic heterogeneity observed herein suggests that contemporary standardized therapeutic regimens may be insufficiently targeted to address the complex polymicrobial ecosystem characteristic of pulpal pathosis. The identification of archaeal and viral constituents provides mechanistic insight into persistent endodontic infections despite technically adequate treatment modalities. These findings establish a comprehensive basis for evidence-based precision endodontics, facilitating the development of patient-specific antimicrobial strategies and novel therapeutic interventions targeting previously unrecognized microbial components. The comprehensive characterization of pulpal microbiome diversity represents a significant advancement toward molecularly informed clinical decision-making, with profound implications for treatment outcome optimization and the mitigation of therapeutic failures in contemporary endodontic practice.},
}

@article {pmid41389850,
year = {2025},
author = {Petrov, VA and Schade, S and Laczny, CC and Hallqvist, J and May, P and Jäger, C and Aho, VTE and Hickl, O and Halder, R and Lang, E and Caussin, J and Lebrun, LA and Schulz, J and Unger, MM and Mills, K and Mollenhauer, B and Wilmes, P},
title = {Resistant starch improves Parkinson's disease symptoms through restructuring of the gut microbiome and modulating inflammation.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {106217},
doi = {10.1016/j.bbi.2025.106217},
pmid = {41389850},
issn = {1090-2139},
abstract = {Alterations in the gut microbiome and a "leaky" gut are associated with Parkinson's disease (PD), which implies the prospect of rebalancing via dietary intervention. Here, we investigate the impact of a diet rich in resistant starch on the gut microbiome through a multi-omics approach. We conducted a randomized, controlled trial with short-term and long-term phases involving 74 PD patients of three groups: conventional diet, supplementation with resistant starch, and high-fibre diet. Our findings reveal associations between dietary patterns and changes in the gut microbiome's taxonomic composition, functional potential, metabolic activity, and host inflammatory proteome response. Resistant starch supplementation led to an increase in Faecalibacterium species and short-chain fatty acids and a reduction of opportunistic pathogens. Long-term supplementation also increased blood APOA4 and HSPA5 and reduced symptoms of PD. Our study highlights the potential of dietary interventions to modulate the gut microbiome and improve the quality of life for PD patients.},
}

@article {pmid41389417,
year = {2025},
author = {Gong, L and Yao, L and Gu, L and Qu, Y and Gao, X and Wang, W and Huang, W and Peng, Y},
title = {Beyond traditional biological nutrient removal limits: achieving ultra-low effluent nitrogen via an anaerobic/Oxic/Anoxic (AOA) process in a pilot-scale system treating municipal wastewater.},
journal = {Water research},
volume = {290},
number = {},
pages = {125123},
doi = {10.1016/j.watres.2025.125123},
pmid = {41389417},
issn = {1879-2448},
abstract = {Developing low-cost and high-efficiency biological nutrient removal (BNR) process remains a major challenge in wastewater treatment plants (WWTPs). In this study, a pilot-scale anaerobic/oxic/anoxic (AOA) process with a treatment capacity of 100 m[3]/day was established and operated continuously for 335 days using real municipal wastewater. Without external carbon addition, the system achieved an average effluent total nitrogen (TN) concentration of 1.2 mg/L, with 90 % of values below 1.8 mg/L. Total phosphorus (TP) and chemical oxygen demand (COD) removal efficiencies reached 92.8 % and 94.1 %, respectively. A sufficient influent organic load (C/N ratio of 8.6) and extremely low nitrate concentrations enabled effective carbon storage in the anaerobic zone. Precise aeration control in the aerobic zone maintained low residual ammonium concentration, minimizing the consumption of internal carbon sources. Therefore, the anoxic zone in the AOA system fully utilized internal carbon sources for denitrification, resulting in ultra-low effluent total nitrogen concentrations. Metagenomic analysis revealed that multiple unclassified microorganisms, such as Unclassified Saccharimonadales, Unclassified Saprospiraceae, and Unclassified Myxococcales, encoded complete Gly and polyhydroxyalkanoate (PHA) metabolism as well as denitrification genes, and potentially contributed to endogenous denitrification. The AOA system overcame the nitrogen removal limitations of conventional processes by eliminating internal nitrate recirculation, while simultaneously reducing chemical dosing and energy consumption. This finding providing a scalable, energy-efficient, and economically viable strategy for next-generation WWTPs aiming to meet increasingly stringent discharge standards.},
}

