@article {pmid40289092,
year = {2025},
author = {Qiu, J and Hu, P and Li, F and Huang, Y and Yang, Y and Sun, F and Wu, P and Lai, Y and Wang, Y and He, X and Dong, Y and Zhang, P and Zhang, S and Wu, N and Wang, T and Yang, S and Li, S and Yuan, J and Liu, X and Liu, G and Hu, Y and Wu, JHY and Chen, D and Pan, A and Pan, XF},
title = {Circulating linoleic acid and its interplay with gut microbiota during pregnancy for gestational diabetes mellitus.},
journal = {BMC medicine},
volume = {23},
number = {1},
pages = {245},
pmid = {40289092},
issn = {1741-7015},
support = {2022YFC2702905//National Key R&D Program of China/ ; 82325043//the National Science Fund for Distinguished Young Scholars/ ; 82473646//Natural Science Foundation of China/ ; 2024NSFSC0578//Sichuan Provincial Natural Science Foundation/ ; YJ202346//Fundamental Research Funds for the Central Universities/ ; },
abstract = {BACKGROUND: Circulating linoleic acid (LA) levels have been reported to be associated with various metabolic outcomes. However, the role of LA and its interplay with gut microbiota in gestational diabetes mellitus (GDM) remains unclear. This study aimed to investigate the longitudinal association between circulating LA levels during pregnancy and the risk of GDM, and the potential role of gut microbiota.

METHODS: A nested case-control study was conducted within the ongoing Tongji-Huaxi-Shuangliu Birth Cohort in Chengdu, China. Blood and fecal samples were collected during early and middle pregnancy from 807 participants. GDM was diagnosed in middle pregnancy using the International Association of Diabetes and Pregnancy Study Groups criteria. Plasma LA levels were measured using gas chromatography-mass spectrometry, and gut microbiota was analyzed through 16S rRNA gene sequencing and shotgun metagenomic sequencing. A two-sample Mendelian randomization study was conducted using data from the IEU OpenGWAS database and the FinnGen consortium.

RESULTS: Elevated plasma LA levels were associated with a lower risk of GDM in both early (P for trend = 0.002) and middle pregnancy (P for trend = 0.02). Consistently, Mendelian randomization analysis revealed that each unit increase in LA was associated with a 16% reduction in GDM risk (odds ratio: 0.84, 95% confidence interval: 0.72, 0.95). In early pregnancy, higher plasma LA levels were correlated with higher adiponectin levels (P < 0.001) and lower levels of triglycerides (P < 0.001), HbA1c (P = 0.04), and C-peptide (P = 0.04). The LA-accociated microbiota mediated the relationship between LA and C-peptide (P = 0.01). Additionally, the inverse association between LA and GDM was modified by Bilophila (P for interaction = 0.03), with a stronger association observed in participants with lower Bilophila levels in early pregnancy. Metagenomic analyses further showed that the LA-associated pathway (D-galacturonate degradation I) and its key enzyme (EC 4.2.1.7) were associated with metabolic traits.

CONCLUSIONS: Our study provides evidence for an inverse causal association between plasma LA levels during pregnancy and GDM risk, which is both mediated and modified by gut microbiota.},
}

@article {pmid40289075,
year = {2025},
author = {Wu, J and Xiang, Y and Li, F and Liu, X and Dang, N and Guo, J},
title = {Phialophora americana infection in a patient with a compound heterozygous CARD9 mutation.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {613},
pmid = {40289075},
issn = {1471-2334},
support = {2022M710852//China Postdoctoral Science Foundation/ ; 82102420//National Natural Science Foundation of China/ ; ZR2024QH034//Natural Science Foundation of Shandong Province/ ; },
abstract = {Phaeohyphomycosis caused by Phialophora americana is relatively rare in clinical practice. Deficiency in the human caspase recruitment domain-containing protein 9 (CARD9) is associated with infections caused by Phialophora americana. In this case, the patient has had a decade-long history of recurrent tinea corporis and recently presented with an invasive, deep subcutaneous infection in the right axilla caused by Phialophora americana. Metagenomic next-generation sequencing (mNGS) confirmed that the pathogen infecting the patient was Phialophora americana. Whole exome sequencing (WES) revealed that the patient had compound heterozygous CARD9 gene mutations, with a c.952-1G > A mutation in intron 6 and a c.184 + 5G > T mutation in intron 2. The expression of the CARD9 protein and the levels of cytokines, including IL-17 and IFN-γ, were observed to be decreased in the patient. After an ineffective treatment with amphotericin B, voriconazole was administered for antifungal therapy and yielded satisfactory results. Following discharge, the patient continued oral voriconazole for ongoing antifungal treatment. One month after discharge, the patient returned to the hospital for a follow-up examination, during which it was observed that the symptoms had been successfully resolved. The novel compound heterozygous mutations may lead to CARD9 deficiency, which in turn results in susceptibility to Phialophora americana infection.},
}

@article {pmid40288855,
year = {2025},
author = {Prisacar, M and Leichert, LI},
title = {Functional metaproteomics for enzyme discovery.},
journal = {Methods in enzymology},
volume = {714},
number = {},
pages = {61-82},
doi = {10.1016/bs.mie.2025.01.029},
pmid = {40288855},
issn = {1557-7988},
abstract = {Discovery of microbial biocatalysts traditionally relied on activity screening of isolated bacterial strains. However, since most microorganisms cannot be cultivated in the lab, such an approach leaves the majority of the microbial enzyme diversity untapped. Metagenomic approaches, in which the DNA from a microbial community is directly isolated and then used either for the creation of an expression library or for sequencing and metagenome annotation have alleviated this shortcoming to an extent, but have their own limitations: the generation of large expression libraries is time-consuming and their screening is costly, while metagenome annotation can infer biocatalytic function only from prior knowledge. We have thus developed a functional metaproteomic approach, which combines the immediacy of traditional activity screening with the comprehensiveness of a meta-omics approach. Briefly, the whole metaproteome of an environmental sample is separated on a 2-D gel, biocatalytically active proteins are visualized in-gel through zymography, and those candidate biocatalysts are then identified through mass spectrometry, searching against a metagenome-derived database obtained from the very same environmental sample. Here we explain the process in detail, with a focus on esterases, and give guidelines on how to develop a functional metaproteomic workflow for enzyme discovery.},
}

@article {pmid40288854,
year = {2025},
author = {Lorente-Arévalo, Á and Gimeno-Pérez, M and Ortega, C and Finnigan, J and Charnock, S and Hidalgo, A},
title = {Ultrahigh-throughput screening assay for PET-degrading enzymes.},
journal = {Methods in enzymology},
volume = {714},
number = {},
pages = {489-503},
doi = {10.1016/bs.mie.2025.01.021},
pmid = {40288854},
issn = {1557-7988},
abstract = {In recent years, several PET-degrading enzymes have been identified from both known microorganisms and metagenomic sources in response to the growing environmental issue of polyethylene terephthalate (PET) accumulation. Despite this progress, there is a limited number of (ultra)high-throughput screening methods for assessing PET-hydrolyzing activity without relying on surrogate substrates. This method utilizes the coupled activity of ketoreductases (KREDs) and diaphorase to produce a fluorescent compound (resorufin) in the presence of PET degradation products, offering a more direct and efficient screening approach. A metagenomic KRED was coupled with the diaphorase from Clostridium kluyveri to enable the detection of the hydrolysis of PET degradation products catalyzed by the Bacillus subtilis BS2 esterase. The coupled reaction was established in water-in-oil microdroplets, encapsulating a single E. coli cell per droplet, demonstrating its potential for use in the ultrahigh-throughput screening of metagenomic libraries or randomized libraries for directed evolution campaigns.},
}

@article {pmid40288852,
year = {2025},
author = {Ashcroft, E and Poma, M and Tischler, D and Munoz-Munoz, J},
title = {Mining metagenomes from extremophiles as a resource for novel glycoside hydrolases for industrial applications.},
journal = {Methods in enzymology},
volume = {714},
number = {},
pages = {45-60},
doi = {10.1016/bs.mie.2025.02.008},
pmid = {40288852},
issn = {1557-7988},
abstract = {The exploration of metagenomes from extremophiles has emerged as a promising approach for discovering novel glycoside hydrolases (GHs) with potential industrial applications. Extremophiles, which thrive in harsh conditions such as high salinity, extreme temperatures, and acidic or alkaline environments, produce enzymes naturally adapted to function under these conditions. This unique adaptability makes them highly desirable for industrial processes requiring robust and efficient biocatalysts. These biocatalysts reduce reliance on harsh chemicals and energy-intensive processes, contributing to greener industrial operations. This review underscores the power of metagenomics in bypassing the need to culture large libraries of extremophiles in the lab. High-throughput sequencing and bioinformatics enable the identification of novel GH-encoding genes directly from environmental DNA. While metagenomic mining has yielded promising results, challenges such as the expression of extremophile-derived genes in mesophilic hosts, low activity yields, and scalability remain. Advances in synthetic biology and protein engineering could address these bottlenecks, enabling more efficient utilization of GHs. Additionally, integrating machine learning for predictive functional annotation may accelerate the identification of high-value candidates.},
}

@article {pmid40288735,
year = {2025},
author = {Wang, M and Masoudi, A and Wang, C and Feng, J and Yu, Z and Liu, J},
title = {Urban afforestation converges soil resistome and mitigates the abundance of human pathogenic bacteria.},
journal = {Environmental research},
volume = {},
number = {},
pages = {121693},
doi = {10.1016/j.envres.2025.121693},
pmid = {40288735},
issn = {1096-0953},
abstract = {Afforestation has emerged as a nature-based strategy for climate mitigation and urban sustainability, yet its effects on antibiotic resistance genes (ARGs) in soils remain underexplored. This study investigates how the conversion of croplands into plantation forests affects the soil resistome, bacterial communities, and physicochemical properties in an urban environment. Using high-throughput metagenomic and 16S rRNA amplicon sequencing, we analyzed soil samples from croplands and afforested plots with Chinese pine (Pinus tabulaeformis) and Chinese scholar (Sophora japonica) trees, across two-time points post-afforestation. Our results show that afforestation promotes the convergence of both bacterial and ARG communities over time, accompanied by a significant reduction in the relative abundance of human pathogenic bacteria. Afforested soils exhibited a lower prevalence of high-risk ARGs (e.g., qnrA, qnrB from the quinolone class) and reduced co-occurrence between ARGs and mobile genetic elements (MGEs), particularly transposases and recombinases, suggesting diminished horizontal gene transfer. Additionally, afforestation-induced changes in soil pH and nutrient dynamics emerged as key ecological factors shaping ARG profiles. Differences between afforestation types were also observed, with Pinus plantations presenting lower ARG-derived risks than Sophora forests. This study supports afforestation as a nature-based solution for enhancing urban sustainability, reducing public health risks, and achieving resilient ecosystems under anthropogenic influence.},
}

@article {pmid40288632,
year = {2025},
author = {Gao, Y and Cheng, Z and Huang, B and Mao, Y and Hu, J and Wang, S and Wang, Z and Wang, M and Huang, S and Han, M},
title = {Deciphering the profiles and hosts of antibiotic resistance genes and evaluating the risk assessment of general and non-general hospital wastewater by metagenomic sequencing.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126313},
doi = {10.1016/j.envpol.2025.126313},
pmid = {40288632},
issn = {1873-6424},
abstract = {Hospital wastewater (HWW) is a substantial environmental reservoir of antibiotic resistance genes (ARGs) and poses risks to public health and aquatic ecosystems. However, research on the diversity, transmission mechanisms, pathogenic hosts, and risks of ARGs in different HWW types is limited. This study involved the collection of HWW samples from 15 hospitals in Hefei, China, which were subsequently categorized as general hospitals (GHs) and non-general hospitals (NGHs). A 280.28-Gbp sequencing dataset was generated using a metagenomic sequencing strategy and analyzed using metagenomic assembly and binning approaches to highlight these issues in GHs and NGHs. Results showed significant differences between GHs and NGHs in ARG distribution, microbial community composition, and hosts of ARGs. Potential pathogens such as Rhodocyclaceae bacterium ICHIAU1 and Acidovorax caeni were more abundant in GHs. Furthermore, plasmid-mediated ARGs (45.21%) were more prevalent than chromosome-mediated ARGs (25.74%) in HWW, with a significantly higher proportion of plasmid-mediated ARGs in GHs compared to NGHs. The co-occurrence of ARGs and mobile genetic elements was more frequent in GHs. Additionally, the antibiotic resistome risk index was higher in GHs (38.73 ± 12.84) than NGHs (22.53 ± 11.80), indicating a greater risk of ARG transmission in GHs. This pioneering study provides valuable insights into the transmission mechanisms and hosts of ARGs in hospital settings, emphasizing the increased risk of ARG transmission in GHs.},
}

@article {pmid40288628,
year = {2025},
author = {Zhou, S and Li, Y and Yang, S and Lin, L and Deng, T and Gan, C and An, W and Xu, M},
title = {The role of electroactive biofilms in enhanced para-chlorophenol transformation collaborated with biosynthetic palladium nanoparticles.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126312},
doi = {10.1016/j.envpol.2025.126312},
pmid = {40288628},
issn = {1873-6424},
abstract = {Bioremediation is a cost-effective strategy for decomposition of chlorinated organic contaminants, but its application is often hindered by the generation of toxic chlorinated byproducts. Though the design of functional biofilms, incorporating microbially-inspired catalytic materials, has emerged as a promising solution for tackling the byproducts issues, the microbial mechanisms driving these processes remain inadequately understood. This study demonstrates a hybrid electroactive biofilm (EAB)-palladium nanoparticles (Pd NPs) system that effectively separates the dechlorination and mineralization of para-chlorophenol (4-CP), and most importantly, it provides new insights into the microbial and genetic roles of EABs in this process. Under an applied potential of -0.6 V, Pd NPs via palladate reduction were biogenically synthesized and deposited on the cytomembranes within the biofilm, achieving an 82% decrease in 4-CP concentration within 48 hours. The ultra-performance liquid chromatogram and mass spectrum confirmed that 4-CP was initially dechlorinated to phenol by the biogenic Pd NPs before undergoing further degradation by the biofilm, effectively preventing toxic chlorinated byproducts. The Dechloromonas, Pseudomonas, and Geobacter were identified as predominant genera in the system and the metagenomics analysis noted increased relative abundance of ring-cleavage genes like pcaG, dmpB/xylE, and catA. Importantly, the abundance of dmpB/xylE was primarily associated with Dechloromonas and Pseudomonas, further highlighted that the dmpB/xylE-pathway was important for rapid 4-CP decomposition in the system. This study advances the understanding of EAB-Pd NPs synergy, showcasing an innovative and sustainable approach for the efficient removal of halogenated pollutants.},
}

@article {pmid40288249,
year = {2025},
author = {Wang, K and Ding, W and Yang, X and Lü, W and Ren, H and Jiang, X},
title = {The components and aromaticity of dissolved organic matter derived from aquatic plants determine the CO2 and CH4 emission potential.},
journal = {Water research},
volume = {281},
number = {},
pages = {123685},
doi = {10.1016/j.watres.2025.123685},
pmid = {40288249},
issn = {1879-2448},
abstract = {Lakes are integral to the carbon cycle through the processing of dissolved organic matter (DOM). However, the specific contributions of various aquatic plants to carbon emissions during their decomposition remain inadequately understood. In this study, decomposition experiments were performed on three aquatic plants-algae, Phragmites australis (PA), and Potamogeton crispus L. (PC)-using advanced techniques, including FT-ICR-MS and metagenomics, to investigate the mechanisms of carbon dioxide (CO2) and methane (CH4) emissions. The results indicate that algae exhibit a substantial potential for CO2 emissions, with emissions reaching up to 2193 μmol·g[-1]. Conversely, PA contributes the highest CH4 emissions, reaching up to 2397 μmol·g[-1]. Factors such as the protein-like content and aromaticity of DOM molecules significantly influence emission levels. DOM with lower aromaticity undergoes easier decomposition in the first 6 days, leading to increased CO2 production. Elevated C/N and C/P ratios in plants enhance the abundance of methanogenic bacteria and genes. Surplus carbon will be mineralized under anaerobic conditions, giving rise to mineralization of organics to CH4. These findings elucidate the mechanisms underlying CO2 and CH4 emissions during the decomposition of different aquatic plants and provide valuable insights for lake water environment management.},
}

@article {pmid40288073,
year = {2025},
author = {Song, Y and Baniakina, LFT and Jiang, L and Chai, L},
title = {Metagenomic insights into the alterations of gut microbial community in Bufo gargarizans tadpoles following lead exposure.},
journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics},
volume = {55},
number = {},
pages = {101522},
doi = {10.1016/j.cbd.2025.101522},
pmid = {40288073},
issn = {1878-0407},
abstract = {Lead (Pb), a prevalent heavy metal contaminant in aquatic environments, has complex effects on the gut microbiome function of aquatic animals. In this study, metagenomic analysis of Bufo gargarizans tadpoles was carried out following Pb exposure. Moreover, histological analysis was performed on the intestines. The results showed that Pb exposure induced histological damage to the intestinal epithelium. Significant differences in microbial abundance and function were detected in the 200 μg/L Pb group compared to the control group. Specifically, an increase in Bosea and Klebsiella was noted at 200 μg/L Pb, which potentially could induce inflammation in tadpoles. Notably, the decrease in the abundance of glycoside hydrolases subsequent to exposure to 200 μg/L Pb is likely to attenuate carbohydrate metabolism. Furthermore, increased fluoroquinolone-related antibiotic resistance genes (ARGs), phenolic-related ARGs, and iron uptake systems following 200 μg/L Pb exposure might heighten the disease risk for tadpoles. These discoveries augment our comprehension of the influences of Pb on the intestinal well-being of amphibians and offer valuable insights for further assessment of the ecological risks that Pb poses to amphibians.},
}

@article {pmid40287860,
year = {2025},
author = {Li, Y and Liu, C and Wang, Y and Li, M and Zou, S and Hu, X and Chen, Z and Li, M and Ma, C and Obi, CJ and Zhou, X and Zou, Y and Tang, M},
title = {Urban wild bee well-being revealed by gut metagenome data: A mason bee model.},
journal = {Insect science},
volume = {},
number = {},
pages = {},
doi = {10.1111/1744-7917.70051},
pmid = {40287860},
issn = {1744-7917},
support = {//Research Development Fund, Xi'an Jiaotong-Liverpool University/ ; //Summer Undergraduate Research Fellowship (SURF) Programme, Xi'an Jiaotong-Liverpool University/ ; },
abstract = {Wild bees are ecologically vital but increasingly threatened by anthropogenic activities, leading to uncertain survival and health outcomes in urban environments. The gut microbiome contains features indicating host health and reflecting long-term evolutionary adaptation and acute reactions to real-time stressors. Moving beyond bacteria, we propose a comprehensive analysis integrating diet, bacteriome, virome, resistome, and their association to understand the survival status of urban lives better. We conducted a study on mason bees (Osmia excavata) across 10 urban agricultural sites in Suzhou, China, using shotgun gut metagenome sequencing for data derived from total gut DNA. Our findings revealed that most ingested pollen originated from Brassica crops and the unexpected garden tree Plantanus, indicating that floral resources at the 10 sites supported Osmia but with limited plant diversity. Varied city landscapes revealed site-specific flowers that all contributed to Osmia sustenance. The gut bacterial community, dominated by Gammaproteobacteria, showed remarkable structural stability across 8 sites but suggested perturbations at 2 sites. Antibiotic resistance gene profiles highly varied across 10 sites with prevalent unclassified drug classes, highlighting environmental threats to both bees and humans. The virome analysis identified honeybee pathogens, suggesting potential virus spillover. Many unknown bacteriophages were detected, some of which targeted the core gut bacteria, underscoring their role in maintaining gut homeostasis. These multifaceted metagenomic insights hold the potential to predict bee health and identify environmental threats, thereby guiding probiotic development and city management for effective bee conservation.},
}

@article {pmid40287822,
year = {2025},
author = {Sun, C and Qin, Z and Liu, R and Guo, Y and Ge, Y and Du, Y},
title = {MetaHiCNet: a web server for normalizing and visualizing microbial Hi-C interaction networks.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkaf340},
pmid = {40287822},
issn = {1362-4962},
support = {//University of Texas Systems STAR Program/ ; },
abstract = {Metagenomic Hi-C (metaHi-C) enables the reconstruction of microbial genome organization and interspecies interactions by capturing physical contacts between genomic fragments. However, raw metaHi-C data are often confounded by systematic biases and spurious contacts, which can obscure meaningful biological signals. Existing metaHi-C pipelines typically lack user-friendly normalization workflows and intuitive visualization tools, limiting the ability to explore microbial interaction networks. Here, we introduce MetaHiCNet, a web-based platform that supports widely used normalization methods with customizable parameters. MetaHiCNet provides a stepwise workflow for bias correction, spurious contact removal, and interactive visualization of microbial interactions. The platform supports multiple visualization modes, including taxonomic treemaps, cross-taxa networks, and cross-bin networks, enabling seamless transitions from community-wide overviews to detailed analyses of specific taxa or bins. This functionality facilitates the investigation of host-microbe interactions and the relationships between mobile genetic elements and their microbial hosts, offering deeper insights into microbial community structures and dynamics. MetaHiCNet is freely accessible at www.metahicnet.com without login.},
}

@article {pmid40287775,
year = {2025},
author = {Ren, H and Hong, H and Zha, B and Lamlom, SF and Qiu, H and Cao, Y and Sun, R and Wang, H and Ma, J and Zhang, H and Sun, L and Yang, Q and Zhou, C and Liu, X and Wang, X and Zhang, C and Zhang, F and Zhao, K and Yuan, R and Abdelghany, AM and Zhang, B and Zheng, Y and Wang, J and Lu, W},
title = {Soybean productivity can be enhanced by understanding rhizosphere microbiota: evidence from metagenomics analysis from diverse agroecosystems.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {105},
pmid = {40287775},
issn = {2049-2618},
mesh = {*Rhizosphere ; *Metagenomics/methods ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Glycine max/microbiology/growth & development ; *Microbiota/genetics ; China ; Fungi/classification/genetics/isolation & purification ; Plant Roots/microbiology ; Archaea/classification/genetics/isolation & purification ; High-Throughput Nucleotide Sequencing ; },
abstract = {BACKGROUND: Microbial communities associated with roots play a crucial role in the growth and health of plants and are constantly influenced by plant development and alterations in the soil environment. Despite extensive rhizosphere microbiome research, studies examining multi-kingdom microbial variation across large-scale agricultural gradients remain limited.

RESULTS: This study investigates the rhizosphere microbial communities associated with soybean across 13 diverse geographical locations in China. Using high-throughput shotgun metagenomic sequencing on the BGISEQ T7 platform with 10 GB per sample, we identified a total of 43,337 microbial species encompassing bacteria, archaea, fungi, and viruses. Our analysis revealed significant site-specific variations in microbial diversity and community composition, underscoring the influence of local environmental factors on microbial ecology. Principal coordinate analysis (PCoA) indicated distinct clustering patterns of microbial communities, reflecting the unique environmental conditions and agricultural practices of each location. Network analysis identified 556 hub microbial taxa significantly correlated with soybean yield traits, with bacteria showing the strongest associations. These key microorganisms were found to be involved in critical nutrient cycling pathways, particularly in carbon oxidation, nitrogen fixation, phosphorus solubilization, and sulfur metabolism. Our findings demonstrate the pivotal roles of specific microbial taxa in enhancing nutrient cycling, promoting plant health, and improving soybean yield, with significant positive correlations (r = 0.5, p = 0.039) between microbial diversity and seed yield.

CONCLUSION: This study provides a comprehensive understanding of the diversity and functional potential of rhizosphere microbiota in enhancing soybean productivity. The findings underscore the importance of integrating microbial community dynamics into crop management strategies to optimize nutrient cycling, plant health, and yield. While this study identifies key microbial taxa with potential functional roles, future research should focus on isolating and validating these microorganisms for their bioremediation and biofertilization activities under field conditions. This will provide actionable insights for developing microbial-based agricultural interventions to improve crop resilience and sustainability. Video Abstract.},
}

*Rhizosphere
*Metagenomics/methods
*Soil Microbiology
*Bacteria/classification/genetics/isolation & purification
*Glycine max/microbiology/growth & development
*Microbiota/genetics
China
Fungi/classification/genetics/isolation & purification
Plant Roots/microbiology
Archaea/classification/genetics/isolation & purification
High-Throughput Nucleotide Sequencing

@article {pmid40287690,
year = {2025},
author = {Mohamed, FS and Jalal, D and Fadel, YM and El-Mashtoly, SF and Khaled, WZ and Sayed, AA and Ghazy, MA},
title = {Characterization and comparative profiling of piRNAs in serum biopsies of pediatric Wilms tumor patients.},
journal = {Cancer cell international},
volume = {25},
number = {1},
pages = {163},
pmid = {40287690},
issn = {1475-2867},
abstract = {Piwi-interacting RNAs (piRNAs) are small non-coding RNAs involved in transposon silencing and linked to cancer progression. However, their role in Wilms tumors (WT) remains unexplored. We conducted a thorough analysis and characterization of piRNAs in serum liquid biopsies of WT patients. Our study examined their expression patterns and functional annotations related to WT pathogenesis, as well as their clinical potential for diagnosis and monitoring. We identified 307 piRNAs expressed in WT serum samples, with 4% classified as repeat-related and 96% as non-repeat-related. The most abundant repeat-related piRNAs originated from LINEs retrotransposon, while tRNA-derived piRNAs were the most prevalent among non-repeat-related piRNAs. Furthermore, a distinct profile of 34 piRNAs showed significant differential expression in WT patients compared to healthy controls-22 downregulated and 12 upregulated. The target genes of differentially expressed piRNAs exhibited significant enrichment in biological pathways related to cytokine activity, inflammatory responses, TGF-beta signaling, p38 MAPK, and ErbB signaling. These genes are also involved in DNA damage response, DNA methylation, cell cycle regulation, as well as kidney development and function. Low expression levels of several piRNAs, especially piR-hsa-1,913,711, piR-hsa-28,190, piR-hsa-28,849, piR-hsa-28,848, and piR-hsa-28,318, showed significant diagnostic potential as non-invasive biomarkers for WT (AUC > 0.8, p < 0.05). Their expression levels also significantly correlated with adverse pathological features, including metastasis, anaplasia, and bilateral WT development. In conclusion, non-transposon-related piRNAs may serve as reliable biomarkers for WT and possess potential non-germline functions, particularly in regulating DNA methylation, cell growth, immune responses, and immune responses. Further studies are warranted to elucidate their functional significance.},
}

@article {pmid40287117,
year = {2025},
author = {Lu, W and Liu, Z and Song, Z and Wang, C and Yu, Z and Peng, S and Tian, Z and Lyu, A and Ning, Z},
title = {Vinegar-processed frankincense ameliorates ulcerative colitis by targeting BSH-active bacteria preference-mediated GDCA hydrolysis.},
journal = {Journal of ethnopharmacology},
volume = {},
number = {},
pages = {119845},
doi = {10.1016/j.jep.2025.119845},
pmid = {40287117},
issn = {1872-7573},
abstract = {Frankincense, is extensively used in both traditional Chinese medicine (TCM) and Indian practices for the treatment of ulcerative colitis (UC). In TCM, it is typically subjected to process with vinegar, which is believed to enhance its therapeutic efficacy. However, the underlying mechanism has yet to be elucidated.

