@article {pmid41418867,
year = {2025},
author = {Ma, X and Xu, Q and Wang, Y and Lu, J and Zhu, K and Deng, J and Wu, S and Wang, Y and Wang, B and Zhang, H},
title = {Profiling of soil bio-composite pollution and driving factors in China.},
journal = {Environmental research},
volume = {},
number = {},
pages = {123578},
doi = {10.1016/j.envres.2025.123578},
pmid = {41418867},
issn = {1096-0953},
abstract = {Soil biological contamination driven by antibiotic resistance poses escalating global health threats, yet national-scale assessments remain scarce. To bridge this knowledge gap, metagenomic analysis of 300 samples spanning five ecosystems (agricultural, bare land, forest, grassland, wetland) was employed to study the diversity, co-occurrence patterns, and driving factors of the soil resistome and pathogens across China. Our analyses revealed that antibiotic resistance genes (ARGs) were ubiquitously detected (23 types; 0.03-2.6 copies/cell), with multidrug (mexF, mexW), vancomycin (vanR/S), and bacitracin (bacA) resistance dominating. Eleven major mobile genetic element (MGE) types were identified, and co-occurrence network analysis confirmed robust ARG-MGE associations. Notably, 272 ARG-carrying pathogens (APs) were identified as a severe consequence mediated by bio-composite contamination, with widely distributed genera including Enterobacter, Klebsiella, Nocardia, Pseudomonas, exhibiting potential for multidrug and vancomycin resistance. AP richness peaked in agricultural soils and was lowest in bare lands. Random forest modeling and correlation analysis revealed mean annual precipitation (MAP; ρ = 0.19, P < 0.05) and grain production (GP; ρ = 0.18, P < 0.05) were weakly but significantly associated with ARG abundance, while soil pH, organic carbon and meat production governed AP richness. These findings demonstrate nationwide soil bio-composite pollution and underscore the need for prioritized interventions in high-risk ecosystems, though further mechanistic studies are required to validate the observed correlations.},
}

@article {pmid41418855,
year = {2025},
author = {Laue, HE and Kook, D and Khatchikian, C and Coto, SD and Jackson, BP and Palys, TJ and Peacock, JL and Karagas, MR and O'Toole, GA and Hoen, AG and Madan, JC},
title = {Early-life arsenic exposure modulates the developing microbiome in a rural cohort.},
journal = {Environmental research},
volume = {},
number = {},
pages = {123588},
doi = {10.1016/j.envres.2025.123588},
pmid = {41418855},
issn = {1096-0953},
abstract = {BACKGROUND: Studies reported associations between arsenic and the infant gut microbiome measured contemporaneously. We tested the hypothesis that early-life arsenic associates with longitudinal microbiome differences and examined sex-specific effects.

METHODS: Participants provided urine and fecal samples at six weeks (6W; n=219) or twelve months (12M; n=219), a subset of whom provided samples at both (n=167). Total arsenic (tAs), inorganic arsenic, monomethylarsinic acid, and dimethylarsinic acid (DMA) were quantified in 6W and 12M urine with high-performance liquid chromatography with inductively-coupled plasma mass spectrometry. We estimated gut microbiome composition at 6W and 12M with metagenomic sequencing. Using generalized linear and mixed-effect models, we evaluated cross-sectional and longitudinal associations of arsenic concentrations with bacterial diversity and species/ gene pathway relative abundance.

RESULTS: DMA and tAs at 6W were associated with bacterial species at 6W but similar associations were not observed at 12M. At 6W, associations between arsenic and metabolic pathways tended to be sex-specific. In longitudinal analyses, tAs associated with higher Shannon diversity [β=0.07 per doubling (95%CI: 0.05, 0.09)], with a diminishing trend in this association with sampling age [β=-0.04 per doubling (95%CI: -0.07, -0.004)]. We observed a similar longitudinal pattern between at least one arsenic measure and ten bacterial species, with stronger associations among males than females.

CONCLUSIONS: We observed longitudinal and cross-sectional associations of arsenic and the gut microbiome in the first year of life. Early-life arsenic concentrations were more strongly associated with disruptions in the infant gut microbiome than later infancy, highlighting the importance of early-life exposures in microbiome dysbiosis.},
}

@article {pmid41418614,
year = {2025},
author = {Ahmed, I and Zhang, D and Farooq, MU and Sheikh, Z and Dai, X},
title = {Microplastics exacerbate antibiotic resistance by regulating microbial and functional gene dynamics in sludge and food waste composting.},
journal = {Water research},
volume = {291},
number = {},
pages = {125161},
doi = {10.1016/j.watres.2025.125161},
pmid = {41418614},
issn = {1879-2448},
abstract = {The presence of antibiotic resistance genes (ARGs) and microplastics (MPs) as co-contaminants in sewage sludge possess environmental concern. Nevertheless, the effect of specific MP types on ARGs propagation and the mechanistic drivers during composting require further elucidation. This study analyzed the impact of MPs polyethylene (PE), polypropylene (PP), and their mixture (PE+PP) on the propagation of ARGs and mobile genetic elements (MGEs) during sludge composting. Results revealed that MPs significantly increased ARGs abundance, with the highest enrichment observed in PE (2.06 log-fold), followed by PP (1.74) and PE+PP (1.65), compared to control trial. MGEs also increased by up to 1.3 log-fold in MP-treated groups. MPs altered bacterial community composition, enhancing the abundance of Brevibacterium, Microbacterium, and Streptomyces. MPs exhibited a partial reduction of up to 30.2 % during composting which modified the compost's chemical properties, elevating carbon content and depleting oxygen. Metagenomic analysis revealed MPs affected microbial functional pathways, upregulating ABC transporters, two-component regulatory systems, and the conjugation gene VirD4. Functionally, MPs enhanced denitrification and dissimilatory nitrate reduction to ammonium, inhibited assimilatory nitrate reduction, and promoted inorganic nitrogen assimilation. Redundancy analysis exhibited MGEs as the primary drivers of ARGs proliferation in MP-amended compost, while temperature was dominant in the control. Network analysis identified key bacterial hosts Staphylococcus, Weissella, Lactiplantibacillus, Sphingobacterium carrying multiple ARGs and MGEs. This study highlights the potential of MPs, even at low concentrations, to promote ARG dissemination by altering microbial communities and enhancing gene transfer, offering new insights into ecological risks associated with MP-contaminated composting systems.},
}

@article {pmid41418611,
year = {2025},
author = {Du, R and Tang, M and Cao, S and Peng, Y},
title = {Overcoming temperature and substrate limitations of anammox via partial denitrification: Stable performance, microbial structure, and N2O mitigation.},
journal = {Water research},
volume = {291},
number = {},
pages = {125186},
doi = {10.1016/j.watres.2025.125186},
pmid = {41418611},
issn = {1879-2448},
abstract = {The widespread application of the anaerobic ammonium oxidation (anammox) process remains constrained by its narrow substrate range (nitrite-to-ammonia ratio of 1.32), sensitivity to low temperatures, and difficulty in controlling nitrous oxide (N2O). This study demonstrated that under different substrate types and proportions (nitrate-nitrite, NOx[-]-N), the partial denitrification coupled with anammox (PD/A) process with high nitrogen load (1.35 kg N/m[3]/d) still maintained stable nitrogen removal efficiencies (83.5 %∼98.5 %), even at long-term continuous cooling (29.4∼11.6°C) and persistent low temperature (15.1∼9.6°C). In the presence of coexisting NO3[-]-N and NO2[-]-N (NO3[-]-N: NO2[-]-N of 1:1), carbon sources were preferentially utilized for the reduction of NO3[-]-N to NO2[-]-N, effectively circumventing the strict substrate dependence inherent to anammox. The stable nitrogen removal of the PD/A process at low temperatures was attributed to the low activation energy (35.1 kJ/mol) of partial denitrification and the cold-resistant granular sludge, ensuring a highly efficient supply of the essential NO2[-]-N for anammox. Cold-resistant granule sludge provided a spatial environment for the synergistic symbiosis of partial denitrification, anammox, and other heterotrophic bacteria, facilitating anammox adaptation to persistent low-temperature conditions. Metagenomic sequencing revealed a high relative abundance of Candidatus Brocadia (14.9 %) within the granular sludge, while Thauera (18.0 %) dominated the flocculent sludge at low temperatures. It further revealed the cross-feeding relationship of the bacterial community between granular and flocculent sludge. Notably, N2O emissions from the PD/A process can be effectively regulated by controlling the COD/NO3[-]-N ratio, achieving a balance between improving nitrogen removal efficiency and mitigating N2O emissions. This research provides a theoretical foundation for the stable operation and N2O control of non-specifically dependent PD/A process under long-term low-temperature conditions.},
}

@article {pmid41418312,
year = {2026},
author = {Braga, LPP and Wang, Y and Huang, Z and Willerslev, E and Tanentzap, AJ},
title = {The Contributions of Microbial Interactions to Abrupt Ecosystem Changes during the Late Quaternary.},
journal = {The American naturalist},
volume = {207},
number = {1},
pages = {182-195},
doi = {10.1086/738433},
pmid = {41418312},
issn = {1537-5323},
mesh = {*Soil Microbiology ; *Ecosystem ; *Climate Change ; Europe ; *Microbial Interactions ; Fungi ; Mycorrhizae/physiology ; Grassland ; Forests ; },
abstract = {AbstractAbrupt ecosystem shifts during the Late Quaternary coincided with major climatic changes and intensified human activities, but the precise causes of these shifts remain debated. Here, building on previous hypotheses and work, we propose a new hypothesis that both plant beneficial and antagonistic soil microorganisms were the proximate drivers of Late Quaternary change. We synthesized evidence from paleoecological studies and contemporary ecosystems to understand how microbes and their interactions with plants shift ecosystem function. Because relevant paleoecological data are nonexistent, we reanalyzed a contemporary survey from grasslands and woodlands across Europe to test the general role of microbial diversity versus climate in controlling ecosystem function. Our models found that the richness of different microbial groups, including Proteobacteria, mycorrhizas, and plant fungal pathogens, were more strongly associated with the magnitude of direct effects on net primary productivity than temperature and precipitation. The richness of most of these groups was also influenced by climate, supporting our hypothesis that climate change may have indirectly caused past ecosystem shifts by changing microbial composition and function. We end by highlighting the potential of environmental DNA to reconstruct the biota and conditions of past ecosystems. Ultimately, improving our understanding of how microbes drove past ecosystem shifts may improve our ability to respond to future environmental changes.},
}

*Soil Microbiology
*Ecosystem
*Climate Change
Europe
*Microbial Interactions
Fungi
Mycorrhizae/physiology
Grassland
Forests

@article {pmid41417461,
year = {2025},
author = {Drew, G and Kraft, CS and Mehta, N},
title = {Fecal Microbiota Therapy: Clinical Laboratory Testing and Metabolomic Approaches for Donor Screening, Product Assessment, and Patient Monitoring.},
journal = {Clinical chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1093/clinchem/hvaf156},
pmid = {41417461},
issn = {1530-8561},
abstract = {BACKGROUND: The safety and efficacy of fecal microbiota transplantation for prevention of recurrent Clostridioides difficile infection relies on complex interactions between the donor and recipient microbiome.

CONTENT: Screening of donor stool has largely aimed to ensure safety; however, metagenomic and metabolic features of the stool, which may affect efficacy of the fecal microbiota transplantation (FMT), have been largely overlooked.