@article {pmid41390369,
year = {2025},
author = {Yuan, X and Fang, M and Lan, W and Zhou, X and Yang, S and Wang, T},
title = {From urinary tract infection to deafness: community-acquired meningitis in an adult caused by hypervirulent Klebsiella pneumoniae-a case report.},
journal = {BMC infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12879-025-12340-0},
pmid = {41390369},
issn = {1471-2334},
abstract = {BACKGROUND: Hypervirulent Klebsiella pneumoniae (hvKP) is an emerging pathogen capable of causing lethal metastatic infections in healthy individuals. While liver abscesses are well-described, the urinary tract is increasingly recognized as a primary portal for hematogenous dissemination.

CASE PRESENTATION: A 46-year-old man with previously undiagnosed diabetes mellitus presented with community-acquired urinary tract infection (CA-UTI) that rapidly progressed to bilateral sensorineural deafness and meningitis. Metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF) identified K. pneumoniae harboring hypervirulence genes rmpA and iucA. Blood, urine, and CSF cultures yielded an ESBL-negative, pansensitive hvKP strain. Brain MRI revealed septic emboli, consistent with hematogenous dissemination.

CONCLUSIONS: This case highlights the urinary tract as an underrecognized but lethal source of hvKP dissemination, particularly in diabetic patients. The rapid neurologic decline and permanent deafness highlight the need for early recognition and aggressive management. Virulence gene profiling should complement routine susceptibility testing. mNGS enabled rapid pathogen identification and guided targeted therapy. Clinicians must remain vigilant for CNS complications in diabetic patients with CA-UTI.},
}

@article {pmid41389890,
year = {2025},
author = {Xu, D and Zhang, W and Tao, XR and Gao, K and Zhao, MN and Wang, JW},
title = {Shenqi funeng xingnao prescription regulated the TNF/NOD‒like receptor signaling pathway and brain-gut axis dysfunction caused by exercise-induced fatigue.},
journal = {Journal of ethnopharmacology},
volume = {},
number = {},
pages = {121035},
doi = {10.1016/j.jep.2025.121035},
pmid = {41389890},
issn = {1872-7573},
abstract = {BACKGROUND: Central fatigue is a phenomenon in which changes in the function of the central nervous system lead to decreased athletic ability and increased fatigue symptoms. Shenqi Funeng Xingnao Prescription (SQFNXNP) is a traditional Chinese medicine prescription applied to alleviate exercise-induced fatigue; however, the molecular mechanism underlying its effects on central fatigue remain elusive.

PURPOSE: This study explored the therapeutic effects and potential molecular mechanisms of SQFNXNP on central fatigue.

METHODS: A chronic fatigue model was constructed to evaluate the therapeutic effects of SQFNXNP at alleviating central fatigue, including pathological changes in the hippocampus and intestine, as well as abnormal levels of neurotransmitters and inflammation. Transcriptomic analysis revealed core gene targets, which were further validated using reverse transcription quantitative polymerase chain reaction (RT-qPCR). Furthermore, metagenomics was applied to explore changes in gut microbial composition and associated signaling pathways. Further validation of key proteins was conducted using western blotting (WB). Correlation analysis was further applied to identify differentially abundant metabolites related to the core targets. Compounds with prototype structures in the brain tissue after SQFNXNP administration were identified by ultra-high performance liquid chromatography-mass spectrometry analysis. A virtual screening procedure was used to screen for potential ingredients of SQFNXNP that could alleviate central fatigue.