AIM OF THE STUDY: To elucidate the underlying mechanism of frankincense vinegar processing from the perspective of bile salt hydrolase (BSH)-active bacteria preference and glycodeoxycholic acid (GDCA) hydrolysis.

MATERIALS AND METHODS: Dextran sodium sulfate (DSS)-induced UC model was used to elucidate the superior improving effects of vinegar-processed frankincense (PF). 16S rRNA and metagenomic sequencing along with ultra-high performance liquid chromatography-triple quadrupole mass spectroscopy (UHPLC-TQ-MS) were employed to reveal the differential bacteria and its related disturbance of GDCA. The effects of PF and GDCA on BSH-active bacteria were confirmed using real-time quantitative polymerase chain reaction (RT-qPCR) and in vitro experiments. Finally, the pro-inflammatory effects of GDCA and the mechanisms by which PF ameliorates UC were verified by establishing a UC pseudo-sterile mice model with GDCA intervention.

RESULTS: PF exhibited remarkable mitigating effects on UC (P<0.05 or P<0.01). Specifically, PF enhanced the BSH activity of Bifidobacterium longum and Lactobacillus acidophilus (P<0.01), thereby promoting their dissociation efficiency toward glycine-conjugated bile acids (G-CBAs), particularly GDCA (P<0.01). Furthermore, PF reduced GDCA levels by regulating the dissociation efficiency of Bifidobacterium longum and Lactobacillus acidophilus toward GDCA, thereby alleviating GDCA-induced exacerbation of UC.

CONCLUSION: PF exhibits its superior amelioration effects on UC by enhancing the dissociation efficiency of Bifidobacteruum longum and Lactobacillus acidophilus towards G-CBAs, particularly GDCA.},
}

@article {pmid40286758,
year = {2025},
author = {Gan, Y and Cui, J and Nie, A and Yang, Y and Zhao, X},
title = {Revealing the influence of Lacticaseibacillus paracasei C5 on the flavor formation of bread dough by metagenomics and flavouromics.},
journal = {International journal of food microbiology},
volume = {437},
number = {},
pages = {111220},
doi = {10.1016/j.ijfoodmicro.2025.111220},
pmid = {40286758},
issn = {1879-3460},
abstract = {This study investigated the impact of L. paracasei C5 on the generation of flavor compounds in bread through metagenomics and flavouromics. Metagenomic profiling revealed that L. paracasei C5 facilitated carbohydrate, amino acid, and lipid metabolism in the dough. Correlative analyses between specific microbial species and flavor compounds demonstrated a positive association between L. paracasei and key flavor compounds in bread, such as 2-nonenal,(E)-, 2-octenal,(E)-, benzeneacetaldehyde, and hexanoic acid, ethyl ester. A predictive network outlining the metabolic pathways responsible for L. paracasei C5 sourdough bread flavor compounds was established, elucidating the microbial annotation of pertinent genes and enzymes. The findings underscored the synergistic role of L. paracasei and S. cerevisiae in enhancing the activity of encoded enzymes involved in carbohydrate degradation, acetyl-CoA synthesis, succinate conversion, acyl-CoA production, transaminases, alcohol dehydrogenase, and carboxylesterases. These results offer novel insights into the mechanisms by which L. paracasei C5 augments bread flavor.},
}

@article {pmid40286682,
year = {2025},
author = {Xin, Y and Gao, Q and Zhang, S and Zhang, Z and Wang, J and Xia, X},
title = {Microbial regulatory mechanisms underlying methane emission in rivers with different land covers.},
journal = {Water research},
volume = {281},
number = {},
pages = {123680},
doi = {10.1016/j.watres.2025.123680},
pmid = {40286682},
issn = {1879-2448},
abstract = {Inland rivers play a crucial role in regulating the methane (CH4) budget via microbial carbon cycling. CH4 emissions vary significantly among rivers with different land covers, yet the regulatory mechanisms of CH4-cycling microorganisms across different land covers remain less understood. This study intergrates in-situ CH4 measurements with amplicon and metagenomic sequencing to investigate CH4-cycling microbial community composition and metabolic functions in regulating CH4 emissions across rivers with different land covers. Our results show that agricultural and urban rivers significantly increase riverine CH4 emission fluxes by 14 and 34 times than forest rivers, respectively. Urban and agricultural river sediments exhibited higher methanogenic abundance, but lower methanotrophic abundance than forest river sediments. Acetoclastic methanogens dominate the methanogenic communities of agricultural rivers, enhanced by high NO3[-] and DOC concentrations. Furthermore, methanogenic metagenome-assembled genomes (MAGs) recovered from agricultural rivers, which affiliated to Methanosarcina, carried the complete set of genes encoding for the enzymes in acetoclastic methanogenesis. In contrast, hydrogenotrophic methanogens drive CH4 production in urban rivers, favored by low DOC: NH4[+] ratios that enable methanogenesis independent of organic carbon. Lower CH4 emissions in agricultural rivers compared to urban rivers might be partly due to the greater sulfate-dependent anaerobic methane-oxidation. In forest rivers, type I methanotrophs outcompetes methanogens, aided by suitable sediment pH and larger sediment particle sizes, fostering oxic conditions that suppress CH4 emissions. This study reveals versatile microbial mechanisms underlying riverine CH4 emissions across land covers, enhancing understanding of microbial-mediated riverine CH4 cycling.},
}

@article {pmid40286059,
year = {2025},
author = {Men, C and Pan, Z and Liu, J and Miao, S and Yuan, X and Zhang, Y and Yang, N and Cheng, S and Li, Z and Zuo, J},
title = {Single and Combined Effects of Aged Polyethylene Microplastics and Cadmium on Nitrogen Species in Stormwater Filtration Systems: Perspectives from Treatment Efficiency, Key Microbial Communities, and Nitrogen Cycling Functional Genes.},
journal = {Molecules (Basel, Switzerland)},
volume = {30},
number = {7},
pages = {},
doi = {10.3390/molecules30071464},
pmid = {40286059},
issn = {1420-3049},
support = {52400245//National Natural Science Foundation of China/ ; 2017ZX07103-007//National Key Research and Development Program of China/ ; 5221101156//National Natural Science Foundation of China/ ; },
mesh = {*Cadmium/chemistry ; *Microplastics/chemistry ; *Nitrogen Cycle/genetics/drug effects ; *Water Pollutants, Chemical ; *Nitrogen ; Filtration ; *Polyethylene/chemistry ; *Microbiota/drug effects ; Denitrification ; Water Purification/methods ; },
abstract = {Microplastics and heavy metal contamination frequently co-occur in stormwater filtration systems, where their interactions may potentially compromise nitrogen removal. Current research on microplastics and Cd contamination predominantly focuses on soils and constructed wetlands, with limited attention given to stormwater filtration systems. In this study, the single and synergistic effects of aged polyethylene microplastics (PE) and cadmium (Cd) contamination in stormwater infiltration systems were investigated from perspectives of nitrogen removal, microbial community structures, and predicted functional genes in nitrogen cycling. Results showed that PE single contamination demonstrated stronger inhibition on NO3[-]-N removal than Cd. Low-level PE contamination (PE content: 0.1% w/w) in Cd-contaminated systems showed stronger inhibitory effect than high-level PE contamination (PE content: 5% w/w). The mean NO3[-]-N removal efficiency under combined Cd50 (Cd concentration: 50 μg/L) and PE5 contamination during the sixth rainstorm event was 1.04 to 34.68 times that under other contamination scenarios. Metagenomic analysis identified keystone genera (Saccharimonadales, Enterobacter, Aeromonas, etc.), and critical nitrogen transformation pathways (nitrate reduction to ammonium, denitrification, nitrogen fixation, and nitrification) govern system performance. PE and Cd contamination effects were most pronounced on nitrification/denitrification enzymes beyond nitrite oxidase and nitrate reductase. These mechanistic findings advance our understanding of co-contaminant interactions in stormwater filtration systems.},
}

*Cadmium/chemistry
*Microplastics/chemistry
*Nitrogen Cycle/genetics/drug effects
*Water Pollutants, Chemical
*Nitrogen
Filtration
*Polyethylene/chemistry
*Microbiota/drug effects
Denitrification
Water Purification/methods

@article {pmid40285962,
year = {2025},
author = {Liao, J and Wei, JH and Liu, J and Ren, L and Zang, N and Liu, E},
title = {Respiratory virome in hospitalized children and analysis of its correlation with disease severity.},
journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {},
number = {},
pages = {},
pmid = {40285962},
issn = {1435-4373},
support = {Grant No. 82341111//The National Natural Science Foundation of China Special Project/ ; },
abstract = {PURPOSE: To investigate the composition of respiratory viromes and their association with disease severity among hospitalized pediatric patients.

METHODS: Clinical data and metagenomic next-generation sequencing (mNGS) results were collected from pediatric patients hospitalized at the Children's Hospital of Chongqing Medical University between January 2022 and September 2023. The analyzed specimens included sputum and bronchoalveolar lavage fluid (BALF).

RESULTS: The study included 229 patients (65.07% male, median age 3 years) with 25 sputum and 204 BALF samples, of whom 40.17% met the WHO criteria for severe acute respiratory infection (SARI). Herpesviruses were detected in 166 cases (72.49%), including 85 cases of cytomegalovirus (CMV), 64 cases of Epstein-Barr virus (EBV), 34 cases of human herpesvirus-7 (HHV-7), 12 cases of human herpesvirus-6 (HHV-6), and 6 cases of herpes simplex virus type 1 (HSV-1). Additionally, 53 cases of torque teno virus (TTV) and 7 cases of torque teno mini virus (TLMV) were detected. CMV prevalence was highest in neonates, while EBV peaked in the 3-6 year group (37.78%). HSV-1 and HHV-6 were predominantly identified in severe infections.

CONCLUSION: Herpesviruses, particularly CMV and EBV, were the most frequently detected viruses, followed by anelloviruses. The age-specific viral distribution patterns provide novel epidemiological perspectives for understanding pediatric respiratory pathogenesis, though their clinical significance requires validation through mechanistic studies.

CLINICAL TRIAL NUMBER: Not applicable.},
}

@article {pmid40285778,
year = {2025},
author = {Alotaib, AS and Anwar, W and Albalawi, HQ and Albalawi, HS and Alshehri, MA and Al-Atawi, FM and Al Joundi, IT and Y Al Samini, A and Alqarni, RZ and Alzahrani, NE and Huraysi, MA},
title = {Metagenomic analysis microbial biodiversity of Trojena' the Mountains of Neom.},
journal = {Cellular and molecular biology (Noisy-le-Grand, France)},
volume = {71},
number = {4},
pages = {100-110},
doi = {10.14715/cmb/2025.71.4.13},
pmid = {40285778},
issn = {1165-158X},
mesh = {*Metagenomics/methods ; *Biodiversity ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification ; Saudi Arabia ; Soil Microbiology ; *Metagenome/genetics ; Phylogeny ; High-Throughput Nucleotide Sequencing ; Microbiota/genetics ; },
abstract = {About 80% of the biosphere is constantly exposed to temperatures below 5 °C in cold environments. Microorganisms in cold environments can grow and decompose various organic compounds at sub-zero temperatures despite exposure to conditions that are harmful to their survival, such as sub-zero temperatures and low nutrient and water availability. The present study was designed to investigate metagenomic insights into the microbial diversity in (Al-Lawz Mountains / Trojena Mountains) Saudi Arabia. Metagenomic data sets are obtained by high-throughput sequencing of environmental soil samples and provide an aggregation of all the conceptually genetic materials of the intended area of this project. This study easily overcomes the bottlenecks associated with conventional molecular methods of retrieving genetic information and the unscientific shortage of microbial biodiversity research at Tabuk. High throughput bioinformatic analysis has been highlighted as the accurate exploration of the abundance and diversity of bacterial communities. Environmental DNA can be sequenced to identify the recent presence, relative abundance & distribution of a prokaryotic species or whole communities of bacteria. A total of 333 bacterial metagenomes were sequenced over two seasons, fall and winter. The 16S rRNA genes were quantified during this period. The most significant species regarding the relative abundance and diversity were in the location of sample1 by, Klebsiella michiganensis (251), stenotrophomonass maltophilia (110), Escherichia coli USML2 (88), Zhongshania aliphaticivorans (40), Acidibrevibacterium fodinaquatile (12) Calothrix spp. & Nibribacter ruber (10) Bacillus spp (10) respectively. On the other hand, the lowest abundances were in sample 4 location with Pseudomonas fluorescens (5) and Corynebacterium glutamicum (3) with (NA) species. This means these were unidentified yet. All these species have a growing demand for microbial biodiversity evaluations, given the pronounced impact of climate change in this region (Al-Lawz Mountains/Trojena Mountain). Benthic microbial communities are to be considered, given they have a potential role in CO2 and nitrogen fixation, which is related to plant growth-promoting properties. They can resist salinity, radiation, low-temperature adaptation, and biocontrol properties. Thus, eDNA cold-mountain biodiversity is a fraction of the time it costs to conduct conventional ecological monitoring.},
}

*Metagenomics/methods
*Biodiversity
RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification
Saudi Arabia
Soil Microbiology
*Metagenome/genetics
Phylogeny
High-Throughput Nucleotide Sequencing
Microbiota/genetics

@article {pmid40285533,
year = {2025},
author = {Liao, X and Wang, H and Wu, D and Grossart, HP and Yang, X and Li, L and Wang, Y and Li, S and Li, J and Cao, M and Chen, N and Hu, A},
title = {Geographical and Environmental Factors Differentially Shape Planktonic Microbial Community Assembly and Resistomes Composition in Urban Rivers.},
journal = {Global change biology},
volume = {31},
number = {4},
pages = {e70211},
doi = {10.1111/gcb.70211},
pmid = {40285533},
issn = {1365-2486},
support = {//the Ocean Negative Carbon Emissions (ONCE) Program/ ; 2021QZKK0103//the Second Tibetan Plateau Scientific Expedition and Research Program/ ; 2019QZKK0503//the Second Tibetan Plateau Scientific Expedition and Research Program/ ; 2023YFC3804904//National Key Research and Development Program/ ; },
mesh = {*Microbiota ; *Plankton ; China ; *Rivers/microbiology ; Bacteria/genetics/drug effects ; Urbanization ; },
abstract = {Global urbanization accelerates pollution challenges in urban rivers, including increased transmission of bacterial antibiotic resistance genes (ARGs), severely threatening the health of aquatic ecosystems and human health. Yet, systematic knowledge of differences in distribution and community assembly patterns of bacterial resistance across urban rivers at a continental scale is still insufficient. In this study, we conducted extensive sampling in nine representative urban rivers across China. We used amplicon and shotgun metagenomic sequencing, state-of-the-art bioinformatics, and multivariate statistics to investigate distribution patterns and community assembly mechanisms of planktonic microbiomes (i.e., bacterioplankton and planktonic microeukaryotes), including their resistomes, i.e., ARGs and metal resistance genes (MRGs). Geographical and environmental factors played a pivotal role in shaping distribution patterns of planktonic microbiomes vs. resistomes in the studied urban rivers. Phylogenetic-bin-based null model analysis (iCAMP) indicated that planktonic microbiomes, dominated by dispersal limitation and drift, tend toward spatial heterogeneity. In contrast, planktonic resistomes, driven by deterministic processes, display more similar distribution patterns. Cross-validated Mantel tests revealed that geographical factors (i.e., geographic distance) were the primary regulators of planktonic microbial community assembly, while environmental factors (i.e., temperature) control assembly processes of planktonic resistomes. Our findings provide crucial insights into the mechanisms driving the biogeographical distribution and community assembly of planktonic microbial entities in urban rivers at a continental scale, offering valuable implications for mitigating and managing the spread of ARGs from the environment to humans.},
}

*Microbiota
*Plankton
China
*Rivers/microbiology
Bacteria/genetics/drug effects
Urbanization

@article {pmid40285445,
year = {2025},
author = {Pérez Díaz, M and de Azevedo Gomes, AM and Quiroga Berdeal, MI and Bermúdez Pose, R},
title = {How to Dissect Zebrafish: A Standardized Sampling Protocol for Histological and Molecular Studies in Adult Zebrafish.},
journal = {Zebrafish},
volume = {},
number = {},
pages = {},
doi = {10.1089/zeb.2024.0184},
pmid = {40285445},
issn = {1557-8542},
abstract = {The zebrafish (Danio rerio) has become an essential model in fields such as developmental biology, toxicology, genetics, and regenerative medicine due to its low cost, small size, transparent embryos, and genetic similarity to humans. Nowadays, this model is increasingly recognized as a valuable tool in other fields, including veterinary medicine and animal production research, particularly aquaculture, due to its unique characteristics that make it suitable for studying economically significant diseases affecting production species. However, unlike established models such as mice, zebrafish lack standardized protocols for housing, feeding, anesthesia, and sample collection, which affects study reproducibility. In addition, it is a common practice to use whole zebrafish larvae or juveniles for metagenomic studies rather than analyzing individual organs, despite the fact that gene expression can vary between organs. This approach complicates the attribution of findings to specific biological processes. To address this, various authors proposed protocols for sample collection in larvae, juveniles, and adult zebrafish; however, comprehensive studies encompassing nearly all fish organs are scarce. Understanding zebrafish anatomy and the technical requirements of the study is essential for accurate sample collection. Some challenges present during zebrafish dissection include the small size of the fish, the fragility of their organs, and the faster onset of autolysis and heterolysis after the death of the animal. Using magnifying lenses, microdissection tools, and conducting dissections on cold surfaces can help mitigate these issues. This article aims to improve sample collection for histopathological and genetic studies in adult zebrafish by establishing a comprehensive, organized, and systematic dissection protocol that accounts for the anatomical specifics of this experimental model.},
}

@article {pmid40285000,
year = {2025},
author = {VanAcker, MC and Ergunay, K and Webala, PW and Kamau, M and Mutura, J and Lebunge, R and Ochola, GO and Bourke, BP and McDermott, EG and Achee, NL and Jiang, L and Grieco, JP and Keter, E and Musanga, A and Murray, S and Stabach, JA and Craft, ME and Fèvre, EM and Linton, YM and Hassell, J},
title = {A Novel Nobecovirus in an Epomophorus wahlbergi Bat from Nairobi, Kenya.},
journal = {Viruses},
volume = {17},
number = {4},
pages = {},
doi = {10.3390/v17040557},
pmid = {40285000},
issn = {1999-4915},
support = {W81XWH-21-C-0001, W81XWH-22-C-0093 and HT9425-23-C-0059//United States Army Medical Research and Development Command/ ; George E. Burch Fellowship//Smithsonian Institution/ ; G1100783/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; CGIAR Trust Fund//CGIAR/ ; },
mesh = {Kenya ; *Chiroptera/virology ; Animals ; Phylogeny ; Genome, Viral ; Feces/virology ; *Coronaviridae/genetics/classification/isolation & purification ; },
abstract = {Most human emerging infectious diseases are zoonotic, originating in animal hosts prior to spillover to humans. Prioritizing the surveillance of wildlife that overlaps with humans and human activities can increase the likelihood of detecting viruses with a high potential for human infection. Here, we obtained fecal swabs from two fruit bat species-Eidolon helvum (n = 6) and Epomophorus wahlbergi (n = 43) (family Pteropodidae)-in peridomestic habitats in Nairobi, Kenya, and used metagenome sequencing to detect microorganisms. A near-complete genome of a novel virus assigned taxonomically to the Coronaviridae family Betacoronavirus genus and Nobecovirus subclade was characterized from E. wahlbergi. Phylogenetic analysis indicates this unique Nobecovirus clade shares a common ancestor with Eidolon/Rousettus Nobecovirus subclades isolated from Madagascar, Kenya, and Cameroon. Recombination was detected across open reading frames, except the spike protein, in all BOOTSCAN analyses, indicating intra-host coinfection and genetic exchange between genome regions. Although Nobecoviruses are currently bat-specific and are not known to be zoonotic, the propensity of coronaviruses to undergo frequent recombination events and the location of the virus alongside high human and livestock densities in one of East Africa's most rapidly developing cities justifies continued surveillance of animal viruses in high-risk urban landscapes.},
}

Kenya
*Chiroptera/virology
Animals
Phylogeny
Genome, Viral
Feces/virology
*Coronaviridae/genetics/classification/isolation & purification

@article {pmid40284976,
year = {2025},
author = {Ibañez, JM and Zambrana, R and Carreras, P and Obregón, V and Irazoqui, JM and Vera, PA and Lattar, TE and Blanco Fernández, MD and Puebla, AF and Amadio, AF and Torres, C and López Lambertini, PM},
title = {Phylodynamic of Tomato Brown Rugose Fruit Virus and Tomato Chlorosis Virus, Two Emergent Viruses in Mixed Infections in Argentina.},
journal = {Viruses},
volume = {17},
number = {4},
pages = {},
doi = {10.3390/v17040533},
pmid = {40284976},
issn = {1999-4915},
support = {INTA 2023-PEM-L01-I704//National Agricultural Technology Institute/ ; },
mesh = {Argentina ; *Solanum lycopersicum/virology ; *Plant Diseases/virology ; Genome, Viral ; Phylogeny ; *Crinivirus/genetics/classification/isolation & purification ; Genetic Variation ; *Tobamovirus/genetics/classification/isolation & purification ; Metagenomics ; Coinfection/virology ; Sewage/virology ; Evolution, Molecular ; },
abstract = {Tobamovirus fructirugosum (ToBRFV) and Crinivirus tomatichlorosis (ToCV) are emerging viral threats to tomato production worldwide, with expanding global distribution. Both viruses exhibit distinct biological characteristics and transmission mechanisms that influence their spread. This study aimed to reconstruct the complete genomes of ToBRFV and ToCV from infected tomato plants and wastewater samples in Argentina to explore their global evolutionary dynamics. Additionally, it compared the genetic diversity of ToBRFV in plant tissue and sewage samples. Using metagenomic analysis, the complete genome sequences of two ToBRFV isolates and two ToCV isolates from co-infected tomatoes, along with four ToBRFV isolates from sewage, were obtained. The analysis showed that ToBRFV exhibited higher genetic diversity in environmental samples than in plant samples. Phylodynamic analysis indicated that both viruses had a recent, single introduction in Argentina but predicted different times for ancestral diversification. The evolutionary analysis estimated that ToBRFV began its global diversification in June 2013 in Israel, with rapid diversification and exponential growth until 2020, after which the effective population size declined. Moreover, ToCV's global expansion was characterized by exponential growth from 1979 to 2010, with Turkey identified as the most probable location with the current data available. This study highlights how sequencing and monitoring plant viruses can enhance our understanding of their global spread and impact on agriculture.},
}

Argentina
*Solanum lycopersicum/virology
*Plant Diseases/virology
Genome, Viral
Phylogeny
*Crinivirus/genetics/classification/isolation & purification
Genetic Variation
*Tobamovirus/genetics/classification/isolation & purification
Metagenomics
Coinfection/virology
Sewage/virology
Evolution, Molecular