SUMMARY: In this review, we discuss the nascent field of metagenomic and metabolic donor and recipient characteristics that may affect efficacy of FMT and future directions for this field to allow for more precise and personalized therapies.},
}

@article {pmid41416507,
year = {2025},
author = {Wang, Y and Wan, Y and Wang, H and Yan, J and Sun, J and Yang, J and Zhang, F and Cao, H and Li, D},
title = {Oral Supplementation of Indole-3-acetic Acid Alleviates High-Fat-Induced Obesity by Activating the Gpha2-Mediated Thyroid-Stimulating Hormone Pathway.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c14556},
pmid = {41416507},
issn = {1520-5118},
abstract = {Obesity is a major global public health challenge. Indole-3-acetic acid (IAA), a gut microbiota-derived tryptophan metabolite, exhibits antiobesogenic potential. In this study, we found that in high-fat-diet-induced obese mice, oral IAA supplementation dose dependently attenuated body weight gain, adiposity, hepatic steatosis, and dyslipidemia while improving insulin sensitivity. Notably, intraperitoneal administration of IAA (50 mg/kg/day) paradoxically exacerbated weight gain. Metagenomic sequencing showed that oral IAA selectively enriched beneficial genera (Ileibacterium, Anaerotignum, and Clostridium) and significantly increased short-chain fatty acid (SCFA) production, particularly acetate and butyrate. In vitro experiments in Saccharomyces cerevisiae further confirmed that IAA directly suppresses de novo fatty acid biosynthesis and triacylglycerol assembly. Mechanistically, IAA upregulated hepatic Gpha2 expression, thereby activating the TSH-THR-PGC-1α-PPARγ signaling cascade and concomitantly repressing key lipogenic genes (Fasn, Acaca, and Srebp-1c). Collectively, these findings position IAA as a promising microbiota-derived metabolite with substantial preventive and therapeutic potential for obesity and related metabolic disorders.},
}

@article {pmid41416110,
year = {2025},
author = {Jun, L and Wan, X and Zhang, D and Zheng, Y and Chen, X and Mi, L and Xiao, B},
title = {Mixed vaginal infection status in women infected with Trichomonas vaginalis: comparison of microscopy method and metagenomic sequencing analysis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1638464},
pmid = {41416110},
issn = {2235-2988},
mesh = {Female ; Humans ; *Trichomonas vaginalis/genetics/isolation & purification ; *Metagenomics/methods ; Adult ; *Vagina/microbiology/parasitology/pathology ; *Trichomonas Vaginitis/diagnosis/microbiology ; *Microscopy/methods ; Microbiota/genetics ; *Coinfection/microbiology/diagnosis/parasitology ; Young Adult ; Middle Aged ; Lactobacillus/isolation & purification/genetics ; },
abstract = {Trichomonas vaginalis (TV) infection is a common non-viral sexually transmitted infection, often combined with mixed vaginal infections. These mixed infections worsen inflammation, disrupt vaginal microbiota, and affect treatment. Currently, TV and its mixed infections are mainly diagnosed by wet mount microscopy, which has low sensitivity and cannot identify complex microbes well. This study compared microscopy with metagenomic sequencing to explore vaginal microbiota changes and improve diagnosis of TV-related mixed infections. We enrolled 30 participants: 20 TV-infected patients (diagnosed by wet mount microscopy) and 10 healthy controls (with Lactobacillus as dominant vaginal microbiota). Then tested by Gram staining, microscopy, and metagenomic sequencing. We analyzed microbial composition and identified different abundant taxa. We also measured clinical indices (Lactobacillus grade, vaginal pH, Nugent score for BV, Donders score for AV) to assess vaginal microecology. Among 20 TV patients, microscopy and clinical criteria found a 65% mixed infection rate (13/20), including TV+AV (5 cases), TV+BV+AV (7 cases), and TV+VVC (1 case). Metagenomic sequencing showed TV patients had higher alpha diversity (Shannon index: p=0.0276) and different beta diversity (ANOSIM, r=0.21, p=0.000167) than controls. At the genus level, TV patients had more anaerobic taxa (Fannyhessea, Atopobium, Peptostreptococcus, FDR<0.05) and less Lactobacillus (FDR<0.05) than controls. All TV patients were CST IV (low Lactobacillus, high mixed bacteria), including 12 cases of CST IV-C and 7 cases of CST IV-B. Microscopy and sequencing had low diagnostic consistency in diagnosing mixed infections, especially for mixed vaginitis. TV infection causes significant vaginal microecological imbalance (less Lactobacillus, more anaerobes, high mixed infection rate). Metagenomic sequencing is better than microscopy at identifying complex microbes and low-abundance pathogens, making it more accurate for diagnosing TV-related mixed infections. These results suggest molecular diagnostic methods should be used as complementary tools for precise analysis improve TV and its mixed infection diagnosis and treatment.},
}

Female
Humans
*Trichomonas vaginalis/genetics/isolation & purification
*Metagenomics/methods
Adult
*Vagina/microbiology/parasitology/pathology
*Trichomonas Vaginitis/diagnosis/microbiology
*Microscopy/methods
Microbiota/genetics
*Coinfection/microbiology/diagnosis/parasitology
Young Adult
Middle Aged
Lactobacillus/isolation & purification/genetics

@article {pmid41416071,
year = {2025},
author = {Zheng, Y and Hou, J and Yang, L and Jiang, Y and Wang, S and Yu, J and Ye, X},
title = {Cavitary pulmonary tuberculosis with Orientia tsutsugamushi coinfection in a non-endemic region: a case report.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1692918},
pmid = {41416071},
issn = {2296-858X},
abstract = {INTRODUCTION: Coinfection of pulmonary tuberculosis and scrub typhus caused by Orientia tsutsugamushi is exceptionally rare. Overlapping clinical and radiologic features, together with the frequent absence of clear epidemiologic clues, complicate timely diagnosis.

CASE PRESENTATION: A 57-year-old man residing in a non-endemic region presented with a left-sided cavitary lung lesion on imaging. Computed tomography (CT)-guided percutaneous lung biopsy, acid-fast bacillus staining, and Mycobacterium tuberculosis DNA PCR established the diagnosis of active cavitary pulmonary tuberculosis. Despite initiation of a standard first-line anti-tuberculosis regimen, high-grade fever persisted. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) detected O. tsutsugamushi, which was subsequently confirmed by a positive IgM indirect immunofluorescence assay (IFA). Doxycycline was added, leading to defervescence within 48 h and marked symptomatic improvement. On follow-up, chest CT demonstrated lesion absorption and cavity shrinkage, while new fibrotic changes emerged. The patient was started on maintenance pirfenidone and prescribed home oxygen therapy.

CONCLUSION: In patients with pulmonary tuberculosis who exhibit persistent fever or suboptimal response despite appropriate therapy-and after excluding drug resistance-scrub typhus should be included in the differential diagnosis, even in non-endemic settings without a typical exposure history. Longitudinal imaging in this case also shows that irreversible structural remodeling may occur despite microbiologic control, underscoring the need to pair prompt pathogen-directed therapy with ongoing monitoring and early strategies to preserve lung function.},
}

@article {pmid41415824,
year = {2025},
author = {Lai, W and Guo, J and Zhou, X and Luo, Y and Zheng, M and Mai, Q and Xiong, J and Luo, M},
title = {Co-infection in pediatric pertussis during 2023 and 2024 in southern China: pathogen distribution characteristic and influence on manifestation of pertussis.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1722003},
pmid = {41415824},
issn = {1664-302X},
abstract = {OBJECTIVE: We sought to examine the pathogen composition of co-infections in pertussis during 2023 and 2024 and assess the impacts of co-infection on pertussis.

METHODS: Clinical data of pediatric pertussis patients were retrospectively analyzed. The impact of co-infections on pertussis, the detection rate and composition of co-pathogens were analyzed. Culture, polymerase chain reaction, or metagenomic sequencing were used in pertussis or co-pathogens detection.

RESULTS: Among 620 pertussis patients, 110 patients co-infected with bacteria, 106 co-infected with virus, and 98 co-infected with both bacteria and virus. M. pneumoniae (114, 18.39%), M. catarrhalis (44, 7.1%), and H. influenzae (26, 4.19%) were the most common bacterial co-pathogens, and Rhinovirus (100, 16.12%), Cytomegalovirus (31, 5%), and Influenza virus A&B (28, 4.52%) were the most common viral co-pathogens. Patients with co-infections exhibited more severe manifestations than those with pertussis alone, and the severity was associated with the type and number of pathogens. The composition of co-pathogens linked to the age and hospitalization status of the patients. M. pneumoniae (91, 21.06%), M. catarrhalis (32, 7.41%), and Influenza virus A&B (22, 5.09%) primarily caused co-infections in older, non-hospitalized patients, whereas Cytomegalovirus [(19, 14.39%) non-ICU, (12, 21.43%) ICU] and Respiratory syncytial virus [(8, 6.06%) non-ICU, (8, 14.28%) ICU] were more common in younger, hospitalized patients.

CONCLUSION: Co-infections are common among pertussis and can intensify clinical symptoms. Distribution of co-infecting pathogens is associated with age and hospitalization status, and the impacts of co-infection on the manifestations of pertussis varied according to the types and number of co-pathogens.},
}

@article {pmid41415820,
year = {2025},
author = {Bao, Y and Wang, T and Adina, W and Yao, R and Chu, H and Yao, X and Meng, J and Wang, J and Ren, W and Zeng, Y},
title = {Gut microbial signatures and cardiac-microbiota axis in Yili horses with divergent exercise-induced cardiac remodeling.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1689293},
pmid = {41415820},
issn = {1664-302X},
abstract = {This study aimed to investigate how different training outcomes affect the gut microbiota composition in racehorses. Twenty-six Yili horses underwent a 9-month conditioning training regimen under uniform husbandry and management conditions. Post-training, the horses were divided into an excellence group (D. Y group) and a general group (D. P group) based on their athletic performance, with the top 10 performers constituting the D. Y group and the bottom 10 the D. P group. Cardiac morphology and function were quantitatively assessed via echocardiography, and metagenomic sequencing was performed on fresh fecal samples. Results indicated that there were no significant differences in gut microbiota and echocardiographic parameters between the two groups prior to training. However, significant differences were observed post-training (p < 0.05). At the genus level, Parabacteroides, Bacteroides, and Prevotella exhibited significantly greater abundance n the D. Y group. LEfSe analysis showed that Prevotella was markedly enriched in the D. Y group (LDA > 4). Functional profiling indicated that multiple metabolic pathways were significantly enriched in global and overview maps, with map00534 and map00190 being particularly enriched in the D. Y group (LDA > 2). Within CAZymes genes, eight were significantly enriched in the D. Y group, including four glycoside hydrolase genes, two carbohydrate esterase genes, and two carbohydrate-binding module genes. Echocardiography revealed significant differences in seven parameters between the groups, with the D. Y group exhibiting notably higher LV_MASS_I and LVM values (p < 0.01). dbRDA analysis demonstrated a significant association between LV_MASS_I and LVM and the gut microbiota profile (p < 0.01). These findings suggest that training-induced cardiac remodeling, particularly the increase in LV_MASS_I and LVM, is closely related to alterations in gut microbiota, with Prevotella enrichment potentially serving as a marker of favorable adaptation to the training regimen. The study provides robust evidence for understanding the interaction between aerobic training, gut microbiota, and cardiac characteristics in racehorses, and highlights potential directions for optimizing athletic performance and probiotic strategies in equine athletes.},
}

@article {pmid41415819,
year = {2025},
author = {Miao, M and Ma, C and Yang, J and Yang, X and Liu, Z and Liu, A and Qian, Z and Ge, Y and Chen, Y and Yin, G and Hu, Z},
title = {BALF metagenomic next-generation sequencing for the diagnosis of pulmonary mycobacterial infection in persons with HIV: a retrospective, diagnostic accuracy study.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1689997},
pmid = {41415819},
issn = {1664-302X},
abstract = {Severely immunocompromised persons with HIV (PWH) are vulnerable to pulmonary mycobacterial infections (MBI), including Mycobacterium tuberculosis (MTB) and non-tuberculous mycobacteria (NTM). This study aimed to assess the effectiveness of metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) in aiding the diagnosis of pulmonary mycobacterial infections in PWH. This study encompassed 146 hospitalized PWH who had a CD4+ T cell count of less than 200 cells/μL. We employed BALF mNGS to pinpoint the causative pathogens of pulmonary infections, with particular focus on pulmonary mycobacterial infections. We evaluated the diagnostic performance of BALF mNGS, and interpreted its clinical significance in detecting mixed infections as appropriate. The median CD4+ T cell count of the participants was 22.5 (IQR: 7.0-63.0) cells/uL. BALF mNGS analysis of 146 severely immunocompromised PWH identified Mycobacterium tuberculosis (13.0%) and M. avium complex (7.5%) as the predominant mycobacterial species, with 9.3% (4/43) of mycobacterial infections showing mixed speciation including TB-NTM co-infections or interspecies NTM coinfections. Furthermore, mNGS demonstrated 78.8% sensitivity (95% CI: 62.2%-89.3%) for proven mycobacterial infections, outperforming conventional culture (68.4% vs. 42.1%, P < 0.01), though missing 7 proven MBI cases. Finally, among 158 co-detected pathogens, Pneumocystis jirovecii (67.1%) and cytomegalovirus (63.0%) were most prevalent, demonstrating co-occurrence rates of 53.5% and 55.8%, respectively in mycobacterial-infected patients. These rates were elevated to 81.2% (P. jirovecii) and 65.3% (CMV) in the subset of 101 patients with CD4+ counts <50 cells/μL. The presence of atypical clinical presentations, along with the coexistence of multiple opportunistic pathogens in BALF, complicates the management of pulmonary MBI in PWH. In this context, mNGS has emerged as a highly promising microbiological test that could revolutionize the management of pulmonary MBI in PWH.},
}

@article {pmid41415818,
year = {2025},
author = {Wu, H and Du, X and Zheng, J and Li, X and Song, Q and Yan, Y and Ma, A and Xu, A and Li, J},
title = {Top-down enrichment of oil-degrading microbial consortia reveals functional streamlining and novel degraders.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1656448},
pmid = {41415818},
issn = {1664-302X},
abstract = {INTRODUCTION: Top-down microbial enrichment is a reliable approach for understanding and designing microbiomes for crude oil remediation. Environmental variables serve as valuable determinants for selecting desired microbiomes with superior performance. However, the linkages between selection methods and the structure and function of desired microbiomes remain unclear.