RESULTS: SQFNXNP alleviated exercise-induced histopathological damage and mitochondrial injury in the hippocampi of mice, decreased cell apoptosis and necrosis, increased cell proliferation, and restored abnormal levels of monoamine neurotransmitters. Moreover, SQFNXNP treatment decreased inflammatory levels in the body, alleviated histopathological damage to the intestine, reduced cell apoptosis in the intestine, increased the expression of key intestinal barrier proteins, restored the goblet cell density and mucus layer integrity in the intestine, and regulated the imbalance in the gut microbiota and central fatigue-related signaling pathways. RT-qPCR and WB further revealed that SQFNXNP regulated the TNF and NOD-like receptor (NLR) signaling pathways by targeting MMP9, PTGS2, MAPK14, BCL2, TLR4, TNF, IL1B, P-AKT1, NIKBIA, and IL6 proteins. The virtual screening procedure revealed that the potential components of SQFNXNP for alleviating central fatigue were oleanolic acid and ginsenoside re.

CONCLUSION: SQFNXNP regulated the TNF/NOD‒like receptor signaling pathway and brain-gut axis dysfunction caused by exercise-induced fatigue, thus providing a traditional Chinese medicine strategy for treating central fatigue in the clinic.},
}

@article {pmid41389554,
year = {2025},
author = {Yang, T and Zhan, Y and Sha, J and Zhao, J and Wang, C and Peng, T and Zhang, L},
title = {Integrative multi-omics elucidates the impact of microalgae on growth, quality, phytohormones, and rhizosphere microbiome of Angelica sinensis.},
journal = {Microbiological research},
volume = {304},
number = {},
pages = {128418},
doi = {10.1016/j.micres.2025.128418},
pmid = {41389554},
issn = {1618-0623},
abstract = {Microalgae have recently been recognized as sustainable biofertilizers that improve soil fertility while enhancing crop performance. However, their roles in regulating medicinal plant growth and quality, as well as the underlying ecological mechanisms, remain poorly understood. In this study, we systematically assessed the effects of three representative microalgae-Anabaena cylindrica (AC), Phormidium tenue (PT), and Chlorella vulgaris (CV)-on the growth, quality, hormonal regulation, soil nutrient dynamics, and rhizosphere microbiome of Angelica sinensis. Field inoculation trials demonstrated that all three microalgae significantly promoted biomass accumulation and increased antioxidant capacity. AC and CV further enhanced the accumulation of ferulic acid and flavonoids, which are two key quality determinants. Microalgal inoculation significantly altered rhizosphere soil properties by increasing total organic carbon and alkali-hydrolyzable nitrogen, with AC uniquely elevating available phosphorus and iron. Metagenomic analysis revealed that AC and PT stimulated nitrification while suppressing denitrification, thereby reducing nitrogen loss and stabilizing the soil nitrogen pools. Distinct microbial taxa, including Rhodanobacter, Streptomyces, and Pseudomonas, were identified as the major contributors to carbon and nitrogen cycling. Hormone metabolomics showed that microalgal inoculation reprogrammed A. sinensis phytohormone profiles in a species-specific manner. Partial least squares path modeling suggested that AC and CV promote ferulic acid biosynthesis through distinct mechanisms, with AC associated with reduced investment in C-mineralization processes and CV associated with lower salicylic acid levels, whereas PT enhances biomass accumulation mainly by stimulating N-cycle processes. Collectively, this study provides integrated evidence linking microalgae-mediated nutrient cycling, rhizosphere microbiome shifts and hormonal regulation to enhanced quality formation in A. sinensis.},
}

@article {pmid41389146,
year = {2025},
author = {Vorobeva, M and iAkushev, A and Chen, CC and Orihara, M and Akbar, N and Colley, P and Sehanobish, E and Chung, CHY and Scott, A and O'Brien, E and Chang, CB and Kita, H and Voyich, J and Knoop, K and Jerschow, E},
title = {Impact of Sinus Surgery on Bacteriome Composition in Patients With Chronic Rhinosinusitis With Nasal Polyps.},
journal = {International forum of allergy & rhinology},
volume = {},
number = {},
pages = {},
doi = {10.1002/alr.70082},
pmid = {41389146},
issn = {2042-6984},
support = {R21AI171306 to E.J./TR/NCATS NIH HHS/United States ; CTSA 5KL2TR001071/TR/NCATS NIH HHS/United States ; /NH/NIH HHS/United States ; },
}