@article {pmid40284912,
year = {2025},
author = {Guo, M and Li, M and Liu, T and Sun, W and Du, K and Yang, S and Fu, Z and Kou, Z},
title = {Epidemiological and Genetic Characteristics of Sapovirus in Shandong, China, 2022-2023.},
journal = {Viruses},
volume = {17},
number = {4},
pages = {},
doi = {10.3390/v17040469},
pmid = {40284912},
issn = {1999-4915},
support = {2021YFC2302003//National Key Research and Development Program of China/ ; },
mesh = {Humans ; *Sapovirus/genetics/classification/isolation & purification ; China/epidemiology ; *Caliciviridae Infections/epidemiology/virology ; Child, Preschool ; Child ; Infant ; *Gastroenteritis/epidemiology/virology ; Male ; Female ; Adolescent ; Adult ; Phylogeny ; Middle Aged ; Young Adult ; Diarrhea/virology/epidemiology ; Genotype ; Prevalence ; Aged ; Genome, Viral ; Infant, Newborn ; Incidence ; Whole Genome Sequencing ; Feces/virology ; },
abstract = {Sapovirus (SaV) is a major pathogen responsible for acute gastroenteritis (AGE), and its incidence has been increasing in recent years. This study investigates the prevalence and the genetic characteristics of SaV in Shandong Province during 2022-2023, based on a surveillance network covering all age groups. Samples were obtained from a viral diarrhea surveillance network in Shandong Province during 2022-2023. SaVs were identified through quantitative reverse-transcription polymerase chain reaction (RT-qPCR). PCR amplification and Sanger sequencing were performed on positive samples, and whole-genome sequencing was conducted using metagenomic sequencing technology. Sequence analysis was conducted using BioEdit 7.0.9.0 and MEGA X, while statistical analysis was performed with SPSS 26.0. A total of 157 SaV-positive cases were identified, resulting in a positivity rate of 1.12%. The positivity rate for SaV was 0.75% in 2022 and it increased significantly to 1.42% in 2023. The highest positivity rates for both 2022 and 2023 were observed in November. The highest positivity rate was observed in the 3-5-year-old age group. In 2022, Dongying City had the highest positivity rate, while Zaozhuang City exhibited the highest rate in 2023. The incidence of vomiting in SaV-positive patients was significantly higher compared to SaV-negative patients (P = 0.002). Eight genotypes were identified in both the VP1 and RdRp regions. The complete genome sequence analysis of a GI.3 strain showed that NS1 (5.88%, 4/68) was the region most prone to amino acid variation, followed by VP2 (5.45%, 9/165) within the same genotype. SaV infections are more prevalent in cold weather, with young children being particularly susceptible. The SaV positivity rate in 2023 increased significantly accompanied by an increased diversity of genotypes, compared to that of 2022. The NS1 region exhibits the biggest variation within the same genotype, indicating that more attention should be paid to other regions besides VP1 in the future study. Ongoing surveillance of SaV is recommended for effective prevention and control.},
}

Humans
*Sapovirus/genetics/classification/isolation & purification
China/epidemiology
*Caliciviridae Infections/epidemiology/virology
Child, Preschool
Child
Infant
*Gastroenteritis/epidemiology/virology
Male
Female
Adolescent
Adult
Phylogeny
Middle Aged
Young Adult
Diarrhea/virology/epidemiology
Genotype
Prevalence
Aged
Genome, Viral
Infant, Newborn
Incidence
Whole Genome Sequencing
Feces/virology

@article {pmid40284799,
year = {2025},
author = {Wang, Y and Cui, Q and Hou, Y and He, S and Zhao, W and Lancuo, Z and Sharshov, K and Wang, W},
title = {Metagenomic Insights into the Diverse Antibiotic Resistome of Non-Migratory Corvidae Species on the Qinghai-Tibetan Plateau.},
journal = {Veterinary sciences},
volume = {12},
number = {4},
pages = {},
doi = {10.3390/vetsci12040297},
pmid = {40284799},
issn = {2306-7381},
support = {2022-HZ-812//the program of science and technology international cooperation project of Qinghai province/ ; },
abstract = {Antibiotic resistance represents a global health crisis with far-reaching implications, impacting multiple domains concurrently, including human health, animal health, and the natural environment. Wild birds were identified as carriers and disseminators of antibiotic-resistant bacteria (ARB) and their associated antibiotic resistance genes (ARGs). A majority of studies in this area have concentrated on migratory birds as carriers for the spread of antibiotic resistance over long distances. However, there has been scant research on the resistome of non-migratory Corvidae species that heavily overlap with human activities, which limits our understanding of antibiotic resistance in these birds and hinders the development of effective management strategies. This study employed a metagenomics approach to examine the characteristics of ARGs and mobile genetic elements (MGEs) in five common Corvidae species inhabiting the Qinghai-Tibetan Plateau. The ARGs were classified into 20 major types and 567 subtypes. Notably, ARGs associated with multidrug resistance, including to macrolide-lincosamide-streptogramins, tetracyclines, beta-lactam, and bacitracin, were particularly abundant, with the subtypes acrB, bacA, macB, class C beta-lactamase, and tetA being especially prevalent. A total of 5 types of MGEs (166 subtypes) were identified across five groups of crows, and transposase genes, which indicated the presence of transposons, were identified as the most abundant type of MGEs. Moreover, some common opportunistic pathogens were identified as potential hosts for these ARGs and MGEs. Procrustes analysis and co-occurrence network analysis showed that the composition of the gut microbiota shaped the ARGs and MGEs, indicating a substantial association between these factors. The primary resistance mechanisms of ARGs in crows were identified as multidrug efflux pumps, alteration of antibiotic targets, and enzymatic inactivation. High-risk ARGs which were found to potentially pose significant risks to public health were also analyzed and resulted in the identification of 81 Rank I and 47 Rank II ARGs. Overall, our study offers a comprehensive characterization of the resistome in wild Corvidae species, enhancing our understanding of the potential public health risks associated with these birds.},
}

@article {pmid40284724,
year = {2025},
author = {Brinkerhoff, RJ and Pandian, J and Leber, M and Hauser, ID and Gaff, HD},
title = {Impacts of Tick Parasitism on the Rodent Gut Microbiome.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/microorganisms13040888},
pmid = {40284724},
issn = {2076-2607},
support = {5R01AI136035/GF/NIH HHS/United States ; },
abstract = {Host microbiota may impact disease vector behavior and pathogen transmission, but little is known about associations between ectoparasites and microbial communities in wildlife reservoir species. We used Illumina metagenomic sequencing to explore the impacts of tick parasitism on the rodent fecal microbiome in both a field and laboratory setting. We found that tick parasitism on wild hosts was associated with variation in the fecal microbiota of both the white-footed deermouse, Peromyscus leucopus, and the southern cotton rat, Sigmodon hispidus. In a lab experiment, we detected significant changes to the fecal microbiome after experimental exposure to immature ticks in treated versus control BALB/c mice. Whereas there is variation in the fecal microbiome associated with each of the host species we tested, some of the same microbial taxa, notably members of the family Muribaculaceae, occurred at higher relative abundance in tick-parasitized hosts in both the field and laboratory studies, suggesting that there are consistent impacts of tick parasitism on the host gut microbiome. We recommend future studies to test the hypothesis that epithelial cell secretions, generated as part of the host's immune response to tick parasitism, could provide resources that allow particular microbial lineages in the mammalian gut to flourish.},
}

@article {pmid40284718,
year = {2025},
author = {Wu, X and Liao, H and Zhang, X and Ma, Z and Fu, Z},
title = {Unraveling the Impact of Microplastic-Tetracycline Composite Pollution on the Moon Jellyfish Aurelia aurita: Insights from Its Microbiome.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/microorganisms13040882},
pmid = {40284718},
issn = {2076-2607},
support = {2022GXNSFBA035473//Natural Science Foundation of Guangxi Province China/ ; 2023A1515011859//Guangdong Natural Science Foundation of China/ ; 2021KJQD18//Guangxi Minzu University Research Fund/ ; },
abstract = {Microplastics have emerged as a pervasive marine contaminant, with extreme concentrations reported in deep-sea sediments (e.g., 1.9 million particles/m[2]) and localized accumulations near Antarctic research stations. Particular concern has been raised regarding their synergistic effects with co-occurring antibiotics, which may potentiate toxicity and facilitate antibiotic resistance gene dissemination through microbial colonization of plastic surfaces. To investigate these interactions, a 185-day controlled exposure experiment was conducted using Aurelia aurita polyps. Factorial combinations of microplastics (0, 0.1, 1 mg/L) and tetracycline (0, 0.5, 5 mg/L) were employed to simulate environmentally relevant pollution scenarios. Microbiome alterations were characterized using metagenomic approaches. Analysis revealed that while alpha and beta diversity measures remained unaffected at environmental concentrations, significant shifts occurred in the relative abundance of dominant bacterial taxa, including Pseudomonadota, Actinomycetota, and Mycoplasmatota. Metabolic pathway analysis demonstrated perturbations in key functional categories including cellular processes and environmental signal transduction. Furthermore, microplastic exposure was associated with modifications in polyp life-stage characteristics, suggesting potential implications for benthic-pelagic population dynamics. These findings provide evidence for the impacts of microplastic-antibiotic interactions on cnidarian holobionts, with ramifications for predicting jellyfish population responses in contaminated ecosystems.},
}

@article {pmid40284693,
year = {2025},
author = {Olivos-Caicedo, KY and Fernandez-Materan, FV and Daniel, SL and Anantharaman, K and Ridlon, JM and Alves, JMP},
title = {Pangenome Analysis of Clostridium scindens: A Collection of Diverse Bile Acid- and Steroid-Metabolizing Commensal Gut Bacterial Strains.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/microorganisms13040857},
pmid = {40284693},
issn = {2076-2607},
support = {1R03AI147127-20A1/NH/NIH HHS/United States ; },
abstract = {Clostridium scindens is a commensal gut bacterium capable of forming the secondary bile acids as well as converting glucocorticoids to androgens. Historically, only two strains, C. scindens ATCC 35704 and C. scindens VPI 12708, have been characterized to any significant extent. The formation of secondary bile acids is important in the etiology of cancers of the GI tract and in the prevention of Clostridioides difficile infection. We determined the presence and absence of bile acid inducible (bai) and steroid-17,20-desmolase (des) genes among C. scindens strains and the features of the pangenome of 34 cultured strains of C. scindens and a set of 200 metagenome-assembled genomes (MAGs) to understand the variability among strains. The results indicate that the C. scindens cultivars have an open pangenome with 12,720 orthologous gene groups and a core genome with 1630 gene families, in addition to 7051 and 4039 gene families in the accessory and unique (i.e., strain-exclusive) genomes, respectively. The pangenome profile including the MAGs also proved to be open. Our analyses reveal that C. scindens strains are distributed into two clades, indicating the possible onset of C. scindens separation into two species, as suggested by gene content, phylogenomic, and average nucleotide identity (ANI) analyses. This study provides insight into the structure and function of the C. scindens pangenome, offering a genetic foundation of significance for many aspects of research on the intestinal microbiota and bile acid metabolism.},
}

@article {pmid40284690,
year = {2025},
author = {Galanova, OO and Mitkin, NA and Danilova, AA and Pavshintsev, VV and Tsybizov, DA and Zakharenko, AM and Golokhvast, KS and Grigoryeva, TV and Markelova, MI and Vatlin, AA},
title = {Assessment of Soil Health Through Metagenomic Analysis of Bacterial Diversity in Russian Black Soil.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/microorganisms13040854},
pmid = {40284690},
issn = {2076-2607},
support = {202760-2-000//RUDN University Scientific Projects Grant System/ ; },
abstract = {Soil health is a critical determinant of agricultural productivity and environmental sustainability. Traditional assessment methods often fail to provide a comprehensive understanding of soil microbial communities and their functions. This study addresses this challenge by employing metagenomic techniques to assess the functionality of soil microbiomes in Russian black soil, renowned for its high fertility. We utilized shotgun metagenomic sequencing to analyze soil samples from Western Siberia subjected to different degrees of agro-soil disturbance. We identified functional genes involved in carbon (accA, argG, acsA, mphE, miaB), phosphorus (phoB, ppa, pstB, pnp, phnJ), and nitrogen (queC, amiF, pyrG, guaA, guaB, napA) metabolic pathways and associated with changes in microbial diversity, in general, and higher representation of certain bacterial species-Bradyrhizobium spp. The results demonstrated significant differences in microbial composition and functional potential between tillage treatments. No-Till technology and conventional tillage practices promoted beneficial microbial communities and enhanced soil health compared to long-term fallow soil. This work underscores the potential of metagenomic analysis in providing a comprehensive understanding of soil health, marking a significant advancement in the field.},
}

@article {pmid40284681,
year = {2025},
author = {Wang, X and Li, Y and Zuo, L and Li, P and Lou, H and Zhao, R},
title = {Revealing the Characteristics and Correlations Among Microbial Communities, Functional Genes, and Vital Metabolites Through Metagenomics in Henan Mung Bean Sour.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/microorganisms13040845},
pmid = {40284681},
issn = {2076-2607},
support = {231100110300//the Major Science and Technology Project of Henan, China/ ; 221100110700//Major Science and Technology Project of Henan, China/ ; },
abstract = {Henan mung bean sour (HMBS) is the raw material for mung bean sour noodles (MBSNs), a traditional fermented food. To investigate the characteristic flavor compounds, we have detected the content of free amino acids (FAAs) and key metabolites including organic acids, sugars, and alcohols. The results revealed that the content associated with umami, sweetness, and bitterness (TVA > 1) showed significant differences. Metagenomic analysis indicated that Lactobacillus delbrueckii was the dominant and characteristic species in WJ and LY15, whereas Bifidobacterium mongoliense, Lactiplantibacillus plantarum, and Acetobacter indonesiensis were the dominant species in GY. The abundance of functional genes related to carbohydrate and amino acid metabolism was higher in WJ and LY15. There was a strong correlation between dominant genera and vital metabolites (r |>| 0.7). This study provides a theoretical foundation for the development of HMBS.},
}

@article {pmid40284671,
year = {2025},
author = {de Obeso Fernández Del Valle, A and Membrillo-Hernández, J},
title = {Metagenomics Analysis of the Microbial Consortium in Samples from Lake Xochimilco, a World Cultural Heritage Site.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/microorganisms13040835},
pmid = {40284671},
issn = {2076-2607},
support = {1/CX/CSRD VA/United States ; },
abstract = {Since ancient times, the community of Xochimilco in the south of Mexico City has provided vegetables for the entire city. Today, Lake Xochimilco is listed as a UNESCO World Heritage Site because it is the last remaining bastion of Aztec culture and preserves the extraordinary ecological landscape of chinampas, a system of arable islands that has endured for over 1000 years. Here, we report on the microbiological communities currently existing in the lake. This is relevant since the water irrigates crops on the islands, known as chinampas. To achieve this, samples from the lake were collected at two different sites, and metagenomics analysis of the 16S gene was conducted. The results indicate the presence of five dominant bacterial phyla: Actinobacteria (44.5%), Proteobacteria (22.5%), Firmicutes (13%), Bacteroidota (6%), and Chloroflexi (4.6%). The most abundant families were Micrococcaceae, Intrasporangiaceae, and Rhodobacteraceae. The results correlate with current anthropogenic activity, indicating a moderate problem associated with contamination. Our findings suggest that immediate actions and increased awareness are necessary to preserve this cultural and natural heritage site and to take steps to comply with Sustainable Development Goal 11 (Sustainable Cities and Communities). Furthermore, this is the first report to characterize microbial communities in the water of Lake Xochimilco using 16S rRNA gene sequencing.},
}

@article {pmid40284644,
year = {2025},
author = {Xin, ZZ and Ma, K and Che, YZ and Dong, JL and Xu, YL and Zhang, XT and Li, XY and Zhang, JY},
title = {Differences in Microbial Community Structure Determine the Functional Specialization of Gut Segments of Ligia exotica.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/microorganisms13040808},
pmid = {40284644},
issn = {2076-2607},
support = {CARS-47//the earmarked fund for the China Agriculture Research System/ ; ZR2022QC250//the Natural Science Foundation of Shandong Province/ ; 32173019//National Natural Science Foundation of China/ ; },
abstract = {Ligia feed on seashore algae and remove organic debris from the coastal zone, thereby playing an important role in the intertidal ecosystem. Nevertheless, the specific roles of distinct gut segments in the gut transit remain unclear. We collected and identified Ligia exotica specimens in the coast of Aoshanwei, Qingdao, Shandong Province, and analyzed their foreguts and hindguts for 16S rRNA, metagenomics, metabolomics, and proteomics. The concentrations of common metabolites, NO3[-]-N and NH4[+]-N, and the contents of C and N were measured. The gut transit decreased the abundances of the dominant phyla Cyanobacteria but increased Proteobacteria, Firmicutes, and Actinobacteria, and Planctomycetes and Bacteroidetes remained relatively constant. The foregut gut microbiota is involved in the carbohydrates and amino acids metabolism, as well as the decomposition of polysaccharides. The hindgut gut microbiota performs a variety of functions, including carbohydrate and amino acid metabolism, fermentation, cell motility, intracellular transport, secretion, and vesicular translocation, and the decomposition of polysaccharides, disaccharides, and oligosaccharides. The results of omics analyses and molecular experiments demonstrated that the metabolic processes involving amino acids and carbohydrates are more active in the foregut, whereas the fermentation, absorption, and assimilation processes are more active in the hindgut. Taken together, the differences in microbial community structure determine the functional specialization of different gut segments, i.e., the foregut appears to be the primary site for digesting food, while the hindgut further processes and absorbs nutrients and then excretes them.},
}

@article {pmid40284617,
year = {2025},
author = {Mohapatra, A and Trivedi, S and Tejpal, CS and Aware, MJ and Vaswani, S and Prajapati, VJ and Kolte, AP and Malik, PK and Sahoo, A and Ravishankar, CN and Bhatta, R},
title = {Effect of Two Selected Levels of Padina gymnospora Biowaste and Enteric Methane Emission, Nutrient Digestibility, and Rumen Metagenome in Growing Sheep.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/microorganisms13040780},
pmid = {40284617},
issn = {2076-2607},
support = {Outreach Methane//Indian Council of Agricultural Research/ ; },
abstract = {A study was conducted on growing sheep to investigate the effect of two selected levels of biowaste of Padina gymnospora on feed intake, digestibility, daily enteric methane (CH4) emission, growth performance, and rumen metagenome. We randomly divided the 18 growing male sheep into three groups of six animals each. The animals were fed on a basal diet comprising finger millet straw (Eleusine coracana) and a concentrate mixture in a 35:65 ratio. The sheep in the control group (C) were offered a concentrate mixture without waste, whereas the wheat bran in the concentrate mixture in test group I (A2) and test group II (A5) was replaced (w/w) with the biowaste of Padina gymnospora at a level of 3.07 and 7.69%, respectively. The biowaste of Padina gymnospora at the above levels in concentrate constituted 2 and 5% of the diet. A significant decrease of 28.4% in daily enteric CH4 emission (g/d) was reported in the A5 group, whereas the difference in daily enteric CH4 emission between the C and A2 & A2 and A5 groups did not prove significant. The inclusion of Padina gymnospora biowaste did not affect the nutrient intake and digestibility among the groups. The inclusion of Padina gymnospora biowaste in the A5 group resulted in a significant reduction (p = 0.0012) in daily CH4 emissions compared with group C; however, no significant differences were observed in daily CH4 emissions between groups C-A2 (p = 0.0793) and A2-A5 (p = 0.3269). Likewise, the adjustment of data to CH4 emissions per 100 g of organic matter intake indicated a substantial decrease in the A5 group relative to C. The energy loss in CH4 as a percentage of GE relative to group C decreased significantly (-23.4%) in the A5 group; however, this reduction was not associated with an increase in productivity, as almost similar average daily gain (p = 0.827) was observed in the groups. The replacement of wheat bran with the biowaste of Padina gymnospora significantly decreased the numbers of total protozoa and holotrichs in the A5 group. Irrespective of the group, the Bacteroidota was the single largest phylum in the rumen metagenome, representing >60% of the microbiota. However, the abundance of Bacteroidota was similar among the groups. The methanogenic phyla Euryarchaeota was the 5th most abundant; however, it constituted only 3.14% of the metagenome. The abundance of Desulfovibrio was significantly higher in the A5 group as compared with the control. In conclusion, the significant increase in the abundance of sulfate-reducing bacteria and reduction in protozoal numbers led to a significant reduction in CH4 emissions with the incorporation of biowaste of Padina gymnospora at a 5% level of the diet.},
}

@article {pmid40284605,
year = {2025},
author = {Xiao, C and Wan, K and Chen, Y and Jin, Y and Zhou, F and Yu, J and Chi, R},
title = {Metagenomic Analysis Revealed the Changes in Antibiotic Resistance Genes and Heavy Metal Resistance Genes in Phosphate Tailings Compost.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/microorganisms13040768},
pmid = {40284605},
issn = {2076-2607},
abstract = {Phosphate tailings are usually rich in phosphorus and some other mineral nutrients, which is very suitable for composting. In this study, 60 days of composting using phosphate tailings, chicken manure, and straw resulted in a significant decrease in total nitrogen (TN) content from 1.75 ± 0.12 g/kg to 0.98 ± 0.23 g/kg (p < 0.01), with a nitrogen retention of 56%, an increase in water-soluble phosphorus (Ws-P) from 3.24 ± 0.14 mg/kg to 7.21 ± 0.09 mg/kg, and an increase in immediate potassium (AK) from 0.56 ± 0.21 mg/kg to 1.90 ± 0.11 mg/kg (p < 0.05). Metagenomic sequencing showed little changes in the diversity and abundance of microbial communities before and after composting, but changes in species composition and the abundance of archaea, bacteria, and fungi resulted in differences in community structure before and after composting. Composting contributed to a lower gene abundance of ARGs and MRGs. The addition of phosphate tailings combined the functions of chemical regulation and nutrient enrichment, and its synergistic effect significantly optimized the nutrient cycling in the composting system.},
}

@article {pmid40284601,
year = {2025},
author = {Song, Z and Zhang, T and Liang, Y and Mcminn, A and Wang, M and Jiao, N and Luo, T},
title = {Seasonal Variations of Community Structure and Functional Genes of Synechococcus in the Subtropical Coastal Waters: Insights from FACS and High-Throughput Sequencing.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/microorganisms13040764},
pmid = {40284601},
issn = {2076-2607},
abstract = {Synechococcus plays a pivotal role in the marine biogeochemical cycle. Advances in isolation techniques and high-throughput sequencing have expanded our understanding of the diversity of the Synechococcus community. However, their genomic diversity, functional dynamics and seasonal variations in the coastal waters are still not well known. Here, seawater samples were collected seasonally (March, June, August, December) from three stations in the coastal waters of Xiamen. Using fluorescence-activated cell sorting (FACS), we isolated 1000 Synechococcus cells per sample and performed ITS amplicon sequencing and metagenomic sequencing to analyze the seasonal variations in community structure and functional genes of Synechococcus. Firstly, we conducted a comparative analysis of in situ data and FACS data from three sampling sites in August. FACS samples revealed low-abundance Synechococcus strains underdetected by in situ samples. In addition, 24 clades representing Synechococcus subclusters S5.1, S5.2, and S5.3 were detected from three in situ samples and twelve FACS samples, suggesting the high diversity of Synechococcus in the coastal waters of Xiamen. Furthermore, the Synechococcus community displayed pronounced seasonal variations, and temperature significantly influenced the variations in Synechococcus community composition. Additionally, Synechococcus populations exhibit seasonal functional dynamics, with enhanced metabolic activity in summer characterized by higher numbers of functional genes associated with metabolic pathways compared to winter samples. Altogether, this study underscored the significance of FACS and high-throughput sequencing to reveal the diversity and functional dynamics of Synechococcus.},
}

@article {pmid40284573,
year = {2025},
author = {Russell, G and Alegoz, R and Hester, K and Sierzega, KL and Szul, MJ and Hubert, N and Rylander, T and Jensen, S and Ciancio, MJ and Martinez-Guryn, K and Evans, CC},
title = {The Microbiome of an Outpatient Sports Medicine Clinic During a Global Pandemic: Effects of Implementation of a Microbiome-Specific Cleaning Program.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/microorganisms13040737},
pmid = {40284573},
issn = {2076-2607},
support = {2018//Illinois Physical Therapy Association/ ; 2020//Illinois Physical Therapy Association/ ; },
abstract = {Outpatient healthcare facilities represent potential sources of healthcare-associated infections (HAIs). The purpose of this study was to survey high-contact surfaces in an outpatient physical therapy clinic, characterize the microbiome of those surfaces, and investigate the effects of a microbiome-specific cleaning and hygiene plan. Hand sanitizer containing a fluorescent probe used by patients and staff identified surface contact. High-contact surfaces were analyzed for bacterial DNA and SARS-CoV-2. A microbiome-specific cleaning and hygiene plan was developed based on initial analysis. After the implementation of the revised cleaning regimen, microbial community diversity and predicted metagenome content (PICRUSt) were employed for differential analysis. Patients had greater surface contact than staff. Ralstonia pickettii was the dominant species pre-cleaning, comprising 49.76% of the total, and observed on 79.5% of surfaces. The cleaning and hygiene plan significantly increased Shannon diversity, and R. pickettii decreased to 4.05% of total bacteria. SARS-CoV-2 was not observed on any surfaces. This study found ecological dominance by a single species in this outpatient clinic, suggesting a potential source of HAIs. However, a microbiome-specific cleaning strategy was successful in diversifying the microbiome and reducing ecological dominance. Additional research is needed to confirm these findings.},
}

@article {pmid40284568,
year = {2025},
author = {Ma, W and Han, Z and Liu, X and Cui, W and Zhen, D and Zhou, X and Song, Y and Jiang, S},
title = {Distinct Effects of Lactiplantibacillus plantarum HNU082 on Microbial Single-Nucleotide Variants in Large Intestine and Small Intestine.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/microorganisms13040731},
pmid = {40284568},
issn = {2076-2607},
abstract = {The intestinal tract extends several times the length of bodies, with varying environmental conditions across different segments (small intestinal and large intestinal), thereby harboring distinct gut microbiota. Most studies focused on the quantitative responses of gut microbiota upon probiotics entering the gut, without an in-depth analysis of how the genetic change in local gut microbiota. Therefore, in this experiment, C57BL/6J male mice were once administered Lactiplantibacillus plantarum HNU082 (Lp082). Then, the mice were euthanized on the 1st, 3rd, and 7th days after gavage, and the contents of the small and large intestines of the mice were scraped for metagenomic analysis. Based on the characterization of large intestine and small intestine bacteria, changes in the diversity and abundance of single-nucleotide variants (SNVs) of microbiota were analyzed. There were observable distinct responses at the genetic level. A significant number of SNVs were identified in Ligilactobacillus murinus in the large intestine. These SNVs may impact the utilization of carbohydrates in L. murinus. Ingested probiotics traversed the entire gut and interacted with the indigenous microbiota, driving the evolution of the indigenous gut microbiota in the different intestinal segments, thereby influencing microbial growth and metabolism. This study investigates the role of probiotics in the evolution of gut microbiota. It offers new probiotic insights and a basis for targeted interventions.},
}

