@article {pmid40715782,
year = {2025},
author = {Tonkin-Hill, G and Ruis, C and Bentley, SD and Lythgoe, KA and Bryant, JM},
title = {Within-host bacterial evolution and the emergence of pathogenicity.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {40715782},
issn = {2058-5276},
support = {2025515//Department of Health | National Health and Medical Research Council (NHMRC)/ ; 220540/Z/20/A//Wellcome Trust (Wellcome)/ ; 220540/Z/20/A//Wellcome Trust (Wellcome)/ ; },
abstract = {The use of whole-genome sequencing to monitor bacterial pathogens has provided crucial insights into their within-host evolution, revealing mutagenic and selective processes driving the emergence of antibiotic resistance, immune evasion phenotypes and adaptations that enable sustained human-to-human transmission. Deep genomic and metagenomic sequencing of intra-host pathogen populations is also enhancing our ability to track bacterial transmission, a key component of infection control. This Review discusses the major processes driving bacterial evolution within humans, including both pathogenic and commensal species. Initially, mutational processes, including how mutational signatures reveal pathogen biology, and the selective pressures driving evolution are considered. The dynamics of horizontal gene transfer and intra-host pathogen competition are also examined, followed by a focus on the emergence of bacterial pathogenesis. Finally, the Review focuses on the importance of within-host genetic diversity in tracking bacterial transmission and its implications for infectious disease control and public health.},
}

@article {pmid40715695,
year = {2025},
author = {Yu, L and Guo, Q and Gu, X and Wang, Z and Li, J and Wang, X and Xu, Z and Wang, Y and Zhang, Y and Zhang, Y and Ding, Y and Chen, Z and Chen, K and Ding, Y},
title = {Impact of gut microbiome on radiotherapy and immunotherapy efficacy in microsatellite-stable colorectal cancer: role of propionic acid and B. fragilis.},
journal = {British journal of cancer},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41416-025-03105-2},
pmid = {40715695},
issn = {1532-1827},
abstract = {BACKGROUND: Colorectal cancer (CRC) is the third most common cancer and the second leading cause of cancer-related deaths worldwide. While immunotherapy is effective in microsatellite instability-high (MSI-H) CRC, its benefits in microsatellite-stable (MSS) CRC are limited. Radiotherapy may modify the immune microenvironment in MSS-CRC, enhancing immunotherapy efficacy, but individual responses vary.

METHODS: We employed MSS-CRC mouse models to examine the effects of combined radiotherapy and immunotherapy, with and without antibiotics (ABX). Various analyses, including metagenomic, nontargeted metabolomic, and gas chromatography-mass spectrometry (GC-MS), were performed to identify factors influencing treatment outcomes. Flow cytometry, immunohistochemistry and in vivo antibody blockade experiments assessed the role of metabolites and bacteria on CD8[+] T cell infiltration and treatment responses, complemented by transcriptomic sequencing and molecular biology experiments.

RESULTS: Our analyses identified propionic acid and Bacteroides fragilis (B. fragilis) as crucial factors enhancing the efficacy of combined therapies in MSS-CRC. Both propionic acid and B. fragilis improved CD8[+] T cell infiltration and treatment outcomes, with molecular assays indicating that propionic acid facilitates H3K14 acetylation, activating the Meox1-Cxcr6/Ccl5 axis.

CONCLUSIONS: This study highlights the pivotal role of the gut microbiome, specifically propionic acid and B. fragilis, in modulating the efficacy of combined radiotherapy and immunotherapy in MSS-CRC.},
}

@article {pmid40715670,
year = {2025},
author = {Yao, X and Huang, Y and Yuan, L and Han, D and Zhang, X},
title = {Clinical performance of metagenomic next-generation sequencing in the diagnosis of Epstein-Barr virus central nervous system infections.},
journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {},
number = {},
pages = {},
pmid = {40715670},
issn = {1435-4373},
abstract = {Metagenomic next-generation sequencing (mNGS) has been widely utilized for diagnosing infectious diseases. However, studies employing mNGS to detect EBV central nervous system (CNS) infections remain scarce. Therefore, this study aimed to evaluate the diagnostic performance of mNGS in EBV CNS infections. Patients discharged with the diagnosis of CNS viral infection and underwent lumbar puncture for mNGS of cerebrospinal fluid between January 2021 and May 2024 were selected. The selected cerebrospinal fluid samples were subjected to PCR, including those that were EBV-negative in mNGS. Clinical data were collected for analysis. A total of 96 samples were included: 18 samples in the EBV infection group (PCR EBV DNA +), 30 samples in the suspected EBV infection group (PCR EBV DNA - but mNGS +), and 48 samples in the non-EBV-infected group (PCR EBV DNA - and mNGS -). All PCR-positive samples were also positive by mNGS, and in the EBV infection group, the viral load detected by PCR was strongly correlated with the number of sequences identified by mNGS (ρ = 0.752, p = 0.00). The number of sequences in the EBV infection group was higher than that in the suspected EBV infection group (14 vs. 4, p = 0.04). Patients in the EBV high sequence group experienced fewer headaches, nausea, and vomiting, had less elevated intracranial pressure, but required longer hospitalization (p = 0.003, 0.005, 0.03, and 0.03, respectively). The mNGS method is a sensitive tool for detecting EBV CNS infections.},
}

@article {pmid40715283,
year = {2025},
author = {Tan, JH and Liew, KJ and Sani, RK and Samanta, D and Pointing, SB and Chan, KG and Goh, KM},
title = {Microbial diversity and metabolic predictions of high-temperature streamer biofilms using metagenome-assembled genomes.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {27297},
pmid = {40715283},
issn = {2045-2322},
abstract = {High-temperature streamer biofilm communities (SBCs) are often dominated by Aquificota, which can comprise over 90% of the microbial population in shallow water channels, such as those found at Mammoth hot springs of Yellowstone National Park and the Rehai hot springs in China. This study examines SBCs from the Dusun Tua (DT) hot spring in Malaysia (75 °C, pH 7.6), where Aquificota accounted for only ~ 35% of the total amplicon sequence variants. Amplicon and hybrid metagenomic sequencing revealed a more balanced microbial community, co-dominated by Aquificota, Chloroflexota, Desulfobacterota, Bacteroidota, Deinococcota, and Candidatus Hydrothermae, along with Thermoproteota and Micrarchaeota. To our knowledge, the co-dominance of Aquificota and Chloroflexota in SBCs has not been previously reported. The unexpected abundance of Chloroflexota may stem from dispersal from upstream Cyanobacteriota-Chloroflexota biofilms, contributing to community diversification. Genome-resolved analyses identified more than 60 medium- to high-quality metagenome-assembled genomes (MAGs), suggesting that biofilm formation was initially driven by chemoautotrophic sulfur oxidation and CO2 fixation, followed by the gradual integration of heterotrophic taxa. Nitrogen cycling and hydrogen oxidation are likely to contribute additional sources of energy. The presence of diverse CAZymes suggests that plant litter may serve as an additional carbon source. Genome-centric analyses across multiple phyla indicated that extracellular polymeric substances (EPS), curli fibers, and other matrix components contribute to the biofilm matrix, enhancing structural resilience and supporting persistence under harsh conditions. Overall, this study highlights the distinct microbial ecology of the DT SBC and broader metabolic roles beyond Aquificota dominance. The genes identified in this study may hold biotechnological potential and serve as a valuable resource for future enzyme discovery and functional screening.},
}

@article {pmid40715125,
year = {2025},
author = {Jie, Z and Liang, H and Meng, Y and Zhang, J and Zhang, T and Li, W and Lin, X and Hu, T and Han, M and Liang, W and Ju, Y and Tong, X and Jin, X and Xu, X and Zhang, W and Wang, J and Yang, H and Kristiansen, K and Xiao, L and Zou, Y},
title = {Integrating metagenomics and cultivation unveils oral phage diversity and potential impact on hosts.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {145},
doi = {10.1038/s41522-025-00773-z},
pmid = {40715125},
issn = {2055-5008},
support = {XMHT20220104017//Shenzhen Municipal Government of China/ ; XMHT20220104017//Shenzhen Municipal Government of China/ ; XMHT20220104017//Shenzhen Municipal Government of China/ ; 2018YFC1313801//National Key Research and Development Program of China/ ; 2018YFC1313801//National Key Research and Development Program of China/ ; 2018YFC1313801//National Key Research and Development Program of China/ ; 2019B020230001//Natural Science Foundation of Guangdong Province/ ; 2019B020230001//Natural Science Foundation of Guangdong Province/ ; 2019B020230001//Natural Science Foundation of Guangdong Province/ ; },
abstract = {Bacteriophages play important roles in the regulation of bacterial communities and may thus impact human health. However, the scarcity of genomic data of oral microorganism has limited information on oral phages. We collected data on 5427 metagenomic samples and 2178 cultivated bacterial genomes across different geographical areas and populations, generating the Oral Phage Database (OPD), comprising 189,859 representative phage genome sequences, including 3416 huge phages (genome size > 200 kbp). OPD reveals that most oral viruses are unknown and encode an enormous variety of dark proteins. Numerous oral phages infecting a broad range of hosts carry anti-defense genes, auxiliary metabolic genes, and virulence factors that may affect bacterial metabolism and influence human health. The composition of oral phages varies among different populations, and several phages have the potential to act as biomarkers for disease. OPD expands our knowledge of phage-bacteria interactions, huge phages diversity, and potential impacts on human health.},
}

@article {pmid40715043,
year = {2025},
author = {Duchesneau, K and Aldeguer-Riquelme, B and Petro, C and Makke, G and Green, M and Tfaily, M and Wilson, R and Roth, SW and Johnston, ER and Kluber, LA and Schadt, CW and Trejo, JB and Callister, SJ and Purvine, SO and Chanton, JP and Hanson, PJ and Tringe, S and Eloe-Fadrosh, E and Glavina Del Rio, T and Konstantinidis, KT and Kostka, JE},
title = {Northern peatland microbial communities exhibit resistance to warming and acquire electron acceptors from soil organic matter.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {6869},
pmid = {40715043},
issn = {2041-1723},
support = {DE-SC0023297//U.S. Department of Energy (DOE)/ ; DE-SC0012088//U.S. Department of Energy (DOE)/ ; DE-AC05-76RL01830//U.S. Department of Energy (DOE)/ ; },
abstract = {The response of microbial communities that regulate belowground carbon turnover to climate change drivers in peatlands is poorly understood. Here, we leverage a whole ecosystem warming experiment to elucidate the key processes of terminal carbon decomposition and community responses to temperature rise. Our dataset of 697 metagenome-assembled genomes (MAGs) represents the microbial community from the surface (10 cm) to 2 m deep into the peat column, with only 3.7% of genomes overlapping with other well-studied peatlands. Community composition has yet to show a significant response to warming after 3 years, suggesting that metabolically diverse soil microbial communities are resistant to climate change. Surprisingly, abundant and active methanogens in the genus Candidatus Methanoflorens, Methanobacterium, and Methanoregula show the potential for both acetoclastic and hydrogenotrophic methanogenesis. Nonetheless, the predominant pathways for anaerobic carbon decomposition include sulfate/sulfite reduction, denitrification, and acetogenesis, rather than methanogenesis based on gene abundances. Multi-omics data suggest that organic matter cleavage provides terminal electron acceptors, which together with methanogen metabolic flexibility, may explain peat microbiome composition resistance to warming.},
}

@article {pmid40714610,
year = {2025},
author = {Li, L and Li, H and Cui, J and Bao, M},
title = {A critical review on the application of environmental DNA (eDNA) metagenomics in monitoring and assessing biological communities post marine oil spills.},
journal = {The Science of the total environment},
volume = {995},
number = {},
pages = {180110},
doi = {10.1016/j.scitotenv.2025.180110},
pmid = {40714610},
issn = {1879-1026},
abstract = {Oil spills pose a serious threat to marine communities, and there is an urgent need for an effective technique to monitor and assess the impacts on biological communities. While traditional methods with low sensitivity, being time-consuming and limited resolution are difficult to meet the application requirements, environmental DNA (eDNA) metagenomics provides an effective tool for comprehensive and long-term monitoring of biomes through non-destructive sampling, which can detect multiple trophic levels at the same time. Meanwhile, this technology provides significant advantages in diversity analysis, community composition and abundance change assessment, and functional gene annotation, enabling a more comprehensive evaluation of oil spills' impacts on marine communities. This review critically summarizes the workflow, including sample collection, DNA extraction, sequencing and data analysis, provides a systematic overview of the application of eDNA metagenomics in marine oil spills, and explores the latest advances in current technologies. Here, we also discuss the technical challenges and future development potential of the method, and emphasize the importance of process standardization, the construction of a global DNA reference database, and artificial intelligence-assisted analysis, which establish a robust theoretical foundation for the systematic application of eDNA metagenomics in marine oil spills monitoring, and new research perspectives on marine ecological pollution management and remediation assessment. Although the method still faces certain technical challenges, its unique advantages in pollution prevention and remediation make it expected to become a core tool for global marine pollution monitoring and assessment.},
}

@article {pmid40714470,
year = {2025},
author = {Yuan, F and Wang, J and Lu, M and Liao, Q and Wang, T and Xue, Y and Chen, H and Ding, Y and Fu, G and Qiu, P and Zou, X},
title = {Metagenomic insight into the ecological effects of the plastisphere in coastal salt marshes.},
journal = {Marine pollution bulletin},
volume = {221},
number = {},
pages = {118476},
doi = {10.1016/j.marpolbul.2025.118476},
pmid = {40714470},
issn = {1879-3363},
abstract = {Microplastics (MPs) introduce a unique ecological niche for microorganisms, termed the "plastisphere". Coastal salt marshes are critical blue‑carbon systems and MP sinks. However, the impacts of the plastisphere on major elemental cycling in coastal salt marshes remain poorly understood. To answer this important question, we conducted a 1-year field experiment in both the intertidal (Spartina alterniflora, SA) and supratidal (Phragmites australis, PA) zones of Yancheng salt marshes in China and investigated the dynamics using metagenomics. Results show pronounced heterogeneity in the ecological effects of the plastisphere in intertidal and supratidal zones. At the SA site, plastisphere communities showed increased gene abundance for nitrogen fixation, assimilatory nitrate reduction to ammonium, and thiosulfate oxidation (by sulfur oxidation complex). In contrast, at the PA site, plastisphere communities exhibited elevated gene abundance for carbon degradation, dissimilatory nitrate reduction to ammonium, and sulfite oxidation. Antibiotic resistance genes (ARGs) and pathogens were enriched in the plastisphere, with different compositions at SA and PA sites and some taxa exclusively present in the plastisphere despite low abundance. These findings highlight the plastisphere's potential to modulate biogeochemical processes and antibiotic resistance in salt marshes, providing a foundation for assessing MPs' ecological roles in these critical habitats.},
}

@article {pmid40714398,
year = {2025},
author = {Wu, L and Yan, M and Huang, X and Liao, H and Bao, D and Ge, Y and Wang, S and Xia, X},
title = {Temperature-mediated shift from competitive to facilitative interactions between lactic acid bacteria and bacillus species in daqu fermentation: Insights from metagenomics, dual RNA-seq, and coculture analysis.},
journal = {International journal of food microbiology},
volume = {442},
number = {},
pages = {111352},
doi = {10.1016/j.ijfoodmicro.2025.111352},
pmid = {40714398},
issn = {1879-3460},
abstract = {Daqu, a pivotal starter that defines the flavor profile and quality of Baijiu, undergoes dynamic temperature changes during its production, significantly influencing the microbial community structure and function. Although the importance of fermentation temperature in shaping microbial biodiversity is well-recognized, its impact on microbial interaction dynamics and the underlying mechanisms remains poorly understood. This study integrates metagenomics, dual RNA-seq, and coculture experiments to elucidate temperature-dependent microbial interactions during Daqu fermentation. Metagenomic analysis revealed that lactic acid bacteria (LAB) and Bacillus are dominant genera with distinct thermal preferences that nevertheless coexist throughout the fermentation process. Elevated temperature stress was found to enhance positive microbial interactions within the Daqu ecosystem. Dual RNA-seq analysis uncovered temperature-responsive gene expression patterns associated with oxidative stress, metabolic capacity, and environmental information processing in representative LAB and Bacillus strains. Guided by these multi-omics findings, co-culture assays demonstrated a temperature-dependent shift in microbial interaction modes. At 30 °C, Lactococcus lactis secretes lactic acid that inhibits the growth of Bacillus subtilis, whereas at 50 °C, B. subtilis alleviates oxidative stress in L. lactis by producing cobalamin, thereby enabling short-term rescue and sustained coexistence over serial transfers. These findings provide critical insights into the temperature-driven modulation of microbial interactions, enhancing the precision and manageability of the Daqu fermentation process.},
}

@article {pmid40714076,
year = {2025},
author = {Wei, R and Liu, J and Li, M and Xie, W and Li, J and Liu, L and Jiang, Y and Sun, S and Deng, T and Wang, S and Tang, Y and Lin, Q and Ni, Z and Liu, T and Qiu, R},
title = {Insights into toxic elements mobilization in Karstic paddy soil of southwest China: The overlooked significance of iron-organic matter colloids.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {383},
number = {},
pages = {126897},
doi = {10.1016/j.envpol.2025.126897},
pmid = {40714076},
issn = {1873-6424},
abstract = {Due to their large specific surface area, variable surface charge, and abundant reactive functional groups, soil colloids are important "carriers" for the migration of HMs (heavy metals) in the soil. This study systematically investigates the migration-transformation mechanisms of colloidal As, Cd, Tl and their driving factors in paddy soils of the Karst region in southwest China. Results show that colloidal Fe and OM are the primary environmental factors influencing the formation and distribution of these three colloidal heavy metals, with significant positive correlations (correlation coefficients r[2] = 0.56-0.79). TEM-EDS and XRD analyses confirm that As/Cd are closely associated with Fe oxides (e.g., magnetite, goethite) at the nanoscale. AF4-UV-ICP-MS technology reveals that colloidal HMs primarily occur in the 100-350 nm size range, and anthropogenic activities in artisanal smelting areas promote the formation of smaller-sized colloids (20-350 nm), enhancing their migration potential. Metagenomic analysis indicates that N/S metabolic genes (e.g., narA, cysN) are significantly correlated with colloidal HMs concentrations, and microbial metabolites affect the binding of HMs to soil colloids. Traditional assessments overlook the high mobility and stability of colloidal HMs (e.g., 100-350 nm), leading to underestimation of potential risks to paddy ecosystems and adjacent water bodies. Future biogeochemical research should prioritize colloid - and nanoparticle - bound HMs to improve risk assessment and remediation strategies.},
}

@article {pmid40713906,
year = {2025},
author = {Guan, F and Liu, J and Zhou, L and Tong, Q and Wu, N and Tu, T and Wang, Y and Yao, B and Luo, H and Tian, J and Huang, H},
title = {Strain-resolved comparison of beef and draft cattle rumen microbiomes using single-microbe genomics.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {80},
pmid = {40713906},
issn = {2524-4671},
support = {2023YFD1302200//the National Key R&D Program of China/ ; 32222082//the National Natural Science Foundation of China/ ; CARS-41//the China Agriculture Research System of MOF and MARA/ ; CAAS-ZDRW202304//the Agricultural Science and Technology Innovation Program/ ; },
abstract = {BACKGROUND: Beef and draft cattle have distinct rumen microbiota that can influence their metabolic processes and body composition. However, traditional metagenomic sequencing methods only provide broad surveys of the rumen microbial genomic contents. In this study, we utilized high-throughput single-cell genome sequencing to investigate these differences at the strain level.

RESULTS: Following quality control and contig assembly, we obtained 97 bacterial genomes, 17 archaeal genomes, and 241 subspecies genomes from the rumen samples of Angus and Wuling cattle. Our analysis revealed a higher bacterial abundance in Angus rumen, characterized by an enrichment of the Succiniclasticum and Limivicinus genera. In contrast, the rumen of Wuling cattle exhibited a higher archaeal abundance. Additionally, we observed variations in the types and abundance of microbial-derived enzymes responsible for plant fiber degradation and volatile fatty acid (VFA) production between the two cattle breeds. The Angus rumen was found to harbor a higher diversity and abundance of cellulases and hemicellulases, particularly from the Ruminococcus unknown_0 genus. Furthermore, genera such as Succiniclasticum, Butyrivibrio, Limivicinus, UBA2868, and Prevotella were identified as key contributors to VFA production. Our findings suggest that the Angus rumen may have a stronger VFA production capacity due to the higher abundance of acidogenic genera. Interestingly, we also observed a greater abundance of Methanobrevibacter_A methanogens, which play a crucial role in energy flow in the rumen ecosystem, in Wuling cattle compared to Angus cattle.

CONCLUSION: Our study highlights differences in the rumen microbiome of Angus and Wuling cattle. This difference could, at least partially, account for the variation in fat content that ultimately results in the superior meat quality of Angus cattle and the sustained muscle activity required by draft cattle. Overall, single-cell genome sequencing reveals distinct microbial composition and metabolic pathways between the two breeds, providing insights into their unique physiological and metabolic needs.},
}

@article {pmid40713905,
year = {2025},
author = {Zhou, J and Zhang, CJ and Zou, D and Gu, C and Li, M},
title = {Magnetite drives microbial community restructuring and stimulates aceticlastic methanogenesis of type II Methanosarcina in mangrove sediments.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {174},
doi = {10.1186/s40168-025-02157-z},
pmid = {40713905},
issn = {2049-2618},
support = {42207144//National Natural Science Foundation of China/ ; 32225003, 32393971, and 32393970//National Natural Science Foundation of China/ ; 2024A1515010843//Guangdong Basic and Applied Basic Research Foundation/ ; 2023B0303000017//Guangdong Major Project of Basic and Applied Basic Research/ ; KCXFZ20240903092800002//Shenzhen Science and Technology Program/ ; 2022B002//Shenzhen University 2035 Program for Excellent Research/ ; },
mesh = {*Methane/metabolism/biosynthesis ; *Ferrosoferric Oxide/pharmacology/metabolism ; *Geologic Sediments/microbiology ; Wetlands ; *Methanosarcina/metabolism/genetics/classification/isolation & purification/drug effects ; *Microbial Consortia/drug effects ; *Microbiota/drug effects ; Acetates/metabolism ; Lactic Acid/metabolism ; },
abstract = {BACKGROUND: Mangrove wetlands are critical hotspots of methane emissions, yet the role of naturally occurring minerals in shaping their microbial communities and methanogenic processes is poorly understood. Magnetite, a common iron mineral in soils and sediments, has been reported to enhance aceticlastic methanogenesis and facilitate syntrophic methanogenesis. In this study, we integrated multi-omic profiling with cultivation-based approaches to investigate the impact of magnetite on methanogenesis of microbial consortia derived from mangrove sediments, using lactate as a substrate.

RESULTS: Across five serial transfers, mangrove microbial consortia converted lactate to propionate and acetate, which were subsequently degraded into methane. Magnetite addition significantly stimulated methane production, leading to notable changes in community structure, particularly for aceticlastic methanogens, with Methanosarcina predominating in the magnetite-amended cultures and Methanothrix in controls. Four Methanosarcina strains T3, T4, T13, and MeOH were subsequently isolated from magnetite-amended cultures. Combined analyses of metagenome-assembled genomes and the genomes of these isolates revealed that the enriched Methanosarcina in magnetite-amended cultures belonged to type II deficient in hydrogenotrophic methanogenesis pathway. Metatranscriptomic analyses suggested that magnetite addition stimulated aceticlastic methanogenesis of type II Methanosarcina and hydrogenotrophic methanogenesis of Methanomicrobiales in the consortia. Furthermore, pure culture experiments confirmed that magnetite stimulated aceticlastic methanogenesis by Methanosarcina sp. T3, although its gene expression patterns differed from those observed in the microbial consortia. Additionally, Methanofastidiosales, an uncultured archaeal lineage possessing H2-dependent methylotrophic methanogenesis, was detected in all transfers.

