@article {pmid40469735,
year = {2025},
author = {Heisel, T and Gonia, S and Dillon, A and Hoops, SL and Al-Ghalith, GA and Gohl, D and Mukhopadhyay, S and Puopolo, K and Kennedy, P and Sadowsky, MJ and Knights, D and Johnson, AJ and Gerber, JS and Gale, CA},
title = {Gut mycobiome maturation and its determinants during early childhood: a comparison of ITS2 amplicon and shotgun metagenomic sequencing approaches.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1539750},
pmid = {40469735},
issn = {1664-302X},
abstract = {INTRODUCTION: Microbial colonization of the gut in early life is important for the development of metabolism, immunity, and the brain. Fungi and bacteria both colonize the human infant gut. The relatively smaller contribution of fungi to the gut microbiome, as compared to bacteria, has posed technical challenges for the precise characterization of fungal communities (mycobiomes) and limited the ability to longitudinally examine mycobiome development.

BACKGROUND: The aims of this study were to (1) characterize mycobiome maturation and identify clinical determinants of mycobiome compositional variation during the first 2 years of life and (2) compare two sequencing approaches (ITS2 amplicon and whole genome metagenomics) for characterizing mycobiome maturational features. Longitudinal fecal samples and associated clinical metadata were obtained from subjects enrolled as part of the MAGIC (Microbiome, Antibiotics and Growth Infant Cohort) study.

RESULTS: Overall, fungal richness increased and mycobiome composition changed in a similar ordered pattern during the first 2 years of life utilizing either amplicon or metagenomic sequencing approaches. Less resolution of taxa to species and genera levels was observed for the metagenomic dataset. The predominant taxa identified by both sequencing approaches, Candida albicans, Saccharomyces/S. cerevisiae, and Malassezia restricta, each exhibited similar dynamics in abundances and prevalences over the first 2 years of life, irrespective of sequencing approach. Antibiotic exposure and breastfeeding status contributed to time-specific mycobiome compositional variation, results that were consistent for both types of sequence datasets. Candida albicans exhibited altered abundance dynamics in association with perinatal antibiotic exposure and birth mode for both sequencing approaches. Post hoc analyses suggested that the birth mode association could be driven by exposure to perinatal antibiotics in children delivered by cesarean section rather than by birth mode itself.

DISCUSSION: In summary, amplicon and metagenomic sequencing approaches provide generally similar results with respect to mycobiome maturational dynamics and the contribution of clinical variables to variation. Differences in taxa identification by the two approaches likely due to sequence database differences, primer/genome sequence variation, and/or sequencing depth should be taken into consideration.},
}

@article {pmid40469725,
year = {2025},
author = {Moumi, NA and Ahmed, S and Brown, C and Pruden, A and Zhang, L},
title = {ARGContextProfiler: extracting and scoring the genomic contexts of antibiotic resistance genes using assembly graphs.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1604461},
pmid = {40469725},
issn = {1664-302X},
abstract = {Antibiotic resistance (AR) presents a global health challenge, necessitating an improved understanding of the ecology, evolution, and dissemination of antibiotic resistance genes (ARGs). Several tools, databases, and algorithms are now available to facilitate the identification of ARGs in metagenomic sequencing data; however, direct annotation of short-read data provides limited contextual information. Knowledge of whether an ARG is carried in the chromosome or on a specific mobile genetic element (MGE) is critical to understanding mobility, persistence, and potential for co-selection. Here we developed ARGContextProfiler, a pipeline designed to extract and visualize ARG genomic contexts. By leveraging the assembly graph for genomic neighborhood extraction and validating contexts through read mapping, ARGContextProfiler minimizes chimeric errors that are a common artifact of assembly outputs. Testing on real, synthetic, and semi-synthetic data, including long-read sequencing data from environmental samples, demonstrated that ARGContextProfiler offers superior accuracy, precision, and sensitivity compared to conventional assembly-based methods. ARGContextProfiler thus provides a powerful tool for uncovering the genomic context of ARGs in metagenomic sequencing data, which can be of value to both fundamental and applied research aimed at understanding and stemming the spread of AR. The source code of ARGContextProfiler is publicly available at GitHub.},
}

@article {pmid40469537,
year = {2025},
author = {Yu, X and Zou, Y and Li, M and Wang, L and Feng, W and Wei, L and Yang, L and He, J and Bu, H and Li, Y},
title = {Auto-Immune Glial Fibrillary Acidic Protein Astrocytopathy with Active Intrathecal Epstein-Barr Virus: A Single-Center Case Series Report.},
journal = {Neuropsychiatric disease and treatment},
volume = {21},
number = {},
pages = {1119-1130},
pmid = {40469537},
issn = {1176-6328},
abstract = {PURPOSE: Auto-immune glial fibrillary acidic protein (GFAP) astrocytopathy is a disease with unclear mechanisms and no diagnostic and treatment guidelines. Epstein-Barr virus (EBV) infection is reportedly involved in glial activities. However, the relationship between GFAP astrocytopathy and EBV infection is not clear. This study reports a case series of auto-immune GFAP astrocytosis with positive cerebrospinal fluid (CSF) EBV DNA, describing its clinical manifestations and treatment experience.

PATIENTS AND METHODS: In the serial case study, we reported six patients diagnosed with GFAP astrocytopathy having intrathecal EBV.

RESULTS: The significant signs included headache, fever and urination disorder, ataxia, limb weakness, numbness, consciousness disorder, psychological disorder, and blindness, among others. CSF analysis showed increased pressure, white blood cell count, abnormal biochemical components, positive GFAP antibody, and EBV. The positive results of metagenomic next-generation sequencing (mNGS) and PCR in CSF indicated that there might be active replication of EBV in the CSF of patients. The results of EBV-associated antibodies in blood suggest no evidence of acute primary EBV infection in six patients. Initial single antivirus therapy did not show satisfactory effects, but all patients showed improvement in clinical features and laboratory analysis after immunotherapy.

CONCLUSION: This study indicated that intrathecal EBV activity was closely related to auto-immune GFAP astrocytopathy, of which the mechanism remains to be further studied.},
}

@article {pmid40469517,
year = {2025},
author = {Zhang, F and Li, R and Liu, Y and Liang, J and Gong, Y and Xiao, C and Cai, J and Wang, T and You, Q and Zhang, J and Chen, H and Xiao, J and Zhang, Y and Yang, Y and Li, H and Yao, J and Zhang, Q and Zheng, J},
title = {Integrative cross-tissue analysis unveils complement-immunoglobulin augmentation and dysbiosis-related fatty acid metabolic remodeling during mammalian aging.},
journal = {iMeta},
volume = {4},
number = {3},
pages = {e70027},
pmid = {40469517},
issn = {2770-596X},
abstract = {Aging-related decline and adaptation are complex, multifaceted processes that affect various tissues and increase risk of chronic diseases. To characterize key changes in cross-tissue aging, we performed comprehensive proteomic and metabolomic analyses across 21 solid tissues and plasma samples, alongside shotgun metagenomic profiling of fecal microbial communities in young and aged mice. Our findings revealed widespread aging-rewired chronic inflammation, characterized by complement system activation in plasma and universal immunoglobulins accumulation across multiple solid tissues. This inflammatory remodeling significantly enhanced vulnerability to aging-related tissue injury. Moreover, we identified organ-specific and organ-enriched proteins with high functional specificity. Among these, aging-related proteins were closely linked to disorders arising from lipid metabolism dysfunction. Analysis of multi-tissue metabolomic and fecal metagenomic profiles revealed that aging significantly disrupted inter-tissue metabolic coupling, activities of polyunsaturated fatty acids metabolism, and gut microbiota homeostasis. Aged mice exhibited a marked decrease in Escherichia and an increase in Helicobacter, strongly correlating with alterations in omega-3 and omega-6 fatty acid abundances. Through multi-omics integration, we identified key molecular hubs driving organismal responses to aging. Collectively, our study uncovers extensive aging-associated alterations across tissues, emphasizing the interplay between systemic inflammation and dysbiosis-driven fatty acid remodeling. These findings provide deeper insights into the development of healthy aging from a cross-tissue perspective.},
}

@article {pmid40469508,
year = {2025},
author = {Zhao, S and Zhong, H and He, Y and Li, X and Zhu, L and Xiong, Z and Zhang, X and Zheng, N and Morgavi, DP and Wang, J},
title = {Leveraging core enzyme structures for microbiota targeted functional regulation: Urease as an example.},
journal = {iMeta},
volume = {4},
number = {3},
pages = {e70032},
pmid = {40469508},
issn = {2770-596X},
abstract = {Microbial communities play critical roles in various ecosystems. Despite extensive research on the taxonomic and functional diversity of microbial communities, effective approaches to regulate targeted microbial functions remain limited. Here, we present an innovative methodology that integrates core enzyme identification, protein structural characterization, regulator virtual screening, and functional validation to achieve precise microbiome functional regulation. As a proof of concept, we focused on the regulation of urea decomposition by the rumen microbiota in ruminants. Through metagenomic analysis, we identified the core urease gene and its corresponding microbial genome (MAG257) affiliated with the unclassified Succinivibrionaceae, and reconstructed its complete gene cluster. Structural analysis of the urease catalytic subunit (UreC) via cryo-electron microscopy (cryo-EM) revealed detailed features of its active site, guiding molecular docking studies that identified epiberberine, a natural compound with potent urease inhibitory activity. Validation in a rumen simulation system demonstrated that epiberberine significantly reduced urea decomposition and enhanced nitrogen utilization. This study establishes a robust framework that combines structural biology and computational screening to achieve targeted microbiome functional regulation, offering a promising tool for microbiome engineering and broader applications in animal productivity, human health, environmental improvement, and biotechnology.},
}

@article {pmid40469506,
year = {2025},
author = {Li, X and Wu, Y and Yi, B and Chen, M and Zhang, G and Shao, X and Jiang, X and Cui, Y and Chen, L and Dong, X and Zhang, S and Zhao, Y and Deng, Y and Li, X and Wang, Y and Wu, L and Fu, Y and Ran, D and Peng, C and Yang, X and Zhang, L and Wang, Y and Zhu, Y and Sun, D and Ran, Y and Zheng, D and Yin, X and Chen, Y and Long, Y and Wang, W and Zhao, X and Liu, E and Xu, T and Li, Q and Zhong, W},
title = {A multi-centered prospective birth cohort study in Western China.},
journal = {iMeta},
volume = {4},
number = {3},
pages = {e70049},
pmid = {40469506},
issn = {2770-596X},
abstract = {The Western China Birth Cohort (WCBC) is a large-scale, multi-centered, prospective birth cohort study designed to address critical gaps in maternal and child health research in Western China, a region with diverse altitudes, ethnic groups, and unique environmental exposures. WCBC had enrolled 15,093 pregnant women across eight clinical centers in five provinces (Qinghai, Gansu, Guizhou, Chongqing, and Sichuan), spanning from the high-altitude Qinghai-Tibet Plateau to lowland regions. WCBC has collected over 220,000 medical records, 80,000 questionnaires, and 12 different types of biological samples, including peripheral blood, cord blood, dried blood spots, placenta, umbilical cord, decidua, saliva, feces, throat and nasal swabs, vaginal swabs, and breast milk. By integrating advanced multi-omics measurement, including genomics, proteomics, exosome profiling, metabolomics, spatial transcriptomics, single-cell RNA sequencing, culturome, metagenomics, and virosome analysis, WCBC provides a valuable platform to explore gene-environment interplay, early-life determinants of health, and long-term disease risks in diverse populations in Western China.},
}

@article {pmid40468884,
year = {2025},
author = {Lee, Y and Ko, YM and Kwak, YS},
title = {Genetic and Nutritional Dynamics of SynCom in Suppressing Apple Fire Blight.},
journal = {The plant pathology journal},
volume = {41},
number = {3},
pages = {380-391},
doi = {10.5423/PPJ.OA.03.2025.0040},
pmid = {40468884},
issn = {1598-2254},
support = {RS-2020-RD009282//Rural Development Administration/ ; RS-2025-00516084//National Research Foundation of Korea/ ; },
abstract = {Fire blight disease, caused by Erwinia amylovora, occurs in apples and other Rosaceae plants and is known to cause significant economic damage. The pathogen usually infects flowers during the reproductive growth period of plants, colonizes, and penetrates by producing exopolysaccharides in the stigma. A synthetic microbial community (SynCom) is an artificial community of microorganisms designed to enhance host viability. To construct SynCom, we attempted to identify and utilize the microbial characteristics of apple trees that are not infected with the pathogen compared to those that are infected. In our previous study, we composed SynCom with strains expected to reduce the density of fire blight pathogens through microbiome analysis, strain isolation, and continuous replacement culture. We are able to observe the disease control effect of the constructed SynCom. However, no study has been conducted to clearly determine the genetic mechanism underlying this effect of the SynCom. Here, we present that potential secondary metabolite candidates and nutritional competition with the pathogen were confirmed as biochemical mechanisms through whole genome analysis of SynCom strains. Additionally, by co-cultivating SynCom with the pathogen in limited nutrient conditions, such as apple blossom extracts, which are susceptible to the pathogen, we confirmed the potential of SynCom treatment to reduce the pathogen densities. This study demonstrates that genetic selection using metagenomics can effectively identify microorganisms with potential functional capabilities.},
}

@article {pmid40468453,
year = {2025},
author = {Hu, F and Gebeyew, K and Wu, Z and Chen, B and Jiao, J and Tan, Z and Tian, D and He, Z},
title = {Fat-rich diet promotes microbiome-dependent ATP synthesis in sheep model.},
journal = {Journal of animal science and biotechnology},
volume = {16},
number = {1},
pages = {81},
pmid = {40468453},
issn = {1674-9782},
support = {XDA26040304//Strategic Priority Research Program/ ; XDA26050102//Strategic Priority Research Program/ ; 32072760//National Natural Science Foundation of China/ ; 2022JJ10054//Natural Science Foundation of Hunan Province of China/ ; },
abstract = {BACKGROUND: The ketogenic diet that forces adenosine triphosphate (ATP) production by beta-oxidation of fatty acids instead of carbohydrate glycolysis, has gained consensus on host metabolism. However, the mechanisms how a ketogenic diet alters gastrointestinal microbiome and its downstream consequences on microbial nutrient availability and energy metabolism remain to be elucidated. Here, we used the sheep model fed with fat-rich diet to evaluate the symbiotic microbiome across three regions of the gastrointestinal tract (rumen, ileum, and colon) to gain a comprehensive understanding of the microbial energy metabolism and microbe-mediated ATP biosynthesis.

RESULTS: Results showed that sheep fed a fat-rich diet had a greater ADG and increased reliance on fat oxidation for fuel utilization. Metagenomics analysis showed the loss of the specialized fiber-degrading bacteria (genus_Fibrobacter) in the rumen and enrichment of genera RUG420 and Eubacterium, which are involved in lipid metabolism and bile acid processing, in the ileum. A significant functional shift related to energy metabolism was shared across three regions of the gastrointestinal microbiomes. These shifts were dominated by glycolysis/gluconeogenesis and TCA cycle in the rumen and by fatty acid degradation and bile acid transformation in the ileum, indicating adaptation to nutrient availability and energy acquisition. Notably, the abundance of substrate-level phosphorylation (SLP) enzymes was significantly increased in the rumen, ileum and colon, while the ATP-producing capacity through electron transport phosphorylation (ETP) by family_Bacteroidaceae in rumen and Acutalibacteraceae in ileum of sheep with fat-rich diet.

CONCLUSIONS: Altogether, the ATP-related microbiome encoding SLP and ETP in rumen, ileum, and colon contributed 36.95% to the host's weight variation. Our study is the first one demonstrating the microbial potential in the ATP synthesis under the shift in dietary energy source, providing a new perspective on the energy metabolism and precise human macronutrients nutrition.},
}

@article {pmid40468444,
year = {2025},
author = {Tang, Q and Yin, X and Wen, G and Luo, Z and Zhang, L and Tan, S},
title = {Unraveling the composition and function of pig gut microbiome from metagenomics.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {60},
pmid = {40468444},
issn = {2524-4671},
support = {No. [2023] 211//2022 Hunan Province Vocational Education "Chuyi" Action High Level Teacher Team Construction Project/ ; No. [2023] 211//2022 Hunan Province Vocational Education "Chuyi" Action High Level Teacher Team Construction Project/ ; },
abstract = {The gut microbiome plays a crucial role in intestinal maturation, metabolism, and immunoregulation, significantly influencing the host's health and growth performance. This review highlights the use of metagenomic techniques to the composition, function, and dynamic changes of the pig gut microbiota. Research has revealed that environmental and host factors, particularly diet, drive significant variations in microbial composition, which in turn shape host epigenetics through microbial components and metabolites. Furthermore, the strong correlation between the gut microbiota and host health presents opportunities for improving growth performance in the livestock industry.},
}

@article {pmid40468439,
year = {2025},
author = {Ravelo, AD and Ruch, M and Suazo, M and Ferm, P and Su, R and Chen, C and Crooker, BA and Noyes, NR and Salfer, IJ and Caixeta, LS},
title = {Associations between hyperketonemia and the rumen metagenome and metabolome in Holstein cows during the first 2 weeks postpartum.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {59},
pmid = {40468439},
issn = {2524-4671},
support = {1025222//U.S. Department of Agriculture/ ; },
abstract = {Hyperketonemia (HYK) is characterized by elevated levels of blood ketone bodies in dairy cows. Despite previous research on the physiological events related to HYK, associations between the rumen metagenome, metabolome, and HYK have not been well described. Therefore, the objective of this study was to compare rumen metagenome and metabolome profiles of cows with naturally occurring HYK to those without HYK during the first two weeks postpartum. Blood beta-hydroxybutyrate (BHB) concentrations at d 5, 10 and 14 postpartum were used to classify 16 rumen cannulated Holstein cows as either hyperketonemic (+ HYK; ≥1.2 mmol/L BHB at any of the collection days) or non-hyperketonemic (-HYK). Five + HYK cows were identified and were paired with 5 -HYK cows based on parity and calving date. Microbial DNA was extracted from rumen fluid and sequenced using shotgun metagenomics with the Illumina platform. Kraken2 was used to map reads to microbial taxonomic groups and Humann3.8 was used to predict potential functions. Metabolome profiling of rumen fluid was conducted using high-resolution liquid chromatography-mass spectroscopy. MetaboAnalyst6.0 was used to identify potential changes in metabolic pathways. Metagenomes and metabolomes comparisons were conducted using mixed models that included the fixed effects of group, day, their interaction, and the random effect of cow. There was minimal difference detected in alpha diversity for the metagenome, but differences in the metabolome were detected by HYK status. The concentration of asparagine and p-cresol was greater in + HYK cows compared to -HYK, but citrulline was greater in -HYK cows throughout all days considered. On d5 the concentration of ornithine was greater in + HYK compared to-HYK cows, and on d10 acetate was greater in the -HYK cows. There were no differences detected in the pathway analysis from the metabolites quantified by HYK status. Overall, modest differences in rumen metabolome were observed between + HYK and -HYK cows in early lactation. Future studies should explore associations between the rumen environment and HYK as this could be informative for treatment and management practices.},
}

@article {pmid40468436,
year = {2025},
author = {Kilama, J and Islam, MS and Amat, S},
title = {Bovine ocular microbiome: the next frontier in managing Pinkeye in cattle.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {58},
pmid = {40468436},
issn = {2524-4671},
abstract = {Infectious bovine keratoconjunctivitis (IBK), or pinkeye, represents a significant economic challenge to dairy and beef cattle industries resulting in decreased productivity and increased treatment costs. The current IBK prevention and control strategies in cattle face challenges owing to the multifactorial nature of the disease, the rise of antibiotic resistance in IBK pathogens, and inconsistent efficacy of IBK vaccines. Recent efforts in metagenomic characterization of the eye microbiome in humans and animals, including cattle, have revealed that the ocular surface is colonized by relatively diverse and dynamic microbial community that is essential for maintaining ocular health and can be leveraged to enhance resistance against infectious ocular diseases. In this narrative review, we provide comprehensive insights into the ocular microbiota by summarizing the amplicon and metagenomic sequencing- and culture-based studies conducted in cattle, and by reviewing relevant findings from humans and other animal species. We also explore the potential of the ocular microbiome as a new frontier in managing IBK. Finally, we examine the gut-eye-microbiome axis and discuss its potential contribution in improving the resistance of cattle against IBK.},
}

@article {pmid40468430,
year = {2025},
author = {Khoiri, AN and Costa, NR and Crusciol, CAC and Pariz, CM and Costa, C and Calonego, JC and de Castilhos, AM and de Souza, DM and de Lima Meirelles, PR and Cru, IV and Moretti, LG and Bossolani, JW and Kuramae, EE},
title = {Pigeon pea-mediated soil microbial shifts improve agroecosystem multifunctionality in long-term maize-palisade grass intercropping.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {60},
pmid = {40468430},
issn = {2524-6372},
support = {#2014/21772-4 and #2014/14935-4//São Paulo Research Foundation (FAPESP)/ ; #458225/2014-2//National Council for Scientific and Technological Development (CNPq)/ ; 1378/14//Fundação Agrisus/ ; },
abstract = {BACKGROUND: Intercropping systems enhance agricultural sustainability by promoting ecosystem multifunctionality (EMF). This study examined the impact of adding pigeon pea (M + PG + PP) into a maize-palisade grass (M + PG) intercropping system under a no-till system (NTS) on soil microbial communities and ecosystem services. After five consecutive growing seasons, bulk soil samples from a soybean-based crop-livestock system were analyzed using metagenomics.

RESULTS: The inclusion of pigeon pea significantly improved the EMF index, with higher plant productivity and slightly enhanced outcomes in soil health, lamb meat productivity, and climate protection. The M + PG + PP treatment enriched Bradyrhizobium spp., which were positively correlated with soil health, plant productivity, and EMF index. Functional analysis indicated that M + PG + PP treatment enhanced nitrogen metabolism, biofilm formation, and exopolysaccharide (EPS) biosynthesis, improving soil fertility and microbial activity. Similarly, functional analysis of microbial plant growth-promoting traits revealed that the M + PG + PP treatment promoted microbial functions related to nitrogen and iron acquisition, sulfur assimilation, and plant colonization, all essential for plant growth and nutrient cycling. In contrast, the M + PG treatment primarily enhanced pathways related to competitive exclusion and phytohormone production.

CONCLUSIONS: These findings highlight the importance of incorporating legumes such as pigeon pea into intercropping systems to optimize ecosystem services, enhance soil health, and promote long-term agricultural productivity and sustainability.},
}

@article {pmid40468269,
year = {2025},
author = {Li, B and Yang, Y and Xu, B and Song, P and Jiang, F and Gao, H and Cai, Z and Gu, H and Zhang, T},
title = {Comparative macrogenomics reveal plateau adaptation of gut microbiome in cervids.},
journal = {BMC biology},
volume = {23},
number = {1},
pages = {154},
pmid = {40468269},
issn = {1741-7007},
mesh = {*Gastrointestinal Microbiome/genetics ; Animals ; *Deer/microbiology/genetics ; Phylogeny ; Metagenome ; Metagenomics ; *Adaptation, Physiological/genetics ; Energy Metabolism ; Biological Evolution ; },
abstract = {BACKGROUND: Diverse gut microbiota in animals significantly influences host physiology, ecological adaptation, and evolution. However, the specific functional roles of gut microbiota in facilitating host adaptation, as well as the coevolutionary dynamics between microbiota and their hosts, remain largely understudied.

RESULTS: A total of 41,847 metagenome-assembled genomes and 3193 high-quality species-level genome bins were generated, establishing a comprehensive gut microbiome catalog for cervids in this study. Phylogenetic analysis revealed a coevolutionary relationship between cervids and their gut microbiota. Comparative metagenomic analyses further indicated that the gut microbiota of plateau cervids have undergone genome-level adaptations related to energy metabolism. At the genus level, species-level genome bins from the genera Alistipes and Faecousia in plateau cervids exhibit enhanced energy metabolism capabilities. Structural variations analysis revealed that the insertion and duplications structural variations in the gut microbiota of plateau cervids were significantly enriched in energy metabolism pathways. In contrast, the deletions and contractions in structural variations were predominantly enriched with metabolic pathways involved in the biosynthesis of diverse biochemical molecules.

CONCLUSIONS: Our study provides a comprehensive gut microbiome catalog of the cervid gut microbiota, revealing the coevolutionary relationship between cervid gut microbiota and hosts. These findings highlight the adaptive genomic evolution of the gut microbiota in contributing to the plateau adaptability of cervids and offer new insights into the mechanisms by which the gut microbiota help hosts adapt to extreme environments.},
}

*Gastrointestinal Microbiome/genetics
Animals
*Deer/microbiology/genetics
Phylogeny
Metagenome
Metagenomics
*Adaptation, Physiological/genetics
Energy Metabolism
Biological Evolution

@article {pmid40468214,
year = {2025},
author = {Yang, X and Chen, H and Wu, L and Guo, X and Xue, D},
title = {Diversity and correlation analysis of microbiomes and metabolites of Sphagnum palustre in various microhabitats.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {761},
pmid = {40468214},
issn = {1471-2229},
support = {2019QZKK0304//Second Tibetan Plateau Scientific Expedition/ ; QNTS202201//Youth Innovation Program of CIB/ ; 2022376//Youth Innovation Promotion Association of the Chinese Academy of Sciences/ ; 2021JDTD011//Youth Science and Technology Innovation Team Program of Sichuan Province of China/ ; },
mesh = {*Microbiota ; *Sphagnopsida/microbiology/metabolism ; Ecosystem ; Soil Microbiology ; Bacteria/genetics/metabolism ; },
abstract = {BACKGROUND: Sphagnum peat mosses are crucial contributors to global carbon sequestration and are a dominant presence in many northern peatland environments. These mosses host a wide variety of microorganisms, which reside within their tissues and on their surfaces. Despite this close association, the connection between these microorganisms and the production of metabolites across different parts of Sphagnum remains unclear.

