@article {pmid40740339,
year = {2025},
author = {Shen, J and Hu, Y and Zhang, Y and Li, L and Deng, X and Chen, M and Li, L and Xie, P and Shao, M},
title = {Metagenomics-based analysis of microbial community structure and functional differences in fermented grains of Jiang-flavored baijiu from different production regions and policy recommendations for industrial development.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1619035},
pmid = {40740339},
issn = {1664-302X},
abstract = {INTRODUCTION: Recently, some regions that originally focused on strong-flavor baijiu production started producing Jiang-flavored baijiu, providing a new perspective for studying the dynamic changes in the microbial community during brewing.

METHODS: This study used second-round fermented grains of Jiang-flavored baijiu from three Guizhou production regions (Renhuai, Duyun, and Bijie). By applying metagenomics technology and various analytical and statistical methods, we analyzed the community structures of bacteria and fungi in fermented grains, their functional genes, and their correlations with environmental factors.

RESULTS: We identified 1063 bacterial genera and 411 fungal genera. Although the dominant microbial species were similar across regions, their relative abundances differed significantly. α-diversity analysis showed that grains from the Bijie region had higher species richness and evenness indices, indicating the significant impact of geographical location and the strong-flavor baijiu-brewing background on microbial structure and composition. Analysis of similarity and the Wilcoxon rank-sum test revealed significant differences in the microbial communities of different regions, and we identified genera with large differences in abundance, such as Desmospora and Kroppenstedtia among bacteria, and Pyrenophora and Blyttiomyces among fungi. Based on our Kyoto Encyclopedia of Genes and Genomes (KEGG) database analysis, the Duyun region had a significantly higher abundance of metabolism-related genes at the tertiary KEGG level. Redundancy analysis showed that six environmental factors (relative humidity, daily temperature difference, elevation, annual mean temperature, extreme cold temperature, and annual precipitation) exerted complex effects on microbial functional genes in fermented grains. Carbon metabolism, antibiotic biosynthesis, and elevation were positively correlated with microbial functional genes. Actinobacteria are crucial for carbon metabolism, followed by Proteobacteria and Chloroflexi.

DISCUSSION: This study elucidated the structural and functional characteristics of microbial communities in second-round fermented grains of Jiang-flavored baijiu under production area transitions and proposed policy recommendations to promote the differentiated development of the baijiu industry.},
}

@article {pmid40740338,
year = {2025},
author = {Mancabelli, L and Tarracchini, C and Longhi, G and Alessandri, G and Ventura, M and Turroni, F},
title = {Dissecting the molecular interactions between botanical extracts and the human gut microbiota.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1610170},
pmid = {40740338},
issn = {1664-302X},
abstract = {Over millions of years, humans and their gut microbes have developed a symbiotic relationship that benefits both organisms. Many plants and herbs consumed as food by humans, such as aloe vera gel and dandelion root extracts, contain bioactive compounds with recognized therapeutic or preventive effects. However, the impact of these botanicals on the composition and functionality of the human gut microbiota is not yet understood. In this study, the molecular impact of these botanicals on reconstructed human gut microbiota was assessed by in-vitro bioreactor experiments followed by metagenomics and transcriptomic approaches, highlighting both taxonomic and functional changes in the human gut microbiome. Furthermore, cross-feeding activities established by common human gut microbial taxa like Bacteroides spp. when cultivated on these extracts were assessed. In conclusion, the results show that botanicals affect intestinal populations that are highly dependent on the microbial taxa present and that trophic interactions are established in few key gut members.},
}

@article {pmid40740321,
year = {2025},
author = {Wang, Y and Radosevich, M and Yang, L and Zhang, Y and Xie, N and Liang, X},
title = {The interplay of nitrogen sources and viral communities in the biodegradation of atrazine in agricultural soils.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1645559},
pmid = {40740321},
issn = {1664-302X},
abstract = {Atrazine is a widely used herbicide, and its degradation is primarily mediated by microbial activity. However, the interplay between nutrient availability and viral infections on microbial degradation of atrazine remains unexplored. Here, we investigated atrazine degradation under different nitrogen amendments (ammonium, nitrate, and urine) and the influence of soil viruses (intracellular and extracellular viruses). The results showed that atrazine degradation was greater with the addition of extracellular viruses without exogenous nitrogen sources. The added nitrogen sources (nitrate and urine) completely inhibited atrazine degradation. Ammonium impeded atrazine degradation, which was promoted with the addition of intracellular viruses. The metagenomic-based evidence revealed that nitrogen amendments significantly alter bacterial and viral community composition. Peduoviridae emerged as the predominant viral family, with its prevalence and temperate phage ratio strongly influenced by nitrogen availability, underscoring the role of nutrient dynamics in shaping virus-host interactions. The presence of viruses selectively enriched atrazine degradation genes and auxiliary metabolic genes (AMGs) associated with key microbial metabolic pathways, revealing potential mechanisms by which viral infections contribute to pollutant biodegradation. The findings highlight the complex interplay between viral predation, microbial adaptation, and nitrogen-driven shifts in microbial community structure and function, offering new perspectives on how viruses shape bioremediation processes in agroecosystems.},
}

@article {pmid40739825,
year = {2025},
author = {Xiang, T and Chi, J and Pan, J},
title = {Cooperative effect of N2H4 on anaerobic ammonium-oxidizing bacteria and heterotrophic bacteria and the underlying mechanism.},
journal = {Water science and technology : a journal of the International Association on Water Pollution Research},
volume = {92},
number = {2},
pages = {285-300},
pmid = {40739825},
issn = {0273-1223},
support = {Youth Project（No.JYTQN2023395）//Department of Education of Liaoning Province/ ; Natural Science Foundation - Doctoral Research Launch Project (No. 2024-BSLH-237)//Department of Education of Liaoning Province/ ; },
mesh = {*Ammonium Compounds/metabolism ; *Hydrazines/pharmacology/chemistry ; Nitrogen/metabolism ; Oxidation-Reduction ; *Bacteria/metabolism ; *Bacteria, Anaerobic/metabolism/drug effects ; Heterotrophic Processes ; Anaerobiosis ; Bioreactors/microbiology ; },
abstract = {Batch experiments investigated cooperative nitrogen removal between anaerobic ammonium-oxidizing bacteria (AnAOB) and heterotrophs under hydrazine (N2H4) and sodium acetate effects. A single addition of sodium acetate (optimal C/N = 2) or N2H4 (1 mg/L) achieved peak total nitrogen removal efficiency of 89.74 and 79.95%, respectively, showing initial enhancement followed by decline with increasing dosage. Combined additions exhibited a V-shaped efficiency trend, with the NH01_CN2 group (C/N = 2, N2H4 = 1 mg/L) achieving 76.76% removal efficiency. Appropriate carbon-to-nitrogen (C/N) ratios allowed hydrazine to promote synergistic interactions. These interactions improved the activity of critical nitrogen-converting genes. The enhanced genes included nitrite oxidoreductase (EC 1.7.99.-), nitrate reductase (EC 1.7.5.1), and cytochrome nitrate reductase (EC 1.9.6.1). Metagenomic analysis revealed that AnAOB primarily engaged in core metabolic pathways, while heterotrophs dominated nucleotide metabolism. Exogenous additives induced metabolic shifts in AnAOB toward versatile environmental adaptations. These findings elucidate the carbon-nitrogen coordination mechanisms governing AnAOB-heterotroph partnerships during nitrogen cycle optimization.},
}

*Ammonium Compounds/metabolism
*Hydrazines/pharmacology/chemistry
Nitrogen/metabolism
Oxidation-Reduction
*Bacteria/metabolism
*Bacteria, Anaerobic/metabolism/drug effects
Heterotrophic Processes
Anaerobiosis
Bioreactors/microbiology

@article {pmid40739820,
year = {2025},
author = {de Sousa, IB and Malvestiti, JA and Cavalcante, RP and Luchessi, AD and Tornisielo, VL and Dantas, RF},
title = {Biological activated carbon: E. coli and helminth eggs removal from urban wastewater and its impact on ecotoxicity.},
journal = {Water science and technology : a journal of the International Association on Water Pollution Research},
volume = {92},
number = {2},
pages = {205-219},
pmid = {40739820},
issn = {0273-1223},
support = {2022/00454-0//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2019/26210-8//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2022/04015-1//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 403211/2023-9//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 2022/16554-4//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; },
mesh = {*Wastewater/parasitology/microbiology ; *Escherichia coli/isolation & purification ; Animals ; *Helminths/isolation & purification ; *Waste Disposal, Fluid/methods ; *Charcoal/chemistry ; Ovum ; Filtration ; Biodegradation, Environmental ; Cities ; Water Purification/methods ; Biofilms ; Raphanus/drug effects/growth & development ; },
abstract = {The main objective of this study was to characterize metagenomically and evaluate the biofilter effectiveness for COD, total coliforms, Escherichia coli, and Helminth eggs removal from urban wastewater using different configurations. Several contact times of wastewater with the biofilm were tested, as well as physicochemical and biological parameters. The optimal treatment time for COD removal was 480 min for BAC1 and 360 min for BAC2, while for E. coli removal, it was 90 and 120 min by BAC1 and BAC2, respectively, and 200 min for Helminth eggs by both BACs. The metagenomic analysis revealed a diverse microbial community within the biofilms, which contributed to the biodegradation process. BAC1 exhibited greater microbiological diversity and better performance than BAC2. Key microbial species identified, such as Lysinibacillus sphaericus, Citrobacter freundii, and Saccharomyces sp. possess notable biodegradative and antimicrobial properties, further enhancing the filter's efficacy. The effluents treated by both BACs did not exhibit toxicity for germination and root elongation of radish seeds.},
}

*Wastewater/parasitology/microbiology
*Escherichia coli/isolation & purification
Animals
*Helminths/isolation & purification
*Waste Disposal, Fluid/methods
*Charcoal/chemistry
Ovum
Filtration
Biodegradation, Environmental
Cities
Water Purification/methods
Biofilms
Raphanus/drug effects/growth & development

@article {pmid40739342,
year = {2025},
author = {Ruffolo, JA and Nayfach, S and Gallagher, J and Bhatnagar, A and Beazer, J and Hussain, R and Russ, J and Yip, J and Hill, E and Pacesa, M and Meeske, AJ and Cameron, P and Madani, A},
title = {Design of highly functional genome editors by modelling CRISPR-Cas sequences.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {40739342},
issn = {1476-4687},
abstract = {Gene editing has the potential to solve fundamental challenges in agriculture, biotechnology and human health. CRISPR-based gene editors derived from microorganisms, although powerful, often show notable functional tradeoffs when ported into non-native environments, such as human cells[1]. Artificial-intelligence-enabled design provides a powerful alternative with the potential to bypass evolutionary constraints and generate editors with optimal properties. Here, using large language models[2] trained on biological diversity at scale, we demonstrate successful precision editing of the human genome with a programmable gene editor designed with artificial intelligence. To achieve this goal, we curated a dataset of more than 1 million CRISPR operons through systematic mining of 26 terabases of assembled genomes and metagenomes. We demonstrate the capacity of our models by generating 4.8× the number of protein clusters across CRISPR-Cas families found in nature and tailoring single-guide RNA sequences for Cas9-like effector proteins. Several of the generated gene editors show comparable or improved activity and specificity relative to SpCas9, the prototypical gene editing effector, while being 400 mutations away in sequence. Finally, we demonstrate that an artificial-intelligence-generated gene editor, denoted as OpenCRISPR-1, exhibits compatibility with base editing. We release OpenCRISPR-1 to facilitate broad, ethical use across research and commercial applications.},
}

@article {pmid40739184,
year = {2025},
author = {Tang, HB and Si, YX and Li, HD and Dang, W and Lu, HL},
title = {Intestinal microbial dysbiosis under nitrite stress in juvenile three-keeled pond turtles, Mauremys reevesii.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {466},
doi = {10.1186/s12866-025-04198-8},
pmid = {40739184},
issn = {1471-2180},
support = {32471577//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Turtles/microbiology ; *Nitrites/toxicity ; *Gastrointestinal Microbiome/drug effects ; *Dysbiosis/microbiology/veterinary/chemically induced ; *Bacteria/classification/genetics/drug effects/isolation & purification ; Stress, Physiological ; Intestines/microbiology ; *Water Pollutants, Chemical/toxicity ; Aquaculture ; },
abstract = {BACKGROUND: Nitrite is one of the primary pollutants in high-density aquaculture systems, and may cause various toxic effects (e.g., oxidative damage, metabolic and immune dysregulation, histological inflammation, etc.) on economically important aquaculture species, such as echinoderms, crustaceans and fish. Nitrite can also disrupt the intestinal function and microbiota in some fish and amphibians. However, intestinal physiological and microbial responses of cultured turtles under nitrite stress were rarely explored.