CONCLUSIONS: Our findings demonstrate that magnetite alters methanogenic consortia in mangrove sediments, selectively stimulating aceticlastic methanogenesis of type II Methanosarcina and modulating hydrogenotrophic activity in Methanomicrobiales. By integrating multi-omics analyses with pure culture validation, we demonstrate, for the first time, that magnetite directly enhances the aceticlastic methanogenesis of type II non-hydrogenotrophic Methanosarcina. This study provides new insights into the influence of magnetite on complex microbial consortia, offers a deeper understanding of the physiology of type II non-hydrogenotrophic Methanosarcina, and advances knowledge of mineral-mediated regulation of methanogenic networks in anoxic environments. Video Abstract.},
}

*Methane/metabolism/biosynthesis
*Ferrosoferric Oxide/pharmacology/metabolism
*Geologic Sediments/microbiology
Wetlands
*Methanosarcina/metabolism/genetics/classification/isolation & purification/drug effects
*Microbial Consortia/drug effects
*Microbiota/drug effects
Acetates/metabolism
Lactic Acid/metabolism

@article {pmid40713701,
year = {2025},
author = {Bhardwaj, K and Niharika, and Garg, A and Jain, A and Kumar, M and Datt, M and Singh, V and Vrati, S},
title = {Identification and profiling of novel metagenome assembled uncultivated virus genomes from human gut.},
journal = {Virology journal},
volume = {22},
number = {1},
pages = {254},
pmid = {40713701},
issn = {1743-422X},
support = {BT/PR18657/BIC/101/507/2016//Department of Biotechnology, Ministry of Science and Technology, India/ ; JCB/2021/000015//Science and Engineering Research Board/ ; },
mesh = {Humans ; *Genome, Viral ; *Metagenome ; Feces/virology ; *Virome ; Metagenomics ; *Gastrointestinal Tract/virology ; *Viruses/genetics/classification/isolation & purification ; Gastrointestinal Microbiome ; Phylogeny ; },
abstract = {Metagenomics has revealed an unprecedented viral diversity in human gut although, most of the sequence data remains uncharacterized. In this study, we mined a collection of 1090 metagenome assembled "high quality" viral genomes (> 90% completeness, as determined by CheckV) derived from human fecal samples. Sequence analysis revealed eight new species spanning seven genera within the class, Caudoviricetes and nineteen new species from fourteen genera within the ssDNA virus family, Microviridae. Additionally, four "high quality" genomes were not found in any of the four major viral databases, NCBI viral RefSeq, IMG-VR, Gut Phage Database (GPD) and Gut Virome Database (GVD). Further, annotation and KEGG pathway analysis of the "high-quality" genomes identified seven core genes (antB, dnaB, DNMT1, DUT, xlyAB, xtmB and xtmA) associated with metabolism and fundamental viral processes. Moreover, genes for virulence, host-takeover, drug resistance, tRNA, tmRNA and CRISPR elements were also detected. Host prediction analysis suggest bacterial hosts for approximately 40% of the genomes. Overall, this study reports the discovery of novel viral genomes and provides a comprehensive genome profiling of human gut viruses in a subpopulation from India. These findings serve as a foundation for future biological investigations to elucidate the role of these viruses in host physiology.},
}

Humans
*Genome, Viral
*Metagenome
Feces/virology
*Virome
Metagenomics
*Gastrointestinal Tract/virology
*Viruses/genetics/classification/isolation & purification
Gastrointestinal Microbiome
Phylogeny

@article {pmid40713093,
year = {2025},
author = {Sepulveda, BJ and González-Recio, O and Chamberlain, AJ and Khansefid, M and Cocks, BG and Wang, J and Prowse-Wilkins, CP and Marett, LC and Williams, SRO and Jacobs, JL and García-Rodríguez, A and Jiménez-Montero, JA and Pryce, JE},
title = {Rumen metagenome as a genomic selection target to reduce enteric methane emissions.},
journal = {Journal of dairy science},
volume = {108},
number = {8},
pages = {8619-8636},
doi = {10.3168/jds.2024-25436},
pmid = {40713093},
issn = {1525-3198},
mesh = {Animals ; *Methane/metabolism ; Cattle ; *Rumen/microbiology/metabolism ; *Metagenome ; Female ; Spain ; Breeding ; Australia ; },
abstract = {Ruminant digestion emits methane, a potent greenhouse gas contributing to global warming and reducing feed efficiency. Reducing enteric methane emissions (EME) through breeding decisions is theoretically possible, yet measuring these emissions on commercial farms is currently challenging and costly. It is common for EME to be measured using different technologies, which may show weak correlations between them, complicating the combination of reference populations, especially between countries. Here, using the same sequencing strategy, we identified a group of ruminant metagenomic features (a core) present in at least 90% of 410 dairy cows in Australia and 434 in Spain. With subsets of this core (the breeding core subsets) we estimated larger reductions on EME than using direct selection on EME. A combination of direct selection on EME and indirect selection on the breeding core subsets was estimated to produce even larger reductions. Combining the principal components of the core with some genera, Kyoto Encyclopedia of Genes and Genomes ontology and Clusters of Orthologous Groups could enhance EME reductions in breeding programs. We estimated an EME reduction of 0.41 phenotypic standard deviations per generation by selecting the top 30% of individuals with desirable ruminal microbiota profiles. An R Shiny application to estimate those reductions is provided. Additionally, the breeding core subsets could predict EME irrespective of each population's EME trait (sulfur hexafluoride in Australia and sniffers in Spain). These results suggest that rumen metagenome features could be used as selection criteria for genomic selection programs to reduce EME, as many of these features are heritable and correlated with EME. Features in the core could connect EME from different cattle populations, irrespective of the methane phenotype used in those populations. We propose that our methodology should be applied to much larger datasets to improve the accuracy of identifying a breeding core. Therefore, we propose a global effort to validate a common core of EME-associated ruminal features.},
}

Animals
*Methane/metabolism
Cattle
*Rumen/microbiology/metabolism
*Metagenome
Female
Spain
Breeding
Australia

@article {pmid40712965,
year = {2025},
author = {Kong, F and Gao, J and Yang, Z and Li, X and Zhang, Y and Chen, Y},
title = {Removing macromolecular organic matter from biogas slurry prior to its application reduces organic N leaching and soil N2O emissions.},
journal = {Environmental research},
volume = {285},
number = {Pt 2},
pages = {122427},
doi = {10.1016/j.envres.2025.122427},
pmid = {40712965},
issn = {1096-0953},
abstract = {Biogas slurry is an organic fertilizer with a low C/N ratio and a high water content. It can promote soil nitrous oxide (N2O) emissions and the leaching of small-molecule organic N compounds. In this study, membrane micro- and ultrafiltration were performed to separate organic matter from biogas slurry. The effects of the application of biogas slurry with organic matter compounds of different sizes on soil N2O emissions and N leaching were observed via simulating leaching through a 30-cm-high soil column over 62 days. In the treatment with filtrated biogas slurry (BS-F), the total N2O emissions and dissolved organic N leaching were significantly increased by 63.74 % and 153.85 %, respectively, over the experimental period compared to the mineral fertilizer treatment (MF). In contrast, the removal of particulate organic matter and large-molecular-weight humic substance from the original biogas slurry (BS-U) resulted in a 30.87 % reduction in soil N2O emissions and a 30.30 % reduction in dissolved organic N leaching, along with a 90.75 % increase in the soil microbial biomass nitrogen (MBN) content. The relative abundances of the genera Methyloversatilis (26.05 %) and Thauera (2.41 %) were higher in the BS-U treatment, whereas those of the functional genes narG/H and nirK/S, involved in denitrification, were lower. The relative abundance of the functional gene nifD, which plays a role in N fixation, was higher. The removal of large-molecular-weight (>100 kDa) organic substances from biogas slurry can reduce soil N2O emissions by impeding denitrification and facilitating other N reduction pathways. Our study provides a theoretical foundation for enhancing the environmental sustainability of biogas slurry in agricultural practices.},
}

@article {pmid40712891,
year = {2025},
author = {Ishibashi, N and Akase, Y and Watanabe, S and Yokoyama, H and Mekata, T},
title = {Genomic and molecular epidemiological characterization of a novel piscine poxvirus in the red seabream, Pagrus major.},
journal = {Journal of virological methods},
volume = {338},
number = {},
pages = {115229},
doi = {10.1016/j.jviromet.2025.115229},
pmid = {40712891},
issn = {1879-0984},
abstract = {Since 2020, unexplained mortality has been recorded in a red seabream hatchery. Affected juveniles exhibit skin darkening and sleep-like symptoms, which occasionally cause mass mortality. In this study, we detected a novel poxvirus genome in diseased fish via next-generation sequencing. Transcriptome analysis of moribund individuals revealed multiple contigs with sequence homology to the salmon gill poxvirus, suggesting the presence of a related viral agent. Subsequent metagenomic analysis led to the assembly of a 308-kbp viral genome of a novel piscine poxvirus, designated Japanese seabream poxvirus (JSPV), containing 338 predicted open reading frames. DNA polymerase of JSPV shared 62 and 44 % amino acid identity with those of the salmon gill poxvirus and carp edema virus, respectively. Comparative genomic analysis of piscine poxviruses revealed that genome synteny was highly conserved in the central region. Subsequently, a PCR method was developed and I7L, which encodes the virion core cysteine protease, was successfully detected in all JSPV genogroups. Based on the partial sequence of I7L, JSPV was classified into two major genogroups: I and II. Genogroup I was further subdivided into genogroups Ia and Ib.},
}

@article {pmid40712732,
year = {2025},
author = {Pérez-Molina, JA and Moreno, E and Crespillo-Andújar, C and Chamorro-Tojeiro, S and Arsuaga, M and Olavarrieta, L and Martín, O and Monge-Maillo, B and Norman, F and Lanza, VF and Serrano-Villar, S},
title = {Chagas disease induces gut microbial metabolic stress: Disruption of energy and nucleotide pathways and partial reversal by antiparasitic therapy (TRIPOBIOME-2 study).},
journal = {Travel medicine and infectious disease},
volume = {67},
number = {},
pages = {102881},
doi = {10.1016/j.tmaid.2025.102881},
pmid = {40712732},
issn = {1873-0442},
abstract = {Chagas disease (CD) can alter gut microbiota composition, although its functional impact is poorly defined. We conducted whole-genome metagenomic sequencing of stool samples from 55 adults with chronic CD (23 treated with benznidazole) and 17 non-infected controls. Functional pathways were annotated with HUMAnN 3, and their differential abundance was assessed using ANCOM-BC2. Diversity metrics (Chao1/ACE indices and multidimensional scaling) and sPLS-DA modelling were used to explore community structure. No significant group differences were observed for alpha- and beta-diversity of bacterial functions; only 6-7 % of variance was attributable to infection status or prior benznidazole therapy. Nevertheless, chronic CD produced a distinctive functional signature marked by depletion of energy-yielding pathways (reductive and canonical tricarboxylic-acid cycles, fatty-acid β-oxidation, haem and 2-methylcitrate metabolism) and modest enrichment of purine and pyrimidine biosynthetic routes. These shifts may imply a microbiome adapting to hypoxia, nutrient scarcity, and metabolic competition with Trypanosoma cruzi. Compared with untreated patients and controls, benznidazole-treated individuals exhibited partial metabolic restoration, namely, up-regulated nucleotide and carbohydrate-degradation pathways, enhanced (5Z)-dodecenoate synthesis, and reduced reliance on the reductive tricarboxylic acid cycle, suggesting renewed microbial growth and improved short-chain-fatty-acid potential. Collectively, our results seem to portray a resource-limited, metabolically stressed gut ecosystem in chronic CD whose functional imbalance is partially reversible with antiparasitic therapy. The affected pathways, particularly those governing energy and nucleotide metabolism, could be used as candidate surrogate markers for disease monitoring and therapeutic response and as targets for microbiota-directed adjuvant strategies.},
}

@article {pmid40712549,
year = {2025},
author = {Fan, J and Guo, Y and Yang, H and Zhang, X and Liu, H and Ren, L and Wang, M},
title = {Dynamic changes of resistance genes and carbohydrate enzyme genes in different agricultural waste fermentation beds based on metagenomics analysis.},
journal = {Ecotoxicology and environmental safety},
volume = {302},
number = {},
pages = {118731},
doi = {10.1016/j.ecoenv.2025.118731},
pmid = {40712549},
issn = {1090-2414},
abstract = {Waste fermentation bed materials from pig farms are often used as organic fertilizers; however, they are a significant source of microorganisms carrying antibiotic-resistance genes (ARGs). Microbes from fermentation bed materials readily introduce ARGs into the soil, causing environmental pollution. We designed four treatments, including RH (rice husk 100 %), RS (rice stalks 50 %, sawdust 40 %, and rice husk 10 %), CS (corn stalks 50 %, sawdust 40 %, and rice husk 10 %), and CTS (cotton stalks 50 %, sawdust 40 %, and rice husk 10 %). The dynamic changes and distribution mechanisms of ARGs in different material fermentation beds are revealed through metagenomic sequencing. The research results indicate that (1) Glycoside hydrolases can increase the abundance of ARGs, while glycosyl transferases can decrease the abundance of ARGs. (2) Lignin promotes the accumulation of glycoside hydrolases, while cellulose and hemicellulose promote the accumulation of glycosyl transferases. (3) At the genus level, Pseudomonas, Parapedobacter, Sphingobacterium, Flavobacterium, Lysobacter, and Myroides mainly rely on their cell membranes to develop ARGs. (4) High lignin content can reduce the accumulation of ARGs, while high cellulose and hemicellulose content can increase the accumulation of ARGs. The results provide a theoretical basis for selecting padding materials that can be widely applied in fermentation bedding systems.},
}

@article {pmid40712359,
year = {2025},
author = {Liu, Y and Li, S and Song, X and Bartlam, M and Wang, Y},
title = {Differential responses of bacterial and archaeal communities to biodegradable and non-biodegradable microplastics in river.},
journal = {Journal of hazardous materials},
volume = {496},
number = {},
pages = {139327},
doi = {10.1016/j.jhazmat.2025.139327},
pmid = {40712359},
issn = {1873-3336},
abstract = {Microplastics are widespread environmental pollutants that pose risks to ecosystems, yet their effects on bacterial and archaeal communities in aquatic ecosystems remain understudied. In this study, we performed a 14-day microcosm experiment combined with metagenomic sequencing to compare bacterial and archaeal responses to a biodegradable microplastic (polylactic acid, PLA) and a non-biodegradable microplastic (polyvinyl chloride, PVC). Microplastics selectively enriched distinct microbial assemblages, with Pseudomonadota and Euryarchaeota identified as the dominant bacterial and archaeal phyla, accounting for 67.83 % and 15.95 %, respectively. Archaeal community in surrounding water were more sensitive to colonization time than bacterial community. Compared to the surrounding water, the plastisphere displayed simpler and more loosely connected microbial networks. Notably, co-occurrence networks of both bacteria and archaea in the PVC plastisphere were predominantly shaped by symbiotic interactions. Both bacteria and archaea carried diverse antibiotic resistance genes (ARGs), but PLS-PM indicated that bacteria were the primary drivers of ARG dissemination (path coefficient = 0.952). While the PVC plastisphere showed higher ARG abundance than the PLA plastisphere, elevated intI1 expression in the PLA plastisphere suggests a potentially greater risk of ARG dissemination associated with PLA microplastics. These findings reveal the distinct effects of PLA and PVC microplastics on microbial communities and highlight the role of microplastics in ARG dissemination, emphasizing their ecological risks in aquatic ecosystems.},
}

@article {pmid40712253,
year = {2025},
author = {Chen, Y and Mo, S and Li, J and Zhong, H and Chao, C and Liu, T and Ma, H},
title = {A challenging case of refractory infection following fish fin injury: Successful treatment through combined therapy.},
journal = {Diagnostic microbiology and infectious disease},
volume = {113},
number = {3},
pages = {117021},
doi = {10.1016/j.diagmicrobio.2025.117021},
pmid = {40712253},
issn = {1879-0070},
abstract = {We report a case of refractory infection caused by Mycobacterium marinum and Mycobacterium shottsii following a fish fin injury. The diagnosis was confirmed by acid-fast bacilli staining and metagenomic next-generation sequencing. This case posed challenges in diagnosis and treatment due to the simultaneous infection by acute and chronic pathogens, uncommon skin and joint symptoms, and multiple lesions involving deep fascia and intermuscular spaces caused by special pathogens. Ultimately, resolution of the lesions without recurrence was achieved after the thorough surgical debridement and excision of the affected tissue in conjunction with dual antibiotic therapy. This success highlights that optimal outcomes require both the most thorough lesion clearance possible and adequate antibacterial therapy administered concurrently. Notably, M. shottsii-previously undocumented as a human pathogen-was identified in this case, expanding the known spectrum of mycobacterial pathogens and highlighting a previously unrecognized zoonotic risk.},
}

@article {pmid40711997,
year = {2025},
author = {Hansen, AK and Percy, DM and Mao, S and Degnan, PH},
title = {Effect of oceanic islands on an insect symbiont genome in transition to a host-restricted lifestyle.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evaf153},
pmid = {40711997},
issn = {1759-6653},
abstract = {Islands offer unique opportunities to study adaptive radiations and their impacts on host genome evolution. In Hawaiian Pariaconus psyllids, all species harbor the ancient nutritional symbiont Carsonella, while only free-living and open-gall species on younger islands host a second stable co-symbiont, Makana. In contrast, a third co-symbiont, Malihini, appears to be in an early-stage of host restriction and genome degradation, making it a valuable model for understanding symbiont evolution during island radiations. Here, we examine Malihini genome evolution across multiple Pariaconus lineages using 16S rRNA sequencing, metagenomics, phylogenetic reconstruction, and microscopy. We find that Malihini is co-diversifying with its hosts on the oldest island Kaua'i (kamua group; open- and closed-gall makers) and on the younger islands only in free-living species (bicoloratus group). Comparison of five Malihini genomes-including three newly assembled in this study-shows ongoing genome reduction from a large-genome ancestor (>3,900 protein-coding genes), likely driven by relaxed selection, vertical transmission bottlenecks, and island dispersal over the past 5-million-years. On Kaua'i, the galling psyllids appear to depend more heavily on co-symbiont (Malihini) for the biosynthesis of amino acids and B-vitamins than galling species on younger islands-especially closed-gall species, which only have Carsonella. Surprisingly, free-living psyllids on younger islands with all three symbionts, show metabolic reliance similar to Kaua'i gall-makers. Together, our results demonstrate that island biogeography and host plant ecology shape symbiont losses and co-diversification patterns. Malihini represents an early-stage of symbiont genome degradation during host restriction, in sharp contrast to its more stable co-residents, Carsonella and Makana.},
}

@article {pmid40711892,
year = {2025},
author = {Turner, D and Adriaenssens, EM and Amann, RI and Bardy, P and Bartlau, N and Barylski, J and Błażejak, S and Bouzari, M and Briegel, A and Briers, Y and Carrillo, D and Chen, X and Claessen, D and Cook, R and Crisci, MA and Dechesne, A and Deptula, P and Dutilh, BE and Ely, B and Fieseler, L and Fogg, PCM and Fukudome, A and Ganjoor, MS and Gientka, I and Holmfeldt, K and Kalatzis, PG and Kauffman, KM and Kempff, A and Knezevic, P and Koonin, EV and Kropinski, AM and Krupovic, M and Kurtböke, I and Lambon, K and Lavigne, R and Lehman, SM and Liu, HT and Lood, C and Lurz, R and Mäntynen, S and Matrishin, CB and Middelboe, M and Millard, AD and Moraru, C and Nielsen, DS and Nobrega, FL and Nunoura, T and Oksanen, HM and Ongenae, V and Parra, B and Pas, C and Pogliano, J and Poranen, MM and Potipimpanon, S and Prichard, A and Pye, HV and Rothschild-Rodriguez, D and Rozen, DE and Santini, JM and Sha, Y and Shymialevich, D and Sokołowska, B and Soleimani-Delfan, A and Średnicka, P and Tavares, P and Telatin, A and Tolstoy, I and Urayama, SI and van Neer, V and Vogensen, FK and Wen, Q and Wichels, A and Wójcicki, M and Ictv Taxonomy Summary Consortium, and Ictv Taxonomy Summary Consortium, and , },
title = {Summary of taxonomy changes ratified by the International Committee on Taxonomy of Viruses (ICTV) from the Bacterial Viruses Subcommittee, 2025.},
journal = {The Journal of general virology},
volume = {106},
number = {7},
pages = {},
doi = {10.1099/jgv.0.002111},
pmid = {40711892},
issn = {1465-2099},
mesh = {*Viruses/classification/genetics ; *Bacteria/virology ; Phylogeny ; *Classification/methods ; },
abstract = {This article summarises the activities of the International Committee on Taxonomy of Viruses Bacterial Viruses Subcommittee, detailing developments in the classification of bacterial viruses. We provide here an overview of all new, abolished, moved and renamed taxa proposed in 2024, approved by the Executive Committee, and ratified by membership vote in 2025. Through the collective efforts of 74 international contributors of taxonomy proposals in this round, 43 ratified proposals have led to the creation of one new phylum, one class, four orders, 33 families, 14 subfamilies, 194 genera and 995 species. These proposals mark significant progress in refining the taxonomy of bacterial viruses. Key updates include the creation of new orders and families that include existing taxa to better reflect genomic and evolutionary relationships. As sequencing and bioinformatics approaches continue to advance, further expansion and refinements in viral taxonomy can be anticipated in the coming years.},
}

*Viruses/classification/genetics
*Bacteria/virology
Phylogeny
*Classification/methods

@article {pmid40711890,
year = {2025},
author = {Krupovic, M and Baquero, DP and Bignon, EA and Bize, A and Borrel, G and Cai, M and Chen, L and Coves, M and Duan, C and Gribaldo, S and Koonin, EV and Li, M and Liu, L and Liu, Y and Medvedeva, S and Ni, Y and Prabhu, A and Rinke, C and Wang, Y and Xu, T and Yan, S and Zeng, Q and Zhang, R and Ictv Taxonomy Summary Consortium, and Ictv Taxonomy Summary Consortium, },
title = {Summary of taxonomy changes ratified by the International Committee on Taxonomy of Viruses (ICTV) from the Archaeal Viruses Subcommittee, 2025.},
journal = {The Journal of general virology},
volume = {106},
number = {7},
pages = {},
doi = {10.1099/jgv.0.002117},
pmid = {40711890},
issn = {1465-2099},
mesh = {*Archaeal Viruses/classification/genetics/isolation & purification ; *Archaea/virology ; Phylogeny ; },
abstract = {The International Committee on Taxonomy of Viruses (ICTV) holds a ratification vote annually following the review of newly proposed taxa by ICTV Study Groups and members of the virology community. This article reports changes to the taxonomy of viruses infecting archaea that were approved and ratified by the ICTV in March 2025. Six new families of head-tailed viruses expanded the order Caudoviricetes (realm Duplodnaviria); one new family of filamentous viruses was added to the order Ligamenvirales (realm Adnaviria); one new family of viruses with pleomorphic virions was included within a new phylum, new order and new class in the kingdom Trapavirae (realm Monodnaviria); finally, three new families were created for spindle-shaped viruses that remain unassigned to higher level taxa. The 25 new species represent viruses infecting a broad range of archaea, including members of the classes Archaeoglobi, Bathyarchaeia, Methanobacteria, Methanomicrobia, Nitrososphaeria and Poseidoniia. Most of these viruses have been discovered by metagenomics in samples derived from diverse environments, including ambient and extreme marine ecosystems, the gastrointestinal tract of humans and animals, anaerobic digesters and terrestrial hot springs. Following this taxonomic update, archaeal viruses are officially classified into a total of 163 virus species in 94 genera within 62 families.},
}

*Archaeal Viruses/classification/genetics/isolation & purification
*Archaea/virology
Phylogeny

@article {pmid40711863,
year = {2025},
author = {Habiba, MU and Augustin, MA and Varela, C and Morris, H and Rahman, MM and Bozkurt, H},
title = {Probiotic Dairy Innovations: Exploring Buffalo Milk Potential for Food Product Development.},
journal = {Comprehensive reviews in food science and food safety},
volume = {24},
number = {4},
pages = {e70236},
doi = {10.1111/1541-4337.70236},
pmid = {40711863},
issn = {1541-4337},
support = {//School of Agriculture, Food and Wine, University of Adelaide/ ; },
mesh = {*Probiotics ; Animals ; *Buffaloes ; *Milk/microbiology/chemistry ; *Dairy Products/microbiology/analysis ; Humans ; Nutritive Value ; },
abstract = {Buffalo milk has emerged as a promising substrate for probiotic dairy innovations due to its distinctive nutritional profile and diverse microbial community. This review critically examines the current knowledge on buffalo milk and its potential applications in developing functional probiotic dairy products. Buffalo milk offers a rich matrix of bioactive components, with higher levels of fat, vitamin A, and biotin, along with comparable calcium content but lower sodium levels relative to cow milk. These compositional differences may have implications for calcium absorption and retention. Lower sodium levels support calcium balance, whereas higher saturated fat content may reduce calcium absorption efficiency, highlighting the need for further study. The review explores the microbial diversity of buffalo milk, emphasizing the prevalence of lactic acid bacteria and other probiotic candidates, and discusses their suitability for use in fermented dairy products such as yoghurt, kefir, and cheese. Innovative processing strategies, including microencapsulation and non-thermal technologies, are assessed for their roles in enhancing probiotic survival and product quality. Additionally, global regulatory frameworks and safety considerations for probiotic dairy products are outlined, along with advanced analytical approaches such as metagenomics and metabolomics for product evaluation. Despite its promising attributes, significant knowledge gaps remain, particularly regarding probiotic strain performance, nutrient bioavailability, consumer acceptance, and clinical validation of health benefits specific to buffalo milk-based products. Addressing these gaps through targeted research will support the development of high-value, health-promoting functional dairy products derived from buffalo milk, particularly in regions where buffalo farming contributes to sustainable food systems.},
}

*Probiotics
Animals
*Buffaloes
*Milk/microbiology/chemistry
*Dairy Products/microbiology/analysis
Humans
Nutritive Value

@article {pmid40711674,
year = {2025},
author = {Xiong, Q and Wang, R and Lai, D and Cai, S and Wang, H and Zhou, N},
title = {Metagenomic Insights into the Root‒Soil Response Mechanisms of Indica and Japonica Rice Under Nitrogen Deficiency and High-Efficiency Nitrogen Compensation.},
journal = {Rice (New York, N.Y.)},
volume = {18},
number = {1},
pages = {72},
pmid = {40711674},
issn = {1939-8425},
support = {32101816//National Natural Science Foundation of China/ ; 2021M702768//China Postdoctoral Science Foundation/ ; 2021K292B//Jiangsu Province Postdoctoral Research Funding/ ; 2021KY47//Jiangxi Province Postdoctoral Scientific Research Funding/ ; 202425YBKT17//Jiangxi Provincial Water Resources Department Science and Technology Project/ ; 20242BAB20263//Natural Science Foundation of Jiangxi Province/ ; PAPD//Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; },
abstract = {Nitrogen (N) dynamics critically regulate rice productivity through root-mediated absorption and assimilation processes. This study investigates the differential responses of japonica (Suxiu 867) and indica (Yangxianyou 918) rice to N deficiency and subsequent high-efficiency compensation, integrating metagenomic analysis with physiological assessments of N metabolism. Building on an established high-efficiency N compensation period (18 days after tillering for japonica and 12 days for indica), we demonstrate that optimized N compensation significantly enhances dry matter accumulation and yield in both subspecies through distinct biological mechanisms. Compensation treatment elevated key metabolic indicators including soluble protein content (Cpr), glutamine synthetase (GDH) activity, soil urease (S-UE) activity, glutamate synthase (GOGAT) activity, and glutamine synthetase (GS) activity, collectively enhancing N assimilation efficiency. Rhizosphere microbiome restructuring showed subspecies-specific patterns, with Chloroflexi and Betaproteobacteria abundance positively correlating with N metabolic enzymes in indica, versus Actinomycetia, Deltaproteobacteria associations in japonica. Functional microbial analysis revealed divergent keystone taxa, with Noviherbaspirillum (indica) and Bacillus (japonica) driving N conversion efficiencies through niche-specific community synergies. Notably, indica rice presented a relatively high N absorption capacity and conversion efficiency, while japonica rice presented relatively stable N absorption and distribution mechanisms, and relatively high N fertilizer application significantly increased the abundance of specific microbial communities in japonica rice. These findings elucidate how subspecies-specific root physiology coordinates with rhizosphere microbial ecology to optimize N utilization, providing actionable insights for precision N management strategies tailored to rice genetic types.},
}