RESULTS: This research explored the connection between microbial diversity and metabolite production in various microhabitats of Sphagnum palustre by employing metagenomic and metabolomic techniques. Our results indicate that the S. palustre microbiome composition is more strongly influenced by microhabitat than by geographic location. Microbiome diversity microbiomes related to S. palustre showed a steady decrease from soil to near soil, from X to CAP, and from belowground to aboveground habitats. In contrast, network complexity increased. Species abundance analysis indicated that Proteobacteria was the most prevalent bacterial phylum across CAP, S, Z, and X. Additionally, Ascomycota emerged as the predominant fungal phylum. There were significant differences in nitrogen fixation activity, methane oxidation activity, total nitrogen, and total carbon among different microhabitats. The FAPROTAX analysis revealed differences in the metabolic potential of the carbon (C) and nitrogen (N) cycles across the four microhabitats. LC-MS/MS technology was employed to quantitatively assess metabolites across various S. palustre microhabitats. A total of 3,822 metabolites and 353 differential metabolites were detected, predominantly including lipids, organic acids, and carboxylic acids. The majority of these differential metabolites were associated with metabolic pathways such as carotenoid biosynthesis, steroid biosynthesis, secondary bile acid biosynthesis, as well as the biosynthesis of neomycin, kanamycin, and gentamicin. Correlation analysis revealed both positive and negative relationships between microorganisms and differential metabolites. Methylocystis, which was significantly enriched in X and T, showed a strong positive correlation with differential metabolites in S vs T and Z vs X, but a negative correlation with those in X vs T (p < 0.05).

CONCLUSION: In summary, our study demonstrates that Sphagnum palustre microbiomes are primarily influenced by microhabitats rather than specific environmental conditions at different sites. We identified significant variations in microbial community diversity across various S. palustre microhabitats. Correlation analysis revealed links between microorganisms and differential metabolic processes. This comprehensive investigation of aboveground and belowground microbiomes and metabolites in S. palustre provides new insights into the distribution of microbial communities and metabolites across different microhabitats.},
}

*Microbiota
*Sphagnopsida/microbiology/metabolism
Ecosystem
Soil Microbiology
Bacteria/genetics/metabolism

@article {pmid40468175,
year = {2025},
author = {Lin, Z and Chen, Y and Yu, Z and Zhang, Z and Lin, Y and Zhang, W and Li, W and Guo, Y and Fang, X},
title = {Early and Accurate Pathogen Identification Based on mNGS: Key to Timely Therapy for Mycoplasma Prosthetic Joint Infection.},
journal = {Orthopaedic surgery},
volume = {},
number = {},
pages = {},
doi = {10.1111/os.70069},
pmid = {40468175},
issn = {1757-7861},
support = {2023J01597,2023J01315//Natural Science Foundation of Fujian Province/ ; 2023CXA020//Fujian Medical Innovation Grant, China/ ; },
abstract = {OBJECTIVES: Prosthetic joint infection (PJI) caused by Mycoplasma infection is relatively rare in clinical practice; all cases are primarily reported as individual case reports, and the characteristics of PJI induced by Mycoplasma infection have not been clearly studied. This case-control study was designed to systematically compare demographic profiles, clinical histories, diagnostic modalities, and therapeutic outcomes between Mycoplasma PJI and conventional bacterial PJI through retrospective analysis.

METHODS: This retrospective single-center study included 6 cases of simplex Mycoplasma PJI, 4 cases of mixed Mycoplasma PJI, 33 cases of Staphylococcus aureus, and 21 cases of Staphylococcus epidermidis infection from January 1, 2017 to January 1, 2024. Perioperative inflammatory markers, pathogen cultures, metagenomic next-generation sequencing (mNGS) results, history of invasive urinary catheterization, clinical presentation, treatment, and rate of treatment success were recorded and analyzed for the four groups. Continuous variables were compared two-by-two between the four groups using independent t-tests or the Mann-Whitney U test based on the distribution of the data. The categorical variables were compared using the chi-square test or Fisher's exact test.

RESULTS: The proportion of invasive urinary catheterization history in the mixed versus simplex Mycoplasma group was significantly higher than that in the Staphylococcus aureus and Staphylococcus epidermidis control groups (p < 0.05). Routine microbial culture positivity was significantly lower in the mixed versus simplex Mycoplasma group than in the control group (p < 0.01), but positive results for Mycoplasma can be detected by mNGS. Of note, one patient in the simplex Mycoplasma group was cured with targeted antibiotic-only therapy and avoided surgery. There was no statistically significant difference in cure rates between the mixed and simplex Mycoplasma groups and the Staphylococcus aureus and Staphylococcus epidermidis control groups (p = 1.000).

CONCLUSION: Prior invasive urinary catheterization represents a significant risk factor for Mycoplasma PJI. The synergistic use of mNGS, optimized culture methods, and 16S rRNA PCR enables early detection of Mycoplasma. This multimodal diagnostic approach significantly enhances pathogen identification accuracy, minimizes diagnostic oversights, and provides essential guidance for effective therapeutic intervention.},
}

@article {pmid40468098,
year = {2025},
author = {Srivastava, A and Rai, PK and Agnihotri, VK and Choure, K and Vishvakarma, R},
title = {Metagenomic analysis of viral communities in the polluted Varuna River reveals site-specific diversity patterns associated with environmental aspects.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {40468098},
issn = {1618-1905},
abstract = {Varuna River, which is native to Varanasi, is of great importance as a water reservoir for the people and is contaminated with heavy pollutants due to urbanization. In this study, four sites (VR1, VR2, VR3, and VR4) of Varuna River water were sampled to assess the viral diversity. The metagenomics approach was used to study the viral diversity and functional analysis, suggesting the overall quality of the water at the sampled location. The analysis shows that VR1 had the most species richness (3000 species), followed by VR3 (2500), VR2 (2000), and VR4 (1500). The PCA analysis revealed distinct spatial patterns and community differentiation where VR2 and VR4 clustered while VR1 and VR3 were distant.Diversity analysis showed that Negarnaviricota dominated all samples at the phylum level. Yunchangviricetes, a non-reported virus, and Insthoviricetes were the dominant classes. Pakpunavirus was the leading genus, followed by the human pathogen Mimivirus. The highest species abundance in VR1 and VR2 was Mimivirus, Megavirus, chilensis, while VR3 and VR4 had Hpunavirus and Pseudomonas phage O4, indicating human involvement. Functional analyses of enzymatic activity and KEGG Orthology in microbial communities from VR1 to VR4 samples showed that VR4 exhibited maximal enzymatic activity, genetic flexibility, and advanced regulatory control compared to the other samples. The increased presence of transporter genes alongside signal transduction proteins and metabolic enzymes in VR4 indicates enhanced functional diversity, which aids in coping with environmental stresses. On the basis of viral species, ecological, biotechnological aspects were also interpreted. This study concluded that the Negarnaviricota plays a key role in maintaining the overall water quality and there is an urgent need for remediation of the Varuna River especially at site VR4 (25° 19' 46.7″ N 83° 02' 38.3″ E).},
}

@article {pmid40468041,
year = {2025},
author = {Lin, D and Du, S and Zhao, Z and Zhang, T and Wang, L and Zhang, Q and Zhou, SY and Graham, DW and Tissue, DT and Zhu, D and Zhu, YG and Penuelas, J and Reich, PB},
title = {Climate warming fuels the global antibiotic resistome by altering soil bacterial traits.},
journal = {Nature ecology & evolution},
volume = {},
number = {},
pages = {},
pmid = {40468041},
issn = {2397-334X},
support = {2023321//Youth Innovation Promotion Association of the Chinese Academy of Sciences (Youth Innovation Promotion Association CAS)/ ; 42222701//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42090063//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Understanding the implications of global warming on the spread of antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) within soil ecosystems is crucial for safeguarding human well-being and sustaining ecosystem health. However, there is currently a lack of large-scale, systematic underpinning data needed to examine this issue. Here, using an integrative approach that combines field experiments, extensive global metagenomic data and microbial culturing, we show that warming enriches bacteria with ARGs and VFGs, increases metabolic complexity and adaptability in bacteria, and accelerates genetic alterations related to ARG and VFGs development. Our validation experiments confirm that the warming effect is more pronounced in colder regions. Machine learning predictions further suggest that warming will increase the soil ARG abundance, especially in some areas that rely heavily on fossil fuels. These results suggest another major negative consequence of global warming, highlighting the importance of developing and implementing sustainability policies that simultaneously combat climate change and antibiotic resistance.},
}

@article {pmid40467587,
year = {2025},
author = {Xiong, S and Xie, B and Yin, N and Zhu, H and Gao, H and Xu, X and Xiao, K and Cai, X and Sun, G and Sun, X and Cui, Y and Van de Wiele, T and Zhu, Y},
title = {Prenatal exposure to trace elements impacts mother-infant gut microbiome, metabolome and resistome during the first year of life.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {5186},
pmid = {40467587},
issn = {2041-1723},
support = {No. L232076//Natural Science Foundation of Beijing Municipality (Beijing Natural Science Foundation)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/genetics ; Female ; Pregnancy ; Infant ; *Trace Elements/adverse effects ; *Metabolome/drug effects ; Feces/microbiology ; *Prenatal Exposure Delayed Effects/microbiology/metabolism ; Adult ; Male ; Metagenomics ; Hair/chemistry ; *Maternal Exposure/adverse effects ; Infant, Newborn ; Bacteria/genetics/classification/drug effects ; Copper ; },
abstract = {Infancy is a critical window for the colonization of gut microbiome. However, xenobiotic impacts on gut microbiome development in early life remain poorly understood. Here, we recruit 146 mother-infant pairs and collect stool samples at 3, 6, and 12 months after delivery for amplicon sequencing (N = 353), metagenomics (N = 65), and metabolomics (N = 198). Trace elements in maternal hair samples (N = 119) affect diversity and composition of the infant gut microbiome. Shannon diversity in 3 month-old infants is correlated positively with selenium and negatively with copper, and relative abundance of Bifidobacterium increases under high exposure to aluminum and manganese. During the first year of life, infants and their paired mothers have distinct microbial diversity and composition, and their bacterial community structures gradually approach. here are 56 differential metabolites between the first and second visit and 515 differential metabolites between the second and third visit. The typical profile of antibiotic resistance genes (ARGs) significantly differs between infants and their mothers. High levels of copper and arsenic exposure may induce the enrichment of ARGs in the infant gut. Our findings highlight the dynamics of the gut microbiome, metabolites, and ARG profiles of mother-infant pairs after delivery, associated with prenatal exposure to trace elements.},
}

Humans
*Gastrointestinal Microbiome/drug effects/genetics
Female
Pregnancy
Infant
*Trace Elements/adverse effects
*Metabolome/drug effects
Feces/microbiology
*Prenatal Exposure Delayed Effects/microbiology/metabolism
Adult
Male
Metagenomics
Hair/chemistry
*Maternal Exposure/adverse effects
Infant, Newborn
Bacteria/genetics/classification/drug effects
Copper

@article {pmid40467492,
year = {2025},
author = {Tonomura, S and Hattori, Y and Ishibashi, T and Ikeda, S and Noda, K and Chiba, T and Kato, Y and Asano, R and Fukuma, K and Edamoto-Taira, Y and Motooka, D and Inagaki, T and Okazawa, M and Nakamura, S and Koga, M and Toyoda, K and Nomura, R and Nakano, K and Friedland, RP and Takeda, K and Takahashi, R and Ihara, M and Nakaoka, Y},
title = {Oral Pathobiont Streptococcus Anginosus Is Enriched in the Gut of Stroke Patients and Predicts 2-Year Cardiovascular Outcome.},
journal = {Circulation journal : official journal of the Japanese Circulation Society},
volume = {},
number = {},
pages = {},
doi = {10.1253/circj.CJ-24-0872},
pmid = {40467492},
issn = {1347-4820},
abstract = {BACKGROUND: Several cross-sectional studies have implicated gut dysbiosis caused by an abundance of oral commensals in stroke, but the effect on long-term prognosis is still unknown. Therefore, we longitudinally investigated oral pathobionts in the gut and their clinical relevance to stroke.

METHODS AND RESULTS: We analyzed the salivary and gut microbiomes collected from 189 acute stroke and 55 non-stroke subjects, and found that Streptococcus anginosus was significantly more abundant in both the saliva (median [IQR], 0.01 [0.00-0.14] vs. 0.00 [0.00-0.03], P=0.02) and gut (0.09 [0.00-0.28] vs. 0.00 [0.00-0.02], P<0.001) of the stroke patients compared with their non-stroke counterparts. Network analysis revealed S. anginosus as a central hub in gut dysbiosis. After adjusting for vascular risks, S. anginosus (odds ratio 1.20, 95% confidence interval 1.06-1.36, P<0.01), Anaerostipes hadrus (0.82, [0.73-0.93], P<0.01), and Bacteroides plebeius (0.86, [0.86-0.93], P=0.01) in the gut were independent predictors of stroke. Longitudinally, S. anginosus in the gut was significantly associated with increased rates of death and major cardiovascular events (P=0.04; log-rank test), whereas A. hadrus and B. plebeius were not (P=0.45 and P=0.19). After adjusting for vascular risks, S. anginosus in the gut was a residual risk for increased rates of death and major cardiovascular events (hazard ratio 4.78, 95% confidence interval 1.08-21.18, P=0.04)Conclusions: S. anginosus in the gut may increase the risk of stroke and a poor prognosis.},
}

@article {pmid40467356,
year = {2025},
author = {Messadi, A and Sayhi, S and Ghedira, K and Zaouaoui, C and Arfaoui, B and Khouikhi, S and Rebai, M and Guediche, NEH and Abdelhafidh, N and Louzir, B and Faida, A},
title = {Microbial diversity investigation using 16S metagenomics in Tunisian patients with systemic lupus erythematosus.},
journal = {Revista Argentina de microbiologia},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ram.2025.04.002},
pmid = {40467356},
issn = {0325-7541},
abstract = {Systemic lupus erythematosus (SLE) is a multisystemic autoimmune disease associated with significant morbidity and mortality. It is characterized by a loss of self-immune tolerance and autoantibody production, leading to multiple organ damage. Emerging investigations have confirmed the role of gut microbiota dysbiosis in patients with SLE, although the underlying mechanisms remain unclear to date. In this study, we aim to investigate the bacterial profile of SLE including phylum/class/genus relative abundance and diversity, to compare them with healthy controls and to study the correlation of relative abundance of different patterns with clinical/biological parameters. In this case-control study, the bacterial profile was investigated in 7 SLE patients and 7 healthy controls using 16S metagenomics clustering. The present study reported a low abundance of the class Bacilli (0.58% in SLE vs 1.26% in the controls), the genus Lactobacillus (0.43% vs 0.74%), as well as a higher abundance of the genera Gammaproteobacteria (2.37% vs 0.77%) and Escherichia-Shigella (2.04% vs 0.51%) in SLE samples compared to the controls (p<0.05). We also found an association between the class Betaproteobacteria (4.42% vs 1.57%) and the genus Faecalibacterium (11.34% vs 3.35%) and renal manifestations (p<0.05). The phylum Actinobacteria (0.21% vs 3.8%, p=0.036) and the genus Bifidobacterium levels were lower in active SLE compared to the healthy controls. This study is the first report on the gut microbiota of SLE and the first case-control study in Tunisia and North Africa. We obtained a particular profile of bacterial gut microbiota for the SLE group. We found a specific clustering when compared to the healthy controls.},
}

@article {pmid40467297,
year = {2025},
author = {Waterworth, SC and Egbert, S and Sorensen, J and O'Keefe, BR and Beutler, JA},
title = {A Biosynthetic and Taxonomic Atlas of the Global Lichen Holobiont.},
journal = {Environmental microbiology},
volume = {27},
number = {6},
pages = {e70112},
doi = {10.1111/1462-2920.70112},
pmid = {40467297},
issn = {1462-2920},
support = {//Natural Sciences and Engineering Research Council of Canada/ ; ZIA BC 011471/CA/NCI NIH HHS/United States ; ZIA BC 011469/CA/NCI NIH HHS/United States ; },
mesh = {*Lichens/microbiology/classification/genetics ; *Bacteria/genetics/classification/metabolism/isolation & purification ; *Fungi/genetics/classification/metabolism/isolation & purification ; Multigene Family ; Biosynthetic Pathways/genetics ; Phylogeny ; Secondary Metabolism ; Metagenomics ; Metagenome ; Symbiosis ; },
abstract = {Lichens are pioneer species in several ecosystems, and as such are found in a variety of geographic regions and environments. Here, inspection of metagenomic data from 794 lichen samples from 34 countries reveals the presence of a complex holobiont harbouring remarkable biosynthetic capabilities, particularly in the bacterial consortia, a component that has been somewhat underappreciated. While bacteria were consistently present, their abundance varied among lichen taxa. Common bacterial genera included Microbacterium, Terribacillus, and JABEUN01 (an Acidimicrobiaceae bacterium awaiting Latin binomial naming assignment) albeit in low abundance. Lichenihabitans and Sphingomonas genera were moderately abundant, present in approximately 30% of samples, and exhibited an enrichment in the number of biosynthetic gene clusters (BGCs) predicted to encode secondary metabolites (biosynthetic potential). We found that both fungal and bacterial biosynthetic repertoires appeared to follow genus-specific patterns but that there was greater relative homogeneity of BGCs in the fungal genera. The substantial biosynthetic diversity within lichen holobionts is evident in our findings, with the lichen-associated bacteria emerging as a promising potential source for sustainable drug discovery.},
}

*Lichens/microbiology/classification/genetics
*Bacteria/genetics/classification/metabolism/isolation & purification
*Fungi/genetics/classification/metabolism/isolation & purification
Multigene Family
Biosynthetic Pathways/genetics
Phylogeny
Secondary Metabolism
Metagenomics
Metagenome
Symbiosis

@article {pmid40467244,
year = {2025},
author = {Li, S and Rao, C and Zang, X and Yang, Y and Yang, W and Huang, X and Li, J and Sun, J and Liu, Y and Ye, D},
title = {Characterization of aroma active compounds and microbial communities in spontaneously fermented Vitis quinquangularis wines.},
journal = {Food research international (Ottawa, Ont.)},
volume = {214},
number = {},
pages = {116676},
doi = {10.1016/j.foodres.2025.116676},
pmid = {40467244},
issn = {1873-7145},
mesh = {*Wine/analysis/microbiology ; *Fermentation ; *Vitis/microbiology/chemistry ; *Odorants/analysis ; *Volatile Organic Compounds/analysis ; Gas Chromatography-Mass Spectrometry ; *Microbiota ; *Food Microbiology ; },
abstract = {This study comprehensively investigated volatile compounds and microbial communities of spontaneously fermented Vitis quinquangularis wines from the Guangxi production regions. The aroma profiles of V. quinquangularis wines were analyzed by GC-O-MS, GC-QQQ-MS/MS, and quantitative descriptive analysis. The wines exhibit predominantly fruity and floral notes, with contributions from esters and (E)-β-damascenone. A distinctive and typical "green and earthy" aroma was observed, with contributions from C6 compounds and volatile phenols such as 1-hexanol, (E)-3-hexen-1-ol, hexanoic acid, 4-vinylguaiacol, eugenol, and isoeugenol. Metagenomics and culturomics analyses indicated that the dominant strains involved in the spontaneous fermentation process were Hanseniaspora opuntiae, Saccharomyces cerevisiae, Paenibacillus sp., Sphingomonas sp., and Bacillus sp. Additionally, microorganisms from sixteen generas, including Actinomycetospora and Ameyamaea, etc., along with six enzymes like EC 1.1.1.1 and EC 1.1.1.318, etc., were implicated in the production of the "green and earthy" aroma in V. quinquangularis wines.},
}

*Wine/analysis/microbiology
*Fermentation
*Vitis/microbiology/chemistry
*Odorants/analysis
*Volatile Organic Compounds/analysis
Gas Chromatography-Mass Spectrometry
*Microbiota
*Food Microbiology

@article {pmid40467108,
year = {2025},
author = {Ghensi, P and Heidrich, V and Bazzani, D and Asnicar, F and Armanini, F and Bertelle, A and Dell'Acqua, F and Dellasega, E and Waldner, R and Vicentini, D and Bolzan, M and Trevisiol, L and Tomasi, C and Pasolli, E and Segata, N},
title = {Shotgun Metagenomics Identifies in a Cross-Sectional Setting Improved Plaque Microbiome Biomarkers for Peri-Implant Diseases.},
journal = {Journal of clinical periodontology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jcpe.14121},
pmid = {40467108},
issn = {1600-051X},
support = {//Italian Society of Periodontology and Implantology (SIdP)/ ; //Eklund Foundation/ ; //International Team for Implantology (ITI)/ ; /ERC_/European Research Council/International ; //CLC Scientific S.r.l./ ; //PreBiomics S.r.l./ ; },
abstract = {AIM: This observational study aimed to verify and improve the predictive value of plaque microbiome of patients with dental implant for peri-implant diseases.

MATERIALS AND METHODS: Patients were included in one of the following study groups according to the health status of their dental implants: (a) healthy, (b) affected by mucositis and (c) affected by peri-implantitis. From each patient, submucosal plaque microbiome samples were collected from the considered dental implant and from a contralateral healthy implant/tooth. After shotgun metagenomic sequencing, the plaque microbiome was profiled taxonomically and functionally with MetaPhlAn 4 and HUMAnN 3, respectively. Taxonomic and functional profiles were fed into machine-learning models, which were then evaluated with cross-validation to assess the extent to which the plaque microbiome could be used to pinpoint peri-implant diseases.

RESULTS: Shotgun metagenomics sequencing was performed for a total of 158 samples spanning 102 individuals. Four-hundred and forty-seven prokaryotic species were identified as part of the peri-implant microbiome, 34% of which were currently uncharacterized species. At the community level, the peri-implant microbiome differed according to the health status of the implant (p ≤ 0.006 for all pairwise comparisons) but this was site-specific, as healthy contralateral sites showed no discriminating microbiome features. Peri-implantitis microbiomes further showed lower inter-subject variability than healthy plaque microbiomes (p < 0.001), while mucositis-associated microbiomes were in the middle of the continuum between health and peri-implantitis. Each health condition was associated with a strong signature of taxonomic and functional microbiome biomarkers (log10 LDA score ≥ 2.5), 30% and 13% of which represented uncharacterized microbial functions and unknown species, respectively. Distinct Fusobacterium nucleatum clades were associated with implant status, highlighting the subspecies F. nucleatum's functional and phenotypic diversity. Machine-learning models trained on taxonomic or functional plaque microbiome profiles were highly accurate in differentiating clinical groups (AUC = 0.78-0.96) and highlighted the extent to which the peri-implant microbiome is associated with peri-implant clinical parameters (AUC = 0.79-0.87).

CONCLUSIONS: Plaque microbiome profiling with shotgun metagenomics revealed consistent associations between microbiome composition and peri-implant diseases. In addition to pointing to peri-implant-associated microbes, warranting further mechanistic studies, we showed high-resolution plaque microbiome evaluation via metagenomics as an effective tool. Its utility within protocols for clinical management of peri-implant diseases should be explored in the future.},
}

@article {pmid40467013,
year = {2025},
author = {Valmas, MI and Kormas, K and Karpouzas, DG and Konstantinidis, KT and Rozman, SD and Udiković-Kolić, N and Remus-Emsermann, MNP and Vasileiadis, S},
title = {Targeted analysis of metagenomes: divide and conquer.},
journal = {Biotechnology advances},
volume = {},
number = {},
pages = {108619},
doi = {10.1016/j.biotechadv.2025.108619},
pmid = {40467013},
issn = {1873-1899},
abstract = {The rapidly developing field of targeted analysis of metagenomes focuses on retrieving information about specific genes and/or genome(s) from environmental DNA. The traditional shotgun sequencing methods overemphasise dominant microorganisms and often fail to confidently assign the entirety of the analysed genetic material to specific species, genomovars, or strains. The ultimate goal of the targete methods is to overcome this limitation of throughput and precision of current shotgun metagenomics when analysing complex microbial communities in the quest of refined information. Here, we discuss recent technological advances that are designed to focus the analytical power of diagnostic tools like sequencing, towards phylogenetically or functionally distinct and rare microbial groups and enhance e.g. the confidence in the assignment of genetic elements to their respective owning organisms. We specifically showcase the capabilities of these technological advances for targeted analysis of metagenomes, identify suitable related applications, discuss methodological limitations, and propose solutions for addressing these limitations. This review aspires to inspire highly relevant experimental designs in the future that will unlock unknown and important aspects of microbial ecology, and the yet-uncultivated microbial majority.},
}

@article {pmid40467000,
year = {2025},
author = {Potrykus, M and Kurpas, M and Gałęzowska, G and Gajewska, M},
title = {Linking Chemical Contamination to Composition of Bacterial Communities in Urban Beach Sands of a Brackish Sea Under Anthropogenic Pressure.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126596},
doi = {10.1016/j.envpol.2025.126596},
pmid = {40467000},
issn = {1873-6424},
abstract = {The water quality on recreational beaches is constantly monitored. However, given that beachgoers often spend more time in contact with the sand than the seawater, it is essential to also regularly assess beach sand quality. In this study, 34 beach sand samples were collected in seven locations along the south shore of the Baltic Sea (Europe) between 2022 and 2023. The samples were obtained from recreational beaches with significant anthropogenic pressure. Since the use of new chemicals is widespread, it is imperative to not only monitor known contaminants but also to actively search for the presence of new ones in the environment. In order to establish the connection between the bacterial biodiversity and their possible resilience in the contaminated marine environment, the bacterial abundances in the beach sand were compared based on 16S rDNA sequencing with chemical contamination examined with non-targeted GC-MS. One hundred forty-nine (149) distinct chemicals were detected, many of which are of human health concern. The presence of polycyclic aromatic hydrocarbons, plasticizers and benzothiazoles in the sand samples was observed, and these contaminants were found to be associated with alterations in the bacterial community structure, characterized by a decrease or increase in certain taxonomic groups. Notably, the bacterial communities exhibited specificity to each location and demonstrated stability throughout the seasons. Furthermore, the presence of DNA from 31 potential human pathogens was detected in the sand. These findings emphasize the necessity for regular monitoring of beach sand for the presence of toxic chemicals and pathogens to safeguard public health and the environment.},
}