METHOD: Twenty Mauremys reevesii juveniles were exposed to different nitrite levels and fed with a commercial diet. Their intestinal content samples were analyzed for microbial diversity and composition.

RESULTS: Nitrite exposure reduced intestinal microbial diversity, with lower α-diversity values in higher-concentration exposed turtles. It also changed the microbial composition. After exposure, the abundances of Bacteroidetes and Firmicutes decreased, but that of Proteobacteria increased at the phylum level. Similarly, abundances of some potentially beneficial bacterial genera, e.g., Prevotella_1, Christensenellaceae_R-7, Muribaculaceae_ge, were shown to decrease, but those of putatively pathogenic genera, e.g., Halomonas, Nesterenkonia, increased at the genus level. Furtherly, potentially altered metabolic pathways (e.g., biosynthesis of ansamycins and vancomycin group antibiotics) were revealed by functional predictions of intestinal microbiota.

CONCLUSION: This study highlighted intestinal microbial dysbiosis and prevalence of putatively pathogenic bacteria in cultured turtles under nitrite stress. Excessive levels of nitrite would alter the health status of aquatic animals by disrupting their intestinal microbiome.},
}

Animals
*Turtles/microbiology
*Nitrites/toxicity
*Gastrointestinal Microbiome/drug effects
*Dysbiosis/microbiology/veterinary/chemically induced
*Bacteria/classification/genetics/drug effects/isolation & purification
Stress, Physiological
Intestines/microbiology
*Water Pollutants, Chemical/toxicity
Aquaculture

@article {pmid40739125,
year = {2025},
author = {Jiang, W and Xiong, M and Feng, S and Liu, Q and Chen, Y and Zou, S and Kang, D},
title = {Water content alters soil organic carbon metabolism via microbial traits in Tibetan alpine peatlands.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {27793},
doi = {10.1038/s41598-025-13788-5},
pmid = {40739125},
issn = {2045-2322},
support = {No. 2023NSFSC0143//the Natural Science Foundation of Sichuan Provence/ ; No. 31800458//the National Natural Science Foundation of China/ ; No. 2019-ZL-19//Sichuan Province Transportation Science and Technology Project: Research and Demonstration on Crucial Technologies of Wetland Eco-environment Protection Under the Influence of Highway Engineering on the Western Sichuan Plateau/ ; },
mesh = {*Soil Microbiology ; *Soil/chemistry ; *Carbon/metabolism ; Tibet ; *Water/analysis ; Carbon Cycle ; Archaea/metabolism/genetics ; Bacteria/metabolism/genetics ; Fungi/metabolism/genetics ; Microbiota ; },
abstract = {Alpine peatlands on the eastern Tibetan Plateau are vital carbon sinks, with soil moisture playing a key role in peatland carbon cycling. However, they face disruptions in their carbon balance due to drought, which reduces soil water content. Therefore, this study investigated microbially driven water-carbon interactions through field surveys, laboratory incubations, and metagenomics. Soil drying contributes to changes in both the metabolic quotient (qCO2) and the microbial quotient (Cmic: Corg), as well as the microbial abundance. As the soil water content decreased, both qCO2 and Cmic: Corg exhibited an overall increasing trend. Moreover, soil water content had a more significant effect on soil bacteria, while its effect on fungi and archaea was minimal. Soil microbial carbon decomposition genes were also influenced by changes in soil water content. Next, we used RDA to analyze the relationship between soil respiration quotient values and microbial traits. The results revealed that Actinobacteria were strongly negatively correlated with qCO2, whereas Archaea and Candidatus_R were positively correlated with qCO2. Additionally, Cmic: Corg was closely linked to fungi, and both Proteobacteria and Acidobacteria exhibited positive correlations. qCO2 had a strong negative correlation with genes involved in the degradation of monosaccharides and hemicellulose, whereas Cmic: Corg was positively correlated with genes related to the degradation of cellulose and lignin. Moreover, droughts affected microbial residue carbon and associated carbon metabolic pathways. Therefore, changes in soil water content may be an important factor influencing carbon metabolism processes in peatlands. This study deepens our understanding of the effects of drought on soil metabolism and microbial dynamics in alpine peatlands and provides new insights into the microecological mechanisms of soil carbon cycling in these ecosystems in the context of global change.},
}

*Soil Microbiology
*Soil/chemistry
*Carbon/metabolism
Tibet
*Water/analysis
Carbon Cycle
Archaea/metabolism/genetics
Bacteria/metabolism/genetics
Fungi/metabolism/genetics
Microbiota

@article {pmid40739039,
year = {2025},
author = {Quijada, NM and Cobo-Díaz, JF and Valentino, V and Barcenilla, C and De Filippis, F and Cabrera-Rubio, R and Carlino, N and Pinto, F and Dzieciol, M and Calvete-Torre, I and Sabater, C and Rubino, F and Knobloch, S and Skirnisdottir, S and Ruiz, L and López, M and Prieto, M and Marteinsson, VT and Margolles, A and Segata, N and Cotter, PD and Wagner, M and Ercolini, D and Alvarez-Ordóñez, A},
title = {The food-associated resistome is shaped by processing and production environments.},
journal = {Nature microbiology},
volume = {10},
number = {8},
pages = {1854-1867},
doi = {10.1038/s41564-025-02059-8},
pmid = {40739039},
issn = {2058-5276},
mesh = {Anti-Bacterial Agents/pharmacology ; *Food Microbiology ; *Bacteria/genetics/drug effects/classification/isolation & purification ; *Food Handling ; *Drug Resistance, Bacterial/genetics ; Animals ; Metagenome ; Vegetables/microbiology ; Humans ; Plasmids/genetics ; Meat/microbiology ; },
abstract = {Food production systems may act as transmission routes for antimicrobial-resistant (AMR) bacteria and AMR genes (AMRGs) to humans. However, the food resistome remains poorly characterized. Here 1,780 raw-material (milk, brine, fresh meat and so on), end-product (cheese, fish, meat products and vegetables) and surface (processing, cooling, smoking, ripening and packing rooms) samples from 113 food processing facilities were subjected to whole-metagenome sequencing. Assembly-free analyses demonstrated that >70% of all known AMRGs, including many predicted to confer resistance to critically important antibiotics, circulate throughout food production chains, with those conferring resistance to tetracyclines, β-lactams, aminoglycosides and macrolides being the most abundant overall. An assembly-based analysis highlighted that bacteria from the ESKAPEE group, together with Staphylococcus equorum and Acinetobacter johnsonii, were the main AMRG carriers. Further evaluation demonstrated that ~40% of the AMRGs were associated with mobile genetic elements, mainly plasmids. These findings will help guide the appropriate use of biocides and other antimicrobials in food production settings when designing efficient antimicrobial stewardship policies.},
}

Anti-Bacterial Agents/pharmacology
*Food Microbiology
*Bacteria/genetics/drug effects/classification/isolation & purification
*Food Handling
*Drug Resistance, Bacterial/genetics
Animals
Metagenome
Vegetables/microbiology
Humans
Plasmids/genetics
Meat/microbiology

@article {pmid40738886,
year = {2025},
author = {Wang, S and Zhang, Z and Zhao, J and Yang, K and Zhang, W and Wang, Z and Liang, Z and Zhang, Y and Zhang, Y and Liu, J and Zhang, L},
title = {Metaproteomic Insights into Bioenergy Conversion Enzymes of Bathypelagic Microbial Communities in the South China Sea.},
journal = {Journal of proteome research},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jproteome.5c00551},
pmid = {40738886},
issn = {1535-3907},
abstract = {Marine microorganisms inhabiting the bathypelagic zone (1000-4000 m) exhibit distinctive environmental adaptability and serve as a valuable reservoir of bioenzymes. However, a limited understanding of deep-sea microbial community composition and metabolic activities hinders the broad application of their enzymatic potential. In this study, we employed a metaproteomic approach to investigate the protein profiles of microbial communities in the bathypelagic layers of the South China Sea (SCS), and we compared them with the corresponding metagenomic data. Our findings revealed a strong phylum-level correlation between metaproteomic and metagenomic datasets, along with a significant enrichment of proteins associated with inorganic ion metabolism and energy conversion. Deep-sea microbial communities are characterized by unique dominant taxa, such as Propionibacteriales, and exhibit diverse strategies for energy utilization. Notably, we identified several enzymes involved in energy conversion, including RuBisCO and carbon monoxide dehydrogenase in Proteobacteria and ammonia monooxygenase in Thaumarchaeota for carbon fixation. These enzymes catalyze reactions utilizing various inorganic substrates as energy sources. Additionally, the deep-sea environment significantly enhanced the expression of methane monooxygenase in methylotrophs, suggesting that such conditions may promote the development of methane-utilizing cell factories. This study not only deepens our understanding of energy conversion mechanisms in deep-sea microorganisms but also offers valuable enzymatic resources for the development of novel bioenergy technologies.},
}

@article {pmid40738767,
year = {2025},
author = {Cauwenberghs, E and De Boeck, I and Delanghe, L and Van Rillaer, T and Demuyser, T and Spacova, I and Verhulst, S and Van Hoorenbeeck, K and Lebeer, S},
title = {Shallow metagenomic shotgun sequencing improves detection of pathogenic species in cystic fibrosis respiratory samples.},
journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jcf.2025.07.011},
pmid = {40738767},
issn = {1873-5010},
abstract = {BACKGROUND: Chronic infection and inflammation of the lungs contribute significantly to disease progression in persons with cystic fibrosis (pwCF). Treatment regimens are largely based on isolating the putative causative pathogen(s) from respiratory samples using basic culturing methods. While this strategy has shown to be highly valuable in the management of CF, the approach is time-consuming and often misses detection of pathogenic microbes that are more difficult to culture, including Mycobacterium spp.

METHODS: In our proof-of-concept study, we evaluated shallow metagenomic shotgun sequencing to detect potential infection-causing pathogens at species level in sputum, oropharyngeal and salivary samples of pwCF (n = 13), and compared it to culture results from the clinic and standard 16S rRNA V4 amplicon sequencing.