@article {pmid40711419,
year = {2025},
author = {Licata, AG and Zoppi, M and Dossena, C and Rossignoli, F and Rizzo, D and Marra, M and Gargari, G and Mantegazza, G and Guglielmetti, S and Bergamaschi, L and Nigro, O and Chiaravalli, S and Massimino, M and De Cecco, L},
title = {QIIME2 enhances multi-amplicon sequencing data analysis: a standardized and validated open-source pipeline for comprehensive 16S rRNA gene profiling.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0167325},
doi = {10.1128/spectrum.01673-25},
pmid = {40711419},
issn = {2165-0497},
abstract = {Multi-amplicon sequencing is a cost-effective method for profiling multiple regions of the 16S rRNA gene, offering a more comprehensive view of microbial diversity. However, implementing such pipelines on open-source platforms (e.g., QIIME2) is often hindered by limited documentation and lack of validation against established tools. This lack of standardization poses challenges for researchers, particularly in clinical and experimental settings. This study aims to: (i) develop and benchmark a standardized, open-source QIIME2- and R-based pipeline for 16S rRNA gene profiling using semiconductor-based sequencing, comparing it with a commercial, closed-source software; and (ii) validate its effectiveness in a pediatric cancer cohort to examine parental influence on the microbiome and child-caregiver microbial relationships. We generated 16S rRNA profiles from 5 mock communities and 12 child-caregiver fecal sample pairs. Benchmarking against commercial software showed that the multi-region (V2-9) approach produced microbial profiles nearly identical to proprietary outputs, with higher sequencing depth and improved taxonomic resolution compared to single-region analyses. Both approaches demonstrated similar microbial richness, accurate mock community reconstruction, and high reproducibility (R = 0.99, P < 0.0001). These findings were further validated using fecal samples. Application of the pipeline to pediatric samples revealed distinct, differentially abundant Bifidobacterium bifidum and Bifidobacterium adolescentis variants in children whose microbiota closely resembled that of their caregivers. Overall, this study presents a validated, open-source QIIME2 and R pipeline for multi-amplicon sequencing, providing a standardized and reproducible framework for 16S rRNA gene profiling in clinical and research contexts.IMPORTANCEMulti-amplicon sequencing comprehensively characterizes microbial communities by targeting multiple regions of the 16S rRNA gene. However, analytical workflows and reference databases provided by commercial library preparation kits frequently rely on proprietary primers and closed-source pipelines, which can limit transparency, reproducibility, and adaptability. To address these limitations, we developed and validated an open-source bioinformatics pipeline utilizing QIIME2 and R. Our pipeline integrates data from all targeted 16S regions, generating microbial profiles comparable to those produced by proprietary software. Validation was performed using mock samples and fecal samples collected from pediatric cancer patients and their caregivers, confirming the pipeline's reliability and broad applicability. Furthermore, our pipeline enables detailed analysis of microbial variants, surpassing traditional genus-level restrictions and fully leveraging the enhanced coverage offered by multi-amplicon sequencing. Our findings highlight the necessity of adopting open-source solutions to ensure scientific reproducibility and adaptability to emerging methodologies.},
}

@article {pmid40709814,
year = {2025},
author = {Labisa-Morais, F and Valente, D and Blanco-Míguez, A and Manghi, P and Garcia-Valiente, A and Andriamaniraka, H and Armanini, F and Asnicar, F and De Gregorio, C and Golzato, D and Manara, S and Modesto, M and Piperni, E and Punčochář, M and Scarafile, D and Torti, V and Borruso, L and Mattarelli, P and Giacoma, C and Sandri, C and Spiezio, C and Segata, N and Valles-Colomer, M},
title = {Bacterial transmission within social groups shapes the underexplored gut microbiome in the lemur Indri indri.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf136},
pmid = {40709814},
issn = {1751-7370},
abstract = {The Indri indri is a critically endangered lemur species that has not successfully been maintained or bred under human care. Investigating this lemur's virtually unexplored gut microbiome will deepen our understanding of the species' health determinants and inform conservation efforts. Through metagenomic assembly and integration into an updated reference database, we found the I. indri faecal microbiome remains largely uncultivated (cultivated species representing <0.1% relative abundance) and is largely specific to this primate species. After reconstructing 342 metagenome-assembled genomes encompassing 48 candidate species from a total of 22 samples (18 of which newly sequenced), we substantially improved microbiome mappability to 85% on average and found evidence for a proportionally large core microbiome. Social group membership emerged as the main determinant of both their taxonomic and functional gut microbiome composition. Using strain-level profiling, we detected extensive microbiome transmission within social groups, suggesting physical interaction is key in promoting microbiome acquisition. Strain sharing rates were highest between mothers and their offspring. Intergroup strain sharing was minimal and inversely correlated with geographical distance, aligning with the rare intergroup interactions and stable territory occupancy coupled with ongoing habitat fragmentation. No evidence of microbiome acquisition through geophagy was detected. These findings underscore the profound influence of social structure on microbiome transmission and composition in I. indri, and highlight the importance of considering social dynamics into research and conservation strategies.},
}

@article {pmid40708906,
year = {2025},
author = {Jiang, Y and Chang, M and Fu, Q and Wang, H},
title = {Xanthogranulomatous pyelonephritis in a 47-day-old male infant: a case report.},
journal = {Frontiers in pediatrics},
volume = {13},
number = {},
pages = {1625781},
pmid = {40708906},
issn = {2296-2360},
abstract = {BACKGROUND: Xanthogranulomatous pyelonephritis (XGP), a rare granulomatous renal disease linked to bacterial infection (e.g., Escherichia coli), presents challenges in pediatric diagnosis, especially in infants, due to overlap with neoplastic renal masses like Wilms tumor.

CASE SUMMARY: A 47-day-old male infant with fever, elevated inflammatory markers (WBC 13.94 × 10[9]/L, CRP 110.43 mg/L), and urinary leukocytes/hematuria showed a left renal mass (1.7 × 1.8 × 2.1 cm) on imaging. Biopsy revealed histiocytic-neutrophilic infiltration with focal necrosis, and metagenomic sequencing identified dominant E. coli. Antibiotic therapy (cefoperazone-sulbactam followed by cefdinir) induced regression (1.1 × 0.8 × 1.1 cm at 2 weeks). Elevated AFP (888.27 ng/ml) normalized, excluding malignancy.

CONCLUSION: This case highlights XGP as a critical differential diagnosis for febrile infants with renal masses. Integration of histopathology, metagenomic sequencing, and prolonged follow-up confirms that focal XGP can be managed successfully with targeted antibiotics, avoiding nephrectomy.},
}

@article {pmid40708849,
year = {2025},
author = {Lataretu, M and Krautwurst, S and Huska, MR and Marquet, M and Viehweger, A and Braun, SD and Brandt, C and Hölzer, M},
title = {Targeted decontamination of sequencing data with CLEAN.},
journal = {NAR genomics and bioinformatics},
volume = {7},
number = {3},
pages = {lqaf105},
pmid = {40708849},
issn = {2631-9268},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Decontamination/methods ; *Software ; Metagenomics/methods ; RNA, Ribosomal/genetics ; Sequence Analysis, RNA/methods ; *Sequence Analysis, DNA/methods ; },
abstract = {Many biological and medical questions are answered based on the analysis of sequence data. However, we can find contamination, artificial spike-ins, and overrepresented rRNA (ribosomal RNA) sequences in various read collections and assemblies. In particular, spike-ins used as controls, as those known from Illumina or Nanopore data, are often not considered as contaminants and also not appropriately removed during analyses. Additionally, removing human host DNA may be necessary for data protection and ethical considerations to ensure that individuals cannot be identified. We developed CLEAN, a pipeline to remove unwanted sequences from both long- and short-read sequencing techniques. While focusing on Illumina and Nanopore data with their technology-specific control sequences, the pipeline can also be used for host decontamination of metagenomic reads and assemblies, or the removal of rRNA from RNA-Seq data. The results are the purified sequences and sequences identified as contaminated with statistics summarized in a report. The output can be used directly in subsequent analyses, resulting in faster computations and improved results. Although decontamination seems mundane, many contaminants are routinely overlooked, cleaned by steps that are not fully reproducible or difficult to trace. CLEAN facilitates reproducible, platform-independent data analysis in genomics and transcriptomics and is freely available at https://github.com/rki-mf1/clean under a BSD3 license.},
}

Humans
*High-Throughput Nucleotide Sequencing/methods
*Decontamination/methods
*Software
Metagenomics/methods
RNA, Ribosomal/genetics
Sequence Analysis, RNA/methods
*Sequence Analysis, DNA/methods

@article {pmid40708635,
year = {2025},
author = {Sun, X and Gong, Q},
title = {A case report of AIDS complicated by Pneumocystis jirovecii and Tropheryma whipplei mixed pulmonary infection identified via metagenomic next-generation sequencing.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1599261},
pmid = {40708635},
issn = {2296-858X},
abstract = {Tropheryma whipplei (TW) is a Gram-positive bacterium that is rarely encountered in clinical practice. It primarily affects the digestive and nervous systems, with pulmonary infections being infrequently reported. This case report describes a patient with HIV/AIDS who developed a mixed pulmonary infection involving Pneumocystis jirovecii pneumonia (PJP) and TW. The diagnosis was confirmed via metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid obtained through bronchoscopy. Following appropriate treatment, the patient's symptoms and pulmonary imaging findings showed marked improvement.},
}

@article {pmid40708049,
year = {2025},
author = {Riccardi, C and Wang, Y and Yooseph, S and Sun, F},
title = {Bidirectional subsethood of shared marker profiles enables accurate virus classification.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {170},
pmid = {40708049},
issn = {2049-2618},
support = {EF-2125142//National Science Foundation/ ; },
mesh = {*Viruses/classification/genetics ; *Metagenomics/methods ; *Software ; *Computational Biology/methods ; Phylogeny ; Genome, Viral ; Humans ; },
abstract = {BACKGROUND: Due to the impact of viral metagenomic sequencing, the official virus taxonomy is updated several times a year, with labels being renamed even substantially across releases. While this helps reveal newer aspects on the classification of viruses, existing bioinformatic methods for classification struggle to stay in sync with this ever-improving resource.

RESULTS: We developed a new computer program, named VIRGO, that is able to correctly predict virus families from metagenomic data with an F1 score above 0.9 using a novel viral sequence similarity metric proposed in this work. Moreover, it ensures compatibility with any version of the official taxonomy of viruses.

CONCLUSIONS: Virgo is designed to easily incorporate newer releases of the official taxonomy, thus representing a valuable resource in the virology community while raising awareness to develop computational methods that evolve alongside manually curated resources. Video Abstract.},
}

*Viruses/classification/genetics
*Metagenomics/methods
*Software
*Computational Biology/methods
Phylogeny
Genome, Viral
Humans

@article {pmid40708022,
year = {2025},
author = {Wang, R and Cheng, S and Du, W and Sun, F and Gao, Y and Zhu, Z and He, C and Chen, J and Tian, S and Chu, Y and Zhou, G and Miao, H and Li, L and Dong, X and Han, X},
title = {An innovative fungal-specific targeted next-generation sequencing method: analytical performance and a single-center prospective clinical study.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {820},
pmid = {40708022},
issn = {1479-5876},
support = {2024ZD0533106//National Science and Technology Major Project/ ; 2019-I2M-5-027//CAMS Innovation Fund for Medical Sciences/ ; 2021YFC2300400//National Key Research and Development Program of China/ ; },
abstract = {BACKGROUND: Invasive pulmonary fungal infections (IPFIs) pose significant diagnostic challenges, particularly in immunocompromised patients. Accurate and timely diagnosis is crucial to improve outcomes. While metagenomic next-generation sequencing (mNGS) is widely utilized, it is expensive and affected by host DNA interference. Targeted next-generation sequencing (tNGS) offers a cost-effective and efficient alternative for fungal pathogen detection.

METHODS: We developed the Fi-tNGS assay, a targeted next-generation sequencing method, specifically designed to detect 64 fungal species. Analytical performance was validated by assessing its limit of detection (LoD), reproducibility, and resistance to host DNA interference. Subsequently, a prospective clinical study was conducted, enrolling 104 patients with suspected IPFIs. Clinical diagnostic performance was evaluated by comparing Fi-tNGS, mNGS, and conventional microbial culture against a comprehensive diagnostic standard.

RESULTS: Fi-tNGS detected 109 pathogens, compared to 110 for mNGS and 77 for culture. The sensitivity and specificity of tNGS were 89.7% and 94.2%, respectively, outperforming culture (65.8% sensitivity, 100% specificity). Combining culture with tNGS or mNGS significantly improved sensitivity to 94.8% and 94.0%, respectively. These findings demonstrate the added diagnostic value of NGS methods for IPFIs.

CONCLUSIONS: tNGS provides accurate and efficient fungal pathogen detection, with sensitivity comparable to mNGS and superior to culture. Its cost-effectiveness and shorter turnaround time highlight its potential as a practical tool for the rapid and precise diagnosis of IPFIs in clinical settings.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12967-025-06784-w.},
}

@article {pmid40708004,
year = {2025},
author = {Holm, JB and Paragkamian, S and Humphreys, M and Chatterjee, A and Yarwood, S and Gaimaro, J and Stavroulaki, M and Tsaparis, D and Plaitis, M and Kasapidis, P and Darivianakis, S and Kotoulas, G and Magoulas, A and Oulas, A and Kyrpiotakis, Z and Pavlidis, P and Ten Hoopen, P and Cochrane, G and Kooistra, HCFW and Schriml, JR and Schriml, BE and Lagkouvardos, I and Gkorezis, P and Davies, N and Laney, C and Stanish, L and Sutton, G and Tighe, S and Mizrachi, IK and Parks, D and Yilmaz, P and Carey, C and Buttigieg, P and Goldstein, P and Pafilis, E and Schriml, LM},
title = {First island-wide, single-day soil collection study on Crete reveals environmental drivers of microbial diversity.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {94},
pmid = {40708004},
issn = {2524-6372},
support = {5726//Hellenic Foundation for Research and Innovation Scholarships for PHD Candidates/ ; 730984//the European Union's Horizon 2020/ ; },
abstract = {Understanding how environmental and ecological factors shape variability in soil-associated microbial communities is a complex problem, particularly on islands, which contain a wide range of diverse and unique geology, fauna, and flora. The island of Crete features sharp altitudinal gradients, diverse landscapes, and distinct ecological zones shaped by its complex geological history making it an ideal natural laboratory for studying how environmental variation influences soil microbial communities. In this study, we characterized the soil microbial communities across Crete's ecozones and identify environmental factors associated with their diversity and composition. We performed a single-day, island-wide soil microbiota investigation, the first of its kind, to address this challenge by eliminating sources of variability including seasonality, weather conditions, anthropogenic or land use changes over time, and ecological succession of microbial communities. This island collection event (Island Sampling Day, ISD) was conducted in conjunction with the annual meeting of the Genomic Standards Consortium, on the island of Crete, and utilized standard data and metadata collection protocols. We generated amplicon sequences (V3-V4 regions of the 16 S ribosomal RNA gene) and a metadata-enriched dataset from 435 soil samples across 72 sites and four distinct ecozones for future whole-island microbiome studies. Here we report on the study design and sample collection process along with our initial examination of the ecological drivers of soil microbial community variability (e.g., elevation, soil types, soil pH, soil moisture, vegetation type, land use) across the Crete ecozones (defined by elevation and distinct habitats).},
}

@article {pmid40707990,
year = {2025},
author = {Drevland, OM and de Muinck, EJ and Trosvik, P and Hammerstad, M and Kvitne, KE and Midtvedt, K and Åsberg, A and Robertsen, I},
title = {Microbiome-derived reactivation of mycophenolate explains variations in enterohepatic recirculation in kidney transplant recipients.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {169},
pmid = {40707990},
issn = {2049-2618},
support = {315792//Norges Forskningsråd/ ; 315792//Norges Forskningsråd/ ; },
mesh = {*Mycophenolic Acid/pharmacokinetics/analogs & derivatives/metabolism ; *Kidney Transplantation ; Humans ; *Gastrointestinal Microbiome/drug effects ; Male ; Female ; *Immunosuppressive Agents/pharmacokinetics/therapeutic use ; Middle Aged ; Feces/microbiology ; Adult ; Transplant Recipients ; Glucuronidase/metabolism/genetics ; Glucuronides/metabolism ; Metagenomics/methods ; *Enterohepatic Circulation ; },
abstract = {BACKGROUND: The pivotal role of microbes in drug metabolism is increasingly recognized, as variation in the gut microbiome composition between individuals has been shown to impact systemic drug exposure, efficacy and toxicity. Mycophenolate mofetil (MMF) is a cornerstone in immunosuppressive therapy following solid organ transplantation. However, dosing and tolerance are challenged by significant pharmacokinetic variability among patients, largely due to variable degrees of enterohepatic recirculation of mycophenolic acid (MPA), the active moiety of MMF. It is hypothesized that the variability in MPA recirculation is driven by gut microbiome-derived β-glucuronidase (β-GUS) mediated cleavage of MPA-glucuronide (MPAG) excreted in the bile. Here, we investigated the bidirectional interaction between MPA and the gut microbiome in kidney transplant recipients, using a combination of in vivo and in vitro data.

RESULTS: We compared the fecal microbiomes of kidney transplant recipients (n = 21) both pre- and post-transplantation to healthy individuals (n = 15) using shotgun metagenomic sequencing. We also determined the individual microbiome-derived reactivation rate of MPAG to MPA and show a strong positive correlation between this reactivation rate and the degree of MPA enterohepatic recirculation in vivo. Through metagenomic analysis, the reactivation rate of MPA was linked to specific gut microbial species. In particular, specific β-GUS gene variants associated with Faecalibacterium prausnitzii showed a strong impact on the conversion of MPAG to MPA. Furthermore, our study confirmed a significant shift in microbial composition post-transplantation and revealed notable fluctuations in species such as F. prausnitzii and Akkermansia muciniphila across different time points after transplantation. Lastly, we provide evidence that the microbiome-derived reactivation rate of MPA is linked to specific beta-glucuronidase alleles.

CONCLUSIONS: We highlight for the first time that the ex vivo determined reactivation rate of MPA explains the variation of enterohepatic recirculation, emphasizing the important role of F. prausnitzii in this process. More broadly, our findings suggest that the gut microbiome significantly influences the degree of enterohepatic recirculation of MPA, providing valuable insights that could be relevant for optimizing individualized immunosuppressive drug dosing in transplant patients. Video Abstract.},
}

*Mycophenolic Acid/pharmacokinetics/analogs & derivatives/metabolism
*Kidney Transplantation
Humans
*Gastrointestinal Microbiome/drug effects
Male
Female
*Immunosuppressive Agents/pharmacokinetics/therapeutic use
Middle Aged
Feces/microbiology
Adult
Transplant Recipients
Glucuronidase/metabolism/genetics
Glucuronides/metabolism
Metagenomics/methods
*Enterohepatic Circulation

@article {pmid40707831,
year = {2025},
author = {Sereika, M and Mussig, AJ and Jiang, C and Knudsen, KS and Jensen, TBN and Petriglieri, F and Yang, Y and Jørgensen, VR and Delogu, F and Sørensen, EA and Nielsen, PH and Singleton, CM and Hugenholtz, P and Albertsen, M},
title = {Genome-resolved long-read sequencing expands known microbial diversity across terrestrial habitats.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41564-025-02062-z},
pmid = {40707831},
issn = {2058-5276},
support = {130690//Villum Fonden (Villum Foundation)/ ; 50093//Villum Fonden (Villum Foundation)/ ; },
abstract = {The emergence of high-throughput, long-read DNA sequencing has enabled recovery of microbial genomes from environmental samples at scale. However, expanding the terrestrial microbial genome catalogue has been challenging due to the enormous complexity of these environments. Here we performed deep, long-read Nanopore sequencing of 154 soil and sediment samples collected during the Microflora Danica project, yielding genomes of 15,314 previously undescribed microbial species, recovered using our custom mmlong2 workflow. The recovered microbial genomes span 1,086 previously uncharacterized genera and expand the phylogenetic diversity of the prokaryotic tree of life by 8%. The long-read assemblies also enabled the recovery of thousands of complete ribosomal RNA operons, biosynthetic gene clusters and CRISPR-Cas systems. Furthermore, the incorporation of the recovered genomes into public genomic databases substantially improved species-level classification rates for soil and sediment metagenomic datasets. These findings demonstrate that long-read sequencing allows cost-effective recovery of high-quality microbial genomes from highly complex ecosystems, which remain an untapped source of biodiversity.},
}

@article {pmid40707808,
year = {2025},
author = {Liu, Y and Shen, J and Zhang, X and Ping, F and Qyu, K and Shen, X},
title = {Xiaoyao Pill Regulates Gut Microbiota and Tryptophan Metabolism to Alleviate Depression Induced by Chronic Stress in Rats.},
journal = {Chinese journal of integrative medicine},
volume = {},
number = {},
pages = {},
pmid = {40707808},
issn = {1993-0402},
abstract = {OBJECTIVE: To investigate the antidepressant effects of Xiaoyao Pill (XYP) by exploring its interactions with gut microbiota and tryptophan metabolism.

METHODS: Utilizing network pharmacology, the functional substance groups, key targets, and pathways of XYP in the treatment of depression were identified. The chronic unpredictable mild stress (CUMS) protocol was implemented in male Sprague-Dawley rats to establish depression model. Thirty rats were randomly divided into 3 groups according to their body weight (10 for each): control, CUMS and XYP groups (1.8 g/kg). After 28-day interventions, behavioral phenotyping including sucrose preference test (SPT) and open field test (OFT) were performed. Biochemical validation encompassed enzyme-linked immunosorbent assay for serum cortisol, hematoxylin-eosin histopathology, and immunohistochemistry. Liquid chromatography-mass spectrometry was utilized to profile serum metabolites, while fecal samples underwent metagenomic sequencing for gut microbiota characterization.

RESULTS: Network pharmacology studies predicted that key components can protect the nervous system by regulating inflammatory pathways through the blood-brain barrier. SPT and OFT showed that XYP treatment significantly ameliorated depressive-like behaviors (all P<0.05). XYP treatment also restored hippocampal neuronal density, increased serum neurotransmitter levels of neurotransmitters such as 5-hydroxytryptamine and vasoactive intestinal peptide, and while suppressing inflammatory markers such as tumor necrosis factor-alpha, interleukin-1 beta (IL-1 β), and IL-6 (all P<0.05). Metagenomics revealed significant restructuring of gut microbiota, notably the regulation of Parabacteroides distasonis (P<0.05). Non-targeted metabolomics analysis showed that the level of metabolites in the tryptophan and kynurenine pathway significantly changed (variable importance in the projection >1, P<0.05), and the change of metabolic flux was significantly correlated with behavioral improvement (P<0.05).