@article {pmid40466780,
year = {2025},
author = {Yang, Y and Abdelfattah, A and Jia, H and Kumar, V and Jiang, Y and Cheng, L},
title = {Enhanced nitrogen removal by Comamonas 110 colonization and bioaugmentation in sequencing batch activated sludge bioreactor.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132759},
doi = {10.1016/j.biortech.2025.132759},
pmid = {40466780},
issn = {1873-2976},
abstract = {While pure functional strains demonstrate high pollutant removal efficiency, their environmental persistence remains challenging. This study optimized Comamonas 110 inoculation strategies in activated sludge systems, enhancing nitrogen removal efficiency (44 % of nitrogen removal at day 180) and achieving stable colonization (15.22 % abundance at day 180) through 30 % initial dosage combined with operational parameter regulation. Monod modeling and 16S rRNA sequencing revealed Comamonas 110 suppressed Nitrite-Oxidizing Bacteria (NOB) while boosting Ammonia-Oxidizing Bacteria (AOB). Denitrifying enzymes (NAR and NIR) increased significantly in inoculated reactors, attributing to the substantial presence of Comamonas 110. Metagenomics revealed upregulated (tricarboxylic acid) TCA cycle genes and nitrogen metabolism pathways, optimizing electron transfer for denitrification. Concurrently, Extracellular Polymeric Substance (EPS) synthesis-related genes were activated, promoting co-aggregation with native EPS-producing microbes. This study provides new insights into colonization dynamics of bioaugmentation strains through microbiome-environment interplay.},
}

@article {pmid40466474,
year = {2025},
author = {Zhang, J and Zeng, W and Meng, Q and Liu, H and Lu, Y and Li, S and Peng, Y},
title = {Insights into synergistic metabolism mechanisms of carbon, nitrogen and phosphorus in Tetrasphaera-dominated partial denitrifying phosphorus removal and anammox (PDPRA) process.},
journal = {Water research},
volume = {284},
number = {},
pages = {123901},
doi = {10.1016/j.watres.2025.123901},
pmid = {40466474},
issn = {1879-2448},
abstract = {The partial denitrifying phosphorus removal coupled with anammox (PDPRA) technology holds great promise for the simultaneous removal of carbon, nitrogen, and phosphorus. However, its widespread application is hindered by the instability of nitrite accumulation and the strong dependence on volatile fatty acids (VFAs) of traditional denitrifying polyphosphate accumulating organisms (DPAOs). This study first proposes coupling partial denitrifying phosphorus removal, driven by Tetrasphaera, a novel fermentative DPAO, with anammox for efficiently treating wastewater rich in complex organic matter (e.g., amino acids and proteins). A comprehensive investigation was conducted on the synergistic metabolic mechanisms between DPAOs and anammox bacteria (AnAOB). Under a low carbon to nitrogen (C/N) ratio of 3.1 ± 0.1, Tetrasphaera utilized intracellular amino acids, particularly proline, to drive the stable and efficient nitrite accumulation, leading to a contribution of 82.64 % to total nitrogen removal through anammox. This PDPRA system ultimately achieved remarkable removal efficiency of chemical oxygen demand (COD, 84.8 ± 0.8 %), total inorganic nitrogen (TIN, 92.3 ± 0.9 %) and orthophosphate (PO4[3-]-P, 92.0 ± 1.5 %). Microbial community analysis and metagenomic sequencing revealed the high abundance of Tetrasphaera and Candidatus Brocadia, with their high contribution to key functional genes (narGHI, napAB, ppk1, ppk2, hzs, hdh) confirming the co-existence and co-prosperity metabolic relationship between DPAO and AnAOB. Additionally, an even spatial distribution of Tetrasphaera and AnAOB within the biofilm was developed, further ensuring the stable and efficient removal performance. The findings of this study contribute to the broader application of the PDPRA process and provide a new approach for treating wastewater containing complex organic matter.},
}

@article {pmid40465720,
year = {2025},
author = {de Porto, AP and Dylla, NP and Stutz, M and Lin, H and Khalid, M and Mullowney, MW and Little, J and Rose, A and Moran, D and McMillin, M and Burgo, V and Smith, R and Woodson, C and Metcalfe, C and Ramaswamy, R and Lehmann, C and Odenwald, M and Bandealy, N and Zhao, J and Kim, M and Adler, E and Sundararajan, A and Sidebottom, A and Kress, JP and Wolfe, KS and Pamer, EG and Patel, BK},
title = {Fecal metabolite profiling identifies critically ill patients with increased 30-day mortality.},
journal = {Science advances},
volume = {11},
number = {23},
pages = {eadt1466},
doi = {10.1126/sciadv.adt1466},
pmid = {40465720},
issn = {2375-2548},
mesh = {Humans ; *Critical Illness/mortality ; *Feces/microbiology/chemistry ; Male ; Female ; Middle Aged ; *Gastrointestinal Microbiome ; Aged ; Intensive Care Units ; *Metabolome ; Dysbiosis/mortality/microbiology ; Metabolomics/methods ; Prospective Studies ; },
abstract = {Critically ill patients admitted to the medical intensive care unit (MICU) have reduced intestinal microbiota diversity and altered microbiome-associated metabolite concentrations. Metabolites produced by the gut microbiota have been associated with survival of patients receiving complex medical treatments and thus might represent a treatable trait to improve clinical outcomes. We prospectively collected fecal specimens, defined microbiome compositions by shotgun metagenomic sequencing, and quantified microbiota-derived fecal metabolites by mass spectrometry from 196 critically ill patients admitted to the MICU for non-COVID-19 respiratory failure or shock to correlate microbiota features and metabolites with 30-day mortality. Microbiota compositions of the first fecal sample after MICU admission did not independently associate with 30-day mortality. We developed a metabolic dysbiosis score (MDS) that uses fecal concentrations of 13 microbiota-derived metabolites, which predicted 30-day mortality independent of known confounders. The MDS complements existing tools to identify patients at high risk of mortality by incorporating potentially modifiable, microbiome-related, independent contributors to host resilience.},
}

Humans
*Critical Illness/mortality
*Feces/microbiology/chemistry
Male
Female
Middle Aged
*Gastrointestinal Microbiome
Aged
Intensive Care Units
*Metabolome
Dysbiosis/mortality/microbiology
Metabolomics/methods
Prospective Studies

@article {pmid40465264,
year = {2025},
author = {Liu, M and Geng, J and Jin, S and Hu, P and Wang, X and Liu, X},
title = {Alterations of the Enteric Virome in Vogt-Koyanagi-Harada Disease.},
journal = {Investigative ophthalmology & visual science},
volume = {66},
number = {6},
pages = {15},
doi = {10.1167/iovs.66.6.15},
pmid = {40465264},
issn = {1552-5783},
mesh = {Humans ; *Uveomeningoencephalitic Syndrome/virology/microbiology ; Male ; Female ; *Virome/genetics ; Adult ; Case-Control Studies ; RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome ; Middle Aged ; Bacteria/genetics ; Metagenomics ; Young Adult ; },
abstract = {PURPOSE: This study aims to explore the enteric virome characteristics of Vogt Koyanagi Harada (VKH) disease and its potential role in this disease.

METHODS: Shotgun metagenomic sequencing was used to detect the enteric virome and 16S rRNA to detect the bacteriome in new-onset, untreated patients with VKH (n = 25) and age- and sex-matched healthy controls without autoimmune diseases (n = 25).

RESULTS: Patients with VKH exhibited different enteric viral communities from healthy controls, characterized by decreased richness of core viral communities (present in > 80% of samples) and increased richness of common viral communities (present in 50%-80% of samples). Notably, within the core virus community, bacteriophage richness was markedly reduced, whereas eukaryotic virus richness significantly increased in patients with VKH. The case-control analysis identified 42 differentially abundant viruses, including a decrease in crAss-like phages, the eukaryotic virus Moumouvirus_moumou, and an enrichment of the Chlamydiamicrovirus_CPG1. Most of the differential phages predominantly targeted bacteria from the phyla Pseudomonadota and Firmicutes. The gut virome-bacteria community correlation analysis revealed a shift in the interactions between the core viruses and bacterial communities. Additionally, Wroclawvirus PA5oct (a Pseudomonas phage) correlated with leukotrichia, a clinically relevant symptom of VKH (P = 0.042). The impact of multiple Pseudomonas phages on the host folate biosynthesis was significantly enhanced in patients with VKH. Moreover, the protein (Earp361-372) encoded by VKH-enriched Pseudomonas was identified to share homology with the melanin antigen gp10044-59.

CONCLUSIONS: The gut virome of patients with VKH differs significantly from healthy controls, suggesting its disturbance may contribute to gut microbiome imbalance and VKH development.},
}

Humans
*Uveomeningoencephalitic Syndrome/virology/microbiology
Male
Female
*Virome/genetics
Adult
Case-Control Studies
RNA, Ribosomal, 16S/genetics
*Gastrointestinal Microbiome
Middle Aged
Bacteria/genetics
Metagenomics
Young Adult

@article {pmid40464977,
year = {2025},
author = {Lewis, R and Hammond, R and Wilkinson, M and Allenby, N},
title = {Technological developments driving industrial natural product discovery.},
journal = {Natural product reports},
volume = {},
number = {},
pages = {},
doi = {10.1039/d4np00072b},
pmid = {40464977},
issn = {1460-4752},
abstract = {Covering: up to 2025Bacterial natural products have long been the foundation for many therapeutic agents. However, traditional culture-based approaches to discovering these products have been deprioritised by pharmaceutical companies, primarily due to the high rates of rediscovery. To revitalise the pipeline of new drugs, especially antibiotics-an area where natural products have historically played a crucial role-new technologies are essential. Culture-independent, or metagenomic, techniques combined with long-read sequencing technologies are now enabling the identification of novel biosynthetic gene clusters (BGCs). When paired with the heterologous expression of DNA extracted directly from environmental samples (eDNA), these approaches may provide access to untapped microbial biosynthetic diversity. This review explores industrial screening for new compounds and examines how modern technologies such as metagenomics, in situ cultivation, and pico-droplet-based screening are advancing the search for novel natural products. These approaches have the potential to greatly expand the discovery of new bioactive compounds, helping to address the growing need for new therapeutic agents.},
}

@article {pmid40464921,
year = {2025},
author = {Shropshire, WC and Hanson, BM and Shelburne, SA},
title = {Genome-wide approaches to bacterial strain typing: a history and review of recent methodological advances.},
journal = {Current opinion in infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1097/QCO.0000000000001118},
pmid = {40464921},
issn = {1473-6527},
abstract = {PURPOSE OF REVIEW: Whole genome sequencing (WGS) has transformed bacterial strain typing, an essential tool for outbreak detection, antimicrobial resistance surveillance, and tracking clonal emergence across clinical, research, and public health settings. Herein, we will review recent advances in WGS-based bacterial strain typing methods for purposes of comparison and classification with a focus on improvements in variant identification, strain classification, and transmission assessment.

RECENT FINDINGS: Advances in sequencing technologies as well as variant calling methodologies and parameter optimization have enhanced the precision and accuracy of single nucleotide variant identification. Hierarchical clustering of gene-by-gene strain typing, combined with novel data management and classification strategies, has improved standardized pathogen typing schemes in an effort to streamline inter-laboratory comparison. Additionally, novel approaches to defining transmission thresholds now better account for species-specific traits, while progress in metagenomic sequencing enables strain identification and tracking within mixed microbial communities.

SUMMARY: Recent developments have enhanced the accuracy, portability, scalability, and standardization of bacterial typing methods, integrating variant calling and gene-by-gene approaches into unified genotyping systems. However, challenges still remain in nomenclature consistency, inter-laboratory variant calling compatibility, and capturing bacterial heterogeneity. Future work should focus on refining genotyping frameworks to enhance surveillance and optimize detection of pathogen transmission while accounting for microbial diversity across various environments.},
}

@article {pmid40464915,
year = {2025},
author = {Kim, R and Oh, S and Woo, KA and Shin, CM and Park, KU and Lee, JY},
title = {Blood microbiome signatures in the REM sleep behavior disorder-Lewy body disease continuum.},
journal = {Journal of neural transmission (Vienna, Austria : 1996)},
volume = {},
number = {},
pages = {},
pmid = {40464915},
issn = {1435-1463},
abstract = {Although systemic inflammation triggered by alterations in microbiota from various body sites has been proposed as a potential mechanism underlying Lewy body diseases (LBDs), the association between the blood microbiome and LBDs remains uncertain. This study aimed to investigate the blood microbiome profiles across the REM sleep behavior disorder (RBD)-LBD continuum and to explore their potential as biomarkers reflecting disease phenotypes and clinical severity. Blood samples were collected from 106 patients across the RBD-LBD continuum, including 41 with isolated RBD (iRBD), 45 Parkinson's disease with probable RBD, and 20 dementia with Lewy bodies with probable RBD, as well as from 94 healthy controls. All patients were evaluated with the Movement Disorder Society-Unified Parkinson's Disease Rating Scale (MDS-UPDRS) and comprehensive neuropsychological tests. Microbiome taxonomic compositions were analyzed using 16 S rRNA metagenomic sequencing. Significant microbial shifts were observed in the RBD-LBD continuum group compared to controls, with reduced microbial alpha diversity and distinct beta diversity patterns. Specifically, the genus Stenotrophomonas was enriched, while the genera Acetobacter, Enhydrobacter, and Lactobacillus were depleted in the RBD-LBD continuum group. The combined model using these genera demonstrated high predictive accuracy for the RBD-LBD continuum, with the area under the receiver-operating-characteristic curve (AUC) of 0.970 (95% confidence interval [CI]: 0.950-0.980). This model also successfully distinguished the iRBD subgroup from controls, achieving an AUC of 0.956 (95% CI, 0.914-0.987). Alpha and beta diversity were significantly associated with MDS-UPDRS Parts I and II scores in the RBD-LBD continuum group. Our findings suggest that patients within the RBD-LBD continuum may share specific blood microbiome signatures.},
}

@article {pmid40464558,
year = {2025},
author = {Ruan, Y and Zhu, T and Yang, R and Su, F and An, C and Hu, Z and Li, X and Li, Y and Chen, P and Shao, X and Qin, J and Chen, H and Chen, R},
title = {Donor-derived microbial engraftment and gut microbiota shifts associated with weight loss following fecal microbiota transplantation.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0012025},
doi = {10.1128/aem.00120-25},
pmid = {40464558},
issn = {1098-5336},
abstract = {Fecal microbiota transplantation (FMT) is a promising treatment for microbiota dysbiosis and may provide metabolic benefits for obesity. However, its mechanisms and variability in clinical outcomes remain poorly understood. This 12-week multicenter, single-arm study evaluated the efficacy of FMT for weight loss and explored the role of donor-derived microbial engraftment and functional shifts in mediating weight loss among overweight and obese individuals. Twenty-three participants (body mass index ≥24 kg/m[2]) without diabetes received three biweekly FMT sessions via a nasojejunal tube. Fecal samples from participants and donors were analyzed using metagenomic sequencing. By week 12, 52% of participants were classified as responders, achieving significant weight loss of ≥5% from baseline, with an average weight loss of 7.98 ± 2.69 kg (P < 0.001). In contrast, non-responders lost 2.90 ± 1.89 kg (P < 0.001). Responders exhibited a significantly higher proportion of donor-derived microbial strains post-FMT compared to non-responders (37.8% vs 15.2%, P = 0.020). Notably, key taxa, including Phascolarctobacterium (P = 0.034) and Acidaminococcaceae (P = 0.012), increased significantly in abundance in responders post-FMT, indicating successful microbial engraftment as a critical determinant of therapeutic success. These findings suggest that FMT is a viable intervention for weight loss in obese individuals. Successful donor-derived microbial engraftment strongly correlates with weight loss efficacy, highlighting the potential of microbiota-targeted therapies in obesity management and providing insights into the mechanisms underlying FMT outcomes.IMPORTANCEPrior research indicates that fecal microbiota transplantation (FMT) is a promising treatment for diseases related to microbiota imbalance, potentially providing metabolic benefits for obesity. However, the specific role of donor-derived microbial engraftment in driving clinical efficacy has remained unclear. In this study, we evaluated the efficacy of FMT in promoting weight loss and explored the role of donor-derived bacterial strains in this process. Our findings demonstrate that the successful engraftment of specific donor-derived taxa, such as Phascolarctobacterium and Acidaminococcaceae, is strongly associated with significant weight loss. This highlights the critical interplay between donor microbiota and recipient gut environment. These findings underscore the potential of microbiota-targeted therapies as a novel strategy for obesity management.CLINICAL TRIALSThis study is registered with the Chinese Clinical Trial Registry as ChiCTR1900024760.},
}

@article {pmid40463963,
year = {2025},
author = {Coblentz, M and Evans, JD and Kothe, CI and Mak, T and Valerón, NR and Chwalek, P and Wejendorp, K and Garg, S and Pless, L and Mak, S and Sörensen, PM and Jahn, LJ and Ekblaw, A},
title = {Food fermentation in space: Opportunities and challenges.},
journal = {iScience},
volume = {28},
number = {4},
pages = {112189},
pmid = {40463963},
issn = {2589-0042},
abstract = {Space exploration is expanding, which demands new technologies and enables new scientific questions. Food, as a bridge between disciplines, can bring these fundamental and applied goals together. Here, we investigate whether food fermentation in space is possible and if so, how it compares with fermentation on Earth. We fermented a miso, a traditional Japanese condiment, on the International Space Station over 30 days and compared it with two earthbound controls. Based on environmental metadata, shotgun metagenomics, whole-genome sequencing, untargeted metabolomics, colorimetry, and sensory analysis, we found that overall, the space miso is recognizable as a miso, indicating fermentation in space is possible. We also found some key microbiological and sensory differences in the space miso, which suggest distinctive features of the space environment. These findings can be harnessed to create more flavorful, nourishing foods for long-term space missions and invite further research questions across science, health, technology, and society.},
}

@article {pmid40463955,
year = {2025},
author = {Zhang, E and Breselge, S and Carlino, N and Segata, N and Claesson, MJ and Cotter, PD},
title = {A genomics-based investigation of acetic acid bacteria across a global fermented food metagenomics dataset.},
journal = {iScience},
volume = {28},
number = {4},
pages = {112139},
pmid = {40463955},
issn = {2589-0042},
abstract = {Developing a better understanding of the genomic and metabolic features of acetic acid bacteria (AABs) has the potential to facilitate an improvement of the taste or flavor of fermented foods. Here, we conducted a high-resolution analysis of AABs present in fermented foods based on the investigation of 337 high-quality metagenomic-assembled genomes (MAGs) recovered from 223 metagenomic samples. Firstly, by integrating these MAGs, we built a phylogenetic tree of high-quality MAGs using GTDB-Tk. We found that AABs MAGs from food-related samples and those from other environments are generally phylogenetically distinct, with the majority of those from fermented foods being assigned to a relatively small number of genera. Functional metagenomic analysis also revealed that the fermented food-associated AABs MAGs are associated with the production of carbohydrate-active enzymes, antibiotic resistance genes, and secondary metabolites. Through these investigations, we have gained substantial insights into the diversity, function, and roles of AABs in fermented food microbiomes.},
}

@article {pmid40463945,
year = {2025},
author = {Wu, C and Mi, Y and Song, J and Zhang, M and Wang, C},
title = {The Regulatory Effect of Human Umbilical Cord Mesenchymal Stem Cells on the Gut Microbiota in Diabetic Nephropathy Rats.},
journal = {Iranian journal of biotechnology},
volume = {23},
number = {1},
pages = {},
pmid = {40463945},
issn = {1728-3043},
abstract = {BACKGROUND: Chronic inflammation is increasingly recognized as a key factor in the progression of diabetic kidney disease (DKD). By discovering that the regulation of gut microbiota plays an important role in diabetic kidney disease, human umbilical cord mesenchymal stem cells (HU-MSCs) explore the mechanism of fibrosis in diabetic kidney disease through the regulation of chronic inflammation, providing new clinical insights for the prediction, diagnosis, and treatment of diabetic kidney disease.

OBJECTIVES: This study explores the regulatory effects of HU-MSCs on gut microbiota and their protective role on the intestinal barrier in diabetic nephropathy rats.

MATERIAL AND METHOD: Diabetic kidney disease (DKD) was induced in SD rats via intraperitoneal injection of streptozotocin. Three groups were established: control group, diabetic kidney disease (DKD) group, and treatment group (DKD+HU-MSCs) (10 rats each). After diabetic kidney disease (DKD) modeling, rats in the treatment group (DKD+HU-MSCs) received 2×10[6] HU-MSCs via tail vein injection weekly for four weeks. Blood, urine, kidney, and colon tissues were collected post-treatment. Pathological changes were observed microscopically; immunohistochemistry detected tight junction proteins ZO-1 and Occludin in colon tissues. DiR-labeled HU-MSCs distribution was assessed with in vivo imaging, and immunohistochemistry evaluated human mesenchymal stem cell markers CD44 and CD90. Fecal samples underwent metagenomic sequencing for gut microbiota analysis.

RESULTS: HU-MSCs transplantation significantly reduced Blood Urea Nitrogen (BUN), Serum Creatinine (SCr), and 24-hour urinary protein levels (all P < 0.05) and improved renal pathology. Markers CD44 and CD90 were present in DKD rat colon tissues. Tight junction proteins Occludin and ZO-1 were decreased in DKD rats but increased following HU-MSCs treatment. Metagenomic analysis showed enhanced abundance of beneficial bacteria (Bifidobacterium and Lactobacillus) with HU-MSCs. Urinary protein was positively correlated with Prevotella and negatively with Ligilactobacillus (p < 0.05).

CONCLUSIONS: HU-MSCs may improve intestinal barrier function in diabetic kidney disease (DKD) rats by restoring gut microbiota structure and increasing intestinal tight junction proteins, offering a potential pathway for enhancing renal function.},
}

@article {pmid40463537,
year = {2025},
author = {De Chiara, L and Doughty, R and Estévez-Gómez, N and Gallego-García, P and Alvariño, P and Díez-Martín, A and Piñón, PD and Treangen, TJ and Cubiella, J and Posada, D},
title = {A Comparison of Methods for the Optimal Recovery of the Human Fecal Virome.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.05.12.25327428},
pmid = {40463537},
abstract = {Human virome studies are gaining attention as viruses are increasingly acknowledged as key modulators of microbial communities and human health. However, viral metagenomics presents distinct challenges, including the low abundance and diversity of viruses in biological samples, the lack of universal marker genes, and protocol-induced biases. Although various virome protocols have been benchmarked using viral particles or nucleic acids from mock communities, these often fail to replicate the complexity and heterogeneity of natural viromes. In this study, we systematically evaluated protocol modifications for the metagenomic analysis of human fecal samples, testing alternatives for viral enrichment, nucleic acid extraction, genome amplification, and library preparation. We assessed the impact of each modification on key inferences, including taxonomic and functional assignment, contig quality, viral diversity, and genome structure. Our results highlight important trade-offs between viral genome recovery and contamination removal, underscoring how methodological choices can shape virome composition. Based on our findings, we propose an optimized protocol that enhances the recovery of viral DNA and RNA genomes while minimizing contamination from non-viral sequences, providing a robust framework for future gut virome studies.},
}

@article {pmid40463520,
year = {2025},
author = {Patel, SM and Farirai, J and Patel, MZ and Boiditswe, S and Tawe, L and Lekalake, S and Matshaba, M and Steenhoff, AP and Arscott-Mills, T and Feemster, KA and Shah, SS and Thielman, N and Cunningham, CK and David, LA and Murdoch, DM and Kelly, MS},
title = {Alterations of the upper respiratory microbiome among children living with HIV infection in Botswana.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2022.12.19.22283664},
pmid = {40463520},
abstract = {Children living with HIV (CLWH) are at high risk of colonization and infection by bacterial respiratory pathogens, though this risk can be reduced by other microbes in the upper respiratory microbiome. The impact of HIV infection on development of the upper respiratory microbiome during childhood is poorly understood, and we sought to address this knowledge gap by identifying associations between HIV infection and the nasopharyngeal microbiomes of children in Botswana. We enrolled Batswana CLWH (<5 years) and age- and sex-matched HIV-exposed, uninfected (HEU) and HIV-unexposed, uninfected (HUU) children in a cross-sectional study. We used shotgun metagenomic sequencing to compare the nasopharyngeal microbiomes of children by HIV status. Among the 143 children in this study, HIV infection and HIV-associated immunosuppression were associated with alterations in nasopharyngeal microbiome composition, including lower abundances of Corynebacterium species associated with respiratory health. These findings suggest that the upper respiratory microbiome may contribute to the high risk of bacterial respiratory infections among CLWH.},
}

@article {pmid40463435,
year = {2025},
author = {Strokach, A and Zoruk, P and Boldyreva, D and Morozov, M and Olekhnovich, E and Veselovsky, V and Babenko, V and Selezneva, O and Zakharevich, N and Larin, A and Koldman, S and Koldman, V and Odorskaya, M and Yunes, R and Pavlov, V and Kudryavtseva, A and Danilenko, V and Klimina, K},
title = {Comparative evaluation of sequencing technologies and primer sets for mouse gut microbiota profiling.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1584359},
pmid = {40463435},
issn = {1664-302X},
abstract = {BACKGROUND: Advancements in sequencing technologies, such as Illumina and Oxford Nanopore Technologies (ONT), have significantly improved microbiome research. However, variations in sequencing platforms, primer selection, and DNA quality may influence microbial diversity assessments, particularly in studies of gut microbiota. This study systematically evaluates these factors in mouse gut microbiota analysis, comparing 16S rRNA gene sequencing and metagenome sequencing (MS) across both platforms.

RESULTS: Our findings highlight the critical influence of primer selection on 16S rRNA sequencing results, with certain primer combinations detecting unique taxa that others miss. Despite these variations in taxonomic resolution, all tested primer sets consistently revealed significant differences between experimental groups, indicating that key microbial shifts induced by bacterial cultures remain detectable regardless of primer choice. A comparative analysis of Illumina and ONT 16S rRNA sequencing revealed notable differences in microbial diversity profiling, with ONT capturing a broader range of taxa. In contrast, MS on both platforms showed a high degree of correlation, indicating that ONT sequencing errors have minimal impact on taxonomic diversity estimations. Furthermore, the type of extracted DNA (high molecular weight vs. standard DNA) had little on microbial diversity outcomes, underscoring the robustness of these sequencing technologies.