RESULTS: Shallow shotgun sequencing improved the detection of pathogenic species in respiratory samples compared to culture methods. In particular, shallow shotgun sequencing could detect pathogenic species associated with CF, specifically Staphylococcus aureus, Pseudomonas aeruginosa, Stenotrophomonas maltophilia, Achromobacter xylosoxidans, Haemophilus influenzae and Mycobacterium spp. in sputum, oropharyngeal and/or salivary samples. Notably, Mycobacterium spp. was not detected based on 16S rRNA amplicon sequencing. Moreover, our approach was able to distinguish S. aureus from S. epidermidis and H. influenzae from H. parainfluenzae. This is not possible with 16S amplicon sequencing, but highly valuable in a clinical setting.

CONCLUSIONS: The improved detection of CF pathogens and other critical microbiome members as well as insights into their relative abundance within the community, could provide more knowledge on patient's disease status leading to more personalized medicine and ultimately benefit patient care.},
}

@article {pmid40738407,
year = {2025},
author = {Wang, Y and Huang, Y and Peng, C and Yang, J and Hui, E and Zhou, J and He, Q and Wan, S and Chen, Y and Peng, M},
title = {Synergistic enhancement of acidogenic fermentation of waste activated sludge by combined nitrite and peracetic acid co-treatment: Insight into interfacial interaction, functional potential, oxidative stress and adaptive mechanisms.},
journal = {Environmental research},
volume = {},
number = {},
pages = {122470},
doi = {10.1016/j.envres.2025.122470},
pmid = {40738407},
issn = {1096-0953},
abstract = {Compared to methane, volatile fatty acids (VFAs) offer superior economic benefits. Therefore, the extraction of VFAs from waste activated sludge (WAS) during anaerobic digestion (AD) has garnered significant attention. This study demonstrates that the NO2[-]-PAA combined treatment technology effectively promotes the accumulation of total volatile fatty acids (TVFAs) in the AD system, achieving a maximum VFAs accumulation of 1551.2 ± 6.6 mg COD/L and an acidification rate (ηa) of 47.8 ± 1.9%. Mechanistic study indicates that the reactive oxygen/nitrogen species (ROS/RNS, including CH3C(O)OO·, ·OH, ·O2[-], [1]O2 and NO·) induced by the combined treatment act synergistically to damage cell membranes, augment membrane permeability, disrupt protein structures, and stimulate lipid peroxidation. This significantly weakens the attraction between microorganisms in WAS, providing the first mechanistic explanation of how it overcomes the energy barrier of WAS dispersion under NO2[-]-PAA exposure (extended Derjaguin-Landau-Verwey-Overbeek (XDLVO) theory). 16S rDNA and metagenomic analyses confirmed that NO2[-]-PAA combined treatment promoted the selective enrichment of hydrolytic-acidogenic bacteria, particularly Petrimonas (27.7%) and Macellibacteroides (17.0%). In addition, the increased abundance of VFAs biosynthesis-related genes and decreased abundance of methanogenic genes contribute to VFAs accumulation. Enhanced regulation of Quorum Sensing (QS) and Two-Component Systems (TCS) gene clusters improved microbial adaptation to NO2[-]-PAA stress. This study elucidated the synergistic effects of NO2[-]-PAA combined treatment on VFAs extraction from the perspectives of interface interactions, functional potential, oxidative stress, and adaptive mechanisms, and provided promising technical solutions for optimizing WAS carbon flux and efficient VFAs recovery.},
}

@article {pmid40738406,
year = {2025},
author = {Xiao, J and He, J and Shen, X and Lei, X and Zhang, H and Li, Y and Sun, C and Shao, Y},
title = {Characterization of the mulberry field antibiotic resistome and mobilome across China.},
journal = {Environmental research},
volume = {},
number = {},
pages = {122471},
doi = {10.1016/j.envres.2025.122471},
pmid = {40738406},
issn = {1096-0953},
abstract = {Antibiotic resistance genes (ARGs) are emerging environmental contaminants that pose increasing risks to ecosystems and human health. However, the distribution and drivers of ARGs associated with woody plants remain underexplored. In this study, we leverage large-scale sampling and metagenomics to provide a comprehensive survey of ARGs in both mulberry (Morus) field soil and rhizosphere across China. Our findings revealed significant regional differences in ARG diversity and composition, exhibiting a distance-decay pattern. The most abundant ARG types identified were multidrug, novobiocin, and macrolide-lincosamide-streptogramin, with the dominant resistance mechanisms being efflux pumps, antibiotic target alteration, and enzymatic inactivation. Structural equation modelling further showed that ARG profiles were primarily influenced by mobile genetic elements (MGEs) and annual mean temperature, with high-risk ARGs increasing significantly. We also observed notable regional and compartmental differences in MGEs, with both richness and abundance being higher in the rhizosphere compared to bulk soil. Moreover, co-occurrence network analysis revealed that ARG-MGE associations in the rhizosphere were stronger and more complex, likely promoting ARG dissemination. Our results not only provide the first overview of ARG profiles in widely planted mulberry but also characterize the factors shaping the antibiotic resistome, paving the way for managing ARG risks in woody plants.},
}

@article {pmid40738384,
year = {2025},
author = {Liang, T and Jiang, T and Liang, Z and Chen, Y and Chen, T and Dong, B and Xie, X and Gu, B and Wu, Q},
title = {Lactiplantibacillus plantarum strain 84-3-derived l-glutamine ameliorates glucose homeostasis via AMPK/PPARγ signaling pathway activation in type 2 diabetes.},
journal = {Metabolism: clinical and experimental},
volume = {172},
number = {},
pages = {156357},
doi = {10.1016/j.metabol.2025.156357},
pmid = {40738384},
issn = {1532-8600},
abstract = {BACKGROUND: Gut microbiota and their metabolites play an essential role in type 2 diabetes (T2D). However, contributions of individual bacterial strains and their metabolites to T2D pathogenesis remain poorly understood. We investigated T2D regulation by Lactobacillus in various animal models to understand its therapeutic effects.

METHODS AND RESULTS: We performed a case-control study of Chinese adults using metabolome profiling and identified an inverse correlation between l-glutamine and T2D serum concentrations. The glnA and GLUL genes encoding glutamine synthetase (GS) in L. plantarum 84-3 were also identified. L. plantarum 84-3 treatment significantly decreased serum inflammation and improved metabolic phenotypes in streptozotocin- or tetraoxypyrimidine-induced T2D rats, including blood glucose, glucose tolerance, insulin resistance, and lipids. We confirmed elevated serum l-glutamine levels in the L. plantarum 84-3 group. RNA sequencing analysis demonstrated that L. plantarum 84-3-derived l-glutamine is a vital bioactive molecule, improving glucose homeostasis by activating the liver AMPK/PPAR signaling pathway and ameliorating T2D. We conducted co-culture fermentation experiments in vitro and in vivo, and metagenomic and metabolomic analyses revealed that resistance starch combined with L. plantarum 84-3 significantly enriched of Lactobacillus abundance and increased the l-glutamine level, affecting of alanine, aspartate, and glutamate metabolism pathways, which was confirmed in vivo in rats. The reduced L. plantarum and l-glutamine levels were validated in a human T2D cohort.

CONCLUSIONS: These findings revealed a novel therapeutic effect of L. plantarum in alleviating T2D-related glucose homeostasis by increasing circulating l-glutamine, which suggests viable preventive and therapeutic strategies for metabolic disorders.},
}

@article {pmid40738105,
year = {2025},
author = {Rodriguez-Rodriguez, L and Pfister, J and Schuck, L and Martin, AE and Mercado-Santiago, LM and Tagliabracci, VS and Forsberg, KJ},
title = {Metagenomic selections reveal diverse antiphage defenses in human and environmental microbiomes.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2025.07.005},
pmid = {40738105},
issn = {1934-6069},
abstract = {To prevent phage infection, bacteria have developed an arsenal of antiphage defenses. Evidence suggests that many examples in nature have not been described. Using plasmid libraries expressing small DNA inserts and functional selections for antiphage defense in Escherichia coli, we identified over 200 putative defenses from 14 bacterial phyla in 9 human and soil microbiomes. Many defenses were unrecognizable based on sequence or predicted structure and thus could only be identified via functional assays. In mechanistic studies, we show that some defenses encode nucleases that distinguish phage DNA via diverse chemical modifications. We also identify outer membrane proteins that prevent phage adsorption and a set of unknown defenses with diverse antiphage profiles and modalities. Most defenses acted against at least two phages, indicating that broadly acting systems are widely distributed. Collectively, these findings highlight the diversity and interoperability of antiphage defense systems.},
}

@article {pmid40738085,
year = {2025},
author = {Li, J and Wang, D and Zhang, Q and He, X and Liu, P and Ye, L and Ren, H and Zhang, XX},
title = {Prevalence and functional impact of the interactions between lysogenic phages and hosts in activated sludge systems: Insights from large-scale metagenomics and experimental evidence.},
journal = {Water research},
volume = {286},
number = {},
pages = {124270},
doi = {10.1016/j.watres.2025.124270},
pmid = {40738085},
issn = {1879-2448},
abstract = {Bacteriophages are the most common biological entities in the activated sludge (AS) of wastewater treatment plants (WWTPs), playing an important role in maintaining or regulating the microbial community. However, the interactions between bacteria and lysogenic phages in AS systems remain poorly understood. In this study, we reconstructed metagenome-assembled genomes (MAGs) from 43 full-scale WWTPs across five countries and found that over 55 % of MAGs in AS were lysogenic, highlighting the widespread interactions between lysogenic phages and their hosts. Additionally, diverse novel prophages embedded in the lysogenic MAGs formed complex phage-host interactions, as revealed by the phage-host network, underscoring the intricate relationships between prophages and their microbial hosts. Through in-silico approaches and experimental validation, we confirmed the inducibility and activity of the prophages, showing that prophage induction significantly contributes to the lysis of microorganisms involved in the aerobic oxidation of organic matter, as well as nitrogen and phosphorus removal. This work represents a pioneering large-scale genome-centric metagenomic study, coupled with experimental validation, that uncovers the predominance of lysogenic phage-host interactions in AS systems. It advances our understanding of the pivotal role of prophages in shaping the AS microbiome, particularly in influencing the microbial processes responsible for pollutant degradation and nitrogen and phosphorus removal.},
}

@article {pmid40736902,
year = {2025},
author = {Gifford, H and Wilson, D and Rhodes, J and Farrer, RA},
title = {Seaside to Bedside: Assembly in Research for Emerging Human Fungal Pathogen Candida auris.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2955},
number = {},
pages = {263-291},
pmid = {40736902},
issn = {1940-6029},
mesh = {Humans ; *Candidiasis/microbiology/diagnosis ; *Candida auris/genetics/pathogenicity ; Animals ; Computational Biology/methods ; Host-Pathogen Interactions ; *Candida/genetics ; },
abstract = {Discovery science in Medical Mycology requires a range of tools, from optimized experimental models to near-patient clinical applications, with the common goal of reducing morbidity and mortality from fungal diseases. Assembly tools underpin bioinformatic discovery across this spectrum of research, setting the scene for genomic enquiry, and promising an unprecedented wave of breakthrough in mechanistic understanding of pathobiology that could unearth critical diagnostic and treatment advances. This chapter examines the investigation of Candida auris, an emerging human fungal pathogen, in the context of clinic detection and treatment of infection. In the laboratory, we cover the use of the Arabian Killifish (AK) as a non-model organism to understand transcriptional responses to both host and pathogen during infection.},
}

Humans
*Candidiasis/microbiology/diagnosis
*Candida auris/genetics/pathogenicity
Animals
Computational Biology/methods
Host-Pathogen Interactions
*Candida/genetics

