@article {pmid40946456,
year = {2025},
author = {Li, C and Yuan, Z and Liu, B and Sun, Y and Wang, Y and Quan, J and Shen, X and Guo, J},
title = {Comparative recovery of carbon, nitrogen, and phosphorus from food waste via anaerobic digestion and Black Soldier Fly Larvae.},
journal = {Water research},
volume = {288},
number = {Pt A},
pages = {124587},
doi = {10.1016/j.watres.2025.124587},
pmid = {40946456},
issn = {1879-2448},
abstract = {With rising global population and energy demands, efficient recovery of carbon (C), nitrogen (N), and phosphorus (P) from food waste has become increasingly critical for sustainable resource management. Although anaerobic digestion (AD) and Black Soldier Fly Larvae (BSFL) conversion have been separately investigated for food waste treatment, direct and systematic comparisons of their nutrient recovery potential across scales remain limited. This study evaluates and compares two treatment pathways, including conventional AD and the emerging BSFL conversion for their potential to recover C-N-P across lab-scale to pilot/full-scale implementations. A full-scale anaerobic system achieved a high methane yield of 667 mL/g VS, recovering 53.2 % of the food waste C with most N and P remained in digestate. In the BSFL system, increased larval density and feeding frequency significantly enhanced larval biomass production, with a peak yield of 309.2 g/kg dry food waste. Pilot-scale trials demonstrated that 29.1 % of C, 34.4 % of N, and 32.7 % of P were effectively converted into larval biomass, which holds value as protein-rich bioresource. Metagenomic analysis revealed that acetate-producing and syntrophic acetate-oxidizing bacteria, along with hydrogenotrophic methanogens, dominated microbial metabolism in AD systems. Meanwhile, a stable gut microbiota composed of Enterococcus, Actinomyces, and Morganella facilitated organic matter assimilation in BSFL conversion. Based on these findings, we propose an integrated technological framework to optimize full-spectrum resource recovery from food waste. This is the first study to systematically compare AD and BSFL technologies for nutrient recovery from food waste, providing a scientific foundation for the development of circular and sustainable food waste management strategies.},
}

@article {pmid40946204,
year = {2025},
author = {Burnett, J and Buckley, D and Grinstead, DA and Oliver, HF},
title = {Microbial Community Associations With Listeria monocytogenes in Food Processing Environments: A Systematic Review and Meta-Analysis.},
journal = {Comprehensive reviews in food science and food safety},
volume = {24},
number = {5},
pages = {e70277},
doi = {10.1111/1541-4337.70277},
pmid = {40946204},
issn = {1541-4337},
support = {//Diversey/ ; },
abstract = {Listeria monocytogenes persistence in food processing environments challenges current understanding of microbial community dynamics. This systematic review and meta-analysis examined peer-reviewed studies that screened for Listeria spp. and performed culture-independent metagenomics on FPE surface samples. Following PRISMA guidelines, we searched PubMed, Web of Science, and Food Science and Technology Abstracts databases, screening 464 studies, with 73 qualifying for full-text review. Seven studies met the inclusion criteria for final analysis, encompassing 1659 environmental samples from meat processing (n = 4 studies) and produce facilities (n = 3 studies). Meta-analysis using random effects models revealed no significant correlation between Listeria presence and overall microbial community alpha diversity (Shannon: z = -0.89, p = 0.40; inverse Simpson and Chao1 indices similarly non-significant). This finding challenges previous assumptions about the relationship between microbial diversity and pathogen persistence. Differential abundance analyses identified three genera most frequently associated with Listeria presence across multiple studies: Pseudomonas, Psychrobacter, and Acinetobacter. These Gammaproteobacteria are characterized as aerobic biofilm formers capable of growth at refrigeration temperatures. One study using rigorous mixed-effects modeling identified Veillonella as significantly associated with L. monocytogenes presence, suggesting potential anaerobic niche interactions within biofilm communities. Synthesis of metabolic capabilities reported in the literature suggests these associated genera may provide structural biofilm matrices and potentially complementary metabolic functions that could facilitate L. monocytogenes survival in FPE conditions. However, the genus-level resolution of 16S rRNA amplicon sequencing data and methodological variations across studies limit definitive conclusions about specific metabolic interactions. These findings indicate that L. monocytogenes persistence appears to be associated with specific microbial partners rather than overall community diversity metrics. Understanding these ecological relationships may inform targeted control strategies focusing on biofilm-forming genera that create favorable conditions for Listeria survival in food processing environments.},
}

@article {pmid40945449,
year = {2025},
author = {Wang, X and Wang, J and Li, Z and Yang, M and Rehman, A},
title = {Alginate-driven co-metabolic degradation mechanism of sulfamethoxazole by marine consortia.},
journal = {Journal of hazardous materials},
volume = {498},
number = {},
pages = {139778},
doi = {10.1016/j.jhazmat.2025.139778},
pmid = {40945449},
issn = {1873-3336},
abstract = {Pharmaceuticals and personal care products (PPCPs), known for their severe ecological risks, are frequently detected in coastal waters worldwide. However, the environmental fate in marine systems remains poorly understood. This study investigated the co-metabolic degradation mechanism of a typical PPCP, sulfamethoxazole (SMX), by a marine consortium SAB using alginate-a natural organic matter-as a co-substrate, aiming to elucidate the biodegradation process of PPCPs in actual marine environments. An integrated approach, including metagenomic sequencing (with binning), RT-qPCR, molecular docking, metabolic modeling, and metabolomics, was employed. Results demonstrated that the SAB consortium efficiently degraded SMX at concentrations from 50 μg/L to 10 mg/L, achieving over 96 % removal within 24 h. SMX degradation was achieved through metabolic cross-feeding of alginate by key species within the SAB consortium. Specifically, alginate is initially converted by Vibrio into the central metabolite 2-keto-3-deoxy-D-gluconate (KDG). KDG is subsequently metabolized by Tritonibacter, Halopseudomonas, and Vibrio, generating key metabolites such as acetyl-CoA, serine, cysteine, and guanine. These metabolites support microbial growth and induce production of SMX-degrading enzymes, such as threonine dehydratase, cysteine S-conjugate β-lyase, and guanine deaminase, leading to SMX cleavage and mineralization. Additionally, acetyl-CoA provides acetyl groups for arylamine N-acetyltransferase-mediated SMX acetylation. These processes collectively drive the co-metabolic degradation of SMX. Overall, this study provides critical insights into PPCPs' fate in marine environments.},
}

@article {pmid40945361,
year = {2025},
author = {Zhang, M and Zhang, D and Zhou, B and Wu, Q and Liu, X and Wang, M and Liang, J and Zhou, L},
title = {Metagenomic insights into fungal enzyme-mediated propionic acid production from food waste via succinic acid pathway.},
journal = {Journal of environmental management},
volume = {393},
number = {},
pages = {127243},
doi = {10.1016/j.jenvman.2025.127243},
pmid = {40945361},
issn = {1095-8630},
abstract = {Employing fungal enzyme additives as a pretreatment for propionic acid (PA) production from food waste is a promising approach to achieving sustainable waste management. This study explored the feasibility and underlying mechanisms of complex enzyme pretreatment in promoting PA-oriented metabolic via mixed cultures. PA-orienting fermentation was achieved under complex enzyme (CE) pretreatment at pH 7, with PA concentration and proportion of 12.6 ± 0.80 g·COD/L and 39.0 ± 1.10 % of total VFAs, respectively. CE addition significantly enhanced hydrolysis and acidogenesis, improving the simultaneous conversion of polysaccharides and proteins. Bacteroides, including B. ovatus, B. sp. M10, and B. xylanisolvens, P. saccharofermentans and E. coil significantly enriched as the dominant species in PA-type fermentation system. Succinic acid pathway emerged as the primary metabolic route for PA production. Functional genes associated with this pathway, including K01676, K01079, frdA, sdhAD, sucCD, MUT, and ACSS, were significantly upregulated with CE addition. The findings provide a practical strategy for designing and optimizing VFA production from food waste, advancing sustainable waste valorization.},
}

@article {pmid40945100,
year = {2025},
author = {Caley, A and Marzinelli, EM and Mayer-Pinto, M},
title = {Limited microbial community responses of marine macroalgae to artificial light at night and moderate warming conditions.},
journal = {Marine environmental research},
volume = {212},
number = {},
pages = {107536},
doi = {10.1016/j.marenvres.2025.107536},
pmid = {40945100},
issn = {1879-0291},
abstract = {Multiple stressors such as Artificial Light at Night (ALAN) and warming are increasingly common in marine systems and can interact in complex ways. Microbial communities play critical roles in the functioning of coastal habitat-forming species such as seaweeds, however the effects of ALAN on seaweed-associated microbial communities remain unknown. We tested the independent and combined effects of ALAN and warming on microbial communities associated with the habitat-forming seaweeds Ecklonia radiata and Sargassum sp. In Ecklonia, ALAN increased the relative abundance of two potentially light-responsive taxa: Dokdonia sp000212355 and an unidentified ASV from Pseudomonadales, whereas warming had the opposite effect. Warming increased microbial community dispersion in Ecklonia and resulted in non-significant increases in relative abundance of putative pathogenic and agarolytic taxa (microbes capable of degrading algal polysaccharides). However, further analyses using metagenomics are needed to confirm functional roles. In contrast, neither ALAN nor warming affected dominant taxa associated with Sargassum. Contrary to expectations, cyanobacteria relative abundance was unaffected by ALAN in either seaweed host, despite their photosynthetic capacity. We found limited evidence for interactive effects of ALAN and warming, and community composition remained unchanged in both seaweed species. Our findings highlight the importance of considering species-specific microbial responses to ALAN and warming, with implications for coastal management.},
}

@article {pmid40945093,
year = {2025},
author = {Niu, Y and Zhang, X and Jiao, M and Storey, KB and Shekhovtsov, SV},
title = {Metabolic plasticity and gut microbiome synergy underlie high-altitude adaptation in the plateau frog Rana kukunoris: A multi-omics perspective.},
journal = {Ecotoxicology and environmental safety},
volume = {303},
number = {},
pages = {119050},
doi = {10.1016/j.ecoenv.2025.119050},
pmid = {40945093},
issn = {1090-2414},
abstract = {Life on the Qinghai-Tibet Plateau is exposed to extreme abiotic stressors, yet endemic frog species such as Rana kukunoris thrive due to specialized adaptations. However, the metabolic and gut microbial mechanisms that enable survival at high altitude remain unclear. Here, we used metabolomic analysis and metagenomic sequencing to compare metabolic profiles of liver and skeletal muscle, as well as gut microbial composition and function, between high- (3730 m) and low-altitude (1990 m) populations. Metabolomic profiling revealed significant altitude-driven shifts, including the down-regulation of glycolysis (fructose-1,6-bisphosphate and glyceraldehyde 3-phosphate decreased by 44.2 % and 40.7 %, respectively) and tricarboxylic acid (TCA) cycle intermediates (fumaric acid and malic acid reduced by 37.7 % and 35.9 %, respectively) in the liver, and enhanced oxidative phosphorylation efficiency via elevated flavins (flavin mononucleotide and flavin adenine dinucleotide increased 1.43- and 1.28-fold, respectively) in skeletal muscle. These findings suggest a conserved strategy of metabolic rate depression and tissue-specific metabolic regulation. Significantly differential metabolites were enriched in glycerophospholipid metabolism and glycosylphosphatidylinositol (GPI)-anchor biosynthesis, highlighting membrane remodeling as a key adaptive response to cold stress at high altitudes. Moreover, gut microbiomes of high-altitude frogs exhibited increased α-diversity and functional enrichment in the biosynthesis of secondary metabolites, cofactors, amino acids, and carbohydrate-active enzymes (GHs/GTs), all likely improving tolerance to stressful environments and maintaining homeostasis. Key microbial taxa, including Candidatus Udaeobacter, Desulfovibrio, Bradyrhizobium, and Akkermansia, showed a specific dominance in high-altitude frogs, which may support host energy homeostasis and fortify gut barrier function. Multi-omics data highlighted the convergence of protective mechanisms in high-altitude frogs, including autophagy and two-component/quorum sensing systems. This study reveals significant adaptive remodeling of metabolism and gut microbiota in high-altitude R. kukunoris, providing novel insights into host-microbe synergistic interactions under extreme environments.},
}

@article {pmid40945085,
year = {2025},
author = {Wang, J and Zhang, Q and Wang, M and Li, W and Zhuang, Y and Huang, T and Yang, Z and Huang, J},
title = {Integrated field-scale natural composite oxidation pond system for livestock wastewater treatment: Microbial insights and nutrient removal dynamics.},
journal = {Ecotoxicology and environmental safety},
volume = {303},
number = {},
pages = {119026},
doi = {10.1016/j.ecoenv.2025.119026},
pmid = {40945085},
issn = {1090-2414},
abstract = {Livestock wastewater rich in organic matter, nitrogen, and phosphorus can cause eutrophication and degrade aquatic ecosystems. Current water management practices in rural areas are insufficient to meet environmental protection requirements, highlighting the urgent need for low-cost, low-energy, ecologically sustainable approaches to livestock wastewater management across diverse settings. However, current hybrid systems are often limited to lab-scale or pilot studies. Therefore, we developed a natural composite oxidation pond system, integrating biological contact, oxidation ponds, and artificial aeration, to treat piggery wastewater, while simultaneously supporting aquaculture. High-resolution in-situ monitoring, metagenomic sequencing, and partial least squares modelling were employed to assess the system's pollutant removal performance and to elucidate the underlying mechanisms. The natural composite oxidation pond systems achieved average removal efficiencies of 76.6 ± 9.5 %, 60.8 ± 23.1 %, 70.8 ± 10.4 %, 74.2 ± 11.6 %, 81.9 ± 13.0 %, and 78.9 ± 39.5 % for total phosphorus, soluble reactive phosphorus, total nitrogen, NH4[+]-N, NO3[-]-N, and NO2[-]-N, respectively (n = 72), improving water quality from inferior Class V (pond 1) to Class IV or V (pond 4 or pond 5). The removal efficiencies of soluble reactive phosphorus, NO3[-]-N, and NO2[-]-N showed significant variation with temperature (p ≤ 0.01). Proteobacteria dominated nitrogen removal through dissimilatory nitrate reduction and denitrification, with sediment microbes playing a more prominent role than water-column communities. Despite seasonal variability challenges, this closed-loop system provides a sustainable, dual-purpose approach to rural wastewater treatment and resource recovery.},
}

@article {pmid40944761,
year = {2025},
author = {Gundogdu, A and Nalbantoglu, OU and Ulgen, M and Sav, MA and Ekinci, G and Kelestimur, F and Türe, U},
title = {Unveiling gut microbiome divergence in sellar-parasellar masses and brain tumors: A link beyond the skull.},
journal = {Neurosurgical review},
volume = {48},
number = {1},
pages = {641},
pmid = {40944761},
issn = {1437-2320},
abstract = {The gut microbiome is increasingly linked to systemic health and central nervous system disorders, including brain tumors. This study investigated gut microbiome composition and metabolic profiles in patients with sellar-parasellar tumors (SPTs), other brain tumor types (OBTs) and healthy controls (HCs) to identify microbial and metabolic biomarkers for brain tumor phenotypes. A cross-sectional study involving 56 participants (17 SPTs, 11 OBTs, 28 HCs) was conducted. Gut microbiota composition was analyzed with 16 S rRNA sequencing, and metabolic activity was inferred via metagenome-scale metabolic models. Multivariable regression and machine learning were used to evaluate microbial and metabolic differences across groups. Taxonomic and metabolic analyses revealed distinct profiles across these groups. The result showed that HCs exhibited higher levels of Lachnospira and Comamonadaceae, while tumor patients had an over-representation of Bacilli. OBT patients showed elevated metabolic exchange scores (MES) for amino acids (D-alanine, L-glutamic acid), carbohydrates (mucin-type O-glycans, alpha-lactose), and lipids (stearic acid, choline), most likely reflecting tumor-associated metabolic demands. Conversely, SPT patients had profiles closer to HCs, with lower MES and reduced systemic disruption. Key taxa such as Akkermansia, Faecalibacterium, and Lachnospira demonstrated tumor-specific adaptive metabolic outputs, emphasizing functional microbial contributions over purely taxonomic roles. These findings highlight the role of gut microbiota in brain tumor progression through altered metabolic pathways, suggesting potential biomarkers and therapeutic targets for neuro- oncology. The study integrates genome-scale metabolic modeling with 16 S profiling to show that functional metabolic divergence can exist even when taxonomic differences are subtle, revealing overlooked biomarkers of the gut-brain axis in neuro-oncology.},
}

@article {pmid40943747,
year = {2025},
author = {Pasricha, ND and Larco, P and Miller, D and Altamirano, DS and Rose-Nussbaumer, JR and Alfonso, EC and Amescua, G},
title = {Infectious Keratitis Management: 10-Year Update.},
journal = {Journal of clinical medicine},
volume = {14},
number = {17},
pages = {},
doi = {10.3390/jcm14175987},
pmid = {40943747},
issn = {2077-0383},
support = {1K08EY033859-05/NH/NIH HHS/United States ; Career Development Award//Research to Prevent Blindness/ ; Grant//All May See Foundation/ ; },
abstract = {Infectious keratitis (IK), including bacterial, fungal, parasitic, and viral etiologies, continues to represent a significant cause of ocular morbidity in the United States and around the world. Corneal scraping for smears and cultures remains the gold standard in diagnosing IK; however, molecular diagnoses, including metagenomic deep sequencing (MDS), are promising emerging diagnostic tools. Despite recent interest in procedural treatment such as riboflavin photoactivated chromophore corneal collagen cross-linking (PACK-CXL) and Rose Bengal photodynamic antimicrobial therapy (RB-PDAT), medical treatment advances have remained stagnant. Methods: This review highlights IK pathogens obtained from corneal cultures at Bascom Palmer Eye Institute (BPEI) from 2011 to 2021 and provides the current BPEI algorithms for initial management of IK or as a referred clinically worsening patient. The roles of corticosteroid therapy, PACK-CXL, and RB-PDAT for IK are also summarized. Results: A total of 9326 corneal cultures were performed at BPEI between 2011 and 2021, and only 3609 (38.7%) had a positive organism identified, of which bacteria were the most common (83.4%). Fortified vancomycin and tobramycin are recommended as first-line medical therapy for IK patients based on culture sensitivity data for the top Gram-negative (Pseudomonas aeruginosa) and Gram-positive (Staphylococcus aureus) bacteria. PACK-CXL and RB-PDAT may benefit IK patients with corneal melting and fungal IK, respectively. Conclusions: Drug holidays, minimizing contamination, and optimizing sample order are crucial to maximizing corneal culture positivity. PACK-CXL and RB-PDAT are promising procedural advancements for IK therapy.},
}

@article {pmid40943646,
year = {2025},
author = {Kovenskiy, A and Katkenov, N and Ramazanova, A and Vinogradova, E and Jarmukhanov, Z and Mukhatayev, Z and Kushugulova, A},
title = {Bacteroides fragilis and Microbacterium as Microbial Signatures in Hashimoto's Thyroiditis.},
journal = {International journal of molecular sciences},
volume = {26},
number = {17},
pages = {},
doi = {10.3390/ijms26178724},
pmid = {40943646},
issn = {1422-0067},
support = {AP19675503//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; },
abstract = {Hashimoto's thyroiditis (HT) and alopecia areata (AA) are organ-specific autoimmune diseases that frequently co-occur, suggesting shared immunological and microbial pathways. The gut microbiome has emerged as a key modulator of immune function, yet disease-specific microbial signatures remain poorly defined. Fecal samples from 51 participants (HT: n = 16, AA: n = 17, healthy controls: n = 18) aged 18-65 years were analyzed using shotgun metagenomic sequencing followed by multivariate statistical analyses. While alpha and beta diversity did not differ significantly across groups, taxonomic profiling revealed disease-specific microbial patterns. Bacteroides fragilis was significantly enriched in HT, suggesting a potential role in immune modulation; although mechanisms such as polysaccharide A production and molecular mimicry have been proposed in previous studies, their involvement in HT remains to be confirmed. Microbacterium sp. T32 was elevated in both HT and AA, indicating its potential as a shared autoimmune marker. Functional analysis showed increased fermentation and amino acid biosynthesis in AA, contrasting with reduced metabolic activity and elevated carbohydrate biosynthesis in HT. HT and AA exhibit distinct gut microbial and metabolic signatures. Bacteroides fragilis and Microbacterium sp. T32 may serve as potential microbial correlates for autoimmune activity, offering new insights into disease pathogenesis and targets for microbiome-based interventions.},
}

@article {pmid40943581,
year = {2025},
author = {Gałęcki, R and Nowak, A and Szulc, J},
title = {Tenebrio molitor Meal-Induced Changes in Rat Gut Microbiota: Microbiological and Metagenomic Findings.},
journal = {International journal of molecular sciences},
volume = {26},
number = {17},
pages = {},
doi = {10.3390/ijms26178663},
pmid = {40943581},
issn = {1422-0067},
support = {LIDER/5/0029/ L-12/20/NCBR/2021//National Centre for Research and Development/ ; },
abstract = {As demand for sustainable protein sources grows, edible insects like Tenebrio molitor (yellow mealworm) are gaining attention as functional feed ingredients. This study investigated how dietary inclusion of T. molitor meal affects gut microbiota composition and diversity in laboratory rats. Wistar rats were divided into three diet groups: standard feed, 35% chicken meal, and 35% T. molitor meal. Fecal samples were collected at weeks 4, 6, and 8. Microbial populations were assessed using culture-based methods, and community structure was analyzed at week 9 via Illumina MiSeq 16S rRNA sequencing. Bioinformatic analyses evaluated microbial diversity and predicted functions. Rats fed T. molitor meal showed significantly reduced counts of total aerobic/anaerobic bacteria, fungi, and coagulase-positive staphylococci. Metagenomics revealed a Firmicutes-dominated microbiota, with enrichment of protein- and cholesterol-metabolizing taxa (e.g., Eubacterium coprostanoligenes, Oscillospiraceae, Ruminococcaceae), and a decline in fiber- and mucin-degrading bacteria like Akkermansia and Muribaculaceae. Functional predictions indicated upregulated amino acid metabolism and chitin degradation. Despite compositional shifts, microbial diversity remained stable, with no signs of dysbiosis. These findings suggest that T. molitor meal supports a safe, functional adaptation of gut microbiota to high-protein, chitin-rich diets, supporting its potential use in monogastric animal nutrition.},
}

@article {pmid40943207,
year = {2025},
author = {Gilyazova, I and Korytina, G and Kochetova, O and Savelieva, O and Mikhaylova, E and Vershinina, Z and Chumakova, A and Markelov, V and Abdeeva, G and Karunas, A and Khusnutdinova, E and Gusev, O},
title = {Advances in Genomics and Postgenomics in Poultry Science: Current Achievements and Future Directions.},
journal = {International journal of molecular sciences},
volume = {26},
number = {17},
pages = {},
doi = {10.3390/ijms26178285},
pmid = {40943207},
issn = {1422-0067},
support = {№ 075-15-2025-484//Government of Russian Federation/ ; },
abstract = {The poultry industry, a globally fast growing agricultural sector, provides affordable animal protein due to high efficiency. Gallus gallus domesticus are the most common domestic birds. Hybrid chicken breeds (crosses) are widely used to achieve high productivity. Maintaining industry competitiveness requires constant genetic selection of parent stock to improve performance traits. Genetic studies, which are essential in modern breeding programs, help identify genome variants linked to economically important traits and preserve population health. Next-generation sequencing (NGS) has identified millions of single nucleotide polymorphisms (SNPs) and insertions/deletions (INDELs), enabling detection of genome-wide regions associated with selection traits. Recent studies have pinpointed such regions using broiler lines, laying hen lines, or pooled genomic data. This review discusses advances in chicken genomic and transcriptomic research focused on traits enhancing meat breed performance and reproductive abilities. Special attention is given to transcriptome studies revealing regulatory mechanisms and key signaling pathways involved in artificial molting, as well as metagenome studies investigating resistance to infectious diseases and climate adaptation. Finally, a dedicated section highlights CRISPR/Cas genomic editing techniques for targeted genome modification in chicken genomics.},
}