METHODS: This study integrated substrate concentration gradients and cultivation patterns to investigate how selection pressures shape top-down enriched crude oil-degrading consortia. The resulting communities were analyzed using 16S rRNA gene sequencing, metagenomics, and co-occurrence network analysis. Key bacterial strains were isolated to validate their individual degradation capabilities.

RESULTS: The top-down process led to a significant reduction in phylogenetic diversity but a notable increase in the potential for xenobiotic degradation and metabolic. The final consortia, GT4, achieved a 55.72% degradation rate of crude oil at an initial concentration of 5 g/L within 7 days. Metagenomic analysis identified Microbacterium as dominant genus harboring key enzymes for the degradation of alkanes and aromatic compounds. Co-occurrence network analysis revealed Mesorhizobium as a keystone genus, showing positive associations with multiple diazotrophic bacteria and hydrocarbon degrading bacteria. Nine bacterial strains were isolated from the consortium. Among them, Microbacterium sp. WS3 and Cellulosimicrobium sp. WS9 exhibited high degradation efficiencies (57.85 and 58.60%, respectively). To the best of our knowledge, this study provides the first experimental evidence for crude oil degradation by Paracandidimonas and Caulobacter, with degradation rates of 51.19 and 40.90%, respectively.

DISCUSSION: These findings highlight the effectiveness of top-down enrichment strategy in generating functionally streamlined consortia and uncover novel oil-degrading microbes with potential for bioremediation applications.},
}

@article {pmid41415809,
year = {2025},
author = {Li, E and Wang, S and Li, Y and Liuli, A and Liang, M and Huang, J and Li, Y and Li, H and Feng, Z},
title = {Characterization of the gut microbiota in people with different levels of obesity.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1679119},
pmid = {41415809},
issn = {1664-302X},
abstract = {PURPOSE: With the evolution of dietary habits, obesity has emerged as a significant global health issue. Numerous studies have demonstrated a close association between obesity and gut microbiota; however, the specific contribution of gut microbiota to varying degrees of obesity remains inadequately understood. Consequently, this study aims to characterize the gut microbiota of individuals across different obesity severity levels.

METHODS: We conducted a comprehensive characterization of the gut microbiome in Chinese obese patients and a healthy control group through the application of 16S rRNA gene sequencing, supplemented by metagenomic sequencing. The study cohort was stratified into five distinct categories based on body mass index (BMI): healthy, overweight, and obesity grades I, II, and III.

RESULTS: In obese populations, the gut microbiome structure shifted significantly, with beneficial genera like Faecalibacterium, Roseburia, and Ruminococcus decreasing, and potentially harmful genera such as Blautia, Collinsella, and Streptococcus increasing. These changes impacted host metabolic pathways, including ribosome synthesis, RNA polymerase activity, and DNA repair. Clinical analyses also revealed strong links between specific genera and metabolic markers like lipid metabolism and insulin resistance.

CONCLUSION: Populations with different obesity traits show unique changes in gut flora. The level of dysbiosis, or imbalance in intestinal microbiota, rises with obesity. These microbial changes are linked to host metabolism, indicating that targeting harmful bacteria and supplementing with beneficial ones from normal-weight populations could effectively reduce obesity.},
}

@article {pmid41415804,
year = {2025},
author = {Zhang, M and Zhu, Y and Sun, Z and Wang, B and Chen, J and Zhou, F and Zeng, J and Li, M and Zou, D and Jiang, Z},
title = {Chemoautotrophic Thermodesulfobacteriota as a key genomic potential group in the hypoxic diazotrophic community of the Changjiang (Yangtze River) estuary.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1671267},
pmid = {41415804},
issn = {1664-302X},
abstract = {Coastal hypoxia, intensified by global warming and eutrophication, profoundly affects marine nitrogen cycling. However, its impact on diazotrophic communities in large river estuaries remains poorly understood. During an unprecedented hypoxia event (minimum dissolved oxygen at 2.70 μmol L[-1]) in August 2016 in the Changjiang Estuary, we sampled across a dissolved oxygen (DO) gradient spanning hypoxic and non-hypoxic waters. Using nifH gene amplicon sequencing, metagenomic binning, and multivariate statistical analyses, we found that higher diazotrophic biodiversity was observed in hypoxia zone, with non-cyanobacterial diazotrophs dominating the communities. The phylum Thermodesulfobacteriota (with relative abundance of 58.93% totally) exhibited significant hypoxia-specific enrichment. LEfSe analysis identified Thermodesulfobacteriota as potential hypoxia biomarkers, while network analysis revealed their keystone role, representing 68.6% of highly connected nodes. Environmental drivers, including low DO concentrations (7.50-61.88 μmol L[-1] in hypoxic vs. 66.56-255.63 μmol L[-1] in non-hypoxic zones), elevated salinity (30.67-34.50), increased dissolved reactive phosphorus (0.39-1.26 μmol L[-1]), and nitrate depletion (0.30-22.50 μmol L[-1]), collectively created favorable conditions for the development of the observed diazotrophic community under hypoxia. Metagenomic analysis revealed a hypoxia-driven increase in nifH gene abundance, with nifH-carrying metagenome-assembled genomes affiliated with Thermodesulfobacteriota showing approximately a 4.7-fold higher relative abundance in hypoxic zone compared to non-hypoxic zone. Reconstruction of metabolic pathways from metagenome-assembled genomes (MAGs) further suggested their potential involvement in both nitrogen fixation and carbon-sulfur cycling. Amplicon and metagenomic datasets consistently demonstrated Thermodesulfobacteriota's predominant in hypoxia. These findings redefine estuarine nitrogen flux models by highlighting hypoxia-driven taxonomic and functional shifts in diazotrophic communities, and provide a foundation for assessing the potential microbial resilience and ecosystem risks in expanding coastal hypoxic zones. Our study underscores the genomic potential of Thermodesulfobacteriota as key players in the nitrogen cycle under hypoxia, a hypothesis that warrants future validation through direct activity measurements.},
}

@article {pmid41415514,
year = {2025},
author = {Chen, X and Wang, L and Li, J and Zhang, Y and Liu, C and Yang, J and Shi, J and Liang, S},
title = {Efficacy of Liposomal Amphotericin B in Treating Pulmonary Aspergillus flavus Infection in Nonneutropenic Adults: Cases Report and Literature Review.},
journal = {Clinical case reports},
volume = {13},
number = {12},
pages = {e71688},
pmid = {41415514},
issn = {2050-0904},
abstract = {Liposomal amphotericin B (L-AmB), as a modified formulation of traditional amphotericin B, have better targeting and lower toxicity. However, clinicians have limited experience with the use of L-AmB for the treatment of Aspergillus flavus (A. flavus) at present. We described two cases of immunocompetent adults; despite undergoing various antibacterial treatments, the symptoms were persistent. Based on the clinical characteristics and results of metagenomic next-generation sequencing and (or) pathology, pulmonary A. flavus infection was confirmed. Subsequently, L-AmB was added to the treatment. Following the initiation of antifungal therapy, the patients' symptoms and images were significantly improved. In conclusion, even in immunocompetent individuals, pathogen detection and pathological examination are crucial when treatment is not effective. In pulmonary A. flavus infection, L-AmB may deserve greater attention and confidence in clinic.},
}

@article {pmid41415494,
year = {2025},
author = {Petrov, TP and Rizzetto, M and Clagnan, E and Dell'Orto, M and De Nisi, P and D'Imporzano, G and Ovani, M and Pina, MP and Kron-Morelli, R and Adani, F},
title = {Trichoderma-Activated Granulated Digestate as an Alternative to Chemical Fertilization: Effects on Tomato Yield and Quality, and Soil Rhizospheric Communities.},
journal = {ACS agricultural science & technology},
volume = {5},
number = {12},
pages = {2383-2392},
pmid = {41415494},
issn = {2692-1952},
abstract = {The use of synthetic fertilizers is always more economically and environmentally unsustainable. It is necessary to improve current agricultural practices. Bioactivated fertilizers are a promising solution to enhance digestate solid fraction's fertilizing properties with an ad hoc microbial consortium and reach yields comparable to chemical fertilization (CF), thus combining circular economy with an upgraded organic agriculture. This study designed a new granulated formulation, obtained using a vacuum drying process at the industrial level, for an improved Trichoderma-activated digestate's solid fraction. This granulation aimed to improve both management operations and Trichoderma activity. After a greenhouse experimentation, yields obtained from the activated digestate (56 ± 7 g FW plant[-1]) were similar to the one obtained with CF (62 ± 9 g FW plant[-1]). Additionally, the bioactivated digestate gave yield production that were 21-30% higher yield than that of digestate alone. Microbial activation further led to higher nutritional values with an increment in the lycopene content between 8.8% and 15.8%. A metagenomic analysis further highlighted the persistence of Trichoderma in the tomato rhizosphere and its ability to establish positive interactions with other beneficial rhizospheric microorganisms. Activated digestate showed its potential to substitute CF, while granulation resulted in a functional formulation to convey this product.},
}

@article {pmid41415413,
year = {2025},
author = {Macias Calix, K and Borges, C and do Nascimento Oliveira, AL and Albuquerque de Luna, SC and Souza Cunha, CM and de Siqueira, AM and Campelo Dos Santos, AL and DeGiorgio, M and Lindo, J and Assis, R},
title = {Genomic insights into ancestry and infectious disease in 17th-century colonial Brazil.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2025.12.10.693243},
pmid = {41415413},
issn = {2692-8205},
abstract = {During urban redevelopment in the historic district of a Brazilian metropolis, archaeologists uncovered a previously undocumented 17th-century cemetery, containing the closely spaced remains of over two dozen young adult males of military age. Historical records suggest the site once housed a makeshift hospital, raising questions about the origins and causes of death of those interred, particularly given the absence of skeletal evidence for violent or fatal trauma. The current study integrates bioarchaeological, historical, and genomic data to investigate the ancestry and putative disease-related mortality of nine individuals whose remains were recovered and subsequently sequenced. Population-genetic analyses revealed strong affinities with Northern European populations, particularly from Norway, Iceland, Estonia, and Czechoslovia, consistent with their likely roles as soldiers or laborers employed by the Dutch West India Company. To explore potential causes of death, we conducted a metagenomic screening with a novel pipeline optimized for degraded DNA, which revealed widespread presence of Klebsiella pneumoniae and Mycobacterium tuberculosis pathogens across all samples. Authenticity was confirmed through post-mortem damage patterns characteristic of historical samples. These findings, together with the absence of combat trauma and the collective burial context at the site, support the hypothesis of an epidemic-related mortality event. This study contributes to the growing field of historical pathogen genomics and offers a rare genomic perspective on life, mobility, and health during a period of colonial upheaval in South America.},
}

@article {pmid41415012,
year = {2025},
author = {Zhang, W and Zhang, L and Liu, H},
title = {Necrotizing enterocolitis in a neonate with severe congenital pulmonary valve stenosis complicated by a postoperative right atrial thrombus: a case report.},
journal = {Frontiers in pediatrics},
volume = {13},
number = {},
pages = {1594899},
pmid = {41415012},
issn = {2296-2360},
abstract = {Congenital heart disease may increase the incidence of necrotizing enterocolitis, especially in low-birth-weight infants. We report a case of a newborn with pulmonary valve stenosis who developed neonatal necrotizing enterocolitis IIIB. The infant underwent initial cardiac surgery followed by a laparotomy. After cardiac surgery, a right atrial thrombus was found by cardiac ultrasound. Enterococcus faecium was identified using metagenomic next-generation sequencing of ascitic fluid. The infant received targeted antibiotic therapy and anticoagulant treatment and was then discharged.},
}