@article {pmid41389008,
year = {2025},
author = {Pryor, JC and Hoedt, EC and Soh, WS and Fowler, S and Caban, S and Minahan, K and Sherwin, S and Nieva, C and McCarthy, H and Horvat, J and Hedley, KE and Duncanson, K and Burns, GL and Talley, NJ and Keely, S},
title = {Antibiotics Alter Duodenal Immune Populations Upon Gluten Exposure in Mice: Implications for Non-Coeliac Gluten Sensitivity.},
journal = {American journal of physiology. Gastrointestinal and liver physiology},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajpgi.00159.2025},
pmid = {41389008},
issn = {1522-1547},
support = {2004860//DHAC | National Health and Medical Research Council (NHMRC)/ ; 2035319//DHAC | National Health and Medical Research Council (NHMRC)/ ; 1170893//DHAC | National Health and Medical Research Council (NHMRC)/ ; },
abstract = {A growing proportion of the non-celiac population experience adverse symptoms to gluten. The pathogenesis of non-celiac gluten sensitivity (NCGS) is unclear, but elevated duodenal eosinophils and altered mucosa-associated microbiota (MAM) populations have been reported. Given the microbiome's role in gluten digestion and its susceptibility to antibiotics, we hypothesised that altering the microbiome with antibiotics would modify immune responses to gluten in mice. BALB/C mice consuming gluten-free chow received amoxicillin/clavulanate (5mg/kg) or PBS-vehicle daily for 5-days. Mice were then treated with a 3mg wheat-gluten suspension, or vehicle, on days 4 and 5 before sacrifice on day 7. Duodenal immune cells were analysed by histology and flow cytometry, while the duodenal MAM and faecal microbiome were characterised via 16S rRNA and shotgun metagenomic sequencing, respectively. Antibiotic treatment followed by gluten reintroduction significantly reduced Staphylococcus in the duodenal MAM, enriched Bacteroides in faeces, and resulted in altered microbial carbohydrate and lipid metabolism, compared to vehicle controls. Treatment with antibiotics and gluten also increased duodenal eosinophils, which positively correlated with the genus Blautia. Flow cytometry revealed that sequential antibiotic and gluten treatment resulted in a greater proportion of active eosinophils and epithelial γδ T-cells, compared to vehicle control mice. This study demonstrated that modulating the microbiome with antibiotics was sufficient to alter the immune response to gluten in mice, suggesting that the microbiome may determine the capacity for gluten to induce immune responses. These findings contribute valuable insights into possible microbial mechanisms underlying NCGS, such as altered gluten metabolism or production of immunomodulatory metabolites.},
}

@article {pmid41388903,
year = {2025},
author = {Wutkowska, M and Nweze, JA and Tláskal, V and Nweze, JE and Daebeler, A},
title = {Uncovering hidden phylo: and ecogenomic diversity of the widespread methanotrophic genus Methylobacter.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf127},
pmid = {41388903},
issn = {1574-6941},
abstract = {The globally distributed genus Methylobacter plays a crucial role in mitigating methane emissions from diverse ecosystems, including freshwater and marine habitats, wetlands, soils, sediments, groundwater, and landfills. Despite their frequent presence and abundance in these systems, we still know little about the genomic adaptations that they exhibit. Here, we used a collection of 97 genomes and metagenome-assembled genomes to ecogenomically characterise the genus. Our analyses suggest that the genus Methylobacter may contain more species than previously thought, with >30 putative species clusters. Some species clusters shared >98.65% sequence identity of the full-length 16S rRNA gene, demonstrating the need for genome-resolved species delineation. The ecogenomic differences between Methylobacter spp. include various combinations of methane monooxygenases, multigene loci for alternative dissimilatory metabolisms related to hydrogen, sulphur cycling, and denitrification, as well as other lifestyle-associated functions. Additionally, we describe and tentatively name the two new Methylobacter species, which we recently cultured from sediment of a temperate eutrophic fishpond, as Methylobacter methanoversatilis, sp. nov. and Methylobacter spei, sp. nov. Overall, our study highlights previously unrecognised species diversity within the genus Methylobacter, their diverse metabolic potential, versatility, as well as the presence of distinct genomic adaptations for thriving in various environments.},
}