@article {pmid40943165,
year = {2025},
author = {Wang, R and Ren, W and Liu, S and Li, Z and Li, L and Ma, S and Yao, X and Meng, J and Zeng, Y and Wang, J},
title = {Metagenomic Analysis Reveals the Anti-Inflammatory Properties of Mare Milk.},
journal = {International journal of molecular sciences},
volume = {26},
number = {17},
pages = {},
doi = {10.3390/ijms26178239},
pmid = {40943165},
issn = {1422-0067},
support = {2022A02007-1 and ZYYD2025JD02.//Xinjiang Uygur Autonomous Region Major Science and Technology Special Project and the Central Guidance for Local Science and Technology Development Fund/ ; },
abstract = {This study aimed to assess the anti-inflammatory properties of mare milk by analyzing immune markers in mice following gavage of mare milk. Metagenomic sequencing was employed to examine variations in the composition and functional profiles of the intestinal microbiota across different experimental groups. Bacterial diversity, abundance, and functional annotations of gut microbiota were evaluated for each group. The results show that, compared to the control group, the mare milk group exhibited a significant decrease in the pro-inflammatory cytokine IL-6 levels and a significant increase in secretory immunoglobulin A (SIgA) levels (p < 0.05). The fermented mare milk group and the pasteurized fermented mare milk group demonstrated a significant downregulation of the pro-inflammatory cytokines TNF-α and IL-1β, along with a significant increase in the anti-inflammatory cytokine IL-10 levels (p < 0.05). Additionally, metagenomic analysis revealed that both the mare milk and fermented mare milk groups were able to regulate the imbalance of the intestinal microenvironment by improving the diversity of the gut microbiota and reshaping its structure. Specifically, the mare milk group enhanced gut barrier function by increasing the abundance of Bacteroides acidifaciens, while the fermented mare milk group increased the proportion of Bacillota and the relative abundance of beneficial bacterial genera such as Faecalibaculum and Bifidobacterium. KEGG pathway annotation highlighted prominent functions related to carbohydrate and amino acid metabolism, followed by coenzyme and vitamin metabolism activities. In conclusion, mare milk and its fermented products demonstrate anti-inflammatory effects, particularly in modulating immune responses and inhibiting inflammatory cascades. Additionally, the administration of mare milk enhances the composition and metabolic activity of intestinal microbiota in mice, supporting intestinal microecological balance and overall gut health, and offering valuable insights for the development of mare milk-based functional foods.},
}

@article {pmid40942030,
year = {2025},
author = {Wang, W and Wei, J and Guo, Z and Bai, X and Song, Y},
title = {Reduction in ARGs and Mobile Genetic Elements Using 2-Bromoethane Sulfonate in an MFC-Powered Fenton System.},
journal = {Molecules (Basel, Switzerland)},
volume = {30},
number = {17},
pages = {},
doi = {10.3390/molecules30173502},
pmid = {40942030},
issn = {1420-3049},
support = {2025YSKY-20//Fundamental Research Funds for Central Public Welfare Scientific Research Institutes of China/ ; 2022-YRUC-01-050206-017//Joint Research Program for Ecological Conservation and High Quality Development of the Yellow River Basin/ ; },
abstract = {The integration of an MFC-powered Fenton (MFC-Fenton) system into the traditional anaerobic composting process can promote excess dewatered sludge (ES) decomposition. However, the antibiotic resistance gene (ARG) profiles in ES treated by MFC-Fenton systems remain poorly understood; in addition, the effect of adding 2-bromoethane sulfonate (BES, a methane inhibitor) during ES treatment using an MFC-Fenton system on ARG levels is largely unexplored. The present work focused on investigating the effects of BES and bioelectrochemical processes on ARG and MGE abundances and unraveling the ARG attenuation mechanism. According to our findings, adding BES promoted ARG reduction in ES in an MFC-Fenton system. The average ARG levels in the MFC-Fenton samples containing high BES contents (0.4 or 0.5 g BES/g VSS) markedly declined relative to those in samples containing lower BES levels. Moreover, macrolide transporter ATP-binding protein, macrolide-efflux protein, and macB levels markedly decreased as BES levels increased. BES supplementation and bioelectrochemical assistance were crucial for altering the ARG composition in the MFC-Fenton system. Changes in the microbial community composition had the greatest effect on the variation in ARG composition. Furthermore, the Actinobacteria and Firmicutes levels accounted for 52.8% of the overall ARG variation. Among MGEs, plasmids, insertion sequences, and integrons showed lower levels within the sludge metagenomes. Typically, sulI, sulII, tetG, and bla TEM levels were positively correlated with metal resistance genes (MRGs), and their levels markedly declined following the MFC-Fenton process. Thus, the collective evidence indicates that BES synergizes with bioelectrogenesis to reduce ARG abundance.},
}

@article {pmid40941824,
year = {2025},
author = {Fernández-Pastrana, VM and González-Reguero, D and Robas-Mora, M and Penalba-Iglesias, D and Alonso-Torreiro, P and Probanza, A and Jiménez-Gómez, PA},
title = {Biotechnological Test of Plant Growth-Promoting Bacteria Strains for Synthesis of Valorized Wastewater as Biofertilizer for Silvicultural Production of Holm Oak (Quercus ilex L.).},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {17},
pages = {},
doi = {10.3390/plants14172654},
pmid = {40941824},
issn = {2223-7747},
abstract = {The degradation of Mediterranean forest ecosystems, such as holm oak forests, has intensified in recent decades due to climate change, forest fires, and deforestation, compromising the natural regeneration of the soil. In this context, it is essential to apply sustainable strategies to restore soil and promote plant growth, thus helping the regeneration of the ecosystem. One of these strategies is the use of plant growth-promoting bacteria (PGPB) in combination with recovered organic waste, such as that from wastewater treatment plants (WWTPs). In this paper, the effects of a biofertilizer formulated from WWTP residue (with and without sterilization), supplemented with two PGPB strains (Bacillus pretiosus and Pseudomonas agronomica), on the growth of holm oak seedlings (Quercus ilex) were evaluated under field conditions. A study was carried out on its nutritional composition, the rhizospheric cenoantibiogram, and its functional and taxonomic microbial diversity. Nine combinations of chemical and biological treatments using irrigation with water as a control were compared. The results showed that treatments with WWTP, especially combined with PGPB strains, promoted greater plant development and a lower seedling mortality rate. The cenoantibiogram exhibited a reduction in the resistance profile in soils treated with biofertilizer, without affecting soil microbial diversity, which remained unaltered across treatments, as confirmed by metagenomic and functional diversity analyses. Overall, this research reinforces the viability of the use of biofertilizers recovered from WWTP as an ecological and effective strategy for the recovery of degraded holm oak forests.},
}

@article {pmid40941779,
year = {2025},
author = {Belevich, TA and Milyutina, IA and Demidov, AB and Vorob'eva, OV and Polukhin, AA and Shchuka, SA and Troitsky, AV},
title = {Distribution and Phylogenetic Diversity of Synechococcus-like Cyanobacteria in the Late Autumn Picophytoplankton of the Kara Sea: The Role of Atlantic and Riverine Water Masses.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {17},
pages = {},
doi = {10.3390/plants14172614},
pmid = {40941779},
issn = {2223-7747},
support = {24-24-00022//Russian Science Foundation/ ; },
abstract = {Increased Atlantic water transport and river discharge are more pronounced effects of global warming at high latitudes. Both phenomena may lead to changes in the species composition of small-celled algae populations in marine ecosystems, as well as to the emergence of new species. This study investigated the spatial distribution of picocyanobacterial (PC) abundance and the phylogenetic diversity of PC Synechococcus in the Kara Sea. PC abundance varied from 2 to 88 cells mL[-1] and increased with warming temperatures and decreasing salinity caused by river water influence. The contribution of Synechococcus to the total picophytoplankton biomass was low (<16%). The Synechococcus community was characterized at deep taxonomic level using amplicon sequencing targeting the petB gene. Diversity was low, revealing only Synechococcus subcluster 5.1 polar lineages I and IV, and euryhaline subcluster 5.2. Synechococcus subcluster 5.1.I represented on average 97% of the total reads assigned to cyanobacteria. For the first time, the presence of estuarine Synechococcus subcluster 5.2 was documented as far north as 82° N. Modified Atlantic water was the main source of cyanobacteria in the Kara Sea, followed by river discharge. Our study contributes to the understanding of PC sources in the Kara Sea and allows for the further monitoring of PC distribution and evolution.},
}

@article {pmid40941733,
year = {2025},
author = {Alatawi, AD and Hetta, HF and Ali, MAS and Ramadan, YN and Alaqyli, AB and Alansari, WK and Aldhaheri, NH and Bin Selim, TA and Merdad, SA and Alharbi, MO and Alatawi, WAH and Algammal, AM},
title = {Diagnostic Innovations to Combat Antibiotic Resistance in Critical Care: Tools for Targeted Therapy and Stewardship.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {15},
number = {17},
pages = {},
doi = {10.3390/diagnostics15172244},
pmid = {40941733},
issn = {2075-4418},
abstract = {Antibiotic resistance is a growing global health threat, with critical care settings representing one of the most vulnerable arenas due to the high burden of infection and frequent empirical antibiotic use. Rapid and precise diagnosis of infectious pathogens is crucial for initiating appropriate therapy, minimizing unnecessary antimicrobial exposure, and supporting effective stewardship programs. This review explores how innovative diagnostic technologies are reshaping infection management and antimicrobial stewardship in critical care. We examine the clinical utility of molecular assays, multiplex PCR, MALDI-TOF mass spectrometry, metagenomic sequencing, point-of-care (POC) diagnostics, and emerging tools like biosensors and AI-powered predictive models. These platforms enable earlier pathogen identification and resistance profiling, facilitating timely and targeted therapy while minimizing unnecessary broad-spectrum antibiotic use. By integrating diagnostics into stewardship frameworks, clinicians can optimize antimicrobial regimens, improve patient outcomes, and reduce resistance selection pressure. Despite their promise, adoption is challenged by cost, infrastructure, interpretation complexity, and inequitable access, particularly in low-resource settings. Future perspectives emphasize the need for scalable, AI-enhanced, and globally accessible diagnostic solutions. In bridging innovation with clinical application, diagnostic advancements can serve as pivotal tools in the global effort to curb antimicrobial resistance in critical care environments.},
}

@article {pmid40941729,
year = {2025},
author = {Hu, L and Li, X and Liu, D and Yao, J and Li, X and Wang, Y},
title = {Beyond the Urogenital Tract, the Role of Ureaplasma parvum in Invasive Infection in Adults: A Case Series and Literature Review.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {15},
number = {17},
pages = {},
doi = {10.3390/diagnostics15172242},
pmid = {40941729},
issn = {2075-4418},
abstract = {Background/Objectives: Ureaplasma parvum (Up) is an opportunistic pathogen associated with urogenital tract infections, pregnancy complications, and reproductive system diseases. Advances in molecular diagnostics have expanded its pathogenic spectrum to include invasive conditions such as arthritis, meningitis, and pneumonia. However, the pathogenic significance of Up remains controversial. Methods: This study retrospectively analyzed nine adult cases of Up detected by metagenomic next-generation sequencing (mNGS) between 2023 and 2024. Results: Patients, aged 21 to 70 years, predominantly had underlying immunosuppressive conditions (66.7%). Infections involved the urinary system (44.4%), respiratory system (33.3%), and peritoneal cavity (22.2%). Symptomatic relief was achieved in five cases following treatment with tetracyclines, quinolones or tigecycline. Conclusions: These findings highlight Up as a potential causative agent of invasive infections, particularly in immunocompromised patients. Up has potential pathogenic significance, whether it is detected as a single pathogen or as a coexisting pathogen.},
}

@article {pmid40941705,
year = {2025},
author = {Wang, Q and Ling, Y and Huang, Y and Zhao, L and Lou, Z and Fan, G and Xue, J},
title = {An Unveiling of the Misdiagnosis of Granulomatosis with Polyangiitis as Acute Sinusitis: A Case Report.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {15},
number = {17},
pages = {},
doi = {10.3390/diagnostics15172218},
pmid = {40941705},
issn = {2075-4418},
abstract = {Background and Clinical Significance: Granulomatosis with polyangiitis (GPA), an immune-mediated systemic small-vessel vasculitis affecting the upper/lower respiratory tracts and kidneys, frequently presents with non-specific nasal symptoms that lead to misdiagnosis. Case Presentation: We report a case of a 55-year-old female with GPA complicated by Bartter syndrome. She presented with one month of left nasal congestion, rhinorrhea, epistaxis, and headache. Initial diagnosis was acute sinusitis. Computed tomography (CT) revealed left maxillary and ethmoid sinus inflammation with bone destruction, while metagenomic next-generation sequencing (mNGS) suggested conventional bacterial infection. Postoperative pathology demonstrated chronic mucosal inflammation with lymphoid tissue hyperplasia. GPA was ultimately diagnosed based on PR3-ANCA seropositivity and chest CT findings of cavitary pulmonary nodules. Postoperatively, severe hypokalemia and hypomagnesemia secondary to Bartter syndrome emerged. Following electrolyte correction, induction therapy with glucocorticoids and cyclophosphamide was initiated. Conclusions: This case underscores that GPA's head and neck manifestations are frequently misdiagnosed as infections or malignancies. Early diagnosis requires vigilance for GPA 'red flags', such as refractory nasal symptoms to conventional therapy (e.g., bloody rhinorrhea), characteristic CT findings (e.g., sinus opacification without ostiomeatal complex obstruction), and nasal endoscopy findings (e.g., ulcers/crusting). Otolaryngologists play a pivotal role in recognizing early disease onset and initiating timely treatment.},
}

@article {pmid40941662,
year = {2025},
author = {Papa Mze, N and Fernand-Laurent, C and Maxence, S and Zanzouri, O and Daugabel, S and Marque Juillet, S},
title = {Optimization of 16S RNA Sequencing and Evaluation of Metagenomic Analysis with Kraken 2 and KrakenUniq.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {15},
number = {17},
pages = {},
doi = {10.3390/diagnostics15172175},
pmid = {40941662},
issn = {2075-4418},
abstract = {Background/Objectives: 16S ribosomal RNA sequencing has, for several years, been the main means of identifying bacterial and archaeal species. Low-throughput Sanger sequencing is often used for the detection and identification of microbial species, but this technique has several limitations. The use of high-throughput sequencers may be a good alternative to improve patient identification, especially for polyclonal infections and management. Kraken 2 and KrakenUniq are free, high-throughput tools providing a very rapid and accurate classification for metagenomic analyses. However, Kraken 2 can present false-positive results relative to KrakenUniq, which can be limiting in hospital settings requiring high levels of accuracy. The aim of this study was to establish an alternative next-generation sequencing technique to replace Sanger sequencing and to confirm that KrakenUniq is an excellent analysis tool that does not present false results relative to Kraken 2. Methods: DNA was extracted from reference bacterial samples for Laboratory Quality Controls (QCMDs) and the V2-V3 and V3-V4 regions of the 16S ribosomal gene were amplified. Amplified products were sequenced with the Illumina 16S Metagenomic Sequencing protocol with minor modifications to adapt and sequence an Illumina 16S library with a small 500-cycle nano-flow cell. The raw files (Fastq) were analyzed on a commercial Smartgene platform for comparison with Kraken 2 and KrakenUniq results. KrakenUniq was used with a standard bacterial database and with the 16S-specific Silva138, RDP11.5, and Greengenes 13.5 databases. Results: Seven of the eight (87.5%) QCMDs were correctly sequenced and identified by Sanger sequencing. The remaining QCMD, QCMD6, could not be identified through Sanger sequencing. All QCMDs were correctly sequenced and identified by MiSeq with the commercial Smartgene analysis platform. QCMD6 contained two bacteria, Acinetobacter and Klebsiella. KrakenUniq identification results were identical to those of Smartgene, whereas Kraken 2 yielded 25% false-positive results. Conclusions: If Sanger identification fails, MiSeq with a small nano-flow cell is a very good alternative for the identification of bacterial species. KrakenUniq is a free, fast, and easy-to-use tool for identifying and classifying bacterial infections.},
}

@article {pmid40941485,
year = {2025},
author = {Wright, SL and Slusanschi, O and Giura, AC and Părlătescu, I and Funieru, C and Gaidula, SM and Moore, NE and Weyrich, LS},
title = {SANA-Biome: A Protocol for a Cross-Sectional Study on Oral Health, Diet, and the Oral Microbiome in Romania.},
journal = {Healthcare (Basel, Switzerland)},
volume = {13},
number = {17},
pages = {},
doi = {10.3390/healthcare13172133},
pmid = {40941485},
issn = {2227-9032},
abstract = {Periodontal disease is a widespread chronic condition linked to systemic illnesses such as cardiovascular disease, diabetes, and adverse pregnancy outcomes. Despite its global burden, population-specific studies on its risk factors remain limited, particularly in Central and Eastern Europe. The SANA-biome Project is a cross-sectional, community-based study designed to investigate the biological and social determinants of periodontal disease in Romania, a country with disproportionately high oral disease rates and minimal microbiome data. This protocol will integrate metagenomic, proteomic, and metabolomic data of the oral microbiome from saliva and dental calculus samples with detailed sociodemographic and lifestyle data collected through a structured 44-question survey. This study is grounded in two complementary frameworks: the IMPEDE model, which conceptualizes inflammation as both a driver and a consequence of microbial dysbiosis, and Ecosocial Theory, which situates disease within social and structural contexts. Our aims are as follows: (1) to identify lifestyle and behavioral predictors of periodontal disease; (2) to characterize the oral microbiome in individuals with and without periodontal disease; and (3) to evaluate the predictive value of combined microbial and sociodemographic features using statistical and machine learning approaches. Power calculations based on pilot data indicate a target enrollment of 120 participants. This integrative approach will help disentangle the complex interplay between microbiological and structural determinants of periodontal disease and inform culturally relevant prevention strategies. By focusing on an underrepresented population, this work contributes to a more equitable and interdisciplinary model of oral health research and supports the development of future precision public health interventions.},
}

@article {pmid40941346,
year = {2025},
author = {Ishii, PE and Teixeira, FA and Lin, CY and Naqvi, SA and Sardi, MI and Norton, SA and Jarett, JK and Khafipour, E and Frantz, N and Chakrabarti, A and Suchodolski, JS},
title = {Effects of a Saccharomyces cerevisiae Fermentation Product on Diet Palatability and Feline Intestinal Health, Immunity, and Microbiome.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {17},
pages = {},
doi = {10.3390/ani15172551},
pmid = {40941346},
issn = {2076-2615},
abstract = {This study evaluated the effects of adding a Saccharomyces cerevisiae fermentation product (SCFP) to adult cat diets on palatability, intestinal health, nutrient digestibility, immune parameters, and the fecal microbiome over 42 days. Sixty-three healthy Domestic Short-hair cats were randomized to three diets: a control diet (CD) without SCFP, or the same diet containing 1.0% or 2.0% SCFP, targeting daily intakes of 150 or 300 mg/kg body weight, respectively. Body weight and blood parameters remained within reference ranges across all groups. Stool quality was largely not affected, although compared with controls, SCFP-supplemented cats had slightly firmer stools at day 21, and increased fecal pH. Shotgun metagenomic sequencing revealed that microbiome diversity remained steady in SCFP-fed cats, whereas diversity in the control group declined over time. Fecal immunoglobulin A concentrations were lower in cats supplemented with SCFP at 150 mg/kg BW by the end of the study, and positive shifts in the circulatory leukocyte profile were observed at both inclusion levels. Apparent total tract macronutrient digestibility did not differ among groups. Palatability tests showed diets with SCFP were generally preferred, indicating a potential benefit for commercial feline feeds, particularly at the 150 mg/kg BW level, which was preferred over 300 mg/kg BW. Overall, these findings suggest that SCFP can act as a functional ingredient in feline nutrition to maintain microbial diversity and enhance diet acceptance without compromising digestibility.},
}

@article {pmid40941237,
year = {2025},
author = {Xu, P and He, Y and Wang, J and Sheng, Y and Wang, J},
title = {Blueberry Anthocyanins Ameliorate Hepatic Dysfunction in High-Fat Diet-Fed Mice: Association with Altered Gut Microbiota and Bile Acid Metabolism.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {17},
pages = {},
doi = {10.3390/foods14173121},
pmid = {40941237},
issn = {2304-8158},
support = {2021DG700024-KF202407//open project titled "Identification of Anti-Damage Functional Factors in Anoectochilus roxburghii and Their Mechanisms of Action"/ ; },
abstract = {The rapid rise in obesity has evolved into a critical global public health concern. Considering the potential adverse effects of current anti-obesity medications, the development of functional foods sourced from natural materials has emerged as a viable alternative. Blueberries, a category of berry fruits, exhibit potential anti-obesity characteristics. In this research, we assessed the impacts of Blueberry extract rich in anthocyanins (BE) on lipid metabolism and liver health in a high-fat diet (HFD)-induced obese mouse model. The findings indicated that BE notably diminished lipid accumulation in both serum and the liver, and mitigated hepatic steatosis and oxidative stress. Integrated proteomic, metagenomic, and metabolomic analyses further revealed the underlying mechanisms. Consumption of BE intake reconfigured the gut microbiota composition and reduced the microbial capacity for secondary bile acid metabolism, thereby interrupting bile acid recycling and facilitating fecal excretion. This process led to a reduction in systemic cholesterol levels and ultimately alleviated hepatic lipid accumulation, resulting in enhanced liver health.},
}

@article {pmid40941211,
year = {2025},
author = {Yu, Z and Zhao, H and Ma, T and Zhang, X and Yan, Y and Zhu, Y and Yu, Y},
title = {Insights into the Composition and Function of Virus Communities During Acetic Acid Fermentation of Shanxi Aged Vinegar.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {17},
pages = {},
doi = {10.3390/foods14173095},
pmid = {40941211},
issn = {2304-8158},
support = {2023M741438//China Postdoctoral Science Foundation/ ; 20220401931002//Open Project Program of Shanxi Provincial Key Laboratory for Vinegar Fermentation Science and Engineering/ ; },
abstract = {Viruses play a regulatory role in microbial ecology. Traditional fermented foods have complex fermentation environments with abundant viral participation, yet current research on viral communities in fermented foods remains insufficient. Traditional, manually produced solid-state fermented vinegar serves as an excellent model for studying the role of viral communities in fermented foods. Using metagenomic approaches, this study investigates the structure and dynamics of viral communities during the acetic acid fermentation process of Shanxi aged vinegar. All identified viruses were bacteriophages, and the dominant families were identified as Herelleviridae, Autographiviridae, and Stanwilliamsviridae. The richness and diversity of viral communities exhibited significant variations during acetic acid fermentation. Furthermore, correlation analysis revealed a strong association (p < 0.01) between core bacteria and core viruses. Functional annotation revealed the presence of viral genes associated with amino acid and carbohydrate metabolism. Notably, abundant auxiliary carbohydrate-active enzyme (CAZyme) genes were identified in viruses, with glycoside hydrolases (GHs), glycosyltransferases (GTs), and carbohydrate-binding modules (CBMs) demonstrating particularly high abundance. Additionally, several antibiotic resistance genes were detected in viruses. This study elucidates the impact of viral communities on microbial dynamics during food fermentation, advancing our understanding of viral roles in traditional fermented food ecosystems.},
}

@article {pmid40941207,
year = {2025},
author = {Kyoung, M and Lee, JI and Kim, SS},
title = {Effects of UVC Treatment on Biofilms of Escherichia coli Strains Formed at Different Temperatures and Maturation Periods.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {17},
pages = {},
doi = {10.3390/foods14173091},
pmid = {40941207},
issn = {2304-8158},
abstract = {In the present study, the biofilm formation and ultraviolet-C (UVC) resistance characteristics of Escherichia coli isolated from an occluded biliary stent were compared with those of four E. coli O157:H7 strains (ATCC 35150, 43889, 43890, and 43895). To evaluate biofilm formation, the E. coli isolated from a stent and four E. coli O157:H7 strains were incubated at 37, 25, and 15 °C for 7 days, revealing that peak biofilm formation occurred at 37 °C (day 1), 25 °C (day 3), and 15 °C (day 5), with the stent-isolated strain consistently exhibiting significantly higher biofilm cell counts than the others (p < 0.05). The UVC treatment was less effective at reducing viable biofilm cells as the formation temperature decreased, with the stent-isolated E. coli biofilm formed at 15 °C showing the lowest reduction levels. Exopolysaccharide quantification revealed that all E. coli strains produced more extracellular polymeric substances (EPSs) at lower temperatures, with the stent-isolated E. coli biofilm formed at 15 °C showing significantly higher EPS levels than the other strains (p < 0.05), potentially explaining its greater UVC resistance. Based on these results, it was confirmed that the biofilm formed by the E. coli isolated from the stent at 15 °C exhibited the highest resistance to UVC, which can be attributed to its elevated exopolysaccharide production. This study demonstrates that both temperature and maturation period significantly influence E. coli biofilm characteristics and provides valuable insights into E. coli isolated from the stent, which may pose a risk of cross-contamination in food-related environments.},
}