@article {pmid40736894,
year = {2025},
author = {Child, HT and Barber, DG and Maneein, S and Clayton, J and Love, J and Tennant, RK},
title = {Laboratory and In-Field Metagenomics for Environmental Monitoring.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2955},
number = {},
pages = {71-88},
doi = {10.1007/978-1-0716-4702-8_5},
pmid = {40736894},
issn = {1940-6029},
mesh = {*Metagenomics/methods ; *Environmental Monitoring/methods ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; Gene Library ; },
abstract = {Direct sequencing of DNA from environmental samples (eDNA) is increasingly utilized to provide a census of natural and industrial habitats. The methodology required to perform metagenomics can be divided into three distinct stages: DNA Purification, Library Preparation and Sequencing, and Bioinformatic Analysis. Here we demonstrate an end-to-end protocol that can be utilized either in the field or laboratory for metagenomic analysis of environmental samples utilizing the Oxford Nanopore Technologies MinION sequencing platform.},
}

*Metagenomics/methods
*Environmental Monitoring/methods
High-Throughput Nucleotide Sequencing/methods
Sequence Analysis, DNA/methods
Computational Biology/methods
Gene Library

@article {pmid40736891,
year = {2025},
author = {Garg, S},
title = {Methods for Chromosome-Scale Haplotype Reconstruction.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2955},
number = {},
pages = {17-36},
doi = {10.1007/978-1-0716-4702-8_2},
pmid = {40736891},
issn = {1940-6029},
mesh = {*Haplotypes ; Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Computational Biology/methods ; *Chromosomes/genetics ; Sequence Analysis, DNA/methods ; Animals ; },
abstract = {Haplotypes are combinations of alleles inherited together on a chromosome. Traditional short-read sequencing methods can identify genotypes but often fail to capture detailed haplotype information, such as allele colocalization or parental origin. Third-generation sequencing technologies, including long-read and long-range methods, offer higher resolution, enabling more accurate haplotype reconstruction in diploid, polyploid, and metagenomic contexts. To achieve this, advanced computational strategies are needed to reconstruct haplotypes from sequencing data. This chapter explores the evolution of sequencing and computational approaches for integrating various sequencing methods to produce chromosome-scale haplotypes, while addressing the challenges and prospects for scaling haplotype analysis across species. Comprehensive haplotype analysis has great potential for enhancing our understanding of complex genetic variations and their roles in diseases.},
}

*Haplotypes
Humans
*High-Throughput Nucleotide Sequencing/methods
*Computational Biology/methods
*Chromosomes/genetics
Sequence Analysis, DNA/methods
Animals

@article {pmid40736175,
year = {2025},
author = {Shi, Q and Wei, Z and Pang, J and Qudsi, AI and Wei, M and Zhang, Z and Zhang, Y and Wang, Z and Chen, K and Xu, X and Lu, X and Liang, Q},
title = {Achromobacter in the Conjunctival Sac Microbiota: Potential Association With Acanthamoeba Keratitis Related to Orthokeratology Lenses.},
journal = {Investigative ophthalmology & visual science},
volume = {66},
number = {9},
pages = {71},
doi = {10.1167/iovs.66.9.71},
pmid = {40736175},
issn = {1552-5783},
mesh = {Humans ; Male ; Female ; *Microbiota ; *Acanthamoeba Keratitis/microbiology/etiology ; *Conjunctiva/microbiology ; Adult ; *Achromobacter/isolation & purification/genetics/physiology ; In Situ Hybridization, Fluorescence ; RNA, Ribosomal, 16S/genetics ; *Orthokeratologic Procedures/adverse effects/instrumentation ; Acanthamoeba ; *Contact Lenses/adverse effects ; Young Adult ; DNA, Bacterial/genetics/analysis ; Dysbiosis/microbiology ; Middle Aged ; },
abstract = {PURPOSE: Acanthamoeba keratitis (AK) is a severe infection linked to orthokeratology lens use, whereas the involvement of conjunctival microbiota in AK remains poorly understood. This study investigates microbiota dysbiosis in AK pathogenesis to inform microbiota-based interventions.

METHODS: Conjunctival swabs from 14 patients with AK and 10 healthy controls underwent 16S rRNA sequencing. Microbiome analysis compared diversity, taxa, and metabolic pathways. Functional assays quantified Achromobacter-enhanced Acanthamoeba adhesion and migration. Metagenomics and fluorescence in situ hybridization (FISH) with species-specific probes confirmed endosymbiosis.

RESULTS: Patients with AK showed reduced bacterial diversity compared with the healthy controls (P < 0.001) but similar richness. Relative abundance of Achromobacter in the AK group was higher compared to the healthy control group (P < 0.001). Achromobacter dominated microbiota among the AK group, being identified as a key biomarker via the linear discriminant analysis effect size (LEfSe). In vitro, Achromobacter increased Acanthamoeba adhesion (P = 0.007) and the migration area (P < 0.05). Metagenomic analysis and FISH further showed Achromobacter spp. as potential endosymbionts of Acanthamoeba. Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed upregulated phenylalanine, fatty acid, and propanoate metabolism in the AK group (all P < 0.001). MetaCyc highlighted enriched pyruvate fermentation to isobutanol, aerobic respiration I, and L-isoleucine biosynthesis II in the AK group (P < 0.001).

CONCLUSIONS: AK-associated conjunctival dysbiosis features Achromobacter dominance, reduced diversity, and altered metabolism. Achromobacter is associated with enhanced adhesion and migration of Acanthamoeba, indicating a possible symbiotic interaction and its potential as a biomarker and therapeutic target.},
}

Humans
Male
Female
*Microbiota
*Acanthamoeba Keratitis/microbiology/etiology
*Conjunctiva/microbiology
Adult
*Achromobacter/isolation & purification/genetics/physiology
In Situ Hybridization, Fluorescence
RNA, Ribosomal, 16S/genetics
*Orthokeratologic Procedures/adverse effects/instrumentation
Acanthamoeba
*Contact Lenses/adverse effects
Young Adult
DNA, Bacterial/genetics/analysis
Dysbiosis/microbiology
Middle Aged

@article {pmid40735808,
year = {2025},
author = {Maffei, VJ and Bertoni, AG and Wood, AC and Rotter, JI and Crago, O and Chen, YI and Petrosino, JF and Hoffman, KL and Goodarzi, MO and Jensen, ET},
title = {Menopause factors and alterations in gut microbiota and insulin homeostasis: A cross-sectional analysis of the microbiome and insulin longitudinal evaluation study (MILES).},
journal = {Diabetes, obesity & metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1111/dom.16578},
pmid = {40735808},
issn = {1463-1326},
support = {P30-DK063491/DK/NIDDK NIH HHS/United States ; R01-DK109588/DK/NIDDK NIH HHS/United States ; UL1-TR001420/TR/NCATS NIH HHS/United States ; UL1-TR001881/TR/NCATS NIH HHS/United States ; 58-3092-5-001//Agricultural Research Service/ ; },
abstract = {AIM: To assess the risk for impaired insulin homeostasis as a function of menopause-related factors and gut microbiota dysbiosis in non-diabetic, post-menopausal women.

MATERIALS AND METHODS: Baseline data (n = 175 women) from the Microbiome and Insulin Longitudinal Evaluation Study (MILES) were used, including insulin and dysglycaemia indices calculated from a 2-h oral glucose tolerance test, untargeted peripheral metabolomics, targeted peripheral short chain fatty-acid levels and faecal bacterial microbiota surveyed by whole-metagenomic sequencing.

RESULTS: After adjustment for covariates, menopause age <50 years and use of hormone replacement therapy (HRT) were associated with lower Matsuda et al. insulin sensitivity index levels (β = -0.232, confidence interval (CI) = [-0.450, -0.014] and β = -0.275, CI = [-0.444, -0.107], respectively) but not pre-menopausal gynaecologic surgery. Pre-menopausal gynaecologic surgery was significantly associated with faecal microbiota beta diversity driven by a relative increase in diabetogenic Ruminococcus gnavus and Clostridium species and a decrease in protective Alistipes species and Akkermansia muciniphila relative abundances. A reduction in two glycerophospholipids in the plasmalogen class significantly statistically mediated an inverse association between gynaecologic surgery before menopause and insulin sensitivity.

CONCLUSIONS: Menopause age and history of HRT are more strongly associated with insulin resistance than gynaecologic surgery before menopause. However, gynaecologic surgery is associated with shifts in gut microbial composition and plasma metabolite levels with a potential to contribute to future diabetes risk.},
}

@article {pmid40735404,
year = {2025},
author = {Meng, D and Wang, P and Zhang, S and Chen, Z and Lai, C and Yi, X and Huang, X and Yu, H and Zhang, M and Gao, X},
title = {Exploring the Prevention of Lipid Deposition Caused by High-Fat Diet and Its Mechanism of Action of Rosa roxburghii Fermented Juice Based on Liver Metabolomics and Gut Microbiota.},
journal = {Food science & nutrition},
volume = {13},
number = {8},
pages = {e70449},
pmid = {40735404},
issn = {2048-7177},
abstract = {Hyperlipidemia has become a prevalent disease in the global epidemic, posing a threat to human health. This study aims to investigate the mechanism by which Rosa roxburghii fermented juice (RRFJ) can prevent lipid deposition induced by a high-fat diet in mice. The results showed that mice in the RRFJ intervention group had significantly reduced body weight as well as lower levels of serum and liver lipid indicators compared to the high-fat diet group. Metagenomic analysis revealed that the RRFJ intervention reversed the decrease in intestinal flora Alistipes and Colidextribacter genes in mice fed a high-fat diet. Liver metabolomics showed that the RRFJ prevented liver dyslipidemia by modulating the biosynthesis of phenylalanine, tyrosine, tryptophan, and phenylalanine metabolism. RRFJ is effective in preventing dyslipidemia through the 'gut-liver axis', which regulates the imbalance of intestinal flora and improves hepatic metabolic profiles. This provides a new intervention strategy for the prevention and treatment of hyperlipidemia.},
}

@article {pmid40733600,
year = {2025},
author = {Debat, H and Bejerman, N},
title = {An Update on RNA Virus Discovery: Current Challenges and Future Perspectives.},
journal = {Viruses},
volume = {17},
number = {7},
pages = {},
pmid = {40733600},
issn = {1999-4915},
mesh = {*RNA Viruses/genetics/isolation & purification/classification ; Humans ; Animals ; *RNA Virus Infections/virology/transmission/epidemiology ; Communicable Diseases, Emerging/virology ; Zoonoses/virology ; Public Health ; },
abstract = {The relentless emergence of RNA viruses poses a perpetual threat to global public health, necessitating continuous efforts in surveillance, discovery, and understanding of these pathogens. This review provides a comprehensive update on recent advancements in RNA virus discovery, highlighting breakthroughs in technology and methodologies that have significantly enhanced our ability to identify novel viruses across diverse host organisms. We explore the expanding landscape of viral diversity, emphasizing the discovery of previously unknown viral families and the role of zoonotic transmissions in shaping the viral ecosystem. Additionally, we discuss the potential implications of RNA virus discovery on disease emergence and pandemic preparedness. Despite remarkable progress, current challenges in sample collection, data interpretation, and the characterization of newly identified viruses persist. Our ability to anticipate and respond to emerging respiratory threats relies on virus discovery as a cornerstone for understanding RNA virus evolution. We address these challenges and propose future directions for research, emphasizing the integration of multi-omic approaches, advanced computational tools, and international collaboration to overcome barriers in the field. This comprehensive overview aims to guide researchers, policymakers, and public health professionals in navigating the intricate landscape of RNA virus discovery, fostering a proactive and collaborative approach to anticipate and mitigate emerging viral threats.},
}