@article {pmid40284547,
year = {2025},
author = {Alzahrani, AJ and Al-Hebshi, BM and Yahia, ZA and Al-Judaibi, EA and Alsaadi, KH and Al-Judaibi, AA},
title = {Impact of Microbiota Diversity on Inflammatory Bowel Disease.},
journal = {Microorganisms},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/microorganisms13040710},
pmid = {40284547},
issn = {2076-2607},
abstract = {Inflammatory bowel disease (IBD) is a chronic condition that includes two main types, Crohn's disease (CD) and ulcerative colitis (UC), involving inflammation of the gastrointestinal (GI) tract. The exact cause of IBD is unknown but could be a combination of genetic, environmental, and immune system factors. This study investigated the impact of IBD on microbiota diversity by evaluating the differences in microbial composition and the microbiota of a control group (A) of healthy individuals and a group (B) of IBD patients. Sixty biopsies were collected from participants recruited from hospitals in Makkah, Saudi Arabia. Biopsy specimens were taken during colonoscopy examination, and bacterial identification was performed by extracting ribosomal DNA from sigmoid colon biopsies using a DNeasy Blood & Tissue Kit. Metagenomics and bioinformatics analyses were then conducted to analyze and compare the microbiota in the two groups. The results showed that the varieties of core microbiome species were 3.81% greater in the IBD patients than in the members of the control group. Furthermore, the differences between the groups were significantly greater than the variations within each group. Differences between the two groups were detected in the relative abundance of Clostridium nexile, Ruminococcus gnavus, Ruminococcus faecis, and Escherichia coli. These results indicate that microbiota could play a role in the pathogenesis of IBD and suggest that microbial diversity can serve as a biomarker for diagnosing the disease and monitoring its progression.},
}

@article {pmid40284188,
year = {2025},
author = {Bonomo, MG and D'Angelo, S and Picerno, V and Carriero, A and Salzano, G},
title = {Recent Advances in Gut Microbiota in Psoriatic Arthritis.},
journal = {Nutrients},
volume = {17},
number = {8},
pages = {},
doi = {10.3390/nu17081323},
pmid = {40284188},
issn = {2072-6643},
mesh = {Humans ; *Arthritis, Psoriatic/microbiology/therapy/immunology ; *Gastrointestinal Microbiome ; Dysbiosis/microbiology ; Probiotics/therapeutic use ; Fecal Microbiota Transplantation ; },
abstract = {Psoriatic arthritis (PsA) is a chronic inflammatory disease characterized by joint inflammation and skin lesions. Recent research has underscored the critical role of gut microbiota-comprising bacteria, fungi, viruses, and archaea-in the pathogenesis and progression of PsA. This narrative review synthesizes the latest findings on the influence of gut microbiota on PsA, focusing on mechanisms such as immune modulation, microbial dysbiosis, the gut-joint axis, and its impact on treatment. Advances in high-throughput sequencing and metagenomics have revealed distinct microbial profiles associated with PsA. Studies show that individuals with PsA have a unique gut microbiota composition, differing significantly from healthy controls. Alterations in the abundance of specific bacterial taxa, including a decrease in beneficial bacteria and an increase in potentially pathogenic microbes, contribute to systemic inflammation by affecting the intestinal barrier and promoting immune responses. This review explores the impact of various factors on gut microbiota composition, including age, hygiene, comorbidities, and medication use. Additionally, it highlights the role of diet, probiotics, and fecal microbiota transplantation as promising strategies to modulate gut microbiota and alleviate PsA symptoms. The gut-skin-joint axis concept illustrates how gut microbiota influences not only gastrointestinal health but also skin and joint inflammation. Understanding the complex interplay between gut microbiota and PsA could lead to novel, microbiome-based therapeutic approaches. These insights offer hope for improved patient outcomes through targeted manipulation of the gut microbiota, enhancing both diagnosis and treatment strategies for PsA.},
}

Humans
*Arthritis, Psoriatic/microbiology/therapy/immunology
*Gastrointestinal Microbiome
Dysbiosis/microbiology
Probiotics/therapeutic use
Fecal Microbiota Transplantation

@article {pmid40284057,
year = {2025},
author = {Lan, W and Ding, H and Zhang, Z and Li, F and Feng, H and Guo, Q and Qin, F and Zhang, G and Xu, M and Xu, Y},
title = {Diversified Soil Types Differentially Regulated the Peanut (Arachis hydropoaea L.) Growth and Rhizosphere Bacterial Community Structure.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {8},
pages = {},
doi = {10.3390/plants14081169},
pmid = {40284057},
issn = {2223-7747},
support = {24-4-4-zrjj-132-jch//Natural Science Foundation of Qingdao/ ; CXGC2025D19//2025 Innovation Project of Shandong Academy of Agricultural Sciences/ ; ZR2024QC012//Natural Science Foundation of Shandong Province/ ; 110202201029(LS-13)//Major Science and Technology Project/ ; },
abstract = {Peanut (Arachis hydropoaea L.) demonstrates a prominent adaptability to diverse soil types. However, the specific effects of soil types on peanut growth and bacterial communities remain elusive. This study conducted a thorough examination of the agronomic traits, the corresponding physicochemical properties, and bacterial structure of rhizosphere soil in acidic (AT), neutral (NT), and saline-alkali (ST) soils, elucidating the internal relationship between soil type and peanut yield. Our results showed that different soil types exhibited significant differences in peanut yield, with ST demonstrating the lowest yield per plant, showing an 85.05% reduction compared to NT. Furthermore, available phosphorus content, urease, and invertase activities were substantially reduced in both ST and AT, particularly in ST by 95.35%, 38.57%, and 62.54%, respectively. Meanwhile, metagenomic sequencing unveiled a notable decline in Bradyrhizobium and Streptomyces in these soils, which is crucial for soil improvement. Further metabolic pathway analysis revealed that the reduction in pathways related to soil remediation, fertility improvement, and stress response in AT and ST may lead to slower peanut growth. In conclusion, peanuts cultivated in acidic and saline-alkali soils can increase yield via implementing soil management practices such as improving soil quality and refining micro-environments. Our study provides practical applications for enhancing peanut yield in low- to medium-yield fields.},
}

@article {pmid40283102,
year = {2025},
author = {Zhao, Y and Wang, Y and Lu, J and Zhu, B and Li, AD},
title = {Exploring the Ecological Impacts of Herbicides on Antibiotic Resistance Genes and Microbial Communities.},
journal = {Life (Basel, Switzerland)},
volume = {15},
number = {4},
pages = {},
doi = {10.3390/life15040547},
pmid = {40283102},
issn = {2075-1729},
support = {BK20230742//the Natural Science Foundation of Jiangsu Province/ ; GWJJ2024100202//2024 Annual Project of the National Health Commission (NHC) Capacity Building and Continuing Education Center/ ; M2022083//Scientific Research Project of Jiangsu Health Committee/ ; ZDXK202249//Jiangsu Provincial Medical Key Discipline/ ; 2024ZB315//Jiangsu Funding Program for Excellent Postdoctor/ ; },
abstract = {The widespread application of herbicides has profound ecological consequences, particularly regarding the distribution of antibiotic resistance genes (ARGs) and microbial communities. In this study, we analyzed herbicide-related metagenomic data to assess the impact of herbicide exposure on ARGs and microbial populations. Our results demonstrate that herbicide application significantly increased the abundance of ARGs, particularly those associated with multidrug resistance, sulfonamides, and bacitracin, with notable increases in subtypes such as bacA and sul1. Microbial community analyses revealed a dominance of Pseudomonadota and Actinomycetota, along with a significant down-regulation of genera like Fibrisoma, Gilsonvirus, Limnobacter, and Wilnyevirus in the experimental group. Additionally, herbicide exposure led to a marked reduction in biodiversity. When threshold values were relaxed, correlation analyses revealed a co-occurrence pattern between multiple genes and sul1, suggesting that horizontal gene transfer plays a pivotal role in the spread of antibiotic resistance in herbicide-contaminated soils. Moreover, environmental factors were found to significantly influence both microbial community composition and ARG distribution. These findings highlight the complex ecological effects of herbicides on microbial diversity and the dissemination of resistance genes, emphasizing the need for further research into the long-term environmental and public health implications of herbicide use.},
}

@article {pmid40282815,
year = {2025},
author = {Lee, JH and Moon, H and Park, HR and Noh, JI and Kim, SS},
title = {Metagenomic Analysis of Raw Milk and the Inactivation of Foodborne Pathogens Using Ultraviolet-C.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {8},
pages = {},
doi = {10.3390/foods14081414},
pmid = {40282815},
issn = {2304-8158},
support = {WISET-2024-056//Ministry of Science and ICT/ ; },
abstract = {The purpose of this study was to identify the microbial community of raw milk samples before and after UV-C irradiation and to establish fundamental data on UV-C treatment to improve the safety and shelf life of raw milk. Metagenomic analysis revealed that Lactococcus spp., Lactobacillus spp., and Staphylococcus spp. were the dominant genera in raw milk, while Pseudomonas spp. became more prevalent after 14 days of refrigerated storage. The microorganisms in raw milk were isolated using selective media and identified as Serratia quinivorans 4364 and Latilactobacillus curvatus DSM 20019. To compare the UV resistance of these microorganisms, Pseudomonas aeruginosa, Staphylococcus aureus, Lactococcus lactis, and Latilactobacillus curvatus were inoculated into sterilized milk and subjected to UV-C treatment. The reduction rates of P. aeruginosa were significantly lower than those of the other strains (S. aureus, L. lactis, and L. curvatus). These findings provide insights into the microbial distribution in raw milk and the degree of resistance to UV treatment, which can serve as fundamental data for the pasteurization of raw milk.},
}

@article {pmid40282811,
year = {2025},
author = {Dong, K and Song, D and Li, S and Wang, X and Dai, L and Pei, X and Yang, X and Jiang, Y},
title = {Significance of Whole-Genome Sequencing for the Traceability of Foodborne Pathogens: During the Processing of Meat and Dairy Products.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {8},
pages = {},
doi = {10.3390/foods14081410},
pmid = {40282811},
issn = {2304-8158},
support = {No. 2023-JSGG-29//National Center of Technology Innovation for Dairy/ ; },
abstract = {The complexity of tracing foodborne pathogens in the food chain has increased significantly due to the long and complicated chain, the involvement of numerous links, and the presence of various types of pathogens at different stages and environments. Traditional typing techniques are not sufficient to meet the requirements of tracing pathogens in the food chain. Whole-Genome Sequencing (WGS) has gradually become an important technological tool for characterizing and tracing pathogens in the food chain due to comprehensive information, speed, and superior discriminatory power. This paper provides an overview of the advantages of WGS and its application in foodborne pathogen traceability. This paper focused on foodborne pathogen contamination pathways during the processing of animal foods in commercial restaurant kitchens and the potential contamination of milk, milk powder, and other dairy products by pathogens during processing in the dairy industry chain and environments. Improper handling practices during meat processing (i.e., using cloths, washing hands without soap, and cleaning boards with knives) were a critical point of foodborne pathogen cross-contamination in commercial kitchen premises. However, in dairy products, contamination of pathogens in raw milk was the main cause of foodborne disease outbreaks. Therefore, preventing the contamination of pathogens in food should not only be focused on hygiene measures during processing and in environments but also on the quality and hygiene of raw materials to prevent the spread of foodborne pathogens throughout the entire production chain. Further, Whole-Metagenome Sequencing and DNA sequence markers are considered to be the future direction of WGS. The purpose of this work is to promote the wider application of WGS during the processing of meat and dairy products and provide theoretical support for the rapid investigation and accurate traceability of foodborne pathogen outbreaks in food.},
}

@article {pmid40282779,
year = {2025},
author = {Nie, X and Chen, X and Lu, X and Yang, S and Wang, X and Liu, F and Yang, J and Guo, Y and Shi, H and Xu, H and Zhang, X and Fang, M and Tao, Y and Liu, C},
title = {Metagenomics Insights into the Role of Microbial Communities in Mycotoxin Accumulation During Maize Ripening and Storage.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {8},
pages = {},
doi = {10.3390/foods14081378},
pmid = {40282779},
issn = {2304-8158},
support = {No. 32060710//the National Natural Science Foundation of China/ ; },
abstract = {Mycotoxins are among the primary factors compromising food quality and safety. To investigate mycotoxin contamination, microbial diversity, and functional profiles in maize across distinct geographic regions, this study analyzed samples from Xuanwei, Fuyuan, and Zhanyi. Mycotoxin concentrations were quantified through standardized assays, while microbial community structures were characterized using metagenomics sequencing. Metabolic pathways, functional genes, and enzymatic activities were systematically annotated with the KEGG, eggNOG, and CAZy databases. The results demonstrated an absence of detectable aflatoxin (AF) levels. Deoxynivalenol (DON) concentrations varied significantly among experimental cohorts, although all values remained within regulatory thresholds. Zearalenone (ZEN) contamination exceeded permissible limits by 40%. The metagenomic profiling identified 85 phyla, 1219 classes, 277 orders, 590 families, 1171 genera, and 2130 species of microorganisms, including six mycotoxigenic fungal species. The abundance and diversity of microorganisms were similar among different treatment groups. Among 32,333 annotated KEGG pathways, primary metabolic processes predominated (43.99%), while glycoside hydrolases (GH) and glycosyltransferases (GT) constituted 76.67% of the 40,202 carbohydrate-active enzymes. These empirical findings establish a scientific framework for optimizing agronomic practices, harvest scheduling, and post-harvest management in maize cultivation.},
}

@article {pmid40282295,
year = {2025},
author = {Laguerre, H and Noël, C and Jégou, C and Fleury, Y and Le Chevalier, P},
title = {The Cœlomic Microbiota Among Three Echinoderms: The Black Sea Cucumber Holothuria forskali, the Sea Star Marthasterias glacialis, and the Sea Urchin Sphaerechinus granularis.},
journal = {Biology},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/biology14040430},
pmid = {40282295},
issn = {2079-7737},
abstract = {In this study, the bacterial communities of the cœlomic microbiota were characterized in three Echinoderms: the deposit feeder sea Cucumber Holothuria forskali, the herbivorous sea Urchin Sphaerechinus granularis, and the carnivorous sea Star Marthasterias glacialis. Samples were collected from the same habitat in the Glénan Archipelago (Brittany, France) at different times for 2 years. The cœlomic microbiota were analyzed by targeted metagenomic with V4-16S metabarcoding and by a culturable approach with the isolation of strains and antimicrobial activity assays. Most of the OTUs of the cœlomic microbiota were affiliated with the phylum Proteobacteria and, notably, five orders: Burkholderiales, Flavobacteriales, Alteromonadales, Vibrionales and Pseudomonadales. Significant differences were observed regarding richness, biodiversity and composition between species and sampling dates. They could be explained by sub-abundant taxa that represented the global diversity. Cœlomic microbiota also revealed shared and unshared bacterial communities, validating a potential "specific" microbiota among the three Echinoderm species. Moreover, significant variations of the microbiota occurred among the sampling dates, suggesting a plasticity and, thus, a potential selection of these microbiota. Finally, out of the 831 bacterial strains isolated from culturable microbiota, 20 strains exhibited antibacterial activities, most of them assigned to the genera Shewanella, Pseudoalteromonas and Vibrio.},
}

@article {pmid40281970,
year = {2025},
author = {Khalid, N and Bukhari, SM and Ali, W and Sheikh, AA and Abdullah, HM and Nazmi, A},
title = {Probiotic Lactocaseibacillus casei NK1 Enhances Growth and Gut Microbiota in Avian Pathogenic Escherichia coli Challenged Broilers.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {8},
pages = {},
doi = {10.3390/ani15081136},
pmid = {40281970},
issn = {2076-2615},
abstract = {The present study was conducted to assess the efficacy of Laboratory-Isolated Lactocaseibacillus casei NK1 (Lc. NK1) in broilers hypothesizing that, Lc. NK1 supplementation will enhance growth performance, modulate the gut microbiome, and reduce fecal pathogenic Escherichia coli in broilers. The experiment spanned 35 days where 60 one-day-old broiler chicks were randomly assigned to four treatment groups (n = 15); control-group with no treatment (NC), APEC (challenged with E. coli only), CProb (received commercial probiotics), and LNK1 (treated with Lc. NK1). The APEC, CProb, and LNK1 groups were infected with E. coli O78 strain at 11 days of age. Growth performance analysis revealed that the LNK1 group by day 35 gained body weight similar to the CProb group, with both groups significantly outperforming the APEC group (p < 0.001). Both the LNK1 and CProp groups exhibited similar reduction in E. coli while increasing Lactobacillus colorizations in the cloacal swabs from day 21 to 35 of age (p > 0.05). Metagenomic analysis using 16S rRNA sequencing showed that the LNK1 group maintained a diverse and balanced gut microbiota, characterized by increased Firmicutes and reduced Proteobacteria. In contrast, the APEC group exhibited reduced diversity and dominance of Escherichia-Shigella (p < 0.001). These findings suggest Lc. NK1 could be a promising probiotic for enhancing gut health and growth performance in broilers, even under pathogenic challenges, offering a potential alternative to antibiotics in poultry production.},
}

@article {pmid40281939,
year = {2025},
author = {Hu, J and An, X and Yang, P and Tan, R and Chen, T and Chen, J and Tao, Y and Li, X and Sun, R and Zhang, S and Liu, S and Yang, L},
title = {Analysis of the Primary Pathogenic Bacteria in Abscess Disease of Musk Deer Using Metagenomic Approaches.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {8},
pages = {},
doi = {10.3390/ani15081105},
pmid = {40281939},
issn = {2076-2615},
support = {Grant No. 5242015//Beijing Municipal Natural Science Foundation/ ; 2024HXFWBH-LSQ-03//Zhangzhou Pien Tze Huang Pharmaceutical Co., Ltd/ ; 2024HXFWBH-LSQ-01//Huailai Zhiyangtianbao Technical development Co., Ltd/ ; },
abstract = {Abscesses are among the diseases affecting the survival of captive musk deer and are difficult to identify in their early stages. In this study, metagenomic sequencing, 16S rRNA sequencing, and paraffin sectioning were used to analyze the microbiota in the abscess musk deer pus group (AMP), abscess musk deer oral group (AMO), and healthy musk deer oral group (HMO) to compare the differences in microbiota in musk deer. By detecting differences in the oral microbiota through throat swabs, we aimed to monitor the early onset of abscess disease to facilitate timely intervention and treatment. The results showed that the alpha diversity of HMO microbiota was significantly higher than that of the AMP and AMO samples. Beta diversity results indicated that there were significant differences in the bacterial communities of HMO and AMO samples, and no significant difference was found between AMO and AMP samples. A taxonomic analysis of the bacterial species indicated that differences between HMO and AMP groups were found in the Fusobacterium and Trueperella species. Fusobacterium and Trueperella were the main pathogenic bacteria responsible for the occurrence of abscess diseases in forest musk deer in this study. Furthermore, the appearance of Fusobacterium and Trueperella in the oral cavity can serve as biomarkers for the early diagnosis of abscess disease in musk deer.},
}

@article {pmid40280794,
year = {2025},
author = {Ruppé, E and Lazarevic, V and Schrenzel, J},
title = {9th International Conference on Clinical Metagenomics (ICCMg9): meeting report.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2025.03.012},
pmid = {40280794},
issn = {1878-4380},
}

@article {pmid40280386,
year = {2025},
author = {An, X and Zhao, R and Wang, L and Xiao, X and Xu, Z and Zhang, S and Xie, D and Xiao, Y and Zhang, Q},
title = {Thiocyanate degradation by mixed bacterial consortia: Adaptive mechanism in response to thiocyanate stress and metabolic pathway.},
journal = {Environmental research},
volume = {},
number = {},
pages = {121688},
doi = {10.1016/j.envres.2025.121688},
pmid = {40280386},
issn = {1096-0953},
abstract = {Thiocyanate, frequently detected in various industrial wastewater, poses significant risks to organisms. The activated sludge isolate thiocyanate-degrading bacterial consortia (TDBC) efficiently metabolizes thiocyanate. However, the adaptive mechanism in response to thiocyanate stress and metabolic pathway by TDBC have not been elucidated. Metagenomic analysis showed that Thiobacillus (77.73 %) were the primary degraders for the efficient degradation of thiocyanate. A total of 27 genes related to thiocyanate biodegradation were identified, including SCNase, COSase, sulfur oxidation, denitrification and carbon fixation. Metaproteomic revealed the high expression of chemotaxis protein and thioredoxin enhances cellular oxidative stress and maintains normal physiological metabolism. Additionally, the differentially expressed proteins were primarily involved in metabolic pathways including sphingolipid metabolism, energy metabolism, oxidative phosphorylation, two-component system and amino acid metabolism. Then the lipid, organic acid and amino acid metabolism were up-regulated by metabolomic analysis, thereby achieving the degradation of thiocyanate. Using a combination of qRT-PCR and parallel reaction monitoring (PRM), 27 key genes involved in thiocyanate biodegradation have been identified, providing a theoretical basis for developing microbial strategies to mitigate thiocyanate pollution. Molecular docking deepens the understanding of the interaction between degrading enzyme and thiocyanate. This study provides a theoretical basis for the microbial remediation of thiocyanate-containing wastewater.},
}

@article {pmid40280272,
year = {2025},
author = {Bačnik, K and Kranjc, L and Botella, L and Maguire, I and Pavić, D and Patoka, J and Dragičević, P and Bláha, M and Bielen, A and Kouba, A and Kutnjak, D and Hudina, S},
title = {Crayfish pet trade as a pathway for the introduction of known and novel viruses.},
journal = {Journal of invertebrate pathology},
volume = {},
number = {},
pages = {108345},
doi = {10.1016/j.jip.2025.108345},
pmid = {40280272},
issn = {1096-0805},
abstract = {Expanding international pet trade has emerged as one of the main introduction pathways of aquatic invasive species, with ornamental crayfish species commonly available on the EU and global markets. Besides most frequently studied crayfish pathogens, such as Aphanomyces astaci and white spot syndrome virus (WSSV), ornamental crayfish carry associated microbial communities, which may potentially lead to the emergence of known or even novel diseases following intentional or unintentional release of animals into the wild. This is especially problematic in the case of viruses, which represent an important, yet considerably understudied, group of crayfish pathogens. Here we analyzed viromes of hepatopancreas tissue of four crayfish species acquired in the international pet trade in Europe (Procambarus clarkii, Procambarus alleni, Cherax holthuisi, and Cherax quadricarinatus) using a high throughput sequencing based metagenomic approach. Seven different known viruses were identified, which were previously either directly associated with crayfish (WSSV, Cherax quadricarinatus reovirus, chequa iflavirus, athtab bunya-like virus) or with hosts from subphylum Crustacea or invertebrates associated with freshwater environment (Shahe ispoda virus 5, Dicistroviridae sp.). Additional sequences represented 8 potential novel and divergent RNA viruses, most similar to sequences belonging to members of Picornavirales, Elliovirales, Reovirales, Hepelivirales, Tolivirales and Ghabrivirales orders. We discuss our findings in relation to their phylogenetic relationships, geographical origins, and putative pathogenicity implications. The results highlight the need for further research into the risks related to disease emergence associated with the pet trade.},
}

@article {pmid40280009,
year = {2025},
author = {Gao, FZ and Hu, LX and Liu, YS and Yang, HY and He, LY and Bai, H and Liu, F and Jin, XW and Ying, GG},
title = {Unveiling the prevalence of metal resistance genes and their associations with antibiotic resistance genes in heavy metal-contaminated rivers.},
journal = {Water research},
volume = {281},
number = {},
pages = {123699},
doi = {10.1016/j.watres.2025.123699},
pmid = {40280009},
issn = {1879-2448},
abstract = {Heavy metals can drive antibiotic resistance through co-selection mechanisms. Current knowledge predominantly focuses on relationships between metal resistance genes (MRGs) and antibiotic resistance genes (ARGs) at the river reach scale. It remains unclear the links between MRGs and ARGs at the large river basin scale, as does the role of MRG-ARG colocalization in resistance dissemination. This study employed metagenomics to investigate the prevalence of MRGs in the Xiangjiang River, a historically heavy metal-contaminated river, and their connections with ARGs by combining resistome profiling with colocalization analyses. Results revealed the significant prevalence of MRGs in the river compared to nationwide rivers, but it showed weak correlations with metal concentrations in either water or sediment. The prevalence of MRGs in water was weakly driven by abiotic parameters, but was strongly influenced by microbial composition. The proportion of water MRGs attributable to sewage sources was tightly positively correlated with MRG abundances, suggesting the significant contribution of external waste input. Plasmid-originated MRGs were more abundant in water, while chromosomal MRGs dominated in sediment, indicating medium-specific transfer dynamics. The profile of MRGs were strongly correlated with that of ARGs in both media, encompassing several clinically high-risk ARGs. However, MRG-ARG colocalization events were rarely detected (eight instances in total), consistent with low frequencies in nationwide rivers (3.5 % in sediment; 2.0 % in water), implying their limited roles in resistance dissemination. Overall, the findings enhance our understanding of riverine metal resistome and its associations with antibiotic resistome, while emphasize the rare presence of MRG-ARG colocalization in riverine environments.},
}

@article {pmid40280002,
year = {2025},
author = {Liu, X and Yang, Y and Graham, NJD and Takizawa, S and Ng, HY},
title = {Deciphering membrane biofouling induced by micro-/nano-plastics in nanofiltration: Metagenomic insights and spacer-driven mitigations.},
journal = {Water research},
volume = {281},
number = {},
pages = {123682},
doi = {10.1016/j.watres.2025.123682},
pmid = {40280002},
issn = {1879-2448},
abstract = {Nanofiltration (NF) is an effective process for micro-/nano-plastics (MNPs) interception, but the impact of accumulated MNPs on the microbial community structure and metabolic pathways of biofilms on NF membranes remains unclear. This provides uncertainty with respect to membrane biofouling behavior and the risks to efficient NF operations. In this study, the size-dependent (20 nm-25 μm) and concentration-dependent (0.1-50 mg·L[-1]) effects of MNPs on the biofouling of a NF membrane treating secondary wastewater effluent were studied. Three MNPs-tolerant, hypermetabolic and polystyrene-degradable genera (i.e., Acinetobacter, Novosphingobium and Asticcacaulis) were detected in biofilms as dominant taxonomic compositions. MNPs led to an increase of 19.3 %-76.7 % in biomass contents and a more rapid decrease in permeate flux, with 0.1 mg·L[-1] of 80 nm NPs causing the most severe membrane biofouling. Metagenomic analysis revealed that MNPs upregulated enzymes involved in exopolysaccharide (ExoA/L/M/P/Q/X/Y/Z) and tyrosine (COMT, FeaB and AOC3) biosynthesis and quorum sensing (PhzF and CiaH/R), and suppressed cell motility pathways including flagellar assembly and bacterial chemotaxis. Novel types of perforated column spacer (PCS) enhanced the hydrodynamics of the membrane feed with a lower pressure drop and higher fluid velocity, introduced micro-jets and greater mass transfer inside feed channels, thus eliminating the deposition of MNPs and mitigating membrane biofouling. Overall, a greater understanding of the interaction mechanisms between MNPs and membrane biofouling in secondary effluent filtration will help develop more effective MNPs management strategies and achieve more sustainable NF operations.},
}

@article {pmid40279015,
year = {2025},
author = {Han, X and Ma, P and Liu, C and Yao, C and Yi, Y and Du, Z and Liu, P and Zhang, M and Xu, J and Meng, X and Liu, Z and Wang, W and Ren, R and Xie, L and Han, X and Xiao, K},
title = {Pathogenic profiles and lower respiratory tract microbiota in severe pneumonia patients using metagenomic next-generation sequencing.},
journal = {Advanced biotechnology},
volume = {3},
number = {2},
pages = {13},
pmid = {40279015},
issn = {2948-2801},
support = {82100096//National Science Foundation/ ; },
abstract = {INTRODUCTION: The homeostatic balance of the lung microbiota is important for the maintenance of normal physiological function of the lung, but its role in pathological processes such as severe pneumonia is poorly understood.