@article {pmid40941186,
year = {2025},
author = {Dissook, S and Thongkumkoon, P and Noisagul, P and Sriaporn, C and Suwannapat, S and Pramoonchakko, W and Suksawat, M and Kulthawatsiri, T and Phetcharaburanin, J and Chewonarin, T and Ruangsuriya, J},
title = {Insights into Microbial and Metabolite Profiles in Traditional Northern Thai Fermented Soybean (Tuanao) Fermentation Through Metagenomics and Metabolomics.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {17},
pages = {},
doi = {10.3390/foods14173070},
pmid = {40941186},
issn = {2304-8158},
support = {FF66/023//Fundamental Fund 2023, Chiang Mai University/ ; },
abstract = {Tuanao, a traditional Northern Thai fermented soybean product, was profiled with an integrated multi-omics workflow to clarify how microbes and metabolites co-evolve during household fermentation. Soybeans were fermented spontaneously for three days; samples from four time points were analyzed by shotgun metagenomics alongside 1H-NMR and UHPLC-ESI-QTOF-MS/MS metabolomics. Bacillus spp. (phylum Bacilliota) quickly supplanted early Enterobacterales and dominated the mature microbiome. The rise of Bacillus coincided with genes for peptide and carbohydrate utilization and with the accumulation of acetate, free amino acids (glutamine, leucine, alanine, valine) and diverse oligopeptides, whereas citrate and glucose-1-phosphate were depleted. This Bacillus-linked metabolic shift indicates that Tuanao is a promising source of probiotics and bioactive compounds. Our study provides the first system-level view of Tuanao fermentation and offers molecular markers to guide starter-culture design and quality control.},
}

@article {pmid40940618,
year = {2025},
author = {Valiauga, B and Žulpaitė, D and Sharrock, AV and Ackerley, DF and Čėnas, N},
title = {Novel TdsD nitroreductase: characterization of kinetics and substrate specificity.},
journal = {Biotechnology letters},
volume = {47},
number = {5},
pages = {103},
pmid = {40940618},
issn = {1573-6776},
abstract = {The reduction of quinones and nitroaromatic compounds catalyzed by Type I nitroreductases is important due to its role in their potential cytotoxic effects and/or biodegradation. The main goal of this work was to investigate the mechanism of catalysis of a TdsD nitroreductase (NR) (TdsD1), a member from an understudied branch of the nitroreductase superfamily, derived from a soil metagenome study. Like the Type I NRs NfsA and NfsB, TdsD1 performed two-electron reduction of quinones and four-electron reduction of nitroaromatic compounds according to a "ping-pong" mechanism with a rate-limiting oxidative half-reaction. TdsD1 was also inhibited by the classical inhibitors of other NRs, dicoumarol and Cibacron blue. Despite sharing only a low degree of homology with the NfsA and NfsB subfamily enzymes, sequence comparisons and computer modelling point to the possibility of an analogous FMN isoalloxazine ring location within the intersubunit space of TdsD1. It also possesses similar specificity for nitroaromatic compounds and quinones, in particular the shared characteristic of being especially active with 2-hydroxy-1,4-naphthoquinone derivatives. It is possible that the similar character of binding of oxidants and other ligands relative to the NfsA and NfsB subfamily enzymes may be related to the conserved Arg27 and Ser53 residues in the active site of TdsD1.},
}

@article {pmid40940575,
year = {2025},
author = {Abenaim, L and Mercati, D and Mandoli, A and Carpentier, J and Noël, G and Conti, B and Caparros Megido, R and Dallai, R},
title = {Exploring the plastivorous activity of Hermetia illucens (Diptera Stratiomyidae) larvae.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {40940575},
issn = {1614-7499},
abstract = {Hermetia illucens (Diptera Stratiomyidae), also known as Black Soldier Fly (BSF), is one of the insect species most investigated for biodegradation ability in its larvae. H. illucens larvae can biodegrade organic waste but also contaminants like pesticides, antibiotics, and mycotoxins. This study wants to investigate the ability of these larvae to degrade polystyrene (PS). Experiments evaluated the growth performance, survival rates, intestinal and intracellular morphological alterations, degradation by-product formation and intestinal microbiota alterations of larvae fed a PS-enriched diet. Despite the addition of PS microparticles, no significant differences in growth or survival were observed compared to the standard diet (p > 0.05). Confocal Laser Scanning Microscopy and Transmission Electron Microscopy confirmed the presence of PS microparticles in the larval gut, with potential signs of biodegradation. Metabolomic analyses identified styrene in the gut after 1 and 3 days of PS feeding, but its occurrence was likely due to thermal depolymerisation of the PS microparticles under GC-MS conditions. Metagenomic analysis revealed significant shifts in the intestinal microbiota. Notably, an enrichment of Corynebacterium, known for its role in aerobic PS degradation, and the abundance increase of other genera (Enterococcus, Enterobacteriaceae, Enterobacter, and Escherichia-Shigella) associated with synthetic polymer metabolism was observed. These results confirm the potential of BSF larvae to manage plastic waste through the interaction between their gut microbiota and synthetic materials. This study provides a foundation for future research focusing on isolating bacterial communities and enzymatic processes involved in polymer degradation, aiming to develop sustainable strategies for plastic waste management.},
}

@article {pmid40940533,
year = {2025},
author = {Burian, J and Boer, RE and Hernandez, Y and Morales-Amador, A and Jiang, L and Bhattacharjee, A and Panfil, C and Ternei, MA and Brady, SF},
title = {Bioactive molecules unearthed by terabase-scale long-read sequencing of a soil metagenome.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {40940533},
issn = {1546-1696},
support = {R35GM122559//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; },
abstract = {Metagenomics provides access to the genetic diversity of uncultured bacteria through analysis of DNA extracted from whole microbial communities. Long-read sequencing is advancing metagenomic discovery by generating larger DNA assemblies than previously possible. However, harnessing the potential of long-read sequencing to access the vast diversity within soil microbiomes is hampered by the challenge of isolating high-quality DNA. Here we introduce a method that can liberate large, high-quality metagenomic DNA fragments from soil bacteria and pair them with optimized nanopore long-read sequencing to generate megabase-sized assemblies. Using this method, we uncover hundreds of complete circular metagenomic genomes from a single soil sample. Through a combination of bioinformatic prediction and chemical synthesis, we convert nonribosomal peptide biosynthetic gene clusters directly into bioactive molecules, identifying antibiotics with rare modes of action and activity against multidrug-resistant pathogens. Our approach advances metagenomic access to the vast genetic diversity of the uncultured bacterial majority and provides a means to convert it to bioactive molecules.},
}

@article {pmid40940504,
year = {2025},
author = {Ruiz-Malagón, AJ and Rodríguez-Sojo, MJ and García-García, J and Ho-Plagaro, A and García, F and Vezza, T and Redondo-Cerezo, E and Griñán-Lisón, C and Marchal, JA and Rodríguez-Cabezas, ME and Rodríguez-Nogales, A and Gálvez, J},
title = {Tigecycline suppresses colon cancer stem cells and impairs tumor engraftment by targeting SNAI1-regulated epithelial-mesenchymal transition.},
journal = {Acta pharmacologica Sinica},
volume = {},
number = {},
pages = {},
pmid = {40940504},
issn = {1745-7254},
abstract = {Cancer stem cells (CSCs) play a key role in the progression of colorectal cancer (CRC). The high heterogeneity of CSCs has hindered the clinical application of CSC-targeting therapies. Tetracyclines are drugs with therapeutic potentials beyond their antibiotic activity. We previously demonstrated the efficacy of tigecycline, a third-generation tetracycline, against a model of colitis-associated colorectal cancer, primarily focusing on its immunomodulatory role with a preliminary assessment of its impact on stemness. In this study we characterize the effects of tigecycline on colon CSCs in vitro and in a CRC xenograft model, with special attention on the signaling pathways involved and the modulation of the gut microbiota. We generated secondary colonospheres from two colon tumor cell lines HCT116 and CMT93, and evaluated the effect of tigecycline on CSCs properties. We showed that tigecycline (25, 50 μM) effectively reduced colon CD133[+]CD44[+]LGR5[+]ALDH[+] subpopulations and their viability, self-renewal and migratory capacity. Moreover, tigecycline treatment hindered epithelial-mesenchymal transition (EMT) process through targeting SNAI1 and β-catenin, resulting in an upregulation of epithelial markers (E-cadherin) and a downregulation of pluripotency and mesenchymal ones (Vimentin, N-cadherin, SOX2, NANOG, MIR155, MIR146). This effect was confirmed in two independent CRC-xenograft murine models in which tigecycline administration led to a reduction in tumor volume. Finally, CRC samples were taken from HCT116 xenograft model mice for analysis of CSCs-related signaling pathways and stools were collected for gut microbiome metagenomic analysis. We found that the antibiotic modulated gut dysbiosis by increasing the abundance of beneficial bacterial species such as Parabacteroides sp., which were involved in metabolic pathways that hindered SNAI1-Wnt-β-catenin signaling. These results reinforce the new role of tigecycline in the therapy of CRC and demonstrate for the first time the effect of tigecycline on colon CSCs and their malignancies.},
}

@article {pmid40940455,
year = {2025},
author = {He, P and Wang, S and Mao, R and Jiang, M and Siegel, S and Pedretti, G and Ignowski, J and Strachan, JP and Luo, R and Li, C},
title = {Real-time raw signal genomic analysis using fully integrated memristor hardware.},
journal = {Nature computational science},
volume = {},
number = {},
pages = {},
pmid = {40940455},
issn = {2662-8457},
support = {C7003-24Y, 17207925, 27210321, C1009-22GF, T45-701/22-R, GHKU707/23//Research Grants Council, University Grants Committee (RGC, UGC)/ ; 62122005//National Science Foundation of China | National Natural Science Foundation of China-Yunnan Joint Fund (NSFC-Yunnan Joint Fund)/ ; },
abstract = {Advances in third-generation sequencing have enabled portable and real-time genomic sequencing, but real-time data processing remains a bottleneck, hampering on-site genomic analysis. These technologies generate noisy analog signals that traditionally require basecalling and read mapping, both demanding costly data movement on von Neumann hardware. Here, to overcome this, we present a memristor-based hardware-software codesign that processes raw sequencer signals directly in analog memory, combining the two separated steps. By exploiting intrinsic device noise for locality-sensitive hashing and implementing parallel approximate searches in content-addressable memory, we experimentally showcase on-site applications, including infectious disease detection and metagenomic classification on a fully integrated memristor chip. Our experimentally validated analysis confirms the effectiveness of this approach on real-world tasks, achieving a 97.15% F1 score in virus raw signal mapping, with 51× speed-up and 477× energy saving over an application-specific integrated circuit. These results demonstrate that in-memory computing hardware provides a viable solution for integration with portable sequencers, enabling real-time and on-site genomic analysis.},
}

@article {pmid40940422,
year = {2025},
author = {Kumar Nath, A and da Silva, RR and Gauvin, CC and Akpoto, E and Dlakić, M and Lawrence, CM and DuBois, JL},
title = {Commensal gut bacteria employ de-chelatase HmuS to harvest iron from heme.},
journal = {The EMBO journal},
volume = {},
number = {},
pages = {},
pmid = {40940422},
issn = {1460-2075},
support = {P30GM140963//HHS | National Institutes of Health (NIH)/ ; R35GM136390//HHS | National Institutes of Health (NIH)/ ; DBI-1828765//National Science Foundation (NSF)/ ; },
abstract = {Iron is essential for almost all organisms, which have evolved different strategies for ensuring a sufficient supply from their environment and using it in different forms, including heme. The hmu operon, primarily found in Bacteroidota and ubiquitous in gastrointestinal tract metagenomes of healthy humans, encodes proteins involved in heme acquisition. Here, we provide direct physiological, biochemical, and structural evidence for the anaerobic removal of iron from heme by HmuS, a membrane-bound, NADH-dependent de-chelatase that deconstructs heme to protoporphyrin IX (PPIX) and Fe(II). Heme can serve as the sole iron source for the model gastrointestinal bacterium Bacteroidetes thetaiotaomicron, when active HmuS is present. Heterologously expressed HmuS was isolated with bound heme molecules under saturating conditions. Its cryo-EM structure at 2.6 Å resolution revealed binding of heme and a pair of cations at distant sites. These sites are conserved across the HmuS family and chelatase superfamily, respectively. The proposed structure-based mechanism for iron removal by HmuS is chemically analogous to the chelatases in both unrelated heme biosynthetic pathways and homologous enzymes in the biosynthetic pathways for chlorophyll and vitamin B12, although the reaction proceeds in the opposite direction. Taken together, our study identifies a widespread mechanism via which anaerobic bacteria can extract nutritional iron from heme.},
}

@article {pmid40940010,
year = {2025},
author = {Ellis, EK and Ióca, LP and Liu, J and Chen, M and Bruner, SD and Ding, Y and Paul, VJ and Donia, MS and Luesch, H},
title = {Structure Determination and Biosynthesis of Dapalides A-C, Glycosylated Kahalalide F Analogues from the Marine Cyanobacterium Dapis sp.},
journal = {Journal of natural products},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jnatprod.5c00757},
pmid = {40940010},
issn = {1520-6025},
abstract = {Kahalalides were originally isolated from the marine mollusk Elysia rufescens and its green algal diet Bryopsis sp., but the true producer was revealed as the obligate bacterial symbiont Candidatus Endobryopsis kahalalidefaciens, residing within Bryopsis sp. The most notable is kahalalide F, a broad-spectrum antitumor depsipeptide that entered the clinic but failed from lack of efficacy. We have isolated three new glycosylated analogues of kahalalide F, termed dapalides A-C (1-3), from a marine cyanobacterium, Dapis sp., collected from Guam. The planar structures were determined by extensive NMR coupled with mass spectrometry. Acid hydrolysis of 1 using amino acid analysis revealed the absolute configuration of singlet and a mixture of duplicate amino acids. Metagenomic analysis unveiled a biosynthetic gene cluster (BGC) with a nonribosomal peptide synthetase (NRPS) system and downstream glycosylation enzymes, which assisted the configurational assignment through epimerization domain analysis. The discovered BGC, termed dap, was assigned to a high-quality metagenome-assembled genome of the Dapis sp. Dapalide A (1) was subjected to phenotypic bioassays and exhibited weak anticancer cytotoxicity. This discovery expands the chemical diversity of the kahalalide F family, suggests their broad ecological role across diverse organisms, and presents an intriguing case of natural product biosynthesis evolution.},
}

@article {pmid40939728,
year = {2025},
author = {de Souza, MA and Pereira, DE and da Silva, ECA and Medeiros, RG and Duarte, AM and Dutra, LMG and Araújo, DFS and de Araújo, WJ and de Oliveira, CJB and Guerra, GCB and Alves, AF and Viera, VB and Soares, JKB},
title = {Consumption of Brazilian palm fruit (Acrocomia intumescens drude) improves biochemical and gut microbiome parameters, reducing cardiovascular risk in exercised rats.},
journal = {Physiology & behavior},
volume = {},
number = {},
pages = {115102},
doi = {10.1016/j.physbeh.2025.115102},
pmid = {40939728},
issn = {1873-507X},
abstract = {OBJECTIVE: This study aimed to evaluate the effects of macaiba pulp on physical, biochemical, intestinal health, and oxidative stress parameters in exercised rats.

METHODOLOGY: Forty-four male rats were divided into four groups (n = 11): sedentary control (CT), exercised control (CT-EX), sedentary macaiba (MC), and exercised macaiba (MC-EX). MC and MC-EX groups received 1000 mg/kg/day of macaiba pulp, while CT and CT-EX received distilled water for eight weeks. Exercised animals underwent swimming for five days a week, beginning with 10 minutes and progressing to 60 minutes. Blood was collected to measure cholesterol (TC, HDL, LDL, VLDL), glucose, urea, liver enzymes (AST, ALT), and cardiovascular risk factors. Liver samples were analyzed for malonaldehyde (MDA), total fat, and cholesterol, while feces were collected for metagenome analysis. Body fat and adiposity index were also measured.

RESULTS: Macaiba-treated groups showed improved gut microbiome balance, reduced TC, LDL, VLDL, glucose, urea, liver enzymes, cardiovascular risks, body fat, MDA, and liver fat, with an increase in HDL.

CONCLUSION: Macaiba pulp effectively improved biochemical parameters, reduced lipid peroxidation from exercise, and lowered adipose tissue and cardiovascular risks.},
}

@article {pmid40939672,
year = {2025},
author = {Ai, C and He, Y and Cheng, Z and Wu, J and Liu, C and Wang, N and Yu, Z and Liao, H and Zhou, S},
title = {Unveiling of active bacteria associated with nutrient cycling during cattle manure composting.},
journal = {Environmental research},
volume = {},
number = {},
pages = {122810},
doi = {10.1016/j.envres.2025.122810},
pmid = {40939672},
issn = {1096-0953},
abstract = {Bacteria play a pivotal role in nutrient turnover during the composting process. However, studies relying on total DNA analysis for bacterial community may be confounded by the presence of extracellular DNA from dead cells. In this study, ethidium monoazide (EMA) was employed to extract intracellular DNA from composting samples for amplicon and metagenomic sequencing, enabling the assessment of active bacterial community dynamics during cattle manure composting. The results revealed that total DNA-based 16S rRNA sequencing could only represent 36.9%-81.6% of the active bacterial communities. In contrast, EMA-based 16S rRNA sequencing identified Proteobacteria as the dominant active bacterial phylum throughout the composting process, with Actinobacteria exhibiting increased activity during the maturation phase. EMA-based metagenomic sequencing further showed that carbon and nitrogen metabolism genes showed the highest activity during the initial phase. Proteobacteria were identified as key functional bacteria in nutrient turnover, with its contribution reaching 55.4% and participating in 82.1% (23/28) of metabolic pathways. Meanwhile, Firmicutes (bin-23, g_Capillibacterium, bin-66, c_Bacilli) were the sole active nitrogen-fixing bacteria, harboring nitrogenase genes (nifH and nifD). This study offers novel understandings regarding the contribution of active bacteria in nutrient turnover and highlights the importance of distinguishing between active and total bacterial communities for a better understanding of microbial processes in composting systems.},
}

@article {pmid40939661,
year = {2025},
author = {Feng, F and Zhao, C and Chen, Y and Zhang, Y and Hu, X and Mu, H and Zhang, W},
title = {Mechanistic insights into sulfidated nanoscale zero-valent iron enhanced methanogenesis: Electron redistribution and direct interspecies electron transfer-driven metabolic reconfiguration.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133300},
doi = {10.1016/j.biortech.2025.133300},
pmid = {40939661},
issn = {1873-2976},
abstract = {Sulfidated nanoscale zero-valent iron (S-nZVI) enhances methanogenesis, yet the underlying mechanisms linking its interfacial structure to microbial metabolic responses remain unclear. This study elucidated S-nZVI's role via electron redistribution, microbial syntrophy enhancement, and metabolic pathway reconfiguration. Density functional theory revealed that sulfur-induced Fe-3d and S-3p orbital coupling, bandgap opening, and valence band shift collectively improved interfacial conductivity. At 5 g·L[-1], S-nZVI increased methane yield by 15 % and 68 % over nZVI and control, respectively. It also shortened lag phase, promoted extracellular polymeric substances secretion, and shifted electron transfer from cytochrome-based to abiotic pathways. Metagenomics confirmed enrichment of direct interspecies electron transfer (DIET)-associated genera and acetoclastic methanogenesis genes. Furthermore, the in-situ formation of conductive Fe3O4 and enhanced microbe colonization collectively reinforced DIET and methanogenesis. Overall, S-nZVI facilitated electron redistribution and drove the reconfiguration of syntrophic metabolism toward more efficient methanogenesis, offering mechanistic insights into material-microbe synergy for enhanced bioenergy recovery.},
}

@article {pmid40939657,
year = {2025},
author = {Tan, HT and Lei, Y and Chek, MF and He, M and Pow, KC and Gong, S and Hao, Q and Hakoshima, T and Sudesh, K and Liu, G},
title = {Engineering chimeric polyhydroxyalkanoate synthases for enhanced copolymerization of poly(3-hydroxybutyrate-co-3-hydroxyhexanoate): A promising biotechnological approach.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133307},
doi = {10.1016/j.biortech.2025.133307},
pmid = {40939657},
issn = {1873-2976},
abstract = {The escalating health and environmental threats posed by microplastics and nanoplastics (MNPs) highlight the urgent need for sustainable alternatives like polyhydroxyalkanoates (PHAs), biodegradable polyesters synthesized by bacterial PHA synthases (PhaCs). However, natural PhaCs exhibit suboptimal substrate specificity and polymer heterogeneity, limiting industrial scalability. To address this, chimeric PhaCs were engineered by swapping N-terminal domains between PhaC from mangrove soil metagenome (PhaCBP-M-CPF4; low 3-hydroxyhexanoate [3HHx] content, fewer but larger granules) and PhaC2 of Rhodococcus aethirovorans I24 (PhaC2Ra; high 3HHx, numerous small granules). This strategy aimed to combine enhanced 3HHx incorporation with controlled granule morphology. Using structural predictions, chimeric enzymes were constructed and tested, revealing that the C-terminal domain retained compatibility with diverse N-terminal regions. The resulting chimeras exhibited improved PHA production, enhanced 3HHx incorporation, and optimized granule formation, overcoming historical challenges in chimeric enzyme design by avoiding β-strand interference. Among the chimeras, distinct strains achieved: (i) up to 200 % increase in PHA production; (ii) up to 45 mol% 3HHx incorporation; and (iii) optimized granule formation, approaching a single-granule-per-cell phenotype (mean count: 1.079) and a granule size increase of up to 7.2-fold (mean area: 1.272 µm[2]). This approach provides a robust framework for tailoring PhaCs to produce high-performance copolymers. By elucidating domain compatibility, the study advances strategies in synthetic biology for creating modular enzymes with tailored functionalities, offering transformative potential in sustainable materials, protein engineering, and innovation in biodegradable plastics.},
}

@article {pmid40939655,
year = {2025},
author = {Hu, F and Qin, J and Yang, H and Al-Dhabi, NA and Dong, Y and Bai, Z and Liu, L and Chai, F and Jin, B and Tang, W and Ji, J},
title = {An effective strategy for restoring the biofilm system of anammox/endogenous partial denitrification combined with continuous-flow partial nitration from deterioration.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133311},
doi = {10.1016/j.biortech.2025.133311},
pmid = {40939655},
issn = {1873-2976},
abstract = {Hydroxylamine supplementation has recently emerged as a potential strategy to persistent sustain partial nitration (PN), but its feasibility in the biofilm system of anammox/endogenous partial denitrification combined with continuous-flow partial nitration (SAEPD-CFPN) systems remains unexplored. Thus, this study assessed the feasibility of hydroxylamine dosing for restoring PN in continuous-flow biofilm reactor and investigated the impact of continuous-flow partial nitration (CFPN) deterioration on biofilm system of SAEPD-CFPN. Results showed that nitrogen removal efficiency (NRE) decreased from 88.86 % to 39.56 %, with the nitrite accumulation rate (NAR) dropping from 87.28 % to 34.33 % due to the deterioration of CFPN. After effective hydroxylamine dosing, the average NRE increased to 89.90 %, while the average NAR rose to 83.83 %. The SAEPD biofilm system could handle insufficient NO2[-]-N supply caused by CFPN performance insignificant deterioration; however, its effectiveness diminished when CFPN performance severely deteriorated over the long term due to lower influent COD concentrations. Metagenomic analysis revealed that CFPN recovery was attributed to the effective inhibition of Nitrobacter and NxrAB. The robustness of the SAEPD biofilm reactor against fluctuations in influent NO2[-]-N was attributable to its complex microbial community structure. Additionally, intermittent hydroxylamine dosing was proposed as a sustainable strategy to ensure stable SAEPD-CFPN biofilm process operation.},
}

@article {pmid40938427,
year = {2025},
author = {Sharma, S and Gajjar, B and Desai, C and Madamwar, D},
title = {Metagenomic analysis reveals the influence of wastewater discharge on the microbial community structures and spread of antibiotic-resistant bacteria at Mohar river, Gujarat.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {10},
pages = {1112},
pmid = {40938427},
issn = {1573-2959},
support = {GSBTM/JD(R&D)/616/21-22/1236//Gujarat State Biotechnology Mission, Department of Science and Technology, Government of Gujarat/ ; },
abstract = {An extensive use of antibiotics has evolved bacterial antimicrobial resistance (AMR) and its spread through horizontal gene transfer within microbial communities of the natural environment. The water bodies receiving wastewater from sewage treatment plant (STP) serve as a conducive reservoir for the spread of antibiotic-resistant bacteria (ARB). This study revealed occurrence of multidrug-resistant and extended spectrum β-lactamase (ESBL) producing bacteria present in STP inlet (SI1), outlet (SO1), riverine environment receiving the STP wastewater (MP1), and control site (C1) of the river Mohar, Gujarat. Microbial community analysis revealed Proteobacteria and Firmicutes as dominating phyla in water samples of Mohar River sites. Shotgun analysis showed presence of antibiotic-degrading enzymes and pathways. The resistance profiling of ARBs showed the higher resistance towards cefotaxime at MP1 (77.4%), followed by SO1 (70.5%), SI1 (64.14%), and the least at C1 (57.13%). The highest ESBL isolates were observed at MP1 (96.42%), followed by SI1 (84.51%), SO1 (80.55%), and C1 (78.57%). Moreover, the RT-qPCR analysis for abundance of intI1 gene (responsible for HGT) showed a descending pattern from SI1 to the C1. The abundance of intI1 was found to correlate positively with mercury, chromium, and chlorine, and a negative correlation was observed with arsenic. The results obtained in this research suggest that AMR spreads and evolves in the water environment via discharge of wastewaters from STPs into the river ecosystems.},
}

@article {pmid40938103,
year = {2025},
author = {Desingu, PA and Arunkumar, S and Nagarajan, K and Saikumar, G},
title = {Metagenomic detection of the complete coding regions of Tanay virus from mosquitoes (Armigeres subalbatus) in India.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0038925},
doi = {10.1128/mra.00389-25},
pmid = {40938103},
issn = {2576-098X},
abstract = {So far, the Tanay virus has only been detected in the Philippines and China. Here, we report that a complete coding region-wide virus with 3.7-16.7% nucleotide diversity to the Tanay viruses identified in China and 25.2% nucleotide diversity to those identified in the Philippines is circulating in mosquitoes (Armigeres subalbatus) in India.},
}

@article {pmid40937156,
year = {2025},
author = {Anselmi, S and Ni, Y and Tonoli, A and Wu, J and Wang, Y and Prout, L and Miodownik, M and Jeffries, JWE and Hailes, HC},
title = {The discovery of new metagenomic urethanases utilising a novel colorimetric assay for applications in the biodegradation of polyurethanes.},
journal = {Green chemistry : an international journal and green chemistry resource : GC},
volume = {},
number = {},
pages = {},
pmid = {40937156},
issn = {1463-9262},
abstract = {The enzymatic molecular recycling of plastics is of increasing interest, where polymers are converted into monomers for reuse or upcycled into value added chemicals. Polyurethanes are an important class of synthetic hydrolysable polymers found in textiles as an elastane component, also known as lycra and spandex, with most post-consumer waste currently disposed of in landfill. Here we have identified three active novel urethane hydrolytic enzymes from a drain metagenome able to breakdown methylenedianiline-based elastane model substrates. In addition, we have established a new colorimetric assay, suitable for high-throughput applications using tyrosinases. For the urethanases identified, the reaction conditions and substrate scope were explored. Finally, the urethanases and assay were used with commercial fabrics, demonstrating breakdown of the polymer.},
}

@article {pmid40936885,
year = {2025},
author = {Ye, X and Li, C and Zhou, Z and Yang, J and Jiang, H and Hu, L and Pan, H and Wei, X and Huang, Y and Lin, Y and Wang, L},
title = {Metagenomic Next-Generation Sequencing-Assisted Risk Prediction and Stratification of Infections After Kidney Transplantation: A Case Study of COVID-19.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {4763-4776},
pmid = {40936885},
issn = {1178-6973},
abstract = {BACKGROUND: During the COVID-19 pandemic, COVID-19 infection has severely damaged the transplanted kidney function and health of kidney transplant patients. This study aims to investigate the clinical characteristics, risk factors and predictors of severe COVID-19 in patients after kidney transplantation.