@article {pmid41388659,
year = {2025},
author = {Wallbank, JA and Kingsbury, JM and Pantos, O and Weaver, L and Smith, DA and Barbier, M and Theobald, B and Gambarini, V and Lear, G},
title = {Plastic Type and Condition Have Minimal Impact on Associated Marine Biofilm Communities.},
journal = {Environmental microbiology},
volume = {27},
number = {12},
pages = {e70214},
doi = {10.1111/1462-2920.70214},
pmid = {41388659},
issn = {1462-2920},
support = {C03X1802//Ministry of Business, Innovation and Employment/ ; },
mesh = {*Biofilms/drug effects/growth & development ; *Seawater/microbiology ; *Plastics ; Fungi/genetics/classification/drug effects/isolation & purification ; *Bacteria/genetics/classification/isolation & purification/drug effects ; RNA, Ribosomal, 16S/genetics ; *Microbiota/drug effects ; },
abstract = {The ecological impacts of plastics and their additives on marine microbiota remain unclear. We applied prokaryotic 16S rRNA gene and fungal ITS2 region amplicon sequencing, alongside shotgun metagenomic sequencing, to identify compositional and functional changes in microbial communities on marine plastic. Five common plastics, both non-aged and artificially aged, were submerged in Auckland Harbour, Aotearoa-New Zealand. Biofilms on linear low-density polyethylene (LLDPE), nylon-6 (PA), polyethylene terephthalate (PET), polylactic acid (PLA), oxo-biodegradable LLDPE (OXO) and glass were sampled over 12 months. The taxonomy and functional potential of biofilm communities differed from surrounding seawater communities and varied with biofilm age. Younger biofilms were more diverse, with Proteobacteria, unknown fungi and unclassified Metazoa dominating prokaryotic, fungal and eukaryotic communities, respectively. Taxa related to previously reported plastic-degraders were found in very low abundance across all substrates. Plastic type and UV-ageing did not significantly shape biofilm communities over a year. Although some genes differed in relative abundance due to UV-ageing, overall functional profiles remained consistent across plastics. Genes conferring reported plastic-degrading traits were present regardless of plastic type, UV-ageing and biofilm age. Nevertheless, nylon hydrolases were notably associated with PA, suggesting marine plastic impacts may be restricted to taxa or functions involved in its degradation.},
}

*Biofilms/drug effects/growth & development
*Seawater/microbiology
*Plastics
Fungi/genetics/classification/drug effects/isolation & purification
*Bacteria/genetics/classification/isolation & purification/drug effects
RNA, Ribosomal, 16S/genetics
*Microbiota/drug effects

@article {pmid41388485,
year = {2025},
author = {Khan, MAS and Bishir, M and Huang, W and Chidambaram, SB and Chang, SL},
title = {Early upregulation of alpha-7 nicotinic acetylcholine receptor in limbic system correlates with gut dysbiosis in mice exposed to binge ethanol.},
journal = {Alcohol, clinical & experimental research},
volume = {},
number = {},
pages = {},
doi = {10.1111/acer.70210},
pmid = {41388485},
issn = {2993-7175},
support = {AA029925/AA/NIAAA NIH HHS/United States ; },
abstract = {BACKGROUND: Alcohol use disorder (AUD) causes neuroinflammation and disrupts the gut microbiome through bidirectional communication between the brain and gut. However, it remains unclear whether the brain or gut responds first to alcohol exposure. We hypothesized that brain regions respond to alcohol first, preceding changes in the gut microbiome.