METHODS: We screened 34 patients with community-acquired pneumonia (CAP) and 12 patients with hospital-acquired pneumonia (HAP), all of whom were admitted to the respiratory intensive care unit. Clinical samples, including bronchoalveolar lavage fluid (BALF), sputum, peripheral blood, and tissue specimens, were collected along with traditional microbiological test results, routine clinical test data, and clinical treatment information. The pathogenic spectrum of lower respiratory tract pathogens in critically ill respiratory patients was characterized through metagenomic next-generation sequencing (mNGS). Additionally, we analyzed the composition of the commensal microbiota and its correlation with clinical characteristics.

RESULTS: The sensitivity of the mNGS test for pathogens was 92.2% and the specificity 71.4% compared with the clinical diagnosis of the patients. Using mNGS, we detected more fungi and viruses in the lower respiratory tract of CAP-onset severe pneumonia patients, whereas bacterial species were predominant in HAP-onset patients. On the other hand, using mNGS data, commensal microorganisms such as Fusobacterium yohimbe were observed in the lower respiratory tract of patients with HAP rather than those with CAP, and most of these commensal microorganisms were associated with hospitalization or the staying time in ICU, and were significantly and positively correlated with the total length of stay.

CONCLUSION: mNGS can be used to effectively identify pathogenic pathogens or lower respiratory microbiome associated with pulmonary infectious diseases, playing a crucial role in the early and accurate diagnosis of these conditions. Based on the findings of this study, it is possible that a novel set of biomarkers and predictive models could be developed in the future to efficiently identify the cause and prognosis of patients with severe pneumonia.},
}

@article {pmid40278577,
year = {2025},
author = {Yang, Z and Zhang, Y and Ran, S and Zhang, J and Tian, F and Shi, H and Wei, S and Li, X and Li, X and Gao, Y and Jia, G and Lin, H and Chen, Z and Zhang, Z},
title = {A Multi-Omics Study of Neurodamage Induced by Growth-Stage Real-Time Air Pollution Exposure in Mice via the Microbiome-Gut-Brain Axis.},
journal = {Toxics},
volume = {13},
number = {4},
pages = {},
pmid = {40278577},
issn = {2305-6304},
support = {82203988//National Natural Science Foundation of China/ ; 2022A1515010695//Guangdong Basic and Applied Basic Research Foundation/ ; 2024A1515010465//Guangdong Basic and Applied Basic Research Foundation/ ; 2023A04J2071//Science and Technology Program of Guangzhou/ ; 23qnpy107//the Fundamental Research Funds for the Central Universities of Sun Yat-sen University/ ; },
abstract = {Air pollution has been widely recognized as a risk factor for neurological disorders, and the gut microbiome may play a mediating role. However, current evidence remains limited. In this study, a mouse model was employed with continuous exposure to real-time air pollution from conception to late adolescence. Effects of growth-stage air pollution exposure on the gut microbiome, host metabolites, and brain tissue were assessed. Pathological damage in the hippocampus and cortex was observed. Fecal metagenomic sequencing revealed alterations in both compositions and functions of the gut microbiome. Metabolic disturbances in unsaturated fatty acids and glycerophospholipids were identified in the intestine, serum, and brain tissues, with significant changes in metabolites (e.g., gamma-linolenic acid, alpha-linolenic acid, docosahexaenoic acid (DHA), phosphatidylethanolamine (PE), phosphatidylcholine (PC) and phosphatidylserine (PS). Serum levels of the pro-inflammatory mediator leukotriene C4 were also elevated. Correlation analysis identified a group of different gut microbiome species that were associated with host metabolites. Furthermore, mediation analysis showed that intestinal and serum metabolites mediated the associations between the key gut microbiome and brain microbiome. These findings indicate that the metabolic crosstalk in the gut-brain axis mediates the neuronal damage in mice induced by growth-stage air pollution exposure, potentially through pathways involving lipid metabolism and inflammation.},
}

@article {pmid40278377,
year = {2025},
author = {Xiong, S},
title = {Gut-Microbiota-Driven Lipid Metabolism: Mechanisms and Applications in Swine Production.},
journal = {Metabolites},
volume = {15},
number = {4},
pages = {},
pmid = {40278377},
issn = {2218-1989},
support = {32272831//National Natural Science Foundation of China/ ; },
abstract = {Background/Objectives: The gut microbiota plays a pivotal role in host physiology through metabolite production, with lipids serving as essential biomolecules for cellular structure, metabolism, and signaling. This review aims to elucidate the interactions between gut microbiota and lipid metabolism and their implications for enhancing swine production. Methods: We systematically analyzed current literature on microbial lipid metabolism, focusing on mechanistic studies on microbiota-lipid interactions, key regulatory pathways in microbial lipid metabolism, and multi-omics evidence (metagenomic/metabolomic) from swine models. Results: This review outlines the structural and functional roles of lipids in bacterial membranes and examines the influence of gut microbiota on the metabolism of key lipid classes, including cholesterol, bile acids, choline, sphingolipids, and fatty acids. Additionally, we explore the potential applications of microbial lipid metabolism in enhancing swine production performance. Conclusions: Our analysis establishes a scientific framework for microbiota-based strategies to optimize lipid metabolism. The findings highlight potential interventions to improve livestock productivity through targeted manipulation of gut microbial communities.},
}

@article {pmid40278299,
year = {2025},
author = {Wu, K and Xu, G and Tian, Y and Li, G and Yi, Z and Tang, X},
title = {Synthesis and Evaluation of Aquatic Antimicrobial Peptides Derived from Marine Metagenomes Using a High-Throughput Screening Approach.},
journal = {Marine drugs},
volume = {23},
number = {4},
pages = {},
pmid = {40278299},
issn = {1660-3397},
support = {2021J02015//Fujian Provincial Natural Science Foundation of China/ ; 23CZB005HJ08//Xiamen Southern Oceanographic Center/ ; K240301(1)//Xiamen Ocean Research and Development Institute/ ; },
mesh = {Animals ; High-Throughput Screening Assays/methods ; *Antimicrobial Peptides/pharmacology/chemical synthesis/chemistry ; *Metagenome ; Penaeidae ; *Anti-Bacterial Agents/pharmacology/chemistry ; Aquaculture ; Aquatic Organisms ; Microbial Sensitivity Tests ; *Antimicrobial Cationic Peptides/pharmacology ; Machine Learning ; },
abstract = {Bacterial diseases cause high mortality and considerable losses in aquaculture. The rapid expansion of intensive aquaculture has further increased the risk of large-scale outbreaks. However, the emergence of drug-resistant bacteria, food safety concerns, and environmental regulations have severely limited the availability of antimicrobial. Compared to traditional antibiotics, antimicrobial peptides (AMPs) offer broad spectrum activity, physicochemical stability, and lower resistance development. However, their low natural yield and high extraction costs along with the time-consuming and expensive nature of traditional drug discovery, pose a challenge. In this study, we applied a machine-learning macro-model to predict AMPs from three macrogenomes in the water column of South American white shrimp aquaculture ponds. The AMP content per megabase in the traditional earthen pond (TC1) was 1.8 times higher than in the biofloc pond (ZA1) and 63% higher than in the elevated pond (ZP11). A total of 1033 potential AMPs were predicted, including 6 anionic linear peptides, 616 cationic linear peptides, and 411 cationic cysteine-containing peptides. After screening based on structural, and physio-chemical properties, we selected 10 candidate peptides. Using a rapid high-throughput cell-free protein expression system, we identified nine peptides with antimicrobial activity against aquatic pathogens. Three were further validated through chemical synthesis. The three antimicrobial peptides (K-5, K-58, K-61) showed some inhibitory effects on all four pathogenic bacteria. The MIC of K-5 against Vibrio alginolyticus was 25 μM, the cell viability of the three peptides was higher than 70% at low concentrations (≤12.5 μM), and the hemolysis rate of K-5 and K-58 was lower than 5% at 200 μM. This study highlights the benefits of machine learning in AMP discovery, demonstrates the potential of cell-free protein synthesis systems for peptide screening, and provides an efficient method for high-throughput AMP identification for aquatic applications.},
}

Animals
High-Throughput Screening Assays/methods
*Antimicrobial Peptides/pharmacology/chemical synthesis/chemistry
*Metagenome
Penaeidae
*Anti-Bacterial Agents/pharmacology/chemistry
Aquaculture
Aquatic Organisms
Microbial Sensitivity Tests
*Antimicrobial Cationic Peptides/pharmacology
Machine Learning

@article {pmid40278100,
year = {2025},
author = {El Jaddaoui, I and Sehli, S and Al Idrissi, N and Bakri, Y and Belyamani, L and Ghazal, H},
title = {The Gut Mycobiome for Precision Medicine.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {11},
number = {4},
pages = {},
pmid = {40278100},
issn = {2309-608X},
abstract = {The human gastrointestinal tract harbors a vast array of microorganisms, which play essential roles in maintaining metabolic balance and immune function. While bacteria dominate the gut microbiome, fungi represent a much smaller, often overlooked fraction. Despite their relatively low abundance, fungi may significantly influence both health and disease. Advances in next-generation sequencing, metagenomics, metatranscriptomics, metaproteomics, metabolomics, and computational biology have provided novel opportunities to study the gut mycobiome, shedding light on its composition, functional genes, and metabolite interactions. Emerging evidence links fungal dysbiosis to various diseases, including inflammatory bowel disease, colorectal cancer, metabolic disorders, and neurological conditions. The gut mycobiome also presents a promising avenue for precision medicine, particularly in biomarker discovery, disease diagnostics, and targeted therapeutics. Nonetheless, significant challenges remain in effectively integrating gut mycobiome knowledge into clinical practice. This review examines gut fungal microbiota, highlighting analytical methods, associations with human diseases, and its potential role in precision medicine. It also discusses pathways for clinical translation, particularly in diagnosis and treatment, while addressing key barriers to implementation.},
}

@article {pmid40278085,
year = {2025},
author = {Guo, MC and Wu, BC and Luo, CY and Sa, W and Wang, L and Li, ZH and Shang, QH},
title = {The Effects of Fungal Pathogen Infestation on Soil Microbial Communities for Morchella sextelata Cultivation on the Qinghai-Xizang Plateau.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {11},
number = {4},
pages = {},
doi = {10.3390/jof11040264},
pmid = {40278085},
issn = {2309-608X},
support = {2023-NK-134//Key R & D and Transformation Projects of Science and Technology Department of Qinghai Province/ ; },
abstract = {Fungi infestation as a disease has serious impacts on the cultivation of Morchella species. To investigate the effects of fungi infestation on the microbial diversity and community structure of soil when cultivating Morchella sextelata, we sampled soil samples of Morchella cultivars in the Qinghai-Xizang Platea and used metagenome sequencing technology to identify the disease fungi and analyze the differences in microbial diversity and structure between disease-infested and healthy soils. The disease fungi identified were Tricharina gilva and Peziza lohjaoensis, and the microbial diversity of T. gilva-infected soil was higher than that of healthy soil, while the diversity of P. lohjaoensis-infected soil was lower. Interestingly, whether infected with T. gilva or P. lohjaoensis, the soil microbial community was changed, and the dominant phyla and genera were different in different soil samples. When infected with P. lohjaoensis, the dominant phyla with relatively high abundances included Proteobacteria, Bacteroidetes, and Ascomycota, with average relative abundances of 44%, 18%, and 15%, respectively, and the dominant genera with high relative abundances encompassed Pseudomonadaceae, Terfezia, and Pedobacter, with average relative abundances of 8%, 9%, and 5%, respectively. Following infection with T. gilva, the dominant phyla with higher relative abundances were Proteobacteria, Acidobacteria, and Bacteroidetes, with average relative abundances of 46%, 15%, and 12%, respectively, and the dominant genera with high relative abundances included Hydrogenophaga, Sphingomonas, and Polaromonas, with average relative abundances of 9%, 3%, and 2%, respectively. Additionally, we found that lipid-metabolism-related genes were less abundant in the soil infected with P. lohjaoensis than in the other soil samples, and glycoside hydrolase diversity was lower in the soil infected with T. gilva than in other healthy soils. The results showed that the effects of different disease fungi on soil microbial communities and functional genes were different, which provided a theoretical basis for the sustainable cultivation of Morchella.},
}

@article {pmid40278081,
year = {2025},
author = {Wicaksono, S and Ngokwe, ZB and McCullough, M and Yap, T},
title = {The Role of Oral Yeasts in the Development and Progression of Oral Squamous Cell Carcinoma: A Scoping Review.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {11},
number = {4},
pages = {},
doi = {10.3390/jof11040260},
pmid = {40278081},
issn = {2309-608X},
support = {202403220801271//Lembaga Pengelola Dana Pendidikan/ ; },
abstract = {The role of oral yeasts in oral squamous cell carcinoma (OSCC) has gained attention due to evidence linking fungal dysbiosis to carcinogenesis. While Candida albicans has been the primary focus, emerging studies highlight the importance of non-Candida species yeast genera. This scoping review synthesises the evidence on the role of oral yeasts, including Candida spp. and non-Candida species, in the development and progression of OSCC. A PRISMA-ScR-guided search was conducted in Medline, Embase, EBM Reviews, and CINAHL. Observational and experimental studies involving humans with OSCC, oral potentially malignant disorders (OPMDs), or oral epithelial dysplasia (OED) were included. This review analysed 75 studies. Research on oral yeast in OSCC has progressed since the 1970s, with advancements in identification techniques-from conventional culture methods to metagenomic sequencing and multi-omics approaches-alongside improved animal and cellular models of OSCC. These methodological advancements have identified notable distinctions in the oral mycobiome between carcinomatous and healthy states. Clinical findings reinforce the hypothesis that oral yeasts, particularly Candida spp., actively contribute to the dysplasia-carcinoma sequence. Emerging evidence suggests that oral yeasts may significantly modulate events contributing to OSCC progression. However, further mechanistic studies and robust clinical evidence are essential to establish causality and clarify their role in OSCC.},
}

@article {pmid40278065,
year = {2025},
author = {Li, XZ and Li, YL and Zhu, JS},
title = {Three-Dimensional Structural Heteromorphs of Mating-Type Proteins in Hirsutella sinensis and the Natural Cordyceps sinensis Insect-Fungal Complex.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {11},
number = {4},
pages = {},
doi = {10.3390/jof11040244},
pmid = {40278065},
issn = {2309-608X},
support = {2021-SF-A4//the Major Science and Technology Projects of Qinghai Province, China/ ; LHZX-2022-01//the Joint Science Project of the Chinese Academy of Sciences, Qinghai Provincial Government, and Sanjiangyuan National Park/ ; QHCY-2023-057//Qinghai Province of China/ ; 2024-NK-P67//Qinghai Province Science and Technology Commissioner Special Project/ ; },
abstract = {The MAT1-1-1 and MAT1-2-1 proteins are essential for the sexual reproduction of Ophiocordyceps sinensis. Although Hirsutella sinensis has been postulated to be the sole anamorph of O. sinensis and to undergo self-fertilization under homothallism or pseudohomothallism, little is known about the three-dimensional (3D) structures of the mating proteins in the natural Cordyceps sinensis insect-fungal complex, which is a valuable therapeutic agent in traditional Chinese medicine. However, the alternative splicing and differential occurrence and translation of the MAT1-1-1 and MAT1-2-1 genes have been revealed in H. sinensis, negating the self-fertilization hypothesis but rather suggesting the occurrence of self-sterility under heterothallic or hybrid outcrossing. In this study, the MAT1-1-1 and MAT1-2-1 proteins in 173 H. sinensis strains and wild-type C. sinensis isolates were clustered into six and five clades in the Bayesian clustering trees and belonged to 24 and 21 diverse AlphaFold-predicted 3D structural morphs, respectively. Over three-quarters of the strains/isolates contained either MAT1-1-1 or MAT1-2-1 proteins but not both. The diversity of the heteromorphic 3D structures of the mating proteins suggested functional alterations of the proteins and provided additional evidence supporting the self-sterility hypothesis under heterothallism and hybridization for H. sinensis, Genotype #1 of the 17 genome-independent O. sinensis genotypes. The heteromorphic stereostructures and mutations of the MAT1-1-1 and MAT1-2-1 proteins in the wild-type C. sinensis isolates and natural C. sinensis insect-fungi complex suggest that there are various sources of the mating proteins produced by two or more cooccurring heterospecific fungal species in natural C. sinensis that have been discovered in mycobiotic, molecular, metagenomic, and metatranscriptomic studies, which may inspire future studies on the biochemistry of mating and pheromone receptor proteins and the reproductive physiology of O. sinensis.},
}

@article {pmid40277368,
year = {2025},
author = {Martins, DT and Alegria, OVC and Dantas, CWD and De Los Santos, EFF and Pontes, PRM and Cavalcante, RBL and Ramos, RTJ},
title = {CrAssphage distribution analysis in an Amazonian river based on metagenomic sequencing data and georeferencing.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0147024},
doi = {10.1128/aem.01470-24},
pmid = {40277368},
issn = {1098-5336},
abstract = {UNLABELLED: Viruses are the most abundant biological entities in all ecosystems of the world. Their ubiquity makes them suitable candidates for indicating fecal contamination in rivers. Recently, a group of Bacteroidetes bacteriophages named CrAssphages, which are highly abundant, sensitive, and specific to human feces, were studied as potential viral biomarkers for human fecal pollution in water bodies. In this study, we evaluated the presence, diversity, and abundance of viruses with a focus on crAssphages via metagenomic analysis in an Amazonian river and conducted correlation analyses on the basis of physicochemical and georeferencing data. Several significant differences in viral alpha diversity indexes were observed among the sample points, suggesting an accumulation of viral organisms in the river mouth, whereas beta diversity analysis revealed a significant divergence between replicates of the most downstream point (IT4) when compared to the rest of the samples, possibly due to increased human impact at this point. In terms of the presence of crAssphage, the analysis identified 61 crAssphage contigs distributed along the Itacaiúnas River. Moreover, our analysis revealed significant correlations between 19 crAssphage contigs and human population density, substantiating the use of these viruses as possible markers for human fecal pollution in the Itacaiúnas River. This study is the first to assess the presence of crAssphages in an Amazonian river, with results suggesting the potential use of these viruses as markers for human fecal pollution in the Amazon.

IMPORTANCE: The Amazon biome is one of the most diverse ecosystems in the world and contains the most vast river network; however, the continuous advance of urban centers toward aquatic bodies exacerbates the discharge of pollutants into these water bodies. Fecal contamination contributes significantly to water pollution, and the application of an improved fecal indicator is essential for evaluating water quality. In this study, we evaluated the presence, diversity, and abundance of crAssphages in an Amazonian river and performed correlation analysis on the basis of physicochemical and georeferencing data to test whether crAssphages are viable fecal pollution markers. Our analysis revealed both the presence of crAssphages and their correlation with physicochemical data and showed significant correlations between the relative abundance of crAssphages and human density. These results suggest the potential use of these viruses as markers for water quality assessment in Amazonian rivers.},
}

@article {pmid40276513,
year = {2025},
author = {Xu, X and Li, Y and Huang, X},
title = {Case Report: A rare case of community-acquired Roseomonas mucosa sepsis that presented with persistently normal host-response biomarkers.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1521161},
pmid = {40276513},
issn = {1664-3224},
mesh = {Humans ; Female ; Middle Aged ; Biomarkers/blood ; *Gram-Negative Bacterial Infections/diagnosis/microbiology/drug therapy ; *Community-Acquired Infections/microbiology/diagnosis/drug therapy ; Anti-Bacterial Agents/therapeutic use ; *Methylobacteriaceae ; *Sepsis/microbiology/diagnosis/drug therapy ; Meropenem/therapeutic use ; },
abstract = {Community-acquired Roseomonas mucosa sepsis can lead to significant morbidity and mortality if not diagnosed promptly. We report a case of a 59-year-old woman with community-acquired Roseomonas mucosa sepsis who presented with persistent fever progressing to septic shock, despite repeatedly negative host-response biomarker results. Initial metagenomic analysis of peripheral blood suggested Pseudomonas aeruginosa infection. However, a peripheral blood culture identified Roseomonas mucosa as the causative pathogen. She was cured after switching to meropenem according to blood cultures and antimicrobial susceptibility testing.},
}

Humans
Female
Middle Aged
Biomarkers/blood
*Gram-Negative Bacterial Infections/diagnosis/microbiology/drug therapy
*Community-Acquired Infections/microbiology/diagnosis/drug therapy
Anti-Bacterial Agents/therapeutic use
*Methylobacteriaceae
*Sepsis/microbiology/diagnosis/drug therapy
Meropenem/therapeutic use

@article {pmid40276369,
year = {2025},
author = {Boshuizen, B and De Maré, L and Oosterlinck, M and Van Immerseel, F and Eeckhaut, V and De Meeus, C and Devisscher, L and Vidal Moreno de Vega, C and Willems, M and De Oliveira, JE and Hosotani, G and Gansemans, Y and Meese, T and Van Nieuwerburgh, F and Deforce, D and Vanderperren, K and Verdegaal, EL and Delesalle, C},
title = {Aleurone supplementation enhances the metabolic benefits of training in Standardbred mares: impacts on glucose-insulin dynamics and gut microbiome composition.},
journal = {Frontiers in physiology},
volume = {16},
number = {},
pages = {1565005},
pmid = {40276369},
issn = {1664-042X},
abstract = {INTRODUCTION: Aleurone, derived from the bran layer of grains like wheat and barley, has demonstrated positive effects on energy metabolism in pigs, mice, and untrained horses, influencing glucose-insulin dynamics and gut microbiome composition. Training itself enhances insulin sensitivity in horses, similar to the improvements in performance capacity observed in human athletes. This study aimed to investigate whether aleurone supplementation provides additional benefits to training by modulating insulin metabolism and gut microbiota in Standardbred mares.

METHODS: Sixteen Standardbred mares (aged 3-5 years) participated in a cross-over study with two 8-week training periods separated by 8 weeks of detraining. Each horse received either 200 g/day aleurone supplementation or a control diet. Insulin metabolism was evaluated using oral (OGTT) and intravenous (FSIGTT) glucose tolerance tests, measuring parameters such as Maximumglucose, AUCglucose, Maximuminsulin, AUCinsulin, Time to peakinsulin (OGTT), Acute Insulin Response to Glucose (AIRg), glucose effectiveness (Sg), and disposition index (DI) (FSIGTT). Fecal samples underwent metagenomic analysis to assess alpha and beta diversity and microbial composition.