*RNA Viruses/genetics/isolation & purification/classification
Humans
Animals
*RNA Virus Infections/virology/transmission/epidemiology
Communicable Diseases, Emerging/virology
Zoonoses/virology
Public Health

@article {pmid40733506,
year = {2025},
author = {Tóth, F and Pankovics, P and Urbán, P and Herczeg, R and Albert, E and Reuter, G and Boros, Á},
title = {Genomic Characterization and Molecular Epidemiology of Tusaviruses and Related Novel Protoparvoviruses (Family Parvoviridae) from Ruminant Species (Bovine, Ovine and Caprine) in Hungary.},
journal = {Viruses},
volume = {17},
number = {7},
pages = {},
pmid = {40733506},
issn = {1999-4915},
support = {PTE ÁOK-KA No:2025/09//University of Pécs Medical School/ ; },
mesh = {Animals ; Cattle ; Phylogeny ; Sheep/virology ; Goats/virology ; *Genome, Viral ; *Parvoviridae Infections/epidemiology/veterinary/virology ; Hungary/epidemiology ; Molecular Epidemiology ; *Sheep Diseases/virology/epidemiology ; Ruminants/virology ; *Cattle Diseases/virology/epidemiology ; Feces/virology ; Genomics ; *Parvoviridae/genetics/classification/isolation & purification ; *Goat Diseases/virology/epidemiology ; High-Throughput Nucleotide Sequencing ; },
abstract = {Tusavirus 1 of species Protoparvovirus incertum 1 (family Parvoviridae) was first identified in humans and later in small ruminants (caprine and ovine). This study reports the full-length coding sequences (~4400-4600 nt) of three novel tusavirus-related protoparvoviruses from ovine ("misavirus", PV540792), for the first time bovine ("sisavirus", PV540793) and subsequently from caprine ("gisavirus" PV540850/51) fecal samples, using next-generation sequencing (NGS) and PCR techniques. Their NS1, VP1 and VP2 proteins shared 61-63% amino acid identities with each other and with tusaviruses, suggesting these three viruses belong to three novel species in the genus Protoparvovirus. Phylogenetic analyses placed them with tusaviruses on a separate main branch, implying a shared origin among these most likely ruminant protoparvoviruses. A small-scale epidemiological investigation on 318 ruminant enteric samples using novel generic NS1 primers found misavirus in 14/51 (27.5%) ovine and sisavirus in 19/203 (9.4%) bovine samples from multiple Hungarian farms. Tusavirus was present in 5/51 (9.8%) ovine and 15/62 (24.2%) caprine samples, all from one farm. The highest prevalences for all three viruses were found in animals aged 2-12 months, though sporadic cases were also found in other age groups. Partial NS and VP sequence-based phylogenetic trees showed virus-specific lineages for misa-, sisa-, gisa- and tusaviruses, with various strains forming sub-lineages. These findings suggest the presence of multiple genotypes and/or members of additional species, which was supported by a VP sequence-based hierarchical cluster analysis. The study's viruses were mostly phylogenetically separated by host; however, two bovine sisavirus strains with diverse phylogenetic localizations in the NS (belonging to bovine sisaviruses) and VP1 trees (distantly related to ovine misaviruses) could indicate previous (interspecies?) recombination events.},
}

Animals
Cattle
Phylogeny
Sheep/virology
Goats/virology
*Genome, Viral
*Parvoviridae Infections/epidemiology/veterinary/virology
Hungary/epidemiology
Molecular Epidemiology
*Sheep Diseases/virology/epidemiology
Ruminants/virology
*Cattle Diseases/virology/epidemiology
Feces/virology
Genomics
*Parvoviridae/genetics/classification/isolation & purification
*Goat Diseases/virology/epidemiology
High-Throughput Nucleotide Sequencing

@article {pmid40732945,
year = {2025},
author = {Kulecka, M and Jaworski, P and Zeber-Lubecka, N and Bałabas, A and Piątkowska, M and Czarnowski, P and Frączek, B and Tarnowski, W and Mikula, M and Ostrowski, J},
title = {The Gut Microbiome Obesity Index: A New Analytical Tool in the Metagenomics Workflow for the Evaluation of Gut Dysbiosis in Obese Humans.},
journal = {Nutrients},
volume = {17},
number = {14},
pages = {},
pmid = {40732945},
issn = {2072-6643},
support = {2018/29/B/NZ7/00809//National Science Center/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Obesity/microbiology ; Male ; Female ; *Metagenomics/methods ; Adult ; Feces/microbiology ; *Dysbiosis/microbiology/diagnosis ; Body Mass Index ; Middle Aged ; Bacteria/classification/genetics ; Workflow ; Case-Control Studies ; Young Adult ; },
abstract = {Background/Objectives: Our aim was to create a new method for analyzing metagenomics data, named the gut microbiome obesity index, using a set of taxa/biological functions that correlated with BMI. Methods: A total of 109 obese patients (73 women and 36 men, median BMI 43.0 kg/m[2]), 87 healthy control (HC) individuals (39 females and 48 males, median BMI 22.7 kg/m[2]), and 109 esports players (five females and 104 males, median BMI 23.0 kg/m[2]) were included in the study. To conduct metagenomic and metabolomic analyses, DNA and selected metabolites were isolated from fecal samples and used for whole-genome shotgun sequencing and gas chromatography/mass spectrometry, respectively. Results: Compared with HCs and esports players, obese patients with a BMI > 40 kg/m[2] had a significantly higher alpha diversity, as analyzed by the Shannon index, and significant dissimilarities in beta diversity. Both richness and diversity measures were correlated with BMI. Compared with HCs and esports players, 12 differential bacteria were found in the overall obesity group and 42 were found in those with a BMI > 40 kg/m[2]. Most of the altered species belonged to the Lachnospiraceae family. When the logarithmic relationship of the sums of the bacteria correlated with BMI was calculated to establish a taxonomic health index, it better differentiated between the obesity groups than a standard analytical pipeline; however, it did not differentiate between the HC and the BMI < 35 kg/m[2] obesity group. Therefore, we created a functional index based on BMI-associated biological pathways, which differentiated between all obesity groups. Conclusions: Of the obesity indices used to distinguish between healthy and obese microbiota analyzed in this study, a function-based index was more useful than a taxonomy-based index. We believe that gut microbiome indexes could be useful as part of routine metagenomics evaluations. However, an index developed in one geographical area might not be applicable to individuals in a different region and, therefore, further studies should develop separate indices for different populations or geographical regions rather than relying on a single index.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Obesity/microbiology
Male
Female
*Metagenomics/methods
Adult
Feces/microbiology
*Dysbiosis/microbiology/diagnosis
Body Mass Index
Middle Aged
Bacteria/classification/genetics
Workflow
Case-Control Studies
Young Adult

@article {pmid40732703,
year = {2025},
author = {Chen, Y and Fu, H and Zhu, Q and Ren, Y and Liu, J and Wu, Y and Xu, J},
title = {Clinical Features of Pulmonary Nocardiosis and Diagnostic Value of Metagenomic Next-Generation Sequencing: A Retrospective Study.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {7},
pages = {},
pmid = {40732703},
issn = {2076-0817},
support = {76080151//the Pfizer Global Medical Grants/ ; },
mesh = {Humans ; *Nocardia Infections/diagnosis/microbiology/drug therapy ; Retrospective Studies ; Male ; Female ; Middle Aged ; *Nocardia/genetics/isolation & purification ; *High-Throughput Nucleotide Sequencing/methods ; Aged ; *Metagenomics/methods ; Adult ; Anti-Bacterial Agents/therapeutic use ; Trimethoprim, Sulfamethoxazole Drug Combination/therapeutic use ; Coinfection/microbiology/diagnosis ; },
abstract = {Pulmonary nocardiosis (PN) is a rare, opportunistic, and potentially life-threatening infection, especially in disseminated cases. This retrospective study aimed to characterize the clinical features of PN and assess the diagnostic utility of metagenomic next-generation sequencing (mNGS). We reviewed data from 19 patients diagnosed with PN between September 2019 and August 2022, including 3 with disseminated disease. Common symptoms included fever, cough, and sputum production, while chest imaging frequently revealed nodules, consolidations, exudates, cavities, and pleural effusions. The sensitivity of mNGS for detecting Nocardia was significantly higher than that of culture (100% vs. 36.84%, p < 0.001). mNGS successfully identified Nocardia species and co-infected pathogens. The most common species was Nocardia farcinica. Four PN cases were co-infected with Rhizomucor pusillus, Cryptococcus neoformans, Lichtheimia ramosa, and Aspergillus spp. Eighteen patients (94.7%) received trimethoprim-sulfamethoxazole (TMP-SMZ). Sixteen cases (84.2%) were improved or cured. Misdiagnosis is common due to the nonspecificity of clinical and imaging presentations of pulmonary nocardiosis. The timely combination of mNGS represents a promising approach to enhance the diagnosis of pulmonary nocardiosis and inform targeted antimicrobial therapy. TMP-SMZ is the first line of treatment.},
}

Humans
*Nocardia Infections/diagnosis/microbiology/drug therapy
Retrospective Studies
Male
Female
Middle Aged
*Nocardia/genetics/isolation & purification
*High-Throughput Nucleotide Sequencing/methods
Aged
*Metagenomics/methods
Adult
Anti-Bacterial Agents/therapeutic use
Trimethoprim, Sulfamethoxazole Drug Combination/therapeutic use
Coinfection/microbiology/diagnosis

@article {pmid40732219,
year = {2025},
author = {Hu, W and Zhou, X and Liu, Y and Zhang, Y and Wang, Y},
title = {Effects of Salinity Fluctuation on Antimicrobial Resistance and Virulence Factor Genes of Low and High Nucleic Acid-Content Bacteria in a Marine Environment.},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/microorganisms13071710},
pmid = {40732219},
issn = {2076-2607},
support = {252102320216//Henan Province Science and Technology Research Project/ ; },
abstract = {Salinity, as one of the critical environmental factors in marine ecosystems, has complex and wide-ranging biological effects. However, the effects of salinity fluctuation on antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) in the marine environment are not well understood. In this study, metagenomic sequencing analysis was used to reveal the response of ARGs and VFGs, hosted by low and high nucleic acid-content bacteria (HNA and LNA bacteria), to salinity, as it decreased from 26‱ to 16‱. The results showed that a total of 27 ARG types and 13 VFG types in HNA and LNA bacteria were found. Salinity changes had significant effects on the ARGs' and VFGs' composition and their hosts' composition. In the network topology relationship, the complexity of the network between the ARGs and their host as well as the VFGs and their host differed with the decrease in salinity. The abundance of most genera of HNA and LNA bacteria was significantly corrected with the abundance of ARGs and VFGs, respectively. Overall, this study demonstrates the effects of salinity on ARGs and VFGs hosted by HNA and LNA bacteria in the marine environment and suggests the importance of salinity in regulating HNA and LNA bacterial communities and functions.},
}