@article {pmid41414025,
year = {2025},
author = {Bian, J and Cao, YN and Han, YP and Liu, JG and Chen, Q and Liu, ZP and Li, MY},
title = {[Screening, Identification, and Performance of Microplastic-degrading Functional Bacteria in Saline-alkali Soil Environment].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {46},
number = {12},
pages = {8082-8092},
doi = {10.13227/j.hjkx.202411208},
pmid = {41414025},
issn = {0250-3301},
mesh = {*Soil Microbiology ; Biodegradation, Environmental ; *Soil Pollutants/metabolism/isolation & purification ; *Microplastics/metabolism/isolation & purification ; Soil/chemistry ; *Bacteria/metabolism/isolation & purification/classification ; Alkalies ; Polyethylene Terephthalates/metabolism ; Salinity ; },
abstract = {The combined effects of salinization and microplastic pollution will have a detrimental impact on soil fertility and the ecological integrity of soil ecosystems. Three strains of salt-resistant microplastic-degrading functional bacteria were obtained from the soil of the Hetao irrigation area, which served as a source of inoculum. The strains were identified using metagenomics and were found to belong to the genera Agrobacterium, Aspergillus fumigatus, and Streptomyces. The strains were designated Agrobacterium_salinitolerans strain （A）, Aspergillus fumigatus strain （F）, and Streptomyces sudanensis strain （S）, respectively. The degradation of polyethylene （PE） and polyethylene terephthalate （PET） by single and mixed bacteria was compared using the weight loss rate of microplastics as a constraint. The findings revealed that the weight loss rates of PE and PET under the combined conditions of the three strains of functional bacteria were 21.900% and 23.800% at 60 d, which was significantly better than that of single bacteria and the mixture of two strains. Based on the growth process of functional bacteria, the characteristics of key enzyme genes, and the changes of surface morphology and functional groups during the degradation of PE and PET, the mechanism of PE and PET being degraded after long-chain depolymerization, β oxidation cycle, and tricarboxylic acid cycle under the action of mixed functional bacteria was revealed. These findings provide a theoretical basis and technical support for the control of microplastic pollution in salinized soil.},
}

*Soil Microbiology
Biodegradation, Environmental
*Soil Pollutants/metabolism/isolation & purification
*Microplastics/metabolism/isolation & purification
Soil/chemistry
*Bacteria/metabolism/isolation & purification/classification
Alkalies
Polyethylene Terephthalates/metabolism
Salinity

@article {pmid41413769,
year = {2025},
author = {Medina-Méndez, JM and Iruzubieta, P and Fernández-López, R and Crespo, J and de la Cruz, F},
title = {Bacterial metabolic signatures in MASLD predicted through gene-centric studies in stool metagenomes.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-025-04549-5},
pmid = {41413769},
issn = {1471-2180},
support = {PI22/01853//Spanish Carlos III Health Institute (ISCIII)/ ; PID2020-1179236B-100//Spanish MINECO/ ; },
}

@article {pmid41413663,
year = {2025},
author = {McAdams, Z and Gustafson, K and Ericsson, A},
title = {Biological and technical variability in mouse microbiota analysis and implications for sample size determination.},
journal = {Lab animal},
volume = {},
number = {},
pages = {},
pmid = {41413663},
issn = {1548-4475},
support = {U42 OD010918/CD/ODCDC CDC HHS/United States ; U42 OD010918/CD/ODCDC CDC HHS/United States ; U42 OD010918/CD/ODCDC CDC HHS/United States ; },
abstract = {The gut microbiota (GM) affects host development, behavior and disease susceptibility. Biomedical research investigating GM-mediated influences on host phenotypes often involves collecting fecal samples from laboratory mice. Many environmental factors can affect the composition of the GM in mice. While efforts are made to minimize this variation, biological and technical variability exists and may influence outcomes. Here we employed a hierarchical fecal sampling strategy (that is, sequenced multiple libraries generated from multiple pellets collected from multiple mice) to quantify the effect size of biological and technical variation and to provide practical guidance for the development of microbiome studies involving laboratory mice. We found that while biological and technical sources of variation contribute significant variability to alpha- and beta-diversity outcomes, their effect size is 3-30-times lower than that of the experimental variable in the context of an experimental group with high intergroup variability. After quantifying the variability of alpha-diversity metrics at the technical and biological levels, we simulated whether sequencing multiple fecal samples from mice improves effect size in a two-group experimental design. Our simulation determined that collecting five fecal samples per mouse increased effect size, reducing the minimum number of animals per group required by 5% while dramatically increasing sequencing costs. Our data suggest that the effect size of biological and technical factors may contribute appreciable variability to an experimental paradigm with relatively low mean differences. In addition, repeated sampling improves statistical power; however, its application is probably impractical given the increased sequencing costs.},
}

@article {pmid41413233,
year = {2025},
author = {Ikagawa, Y and Okamoto, S and Taniguchi, K and Mizoguchi, R and Hashimoto, A and Imamura, R and Arakawa, H and Ogura, K and Yanagihara, M and Tsujiguchi, H and Hara, A and Nakamura, H and Hosomichi, K and Karashima, S},
title = {Gut microbiota-derived polyamine pathways associated with mean blood pressure.},
journal = {Hypertension research : official journal of the Japanese Society of Hypertension},
volume = {},
number = {},
pages = {},
pmid = {41413233},
issn = {1348-4214},
abstract = {Hypertension is a common lifestyle-related disease and is influenced by various factors, including excessive salt intake. Recently, the gut microbiota (GM) has gained attention for its potential involvement in blood pressure regulation; however, polyamine metabolism involvement remains poorly understood. Sixty participants aged ≥40 years from Shika Town, Japan, were stratified into four groups (n = 15 each) based on mean blood pressure and urinary sodium chloride (u-NaCl) excretion. The clinical parameters were evaluated, and fecal samples were analyzed using shotgun metagenomic sequencing to assess the microbial composition and abundance of genes related to arginine-polyamine metabolism. Three major findings were observed: (1) Significant differences in the α-diversity of GM were observed between salt-sensitive and non-salt-sensitive hypertensive groups; (2) The abundance of spermidine synthase (EC 2.5.1.16), a key enzyme in polyamine metabolism with known antihypertensive effects, was significantly higher in normotensive individuals, independent of u-NaCl excretion; and (3) Bacterial species harboring polyamine metabolic enzyme genes, including EC 2.5.1.16, differed significantly between groups, suggesting group-specific microbial metabolic traits. These findings suggest that GM-mediated polyamine metabolism may contribute to the regulation of salt-sensitive blood pressure. While variations in spermidine-producing bacteria and the involvement of EC 2.5.1.16 were observed, these factors alone do not fully account for the intergroup differences related to salt intake. Thus, polyamine metabolism likely plays a part in salt sensitivity, but additional microbial and host factors are also involved. Further studies are needed to validate these findings and to explore microbiota-targeted strategies for the prevention and treatment of hypertension.},
}

@article {pmid41412926,
year = {2025},
author = {Autenrieth, IB and Bury, L and Rooney, AM and Willmann, M and Vehreschild, MJGT and Egli, A},
title = {Paradigms for microbiome analysis in infectious and non-communicable diseases.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2025.11.016},
pmid = {41412926},
issn = {1878-4380},
abstract = {Next-generation sequencing and bioinformatics paved the way in deciphering the human gut microbiome and challenged fundamental postulates on the causal role of the microbiota for health and pathogenesis of infectious and noncommunicable diseases. To exploit the clinical relevance and potential of microbiome diagnostics and therapy, deep metagenomic sequencing with standardized, validated laboratory procedures, aiming at deciphering the microbiome at strain level and applying index-scores to allow classification of individual microbiomes as dysbiotic (associated with disease) or eubiotic (associated with health) should be implemented. By this means, metagenomically informed therapies with live biotherapeutic products, fecal microbiota transfer, pro-, pre-, or postbiotics might become a standard in personalized prevention and treatment of infectious and non-communicable diseases.},
}

@article {pmid41412727,
year = {2025},
author = {Osswald, A and Wortmann, E and Wylensek, D and Kuhls, S and Coleman, OI and Peuker, K and Strigli, A and Ducarmon, QR and Larralde, M and Liang, W and Treichel, NS and Schumacher, F and Volet, C and Matysik, S and Kleigrewe, K and Gigl, M and Rohn, S and Guo, CJ and Kleuser, B and Liebisch, G and Schnieke, A and Ridlon, JM and Bernier-Latmani, R and Zeller, G and Zeissig, S and Haller, D and Flisikowski, K and Clavel, T and Ocvirk, S},
title = {Secondary bile acid production by gut bacteria promotes Western diet-associated colorectal cancer.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2024-332243},
pmid = {41412727},
issn = {1468-3288},
abstract = {BACKGROUND: Western diet and associated production of secondary bile acids (BAs) have been linked to the development of sporadic colorectal cancer (CRC). Despite observational studies showing that secondary BAs produced by 7α-dehydroxylating (7αDH+) gut bacteria are increased in CRC, a causal proof of their tumour-promoting effects is lacking.

OBJECTIVE: Investigate the causal role of BAs produced by 7αDH+ gut bacteria in CRC.

DESIGN: We performed feeding studies in a porcine model of CRC combined with multi-omics analyses and gnotobiotic mouse models colonised with 7αDH+ bacteria or a genetically modified strain to demonstrate causality.

RESULTS: Western diet exacerbated the CRC phenotype in APC [1311/+] pigs. This was accompanied by increased levels of the secondary BA deoxycholic acid (DCA) and higher colonic epithelial cell proliferation. The latter was counteracted by the BA-scavenging drug colestyramine. Metagenomic analysis across multiple human cohorts revealed higher occurrence of bai (BA inducible) operons from Clostridium scindens and close relatives in faeces of patients with CRC. Addition of these specific 7αDH+ bacteria (C. scindens/Extibacter muris) to defined communities of gut bacteria led to DCA production and increased colon tumour burden in mouse models of chemically or genetically induced CRC. A mutant strain of Faecalicatena contorta lacking 7αDH caused fewer colonic tumours in azoxymethane/dextran sodium sulfate treated mice and triggered less epithelial cell proliferation in human colon organoids compared with wild-type F. contorta.

CONCLUSION: This work provides functional evidence for the causal role of secondary BAs produced by gut bacteria through 7αDH in CRC under adverse dietary conditions, opening avenues for future preventive strategies.},
}

@article {pmid41412669,
year = {2026},
author = {Li, W and Chen, J and Zhang, J and Peng, Z},
title = {Multi-omics insights into the formation mechanism of aging quality in white tea (Bai Mudan) during storage: Integrating sensory evaluation, volatilomics, metabolomics, and metagenomics.},
journal = {Food research international (Ottawa, Ont.)},
volume = {224},
number = {},
pages = {117996},
doi = {10.1016/j.foodres.2025.117996},
pmid = {41412669},
issn = {1873-7145},
mesh = {*Metabolomics/methods ; *Food Storage ; *Tea/chemistry/microbiology ; Volatile Organic Compounds/analysis ; Taste ; *Metagenomics ; Odorants/analysis ; Humans ; *Camellia sinensis/microbiology/chemistry ; Bacteria/genetics ; Multiomics ; },
abstract = {White tea (WT) develops unique aged quality during long-term storage, characterized by progressive changes in sensory properties and chemical composition. However, integrated insights into the sensory, metabolites, and microbial contribution underlying this process remain limited. This study systematically investigated the quality evolution of Bai Mudan tea (a typical WT) over 0 to 11 years of storage using an integrated multi-omics approach. Sensory analysis revealed a flavor transition from fresh (grassy, fruity) to aged (woody, stale) characteristics. Volatilomics identified 72 volatile compounds, with cedrol and isophorone as aged characteristic aroma compounds (rOAV ≥1, VIP ≥ 1, p ≤ 0.05). Metabolomics identified 1146 non-volatile metabolites, showing accumulation of fatty acyls and flavonoids, and a decrease in amino acids. Metagenomic sequencing analysis revealed that bacterial communities (mainly Sphingomonas, Pedobacter, Methylobacterium, and Chryseobacterium) dominated during the first 7 years of storage, followed by a potential shift toward a bacterial-fungal synergy pattern in later stages as the abundances of Monascus and Aspergillus increased. KEGG annotation highlighted the roles of carbohydrate metabolism and amino acid metabolism, and flavonoid biosynthesis was activated during storage. Multi-omics correlation networks demonstrated that fungi positively regulated volatile flavors, while bacteria may be involved in taste balance. Monascus, Sphingomonas, Sphingobium, and Novosphingobium were identified as core functional taxa that may contribute to WT quality formation during storage through aged flavor synthesis, flavonoid accumulation, and lipid degradation. In conclusion, this study provides a multi-dimensional scientific basis for a comprehensive understanding of the formation mechanism of aged quality in white tea during storage.},
}