CONCLUSION: These results highlight the advantages and limitations of different sequencing strategies in microbiota research. While 16S rRNA sequencing remains a cost-effective tool for assessing bacterial diversity, MS provides superior taxonomic resolution and more precise species identification. Our study advocates for a hybrid approach that combines multiple sequencing technologies to achieve a more comprehensive and accurate representation of microbial communities.},
}

@article {pmid40463374,
year = {2025},
author = {Gu, J and Ma, Y and Chang, Q and Chen, L},
title = {Influence of programmed death ligand 1 (PD-L1) knockout on gut microbiota in experimental autoimmune uveitis.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1600673},
pmid = {40463374},
issn = {1664-3224},
mesh = {Animals ; *Gastrointestinal Microbiome/immunology ; *Uveitis/immunology/microbiology/genetics ; *B7-H1 Antigen/genetics/deficiency ; *Autoimmune Diseases/immunology/microbiology/genetics ; Mice, Knockout ; Mice ; Female ; Disease Models, Animal ; Mice, Inbred C57BL ; },
abstract = {PURPOSE: Programmed death ligand 1 (PD-L1) is a potential target for autoimmune disease therapies. The gut microbiota plays a critical role in autoimmunity, and may influence therapeutic outcomes of immune therapies in cancer. However, the relationship between PD-L1 and gut microbiota in autoimmune conditions remains unclear. This study aims to investigate the effect of PD-L1 knockout on gut microbiota in an experimental autoimmune uveitis (EAU) model.

METHODS: EAU was induced via immunization with interphotoreceptor retinoid-binding protein peptide 651-670 (IRBP651-670) in either wild type (WT) or PD-L1 knockout (KO) C57BL/6J female mice. Sham adjuvant was administered to WT or PD-L1 KO mice as healthy controls. The severity of EAU was evaluated through clinical evaluation and histopathological gradings. The characteristics of gut microbiota was analyzed using metagenomic sequencing.

RESULTS: Each group consisted of three biological replicates. The clinical and histopathological scores of EAU were significantly higher in KO_EAU mice than in WT_EAU mice. WT_EAU mice exhibited lower microbial richness than their healthy controls (WT mice), while PD-L1 KO in EAU mice (KO_EAU group) led to increased richness when compared to wild type EAU mice (WT_EAU group). EAU induced a reduction in the abundance of Akkermansia muciniphila A and an increased in CAG-485 sp002362485. PD-L1 knockout in EAU led to an increased abundance of families Bacteroidaceae, Lachnospiraceae and Ruminococcaceae. EAU was associated with declining microbial tryptophan metabolism and up-regulated functions related to lipid and carbohydrate metabolism; PD-L1 knockout in EAU further increased the metabolism of glycan and biosynthesis of 3-deoxy-α-D-manno-2-octulosonate (Kdo), a key component of bacterial lipopolysaccharide (LPS).

CONCLUSION: Both EAU and PD-L1 knockout modulate gut microbiota, affecting microbial composition - particularly Akkermansia, CAG-485, Bacteroidaceae, Lachnospiraceae and Ruminococcaceae - and microbial functions such as lipid, carbohydrate and glycan metabolism.},
}

Animals
*Gastrointestinal Microbiome/immunology
*Uveitis/immunology/microbiology/genetics
*B7-H1 Antigen/genetics/deficiency
*Autoimmune Diseases/immunology/microbiology/genetics
Mice, Knockout
Mice
Female
Disease Models, Animal
Mice, Inbred C57BL

@article {pmid40462844,
year = {2025},
author = {Morra, M and Marradi, D and Gandini, L and Ivagnes, V and Ottolini, G and Bovio, A and Jabali, G and Maraschi, L and Dada, IA and Chawanda, TV and Gorla, M and Tarasiuk, O and Mocchetti, C and Soluri, MF and Boccafoschi, F and Sblattero, D and Cotella, D},
title = {A non-hypothesis-driven practical laboratory activity on functional metagenomics: "fishing" protein-coding DNA sequences from microbiomes.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {13},
number = {},
pages = {1602982},
pmid = {40462844},
issn = {2296-4185},
abstract = {Practical laboratory of the most functional metagenomics courses focuses on activities aimed at providing specific skills in bioinformatics through the analysis of genomic datasets. However, sequence-based analyses of metagenomes should be complemented by function-based analyses, to provide evidential knowledge of gene function. A "true" functional metagenomic approach relies on the construction and screening of metagenomic libraries - physical libraries that contain DNA cloned from metagenomes of various origin. The information obtained from functional metagenomics will help in future annotations of gene function and serve as a complement to sequence-based metagenomics. Here, we describe a simple protocol for the construction of a metagenomic DNA library, optimized and tested by a team of undergraduate biotechnology students. This protocol is based on a technique developed in our laboratory and currently used for research. Using this protocol, libraries of protein domains can be quickly generated, from the DNA of any intron-less genome, such as those of bacteria or phages. Therefore, these libraries provide a valuable platform for training students in various validation tools, including computational methods - for example, metagenome assembly, functional annotation - and proteomics techniques, including protein expression and analysis. By varying the biological source and validation pipeline, this approach offers virtually limitless opportunities for innovative thesis research projects.},
}

@article {pmid40462511,
year = {2025},
author = {Qian, LM and Wang, SX and Zhou, W and Qin, ZX and Wang, YN and Zhao, Q and Xu, RH},
title = {Individualized metagenomic network model for colorectal cancer diagnosis: insights into viral regulation of gut microecology.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {3},
pages = {},
doi = {10.1093/bib/bbaf208},
pmid = {40462511},
issn = {1477-4054},
support = {Y-HR2020QN-0474//Beijing Xisike Clinical Oncology Research Foundation/ ; 84000-31630002//Sun Yat-sen University clinical research 5010 program/ ; CIRP-SYSUCC-0004//Cancer Innovative Research Program of Sun Yat-sen University Cancer Center/ ; 2019-I2M-5-036//CAMS Innovation Fund for Medical Sciences (CIFMS)/ ; 82173128//National Natural Science Foundation of China/ ; 81930065//National Natural Science Foundation of China/ ; 82321003//National Natural Science Foundation of China/ ; },
mesh = {*Colorectal Neoplasms/diagnosis/virology/microbiology/genetics ; Humans ; *Gastrointestinal Microbiome ; *Metagenomics/methods ; *Metagenome ; Dysbiosis/virology ; },
abstract = {The role of gut microbiota, especially viruses, in colorectal cancer (CRC) pathogenesis remains unclear. This study investigated the interplay between gut microbiota and CRC development. We developed a viral/bacterial sequence analysis pipeline to reanalyze gut metagenomic datasets from eight CRC studies. A multisample co-occurrence network was constructed to delineate microbiota species interconnections. Our analysis confirmed dysbiosis in CRC patients and revealed enrichment of viral species, particularly those hosted by Lactococcus and Escherichia. These viruses were identified as central hubs in the multikingdom interaction network. We developed a network-based model using single sample networks (SSN) that distinguished CRC patients from controls with an area under the curve (AUC) of 0.93. Models combining relative abundance and SSN assessment achieved an AUC of 0.97, outperforming SSN-based models without viral data. This study highlights the crucial role of viruses in the gut microbiome network and their potential as targets for CRC prevention and intervention. Our approach offers a new perspective on noninvasive diagnostic criteria for CRC.},
}

*Colorectal Neoplasms/diagnosis/virology/microbiology/genetics
Humans
*Gastrointestinal Microbiome
*Metagenomics/methods
*Metagenome
Dysbiosis/virology

@article {pmid40462354,
year = {2025},
author = {Li, X and Xu, L and Demaree, B and Noecker, C and Bisanz, JE and Weisgerber, DW and Modavi, C and Turnbaugh, PJ and Abate, AR},
title = {Microbiome Single Cell Atlases Generated with a Commercial Instrument.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e2409338},
doi = {10.1002/advs.202409338},
pmid = {40462354},
issn = {2198-3844},
support = {//Florida State University Start-up fund/ ; COA7000-138420-7030928-45-A73H5//UCSF Benioff Center for Microbiome Medicine (BCMM) Trainee Pilot Award/ ; R01HG008978//Foundation for the National Institutes of Health/ ; U01AI129206//Foundation for the National Institutes of Health/ ; R01AI149699//Foundation for the National Institutes of Health/ ; R01EB019453//Foundation for the National Institutes of Health/ ; R01HL122593//Foundation for the National Institutes of Health/ ; R01AT011117//Foundation for the National Institutes of Health/ ; F32GM140808//Foundation for the National Institutes of Health/ ; },
abstract = {Single-cell sequencing is useful for resolving complex systems into their composite cell types and computationally mining them for unique features that are masked in pooled sequencing. However, while commercial instruments have made single-cell analysis widespread for mammalian cells, analogous tools for microbes are limited. Here, EASi-seq (Easily Accessible Single microbe sequencing) is presented. By adapting the single-cell workflow of the commercial Mission Bio Tapestri instrument, this method allows for efficient sequencing of individual microbial genomes. EASi-seq allows tens of thousands of microbes to be sequenced per run and, as it is shown, can generate detailed atlases of human and environmental microbiomes. The ability to capture large genome datasets from thousands of single microbes provides new opportunities in discovering and analyzing species subpopulations. To facilitate this, a companion bioinformatic pipeline is developed that clusters genome by sequence similarity, improving whole genome assembly, strain identification, taxonomic classification, and gene annotation. In addition, the integration of metagenomic contigs with the EASi-seq datasets is demonstrated to reduce capture bias and increase coverage. EASi-seq enables high-quality single-cell genomic sequencing for microbiome samples using a simple workflow run on a commercially available platform.},
}

@article {pmid40462165,
year = {2025},
author = {Gao, H and Bai, H and Su, Y and Gao, Y and Fang, H and Li, D and Yu, Y and Lu, X and Xia, D and Mao, D and Luo, Y},
title = {Fecal microbiota transplantation from Helicobacter pylori carriers following bismuth quadruple therapy exacerbates alcohol-related liver disease in mice via LPS-induced activation of hepatic TLR4/NF-κB/NLRP3 signaling.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {627},
pmid = {40462165},
issn = {1479-5876},
support = {42377426//National Natural Science Foundation of China/ ; 42077382//National Natural Science Foundation of China/ ; 21JCYBJC01200//Tianjin Municipal Natural Science Foundation/ ; 2023220//Research Project on Integrated Traditional Chinese and Western Medicine of Tianjin Municipal Health Commission/ ; },
mesh = {Animals ; *Fecal Microbiota Transplantation/adverse effects ; *NLR Family, Pyrin Domain-Containing 3 Protein/metabolism ; *Helicobacter pylori/physiology/drug effects ; *Signal Transduction/drug effects ; Lipopolysaccharides/pharmacology ; *Bismuth/therapeutic use/pharmacology ; *Toll-Like Receptor 4/metabolism ; Gastrointestinal Microbiome/drug effects ; *NF-kappa B/metabolism ; *Liver/pathology/metabolism/drug effects ; *Liver Diseases, Alcoholic/microbiology/therapy/pathology ; Male ; Mice ; Mice, Inbred C57BL ; Helicobacter Infections/microbiology ; Disease Models, Animal ; Humans ; Dysbiosis ; },
abstract = {BACKGROUND: Helicobacter pylori infection is common in patients with alcohol-related liver disease (ALD), and bismuth quadruple therapy (BQT) is widely used for eradication. However, its impact on ALD remains unclear. This study aims to characterize BQT-induced gut microbiota alterations in asymptomatic H. pylori carriers and evaluate their effect on an ALD mouse model.

METHODS: Metagenomic sequencing was conducted to assess the gut microbiota composition of individuals before and after BQT. Fecal microbiota transplantation (FMT) from these donors was performed in an ALD mouse model. Gut microbiota in mice was analyzed by 16S rRNA sequencing. Liver and intestinal parameters were assessed using western blot, RT-qPCR, histopathology, ELISA, and flow cytometry.

RESULTS: BQT treatment significantly altered the gut microbiota in H. pylori carriers, increasing the abundance of opportunistic pathogens, including Klebsiella pneumoniae, Escherichia coli, Klebsiella quasipneumoniae, and Klebsiella variicola, while decreasing beneficial bacteria such as Bifidobacterium, Eubacterium, Bacteroides, Faecalibacterium, and Blautia. In ALD mice receiving FMT from post-BQT donors, exacerbated gut dysbiosis was observed, marked by an enrichment of Enterobacteriaceae and Escherichia-Shigella. These microbiota changes were associated with impairment of intestinal barrier integrity, as evidenced by reduced levels of mucins, tight junction proteins, and antimicrobial peptides, along with a decrease in Treg cells and an increase in Th17 and Th1 cells. Additionally, this dysbiosis led to elevated serum lipopolysaccharide (LPS) levels, which activated the hepatic NLRP3 inflammasome pathway and subsequently increased IL-18 and IL-1β levels. Furthermore, liver function and oxidative stress markers, including ALT, AST, MDA, GSSG/GSH ratio, and SOD, were significantly elevated, indicating severe liver dysfunction and increased oxidative stress. Finally, probiotic supplementation effectively mitigated the negative effects of BQT-induced gut microbiota remodeling on ALD in mice.

CONCLUSIONS: BQT markedly alters the gut microbiota in H. pylori carriers, promoting dysbiosis that exacerbates ALD in mice via LPS-mediated activation of hepatic inflammatory pathways. These findings highlight the need for careful consideration of BQT use in ALD patients.},
}

Animals
*Fecal Microbiota Transplantation/adverse effects
*NLR Family, Pyrin Domain-Containing 3 Protein/metabolism
*Helicobacter pylori/physiology/drug effects
*Signal Transduction/drug effects
Lipopolysaccharides/pharmacology
*Bismuth/therapeutic use/pharmacology
*Toll-Like Receptor 4/metabolism
Gastrointestinal Microbiome/drug effects
*NF-kappa B/metabolism
*Liver/pathology/metabolism/drug effects
*Liver Diseases, Alcoholic/microbiology/therapy/pathology
Male
Mice
Mice, Inbred C57BL
Helicobacter Infections/microbiology
Disease Models, Animal
Humans
Dysbiosis

@article {pmid40462041,
year = {2025},
author = {Luo, Y and Wu, R and Wu, W and Zhao, D and Jiang, Y and Gu, H},
title = {Differences in pulmonary microbiota of severe community-acquired pneumonia with different pathogenic microorganisms in children.},
journal = {BMC pediatrics},
volume = {25},
number = {1},
pages = {449},
pmid = {40462041},
issn = {1471-2431},
support = {82200008//the Youth Program of National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Community-Acquired Infections/microbiology ; Male ; Female ; Child, Preschool ; Haemophilus influenzae/isolation & purification ; Infant ; Bronchoalveolar Lavage Fluid/microbiology ; *Microbiota ; *Lung/microbiology ; Streptococcus pneumoniae/isolation & purification ; Mycoplasma pneumoniae/isolation & purification ; *Pneumonia, Bacterial/microbiology ; Child ; Severity of Illness Index ; Pneumonia, Mycoplasma/microbiology ; C-Reactive Protein/analysis ; Community-Acquired Pneumonia ; },
abstract = {BACKGROUND: Community-acquired pneumonia (CAP) is the leading cause of hospitalization and death in children under 5 years old. Recently, the number of children with severe CAP (SCAP) has increased significantly, and local or systemic complications may occur. However, changes in the pulmonary microbiota of SCAP with different pathogens and their relationship with the clinical features of SCAP remain unclear.

METHODS: This study collected bronchoalveolar lavage fluid (BALF) from 105 children with SCAP for metagenomics next generation sequencing (mNGS). According to the first pathogen of mNGS, the enrolled children were divided into the Streptococcus pneumoniae (SP), Mycoplasma pneumoniae (MP) and Haemophilus influenzae (HI) groups. We aimed to explore differences in clinical features and pulmonary microbiota of SCAP with different pathogens, and clarify the correlation between pulmonary microbiota and clinical features.

RESULTS: Fever days and the levels of C-reactive protein (CRP), procalcitonin (PCT), lactate dehydrogenase (LDH), D-dimer and heparin-binding protein (HBP) of children in MP group were significantly higher than those in HI group. The level of LDH of children in MP group was significantly higher than that in SP group. The abundance of MP was also positively correlated with fever days and the levels of PCT, LDH and D-dimer. The α diversity of SP group was significantly increased compared to MP group and HI group.

CONCLUSION: Compared to SP-infected and HI-infected children with SCAP, children with SCAP infected with MP tend to have a more intense inflammatory response. The α diversity was higher in the lower airways of children with SCAP and SP infections compared to MP-infected and HI-infected children with SCAP.},
}

Humans
*Community-Acquired Infections/microbiology
Male
Female
Child, Preschool
Haemophilus influenzae/isolation & purification
Infant
Bronchoalveolar Lavage Fluid/microbiology
*Microbiota
*Lung/microbiology
Streptococcus pneumoniae/isolation & purification
Mycoplasma pneumoniae/isolation & purification
*Pneumonia, Bacterial/microbiology
Child
Severity of Illness Index
Pneumonia, Mycoplasma/microbiology
C-Reactive Protein/analysis
Community-Acquired Pneumonia

@article {pmid40461820,
year = {2025},
author = {Piccinno, G and Thompson, KN and Manghi, P and Ghazi, AR and Thomas, AM and Blanco-Míguez, A and Asnicar, F and Mladenovic, K and Pinto, F and Armanini, F and Punčochář, M and Piperni, E and Heidrich, V and Fackelmann, G and Ferrero, G and Tarallo, S and Nguyen, LH and Yan, Y and Keles, NA and Tuna, BG and Vymetalkova, V and Trompetto, M and Liska, V and Hucl, T and Vodicka, P and Bencsiková, B and Čarnogurská, M and Popovici, V and Marmorino, F and Cremolini, C and Pardini, B and Cordero, F and Song, M and Chan, AT and Derosa, L and Zitvogel, L and Huttenhower, C and Naccarati, A and Budinska, E and Segata, N},
title = {Pooled analysis of 3,741 stool metagenomes from 18 cohorts for cross-stage and strain-level reproducible microbial biomarkers of colorectal cancer.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
pmid = {40461820},
issn = {1546-170X},
support = {101045015//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 825410//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; CGCATF-2023/100036//Cancer Research UK (CRUK)/ ; CGCATF-2023/100041//Cancer Research UK (CRUK)/ ; 1OT2CA297205-01//U.S. Department of Health & Human Services | NIH | NCI | Division of Cancer Epidemiology and Genetics, National Cancer Institute (National Cancer Institute Division of Cancer Epidemiology and Genetics)/ ; OT2CA297680//U.S. Department of Health & Human Services | NIH | NCI | Division of Cancer Epidemiology and Genetics, National Cancer Institute (National Cancer Institute Division of Cancer Epidemiology and Genetics)/ ; },
abstract = {Associations between the gut microbiome and colorectal cancer (CRC) have been uncovered, but larger and more diverse studies are needed to assess their potential clinical use. We expanded upon 12 metagenomic datasets of patients with CRC (n = 930), adenomas (n = 210) and healthy control individuals (n = 976; total n = 2,116) with 6 new cohorts (n = 1,625) providing granular information on cancer stage and the anatomic location of tumors. We improved CRC prediction accuracy based solely on gut metagenomics (average area under the curve = 0.85) and highlighted the contribution of 19 newly profiled species and distinct Fusobacterium nucleatum clades. Specific gut species distinguish left-sided versus right-sided CRC (area under the curve = 0.66) with an enrichment of oral-typical microbes. We identified strain-specific CRC signatures with the commensal Ruminococcus bicirculans and Faecalibacterium prausnitzii showing subclades associated with late-stage CRC. Our analysis confirms that the microbiome can be a clinical target for CRC screening and characterizes it as a biomarker for CRC progression.},
}

@article {pmid40461259,
year = {2025},
author = {Esser, SP and Turzynski, V and Plewka, J and Nuy, J and Moore, CJ and Banas, I and Soares, AR and Lee, J and Woyke, T and Probst, AJ},
title = {Differential Expression of Core Metabolic Functions in Candidatus Altiarchaeum Inhabiting Distinct Subsurface Ecosystems.},
journal = {Environmental microbiology reports},
volume = {17},
number = {3},
pages = {e70096},
doi = {10.1111/1758-2229.70096},
pmid = {40461259},
issn = {1758-2229},
support = {DFG PR1603/2-1//Ministerium für Kultur und Wissenschaft des Landes Nordrhein- Westfalen ("Nachwuchsgruppe Dr. Alexander Probst") and the German Research Foundation/ ; //Aker B.P.: GeneOil Project/ ; //U.S. Department of Energy Joint Genome Institute/ ; //DOE Office of Science User Facility/ ; //the Office of Science of the U.S. Department of Energy operated/ ; },
mesh = {*Ecosystem ; Germany ; Groundwater/microbiology ; Symbiosis ; Transcriptome ; Gene Expression Profiling ; Genome, Archaeal ; Multigene Family ; },
abstract = {Candidatus Altiarchaea are widespread across aquatic subsurface ecosystems and possess a highly conserved core genome, yet adaptations of this core genome to different biotic and abiotic factors based on gene expression remain unknown. Here, we investigated the metatranscriptome of two Ca. Altiarchaeum populations that thrive in two substantially different subsurface ecosystems. In Crystal Geyser, a high-CO2 groundwater system in the USA, Ca. Altiarchaeum crystalense co-occurs with the symbiont Ca. Huberiarchaeum crystalense, while in the Muehlbacher sulfidic spring in Germany, an artesian spring high in sulfide concentration, Ca. A. hamiconexum is heavily infected with viruses. We here mapped metatranscriptome reads against their genomes to analyse the in situ expression profile of their core genomes. Out of 537 shared gene clusters, 331 were functionally annotated and 130 differed significantly in expression between the two sites. Main differences were related to genes involved in cell defence like CRISPR-Cas, virus defence, replication, transcription and energy and carbon metabolism. Our results demonstrate that altiarchaeal populations in the subsurface are likely adapted to their environment while influenced by other biological entities that tamper with their core metabolism. We consequently posit that viruses and symbiotic interactions can be major energy sinks for organisms in the deep biosphere.},
}

*Ecosystem
Germany
Groundwater/microbiology
Symbiosis
Transcriptome
Gene Expression Profiling
Genome, Archaeal
Multigene Family

@article {pmid40461059,
year = {2025},
author = {Laiola, M and Koppe, L and Larabi, A and Thirion, F and Lange, C and Quinquis, B and David, A and Le Chatelier, E and Benoit, B and Sequino, G and Chanon, S and Vieille-Marchiset, A and Herpe, YE and Alvarez, JC and Glorieux, G and Krukowski, H and Geert, HRB and Raes, J and Fouque, D and Massy, ZA and Ehrlich, SD and Stengel, B and Wagner, S and , },
title = {Toxic microbiome and progression of chronic kidney disease: insights from a longitudinal CKD-Microbiome Study.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2024-334634},
pmid = {40461059},
issn = {1468-3288},
abstract = {BACKGROUND: The gut microbiota has been linked to non-communicable diseases, including chronic kidney disease (CKD). However, the relationships between gut microbiome composition changes, uraemic toxins (UTs) accumulation, and diet on CKD severity and progression remain underexplored.

OBJECTIVE: To characterise relationships between gut microbiome composition and functionality, UTs diet, and CKD severity and progression, as well as assess microbial contributions to UTs accumulation through mice faecal microbiota transplantation (FMT).

DESIGN: This study profiled the gut microbiome of 240 non-dialysis patients with CKD (CKD-REIN cohort) using shotgun metagenomics, with follow-up in 103 patients after 3 years, with comparisons with healthy volunteers from the Milieu Intérieur cohort. A multiomics approach identifies features associated with CKD severity (and progression), with validation in an independent Belgian cohort. Experimental models used FMT to test CKD gut microbiome effects on UTs and kidney fibrosis. Changes in gut microbiome over time were evaluated, and the impact of diet on these changes was assessed.

RESULTS: Compared with matched healthy controls, patients with CKD exhibited gut microbiota alteration, with enrichment of UT precursor-producing species. Patients with severe CKD exhibited higher UT levels and greater enrichment of UT (precursor)-producing species in the microbiota than patients with moderate CKD. Over time, UT (precursor)-producing species increased, and a plant-based low protein diet appeared to mitigate these changes. FMT from patients with CKD to antibiotic-treated CKD model mice increased serum UT levels and exacerbated kidney fibrosis.

CONCLUSIONS: This study highlights the role of the microbiome and UTs in CKD, suggesting a potential therapeutic target to slow disease progression.},
}

@article {pmid40460917,
year = {2025},
author = {Lian, ZH and You, Z and Han, PY and Qiu, Y and Zhang, YZ and Ge, XY},
title = {Decoding the virome reveals diverse novel viruses in tree shrews (Tupaia belangeri) in Yunnan Province.},
journal = {Virologica Sinica},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.virs.2025.05.011},
pmid = {40460917},
issn = {1995-820X},
abstract = {Viruses circulating in small mammals possess the potential to infect humans. Tree shrews are a group of small mammals inhabiting widely in forests and plantations, but studies on viruses in tree shrews are quite limited. Herein, viral metagenomic sequencing was employed to detect the virome in the tissue and swab samples from seventy-six tree shrews that we collected in Yunnan Province. As the results, genomic fragments belonging to eighteen viral families were identified, thirteen of which contain mammalian viruses. Through polymerase chain reaction (PCR) and Sanger sequencing, twelve complete genomes were determined, including five parvoviruses, three torque teno viruses (TTVs), two adenoviruses, one pneumovirus, and one hepacivirus, together with three partial genomes, including two hepatitis E virus and one paramyxovirus. Notably, the three TTVs, named TSTTV-HNU1, TSTTV-HNU2, and TSTTV-HNU3, may compose a new genus within the family Anelloviridae. Notably, TSParvoV-HNU5, one of the tree shrew parvoviruses detected, was likely to be a recombination of two murine viruses. Divergence time estimation further revealed the potential cross-species-transmission history of the tree shrew pneumovirus TSPenV-HNU1. Our study provides a comprehensive exploration of viral diversity in wild tree shrews, significantly enhancing our understanding of their role as natural virus reservoirs.},
}

@article {pmid40460905,
year = {2025},
author = {Memon, FU and Li, C and Ahmad, S and Cui, Y and Feng, X and Zeng, P and Nabi, F and Huang, Z and Tettamanti, G and Chen, T and Tian, L},
title = {Efficiency of microbial fermentation on microbial shifts, enzymatic activity, and transcriptions in black soldier fly larvae during the sugarcane waste conversion.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126588},
doi = {10.1016/j.envpol.2025.126588},
pmid = {40460905},
issn = {1873-6424},
abstract = {Sugarcane trash, consisting mainly of dried leaves, tops and cans, is often burned in fields, posing serious risks to human health, contributing to environmental pollution, and depleting soil nutrients. Black soldier fly larvae (BSFL) offer a promising solution for organic waste management by converting it into insect proteins. This study aimed to develop a microbial fermentation method to utilize sugarcane waste as feed for BSFL and investigate underlying mechanisms. Our results revealed that all fermented groups exhibited enhanced growth and developmental performance, with the combination of Bacillus subtilis, Enterococcus faecalis, and Saccharomyces cerevisiae leading to the highest increases in larval body weight, survival rate, substrate conversion efficiency, and protein content compared to the unfermented group. Metagenomic analysis revealed a notable increase in the phylum Firmicutes, along with its beneficial strains such as Bacillus licheniformis, B. safensis, B. pumilus, Cytobacillus kochii, and Lysinibacillus fusiformis, in the gut of BSFL reared on fermented sugarcane waste, leading to improved gut homeostasis and reduced pathogenic loads. Additionally, the BSFL fed with fermented sugarcane waste exhibited high abundances of carbohydrate-active enzymes (CAZymes) involved in cellulose, hemicellulose, and starch degradation at both class and family levels. Transcriptome analysis further indicated the upregulation of key genes associated with key physiological processes, such as carbohydrate metabolism, chitin biosynthesis, and defense mechanisms. Collectively, these findings demonstrate the synergistic potential of microbial fermentation and BSFL for sustainable sugarcane waste management while advancing the understanding of host-microbe-diet interactions in insect-based bioconversion systems.},
}

@article {pmid40460824,
year = {2025},
author = {Gogokhia, L and Tran, N and Grier, A and Nagayama, M and Xiang, G and Funez-dePagnier, G and Lavergne, A and Ericsson, C and Ben Maamar, S and Zhang, M and Battat, R and Scherl, E and Lukin, DJ and Longman, RS},
title = {Donor composition and fiber promote strain engraftment in a randomized controlled trial of fecal microbiota transplant for ulcerative colitis.},
journal = {Med (New York, N.Y.)},
volume = {},
number = {},
pages = {100707},
doi = {10.1016/j.medj.2025.100707},
pmid = {40460824},
issn = {2666-6340},
abstract = {BACKGROUND: Fecal microbiota transplantation (FMT) is an emerging treatment for ulcerative colitis (UC), but the impact of prebiotic fiber on FMT efficacy for UC is unclear. We performed a randomized, double-blind, placebo-controlled clinical trial to examine the efficacy of FMT with and without dietary fiber supplementation in patients with UC.