CONCLUSIONS: XYP exerts antidepressant effects by increasing neurotransmitter levels, reducing inflammatory makers and modulating Parabacteroides distasonis. Through further exploration of metabolomics, we found that XYP may play a protective role in depression by regulating tryptophan metabolism.},
}

@article {pmid40707722,
year = {2025},
author = {Mangnier, L and Bodein, A and Mariaz, M and Mathieu, A and Scott-Boyer, MP and Vashist, N and Bramble, MS and Droit, A},
title = {A systematic benchmark of integrative strategies for microbiome-metabolome data.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {1100},
pmid = {40707722},
issn = {2399-3642},
mesh = {Humans ; *Metabolomics/methods ; *Metabolome ; *Gastrointestinal Microbiome ; Benchmarking ; *Metagenomics/methods ; *Microbiota ; Computational Biology/methods ; },
abstract = {The rapid advancement of high-throughput sequencing technologies has enabled the integration of various omic layers into computational frameworks. Among these, metagenomics and metabolomics are increasingly studied for their roles in complex diseases. However, no standard currently exists for jointly integrating microbiome and metabolome datasets within statistical models. We benchmarked nineteen integrative methods to disentangle the relationships between microorganisms and metabolites. These methods address key research goals, including global associations, data summarization, individual associations, and feature selection. Through realistic simulations, we identified the best-performing methods and validated them on real gut microbiome datasets, revealing complementary biological processes across the two omic layers. Practical guidelines are provided for specific scientific questions and data types. This work establishes a foundation for research standards in metagenomics-metabolomics integration and supports future methodological developments, while also providing guidance for designing optimal analytical strategies tailored to specific integration questions.},
}

Humans
*Metabolomics/methods
*Metabolome
*Gastrointestinal Microbiome
Benchmarking
*Metagenomics/methods
*Microbiota
Computational Biology/methods

@article {pmid40707492,
year = {2025},
author = {Villette, R and Novikova, PV and Laczny, CC and Mollenhauer, B and May, P and Wilmes, P},
title = {Human gut microbiome gene co-expression network reveals a loss in taxonomic and functional diversity in Parkinson's disease.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {142},
pmid = {40707492},
issn = {2055-5008},
support = {863664//HORIZON EUROPE European Research Council/ ; 863664//HORIZON EUROPE European Research Council/ ; CORE/16/BM/11333923//Fonds National de la Recherche Luxembourg/ ; CORE/16/BM/11333923//Fonds National de la Recherche Luxembourg/ ; },
mesh = {*Parkinson Disease/microbiology ; *Gastrointestinal Microbiome/genetics ; Humans ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Gene Regulatory Networks ; Metagenomics ; Gene Expression Profiling ; Male ; Female ; Aged ; Middle Aged ; },
abstract = {Gut microbiome alterations are linked to various diseases, including neurodegeneration, but their ecological and functional impacts remain unclear. Using integrated multi-omics (metagenomics and metatranscriptomics), we analyse microbiome gene co-expression networks in Parkinson's disease (PD) and healthy controls (HC). We observe a significant depletion of hub genes in PD, including genes involved in secondary bile acid biosynthesis, bacterial microcompartments (BMCs), polysaccharides transport and flagellar assembly (FA). Blautia, Roseburia, Faecalibacterium and Anaerobutyricum genera are the main contributors to these functions, showing significantly lower expression in PD. Additionally, we identify a strong correlation between BMC and FA expression, and an apparent dysregulation in cross-feeding between commensals in PD. Finally, PD also exhibits reduced gene expression diversity compared to HC, whereby higher gene expression correlates with greater diversity. We identify disruptions in gut metabolic functions, at both taxonomic and functional level, and microbiome-wide ecological features, highlighting targets for future gut microbiome restoration efforts.},
}

*Parkinson Disease/microbiology
*Gastrointestinal Microbiome/genetics
Humans
*Bacteria/classification/genetics/isolation & purification/metabolism
*Gene Regulatory Networks
Metagenomics
Gene Expression Profiling
Male
Female
Aged
Middle Aged

@article {pmid40707215,
year = {2025},
author = {Li-Hau, F and Nakagawa, M and Kakegawa, T and Ward, LM and Ueno, Y and McGlynn, SE},
title = {Metabolic Potential and Microbial Diversity of Late Archean to Early Proterozoic Ocean Analog Hot Springs of Japan.},
journal = {Microbes and environments},
volume = {40},
number = {3},
pages = {},
doi = {10.1264/jsme2.ME24067},
pmid = {40707215},
issn = {1347-4405},
mesh = {*Hot Springs/microbiology/chemistry ; Japan ; *Bacteria/classification/metabolism/genetics/isolation & purification ; *Archaea/classification/metabolism/genetics/isolation & purification ; Oxidation-Reduction ; Phylogeny ; Nitrogen Fixation ; Oceans and Seas ; Iron/metabolism ; *Biodiversity ; Carbon Cycle ; RNA, Ribosomal, 16S/genetics ; Nitrogen Cycle ; Hydrogen/metabolism ; },
abstract = {Circumneutral iron-rich hot springs may represent analogues of Neoarchean to Paleoproterozoic oceans of early Earth, potentially providing windows into ancient microbial ecology. Here we sampled five Japanese hot springs to gain insights into functional processes and taxonomic diversity in these analog environments. Amplicon and metagenomic sequencing confirm a hypothesis where taxonomy is distinct between sites and linked to the geochemical setting. Metabolic functions shared among the springs include carbon fixation via the reductive pentose phosphate cycle, nitrogen fixation, and dissimilatory iron oxidation/reduction. Among the sites, Kowakubi was unique in that it was dominated by Hydrogenophilaceae, a group known for performing hydrogen oxidation, motivating a hypothesis that H2 as an electron donor may shape community composition even in the presence of abundant ferrous iron. Evidence for nitrogen cycling across the springs included N2 fixation, dissimilatory nitrate reduction to ammonia (DNRA), and denitrification. The low-salinity springs Furutobe and OHK lacked evidence for ammonium oxidation by ammonia monooxygenase, but evidence for complete nitrification existed at Kowakubi, Jinata, and Tsubakiyama. In most sites, the microaerophilic iron-oxidizing bacteria from the Zetaproteobacteria or Gammaproteobacteria classes had higher relative abundances than Cyanobacteria. Microaerophilic iron oxidizers may outcompete abiotic Fe oxidation, while being fueled by oxy-phototrophic Cyanobacteria. Our data provide a foundation for considering which factors may have controlled productivity and elemental cycling as Earth's oceans became oxygenated at the onset of the Great Oxidation Event.},
}

*Hot Springs/microbiology/chemistry
Japan
*Bacteria/classification/metabolism/genetics/isolation & purification
*Archaea/classification/metabolism/genetics/isolation & purification
Oxidation-Reduction
Phylogeny
Nitrogen Fixation
Oceans and Seas
Iron/metabolism
*Biodiversity
Carbon Cycle
RNA, Ribosomal, 16S/genetics
Nitrogen Cycle
Hydrogen/metabolism

@article {pmid40706942,
year = {2025},
author = {Xiong, J and Wu, Y and Chen, J and Cheng, D and Liu, X},
title = {Influence mechanism of sludge composting on antibiotic resistance genes under antibiotic stress: A comprehensive analysis.},
journal = {Comparative biochemistry and physiology. Toxicology & pharmacology : CBP},
volume = {},
number = {},
pages = {110297},
doi = {10.1016/j.cbpc.2025.110297},
pmid = {40706942},
issn = {1532-0456},
abstract = {Antibiotic resistance genes (ARGs) are increasingly recognized as emerging contaminants that enter agricultural lands and surrounding ecosystems through the application of sewage sludge containing residual antibiotics. Composting is an effective method for reducing antibiotics and ARGs in sludge; however, the impact of residual antibiotics on the efficiency of ARG removal remains unclear. This study explored the reduction of oxytetracycline (OTC), sulfamerazine (SM1), and ciprofloxacin (CIP), as well as their impact on the removal of ARGs during sewage sludge composting. Our results demonstrated that composting achieved average removal efficiencies of 89.37 %, 72.63 %, and 82.98 % for OTC, CIP, and SM1, respectively. Metagenomic sequencing revealed that antibiotic residues significantly promoted the elimination of ARGs by 26.05-40.81 %. In contrast, the CK treatment resulted in a notable increase in tetracycline-resistant genes, particularly adeF, tetX, and soxR, compared to the levels reduced under antibiotic-induced selective pressure. Redundancy analysis (RDA) indicated that temperature, pH, C/N, CIP, and Proteobacteria, Tenericutes, and Chloroflexi were significant factors influencing the reduction of ARGs (P < 0.05). Network analysis further confirmed that Proteobacteria, particularly genera such as Pseudomonas and Pseudoxanthomonas, were predominantly associated with ARGs. These findings indicated that antibiotic residues can effectively promote the rebound of related ARGs, and offer valuable insights for the source control of ARGs.},
}

@article {pmid40706837,
year = {2025},
author = {Yu, F and Zhang, Y and Wen, Y and Peng, Z and Xu, D and Xiao, J},
title = {Divergent risk gene profiles in smallholder and large-scale paddy farms.},
journal = {Environmental research},
volume = {285},
number = {Pt 2},
pages = {122406},
doi = {10.1016/j.envres.2025.122406},
pmid = {40706837},
issn = {1096-0953},
abstract = {The proliferation of microbial resistance and virulence genes in agricultural soils poses an increasing threat to soil quality, food security, and public health. Smallholder and large-scale farming systems represent the two dominant modes of rice cultivation in many developing countries, yet the impact of their contrasting management practices on soil microbial risk gene reservoirs remains poorly understood. In this study, we systematically compared the profiles and ecological dynamics of antibiotic resistance genes (ARGs), biocide resistance genes (BRGs), metal resistance genes (MRGs), and virulence factor genes (VFGs) in paddy soils from paired smallholder and large-scale farms in Jiangsu, China. Metagenomic sequencing revealed significantly higher abundances of all four gene categories in smallholder farms, with ARGs 5.42 %, BRGs 8.66 %, MRGs 4.81 %, and VFGs 7.81 % more abundant compared with large-scale farms. Co-occurrence network analysis based on strong correlations (Spearman's ρ > 0.8) and high significance (q-value <0.001) revealed a lower average degree (11.83 vs. 20.98) and higher modularity (0.65 vs. 0.52) in smallholder farm soils, indicating a more compartmentalized and localized structure of gene interactions. Neutral community modeling and normalized stochasticity ratio analyses indicated that stochastic processes dominated gene community assembly in both systems, with stronger dispersal signals in smallholder soils. Random forest analysis identified total carbon, total nitrogen, nitrate, available phosphorus, and heavy metals as key environmental predictors of risk gene abundance, with total carbon and total nitrogen contributing the most (8.31-10.78 % and 6.79-9.80 % increase in MSE across the four gene categories). Together, these findings highlight the elevated ecological risks associated with poorly regulated farming practices and emphasize the importance of standardized management in reducing the enrichment and dissemination of microbial risk genes.},
}

@article {pmid40706488,
year = {2025},
author = {Tong, Y and Wang, Y and Zhang, J and Guo, Y and Yuan, T and Chen, H and Zhang, H and Zhan, K and Zhao, L and Ma, Q and Huang, S},
title = {Comprehensive study on the impact of ginger extract on laying performance, egg quality, inflammatory responses, intestinal barrier function, and cecal microbiome and resistome in laying hens.},
journal = {Poultry science},
volume = {104},
number = {10},
pages = {105448},
doi = {10.1016/j.psj.2025.105448},
pmid = {40706488},
issn = {1525-3171},
abstract = {Experimental models have been extensively used to explore the effects of ginger extract (GE) on oxidative stress and immune response. However, the influence of GE dietary supplementation on gut microbial composition, function, and the resistome in laying hens remains not fully understood. This research investigated the impact of GE supplementation on laying performance, egg quality, metabolism, inflammation, and the gut microbiome and resistome in laying hens. Thirty healthy, 35-week-old Jingfen No.6 laying hens with consistent body weight and laying rate were randomly allocated to either the control group (Con; basal diet) or the ginger extract supplementation group (Con-G; basal diet with 5 g/kg GE), each with fifteen replicates (one hen per replicate). The pre-feeding period lasted one week, followed by an eight-week trial. The results revealed that average laying rate (P = 0.051) and egg mass (P < 0.05) significantly increased, while feed conversion efficiency improved (P < 0.05) in the GE-supplemented group during the study period. Additionally, egg quality, host metabolism, serum antioxidant levels, and histological assessments of the jejunum, ileum, and cecum tissues were positively affected by GE (P < 0.05). Notably, GE supplementation significantly decreased (P < 0.05) serum pro-inflammatory cytokines (IL-6, IL-1β, and TNF-α) and increased (P < 0.05) IgA, IgG, and IL-10 levels. LEfSe analysis revealed that the relative abundance of genera such as Ligilactobacillus salivarius, Limosilactobacillus vaginalis, Butyricimonas virosa, and Limosilactobacillus alvi were significantly increased (P < 0.05) in the Con-G group. Furthermore, ginger extract significantly enhanced (P < 0.05) the production of short-chain fatty acids(including acetate, propionate, butyrate, isovalerate, valerate, and lactate) in the cecum, modulated the expression profile of antibiotic resistance genes in the intestines of laying hens, and inhibited pathogen colonization. The study concludes that ginger extract supplementation in laying hen diets improves laying performance, egg quality, host metabolism, and immune responses, positively alters gut microbiota composition and functionality, and modulates the poultry resistome. Metagenomic analysis underscores the potential of GE as a safe and effective additive.},
}

@article {pmid40706388,
year = {2025},
author = {Elad, T and Tang, K and Pierrelée, M and Jensen, MM and Bentzon-Tilia, M and Smets, BF and Dechesne, A and Valverde-Pérez, B},
title = {An integrated meta-omics approach for identifying candidate organic micropollutant degraders in complex microbial communities.},
journal = {Water research},
volume = {286},
number = {},
pages = {124217},
doi = {10.1016/j.watres.2025.124217},
pmid = {40706388},
issn = {1879-2448},
abstract = {Biotransformation is a significant determinant of the fate of organic micropollutants (OMPs) in natural and engineered environments. Here we propose a genome-resolved metatranscriptomics approach for the identification of candidate OMP-transforming microorganisms based on positive relations between biotransformation rate constants and the activity of metagenome-assembled genomes (MAGs). To demonstrate the approach, we used five nitrifier-rich batch cultures, first validating with ammonia (a macropollutant) before applying it to atenolol (an OMP). As expected, the biotransformation rate constant of ammonia was correlated with the activity of an ammonia-oxidizing bacterium, namely Nitrosomonas europaea; it was not correlated with the activity of other bacteria, including several ammonia oxidizers. Additionally, the biotransformation rate constant of ammonia was correlated with the transcript relative abundance of the ammonia monooxygenase (AMO) expressed by N. europaea but not with the transcript abundance of AMO at the community level. The biotransformation rate constant of atenolol was correlated with the activity of four MAGs representing three heterotrophic genera: Terrimonas, Flavobacterium, and Zeimonas. It was not correlated with the total transcript relative abundance of any member of a comprehensive set of amidohydrolases, which are predicted to transform this drug. By contrast, it was correlated with the expression of the amidohydrolase asparagine synthase (AsnB) identified in the Terrimonas and Flavobacterium MAGs. In summary, we present a novel association-based method for investigating biotransformation processes robust to variability in enzyme reaction kinetics with implications for OMP control.},
}

@article {pmid40706155,
year = {2025},
author = {Wang, YC and He, LY and Wu, HY and Qiao, LK and Huang, Z and Bai, H and Gao, FZ and Shi, YJ and Zhao, JL and Liu, YS and Ying, GG},
title = {High-risk plasmid-borne resistance genes from swine farm environments infiltrate deep soil and interact with the human gut microbiome via horizontal transfer.},
journal = {Journal of hazardous materials},
volume = {496},
number = {},
pages = {139281},
doi = {10.1016/j.jhazmat.2025.139281},
pmid = {40706155},
issn = {1873-3336},
abstract = {Swine farms serve as critical reservoirs of antibiotic resistance genes (ARGs), yet the frequency of horizontal gene transfer (HGT) remains poorly understood. In this study, we explored the gene exchange within the "swine farm-human-pig" network and assessed its risks. We identified 16,612 plasmid contigs from 107 field samples, revealing a significant presence of previously uncharacterized plasmid types. Notably, 52.88 % of acquired ARGs were located on plasmids, with 71.22 % containing at least one mobile genetic element (MGE). We quantified HGTs at the microbial community level among the human gut, pig gut, and swine farm environments. Among 4687 metagenome-assembled genomes (MAGs), 3008 were involved in 11,250 HGTs. HGT linkages were most frequently identified between microbial genomes from the swine farm and the human gut microbiome. ARGs were involved in 91 HGT events, with 645 events linked to MGEs and 16 related to virulence factors, suggesting potential cross-species transmission of clinical pathogens. The detection of 32 Rank I ARGs and the identification of increased resistome risks underscore the extensive dispersion of livestock-related contaminants into more distant environmental compartments. This study elucidates the complexities of gene exchange networks in swine farm environments, underscoring the urgent need for strategies to mitigate risks associated with the antibiotic resistome.},
}

@article {pmid40705419,
year = {2025},
author = {Iqbal, NT and Sawatzki, K and Ahmed, K and Tisoncik-Go, J and Smith, E and Voss, K and Cornelius, J and Wang, L and Spaulding, AB and Serebryannyy, L and Douek, DC and Syed, MA and Mahmood, SF and Khan, E and Van Voorhis, WC and Gale, M},
title = {Identification of Co-Circulating Dengue and South America-Origin Zika Viruses, Pakistan, 2021-2022.},
journal = {Emerging infectious diseases},
volume = {31},
number = {8},
pages = {1648-1651},
doi = {10.3201/eid3108.250342},
pmid = {40705419},
issn = {1080-6059},
mesh = {Humans ; Pakistan/epidemiology ; *Zika Virus Infection/epidemiology/virology/history ; *Dengue/epidemiology/virology/history ; *Zika Virus/genetics/classification/isolation & purification ; *Dengue Virus/genetics/classification/isolation & purification ; Phylogeny ; Male ; Female ; Disease Outbreaks ; Adult ; South America/epidemiology ; Middle Aged ; },
abstract = {We collected samples from febrile patients in Karachi, Pakistan, in 2021-2022. Sequencing, molecular, and serologic screens revealed dengue serotype 2 and Zika virus. The Zika lineage was inferred to be from Brazil in 2016, indicating unobserved circulation. We conclude that Zika virus contributes to perceived dengue outbreak burden in Pakistan.},
}

Humans
Pakistan/epidemiology
*Zika Virus Infection/epidemiology/virology/history
*Dengue/epidemiology/virology/history
*Zika Virus/genetics/classification/isolation & purification
*Dengue Virus/genetics/classification/isolation & purification
Phylogeny
Male
Female
Disease Outbreaks
Adult
South America/epidemiology
Middle Aged

@article {pmid40705360,
year = {2025},
author = {Feierabend, M and Töpfer, N},
title = {In silico encounters: Harnessing metabolic modelling to understand plant-microbe interactions.},
journal = {FEMS microbiology reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsre/fuaf030},
pmid = {40705360},
issn = {1574-6976},
abstract = {Understanding plant-microbe interactions is vital for developing sustainable agricultural practices and mitigating the consequences of climate change on food security. Plant-microbe interactions can improve nutrient acquisition, reduce dependency on chemical fertilizers, affect plant health, growth, and yield, and impact plants' resistance to biotic and abiotic stresses. These interactions are largely driven by metabolic exchanges and can thus be understood through metabolic network modelling. Recent developments in genomics, metagenomics, phenotyping, and synthetic biology now enable researchers to harness the potential of metabolic modelling at the genome scale. Here, we review studies that utilize genome-scale metabolic modelling to study plant-microbe interactions in symbiotic, pathogenic, and microbial community systems. This review catalogues how metabolic modelling has advanced our understanding of the plant host and its associated microorganisms as a holobiont. We showcase how these models can contextualize heterogeneous datasets and serve as valuable tools to dissect and quantify underlying mechanisms. Finally, we consider studies that employ metabolic models as a testbed for in silico design of synthetic microbial communities with predefined traits. We conclude by discussing broader implications of the presented studies, future perspectives, and outstanding challenges.},
}

@article {pmid40704918,
year = {2025},
author = {Pan, J and Tian, X and Wu, K and Ji, J and Dong, M and Sun, T and Lv, D and Yao, P and Lv, L and Yao, H},
title = {Gut microbiota-associated non-cholesterol sterol dysregulation modulates immune reconstitution during antiretroviral therapy in people living with HIV.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0140425},
doi = {10.1128/spectrum.01404-25},
pmid = {40704918},
issn = {2165-0497},
abstract = {Non-cholesterol sterol metabolism plays a crucial role in immune regulation. However, the non-cholesterol sterol profiles, its association with gut dysbiosis, and its impact on the CD4[+] T cell recovery in people living with HIV (PLWH) are yet to be elucidated. In this study, we recruited 37 PLWH and 50 healthy controls to characterize non-cholesterol sterol profiles and gut microbiota composition using targeted liquid chromatography-mass spectrometry and metagenomic analysis. Correlations between sterol profiles and immune cell subsets were assessed. In vitro peripheral blood mononuclear cell (PBMC) model was used to validate key findings. We identified a distinct dysregulation of non-cholesterol sterol metabolism in PLWH, characterized by elevated levels of cholesterol precursors and metabolites and depleted levels of plant sterols, which were linked to gut dysbiosis. Our study results highlighted Oscillibacter spp. as the key regulator of sterol metabolism. Specifically, plant sterols (e.g., brassicasterol and campesterol) were found to be associated with impaired CD4[+] T cell recovery during antiretroviral therapy (ART). These findings were validated using ex vivo PBMC models, which revealed that brassicasterol stimulates T cell abnormal activation and pro-inflammatory cytokine release, whereas lathosterol dampens immune activation and inflammation. In summary, our study highlights the interplay between gut dysbiosis and sterol dysregulation in PLWH, demonstrating that higher brassicasterol levels impair immune recovery post-ART by promoting CD4[+] T cell hyperactivation. Hence, targeting microbial sterol metabolism-through Oscillibacter spp. enrichment or plant sterol modulation-may offer novel therapeutic strategies to optimize ART outcomes by balancing immune activation and resolution.IMPORTANCEThis study is the first to integrate non-cholesterol sterol profiling with gut microbiota analysis in people living with HIV (PLWH), uncovering a unique sterol dysregulation characterized by elevated cholesterol precursors and depleted plant sterols in this population. We demonstrate that Oscillibacter spp. were associated with these metabolic shifts and that specific sterols differentially affect immune recovery: plant sterols such as brassicasterol impede CD4[+] T cell restoration by promoting hyperactivation, whereas the cholesterol derivative lathosterol mitigates inflammation and supports immune reconstitution. These insights reveal novel microbiome-sterol interactions that can be leveraged to develop targeted microbiome- and sterol-based interventions aimed at enhancing antiretroviral therapy efficacy and long-term immune health in PLWH.},
}

@article {pmid40703671,
year = {2025},
author = {Wang, Y and Lu, J and Dai, W and Yang, S},
title = {Jian-Pi-Yi-Shen formula improves kidney function by regulating gut microbiome in rats with chronic kidney disease.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1526863},
pmid = {40703671},
issn = {2235-2988},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Renal Insufficiency, Chronic/drug therapy/microbiology ; *Drugs, Chinese Herbal/pharmacology/administration & dosage ; Rats ; *Kidney/drug effects/physiopathology ; Disease Models, Animal ; Feces/microbiology ; Male ; Creatinine/blood ; Rats, Sprague-Dawley ; Metagenomics ; Medicine, Chinese Traditional ; },
abstract = {INTRODUCTION: Recent studies have underscored the role of interactions between Traditional Chinese Medicine (TCM) and the gut microbiome (GM) in mediating therapeutic effects. Jian-Pi-Yi-Shen Formula (JPYSF) has shown efficacy in ameliorating chronic kidney disease (CKD) symptoms, but its mechanisms via GM modulation remain unclear.

METHODS: In this study, 8-week-old rats were assigned to three groups after a two-week acclimation: C (normal diet for six weeks), M (adenine diet for four weeks then normal diet for two weeks), and T (same as M, with JPYSF administered during the final three weeks). Fecal samples were collected at three timepoints (T1: post-acclimation; T2: after three weeks on respective diets; T3: after three weeks of JPYSF treatment) for metagenomic sequencing. Serum creatinine (SCR) was measured at T2 and T3.

RESULTS: At T2, adenine-fed rats showed elevated SCR (C: 28.4 ± 1.5 µmol/L; M: 189.6 ± 25.8µmol/L; T: 186.4 ± 32.5µmol/L; p < 0.001). By T3, SCR decreased more in T (86.0 ± 14.9µmol/L) than in M (119.6 ± 16.3µmol/L; p = 0.012), with C remaining stable (30.8 ± 4.4µmol/L). Adenine feeding induced significant GM shifts, evidenced by increased Aitchison distance (p < 0.01) and altered co-abundance interaction groups (CIGs): CIG3, 6, 9, 10 increased; CIG1, 2, 4, 12 decreased (all p < 0.05). After JPYSF treatment, only CIG4 significantly rebounded (T3 vs. M, p = 0.0079), and T3-T1 dissimilarity was lower in T than M (p < 0.05). SCR levels were significantly lower in T than M after returning to a normal diet, suggesting a renoprotective effect of JPYSF. Co-occurrence analysis linked SCR positively with toxin-associated CIGs (CIG3, 6, 7, 9, 10) and pathways (purine metabolism, toluene degradation), and negatively with CIG4.