MATERIAL AND METHODS: The clinical data of patients with COVID-19 after kidney transplantation were collected from December 2022 to January 2023 at the First Affiliated Hospital of Soochow University. Logistic regression analysis was performed to identify risk factors for severe disease and to construct a nomogram model. Concurrently, metagenomic next-generation sequencing (mNGS) was employed to detect the sputum microbiome.

RESULTS: A total of 58 patients were enrolled and were categorized into the common group (n=35) and the severe group (n=23) based on infection severity. The common group comprised 23 males with a mean age of 45.60 ± 9.11 years, while the severe group included 16 males with a mean age of 48.22 ± 9.95 years. Multivariate logistic analysis revealed that days of fever before hospitalization, C-reactive protein (CRP) and interleukin-10 (IL-10) on admission were significantly independent risk factors for severity, with an area under the ROC curve at 0.906. Comparison of the sputum microbiome revealed that there were no significant differences in α and β diversity between the two groups. Streptococcus parasanguinis was significantly more abundant in the specimens from the severe group, while Gemella sanguinis and Gemella haemolysans were significantly more abundant in the common group.

CONCLUSION: The severity of COVID-19 in kidney transplant patients is associated with days of fever before hospitalization, and the levels of CRP and IL-10 at admission, which also alter the abundance of certain species in the sputum microbiome. Therefore, it is necessary to actively monitor the clinical indicators of kidney transplant patients admitted with COVID-19 to reduce the risk of progression to severe disease.},
}

@article {pmid40936884,
year = {2025},
author = {Wu, Y and Yu, X and Zhang, Y and Liu, J and Chen, Y and Wang, R and Zhang, W},
title = {Challenges in Management of Disseminated Mucormycotic Infection with Endocarditis in an Adult Patient Receiving Liver Transplantation.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {4711-4721},
pmid = {40936884},
issn = {1178-6973},
abstract = {Mucormycosis is a rare fungal infection. With the recent advancements in diagnostic technologies, including molecular diagnostic techniques, such as PCR and metagenomic next-generation sequencing, the detection rates of mucormycosis have increased. However, its mortality rates remain alarmingly high. Although post-liver transplantation mucormycosis cases are infrequently reported (less than 1%), their mortality rate ranges from 60% to 90%, while mucormycotic endocarditis is even rarer. This article summarizes the clinical manifestations of mucormycosis in a post-liver transplantation adult patient and reviews the existing literature on mucormycotic endocarditis, with the aim of outlining its clinical features, diagnostic challenges, and therapeutic strategies.},
}

@article {pmid40936227,
year = {2025},
author = {Liu, C and Long, J and Li, Y and Leng, X and Zhang, J and Chen, S and Fu, J and Li, C and Zhou, Y and Feng, C and Huang, B},
title = {The Comparison of Diagnostic Performance Between Next-Generation Sequencing of Blood and Tissues for Primary Spinal Infections.},
journal = {Global spine journal},
volume = {},
number = {},
pages = {21925682251375446},
doi = {10.1177/21925682251375446},
pmid = {40936227},
issn = {2192-5682},
abstract = {Study designprospective study.ObjectivesThe hematogenous spread of pathogens from a distant infected area is the main route of primary spinal infections. It is expected that blood metagenomic next-generation sequencing (mNGS) has potential in the pathogen detection of primary spinal infections. The aim of this study is to compare the diagnostic performance of blood and tissue mNGS in primary spinal infections.MethodsA total of 21 patients with primary spinal infections were analyzed. The results of mNGS and culture of blood and spinal specimens were used to calculate the diagnostic efficiency-related parameters.ResultsThe positive rate, sensitivity and specificity of blood mNGS were significantly lower than those of tissue mNGS (42.86% vs 90.48%, 9.52% vs 95%, 12.5% vs 100%). The positive rate and sensitivity of blood mNGS were higher (42.86% vs 4.76, 9.52% vs 5%) than those of blood pathogen culture. Also, the sensitivity and specificity of blood mNGS were lower than tissue pathogen culture (9.52% vs 45%, 12.5% vs 100%). Moreover, the specificity of blood mNGS was the lowest among the 4 pathogen identification techniques.ConclusionsThe diagnostic performance of blood mNGS is worse than tissue mNGS in primary spinal infections. The application prospects of blood mNGS in pathogen identification of primary spinal infections are limited. Further studies will be required to investigate the diagnostic values of blood mNGS in other types of spinal infections or in subpopulations of spinal infections.},
}

@article {pmid40935925,
year = {2025},
author = {Zhou, Y and Wang, H and Sun, J and Wicaksono, WA and Liu, C and He, Y and Qin, Y and Berg, G and Li, L and Lin, H and Chai, Y and Bai, Y and Ma, Z and Cernava, T and Chen, Y},
title = {Phenazines contribute to microbiome dynamics by targeting topoisomerase IV.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {40935925},
issn = {2058-5276},
support = {LZ23C140004//Natural Science Foundation of Zhejiang Province (Zhejiang Provincial Natural Science Foundation)/ ; U21A20219//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Phenazines are highly prevalent, natural bioactive substances secreted by microbes. However, their mode of action and potential involvement in shaping microbiomes remain elusive. Here we performed a comprehensive analysis of over 1.35 million bacterial genomes to identify phenazine-producing bacteria distributed across 193 species in 34 families. Analysis of rhizosphere microbiome and public rhizosphere metagenomic datasets revealed that phenazines could shape the microbial community by inhibiting Gram-positive bacteria, which was verified by pairwise interaction assays using Phenazine-1-carboxamide (PCN)-producing Pseudomonas chlororaphis. PCN induced DNA damage in Bacillus subtilis, a model Gram-positive target, where it directly bound to the bacterial topoisomerase IV, inhibiting its decatenation activity and leading to cell death. A two-species consortium of phenazine-producing Pseudomonas and resistant B. subtilis exhibited superior synergistic activity in preventing Fusarium crown rot in wheat plants. This work advances our understanding of a prevalent microbial interaction and its potential for biocontrol.},
}

@article {pmid40935888,
year = {2025},
author = {Otani, K and Nakatsu, G and Fujimoto, K and Miyaoka, D and Sato, N and Nadatani, Y and Nishida, Y and Maruyama, H and Ominami, M and Fukunaga, S and Hosomi, S and Tanaka, F and Imoto, S and Uematsu, S and Watanabe, T and Fujiwara, Y},
title = {Development of gastric mucosa-associated microbiota in autoimmune gastritis with neuroendocrine tumors.},
journal = {Journal of gastroenterology},
volume = {},
number = {},
pages = {},
pmid = {40935888},
issn = {1435-5922},
support = {JP22K08040//Japan Society for the Promotion of Science/ ; },
abstract = {BACKGROUND: Autoimmune gastritis (AIG) is a chronic atrophic gastritis that affects the gastric corpus, leading to achlorhydria, hypergastrinemia, and a precursor of neuroendocrine tumors (NETs). This study aimed to elucidate the underlying mechanisms of gastric NET formation in AIG by analyzing gastric mucosa-associated microbiota and host tissue-derived metabolite profiles.

METHODS: A total of 19 patients diagnosed with AIG and 12 controls uninfected with Helicobacter pylori underwent gastric mucosal biopsies for microbiome analysis using next-generation sequencing with primers targeting the V3-V4 region of the 16S rRNA gene, and metabolome analysis using capillary electrophoresis time-of-flight mass spectrometry.

RESULTS: Microbiome analysis revealed significantly reduced α-diversity indices in patients with AIG when compared with the control group. β-Diversity analysis showed distinct microbial compositions among the control, NET-negative, and NET-positive groups. The NET-positive group exhibited a significantly higher abundance of Proteobacteria and Fusobacteriota, particularly Haemophilus parainfluenzae, Fusobacterium periodonticum, and Fusobacterium nucleatum, whereas Firmicutes, including Streptococcus salivarius and Veillonella atypica, were significantly decreased compared with the NET-negative group. Metabolome analysis revealed a shift away from glycolysis and tricarboxylic acid cycle activity toward alternative metabolic pathways in patients with AIG. Integrated analysis of gastric microbiota signatures (GMS) and tissue metabotypes demonstrated significant associations among GMS, tissue metabotypes, and NET diagnosis.

CONCLUSIONS: These findings highlight marked shifts in gastric mucosa-associated microbiota profiles in patients with AIG who developed gastric NETs. Tissue-specific metabolic alterations may precede mucosal dysbiosis in patients with AIG and promote the development of a microenvironment implicated in NET formation.},
}

@article {pmid40935532,
year = {2025},
author = {Webster, AM and Triumph, Z and Wei, B and Martin, RM and Smith, LE and Wilhelm, SW and Cleckner, LB and Razavi, NR and Boyer, GL},
title = {First report of nodularin production by Nostochopsis sp. in a temperate eutrophic lake.},
journal = {Harmful algae},
volume = {149},
number = {},
pages = {102956},
doi = {10.1016/j.hal.2025.102956},
pmid = {40935532},
issn = {1878-1470},
abstract = {Benthic cyanobacteria are understudied in comparison to their planktonic counterparts. Consequently, our understanding of cyanotoxin production in benthic mats remains limited. We detected nodularin-R (NOD-R) in a population of Nostochopsis from Honeoye Lake (New York, United States). Identification as Nostochopsis was supported by morphological (see section 3.1 for a detailed description) and metagenomic analyses. The first metagenome assembled genome of Nostochopsis was drafted and estimated at 99.28 % complete. Cyanotoxin testing of Nostochopsis biomass showed production of NOD-R but not microcystins, anatoxins, or cylindrospermopsins. The complete nodularin synthetase cluster was confirmed in the Nostochopsis genome. To our knowledge, this is the first report of nodularin production, or any cyanotoxin production, by the benthic cyanobacteria Nostochopsis. This is the fourth genus of cyanobacteria reported to produce nodularins.},
}

@article {pmid40935105,
year = {2025},
author = {Zhao, J and Guo, Z and Tang, L and Lu, X and Li, Y and Yang, K},
title = {Dynamic evolution of antibiotic resistance risk in sewage sludge-amended soil during crop growth: a field-based metagenomic perspective.},
journal = {Environmental research},
volume = {},
number = {},
pages = {122799},
doi = {10.1016/j.envres.2025.122799},
pmid = {40935105},
issn = {1096-0953},
abstract = {Sewage sludge, a ubiquitous by-product of wastewater treatment, accumulates globally. Land application, a prominent waste valorization strategy, inadvertently disseminates the sludge antibiotic resistome into ecosystems, threatening ecological security and public health. Risk assessment of antibiotic resistance (AR) during sludge land application is urgently needed. Herein, we conducted a field study by planting three crops in sludge-amended soil, and monitoring the dynamic evolution of AR risk throughout their growth cycles. Metagenomic sequencing assessed antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), virulence factors (VFs), and their co-occurrence. Sludge amendment exerted persistent, yet largely recoverable, impacts on soil microbial community and the resistome. The resulting AR risk evolution was nonlinear and fluctuating, dominated by soil microbial community reconstruction. Given the differences in crop edible parts, growth periods of crops, complex AR risk dynamics, and external factors like weather, we propose a time-sensitive control strategy targeting critical risk windows. This strategy aims to mitigate AR risk under the "One Health" paradigm for sustainable sludge land application.},
}

@article {pmid40935093,
year = {2025},
author = {Marangi, M and Palladino, G and Valzano, F and Scicchitano, D and Turroni, S and Rampelli, S and Candela, M and Arena, F},
title = {Genetic characterization of enteric protozoan microorganisms in newly arrived migrants in Italy and correlation with the gut microbiome layout.},
journal = {Travel medicine and infectious disease},
volume = {},
number = {},
pages = {102901},
doi = {10.1016/j.tmaid.2025.102901},
pmid = {40935093},
issn = {1873-0442},
abstract = {The prevalence of the enteric protozoan microorganisms, its genetic characterization as well as its associated gut microbiome has been molecularly and 16S metagenomic characterized in a cohort of newly arrived migrants in Italy from African countries over the period 2022-2024. Out of 199 individuals, 92 (46.2 %) were found to be carrier of protozoan microorganisms with a higher prevalence of Blastocystis sp. (15.5 %), followed by Giardia duodenalis (12.6 %), Dientamoeba fragilis (7.5 %), Cryptosporidium parvum (6.5 %), and Entamoeba histolytica (4 %). Subtypes ST1, ST2 and ST3 were genetically characterized for Blastocystis sp., assemblages A and B for G. duodenalis, subtypes families IIa and IIc for C. parvum and genotype 1 for D. fragilis. High prevalence of Butyrivibrio, Lachnospiraceae UGC 10 and Paraprevotella, were identified in the protozoan non-carrier individual group. This work shed lights on the circulation of enteric protozoan microorganisms in apparently healthy migrants from African countries and the potential relationship with the host-microbiome composition. Moreover, these results give an overview of the importance of microbiological surveys among migrants and asylum seekers arriving to hosting countries in order to evaluate the reliable risk of several microorganisms introduction though migration. Ultimately, further investigation of interplays between the intestinal microbiota and protozoan microorganisms will provide new approaches in the diagnosis and treatment of intestinal infections.},
}

@article {pmid40934662,
year = {2025},
author = {Zhang, J and Zhao, J and Gao, Z and Ding, X and Li, Y and Shi, J and Zhao, D and Shi, L and Bi, X and Miao, Y},
title = {An effective method for enhancing metabolic activity of anammox bacteria: Accelerating heme biosynthesis by glutamate.},
journal = {Journal of environmental management},
volume = {393},
number = {},
pages = {127301},
doi = {10.1016/j.jenvman.2025.127301},
pmid = {40934662},
issn = {1095-8630},
abstract = {Enhancing and maintaining anammox bacteria (AnAOB) activity is a major challenge for application of anammox process, which could be achieved by accelerating heme biosynthesis. Heme is crucial for electron transport and redox reaction and its biosynthesis may be promoted by glutamate. To explore the effect of glutamate on AnAOB activity, four parallel anammox systems (named R0, R1, R2, and R3) with different concentrations of glutamate (0, 0.125, 0.25, and 0.5 mM) were set up. The results showed that AnAOB activities and nitrogen removal efficiencies of R1 and R2 were about 58.3 % and 48.8 %, and 80.5 % and 64.1 % higher than that of R0, respectively, whereas excessive glutamate (0.5 mM) deteriorated the system performance. Moreover, heme content, activities of hydrazine synthase and hydrazine dehydrogenase, and sludge particle size in R1 and R2 were significantly higher than R0. Metagenomic sequencing analysis further revealed that the moderate amount of glutamate (0.125 mM, 0.25 mM) could effectively improve AnAOB activity by enhancing heme biosynthesis, accelerating electron transport and energy synthesis, and promoting the aggregation of microorganisms. This study provides an effective method for enhancing AnAOB metabolic activity and clarifies the underlying mechanism.},
}

@article {pmid40934587,
year = {2025},
author = {Wang, F and Xiong, J and Lin, L and Xu, W and Liu, L and Yang, S and Cao, W},
title = {Antibiotic resistance genes link to nitrogen removal potential via co-hosting preference for denitrification genes in a subtropical estuary.},
journal = {Journal of hazardous materials},
volume = {498},
number = {},
pages = {139801},
doi = {10.1016/j.jhazmat.2025.139801},
pmid = {40934587},
issn = {1873-3336},
abstract = {Estuaries are important sinks for antibiotic resistance genes (ARGs) and hotspots of nitrogen cycling. However, the interactions between nitrogen cycling functional genes (NCGs) and ARGs in estuaries remain poorly understood. This study employed metagenomic sequencing to explore potential interactions between nitrogen, ARGs, and microbial-mediated nitrogen cycling processes in estuarine waters. Results showed beta-lactam was the predominant subtype of ARGs (407 species), and sul1 exhibited the highest relative abundance (4.11 %). Nitrogen was the important factor driving spatiotemporal variation of ARGs, promoting their proliferation and dispersal by enhancing microbial growth and reproduction. Network analysis revealed wide and complex correlations between ARGs and NCGs. Nitrate-reducing bacteria were the main hosts of ARGs, and the greatest number of potential hosts were those involved in assimilatory nitrate reduction to ammonium (17.44 %), dissimilatory nitrate reduction to nitrite (16.59 %), and denitrification (15.71 %). Compared with dissimilatory nitrite reduction to ammonium genes, ARGs prefer to form co-hosting relationships with denitrification genes, indicating that ARGs had a stronger effect on the nitrogen removal potential than on the nitrogen retention potential. This study highlights the complex interactions between ARGs and nitrogen cycling processes in subtropical estuaries, and will provide a scientific base for couple management strategies of nitrogen and antibiotic pollution.},
}

@article {pmid40934284,
year = {2025},
author = {Lucas, A and Schäffer, DE and Wickramasinghe, J and Auslander, N},
title = {kMermaid: Ultrafast metagenomic read assignment to protein clusters by hashing of amino acid k-mer frequencies.},
journal = {PLoS computational biology},
volume = {21},
number = {9},
pages = {e1013470},
doi = {10.1371/journal.pcbi.1013470},
pmid = {40934284},
issn = {1553-7358},
abstract = {Shotgun metagenomic sequencing can determine both the taxonomic and functional content of microbiomes. However, functional classification for metagenomic reads remains highly challenging as protein mapping tools require substantial computational resources and yield ambiguous classifications when short reads map to homologous proteins originating from different bacteria. Here we introduce kMermaid for the purpose of uniquely mapping bacterial short reads to taxa-agnostic clusters of homologous proteins, which can then be used for downstream analysis tasks such as read quantification and pathway or global functional analysis. Using a nested hash map containing amino acid k-mer profiles as a model for protein assignment, kMermaid achieves the sensitivity of popular existing protein mapping tools while remaining highly resource efficient. We evaluate kMermaid on simulated data and data from human fecal samples as well as demonstrate the utility of kMermaid for classifying reads originating from new, unseen proteins. kMermaid allows for highly accurate, unambiguous and ultrafast metagenomic read assignment into protein clusters, with a fixed memory usage, and can easily be employed on a typical computer.},
}

@article {pmid40933810,
year = {2025},
author = {Tigrero-Vaca, J and Villavicencio-Vásquez, M and Coronel, J and Cevallos-Cevallos, JM},
title = {Multi-platform metagenomic characterization of the microbial community during spontaneous cacao fermentation.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {13},
number = {},
pages = {1630515},
doi = {10.3389/fbioe.2025.1630515},
pmid = {40933810},
issn = {2296-4185},
abstract = {Cacao fermentation is a spontaneous process in which microorganisms play a key role in the development of distinctive chocolate flavors. The microbiota acting during cacao fermentation has been routinely characterized by culture-based techniques and next-generation sequencing using Illumina's platform. However, the potential of in situ sequencing technologies to monitor microbial dynamics during cacao fermentation has not been assessed. In this study, cacao bean samples were collected at 0, 24, 48, 72, and 96 h after the start of the fermentation. Total DNA was extracted, and sequencing libraries were prepared for further sequencing using Illumina's and Nanopore's MinION sequencing platforms. Additionally, microorganisms were isolated using traditional culture-based methods. At the order and family taxonomic levels, Illumina and MinION sequencing revealed similar microbial composition in the samples. However, discrepancies were observed at the genus and species levels. In this sense, Illumina sequencing revealed a predominance of Limosilactobacillus, Levilactobacillus, Lactiplantibacillus, Frauteria, Saccharomyces and Acetobacter, while MinION sequencing showed a prevalence of Escherichia, Salmonella, Liquorilactobacillus, Lentilactobacillus, Acetobacter and Komagataeibacter during fermentation. The three methods were consistent in detecting the major yeast (Saccharomyces cerevisiae), lactic acid bacteria (Lactiplantibacillus plantarum, Leuconostoc pseudomesenteroides, Levilactobacillus brevis, Liquorilactobacillus mali, and Lentilactobacillus hilgardii) and acetic acid bacteria (Acetobacter pasteurianus) species during fermentation. Functional analysis based on a hybrid assembly of Illumina and MinION data revealed the roles of lactic acid bacteria and acetic acid bacteria in the metabolism of carbohydrates, amino acids, and secondary metabolites such as polyphenols and theobromine. This study represents the first report assessing the applicability of MinION sequencing for the characterization of microbial populations during cacao fermentation, demonstrating its potential as a complementary tool to established sequencing platforms.},
}

@article {pmid40933579,
year = {2025},
author = {Lin, B and Zhong, D and Qin, L and Liu, Q and Wu, L and Wang, B and Wang, K and Lu, X and Deng, S and Pan, L},
title = {Application of metagenomics sequencing to diagnose paralytic rabies with stroke-like onset: a case report.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1639262},
doi = {10.3389/fmed.2025.1639262},
pmid = {40933579},
issn = {2296-858X},
abstract = {BACKGROUND: Rabies is an acute zoonotic infectious disease caused by infection with a virus of the genus Lyssavirus. We report a case of paralytic rabies with a stroke-like onset, which was diagnosed using metagenomics next-generation sequencing (mNGS).

CASE PRESENTATION: A 58-year-old man was admitted to the hospital with "numbness and weakness in the right upper extremity for 2 days, aggravated for 1 day." Twenty-five days before his admission, the patient was bitten on the back of right hand by an unvaccinated domestic dog, resulting in a penetrating injury, classified as grade III according to the rabies exposure classification method. Following admission, the patient exhibited rapidly progressive stroke symptoms, and on the second day, he suffered a sudden respiratory arrest accompanied by a weakened heartbeat and a decreased heart rate. He was treated with emergency tracheal intubation, cardiopulmonary resuscitation, and dehydration to lower cranial pressure.