@article {pmid40732185,
year = {2025},
author = {Yaguchi, E and Komiyama, Y and Inami, S and Shibasaki, I and Shintani, T and Shiraishi, R and Hyodo, T and Shiba, H and Hamaguchi, S and Fukuda, H and Toyoda, S and Fukumoto, C and Izumi, S and Wakui, T and Kawamata, H},
title = {Oral Dysbiosis Is Associated with the Pathogenesis of Aortic Valve Diseases.},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/microorganisms13071677},
pmid = {40732185},
issn = {2076-2607},
abstract = {The involvement of oral bacteria in the pathogenesis of distant organs, such as the heart, lungs, brain, liver, and intestine, has been shown. We analyzed the distribution of bacterial species in the resected aortic valve by 16S rRNA metagenomic analysis and directly compared their gene sequences with those in the oral cavity. Thirty-two patients with aortic stenosis or aortic regurgitation who underwent aortic valve replacement were enrolled in this study. Antibody titer against periodontal pathogenic bacteria in the patient's serum was analyzed. The genetic background and distribution of bacterial species on subgingival plaque, the dorsal surface of the tongue, and the resected aortic valve were analyzed. Patients with aortic valve disease were shown to have more severe periodontal disease by the detection of antibodies against Socransky's red-complex bacteria of periodontitis. Bacterial DNA was detected in the aortic valves of 12 out of 32 patients. The genomic sequences of the V3-V4 region of the 16S rRNA in some bacteria isolated from the aortic valves of six patients who underwent metagenomic analysis were identical to those found in the oral cavity. The findings indicate that bacteria detected in the aortic valve may be introduced through oral dysbiosis, a condition characterized by an imbalance in the oral microbiota that increases the risk of periodontal disease and dental caries. Oral dysbiosis and the resulting potential bacteremia are associated with the pathogenesis of aortic valve diseases.},
}

@article {pmid40732173,
year = {2025},
author = {Harahap, AFP and Treinen, C and Zyl, LJV and Williams, WT and Conrad, J and Pfannstiel, J and Klaiber, I and Grether, J and Hiller, E and Vahidinasab, M and Perino, EHB and Lilge, L and Burger, A and Trindade, M and Hausmann, R},
title = {Glucoselipid Biosurfactant Biosynthesis Operon of Rouxiella badensis DSM 100043[T]: Screening, Identification, and Heterologous Expression in Escherichia coli.},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/microorganisms13071664},
pmid = {40732173},
issn = {2076-2607},
support = {01DG17018//German Federal Ministry of Education and Research/ ; UID105876//South African National Research Foundation/ ; 57552340//German Academic Exchange Service (DAAD)/ ; 317898569//Deutsche Forschungsgemeinschaft/ ; },
abstract = {Rouxiella badensis DSM 100043[T] had been previously proven to produce a novel glucoselipid biosurfactant which has a very low critical micelle concentration (CMC) as well as very good stability against a wide range of pH, temperature, and salinity. In this study, we performed a function-based library screening from a R. badensis DSM 100043[T] genome library to identify responsible genes for biosynthesis of this glucoselipid. The identified open reading frames (ORFs) were cloned into several constructs in Escherichia coli for gene permutation analysis and the individual products were analyzed using high-performance thin-layer chromatography (HPTLC). Products of interest from positive expression strains were purified and analyzed by liquid chromatography/electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS) and nuclear magnetic resonance (NMR) for further structure elucidation. Function-based screening of 5400 clones led to the identification of an operon containing three ORFs encoding acetyltransferase GlcA (ORF1), acyltransferase GlcB (ORF2), and phosphatase/HAD GlcC (ORF3). E. coli pCAT2, with all three ORFs, resulted in the production of identical R. badensis DSM 100043[T] glucosedilipid with Glu-C10:0-C12:1 as the main congener. ORF2-deletion strain E. coli pAFP1 primarily produced glucosemonolipids, with Glu-C10:0,3OH and Glu-C12:0 as the major congeners, predominantly esterified at the C-2 position of the glucose moiety. Furthermore, fed-batch bioreactor cultivation of E. coli pCAT2 using glucose as the carbon source yielded a maximum glucosedilipid titer of 2.34 g/L after 25 h of fermentation, which is 55-fold higher than that produced by batch cultivation of R. badensis DSM 100043[T] in the previous study.},
}

@article {pmid40732167,
year = {2025},
author = {He, W and Wang, X and Cao, Y and Liu, C and Qin, Z and Zuo, Y and Li, Y and Tang, F and Dai, J and Wang, S and Xue, F},
title = {Effects of Antibiotic Residues on Fecal Microbiota Composition and Antimicrobial Resistance Gene Profiles in Cattle from Northwestern China.},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/microorganisms13071658},
pmid = {40732167},
issn = {2076-2607},
support = {2023YFF0611501//National Key Research and Development Program of China/ ; },
abstract = {Grazing is a free-range farming model commonly practiced in low-external-input agricultural systems. The widespread use of veterinary antibiotics in livestock farming has led to significant environmental accumulation of antibiotic residues and antibiotic resistance genes (ARGs), posing global health risks. This study investigated the antibiotic residues, bacterial community, ARG profiles, and mobile genetic elements (MGEs) in cattle feces from three provinces in western China (Ningxia, Xinjiang, and Inner Mongolia) under grazing modes. The HPLC-MS detection showed that the concentration of tetracycline antibiotics was the highest in all three provinces. Correlation analysis revealed a significant negative correlation between antibiotic residues and the diversity and population abundance of intestinal microbiota. However, the abundance of ARGs was directly proportional to antibiotic residues. Then, the Sankey analysis revealed that the ARGs in the cattle fecal samples were concentrated in 15 human pathogenic bacteria (HPB) species, with 9 of these species harboring multiple drug resistance genes. Metagenomic sequencing revealed that carbapenemase-resistant genes (blaKPC and blaVIM) were also present in considerable abundance, accounting for about 10% of the total ARGs detected in three provinces. Notably, Klebsiella pneumoniae strains carrying blaCTX-M-55 were detected, which had a possibility of IncFII plasmids harboring transposons and IS19, indicating the risk of horizontal transfer of ARGs. This study significantly advances the understanding of the impact of antibiotic residues on the fecal microbiota composition and ARG profiles in grazing cattle from northwestern China. Furthermore, it provides critical insights for the development of rational antibiotic usage strategies and comprehensive public health risk assessments.},
}

@article {pmid40732166,
year = {2025},
author = {Deng, L and Xu, J and Xue, Q and Wei, Y and Wang, J},
title = {Healthy Ageing and Gut Microbiota: A Study on Longevity in Adults.},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/microorganisms13071657},
pmid = {40732166},
issn = {2076-2607},
support = {2020//National Project of Multidisciplinary Management of Major Diseases/ ; JKCJ202303//International Institute of Population Health, Peking University Health Science Center/ ; },
abstract = {Many studies have focused on ageing and gut microbiota, but the correlation between gut microbiota and physical function in older adults, especially those with longevity, remains obscure and deserves further exploration. In this study we investigated changes in the gut microbiota and the association between gut microbiota and physical function in adults with longevity. This is a prospective observational study. Fifty-one older adults aged ≥ 60 years (including 27 participants aged 90 years and above) were enrolled. Information on clinical data, physical function including intrinsic capacity by Integrated Care for Older People (ICOPE) tool, and dietary habits of participants was collected and analysed. Gut microbiota structure and functional pathways were analysed by Metagenomics. Intrinsic capacity (measured as ICOPE scores) of adults' longevity (aged 90-98, longe group) was significantly lower than older adults aged 60-89 years (CON group) (5.44 ± 2.15 vs. 6.71 ± 1.46, p = 0.017). Gut microbiota of the longe group is enriched in Akkermansia and Bifidobacterium, which may be beneficial to health. Gut microbiota was closely related to daily milk (including plain milk, flavoured milk with a content of cow's milk or reconstituted milk of ≥80%, or reconstituted milk or fermented milk with a content of cow's milk or milk powder of ≥80%) consumption, anxiety, and physical function including grip strength by the Short Physical Performance Battery (SPPB). Bacteroides plebeius and Bacteroides eggerthii were increased in long-living adults with better physical function. Escherichia coli was more abundant in frail young-old adults. Grip strength is positively correlated with the abundance of Roseburia hominis, Eubacterium rectale, Eubacterium eligens, and Roseburia intestinalis (p < 0.05). Pathways related to amino acid synthesis that include L-isoleucine, L-valine, and L-threonine were over-presented in long-living adults of better physical function. Adults with longevity showed comparable gut microbiota abundance to younger elderly individuals. The gut microbiota of long-living adults showed higher abundance of potentially beneficial bacteria, and the altered bacteria are closely associated with physical function. Changes in the gut microbiota may precede clinical indicators during the process of ageing. Gut microbiota may be a potential biomarker for longevity and healthy ageing. Nutrition and emotional state can be important influencing factors.},
}

@article {pmid40732140,
year = {2025},
author = {Madney, Y and Mahfouz, S and Bayoumi, A and Hassanain, O and Hassanain, O and Sayed, AA and Jalal, D and Lotfi, M and Tolba, M and Ziad, GA and Elanany, M and Hashem, M and Taha, G and Shalaby, L and Elhaddad, A},
title = {Carbapenem-Resistant Enterobacteriaceae (CRE) in Children with Cancer: The Impact of Rapid Diagnostics and Targeted Colonization Strategies on Improving Outcomes.},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/microorganisms13071627},
pmid = {40732140},
issn = {2076-2607},
support = {54699605//Pfizer Global Medical Grants/ ; },
abstract = {Carbapenem-resistant Enterobacteriaceae (CRE) pose an emerging threat, with a high mortality rate among children with cancer. This study aimed to evaluate the impact of routine rectal swab surveillance and rapid PCR-based detection of carbapenemase genes to facilitate the early initiation of appropriate treatment and assess its effects on outcomes. The study compared two groups of pediatric cancer patients with CRE bloodstream infections: a retrospective cohort of 254 patients from 2013 to 2017, and a prospective cohort of 186 patients from 2020 to 2022, following the implementation of these tools. A rapid diagnostic test in the prospective cohort resulted in the early initiation of proper antibiotics in 85% (165/186) of patients, compared to only 58% (147/254) in the retrospective group. This led to a decrease in the need for ICU admission related to sepsis from CRE and a significant reduction in the 30-day mortality rate (16% vs. 30%, p ≤ 0.01). Genotypic profiling revealed that class B carbapenemases were the most prevalent (69%), with the NDM type being identified in 67% of patients. OXA-48 and KPC enzymes were detected in 59% and 4% of patients, respectively. Multivariate analysis revealed that patients having Klebsiella pneumoniae, NDM genotype carbapenemases, presence of pneumonia, and septic shock requiring ICU admission were predictors of poor outcomes. Rapid diagnostics and targeted colonization lead to the appropriate use of targeted antibiotics, resulting in improved patient outcomes. Understanding carbapenemase-producing microorganisms and administering newer antibiotics may further reduce mortality and enhance treatment strategies for high-risk patients.},
}