*Metabolomics/methods
*Food Storage
*Tea/chemistry/microbiology
Volatile Organic Compounds/analysis
Taste
*Metagenomics
Odorants/analysis
Humans
*Camellia sinensis/microbiology/chemistry
Bacteria/genetics
Multiomics

@article {pmid41412647,
year = {2026},
author = {Chen, T and Mo, S and Shen, M and Du, W and Yu, Q and Chen, Y and Xie, J},
title = {Therapeutic potential of Ficus pumila L. in chronic obstructive pulmonary disease through modulation of the gut microbiota-SCFA-lung signaling pathway.},
journal = {Food research international (Ottawa, Ont.)},
volume = {224},
number = {},
pages = {117952},
doi = {10.1016/j.foodres.2025.117952},
pmid = {41412647},
issn = {1873-7145},
mesh = {*Pulmonary Disease, Chronic Obstructive/drug therapy/microbiology/metabolism ; *Gastrointestinal Microbiome/drug effects ; Animals ; *Ficus/chemistry ; *Signal Transduction/drug effects ; *Lung/metabolism/drug effects ; Mice ; *Fatty Acids, Volatile/metabolism ; *Plant Extracts/pharmacology ; Male ; Mice, Inbred C57BL ; Disease Models, Animal ; Polysaccharides/pharmacology ; },
abstract = {Ficus pumila L. has been reported to alleviate pulmonary inflammation, its impact on chronic obstructive pulmonary disease (COPD) pathobiology-specifically via modulation of the gut-lung signaling pathway-has yet to be mechanistically defined. This study investigated how Ficus pumila L. polysaccharides (FP-P) and aqueous extracts (FP-E) remodel the gut microbiome-SCFA network and restore microbial metabolic function in a cigarette smoke-induced COPD mouse model. Microbiota composition was profiled by high-resolution 16S rRNA amplicon sequence variant (ASV) analysis, with concomitant quantification of caecal SCFA using targeted gas chromatography-mass spectrometry (GC-MS) and inference of metagenome function by PICRUSt2. Results demonstrated that FP-P and FP-E alleviated pulmonary pathology, reduced inflammatory cytokine secretion, and significantly restored gut microbiota α-diversity in COPD mice. At the family level, FP-P selectively expanded SCFA-producing Clostridiaceae, and Staphylococcaceae, whereas it contracted pro-inflammatory Helicobacteraceae and Campylobacteraceae. Caecal total SCFA concentration increased by 41.90 %, driven primarily by elevations in butyrate (+23.41 %) and propionate (+45.45 %), without significant changes in acetate. PICRUSt2-inferred metagenomes showed up-regulation of butanoate biosynthesis (PWY-5677), metabolism of cofactors and amino acid (P162-PWY and NAD-BIOSYNTHESIS-II), and carbohydrate degradation (P341-PWY), all of which underpin SCFA production. These functional shifts were accompanied by increased abundance of microbial genes encoding ribosomal proteins and ATP-binding cassette transporters, indicating barrier reinforcement. Collectively, FP-P and FP-E mitigate CS-induced COPD pathology through a gut microbiota-SCFA-lung signaling signaling pathway, highlighting the gut-to-lung communication within the broader gut-lung axis. These findings establish a mechanistic link between microbial metabolism and pulmonary inflammation while acknowledging that the reverse lung-to-gut feedback remains to be elucidated. Future studies will investigate this bidirectional crosstalk and the receptor-mediated signaling of SCFAs in lung tissue.},
}

*Pulmonary Disease, Chronic Obstructive/drug therapy/microbiology/metabolism
*Gastrointestinal Microbiome/drug effects
Animals
*Ficus/chemistry
*Signal Transduction/drug effects
*Lung/metabolism/drug effects
Mice
*Fatty Acids, Volatile/metabolism
*Plant Extracts/pharmacology
Male
Mice, Inbred C57BL
Disease Models, Animal
Polysaccharides/pharmacology

@article {pmid41412637,
year = {2026},
author = {Ferrocino, I and Biolcati, F and Giordano, M and Bertolino, M and Zeppa, G and Cocolin, L},
title = {Dairy environment and seasons affect the microbiome of a traditional artisanal cheese.},
journal = {Food research international (Ottawa, Ont.)},
volume = {224},
number = {},
pages = {117927},
doi = {10.1016/j.foodres.2025.117927},
pmid = {41412637},
issn = {1873-7145},
mesh = {*Cheese/microbiology/analysis ; *Seasons ; *Microbiota ; Animals ; *Food Microbiology ; Italy ; Fungi/classification/genetics/isolation & purification ; *Dairying/methods ; Bacteria/classification/genetics ; Milk/microbiology ; Food Handling/methods ; Cattle ; Metagenomics ; },
abstract = {Cheese microbiome is a complex community shaped by raw ingredients and by the production environment that significantly influences final product characteristics. While environmental microbiome can establish stable resident populations, their composition remains susceptible to seasonal shifts, hygienic practices and other external factors. In this study we investigate the interplay of these factors on the bacterial and fungal communities throughout the production of a full-fat semi cooked semi-hard cow's milk cheese produced in the Piedmont region, North-West of Italy, named Maccagno. Amplicon based sequencing was used to characterize bacterial and fungal diversity across environmental surfaces (contact and non-contact) and during the manufacturing and ripening of Maccagno cheeses over three seasons (autumn, winter and summer). Metabolomic profiling and texture analysis of the ripened cheeses allowed for direct correlation with microbial community shifts. The facility environment maintained a remarkably stable core microbiota, including Staphylococcus, Streptococcus thermophilus, Lactococcus lactis, Debaryomyces, Penicillium and Cladosporium. Among the monitored processing plant sampling sites, the metal stirring tool, milk inlet pipe and the ripening room ventilation system emerged as critical points for microbial transfer and persistence. During ripening, core microbial taxa including Lc. lactis, S. thermophilus and Debaryomyces were observed. Shotgun metagenomics was then performed on final cheeses and genome reconstruction highlighted that Lc. lactis genomes showed impressive seasonal genomic adaptability, particularly in autumn, where it contributed to favorable texture and flavor through proteolytic activity and production of aroma-associated metabolites like acetoin and linear ketons. Conversely, summer production exhibiting the highest prevalence of spoilage-associated microbes such as Acinetobacter and Enterobacteriaceae, mainly of facility origin that led to off-flavor profiles inconsistent with the typical Maccagno sensory identity. The fungal communities, mainly composed by Debaryomyces and Penicillium, also varied seasonally, influenced significantly by the ventilation system in the ripening room. Maccagno cheese quality is a direct reflection of these complex microbial dynamics. Seasonal variations in raw milk microbiome and microbial populations established in specific environmental niches significantly affected the final product's sensory and textural attributes. To this end, understanding seasonal influences and the role of resident environmental populations is crucial for optimizing production protocols, mitigating spoilage risks, and ensuring the consistent quality of traditional cheeses.},
}

*Cheese/microbiology/analysis
*Seasons
*Microbiota
Animals
*Food Microbiology
Italy
Fungi/classification/genetics/isolation & purification
*Dairying/methods
Bacteria/classification/genetics
Milk/microbiology
Food Handling/methods
Cattle
Metagenomics

@article {pmid41412435,
year = {2025},
author = {Dolci, M and Frosio, F and Signorini, L and Soggiu, A and Meroni, G and Favi, E and Alavrez, EC and Ferrante, P and Delbue, S},
title = {Human polyomavirus 6 differentially infects healthy and tumor tissue in the colon: A case report.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {},
number = {},
pages = {105865},
doi = {10.1016/j.meegid.2025.105865},
pmid = {41412435},
issn = {1567-7257},
abstract = {INTRODUCTION: Human polyomavirus 6 (HPyV6) is part of the human skin virome. Like other HPyVs, it encodes proteins with oncogenic properties.

MATERIALS AND METHODS: A 73-year-old Italian female patient with stage II right-sided colon adenocarcinoma underwent hemicolectomy; she died one month later because of bacterial sepsis. Colon tumor (T), adjacent healthy (AH) tissue, and serum samples were collected. Total nucleic acids were subjected to next-generation sequencing, followed by metagenomics analysis. HPyV detection was confirmed by real-time PCR and Rolling Circle Amplification (RCA); HPyV6 transcripts and proteins were identified by means of PCR and Western blot/mass spectrometry, respectively.

RESULTS: Viral metagenomics analysis revealed the presence of several viral genomes, mainly belonging to unclassified viruses and phages, in both AH and T tissues. HPyV6 DNA was detected in the T tissue, representing 7 % of the viral sequences, but not in the AH tissue. Subsequent molecular analysis confirmed the presence of the HPyV6 genomes (3.3x10[6]copies/ug) as episomes, infecting 19.8 % of the tumor cells; LT-Ag and VP1 transcripts were expressed in the T tissue, and the LT-Ag protein was expressed twice as highly in the T tissue as in the AH tissue.

CONCLUSIONS: This is the first report of the differential presence and expression of the HPyV6 genome in colon tumors but not in the AH tissue. These results are indicative of ongoing active replication of the virus, which might play a triggering role in malignant transformation.},
}

@article {pmid41412398,
year = {2025},
author = {Zhang, H and Jing, X and Gong, Y and Zheng, P and Ren, Y and Chen, R and Wu, Y and Liu, S and Zhang, L and Xu, J and Xu, Y},
title = {Single-cell phenotyping and sequencing uncover metabolically active low-abundance yeasts in thermophilic fermentation.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133803},
doi = {10.1016/j.biortech.2025.133803},
pmid = {41412398},
issn = {1873-2976},
abstract = {Microbiota-driven fermentation is a global biomanufacturing process that often operates under extreme and fluctuating temperatures. To understand how such systems maintain productivity, this study investigated the Chinese fermentation starter high-temperature Daqu (HTD) as a model system. By combining metagenomics and Raman microspectroscopy, the analysis revealed a drastic decoupling between phylogenetic composition and metabolic activity, with only 10-32 % of yeast species detected by sequencing remaining metabolically active under heat stress. Raman-activated cell sorting and culture (RACS-Culture) recovered three yeasts that consistently maintained viability throughout HTD production: Pichia kudriavzevii, Wickerhamomyces anomalus, and Saccharomycopsis fibuligera. Mono-species and synthetic-community fermentation further revealed a sophisticated mechanism of temporal niche partitioning: in the moderate-temperature early and late stages, S. fibuligera and W. anomalus dominated substrate degradation and flavor precursor biosynthesis, respectively. However, as temperatures rose above 45 °C, both species exhibited low metabolic activity and survival rates. In contrast, only P. kudriavzevii sustained robust growth at this elevated temperature. Genomic analysis revealed a remarkable expansion of heat-resistance and cell-clustering-related genes of wos2 and FLO8 in P. kudriavzevii. These genetic characteristics underpin its enhanced viability, which enables the initially low-abundance species to thrive as a primary ethanol producer and ultimately establish numerical dominance. Thus, temporally overlaying single-cell metabolic vitality profiles onto the corresponding metagenomes can unravel novel functional species and reveal their ecological roles in a complex ecosystem.},
}