RESULTS: The patient's condition deteriorated rapidly after admission. A lumbar puncture was conducted on the morning of the second day of admission, and cerebrospinal fluid (CSF) was sent to Weiyuan Genetic Laboratories (Guangzhou, China) for rabies virus identification. The patient died on the third day of admission. Pathogen capture macro-genomics was performed on CSF using an Illumina NextSeq second-generation sequencer, and nine rabies virus sequences, which shared more than 99% nucleotide homology with the genome sequence of the rabies virus Rabies lyssavirus (NCBI accession no. MN175989.1), were detected. The Q30 ratio of this test was 98.3%.

CONCLUSION: Compared to polymerase chain reaction (PCR) and direct fluorescent antibody (DFA) test, mNGS shortens the diagnostic window and improves sensitivity to low-virus or seronegative manifestations by simultaneously capturing and sequencing the entire pathogen genome. The mNGS technology can effectively aid in the diagnosis of paralytic rabies.},
}

@article {pmid40933366,
year = {2025},
author = {Gutleben, J and Podell, S and Mizell, K and Sweeney, D and Neira, C and Levin, LA and Jensen, PR},
title = {Extremophile hotspots linked to containerized industrial waste dumping in a deep-sea basin.},
journal = {PNAS nexus},
volume = {4},
number = {9},
pages = {pgaf260},
doi = {10.1093/pnasnexus/pgaf260},
pmid = {40933366},
issn = {2752-6542},
abstract = {Decaying barrels on the seafloor linked to DDT contamination have raised concerns about the public health implications of decades old industrial waste dumped off the coast of Los Angeles. To explore their contents, we collected sediment cores perpendicular to five deep-sea barrels. The concentration of DDT and its breakdown products were highly elevated relative to control sites yet did not vary with distance from the barrels, suggesting that they were not associated with the contamination. Sediment cores collected through white halos surrounding three barrels were enriched in calcite and had elevated pH. The associated microbial communities were low diversity and dominated by alkalophilic bacteria with metagenome-assembled genomes adapted to high pH. A solid concretion sampled between a white halo and barrel was composed of brucite, a magnesium hydroxide mineral that forms at high pH. Based on these findings, we postulate that leakage of containerized alkaline waste triggered the formation of mineral concretions that are slowly dissolving and raising the pH of the surrounding sediment pore water. This selects for taxa adapted to extreme alkalinity and drives the precipitation of "anthropogenic" carbonates forming white halos, which serve as a visual identifier of barrels that contained alkaline waste. Remarkably, containerized alkaline waste discarded >50 years ago represents a persistent pollutant creating localized mineral formations and microbial communities that resemble those observed at some hydrothermal systems. These formations were observed at one-third of the visually identified barrels in the San Pedro Basin and have unforeseen, long-term consequences for benthic communities in the region.},
}

@article {pmid40933132,
year = {2025},
author = {Li, X and Lu, H},
title = {Enhanced metagenomic strategies for elucidating the complexities of gut microbiota: a review.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1626002},
doi = {10.3389/fmicb.2025.1626002},
pmid = {40933132},
issn = {1664-302X},
abstract = {The human gastrointestinal tract (GIT) is inhabited by a heterogeneous and dynamic microbial community that influences host health at multiple levels both metabolically, immunologically and via neurological pathways. Though the gut microbiota-overwhelmingly Bacteroidetes and Firmicutes-has essential functions in nutrient metabolism, immune regulation, and resistance to pathogens, its dysbiosis is likewise associated with pathologies, such as inflammatory bowel disease (IBD), obesity, type 2 diabetes (T2D), and neurodegenerative diseases. While conventional metagenomic techniques laid the groundwork for understanding microbial composition, next-generation enhanced metagenomic techniques permit an unprecedented resolution in exploring the functional and spatial complexity of gut communities. Advanced frameworks such as high-throughput sequencing, bioinformatic and multi-omics technologies are expanding the understanding of microbial gene regulation, metagenomic pathways, and host-microbe communication. Beyond taxonomic profiling, they map niche-specific activities of gut microbiota along a dichotomy of facultative mutualism, evidenced by relations of beneficial symbionts, represented here by Enterobacteriaceae. In this review, we critically consider the latest approaches (e.g., long-read sequencing, single-cell metagenomics and AI-guided annotation) that mitigate biases stemming from DNA extraction, sequencing depth and functional inference.},
}

@article {pmid40933127,
year = {2025},
author = {Akhtar, MF and Wenqiong, C and Umar, M and Changfa, W},
title = {Biochemical properties of lactic acid bacteria for efficient silage production: an update.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1581430},
doi = {10.3389/fmicb.2025.1581430},
pmid = {40933127},
issn = {1664-302X},
abstract = {Ensiling, a microbial-driven process employed for preserving fresh forage in both bio-refineries and animal production, triggers significant biochemical transformations. These changes have spurred the exploration of novel silage additives, with a particular emphasis on the potential of microbial strains that exhibit superior biopreservation capabilities. Lactic acid bacteria (LAB) species have gained widespread recognition for their diverse applications as additives in the fermentation of crops and forage biomasses during ensiling. Nonetheless, recent variations in silage quality might be attributed to a lack of comprehensive information on the gene expression and molecular mechanisms of the microbiota involved in silage production. Contemporary research efforts have been directed toward uncovering nutrient-rich animal feed solutions through enhanced LAB inoculants. This review aims to shed light on the role of LAB inoculants in silage production and the modern biotechnological methods, including metabolomics, proteomics, metagenomics, genomics, transcriptomics, and genetic manipulation. These powerful tools are instrumental in the identification, enhancement, and development of high-performance LAB strains. Additionally, the review outlines emerging trends and prospective developments in LAB advancement for the enhancement of silage, which holds significant promise for breakthroughs in sustainable agriculture and improved animal feed production.},
}

@article {pmid40933007,
year = {2025},
author = {Le, J and Hakimjavadi, H and Parsana, R and Chamala, S and Michail, S},
title = {Fecal Microbiota Transplantation Induces Sustained Gut Microbiome Changes in Pediatric Ulcerative Colitis: A Combined Randomized and Open-Label Study.},
journal = {Gastro hep advances},
volume = {4},
number = {10},
pages = {100741},
doi = {10.1016/j.gastha.2025.100741},
pmid = {40933007},
issn = {2772-5723},
abstract = {BACKGROUND AND AIMS: Fecal microbiota transplantation (FMT) is a promising tool to modulate the gut microbiome in pediatric ulcerative colitis (UC). We investigated the long-term impact of FMT on the gut microbiome and identified microbial signatures associated with disease severity and clinical outcomes.

METHODS: This study combined a randomized, double-blind trial comparing FMT to autologous placebo with an open-label extension to assess FMT's effects on the gut microbiome in pediatric UC patients over 48 weeks. Stool samples were collected at baseline and postintervention, and clinical response was evaluated using the Pediatric Ulcerative Colitis Activity Index. Shotgun metagenomic sequencing characterized the fecal microbiome's composition and functional potential. Taxon set enrichment analysis identified microbial taxon sets associated with UC and FMT.

RESULTS: FMT induced significant, sustained increases in gut microbial diversity over 48 weeks. Key changes included decreases in Klebsiella oxytoca and increases in Coprobacter fastidiosus post-FMT. Microbial signatures were associated with disease severity, including increased indole producers and decreased mucin degraders in mild UC compared to remission. Patients with clinical improvement post-FMT showed decreased Fusobacterium nucleatum and Veillonella parvula. Klebsiella pneumoniae and Klebsiella variicola decreased after open-label FMT.

CONCLUSION: FMT induces sustained changes in the pediatric UC gut microbiome, with distinct microbial signatures associated with disease severity and clinical outcomes. However, the high autologous placebo response rate underscores the need for further research to elucidate the mechanisms underlying FMT and placebo responses. Our study provides insights into the gut microbiome's role in pediatric UC, laying the foundation for developing personalized microbiome-targeted therapies. ClinicalTrials.gov number, NCT02291523.},
}

@article {pmid40932661,
year = {2025},
author = {Sachdeva, S and Sarethy, IP},
title = {Antibiotic resistance profiling in an ancient Indian sulfur-rich stepwell: a case study of Gandhak-ki-Baoli.},
journal = {Molecular biology reports},
volume = {52},
number = {1},
pages = {895},
pmid = {40932661},
issn = {1573-4978},
mesh = {India ; *Sulfur/analysis ; *Bacteria/genetics/drug effects ; Anti-Bacterial Agents/pharmacology ; Metagenomics/methods ; *Drug Resistance, Microbial/genetics ; *Drug Resistance, Bacterial/genetics ; Water Microbiology ; Metagenome ; },
abstract = {BACKGROUND: Antimicrobial resistance (AMR) is a growing global health concern, increasingly recognized to emerge not only from clinical and agricultural sources but also from natural and historical environments. Despite their ecological and cultural significance, ancient water bodies such as stepwells remain largely unexplored in the context of environmental resistomes.

METHOD: This study investigates AMR in Gandhak-ki-Baoli, an ancient sulfur-rich stepwell located in Delhi, India. A combined methodological approach involving culture-based microbial isolation and metagenomics sequencing was used to identify bacterial taxa and associated antibiotic resistance genes (ARGs).

RESULTS: The analysis revealed a diverse microbial community harboring ARGs, including those conferring multidrug resistance. Several genes showed evidence of co-selection mechanisms with heavy metals and biocides. The stepwell's unique environmental conditions characterized by stagnant water, low light, variable moisture, and limited nutrients that likely contribute to the persistence and potential horizontal transfer of resistance traits.

CONCLUSIONS: This is the first study to profile AMR in a historical stepwell, revealing the presence of a complex environmental resistome. The findings suggest that ancient water structures like stepwells can act as hidden reservoirs of AMR. These insights highlight the need to include such environments in future AMR surveillance efforts to better understand the broader ecological landscape of resistance.},
}

India
*Sulfur/analysis
*Bacteria/genetics/drug effects
Anti-Bacterial Agents/pharmacology
Metagenomics/methods
*Drug Resistance, Microbial/genetics
*Drug Resistance, Bacterial/genetics
Water Microbiology
Metagenome

@article {pmid40932534,
year = {2025},
author = {Wang, F and Xia, J and Sun, J},
title = {Microbiological diagnostics and their impact on hematology nursing.},
journal = {Folia microbiologica},
volume = {},
number = {},
pages = {},
pmid = {40932534},
issn = {1874-9356},
abstract = {Microbiological diagnostics have become a foundational element in hematology nursing, where early and accurate infection detection is vital for immunocompromised patients. This review explores how both traditional techniques, such as microscopy, culture, and antigen detection, and emerging technologies, including polymerase chain reaction (PCR), metagenomic next-generation sequencing (mNGS), and MALDI-TOF mass spectrometry, contribute to clinical decision-making and infection control. These tools not only accelerate pathogen identification and resistance profiling but also support precision medicine approaches tailored to hematologic patient needs. The expanding role of hematology nurses is emphasized, particularly in diagnostic stewardship, specimen collection, result interpretation, and coordination of infection management strategies. Educational interventions have proven effective in reducing contamination rates and improving antimicrobial targeting. Furthermore, novel point-of-care platforms, such as CRISPR-based diagnostics and AI-enhanced digital PCR, are shifting diagnostic capabilities closer to the bedside, redefining nursing workflows and responsibilities. These innovations empower nurses to engage in real-time clinical decisions, monitor therapy responses, and enhance patient education regarding diagnostic procedures and infection risks. However, gaps remain in microbiology-related training and confidence among nurses, highlighting the need for integrated educational curricula and interdisciplinary collaboration. By aligning technological advancements with frontline nursing practice, microbiological diagnostics not only optimize patient outcomes but also elevate the role of nurses as key stakeholders in infection prevention, antimicrobial stewardship, and evidence-based care. This review underscores the urgent need to equip hematology nurses with the skills and tools necessary to adapt to the rapidly evolving diagnostic landscape in order to support safe, timely, and personalized healthcare delivery.},
}

@article {pmid40932289,
year = {2025},
author = {Zhao, Y and Du, L and Song, J and Sun, W and Chen, Y and Yu, X and Huang, H and Huang, G and Huang, E and Wang, N and An, S and Ai, L and Chen, P},
title = {Hierarchical integration of mNGS, PCR, and other conventional methods for precision TB diagnostics.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0193125},
doi = {10.1128/spectrum.01931-25},
pmid = {40932289},
issn = {2165-0497},
abstract = {UNLABELLED: This study systematically compared the diagnostic accuracy of seven assays for detecting the Mycobacterium tuberculosis complex, including metagenomic next-generation sequencing (mNGS), droplet digital polymerase chain reaction, real-time quantitative polymerase chain reaction, EasyNAT MTC, GeneXpert MTB/RIF, interferon-gamma release assay (IGRA), and acid‒fast staining (AFS). We try to select appropriate combinations of tuberculosis (TB) detection methods for regions with varying levels of medical resources, based on sensitivity, cost-effectiveness, and operational feasibility. A retrospective analysis was conducted on 141 samples collected from patients with suspected active TB at The First Affiliated Hospital of Sun Yat-sen University between April 2022 and April 2024. Among these samples, there were 100 cases assigned to the case group and 41 cases to the control group, based on the tuberculosis diagnostic criteria. Historical data for Xpert, IGRA, and AFS were collected, and parallel experiments using mNGS, droplet digital PCR (ddPCR), real-time quantitative polymerase chain reaction (RT-qPCR), and EasyNAT were conducted on all samples. Diagnostic performance was evaluated by comparing it with the final clinical diagnoses. Sensitivity, specificity, positive predictive value, negative predictive value, and receiver operating characteristic (ROC) curve analysis were conducted, along with DeLong tests for statistical comparison. Compared with the final clinical diagnosis, mNGS demonstrated the highest sensitivity (100%), followed by IGRA (79.2%), EasyNAT (79.1%), RT-qPCR (78.0%), ddPCR (75.8%), Xpert (75.3%), and AFS (16.7%). The specificity was 100% for both Xpert and AFS, followed by ddPCR (97.6%), RT-qPCR (95.1%), EasyNAT (92.7%), IGRA (72.7%), and mNGS (75.6%). ROC analysis revealed a significantly greater area under the ROC curve for mNGS (0.878) than for ddPCR (0.817, P = 0.031). DeLong tests revealed statistically significant differences in diagnostic performance between mNGS and ddPCR (P < 0.05) and between IGRA and AFS (P < 0.01). mNGS uniquely identified the pathogens involved in co-infection and quantified pathogen-specific sequencing reads. Through a comprehensive evaluation of the diagnostic efficacy, cost-effectiveness, and timeliness of tuberculosis detection methods, we propose corresponding combinations of TB testing approaches for regions with different healthcare resources. For undeveloped regions with limited resources, a combination of AFS +EasyNAT + chest X-ray is recommended. Primary care facilities may additionally employ IGRA + RT-qPCR. Intermediate-level hospitals can incorporate Xpert MTB/RIF for drug resistance testing, while tertiary hospitals or specialized centers should, on the basis of these fundamental tests, utilize mNGS for diagnosis and ddPCR for therapeutic monitoring in patients with complex mixed infections.

IMPORTANCE: This study is the first to comprehensively evaluate the diagnostic efficacy, cost-effectiveness, and timeliness of seven TB detection methods in a single-center cohort. Our findings provide actionable solutions for optimizing TB diagnostics in diverse healthcare ecosystems, aligning with the WHO's End TB Strategy to ensure equitable access to rapid diagnostics.},
}

@article {pmid40931802,
year = {2025},
author = {Gernert, JA and Klein, M and Schöberl, F and Müller, KJ and Schmidbauer, ML and Forbrig, R and Roeber, S and Herms, J and Terpolilli, N and Milakovic Obradovic, M and Graf, A and Dächert, C and Keppler, OT and Münchhoff, M and Dimitriadis, K},
title = {Severe course of tick-borne encephalitis (TBE) in a patient with relapsing multiple sclerosis (MS) treated with ocrelizumab.},
journal = {Multiple sclerosis (Houndmills, Basingstoke, England)},
volume = {},
number = {},
pages = {13524585251369425},
doi = {10.1177/13524585251369425},
pmid = {40931802},
issn = {1477-0970},
abstract = {Description of a patient with multiple sclerosis (MS) who underwent immunotherapy with ocrelizumab and suffered a severe course of tick-borne encephalitis (TBE): A 33-year-old man presented with acute cerebellitis with tonsillar herniation. The initial suspected diagnosis of TBE was confirmed after a significant diagnostic delay, likely caused by negative serological testing due to B-cell depletion from ocrelizumab treatment for underlying MS. TBE diagnosis was made using polymerase chain reaction (PCR) and oligo-hybrid capture metagenomic next-generation sequencing (mNGS) of cerebral spinal fluid and brain biopsy samples which yielded a near-full length TBE Virus (TBEV) genome.},
}

@article {pmid40931531,
year = {2025},
author = {Gasparini, J},
title = {Targeted 'infectiosome' for disease ecology: A new tool to answer old questions.},
journal = {The Journal of animal ecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1365-2656.70130},
pmid = {40931531},
issn = {1365-2656},
abstract = {Research Highlight: Bralet, T., Aaziz, R., Tornos, J., Gamble, A., Clessin, A., Lejeune, M., Galon, C., Michelet, L., Lesage, C., Jeanniard du Dot, T., Desoubeaux, G., Guyard, M., Delannoy, S., Moutailler, S., Laroucau, K. and Boulinier, T. (2025). High-throughput microfluidic real-time PCR as a promising tool in disease ecology. Journal of Animal Ecology, https://doi.org/10.1111/1365-2656.70088. Disease ecology aims to understand the causes and consequences of the maintenance and transmission of pathogenic infectious agents. A crucial step in studying disease ecology is identifying the 'infectiosome', which I define as all infectious agents circulating among individuals, populations and the community of a given ecosystem. In a recent study, Bralet et al. (2025) propose a new, cheap and adaptable toolkit for determining a targeted 'infectiosome', which appears very useful in disease ecology approaches: high-throughput microfluidic real-time PCR (Htrt PCR). This method is a good alternative to costly metagenomic approaches and consists of running several dozen PCRs from a single tissue sample. This technique enables screening, from a single sample, the presence of dozens of targeted infectious agents: the targeted 'infectiosome', allowing one to answer several questions. For example, Bralet et al. (2025) applied this method to 274 seabirds and 80 mammals samples collected from the Southern Ocean islands and detected pathogenic infectious agents in new locations. The results also show that some species are potential 'reservoirs' of several infectious agents in this ecosystem. This method is really promising and can be easily adapted and used to test different hypotheses in disease ecology at the scales of the population and the community in other ecosystems, such as the urban ecosystem.},
}

@article {pmid40931350,
year = {2025},
author = {Ye, G and Hong, H and Li, T and Li, J and Wu, JQ and Jiang, S and Meng, ZT and Yuan, HT and Xue, W and Li, AL and Zhou, T and Li, TT and Li, T},
title = {MAGdb: a comprehensive high quality MAGs repository for exploring microbial metagenome-assemble genomes.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {276},
pmid = {40931350},
issn = {1474-760X},
support = {No. 32100421//China National Natural Science Foundation/ ; No. 82341098//China National Natural Science Foundation/ ; No. 82130052//China National Natural Science Foundation/ ; No. NSS2021CI05002//Nanhu Laboratory/ ; No. 2024ZYYDSA400333//The Central Government Guides Local Science and Technology Development Fund Projects/ ; },
mesh = {*Metagenome ; *Metagenomics/methods ; *Databases, Genetic ; *Microbiota ; },
abstract = {Metagenomic analyses of microbial communities have unveiled a substantial level of interspecies and intraspecies genetic diversity by reconstructing metagenome-assembled genomes (MAGs). The MAG database (MAGdb) boasts an impressive collection of 74 representative research papers, spanning clinical, environmental, and animal categories and comprising 13,702 paired-end run accessions of metagenomic sequencing and 99,672 high quality MAGs with manually curated metadata. MAGdb provides a user-friendly interface that users can browse, search, and download MAGs and their corresponding metadata information. It represents a valuable resource for researchers in discovering potential novel microbial lineages and understanding their ecological roles. MAGdb is publicly available at https://magdb.nanhulab.ac.cn/ .},
}

*Metagenome
*Metagenomics/methods
*Databases, Genetic
*Microbiota

@article {pmid40931024,
year = {2025},
author = {Tan, MH and Bangre, O and Rios-Teran, CA and Tiedje, KE and Deed, SL and Zhan, Q and Rasyidi, F and Pascual, M and Ansah, PO and Day, KP},
title = {Metagenomic complexity of high, seasonal transmission of Plasmodium spp. in asymptomatic carriers in Northern Sahelian Ghana.},
journal = {Communications medicine},
volume = {5},
number = {1},
pages = {386},
pmid = {40931024},
issn = {2730-664X},
support = {R01-AI149779//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R01-AI149779//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; },
abstract = {BACKGROUND: Mixed-species, mixed-strain plasmodia infections are known to occur in humans in malaria endemic areas. It may be surprising that to date, the extent of this complexity has not been systematically explored in high-burden countries of sub-Saharan Africa, especially in the reservoir of asymptomatic infections in all ages, which sustains transmission.

METHODS: Here we take a metagenomic lens to these infections by sampling variable blood volumes from 188 afebrile residents living in high, seasonal transmission in Northern Sahelian Ghana. We estimated multiplicity of infection for different Plasmodium spp. through genotyping of antigens and microsatellites. We further defined 'metagenomic complexity' as a measure of overall within-host complexity across the combination of species and strains.

RESULTS: We show that prevalence of Plasmodium spp. and inter-/intra-species complexity is significantly higher in larger blood volumes from these individuals. Overall, malaria infections display high levels of metagenomic complexity comprising single-, double-, and triple-species infections with varying levels of intra-species complexity for P. falciparum, P. malariae, P. ovale curtisi, and P. ovale wallikeri. We also report a subset of individuals with highly-complex infections that cannot be explained by age or location. The implications of these findings to malaria epidemiology and control are illustrated by a geographic scaling exercise to district and region levels in northern Ghana.