DISCUSSION: These results demonstrate that JPYSF lowers SCR and selectively modulates GM modules, particularly CIG4, which inversely correlates with uremic toxin-producing pathways, suggesting improved renal function and specific gut microbiota modulation in CKD rats.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Renal Insufficiency, Chronic/drug therapy/microbiology
*Drugs, Chinese Herbal/pharmacology/administration & dosage
Rats
*Kidney/drug effects/physiopathology
Disease Models, Animal
Feces/microbiology
Male
Creatinine/blood
Rats, Sprague-Dawley
Metagenomics
Medicine, Chinese Traditional

@article {pmid40703293,
year = {2025},
author = {Zhang, Z and Wang, M},
title = {Three case reports of pulmonary mucormycosis with a review of the literature.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1580912},
pmid = {40703293},
issn = {2296-858X},
abstract = {Pulmonary mucormycosis (PM) is an invasive and life-threatening fungal infection that predominantly affects immunocompromised individuals. This study thoroughly examined the disease through three case reports and a literature review. Case 1 involved a patient with type 1 diabetes mellitus diagnosed through bronchoscopic histopathology, who succumbed despite a combination of oral isavuconazole, nebulized amphotericin B, and intravenous amphotericin B cholesteryl sulfate complex. Case 2 involved a patient with follicular non-Hodgkin lymphoma who had a concurrent coronavirus disease 2019 (COVID-19) infection, which was confirmed through metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF). The patient experienced clinical improvement following sequential intravenous voriconazole, amphotericin B cholesteryl sulfate complex, and oral isavuconazole. Case 3 involved a patient diagnosed with mNGS in a lung cancer patient with chronic obstructive pulmonary disease, who showed poor therapeutic response to combined intravenous voriconazole, amphotericin B cholesteryl sulfate complex, and oral isavuconazole, resulting in fatal outcomes. Literature synthesis revealed mortality rates of 28.3% with antifungal monotherapy compared to 23.7% when antifungal monotherapy was combined with bronchoscopic intervention; the mortality rate for antifungal-surgical combination therapy was 9%. Notably, all 13 patients receiving multimodal treatment (antifungals, bronchoscopy, and surgery) survived. These findings underscore that combination therapy integrating pharmacotherapy, bronchoscopic intervention, and surgical resection demonstrated significantly superior survival outcomes compared to monotherapy.},
}

@article {pmid40703238,
year = {2025},
author = {Rangasamy, K and Saleh, AM},
title = {Bio-priming of tomato seedlings with bacterial consortium against Fusarium oxysporum: a study on morphological parameters and molecular profiling.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1606896},
pmid = {40703238},
issn = {1664-302X},
abstract = {Soil-borne diseases significantly threaten global crop production, resulting in substantial economic losses. Among these, Fusarium oxysporum, a major pathogen responsible for wilt in the root zones, severely affects tomato (Solanum lycopersicum), a widely consumed yet vulnerable vegetable. Conventional management strategies rely on fungicides and synthetic chemicals, which pose environmental and health risks, prompting the exploration of safer alternatives such as plant growth-promoting rhizobacteria (PGRP). In this study, we investigated the efficacy of two bacterial isolates, Pseudomonas aeruginosa VITK-1 and Burkholderia cepacia VITK-3, both individually and as a consortium, in the presence of Fusarium oxysporum under greenhouse conditions. In vitro assays revealed that the isolates inhibited Fusarium oxysporum, with rates ranging from 64.1 to 76.5%. Additionally, significant inhibition was observed against Ralstonia solanacearum, Septoria protearum (57.2%), Verticillium dahlia (88.5 to 81%), and Cercospora canescens (66.1 to 47.7%) in vitro. Both strains produced bioactive compounds against the test pathogens and formed biofilms, which enhanced plant growth and suppressed phytopathogens. Consortium treatment with Fusarium oxysporum significantly improved tomato seedlings' antioxidant activity, including superoxide dismutase (SOD), catalase (CAT), phenolic, and flavonoid content, along with enhanced physiological parameters. Gene expression analysis confirmed the up-regulation of defense-related genes, while metagenomic profiling indicated improvements in the soil microbial community under consortium treatment with Fusarium oxysporum compared to individual treatments and untreated controls. These findings underscore the potential of bacterial consortia as effective biocontrol agents that promote plant health and soil microbiome integrity.},
}

@article {pmid40703235,
year = {2025},
author = {Pan, J and Huang, MD and Wang, J and Zhao, JX and Yang, B and Yang, HH and Huang, JS and Su, YL and Song, XR and Wang, WG and Bu, LD},
title = {Unraveling the microbiome-aroma Nexus: a metagenomic and volatile compound analysis of Yunnan cigars.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1597501},
pmid = {40703235},
issn = {1664-302X},
abstract = {INTRODUCTION: Understanding how microbial communities influence aroma profiles is critical to improving cigar quality. However, comparative studies examining the microbiome-aroma nexus across major cigar-producing regions remain limited.

METHODS: We integrated high-throughput metagenomic sequencing with volatile organic compound (VOC) profiling to investigate microbial community structure and aroma compounds in four Yunnan cigars and two Cuban cigars.

RESULTS: Bacillus spp. was consistently dominant across all samples, while Yunnan cigars exhibited higher microbial diversity. A total of 121 VOCs were detected, with nicotine, ylangene, δ-elemene, (R,S)-anatabine, and phenethyl alcohol identified as key aroma components. Nicotine, accounting for 29.7-55.0% of total VOC content, was positively correlated with Enterobacter and Escherichia, and negatively with Corynebacterium and Brachybacterium. Ylangene showed strong positive associations with Brachybacterium and Yaniella. After FDR correction, 26 differential VOCs were identified across cigar groups. KEGG pathway analysis revealed functional enrichment in carbohydrate, amino acid, and lipid metabolism. Principal component analysis indicated that the aroma complexity of certain Yunnan cigars, particularly YX4, approached that of Cuban cigars.

DISCUSSION: Our findings demonstrate that region-specific fermentation microbiota are intricately linked to the production of key VOCs. This work provides a scientific framework for optimizing cigar fermentation through microbial regulation and supports the potential for targeted microbial inoculation to enhance sensory quality and global competitiveness.},
}

@article {pmid40702703,
year = {2025},
author = {Liu, X and Kong, J and Shan, Y and Yang, Z and Miao, J and Pan, Y and Luo, T and Shi, Z and Wang, Y and Gou, Q and Yang, C and Li, H and Li, C and Li, S and Zhang, X and Sun, Y and Holmes, EC and Guo, D and Shi, M},
title = {SegFinder: an automated tool for identifying complete RNA virus genome segments through co-occurrence in multiple sequenced samples.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {4},
pages = {},
doi = {10.1093/bib/bbaf358},
pmid = {40702703},
issn = {1477-4054},
support = {82341118//National Natural Science Foundation of China/ ; KQTD20200820145822023//Shenzhen Science and Technology Program/ ; MRP/071/20X//Hong Kong Innovation and Technology Fund/ ; GZNL2023A01001//Major Project of Guangzhou National Laboratory/ ; GZNL2023A01008//Major Project of Guangzhou National Laboratory/ ; 2019ZT08Y464//Guangdong Province 'Pearl River Talent Plan' Innovation, Entrepreneurship Team Project/ ; ZDSYS20220606100803007//Fund of Shenzhen Key Laboratory/ ; GNT2017197//NHMRC Investigator Award/ ; //Innovation and Technology Commission, Hong Kong Special Administrative Region, China/ ; },
mesh = {*Genome, Viral ; *RNA Viruses/genetics ; Animals ; *Computational Biology/methods ; Metagenomics/methods ; *Software ; RNA, Viral/genetics ; },
abstract = {Metagenomic sequencing has expanded the ribonucleic acid (RNA) virosphere, but many identified viral genomes remain incomplete, especially for segmented viruses. Traditional methods relying on sequence homology struggle to identify highly divergent segments and group them confidently within a single virus species. To address this, we developed a new bioinformatic tool-SegFinder-that identifies virus genome segments based on their common co-occurrence at similar abundance within segmented viruses. SegFinder successfully re-discovered all segments from a test data set of individual mosquito transcriptomes, which was also used to establish parameter thresholds for reliable segment identification. Using these optimal parameters, we applied SegFinder to 858 libraries from eight metagenomic sequencing projects, including vertebrates, invertebrates, plants, and environmental samples. Excluding the RdRP segment, we identified 106 unique viral genome segments from these samples. Among them, 53 were novel, including 30 segments that showed no recognizable sequence homology to any known viruses. However, the viral origin of these highly divergent segment was supported by the presence of conserved terminal sequences. SegFinder identifies segmented genome structures in viruses previously considered to be predominantly unsegmented, and in doing so expanded the number of known families and orders of segmented RNA viruses, making it a valuable tool in an era of large-scale parallel sequencing.},
}

*Genome, Viral
*RNA Viruses/genetics
Animals
*Computational Biology/methods
Metagenomics/methods
*Software
RNA, Viral/genetics

@article {pmid40702553,
year = {2025},
author = {Martí-Carreras, J and Carrasco, M and Noguera-Julian, M and Francino, O and Leal, RO and Ferrer, L and Oliva, G and Molina, J and Roura, X},
title = {Effects of meglumine antimoniate and allopurinol treatment on the fecal microbiome profile in dogs with leishmaniosis.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {78},
pmid = {40702553},
issn = {2524-4671},
abstract = {BACKGROUND: The combination of meglumine antimoniate and allopurinol is considered one of the most effective treatments for canine leishmaniosis caused by Leishmania infantum. This study investigated the effects of this treatment on the gut microbiome of 10 dogs from Spain, Portugal, and Italy via fecal shotgun metagenomic sequencing over six months.

METHODS: Dogs were sampled at baseline (BL), after one month of combined treatment with meglumine antimoniate and allopurinol (M1) and after six months of allopurinol treatment (M6). Fecal samples had their total DNA extracted and sequenced by Illumina sequencing. Posteriorly, a microbiome analysis was conducted to analyze bacterial abundance, diversity and enrichment.

RESULTS: The gut microbiome of Leishmania-infected dogs (BL) is dominated by Prevotella, Collinsella, Bacteroides, and Blautia, with individual variability being the primary determinant of microbiome composition. No significant changes in alpha diversity (Shannon index, gene number) or beta diversity (Bray-Curtis dissimilarity, UniFrac distance) were detected between pre- and post-treatment time points, suggesting that treatment with meglumine antimoniate and allopurinol does not disrupt the gut microbiota. Minor trends in taxonomic shifts were noted, with slight increases in Bifidobacterium pseudocantenulatum, Collinsella tanakaei, and Slackia piriformis after treatment, but these changes were not statistically significant after correction for multiple testing. Linear discriminant analysis and multivariable modeling confirmed that the microbial community structure was resilient to treatment effects. Individual-specific microbiome differences in diversity accounted for 52% of the observed variability, underscoring the personalized nature of the gut microbiota in dogs. Importantly, no adverse microbiome disruptions were detected, even with prolonged allopurinol use.

CONCLUSIONS: This study highlights the robustness of the canine gut microbiome during antileishmanial therapy and highlights the use of meglumine antimoniate and allopurinol without compromising gut microbial diversity or health. Further studies with larger cohorts are recommended to confirm these findings and explore the functional roles of the gut microbiota in modulating immune responses in Leishmania-infected dogs.},
}

@article {pmid40702426,
year = {2025},
author = {Ye, J and Jin, S and Li, Y and Gao, W and Zheng, C and Zuo, H and Zhang, C and Song, M and Hao, J and Liu, Y and Feng, Z and Zhang, H and Zhao, Z and Guo, Y and Zhang, L},
title = {Scedosporium boydii pulmonary infection in an immunocompetent patient with COPD confirmed by next-generation metagenomic sequencing and culture: a case report.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {938},
pmid = {40702426},
issn = {1471-2334},
support = {H2020206449//Precision Medicine Joint Fund Cultivation Project of the Natural Science Foundation of Hebei Province/ ; YNXJYJKF-001//Open Research Project of Hebei Key Laboratory of Intractable Pathogens, Shijiazhuang Center for Disease Control and Prevention/ ; 20180460//Key Project of the Hebei Provincial Medical Science Research Program/ ; 2024143//Scientific Research Project of the Hebei Provincial Administration of Traditional Chinese Medicine/ ; },
mesh = {Humans ; *Scedosporium/genetics/isolation & purification/classification ; *Pulmonary Disease, Chronic Obstructive/complications/microbiology ; Male ; Antifungal Agents/therapeutic use ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Bronchoalveolar Lavage Fluid/microbiology ; *Mycoses/diagnosis/microbiology/drug therapy ; *Lung Diseases, Fungal/diagnosis/microbiology/drug therapy ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Tomography, X-Ray Computed ; Aged ; Invasive Fungal Infections ; },
abstract = {Scedosporium boydii infections pose diagnostic challenges due to their nonspecific clinical manifestations and slow growth characteristics in conventional cultures. This paper highlights the diagnostic value of molecular technology combined with targeted prolonged culture for rare fungi. Unitl now, only one case was identified using metagenomic next-generation sequencing (mNGS). This case represents the first report of a 20-day delayed culture confirmation of S. boydii guided by mNGS results in a non-immunocompromised chronic obstructive -with history of COPD who was admitted with fever and cough. Despite two weeks of antibacterial treatment, chest computed tomography (CT) showed worsening infection. To clarify the pathogen, mNGS and bacterial culture of bronchoalveolar lavage fluid (BALF) were performed. Subsequent culture and Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) confirmed the growth of Scedosporium species. Based on clinical presentation, chest CT findings, mNGS results, pulmonary Scedosporiosis was diagnosed, and an antifungal treatment regimen (200 mg BID orally) was initiated. Subsequent culture confirmed S. boydii growth and antifungal susceptibility results were also obtained. After six weeks of voriconazole treatment, he was discharged from the hospital and continued to take oral medication for three months. He was fully recovered without recurrence after six months of follow-up. The present case suggests that mNGS findings can unveil cryptic pathogens like Scedosporium. Use mNGS results to trigger intentional, extended targeted cultivation- challenging standard incubation times- especially in non-immunocompromised hosts with underlying lung disease. Seamless clinician-laboratory collaboration is paramount for treatment success.},
}

Humans
*Scedosporium/genetics/isolation & purification/classification
*Pulmonary Disease, Chronic Obstructive/complications/microbiology
Male
Antifungal Agents/therapeutic use
High-Throughput Nucleotide Sequencing
Metagenomics
Bronchoalveolar Lavage Fluid/microbiology
*Mycoses/diagnosis/microbiology/drug therapy
*Lung Diseases, Fungal/diagnosis/microbiology/drug therapy
Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
Tomography, X-Ray Computed
Aged
Invasive Fungal Infections

@article {pmid40701508,
year = {2025},
author = {Chen, WJ and Wang, JP and Zhou, JR and He, Y and An, DQ and Tian, TT and Liang, MT and Aikepa, D and Kahaer, M and Sun, YP},
title = {Efficacy and Mechanisms of Compound Bai Mao Yin in Regulating Uric Acid Transport and Improving the Intestinal Microbiota to Alleviate Hyperuricemia via the Enterorenal Axis.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107922},
doi = {10.1016/j.micpath.2025.107922},
pmid = {40701508},
issn = {1096-1208},
abstract = {BACKGROUND: The compound Bai Mao Yin (BMY) has demonstrated therapeutic efficacy in reducing uric acid (UA) levels; however, its underlying mechanisms remain unclear.

METHODS: The UA-lowering effects of BMY were evaluated in a cohort of 40 patients with hyperuricemia (HUA) who received BMY treatment for 90 days. Fecal samples were collected at baseline (day 0), mid-treatment (day 30), and post-treatment (day 90) for metagenomic sequencing to analyze changes in gut microbiota and identify potential BMY targets in HUA. These clinical findings were validated in a hyperuricemic mouse model induced by xanthine and potassium oxonate. Mouse fecal samples were analyzed via 16S rDNA (V3-V4 region) sequencing to assess microbiota shifts. Additionally, fecal microbiota transplantation (FMT) from BMY-treated mice to HUA mice and in vitro cell experiments using HK2 cells were conducted to investigate the roles of BMY and the reconstructed microbiota in UA metabolism, renal UA transport, and inflammation through upstream signaling pathways.

RESULTS: Clinical cohort studies demonstrated that the BMY effectively lowers UA levels in patients with HUA without inducing hepatorenal toxicity. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of metagenomic data revealed that BMY modulates the gut microbiota and influences ATP-binding cassette transporters and UA metabolism-related pathways. In animal models, BMY increased the relative abundance of beneficial gut bacteria, reduced intestinal permeability, and regulated UA transporters in both intestinal and renal systems, contributing to UA reduction. In vitro assays showed that BMY directly decreased UA levels in the cell supernatant and suppressed interleukin-1β (IL-1β) and interleukin-6 (IL-6) expression by downregulating the TLR4/MYD88/NFκB signaling pathway, thereby alleviating inflammation.

CONCLUSIONS: Compound BMY was found to improve the intestinal microenvironment and modulate UA transport via the enterorenal axis, effectively reducing HUA.},
}

@article {pmid40701495,
year = {2025},
author = {Feng, B and Chen, J and Wang, C and Wang, P and Gao, H and Zhang, B and Zhang, J and Zhang, S and Fu, J},
title = {High pollution and health risk of antibiotic resistance genes in rural domestic sewage in southeastern China: A study combining national-scale distribution and machine learning.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126865},
doi = {10.1016/j.envpol.2025.126865},
pmid = {40701495},
issn = {1873-6424},
abstract = {Rural domestic sewage has emerged as an important reservoir of antibiotic resistance genes (ARGs) under rapid urbanization, while the national-scale geographical patterns and risks of ARGs remaining unclear. We investigated ARG pollution in rural domestic sewage across 39 sites in 22 Chinese provinces using metagenomic sequencing, identifying 702 ARG subtypes across 21 types. Multidrug resistance genes were predominant in the shared ARGs, accounting for 58.96% of the total ARG abundance. Host bacteria analysis revealed Klebsiella pneumoniae and Escherichia coli were the main pathogenic-resistant bacteria. Southeastern China exhibited the highest level of ARG pollution in rural domestic sewage, followed by south-central, northern, and western. This ARG pollution was primarily caused by human/animal feces based on ARG indicators. Partial least-squares path model and partial redundancy analysis highlighted antibiotics as the primary driver, explaining 24.16% of ARG variation, with sulfamethazine, norfloxacin, and ofloxacin identified as priority control targets. Risk assessment by calculating the risk index indicated 24.58% of detected ARGs posed potential health threats, particularly multidrug resistance. Machine learning models predicted higher ARG risks in rural domestic sewage from southeastern China with intensive human activity. This study underscores the crucial impact of antibiotics in ARG proliferation and risk in rural domestic sewage.},
}

@article {pmid40701415,
year = {2025},
author = {Ma, J and Zi, X and Wu, S and Ma, Y and Liang, R and Yang, J and Yao, J and Li, M and Li, Z},
title = {Multi-omics insights into the regulatory mechanism of citric acid in silage fermentation.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133025},
doi = {10.1016/j.biortech.2025.133025},
pmid = {40701415},
issn = {1873-2976},
abstract = {A meta-analysis was conducted to assess the effects of citric acid (CA) on silage fermentation, and then used whole-plant cassava silage as a model to explore the underlying microbiological mechanisms with metagenomic and metabolomic data. The meta-analysis revealed that CA supplementation increased the dry matter, crude protein, water-soluble carbohydrate, and lactic acid contents in silage, but decreased the pH, dry matter loss, and the contents of fiber, NH3-N, and acetic acid, all of which meet the expectations for an ideal silage additive. The fermentation parameter responses of whole-plant cassava silage to CA were consistent with those in the meta-analysis. Metabolomic analysis revealed that CA increased the level of antimicrobial metabolites and decreased the level of amino acids and their derivatives in cassava silage. By constructing microbial genome and gene catalogs, we found that CA supplementation increased the abundance of lactic acid-rods (Levilactobacillus, Lentilactobacillus, and Companillactobacillus) and inhibited the abundance of lactic acid cocci (Leuconostoc, Pediococcus, and Weissella) and undesirable bacteria (Acinetobacter, Serratia, Klebsiella, and Pantoea), which resulted in an increased abundance of genes involved in structural carbohydrate hydrolysis (cellulase and pectinase), lactic acid production (ldh), and amino acid synthesis (CKase and CPS1) and a decreased abundance of genes involved in acetate (porA, acs, pdhC, and pct) and NH3 production (glsA). Additionally, CA reduced the abundance of antibiotic resistance genes in silage by inhibiting the bacteria that hosted more resistance genes. Accordingly, CA supplementation could improve the nutritional value, preservation, and biosafety of silage by regulating its microbial composition and function.},
}

@article {pmid40701414,
year = {2025},
author = {Yuan, CY and Yu-Xia, and Huo, JH and Nie, CL and Zhang, KX and Liang-Feng, and Su, XL and Song, Z and Yi, GP and Sun, FY},
title = {Integrating methane conversion with multi-pathway nitrogen removal for wastewater in membrane-enabled stratified biofilm: System development and microbial dynamics.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133021},
doi = {10.1016/j.biortech.2025.133021},
pmid = {40701414},
issn = {1873-2976},
abstract = {Global demands for energy-neutral wastewater treatment drive innovation in sustainable nitrogen removal. A single-biofilm membrane biofilm reactor (MBfR) was constructed for efficient aerobic methane oxidation coupled with simultaneous ammonia oxidation and denitrification (AME-AOD). Through meticulous refinement in aspects such as membrane materials and gas-to-feed ratios, the best-performing biofilm achieved a high total nitrogen (TN) removal efficiency of 97 % ± 2 %. The system ultimately reduced TN from 51.6 ± 0.7 mg l[-1] to approximately 5 mg l[-1] within 16 h with a methane conversion efficiency of 30.0 ± 0.9 mg-CH4/mg-N. From startup, the biofilm supported stable coexistence of aerobic and anoxic processes, with gene abundances related to nitrification and denitrification increasing by 1.6-fold and 1.2-fold, respectively. After long-term operation, ecological niche differentiation enabled coexistence and synergistic interaction of methanotrophs, anaerobic ammonium oxidation (anammox), denitrifiers, and nitrifiers within each layer of the biofilm. Overall, this study offers a new strategy to advance sustainable mainstream nitrogen removal in wastewater.},
}

@article {pmid40701047,
year = {2025},
author = {Sun, J and He, Z},
title = {Light stimulated H2O2 inhibition on methanogenesis during anaerobic digestion towards enhanced VFAs production.},
journal = {Water research},
volume = {286},
number = {},
pages = {124229},
doi = {10.1016/j.watres.2025.124229},
pmid = {40701047},
issn = {1879-2448},
abstract = {Producing volatile fatty acids (VFAs) from anaerobic digestion (AD) of sewage sludge is of strong interest and can be realized via arresting methanogens. Herein, in situ hydrogen peroxide (H2O2) dosage has been demonstrated to be an effective approach to suppress methanogenesis and promote VFAs accumulation in the presence of illumination. Two AD reactors operating under different conditions produced average VFAs concentrations of 11,456.5 mg COD L[-1] (RLight, 80 mg L[-1] H2O2) and 11,896.5 mg COD L[-1] (RDark, 380 mg L[-1] H2O2). The comparable VFAs concentrations indicated that methanogenic activity was effectively inhibited under both conditions, thereby preventing further conversion of VFAs to methane. However, visible light significantly reduced the H2O2 dosage level from 380 to 80 mg L[-1] to achieve complete methane inhibition, likely due to light-activated H2O2 producing ·OH. The light-exposed H2O2 elevated intracellular reactive oxygen species (ROS) levels, leading to a sharp decline in methanogen abundance (only 5.02 % remained compared to the inoculum). Firmicutes became dominant, increasing from 14.03 % (inoculum) to 52.35 % under high oxidative stress. Metagenomic functional predictions inferred microbial communities that tended to mitigate oxidative stress by reducing ROS generation, as shown by the relative gene abundance reduced from 0.0577 to 0.0472 %. A side-effect of H2O2 inhibition was the enrichment of NH4[+] and PO4[3-], increased by 1.44 and 5.26 times, respectively; those nutrient compounds could be potentially recovered.},
}

@article {pmid40701001,
year = {2025},
author = {Shang, H and Gou, W and Liu, S and Yuan, W and Cao, Z and Guo, Y and Zhang, N},
title = {Integrated metagenomics and metabolomic to reveal the effects of dietary comfrey polysaccharides on the oxidative stability and fatty acid composition of egg yolks in laying hens.},
journal = {Poultry science},
volume = {104},
number = {10},
pages = {105553},
doi = {10.1016/j.psj.2025.105553},
pmid = {40701001},
issn = {1525-3171},
abstract = {This study investigated the influences of comfrey (Symphytum officinale L.) polysaccharides (CPs) in the diet of laying hens on the oxidation stability and fatty acid composition of the egg yolks based on metagenomic and metabolomics techniques. Dietary CPs improved the total phenolic content in fresh and stored eggs. The activity of superoxide dismutase was increased, and the content of malondialdehyde was reduced in the stored eggs of the 1.0 % group of CPs. Dietary supplementation with 1.0 % CPs increased some polyunsaturated fatty acid (PUFA) contents in stored egg yolk, including dihomo-γ-linolenic acid (C20:3n6), arachidonic acid (C20:4n6), and docosahexaenoic acid (C22:6n3). The abundances of Methanobrevibacter, Parabacteroides, and Merdibacter in the caecum were increased in the 1.0 % group of CPs. The content of melatonin was increased, and the contents of palmitic acid and myristic acid in the caecum were decreased by CPs. These results suggested that CPs could improve the antioxidant status and fatty acid composition of egg yolks.},
}

@article {pmid40700599,
year = {2025},
author = {Mofidifar, S and Tefagh, M},
title = {Reducing Redundancy and Enhancing Accuracy through a Phylogenetically-Informed Microbial Community Metabolic Modeling Approach.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaf328},
pmid = {40700599},
issn = {1367-4811},
abstract = {MOTIVATION: Metabolic modeling has emerged as a powerful tool for predicting community functions. However, current modeling approaches face significant challenges in balancing the metabolic trade-offs between individual and community-level growth. In this study, we investigated the effect of metabolic relatedness among taxa on growth rate calculations by merging related taxa based on their metabolic similarity, introducing this approach as PhyloCOBRA.

RESULTS: This approach enhanced the accuracy and efficiency of microbial community simulations by combining genome-scale metabolic models (GEMs) of closely related organisms, aligning with the concepts of niche differentiation and nestedness theory. To validate our approach, we implemented PhyloCOBRA within the MICOM and OptCom package (creating PhyloMICOM and PhyloOptCom, respectively), and applied it to metagenomic data from 186 individuals and four-species synthetic community (SynCom). Our results demonstrated significant improvement in the accuracy and reliability of growth rate predictions compared to the standard methods. Sensitivity analysis revealed that PhyloMICOM models were more robust to random noise, while Jaccard index calculations showed a reduction in redundancy, highlighting the enhanced specificity of the generated community models. Furthermore, PhyloMICOM reduced the computational complexity, addressing a key concern in microbial community simulations. This approach marks a significant advancement in community-scale metabolic modeling, offering a more stable, efficient, and ecologically relevant tool for simulating and understanding the intricate dynamics of microbial ecosystems.