METHODS: 27 patients with mild to moderate UC were randomized to receive a single FMT or placebo with or without psyllium fiber supplementation for 8 weeks. The primary outcome was clinical response at week 8, and secondary outcomes included endoscopic improvement and clinical remission. Metagenomic sequencing of fecal DNA was analyzed to determine taxonomic profiles and donor strain engraftment.

FINDINGS: The trial was terminated early due to manufacturer discontinuation of FMT product. FMT induced clinical response, remission, and endoscopic improvement in UC patients compared to placebo (p < 0.05), but fiber did not improve clinical outcomes of FMT. Recipient microbiome composition post-FMT shifted toward donor composition in responders and non-responders, but the durability of this change was stronger in responders. Clinical response and durable change in microbiome composition following FMT was donor dependent. Strain tracking analysis also demonstrated a donor-dependent variability in the rate of successful engraftment and identified a consortium of engrafted bacteria associated with treatment response or fiber supplementation.

CONCLUSIONS: Single-dose FMT demonstrated clinical efficacy for mild to moderate UC compared to placebo but revealed no benefit of fiber supplementation. These results highlight proof of concept that donor selection and prebiotic fiber can shape strain-level engraftment. This study was registered at ClinicalTrials.gov: NCT03998488.

FUNDING: National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Diseases (R01 DK128257, to R.S.L.).},
}

@article {pmid40460798,
year = {2025},
author = {Vermote, L and Chun, BH and Khan, SA and De Vuyst, L and Jeon, CO and Weckx, S},
title = {Metagenomic and meta-metabolomic analysis of traditional Korean rice vinegar productions shows a large variability between producers.},
journal = {International journal of food microbiology},
volume = {440},
number = {},
pages = {111283},
doi = {10.1016/j.ijfoodmicro.2025.111283},
pmid = {40460798},
issn = {1879-3460},
abstract = {Cereal vinegars have been used for thousands of years, especially in Asian countries. These vinegars are still produced in a traditional way by a spontaneous, consecutive, alcoholic and acetic acid fermentation process in open vats under non-sterile conditions, which can lead to an unstable and inconsistent flavor and quality. The present study characterized the microbial diversity of complete, traditional Korean rice vinegar productions at two producers (A and B), from steamed rice to rice vinegar, applying high-throughput amplicon-based and shotgun metagenomic sequencing, in combination with meta-metabolomic analysis. Functional analysis based on metagenome-assembled genomes provided insights into the genetic potential of the different microorganisms involved. Producer A used nuruk, a traditional starter, and seed vinegar to start the alcoholic and acetic acid fermentation phases, respectively, which resulted in highly controlled productions even when different fermentation vessels were used. Producer B used only nuruk to start the vinegar productions, and the spontaneous inoculation of acetic acid bacteria did fail in one of the productions. The addition of nuruk resulted in a simultaneous rice starch saccharification and alcoholic fermentation phase characterized by producer-specific moulds, yeasts, and lactic acid bacteria (LAB). During the acetic acid fermentation phase at both producers (a) novel Acetobacter species, related to A. pasteurianus was found. The simultaneous presence of several LAB species made it hard to link them with the production of specific metabolites. Also, the species contributing to ester formation, important for the flavor, was not clear and requires further research.},
}

@article {pmid40460633,
year = {2025},
author = {Zheng, Z and Lyu, H and Wang, L and Tang, J},
title = {Microplastic biofilm may shape microbial community enriched with antibiotic resistance genes to enhance nitrogen transformation under antibiotic stress.},
journal = {Journal of hazardous materials},
volume = {494},
number = {},
pages = {138796},
doi = {10.1016/j.jhazmat.2025.138796},
pmid = {40460633},
issn = {1873-3336},
abstract = {The response of nitrogen transformation to microplastic biofilm under antibiotics (ATs) stress as well as the interrelationships between functional genes and microorganisms in surface water are not very well understood and need further investigation. This study investigated the response of nitrogen transformation by analyzing changes in various nitrogen forms and explored the interaction between nitrogen transformation functions and antibiotic resistance genes (ARGs) under exposure to ATs (ciprofloxacin (CIP) and tetracycline (TC)) and PVC biofilm. Compared to the control, exposure to mature polyvinyl chloride (PVC) biofilm increased nitrate nitrogen (NO3[-]-N) and ammonia nitrogen (NH4[+]-N) removal by 12.48 % and 8.79 %, with the NO3[-]-N removal rate constant reaching 0.17. However, co-exposure to CIP significantly inhibited nitrogen transformation, reducing the NO3[-]-N removal rate constant to 0.08. In PVC biofilm, more active nitrogen transformation and enhanced horizontal transfer of ARGs led to a stronger positive correlation between nitrogen transformation genes (NTGs) and ARGs. Microorganisms carrying NTGs largely overlapped with ARGs host species, including Hydrogenophaga, Rhodococcus, and Ignavibacterium, which exhibited high abundance of both gene types. This indicated that PVC biofilm facilitated nitrogen transformation under ATs stress by enriching nitrogen transformation microorganisms carrying high ARGs abundance. These results extended knowledge of effects of ATs and microplastics (MPs) on nitrogen transformation in surface water and provided theoretical support for unique ecological effects of microplastic biofilm.},
}

@article {pmid40460618,
year = {2025},
author = {Achudhan, AB and Saleena, LM},
title = {In silico analysis to identify novel amidase enzymes from unclassified bacteria present in coal metagenome.},
journal = {Computational biology and chemistry},
volume = {119},
number = {},
pages = {108525},
doi = {10.1016/j.compbiolchem.2025.108525},
pmid = {40460618},
issn = {1476-928X},
abstract = {Amidase enzymes are essential for converting amide groups into carboxylic acids, which have a variety of applications in various industries, including food, flavorings, and pharmaceuticals. The purpose of this study is to utilize metagenomic analysis to identify and analyze novel amidase enzymes produced by unclassified bacteria present in the coal. Initially, metagenomic DNA was extracted from coal and sequenced using the Illumina platform. Analysis of the annotated coal metagenomic data revealed two novel amidase enzymes from microorganisms belonging to the unclassified Oxalobacteraceae family and the unclassified Betaproteobacteria class. These enzymes belong to the amidase signature family, as identified using the InterProScan database. The three-dimensional (3D) structures of these enzymes were predicted with high per-residue confidence scores of approximately 97.34 and 95.31 using the neural network-based AlphaFold2. Molecular docking analysis suggested caprolactam has the highest binding affinity with the enzymes. Molecular dynamics simulations were performed for 200 ns to assess the protein stability. The modelled protein Amidase 1 and Amidase 2 complexes showed higher binding free energy and better stability when compared with the PDB database amidase structures. Overall, this study demonstrates the identification of novel enzymes from unclassified bacteria belonging to the amidase signature family through in-silico mining of the coal metagenome. Novel amidase enzymes found in the coal metagenome exhibit good stability and high substrate binding affinity compared to the crystal structures in the PDB, indicating potential applications in various industries.},
}

@article {pmid40460542,
year = {2025},
author = {Smirnova, AV and Verbeke, TJ and Furgason, CC and Albakistani, EA and Nwosu, FC and Kim, JJ and Haupt, ES and Sheremet, A and Lee, ES and Trang, E and Richardson, E and Dacks, JB and Dunfield, PF},
title = {Microbial community development in an oil sands pit lake.},
journal = {The Science of the total environment},
volume = {987},
number = {},
pages = {179764},
doi = {10.1016/j.scitotenv.2025.179764},
pmid = {40460542},
issn = {1879-1026},
abstract = {Surface mining and extraction of oil sands in Canada produces fluid tailings that contain several compounds of concern for the environment. One option for mine reclamation is the construction of Pit Lakes (PLs) to contain and remediate these tailings. Ultimately, PLs should support food webs typical of boreal lakes. From 2015 to 2021, we applied 16S/18S rRNA gene amplicon sequencing and metagenomics to monitor prokaryotic and eukaryotic microbes in the only full-scale PL of the oil sands industry (Base Mine Lake or BML), and compared it to two control environments: a freshwater reservoir unaffected by tailings, and active tailings ponds receiving regular industrial input. Microbial communities in BML were always intermediate to the two control environments based on alpha and beta diversity analyses. BML communities were highly variable with year, season, and water depth, and contained fewer core species than the freshwater reservoir. Several hydrocarbon degraders and sulfur cycling bacteria were identified as indicator species of tailings ponds, while several phototrophs were indicative of freshwater. However, all of these species were abundant in BML, suggesting that the PL supports food webs characteristic of each control environment. Over the 6-year study, the relative abundances of some common freshwater phytoplankton (Cryptomonas, Mychonastes, Trebouxiophyceae, Cyanobium) and heterotrophic bacteria (Sporichthyaceae, Ca. Fonsibacter, Ilumatobacteraceae, Microbacteriaceae, Ca. Planktophila) increased in BML. The results suggest that microbial communities and processes in BML represent an intermediate state between a tailings pond and a natural freshwater system, and did not stabilize within 10 years of its creation.},
}

@article {pmid40460541,
year = {2025},
author = {Kang, MG and Kwak, MJ and Kang, A and Park, J and Lee, DJ and Mun, J and Kim, S and Mun, D and Lee, W and Choi, H and Seo, E and Choi, Y and Jeong, KC and Oh, S and Kim, J and Kim, Y},
title = {Metagenome-based microbial metabolic strategies to mitigate ruminal methane emissions using Komagataeibacter-based symbiotics.},
journal = {The Science of the total environment},
volume = {987},
number = {},
pages = {179793},
doi = {10.1016/j.scitotenv.2025.179793},
pmid = {40460541},
issn = {1879-1026},
abstract = {Global warming increasingly threatens organisms in equatorial regions, where temperatures often exceed physiological limits. Rumen methanogens are a major biological source of anthropogenic methane, a potent greenhouse gas. Therefore, ruminal methane mitigation strategies that preserve animal productivity are urgently needed. Our In vitro analysis of Holstein steer rumen fluid-integrating gas production, volatile fatty acid (VFA) profiles, and metagenomic data-demonstrated that kombucha, a fermented beverage, effectively reduces methane emissions by modulating ruminal fermentation. Rumen fluid was incubated for 60 h under three treatments (control, 3-NOP, and kombucha). During the initial 30 h, kombucha reduced methane by 15.07 % compared to the control but was 17.54 % higher than 3-NOP. In the subsequent 30 h, kombucha achieved sustained reductions of 34.72 % versus the control and 26.28 % versus 3-NOP, highlighting its uniquely sustained methane-reducing effect. A metagenomics-guided screening and in vitro validation identified Komagataeibacter intermedius SLAM-NK6B as a key strain underlying the methane-reducing effect of kombucha. The genome of SLAM-NK6B encodes biosynthetic gene clusters for cellulose, malate, citrate, and methanobactin-metabolites that can modulate the rumen microbiota. SLAM-NK6B supplementation reduced methanogen abundance by 53.32 % and increased hydrogen pressure, shifting microbial metabolism. Excluding acetate, VFA production increased significantly, with propionate levels elevated by 15.39-43.81 %. Metagenomic data further indicated activation of alternative hydrogen sink pathways, including citrate-to-propionate and malate-to-propionate conversions. This study proposes a novel microbial metabolic strategy for methane mitigation, enabling both methane reduction and enhanced fermentation efficiency. Such metabolic guidance of the rumen microbiome offers a sustainable approach to low-emission ruminant production.},
}

@article {pmid40459709,
year = {2025},
author = {Quoc, NB and Nhu, LTT and Chau, NNB},
title = {Identification of diet resources of big-eyed bug Geocoris ochropterus (Fieber) (Hemiptera: Geocoridae) by multiplex PCR and shotgun metagenomic approaches.},
journal = {Molecular biology reports},
volume = {52},
number = {1},
pages = {537},
pmid = {40459709},
issn = {1573-4978},
support = {E2022.02.1//Đại học Mở Thành phố Hồ Chí Minh/ ; },
mesh = {Animals ; *Metagenomics/methods ; Multiplex Polymerase Chain Reaction/methods ; *Hemiptera/genetics ; Diet ; Gastrointestinal Microbiome/genetics ; Metagenome/genetics ; },
abstract = {BACKGROUND: Big-eyed bugs (Geocoris spp.) are important generalist predators in agricultural ecosystems, playing a crucial role in natural pest control.

METHODS: To better understand their dietary sources, we assessed the plant and animal food sources in the gut of Geocoris ochropterus using multiplex PCR and shotgun metagenomic analysis. The PCR assays targeted genetic markers from both animal (COI) and plant (matK and rbcL) DNA.

RESULTS: Results revealed the presence of both animal and plant-derived DNA in the gut samples, indicating that Geocoris ochropterus feeds on a mixed diet. Additionally, the results of shotgun metagenomic sequencing of the gut microbiota showed a predominance of Eukaryota, with over 80% of sequences belonging to this domain, while a diverse range of taxonomic groups were identified, including arthropods, plants, bacteria, and fungi. Arthropods particularly insects from the orders Lepidoptera, Hemiptera, Hymenoptera, Coleoptera, Phasmatodea and plants belonging to the orders Brassicales, Cucurbitales, and Poales constituted the most abundant dietary components. At the genus level, notable taxa included Maniola (family Nymphalidae), Carposina (Carposinidae), Helicoverpa (Noctuidae), and Solanum (Solanaceae). Species-level analysis confirmed the dominance of several insect species, including Maniola hyperanthus, Carposina sasakii, and Bombyx mori, alongside plant species such as Cucumis melo, Gossypium hirsutum, and Digitaria exilis.

CONCLUSIONS: These findings provide a comprehensive characterization of the diet of Geocoris ochropterus, highlighting its role as a generalist predator with a diverse diet consisting of both insect and plant food sources. This study contributes to the understanding of Geocoris ochropterus as a potential biocontrol agent in agricultural systems.},
}

Animals
*Metagenomics/methods
Multiplex Polymerase Chain Reaction/methods
*Hemiptera/genetics
Diet
Gastrointestinal Microbiome/genetics
Metagenome/genetics

@article {pmid40458954,
year = {2025},
author = {Wang, Y and Pan, Z and Shi, Y and Bai, Y and Liang, J and Wang, A and Qu, J},
title = {MnOxGeneTool: A Comprehensive Tool for Identifying and Quantifying Mn(II)-Oxidizing Genes, Revealing Phylogenetic Diversity and Environmental Drivers of Mn(II)-Oxidizers.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c01235},
pmid = {40458954},
issn = {1520-5851},
abstract = {Manganese (Mn) oxides are crucial for degrading organic pollutants and driving biogeochemical cycles. Microorganisms drive Mn(II) oxidation, but traditional cultivation-dependent identification methods are inefficient and error-prone. To overcome these limitations, we developed MnOxGeneTool, a bioinformatics tool for identifying and quantifying Mn(II)-oxidizing genes from genomic and metagenomic data. MnOxGeneTool consists of three main components: (1) a curated database of known Mn(II)-oxidizing proteins and their homologues, (2) a hidden Markov models (HMMs) database derived from this protein data set, and (3) a computational pipeline that integrates bioinformatics tools (e.g., HMMER and BLASTX) to identify and quantify Mn(II)-oxidizing genes. We assessed the accuracy and sensitivity of these HMMs through cross-validation, demonstrating their effectiveness in identifying Mn(II)-oxidizing genes in bacterial genomes. Using MnOxGeneTool, we explored the phylogenetic diversity of Mn(II)-oxidizers and identified 824 bacterial genera containing Mn(II)-oxidizing genes, significantly expanding previous knowledge in this field. Additionally, we analyzed metagenomic data from various environments to explore environmental drivers of Mn(II)-oxidizing genes, identifying two potential drivers: oligotrophic conditions and alkaline environments. These findings enable targeted discovery of novel Mn(II)-oxidizers and genetic determinants through identification of their ecological niches and expression optima, thereby expanding MnOxGeneTool's predictive coverage of uncatalogued Mn(II)-oxidizing proteins. By providing an innovative bioinformatics tool that enables efficient identification and quantification of Mn(II)-oxidizing genes from both genomic and metagenomic data, this study offers significant advancements in the research of biogenic Mn(II) oxidation. The tool is available at https://github.com/wyh19990121/MnOxGeneTool.},
}

@article {pmid40458218,
year = {2025},
author = {Qush, A and Assaad, N and Alkhayat, FA and Al-Kuwari, MS and Al-Khalaf, N and Bassil, M and Yassine, HM and Zeidan, A and Razali, R and Kamareddine, L},
title = {Insects in agricultural greenhouses: a metagenomic analysis of microbes in Trialeurodes vaporariorum infesting tomato and cucumber crops.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1581707},
pmid = {40458218},
issn = {1664-462X},
abstract = {INTRODUCTION: With the predicted 9-10 billion world population increase by 2050 and its accompanying need for sustainable food production, and with the harsh climate conditions challenging agriculture and food security in many countries world-wide, employing "horticultural protected cultivation practices" in farming for seasonal and off-seasonal crop production is on the rise, among which is the use of agricultural greenhouses. The importance of greenhouse farming has been, indeed, evident by the perceived increase in year-round crops production, curtail in production risks, upsurge in agricultural profits, outreaching food stability and security in many countries globally. Yet, and despite this acknowledged success of employing greenhouses in farming, many constraints, including the presence of insect pests, still chaperoned this practice over the years, significantly impacting crop quality and production.

METHODS: As such, we assessed in this study the status of "insect pests" in the greenhouse model by collecting insects from different greenhouse sectors grown with tomatoes and cucumbers and identified the collected insects using relevant identification keys. To further explore the pest paradigm in greenhouses, we then focused on particularly studying Trialeurodes vaporariorum (TRIAVA), a key insect species among the collected and identified insects in the studied greenhouse model and a significant pest with an impactful effect on many crops worldwide. To do so, we traced the abundance of TRIAVA in the tomato and cucumber grown greenhouse sectors over the period of the study, analyzed its metagenome and associated its abundance with crop yield.

RESULTS AND DISCUSSION: Our findings revealed TRIAVA hosted microbes with aptitudes to either serve as symbiotic microorganisms and protect TRIAVA against pathogens or to potentially cause damage to crops. This work provides additional insight into the insect pests paradigm in greenhouses, an upshot that could serve integrated insect pest management strategies in greenhouses for optimal agricultural practices.},
}

@article {pmid40456950,
year = {2025},
author = {Kocharovskaya, Y and Delegan, Y and Sevostianov, S and Bogun, A and Demin, DV},
title = {Metagenomic Analysis of Pulp and Paper Wastes and Prospects for Their Self-purification.},
journal = {Current microbiology},
volume = {82},
number = {7},
pages = {320},
pmid = {40456950},
issn = {1432-0991},
mesh = {*Paper ; *Metagenomics ; Lignin/metabolism ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Industrial Waste/analysis ; Biodegradation, Environmental ; *Microbiota ; High-Throughput Nucleotide Sequencing ; },
abstract = {Thousands of tons of waste accumulate, as a result of the activities of the pulp and paper industry, which is often stored in the form of dumps. However, intensifying the use of lignocellulose for more efficient bioremediation remains highly challenging. Therefore, the study of microbiomes with potentially desirable characteristics for the decomposition of pulp and paper wastes is currently an important task. In this study, a comprehensive assessment of the microbiota biodiversity of these dumps was carried out using high-throughput, high-resolution sequencing. In study 472 million high-quality clean reads assembled into 6,413,337 contigs with a total length of 4306 Mb, of which 3,633,174 open reading frames (ORFs) were identified. The core microbiome was composed of four phyla from Proteobacteria, Actinobacteria, Bacteroidetes, and Verrucomicrobia. Representatives of phylum Proteobacteria prevailed in samples. Annotation using the KEGG database in the Metabolism category resulted in 654,234 ORFs and 5138 ORFs encoding enzymes/proteins involved in degradation of lignocellulose which formed main pool of the wastes. By use of the created database, the search for lignocellulose degradation genes showed that genera Shewanella, Achromobacter, and Delftia covered significant part of the reads. The results indicate that the established microbiome of local landfills can be considered as an important source for improving lignocellulose bioremediation, provided that lignocellulosic fungi are sufficiently active. In whole, these new data can be used as a scientific basis to form an efficient eco-biotechnology for auto-remediation of pulp and paper industry waste.},
}

*Paper
*Metagenomics
Lignin/metabolism
*Bacteria/classification/genetics/metabolism/isolation & purification
*Industrial Waste/analysis
Biodegradation, Environmental
*Microbiota
High-Throughput Nucleotide Sequencing

@article {pmid40456770,
year = {2025},
author = {Zhou, XQ and Chen, KH and Yu, RQ and Yang, M and Liu, Q and Hao, YY and Li, J and Liu, HW and Feng, J and Tan, W and Huang, Q and Gu, B and Liu, YR},
title = {Microbial potential to mitigate neurotoxic methylmercury accumulation in farmlands and rice.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {5102},
pmid = {40456770},
issn = {2041-1723},
support = {42425701//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42177022//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Methylmercury Compounds/metabolism/toxicity ; *Oryza/metabolism/microbiology ; *Soil Microbiology ; Biodegradation, Environmental ; Metagenomics ; *Soil Pollutants/metabolism/toxicity ; *Bacteria/metabolism/genetics/classification ; Soil/chemistry ; },
abstract = {Toxic methylmercury (CH3Hg[+]) is produced by microbial conversion of inorganic mercury in hypoxic environments such as rice paddy soils, and can accumulate in rice grains. Although microbial demethylation has been recognized as a crucial pathway for CH3Hg[+] degradation, the identities of microbes and pathways accountable for CH3Hg[+] degradation in soil remain elusive. Here, we combine [13]CH3Hg[+]-DNA stable-isotope probing experiments with shotgun metagenomics to explore microbial taxa and associated biochemical processes involved in CH3Hg[+] degradation in paddy and upland soils. We identify Pseudarthrobacter, Methylophilaceae (MM2), and Dechloromonas as the most significant taxa potentially engaged in the degradation of [13]CH3Hg[+] in paddy soil with high mercury contamination. We confirm that strains affiliated with two of those taxa (species Dechloromonas denitrificans and Methylovorus menthalis) can degrade CH3Hg[+] in pure culture assays. Metagenomic analysis further reveals that most of these candidate [13]CH3Hg[+] degraders carry genes associated with the Wood-Ljungdahl pathway, dicarboxylate-hydroxybutyrate cycle, methanogenesis, and denitrification, but apparently lack the merB and merA genes involved in CH3Hg[+] reductive demethylation. Finally, we estimate that microbial degradation of soil CH3Hg[+] contributes to 0.08-0.64 fold decreases in CH3Hg[+] accumulation in rice grains across China (hazard quotient (HQ) decrements of 0.62-13.75%). Thus, our results provide insights into microorganisms and pathways responsible for CH3Hg[+] degradation in soil, with potential implications for development of bioremediation strategies.},
}

*Methylmercury Compounds/metabolism/toxicity
*Oryza/metabolism/microbiology
*Soil Microbiology
Biodegradation, Environmental
Metagenomics
*Soil Pollutants/metabolism/toxicity
*Bacteria/metabolism/genetics/classification
Soil/chemistry

@article {pmid40456641,
year = {2025},
author = {Wen, M and Liu, Y and Feng, CY and Ji, W and Li, ZQ},
title = {Differences of key processes in soil nitrogen cycling and their driving factors under different land-use types.},
journal = {Ying yong sheng tai xue bao = The journal of applied ecology},
volume = {36},
number = {5},
pages = {1387-1397},
doi = {10.13287/j.1001-9332.202505.036},
pmid = {40456641},
issn = {1001-9332},
mesh = {*Soil/chemistry ; *Soil Microbiology ; *Nitrogen Cycle ; *Nitrogen/analysis/metabolism ; China ; Nitrification ; *Ecosystem ; Denitrification ; Forests ; Wetlands ; Grassland ; Agriculture ; Nitrogen Fixation ; },
abstract = {To investigate the responses and drivers of soil microbial nitrogen (N)-cycling functional genes under different land-use types, we analyzed five representative ecosystems in the Yellow River alluvial plain: Tamarix chinensis forests, Fraxinus chinensis forests, grasslands, wetlands, and farmlands. With metagenomic sequencing, we quantified the relative abundances of 22 functional genes associated with six critical N-cycling processes. Soil physicochemical properties were characterized. There were significant variations in soil nitrogen (N)-cycling functional gene abundances across land-use types. Wetlands exhibited the highest relative abundances of nitrogen fixation (1.28×10[-5]), nitrification (4.91×10[-4]), and denitrification (7.03×10[-4]) genes, but the lowest assimilatory nitrate reduction potential (1.84×10[-4]). Farmlands showed maximal assimilatory nitrate reduction gene abundance (3.31×10[-4]), while grasslands dominated in ammonification gene expression (2.35×10[-4]), significantly higher than other ecosystems. T. chinensis forests maintained the most constrained N-cycling profile, with minimal nitrification (2.77×10[-4]) and denitrification (5.25×10[-4]) relative gene abundances. Redundancy analysis identified soil total nitrogen, organic carbon, total potassium, and electrical conductivity as the key environmental drivers of these variations. Our findings demonstrated that land-use types could shape microbial N-cycling functional gene abundances by altering soil nutrient conditions, with consequence on fundamental processes of soil nitrogen transformation.},
}