CONCLUSIONS: Our metagenomic investigation underscores the need to more sensitively measure within-host Plasmodium spp. complexity in asymptomatic carriers of infection. This will optimise strategies for malaria surveillance and control.},
}

@article {pmid40930091,
year = {2025},
author = {Minich, JJ and Allsing, N and Din, MO and Tisza, MJ and Maleta, K and McDonald, D and Hartwick, N and Mamerto, A and Brennan, C and Hansen, L and Shaffer, J and Murray, ER and Duong, T and Knight, R and Stephenson, K and Manary, MJ and Michael, TP},
title = {Culture-independent meta-pangenomics enabled by long-read metagenomics reveals associations with pediatric undernutrition.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2025.08.020},
pmid = {40930091},
issn = {1097-4172},
abstract = {The human gut microbiome is linked to child malnutrition, yet traditional microbiome approaches lack resolution. We hypothesized that complete metagenome-assembled genomes (cMAGs), recovered through long-read (LR) DNA sequencing, would enable pangenome and microbial genome-wide association study (GWAS) analyses to identify microbial genetic associations with child linear growth. LR methods produced 44-64× more cMAGs per gigabase pair (Gbp) than short-read methods, with PacBio (PB) yielding the most accurate and cost-effective assemblies. In a Malawian longitudinal pediatric cohort, we generated 986 cMAGs (839 circular) from 47 samples and applied this database to an expanded set of 210 samples. Machine learning identified species predictive of linear growth. Pangenome analyses revealed microbial genetic associations with linear growth, while genome instability correlated with declining length-for-age Z score (LAZ). This resource demonstrates the power of comparing cMAGs with health trajectories and establishes a new standard for microbiome association studies.},
}

@article {pmid40929977,
year = {2025},
author = {Han, F and Guo, Y and Zhao, C and Zhang, W and Zhang, M and Zhou, W},
title = {Halophilic heterotrophic ammonia assimilation biosystem shows stronger resilience and decreased ARGs abundance under sulfamethoxazole gradient stress compared with halophilic nitrification biosystem.},
journal = {Journal of hazardous materials},
volume = {498},
number = {},
pages = {139749},
doi = {10.1016/j.jhazmat.2025.139749},
pmid = {40929977},
issn = {1873-3336},
abstract = {Differences of niche and nitrogen metabolism between halophilic nitrification (AN) and heterotrophic ammonia assimilation (HAA) biosystems determine microbiome resilience and antibiotic resistance genes (ARGs) transfer under antibiotic stress. However, the underlying mechanism of this difference remains unclear. This study compared the bioresponses and ARGs characteristics of the two biosystems under sulfamethoxazole (SMX) stress. Results revealed that both biosystems maintained above 90 % NH4[+] -N and 95 % SMX removal efficiencies at SMX concentrations below 1 mg/L. However, exposure to 5 mg/L SMX impaired both NH4[+]-N and SMX removal efficiencies. HAA biosystem exhibited stronger robustness and resilience than the AN biosystem under SMX stress. The microbial products synthesis, extracellular protein structure, and extracellular electron transfer in both biosystems displayed distinct responses to SMX. Metagenomic results revealed SMX shock decreased the abundance of ammonia-oxidizing bacteria and ammonia-monooxygenase gene in the AN biosystem, while the rapid turnover of heterotrophic microorganisms and the flexibility of ammonia assimilation genes maintained the HAA function in the HAA biosystem. Furthermore, SMX stress induced ARGs enrichment in the AN biosystem, whereas the abundance and diversity of ARGs in the HAA biosystem decreased under SMX stress. These findings highlighted the potential of novel HAA biosystem for antibiotics degradation and ARGs control.},
}

@article {pmid40929972,
year = {2025},
author = {Liu, K and Wang, X and Li, F and Tao, J and Weng, CH and Hu, Q and Kang, D and Luo, Z and Tang, Z and Liu, N and Qiu, J},
title = {Metagenomic characterization of antibiotic resistance genes and human bacterial pathogens in groundwater from agricultural, landfill, and hazardous waste disposal sites (HWDS) sources: Drivers, risks, and source tracking.},
journal = {Journal of hazardous materials},
volume = {498},
number = {},
pages = {139803},
doi = {10.1016/j.jhazmat.2025.139803},
pmid = {40929972},
issn = {1873-3336},
abstract = {Agricultural sources, landfills, and hazardous waste disposal sites (HWDS) are major hotspots for the spread of groundwater antibiotic resistance genes (ARGs) and human bacterial pathogens (HBPs). However, there is a lack of systematic understanding regarding the environmental behavior of groundwater ARGs, the pathogenic risks of HBPs, and the relative contribution mechanisms of different sources, presenting critical scientific challenges for developing targeted groundwater pollution control strategies. To address this, this study collected 26 groundwater metagenomic samples to characterize the composition, influencing factors, and health risks of ARGs and HBPs near key ARG reservoirs, and constructed a source-tracking indicator system. The research identified 16 clinically critical high-risk ARGs (e.g., tetM, sul1) and 14 priority HBPs (e.g., Escherichia coli, Klebsiella pneumoniae) associated with severe human diseases and high transmissibility. Screening ARG source-specific indicators demonstrated high accuracy in predicting contributions from artificially mixed sources (prediction errors < 4 %). Validation with real groundwater samples showed that landfills contributed more significantly to groundwater ARGs pollution than other sources. This study deepens our understanding of antibiotic resistance risks in groundwater near key ARG reservoirs and provides a robust framework for tracing ARGs in complex groundwater environments by integrating microbe-gene-environment interactions across multiple pollution sources.},
}

@article {pmid40929881,
year = {2025},
author = {Liu, Y and Li, K and Xu, J and Shen, W and Li, Y and Ma, J and Wang, T and Liu, J and Li, T and Zhang, X and Tian, W and Tian, J and Wang, H and Zhang, X},
title = {Alpha-linolenic acid ameliorates T2DM via reshaping gut-liver axis and inflammatory GPR120-NF-κB/NLRP3 pathway in mouse and rat models.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {147},
number = {},
pages = {157214},
doi = {10.1016/j.phymed.2025.157214},
pmid = {40929881},
issn = {1618-095X},
abstract = {BACKGROUND: The gut-liver axis, pivotal in managing glucose balance and insulin responsiveness, is central to the development of type 2 diabetes mellitus (T2DM). Research has highlighted the regulatory effects of dietary alpha-linolenic acid (ALA), but it remains unclear how ALA modulates gut microbiota and liver inflammation in T2DM.

PURPOSE: This study aimed to systematically investigate ALA's influence on liver inflammation, intestinal barrier integrity, gut microbial composition, and metabolic homeostasis in T2DM, with a focus on the underlying molecular mechanisms.

STUDY DESIGN: A dual-model approach was employed using both db/db mouse model and the SCZ/NA-induced T2DM rat model to ensure robust species and model validation.

METHODS: Animals received oral ALA supplementation, followed by assessments of glucose tolerance, insulin sensitivity, hepatic histology, and inflammatory markers. Intestinal barrier function, permeability, and systemic LPS levels were evaluated. Mechanistic analysis focused on the GPR120-NF-κB/NLRP3 signaling pathway. Multi-omics profiling including fecal metagenomics, SCFA quantification, and plasma metabolomics were conducted to assess gut microbiota and host metabolic responses.

RESULTS: Our results revealed that ALA therapy significantly mitigated insulin resistance and glucose intolerance in db/db mice. Histopathological analysis revealed a decrease in hepatic steatosis following ALA administration, alongside a reduction in inflammatory markers indicative of T2DM. Importantly, our findings demonstrated that ALA mitigates liver inflammation by inhibiting the NF-κB/NLRP3 pathway, possibly via its interaction with GPR120. Beyond this, augmenting ALA bolstered intestinal integrity, minimized permeability, curbed lipopolysaccharide leakage, and suppressed pro-inflammatory cytokine expression within the intestines. Significantly, an integrated multi-omics investigation, encompassing fecal metagenomic sequencing, SCFA evaluation, and plasma non-targeted metabolomics, disclosed a potent correlation between ALA's hypoglycemic efficacy and the modulation of gut microbial community structure, elevation of SCFA synthesis, and enhancement of metabolic signatures.

CONCLUSION: Our study's initial insights indicated that dietary ALA modulates inflammation and metabolism in T2DM via the gut-liver axis, specifically through the GPR120-NF-κB/NLRP3 pathway. This elucidates ALA's dual function in reshaping the gut microbiota and combating systemic inflammation, positioning it as a potentially efficacious dietary component for managing T2DM.},
}

@article {pmid40929831,
year = {2025},
author = {Liu, F and Yang, B and Han, T and Li, F and Wang, L and Xu, H},
title = {Metagenomic and Micro-CT insights into Fe(III)-modulated extracellular polymeric substances driving anammox granulation and enhancement of nitrogen removal.},
journal = {Journal of environmental management},
volume = {393},
number = {},
pages = {127283},
doi = {10.1016/j.jenvman.2025.127283},
pmid = {40929831},
issn = {1095-8630},
abstract = {Multivalent cations are commonly employed to accelerate sludge aggregation and granulation, yet they often compromise intragranular mass transfer and diminish microbial activity. Here, the effect of Fe(III) dosing on granule formation and anammox-driven nitrogen removal over a 110-day continuous operation was investigated. Fe(III) supplementation enhanced interactions with extracellular polymeric substances (EPS), transforming flocculent biomass into highly porous granules and yielding a 67.9 % increase in specific anammox activity (SAA). During the first 30 days of Fe(III) dosing, the Zeta potential shifted from -12.0 to -9.3 mV and EPS content surged from 32.8 mg/g VSS to 49.0 mg/g VSS, accelerating primary floc aggregation. Subsequently, the protein-to-polysaccharide ratio of EPS escalated from 1.7 to 5.3, reflecting a transition from a carbohydrate-rich, hydrophilic gel to a protein-dominated, hydrophobic network that facilitated granulation. Micro-computed tomography revealed that smaller (1.5 mm) granules exhibited dense architectures, whereas larger (2.5 mm) granules developed internal cavities as a result of mass transfer limitations, approaching structural fragmentation. Metagenomic analysis showed that Fe(III) upregulated pathways for hydrophobic amino acids (e.g., isoleucine, leucine, valine) synthesis and downregulated polysaccharide biosynthesis, thereby increasing EPS hydrophobicity and promoting granulation. The observed SAA enhancement was linked to Fe(III)-dependent activation of iron-containing enzymes (e.g., hzs ABC), cytochrome c maturation, and Fe-S cluster assembly. Concurrently, the relative abundance of Ca. Kuenenia rose from 14.1 % during aggregation to 18.6 % after sludge granulation. This work elucidates the mechanism of Fe(III)-EPS-mediated granulation and offers a sustainable strategy to reconcile structural integrity with metabolic efficiency in metal-driven anammox wastewater treatment processes.},
}

@article {pmid40929513,
year = {2025},
author = {Bhaya, D and Birzu, G and Rocha, EPC},
title = {Horizontal Gene Transfer and Recombination in Cyanobacteriota.},
journal = {Annual review of microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-micro-041522-100420},
pmid = {40929513},
issn = {1545-3251},
abstract = {Cyanobacteria played a pivotal role in shaping Earth's early history and today are key players in many ecosystems. As versatile and ubiquitous phototrophs, they are used as models for oxygenic photosynthesis, nitrogen fixation, circadian rhythms, symbiosis, and adaptations to harsh environments. Cyanobacterial genomes and metagenomes exhibit high levels of genomic diversity partly driven by gene flow within and across species. Processes such as recombination and horizontal transfer of novel genes are facilitated by the mobilome that includes plasmids, transposable elements, and bacteriophages. We review these processes in the context of molecular mechanisms of gene transfer, barriers to gene flow, selection for novel traits, and auxiliary metabolic genes. Additionally, Cyanobacteriota are unique because ancient evolutionary innovations, such as oxygenic photosynthesis, can be corroborated with fossil and biogeochemical records. At the same time, sequencing of extant natural populations allows the tracking of recombination events and gene flow over much shorter timescales. Here, we review the challenges of assessing the impact of gene flow across the whole range of evolutionary timescales. Understanding the tempo and constraints to gene flow in Cyanobacteriota can help decipher the timing of key functional innovations, analyze adaptation to local environments, and design Cyanobacteriota for robust use in biotechnology.},
}

@article {pmid40929468,
year = {2025},
author = {Xiang, Y and Man, X and Zhang, H and Chen, M and Yang, R},
title = {Nitrogen removal efficiency and pathways of the simultaneous nitrification and denitrification process under ultra-low oxygen conditions.},
journal = {Environmental technology},
volume = {},
number = {},
pages = {1-12},
doi = {10.1080/09593330.2025.2556497},
pmid = {40929468},
issn = {1479-487X},
abstract = {To explore strategies for further reducing aeration energy consumption in the simultaneous nitrification and denitrification (SND) process, an SND reactor was constructed to treat low carbon-to-nitrogen (C/N) ratio domestic wastewater under ultra-low dissolved oxygen (DO) conditions (DO < 0.05 mg·L[-][1]). The effects of hydraulic retention time (HRT) and C/N ratio on nitrogen removal performance were systematically evaluated, and batch experiments were conducted to determine nitrification and denitrification rates. Under influent condition of 50.0 mg·L[-][1] ammonia and a C/N ratio of 2.2, the reactor maintained stable ultra-low DO levels, achieved effluent ammonia concentrations below 5.0 mg·L[-][1], and attained optimal SND efficiencies exceeding 80.0%. Although a shortened HRT destabilised performance, increasing the C/N ratio successfully restored nitrogen removal stability. Nitrification and denitrification rates ranged from 4.20-30.89 mg·L[-][1]·h[-][1] and 1.57-21.92 mg·L[-][1]·h[-][1], respectively, under C/N ratios from 2.2-8.0. High-throughput sequencing and metagenomic analysis revealed that heterotrophic nitrification and aerobic denitrification dominated nitrogen transformation, with microorganisms utilising low-energy nap and nirK enzymes to adapt to the ultra-low DO environment. These findings provide novel insights into energy-efficient nitrogen removal pathways under ultra-low oxygen conditions.},
}

@article {pmid40929372,
year = {2025},
author = {Huereca, A and Allen, CCG and McMullin, RT and Simon, A and Belosokhov, A and Spribille, T},
title = {Evidence for extensive diversity in the pollen-parasitic genus Retiarius in western North America, including two new species associated with lichens.},
journal = {Mycologia},
volume = {},
number = {},
pages = {1-27},
doi = {10.1080/00275514.2025.2513197},
pmid = {40929372},
issn = {1557-2536},
abstract = {Understanding the diversity of microscopic hyphomycetes is an ongoing effort, and many species remain undescribed. While studying lichen organismal composition in western Canada, metagenomic data revealed the presence of an unknown species of Retiarius (Orbiliaceae, Ascomycota), a genus of pollen-parasitic fungus with no previous records in the region. We developed genus-specific primers to amplify Retiarius DNA in lichen and adjacent substrate extractions, successfully detecting multiple lineages of Retiarius across a wide geographic range within North America. We proceeded to screen accumulations of pollen on the undersurface of lichen thalli to isolate any pollen-associated fungi. Using dilution series and PCR for identification, we isolated two specifically distinct strains of Retiarius with morphology unlike any described member of the genus. Inclusion of DNA from these strains in a multilocus phylogeny using the internal transcribed spacer regions ITS1-5.8S-ITS2 (ITS), partial nuc 28S rDNA (28S), and nuc small subunit (18S) confirmed their evolutionarily distinct position in the genus. We describe these two species here as Retiarius canadensis and R. crescentus. The former possesses trinacrium-shaped conidia, similar to those of R. bovicornutus and R. revayae but morphometrically different, and the latter is distinguished by its canoe-shaped conidia, a morphological character heretofore unknown from Retiarius.},
}

@article {pmid40929115,
year = {2025},
author = {Gonzalez, FL and Kettenburg, G and Ranaivoson, HC and Andrianiaina, A and Andry, S and Raharinosy, V and Randriambolamanantsoa, TH and Lacoste, V and Dussart, P and Héraud, JM and Brook, CE},
title = {Genomic characterization of novel bat kobuviruses in Madagascar: Implications for viral evolution and zoonotic risk.},
journal = {PloS one},
volume = {20},
number = {9},
pages = {e0331736},
doi = {10.1371/journal.pone.0331736},
pmid = {40929115},
issn = {1932-6203},
mesh = {*Chiroptera/virology ; Animals ; Madagascar ; Phylogeny ; *Zoonoses/virology ; *Genome, Viral ; *Evolution, Molecular ; *Viral Zoonoses/virology ; Humans ; Genomics ; High-Throughput Nucleotide Sequencing ; *Picornaviridae Infections/virology/veterinary/epidemiology ; },
abstract = {Kobuviruses (family Picornaviridae, genus Kobuvirus) are enteric viruses that infect a wide range of both human and animal hosts. Much of the evolutionary history of kobuviruses remains elusive, largely due to limited screening in wildlife. Bats have been implicated as major sources of virulent zoonoses, including coronaviruses, henipaviruses, lyssaviruses, and filoviruses, though much of the bat virome still remains uncharacterized. While most bat virus research has historically focused on immediately recognizable zoonotic clades (e.g., SARS-related coronaviruses), a handful of prior reports catalog kobuvirus carriage in bats and posit the role of bats as progenitors of downstream kobuvirus evolution. As part of a multi-year study, we carried out metagenomic Next Generation Sequencing (mNGS) on fecal samples obtained from endemic, wild-caught Madagascar fruit bats to characterize potentially zoonotic viruses circulating within these populations. The wild bats of Madagascar represent diverse Asian and African phylogeographic histories, presenting a unique opportunity for viruses from disparate origins to mix, posing a significant public health threat. Here, we report detection of kobuvirus RNA in Malagasy fruit bats (Eidolon dupreanum) and undertake phylogenetic characterization of Malagasy kobuvirus sequences, which nest within the Aichivirus A clade - a kobuvirus clade known to infect a wide range of hosts including humans, rodents, canids, felids, birds, and bats. Given the propensity of kobuviruses for recombination and cross-species transmission, further characterization of this clade is critical for accurate evaluation of future zoonotic threats.},
}

*Chiroptera/virology
Animals
Madagascar
Phylogeny
*Zoonoses/virology
*Genome, Viral
*Evolution, Molecular
*Viral Zoonoses/virology
Humans
Genomics
High-Throughput Nucleotide Sequencing
*Picornaviridae Infections/virology/veterinary/epidemiology

@article {pmid40928986,
year = {2025},
author = {Miao, Q and Qu, L and Jiang, J and Liu, Q and Zhao, W and Tan, L and Li, J and Cao, W and Wang, B and Xia, X},
title = {Identification and Molecular Characterization of Two Novel Picorna-Like Viruses in Armigeres subalbatus Mosquitoes in Yunnan, China.},
journal = {Vector borne and zoonotic diseases (Larchmont, N.Y.)},
volume = {},
number = {},
pages = {},
doi = {10.1177/15303667251372308},
pmid = {40928986},
issn = {1557-7759},
abstract = {Background: Mosquitoes harbor diverse insect-specific viruses (ISVs) frequently overlooked in arbovirus surveillance. Comprehensive characterization of ISVs is crucial for understanding their impact on host ecology and potential roles in arbovirus transmission. Methods: Using metagenomic sequencing on Armigeres subalbatus from Yunnan, China, we identified two novel picorna-like viruses, assembled their genomes, and conducted phylogenetic analysis. Detection was confirmed via RT-PCR and Sanger sequencing. Results: Both viruses are closely related to Hubei picorna-like virus 59, previously reported in spiders but unconfirmed. This work provides the first genomic evidence of this lineage in mosquitoes. Conclusion: This study characterizes two novel ISVs, expanding known picorna-like virus diversity and offering insights into cross-species virus evolution and arbovirus ecology.},
}

@article {pmid40928296,
year = {2025},
author = {Martinez, A and Ruth, N and Hatch, A and Chain, P and Shakya, M},
title = {Aerosol biome of a cafeteria and medical facility in Los Alamos, New Mexico, USA.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0076625},
doi = {10.1128/mra.00766-25},
pmid = {40928296},
issn = {2576-098X},
abstract = {Aerosol sampling with next-generation sequencing was used to characterize microbial communities in a cafeteria and medical facility waiting room in Los Alamos, New Mexico, USA. We detected sequences from human, bacteria, archaea, fungi, other eukaryotes, and viruses, providing insights into the diversity of the aerosol microbiome.},
}

@article {pmid40928292,
year = {2025},
author = {Fujii, C and Vernon, S and Félix, M-A and Wang, D},
title = {Orsay virus variants isolated from wild Caenorhabditis elegans nematodes, France.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0055025},
doi = {10.1128/mra.00550-25},
pmid = {40928292},
issn = {2576-098X},
abstract = {Four new variants of Orsay virus were identified from wild isolates of Caenorhabditis elegans nematodes collected from decaying plant matter in France. Near-complete genomes of the viruses were determined by metagenomic sequencing. The four genomes share 96.1-98.9% nucleotide identity with the reference Orsay virus sequence JUv1580.},
}

@article {pmid40928236,
year = {2025},
author = {Liu, D and Hu, J and Zhang, D and Ren, S and Zhao, L and Gao, H and Hu, S and Xu, S and Liang, G},
title = {Use of the CHM13-T2T genome improves metagenomic analysis by minimizing host DNA contamination.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0084025},
doi = {10.1128/msystems.00840-25},
pmid = {40928236},
issn = {2379-5077},
abstract = {Human-associated metagenomic data often contain human nucleic acid information, which can affect the accuracy of microbial classification or raise ethical concerns. These reads are typically removed through alignment to the human genome using various metagenomic mapping tools or human reference genomes, followed by filtration before metagenomic analysis. In this study, we conducted a comprehensive analysis to identify the optimal combination of alignment software and human reference genomes using benchmarking data. Our findings show that the combination of bwa-mem and the telomere-to-telomere human genome (CHM13-T2T) is the most effective in removing human reads in simulated data. We also analyzed CHM13-T2T-derived sequences in RefSeq to understand how CHM13-T2T reduces false positive results. Finally, we assessed clinical samples and found that CHM13-T2T effectively reduces host-derived contamination, particularly in low microbial biomass samples. This study provides a thorough overview of the application of CHM13-T2T in metagenomic analysis and highlights its significance in improving microbial classification accuracy.IMPORTANCEHuman gene sequences account for a large proportion of metagenomic sequences. To gain accurate and precise microbiome information, effective host-derived contamination removal methods are required. Both the alignment algorithm and the reference genome could influence the effectiveness of this process. The telomere-to-telomere human genome (CHM13-T2T) is a state-of-the-art human genome with 216 Mbp of additional new sequences compared with the commonly used GRCh38.p14. Our findings show the optimal dehosting effect of CHM13-T2T combined with the bwa-mem software in metagenomic analysis. We also investigate the reasons for the superiority of CHM13-T2T. Our study provides insights into optimal strategies for host sequence removal from metagenomic data. A standard reference is proposed for future metagenomic analysis, which can improve the accuracy of microbial identification.},
}

@article {pmid40928232,
year = {2025},
author = {Allman, HM and Bernate, EP and Franck, E and Oliaro, FJ and Hartmann, EM and Crofts, TS},
title = {Preparation of functional metagenomic libraries from low biomass samples using METa assembly and their application to capture antibiotic resistance genes.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0103925},
doi = {10.1128/msystems.01039-25},
pmid = {40928232},
issn = {2379-5077},
abstract = {A significant challenge in the field of microbiology is the functional annotation of novel genes from microbiomes. The increasing pace of sequencing technology development has made solving this challenge in a high-throughput manner even more important. Functional metagenomics offers a sequence-naive and cultivation-independent solution. Unfortunately, most methods for constructing functional metagenomic libraries require large input masses of metagenomic DNA, putting many sample types out of reach. Here, we show that our functional metagenomic library preparation method, METa assembly, can be used to prepare useful libraries from much lower input DNA quantities. Standard methods of functional metagenomic library preparation generally call for 5-60 µg of input metagenomic DNA. We demonstrate that the threshold for input DNA mass can be lowered at least to 30.5 ng, a 3-log decrease from prior art. We prepared functional metagenomic libraries using between 30.5 ng and 100 ng of metagenomic DNA and found that despite their limited input mass, they were sufficient to link MFS transporters lacking substrate-specific annotations to tetracycline resistance and capture a gene encoding a novel GNAT family acetyltransferase that represents a new streptothricin acetyltransferase, satB. Our preparation of functional metagenomic libraries from aquatic samples and a human stool swab demonstrates that METa assembly can be used to prepare functional metagenomic libraries from microbiomes that were previously incompatible with this approach.IMPORTANCEBacterial genes in microbial communities, including those that give resistance to antibiotics, are often so novel that sequencing-based approaches cannot predict their functions. Functional metagenomic libraries offer a high-throughput, sequence-naive solution to this problem, but their use is often held back due to their need for large quantities of metagenomic DNA. We demonstrate that our functional metagenomic library preparation method, METa assembly, can prepare these libraries using as little as ~30 ng of DNA, approximately 1,000-fold less than other methods. We use METa assembly to prepare functional metagenomic libraries from low-biomass aquatic and fecal swab microbiomes and show that they are home to novel tetracycline efflux pumps and a new family of streptothricin resistance gene, respectively. The efficiency of the METa assembly library preparation method makes many otherwise off-limits, low-biomass microbiome samples compatible with functional metagenomics.},
}

@article {pmid40928220,
year = {2025},
author = {Dong, L and Yang, J and Wu, H and Sun, Y and Liu, J and Yuan, H and Wang, M and Dai, Y and Teng, F and Jing, G and Yang, F},
title = {Metagenomic research on the structural difference of plaque microbiome from different caries stages and the construction of a caries diagnostic model.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0004425},
doi = {10.1128/msystems.00044-25},
pmid = {40928220},
issn = {2379-5077},
abstract = {Development of dental caries is a dynamic process; yet, there is limited knowledge on microbial differences at various stages of caries at higher resolution. To investigate the shifting microbiome profiles across different caries stages, 30 children were enrolled in this study, including 15 caries-active patients and 15 caries-free individuals. Plaque samples were collected from the buccal surface of caries-free subjects, defined as confident health (CH; n = 15). For caries-active individuals, plaque samples were collected from non-cavitated surfaces (defined as relative health [RH], n = 15), enamel caries (EC; n = 15), and dentin caries samples (DC; n = 15). All the above samples were sequenced through the 2bRAD sequencing platform to reveal the microbial community structures in each group. We identified significant differences in microbial community structures from different caries stages. First, the CH group showed the highest species richness (P < 0.05), and then followed by the RH and EC groups with lower richness, and the lowest richness was found in the DC group, yet no significant difference was found among the last three groups (P > 0.05). Second, the microbial structure exhibited the greatest difference between CH and DC groups, followed by the distance between RH/EC and DC groups, and the smallest difference was found between RH and EC groups. Third, specific species were found with a significant difference during the different caries stages. Therefore, we developed a diagnostic model using deep learning methods based on neural networks to diagnose different caries stages with an AUC of over 98%. This may provide methodological support for the understanding of the etiological factor in the pathological progression of dental caries.IMPORTANCEThe diagnosis and treatment of dental caries are crucial for human oral health. Previous studies have focused on the microbial differences between caries and healthy teeth, but there was not enough knowledge on the microbial differences at different stages of dental caries. Our findings could provide a high-resolution understanding of the microbial divergencies among different stages of dental caries and thus build microbial-based diagnostic models for differentiating dental caries status using deep learning methods with an accuracy of over 98%. This may provide methodological support for the understanding of the etiological factor in the pathological progression of dental caries.},
}

@article {pmid40928217,
year = {2025},
author = {Russell, JN and Kos, D and Yacoub, E and Sies, AN and Warr, B and Jelinski, M and Ruzzini, A and Cameron, ADS},
title = {Enhanced metagenomic surveillance for bovine respiratory disease pathogens and antimicrobial resistance by hybridization capture sequencing.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0097725},
doi = {10.1128/aem.00977-25},
pmid = {40928217},
issn = {1098-5336},
abstract = {UNLABELLED: Bovine respiratory disease (BRD) is the primary disease of cattle and is responsible for most of the antibiotic use in the beef industry, both for metaphylaxis and treatment. Infection prevention and targeted treatments would benefit from detecting and identifying bacterial pathogens and, ideally, assessing antibiotic sensitivity. Here, we report success refining targeted metagenomics by hybridization capture sequencing (CapSeq) to detect and genotype bacterial pathogens and genes for antibiotic resistance in BRD. We developed a novel multi-locus sequence typing (MLST) strategy to both enhance assay sensitivity and provide epidemiological data compatible with traditional typing assays. Phylogenetically informed panel design by ProbeTools coupled with hybridization capture enabled the sequencing of novel genotypes and elucidated coinfection by distinct strains of Mycoplasmopsis bovis. CapSeq was orders of magnitude more sensitive than classical metagenomics at a scale compatible with low-throughput DNA sequencing capacity in diagnostic laboratories. Iterative design and testing of longer typing loci confirmed improvements in locus detection through a strategy applicable to future target selection. CapSeq detected bacterial pathogens that evaded detection by traditional metagenomics, and it demonstrated greater range and sensitivity for antibiotic resistance gene detection.