AVAILABILITY: PhyloCOBRA implementations are available as extensions to the MICOM packages and can be accessed at https://github.com/sepideh-mofidifar/PhyloCOBRA.},
}

@article {pmid40700380,
year = {2025},
author = {Soto-Hernández, A and Muriel-Millán, LF and Gracia, A and Sánchez-Flores, A and Pardo-López, L},
title = {Enzymatic characterization and polyurethane biodegradation assay of two novel esterases isolated from a polluted river.},
journal = {PloS one},
volume = {20},
number = {7},
pages = {e0327637},
doi = {10.1371/journal.pone.0327637},
pmid = {40700380},
issn = {1932-6203},
mesh = {*Polyurethanes/metabolism/chemistry ; Biodegradation, Environmental ; *Rivers/microbiology/chemistry ; *Esterases/metabolism/genetics/isolation & purification/chemistry ; *Acinetobacter/enzymology/genetics ; Mexico ; *Bacterial Proteins/metabolism/genetics ; },
abstract = {The environmental ubiquity of plastic materials generates global concern, pollution, and health problems. Microorganisms and enzymes with plastic biodegradation potential are considered as environmentally friendly alternatives to address these issues. Interestingly, polluted environments exert selective pressure on native microbial communities that have the metabolic capacity to tolerate and transform different contaminants, including plastics. A number of enzymes have been described as polyurethane degraders. However, some of them do not possess complete characterization or efficient degradation rates. Hence, there is still a need to identify and characterize efficient enzymes for application in green processes for plastic recycling. Here, we used an environmental DNA sample isolated from the sediments of a polluted river in Mexico (Apatlaco River), which was used to construct a metagenomic fosmid library to explore the metabolic potential of microbial communities for polyurethane biodegradation. Functional screenings were performed on agar media containing the polyester polyurethane Impranil DLN (Impranil), and positively selected fosmid DNA was identified and sequenced by Illumina. Bioinformatic analyses identified two Acinetobacter genes (epux1 and epux2) encoding alpha/beta hydrolases. The genes were heterologously expressed to determine the capacity of their encoded proteins for Impranil clearing. Both Epux1 and Epux2 enzymes exhibited Impranil cleavage at 30 °C and 15 °C and ester group modifications were validated by infrared spectroscopy. Furthermore, the release of building blocks of the polymer was determined by GC-MS analysis, thus indicating their esterase/polyurethanase activity. Overall, our results demonstrate the potential of these novel bacterial enzymes for the hydrolysis of polyurethane with potential applications in the circular plastics economy.},
}

*Polyurethanes/metabolism/chemistry
Biodegradation, Environmental
*Rivers/microbiology/chemistry
*Esterases/metabolism/genetics/isolation & purification/chemistry
*Acinetobacter/enzymology/genetics
Mexico
*Bacterial Proteins/metabolism/genetics

@article {pmid40699657,
year = {2025},
author = {Baev, V},
title = {Bioinformatics Research in Bacterial Genomics and Metagenomics.},
journal = {Current issues in molecular biology},
volume = {47},
number = {4},
pages = {},
doi = {10.3390/cimb47040258},
pmid = {40699657},
issn = {1467-3045},
abstract = {Bioinformatics plays a crucial role in bacterial genomics and metagenomics research, transforming our understanding of microbial communities and their functions [...].},
}

@article {pmid40699423,
year = {2025},
author = {Pimenta, M and Gaschet, M and Meyer, S},
title = {Targeted 16S rRNA Gene Sequencing for Water Samples.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2962},
number = {},
pages = {65-82},
pmid = {40699423},
issn = {1940-6029},
mesh = {*RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; *Sequence Analysis, DNA/methods ; *Water Microbiology ; Gene Library ; Polymerase Chain Reaction/methods ; *Bacteria/genetics ; DNA, Bacterial/genetics ; },
abstract = {The choice of variable region to amplify in 16S rRNA-targeted amplicon sequencing has long been a matter of debate. Here, we describe a method for sequencing multiple variable regions with the Ion 16S Metagenomics kit, which amplifies six different amplicons covering seven 16S variable regions. We present the full protocol of water sequencing from sample collection to library preparation.},
}

*RNA, Ribosomal, 16S/genetics
*Metagenomics/methods
High-Throughput Nucleotide Sequencing/methods
*Sequence Analysis, DNA/methods
*Water Microbiology
Gene Library
Polymerase Chain Reaction/methods
*Bacteria/genetics
DNA, Bacterial/genetics

@article {pmid40698993,
year = {2025},
author = {Castejon-Ramirez, S and Maron, G},
title = {Targeted strategies for pediatric cancer and post-transplant fever: the role of host and pathogen biomarkers.},
journal = {Current opinion in infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1097/QCO.0000000000001132},
pmid = {40698993},
issn = {1473-6527},
abstract = {PURPOSE OF REVIEW: Host and pathogen biomarkers may lead to improved management of fever in children with cancer and post hematopoietic cell transplant (HCT). This review summarizes current evidence on biomarkers for predicting infections.

RECENT FINDINGS: Host biomarkers show promise for distinguishing between infectious and noninfectious causes of fever in patients with cancer or post HCT. Combining multiple biomarkers and integrating them into risk-stratification clinical scores may enhance predictive accuracy with the potential of individualizing antimicrobial treatment. Molecular diagnostic methods like multiplex PCR provide rapid detection of many pathogens. Emerging technologies such as transcriptomics, metabolomics, and microbial metagenomic next-generation sequencing demonstrate potential but require further evaluation. Large prospective studies are needed to validate standardized cutoffs and algorithms incorporating biomarkers into clinical decision-making. The integration of host and pathogen biomarkers holds the promise of optimizing antimicrobial therapy by tailoring treatment when indicated and minimizing unnecessary antimicrobials, ultimately enhancing patient outcomes.

SUMMARY: Targeted biomarker-based strategies have the potential to improve antimicrobial stewardship and outcomes in immunocompromised pediatric patients.},
}

@article {pmid40698950,
year = {2025},
author = {Niknejad, DJ and Martin, RM and Chase, EE and Morse, RH and Lucas, GM and DeBruyn, JM and Walker, FR and Webb, EA and Wilhelm, SW},
title = {Metagenome-assembled genome of Synechococcus sp. "Tanasi" from the Tellico Reservoir, Tennessee, USA.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0041725},
doi = {10.1128/mra.00417-25},
pmid = {40698950},
issn = {2576-098X},
abstract = {Synechococcus-like cyanobacteria are vital to aquatic ecosystems. Taxonomists have begun to reassign genomic clades within this group to new taxa. This process depends on genomic data from diverse habitats. Here, we present a metagenome-assembled genome of a Synechococcus sp. strain from the Tennessee River Basin, an ecosystem under-represented in databases.},
}

@article {pmid40698947,
year = {2025},
author = {Coleine, C and Micheletti, D and Pindo, M and Larger, S and Stefani, E and Biagioli, F and Stajich, JE and Donati, C},
title = {Draft genome sequence of an uncultured archaeon from Antarctic endolithic communities.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0042725},
doi = {10.1128/mra.00427-25},
pmid = {40698947},
issn = {2576-098X},
abstract = {A draft genome sequence was assembled and annotated for an uncultured archaeon reconstructed from shotgun metagenomes obtained from Antarctic endoliths. The assembled genome is 1.99 megabases and encodes 2,405 predicted protein-coding genes. This genome sequence provides insights into the microbial diversity and functional potential of extremophiles inhabiting Antarctic rock environments.},
}

@article {pmid40698938,
year = {2025},
author = {Lei, L and Li, X and Xiong, Z and Li, J and Liu, L and Chen, L and Zhong, Q and Jiang, H and Cheng, Z and Xiao, S},
title = {Distinctive structure of endophytic microbial communities in two species of wild and cultivated rice.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0297824},
doi = {10.1128/spectrum.02978-24},
pmid = {40698938},
issn = {2165-0497},
abstract = {Endophytic microbial communities play an important role in plant development, nutrient acquisition, and oxidative stress tolerance. Oryza officinalis and Oryza meyeriana are unique wild rice varieties in China with many high-quality resistance genes, rich endophyte diversity, and potential resources for sustainable agriculture. In the present study, the endophytic microbial community structures of O. officinalis, O. meyeriana, and cultivated rice were compared using metagenomic sequencing. Dechloromonas, Salmonella, Klebsiella, and Listeria were the core microbial groups in wild and cultivated rice. The relative abundances of Ligilactobacillus, Escherichia, and Bradyrhizobium in O. meyeriana were higher than those in cultivated rice. The relative abundances of Listeria, Acinetobacter, Escherichia, and Dechloromonas in O. officinalis were also higher. Compared to that of cultivated rice, the microbiota of wild rice had a more complex and stable community network. At the pathway level 2 based on the Kyoto Encyclopedia of Genes and Genomes classification system, the relative abundance of metabolic categories was dominant. Most pathways showed that the O. officinalis relative abundance was higher than those of the other two species. Our study revealed differences in the leaf endophyte community structure and function between wild and cultivated rice in the same habitat, demonstrating the potential of wild rice in recruiting specific microorganisms to improve crop performance and promote safe and sustainable food production.IMPORTANCEUnder the current climate change environment, plant-beneficial endophytes are of great significance for promoting food production. Modern cultivars may have lost many beneficial endophytes compared to their ancestors. However, relatively few studies have been conducted on the community structure and function of modern ancestral crop endophytes. In this study, the composition and function of the microbial communities of two wild rice species were analyzed; the differences between them and cultivated rice were determined; and the patterns of microbial interactions and their core microbiomes were determined. Our findings can aid in the exploration of the beneficial endophytes in wild rice and use them to improve crop stress resistance and sustainability. These results provide relevant insights into the role of endophytes in the mechanism of high-stress resistance in wild rice.},
}

@article {pmid40698936,
year = {2025},
author = {Maghini, DG and Kiguchi, Y and Darling, AE and Monahan, LG and Halpern, AL and Burke, CM and Jaeger, E and Statham, A and Truong, T and Ying, K and Bruinsma, SP and Schroth, GP and Bhatt, AS},
title = {Illumina complete long read assay yields contiguous bacterial genomes from human gut metagenomes.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0153124},
doi = {10.1128/msystems.01531-24},
pmid = {40698936},
issn = {2379-5077},
abstract = {Metagenomics enables direct investigation of the gene content and potential functions of gut bacteria without isolation and culture. However, metagenome-assembled genomes are often incomplete and have low contiguity due to challenges in assembling repeated genomic elements. Long-read sequencing approaches have successfully yielded circular bacterial genomes directly from metagenomes, but these approaches require high DNA input and can have high error rates. Illumina has recently launched the Illumina Complete Long Read (ICLR) assay, a new approach for generating kilobase-scale reads with low DNA input requirements and high accuracy. Here, we evaluate the performance of ICLR sequencing for gut metagenomics for the first time. We sequenced a microbial mock community and 10 human gut microbiome samples with standard, shotgun 2 × 150 paired-end sequencing, ICLR sequencing, and nanopore long-read sequencing and compared performance in read lengths, assembly contiguity, and bin quality. We find that ICLR human metagenomic assemblies have higher N50 (119.5 ± 24.8 kilobases) than short read assemblies (9.9 ± 4.5 kilobases; P = 0.002), and comparable N50 to nanopore assemblies (91.0 ± 43.8 kilobases; P = 0.32). Additionally, we find that ICLR draft microbial genomes are more complete (94.0% ± 20.6%) than nanopore draft genomes (85.9% ± 23.0%; P ≤ 0.001), and that nanopore draft genomes have truncated gene lengths (924.6 ± 114.7 base pairs) relative to ICLR genomes (954.6 ± 71.5 base pairs; P ≤ 0.001). Overall, we find that ICLR sequencing is a promising method for the accurate assembly of microbial genomes from gut metagenomes.IMPORTANCEMetagenomic sequencing allows scientists to directly measure the genome content and structure of microbes residing in complex microbial communities. Traditional short-read metagenomic sequencing methods often yield fragmented genomes, whereas advanced long-read sequencing methods improve genome assembly quality but often suffer from high error rates and are logistically limited due to high input requirements. A new method, the Illumina Complete Long Read (ICLR) assay, is capable of generating highly accurate kilobase-scale sequencing reads with minimal input material. To evaluate the utility of ICLR in metagenomic contexts, we applied short-read, long-read, and ICLR methods to simple and complex microbial communities. We found that ICLR outperforms short-read methods and yields comparable metagenomic assemblies to standard long-read approaches while requiring less input material. Overall, ICLR represents an additional option for assembling complete genomes from complex metagenomes.},
}

@article {pmid40698877,
year = {2025},
author = {Rimet, F and Lemonnier, C and Alric, B and Beja, P and Bittner, L and Bylemans, J and Leese, F and Logares, R and Meissner, K and Not, F and Orsini, L and Paix, B and Rodríguez-Ezpeleta, N and Siano, R and Thalinger, B and Tromas, N and Vasselon, V and Domaizon, I},
title = {Omics to Study and Manage Aquatic Environments: A Snapshot From the AquaEcOmics Meeting (Evian-les-Bains, 2025).},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e70041},
doi = {10.1111/mec.70041},
pmid = {40698877},
issn = {1365-294X},
abstract = {The AquaEcOmics meeting brought together 280 scientists applying omics tools to aquatic research in March 2025 (Evian-les-Bains, France). We synthesised here the main outcomes from the 167 presentations which were given. A similar number of presentations were about micro- and macroorganisms. While studies on macroorganisms mostly focused on stakeholder-driven research and methodology development, studies on microorganisms tended to focus on fundamental scientific questions. These questions mostly contributed to community ecology studies using metabarcoding; functional ecology studies using metagenomics, metatranscriptomics and metabolomics; and to a lesser degree population genomics studies using metabarcoding and RADseq, ddRADseq. Stakeholder-driven research presentations could be clustered in two groups: those using omics to replace existing standardised monitoring methods-also termed 'retrofitting'-to meet regulatory frameworks (e.g., fish biomonitoring), and those investigating anthropogenic pressures by harnessing the full power of omics, for instance by sequencing the entire microbial diversity or by detecting resistance genes to antibiotics and metals in rivers. The carbon footprint and applicability of omics were also questioned, sparking animated debates among attendees. Finally, some presentations focused on methodological developments and encompassed sampling strategies and devices, issues related to reference libraries (completeness, curation), comparison of short reads versus long reads, and in situ detection and quantification of organisms (dPCR, models). The use of omics to study aquatic ecosystems is a fast-evolving field. Meeting attendees agreed to maintain the generated momentum to promote omics as tools to improve the monitoring and protection of our environment.},
}

@article {pmid40697984,
year = {2025},
author = {Hebbar, P and Han, OB and Yan, NX and Kay, D and Chu, KY and Woon, JS and Lun, PK and Kabekkodu, SP and Prasad, ASB and Prakash, B and Nograles, N and Kanakal, MM and Goodson, M and Nagaraja, S and Mascarenhas, R},
title = {Characterization of microbiome diversity unveils substantial microbial variation in mangrove soil sediments from coastal regions of Malaysia.},
journal = {Access microbiology},
volume = {7},
number = {6},
pages = {},
pmid = {40697984},
issn = {2516-8290},
abstract = {The mangrove ecosystems are of great ecological importance found in tropical and subtropical coasts, including Malaysia. The microbial communities in the mangrove sediments play an indispensable role in maintaining homeostasis and supporting biodiversity. However, mangroves are facing various threats due to increasing anthropogenic activities. Thus, it is important to monitor the microbial community to improve our understanding of anthropogenic pressure on reshaping these ecosystems. This study examines the microbial community diversity in mangrove sediments of southern peninsular Malaysia. High-throughput MinION sequencing of the 16S rRNA gene was performed to compare the soil microbiome diversity in 35 samples from 8 different mangroves representing Sungai Sedili Kecil and Sungai Sedili Besar that flow into the South China Sea; Sungai Pulai, Sungai Melayu, Sungai Danga, Sungai Skudai and Sungai Johor that join the Straits of Johor; and Pulau Kukup from the Straits of Malacca. The metagenomic classification performed with 16S rRNA showed 2,573 taxa comprising 32 phyla. Total abundance analysis showed Pseudomonadota (67-69%), Bacteroidota (6-8%), Bacillota (5-8%), Campylobacterota (4-5%), Acidobacteriota (3-4%), Planctomycetota (2-4%) and Actinomycetota (1-2%) as the relatively common phyla. Alpha diversity indices revealed significantly higher richness in samples from mangroves of the South China Sea. Further, the 'Shannon' index showed a significant difference in diversity between Sungai Melayu and Sungai Pulai. Higher abundance of Burkholderiaceae, Bacillaceae and Enterobacteriaceae suggests a difference in the microbial community structure. This study stands as the first comprehensive analysis of microbial communities for future monitoring and conservation in these mangroves.},
}

@article {pmid40697547,
year = {2025},
author = {Hu, J and Lang, H and Fan, D and Wen, T and Shi, J and Xiao, C and Li, Y and Kang, C and Shi, P and Shen, L and Lin, N},
title = {Curcumin supplementation accelerates high-altitude acclimatization, prevents polycythemia and modulates gut microbiota in male Han population: a randomized controlled trial.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1572376},
pmid = {40697547},
issn = {2296-861X},
abstract = {BACKGROUND: Previous evidence showed that curcumin enhanced the oxygen supply efficiency of hemoglobin and alleviated acute plateau hypoxia injury in animal models. However, its efficacy on human beings is not yet verified. This study aimed to assess the effects of curcumin supplementation on hypoxia injury and gut microbiota in the male Han population.

METHODS: In this 7-week single-blinded randomized trial, 102 male Han population urgently entered the 3,000 meters altitude from the plain and received 812 mg curcumin or placebo per day for 1 week on the plain and 6 weeks on the plateau. Biochemical parameters were assessed and physical examination was carried out at the baseline (T0), and the end of the 1st (T1) and 7th week (T3) of intervention. The score of acute mountain sickness (AMS) was evaluated in the 2nd week after entering the plateau (T2) and T3. Intestine microbial composition was analyzed by metagenomic sequencing.

RESULTS: After a 1-week intervention on the plain, curcumin significantly increased red blood cells (RBC), hematocrit (HCT), and hemoglobin in treatment group as compared to placebo group (p < 0.05). However, curcumin significantly reduced the levels of HCT and hemoglobin compared to that in the placebo group after the 6-week intervention on the plateau (p < 0.05). Furthermore, the score of AMS in the curcumin group were lower than those in the placebo group at T3, although with no significant difference. Gut microbiota analysis indicated that curcumin significantly increased the abundance of butyrate-producing bacteria Roseburia, Lachnospira, and Sellimonas while decreasing the abundance of Alistipes and Escherichia at high-altitude environments. In addition, a higher relative abundance of Bifidobacterium was observed in the curcumin group on the plateau.

CONCLUSION: Curcumin exhibited different regulation of hemoglobin in low- and high-altitude environments. On the plain, curcumin supplementation elevated the RBC and hemoglobin, which is favorable for reducing the incidence of AMS at the early stage of entering the plateau. On the plateau, curcumin suppressed excessive increase of HCT and hemoglobin by modulating the abundance of butyrate-producing bacteria to avoid the occurrence of high-altitude polycythemia.

CLINICAL TRIAL REGISTRATION: https://www.chictr.org.cn/, identifier: ChiCTR220005965.},
}

@article {pmid40696623,
year = {2025},
author = {Jia, B and Liu, R and Wang, Q and Yang, S},
title = {Pterygomaxillary space infection complicated by meningitis due to Streptococcus constellatus: Two case reports and literature review.},
journal = {Medicine},
volume = {104},
number = {29},
pages = {e43468},
doi = {10.1097/MD.0000000000043468},
pmid = {40696623},
issn = {1536-5964},
support = {CSA-W2023-03//the Western Stomatological Clinical Research Fund Project of the Chinese Stomatological Association/ ; },
mesh = {Humans ; Male ; *Streptococcal Infections/complications/diagnosis/drug therapy/microbiology ; *Meningitis, Bacterial/microbiology/diagnosis/drug therapy/complications ; *Streptococcus constellatus/isolation & purification ; Anti-Bacterial Agents/therapeutic use ; Aged ; Middle Aged ; Magnetic Resonance Imaging ; Tomography, X-Ray Computed ; },
abstract = {RATIONALE: Streptococcus constellatus is a common oral bacterium implicated in pterygomaxillary space infections. Due to the deep anatomical location of these infections, they are often misdiagnosed as temporomandibular joint disorders. Although rare, concurrent meningitis in immunocompetent individuals can occur and may be life-threatening.

PATIENT CONCERNS: We report 2 older male patients who presented with facial pain and headache, initially misdiagnosed as temporomandibular joint disorders. Their conditions rapidly progressed to fever, altered mental status, and neurological deficits.

DIAGNOSES: Cerebrospinal fluid analysis and metagenomic next-generation sequencing confirmed S constellatus meningitis. Computed tomography or magnetic resonance imaging revealed concurrent pterygomaxillary space infections.

INTERVENTIONS: Both the patients received targeted antibiotic therapy (meropenem followed by vancomycin/linezolid plus metronidazole); 1 patient also underwent surgical drainage.

OUTCOMES: Both the patients recovered completely without neurological sequelae.

LESSONS: Although S constellatus meningitis is rare, odontogenic sources should be considered in patients with poor oral hygiene. Our report highlights the diagnostic value of next-generation sequencing for early pathogen detection in cerebrospinal fluid.},
}

Humans
Male
*Streptococcal Infections/complications/diagnosis/drug therapy/microbiology
*Meningitis, Bacterial/microbiology/diagnosis/drug therapy/complications
*Streptococcus constellatus/isolation & purification
Anti-Bacterial Agents/therapeutic use
Aged
Middle Aged
Magnetic Resonance Imaging
Tomography, X-Ray Computed

@article {pmid40696533,
year = {2025},
author = {Liu, W and Wang, J and Xue, Y and Li, J and Huang, Y and Zhu, S and Wang, L and Wang, G and Chen, W and Zhao, J},
title = {The impact of Bifidobacterium longum CCFM1112 on chronic constipation: a randomised, double-blind, placebo-controlled study.},
journal = {Beneficial microbes},
volume = {},
number = {},
pages = {1-17},
doi = {10.1163/18762891-bja00085},
pmid = {40696533},
issn = {1876-2891},
abstract = {A mounting body of evidence suggests that probiotics may mitigate constipation through their favourable modulation of gut microbiota and its metabolic byproducts. The precise mechanisms underlying this effect remain to be fully elucidated. This randomised, double-blind, placebo-controlled study investigates the clinical efficacy of Bifidobacterium longum (B. longum) CCFM1112 in treating chronic constipation. Fifty-six volunteers diagnosed with chronic constipation according to the Rome IV criteria were randomly assigned to either the B. longum CCFM1112 group or a placebo group for a 4-week intervention. Key outcomes measured included weekly spontaneous bowel movements (SBM), stool consistency (Bristol Stool Form Scale [BSFS]), Patient Assessment of Constipation-Symptoms (PAC-SYM) questionnaire, and Quality of Life (PAC-QOL) questionnaire. In addition, gut microbiota was detected using metagenomic sequencing, and non targeted metabolomics was used to detect fecal and serum metabolites. Results demonstrated that B. longum CCFM1112 significantly reduced PAC-QOL scores and improved BSFS in patients with chronic constipation. Correlation analyses revealed that B. longum CCFM1112 significantly increased the abundance of the genera Blautia, Anaerobutyricum, and Streptococcus. Furthermore, the abundance of species, including Blautia massiliensis, Blautia sp. SC05B48, Anaerobutyricum hallii, and Streptococcus salivarius, was also significantly elevated. Furthermore, it elevated fecal levels of linoleic acid, gamma-aminobutyric acid (GABA), and arachidonic acid, while increasing L-glutamic acid and decreasing adenosine in serum. Our research findings provide evidence that the intake of B. longum CCFM1112 can alleviate constipation.},
}

@article {pmid40696437,
year = {2025},
author = {Ashton, PM and Mageiros, L and Meiring, JE and Chunga-Chirambo, A and Khanam, F and Dongol, S and Banda, H and Karkey, A and Preciado-Llanes, L and Thomaides-Brears, H and Gibani, M and Rajib, NH and Rahman, N and Biswas, PK and Bhuiyan, MAI and Kay, S and Auger, K and Seret, O and Thomson, NR and Pollard, AJ and Baker, S and Basnyat, B and Clemens, JD and Dolecek, C and Dunstan, SJ and Dougan, G and Heyderman, RS and Pitzer, VE and Qadri, F and Gordon, MA and Holt, KE and Darton, TC and , },
title = {Interplay between the gut microbiome and typhoid fever: insights from endemic countries and a controlled human infection model.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {168},
pmid = {40696437},
issn = {2049-2618},
mesh = {Humans ; *Typhoid Fever/microbiology/epidemiology ; *Gastrointestinal Microbiome ; *Salmonella typhi/pathogenicity ; Prospective Studies ; Male ; Female ; Malawi/epidemiology ; Adult ; Bangladesh/epidemiology ; Nepal/epidemiology ; Adolescent ; Child ; Feces/microbiology ; Young Adult ; Endemic Diseases ; Fatty Acids, Volatile/metabolism ; Middle Aged ; Child, Preschool ; },
abstract = {BACKGROUND: Typhoid fever is a systemic infection caused by Salmonella enterica serovar Typhi (S. Typhi) invasion from the gut lumen. Transmission between people occurs through ingestion of contaminated food and water, particularly in settings with poor water and sanitation infrastructure, resulting in over 10 million illnesses annually. As the pathogen invades via the gastrointestinal tract, it is plausible that the gut microbiome may influence the outcome of S. Typhi exposure. There is some evidence that bacteria producing short-chain fatty acids (SCFAs) may create an environment unfavourable to invasive Salmonella, but data from humans is limited.