@article {pmid40732132,
year = {2025},
author = {Thomas-White, K and Olmschenk, G and Lyttle, D and Markowitz, R and Navarro, P and McLean, K},
title = {Remote BV Management via Metagenomic Vaginal Microbiome Testing and Telemedicine.},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/microorganisms13071623},
pmid = {40732132},
issn = {2076-2607},
abstract = {Bacterial vaginosis (BV) affects 30% of women annually, but many face barriers to in-person care. Here we present real-world outcomes of remote BV diagnosis and management through self-collected vaginal microbiome (VMB) testing and telemedicine visits, focusing on symptom resolution, recurrence, and overall microbial shifts. Among the 1159 study participants, 75.5% experienced symptom resolution at four weeks when managed with our algorithm-guided treatment protocol. At a median follow-up of 4.4 months after the initial visit, 30.0% of patients experienced recurrent BV, which is lower than the typical recurrence rates seen in historical in-person cohorts. Across the entire cohort, metagenomic data demonstrated a significant increase in Lactobacillus abundance (mean of 32.9% to 48.4%, p < 0.0001) and a corresponding decrease in BV-associated taxa such as Gardnerella, Prevotella, and Fannyhessea. A PERMANOVA of pairwise Bray-Curtis distances showed significant separation between pre-and post-treatment samples (pseudo-F = 37.6, p < 0.0001), driven by an increase in Lactobacillus-dominated samples. Treatment adherence was high (a total of 78% reported perfect or near-perfect adherence), and adverse events were generally mild (in total, 22% reported vaginal irritation, and 13% reported abnormal discharge). These results demonstrate that Evvy's at-home metagenomic platform, paired with telemedicine and a smart treatment algorithm, delivers robust clinical and microbial outcomes. This work offers a novel approach to managing bacterial vaginosis, a challenging condition characterized by persistently high recurrence rates.},
}

@article {pmid40732125,
year = {2025},
author = {Feng, W and Gao, C and Cui, X and Yang, B and He, K and Huang, Q and Yang, X and Wen, K and Xie, J and Yang, Z and Zhu, L},
title = {Metagenome Analysis Reveals Changes in Gut Microbial Antibiotic Resistance Genes and Virulence Factors in Reintroduced Giant Pandas.},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/microorganisms13071616},
pmid = {40732125},
issn = {2076-2607},
support = {U21A20193//National Natural Science Foundation of China/ ; 32270546//National Natural Science Foundation of China/ ; },
abstract = {Antibiotic resistance has emerged as a critical global public health challenge. In this study, we employed metagenomic sequencing to analyze fecal samples from giant pandas (Ailuropoda melanoleuca) across three distinct stages-semi-wild, released, and wild populations-to investigate shifts in antibiotic resistance genes (ARGs) and virulence factors (VFs) during the reintroduction process. Our findings revealed significant variations in the composition of ARG and VF across different stages, with released and wild giant pandas exhibiting similar ARG and VF profiles. Further analyses identified that the increased abundance of ARGs and VFs in both released and wild individuals compared to semi-wild individuals was mainly from Pseudomonas. We hypothesized that the same geographic environment in which ARGs and VFs are transmitted between a host and the environment via mobile genetic elements (MGEs) may be responsible for the similar structure of ARGs and VFs in released and wild giant pandas. Additionally, diet may modulate the gut microbial community, thereby influencing the distributions of ARG and VF. This study elucidated the impact of geographic and dietary factors on ARGs and VFs dynamics in giant pandas, offering valuable insights for mitigating antibiotic resistance and virulence gene dissemination.},
}

@article {pmid40732124,
year = {2025},
author = {Tom, A and Yellapu, NK and Rahi, M and Saini, P},
title = {Metagenomic Analyses of Gut Bacteria of Two Sandfly Species from Western Ghats, India, Differing in Their Vector Competence for Leishmaniasis.},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/microorganisms13071615},
pmid = {40732124},
issn = {2076-2607},
abstract = {Phlebotomine sandflies are the primary vectors of Leishmania parasites, the causative agents of leishmaniasis. In India, Phlebotomus argentipes is the confirmed vector of Leishmania donovani. The sandfly gut microbiota plays a crucial role in Leishmania development and transmission, yet it remains largely understudied. This study used a metagenomic approach targeting the V3-V4 region of the 16S rRNA gene to compare the gut bacterial communities of P. argentipes and Sergentomyia babu prevalent in Kerala. A total of 18 distinct bacterial phyla were identified in P. argentipes, and 14 in S. babu, both dominated by Proteobacteria, Actinobacteria, and Firmicutes. A total of 315 genera were identified in P. argentipes, with a high relative abundance of Pseudomonas (6.3%), whereas S. babu harbored 327 genera, with Pseudomonas showing a higher relative abundance of 11%. Unique to P. argentipes, bacterial phyla such as Fusobacteria, Armatimonadetes, Elusimicrobia, Chlamydiae, and Crenarchaeota were identified, whereas Chlorobi was specific to S. babu. Additionally, 145 species were identified in P. argentipes, compared to 164 species in S. babu. These findings provide a comparative baseline of gut microbial diversity between vector and non-vector sandfly species, offering a foundation for future functional investigations into vector competence.},
}

@article {pmid40732102,
year = {2025},
author = {Liu, Y and Ren, J and Yu, B and Liu, S and Cao, X},
title = {Metagenomic and Metabolomic Perspectives on the Drought Tolerance of Broomcorn Millet (Panicum miliaceum L.).},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/microorganisms13071593},
pmid = {40732102},
issn = {2076-2607},
support = {YDZJSX2022A044//the Central Guiding Local Science and Technology Development Funds/ ; CARS-06-14.5-A16//the earmarked fund for CARS/ ; 2025CYJSTX03-23//the earmarked fund for Modern Agro-Industry Technology Research System/ ; },
abstract = {Drought stress is an important abiotic stress factor restricting crop production. Broomcorn millet (Panicum miliaceum L.) has become an ideal material for analyzing the stress adaptation mechanisms of crops due to its strong stress resistance. However, the functional characteristics of its rhizosphere microorganisms in response to drought remain unclear. In this study, metagenomics and metabolomics techniques were employed to systematically analyze the compositional characteristics of the microbial community, functional properties, and changes in metabolites in the rhizosphere soil of broomcorn millet under drought stress. On this basis, an analysis was conducted in combination with the differences in functional pathways. The results showed that the drought treatment during the flowering stage significantly altered the species composition of the rhizosphere microorganisms of broomcorn millet. Among them, the relative abundances of beneficial microorganisms such as Nitrosospira, Coniochaeta, Diversispora, Gigaspora, Glomus, and Rhizophagus increased significantly. Drought stress significantly affects the metabolic pathways of rhizosphere microorganisms. The relative abundances of genes associated with prokaryotes, glycolysis/gluconeogenesis, and other metabolic process (e.g., ribosome biosynthesis, amino sugar and nucleotide sugar metabolism, and fructose and mannose metabolism) increased significantly. Additionally, the expression levels of functional genes involved in the phosphorus cycle were markedly upregulated. Drought stress also significantly alters the content of specific rhizosphere soil metabolites (e.g., trehalose, proline). Under drought conditions, broomcorn millet may stabilize the rhizosphere microbial community by inducing its restructuring and recruiting beneficial fungal groups. These community-level changes can enhance element cycling efficiency, optimize symbiotic interactions between broomcorn millet and rhizosphere microorganisms, and ultimately improve the crop's drought adaptability. Furthermore, the soil metabolome (e.g., trehalose and proline) functions as a pivotal interfacial mediator, orchestrating the interaction network between broomcorn millet and rhizosphere microorganisms, thereby enhancing plant stress tolerance. This study sheds new light on the functional traits of rhizosphere microbiota under drought stress and their mechanistic interactions with host plants.},
}

@article {pmid40732101,
year = {2025},
author = {Elbehiry, A and Marzouk, E and Abalkhail, A and Edrees, HM and Ellethy, AT and Almuzaini, AM and Ibrahem, M and Almujaidel, A and Alzaben, F and Alqrni, A and Abu-Okail, A},
title = {Microbial Food Safety and Antimicrobial Resistance in Foods: A Dual Threat to Public Health.},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/microorganisms13071592},
pmid = {40732101},
issn = {2076-2607},
abstract = {The intersection of microbial food safety and antimicrobial resistance (AMR) represents a mounting global threat with profound implications for public health, food safety, and sustainable development. This review explores the complex pathways through which foodborne pathogens-such as Salmonella spp., Escherichia coli (E. coli), Listeria monocytogenes (L. monocytogenes), and Campylobacter spp.-acquire and disseminate resistance within human, animal, and environmental ecosystems. Emphasizing a One Health framework, we examine the drivers of AMR across sectors, including the misuse of antibiotics in agriculture, aquaculture, and clinical settings, and assess the role of environmental reservoirs in sustaining and amplifying resistance genes. We further discuss the evolution of surveillance systems, regulatory policies, and antimicrobial stewardship programs (ASPs) designed to mitigate resistance across the food chain. Innovations in next-generation sequencing, metagenomics, and targeted therapeutics such as bacteriophage therapy, antimicrobial peptides (AMPs), and CRISPR-based interventions offer promising alternatives to conventional antibiotics. However, the translation of these advances into practice remains uneven, particularly in low- and middle-income countries (LMICs) facing significant barriers to diagnostic access, laboratory capacity, and equitable treatment availability. Our analysis underscores the urgent need for integrated, cross-sectoral action-anchored in science, policy, and education-to curb the global spread of AMR. Strengthening surveillance, investing in research, promoting responsible antimicrobial use, and fostering global collaboration are essential to preserving the efficacy of existing treatments and ensuring the microbiological safety of food systems worldwide.},
}

@article {pmid40732100,
year = {2025},
author = {Mourão, AV and Fernandes, D and de Sousa, T and Calouro, R and Saraiva, S and Igrejas, G and Poeta, P},
title = {Aquatic Resistome in Freshwater and Marine Environments: Interactions Between Commensal and Pathogenic in the Context of Aquaculture and One Health.},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/microorganisms13071591},
pmid = {40732100},
issn = {2076-2607},
support = {UI/00772//Fundacao para a Ciencia e a Tecnologia/ ; LA/P/0059/2020//Fundacao para a Ciencia e a Tecnologia/ ; },
abstract = {Aquatic resistomes are important reservoirs of antibiotic resistance genes (ARGs) and their precursors, which can proliferate and dissipate in pathogenic microorganisms that affect humans and animals, especially due to anthropogenic pressures such as the intensive use of antibiotics in aquaculture, often without effective regulation. This review addresses the mechanisms of horizontal gene transfer (HGT) in the dissemination of ARGs through mobile genetic elements (MGEs). In freshwater, genera such as Aeromonas, Pseudomonas and Microcystis stand out as vectors of ARGs. In the context of One Health, it is essential to implement sound public policies and strict regulations on the use of antibiotics in aquaculture, and the use of monitoring tools such as environmental DNA (eDNA) and metagenomics allows for the early detection of ARGs, contributing to the protection of human, animal and environmental health.},
}

@article {pmid40732084,
year = {2025},
author = {Ning, Z and Liang, J and Ti, J and Zhang, M and Cai, C},
title = {Enhanced Natural Attenuation of Gasoline Contaminants in Groundwater: Applications and Challenges of Nitrate-Stimulating Substances.},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/microorganisms13071575},
pmid = {40732084},
issn = {2076-2607},
support = {42330714//National Natural Science Foundation of China/ ; 242S4201Z//the S&T Program of Hebei/ ; 322074//Sinopec Science Department Project/ ; },
abstract = {Nitrate is a promising enhanced natural attenuation (ENA) material that enhances the microbial degradation of petroleum hydrocarbons by acting as an electron acceptor and nitrogen source. This study evaluated nitrate-containing materials (yeast extract, compound nitrogen fertilizer, and nitrate solutions) in microcosm experiments using gasoline-contaminated aquifer soils. Chemical analysis revealed that yeast extract achieved the highest degradation rate (34.33 mg/(kg·d)), reducing 600 mg/kg of petroleum hydrocarbons to undetectable levels within 18 days. Nitrate materials significantly increased nitrate-reducing activity and upregulated both aerobic/anaerobic hydrocarbon degradation genes, expanding microbial degradation potential. Metagenomic analysis identified Pseudomonas and Achromobacter as dominant genera across treatments, suggesting their critical roles in biodegradation. These findings demonstrate that nitrate-enhanced strategies effectively accelerate hydrocarbon attenuation under facultative anaerobic conditions, offering practical ENA solutions for petroleum-polluted sites.},
}