*Soil/chemistry
*Soil Microbiology
*Nitrogen Cycle
*Nitrogen/analysis/metabolism
China
Nitrification
*Ecosystem
Denitrification
Forests
Wetlands
Grassland
Agriculture
Nitrogen Fixation

@article {pmid40456384,
year = {2025},
author = {Nayyar, J and Bedu-Ferrari, C and Patangia, D and Hurley, E and Feeley, L and Ross, RP and Stanton, C and Brady, P},
title = {Gut and oral microbial profile associations to oral cancer.},
journal = {Journal of dentistry},
volume = {},
number = {},
pages = {105848},
doi = {10.1016/j.jdent.2025.105848},
pmid = {40456384},
issn = {1879-176X},
abstract = {The human microbiome is widely known to be associated with health and disease. The oral microbiome has been linked with oral diseases and infections, though not many studies have explored the relation between oral and gut microbiome with oral cancer based on lesion histology METHODS: This study uniquely explores the oral and gut microbiota in 30 participants (n=30) divided into three groups based on histology; Benign (B) (n=15), Potentially Malignant (PM) (n=8), and Malignant (M) (n=7) oral lesions. Using shotgun metagenomic sequencing, we analysed microbiota profiles to determine their potential as biomarkers for oral malignancy RESULTS: Distinct gut microbial profiles were observed between Benign and Malignant groups and the association of specific microbes in oral saliva, such as Haemophilus parainfluenzae, Veillonella parvula, Fusobacterium nucleatum and Rothia mucilaginosa were strongly associated with malignancy CONCLUSION: The data from this exploratory study suggest that oral and gut microbiomes could act as possible biomarkers and aid in early detection and assessment of oral cancer risk. With regard to potentially malignant lesions, future research could study individual Oral Potentially Malignant Disorders (OPMDs) as distinct entities due to the wide variation in clinical and histological presentation. Further research is required to develop definitive biomarkers in both potentially malignant and malignant oral lesions CLINICAL SIGNIFICANCE: While smoking and alcohol are known risk factors for oral cancer, a biomarker such as the saliva/stool microbiome profile could help identify a risk indicator or a potential risk factor. Additionally such a biomarker could help identify patients with OPMDs that are likely to undergo malignant transformation.},
}

@article {pmid40456327,
year = {2025},
author = {Zhao, F and Yang, Z and Wang, J and Bartlam, M and Wang, Y},
title = {Enantioselective effects of chiral antibiotics on antibiotic resistance gene dissemination and risk in activated sludge.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132749},
doi = {10.1016/j.biortech.2025.132749},
pmid = {40456327},
issn = {1873-2976},
abstract = {Misuse of antibiotics drives the spread of antibiotic resistance genes (ARGs). Although reducing residual antibiotic concentrations can help curb ARG proliferation, the biodegradation and transformation of antibiotic stereoisomers may exacerbate resistance development. However, the impact of antibiotic enantiomers on ARG proliferation remains poorly understood. This study employed metagenomic analysis to investigate the enantiomer-specific selection and resistance risks of chiral antibiotic ofloxacin (OFL) and its (S)-enantiomer, levofloxacin (LEV), in activated sludge. Results showed that LEV primarily promoted the enrichment of ARGs related to aminoglycoside and mupirocin resistance by selecting for pathogenic bacteria carrying virulence factors under high toxicity stress. OFL-driven ARG proliferation involved more diverse mechanisms, including increased gene mobility, co-selection with heavy metals, broader host range, and elevated pathogenicity. The antibiotic resistome risk index (ARRI) further demonstrated a higher environmental risk under OFL treatment than LEV. These findings offer critical insights into the enantioselective resistance risks posed by chiral antibiotics.},
}

@article {pmid40455595,
year = {2025},
author = {Fetters, AM and Cantalupo, PG and Robles, MTS and Pipas, JM and Ashman, TL},
title = {Sharing Pollinators and Viruses: Virus Diversity of Pollen in a Co-Flowering Community.},
journal = {Integrative and comparative biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/icb/icaf073},
pmid = {40455595},
issn = {1557-7023},
abstract = {Co-flowering plant species frequently share pollinators, flower-inhabiting bacteria, and fungi, but whether pollen-associated viruses are shared is unknown. Given that pollen-associated viruses are sexually transmitted diseases, their diversity is expected to increase with pollinator sharing. We conducted a metagenomic study to identify pollen-associated viruses from 18 co-flowering plant species to determine whether 1) life history, floral traits, or pollination generalism were associated with viral richness, and 2) plants shared pollen-associated viruses. We demonstrated that pollination generalism influences pollen-associated virus richness and the extent of pollen virus sharing between plant species. We also revealed that perenniality, multiple flowers, and bilateral floral symmetry were associated with high pollen viral richness locally, confirming and extending patterns observed previously at a continental scale. Our results highlight the importance of plant-pollinator interactions as drivers of plant-viral interaction diversity.},
}

@article {pmid40455399,
year = {2025},
author = {Qayyum, H and Raziq, MF and Manzoor, H and Zaidi, SSA and Ali, A and Kayani, MUR},
title = {Efficient De Novo Assembly and Recovery of Microbial Genomes from Complex Metagenomes Using a Reduced Set of k-mers.},
journal = {Interdisciplinary sciences, computational life sciences},
volume = {},
number = {},
pages = {},
pmid = {40455399},
issn = {1867-1462},
abstract = {De novo assembly and genome binning are fundamental steps for genome-resolved metagenomics analyses. However, the availability of limited computational resources and extensive processing time limit the broader application of these analyses. To address these challenges, the optimization of the parameters employed in these processes can improve the effective utilization of available metagenomics tools. Therefore, this study tested three sets of k-mers (default, reduced, and extended) for their efficiency in metagenome assembly and suitability in recovering metagenome-assembled genomes. The results demonstrate that the reduced set of k-mers outperforms the other two sets in computational efficiency and the quality of results. The assemblies from the default set are comparable with those from the reduced set; however, less complete and highly contaminated metagenome-assembled genomes are obtained at the expense of higher processing time. The extended set of k-mers yields less contiguous but computationally expensive assemblies. This set takes approximately 3-times more processing time than the reduced k-mers and recovers the lowest proportions of high and medium-quality metagenome-assembled genomes. Contrarily, the reduced set produces better assemblies, substantially improving the number and quality of the recovered metagenome-assembled genomes in significantly reduced processing time. Validation of the reduced k-mer set on previously published metagenome datasets further demonstrates its effectiveness not only for human metagenomes but also for the metagenomes of environmental origin. These findings underscore that the reduced k-mer set is optimal for efficient metagenome analyses of varying complexities and origins. This optimization of the k-mer set used in metagenome assemblers significantly reduces computational time while improving the quality of the assemblies and recovered metagenome-assembled genomes. This efficient solution will facilitate the widespread application of genome-resolved analyses, even in resource-limited settings, and help the recovery of better-quality metagenome-assembled genomes for downstream analyses.},
}

@article {pmid40455288,
year = {2025},
author = {Hu, J and Yu, W and Cui, J and Zhang, L and Yu, W},
title = {Recent advances in diagnostic technologies for postoperative central nervous system infections: a review.},
journal = {Neurological sciences : official journal of the Italian Neurological Society and of the Italian Society of Clinical Neurophysiology},
volume = {},
number = {},
pages = {},
pmid = {40455288},
issn = {1590-3478},
abstract = {Postoperative central nervous system infections (PCNSIs), including meningitis, cerebral abscesses, and implant-associated infections, represent critical complications following neurosurgical procedures. These infections pose significant risks to patient outcomes due to delayed diagnosis, escalating antimicrobial resistance, and limited therapeutic efficacy. Conventional diagnostic approaches, such as cerebrospinal fluid (CSF) analysis, microbial cultures, and neuroimaging, exhibit notable limitations in sensitivity, specificity, and rapidity. This review highlights transformative technologies reshaping PCNSI diagnostics, including molecular assays (e.g., quantitative PCR, digital droplet PCR), metagenomic next-generation sequencing (mNGS), CRISPR-based pathogen detection platforms, metabolomics, and advanced molecular imaging modalities. Furthermore, we address translational challenges in clinical adoption, including cost barriers, standardization gaps, and the need for interdisciplinary collaboration. Emerging artificial intelligence (AI)-driven strategies are proposed to optimize pathogen identification, predict antimicrobial resistance profiles, and tailor personalized therapeutic regimens.},
}

@article {pmid40455149,
year = {2025},
author = {da Silva, AF and Wallau, GL},
title = {Bioinformatic Identification of Viral Genomes from High-Throughput Metagenomic Sequencing Data.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2927},
number = {},
pages = {1-22},
pmid = {40455149},
issn = {1940-6029},
mesh = {*Genome, Viral ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; *Computational Biology/methods ; *Viruses/genetics ; Phylogeny ; },
abstract = {Virus identification has historically been performed through cell culture isolation and low-throughput methodologies that are limited often requiring previous information about the investigated viruses. These classical virological methods have been pivotal to many discoveries, but overall, they have a limited capacity for characterization of highly divergent and novel viruses. Nowadays, new technologies such as next-generation sequencing have revolutionized the virology field, enabling unbiased high-throughput viral genome characterization. But although the sequencing bottleneck has been surpassed, we could not say the same for the bioinformatics bottleneck of fishing new viral genomes from these large datasets littered with host and other microbes sequencing data. Here, we describe a bioinformatic framework to process metagenomic or metatranscriptomic data, aiming to assemble, identify, and study the evolutionary relationship of viral sequences and genomes.},
}

*Genome, Viral
*High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
*Computational Biology/methods
*Viruses/genetics
Phylogeny

@article {pmid40454874,
year = {2025},
author = {Pfister, CA and Berlinghof, J and Bogan, M and Cardini, U and Gobet, A and Hamon-Giraud, P and Hart, J and Jimenez, N and Siegel, A and Stanfield, E and Vallet, M and Leblanc, C and Rousseau, C and Thomas, F and Stock, W and Dittami, SM},
title = {Evolutionary history and association with seaweeds shape the genomes and metabolisms of marine bacteria.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0099624},
doi = {10.1128/msphere.00996-24},
pmid = {40454874},
issn = {2379-5042},
abstract = {UNLABELLED: Seaweeds harbor a rich diversity of bacteria, providing them with metabolic resources and a surface for attachment and biofilm development. The host's unique environment potentially shapes the bacterial genomes and promotes adaptations for a symbiotic lifestyle. To investigate whether the genomes of seaweed-associated bacteria are genetically and metabolically distinct from their close free-living relatives in seawater, we compared both the seaweed-associated and free-living counterparts of 72 bacterial genera across 16 seaweed hosts using whole-genome sequences or high-quality metagenome-assembled genomes. While taxonomic affiliation strongly influenced genome characteristics such as GC content, gene number, and size, host association had a lower effect overall. A reduced genome size was suggested only in Nereocystis luetkeana-associated microbes, while only Ascophyllum nodosum-associated bacteria had an increased GC content. Metabolic adaptations were indicated from the genomes of seaweed-associated bacteria, including enriched pathways for B vitamin production, complex carbohydrate utilization, and amino acid biosynthesis. In particular, Flavobacteriia showed the most pronounced differences between host-associated and free-living strains. We further hypothesized that bacteria associated with seaweed might have evolved to complement their host's metabolism and tested this inference by analyzing the genomes of both the seaweed Ectocarpus subulatus and its 28 bacterial associates but found no evidence for such complementarity. Our analyses of 72 paired bacterial genomes highlighted significant metabolic differences in seaweed-associated strains with implications for carbon, nitrogen, and sulfur cycling in the coastal ocean.

IMPORTANCE: We hypothesized that the unique environment of seaweeds in coastal oceans shapes bacterial genomes and promotes a symbiotic lifestyle. We compared the genomes of bacteria isolated from seaweed with bacteria from the same genus found free-living in seawater. For genome features that included the number of genes, the size of the genome, and the GC content, taxonomy was of greater importance than bacterial lifestyle. When we compared metabolic abilities, we again found a strong effect of taxonomy in determining metabolism. Although several metabolic pathways differed between free-living and host-associated bacteria, this was especially prominent for Flavobacteriia in the phylum Bacteroidota. Notably, bacteria living on seaweeds had an increased occurrence of genes for B vitamin synthesis, complex carbohydrate use, and nitrogen uptake, indicating that bacterial genomes reflect both their evolutionary history and the current environment they inhabit.},
}

@article {pmid40454811,
year = {2025},
author = {Millard, SA and Vendrov, KC and Young, VB and Seekatz, AM},
title = {Host origin of microbiota drives functional recovery and Clostridioides difficile clearance in mice.},
journal = {mBio},
volume = {},
number = {},
pages = {e0110825},
doi = {10.1128/mbio.01108-25},
pmid = {40454811},
issn = {2150-7511},
abstract = {UNLABELLED: Colonization resistance provided by the gut microbiota is essential for resisting both initial Clostridioides difficile infection (CDI) and potential recurrent infection (rCDI). Although fecal microbiota transplantation (FMT) has been successful in treating rCDI by restoring microbial composition and function, mechanisms underlying the efficacy of standardized stool-derived products remain poorly understood. Using a combination of 16S rRNA gene-based and metagenomic sequencing alongside metabolomics, we investigated microbiome recovery following FMT from human and murine donor sources in a mouse model of rCDI. We found that a human-derived microbiota was less effective in clearing C. difficile compared to a mouse-derived microbiota, despite recovery of taxonomic diversity, compositional changes, and bacterial functions typically associated with clearance. Metabolomic analysis revealed deficits in secondary metabolites compared to those that received murine FMT, suggesting a functional remodeling between human microbes in their new host environment. Collectively, our data revealed additional environmental, ecological, or host factors to consider in FMT-based recovery from rCDI.

IMPORTANCE: Clostridioides difficile is a significant healthcare-associated pathogen, with recurrent infections presenting a major treatment challenge due to further disruption of the microbiota after antibiotic administration. Despite the success of fecal microbiota transplantation (FMT) for the treatment of recurrent infection, the mechanisms mediating its efficacy remain underexplored. This study reveals that the effectiveness of FMT may be compromised by a mismatch between donor microbes and the recipient environment, leading to deficits in key microbial metabolites. These findings highlight additional factors to consider when assessing the efficacy of microbial-based therapeutics for C. difficile infection (CDI) and other conditions.},
}

@article {pmid40454480,
year = {2025},
author = {Lynch, LE and Lahowetz, R and Maresso, C and Terwilliger, A and Pizzini, J and Melendez Hebib, V and Britton, RA and Maresso, AW and Preidis, GA},
title = {Present and future of microbiome-targeting therapeutics.},
journal = {The Journal of clinical investigation},
volume = {135},
number = {11},
pages = {},
pmid = {40454480},
issn = {1558-8238},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Probiotics/therapeutic use ; *Phage Therapy/trends/methods ; Bacteriophages ; Animals ; },
abstract = {A large body of evidence suggests that single- and multiple-strain probiotics and synbiotics could have roles in the management of specific gastrointestinal disorders. However, ongoing concerns regarding the quality and heterogeneity of the clinical data, safety in vulnerable populations, and the lack of regulation of products containing live microbes are barriers to widespread clinical use. Safety and regulatory issues must be addressed and new technologies considered. One alternative future strategy is the use of synthetic bacterial communities, defined as manually assembled consortia of two or more bacteria originally derived from the human gastrointestinal tract. Synthetic bacterial communities can model functional, ecological, and structural aspects of native communities within the gastrointestinal tract, occupying varying nutritional niches and providing the host with a stable, robust, and diverse gut microbiota that can prevent pathobiont colonization by way of colonization resistance. Alternatively, phage therapy is the use of lytic phage to treat bacterial infections. The rise of antimicrobial resistance has led to renewed interest in phage therapy, and the high specificity of phages for their hosts has spurred interest in using phage-based approaches to precisely modulate the microbiome. In this Review, we consider the present and future of microbiome-targeting therapies, with a special focus on early-life applications, such as prevention of necrotizing enterocolitis.},
}

Humans
*Gastrointestinal Microbiome
*Probiotics/therapeutic use
*Phage Therapy/trends/methods
Bacteriophages
Animals

@article {pmid40454439,
year = {2025},
author = {Rosam, K and Steixner, S and Bauer, A and Lass-Flörl, C},
title = {Non-conventional diagnostic methods for invasive fungal infections.},
journal = {Expert review of molecular diagnostics},
volume = {},
number = {},
pages = {},
doi = {10.1080/14737159.2025.2509026},
pmid = {40454439},
issn = {1744-8352},
abstract = {INTRODUCTION: Biomarkers have revolutionized the field of fungal diagnostics by enabling early detection, risk assessment, and monitoring treatment response. Their value in clinical practice is influenced by a wide range of determinants including diagnostic performance (sensitivity and specificity), predictive value in diverse patient groups, host immune status and comorbidities, technical standardization and antifungal treatment.

AREA COVERED: This review provides a comprehensive overview of the current antigen and DNA-based methods used for the detection of invasive fungal infections (IFIs), with a particular focus on the clinically significant pathogens Aspergillus spp. Candida spp. and Mucorales. It examines the advantages and limitations of the available diagnostic tools, emphasizing their role in early detection, specificity, and clinical application.

EXPERT OPINION: The selection of fungal biomarkers should be tailored based on the patient population, the clinical setting, and the type of fungal infection suspected. Using a combination of biomarkers often improves diagnostic accuracy, particularly in high-risk populations like hematologic malignancy patients. Fungal biomarkers do not provide definitive proof of an active fungal infection; instead, they serve as indirect indicators of the presence of fungal components. Their primary role is to support the diagnosis, assess risk, and guide clinical decisions, but they must be interpreted within the broader clinical context to follow current guidelines for diagnosing fungal infections (EORTC/MSG).},
}

@article {pmid40454309,
year = {2025},
author = {Xu, J and Li, Y and Wang, X and Mu, Y},
title = {Case Report: A Case of Visceral Leishmaniasis Misdiagnosed as Brucellosis.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {2673-2677},
pmid = {40454309},
issn = {1178-6973},
abstract = {Visceral leishmaniasis (VL) is an infectious disease caused by protozoan parasites of the genus Leishmania and transmitted through the bites of infected female sandflies. Due to its nonspecific clinical presentation, VL is prone to misdiagnosis and underdiagnosis. Though rare, VL is endemic in regions of Africa, South America, Asia, and parts of Europe, including the Mediterranean. This report describes a case of VL initially misdiagnosed as brucellosis due to a history of close contact with sheep. The patient tested negative for brucellosis via serum agglutination, blood culture, and bone marrow smear, and showed no improvement with a combination of omadacycline and rifampin therapy. Definitive diagnosis was achieved through metagenomic next-generation sequencing (mNGS) and confirmation with the rk39 antigen test. The patient was successfully treated with amphotericin B cholesterol sulfate complex and recovered fully. This case highlights the need to consider rare pathogens when epidemiological history and clinical response to treatment are incongruent and emphasizes the value of mNGS in timely diagnosis of VL.},
}

@article {pmid40454150,
year = {2025},
author = {Du, R and Mao, H and Li, WM and Liu, D and Wang, K},
title = {Case Report: Empyema secondary to percutaneous transthoracic needle biopsy in three cases.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1531909},
pmid = {40454150},
issn = {2296-858X},
abstract = {Percutaneous transthoracic needle biopsy (PTNB) is a widely utilized diagnostic procedure for pulmonary lesions, with the current literature predominantly documenting pneumothorax and hemorrhage as primary complications. While empyema represents a rare complication, its clinical implications warrant special attention. In this study, we report the cases of three patients with unidentified pulmonary masses who developed empyema after PTNB. All cases exhibited fever (24-48 h post-procedure) and radiographic evidence of pleural effusion progression shortly after the procedure, which was successfully managed through pleural drainage and antibiotic treatment. These findings suggest that pre-procedural infectious foci may be prone to iatrogenic pleural seeding during PTNB. This report emphasizes the necessity of monitoring infectious indicators in patients undergoing biopsy of cavitary or necrotic lesions. Physicians should exercise caution when puncturing lumps suspected of abscesses and remain vigilant for empyema secondary to PTNB if the patient shows signs of infection.},
}

@article {pmid40453877,
year = {2025},
author = {Ma, R and Yin, Y and Zhang, JP and Zhang, MX and Zhou, JR and He, Y and Gai, W and Zhang, XH and Wang, Y and Xu, LP and Liu, KY and Huang, XJ and Sun, YQ},
title = {Metagenomic Next-generation Sequencing Compared With Blood Culture as First-line Diagnostic Method for Bloodstream Infection in Hematologic Patients With Febrile Neutropenia: A Multicenter, Prospective Study.},
journal = {Open forum infectious diseases},
volume = {12},
number = {6},
pages = {ofaf288},
pmid = {40453877},
issn = {2328-8957},
abstract = {Bloodstream infection (BSI) is a frequent but lethal complication in hematologic patients with febrile neutropenia (FN). However, blood culture (BC) only detects an organism in 20%-30% of patients with FN. We aimed to evaluate the diagnostic performance of metagenomic next-generation sequencing (mNGS) as a first-line diagnostic method in BSI. This study was prospectively performed in 4 Chinese hematologic centers. In patients aged ≥15 years with hematologic diseases, peripheral blood specimens were collected per patient for simultaneous BC and mNGS at the onset of FN. The clinical physician and mNGS analysis team were double-blinded, and the adjudication of the clinical diagnosis was evaluated by another expert panel of 4 specialists. The primary endpoint of this study was the diagnostic performance of mNGS. This study was registered on ClinicalTrials.gov. Three hundred FN events were enrolled, including 62 definite BSI, 61 probable BSI, 116 infectious FN other than BSI, 55 noninfectious FN events, and 6 FN of indeterminate cause. Among 62 definite BSI cases, mNGS identified causative pathogens in 59 (95.2%). Concurrent BC initially detected pathogens in 59 cases, and 3 additional pathogens consistent with mNGS were later identified in repeated BC testing. The sensitivity, specificity, positive predictive value, and negative predictive value of mNGS were 95.2%, 94.6%, 95.2%, and 94.6%, respectively. The diagnostic time of mNGS was significantly shorter than that of BC (39.7 ± 15.0 vs 119.8 ± 31.9 hours, P < .0001). The findings suggest that the mNGS approach has excellent diagnostic performance for the first-line diagnosis of BSI in patients with FN. The study will promote early diagnosis and better management of the patients.},
}

@article {pmid40453711,
year = {2025},
author = {Zhou, J and Kamau, E and Wei, Q},
title = {Editorial: Targeted metagenomics in pathogen detection.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1612802},
pmid = {40453711},
issn = {2235-2988},
}

@article {pmid40452057,
year = {2025},
author = {Francioli, D and Kampouris, ID and Kuhl-Nagel, T and Babin, D and Sommermann, L and Behr, JH and Chowdhury, SP and Zrenner, R and Moradtalab, N and Schloter, M and Geistlinger, J and Ludewig, U and Neumann, G and Smalla, K and Grosch, R},
title = {Microbial inoculants modulate the rhizosphere microbiome, alleviate plant stress responses, and enhance maize growth at field scale.},
journal = {Genome biology},
volume = {26},
number = {1},
pages = {148},
pmid = {40452057},
issn = {1474-760X},
support = {031B0514A- E//Bundesministerium für Bildung und Forschung/ ; 031B0514A- E//Bundesministerium für Bildung und Forschung/ ; 031B0514A- E//Bundesministerium für Bildung und Forschung/ ; 031B0514A- E//Bundesministerium für Bildung und Forschung/ ; 031B0514A- E//Bundesministerium für Bildung und Forschung/ ; 031B0514A- E//Bundesministerium für Bildung und Forschung/ ; 031B0514A- E//Bundesministerium für Bildung und Forschung/ ; 031B0514A- E//Bundesministerium für Bildung und Forschung/ ; 031B0514A- E//Bundesministerium für Bildung und Forschung/ ; 031B0514A- E//Bundesministerium für Bildung und Forschung/ ; 031B0514A- E//Bundesministerium für Bildung und Forschung/ ; 031B0514A- E//Bundesministerium für Bildung und Forschung/ ; 031B0514A- E//Bundesministerium für Bildung und Forschung/ ; 031B0514A- E//Bundesministerium für Bildung und Forschung/ ; 031B0514A- E//Bundesministerium für Bildung und Forschung/ ; },
mesh = {*Zea mays/microbiology/growth & development ; *Rhizosphere ; *Microbiota ; *Stress, Physiological ; Bacillus ; Plant Roots/microbiology ; Soil Microbiology ; *Agricultural Inoculants/physiology ; },
abstract = {BACKGROUND: Field inoculation of crops with beneficial microbes is a promising sustainable strategy to enhance plant fitness and nutrient acquisition. However, effectiveness can vary due to environmental factors, microbial competition, and methodological challenges, while their precise modes of action remain uncertain. This underscores the need for further research to optimize inoculation strategies for consistent agricultural benefits.

RESULTS: Using a comprehensive, multidisciplinary approach, we investigate the effects of a consortium of beneficial microbes (BMc) (Pseudomonas sp. RU47, Bacillus atrophaeus ABi03, Trichoderma harzianum OMG16) on maize (Zea mays cv. Benedictio) through an inoculation experiment conducted within a long-term field trial across intensive and extensive farming practices. Additionally, an unexpected early drought stress emerged as a climatic variable, offering further insight into the effectiveness of the microbial consortium. Our findings demonstrate that BMc root inoculation primarily enhanced plant growth and fitness, particularly by increasing iron uptake, which is crucial for drought adaptation. Inoculated maize plants show improved shoot growth and fitness compared to non-inoculated plants, regardless of farming practices. Specifically, BMc modulate plant hormonal balance, enhance the detoxification of reactive oxygen species, and increase root exudation of iron-chelating metabolites. Amplicon sequencing reveals shifts in rhizosphere bacterial and fungal communities mediated by the consortium. Metagenomic shotgun sequencing indicates enrichment of genes related to antimicrobial lipopeptides and siderophores.