METHODS: To investigate the association between the gut microbiome and typhoid fever, we analysed samples collected from three all-age cohorts enrolled in a prospective surveillance study conducted across three settings where typhoid fever is endemic (Dhaka, Bangladesh; Blantyre, Malawi; and Kathmandu, Nepal). Cohorts consisted of acute typhoid fever patients (n = 92), asymptomatic household contacts of typhoid fever patients (representing individuals who were likely exposed to S. Typhi but did not develop the disease, n = 97) and asymptomatic serosurvey participants with high Vi antibody titres (representing individuals who were exposed to S. Typhi and may be carriers, n = 69). The stool microbiomes of each cohort were characterised using shotgun metagenomics, and bacterial diversity, composition and function were compared.

RESULTS: We identified 4 bacterial species that were significantly lower in abundance in typhoid fever patients compared with household contacts (i.e. probably exposed), in two of the three participant populations (Bangladesh and Malawi). These bacteria may represent taxa that provide protection against the development of clinical infection upon exposure to S. Typhi and include the inflammation-associated species Prevotella copri clade A and Haemophilus parainfluenzae. Our functional analysis identified 28 specific metabolic gene clusters (MGCs) negatively associated with typhoid fever in Bangladesh and Malawi, including seven MGCs involved in SCFA metabolism. The putative protection provided by microbiome SCFA metabolism was supported by data from a controlled human infection model conducted in a UK population, in which participants who did not develop typhoid fever following ingestion of S. Typhi had a higher abundance of a putative SCFA-metabolising MGC (q-value = 0.22).

CONCLUSIONS: This study identified the same protective associations between taxonomic and functional microbiota characteristics and non-susceptibility to typhoid fever across multiple human populations. Future research should explore the potential functional role of SCFAs and inflammation-associated bacteria in resistance to S. Typhi and other enteric infections. Video Abstract.},
}

Humans
*Typhoid Fever/microbiology/epidemiology
*Gastrointestinal Microbiome
*Salmonella typhi/pathogenicity
Prospective Studies
Male
Female
Malawi/epidemiology
Adult
Bangladesh/epidemiology
Nepal/epidemiology
Adolescent
Child
Feces/microbiology
Young Adult
Endemic Diseases
Fatty Acids, Volatile/metabolism
Middle Aged
Child, Preschool

@article {pmid40695901,
year = {2025},
author = {Awad, N and Larson, PJ and Sissoko, CA and Bond, LL and Dion, GR},
title = {Metagenomic whole genome shotgun analysis of the airway microbiome in laryngotracheal stenosis: a pilot study.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {26570},
pmid = {40695901},
issn = {2045-2322},
mesh = {Humans ; Pilot Projects ; *Microbiota/genetics ; *Laryngostenosis/microbiology ; *Tracheal Stenosis/microbiology ; Male ; Female ; Middle Aged ; *Metagenomics/methods ; Aged ; Metagenome ; Adult ; Tracheostomy ; Whole Genome Sequencing ; RNA, Ribosomal, 16S/genetics ; Shotgun Sequencing ; },
abstract = {The airway microbiome has been implicated in the pathogenesis of laryngotracheal stenosis (LTS), yet prior studies using 16 S rRNA sequencing have limited sub-genus level resolution. Metagenomic whole genome shotgun sequencing (mWGS) allows for strain-level taxonomic and functional genomic analysis, providing detailed insights into specific organisms and pathways. A pilot study was conducted to explore the advantages and challenges of mWGS in investigating the airway metagenome in LTS. mWGS was conducted on 12 intraoperative swab samples from 8 LTS patients, divided into tracheostomy-dependent (n = 3) and non-tracheostomy (n = 5) groups, and 4 controls. Patient comorbidities, antibiotic use, and medications were documented. Biobakery workflows were used for taxonomic and functional profiling. Species-specific reference databases were constructed for 6 abundant species for strain-level analyses. LTS samples had decreased taxonomic diversity and were dominated by species with previously described roles in other chronic inflammatory processes such as Staphylococcus aureus, Streptococcus parasanguinis, Streptococcus mitis, and Corynebacterium pseudogenitalium. LTS samples were enriched for pathways involved in fatty acid biosynthesis and formaldehyde metabolism. Our results identified tracheostomy as an important potential confounder in airway metagenomics but show mWGS techniques are promising in uncovering microbiota correlates in LTS that could reveal disease-specific biomarkers, comorbidity links, and therapeutic targets.},
}

Humans
Pilot Projects
*Microbiota/genetics
*Laryngostenosis/microbiology
*Tracheal Stenosis/microbiology
Male
Female
Middle Aged
*Metagenomics/methods
Aged
Metagenome
Adult
Tracheostomy
Whole Genome Sequencing
RNA, Ribosomal, 16S/genetics
Shotgun Sequencing

@article {pmid40695592,
year = {2025},
author = {Welsch, EC and Barron, M and Storage, KM and Kazen, AB and Aboulalazm, FA and Kirby, J and Kindel, TL},
title = {Gut microbiome and bile acid changes after male rodent sleeve gastrectomy: what comes first?.},
journal = {American journal of physiology. Regulatory, integrative and comparative physiology},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajpregu.00297.2024},
pmid = {40695592},
issn = {1522-1490},
support = {R01HL158900//HHS | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; HL072483//HHS | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; Clowes Career Development Award//American College of Surgeons (ACS)/ ; },
abstract = {Background Understanding how a sleeve gastrectomy (SG) achieves metabolic improvement is challenging due to the complex relationship between the liver, bile acid (BA) pool, and gut microbiome. We hypothesized that SG alters the gut microbiome which then increases the BA pool leading to metabolic efficacy. Methods We performed fecal material transfer (FMT) from SG or sham mice to surgically-naïve mice with an intact microbiome. We evaluated the effect of surgery and FMT on BA-related liver enzymes, BA concentrations, and gut microbiome composition via 16s and metagenomic analysis. Results SG significantly deflected weight gain compared to sham surgery, 5±2 g vs 10±3 g respectively (p= 0.004). SG significantly increased the BA pool and decreased liver transcription of slc10a1 (p=0.04) and cyp8b1 (p=0.03). Random forest analysis identified several features with significantly increased relative abundance in SG compared to sham mice including Lactobacillus. Examination of metabolic profiles with metagenomic analysis revealed a BA salt hydrolase produced by the Ligilactobacillus species. FMT of SG stool to surgically-naïve mice significantly decreased the BA pool compared to sham FMT (p=0.034). Unlike SG surgery, we found no effect of SG or sham FMT on bile acid related enzymes in the liver after 14 weeks of treatment. Conclusion Overall, we propose that the metabolic benefits of SG surgery are related to decreased liver transcription of cyp8b1and slc10a1 with subsequent increases in the systemic and enterohepatic BA pool including LCA. The gut microbiome adapts to the altered BA pool with associated increases in Ligilactobacillus and bile salt hydrolase production.},
}

@article {pmid40695364,
year = {2025},
author = {Kabil, A and Liu, LT and Xu, C and Nayyar, N and Gonzalez, L and Chopra, S and Brassard, J and Beaulieu, MJ and Li, Y and Damji, A and Zandstra, PW and Blanchet, MR and Hughes, MR and McNagny, KM},
title = {Microbial dysbiosis sculpts a systemic ILC3/IL-17 axis governing lung inflammatory responses.},
journal = {Mucosal immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.mucimm.2025.07.002},
pmid = {40695364},
issn = {1935-3456},
abstract = {Advancements in vaccination and sanitation have significantly reduced the prevalence and burden of infectious diseases; however, these benefits have coincided with a marked rise in autoimmune and allergic disorders. Recent studies have investigated these linked trends through the lens of host-microbiome alterations, proposing these shifts as a potential explanatory mechanism. Previously, we demonstrated that vancomycin-induced depletion of short-chain fatty acid (SCFA)-producing bacteria results in hyperactivation of ILC2s and exacerbated allergic responses. Here we investigate the effects of low-dose streptomycin on innate and adaptive immune cell populations and their activation states. Although streptomycin-treated mice exhibit normal allergic responses, they display heightened susceptibility to Th1/Th17-mediated disease, specifically hypersensitivity pneumonitis (HP). This is characterized by a two-fold increase in ILC3s and Th17 cells in the lungs, alongside activation of antigen-presenting cells (APCs) at steady state-an effect that is further amplified upon exposure to HP-inducing agents. Shotgun metagenomic analysis revealed that streptomycin-induced dysbiosis reduces microbial diversity, depletes bile acid-metabolizing bacteria, and enriches for metabolic pathways involved in branched-chain amino acid biosynthesis, including leucine-a known activator of mTORC1. Strikingly, administration of the secondary bile acid metabolite isolithocholic acid (an inverse agonist of RORγt), or an IL-23 neutralizing antibody, reverses the enhanced susceptibility to HP. Inhibition of mTORC1 significantly reduced Th17/ILC3 responses and histopathology. Our findings underscore microbial equilibrium as a key determinant of susceptibility to HP and uncover a positive feedback loop between IL and 23-producing APCs and ILC3/Th17 cells that mechanistically links dysbiosis to sustained type 3 inflammation, and we identify a simple, actionable means of intervention.},
}

@article {pmid40695181,
year = {2025},
author = {Zhang, Y and Zhang, H and Tao, T and Chen, J and Li, P and Wang, Y and Liu, P and Zhu, Y and Routledge, MN and Yang, C and Zhang, C},
title = {Investigation and insights into the technical strategies for reducing agrochemical inputs in rice farming to enhance agroecosystem resilience and food safety, A case study in China.},
journal = {Journal of environmental management},
volume = {392},
number = {},
pages = {126619},
doi = {10.1016/j.jenvman.2025.126619},
pmid = {40695181},
issn = {1095-8630},
abstract = {The growing demand for cereal production has led to increasing agrochemical inputs; therefore, evaluation and adjustment of current practices are required to maintain and improve sustainable cropping systems. A Four-years study of multiple practices with reduced agrochemical application for rice farming was conducted and investigated in southern China to assess impacts on food safety and ecological resilience. A 30 % reduction in total pesticide use resulted in a 20 % decrease in ecological risk to earthworms, primarily due to reduced application of key pesticides: pymetrozine, pretilachlor, difenoconazole, propiconazole, thifluzamide, tricyclazole, and hexaconazole. A 22 % reduction in total mineral fertilizer use had a slight impact on soil fertility; however, certain practices involving partial replacement of chemical fertilizers with organic manure enhanced soil enzyme activity. This improvement was also linked to changes in the soil bacterial community, particularly the enrichment of Gemmatimonadetes, Actinobacteria, and Cyanobacteria, which contributed to enhanced soil fertility. Additionally, reduction in agrochemical application was accompanied by a declining trend in heavy metal accumulation; however, exposure risks of arsenic and Cd still require consideration. Our study demonstrates that progressive reduction of agrochemical inputs can mitigate pollutant risks and reactivate soil self-restoration processes, thereby enabling the design of adaptable sustainable cropping systems with optimized ecological trade-offs.},
}

@article {pmid40695175,
year = {2025},
author = {Federico, S and Esposito, R and De Rosa, M and Sonnessa, M and Reddel, S and Laurenzi, G and Bertolino, M and Giovine, M and Pozzolini, M and Zupo, V and Costantini, M},
title = {Comparative metagenomic analyses of the microbiome from three Mediterranean sponges to identify genes involved in biosynthesis of bioactive compounds.},
journal = {Marine genomics},
volume = {82},
number = {},
pages = {101202},
doi = {10.1016/j.margen.2025.101202},
pmid = {40695175},
issn = {1876-7478},
abstract = {Marine sponges host a range of microorganisms and among them, bacteria represent a significant part of their biomass. Furthermore, bacteria are promising sources of natural products to be applied in various fields. Often the study their biotechnological potential is relented by low grow rates. For this reason, such cultivation-independent approaches, as metagenomics tools applied to sponges is obtaining wide success. For the first time, here we aimed at having an almost complete information about taxonomic and functional diversity of bacteria associated to three sponges, Agelas oroides, Haliclona (Halichoclona) vansoesti and Geodia cydonium, previously reported as candidate sources of bioactive compounds for pharmacological, nutraceutical and cosmeceutical purposes. Comparative metagenomic analyses were applied, sequencing DNA from the three sponges by ONT GridION X5 Mk1 sequencer. Our findings revealed for all the analyzed sponges the presence of genes/enzymes responsible for the synthesis of vitamins, fatty acids, antioxidant glutathione, terpenes, steroids and carotenoids. Consequently, we demonstrated the three sponges under analysis and their associated microorganisms could be considered good candidates for the isolation and identification of bioactive compounds for biotechnological application in the field of pharmacology, nutraceuticals and cosmeceuticals as well as environmental biotechnologies. Overall, metagenomic data represent a useful tool exploitable to sustainably develop bioactive products.},
}

@article {pmid40695133,
year = {2025},
author = {Shi, F and Fang, H and Cheng, S and Guo, Y and Wang, H and Chen, L and Pu, H and Liu, B},
title = {Cadmium accumulation suppresses rice nitrogen use efficiency by inhibiting rhizosphere nitrification and promoting nitrate reduction.},
journal = {Journal of hazardous materials},
volume = {496},
number = {},
pages = {139298},
doi = {10.1016/j.jhazmat.2025.139298},
pmid = {40695133},
issn = {1873-3336},
abstract = {Cadmium (Cd) pollution significantly disrupts paddy soil nitrogen (N) availability and impairs rice nitrogen use efficiency (NUE). However, most existing studies rely on microcosm or pot experiments, with limited field-based manipulative studies involving Cd addition. The regulatory mechanisms by which N transformation processes influence rice N utilization under Cd stress remain poorly understood. In this study, a field experiment incorporating multiple levels of Cd addition was conducted to address this gap. Plant traits, nutrient content, and microbial community characteristics in rhizosphere and bulk soils were examined through soil chemical analysis, metagenomic sequencing, and bioinformatics approaches. The results demonstrated that microbial communities, soil N transformation potential, and rice NUE responded to Cd addition in a dose-dependent manner, with rhizosphere soils exhibiting greater sensitivity than bulk soils. Cd addition reduced dissolved organic carbon (DOC), NH4[+]-N, and NO3[-]-N in rhizosphere soil, while increasing total and available phosphorus (P) contents in both rhizosphere and bulk soils. Although Cd addition enhanced aboveground biomass and total N uptake, it led to a decline in plant N concentration and NUE. Moreover, Cd accumulation markedly suppressed the abundance of nitrification genes while promoting genes involved in dissimilatory nitrate reduction to ammonium (DNRA) and denitrification. Overall, Cd stress altered microbial community structure and soil N and P availability, thereby impairing rice N uptake and NUE. These findings suggest that acute Cd exposure rapidly disrupts microbial ecology, decouples the soil N cycle, and reduces N supply potential of paddy soils and rice NUE, ultimately threatening agroecosystem stability in southern China. These impacts warrant greater consideration in future farmland management strategies.},
}

@article {pmid40694475,
year = {2025},
author = {Pfeifer, E and d'Humières, C and Lamy-Besnier, Q and Oñate, FP and Denisé, R and Dion, S and Condamine, B and Touchon, M and Ma, L and Burdet, C and Mentré, F and Denamur, E and Rocha, EPC and , },
title = {Antibiotic perturbation of the human gut phageome preserves its individuality and promotes blooms of virulent phages.},
journal = {Cell reports},
volume = {44},
number = {8},
pages = {116020},
doi = {10.1016/j.celrep.2025.116020},
pmid = {40694475},
issn = {2211-1247},
abstract = {Antibiotic use disrupts the gut microbiota, posing risks of long-term health issues and resistance. To study its impact on gut phages, we followed 22 healthy individuals 2 weeks before and up to 6 months after a 3-day course of 3[rd]-generation cephalosporins. Our results show that gut phages rarely encode antibiotic resistance genes and are mostly temperate, including many phage plasmids. Furthermore, phage populations remain individual-specific even after microbiome perturbation. Yet, we report a 20% decline in phage diversity the day after treatment, alongside blooms of a few, mostly virulent, phages. We suggest that some of these phages contribute to the recovery of bacterial diversity via "kill-the-winner" dynamics. This is supported by (temporarily) dominant phages targeting Parabacteroides distasonis, a bacterium that thrives post-treatment only in the absence of these phages. Our findings suggest gut phages are crucial to the microbiome response to antibiotics, aiding the restoration of balance and diversity.},
}

@article {pmid40694390,
year = {2025},
author = {Patrick, S and Filkins, L and Goker, M and Holden, N and Hoskisson, PA and Kiepas, A and Meehan, C and Pallen, M and Pritchard, L and Suchanek, AL and Sutcliffe, I and Trujillo, ME and Tucker, N and Turnbull, JD and Butler-Wu, S},
title = {'What's in a name? Fit-for-purpose bacterial nomenclature': meeting report.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {75},
number = {7},
pages = {},
doi = {10.1099/ijsem.0.006844},
pmid = {40694390},
issn = {1466-5034},
mesh = {*Terminology as Topic ; *Bacteria/classification/genetics ; Phylogeny ; },
abstract = {Rapid and economical DNA sequencing has resulted in a revolution in phylogenomics. The impact of changes in nomenclature can be perceived as an absolute necessity of scientific rigour, coupled with the slight inconvenience of needing to re-learn names. In relation to practical aspects of microbiology, for example, infectious disease diagnosis, there may, however, be potential dangers. Historically, prokaryote classification has been based on multiple metabolic, physiological, biochemical and descriptive characteristics combined with the environmental source. Whole-genome sequence data have transformed our ability to determine evolutionary relationships. In addition, metagenomic and metataxonomic sequencing have resulted in the discovery of novel microbes, many of which are yet to be cultured. As a result, occasional name changes and additional prokaryote discoveries have accelerated at an unprecedented pace. Herein is a report of a Microbiology Society supported meeting of representatives of the communities of specialist taxonomists, phylogeneticists and applied microbiologists. Discussion included: recent advances in phylogenomics and the potential impact of nomenclature change on practical microbiology, e.g. plant pathology, food security, industrial microbiology, clinical microbiology and infectious diseases; the need, or lack thereof, for wider consideration and consultation prior to nomenclature change proposals which impact on practical microbiology; the application of the intricate and highly necessary rules of prokaryote nomenclature, which sometimes appear unfathomable to the non-specialist; and genome-based phylogenomics and the relationship with the International Code of Nomenclature of Prokaryotes. The meeting resulted in the formation of the Ad Hoc Committee for Mitigating Changes in Prokaryotic Nomenclature under the auspices of the International Committee on Systematics for Prokaryotes.},
}

*Terminology as Topic
*Bacteria/classification/genetics
Phylogeny

@article {pmid40694261,
year = {2025},
author = {Tay, DD and Kumar, VS and Shapawi, R and Shah, MD and Ahmad, HF and Mazlan, N},
title = {The Relationship Between the Gut Microbiome and the Aqua Cultured Fish, General Prospects Toward Fish Health: A Systematic Review.},
journal = {Applied biochemistry and biotechnology},
volume = {},
number = {},
pages = {},
pmid = {40694261},
issn = {1559-0291},
support = {Grant Agensi Kerajaan HIC2404//Ministry of Higher Education, Malaysia/ ; },
abstract = {Aquaculture allows the cultivation of aquatic life outside its normal origins which can provide work opportunities, seafood security, as well as conservation efforts for endangered fish species. Numerous factors influence the health of aquaculture fish, with the gut microbiome playing a pivotal role. Research indicates that an imbalance or dysbiosis in the gut microbiome can significantly affect the overall well-being and health outcome of these fish. Despite extensive research utilizing metagenomics across diverse environments and controlled conditions, a clear consensus on the characteristic of "healthy" or "optimal" gut microbiome in domesticated fish has yet to be established. This review will cover 28 studies, which further discusses the findings of the gut microbiome within fish and attempts to provide a general outline of how the gut bacteria may interact and affect fish health within aquaculture environments. The indices as well as pathogens and beneficial bacteria of each study are also listed. This review aims to provide readers with an enhanced understanding of the complex dynamics of the gut microbiome in aquaculture fish, while offering insights that could inform the design of future studies in this field.},
}

@article {pmid40693750,
year = {2025},
author = {Sant, DG and Smith, TP and Wong, ELY and Cohen, J and King, KC and Bell, T and Barraclough, TG},
title = {Eco-evolutionary robustness of wild bacterial communities to experimental perturbation.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf144},
pmid = {40693750},
issn = {1751-7370},
abstract = {Most knowledge about bacterial evolution and ecological interactions comes from laboratory studies. One difference between the wild and most laboratory experiments is the diversity of bacterial taxa present. Understanding how wild bacteria respond to perturbation therefore requires consideration of how ecological sorting, colonization, and genetic changes of constituent species interact. Ecological sorting of species might reduce evolutionary rates and make communities robust to disturbance, or it could amplify selection pressures and lead to unstable co-evolutionary cascades. Even estimates of basic rates of ecological sorting, dispersal, and genetic change are rare. Here, we addressed these knowledge gaps by liming wild decomposer communities living in beech tree holes and tracking ecological and evolutionary responses for 12 weeks. Overall, tree hole communities were extremely robust to liming involving short-term pulses up to 4 pH units and long-term increases up to 2 pH units. Species diversity and composition displayed significant but small changes in treatment tree holes compared to control ones. New bacterial taxa colonized at a low rate that did not vary with liming. Genetic changes in the frequency of single nucleotide polymorphisms in metagenome assembled genomes occurred at rates that were both comparable to and correlated with ecological changes in the same metagenome assembled genomes, but the rate of genetic changes did not vary between limed and control tree holes. Analysis of rates of genetic change estimated low effective population size (~104) and generation times of roughly 1 day. Our study provides estimates of rates of ecological and evolutionary processes in wild bacterial communities, which displayed remarkable robustness to our experimental perturbation.},
}

@article {pmid40693317,
year = {2025},
author = {Fan, S and Zhang, J and Guo, F and Xu, F and Tang, Z and Li, R and Bai, B and Liu, Y and Li, G and Wan, S},
title = {Regulation of DNA Methylation in Peanut Leaves and Roots: Uncovering the Molecular Mechanisms for Increased Yield After Single-Seed Sowing.},
journal = {Plant biotechnology journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/pbi.70264},
pmid = {40693317},
issn = {1467-7652},
support = {CXGC2025C13//The Innovation Program of SAAS/ ; 202333033//The project of "New Colleges and University 20" of Jinan City/ ; SDBX2022017//Shandong Province Postdoctoral Innovation Talent Support Project/ ; tspd20221107//Taishan Scholar Program of Shandong province/ ; tsqn202211275//Taishan Scholar Program of Shandong province/ ; tsqn202312285//Taishan Scholar Program of Shandong province/ ; 2021LZGC026//Key Technology Research and Development Program of Shandong Province/ ; 2022LZGC021//Key Technology Research and Development Program of Shandong Province/ ; },
abstract = {Cytosine methylation is a crucial epigenetic modification that responds to various environmental cues, yet the specific mechanisms influencing planting patterns remain incompletely understood. This study reveals significant growth differences between single-seed (SS) precision sowing and double-seed (DS) sowing observed 42 days after germination under controlled indoor conditions. These differences were eliminated by the application of the DNA methylation inhibitor 5-azacytidine (5-aza), highlighting the role of DNA methylation in these processes. To further investigate the role of DNA methylation in planting pattern, we generated DNA methylation profiles of peanut leaves and roots under both DS and SS planting patterns. The analysis revealed increased CHH methylation in both tissues, caused by the RNA-directed DNA methylation (RdDM) pathway. Further analysis, including differential methylation, transposable element (TE) analysis and methylation-related gene analysis, demonstrated tissue-specific epigenetic responses to planting patterns. Integrating methylome and transcriptome data, we found that DS was associated with hyper-CHH methylation in WRKY gene promoters in leaves, accelerating leaf senescence. Meanwhile, SS reduced CHH methylation in promoters in roots, upregulating genes involved in flavonoid biosynthesis. This upregulation enhanced root nodule formation and improved stress resistance, resulting in increased concentrations of nitrogen and phosphorus in the roots, as confirmed by metagenomic functional analysis. This research provides novel insights into the epigenetic regulation of plant growth and development.},
}

@article {pmid40693040,
year = {2025},
author = {Fan, Q and Tang, G and Jiang, M and Xu, Y and Pan, N and Liang, Z and Zhang, C and Li, P and Xu, F and Chen, Z and Liu, B and Chen, L and Li, Y and Li, C and Hu, F and Li, F},
title = {Clinical prognostic value of TTV and HCMV but not EBV for outcomes in hospitalized HIV-positive patients.},
journal = {Biosafety and health},
volume = {7},
number = {3},
pages = {173-182},
pmid = {40693040},
issn = {2590-0536},
abstract = {Opportunistic infections caused by viruses, bacteria, fungi, and parasites, are commonly reported in hospitalized human immunodeficiency virus (HIV)-positive patients, but their detrimental contribution to disease severity remains under explored. In this study, we examined the coinfection profiles of 126 HIV-positive patients with suspected respiratory, bloodstream, or neurological infections. Lower respiratory tract (LRT) samples, cerebrospinal fluid, and blood samples collected within the first seven days of admission were subjected to metagenomic next-generation sequencing (mNGS). Additionally, a multiplex polymerase chain reaction (PCR) detection kit to identify ten commonly known respiratory pathogens was applied to the LRT samples. Of 126 HIV-positive patients, 111 (88.1 %) were coinfected with at least one known virus. Epstein-Barr virus (EBV) (71/111, 64.0 %), human cytomegalovirus (HCMV) (64/111, 57.7 %), and torque teno virus (TTV) (63/111, 56.8 %) were the three most prevalent coinfected viruses. Fungal coinfections (58/126, 46.0 %) and bacterial coinfections (47/126, 37.3 %) were less frequent than viral coinfections. Higher viral loads of coinfection were associated with fungal coinfections (odds ratio [OR] = 2.573, 95 % confidence interval [CI]: 1.150-5.757, P = 0.0214) and lower CD4[+]/CD8[+] T cell ratios (OR = 0.048, 95 % CI: 0.005-0.429, P = 0.0067). Importantly, patients with higher loads of HCMV and TTV, but not EBV, exhibited worse clinical outcomes. Specifically, patients with HCMV reads per million (RPM) > 0 and TTV RPM > 5 exhibited significantly higher risks of poor prognosis and intensive care unit (ICU) admission. In contrast, EBV RPM showed no association with clinical outcomes in this context. In conclusion, HCMV and TTV may serve as prognostic biomarkers linked to poorer outcomes in HIV-positive patients. Detection of HCMV and TTV could predict clinical outcomes and improve patient management strategies.},
}

@article {pmid40692859,
year = {2025},
author = {Brandon, H and Montelongo-Jauregui, D and Swaminathan, N},
title = {Mycoplasma hominis prosthetic valve infective endocarditis and endophthalmitis in a renal transplant recipient: a case report.},
journal = {Therapeutic advances in infectious disease},
volume = {12},
number = {},
pages = {20499361251357405},
pmid = {40692859},
issn = {2049-9361},
abstract = {Mycoplasma hominis is a rare cause of infective endocarditis, typically reported in immunocompetent patients following valve replacement. We report the first case of post-renal transplant prosthetic valve infective endocarditis and concurrent endophthalmitis caused by M. hominis. A 47-year-old woman with prior aortic valve replacement and renal transplantation presented with fever & atrial fibrillation. She was diagnosed with culture-negative endocarditis complicated by cerebral septic emboli and visual symptoms. Plasma cell-free DNA metagenomic next-generation sequencing identified M. hominis, which was confirmed by culture of aortic abscess tissue. Management included valve replacement surgery and antibiotic therapy with doxycycline and levofloxacin. This case highlights the diagnostic challenges of M. hominis infections, the utility of advanced molecular diagnostics, and the importance of considering M. hominis in immunocompromised patients with culture-negative endocarditis. Donor and recipient screening for M. hominis in recipients with prosthetic heart valves may help prevent infection.},
}

@article {pmid40692682,
year = {2025},
author = {Qin, X and Xi, L and Zhao, L and Han, J and Qu, H and Xu, Y and Weng, W},
title = {Exploring the distinctive characteristics of gut microbiota across different horse breeds and ages using metataxonomics.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1590839},
pmid = {40692682},
issn = {2235-2988},
mesh = {Animals ; Horses/microbiology ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Age Factors ; Metagenomics/methods ; DNA, Bacterial/genetics ; Biodiversity ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Gut microbiota exerts a pivotal function in host nutrient metabolism and maturation of the mucosal immunity. Analyzing the reciprocal interaction between horses and gut microbiota constitutes a crucial aspect of scientific feeding practices. This study aims to investigate the differences in gut microbiota among Hequ horses, Mongolian horses, and Thoroughbred horses, as well as between Thoroughbred horses at two age stages.