METHODS: B6 mice were given ethanol (EtOH; 5 g/kg/day, 42%v/v, i.g.) at various time points. Fecal samples were collected prior to the first EtOH injection (Day 0), at 24 h following the first, second, and third injections (Day 1, Day 2, and Day 3, respectively), and at 96 h after the third injection (Day 6). Brain regions, central amygdala (CeA), hypothalamus (Hyp), and nucleus accumbens (NAc) were isolated at 2 min, 12 h, 24 h, and 192 h following the first and third doses of binge EtOH, respectively. mRNA or protein expression levels of TNF-α, IL-1β, P2Y12, ITGβ2, and α7nAChR were analyzed by qRT-PCR and western blot, respectively. Fecal microbial composition and abundance were assessed using 16S rRNA metagenomic sequencing.

RESULTS: Data revealed increased TNF-α expression in the Amg, Hyp, and NAc and increased IL-1β expression in the Amg and NAc, 12 h after the first EtOH injection. α7nAChR expression in the CeA, Hyp, and NAc was also upregulated at 24 h after the third EtOH dose, compared to the control group. α7nAChR expression in the Hyp was observed at 2 min after the first EtOH dose. CHRNA7 mRNA levels were upregulated 24 h after the third EtOH dose. ITGβ2 showed an increasing trend in the Amg at 12 h after the first dose, followed by a significant reduction at 24 h, and 192 h after the third dose. 16S rRNA sequencing revealed a significant difference in β-diversity on Day 6. The relative abundance of the Prevotellaceae family was higher in EtOH-treated mice compared to controls at Day 3 and Day 6.

CONCLUSION: This study showed that brain inflammation, indicated by α7nAChR upregulation, occurred before EtOH-induced gut dysbiosis, supporting an anterograde sequence of events.},
}

@article {pmid41388438,
year = {2025},
author = {Chiriac, MC and Layoun, P and Fernandes, C and Szőke-Nagy, T and Kasalicky, V and Okazaki, Y and Woodhouse, JN and Grossart, HP and Piwosz, K and Znachor, P and Sonntag, B and Callieri, C and Orlić, S and Sommaruga, R and Lepère, C and Biderre-Petit, C and Tammert, H and Herlemann, DPR and Ślusarczyk, M and Bednarska, A and Banciu, HL and Zalewski, M and Woźniczka, A and Ghai, R and Salcher, MM and Haber, M},
title = {Ecological success in freshwater lakes: insights from novel cultivated lineages of the abundant Nanopelagicales order.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02272-x},
pmid = {41388438},
issn = {2049-2618},
support = {24-12912M//Grantová Agentura České Republiky/ ; 22-03662S//Grantová Agentura České Republiky/ ; 22-33245S//Grantová Agentura České Republiky/ ; 20-12496X//Grantová Agentura České Republiky/ ; 21-21990S//Grantová Agentura České Republiky/ ; 022/2019/P//Grant Agency of the University of South Bohemia/ ; 017/2022/P//Grant Agency of the University of South Bohemia/ ; JPMJFR2273//JST FOREST/ ; 25K18161//Japan Society for the Promotion of Science/ ; GR1540/37-1//Leibniz-Institut für Gewässerökologie und Binnenfischerei/ ; KK.01.1.1.01.0003//European Regional Development Fund - the Operational Programme Competitiveness/ ; HRZZ IP-2020-02-9021//Croatian Science Foundation/ ; 760010/30.12.2022//Ministerul Cercetării şi Inovării/ ; },
abstract = {BACKGROUND: The order Nanopelagicales is the most abundant bacterioplankton lineage in freshwater lakes and exhibits typical streamlined genomic characteristics such as small cell volumes (<0.1 μm[3]), reduced genome sizes (<1.5 Mbp), and low GC content. These characteristics reflect adaptations to a free-living life strategy in oligotrophic environments. While many Nanopelagicales metagenome-assembled genomes and single-amplified genomes are available in public databases, strain-level microdiversity within this lineage remains poorly understood. This is mainly attributed to the incomplete nature of these genomes and the difficulty in isolating and maintaining pure cultures, with only 20 genome-sequenced cultures available to date.