RESULTS: Training alone: Training significantly improved OGTT parameters by decreasing Maximuminsulin (P = 0.005) and AUCinsulin (P = 0.001), while increasing Time to peakinsulin (P = 0.03), indicating enhanced insulin sensitivity. FSIGTT results also showed a decrease in logAIRg (P = 0.044). Training with Aleurone: Aleurone supplementation further reduced FSIGTT AIRg (P = 0.030), logAIRg (P = 0.021) while increasing glucose effectiveness (Sg; P = 0.031). These findings suggest aleurone improves insulin sensitivity, glucose disposal, and fasting glucose regulation beyond training. Microbiome analysis revealed training decreased Pseudomonas, associated with dysbiosis, while aleurone reduced inflammation-associated Desulfovibrio. Beta diversity metrics showed no significant changes.

CONCLUSION: Aleurone supplementation enhances training-induced improvements in glucose metabolism and fecal microbiota composition, which could offer potential benefits for equine athletes by optimizing metabolic flexibility. It also supports improvements in glucose and insulin dynamics, particularly by further enhancing insulin sensitivity and glucose-mediated disposal. Future studies should investigate the mechanisms of aleurone at the muscle and gut level and explore its potential applications for metabolic disorders such as Equine Metabolic Syndrome.},
}

@article {pmid40275546,
year = {2025},
author = {Jungpraditphol, I and Sutthiboonyapan, P and Khamwachirapitak, C and Krasaesin, A and Srithanyarat, S and Porntaveetus, T and Wiriyakijja, P},
title = {Shotgun Metagenomics of Biofilm Microbiome in Oral Lichen Planus With Desquamative Gingivitis.},
journal = {Oral diseases},
volume = {},
number = {},
pages = {},
doi = {10.1111/odi.15349},
pmid = {40275546},
issn = {1601-0825},
support = {68-032,68-059//Health Systems Research Institute/ ; HEA_FF_68_008_3200_001,HEA_FF_68_223_3200_015//Thailand Science Research and Innovation Chulalongkorn University/ ; DRF68_007//Faculty of Dentistry, Chulalongkorn University/ ; },
abstract = {INTRODUCTION: Oral lichen planus (OLP) is a chronic inflammatory condition often associated with desquamative gingivitis (DG). The oral microbiome's role in OLP and DG (OLP-DG) is gaining recognition, but prior 16S rRNA studies lacked taxonomic resolution. This study introduced shotgun metagenomic sequencing to thoroughly compare the supragingival and subgingival plaque microbiomes of individuals with and without OLP-DG.

METHODS: Twenty-seven participants (9 OLP-DG, 18 non-OLP) were recruited. Supra- and subgingival plaque samples were collected separately. Genomic DNA was analyzed using shotgun metagenomic sequencing. Microbial abundance and diversity were assessed through bioinformatic and statistical analyses.

RESULTS: We observed significant changes in the supragingival and subgingival microbiomes in OLP-DG. Supragingival plaque showed reduced Corynebacteriaceae and Porphyromonadaceae, with enrichment of an unnamed Synergistaceae genus and three unnamed species (Candidatus Saccharibacteria bacterium oral taxon 955 and 488 and GGB10852_SGB17523). Subgingival plaque revealed increased Flavobacteriaceae and Rhodocyclaceae, and reduced Actinomycetaceae. Although alpha or beta diversity was not significantly different, common commensals like Corynebacterium matruchotii and Streptococcus mitis were less abundant in OLP-DG patients.

CONCLUSION: This first-time application of metagenomic sequencing revealed a distinct microbiome in OLP-DG, characterized by novel bacterial species and reduced commensals, suggesting a potential role in OLP-DG pathogenesis, and warranting further study.},
}

@article {pmid40275408,
year = {2025},
author = {Pérez-Carrascal, OM and Pratama, AA and Sullivan, MB and Küsel, K},
title = {Unveiling plasmid diversity and functionality in pristine groundwater.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {42},
pmid = {40275408},
issn = {2524-6372},
abstract = {BACKGROUND: Plasmids are key in creating a dynamic reservoir of genetic diversity, yet their impact on Earth's continental subsurface-an important microbial reservoir-remains unresolved. We analyzed 32 metagenomic samples from six groundwater wells within a hillslope aquifer system to assess the genetic and functional diversity of plasmids and to evaluate the role of these plasmids in horizontal gene transfer (HGT).

RESULTS: Our results revealed 4,609 non-redundant mobile genetic elements (MGEs), with 14% (664) confidently classified as plasmids. These plasmids displayed well-specific populations, with fewer than 15% shared across wells. Plasmids were linked to diverse microbial phyla, including Pseudomonadota (42.17%), Nitrospirota (3.31%), Candidate Phyla Radiation (CPR) bacteria (2.56%), and Omnitrophota (2.11%). The presence of plasmids in the dominant CPR bacteria is significant, as this group remains underexplored in this context. Plasmid composition strongly correlated with well-specific microbial communities, suggesting local selection pressures. Functional analyses highlighted that conjugative plasmids carry genes crucial for metabolic processes, such as cobalamin biosynthesis and hydrocarbon degradation. Importantly, we found no evidence of high confidence emerging antibiotic resistance genes, contrasting with findings from sewage and polluted groundwater.

CONCLUSIONS: Overall, our study emphasizes the diversity, composition, and eco-evolutionary role of plasmids in the groundwater microbiome. The absence of known antibiotic resistance genes highlights the need to preserve groundwater in its pristine state to safeguard its unique genetic and functional landscape.},
}

@article {pmid40275402,
year = {2025},
author = {Maaskant, A and Lee, D and Ngo, H and Montijn, RC and Bakker, J and Langermans, JAM and Levin, E},
title = {AI for rapid identification of major butyrate-producing bacteria in rhesus macaques (Macaca mulatta).},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {39},
pmid = {40275402},
issn = {2524-4671},
abstract = {BACKGROUND: The gut microbiome plays a crucial role in health and disease, influencing digestion, metabolism, and immune function. Traditional microbiome analysis methods are often expensive, time-consuming, and require specialized expertise, limiting their practical application in clinical settings. Evolving artificial intelligence (AI) technologies present opportunities for developing alternative methods. However, the lack of transparency in these technologies limits the ability of clinicians to incorporate AI-driven diagnostic tools into their healthcare systems. The aim of this study was to investigate an AI approach that rapidly predicts different bacterial genera and bacterial groups, specifically butyrate producers, from digital images of fecal smears of rhesus macaques (Macaca mulatta). In addition, to improve transparency, we employed explainability analysis to uncover the image features influencing the model's predictions.

RESULTS: By integrating fecal image data with corresponding metagenomic sequencing information, the deep learning (DL) and machine learning (ML) algorithms successfully predicted 16 individual bacterial genera (area under the curve (AUC) > 0.7) among the 50 most abundant genera in rhesus macaques (Macaca mulatta). The model was successful in predicting functional groups, major butyrate producers (AUC 0.75) and a mixed group including fermenters and short-chain fatty acid (SCFA) producers (AUC 0.81). For both models of butyrate producers and mixed fermenters, the explainability experiments revealed no decline in the AUC when random noise was added to the images. Increased blurring led to a gradual decline in the AUC. The model's performance was robust against the impact of fecal shape from smearing, with a stable AUC maintained until patch 4 for all groups, as assessed through scrambling. No significant correlation was detected between the prediction probabilities and the total fecal weight used in the smear; r = 0.30 ± 0.3 (p > 0.1) and r = 0.04 ± 0.36 (p > 0.8) for the butyrate producers and mixed fermenters, respectively.

CONCLUSION: Our approach demonstrated the ability to predict a wide range of clinically relevant microbial genera and microbial groups in the gut microbiome based on digital images from a fecal smear. The models proved to be robust to the smearing method, random noise and the amount of fecal matter. This study introduces a rapid, non-invasive, and cost-effective method for microbiome profiling, with potential applications in veterinary diagnostics.},
}

@article {pmid40275259,
year = {2025},
author = {He, H and Cai, L and Xue, X and Zhang, K and Huang, Q and Qiu, A and Fan, H and Lin, Y and Xu, B and Pan, W},
title = {Disseminated talaromycosis in HIV-negative patients with lung cancer: a rare case report and literature review.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {601},
pmid = {40275259},
issn = {1471-2334},
support = {2024SSY06041//Jiangxi Key Laboratory of oncology/ ; JDLCZDZK-PWH//the National Natural Science Foundation of China/ ; SHDC22022302//the Clinical Research Plan of SHDC/ ; 2023YJBF-FH03, 2020YCGPZ-102//the Clinical Research Project of Second Affiliated Hospital of Naval Medical University/ ; 2023ZD005//2023 Key Project for Science and Technology Innovation of Jiangxi Provincial Health Commission/ ; 2024DZXYYXK-104//the National Key Research and Development Program of China/ ; },
mesh = {Humans ; Male ; *Lung Neoplasms/complications/microbiology ; Talaromyces/isolation & purification ; Fatal Outcome ; *Mycoses/complications/microbiology/diagnosis/drug therapy ; Middle Aged ; Antifungal Agents/therapeutic use ; *Carcinoma, Squamous Cell/complications ; Tomography, X-Ray Computed ; },
abstract = {BACKGROUND: Talaromycosis has long been considered to be exclusively associated with human immunodeficiency virus/acquired immune deficiency syndrome (HIV/AIDS). In recent years, with effective control measures for HIV, the number of talaromycosis patients without HIV infection has been increasing annually. All of these patients have various immunosuppressive factors, including tumors. However, we find that talaromycosis among HIV-negative lung cancer patients remains a rarity and is without comprehensive reviews, contributing to significant gaps in clinical knowledge.

CASE PRESENTATION: We report a case of lung squamous cell carcinoma combined with Talaromyces marneffei (T.marneffei) infection in an HIV-negative patient. The patient, a male with a history of long-term smoking, presented with recurrent fever and cough. Chest computed tomography (CT) scans revealed pleural effusion and nodules. The patient was diagnosed with lung squamous cell carcinoma and talaromycosis through sputum cytology and blood/cerebrospinal fluid metagenomics next-generation sequencing (mNGS). The patient underwent only antifungal therapy and succumbed to respiratory failure, liver and kidney failure, and sepsis in January 2024, before receiving any anti-tumor therapy.

CONCLUSION: The mortality rate of talaromycosis combined with lung cancer is extremely high. Therefore, regardless of whether patients have a history of travel to endemic areas of T. marneffei infection, it is crucial to test for HIV and anti-IFN-γ autoantibodies (AIGA) in patients suspected of having a pulmonary fungal infection, as well as conducting multiple cultures of specimens from different sites and utilizing mNGS to enhance diagnostic accuracy. Additionally, it is essential to perform biopsies in various methods from multiple sites to ascertain the presence of lung cancer. With effective control of T. marneffei infection and timely diagnosis and treatment of lung cancer, there can be a significant improvement in patient survival rates.},
}

Humans
Male
*Lung Neoplasms/complications/microbiology
Talaromyces/isolation & purification
Fatal Outcome
*Mycoses/complications/microbiology/diagnosis/drug therapy
Middle Aged
Antifungal Agents/therapeutic use
*Carcinoma, Squamous Cell/complications
Tomography, X-Ray Computed

@article {pmid40274091,
year = {2025},
author = {Huo, X and He, M and Qiao, J and Zhao, J and Yang, B},
title = {Regulatory effects of nano-carbon on poplar growth and rhizosphere soil organic carbon accumulation.},
journal = {Environmental research},
volume = {},
number = {},
pages = {121628},
doi = {10.1016/j.envres.2025.121628},
pmid = {40274091},
issn = {1096-0953},
abstract = {The positive effects of nano-carbon on plant growth and soil C sequestration within the rhizosphere have been widely recognized. Nevertheless, information is seriously deficient in understanding the underlying mechanisms based on microbial communities and carbon cycle functional genes. Here, metagenomic sequencing was employed to explore different responses of poplar seedling growth and organic carbon fractions to nano-carbon fertilizers at concentrations of 0 ml/kg (CK), 5 ml/kg (NC-5), 10 ml/kg (NC-10) and 20 ml/kg (NC-20). We observed that, after 120 days of nano-carbon fertilizers treatments, the growth indexes (height and biomass) of poplar were significantly increased by 53-173 %, and C fractions in the rhizosphere soil were significantly increased by 1.6-8.2 % with the NC-5 treatment having a greater impact on organic carbon components than the NC-10 and NC-20 treatments. Compared to CK, the additions of nano-carbon fertilizers significantly increased the content of total nitrogen (TN), nitrate nitrogen (NN), and available potassium (AK) in the rhizosphere soil and decreased the pH, and improved stochastic processes in microbial communities, which elevates the abundance of microbes involved in carbon fixation (e.g., Proteobacteria, Actinobacteria) and carbon-cycling genes. In addition, network complexity and stability of microbes were significantly enhanced by nano-carbon treatments. Structural equation model indicated that microbial community assembly processes directly alter rhizosphere SOC accumulation. Carbon functional genes influenced by microbial structure have positive effects on biomass of poplar and SOC contents. Our observations provide key evidence for evaluating how nano-carbon fertilizers may influence functional changes in C cycle that are mediated by microbial synergy.},
}

@article {pmid40273857,
year = {2025},
author = {Yu, H and Zhang, D and Xiong, R and Liu, S and Hu, R and Chen, P and Wu, X and Zou, H and Hu, N and Ding, D and Yan, Q and He, Z},
title = {Soil-dependent responses of bacterial communities, phosphorus and carbon turnover to uranium stress in different soil ecosystems.},
journal = {Journal of hazardous materials},
volume = {493},
number = {},
pages = {138383},
doi = {10.1016/j.jhazmat.2025.138383},
pmid = {40273857},
issn = {1873-3336},
abstract = {Uranium (U) can impact microbially driven soil phosphorus (P) and carbon (C) cycling. However, the response of microbial P and C turnover to U in different soils is not well understood. Through the quantitative assay of P pools and soil organic C (SOC) quantitative assay and sequencing of 16S rRNA gene amplicons and metagenomes, we investigated the effect of U on P and C biotransformation in grassland (GL), paddy soil (PY), forest soil (FT). U (60 mg kg[-1]) impacted the diversity, interaction and stability of soil bacterial communities, leading to a decrease in available P (AP). Under U stress, organophosphate mineralization substantially contributed to the AP in GL and FT, whereas intracellular P metabolism dominated the AP in PY. Also, the reductive citrate cycle (rTCA cycle) promoted the content of SOC in GL, while the rTCA cycle and complex organic C degradation pathways enhanced the SOC in PY and FT, respectively. Notably, functional bacteria carrying organic C degradation genes could decompose SOC to enhance soil AP. Bacteria developed various resistance strategies to cope with U stress. This study reveals soil-dependent response of microbial P and C cycling and its ecological functions under the influence of radioactive contaminants in different soil systems.},
}

@article {pmid40273693,
year = {2025},
author = {Yan, X and Xin, Y and Zhu, L and Tang, Q and Chen, M and Wei, Y and Zhang, J and Richnow, HH},
title = {Neglected role of virus-host interactions driving antibiotic resistance genes reduction in an urban river receiving treated wastewater.},
journal = {Water research},
volume = {282},
number = {},
pages = {123627},
doi = {10.1016/j.watres.2025.123627},
pmid = {40273693},
issn = {1879-2448},
abstract = {Treated wastewater from wastewater treatment plants (WWTPs) is a major contributor to the transfer of antibiotic resistance genes (ARGs) into urban rivers. However, the role of viral communities in this process remains poorly understood. This study focused on North Canal in Beijing, China, which receives over 80 % of its water from treated wastewater, to investigate the impact of viral communities on ARGs transfer. Results showed significant seasonal variation in the abundance and composition of ARGs, with 30 high-risk ARGs detected, accounting for 1.50 % ± 1.28 % of total ARGs. The assembly of ARGs in North Canal followed a stochastic process of homogenizing dispersal, with conjugative mobility playing a key role in horizontal gene transfer with Pseudomonas as primary host for HGT. The potential conjugative mobility of ARGs is significantly higher in wet season (69.4 % ± 17.3 %) compared to dry season (42.9 % ± 17.1 %), with conjugation frequencies ranging from 1.18 × 10[-6] to 2.26 × 10[-4]. Viral species accumulation curves approaching saturation indicated the well captured viral diversity, and no phages carrying ARGs were found among 27,523 non-redundant viral operational taxonomic units. Most of the phages (89.2 % ± 3.8 %) were lytic in North Canal, which were observed to contribute to ARGs reduction by lysing their host bacteria, reflected by higher virus-host ratio and demonstrated by the phage lysis assays in treated wastewater and receiving river. We provided compelling evidence that phage-host interactions can reduce ARGs through host lysis, highlighting their potential role in mitigating ARG transmission in urban rivers receiving treated wastewater.},
}

@article {pmid40273602,
year = {2025},
author = {Hu, C and Lu, JN and Chen, Z and Tian, L and Yin, Y and Jiang, G and Fei, YH and Tang, YT and Wang, S and Jin, C and Qiu, R and Chao, Y},
title = {Viral diversity and auxiliary metabolic genes in rare earth element mine drainage in South China.},
journal = {Water research},
volume = {281},
number = {},
pages = {123666},
doi = {10.1016/j.watres.2025.123666},
pmid = {40273602},
issn = {1879-2448},
abstract = {In extreme environments, viruses play a crucial role in regulating the structure and metabolic activities of microbial communities, thereby impacting the overall biogeochemical cycles. Previous research found that rare earth element acid mine drainage (REE-AMD) harbors a wide array of microbial species. However, our understanding of the viruses that infect these microorganisms remains limited. In this study, we utilized metagenomic analysis to explore the viral diversity, interactions between viruses and their hosts, as well as the viruses encoded auxiliary metabolic genes (AMGs) within REE-AMD. The results demonstrated that viral communities showed increased diversity with REEs pollution. Furthermore, AMGs exhibited habitat and host specificity. Viruses in water samples contaminated with REEs tended to encode AMGs related to cellular metabolic processes and stress responses to protect their hosts. In contrast, viruses in sediment samples were more likely to encode AMGs associated with nutrient competition, thereby expanding the ecological niches of hosts and viruses. Viruses would carry more AMGs from the dominant prokaryotes. Additionally, under REEs stress, viruses encode a greater number of carbon- and sulfur-related AMGs, influencing the carbon and sulfur cycles of microorganisms in REE-AMD. Overall, our study provides a first systematic characterization of the viral community in REE-AMD, which is crucial for understanding the intricate interactions among viruses, their hosts, and the surrounding environment.},
}

@article {pmid40273394,
year = {2025},
author = {Chen, CC and Chiu, JY and Tan, AH and Toh, TS and Lim, SY and Tan, EK and Pettersson, S and Hsu, CC and Liou, JM and Wu, MS and Hsu, CL and Lin, CH},
title = {Investigating Plasma Metabolomics and Gut Microbiota Changes Associated With Parkinson Disease: A Focus on Caffeine Metabolism.},
journal = {Neurology},
volume = {104},
number = {10},
pages = {e213592},
doi = {10.1212/WNL.0000000000213592},
pmid = {40273394},
issn = {1526-632X},
abstract = {BACKGROUND AND OBJECTIVES: Coffee intake is linked to a reduced risk of Parkinson disease (PD), but whether this effect is mediated by gut microbiota and metabolomic changes remains unclear. This study examines PD-associated metabolomic shifts, caffeine metabolism, and their connection to gut microbiome alterations in a multicenter study.

METHODS: We conducted an untargeted serum metabolomic assay using liquid chromatography with high-resolution mass spectrometry on an exploratory cohort recruited from National Taiwan University Hospital (NTUH). A targeted metabolomic assay focusing on caffeine and its 12 downstream metabolites was conducted and validated in an independent cohort from University Malaya Medical Centre (UMMC). In the exploratory cohort, the association of each caffeine metabolite with gut microbiota changes was investigated by metagenomic shotgun sequencing. A clustering-based approach was used to correlate microbiome changes with plasma caffeine metabolite level and clinical severity. Body mass index, antiparkinsonism medication use, and dietary habits (including coffee and tea intake) were recorded.

RESULTS: Sixty-three patients with PD and 54 controls from NTUH formed the exploratory cohort while 36 patients with PD and 20 controls from UMMC served as an validation cohort to replicate the plasma caffeine findings. A total of 5,158 metabolites were detected from untargeted metabolomic analysis, with 3,131 having high confidence for analysis. Compared with controls, the abundance of 56 metabolites was significantly higher and that of 7 metabolites was significantly lower (adjusted p < 0.05 and log2 fold change >1) in patients with PD. Caffeine metabolism was significantly lower in patients with PD (p = 0.0013), and serum levels of caffeine and its metabolites negatively correlated with motor severity (p < 0.01). Targeted metabolomic analysis confirmed reduced levels of caffeine and its metabolites, including theophylline, paraxanthine, 1,7-dimethyluric acid, and 5-acetylamino-6-amino-3-methyluracil, in patients with PD; these findings were replicated in the validation cohort (p < 0.05). A clustering approach found that 56 microbiome species enriched in patients with PD negatively correlated with caffeine and its metabolites paraxanthine and theophylline (both p < 0.05), notably Clostridium sp000435655, Acetatifactor sp900066565, Oliverpabstia intestinalis, and Ruminiclostridium siraeum.

DISCUSSION: This study identifies PD-related changes in microbial-caffeine metabolism compared with controls. Our findings offer insights for future functional research on caffeine-microbiome interactions in PD.},
}

@article {pmid40272442,
year = {2025},
author = {Diao, Z and Zhao, Z and Han, Y and Chen, Y and Huang, T and Feng, L and Ma, Y and Li, J and Zhang, R},
title = {A Comprehensive Assessment of Metagenomic cfDNA Sequencing for Microbe Detection.},
journal = {Clinical chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1093/clinchem/hvaf044},
pmid = {40272442},
issn = {1530-8561},
support = {2024-2-40510//Capital's Funds for Health Improvement and Research/ ; 2022YFC2603800//National Key R&D Program of China/ ; },
abstract = {BACKGROUND: Metagenomic cell-free DNA (cfDNA) sequencing provides a new avenue for diagnosing infectious diseases. Owing to the low concentration and highly fragmented nature of microbial cfDNA in plasma, coupled with methodological complexity, ensuring accurate and comparable metagenomic cfDNA sequencing results has proved challenging. This study aims to evaluate the performance of metagenomic cfDNA sequencing for detecting microorganisms in plasma across various laboratories and to examine factors affecting accuracy.

METHODS: A reference panel consisting of 18 microbial cfDNA communities was designed and used to investigate the performance of metagenomic cfDNA sequencing across 130 laboratories. We comprehensively assessed the accuracy, repeatability, anti-interference, limit of detection (LoD), and linear correlation.

RESULTS: The results showed that the performance of most laboratories was excellent, with an average F1 score of 0.98. Most contamination in metagenomic cfDNA sequencing originated from "wet labs," as 68.25% (475/696) of the false-positive sequences matched reported microorganisms. The chief cause (74.24%, 49/66) of false-negative errors in metagenomic cfDNA sequencing was from "dry labs." Laboratories showed favorable reproducibility, LoD, and linearity. Interference from elevated human cfDNA concentrations was minimal, whereas interference from genetically similar microorganisms was more pronounced. Overall, viral cfDNA detection showed weaker performance compared to bacterial and fungal detection.

CONCLUSIONS: This study presented the performance of metagenomic cfDNA sequencing in real-world settings, identifying key factors critical for its development and optimization. These findings provide valuable guidance for accurate pathogen detection in infectious diseases and promote the adoption of metagenomic cfDNA sequencing in diagnostics.},
}

@article {pmid40272326,
year = {2025},
author = {Adi, A and Lebrun, S and Kondo, M and Alvarez Villela, M and Fontes, JD},
title = {Culture-Negative Subacute Lactobacillus Endocarditis Diagnosed by Microbial Cell-Free DNA Sequencing.},
journal = {JACC. Case reports},
volume = {},
number = {},
pages = {103505},
doi = {10.1016/j.jaccas.2025.103505},
pmid = {40272326},
issn = {2666-0849},
abstract = {BACKGROUND: Lactobacillus endocarditis is a rare infection generally occurring in patients with heart disease and immunosuppression. Although Lactobacillus is typically a benign part of the gastrointestinal and genitourinary flora, it can cause invasive infections.

CASE SUMMARY: We present a case of a 74-year-old patient with low-grade fever and a nonproductive cough following recent cardiac surgery. Transesophageal echocardiography revealed vegetations, suggestive of endocarditis, despite negative blood cultures. Due to high suspicion for endocarditis, advanced genetic testing identified Lactobacillus fermentum as the causative pathogen. The patient disclosed daily probiotic use, likely the infection source. Treatment with intravenous ampicillin resulted in significant symptom improvement.