CONCLUSIONS: Our findings highlight the multifaceted benefits of BMc inoculation on plant fitness, significantly influencing metabolism, stress responses, and the rhizosphere microbiome. These improvements are crucial for advancing sustainable agricultural practices by enhancing plant resilience and productivity.},
}

*Zea mays/microbiology/growth & development
*Rhizosphere
*Microbiota
*Stress, Physiological
Bacillus
Plant Roots/microbiology
Soil Microbiology
*Agricultural Inoculants/physiology

@article {pmid40451466,
year = {2025},
author = {Osogo, AK and Muyekho, F and Were, H and Okoth, P},
title = {Deciphering common bean (Phaseolus Vulgaris L.) microbiome assemblages reveal mechanistic insights into host-pathogen-microbiome interactions.},
journal = {Genomics},
volume = {},
number = {},
pages = {111064},
doi = {10.1016/j.ygeno.2025.111064},
pmid = {40451466},
issn = {1089-8646},
abstract = {Common bean (Phaseolus vulgaris L.) is the primary source of proteins and nutrients in most households in sub-Saharan Africa. However, production of this crop is constrained by several biotic factors. While research on common bean plant-pathogen interactions has predominantly focused on binary relationships, the diversity of microbes naturally inhabiting plant tissues and their interactions has often been overlooked. Recent findings, however, show that these resident microbes actively contribute to plant defense mechanisms, rather than merely acting as passive bystanders. This study aimed to document and explore potential interactions within the common bean microbiome assemblages through field investigations in selected locations across the western regions of Kenya. Common bean leaf samples were collected from farmer's fields along motorable roads 3-5 km apart. Shotgun metagenomic analysis identified a diverse range of microorganisms, including bacteria, fungi, yeast, phytoplasmas, viruses, and bacteriophages, across multiple taxonomic levels-spanning 4 Kingdoms, 136 Phyla, 168 Classes, 360 Orders, 792 Families, 2039 Genera, and 6130 Species-both epiphytic and endophytic, and pathogenic or non-pathogenic. Pseudomonadota consistently showed the highest taxonomic annotation for antimicrobial-resistant organisms, highlighting its central role in resistance across the studied area. The sequences obtained were mapped to the EggNOG, CAZy, and KEGG databases to explore, assign, and predict gene functions. The EggNOG database emphasized the importance of "Replication, recombination, and repair" processes in maintaining genomic stability, along with amino acid transport, energy production, and metabolism. CAZy analysis revealed a significant presence of glycosyltransferases, particularly from GT1 and GT32 families, and noted the role of enzymes like Glycoside Hydrolases in plant defense against pathogens. KEGG pathway analysis underscored the central role of metabolic processes such as energy metabolism, translation, and carbohydrate metabolism. Key pathways linked to plant defense and resilience, including 2-oxocarboxylic acid metabolism, amino acid biosynthesis, and secondary metabolite biosynthesis, were identified. These findings underscore the role of metabolic and enzymatic processes in strengthening plant defenses and stress tolerance while laying the groundwork for multidisciplinary research to advance sustainable agriculture and food safety.},
}

@article {pmid40451005,
year = {2025},
author = {Su, X and Liu, J and Chang, L and Hu, W and Fang, Y and Li, J and Huang, L and Shu, W and Dong, H},
title = {Viral insights into the acidification of sulfidic mine tailings.},
journal = {Journal of hazardous materials},
volume = {494},
number = {},
pages = {138754},
doi = {10.1016/j.jhazmat.2025.138754},
pmid = {40451005},
issn = {1873-3336},
abstract = {The acidification of sulfidic mine tailings, driven primarily by sulfur- and iron-oxidizing microorganisms, can lead to severe environmental pollution and imperil human health. The role of viruses in this process and its underlying mechanisms yet remain poorly understood. In this study, we recovered 623 species-level viral genomes and 322 prokaryotic genomes from seven metagenomes of mine tailings with pH values ranging from 7.51 to 2.13. We observed that acidification drastically altered geochemical properties and degraded environmental quality, characterized by significant decreases in carbon/nitrogen ratio and heavy metal levels. The structure and function of viral communities were significantly correlated with pH and prokaryotic diversity, showing distinct dynamics across different acidification stages, similar to patterns observed in the prokaryotic community. Notably, potential sulfur-oxidizing prokaryotes increased in relative abundance as pH declined, while their virus-host abundance ratio exhibited a significant positive correlation with pH. Results indicated that viral "top-down" predation on sulfur-oxidizing prokaryotes was likely suppressed during acidification, providing a survival advantage to these organisms over iron-oxidizing counterparts. Moreover, viruses likely reprogrammed the sulfur and iron metabolism of prokaryotic hosts and enhanced their adaptability to environmental stressors through auxiliary metabolic genes. Additionally, a pH- and lifestyle-dependent evolutionary scenario for viruses revealed that frequent recombination and the accumulation of synonymous mutations in lytic viruses and chronic Inoviridae, likely increased their intrapopulation diversity and resilience. These findings provide new insights into the multifaceted roles of viruses in mine tailings acidification, deepening understanding of the underlying mechanisms and advancing potential strategies to mitigate associated environmental risks.},
}

@article {pmid40450941,
year = {2025},
author = {Wu, L and Wang, J and Jin, T and Zhou, X and Wang, L},
title = {Lignin-enhanced fungal-bacterial consortium for degradation of petroleum hydrocarbon contaminants.},
journal = {Journal of environmental management},
volume = {388},
number = {},
pages = {125973},
doi = {10.1016/j.jenvman.2025.125973},
pmid = {40450941},
issn = {1095-8630},
abstract = {A lignin-enhanced fungal-bacterial consortium strategy (Bau_Lignin) was proposed to promote the biodegradation of petroleum hydrocarbon contaminants (PHCs), with pyrene and n-docosane selected as representative compounds. Optimal performance was achieved by co-inoculating fungi and bacteria at a 5:5 ratio. Within 12 days, the pyrene removal efficiency of Bau_Lignin was 2.23 times and 1.67 times higher than that of the bacterial consortium (XH40) and the fungal-bacterial consortium (Bau), respectively. Lignin addition enhanced enzyme activities (e.g., ligninolytic enzymes, dioxygenases, dehydrogenases) and increased the abundance of key functional genera (e.g., Pseudomonas, Achromobacter, Stenotrophomonas). Metagenomic sequencing further revealed an enrichment of genes associated with biosurfactant production and oxygenase activity in Bau_Lignin, facilitating mass transfer, hydroxylation, and ring-cleavage processes. Thus, a potential reinforcement mechanism was proposed, highlighting the synergistic interactions among enzyme activities, functional genera, and key functional genes across multiple pathways.},
}

@article {pmid40450938,
year = {2025},
author = {Hou, Y and Jia, R and Zhou, L and Zhang, L and Wei, S and Li, B and Zhu, J},
title = {Alterations in microbial-mediated methane, nitrogen, sulfur, and phosphorus cycling within paddy soil induced by integrated rice-fish farming.},
journal = {Journal of environmental management},
volume = {388},
number = {},
pages = {126056},
doi = {10.1016/j.jenvman.2025.126056},
pmid = {40450938},
issn = {1095-8630},
abstract = {Rice paddies are crucial ecosystems, supporting dense microbial populations and playing a significant role in global food security. Integrated rice-fish farming has been recognized as an important agricultural production pattern to enhance agro-ecosystem stability and food productivity. Using metagenomic sequencing, we compared the microbial-mediated soil CH4, N, S, and P cycles in integrated rice-fish farming versus traditional rice monoculture, exploring their potential coupling mechanisms within microbes. Integrated rice-fish farming has significantly impacted these microbial-mediated cycles in paddy soil, altering the overall functional diversity, sum abundance, and microbial host diversity for the CH4, N, S, and P cycling genes. Specifically, it suppressed the denitrification, assimilatory nitrate reduction (ANR), assimilatory sulfate reduction (ASR), thiosulfate oxidation, organic phosphoester hydrolysis, and two-component system pathways and most of their associated functional genes, while enhanced the acetoclastic methanogenesis and the reduction of tetrathionate to thiosulfate processes. Compared to traditional rice monoculture, integrated rice-fish farming resulted in metagenome-assembled genomes (MAGs) with fewer and more isolated biogeochemical cycling genes, lacking potential couplings among multi-element cycles. Additionally, this farming approach increased the soil nutrient levels including the total carbon (TC), total organic carbon (TOC), total nitrogen (TN), total sulfur (TS), and total phosphorus (TP) concentrations, which have been identified as the most crucial factors driving the alterations in microbial functional genes/pathways involved in biogeochemical cycling processes in our study. Overall, integrated rice-fish farming dynamically altered the microbial-mediated CH4, N, S, and P cycles and their potential couplings within microbes through promoting the soil nutrient levels, which could favor rice growth, thus maintaining food security and providing refined knowledge for maintaining soil sustainability.},
}

@article {pmid40450783,
year = {2025},
author = {Rajput, V and Pramanik, R and Nannaware, K and Shah, P and Bhalerao, A and Jain, N and Shashidhara, LS and Kamble, S and Dastager, S and Dharne, M},
title = {Metagenomics based longitudinal monitoring of antibiotic resistome and microbiome in the inlets of wastewater treatment plants in an Indian megacity.},
journal = {The Science of the total environment},
volume = {986},
number = {},
pages = {179691},
doi = {10.1016/j.scitotenv.2025.179691},
pmid = {40450783},
issn = {1879-1026},
abstract = {The growing threat of antimicrobial resistance (AMR) poses a significant global challenge, undermining advancements in healthcare, agriculture, and life expectancy. Despite its critical importance, data on population-level AMR trends, including seasonal and temporal variations, remain scarce. In this study, we conducted metagenomic analysis on 190 wastewater samples collected monthly from December 2022 to December 2023 in Pune, India, to assess the diversity, dynamics, and co-occurrence of AMR determinants. Using nanopore shotgun sequencing, we generated 87.86 Gbp of data, enabling the taxonomic classification of 157 bacterial phyla and 3291 genera. Proteobacteria dominated the microbial community, with notable seasonal shifts, including increased Streptococcus abundance correlating with SARS-CoV-2 viral surges in March 2023. We identified 637 distinct antimicrobial resistance genes (ARGs) associated with 29 antibiotic classes, with multidrug, macrolide-lincosamide-streptogramin, beta-lactams, and tetracyclines genes being the most prevalent, particularly within WHO priority pathogens such as Enterobacteriaceae and Pseudomonas. Temporal normalization of ARG abundance revealed significant seasonal variability, peaking during winter, potentially driven by increased antibiotic use for respiratory infections. The integration of viral load data with AMR trends highlighted complex interactions between viral outbreaks and AMR dissemination. This study demonstrates the potential of wastewater surveillance as an early warning system for AMR, providing valuable insights into environmental and community resistance dynamics. Our results underscore the importance of integrated AMR surveillance to inform public health strategies aimed at mitigating the global AMR threat.},
}

@article {pmid40450775,
year = {2025},
author = {Han, M and Li, S and Li, Z and Wang, A and Ren, N and Ho, SH},
title = {Layer-specific photo-metabolic specialization of encapsulated microalgae: A strategy for synchronous multi-nitrogen elimination from wastewater.},
journal = {Water research},
volume = {282},
number = {},
pages = {123926},
doi = {10.1016/j.watres.2025.123926},
pmid = {40450775},
issn = {1879-2448},
abstract = {Conventional wastewater treatment (WWT) systems face persistent challenges in simultaneous ammonium (NH4[+]-N) and nitrate (NO3[-]-N) removal due to substrate competition and energy-intensive multi-stage processes. This study presents an innovative strategy leveraging encapsulated microalgal systems to achieve synchronous 94.45 % NH4[+]-N and 98.47 % NO3[-]-N removal within a single reactor through spatial reprogramming of photosynthetic energy allocation. By exploiting the structural heterogeneity within alginate-encapsulated beads, depth-stratified metabolic zones were created that challenge the long-held dogma of microalgae's inherent NH4[+]-N preference. Multidimensional analyses, including spatial distribution mapping, molecular dynamics simulations, metagenomic profiling and photosynthetic regulation, further revealed that light-modulated oxygen gradients, polymer-mediated solute transport, and stratified photo-metabolic specialization synergistically reprogramed microalgal nitrogen metabolism, enabling co-utilization of NH4[+]-N and NO3[-]-N. The system demonstrated robust dual-nitrogen assimilation efficiencies under varying environmental conditions, transcending conventional substrate utilization hierarchies. This transformative approach not only resolves the dilemma of mixed nitrogen pollution but also advances sustainable WWT by integrating pollutant removal with biomass valorization. The findings provide mechanistic insights into microalgal metabolic plasticity and offer a scalable, energy-efficient solution to upgrade traditional denitrification technologies, aligning with urgent demands for circular economy in water resource management.},
}

@article {pmid40450375,
year = {2025},
author = {Kuhar, U and Krapež, U and Slavec, B and Račnik, J and Šenica Kavčič, P and Jamnikar-Ciglenecki, U},
title = {Virome analysis suggests deltacoronaviruses and picornaviruses as a probable cause of severe intestinal disease on three quail farms.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {54},
pmid = {40450375},
issn = {2524-4671},
support = {research core funding No. P4-0092 and research project No. J4-8824//The Slovenian Research and Innovation Agency/ ; research core funding No. P4-0092 and research project No. J4-8824//The Slovenian Research and Innovation Agency/ ; research core funding No. P4-0092 and research project No. J4-8824//The Slovenian Research and Innovation Agency/ ; research core funding No. P4-0092 and research project No. J4-8824//The Slovenian Research and Innovation Agency/ ; research core funding No. P4-0092 and research project No. J4-8824//The Slovenian Research and Innovation Agency/ ; research core funding No. P4-0092 and research project No. J4-8824//The Slovenian Research and Innovation Agency/ ; },
abstract = {BACKGROUND: Quail farming is increasingly popular mainly due to higher market interest in meat and eggs. However, quails are susceptible to several common poultry viral infections, especially in intensive farming systems. Enteric viruses in poultry can cause significant economic losses, particularly in young birds. Mixed viral infections often exacerbate disease severity. Gamma and deltacoronaviruses are known causes of enteritis in quails, although infections with coronaviruses as well as picornaviruses may be also asymptomatic. Advanced diagnostic tools like next-generation sequencing (NGS) and metagenomics have improved understanding of these infections, yet knowledge gaps persist, and new viruses are continually being identified.

RESULTS: Three outbreaks of enteritis with high mortality in quail farms were investigated using NGS with a metagenomic approach. We found that coronaviruses, picornaviruses (anativiruses) and parvoviruses were highly abundant in samples from investigated outbreaks. Viruses belonging to the families Adenoviridae, Astroviridae and Flaviviridae were less abundant and not present in all samples. Coronaviruses and picornaviruses were detected in all outbreaks, while parvovirus was detected only in one. The complete genomes of three quail deltacoronaviruses, three quail anativiruses and one quail chaphamaparvovirus were determined by NGS. Phylogenetic analysis revealed that the coronavirus and anativirus strains from this study were closely related to the other relevant quail virus strains. As for chaphamaparvovirus, this is the first report of this virus in quails.

CONCLUSIONS: The data from this study indicates the presence of numerous viruses in samples from quails with enteritis that have been overlooked by standard diagnostic approaches but could have played a role in the development of enteritis. These results may support further analysis of virome in healthy quails and in those with different clinical signs.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42523-025-00428-6.},
}

@article {pmid40450182,
year = {2025},
author = {Wang, C and Dong, T and Rong, X and Yang, Y and Mou, J and Li, J and Ge, J and Mu, X and Jiang, J},
title = {Microbiome in prostate cancer: pathogenic mechanisms, multi-omics diagnostics, and synergistic therapies.},
journal = {Journal of cancer research and clinical oncology},
volume = {151},
number = {6},
pages = {178},
pmid = {40450182},
issn = {1432-1335},
support = {82172230//the National Natural Science Foundation of China/ ; 21ZGY29//the Changchun Scientific and Technological Development Program/ ; 3R218FM83430//Life Spring AKY Pharmaceuticals/ ; 20240205001YY//the Jilin Scientific and Technological Development Program/ ; 2017F014//the Jilin Health Service Capacity Improvement Program/ ; },
mesh = {Humans ; *Prostatic Neoplasms/microbiology/therapy/diagnosis/pathology ; Male ; *Microbiota ; Metagenomics/methods ; Multiomics ; },
abstract = {BACKGROUND: Prostate cancer (PCa) is a leading cause of cancer-related deaths in men, with the microbiome emerging as a significant factor in its development and progression. Understanding the microbiome's role could provide new insights into PCa pathogenesis and treatment.

OBJECTIVE: This review aims to explore the interactions between the microbiome and PCa, focusing on microbial imbalances and their effects on immune responses, inflammation, and hormone levels. It also discusses advanced research techniques and the potential for microbiome modulation in PCa management.

METHODS: The review synthesizes current literature on the microbiome's role in PCa, highlighting differences in microbial composition between cancerous and healthy prostate tissues. It examines techniques such as high-throughput sequencing and metagenomics and explores the mechanisms through which the microbiome influences PCa.

CONCLUSIONS: The review reveals substantial microbial differences in prostate tissues of PCa patients compared to healthy individuals, indicating a potential link between microbiome alterations and disease progression. It highlights the promise of microbiome-based strategies for diagnosis and treatment and underscores the need for further research into personalized, microbiome-centric approaches for PCa management.},
}

Humans
*Prostatic Neoplasms/microbiology/therapy/diagnosis/pathology
Male
*Microbiota
Metagenomics/methods
Multiomics

@article {pmid40450127,
year = {2025},
author = {Yan, P and Zhu, J and Ji, Q and Hou, G and Liang, G and Liu, X and Liu, R},
title = {Significant impact of bleaching treatment on phage-host interaction dynamics in a full-scale wastewater treatment plant.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {19165},
pmid = {40450127},
issn = {2045-2322},
support = {No. 42377120//National Natural Science Foundation of China/ ; No. 42377120//National Natural Science Foundation of China/ ; No. 42377120//National Natural Science Foundation of China/ ; No. 42377120//National Natural Science Foundation of China/ ; No. 42377120//National Natural Science Foundation of China/ ; No. 42377120//National Natural Science Foundation of China/ ; No. 42377120//National Natural Science Foundation of China/ ; },
mesh = {*Bacteriophages/genetics/physiology ; *Wastewater/microbiology/virology ; Sewage/microbiology/virology ; *Bacteria/genetics/virology ; *Water Purification/methods ; Genome, Viral ; Metagenomics ; *Host Microbial Interactions ; },
abstract = {The temporal dynamics of phage-host interactions within full-scale biological wastewater treatment (BWT) plants remain inadequately characterized. Here, we provide an in-depth investigation of viral and bacterial dynamics over a nine-year period in an activated sludge BWT plant, where bleach addition was applied to control sludge foaming. By conducting bioinformatic analyses on 98 metagenomic time-series samples, we reconstructed 3,486 bacterial genomes and 2,435 complete or near-complete viral genomes, which were classified into 361 bacterial and 889 viral clusters, respectively. Our results demonstrate that the primary bleaching event induced significant shifts in both bacterial and viral communities, as well as in virus-host interactions, as evidenced by alterations in bacteria-virus interaction networks and virus-to-host ratio dynamics. Following bleaching, the bacteria-virus network became less interconnected but more compartmentalized. Viral communities mirrored bacterial dynamics, indicating a strong coupling in phage-host interactions. Among the identified virus-host pairs, many exhibited a decelerating rise in viral abundance relative to host abundance, with virus-to-host ratios generally displaying a negative correlation with host abundance. This trend was particularly pronounced in virus-host pairs where viruses harbored integrase genes, indicative of temperate dynamics resembling a "Piggyback-the-Winner" model. Notably, the bleaching intervention appeared to induce a transition from lysogeny to lysis in viruses associated with some foaming-related bacterial species, suggesting a potential virus-involved indirect mechanism by which bleaching mitigates sludge foaming.},
}

*Bacteriophages/genetics/physiology
*Wastewater/microbiology/virology
Sewage/microbiology/virology
*Bacteria/genetics/virology
*Water Purification/methods
Genome, Viral
Metagenomics
*Host Microbial Interactions

@article {pmid40450092,
year = {2025},
author = {Nesti, DR and Hayashida, K and Sugi, T and Artama, WT and Wijayanto, H and Kawai, N and Yamagishi, J},
title = {Development of a semicomprehensive detection method for paramyxoviruses and its validation using Indonesian bats.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {19154},
pmid = {40450092},
issn = {2045-2322},
support = {0953/E4/KS.00/2021//Ministry of Higher Education, Science and Technology, Indonesia/ ; 0953/E4/KS.00/2021//Ministry of Higher Education, Science and Technology, Indonesia/ ; 0953/E4/KS.00/2021//Ministry of Higher Education, Science and Technology, Indonesia/ ; JPJSBP120208101//Japan Society for the Promotion of Science (JSPS), Japan/ ; JPJSBP120208101//Japan Society for the Promotion of Science (JSPS), Japan/ ; JPJSBP120208101//Japan Society for the Promotion of Science (JSPS), Japan/ ; JPJSBP120208101//Japan Society for the Promotion of Science (JSPS), Japan/ ; 24wm0125008h0005//Japan Agency of Medical Research and Development (AMED)/ ; 24wm0125008h0005//Japan Agency of Medical Research and Development (AMED)/ ; 24wm0125008h0005//Japan Agency of Medical Research and Development (AMED)/ ; },
mesh = {*Chiroptera/virology ; Animals ; Indonesia ; *Paramyxoviridae Infections/virology/veterinary/diagnosis ; *Paramyxoviridae/genetics/isolation & purification/classification ; High-Throughput Nucleotide Sequencing/methods ; Phylogeny ; Reverse Transcriptase Polymerase Chain Reaction/methods ; Genome, Viral ; Zoonoses/virology ; },
abstract = {An outbreak of zoonotic diseases is one of the worldwide threats. Bats were reported as important reservoir hosts for many emerging zoonotic diseases. To mitigate the risk, understanding bat virome and their distribution is indispensable. Universal detection methods that can simultaneously identify multiple viruses are some of the most promising approaches. Here, we developed a semicomprehensive detection method integrating group-wide RT-PCR for paramyxoviruses and multiplex next-generation sequencing. The RT-PCR consists of three sets of degenerative primers covering viruses from Paramyxoviridae, including Pneumoviridae, which have now been reclassified into a distinct family. Index nucleotides were added to the primers to enable cost-effective multiplex sequencing, and the length of index was optimized to increase sensitivity. The method was applied to tracheal and rectal swabs from 135 bats captured in Indonesia. A conventional RT-PCR test validated the NGS results. Collectively, seven sequences of novel paramyxovirus-like similar to Pararubulavirus, Orthorubulavirus, and Henipavirus were successfully identified from seven bat samples. Furthermore, sequences between the two different target locations detected by NGS in the virus genomes were verified by RT-PCR. The similarity of the obtained sequences to the known paramyxoviruses sequences was relatively low, ranging from 70.88 to 82.44%. It suggests that the obtained sequences from novel viruses and the zoonotic risk of those novel viruses remain unknown. This cost-affordable, semi-comprehensive, pan-paramyxovirus test can be applied to other samples for viral genome surveillance, and the same strategy can be implemented to other pathogens for zoonosis control.},
}

*Chiroptera/virology
Animals
Indonesia
*Paramyxoviridae Infections/virology/veterinary/diagnosis
*Paramyxoviridae/genetics/isolation & purification/classification
High-Throughput Nucleotide Sequencing/methods
Phylogeny
Reverse Transcriptase Polymerase Chain Reaction/methods
Genome, Viral
Zoonoses/virology

@article {pmid40450052,
year = {2025},
author = {Kundral, S and Giang, PD and Grundon, LR and Supper, JM and Khare, SK and Bernhardt, PV and Evans, P and Bell, SG and De Voss, JJ},
title = {Characterisation of the thermophilic P450 CYP116B305 identified using metagenomics-derived sequence data from an Australian hot spring.},
journal = {Applied microbiology and biotechnology},
volume = {109},
number = {1},
pages = {133},
pmid = {40450052},
issn = {1432-0614},
support = {FT210100812//Australian Research Council/ ; DP240101500//Australian Research Council/ ; DP240101500//Australian Research Council/ ; },
mesh = {*Cytochrome P-450 Enzyme System/genetics/metabolism/chemistry/isolation & purification ; *Hot Springs/microbiology ; Escherichia coli/genetics/metabolism ; Metagenomics ; Enzyme Stability ; Oxidation-Reduction ; Heme/metabolism ; Recombinant Proteins/genetics/metabolism/chemistry/isolation & purification ; Hot Temperature ; Australia ; Queensland ; },
abstract = {Cytochrome P450 enzymes (P450s) have gained significant attention due to their remarkable ability to oxidise unactivated C-H bonds with high regio- and stereoselectivity. Their industrial utility is often limited by challenges such as low stability, poor expression, and dependence on elusive redox partners. These issues have driven the search for more robust P450s, especially those that are inherently stable under extreme conditions typical of industrial processes. "Self-sufficient P450s" in which the P450 heme domain is naturally fused to redox domains in a single polypeptide chain eliminates the need to identify and separately express required redox partners. Furthermore, P450s from thermophilic organisms are more temperature tolerant with fewer stability issues. This study presents a self-sufficient P450, CYP116B305, identified from metagenomically assembled genomes from Innot Hot Springs (71 °C), located in North Queensland, Australia. CYP116B305 was heterologously expressed in Escherichia coli and purified using standard protocols. Investigation of the thermal stability of CYP116B305 revealed a robust heme domain with a [15]T50 value of 56.9 ± 0.1 °C, while the reductase domain exhibited slightly lower stability, with a [15]T50 value of 52.5 ± 0.5 °C. Further characterisation revealed that CYP116B305 efficiently bound to and hydroxylated 2-hydroxyphenylacetic acid (2-HPA) at the C-5 position, yielding homogentisic acid. The catalytic parameters, including the coupling efficiency and rate of electron transfer from the NADPH cofactor to the P450 heme, were shown to improve at an elevated temperature (45 °C) compared to 25 °C. The combination of the self-sufficiency and improved stability makes CYP116B305 a promising platform for biotechnological applications and biocatalyst engineering. KEY POINTS: • Hot spring metagenomics reveals thermostable P450s of biocatalytic value. • CYP116B305 shows enhanced catalytic activity at elevated temperature (45 °C). • CYP116B305 is a promising platform enzyme for diverse biotechnological use.},
}

*Cytochrome P-450 Enzyme System/genetics/metabolism/chemistry/isolation & purification
*Hot Springs/microbiology
Escherichia coli/genetics/metabolism
Metagenomics
Enzyme Stability
Oxidation-Reduction
Heme/metabolism
Recombinant Proteins/genetics/metabolism/chemistry/isolation & purification
Hot Temperature
Australia
Queensland

@article {pmid40449763,
year = {2025},
author = {Liu, W and Chen, S and Yang, J and Chen, Y and Yang, Q and Lu, L and Li, J and Yang, T and Zhang, G and Hu, J},
title = {Characterization of blood and urine microbiome temporal variability in patients with acute myeloid leukemia.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107734},
doi = {10.1016/j.micpath.2025.107734},
pmid = {40449763},
issn = {1096-1208},
abstract = {BACKGROUND: Investigating the microbiota of blood and urine from acute myeloid leukemia (AML) patients is essential to unravel the complex role of microbiota in systemic host-microbe interactions and implications.