RESULTS: Here, we report the isolation and genome analysis of 72 new Nanopelagicales strains, including members of Planktophila and a novel, previously uncultured genus, Aquilimus. High interspecific diversity and microdiversity were observed in the genus Planktophila, which likely facilitates the coexistence of closely related species within the same habitats by allowing fine-scale niche partitioning. The unusually high diversity of transporters for small organic compounds, along with carbohydrate-active enzymes, suggests that Planktophila members can degrade plant and algal polymers and import the resulting products to support growth. A notable finding is the repeated, independent loss of the oxidative phase of the pentose phosphate pathway in abundant Nanopelagicales species, which may represent an energy-saving adaptation in oligotrophic waters. Two species (Planktophila vernalis and Nanopelagicus abundans) seem to be equally abundant on a global scale, with water pH likely being the most significant factor influencing the predominance of one group over the other in different water bodies. Additionally, P. vernalis may tolerate periods of anoxia due to genomic encoding of respiratory nitrate reductase and nitrate/nitrite antiporters.

CONCLUSIONS: In conclusion, this work increased to a great degree the cultivated diversity of the abundant Nanopelagicales order. Analysis of over 1700 metagenomes showed that only a few cultivated species are globally dominant, and time-series analyses revealed consistent spring and autumn peaks. Key metabolic adaptations, such as loss of the oxidative phase of the pentose phosphate pathway and a high microdiversity of genes involved in cell surface biosynthesis and modifications, are likely to help these species survive periods of starvation and avoid predation. These findings highlight the ecological importance of Nanopelagicales and suggest that microdiversity underpins their adaptability. This work lays a foundation for studying their physiology, ecology, and strain-specific functional variation. Video Abstract.},
}

@article {pmid41388019,
year = {2025},
author = {Chac, D and Heller, FJ and Banna, HA and Kaisar, MH and Markiewicz, SM and Pruitt, EL and Chowdhury, F and Bhuiyan, TR and Akter, A and Khan, AI and Dumayas, MG and Rice, A and Karmakar, PC and Dash, P and LaRocque, RC and Ryan, ET and Xu, L and Minot, SS and Harris, JB and Qadri, F and Weil, AA},
title = {Gut bacteria-derived sphingolipids alter innate immune responses to oral cholera vaccine antigens.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-67388-y},
pmid = {41388019},
issn = {2041-1723},
support = {K08 AI123494/AI/NIAID NIH HHS/United States ; T32HD007233//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; R01 106878//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; R01 AI AI136979//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; R01 AI103055/AI/NIAID NIH HHS/United States ; R01 AI099243/AI/NIAID NIH HHS/United States ; D43 TW005572/TW/FIC NIH HHS/United States ; K43 TW010362/TW/FIC NIH HHS/United States ; R35 GM133420/GM/NIGMS NIH HHS/United States ; },
abstract = {The degree of protection conferred after receiving an oral cholera vaccine (OCV) varies based on age, prior exposure to Vibrio cholerae, and unknown factors. Recent evidence suggests that the microbiota may mediate some of the unexplained differences in oral vaccine responses. Here, we use metagenomic sequencing of the fecal microbiota at the time of vaccination and relate microbial features to immune responses after OCV using a reference-independent gene-level method. We find that the presence of sphingolipid-producing bacteria is associated with the development of protective immune responses after OCV. We test these associations by stimulating human macrophages with Bacteroides xylanisolvens metabolites and find that sphingolipid-containing extracts increase innate immune responses to OCV antigens. Our findings demonstrate a new analytic method for translating metagenomic sequencing data into strain-specific results associated with a biological outcome, and in validating this tool, we identify that microbe-derived sphingolipids impact immune responses to OCV antigens.},
}