@article {pmid41412053,
year = {2025},
author = {Xu, Y and Han, Y and Dong, X and Feng, Y and Wu, F and Xing, F and He, J and Rogers, MJ and Luan, X and Liu, R and He, J and Dang, H and Zhang, D},
title = {Temperature shapes the biogeography of rdhA and reductive dehalogenators in sediment across northwestern Pacific marginal seas.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140847},
doi = {10.1016/j.jhazmat.2025.140847},
pmid = {41412053},
issn = {1873-3336},
abstract = {Dehalogenating microorganisms are crucial in organohalide detoxification in marine sediments. However, the large-scale biogeography and potential environmental adaptability of reductive dehalogenators (RDGs) in marginal sea sediments remain poorly understood. Here, dehalogenating cultures enriched from different marginal sea sediments across northwestern Pacific showed varied dehalogenation patterns, suggesting diverse reductive dehalogenase genes (rdhA). Genome-resolved metagenomic analysis of in situ marginal sea sediments revealed the presence of rdhA-like genes belonging to six distinct categories, with two novel clades more abundant in hypothermal deep-sea sediments (p<0.05). The results of canonical correspondence analysis and distance decay relationship revealed that temperature outweighed geographical contiguity in determining rdhA biogeography and phylogenetic diversity in sediments. A total of 64 putative RDGs were identified across 13 phyla. Low ratios of non-synonymous and synonymous polymorphisms and nucleotide diversity at gene and genome levels indicated the conservation of dehalogenation metabolism in sediment microbiome. RDGs at higher abundance (p<0.05) in mesothermal (≥17.40 ℃) sediments may rely more on sulfate reduction, whereas those with higher abundance (p<0.05) in hypothermal (≤5.5 ℃) sediments (hyp-RDGs) may rely on nitrate utilization. Additionally, hyp-RDGs were prone to external cobalamin acquisition, possibly as an efficient energy-saving strategy. These findings provide insights into the ecological roles of RDGs in marine sediments.},
}

@article {pmid41412046,
year = {2025},
author = {Li, X and Zhang, Y and Zhao, C and Dang, X and Li, B and Hou, S and Gao, X and Hao, J and Lyu, Z and Wang, Y and Hao, L and Zhu, T},
title = {Breaking the cycle of resistance: Hyperthermophilic composting establishes a multi-layered defense against ARG dissemination.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140801},
doi = {10.1016/j.jhazmat.2025.140801},
pmid = {41412046},
issn = {1873-3336},
abstract = {The environmental dissemination of antibiotic residues and antibiotic resistance genes (ARGs) from livestock manure poses major risks to public health. Here, we established a hyperthermophilic composting (HC, >80℃) system alongside conventional composting (CK) to elucidate the mechanisms driving antibiotic and ARG removal. By integrating metagenomics, Quantitative PCR (qPCR), and machine learning, we systematically assessed antibiotic degradation, ARG/MGE dynamics, and microbial functional shifts. HC rapidly reached 87.3 ℃ within 24 h and maintained extreme thermophilic conditions, achieving higher TOC degradation (36.58 % vs. 22.59 % in CK), accelerated humification (HA/FA=2.19 by day 15), and efficient removal of oxytetracycline, enrofloxacin, and sulfamethoxazole (98.44 %, 92.34 %, and 99.63 %, respectively), thereby shortening the selective pressure window. Metagenomics identified 796 ARGs and 128 MGEs; key ARGs (macB, bcrA, tetA(58)) declined markedly in HC, with ARG and MGE abundances strongly correlated and virulence factor genes synchronously reduced. qPCR confirmed rapid ARG/MGE attenuation in HC without the rebound observed in CK. Partial least squares path modeling (GOF=0.858) showed MGEs were the primary driver of ARG dissemination (path coefficient=0.790), while temperature exerted indirect effects by reshaping thermophilic communities, enhancing metabolism, and suppressing antibiotics and MGEs. Random forest further highlighted MGEs (integrase, transposase, IS91/ISCR) and humification indices (HA/FA/HS) as key factors, with Bacillus and Truepera as major contributors under HC. Overall, HC established a multilayered "high temperature-community restructuring-functional metabolism-MGE suppression" barrier, enabling faster, more stable and safer resistance risk control than CK. This provides a scalable pathway for safe manure valorization and ARG mitigation under the One Health framework.},
}

@article {pmid41412032,
year = {2025},
author = {You, F and Yang, S and Ding, Y and Han, J and Xing, D and Jin, C and Zhao, Y and Gao, M and Guo, L},
title = {Comparative insights into denitrification performance and microbial adaptation of heterotrophic, autotrophic, and mixotrophic systems under florfenicol stress for recirculating mariculture wastewater treatment.},
journal = {Water research},
volume = {291},
number = {},
pages = {125172},
doi = {10.1016/j.watres.2025.125172},
pmid = {41412032},
issn = {1879-2448},
abstract = {Wastewater from marine recirculating aquaculture systems (RAS) poses significant treatment challenges due to its high nitrate concentrations and low carbon-to-nitrogen ratio. The additional presence of antibiotic residues such as florfenicol creates mixed pollution that further impairs denitrification and destabilizes microbial communities. This study systematically compared the multi-scale responses of heterotrophic (HDN), sulfur-autotrophic (SADN), and mixotrophic (MDN) denitrification under 4.0 mg L[-1] florfenicol stress in synthetic recirculating mariculture wastewater (salinity = 3.5 %). The MDN system achieved the highest denitrification rate (46.83 mg NOx[-]-N h[-1] g[-1] MLVSS) and maintained nitrate removal efficiency above 98 % with minimal fluctuations under florfenicol stress. Although the HDN system exhibited high NAR/NIR activities and electron transport system activity (ETSA), nitrite accumulation occurred due to functional imbalance. The SADN system, relying on sulfur oxidation, demonstrated limited metabolic flexibility and electron supply capacity under florfenicol stress, resulting in slower nitrate reduction. Metagenomic and KEGG pathway revealed significant differences in microbial community composition and functional potential among HDN, SADN and MDN denitrification systems: HDN was dominated by biofilm-forming Proteobacteria, with broad antibiotic resistance gene (ARG) enrichment and stronger mobile genetic element co-localization; SADN showed enrichment of Campylobacterota, consistent with sulfur oxidation-based pathways, and Mantel tests confirmed tighter ARG-environment coupling; MDN showed the highest microbial diversity with elevated Planctomycetota, functional enrichment in carbohydrate and energy metabolism, and stable quorum sensing-electron transfer coupling with functional redundancy. These findings provide new insights for designing robust treatment strategies for recirculating mariculture wastewater subject to compound pollution from nitrate and antibiotics.},
}

@article {pmid41411799,
year = {2025},
author = {Chen, M and Meng, S and Guan, R and Dong, Q and Dong, X and Shen, X and Fang, L and Zhao, F},
title = {Lead exposure changes carbohydrate and amino acid metabolism corresponding to a disturbed microbiota-gut-brain axis in mice.},
journal = {Ecotoxicology and environmental safety},
volume = {309},
number = {},
pages = {119554},
doi = {10.1016/j.ecoenv.2025.119554},
pmid = {41411799},
issn = {1090-2414},
abstract = {Chronic lead exposure can cause irreversible neurological damage. The brain-gut axis's involvement in lead-induced neurotoxicity, a key factor in cognitive deficits, requires further exploration. To deepen our understanding of how lead exposure influences the brain-gut connection, we carried out the behavioral and morphological analysis, as well as metabolome and metagenome analysis associated with the gut-brain axis. The study results suggested that Pb exposure resulted in inflammation in both the brain and gut, along with decreased cognitive ability. The metagenomic data indicated that Pb exposure impacted microbial diversity and composition, with a marked increase in genes linked to carbohydrate and amino acid metabolism. Compared to control mice, the metabolic profiles of brain, feces and serum samples from Pb-exposed mice were differed, with higher levels of amino acids in serum and soluble sugars in feces, but lower levels of amino acids in brain. Key enriched microbial (eg: Tenericutes, Thermotogae, Alistipes_putredinis) was significantly negatively correlated with brain amino acid (eg: proline, asparagine, tryptophan) but positively correlated with serum amino acids (eg: valine, leucine, tyrosine). This research uncovers new perspectives on how lead exposure alters metabolites in the brain-gut axis, regulated by gut microbiota, highlighting the need for additional research on lead's health risks.},
}

@article {pmid41410816,
year = {2025},
author = {He, JH and Wang, H and Qiu, E and Qi, Q and Wang, Z},
title = {Gut Microbiota and Atherosclerosis: Integrative Multi-Omics and Mechanistic Insights.},
journal = {Current atherosclerosis reports},
volume = {28},
number = {1},
pages = {1},
pmid = {41410816},
issn = {1534-6242},
support = {R01HL170904/HL/NHLBI NIH HHS/United States ; K01HL169019/HL/NHLBI NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Atherosclerosis/microbiology/metabolism ; Metabolomics/methods ; Metagenomics ; Dysbiosis ; Proteomics ; Multiomics ; },
abstract = {PURPOSE OF REVIEW: This review synthesizes and discusses evidence from metagenomics, metabolomics, and proteomics on gut microbiome alterations in atherosclerotic cardiovascular disease (ACVD), with carotid atherosclerosis (CAS) serving as an example.

RECENT FINDINGS: Evidence on gut microbial α-diversity and β-diversity was mixed and differs by disease status. Pro-inflammatory/pathogenic gut bacterial taxa (e.g., Escherichia coli, Klebsiella spp., Streptococcus spp., and Ruminococcus gnavus) were often enriched in patients with ACVD or CAS, whereas short-chain fatty acid (SCFA) producers (e.g., Faecalibacterium prausnitzii, Roseburia spp., Bacteroides spp., and Eubacterium eligens) were depleted. Targeted and untargeted metabolomics implicated multiple microbial-derived metabolites in relation to ACVD and CAS, including trimethylamine N-oxide, short-chain fatty acids, bile acids, lipopolysaccharides, phenylacetylglutamine, indole-3-propionate and imidazole propionate. Gut dysbiosis contributes to ACVD or CAS possibly via metabolite-mediated effects on endothelial function, inflammation, and lipid metabolism. Future research prioritizing longitudinal and interventional studies integrating microbial metagenomics with host multi-omics are needed to elucidate causal pathways and identify clinically actionable targets.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Atherosclerosis/microbiology/metabolism
Metabolomics/methods
Metagenomics
Dysbiosis
Proteomics
Multiomics

@article {pmid41410786,
year = {2025},
author = {Senel, E and Ramos-Barbero, MD and Santos, F and Villamor, J and Mutlu, MB and Antón, J},
title = {Viral diversity of brine and precipitated halite of Tuz Lake, an inland hypersaline lake in Turkey.},
journal = {Archives of virology},
volume = {171},
number = {1},
pages = {28},
pmid = {41410786},
issn = {1432-8798},
support = {208F135//the Anadolu University Research Foundation No. 1208F135. ES. was an MSc student of the Erasmus program./ ; },
mesh = {*Lakes/virology/chemistry ; Salinity ; Turkey ; Salts/chemistry ; *Viruses/genetics/classification/isolation & purification ; Phylogeny ; *Biodiversity ; Metagenomics ; Genome, Viral ; },
abstract = {The diversity of viral communities in inland hypersaline environments remains largely unexplored. Here, we characterized viral assemblages of the thalassohaline inland hypersaline Tuz Lake (Turkey). To identify viral groups and viral sequences present in multiple samples, brine and precipitated salt samples were analysed using microscopy and metagenomics. Viral assemblages showed an abundance and morphology similar to what is commonly found in hypersaline systems. Despite these similarities, the vast majority of sequences remained unknown with regard to taxonomy and function and could not be characterized, highlighting their novelty. A remarkably high fraction of the viral sequences identified were present in both brine and salt samples, indicating viral stability during salt precipitation and dissolution in the lake, suggesting that Tuz Lake might be of considerable astrobiological interest. Alongside this high level of similarity, read recruitments revealed the presence of some sample-specific viral sequences in the salt sample. Tuz Lake viral assemblages displayed a distinct composition when compared to previously described viral metagenomes and haloviral genomes from hypersaline environments, with the highest similarity to the viral assemblages of the crystallizer ponds in the Bras del Port saltern (Spain).},
}

*Lakes/virology/chemistry
Salinity
Turkey
Salts/chemistry
*Viruses/genetics/classification/isolation & purification
Phylogeny
*Biodiversity
Metagenomics
Genome, Viral