IMPORTANCE: Shotgun metagenomic sequencing for infectious disease diagnostics and surveillance benefits from simultaneous detection of multiple pathogens in a sample. Adding a hybridization probe capture step to the metagenomics workflow enriches targeted loci to improve the sensitivity of pathogen detection without compromising the ability to detect pathogen variants. Our custom probe panel enables multi-locus sequence typing of bovine respiratory disease agents as well as capture of antibiotic resistance genes, which improves the sensitivity of metagenomic testing and provides genotyping data compatible with traditional assays. This study demonstrates the utility of new design principles for probe panels; it also demonstrates how targeted metagenomics provides important new insights into co-infections and is equally useful for surveillance of environmental reservoirs of disease agents.},
}

@article {pmid40928095,
year = {2025},
author = {Darwiche, L and Goff, JL},
title = {Beyond tellurite: the multifunctional roles of genes annotated as tellurium resistance determinants in bacteria.},
journal = {Critical reviews in microbiology},
volume = {},
number = {},
pages = {1-21},
doi = {10.1080/1040841X.2025.2555936},
pmid = {40928095},
issn = {1549-7828},
abstract = {The metalloid tellurium (Te) is toxic to bacteria; however, the element is also extremely rare. Thus, most bacteria will never encounter Te in their environment. Nonetheless significant research has been performed on bacterial Te resistance because of the medical applications of the element. The so-called "tellurium resistance (Te[R]) genes" were first described on plasmids isolated from clinically relevant Enterobacteriaceae. With time, it has become apparent that, given the rarity of Te on the planet, these genes may have functions beyond tellurium resistance. Nonetheless, the description of these genes as "tellurium resistance genes" has persisted. In this review, we first examine the history and discovery of the Te[R] genes. We then performed an analysis of 184,000 high-quality, prokaryotic (meta)genomes, which revealed that terZABCDF, telA, and tehAB are relatively common in genome annotations and that they are frequently described as "tellurium resistance genes". We synthesized the literature to describe the functions of these ubiquitous genes beyond tellurium resistance. These genes have functions in diverse cellular processes including phage resistance, antibiotic resistance, virulence, oxidative stress resistance, cell cycle regulation, metal resistance, and metalation of exoenzymes. Considering this analysis, we propose that it is time to appreciate the multifunctional nature of the "tellurium resistance genes".},
}

@article {pmid40927879,
year = {2025},
author = {Wang, X and Wang, J and Chen, J and Bezemer, TM and Song, Z and Wanek, W and Liu, G and Zhang, C},
title = {Environmental Stresses Constrain Soil Microbial Community Functions by Regulating Deterministic Assembly and Niche Width.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e70096},
doi = {10.1111/mec.70096},
pmid = {40927879},
issn = {1365-294X},
support = {2023YFF1305103//National Key Research and Development Program of China/ ; 42130717//National Sciences Foundation of China/ ; 42177449//National Sciences Foundation of China/ ; 2024JC-JCQN-35//Shaanxi Provincial Science Fund for Distinguished Young Scholars/ ; },
abstract = {Increasing evidence indicates that the loss of soil microbial α-diversity triggered by environmental stress negatively impacts microbial functions; however, the effects of microbial α-diversity on community functions under environmental stress are poorly understood. Here, we investigated the changes in bacterial and fungal α- diversity along gradients of five natural stressors (temperature, precipitation, plant diversity, soil organic C and pH) across 45 grasslands in China and evaluated their connection with microbial functional traits. By quantifying the five environmental stresses into an integrated stress index, we found that the bacterial and fungal α-diversity declined under high environmental stress across three soil layers (0-20 cm, 20-40 cm and 40-60 cm). Metagenomic-based analyses showed that the diversity of functional genes decreased along the stress gradients. High stress enhanced the abundance of genes associated with broad functional categories (e.g., glycolysis/gluconeogenesis, TCA cycle, DNA replication/repair and cell growth/death) but reduced the abundance of genes linked to specialised functional categories (e.g., C, N, S and methane metabolism). Phylogenetic null models and niche analyses indicated that stochastic assembly processes predominated in high-diversity communities, in which bacterial and fungal taxa had a narrow ecological niche. However, in low-diversity communities, deterministic assembly processes were dominant, and taxa had wide niches, correlating with the reduction in gene abundance observed for broad and specialised functional categories. Given the essential role of the microbiome in regulating ecosystem functions, our findings suggest that low-diversity-induced deterministic community assembly processes and a wide niche under high environmental stress may regulate microbial functions. These findings emphasise the ecological mechanisms through which microbial biodiversity regulates terrestrial ecosystem functioning.},
}

@article {pmid40927726,
year = {2025},
author = {Eiman, L and Moazzam, K and Anjum, S and Kausar, H and Sharif, EAM and Ibrahim, WN},
title = {Gut dysbiosis in cancer immunotherapy: microbiota-mediated resistance and emerging treatments.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1575452},
pmid = {40927726},
issn = {1664-3224},
mesh = {Humans ; *Dysbiosis/immunology/therapy ; *Gastrointestinal Microbiome/immunology ; *Neoplasms/therapy/immunology/microbiology ; *Immunotherapy/methods ; Animals ; *Drug Resistance, Neoplasm ; Probiotics/therapeutic use ; Fecal Microbiota Transplantation ; Tumor Microenvironment/immunology ; },
abstract = {Cancer is a multifaceted disease driven by a complex interplay of genetic predisposition, environmental factors and lifestyle habits. With the accelerating pace of cancer research, the gut microbiome has emerged as a critical modulator of human health and immunity. Disruption in the gut microbial populations and diversity, known as dysbiosis, has been linked with the development of chronic inflammation, oncogenesis, angiogenesis and metastasis. This review discusses the microbial species associated with various types of cancer and the pathways involved in their tumorigenic effect including mechanisms like inflammatory cytokine response, immune modulation, genotoxicity and modification of the tumor microenvironment. Diagnostic tools such as metagenomics, metabolomics, and the use of dysbiosis indexes help in the detection of gut bacterial imbalances, enabling early detection of cancer and potential intervention. Gut dysbiosis diminishes the efficacy of cancer treatments including immunotherapies, and creates immunotherapy resistance by altering drug metabolism and driving immunometabolic reprogramming, allowing tumor cells to evade immune attack. Immunometabolic reprogramming through gut microbiota modulation provides a new avenue to be explored that can restore anti-tumor immunity and reverse resistance to cancer treatments. This review also highlights the use of fecal microbiota transplantation and probiotics to mitigate chances of dysbiosis-related cancer progression. Through a comprehensive assessment of the role of gut microbiota in cancer, this review underscores the need for the use of gut microbial biomarkers for cancer detection and microbiome-targeting strategies to individualize cancer treatment.},
}

Humans
*Dysbiosis/immunology/therapy
*Gastrointestinal Microbiome/immunology
*Neoplasms/therapy/immunology/microbiology
*Immunotherapy/methods
Animals
*Drug Resistance, Neoplasm
Probiotics/therapeutic use
Fecal Microbiota Transplantation
Tumor Microenvironment/immunology

@article {pmid40927460,
year = {2025},
author = {Feng, Y and Chang, Q and Zhou, H and Zhang, W and Xie, L and Deng, X and Chen, T and Liu, W},
title = {Effects of gut microbiota on cognitive impairment in Parkinson's disease: a comprehensive Mendelian randomization and case-control study.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1620449},
pmid = {40927460},
issn = {1664-302X},
abstract = {BACKGROUND: Increasing evidence suggests a potential role of the gut microbiota in Parkinson's disease (PD). However, the relationship between the gut microbiome (GM) and PD dementia (PDD) remains debated, with their causal effects and underlying mechanisms not yet fully understood.

METHODS: Utilizing data from large-scale genome-wide association studies (GWASs), this study applied bidirectional and mediating Mendelian randomization (MR) to investigate the causal relationship and underlying mechanisms between the GM and PDD. In our analysis, inverse-variance weighting (IVW) was used as the primary method. Clinical validation was performed using metagenomic sequencing and bioinformatic analysis. The relationships between the GM and PDD were visualized using receiver operating characteristic (ROC) curves, confusion matrices, and correlation analyses.

RESULTS: Our study revealed a significant causal impact of five GM genera, 10 metabolites, two metabolite ratios, and 22 immune cells on PDD. Notably, the maltose to sucrose ratio was identified as a mediator of the positive causal effect of Subdoligranulum on PDD, with a mediation value of 13.2%. The clinical samples confirmed the efficacy of Subdoligranulum sp. in distinguishing patients with PDD from normal controls (area under the curve (AUC) = 0.80, 95% CI: 0.674-0.924). In addition, correlation analysis revealed a potential negative association between Subdoligranulum abundance and the Mini-Mental State Examination (MMSE) scores (r = -0.316, p = 0.006). Finally, bioinformatic analysis suggested that Subdoligranulum may influence PDD risk through the regulation of starch and sucrose metabolism pathways.

CONCLUSION: Our study confirms the potential role of Subdoligranulum in PDD progression, potentially mediated through starch and sucrose metabolism. These findings highlight the importance of the gut-brain axis in PDD and may provide insights into targeted interventions for PDD.},
}

@article {pmid40927458,
year = {2025},
author = {Li, Y and Duan, Y and Zhang, J and Petropoulos, E and Zhao, J and Wu, F and Wang, L and Chen, Y and Wang, X},
title = {Structure and function of the topsoil microbiome in Chinese terrestrial ecosystems.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1595810},
pmid = {40927458},
issn = {1664-302X},
abstract = {While soil microorganisms underpin terrestrial ecosystem functioning, how their functional potential adapts across environmental gradients remains poorly understood, particularly for ubiquitous taxa. Employing a comprehensive metagenomic approach across China's six major terrestrial ecosystems (41 topsoil samples, 0-20 cm depth), we reveal a counterintuitive pattern: oligotrophic environments (deserts, karst) harbor microbiomes with significantly greater metabolic pathway diversity (KEGG) compared to resource-rich ecosystems. We provide a systematic catalog of key functional genes governing biogeochemical cycles in these soils, identifying: 6 core CAZyme genes essential for soil organic carbon (SOC) decomposition and biosynthesis; 62 nitrogen (N)-cycling genes (KOs) across seven critical enzymatic clusters; 15 sulfur (S)-cycling genes (KOs) within three key enzymatic clusters. These functional gene abundances exhibit distinct, geography-driven clustering patterns, strongly correlated with eight environmental drivers (latitude, NDVI, pH, EC, SOC, TN, C:N ratio, and MAP). This work provides a predictive framework and actionable genetic targets (e.g., specific CAZyme, N/S cycling genes) for potentially manipulating soil microbiomes to enhance ecosystem resilience and biogeochemical functions under stress.},
}

@article {pmid40926888,
year = {2025},
author = {Chen, WY and Lan, YC and Chen, JW and Wu, JH},
title = {Genomic personalities of Dehalococcoides subspecies and Dehalogenimonas illuminate complete trichloroethene dechlorination in high-salt conditions.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf101},
pmid = {40926888},
issn = {2730-6151},
abstract = {Global salinization increasingly threatens ecosystem integrity and the regulation of biogeochemical cycles. Our study reveals novel insights into the microbial contributions to the organohalide decomposition in saline environments, demonstrating the unprecedented ability of organohalide-respiring bacteria Dehalococcoides and Dehalogenimonas to completely dechlorinate trichloroethene to non-toxic ethene under hypersaline conditions (up to 31.3 g/L) in long-term operations. Using gradient salinity reactors and metagenomic analyses, we identified the evolved genomic features associated with high-salt tolerance. The Cornell subgroup of Dehalococcoides and Dehalogenimonas exhibit significantly lower average protein isoelectric points and retain the ribosomal protein L33p gene, unlike the Victoria and Pinellas subgroups. Dehalococcoides shows subspecies-level genomic divergence and unique codon usage biases. Intriguingly, the L33p gene is found in diverse bacterial phyla from saline environments, suggesting it may provide a growth advantage under salt stress. These genomic traits, hypothesized to enhance salt tolerance and dechlorination efficiency under salt stress, correlate with performance at elevated salinity. Our findings advance the understanding of microbial salt adaptation mechanisms and support the development of bioremediation strategies tailored for saline environments.},
}

@article {pmid40926875,
year = {2025},
author = {Zhao, J and Ye, J},
title = {Diagnostic Challenges of Six-Pathogen Detected by mNGS in an Immunocompromised ICU Patient with Severe Community-Acquired Pneumonia-Induced Sepsis: A Case Report and Literature Review.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {4659-4665},
pmid = {40926875},
issn = {1178-6973},
abstract = {INTRODUCTION: Severe community-acquired pneumonia (SCAP) in immunocompromised patients is often caused by rare atypical pathogens, which are difficult to detect using conventional microbiological tests (CMTs) and can progress to sepsis in severe cases. Metagenomic next-generation sequencing (mNGS), an emerging pathogen detection technique, enables rapid identification of mixed infections and provides valuable guidance for clinical treatment decisions. SCAP-induced sepsis caused by a six-pathogen co-infection has not been previously reported, but interpretation remains a challenge.

CASE PRESENTATION: This report describes a case of SCAP-induced sepsis detected six pathogens by mNGS in a patient with IgA nephropathy who developed immunosuppression following long-term treatment with rituximab and corticosteroids. Bronchoalveolar lavage fluid (BALF) mNGS detected six pathogens, including Pneumocystis jirovecii, Klebsiella pneumoniae, Primate bocaparvovirus 1, Cytomegalovirus, Elizabethkingia anophelis, and Candida albicans. The patient was admitted to the intensive care unit (ICU) and received a combination of meropenem, trimethoprim-sulfamethoxazole, ganciclovir, piperacillin-tazobactam, and caspofungin. Following appropriate treatment, the patient recovered and was successfully discharged.

CONCLUSION: mNGS offers significant advantages for the diagnosis and identification of mixed infections in immunocompromised patients with SCAP-induced sepsis. It enables clinicians to initiate timely and targeted antimicrobial therapy, which facilitates early recovery, reduces the overuse of broad-spectrum antibiotics, and ultimately improves patient prognosis. Nevertheless, its interpretation requires caution, as distinguishing true pathogens from colonizers or contaminants still relies on clinical correlation and complementary diagnostic methods.},
}

@article {pmid40926846,
year = {2025},
author = {Prihambodo, TR and Mulianda, R and Wulandari, W and Anggrahini, S and Qomariyah, N and Ella, A and Winarti, E and Yusriani, Y and Suyatno, S and Firison, J and Fitra, D and Harahap, AE and Sari, DAP and Hidayat, T and Jayanegara, A},
title = {Scopus-based bibliometric analysis of research trends in silage feed and its impact on rumen fermentation in ruminants.},
journal = {Veterinary world},
volume = {18},
number = {7},
pages = {1972-1990},
pmid = {40926846},
issn = {0972-8988},
abstract = {BACKGROUND AND AIM: Silage plays a pivotal role in ruminant nutrition, significantly influencing rumen fermentation, animal productivity, and environmental sustainability. Despite extensive research on silage and fermentation, a comprehensive synthesis of global trends and collaborations in this domain has not been systematically explored. This study aimed to conduct a bibliometric analysis of global research on silage feed and its effects on rumen fermentation in ruminants. It sought to identify publication trends, leading contributors, research themes, and international collaboration networks, thereby informing future directions in ruminant nutrition research.

MATERIALS AND METHODS: A total of 1,007 documents published between 1961 and 2024 were retrieved from the Scopus database using targeted keywords. Bibliometric and network analyses were performed using VOSviewer, Bibliometrix (R package), and Microsoft Excel. Inclusion criteria were limited to peer-reviewed English-language articles focused on silage feed and rumen fermentation in ruminants. Data cleaning and preprocessing involved harmonization of author names, keywords, and institutional affiliations.

RESULTS: Publication output has increased significantly since 2010, with China, the United States, and Canada emerging as the top contributors. Major research themes include silage quality, microbial fermentation, methane mitigation, and feed efficiency. Core journals identified include Journal of Dairy Science and Journal of Animal Science. Leading institutions such as China Agricultural University and the University of Florida demonstrated high productivity and citation impact. Keyword analysis highlighted emerging trends, including microbiome, methanogenesis, and sustainability. Collaboration network analysis revealed strong regional clusters, with North America and Europe forming central hubs, while Asia and South America showed growing but less integrated networks.

CONCLUSION: Research on silage and rumen fermentation has evolved from foundational studies to interdisciplinary approaches integrating microbiology, environmental science, and precision agriculture. The field is rapidly expanding, with increasing emphasis on reducing methane emissions and enhancing livestock performance through improved silage practices. However, global collaboration remains fragmented, particularly in underrepresented regions. Future research should focus on metagenomics, smart technologies (e.g., Artificial Intelligence and Internet of Things), and policy-driven strategies to optimize feed systems and support sustainable livestock production.},
}

@article {pmid40926709,
year = {2025},
author = {Zhao, R and He, G and Zhou, D and Li, X and Kuyper, TW and Zhang, F and Zhang, J},
title = {Arbuscular mycorrhizal fungi enhance nitrate ammonification in hyphosphere soil.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70561},
pmid = {40926709},
issn = {1469-8137},
support = {U23A2054//National Natural Science Foundation of China/ ; 42377128//National Natural Science Foundation of China/ ; 201913043//China Scholarship Council/ ; 201906350223//China Scholarship Council/ ; },
abstract = {Microbial nitrate ammonification is a crucial process to retain nitrogen (N) in soils, thereby reducing N loss. Nitrate ammonification has been studied in enrichment and axenic bacterial cultures but so far has been merely ignored in environmental studies. In particular, the capability of arbuscular mycorrhizal fungi (AMF) to regulate nitrate ammonification has not yet been explored. Here, nitrate ion ([15]NO3 [-]) was used to trace N transformations in hyphosphere and bulk soils. Metagenomic analysis was conducted, and cross-kingdom interactions between AMF and an isolated nirBD-carrying Paenibacillus sp. strain DP01 from hyphosphere soil were investigated. AMF hyphae significantly increased ammonium ion (NH4 [+]) concentration and [15]NH4 [+] derived from [15]NO3 [-] in hyphosphere soil, which were 1.42 and 5.01 times as high as those in bulk soil. Metagenomic analysis showed that the nirB gene involved in nitrite reduction to ammonium was prevalent in hyphosphere and bulk soils. Hyphal exudates enhanced ammonification efficiency and biofilm formation of the nitrite-ammonifying strain DP01. Additionally, accelerated oxygen depletion was detected on hyphal surface. This study demonstrates a novel interaction in which AMF significantly enhanced nitrate ammonification in the hyphosphere. Given the widespread presence of nitrate-ammonifying microbes in soils, this newly described interkingdom interaction offers guidance for agricultural practices aimed at increasing N efficiency and environmental sustainability.},
}

@article {pmid40926344,
year = {2025},
author = {Sarango Flores, S and Cordovez, V and Oyserman, BO and Arias Giraldo, LM and Stopnisek, N and Raaijmakers, JM and van 't Hof, P},
title = {Microbiome-Mediated Resistance of Wild Tomato to the Invasive Insect Prodiplosis longifila.},
journal = {Environmental microbiology reports},
volume = {17},
number = {5},
pages = {e70190},
doi = {10.1111/1758-2229.70190},
pmid = {40926344},
issn = {1758-2229},
support = {024.004.014/NWO_/Dutch Research Council/Netherlands ; CZ07-000440-2018//SENESCYT scholarship/ ; 10093//Chancellor Research Grant/ ; },
mesh = {*Solanum lycopersicum/microbiology/parasitology/immunology ; Animals ; *Microbiota ; *Soil Microbiology ; *Diptera/physiology ; Ecuador ; Plant Roots/microbiology/parasitology ; Introduced Species ; Bacteria/classification/genetics/isolation & purification ; Plant Leaves/parasitology ; },
abstract = {Plant roots are colonised by diverse communities of microorganisms that can affect plant growth and enhance plant resistance to (a) biotic stresses. We investigated the role of the indigenous soil microbiome in the resistance of tomato to the invasive sap-sucking insect Prodiplosis longifila (Diptera: Cecidomyiidae). Native and agricultural soils were sampled from the Andes in Southern Ecuador and tested, in greenhouse bioassays, for leaf tissue damage caused by P. longifila on domesticated Solanum lycopersicum cv. Moneymaker and wild tomato S. pimpinellifolium. We observed no significant differences in insect damage between domesticated and wild tomatoes grown in live native or agricultural soils. However, when grown in sterilised native and agricultural soils, wild tomato was more severely affected by the insect than the domesticated tomato. Microbiome analyses revealed that soil sterilisation impacted overall rhizobacterial diversity and abundance in wild tomato. Particularly, Actinoplanes abundance was reduced upon sterilisation, which significantly correlated with loss of insect resistance. Metagenome analyses and genome assembly of Micromonosporaceae (Actinoplanes family) suggested a putative association between motility, chemotaxis, membrane transport, chorismate, and lanthipeptide biosynthesis and insect resistance. This indicates that wild S. pimpinellifolium, in contrast to domesticated S. lycopersicum, relies on specific members of the root-associated microbiome for P. longifila protection.},
}

*Solanum lycopersicum/microbiology/parasitology/immunology
Animals
*Microbiota
*Soil Microbiology
*Diptera/physiology
Ecuador
Plant Roots/microbiology/parasitology
Introduced Species
Bacteria/classification/genetics/isolation & purification
Plant Leaves/parasitology

@article {pmid40925458,
year = {2025},
author = {Zhao, Z and Gao, B and Henawy, AR and Ur Rehman, K and Ho, JWK and Xue, Y and Wu, J and Jiménez, N and Subirats, J and Zheng, L and Huang, F and Yu, C and Zhang, J and Cai, M},
title = {Effects of chicken manure-derived black soldier fly organic fertilizer on soil carbon and nitrogen cycling: insights from metagenomic and microbial network analysis.},
journal = {Environmental research},
volume = {},
number = {},
pages = {122775},
doi = {10.1016/j.envres.2025.122775},
pmid = {40925458},
issn = {1096-0953},
abstract = {Black soldier fly (BSF) organic fertilizer is known to enhance soil fertility and promote plant growth. However, its effects on soil carbon (C) and nitrogen (N) cycling remains unclear. In this study, we established a BSF chicken manure bioconversion system to produce BSF organic fertilizer and investigate its impacts on soil C and N cycling, as well as microbial ecological networks through metagenomic analysis. Compared to the control, BSF organic fertilizer significantly increased soil organic matter by 16.1% (p < 0.05) and total potassium by 11.0% (p < 0.05). Metagenomic sequencing revealed that BSF organic fertilizer significantly enhanced soil C and N cycling. For instance, the abundance of carbon fixation genes such as Calvin-Benson-Bassham (CBB) cycle genes pyc, pycA, and pycB increased by 35.7% (p < 0.01), 107.1% (p < 0.001), and 14.6% (p < 0.05), respectively. In nitrogen cycling, denitrification genes nirB, nirK, and nirS increased by 181.5 % (p < 0.001), 102.7% (p < 0.001), and 25.9% (p < 0.05), respectively. Furthermore, soils amended with BSF organic fertilizer displayed a 9.9% higher proportion of positive microbial interactions, particularly enhancing synergistic associations between bacteria and fungi, suggesting improved microbial community stability. Importantly, bacteria and fungi were interdependent in regulating C and N cycling processes, together orchestrating soil ecosystem functions. Overall, BSF organic fertilizers effectively promoted soil C and N cycling and maintained the stability of microbial communities. These findings provide valuable insights for the rational selection of fertilizers and the optimization of fertilization management practices, thereby contributing to the sustainable development of agricultural production.},
}