DISCUSSION: This case underscores the importance of considering probiotics as a potential source of bacteremia in patients with negative cultures after surgery and highlights how metagenomic sequencing can identify pathogens and guide effective therapy in challenging cases.},
}

@article {pmid40272234,
year = {2025},
author = {Wang, X and Zhang, J and Yang, B and Mao, H and Yu, Q and Zhang, Y},
title = {Intermittent Microaeration Enhanced Anaerobic Digestion: The Key Role of Fe(III)/Fe(II) Cycle and Reactive Oxygen Species.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c04187},
pmid = {40272234},
issn = {1520-5851},
abstract = {Microaeration has been reported to improve anaerobic digestion, which is generally attributed to increased microbial diversity, but a thorough explanation is lacking. In this study, it was found that intermittent microaeration (IMA) supplied to an anaerobic digester could oxidize Fe(II) produced by dissimilatory iron reduction (DIR) to form a Fe(III)/Fe(II) cycle and generate extracellular reactive oxygen species (ROS) to improve anaerobic treatment of phenol-containing wastewater. The results showed that compared to the control group without IMA, the removal rates of COD and phenol increased by 29.54 and 49.68 percentage points, respectively, and daily average methane production increased by 85.44%. The Fe(III)/Fe(II) cycle slowed down the loss of iron (13.97%) released from sludge due to the lower solubility of Fe(III) and facilitated [•]OH generation (1.22 ± 0.04 μM) via Fenton-like reactions. The DIR and the generation of [•]OH accelerated phenol degradation. Metagenomic analysis revealed that the abundance of methanogens and antioxidant enzymes-encoding genes in response to oxidative stress significantly increased in the IMA group compared to the control, enabling methanogenesis to proceed smoothly under microaeration. This study investigated the extracellular ROS generation induced by microaeration during anaerobic digestion and their roles in promoting anaerobic performance, thereby providing a new perspective for optimizing anaerobic systems with microaeration.},
}

@article {pmid40272147,
year = {2025},
author = {Dai, X and Cao, Y and Li, L and Gao, Y-X and Wang, J-X and Liu, Y-J and Ma, T-T and Zheng, J-M and Zhan, P-P and Shen, Z-Y},
title = {Gut microbiome and metabolome profiles in renal allograft rejection from multiomics integration.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0162624},
doi = {10.1128/msystems.01626-24},
pmid = {40272147},
issn = {2379-5077},
abstract = {UNLABELLED: The gut microbiome and metabolome play crucial roles in renal allograft rejection progression. Integrated multiomics analyses may provide a comprehensive understanding of specific underlying mechanisms, which remain elusive. This study aimed to identify new approaches for clinical renal allograft rejection diagnosis and treatment. Thirty-five patients were divided into three groups: the rejection (n = 16), dysfunction (n = 7), and control (n = 12) groups. Metagenomic sequencing and nontargeted metabolomics were used to analyze stool and plasma samples. Significant microbiota, metabolites, and signaling pathways were identified. LASSO regression was used to construct a diagnostic model, and its diagnostic value was assessed via receiver operating characteristic curves. The microbiota composition and the related genes in the rejection group significantly differed from that in the dysfunction and control groups at the phylum, genus, and species levels (P < 0.001). The core species in the rejection group networks were Escherichia coli and Ruminococcus gnavus, while core species in the dysfunction group networks were Faecalibacterium prausnitzii and Bacteroides ovatus. The balance of specific microbial species was associated with kidney function in rejection patients. Spearman analysis revealed that specific differential species like Agathobaculum butyriciproducens and Gemmiger qucibialis were closely linked to the levels of serum 4-pyridoxic acid, 4-acetamidobutanoate, and fecal tryptamine from specific differential pathways. Finally, we constructed four clinical models to distinguish the rejection and dysfunction groups, and the model had excellent diagnostic performance. Altered gut microbiota may contribute to changes in metabolic pathway activity and metabolite abundance in rejection and dysfunction patients, which are strongly correlated with host immunological rejection. The diagnostic model, developed based on the gut microbiota and metabolites, has high clinical value for diagnosing renal rejection.

IMPORTANCE: This study aimed to screen new markers for non-invasive diagnosis by the gut microbiome and metabolome analysis, providing new insights into rejection mechanisms and identifying new approaches for clinical renal allograft rejection diagnosis.},
}

@article {pmid40271228,
year = {2025},
author = {Liu, J and Wu, X},
title = {Rare Bloodstream Infection of Rhodococcus rhodochrous as the Prodromal Signal for Malignancy.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {1951-1959},
doi = {10.2147/IDR.S512213},
pmid = {40271228},
issn = {1178-6973},
abstract = {Rhodococcus-associated infections are extremely rare, and previous publications have indicated that such infections are primarily observed among individuals with HIV. Limited information is available regarding therapy, and no clear consensus has been reached to guide treatment. Here, we report the first case of bloodstream infection with Rhodococcus rhodochrous in a non-HIV patient with a viral intracranial infection. During follow-up, lymph node biopsy and bone marrow aspiration were performed because superficial lymphadenectasis had failed to regress as expected within 3 months. The patient was newly diagnosed with nodal T-follicular helper cell lymphoma, angioimmunoblastic-type. For cases of rare infection or co-infection, screening for pathogenic microorganisms is the priority, and several methods should be employed, such as microorganism culture, antigen and antibody detection, and metagenomic next-generation sequencing. In retrospect to integrated case management, our case indicated that early malignancy screening is significant for early diagnosis and treatment of occult cancer during patients with rare opportunistic infections.},
}

@article {pmid40270817,
year = {2025},
author = {Onohuean, H and Olot, H and Onohuean, FE and Bukke, SPN and Akinsuyi, OS and Kade, A},
title = {A scoping review of the prevalence of antimicrobial-resistant pathogens and signatures in ready-to-eat street foods in Africa: implications for public health.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1525564},
doi = {10.3389/fmicb.2025.1525564},
pmid = {40270817},
issn = {1664-302X},
abstract = {BACKGROUND AND OBJECTIVE: Despite its critical role in individual and societal health, food hygiene remains underexplored. Antibiotic-resistant pathogenic bacteria in ready-to-eat (RTE) food threaten public health. This scoping review collected data on the epidemiological prevalence of RTE food-contaminated pathogens resistant to antimicrobial drugs and resistance genes in Africa.

METHOD: Using electronic databases, such as PubMed, Scopus, and Web of Science (WoS), handpicked from references, pre-reviewed published articles were retrieved and analyzed according to the PRISMA-ScR guidelines.

RESULTS: The findings indicate 40 previewed published articles qualified for meta-synthesis in the scoping review with a population/case ratio of 11,653/5,338 (45.80%). The most frequently reported RTE foods were meat or beef/beef-soup, chicken or poultry products, salads, vegetable salads, and sandwiches, which harboured pathogens such as E. coli, Salmonella, and Staphylococcus. Antibiotic susceptibility tests revealed the use of 48 antibiotics to manage infections, following CLSI (Clinical and Laboratory Standards Institute) protocols. Moreover, 10 authors reported 54 resistance genes associated with pathogenic resistant bacteria. In addition, only 15 studies received funding or financial support.

CONCLUSION: These findings from several researchers indicate that RTE street foods in African and resource-limited nations harbour enteric pathogens and are a significant concern to the public health system and reservoir of the spread of antibiotic resistance. This underscores the necessity of implementing effective control strategies to address challenges and limit the spread of resistant bacteria in RTE foods. The antimicrobial resistance surveillance system in the region is a significant concern. Notably, Africa needs to strengthen the national and international regulatory bodies and a health surveillance system on antimicrobial resistance, particularly among developing nations.},
}

@article {pmid40270812,
year = {2025},
author = {Fagerlund, A and Møretrø, T and Jensen, MR and Langsrud, S and Moen, B},
title = {Early detection and population dynamics of Listeria monocytogenes in naturally contaminated drains from a meat processing plant.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1541481},
doi = {10.3389/fmicb.2025.1541481},
pmid = {40270812},
issn = {1664-302X},
abstract = {Listeria monocytogenes, a significant foodborne pathogen, often contaminates ready-to-eat foods through cross-contamination in food processing environments, and floor drains represent one of the most common sites of persistence. Subtyping of L. monocytogenes from food processing plants for the purpose of source tracking is usually performed on a single colony obtained after selective enrichment. This study investigates the temporal variation and population dynamics of L. monocytogenes in drains, focusing on the diversity of L. monocytogenes and the impact of the resident microbiota. Six different drains in a meat processing plant were each sampled four times over a period of 8 weeks and subjected to two-step selective enrichment in Half Fraser and Full Fraser broths. The clonal complexes (CCs) of at least 20 individual L. monocytogenes isolates from each positive sample (460 isolates in total) were determined using either the GenoListeria Multiplex qPCR assay or whole genome sequencing (WGS). The microbiota in drains and enrichment cultures was analyzed by 16S rRNA gene amplicon sequencing and metagenomic or quasimetagenomic sequencing. L. monocytogenes was detected in the majority of samples and four different CCs were identified - CC9, CC11 (ST451), CC121 and CC8 - with up to three CCs in the same sample and with different CCs dominating in different drains. The same clones of CC9, CC11, and CC121 had persisted in the facility for 3-5 years. The composition of the drain microbiota remained relatively stable over time, with Pseudomonas, Acinetobacter, Janthinobacterium, Chryseobacterium, Staphylococcus, and Sphingomonas as the most commonly identified genera. There were no apparent differences in the microbial genera present in L. monocytogenes positive and negative drains or samples. The study highlights the use of techniques such as qPCR and quasimetagenomics for monitoring and controlling the risk of L. monocytogenes contamination in processing environments.},
}

@article {pmid40270585,
year = {2025},
author = {Zheng, Z and Gong, Z and Zhang, R and Lin, X and Hong, W and Song, L},
title = {Potential pathogens drive ARGs enrichment during biofilms formation on environmental surfaces.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf057},
doi = {10.1093/ismeco/ycaf057},
pmid = {40270585},
issn = {2730-6151},
abstract = {The enrichment of antibiotic resistance genes (ARGs) on environmental surfaces is a fundamental question in microbial ecology. Understanding the processes driving ARG variations can provide clues into their transfer mechanisms between phases and offer insights for public health management. In this study, we examined microbiota, potential pathogen, and ARG dynamics on two common environment surfaces-polyvinyl chloride (PVC) and carbon steel (CS)-under environmental stress (induced by landfill leachate flow) in a Center for Disease Control and Prevention Biofilm Reactor using metagenomics and quantitative polymerase chain reaction-Chip techniques. Contrary to the expected changes in biofilms morphology and physiochemical properties, microbiota, potential pathogens, and ARGs exhibited a divergence-convergence pattern, primarily shaped by attachment surface properties and, subsequently, biofilm maturity during biofilms formation. During this process, ARG levels in biofilms gradually increased to and exceeded the levels in the surrounding environment, but with a distinct structure (P < .05). Furthermore, 1.93- and 3.05-fold increases in the concentrations of mobile genetic elements intI-1 in PVC and CS biofilms, respectively, suggested their important role in the transfer and spread of ARGs within the biofilm matrix. Although potential pathogens were less abundant (3.48%-5.63%) in the biofilms microbiota, they accounted for 18.28%-45.16% of the ARG hosts and harbored multiple ARGs. Pathogens significantly impacted ARG enrichment (Procrustes analysis: P = .0136, M[2] = 0.34) although microbiota development also influenced this process (P = .0385, M[2] = 0.67). These results suggest that pathogens are key in shaping ARG enrichment in biofilms. Our findings provide dynamic insights into resistome enrichment on environmental surfaces.},
}

@article {pmid40270483,
year = {2025},
author = {McElwee-Adame, A and Esplin-Stout, R and Mugoya, T and Vourlitis, G and Welch, N and Henning, J and Afram, K and Jeshvaghane, MA and Bingham, N and Dockter, A and Eslava, J and Gil, G and Mergens, J and Mohamed, A and Nguyen, T and Noor, F and Salcedo, N and Sethuraman, A},
title = {Evolutionary History and Rhizosphere Microbial Community Composition in Domesticated Hops (Humulus lupulus L.).},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e17769},
doi = {10.1111/mec.17769},
pmid = {40270483},
issn = {1365-294X},
support = {2017-06423//USDA; National Institute of Food and Agriculture/ ; 2022-77040-38529//USDA; National Institute of Food and Agriculture/ ; 1564659//NSF; Division of Biological Infrastructure/ ; 2147812//NSF; Division of Biological Infrastructure/ ; },
abstract = {Humulus lupulus L., commonly known as hop, is a perennial crop grown worldwide and is well known for its pharmacological, commercial, and most importantly brewing applications. For hundreds of years, hop has undergone intense artificial selection, with over 250 cultivated varieties being developed worldwide, all displaying differences in key characteristics such as bitter acid concentrations, flavour and aroma profiles, changes in photoperiod, growth, and pathogen/pest resistances. Previous studies have individually explored differences between cultivars, aiming to identify markers that can quickly and cost-effectively differentiate between cultivars. However, little is known about their evolutionary history and the variability in their associated rhizospheric microbial communities. Coupling phenotypic, genomic, and soil metagenomic data, our study explores the global population structure and domestication history of 98 hop cultivars. We assessed differences in growth rates, rates of viral infection, usage of dissolvable nitrogen, and soil microbial community compositions between US and non-US based cultivars. Our study revealed that worldwide hop cultivars cluster into four subpopulations: Central European, English, and American ancestry as previously reported, and one new group, the Nobles, revealing further substructure amongst Central European cultivars. Modelling the evolutionary history of domesticated hop reveals divergence of the common ancestors of modern US cultivars around 2800 years before present (ybp), and more recent divergences with gene flow across English, Central European, and Noble cultivars, reconciled with key events in human history and migrations. Furthermore, cultivars of US origin were shown to overall outperform non-US cultivars in both growth rates and usage of dissolvable nitrogen and display novel microbial composition under common-garden settings in the United States.},
}

@article {pmid40270118,
year = {2025},
author = {Murtaza, N and Collins, L and Yao, CK and Thwaites, PA and Veitch, P and Varney, JE and Gill, PA and Gibson, PR and Morrison, M and Muir, JG},
title = {Effects of dietary FODMAP content on the faecal microbiome and gastrointestinal physiology in healthy adults: a randomised, controlled cross-over feeding study.},
journal = {The British journal of nutrition},
volume = {},
number = {},
pages = {1-39},
doi = {10.1017/S0007114525000868},
pmid = {40270118},
issn = {1475-2662},
abstract = {The effect dietary FODMAPs (fermentable oligo-, di- and mono-saccharides and polyols) in healthy adults is poorly documented. This study compared specific effects of low and moderate FODMAP intake (relative to typical intake) on the faecal microbiome, participant-reported outcomes and gastrointestinal physiology. In a single-blind cross-over study, 25 healthy participants were randomised to one of two provided diets, 'low' (LFD) <4 g/d or 'moderate' (MFD) 14-18 g/d, for 3 weeks each, with ≥2-week washout between. Endpoints were assessed in the last week of each diet. The faecal bacterial/archaeal and fungal communities were characterised in 18 participants in whom high quality DNA was extracted by 16S rRNA and ITS2 profiling, and by metagenomic sequencing. There were no differences in gastrointestinal or behavioural symptoms (fatigue, depression, anxiety), or in faecal characteristics and biochemistry (including short-chain fatty acids). Mean colonic transit time (telemetry) was 23 (95% confidence interval: 15, 30) h with the MFD compared with 34 (24, 44) h with LFD (n=12; p=0.009). Fungal diversity (richness) increased in response to MFD, but bacterial richness was reduced, coincident with expansion of the relative abundances of Bifidobacterium, Anaerostipes, and Eubacterium. Metagenomic analysis showed expansion of polyol-utilising Bifidobacteria, and Anaerostipes with MFD. In conclusion, short-term alterations of FODMAP intake are not associated with symptomatic, stool or behavioural manifestations in healthy adults, but remarkable shifts within the bacterial and mycobiome populations were observed. These findings emphasise the need to quantitatively assess all microbial Domains and their interrelationships to improve understanding of consequences of diet on gut function.},
}

@article {pmid40270064,
year = {2025},
author = {Basu, A and Chalasani, D and Sarma, PVSRN and Uikey, S and Chenna, VR and Choudhari, PL and Podile, AR},
title = {Influence of genotype, nodule position, and edaphic factors on microbial diversity and assembly of pigeonpea (Cajanus cajan) root nodules in Indian soils.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {41},
pmid = {40270064},
issn = {2524-6372},
abstract = {BACKGROUND: Pigeonpea (Cajanus cajan) is an important legume crop in semi-arid regions with multiple uses. The microbial diversity within its root nodules in Indian soils remains poorly explored. We investigated the bacterial diversity of pigeonpea root nodules across different genotypes and soil types to identify the factors driving their assembly. Using a metagenomic approach and high-throughput sequencing of the 16S rRNA gene, we analyzed the nodule microbiomes of three pigeonpea genotypes (Asha, Durga, and Mannem Konda Kandi) grown in three different soil types (Alfisol, Vertisol, and Inceptisol) and wild pigeonpea (C. scarabaeoides) in its native soil.

RESULTS: Our results indicated that pigeonpea nodules harbor diverse rhizobial and non-rhizobial endophytes and that host genotype, nodule position, soil type, and other edaphic factors influence significant variation in the microbial community structure. The core nodule microbiome was dominated by Proteobacteria and Bacteroidetes. Bradyrhizobium and Ensifer were predominant among the rhizobial taxa, and non-rhizobial genera such as Pseudomonas, Chitinophaga, and Limnobacter were also abundant. Edaphic factors, particularly soil type, pH, and nutrient availability, had a stronger influence on the nodule bacterial community composition than the host genotype. Although bulk soil exhibited higher bacterial diversity, nodule microbiomes were less diverse but more specialized, indicating host-mediated selection. A comparison of the nodule microbiomes of wild and cultivated pigeonpea revealed distinct differences, with the core nodule microbiome of wild pigeonpea dominated by Bradyrhizobium, while that of cultivated pigeonpea exhibited a diverse bacterial community.

CONCLUSIONS: These findings demonstrate that soil properties play a more critical role than host genetics in shaping the pigeonpea nodule microbiome, emphasizing the importance of environmental conditions in symbiotic interactions. The differences between wild and cultivated genotypes suggest that domestication has altered microbial recruitment strategies. This study provides foundational insights into the factors driving microbial assembly in pigeonpea nodules, with implications for improving crop productivity through targeted microbial management. Future research should explore the functional roles of these microbial communities to optimize their use in sustainable agriculture.},
}

@article {pmid40269715,
year = {2025},
author = {Poopedi, E and Pierneef, R and Singh, T and Gomba, A},
title = {Antibiotic resistance profiles and mutations that might affect drug susceptibility in metagenome-assembled genomes of Legionella pneumophila and Aeromonas species from municipal wastewater.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {237},
pmid = {40269715},
issn = {1471-2180},
support = {121333//National Research Foundation/ ; K5/2885//3//Water Research Commission/ ; },
mesh = {*Wastewater/microbiology ; *Aeromonas/genetics/drug effects/isolation & purification ; *Anti-Bacterial Agents/pharmacology ; *Legionella pneumophila/genetics/drug effects/isolation & purification ; Genome, Bacterial ; Mutation ; *Metagenome ; *Drug Resistance, Bacterial/genetics ; Microbial Sensitivity Tests ; },
abstract = {Antibiotic resistance (AR) has emerged as a significant global health issue. Wastewater treatment plants (WWTPs) contain diverse bacterial communities, including pathogens, and have been identified as crucial reservoirs for the emergence and dissemination of AR. The present study aimed to identify antibiotic resistance genes (ARGs) and screen for the presence of mutations associated with AR in Legionella pneumophila and Aeromonas spp. from municipal wastewater. Metagenome-assembled genomes (MAGs) of L. pneumophila and Aeromonas spp. were reconstructed to investigate the molecular mechanisms of AR in these organisms. A total of 138 nonsynonymous single nucleotide variants (SNVs) in seven genes associated with AR and one deletion mutation in the lpeB gene were identified in L. pneumophila. In Aeromonas spp., two (aph(6)-Id and aph(3'')-Ib) and five (blaMOX-4, blaOXA-1143, blaOXA-724, cepH, and imiH) ARGs conferring resistance to aminoglycosides and β-lactams were identified, respectively. Moreover, this study presents β-lactam resistance genes, blaOXA-1143 and blaOXA-724, for the first time in Aeromonas spp. from a municipal WWTP. In conclusion, these findings shed light on the molecular mechanisms through which clinically relevant pathogenic bacteria such as L. pneumophila and Aeromonas spp. found in natural environments like municipal wastewater acquire AR.},
}

*Wastewater/microbiology
*Aeromonas/genetics/drug effects/isolation & purification
*Anti-Bacterial Agents/pharmacology
*Legionella pneumophila/genetics/drug effects/isolation & purification
Genome, Bacterial
Mutation
*Metagenome
*Drug Resistance, Bacterial/genetics
Microbial Sensitivity Tests

@article {pmid40269516,
year = {2025},
author = {Cumbo, F and Truglia, S and Weitschek, E and Blankenberg, D},
title = {Feature selection with vector-symbolic architectures: a case study on microbial profiles of shotgun metagenomic samples of colorectal cancer.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {2},
pages = {},
doi = {10.1093/bib/bbaf177},
pmid = {40269516},
issn = {1477-4054},
support = {U24HG006620/NH/NIH HHS/United States ; },
mesh = {Humans ; *Colorectal Neoplasms/microbiology/genetics ; *Metagenomics/methods ; *Metagenome ; *Microbiota ; *Gastrointestinal Microbiome ; Computational Biology/methods ; Algorithms ; },
abstract = {UNLABELLED: The continuously decreasing cost of next-generation sequencing has recently led to a significant increase in the number of microbiome-related studies, providing invaluable information for understanding host-microbiome interactions and their relation to diseases. A common approach in metagenomics consists of determining the composition of samples in terms of the amount and types of microbial species that populate them, with the goal of identifying microbes whose profiles are able to differentiate samples under different conditions with advanced feature selection techniques. Here, we propose a novel backward variable selection method based on the hyperdimensional computing (HDC) paradigm, which takes inspiration from how the human brain works in the classification of concepts by encoding features into vectors in a high-dimensional space. We validated our method on public metagenomic samples collected from patients affected by colorectal cancer in a case/control scenario, by performing a comparative analysis with other state-of-the-art feature selection methods, obtaining promising results.

AUTHOR SUMMARY: Characterizing the microbial composition of metagenomic samples is crucial for identifying potential biomarkers that can distinguish between healthy and diseased states. However, the high dimensionality and complexity of metagenomic data present significant challenges in the context of accurately selecting features. Our backward variable selection method, based on the HDC paradigm, offers a promising approach to overcoming these challenges. By effectively reducing the feature space while preserving essential information, this method enhances the ability to detect critical microbial signatures associated with diseases like colorectal cancer, leading to more precise diagnostic tools.},
}

Humans
*Colorectal Neoplasms/microbiology/genetics
*Metagenomics/methods
*Metagenome
*Microbiota
*Gastrointestinal Microbiome
Computational Biology/methods
Algorithms

@article {pmid40269515,
year = {2025},
author = {Sirasani, JP and Gardner, C and Jung, G and Lee, H and Ahn, TH},
title = {Bioinformatic approaches to blood and tissue microbiome analyses: challenges and perspectives.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {2},
pages = {},
doi = {10.1093/bib/bbaf176},
pmid = {40269515},
issn = {1477-4054},
support = {2430236//National Science Foundation/ ; },
mesh = {Humans ; *Microbiota/genetics ; *Computational Biology/methods ; High-Throughput Nucleotide Sequencing ; Machine Learning ; Biomarkers/blood ; },
abstract = {Advances in next-generation sequencing have resulted in a growing understanding of the microbiome and its role in human health. Unlike traditional microbiome analysis, blood and tissue microbiome analyses focus on the detection and characterization of microbial DNA in blood and tissue, previously considered a sterile environment. In this review, we discuss the challenges and methodologies associated with analyzing these samples, particularly emphasizing blood and tissue microbiome research. Key preprocessing steps-including the removal of ribosomal RNA, host DNA, and other contaminants-are critical to reducing noise and accurately capturing microbial evidence. We also explore how taxonomic profiling tools, machine learning, and advanced normalization techniques address contamination and low microbial biomass, thereby improving reliability. While it offers the potential for identifying microbial involvement in systemic diseases previously undetectable by traditional methods, this methodology also carries risks and lacks universal acceptance due to concerns over reliability and interpretation errors. This paper critically reviews these factors, highlighting both the promise and pitfalls of using blood and tissue microbiome analyses as a tool for biomarker discovery.},
}

Humans
*Microbiota/genetics
*Computational Biology/methods
High-Throughput Nucleotide Sequencing
Machine Learning
Biomarkers/blood

@article {pmid40269473,
year = {2025},
author = {Khan, MAW and Bohannan, BJM and Meyer, KM and Womack, AM and Nüsslein, K and Grover, JP and Mazza Rodrigues, JL},
title = {Community-Level Metabolic Shifts Following Land Use Change in the Amazon Rainforest Identified by a Supervised Machine Leaning Approach.},
journal = {Environmental microbiology reports},
volume = {17},
number = {2},
pages = {e70088},
doi = {10.1111/1758-2229.70088},
pmid = {40269473},
issn = {1758-2229},
support = {DE-AC02-05CH11231//U.S. Department of Energy/ ; DEB 14422214//National Science Foundation/ ; },
mesh = {*Rainforest ; *Soil Microbiology ; *Bacteria/genetics/metabolism/classification/isolation & purification ; *Microbiota ; Metagenomics/methods ; Metagenome ; *Archaea/genetics/metabolism/classification/isolation & purification ; Soil/chemistry ; Viruses/genetics/classification/metabolism/isolation & purification ; Machine Learning ; Brazil ; },
abstract = {The Amazon rainforest has been subjected to high rates of deforestation, mostly for pasturelands, over the last few decades. This change in plant cover is known to alter the soil microbiome and the functions it mediates, but the genomic changes underlying this response are still unresolved. In this study, we used a combination of deep shotgun metagenomics complemented by a supervised machine learning approach to compare the metabolic strategies of tropical soil microbial communities in pristine forests and long-term established pastures in the Amazon. Machine learning-derived metagenome analysis indicated that microbial community structures (bacteria, archaea and viruses) and the composition of protein-coding genes were distinct in each plant cover type environment. Forest and pasture soils had different genomic diversities for the above three taxonomic groups, characterised by their protein-coding genes. These differences in metagenome profiles in soils under forests and pastures suggest that metabolic strategies related to carbohydrate and energy metabolisms were altered at community level. Changes were also consistent with known modifications to the C and N cycles caused by long-term shifts in aboveground vegetation and were also associated with several soil physicochemical properties known to change with land use, such as the C/N ratio, soil temperature and exchangeable acidity. In addition, our analysis reveals that these alterations in land use can also result in changes to the composition and diversity of the soil DNA virome. Collectively, our study indicates that soil microbial communities shift their overall metabolic strategies, driven by genomic alterations observed in pristine forests and long-term established pastures with implications for the C and N cycles.},
}