@article {pmid41410736,
year = {2025},
author = {Nath, S},
title = {Advanced microbial engineering approaches for biodegradation of pharmaceutical pollutants.},
journal = {Biodegradation},
volume = {37},
number = {1},
pages = {15},
pmid = {41410736},
issn = {1572-9729},
mesh = {*Biodegradation, Environmental ; *Water Pollutants, Chemical/metabolism ; Pharmaceutical Preparations/metabolism ; *Metabolic Engineering/methods ; *Bacteria/metabolism/genetics ; Bioreactors/microbiology ; },
abstract = {Pharmaceutical pollutants have emerged as pervasive environmental contaminants, entering ecosystems via wastewater effluents, agricultural runoff and improper disposal. These pollutants typically belong to classes such as antiepileptics, antibiotics, analgesics, non-steroidal anti-inflammatory drugs, hormones and antiseptics. Their recalcitrance arises from their stable chemical structures, which resist degradation and pose significant challenges for conventional wastewater treatment processes, leading to their persistence in the environment and potentially harmful effects on ecosystems and human health. This study investigates microbial engineering strategies for the efficient degradation of pharmaceutical pollutants. Recent advancements in CRISPR systems, ALE, metabolic engineering, bioaugmentation and bioreactor designs have significantly improved pollutant breakdown. Additionally, novel approaches to address emerging contaminants and the application of advanced biotechnologies like synthetic biology and metagenomics are crucial for developing more effective and sustainable bioremediation strategies. These insights offer a roadmap for developing more effective and sustainable solutions for the bioremediation of pharmaceutical pollutants.},
}

*Biodegradation, Environmental
*Water Pollutants, Chemical/metabolism
Pharmaceutical Preparations/metabolism
*Metabolic Engineering/methods
*Bacteria/metabolism/genetics
Bioreactors/microbiology

@article {pmid41409983,
year = {2025},
author = {Hira, J and Mahbub, NB and Ali, J and Ahmad, R},
title = {Low-cost in-house re-formulated brain heart infusion medium for effective planktonic growth and early detection of bloodstream bacterial pathogens.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1680006},
pmid = {41409983},
issn = {1664-302X},
abstract = {Sepsis, a clinically defined life-threatening condition, is a global contributor to high morbidity and mortality rates in humans. It is caused by systemic bloodstream bacterial infections, primarily involving aerobic pathogens such as Escherichia coli, Staphylococcus aureus, and Klebsiella pneumoniae. Rapid and accurate identification of these pathogens is a high-demand task, as prolonged diagnosis may increase the mortality rate among sepsis patients. Globally, commercial blood culture systems like the BD BACTEC™ FX blood culture system, which utilizes BD BACTEC™ PLUS Aerobic/F culture bottles (used in this study), are commonly used to detect aerobic bloodstream infections. However, due to high costs (∼$10.00-$15.00/bottle), limited availability of culture media (especially in low- and middle-income countries, and war zones), and a lack of customization for antibiotic susceptibility assay and epidemiology research, there is a need for secondary alternatives to facilitate the growth and identification of bloodborne pathogens. Therefore, we developed a low-cost (∼$4-$5/bottle) in-house culture medium with a newly improved formulation of Brain Heart Infusion media that enhances bacterial growth from spiked human blood tested on a panel of bacteria (Escherichia coli, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterococcus faecalis). The growth dynamics of these microbes in in-house formulated BHI-Blood+ culture media coincide with those in BACTEC™ Plus Aerobic/F culture vials, which primarily suggests the compatibility of bloodborne pathogens with this media and can be flagged positive <8 h based on cellular growth rate. Additionally, conventional qPCR-based early detection (<24 h) and validation with the Oxford Nanopore MinION NGS platform highlight the value of this in-house culture media as an alternative to commercial culture media in terms of low-cost availability.},
}

@article {pmid41409546,
year = {2025},
author = {Zhao, L and Peng, S and Ge, M and Xing, B and Zhao, X and Yang, T and Yu, S and Zhang, C and Liu, J and Miao, Z and Ma, H},
title = {Gut-to-tumor translocation of multidrug-resistant Klebsiella pneumoniae shapes the microbiome and chemoresistance in pancreatic cancer.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1694479},
pmid = {41409546},
issn = {2235-2988},
mesh = {Humans ; *Pancreatic Neoplasms/microbiology/drug therapy/pathology ; *Klebsiella pneumoniae/drug effects/genetics/isolation & purification ; *Gastrointestinal Microbiome ; Feces/microbiology ; Male ; Female ; Middle Aged ; Aged ; *Drug Resistance, Multiple, Bacterial ; Metagenomics ; Anti-Bacterial Agents/pharmacology ; Whole Genome Sequencing ; Klebsiella Infections/microbiology ; },
abstract = {BACKGROUND: Despite advances and successes in precision oncology, pancreatic cancer (PC) remains a tumor with extremely low survival rates, and many of these cases experienced postoperative recurrence and metastasis. Alterations in the gut microbiota have been linked to the survival rates of PC patients. Nevertheless, the complexity of gut microbiota composition poses significant challenges in identifying definitive clinical biomarkers for PC.

METHODS: Fecal samples were collected from PC patients, half of whom had metastasis, and their matched healthy controls (HCs). A metagenomic analysis was employed to further investigate the functional features of gut microbiota with both PC and metastatic PC. The clinical correlations, microbial metabolic pathways and antibiotic resistome were further assessed. In a follow-up validation, intraoperative tumor tissue and pancreatic fluid were sampled from PC patients and underwent comprehensive microbiological analysis, including bacterial culture, mass spectrometry-based identification, and third-generation whole-genome sequencing of Klebsiella pneumoniae isolates.

RESULTS: We observed a significant alteration of the gut microbiota in PC patients, highlighted by an overall increase in microbial diversity compared to healthy controls (p < 0.05). Comparative abundance analysis identified 59 differentially abundant microbial species in non-metastatic pancreatic cancer (NMPC) (56 increased, 3 decreased) and 21 in metastatic pancreatic cancer (MPC) (19 increased, 2 decreased), alongside 18 significantly altered microbial metabolic pathways (FDR-adjusted p < 0.05). Notably, Klebsiella pneumoniae, Klebsiella oxytoca, and Akkermansia muciniphila were identified as prominent antibiotic resistance gene (ARG) carriers in the gut microbiota of PC patients, with 653 ARG subtypes detected across fecal samples, 38-47% of which were shared among groups. Strong co-occurrence patterns between ARGs (e.g., acrB, mdtC, cpxA, emr, pmrF) and the above species were observed predominantly in MPC samples (p < 0.05). Whole-genome sequencing of 14 isolates obtained from tumor tissue and pancreatic fluid revealed consistent ARG profiles and virulence genes, corroborating the metagenomic findings and supporting the hypothesis of gut-to-tumor translocation and potential intratumoral colonization.

CONCLUSION: This study provides a comprehensive microbiome-based insight into PC and its metastatic subtypes. By integrating microbiome analysis with microbial culture, this study provides direct evidence of gut-derived multidrug-resistant (MDR) K. pneumoniae colonization in PC tissues.},
}

Humans
*Pancreatic Neoplasms/microbiology/drug therapy/pathology
*Klebsiella pneumoniae/drug effects/genetics/isolation & purification
*Gastrointestinal Microbiome
Feces/microbiology
Male
Female
Middle Aged
Aged
*Drug Resistance, Multiple, Bacterial
Metagenomics
Anti-Bacterial Agents/pharmacology
Whole Genome Sequencing
Klebsiella Infections/microbiology

@article {pmid41409544,
year = {2025},
author = {Liu, J and Qin, SY and Lei, CC and Ma, H and Xie, LH and Liu, Y and Li, JH and Ni, HB and Yu, MY and Liang, HR and Shi, WH and Qin, Y and Jiang, J and Yan, WL and Chen, BN and Li, ZY and Sun, HT},
title = {Blastocystis infection in Tibetan antelopes (Pantholops hodgsonii) alters gut microbiota composition and function.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1719025},
pmid = {41409544},
issn = {2235-2988},
mesh = {*Gastrointestinal Microbiome ; *Antelopes/microbiology/parasitology ; Animals ; *Blastocystis ; *Blastocystis Infections/veterinary/parasitology/microbiology ; Tibet ; Metagenome ; Metagenomics ; Bacteria/classification/genetics/isolation & purification ; Feces/microbiology/parasitology ; },
abstract = {INTRODUCTION: The gut microbiota plays an important role in host environmental adaptation, including defense against pathogens. Parasite infections can disrupt gut microbial communities and thus influence host adaptability. However, most current knowledge of Blastocystis-microbiota interactions comes from humans or domestic animals, and data from wild mammals, especially those inhabiting extreme environments, remain scarce.

METHODS: In this study, we analyzed 68 gut metagenomes from Tibetan antelopes (Pantholops hodgsonii) and screened for infections by four intestinal parasites - Blastocystis, Cryptosporidium, Giardia, and Encephalitozoon bieneusi.

RESULTS: Among them, 26 individuals were solely infected with Blastocystis subtype ST31. Compositional analysis revealed 25 differential families, with 12 enriched in infected and 13 in healthy individuals. LEfSe further identified 38 species-level biomarkers (LDA > 2, p < 0.05), indicating a significant shift in gut microbial diversity following Blastocystis ST31 infection. Notably, the relative abundance of Arthrobacter sp. 08Y14, associated with environmental resilience, was markedly reduced in infected individuals. Functional profiling showed a decrease in metabolic diversity, with 18 CAZy families detected in the healthy group but only 2 in the infected group. KEGG analysis showed that the average relative abundance of K07497 was higher in the infected group (5.16) than in the healthy group (1.03).

DISCUSSION: These findings suggest that Blastocystis ST31 infection reshapes the gut microbiota and may impair the high-altitude adaptability of Tibetan antelopes by reducing plateau-adaptive microbes and functional capacity. This study provides the first evidence of Blastocystis-induced gut microbiota changes in Tibetan antelopes and broadens our understanding of parasite-microbiota interactions across hosts.},
}

*Gastrointestinal Microbiome
*Antelopes/microbiology/parasitology
Animals
*Blastocystis
*Blastocystis Infections/veterinary/parasitology/microbiology
Tibet
Metagenome
Metagenomics
Bacteria/classification/genetics/isolation & purification
Feces/microbiology/parasitology

@article {pmid41409502,
year = {2025},
author = {Pico-Tomàs, A and Sanchís, A and Mejías-Molina, C and Comas-Cufí, M and Balcázar, JL and Bofill-Mas, S and Torrell, H and Canela, N and Borrego, CM and Corominas, L},
title = {Tracking Age-Linked Antibiotic Resistance Patterns through Building-Level Wastewater Analysis.},
journal = {ACS ES&T water},
volume = {5},
number = {12},
pages = {7141-7151},
pmid = {41409502},
issn = {2690-0637},
abstract = {Antimicrobial resistance (AMR) is a global health challenge, and monitoring different demographic populations can improve our understanding of its spread and prevalence in urban settlements. This study applies building-level wastewater-based epidemiology (WBE) to analyze the resistome and mobilome of age-segregated populations from an elementary school (School), a university residence (UnivRes), and an elderly care facility (ElderlyRes) all located in Girona (Catalonia, Spain). Metagenomic analyses were subsequently conducted to investigate differences in bacterial communities, antibiotic resistance genes (ARGs), and mobile genetic elements (MGEs). The results revealed age-linked variations in the relative abundance and diversity of ARGs. The wastewater collected at the School exhibited the highest abundance of ARGs, while the ElderlyRes showed the highest diversity. Furthermore, sequences affiliated with bacterial pathogens were more prevalent in samples from both the School and the ElderlyRes, emphasizing potential public health implications. Among the 12 bacterial genera most strongly correlated with ARGs (Pearson R > 0.7), 11 were identified as members of the gut microbiota, underscoring their predominant role as reservoirs of resistance compared to bacteria of environmental origin. By integrating localized wastewater sampling with metagenomics, our study uncovers demographic-specific resistome patterns, delivering actionable evidence to strengthen AMR surveillance and intervention strategies in urban populations.},
}