METHODS AND RESULTS: Paired-end sequencing with a read length of 2×250 bp targeting the V3-V4 region of the 16S rRNA gene in fecal samples was carried out. Subsequently, differences in the diversity, composition, and metabolic pathways of the gut microbiota among the groups were analyzed. The results showed that: (1) Horse breeds were associated with variations in the gut microbiota. Microbial diversity, the proportion of commensal bacteria from Bacillota and Bacteroidota, and bacterial communities involved in dietary fiber metabolisms were significantly higher in the gut of the Hequ horses than in the gut of the Mongolian and Thoroughbred horses. The highest Bacillota to Bacteroidota (B/B) ratio and enrichment of bacterial communities involved in the metabolism of bile acids, lipids, and amino acids in the gut of the Mongolian horses resulted in significantly higher lipid metabolism and amino acid metabolism than in the other two breeds. The bacterial communities enriched in the gut of Thoroughbred horses were primarily involved in carbohydrate metabolism, but the level of energy metabolism was significantly lower than in Hequ horses. (2) The results also showed an association between age and gut microbiota of Thoroughbred horses. The alpha diversity, B/B ratio, and 83.33% of metabolic pathways did not differ significantly between younger and older Thoroughbred horses. However, there were significant differences between the two age groups in beta diversity, composition of glycolytic bacteria, metabolism of cofactors and vitamins, and energy metabolism of gut microbiota.

CONCLUSIONS: Collectively, these results point to an association between the breed of horses or the age of Thoroughbred horses with variations in gut microbiota. The current findings will serve as a reference for improving feeding strategies for horses.},
}

Animals
Horses/microbiology
*Gastrointestinal Microbiome
RNA, Ribosomal, 16S/genetics
Feces/microbiology
*Bacteria/classification/genetics/isolation & purification/metabolism
Age Factors
Metagenomics/methods
DNA, Bacterial/genetics
Biodiversity
Sequence Analysis, DNA

@article {pmid40692236,
year = {2025},
author = {Shao, XF and Wu, XM and Deng, J and Lei, WB},
title = {[Metagenomic next-generation sequencing technology assists in the diagnosis of Talaromyces marneffei infection in the larynx: a case report].},
journal = {Zhonghua er bi yan hou tou jing wai ke za zhi = Chinese journal of otorhinolaryngology head and neck surgery},
volume = {60},
number = {6},
pages = {666-667},
doi = {10.3760/cma.j.cn115330-20250111-00035},
pmid = {40692236},
issn = {1673-0860},
mesh = {Humans ; Male ; Middle Aged ; *Talaromyces/genetics ; High-Throughput Nucleotide Sequencing ; *Mycoses/diagnosis/microbiology ; Metagenomics ; Larynx/microbiology ; *Laryngeal Diseases/diagnosis/microbiology ; },
}

Humans
Male
Middle Aged
*Talaromyces/genetics
High-Throughput Nucleotide Sequencing
*Mycoses/diagnosis/microbiology
Metagenomics
Larynx/microbiology
*Laryngeal Diseases/diagnosis/microbiology

@article {pmid40692127,
year = {2025},
author = {Vipindas, PV and Venkatachalam, S and Jabir, T and Yang, EJ and Cho, KH and Jung, J and Lee, Y and Moon, JK and Jain, A},
title = {Distribution of Surface-Layer Prokaryotes in the Western Arctic Ocean: Responses to Pacific Water Inflow and Sea Ice Melting.},
journal = {Environmental microbiology},
volume = {27},
number = {7},
pages = {e70154},
doi = {10.1111/1462-2920.70154},
pmid = {40692127},
issn = {1462-2920},
support = {//National Centre for Polar and Ocean Research, Ministry of Earth Sciences, Govt. of India/ ; //Korea Polar Research Institute/ ; //The Ministry of Oceans and Fisheries, Republic of Korea/ ; },
mesh = {Arctic Regions ; *Ice Cover/microbiology ; *Archaea/genetics/classification/isolation & purification ; *Seawater/microbiology ; *Bacteria/genetics/classification/isolation & purification/metabolism ; Pacific Ocean ; Microbiota ; Metagenome ; },
abstract = {Here, we evaluated how microbial community composition and functions vary along the path of Pacific water inflow, starting from the Bering Sea via the Chukchi Sea to the central Arctic Ocean. Our findings reveal that the inflow of Pacific water and sea ice melt significantly influence the environmental settings of the western Arctic Ocean, resulting in distinct prokaryotic communities with varied distribution patterns between the open Chukchi Sea and the Ice-covered central Arctic Ocean. The heterotrophic populations reliant on phytoplankton predominated in the Bering Sea and Southern Chukchi Sea, while in the Central Arctic Ocean, chemoautotrophic bacteria and archaea contributed equally with heterotrophic populations adapted to oligotrophic conditions. Although no specific functional genes were universally enriched across the metagenome libraries of prokaryotic communities, the relative abundance of functional genes varied among oceanic sectors. The assembly processes of prokaryotic communities in the western Arctic Ocean were found to be influenced by both deterministic and stochastic factors, with deterministic processes playing a more significant role. Thus, the ongoing increases in Pacific inflow and sea ice melt could lead to the displacement of native chemoautotrophic and oligotrophic populations in the Arctic Ocean by fast-growing heterotrophic populations better adapted to elevated nutrient concentrations and temperatures.},
}

Arctic Regions
*Ice Cover/microbiology
*Archaea/genetics/classification/isolation & purification
*Seawater/microbiology
*Bacteria/genetics/classification/isolation & purification/metabolism
Pacific Ocean
Microbiota
Metagenome

@article {pmid40691960,
year = {2025},
author = {Goremykin, V and Coleine, C and Ripa, C and Selbmann, L and Donati, C},
title = {Phylogenomic analysis resolves the evolutionary pattern of diversification of cyanobacteria and reveals the evolutionary affinity of novel Antarctic lineages.},
journal = {Molecular phylogenetics and evolution},
volume = {},
number = {},
pages = {108419},
doi = {10.1016/j.ympev.2025.108419},
pmid = {40691960},
issn = {1095-9513},
abstract = {Establishing phylogenetic relationships among the major cyanobacterial lineages remains elusive. Here we report a phylogenetic analysis of a large and well curated dataset, which allowed us to resolve with maximum statistical support the general pattern of cyanobacterial diversification and to address the limited knowledge regarding the diversity of Antarctic cyanobacteria. The analysis included novel Metagenome-Assembled Genomes (MAGs) sampled from diverse lithic habitats across Antarctica at elevations up to 3.4 km. The results presented here revealed previously undetected lineages and provided a robust phylogenetic framework for a natural cyanobacterial classification.},
}

@article {pmid40691525,
year = {2025},
author = {Abdelkader, A and Ferdous, NA and El-Hadidi, M and Burzykowski, T and Mysara, M},
title = {metaGEENOME: an integrated framework for differential abundance analysis of microbiome data in cross-sectional and longitudinal studies.},
journal = {BMC bioinformatics},
volume = {26},
number = {1},
pages = {189},
pmid = {40691525},
issn = {1471-2105},
mesh = {Longitudinal Studies ; *Microbiota/genetics ; *Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; Cross-Sectional Studies ; Humans ; Metagenome ; },
abstract = {BACKGROUND: Detecting biomarkers is a key objective in microbiome research, often done through 16S rRNA amplicon sequencing or shotgun metagenomic analysis. A critical step in this process is differential abundance (DA) analysis, which aims to pinpoint taxa whose abundance significantly differs between groups. However, DA analysis remains challenging due to high dimensionality, compositionality, sparsity, inter-taxa correlations, uneven abundance distributions, and missing values-all which hinder our ability to model the data accurately. Despite the availability of many DA tools, balancing high statistical power with effective false discovery rate (FDR) control remains a major limitation.

RESULTS: Here, we introduce a novel approach for DA analysis that integrates counts adjusted with Trimmed Mean of M-values (CTF) normalization and Centered Log Ratio (CLR) transformation with Generalized Estimating Equation (GEE) model. We benchmarked our approach against eight widely used tools employing both simulated and real datasets in cross-sectional and longitudinal settings. While several tools (e.g. MetagenomeSeq, edgeR, DESeq2 and Lefse) achieved high sensitivity, they often failed to adequately control the FDR. In contrast, our method demonstrated high sensitivity and specificity when compared to other approaches that successfully controlled the FDR, including ALDEx2, limma-voom, ANCOM, and ANCOM-BC2.

CONCLUSIONS: Our approach effectively addresses key challenges in microbiome data analysis across both cross-sectional and longitudinal designs. Integrated into the R package metaGEENOME (https://github.com/M-Mysara/metaGEENOME), our framework provides a flexible, scalable and statistically robust solution for DA analysis, offering improved FDR control and enhanced performance for biomarker discovery in microbiome studies.},
}

Longitudinal Studies
*Microbiota/genetics
*Metagenomics/methods
RNA, Ribosomal, 16S/genetics
Cross-Sectional Studies
Humans
Metagenome

@article {pmid40691449,
year = {2025},
author = {Vázquez-Castellanos, JF and Maciel, LF and Wauters, L and Gregory, A and Van Oudenhove, L and Geboers, K and Verbeke, K and Smokvina, T and Tack, J and Vanuytsel, T and Derrien, M and Raes, J},
title = {Probiotic-mediated modulation of gut microbiome in students exposed to academic stress: a randomized controlled trial.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {140},
pmid = {40691449},
issn = {2055-5008},
mesh = {Humans ; *Probiotics/administration & dosage ; *Gastrointestinal Microbiome/drug effects ; *Stress, Psychological/microbiology ; *Students/psychology ; Male ; Female ; *Lacticaseibacillus rhamnosus/physiology ; RNA, Ribosomal, 16S/genetics ; Young Adult ; Adult ; Feces/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Anxiety ; Metagenomics ; },
abstract = {Probiotics have been widely tested for their effect on mental well-being, albeit with heterogeneous outcomes. Direct and indirect effects through the gut microbiome might lie at the basis of these observations. Here, in a post-hoc analysis, we assessed the effect of 4-week consumption of a probiotic candidate strain on the gut microbiome in students exposed to academic stress. Healthy students were randomized to consume a fermented milk product with Lacticaseibacillus rhamnosus CNCM I-3690 (N = 39) or an acidified non-fermented milk product (N = 40) twice daily for 4 weeks before academic exams. The gut microbiome was analysed by Quantitative Microbiome Profiling based on 16S rRNA gene amplicon and shotgun metagenomic sequencing. Stress and anxiety were assessed using both objective and self-reported markers. Changes of alpha-diversity markers and community shifts from baseline (beta diversity) were lower in L. rhamnosus treated individuals over controls, suggesting lower overall changes of gut microbiota during psychological stress in the Probiotic group. The intake of L. rhamnosus CNCM I-3690 induced differential abundance of some species, such as the maintenance of the quantitative abundance of Ruminococcus bicirculans, and co-varied with species, which differed according to visits (i.e., stress level), suggesting a potential beneficial effect of the strain before the highest increase of stress level. The higher quantitative abundance of F. prausnitzii induced by the probiotic intake was associated with lowered self-reported anxiety levels before the exam. Functional analysis revealed minor changes upon intake of the probiotic strain. Taken together, using a quantitative framework, we found that L. rhamnosus CNCM I-3690 has a potential effect on gut microbiome response to stress, although further studies are needed to better understand the precise interaction.},
}

Humans
*Probiotics/administration & dosage
*Gastrointestinal Microbiome/drug effects
*Stress, Psychological/microbiology
*Students/psychology
Male
Female
*Lacticaseibacillus rhamnosus/physiology
RNA, Ribosomal, 16S/genetics
Young Adult
Adult
Feces/microbiology
*Bacteria/classification/genetics/isolation & purification
Anxiety
Metagenomics

@article {pmid40691217,
year = {2025},
author = {Leung, HKM and Lo, EKK and Chen, C and Zhang, F and Felicianna, and Ismaiah, MJ and El-Nezami, H},
title = {Theabrownin combined with zearalenone suppresses colitis-associated colorectal cancer by inhibiting PI3K/AKT pathway and enhancing microbial propionate production.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {26386},
pmid = {40691217},
issn = {2045-2322},
mesh = {*Zearalenone/pharmacology/administration & dosage ; Animals ; Mice ; *Proto-Oncogene Proteins c-akt/metabolism ; *Phosphatidylinositol 3-Kinases/metabolism ; Gastrointestinal Microbiome/drug effects ; *Propionates/metabolism ; Signal Transduction/drug effects ; *Colorectal Neoplasms/drug therapy/etiology ; *Colitis-Associated Neoplasms/drug therapy/metabolism/pathology ; Male ; Cytokines/metabolism ; Fluorouracil/pharmacology ; *Colitis/complications ; Mice, Inbred C57BL ; },
abstract = {Colorectal cancer (CRC) is both a leading cause of cancer-related mortality and one of the most frequently diagnosed cancers. Previous studies have shown that zearalenone and theabrownin each exert anti-CRC effects. Here, we aimed to evaluate the anti-tumor properties of theabrownin and zearalenone mixture (TZ) and to assess whether supplementing TZ with 5-FU, a commonly used chemotherapeutic drug, could further suppress CRC tumorigenesis. Our results revealed that TZ significantly attenuated AOM/DSS-induced colorectal tumorigenesis. TZ improved survival rate, reduced tumor count, preserved colon length, and mitigated colonic inflammation in AOM/DSS mice. In addition, the concentration of pro-inflammatory cytokines IL-6, TNF-α and IL-17 A/F and proliferative PI3K/AKT were significantly reduced. Metagenomic analyses revealed that TZ modulated the gut microbiota and mycobiota composition and increased the fecal acetate and propionate levels. Furthermore, the enrichment of the bacterial Desulfovibrionaceae bacterium LT0009, Helicobacter sp. MIT 03-1616 and fungal Xylariaceae sp. FL0594 was associated with the reduction of tumor multiplicity and pro-inflammatory cytokines. No additional benefits were observed with combining TZ with 5-FU. Taken together, TZ presented remarkable inhibitory effects on colorectal tumorigenesis, indicating its potential as a novel therapeutic candidate for CRC.},
}

*Zearalenone/pharmacology/administration & dosage
Animals
Mice
*Proto-Oncogene Proteins c-akt/metabolism
*Phosphatidylinositol 3-Kinases/metabolism
Gastrointestinal Microbiome/drug effects
*Propionates/metabolism
Signal Transduction/drug effects
*Colorectal Neoplasms/drug therapy/etiology
*Colitis-Associated Neoplasms/drug therapy/metabolism/pathology
Male
Cytokines/metabolism
Fluorouracil/pharmacology
*Colitis/complications
Mice, Inbred C57BL

@article {pmid40689619,
year = {2025},
author = {Tambovtseva, RS and Arslan, LA and Grigoryeva, TA and Abdulkhakov, SR and Doludin, YV and Stoma, IO and Rizvanov, AA and Miftakhova, RR and Gabdoulkhakova, AG},
title = {Narrative review on bacteria-derived metabolites in the pathogenesis of ulcerative colitis.},
journal = {Clinical microbiology reviews},
volume = {},
number = {},
pages = {e0021024},
doi = {10.1128/cmr.00210-24},
pmid = {40689619},
issn = {1098-6618},
abstract = {SUMMARYThe pathogenesis of ulcerative colitis (UC) is heterogeneous; the causes are considered to be external factors such as stress, infections, antibiotics, and other medications, diet, and intrinsic factors such as genetic predisposition. The aim of this narrative review is to analyze data on intestinal flora and bacteria-derived metabolites in inflammatory bowel diseases and ulcerative colitis in particular. The main focus is on proteolytic, saccharolytic, mucin-degrading, and bile acid-metabolizing bacteria. What types of metabolites are beneficial for intestinal integrity and the patient's health? How can dietary preferences trigger disease and cause complications? What kind of changes in the microbiome promote the disease? We consider what targets/receptors metabolites act on and their physiological role. The knowledge accumulated over the past years on the gut metagenome, metabolome, and signaling mechanisms may allow, in the future, modulating the composition of the intestinal microbiome and suppressing the growth of pathogenic flora without the use of antibiotics, but due to pro- and prebiotics, products of bacterial metabolism, including quorum sensing molecules.},
}

@article {pmid40688523,
year = {2025},
author = {Mwing'a, GP and Kimu, PA and Beti, M and Shayo, M and Kuchaka, D and Mchome, Z and Mahundi, M and Kumalija, C and Sindato, C and Sonda, T and Kazyoba, PE},
title = {Trends and seasonal variation in gastrointestinal infections in Tanzania: Analysis of 5-year DHIS2 data toward implementing the sampling cycles and metagenomic analyses.},
journal = {IJID regions},
volume = {16},
number = {},
pages = {100661},
pmid = {40688523},
issn = {2772-7076},
abstract = {OBJECTIVES: Gastrointestinal (GI) infections, such as diarrhea and dysentery, continue to be major contributors of morbidity and mortality in low-resource countries. Determining trends and seasonality of GI infections provides a better understanding of how interventions can be improved to reduce the burden. To this effect, an analysis of data from the District Health Information System 2 (DHIS2) was conducted to determine the trend and seasonal variations of GI infections in regions located in the Great Lakes of Tanzania.

METHODS: Data from DHIS2 of 22 districts in Tanzania recorded between January 2018 and December 2022 were analyzed for trends and seasonal variations in GI infections. The data were managed and analyzed by STATA and Microsoft Excel.

RESULTS: A total of 1,511,623 GI cases were recorded between January 2018 and December 2022, with diarrhea leading by 84.4%. Data have shown clear seasonal variations of GI infection: peaks during the rainy season and decline in the dry season.

CONCLUSION: Results have revealed that there is a significant decrease in GI infections from January to August, and the cases increase from September to December. This confirmed two sampling cycles, the dry and rainy season, within which pathogen characteristics and diversity will be elucidated.},
}

@article {pmid40688383,
year = {2025},
author = {Liu, S and Rodriguez, JS and Munteanu, V and Ronkowski, C and Sharma, NK and Alser, M and Andreace, F and Blekhman, R and Błaszczyk, D and Chikhi, R and Crandall, KA and Della Libera, K and Francis, D and Frolova, A and Gancz, AS and Huntley, NE and Jaiswal, P and Kosciolek, T and Łabaj, PP and Łabaj, W and Luan, T and Mason, C and Moustafa, AM and Muralidharan, HS and Mutlu, O and Mansouri Ghiasi, N and Rahnavard, A and Sun, F and Tian, S and Tierney, BT and Van Syoc, E and Vicedomini, R and Zackular, JP and Zelikovsky, A and Zielińska, K and Ganda, E and Davenport, ER and Pop, M and Koslicki, D and Mangul, S},
title = {Analysis of metagenomic data.},
journal = {Nature reviews. Methods primers},
volume = {5},
number = {},
pages = {},
pmid = {40688383},
issn = {2662-8449},
support = {R35 GM146980/GM/NIGMS NIH HHS/United States ; },
abstract = {Metagenomics has revolutionized our understanding of microbial communities, offering unprecedented insights into their genetic and functional diversity across Earth's diverse ecosystems. Beyond their roles as environmental constituents, microbiomes act as symbionts, profoundly influencing the health and function of their host organisms. Given the inherent complexity of these communities and the diverse environments where they reside, the components of a metagenomics study must be carefully tailored to yield accurate results that are representative of the populations of interest. This Primer article examines the methodological advancements and current practices that have shaped the field, from initial stages of sample collection and DNA extraction to the advanced bioinformatics tools employed for data analysis, with a particular focus on the profound impact of next-generation sequencing (NGS) on the scale and accuracy of metagenomics studies. We critically assess the challenges and limitations inherent in metagenomics experimentation, available technologies and computational analysis methods. Beyond technical methodologies, we explore the application of metagenomics across various domains, including human health, agriculture and environmental monitoring. Looking ahead, we advocate for the development of more robust computational frameworks and enhanced interdisciplinary collaborations. This Primer serves as a comprehensive guide for advancing the precision and applicability of metagenomic studies, positioning them to address the complexities of microbial ecology and their broader implications for human health and environmental sustainability.},
}

@article {pmid40687859,
year = {2025},
author = {Yu, H and Li, J and Wang, Y and Zhang, T and Mehmood, T and Habimana, O},
title = {Dysbiosis and genomic plasticity in the oily scalp microbiome: a multi-omics analysis of dandruff pathogenesis.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1595030},
pmid = {40687859},
issn = {1664-302X},
abstract = {INTRODUCTION: Dandruff, affecting ~50% of the global population, is a prevalent scalp condition linked to microbial dysbiosis and inflammation, significantly impacting quality of life.

METHODS: This study employed an integrative omics approach, utilizing 16S rRNA and ITS1 amplicon sequencing alongside shotgun metagenomics, to analyze the scalp microbiome of 65 individuals with varying scalp conditions (healthy oily, healthy non-oily, and dandruff oily).

RESULTS: Distinct microbial profiles were identified, with an increased abundance of pathogenic genera such as Staphylococcus in the dandruff oily (DO) group, contrasted with the presence of Cutibacterium in healthy cohorts.

DISCUSSION: Functional profiling revealed elevated DNA repair mechanisms in the DO group, indicative of stress stemming from pathogen overgrowth, while healthy non-oily samples demonstrated enhanced functions for scalp homeostasis. Notably, the increase in genomic plasticity in the DO group, characterized by antimicrobial resistance genes and mobile elements, underscores the complex interplay of microbial dynamics in dandruff pathology, advocating for microbiome-targeted therapies.},
}

@article {pmid40687781,
year = {2025},
author = {Wang, L and Huang, G and Li, G and Yuan, S and Wei, F},
title = {Updating conservation metagenomics on the gut microbiome of threatened mammals.},
journal = {iScience},
volume = {28},
number = {7},
pages = {113000},
pmid = {40687781},
issn = {2589-0042},
abstract = {During the past two decades, much work has characterized the composition and function of the gut microbiome on diverse wildlife in the framework of conservation metagenomics. While promising for conservation, translating theory into practice remains challenging and requires progress. Here, we summarize the progress of gut microbiomes of threatened mammals from ecology and evolution to conservation practice, and propose an integrative framework for future conservation metagenomics within which multi-dimension, multi-scale, multi-technology, and multi-omics can be comprehensively considered to advance our understanding of the patterns and underpinnings of wildlife gut microbiomes. We also propose microbiome banking to archive endangered species' biological information and microbial entities. Moreover, a reference framework for cutting-edge gut metagenomics research on the giant panda is outlined, demonstrating the field's potential. Finally, while microbiome manipulation shows promise, it remains experimental-demanding stringent safety protocols, vigilant oversight, and thorough risk assessment to ensure responsible application.},
}