*Rainforest
*Soil Microbiology
*Bacteria/genetics/metabolism/classification/isolation & purification
*Microbiota
Metagenomics/methods
Metagenome
*Archaea/genetics/metabolism/classification/isolation & purification
Soil/chemistry
Viruses/genetics/classification/metabolism/isolation & purification
Machine Learning
Brazil

@article {pmid40269059,
year = {2025},
author = {Aljutaily, T and Aladhadh, M and Alsaleem, KA and Alharbi, HF and Barakat, H and Aljumayi, H and Moustafa, MMA and Rehan, M},
title = {Gut microbiota diversity in obese rats treated with intermittent fasting, probiotic-fermented camel milk with or without dates and their combinations.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {14204},
pmid = {40269059},
issn = {2045-2322},
support = {QU-APC-2024-9/1//Deanship of Graduate Studies and Scientific Research at Qassim University/ ; QU-APC-2024-9/1//Deanship of Graduate Studies and Scientific Research at Qassim University/ ; QU-APC-2024-9/1//Deanship of Graduate Studies and Scientific Research at Qassim University/ ; QU-APC-2024-9/1//Deanship of Graduate Studies and Scientific Research at Qassim University/ ; QU-APC-2024-9/1//Deanship of Graduate Studies and Scientific Research at Qassim University/ ; QU-APC-2024-9/1//Deanship of Graduate Studies and Scientific Research at Qassim University/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Camelus ; Rats ; *Obesity/microbiology/diet therapy ; *Probiotics/administration & dosage ; *Fasting ; *Milk ; Male ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification ; Biodiversity ; Cultured Milk Products ; Intermittent Fasting ; },
abstract = {Dietary alternatives help effectively in obesity management. The present study examines the gut microbiota diversity in obesity-induced rats treated with intermittent fasting, fermented camel milk (FCM), and FCM-incorporated Sukkari date or their combinations. The metagenomic analysis of the gut microbiome through 16 S rRNA revealed 226 families, 499 genera, and 879 bacterial species. In the taxonomy distributions and heatmap analysis, Bacteroidota (i.e., Prevotella) had the uppermost relative abundance in groups before treatments (Before_Groups, most samples clustered in one sub-cluster) reached 80.50% in sample S11 (Before_G2), whereas Firmicutes (i.e., Lactobacillus) presented the dominant in groups after treatments (After_Groups, generality samples grouped in another sub-cluster) and counted 70.86% in sample S88 (After_G6), reflecting potential short-chain fatty acids production. The alpha and beta diversity explored by Shannon and PCoA indices presented high diversity in most groups after treatment. Deferribacterota and Fusobacteriota, in addition to Stenotrophomonas and Listeria, were the key phylotypes in the treated groups at the Phylum and genus levels, respectively. The proposed functional pathways involving mannan, rhamnose I, glucose, and xylose degradation were the most supported pathways in After_Groups with potential carbohydrate degradation. Eventually, intermittent fasting and probiotic fermented camel milk increased microbiome diversity and accelerated weight loss, preventing health issues.},
}

Animals
*Gastrointestinal Microbiome/genetics
Camelus
Rats
*Obesity/microbiology/diet therapy
*Probiotics/administration & dosage
*Fasting
*Milk
Male
RNA, Ribosomal, 16S/genetics
Bacteria/genetics/classification
Biodiversity
Cultured Milk Products
Intermittent Fasting

@article {pmid40268958,
year = {2025},
author = {Luo, Q and Gao, H and Xiang, Y and Li, J and Dong, L and Wang, X and Liu, F and Guo, Y and Shen, C and Ding, Q and Qin, C and Liang, G and Wen, L},
title = {The dynamics of microbiome and virome in migratory birds of southwest China.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {64},
pmid = {40268958},
issn = {2055-5008},
mesh = {Animals ; China ; *Virome ; Feces/microbiology/virology ; *Gastrointestinal Microbiome ; *Charadriiformes/microbiology/virology ; Animal Migration ; *Bacteria/classification/genetics/isolation & purification ; *Viruses/classification/genetics/isolation & purification ; *Birds/microbiology/virology ; Metagenomics ; Phylogeny ; },
abstract = {Migratory birds carry pathogens, posing a significant threat to environmental and human health. We documented the metatranscriptome and RNA virome of 896 stool samples from migratory birds and environmental samples over four consecutive years in southwest China. Our analysis identified Catellicoccus marimammalium as the predominant bacterium in the gut of black-headed gulls, with an average relative abundance of 79.3%. Strain-level analysis of C. marimammalium revealed a dominant population with some longitudinal diversity over the four years. Additionally, the gut of black-headed gulls was found to harbor numerous viruses, including a novel hepatovirus. Lysates of cells of C. marimammalium but not other bacteria derived from black-headed gulls could inhibit the replication of human hepatovirus, suggesting a potential regulatory role for gut commensal bacteria in modulating viral carriage. These findings enhance our understanding of the microbiome and RNA virome diversity in migratory birds and provide insights into the modulation of asymptomatic infections.},
}

Animals
China
*Virome
Feces/microbiology/virology
*Gastrointestinal Microbiome
*Charadriiformes/microbiology/virology
Animal Migration
*Bacteria/classification/genetics/isolation & purification
*Viruses/classification/genetics/isolation & purification
*Birds/microbiology/virology
Metagenomics
Phylogeny

@article {pmid40268922,
year = {2025},
author = {Patsis, AC and Schuler, CJ and Toner, BM and Santelli, CM and Sheik, CS},
title = {The potential for coupled organic and inorganic sulfur cycles across the terrestrial deep subsurface biosphere.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {3827},
pmid = {40268922},
issn = {2041-1723},
support = {EAR-1813526//National Science Foundation (NSF)/ ; EAR-1813526//National Science Foundation (NSF)/ ; },
mesh = {*Sulfur/metabolism ; Ecosystem ; *Sulfur Compounds/metabolism ; *Bacteria/metabolism/genetics/classification ; Metagenome ; Sulfides/metabolism ; Metagenomics ; Sulfites/metabolism ; Soil Microbiology ; Sulfonium Compounds ; },
abstract = {Organosulfur compounds (OrgS) are fundamental components of life's biomass, yet the cycling of these compounds in the terrestrial deep subsurface, one of Earth's largest ecosystems, has gone relatively unexplored. Here, we show that all subsurface microbial genomes reconstructed from Soudan Underground Mine State Park have the capacity to cycle organic sulfur species. Our findings suggest that OrgS degradation may be an integral link between the organic and inorganic sulfur cycle via the production of sulfite and sulfide. Furthermore, despite isolation from surface ecosystems, most Soudan microorganisms retained genes for dimethylsulfoniopropionate and taurine biosynthesis. Metagenomic analyses of an additional 54 deep subsurface sites spanning diverse lithologies revealed the capacity for OrgS cycling to be widespread, occurring in 89% of assembled metagenomes. Our results indicate that consideration of OrgS cycling may be necessary to accurately constrain sulfur fluxes, discern the energetic limits of deep life, and determine the impact of deep subsurface biogeochemical sulfur cycling on greater Earth system processes.},
}

*Sulfur/metabolism
Ecosystem
*Sulfur Compounds/metabolism
*Bacteria/metabolism/genetics/classification
Metagenome
Sulfides/metabolism
Metagenomics
Sulfites/metabolism
Soil Microbiology
Sulfonium Compounds

@article {pmid40268850,
year = {2025},
author = {Zhao, J and Zhuge, R and Hu, B and Wang, Y and Wang, X and Zhang, Y and Yuan, L and Qiu, C and Yan, Y and Zhang, X and Hua, Z and Tang, J and Guo, K and Sun, Y and Wang, K and Qiu, L and Luo, J and Zhang, W and Zhuge, J and Fang, H},
title = {Clinical impact of bronchoalveolar lavage fluid metagenomic next-generation sequencing in immunocompromised patients with severe community-acquired pneumonia in ICU: a multicenter retrospective study.},
journal = {Infection},
volume = {},
number = {},
pages = {},
pmid = {40268850},
issn = {1439-0973},
support = {2023KY1296//The Project of Zhejiang Provincial Department of Health/ ; 2022K71//Quzhou Bureau of Science and Technology/ ; },
abstract = {BACKGROUND: An increasing number of critically ill patients are immunocompromised. These patients are at high risk of intensive care unit (ICU) admission because of numerous complications. Acute respiratory failure due to severe community-acquired pneumonia (SCAP) is one of the leading causes of admission. Early targeted antibiotic therapy is crucial for improving the prognosis of these patients. Metagenomic next-generation sequencing (mNGS) in bronchoalveolar lavage fluid (BALF) has shown significant value in pathogen detection in recent years. However, there are few studies on summarizing pathogen profiles of SCAP in immunocompromised patients.

METHODS: We performed a multicenter retrospective analysis of patients with SCAP in the ICU diagnosed between May 2021 to October 2024. Bronchoalveolar lavage fluid (BALF), blood, and sputum samples were collected and subjected to mNGS and conventional microbiological tests (CMTs). The pathogen profiles detected by the two methods were compared.

RESULTS: In our study, compared to CMTs, mNGS increased the detection rates of mixed infections in the immunocompromised group (58.82% vs 17.96%, P < 0.05) and immunocompetent group (44.58% vs 18.72%, P < 0.05), while also reducing the rate of no pathogen detected (4.90% vs 38.73%, P < 0.05; 8.37% vs 32.76%, P < 0.05). In both groups, the proportion of positive clinical impacts (diagnosis) resulting from mNGS results exceeded 90% (96.57% vs 93.84%), and the treatment effectiveness rate in the immunocompromised group was higher than in the immunocompetent group (65.69% vs 56.40%, P < 0.05). Further analysis showed that when mNGS-guided treatment was effective, the 28-day mortality rate significantly improved in both the immunocompromised group (31.34% vs 74.29%, P < 0.05) and the immunocompetent group (42.36% vs 40.68%, P < 0.05) compared to when the treatment was ineffective.

CONCLUSION: This study indicates that ICU patients with SCAP, particularly those who are immunocompromised, are more likely to have polymicrobial infections. mNGS in BALF provides rapid and comprehensive pathogen profiling of pulmonary infections, thereby having a positive impact on both the diagnosis, treatment and prognosis of immunocompromised patients with SCAP.},
}

@article {pmid40268777,
year = {2025},
author = {Claverie, JM and Legendre, M and Rigou, S and Abergel, C},
title = {Refining the taxonomy of pithovirus-related giant DNA viruses within the order Pimascovirales.},
journal = {Archives of virology},
volume = {170},
number = {5},
pages = {111},
pmid = {40268777},
issn = {1432-8798},
mesh = {Genome, Viral ; Phylogeny ; *DNA Viruses/classification/genetics/ultrastructure ; *Giant Viruses/classification/genetics/ultrastructure ; DNA, Viral/genetics ; },
abstract = {The first member of the family Pithoviridae (Pithovirus sibericum) was isolated from ancient Siberian permafrost and characterized in 2014. Since then, many relatives have been isolated, characterized, and classified as members of the genera Alphapithovirus, Alphacedratvirus, and Alphaorpheovirus. In addition, one complete circular genome sequence was assembled from metagenomic data (hydrivirus). All of these viruses form distinctive giant elongated ovoid particles, up to 2 µm in length, but they differ significantly in the size of their genome, their nucleotide composition, and their gene content. Based on their shared ovoid virion shape, common replication strategy, and core gene similarity, we recently proposed to update their taxonomic status by classifying them in three distinct families (Pithoviridae, Orpheoviridae, and Hydriviridae) within a new suborder, the Ocovirineae, to separate them clearly from the other more distant families (Marseilleviridae, Ascoviridae, Iridoviridae) of the order Pimascovirales. This new taxonomy, validated by the last ICTV Ratification vote held in March 2025, extends the previous partition from three clades to four (to include hydrivirus) while keeping the genera Alphacedratvirus and Alphapithovirus in the same family, Pithoviridae (but split into two subfamilies), due to their much greater similarity to each other than to orpheovirus and hydrivirus.},
}

Genome, Viral
Phylogeny
*DNA Viruses/classification/genetics/ultrastructure
*Giant Viruses/classification/genetics/ultrastructure
DNA, Viral/genetics

@article {pmid40268631,
year = {2025},
author = {Pemán, J and Ruiz-Gaitán, A},
title = {Diagnosing invasive fungal infections in the laboratory today: It's all good news?.},
journal = {Revista iberoamericana de micologia},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.riam.2025.01.004},
pmid = {40268631},
issn = {2173-9188},
abstract = {Despite the advances in medical science, invasive fungal infections (IFI) remain a diagnostic challenge. The increasing prevalence of IFI, driven by immunosuppressive therapies, advances in intensive care and emerging pathogens, underscores the need for early and accurate diagnosis. This review evaluates current laboratory methods for the diagnosis of IFI, highlighting their strengths and limitations. Conventional techniques, including fungal culture, direct microscopy, and histopathology, remain the gold standard for the diagnosis of proven IFIs. These methods allow pathogen isolation, species identification and antifungal susceptibility testing. However, these techniques have limitations in terms of sensitivity and turnaround times. Although microscopy is a rapid technique, its sensitivity and species discrimination profile are limited. Modern serological assays, such as β-d-glucan and galactomannan detection, have improved the diagnostic accuracy of probable IFI cases. Integration of these assays with clinical and radiological findings, enables earlier intervention, although this is accompanied by an increased risk of false positives and necessitates careful clinical correlation. Molecular diagnostics, particularly polymerase chain reaction (PCR), allow rapid, species-specific identification directly from clinical samples. The advent of MALDI-TOF mass spectrometry has further improved diagnostic efficiency, particularly for yeast identification, although challenges remain for filamentous fungi. Innovative techniques, such as metagenomic sequencing, lateral-flow assays, and loop-mediated isothermal amplification, offer the potential for rapid and precise detection, even in resource-limited settings. The combination of conventional and innovative methods provides a comprehensive diagnostic framework. The continuous refinement of these tools, in conjunction with multidisciplinary collaboration, is imperative to improve the early diagnostic and targeted treatment of patients with IFI.},
}

@article {pmid40268236,
year = {2025},
author = {Emon, MI and Cheung, YF and Stoll, J and Rumi, MA and Brown, C and Choi, JM and Moumi, NA and Ahmed, S and Song, H and Sein, J and Yao, S and Khan, A and Gupta, S and Kulkarni, R and Butt, A and Vikesland, P and Pruden, A and Zhang, L},
title = {CIWARS: a web server for antibiotic resistance surveillance using longitudinal metagenomic data.},
journal = {Journal of molecular biology},
volume = {},
number = {},
pages = {169159},
doi = {10.1016/j.jmb.2025.169159},
pmid = {40268236},
issn = {1089-8638},
abstract = {The rise of antibiotic resistance (AR) poses a substantial threat to human and animal health, food security, and economic stability. Wastewater-based surveillance (WBS) has emerged as a powerful strategy for population-level AR monitoring, providing valuable data to guide public health and policy decisions. Metagenomic sequencing is especially promising, as it can yield comprehensive profiles of antibiotic resistance genes (ARGs) and other genes relevant to AR in a single run. However, online analytical platforms to facilitate analysis of longitudinal metagenomic data are lacking. To address this, we introduce CyberInfrastructure for Waterborne Antibiotic Resistance Surveillance (CIWARS), a web server configured for characterizing key AR trends from longitudinal metagenomic WBS data. CIWARS offers comprehensive profiling of ARGs and taxonomic profiling of pathogen-associated bacterial taxonomic groups, identifies potential associations of ARGs with mobile genetic elements (MGEs) and pathogen-containing taxa, and assesses resistome risk based on the co-occurrence of ARGs, MGEs, and pathogen-like sequences. Additionally, it detects anomalous AR indicators over time, aiding in identifying potential events of concern, such as the emergence of resistant strains or outbreaks. Through interactive temporal data visualization, CIWARS enables AR monitoring and can serve as a tool to inform effective and timely interventions to mitigate the spread and transmission of AR. Here, CIWARS is demonstrated using longitudinal metagenomic data from a wastewater treatment plant (WWTP) influent and effluent, but it can be extended to any environment. CIWARS provides a valuable tool to support global efforts to combat the evolution and spread of AR, while also guiding agricultural and public health efforts aimed at optimizing antibiotic use. The web server is freely available at https://ciwars.cs.vt.edu/.},
}

@article {pmid40271438,
year = {2017},
author = {Lu, J and Breitwieser, FP and Thielen, P and Salzberg, SL},
title = {Bracken: estimating species abundance in metagenomics data.},
journal = {PeerJ. Computer science},
volume = {3},
number = {},
pages = {},
doi = {10.7717/peerj-cs.104},
pmid = {40271438},
issn = {2376-5992},
abstract = {Metagenomic experiments attempt to characterize microbial communities using high-throughput DNA sequencing. Identification of the microorganisms in a sample provides information about the genetic profile, population structure, and role of microorganisms within an environment. Until recently, most metagenomics studies focused on high-level characterization at the level of phyla, or alternatively sequenced the 16S ribosomal RNA gene that is present in bacterial species. As the cost of sequencing has fallen, though, metagenomics experiments have increasingly used unbiased shotgun sequencing to capture all the organisms in a sample. This approach requires a method for estimating abundance directly from the raw read data. Here we describe a fast, accurate new method that computes the abundance at the species level using the reads collected in a metagenomics experiment. Bracken (Bayesian Reestimation of Abundance after Classification with KrakEN) uses the taxonomic assignments made by Kraken, a very fast read-level classifier, along with information about the genomes themselves to estimate abundance at the species level, the genus level, or above. We demonstrate that Bracken can produce accurate species- and genus-level abundance estimates even when a sample contains multiple near-identical species.},
}

@article {pmid40268215,
year = {2025},
author = {Sun, X and Hu, P and Xiao, M and Zhang, S and Shi, J and Cai, D and Wang, D and Xu, L and Liu, L and Liu, Y},
title = {Synergy of Multi-Enzyme Pretreatment and Paraclostridium benzoelyticum Bioaugmentation: A Dual Strategy for Enhancing Methane Production in Dry Anaerobic Digestion of Kitchen Waste.},
journal = {Environmental research},
volume = {},
number = {},
pages = {121671},
doi = {10.1016/j.envres.2025.121671},
pmid = {40268215},
issn = {1096-0953},
abstract = {Dry anaerobic digestion (DAD) of kitchen waste (KW) has low methane production due to the poor mass transfer and the low abundance of functional microorganisms. This study employed multi-enzyme pretreatment (PRE), bioaugmentation with Paraclostridium benzoelyticum (BIO), and their combination (COM) to enhance methane production. Interestingly, the COM group had the highest methane production, which was increased by 18.51%, 9.91% and 12.39% compared with the control, PRE and BIO groups, respectively, which indicated that there was a synergy between multi-enzyme pretreatment and bioaugmentation. Further analysis of microbial community and metagenome was conducted to reveal the synergistic mechanism. The results showed that in COM group, the enrichment of the Rikenellaceae, Methanobacteriaceae and Methanosaetaceae was the directly reason for enhancing methane production. Additionally, key metabolic functions including biosynthesis of cofactors, methane metabolism and oxidative phosphorylation also played a pivotal role in boosting methane production. Furthermore, the enhancement of the hydrogenotrophic methanogenesis pathway has been demonstrated to be a critical factor in the synergistic effects. It provided a reliable theoretical basis for the practical application of the multi-enzyme pretreatment combined with Paraclostridium benzoelyticum bioaugmentation for DAD.},
}

@article {pmid40268122,
year = {2025},
author = {Highmore, C and Cooper, K and Parker, J and Robinson, J and Castangia, R and Webb, JS},
title = {Real-time detection of Foodborne Pathogens and Biofilm in the food processing environment with Bactiscan, a macro-scale fluorescence device.},
journal = {Journal of food protection},
volume = {},
number = {},
pages = {100511},
doi = {10.1016/j.jfp.2025.100511},
pmid = {40268122},
issn = {1944-9097},
abstract = {Food safety relies on rapid detection methods and rigorous sampling of the food processing environment, and is challenged by recurrent biofilm contamination and by sub-lethally injured bacteria that can evade detection. Bactiscan is investigated as an alternative detection approach, a macro-scale and reagentless device that detects microbial contamination through activating green fluorescence of glycoproteins in the bacterial cell wall. The detection capability of Bactiscan was tested on foodborne pathogens Escherichia coli, Listeria monocytogenes, Salmonella enterica, and Staphylococcus aureus. Detection by Bactiscan was assessed using 3 independent observers viewing bacterial samples dried on stainless steel, using 3 biological repeats and 5 technical repeats. Detection by Bactiscan was possible to 1.20*10[6] colony forming units (CFU), compared to 1.36*10[4] CFU by ATP swab testing, where Bactiscan detection limits were defined by the concentration at which 50% of the samples were observed under illumination of the device. Heat-killed and chlorine stressed E. coli and S. enterica caused a 2-log reduction in detection by ATP swab tests (p≤0.05), while detection by Bactiscan was unaffected (p≥0.05). Pathogen biofilms were detectable via Bactiscan with >80% accuracy at 4 days of growth; E. coli and L. monocytogenes biofilms were visible at 2 days of growth. In situ contamination studies determined that Bactiscan can detect microbial contamination on chicken, salmon, and yoghurt samples with stronger fluorescence than a competitor UV torch. The presence of one of the pathogens on the food samples was confirmed by metagenome sequencing, determining that S. aureus was present in 7 samples out of 9 with a relative abundance of >0.5%. These data demonstrate that Bactiscan can effectively detect bacteria present in the food processing environment and can complement existing technologies to improve food industry cleaning practices and infection prevention.},
}

@article {pmid40267797,
year = {2025},
author = {Sun, X and Sun, Y and Li, P and Gao, Y and Han, M and Zhang, P},
title = {Intensive oyster farming alters the microbial-regulated blue carbon storage in sediment.},
journal = {Marine pollution bulletin},
volume = {216},
number = {},
pages = {118016},
doi = {10.1016/j.marpolbul.2025.118016},
pmid = {40267797},
issn = {1879-3363},
abstract = {Intensive oyster farming enhances the organic matter coupling from water to sediment through biodeposition, potentially contributing to carbon storage. Microbes play a key role in regulating biogeochemical cycling in the coastal sediment. However, their specific contributions to carbon storage under oyster farming remain poorly understood. This study investigates microbial necromass and associated biogeochemical processes in sediments from an intensive oyster farm in Sanggou Bay, China, and compares these indicators with adjacent seagrass beds and bare zones. Additionally, carbon use efficiency (CUE) was employed to indicate microbial-regulated carbon cycling and storage in sediment. The results demonstrate that oyster farming promotes organic carbon accumulation in surface sediments but reduces its stability. Microbial necromass was identified as a critical driver of sedimentary organic carbon in oyster farm sediments, supported by enhanced nitrogen and sulfur cycling pathways. Notably, contrasting relationships between CUE and organic carbon were observed between the seagrass bed and the oyster farm. Functional metagenomic analysis further revealed distinct microbial metabolic pathways across habitats, highlighting the role of biodeposition in shaping microbial functions. These findings enhance our understanding of microbial contributions to blue carbon storage in aquaculture systems and provide new insights into coastal carbon storage beyond vegetated ecosystems.},
}

@article {pmid40267563,
year = {2025},
author = {Jian, Z and Wu, H and Yan, S and Li, T and Zhao, R and Zhao, J and Zi, X and Wang, K and Huang, Y and Gu, D and Zhao, S and Ge, C and Jia, J and Liu, L and Xu, Z and Dou, T},
title = {Species and functional composition of cecal microbiota and resistance gene diversity in different Yunnan native chicken breeds: A metagenomic analysis.},
journal = {Poultry science},
volume = {104},
number = {7},
pages = {105138},
doi = {10.1016/j.psj.2025.105138},
pmid = {40267563},
issn = {1525-3171},
abstract = {The gut microbiota of chickens not only modulates host immune function and production performance through nutrient metabolism but also serves as a reservoir for antibiotic resistance genes (ARGs), whose accumulation exacerbates bacterial resistance. This study integrated 108 cecal microbiome samples from six Yunnan native chicken breeds under free-range and caged farming systems, constructing a comprehensive catalog comprising 12,715 microbial genomes. We systematically revealed the dual mechanisms by which the gut microbiota regulates host phenotypes and ARG dissemination. Metagenomic analysis demonstrated that Alistipes, Prevotella, and Spirochaeta synergistically regulate body weight and immune indices through metabolic networks, which are linked to the significant enrichment of carbohydrate-active enzymes. GH23 and GT2 presented the greatest abundance, highlighting their pivotal role in dietary fiber metabolism. A total of 1327 ARGs were identified, spanning seven resistance mechanisms dominated by antibiotic efflux and target alteration. Alistipes_sp._CAG:831 presented the highest ARG abundance and diversity, with ARG levels strongly correlated with host bacterial abundance. Metagenomic-phenotype association networks further revealed that environmental stress drives disparities in ARG enrichment by altering the microbial community structure. This study elucidates the gut microbiota-host interaction network in Yunnan native chickens and provides critical insights into ARG transmission dynamics, offering a theoretical foundation for antibiotic resistance risk assessment and sustainable poultry farming strategies.},
}