@article {pmid40779866,
year = {2025},
author = {Lin, XQ and Li, ZL and Chen, XQ and Wang, L and Yu, L and Wang, AJ},
title = {Microbial synergistic metabolic mechanism of enhanced tetrabromobisphenol A removal by bio-electrochemical system coupled constructed wetland.},
journal = {Journal of hazardous materials},
volume = {496},
number = {},
pages = {139382},
doi = {10.1016/j.jhazmat.2025.139382},
pmid = {40779866},
issn = {1873-3336},
mesh = {Biodegradation, Environmental ; *Bioreactors/microbiology/statistics & numerical data ; Desulfovibrio/metabolism ; Geobacter/metabolism ; Metagenome ; *Microbiota ; Nitrates/metabolism ; *Polybrominated Biphenyls/metabolism ; *Water Pollutants, Chemical/metabolism ; *Water Purification/methods/statistics & numerical data ; Wetlands ; Electrochemical Techniques ; },
abstract = {The widespread existence of tetrabromobisphenol A (TBBPA) in the aquatic environment requires efficient treatment technology. The feasibility and related molecular mechanisms for the simultaneous deep removal of nitrate and TBBPA in a bio-electrochemical system coupled with a constructed wetland (BES-CW) are unclear. This study fabricated the BES-CW to achieve simultaneously deep removal of nitrate and TBBPA. TBBPA majorly went through reductive debromination, hydrolytic debromination, ring-cleavage, and oxidation in the open and closed circuits of BES-CW. Electricity activated key genes encoded in oxidoreductase (pflA, pflX) and oxygenase (dmpB, pobA) from electroactive bacteria (Geobacter and Desulfovibrio), accelerating TBBPA metabolites' oxidation and mineralization. Nitrate enriched the Acinetobacter and stimulated genes encoded in hydrolytic dehalogenase, inducing TBBPA hydrolytic debromination and further mineralization. Electricity and nitrate synergistically enhance TBBPA degradation and mineralization, guiding the advanced treatment of emerging pollutants in the aquatic environment.},
}

Biodegradation, Environmental
*Bioreactors/microbiology/statistics & numerical data
Desulfovibrio/metabolism
Geobacter/metabolism
Metagenome
*Microbiota
Nitrates/metabolism
*Polybrominated Biphenyls/metabolism
*Water Pollutants, Chemical/metabolism
*Water Purification/methods/statistics & numerical data
Wetlands
Electrochemical Techniques

@article {pmid40925130,
year = {2025},
author = {Sahu, KK and Yadav, K and Pradhan, M and Sharma, M and Dubey, A and Sucheta, and Kirubakaran, JJ},
title = {Pharmacological insights into gut microbiota modulation in systemic lupus erythematosus: Mechanisms, treatment strategies, and clinical implications.},
journal = {The Journal of pharmacology and experimental therapeutics},
volume = {392},
number = {9},
pages = {103659},
doi = {10.1016/j.jpet.2025.103659},
pmid = {40925130},
issn = {1521-0103},
abstract = {Systemic lupus erythematosus (SLE) is a complex autoimmune disease characterized by widespread inflammation and immune system dysregulation. Recent research suggests that the gut microbiota may play a role in the development of SLE by modulating immune system responses, affecting cytokine production, and altering the activity of T and B cells lymphocytes. As a result, there is a growing interest in microbiota-targeted therapies, including probiotics, dietary changes, and fecal microbiota transplantation. These methods may help restore the balance of microbes and reduce disease activity, but there are still a number of problems to solve. For example, microbiota composition varies greatly from person to person, and it is not clear how dysbiosis causes disease onset. There are also safety concerns about fecal microbiota transplantation. Experimental and clinical studies have started to shed light on the complicated ways in which microbial communities and immune function affect each other in SLE. These studies provide useful information, but their results are often inconsistent. As research continues, integrative methods like metagenomics and metabolomics may help find microbial signatures linked to disease, helping create more accurate and personalized treatments. The gut microbiome is a promising yet still developing area of research that could help us learn more about autoimmune diseases and their treatment, such as SLE. SIGNIFICANCE STATEMENT: Grasping the complex interplay between gut microbiota and systemic lupus erythematosus (SLE) has provided an avenue for therapeutic intervention. This study emphasizes the importance of gut dysbiosis in immune dysregulation, with connections between microbial translocation, molecular mimicry, and inflammatory pathways as contributing factors to the progression of SLE. This work sets the stage for novel and targeted approaches to treating SLE and improving patient outcomes by investigating microbiota-centric treatment options, such as probiotics, dietary interventions, and fecal microbiota transplantation.},
}

@article {pmid40925069,
year = {2025},
author = {Ji, Y and Gu, J and Xiao, S and Zhao, M and Xu, J and Lin, J and Cui, J and Zhao, W},
title = {Prognostic value of Nanopore sequencing-based metagenomics next-generation sequencing in clinical infectious cases: A retrospective observational study.},
journal = {Diagnostic microbiology and infectious disease},
volume = {114},
number = {1},
pages = {117092},
doi = {10.1016/j.diagmicrobio.2025.117092},
pmid = {40925069},
issn = {1879-0070},
abstract = {OBJECTIVES: This study aimed to evaluate the prognostic value of metagenomic next-generation sequencing(mNGS) using Nanopore sequencing technology (NST) versus traditional culture methods in infectious disease cases.

METHODS: We conducted a retrospective, single-center observational study comparing clinical outcomes between patients and specimen types in NST group and those in culture-based control group. Cox Proportional Hazards regression and Kaplan-Meier survival analysis were conducted to evaluate the association between diagnostic strategy and 28-day mortality. To minimize bias, Propensity Score Matching (PSM) and robust multivariate Cox regression analysis were employed to control for confounding factors. Diagnostic accuracy was quantified by calculating sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV).

RESULTS: The NST-based diagnosis was independently associated with a significantly reduced 28-day mortality rate, as indicated by the robust multivariate Cox regression analysis. (HR = 0.29, 95 %CI:0.09-0.91, p = 0.033). The sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of NST in detecting bacterium were 0.93,0.54, 0.5and 0.94, respectively. Additionally, the NST group was associated with higher Antibiotic De-escalation Rate (ADE) and reduced Duration of Therapy (DOT), with p values of 0.0238 and 0.008, respectively.

CONCLUSION: NST-based mNGS demonstrated superior performance in diagnosing bacterial infections compared to traditional culture methods. The NST group and positive pathogen detection were associated with a reduced 28-day mortality rate. Additionally, higher APACHE II scores upon admission were identified as independent predictors of worse prognosis, highlighting the importance of early severity assessment in patient outcomes.},
}

@article {pmid40924942,
year = {2025},
author = {Hooper, C and Tidy, AM and Jessop, R and Bateman, KS and Green, MJ and Ross, SH and Ward, GM and Hazelgrove, R and Hunt, JE and Parker, M and Bass, D},
title = {Genomic and morphological characterization of a novel iridovirus, bivalve iridovirus 1 (BiIV1), infecting the common cockle (Cerastoderma edule).},
journal = {Microbial genomics},
volume = {11},
number = {9},
pages = {},
doi = {10.1099/mgen.0.001494},
pmid = {40924942},
issn = {2057-5858},
mesh = {Animals ; *Iridovirus/genetics/classification/isolation & purification/ultrastructure ; Phylogeny ; *Cardiidae/virology ; *Genome, Viral ; Base Composition ; Open Reading Frames ; Genomics ; },
abstract = {High rates of mortality of the common cockle, Cerastoderma edule, have occurred in the Wash Estuary, UK, since 2008. A previous study linked the mortalities to a novel genotype of Marteilia cocosarum, with a strong correlation between cockle moribundity and the presence of M. cocosarum. Here, we characterize a novel iridovirus, identified by chance during metagenomic sequencing of a gradient purification of Marteilia cells, with the presence also correlated to cockle moribundity. The novel 179,695 bp iridovirus, bivalve iridovirus 1 (BiIV1), encodes 193 predicted ORFs and has a G+C content of 41 mol%. BiIV1 clusters together with other aquatic invertebrate iridoviruses in phylogenetic analyses and has a similar genome size to other invertebrate iridoviruses. Comparative analysis revealed that BiIV1 has lost three genes that were previously thought to be common amongst all iridoviruses but has also gained genes, potentially from horizontal transfer from its bivalve mollusc host(s). Electron microscopy showed 158 nm icosahedral virions present in the haemocytes of cockles, typical of those observed in host tissues infected with viruses of the family Iridoviridae. Prevalence of BiIV1 in moribund cockles was higher than that in apparently healthy cockles at most sites in the Wash Estuary, with up to 100% PCR prevalence in moribund cockles. Our findings provide the first genome for a bivalve-infecting iridovirus and identify a second bivalve-associated iridovirus in publicly available genomic datasets, adding to the knowledge of invertebrate iridovirus genomics and diversity.},
}

Animals
*Iridovirus/genetics/classification/isolation & purification/ultrastructure
Phylogeny
*Cardiidae/virology
*Genome, Viral
Base Composition
Open Reading Frames
Genomics

@article {pmid40924621,
year = {2025},
author = {Liu, L and Hu, L and Kuzyakov, Y and Rillig, MC and Duan, G and Wei, G and Chen, C},
title = {Microbial Physiological Adaptation to Biodegradable Microplastics Drives the Transformation and Reactivity of Dissolved Organic Matter in Soil.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c09633},
pmid = {40924621},
issn = {1520-5851},
abstract = {The turnover of dissolved organic matter (DOM) in soil regulated by biodegradable microplastics (MPs) has garnered much attention due to its profound impact on the storage and stability of soil organic matter. However, the transformation and reactivity of plant-derived and microbially derived DOM by microorganisms adapted to biodegradable MPs, and the involved microbial physiological processes, remain nearly unknown. Here, we added virgin and aged polylactic acid (PLA) and polyhydroxyalkanoate (PHA) to agricultural soils and incubated for 56 days. Using stable isotope techniques, reactomics, and metagenomics, we found that the addition of both virgin and aged PLA induced hydroxylation, demethylation, and dehydrogenation of lignin-derived DOM, resulting in a 3-fold increase in their oxidation degree. PLA activated the enzymatic pathway for lignin-derived DOM decomposition and downregulated genes involved in bacterial anabolism, such as those related to protein, amino sugar, and peptidoglycan biosynthesis. In contrast, PHA increased the content of microbially derived DOM compounds such as proteins and amino sugars by 2.1-fold relative to the control with peptide chain elongation. PHA resulted in the degradation of lignin-derived DOM into pyruvate and acetyl-CoA, accelerated bacterial ATP synthesis, the de novo biosynthesis of proteins and peptidoglycan, and cell renewal and death, thereby increasing PHA- and soil organic matter-derived microbial necromass carbon. Our study provides new insights into the impact of biodegradable MPs on soil DOM transformation and underscores the importance of the microbial physiological processes involved.},
}

@article {pmid40924014,
year = {2025},
author = {Wei, Y and Chen, Y and Zhao, T and Zhang, X and Wang, N and Shen, L and Liang, Y and Ye, S and He, H},
title = {Treatment of non-sterile biogas slurry from a pig farm using microalgae isolated from the activated sludge of sewage plants.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0068825},
doi = {10.1128/spectrum.00688-25},
pmid = {40924014},
issn = {2165-0497},
abstract = {UNLABELLED: Microalgae treatment is regarded as a green and environmentally acceptable method of treating pig farm biogas slurry (BS). Numerous studies have been conducted on the use of microalgae to treat sterilized BS. Nevertheless, in large-scale application settings, this method will undoubtedly result in high costs and low efficiency. In this study, microalgae were isolated from activated sludge, and their capacity to treat non-sterile BS with high ammonium nitrogen levels was investigated, along with examining alterations in microbial composition within BS. The results showed that both Chlorella sp. HH01 and Chlorella sp. HS02 treatments effectively removed ammonia nitrogen and phosphorus from BS. They also showed some removal capabilities for chemical oxygen demand, heavy metals, and antibiotics. Algal treatment significantly reduced the number of species, richness, variety, and pathogens within the microorganisms of BS, according to the results of metagenomic research. Meanwhile, algal treatment demonstrated a significant removal effect on certain antibiotic resistance genes, while increasing the abundance of some others. This study provides a comprehensive exploration of microalgae-mediated mitigation effects on antibiotic resistance genes in BS.

IMPORTANCE: Numerous studies have been conducted on the use of microalgae to treat sterile biogas slurry (BS). However, in large-scale applications, this approach undoubtedly results in high costs and inefficiencies. Therefore, it is crucial to identify microalgae capable of growing in non-sterilized and undiluted BS while effectively treating major pollutants. The findings of this study reveal that microalgae isolated and purified from activated sludge in sewage treatment plants can withstand crude BS containing high concentrations of ammonia nitrogen and effectively remove ammonia nitrogen and total phosphorus. Additionally, they exhibit some removal capabilities for chemical oxygen demand, heavy metals, pathogens, antibiotics, and certain antibiotic resistance genes.},
}

@article {pmid40923736,
year = {2025},
author = {Zhang, X and He, Q and Mao, G and Liang, M},
title = {Diagnosis of Pulmonary Actinomycosis Caused by Actinomyces graevenitzii: a Case Series of Three Patients.},
journal = {Clinical laboratory},
volume = {71},
number = {9},
pages = {},
doi = {10.7754/Clin.Lab.2025.250254},
pmid = {40923736},
issn = {1433-6510},
mesh = {Humans ; *Actinomycosis/diagnosis/microbiology/drug therapy ; *Actinomyces/isolation & purification/genetics ; Male ; Middle Aged ; Female ; High-Throughput Nucleotide Sequencing ; Bronchoalveolar Lavage Fluid/microbiology ; *Lung Diseases/microbiology/diagnosis ; Aged ; Adult ; Lung/microbiology ; },
abstract = {BACKGROUND: Actinomyces graevenitzii is a relatively uncommon Actinomyces species, which is an oral species and predominantly recovered from respiratory locations [1,2]. It is a gram-positive anaerobic bacteria or microaerobic filamentation bacteria, which can induce pyogenic and granulomatous inflammation characterized by swelling and concomitant pus, sinus formation, and the formation of yellow sulfur granules. All tissues and organs can be infected; the most common type involves the neck and face (55%), followed by the abdominal and pelvic cavities (20%). Chest involvement is the third most common type (15%), affecting the lung parenchyma, central airway, pleura, mediastinum, and chest wall [3-5]. Diagnosis of actinomycosis mainly relies on sputum, pus or biopsy specimens to find actinomycetes. Metagenomics next-generation sequencing (mNGS) in recent years has been increasingly valued and recognized for its application in infectious diseases. It provides a more efficient and accurate means for the pathological diagnosis of respiratory infections, updating the diagnostic strategy for lower respiratory tract infections [6].

METHODS: This study systematically summarized the clinical characteristics of Actinomyces graevenitzii infection by analyzing three cases of this pathogen. Bronchoalveolar lavage fluid (BAL) samples were collected for bacterial culture and mNGS. The isolated strains were routinely identified by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS).

RESULTS: Microbiological analysis demonstrated Actinomyces graevenitzii growth in all three bronchoalveolar la-vage (BAL) cultures. Metagenomic next-generation sequencing (mNGS) results showed concordant detection of A. graevenitzii in two cases, while unexpectedly identifying Tropheryma whipplei as the predominant pathogen in the remaining case.

CONCLUSIONS: Actinomycosis infections often present with subtle and nonspecific clinical manifestations, making them difficult to distinguish from pulmonary tuberculosis, fungal infections, and lung malignancies through imaging studies alone, frequently resulting in misdiagnosis or delayed diagnosis. Early and accurate diagnosis can be achieved through timely analysis of BAL fluid using advanced diagnostic techniques, including MALDI-TOF/MS for bacterial identification and mNGS, facilitating prompt and appropriate treatment.},
}

Humans
*Actinomycosis/diagnosis/microbiology/drug therapy
*Actinomyces/isolation & purification/genetics
Male
Middle Aged
Female
High-Throughput Nucleotide Sequencing
Bronchoalveolar Lavage Fluid/microbiology
*Lung Diseases/microbiology/diagnosis
Aged
Adult
Lung/microbiology

@article {pmid40923351,
year = {2025},
author = {Stensvold, CR},
title = {Aspects of Genetic Diversity, Host Specificity and Public Health Significance of Single-Celled Intestinal Parasites Commonly Observed in Humans and Mostly Referred to as 'Non-Pathogenic'.},
journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica},
volume = {133},
number = {9},
pages = {e70036},
doi = {10.1111/apm.70036},
pmid = {40923351},
issn = {1600-0463},
mesh = {Humans ; *Intestinal Diseases, Parasitic/parasitology ; *Genetic Variation ; *Host Specificity ; *Public Health ; Blastocystis/genetics ; Animals ; },
abstract = {Clinical microbiology involves the detection and differentiation of primarily bacteria, viruses, parasites and fungi in patients with infections. Billions of people may be colonised by one or more species of common luminal intestinal parasitic protists (CLIPPs) that are often detected in clinical microbiology laboratories; still, our knowledge on these organisms' impact on global health is very limited. The genera Blastocystis, Dientamoeba, Entamoeba, Endolimax and Iodamoeba comprise CLIPPs species, the life cycles of which, as opposed to single-celled pathogenic intestinal parasites (e.g., microsporidia and sporozoa), do probably not include gut-invasive stages that could result in pathological processes and thereby disease (except for Entamoeba histolytica). All five genera are parasites in the sense that they use a host to complete their life cycle; still, by many specialists, these are considered to be of limited clinical relevance and could possibly be referred to as 'eukaryotic endobionts' or even 'endosymbionts', in case they would have health-protective effects. The articles included in this thesis exemplify the work and the data that support the view that it might be more relevant to study these genera in a public health and gut ecology context than in a clinical microbiology context. Essential to investigating the impact of intestinal parasites on health and disease are accurate diagnostic tools, including DNA-based technology such as PCR and sequencing, plus accurate reference databases. Small subunit (SSU) ribosomal RNA (rRNA) genes consistently present in both pro- and eukaryotic organisms are today avidly used as taxonomic markers. DNA-based methods have been developed for genetic characterisation of microorganisms and provided data on species/subtypes/genotypes, etc. Metagenomics and metabarcoding (the use of low-specific PCR coupled with next-generation sequencing) can provide information on co-infection/co-colonisation with other organisms and enable screening for genetic diversity, even in complex matrices. By developing and implementing sensitive and specific DNA-based diagnostic tools and typing assays primarily based on the SSU rRNA gene, we have increased insight into the diversity, distribution and significance of CLIPPs. With these tools, we have shown that the genera Blastocystis and Dientamoeba are far more common than previously thought. Only 10-15 years ago, hypotheses on their distribution typically relied on data generated by traditional parasitological diagnostic methods, such as light microscopy. Hence, we have shown that most older children in Nigeria host Blastocystis, and that most children in day-care institutions in Denmark, if not all, get colonised by Dientamoeba at some point. Single-celled non-pathogenic intestinal parasites can be hosted by patients with diarrhoea and functional or inflammatory bowel diseases. However, emerging data appear to suggest that CLIPPs are generally more common in gut-healthy individuals than in patients with gastrointestinal symptoms. The research we have carried out on associations between CLIPPs and gut bacteria suggests that colonisation with these parasites is seen primarily in individuals with a healthy 'gut flora' (eubiosis). This observation should prompt future research projects focusing on the use of CLIPPs as biomarkers, and it should be investigated to which extent manipulation with CLIPPs could lead to changes in the gut flora and thereby be used as probiotics. In the event that it makes sense to speak of 'infection' by CLIPPs, we still lack tools to differentiate between colonisation and infection. We have known for decades that morphologically similar parasites can differ in terms of clinical impact and be genetically distinct, a feature that we refer to as 'cryptic genetic diversity'. One example is E. histolytica, which cannot be differentiated from Entamoeba dispar by cyst morphological features. However, whereas E. histolytica can be invasive and give rise to amoebic dysentery and amoebiasis, E. dispar is by most specialists considered non-invasive and generally non-pathogenic. This insight led us to investigate genetic diversity among other species of Entamoeba as well as other CLIPPs genera. If we could demonstrate similar-or higher-degrees of diversity within Blastocystis, Dientamoeba, Endolimax and Iodamoeba, these differences might be key to explaining differences in parasite phenotype and thereby differences in the ability of the parasites to cause symptoms. Despite the disclosure of striking genetic diversity among some CLIPPs, we have found little support for such theories; however, more studies are needed. As for Dientamoeba, we have observed a more or less clonal expansion of one of the two genotypes known to exist, and this genotype appears to have global predominance. In contrast, extensive genetic diversity is observed between and within subtypes of Blastocystis: to date, more than 30 species, the so-called subtypes, have been acknowledged. We, and many others, have sought to identify whether one or more of these subtypes could be linked to the development of intestinal symptoms, but there is little evidence to support this hypothesis. We know that Subtypes 1-4 reflect about 95% of Blastocystis colonisation in humans, and we have shown that individuals with zoonotic subtypes (e.g., ST6, ST7 and ST8) might typically experience symptoms. We have disclosed astonishing genetic variation among other CLIPPs, which has led to the recognition of Iodamoeba bütschlii, Endolimax nana, Entamoeba coli and Entamoeba hartmanni as species complexes, where each species should be regarded as a complex of species (referred to as 'subtypes' or 'ribosomal lineages') with overlapping morphology. And where E. histolytica and E. dispar differ by only 1%-2% diversity across the SSU rRNA gene, we have observed up to at least 10% and 30% genetic difference among ribosomal lineages within E. coli and I. bütschlii, respectively, challenging species concepts currently applied. Our research has resulted in the recognition of three ribosomal lineages within both E. coli and E. hartmanni, as well as two ribosomal lineages of E. nana and I. bütschlii. Moreover, we have discovered a new lineage of Entamoeba moshkovskii. Molecular characterisation of intestinal parasites collected from different host species (humans, non-human primates, other mammals, birds, etc.) can help identify opportunity for transmission between human and non-human hosts. We have shown that pigs can host a few species/lineages that can readily colonise humans, such as Entamoeba hartmanni and I. bütschlii. Many other species of larger mammals are common hosts of Blastocystis and Entamoeba. However, for the two latter genera, the species/genetic variants observed in non-human hosts are typically different from those observed in humans, which could indicate that many species of CLIPPs have adapted to their respective hosts over a long period, resulting in relatively high host specificity. For Blastocystis, we have shown that even though a given subtype may be found in more than one host species, it is possible to demonstrate cryptic host specificity at allele level. For instance, even though both human and non-human primates can be colonised by ST3, host species-specific strains of ST3 circulate within these two host populations. With regards to E. coli, it is possible that ST1 has adapted to human hosts, while E. coli ST2 has adapted to a broader host range, including non-human primates and rodents. It has become clear that CLIPPs are common colonisers of the human background population, and even though we cannot disprove the existence of infection by any of these, it should be reasonable to consider clinical and medical intervention redundant in most cases. Perhaps it might even be so that one should try not to eradicate these organisms from the gut when first established. However, more studies are warranted to elucidate the significance of the pronounced genetic diversity observed in some CLIPPs with regards to transmission patterns and clinical significance. Future research in CLIPPs should also include studies that can elucidate those factors that favour colonisation with CLIPPs and what role CLIPPs have in host-gut ecology, metabolism and overall health condition. Finally, as human and non-human hosts share these parasitic genera, and as some protozoa possibly contribute to overall gut function in ruminants, it would be interesting to study these in domesticated and wild animals to learn more about the role of these parasites in health and disease, including investigations into whether some CLIPPs might be endosymbionts.},
}

Humans
*Intestinal Diseases, Parasitic/parasitology
*Genetic Variation
*Host Specificity
*Public Health
Blastocystis/genetics
Animals