METHODS: We conducted a longitudinal observational study to characterize the temporal dynamics of blood and urine microbiota in 27 AML patients, utilizing metagenomic analysis pipeline for microbial identification to identify disease-associated microbial signatures.

RESULTS: The composition of blood and urine microbiota of AML was dominated by Proteobacteria phylum in blood, Firmicutes phylum in urine. The species and diversity of blood and urine microbiota did not have difference between AML patients and healthy controls. Restitution of alpha and beta diversity of blood microbiota and urine microbiota to resemble that of healthy controls occurred after cessation of treatment. Temporal variation of urine microbiome was higher than blood after treatment which was closely related to pathogenic bacteria and beneficial bacteria measured by coefficient of variation (CV) of alpha diversity. The temporal variability of urine microbiota was significantly correlated with platelet and exposure of levofloxacin. The variation of microbiome of AML patients with infection was found that the relative abundance of Burkholderia significantly enriched in blood and urine which had high accuracy and sensitivity. The correlation between blood microbiota and serum amino acid metabolites was similar to that between gut microbiota and serum metabolites.

CONCLUSION: This study represents the first comprehensive investigation to quantify the longitudinal variability of blood and urine microbiota in AML patients, revealing distinct patterns compared to gut microbiota and associations with adverse clinical outcomes. Our findings highlight the potential of leveraging stabilizing taxa as a target for microbiome restoration.},
}

@article {pmid40449445,
year = {2025},
author = {Zheng, Z and Gustavsson, DJI and Zheng, D and Holmin, F and Falås, P and Wilén, BM and Modin, O and Persson, F},
title = {Genome-centric metagenomics reveals the effect of organic carbon source on one-stage partial denitrification-anammox in biofilm reactors.},
journal = {Journal of environmental management},
volume = {388},
number = {},
pages = {125972},
doi = {10.1016/j.jenvman.2025.125972},
pmid = {40449445},
issn = {1095-8630},
abstract = {Nitrogen removal from wastewater with anammox saves energy and resources. Partial denitrification-anammox (PDA) is a promising process alternative for municipal wastewater treatment, given that the understanding about how to control the microbiome and its activity reach sufficient level. Here, two moving bed biofilm reactors were fed with either acetate or propionate to study the role of organic carbon type for microbiome composition and nitrogen turnover during development of PDA. With acetate, 87 % of the removed nitrogen was converted via anammox during stable operation at a rate of 0.52 g N/(m[2]·d). With propionate, the anammox contribution was considerably lower (41 %), as was the rate of nitrogen removal (0.27 g N/(m[2]·d)). The microbiome composition in the acetate- and propionate-fed reactors was however similar, with an enrichment of metagenome assembled genomes (MAGs) having genes for nitrate reduction (narG, napA). A large fraction of these MAGs had the potential to accumulate nitrite since they lacked genes for nitrite reduction (nirS, nirK, nrfA). Genes for acetate utilization were common among these MAGs, but the necessary genes for propionate conversion were rare, suggesting that the genetic make-up of the individual denitrifiers had major influence on the nitrogen turnover. One anammox MAG (Ca. Brocadia sapporoensis), harboring genes for organic carbon utilization, prevailed in the PDA reactors. Another three anammox MAGs (Ca. B. fulgida, Ca. B. pituitae and a potentially new species within Ca. Brocadia), lacking genes for organic carbon utilization, decreased in abundance in the reactors, indicating the importance of metabolic versatility for anammox bacteria in PDA.},
}

@article {pmid40449443,
year = {2025},
author = {Hou, M and Gu, X and Lai, W and Fan, Y and Sun, S and Yan, P and Zhang, Y and Zheng, X and He, S},
title = {Sulfur-iron interactions forming activated FexSy pool in-situ to synergistically improve nitrogen removal in denitrification system.},
journal = {Journal of environmental management},
volume = {388},
number = {},
pages = {126047},
doi = {10.1016/j.jenvman.2025.126047},
pmid = {40449443},
issn = {1095-8630},
abstract = {Sulfur-iron coupling has received increasing attention for improving nitrogen removal. However, the boosting mechanisms of denitrification in sulfur-iron coupling biological system are still ambiguous, and no reasonable explanation has been given for the mismatch between the amount of S[0] loss and the amount of SO4[2-] produced in the coupling system. Therefore, this study established sulfur-iron coupling denitrification systems, and investigated the nitrogen removal performances and coupling mechanisms of the systems. The research results showed that the TN removal efficiencies of the sulfur-iron coupling systems were 122.73-149.27 % higher than those of the single electron donor systems. In the process of nitrogen removal, about 26.03-35.32 % of the more leached S[0] and Fe[0] in the coupling systems co-precipitated to form activated FexSy pool in-situ, contributing about 25.41 % of the nitrogen removal and allowing the systems to remove 76.32-100 % of TN without external electron donors; moreover, the oxidation process of S[2-] provided electrons for the reduction of Fe (Ⅲ) to Fe (Ⅱ), generating more electron donors. Metagenomic sequencing results showed significant increases in the richness and diversity of functional microorganisms associated with sulfur and iron autotrophic denitrification in the coupling systems, and their contributions to the key genes in the denitrification, sulfur transformation and iron cycle processes increased substantially. In general, this study offered deeper understanding for assessing the nitrogen removal potential of the sulfur-iron coupling system, as well as investigating the interactions between S[0] and Fe[0] and elucidating nitrogen removal pathways within the system.},
}

@article {pmid40449312,
year = {2025},
author = {Xia, Z and Ng, HY and Bae, S},
title = {Synergistic microalgal-bacterial interactions enhance nitrogen removal in membrane-aerated biofilm photoreactors treating aquaculture wastewater under salt stress: Insights from metagenomic analysis.},
journal = {Water research},
volume = {283},
number = {},
pages = {123878},
doi = {10.1016/j.watres.2025.123878},
pmid = {40449312},
issn = {1879-2448},
abstract = {This study investigates the membrane-aerated biofilm photoreactor (MABPR) for treating aquaculture effluents with low C/N ratio and elevated salinity (0.5%-3.2%). The MABPR integrated biofilm reactors with microalgal-bacterial consortia, achieving superior total inorganic nitrogen (TIN) removal by leveraging counter-diffusional biofilm properties, bubbleless aeration, and enhanced microalgal productivity. The system consistently outperformed conventional reactors, achieving 84.7 ± 1.9% TIN removal at 3.2% salinity with TIN removal flux increasing from 0.82 ± 0.04 to 1.22 ± 0.07 g/m[2] d. The MABPR promoted microalgal proliferation (Chl-a/VSS: 8.08-15.04 mg/g) and higher biomass productivity (1.83 g/m[2] d) compared to SBBPR and MABR. Elevated salinity stimulated extracellular polymeric substance (EPS) production, reinforcing biofilm stability and microbial resilience. The MABPR demonstrated 22%-65% higher nitrogen removal efficiency than controls at the highest salinity. Canonical nitrification-denitrification remained the primary nitrogen removal pathway, with short-cut nitrification-denitrification contributing under salt stress. Metagenomic analysis revealed bidirectional adaptation between microalgae and bacteria, with enriched nitrogen assimilation (GS/GOGAT pathway) compensating for bacterial deficits. Microalgae facilitated pollutant removal through ammonia uptake and dissolved organic matter release, supporting denitrification. At 3.2% salinity, Nitrosomonas and Nitrobacter abundance increased by 42.6% and 35.8%, while denitrifiers Denitromonas and Hoeflea dominated, comprising 59.4% and 35.9% of the population. The MABPR further promoted the synthesis of growth cofactors (vitamins, phytohormones), enhancing microalgal productivity and stress resilience. These synergistic microalgal-bacterial interactions supported pollutant removal, showcasing the MABPR as a robust, sustainable solution for aquaculture wastewater treatment and resource recovery under salt stress.},
}

@article {pmid40449097,
year = {2025},
author = {Cañete-Reyes, Á and González, JG and Alteio, LV and Rodríguez-Lázaro, D and Hernández, M},
title = {Aetiology and environmental factors of the Watery Mouth Disease associated with neonatal diarrhoea in lambs.},
journal = {Veterinary microbiology},
volume = {306},
number = {},
pages = {110542},
doi = {10.1016/j.vetmic.2025.110542},
pmid = {40449097},
issn = {1873-2542},
abstract = {Watery Mouth Disease is the main disease in neonatal lambs, causing great economic losses. Despite this, the cause of the condition remains poorly understood. Therefore, we have analysed the main bacteria found in sick animals, their intestinal and temporal distribution, as well as the main sources of contamination. Twelve different farms were sampled, from which 331 samples were taken in total. From these samples, 184 environments were analyzed using 16S rRNA amplicon sequencing, 164 isolates were identified by whole genome sequencing and 35 bacterial counts were performed. The dominant bacterial groups at the rectal level were Escherichia-Shigella (36 %) and Clostridium (29 %), with a homogeneous distribution along the digestive tract and a maximum abundance ranging between 12 and 24 hours of lamb life. Within Escherichia-Shigella: Escherichia coli and Escherichia fergusonii and within Clostridium: Clostridium perfringens, Clostridium cadaveris, Clostridium tertium and Clostridium paraputricum were identified as the main isolates present in sick animals. The high presence of Clostridium strains, especially potentially pathogenic species like C. perfringens in sick animals, point out Clostridium as a new important protagonist of watery mouth disease and the need of their inclusion in future studies. In particular, bedding was established as the main microbial contaminating factor, reaching the highest increase 48 hours after removal and cleaning of the lambing area (i.e. 8.03 ×10[8], 1.88 ×10[6], 3.88 ×10[6], 4.85 ×10[7] and 4.00 ×10[5] CFU/g for mesophilic aerobes, coliforms, E. coli, mesophilic anaerobes and sporulates, respectively). These results highlight the need to increase cleanliness in bedding to reduce the presence of these bacteria.},
}

@article {pmid40448586,
year = {2025},
author = {Jones, LM and El Aidy, S},
title = {Electroactive ecosystem insights from corrosion microbiomes inform gut microbiome modulation.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf112},
pmid = {40448586},
issn = {1751-7370},
abstract = {Electroactive microorganisms influence environmental and host-associated ecosystems through their ability to mediate extracellular electron transfer. This review explores parallels between EAM-driven microbiologically influenced corrosion systems and the human gut microbiome. In corrosion, EAMs contribute to biofilm formation, redox cycling, and material degradation through mechanisms such as direct electron transfer and syntrophic interactions. Similarly, gut-associated EAMs regulate redox balance, drive short-chain fatty acid production, and shape host-microbe interactions. Despite differing contexts, both systems share traits like anoxic niches, biofilm formation, and metabolic adaptability. Insights from well-characterized corrosion microbiomes offer valuable frameworks to understand microbial resilience, electron transfer strategies, and interspecies cooperation in the gut. Bridging knowledge between these systems can inform microbiome engineering approaches aimed at promoting gut health, highlighting the need for further functional metagenomics and exploration of archaeal contributions to biofilm stability and redox modulation.},
}

@article {pmid40448221,
year = {2025},
author = {Fan, KC and Lin, CC and Chiu, YL and Koh, SH and Liu, YC and Chuang, YF},
title = {Compositional and functional gut microbiota alterations in mild cognitive impairment: links to Alzheimer's disease pathology.},
journal = {Alzheimer's research & therapy},
volume = {17},
number = {1},
pages = {122},
pmid = {40448221},
issn = {1758-9193},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Cognitive Dysfunction/microbiology/pathology/metabolism ; *Alzheimer Disease/microbiology/pathology/metabolism ; Male ; Female ; Aged ; Feces/microbiology ; Biomarkers ; Brain/pathology/metabolism ; Aged, 80 and over ; Dysbiosis ; tau Proteins ; Middle Aged ; },
abstract = {BACKGROUND: Emerging evidence highlights the bidirectional communication between the gut microbiota and the brain, suggesting a potential role for gut dysbiosis in Alzheimer's disease (AD) pathology and cognitive decline. Existing literature on gut microbiota lacks species-level insights. This study investigates gut microbiota alterations in mild cognitive impairment (MCI), focusing on their association with comprehensive AD biomarkers, including amyloid burden, tau pathology, neurodegeneration, and cognitive performance.

METHODS: We analyzed fecal samples from 119 individuals with MCI and 320 cognitively normal controls enrolled in the Taiwan Precision Medicine Initiative on Cognitive Impairment and Dementia cohort. Shotgun metagenomic sequencing was conducted with taxonomic profiling using MetaPhlAn4. Amyloid burden and plasma pTau181 were quantified via PET imaging and Simoa assays, respectively, while APOE genotyping was performed using TaqMan assays. Microbial diversity, differential abundance analysis, and correlation mapping with neuropsychological and neuroimaging measures were conducted to identify gut microbiota species signatures associated with MCI and AD biomarkers.

RESULTS: We identified 59 key microbial species linked to MCI and AD biomarkers. Notably, species within the same genera, such as Bacteroides and Ruminococcus, showed opposing effects, while Akkermansia muciniphila correlated with reduced amyloid burden, suggesting a protective role. Functional profiling revealed microbial pathways contributing to energy metabolism and neuroinflammation, mediating the relationship between gut microbes and brain health. Co-occurrence network analyses demonstrated complex microbial interactions, indicating that the collective influence of gut microbiota on neurodegeneration.

CONCLUSIONS: Our findings challenge genus-level microbiome analyses, revealing species-specific modulators of AD pathology. This study highlights gut microbial activity as a potential therapeutic target to mitigate cognitive decline and neurodegeneration.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Cognitive Dysfunction/microbiology/pathology/metabolism
*Alzheimer Disease/microbiology/pathology/metabolism
Male
Female
Aged
Feces/microbiology
Biomarkers
Brain/pathology/metabolism
Aged, 80 and over
Dysbiosis
tau Proteins
Middle Aged

@article {pmid40447717,
year = {2025},
author = {Lai, LM and Dai, QB and Cao, ML and Liu, Y and Zhao, R and Yuan, L},
title = {Clinical utility of metagenomic next-generation sequencing in pathogen detection for lower respiratory tract infections.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {19039},
pmid = {40447717},
issn = {2045-2322},
support = {2024B1362//the Science and Technology Plan of Jiangxi Provincial Health Commission/ ; 202510284//the Science and Technology Plan of Jiangxi Provincial Health Commission/ ; 20242BAB20430//the Natural Science Foundation of Jiangxi Province/ ; },
mesh = {Humans ; *Respiratory Tract Infections/diagnosis/microbiology ; *High-Throughput Nucleotide Sequencing/methods ; Female ; Male ; *Metagenomics/methods ; Middle Aged ; Retrospective Studies ; Aged ; Adult ; Bronchoalveolar Lavage Fluid/microbiology ; Sensitivity and Specificity ; },
abstract = {Identifying pathogens in patients with lower respiratory tract infections (LRTIs) has always been a major challenge. Metagenomic next-generation sequencing (mNGS) technology is a new diagnostic tool that can assist clinicians in the etiological diagnosis of LRTIs. This study focuses on the clinical value of mNGS in the diagnosis of suspected LRTIs. A total of 400 patients with suspected LRTIs admitted at the First Affiliated Hospital of Nanchang University from July 2020 to February 2023 were enrolled in this retrospective study. Bronchoalveolar lavage fluid (BALF) samples were analyzed using both mNGS and culture methods. The diagnostic accuracy of two approaches was systematically compared against the final clinical diagnosis, which served as the gold-standard reference. Of the 400 enrolled cases, 82.3% (329/400) were diagnosed with LRTIs. From these cases, mNGS identified 76.8% (307/400) truepositive cases, 8.0% (32/400) falsepositive cases, 9.8% (39/400) truenegative cases, and 5.5% (22/400) falsenegative cases. mNGS demonstrated significantly higher sensitivity [93.3% (307/329) vs. 55.6(183/329)%] alongside greater negative predictive values [63.9% (39/61) vs.25.9%(51/197)], whereas culture offered higher specificity [54.9%(39/71) vs. 71.8%(51/71)]. The area under the receiver-operating curve (AUC) of mNGS[0.744(95%CI: 0.67-0.82)]was significantly higher than that of cultures[0.636(95%CI: 0.57-0.71)]. Specifically, mNGS detected more Streptococcus pneumoniae (7.0% vs. 0%), Haemophilus influenzae (6.7% vs. 0%), Aspergillus (9.4% vs. 3.5%), Pneumocystis jirovecii (11.9% vs. 0%) and other intracellular pathogens. Of the 329 patients with LRTIs, antibiotic treatment was modified based on the mNGS results in more than half of the patients(50.5%,166/329), including 20 cases of adjusted antimicrobial regimens, 70 cases de-escalated the empirical antibiotic treatment, and 76 patients escalated the treatment by increasing dosage or medication. 60.8%(101/166) of patients responded to modified antibiotic treatment. Significant benefits of mNGS have been shown in pathogen identification and antimicrobial treatment stewardship in patients with LRTIs. For those with suboptimal therapeutic responses, physicians should be alert to some emerging intracellular pathogens, including Chlamydia psittaci, Mycobacterium tuberculosis, and Pneumocystis jirovecii.},
}

Humans
*Respiratory Tract Infections/diagnosis/microbiology
*High-Throughput Nucleotide Sequencing/methods
Female
Male
*Metagenomics/methods
Middle Aged
Retrospective Studies
Aged
Adult
Bronchoalveolar Lavage Fluid/microbiology
Sensitivity and Specificity

@article {pmid40447596,
year = {2025},
author = {Wang, X and Jiang, Q and Tian, X and Chen, W and Mai, J and Lin, G and Huo, Y and Zheng, H and Yan, D and Wang, X and Li, T and Gao, Y and Mou, X and Zhao, W},
title = {Metagenomic analysis reveals the novel role of vaginal Lactobacillus iners in Chinese healthy pregnant women.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {92},
pmid = {40447596},
issn = {2055-5008},
mesh = {Humans ; Female ; *Vagina/microbiology ; Pregnancy ; *Metagenomics/methods ; China ; *Lactobacillus/genetics/isolation & purification/classification/physiology ; Adult ; Gardnerella vaginalis/growth & development ; Microbiota ; Vaginosis, Bacterial/microbiology ; Biofilms/growth & development ; Asian People ; Pregnant People ; Young Adult ; },
abstract = {This study investigated the relationship between vaginal microbiota and women's health conditions in 95 Chinese pregnant women in their third trimester. We conducted vaginal metagenomic analysis, examining species, functional pathways, and genes, and utilized correlation and LEfSe analyses to link microbiota to health conditions. Results revealed that healthy participants exhibited higher levels of Lactobacillus iners, with its abundance associated with tetrahydrofolate biosynthesis pathways. They also possessed more glycosyltransferase and ErmB antibiotic resistance genes compared to women with diagnosed conditions. Comparative genomics demonstrated that L. iners strains linked to bacterial vaginosis (BV) possessed more genes encoding biofilm-associated YhgE/Pip domain-containing proteins than healthy-associated strains. Notably, three BV-associated L. iners strains exhibited stronger biofilm formation abilities than four healthy-associated strains isolated in this study. Also, four out of seven L. iners strains inhibited the growth of Gardnerella vaginalis. Overall, L. iners may help maintain vaginal ecosystem stability in Chinese pregnant women.},
}

Humans
Female
*Vagina/microbiology
Pregnancy
*Metagenomics/methods
China
*Lactobacillus/genetics/isolation & purification/classification/physiology
Adult
Gardnerella vaginalis/growth & development
Microbiota
Vaginosis, Bacterial/microbiology
Biofilms/growth & development
Asian People
Pregnant People
Young Adult

@article {pmid40447587,
year = {2025},
author = {Paluoja, P and Vaher, M and Teder, H and Krjutškov, K and Salumets, A and Raime, K},
title = {Honey bulk DNA metagenomic analysis to identify honey biological composition and monitor honey bee pathogens.},
journal = {NPJ science of food},
volume = {9},
number = {1},
pages = {91},
pmid = {40447587},
issn = {2396-8370},
support = {616219790085//European Agricultural Fund for Rural Development/ ; 616219790085//European Agricultural Fund for Rural Development/ ; 616219790085//European Agricultural Fund for Rural Development/ ; },
abstract = {Honey's DNA mixture originates from various organisms like plants, arthropods, fungi, bacteria, and viruses. Conventional methods like melissopalynological analysis and targeted honey DNA metabarcoding offer a limited view of honey's biological composition. We conducted a honey bulk DNA metagenomic analysis to characterize the honey's taxonomic composition and identify honey bee-related pathogens and parasites based on 266 Estonian and 103 foreign honey samples. 70.4% of the DNA in Estonian honey was derived from green plant families like Brassicaceae, Rosaceae, Fabaceae, and Pinaceae. Geographical distribution analysis revealed distinct botanical compositions between Estonian mainland and island samples. The bacterial family Lactobacillaceae was prevalent overall, reflecting the honey bee microbiota in honey. We detected 12 honey bee pathogens and parasites, including Paenibacillus larvae, Nosema ceranae, Varroa destructor, and Aethina tumida. In conclusion, the study underscores the potential of bulk DNA-based non-targeted metagenomic approaches for monitoring honey bee health, environment, and honey composition, origin, and authenticity.},
}

@article {pmid40447574,
year = {2025},
author = {Rodríguez Del Río, Á and Scheu, S and Rillig, MC},
title = {Soil microbial responses to multiple global change factors as assessed by metagenomics.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {5058},
pmid = {40447574},
issn = {2041-1723},
mesh = {*Soil Microbiology ; *Metagenomics/methods ; *Bacteria/genetics/classification/drug effects ; Metagenome ; Soil/chemistry ; Droughts ; Microbiota/genetics ; Salinity ; *Climate Change ; Global Warming ; },
abstract = {Anthropogenic activities impose multiple concurrent pressures on soils globally, but responses of soil microbes to multiple global change factors are poorly understood. Here, we apply 10 treatments (warming, drought, nitrogen deposition, salinity, heavy metal, microplastics, antibiotics, fungicides, herbicides and insecticides) individually and in combinations of 8 factors to soil samples, and monitor their bacterial and viral composition by metagenomic analysis. We recover 742 mostly unknown bacterial and 1865 viral Metagenome-Assembled Genomes (MAGs), and leverage them to describe microbial populations under different treatment conditions. The application of multiple factors selects for prokaryotic and viral communities different from any individual factor, favouring the proliferation of potentially pathogenic mycobacteria and novel phages, which apparently play a role in shaping prokaryote communities. We also build a 25 M gene catalog to show that multiple factors select for metabolically diverse, sessile and non-biofilm-forming bacteria with a high load of antibiotic resistance genes. Finally, we show that novel genes are relevant for understanding microbial response to global change. Our study indicates that multiple factors impose selective pressures on soil prokaryotes and viruses not observed at the individual factor level, and emphasizes the need of studying the effect of concurrent global change treatments.},
}

*Soil Microbiology
*Metagenomics/methods
*Bacteria/genetics/classification/drug effects
Metagenome
Soil/chemistry
Droughts
Microbiota/genetics
Salinity
*Climate Change
Global Warming

@article {pmid40446767,
year = {2025},
author = {Adyari, B and Liao, X and Yan, X and Qiu, Y and Grossart, HP and Li, L and Yu, T and Mao, G and Liu, K and Su, J and Liu, Y and Hu, A},
title = {Anthropogenic gene dissemination in Tibetan Plateau rivers: sewage-driven spread, environmental selection, and microeukaryotic inter-trophic driving factors.},
journal = {Water research},
volume = {284},
number = {},
pages = {123887},
doi = {10.1016/j.watres.2025.123887},
pmid = {40446767},
issn = {1879-2448},
abstract = {The spread of anthropogenic genes, such as antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), virulence factor genes (VFGs), and antibiotic-resistant bacteria (ARBs), is a growing public health concern. However, the role of anthropogenic activities in the dissemination of these genes and bacteria in Tibetan Plateau rivers is still unclear. In this study, we analyzed 138 metagenomic samples from water and sediment across nine Tibetan rivers, along with sewage samples from 21 wastewater treatment plants (WWTPs), at both the gene and contig levels, to investigate the spread of the sewage-enriched genes and their bacterial hosts (contigs) in Tibetan rivers. Overall, sewage input was positively correlated with increased the abundance of an average 56 % and 17 % of detected genes in water and sediment, respectively. However, FEAST source tracking analysis revealed that the overall contribution of sewage across all rivers was significantly lower than that of water and sediment. Additionally, sewage's impact varied across rivers, with the Yarlung Zangbo, the largest river, exhibiting limited influence despite receiving inputs from smaller rivers and WWTPs. Neutral community model (NCM) suggested that neutral processes and negative selection predominantly governed the spread of majority of highly abundant sewage-enriched genes and contigs, suggesting restricted environmental spread. In contrast, a subset of genes over-represented relative to neutral expectations (above-neutral prediction) showed lower overall abundance but higher richness, potentially reflecting selection that favor their retention in certain downstream environments. Furthermore, sewage-enriched genes and contigs in water, regardless of their community assembly processes, were linked to microbial interaction modules dominated by microeukaryotic groups associated with sewage, including consumer protists (ciliate), human parasites (e.g., Naegleria), algae, and fungi. These interactions may facilitate the dissemination of antimicrobial resistance in aquatic environments, though this pattern was less pronounced in sediment.},
}