@article {pmid41409175,
year = {2025},
author = {Ng, DZW and Low, A and Khairul Sani, KRB and Liu, L and Zhang, Z and Koh, XQ and Zhu, M and Mitra, K and Muthiah, M and Dan, YY and Lee, JWJ and Chan, ECY},
title = {Dysbiosis-Driven Reprogramming of Secondary Bile Acid Metabolism in Metabolic Dysfunction-Associated Steatotic Liver Disease: Insights from an Ex Vivo Human Fecal Microbiota Model.},
journal = {ACS pharmacology & translational science},
volume = {8},
number = {12},
pages = {4335-4344},
pmid = {41409175},
issn = {2575-9108},
abstract = {Gut microbial dysbiosis-induced perturbations in bile acid (BA) metabolism are implicated in metabolic dysfunction-associated steatotic liver disease (MASLD), yet evidence remains largely associative. Using an optimized ex vivo fecal microbiota model, we modeled the metabolism kinetics of conjugated- and primary-BA between MASLD and healthy donors. Enzymes for known BA metabolic reactions were inferred using functional metagenomics. MASLD cultures exhibited impaired deconjugation capacity but preserved downstream primary-BA clearance and demonstrated a substrate-independent shift that favored oxidative metabolism over 7α-dehydroxylation. This was marked by increased formation clearance of 7-keto-deoxycholic acid (175%) and 3-oxo-cholic acid (51.7%) from cholic acid (CA) and 7-keto-lithocholic acid (77.9%) from chenodeoxycholic acid (CDCA). C7-oxidized BA constituted the major proportion of total BA clearance (CA = 56.0%, CDCA = 72.3%) in MASLD cultures. Enrichment of C3- and C7-hydroxysteroid dehydrogenases in MASLD compared to control corroborated the differential secondary BA profiles. Together, microbes catalyzing C7-oxidation warrants further investigation as potential pharmacological targets of MASLD.},
}

@article {pmid41408693,
year = {2025},
author = {Esener, N},
title = {Omics technologies in mastitis: text mining and topic modelling analysis of global research trends.},
journal = {The Journal of dairy research},
volume = {},
number = {},
pages = {1-11},
doi = {10.1017/S0022029925101830},
pmid = {41408693},
issn = {1469-7629},
abstract = {Mastitis, an inflammation of the mammary gland, is a disease of significant clinical and economic importance. In recent years, advances in omics technologies have provided powerful tools to unravel the complex biological mechanisms underlying mastitis. These approaches encompass diverse fields such as genomics, proteomics, transcriptomics, metagenomics, metabolomics, epigenomics, lipidomics, glycomics, pharmacogenomics, foodomics, interactomics and exposomics. However, despite the rapid growth of omics research, the thematic structure of this literature has not been systematically examined. In this study, latent dirichlet allocation (LDA) was employed to perform topic modelling on publications related to omics and mastitis retrieved from Scopus and Web of Science. The LDA analysis revealed ten distinct topics, labelled according to the most frequent terms within each cluster: 'proteomics', 'pathogen genomics', 'differential expression', 'metabolism', 'genetic selection', 'disease economy', 'molecular diagnostics', 'microbiome', 'antimicrobial resistance' and 'genetic variation.' Among these, the topics of 'genomics', 'differential expression' and 'antimicrobial resistance' accounted for the highest number of publications, while 'metabolism' emerged more recently. All topics exhibited an increasing trend in publication volume over time, likely driven by the declining costs and greater accessibility of high-throughput omics technologies. This study provides a comprehensive thematic overview of omics research on mastitis, identifies key areas of emphasis and emerging directions, and highlights knowledge gaps that may inform future investigations and the development of targeted strategies for disease control and prevention.},
}

@article {pmid41408356,
year = {2025},
author = {Yao, QC and Zhang, DY and Du, YP and Chen, C and Lv, YT and Li, D and Xing, YX and Xu, XY and Lin, QQ and Tan, WF and Bai, FH},
title = {Gut microbiome-metabolome dysregulation in systemic sclerosis: a multi-omics study.},
journal = {Rheumatology (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/rheumatology/keaf668},
pmid = {41408356},
issn = {1462-0332},
abstract = {OBJECTIVES: The interplay between the gut microbiome (GM), plasma metabolites, and systemic sclerosis (SSc) has not been systematically studied. We hypothesized that disruption at the GM-metabolome interface contributes to the pathogenesis of SSc. This study aims to investigate the faecal microbiome composition and plasma metabolite profiles in SSc patients.

METHODS: To evaluate the interactions, deep shotgun metagenomic sequencing was conducted on faecal samples from 15 SSc patients and 33 healthy controls. Simultaneously, untargeted Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) metabolomic profiling was performed on plasma samples from 14 SSc patients and 30 controls.

RESULTS: The analysis revealed significant alterations in 11 microbial species and 266 MS2-identified metabolites in SSc patients vs controls. In SSc, elevated levels of Escherichia coli, Lactobacillus mucosae, and Parabacteroides distasonis were noticed. Conversely, P. plebeius, B. hansenii, and Agathobaculum butyriciproducens were enriched in the control group. Functional predictions indicated a depletion of amino acid biosynthesis pathways, including L-isoleucine and L-methionine, in SSc patients. The metabolomic analysis demonstrated a significant reduction in lipid-like molecules and amino acid levels in SSc patients. Dysregulated pathways, such as alanine, aspartate, and glutamate metabolism, arginine and proline metabolism, and glycine, serine, and threonine metabolism, were associated with the development of SSc. Striking microbiota-metabolite correlations (168 significant associations) were identified, with disease-enriched species showing specific metabolic linkages.

CONCLUSIONS: This study offers a comprehensive characterization of the disrupted GM-metabolite interface in SSc patients, providing new perspectives on SSc pathogenesis and potential therapeutic targets.},
}

@article {pmid41408316,
year = {2025},
author = {Wang, L and Remue, L and Adriaens, N and Soto, A and Verwimp, S and van Bree, J and Trappeniers, K and Delang, L},
title = {Identification of a culturable fungal species and endosymbiotic bacteria in saliva of Aedes aegypti and Culex pipiens and their impact on arbovirus infection in vitro.},
journal = {Parasites & vectors},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13071-025-07158-3},
pmid = {41408316},
issn = {1756-3305},
support = {C22/18/007//KU Leuven/ ; C14/20/108//KU Leuven/ ; STG/19/008//KU Leuven/ ; },
abstract = {BACKGROUND: Mosquito saliva plays a key role in arbovirus transmission and pathogenesis. It was shown that saliva contains several molecules that are essential for blood feeding. Recently, bacteria were also reported to be present in the saliva of Aedes albopictus and Anopheles mosquitoes. Nevertheless, information on the bacterial communities in Aedes and Culex saliva is still scarce.

METHODS: This study isolated and identified culturable fungal and bacterial colonies from saliva harvested from Aedes aegypti (laboratory strain) and Culex pipiens (field-collected) mosquitoes. 16S metagenomic sequencing was performed to identify bacterial communities in saliva and mosquito organs. Furthermore, it was assessed how these microbial communities were affected upon blood feeding and upon oral treatment with antibiotics and an antifungal drug.

RESULTS: The fungal species Penicillium crustosum was identified in mosquito saliva. Culturable bacteria detected in mosquito saliva included Serratia marcescens, Serratia nematodiphila, Enterobacter spp., and Klebsiella spp., which were previously identified as mosquito or insect endosymbionts in the midgut or other organs. Analysis with 16S metagenomics showed that bacterial communities in saliva were more diverse than those in the midgut. Blood feeding did not affect the fungal or bacterial load in mosquito saliva. Oral treatment of adult mosquitoes with antibiotics or an antifungal drug resulted in a significant reduction of bacteria or fungi present in the mosquito saliva. Notably, co-incubation of the mosquito-borne Semliki Forest virus with saliva from antibiotic- or antifungal-treated mosquitoes triggered a decrease in viral infection in human skin fibroblasts compared with nontreated saliva.

CONCLUSIONS: These findings indicate that bacteria and fungi can be present in mosquito saliva and provide a foundation for further exploration of the impact of salivary fungi and bacteria on both vector competence and arbovirus infection in the mammalian host.},
}

@article {pmid41408188,
year = {2025},
author = {Halimi, H and Hesami, Z and Asri, N and Khorsand, B and Rostami-Nejad, M and Houri, H},
title = {Exploring the biliary microbiome in hepatopancreatobiliary disorders: a comprehensive systematic review of microbial signatures and diagnostic potential.},
journal = {BMC gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12876-025-04551-1},
pmid = {41408188},
issn = {1471-230X},
support = {NO. IR.SBMU.RIGLD.REC.1404.036//Shahid Beheshti University of Medical Sciences/ ; },
abstract = {BACKGROUND: Hepatopancreatobiliary (HPB) diseases, encompassing hepatobiliary and pancreatic disorders, pose substantial global health challenges due to their high morbidity and mortality rates. Recent research highlights the crucial role of the biliary microbiome in the development of these diseases.

METHODS: This study provides a comprehensive systematic review of the biliary microbiome's characteristics across various HPB disorders, including cholangiocarcinoma (CCA), pancreatic cancer (PC), primary sclerosing cholangitis (PSC), and gallstone disease (GSD). Following Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines, we screened articles from multiple databases, focusing on original research utilizing 16 S rRNA gene sequencing or metagenomics.

RESULTS: Our review included 24 studies that met stringent inclusion criteria. The results indicate distinct alterations in bacterial diversity and composition associated with different HPB conditions, highlighting potential pathogenic mechanisms and candidate taxa as potential microbial indicators. In lithiasis conditions, elevated levels of Pyramidobacter and Citrobacter were associated with recurrent and giant common bile duct (CBD) stones. Proteobacteria were prevalent in PSC and CCA, potentially contributing to these diseases by promoting chronic inflammation. Sphingomonas was associated with both CCA and PSC, with potential implications for lymph node metastasis in PC.

CONCLUSIONS: These findings suggest the potential of the biliary microbiome as a diagnostic tool, offering insights into the pathophysiology and possible therapeutic targets for HPB diseases. However, given the heterogeneity in methodologies and the limited number of studies including healthy controls, these observations remain preliminary; further prospective validation is required before clinical translation.},
}

@article {pmid41408023,
year = {2025},
author = {Wang, H and Zhang, M and Hua, B and He, J and Yang, Y and Wu, W and Zhang, Y and Wei, F and Cai, Y and Wang, Q},
title = {Exploring the gut microbiome in systemic lupus erythematosus: metagenomic and metabolomic insights into a new pro-inflammatory bacteria Clostridium scindens.},
journal = {Clinical rheumatology},
volume = {},
number = {},
pages = {},
pmid = {41408023},
issn = {1434-9949},
support = {C2301008，C2404002//Shenzhen Medical Research Fund/ ; 2023B1515230002//Guangdong Basic and Applied Basic Research Foundation/ ; 2023A1515010294//Guangdong Basic and Applied Basic Research Foundation/ ; 0102018-2019-YBXM-1499-01-0414//Treatment and Prevention Integration Project of Shenzhen Municipal Health Commission/ ; SZSM202311030//Sanming Project of Medicine in Shenzhen/ ; No. NSFC 82302037//The National Natural Science Foundation of China/ ; KYQD2024355//Shenzhen High-level Hospital Construction Fund and Peking University Shenzhen Hospital Scientific Research Fund/ ; },
abstract = {OBJECTIVES: Systemic lupus erythematosus (SLE) is a complex autoimmune disease with unclear pathogenesis. Emerging evidence indicates that the gut microbiome may play a critical role in immune regulation. This study aimed to investigate gut microbiome and metabolome alterations in SLE patients, with a focus on the pro-inflammatory bacterium Clostridium scindens (C. scindens), and explore its potential contribution to disease pathogenesis.

METHOD: We performed metagenomic sequencing to analyze gut microbial composition in SLE patients and healthy controls, alongside untargeted metabolomic profiling of peripheral blood to assess systemic metabolic changes. We examined species diversity, taxonomic differences at both phylum and species levels, and metabolic alterations. Statistical analyses identified significant associations and potential diagnostic markers.

RESULTS: SLE patients did not show a consistent reduction in species diversity, but exhibited significant microbial compositional differences compared to healthy controls. These patterns suggest potential diagnostic utility. Metabolomic analysis revealed systemic metabolic disturbances linked to gut dysbiosis. Ruminococcus gnavus was associated with altered amino acid, lactose, and sphingolipid metabolism, potentially affecting host immunity. Notably, C. scindens appeared to contribute to immune dysregulation via bile acid metabolism.

CONCLUSIONS: This study reveals distinct microbial and metabolic profiles in SLE, identifying C. scindens as a potential driver of immune imbalance. The findings suggest that targeting the gut microbiome could offer novel strategies for diagnosis and therapeutic intervention in SLE. Key Points • Gut microbial composition is significantly altered in SLE patients compared to healthy controls. • Metabolomic profiling reveals systemic disturbances linked to gut dysbiosis. • Clostridium scindens is associated with bile acid metabolism and immune dysregulation in SLE. • The gut microbiome may serve as a potential target for diagnosis and treatment in SLE.},
}

@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.},
}