@article {pmid40732069,
year = {2025},
author = {Mushtaq, M and Ni, X and Khan, M and Zhao, X and Yang, H and Danzeng, B and Ali, S and Zafar, MH and Quan, G},
title = {Dietary Protein-Induced Changes in Archaeal Compositional Dynamics, Methanogenic Pathways, and Antimicrobial Resistance Profiles in Lactating Sheep.},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/microorganisms13071560},
pmid = {40732069},
issn = {2076-2607},
support = {CARS-39-08//The earmarked fund for the China Agriculture Research System/ ; 202403AP140017//Yunnan International Joint Laboratory of Conservation and Innovative Utilization of Sheep Germplasm Re sources/ ; },
abstract = {Dietary protein levels greatly influence gut microbial ecosystems; however, their effects on gut archaea and associated functions in ruminants require further elucidation. This study evaluated the impact of varying dietary protein levels on gut archaeal composition, antimicrobial resistance (AMR) genes, virulence factors, and functional capacities in sheep. Eighteen ewes (Yunnan semi-fine wool breed, uniparous, 2 years old, and averaging 50 ± 2 kg body weight) were randomly assigned to diets containing an 8.5 (low; H_1), 10.3 (medium; H_m), or 13.9% (high; H_h) crude protein level from the 35th day of pregnancy to the 90th day postpartum. The total duration of the experiment was approximately 202 days. A total of nine fecal samples (three from each group) were analyzed via 16S rRNA and metagenomics sequencing. Higher archaeal alpha diversity and richness were observed in the H_m and H_h groups compared to the H_l group (p < 0.05). A Beta diversity analysis revealed the archaeal community's distinct clustering mode based on protein levels. The methanogenic genera Methanobrevibacter and Methanocorpusculum were dominant across the three groups, and their abundance was influenced by protein intake. A functional prediction analysis indicated moderate changes in amino acid and carbohydrate metabolism, which are particularly associated with methane production, an important source of greenhouse gases. AMR genes (e.g., tetA (60), patA, vat, and Erm methyltransferase) and virulence factors (Bacillibactin, LPS) were significantly enriched when animals were fed high-protein diets. Our results demonstrated that dietary protein levels significantly influence gut archaeal composition, AMR gene enrichment, and related functional pathways. Medium-protein diets promoted greater archaeal diversity, whereas high-protein diets favored resistance gene proliferation and enhanced methanogenic activity. Optimizing dietary protein intake may enhance gut health, mitigate antimicrobial resistance risk, and reduce methane emissions, thereby supporting livestock sustainability and environmental protection.},
}

@article {pmid40732056,
year = {2025},
author = {Cayo, M and Solís-Cornejo, F and Santos, A and Zamorano, P and Valenzuela, B},
title = {The Abundance and Distribution of the acdS Gene in Microbial Communities from the Rhizosphere of Copiapoa solaris, a Native Cactus in the Arid Coastal Region of Antofagasta, Chile.},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/microorganisms13071547},
pmid = {40732056},
issn = {2076-2607},
support = {ANT22991//Fortaleciendo la Formación de Pregrado, Posgrado e Investigación con Estándares de Calidad, Ministerio de Educación/ ; },
abstract = {Copiapoa solaris is an endemic cactus species from the Antofagasta region, Chile, thriving in arid coastal ecosystems known as "fog oases," where the rising marine moisture is the primary water source. This study investigates the role of microbial communities associated with the rhizosphere of C. solaris in adapting to extreme environmental conditions, particularly focusing on the acdS gene, which encodes ACC deaminase-an enzyme that reduces ethylene production under stress. This research aims to elucidate the gene's contribution to the adaptation of C. solaris in these challenging environments. Samples were collected from three sites (El Cobre, Quebrada Botija, and Quebrada Izcuña) that differ in relative humidity, temperature, and topography. Environmental DNA was extracted, phylogenetic diversity was analyzed, and metagenomic annotation of the acdS gene was conducted. The acdS gene was detected in all samples, with the highest relative abundance at Quebrada Izcuña (0.05%), characterized by low relative humidity (<70%) and severe water stress. Phylogenetic analysis revealed conserved sequences across sites, while taxonomic and alpha diversity were similar among them. However, beta diversity indicated that Quebrada Izcuña was the least homogeneous, hosting distinct taxa potentially associated with stress mitigation. The acdS gene was detected on plasmids at El Cobre and Quebrada Izcuña, suggesting its potential mobility within the metagenome. The results of this study highlight the intricate relationships between microbial communities and the resilient cactus species C. solaris in extreme environments. The conservation and abundance of the acdS gene, particularly in low-humidity conditions, suggest its vital role in facilitating stress tolerance through microbial interactions. Understanding these dynamics is crucial for developing strategies to enhance plant resilience in arid ecosystems, with potential applications in sustainable agriculture and ecosystem management under changing climatic conditions.},
}

@article {pmid40732017,
year = {2025},
author = {Lianou, A and Tsantes, AG and Ioannou, P and Bikouli, ED and Batsiou, A and Kokkinou, A and Tsante, KA and Tsilidis, D and Lampridou, M and Iacovidou, N and Sokou, R},
title = {hMPV Outbreaks: Worldwide Implications of a Re-Emerging Respiratory Pathogen.},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/microorganisms13071508},
pmid = {40732017},
issn = {2076-2607},
abstract = {Human metapneumovirus (hMPV), a member of the Pneumoviridae subfamily, has emerged as a significant etiological agent of acute respiratory tract infections across diverse age groups, particularly affecting infants, the elderly, and immunocompromised individuals. Since its initial identification in 2001, hMPV has been recognized globally for its seasonal circulation pattern, predominantly in late winter and spring. hMPV is a leading etiological agent, accounting for approximately 5% to 10% of hospitalizations among pediatric patients with acute respiratory tract infections. hMPV infection can result in severe bronchiolitis and pneumonia, particularly in young children, with clinical manifestations often indistinguishable from those caused by human RSV. Primary hMPV infection typically occurs during early childhood; however, re-infections are frequent and may occur throughout an individual's lifetime. hMPV is an enveloped, negative-sense RNA virus transmitted through respiratory droplets and aerosols, with a 3-5-day incubation period. The host immune response is marked by elevated pro-inflammatory cytokines, which contribute to disease severity. Advances in molecular diagnostics, particularly reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and metagenomic next-generation sequencing (mNGS), have improved detection accuracy and efficiency. Despite these advancements, treatment remains largely supportive, as no specific antiviral therapy has yet been approved. Promising developments in vaccine research, including mRNA-based candidates, are currently undergoing clinical evaluation. This review synthesizes current knowledge on hMPV, highlighting its virological, epidemiological, and clinical characteristics, along with diagnostic advancements and emerging therapeutic strategies, while underscoring the critical role of continued research and sustained preventive measures-including vaccines, monoclonal antibodies, and non-pharmaceutical interventions-in mitigating the global burden of hMPV-related disease.},
}

@article {pmid40731996,
year = {2025},
author = {Asimakis, E and Galiatsatos, I and Apostolopoulou, G and Savvidou, EC and Balatsos, G and Karras, V and Evangelou, V and Dionyssopoulou, E and Augustinos, A and Papadopoulos, NT and Michaelakis, A and Stathopoulou, P and Tsiamis, G},
title = {The Symbiotic Bacterial Profile of Laboratory-Reared and Field-Caught Aedes albopictus Mosquitoes from Greece.},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/microorganisms13071486},
pmid = {40731996},
issn = {2076-2607},
support = {«moSquITo»: Innovative approaches for monitoring and management of the Asian tiger mosquito with emphasis on the Sterile Insect Technique (ΤΑΕΔΚ06173)//National Recovery and Resilience Plan, "Greece 2.0" & EU Funding - Next Generation EU/ ; },
abstract = {The Asian tiger mosquito Aedes albopictus is a highly invasive species capable of transmitting human pathogens. For population management, the sterile insect technique (SIT) is considered an effective and sustainable alternative to conventional methods, such as insecticides and reducing or eliminating breeding sites. The use of symbiotic bacteria to improve the application of SIT or design combined SIT/incompatible insect technique (IIT) approaches is currently considered. In this context, exploring the microbiota of local mosquito populations is crucial for identifying interesting components. This study employed 16S rRNA sequencing and microbiological methods to characterize the diversity of laboratory and wild Ae. albopictus in Greece. Differences were recorded between wild and lab-reared mosquitoes, with laboratory samples exhibiting higher diversity. Laboratory treatment, sex, and developmental stage also resulted in variations between communities. Populations reared in the same facility developed mostly similar bacterial profiles. Two geographically distant wild populations displayed similar bacterial profiles, characterized by seasonal changes in the relative abundance of Pantoea and Zymobacter. Wolbachia was dominant in most groups (63.7% relative abundance), especially in field-caught mosquitoes. It was identified with two strains, wAlbA (21.5%) and wAlbB (42.2%). Other frequent taxa included Elizabethkingia, Asaia, and Serratia. Blood feeding favored an increase in Serratia abundance. Various Enterobacter, Klebsiella, Aeromonas, and Acinetobacter strains were isolated from larval and adult mosquito extracts and could be further characterized as diet supplements. These findings suggest that the microbiota of local populations is highly variable due to multiple factors. However, they retain core elements shared across populations that may exhibit valuable nutritional or functional roles and could be exploited to improve SIT processes.},
}

@article {pmid40731980,
year = {2025},
author = {Karadedos, DM and Mantzios, T and Kiousi, DE and Tsifintaris, M and Giannenas, I and Sakkas, P and Papadopoulos, GA and Antonissen, G and Pappa, A and Galanis, A and Tsiouris, V},
title = {Metagenomic Insight into Cecal Microbiota Shifts in Broiler Chicks Following Eimeria spp. Vaccination.},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/microorganisms13071470},
pmid = {40731980},
issn = {2076-2607},
abstract = {Coccidiosis, caused by Eimeria spp., remains a major challenge in poultry production, significantly affecting poultry health and performance, leading to substantial economic losses. While its impact on gut health is well documented, the interplay of Eimeria spp. challenge and/or vaccination with the intestinal microbiota remain insufficiently understood. Therefore, the aim of this study was to investigate the effects of Eimeria spp. (E. acervulina, E. maxima, and E. tenella) challenge, alone or in combination with a commercially available vaccine, on broiler performance, intestinal gross lesions, and cecal microbiota structure and function in experimentally challenged broiler chicks. A total of 216 Ross 308[®] broilers were randomly divided into three groups, with six replicates per group, according to the following experimental design: (A) negative control, (B) Eimeria spp.-challenged birds on day 16, and (C) Eimeria spp.-vaccinated and -challenged birds. Performance parameters were recorded on a weekly basis, coccidiosis gross lesions in the intestine were evaluated on days 23 and 29, and microbiota samples were collected on day 23. Broilers in the challenged group exhibited significantly (p ≤ 0.05) increased coccidiosis gross lesions in the intestine at both sampling periods (7 and 19 days post-infection, dpi), whereas vaccination significantly (p ≤ 0.05) minimized the severity of lesions at both time points. The challenged-only group showed significantly (p ≤ 0.05) lower average daily weight gain (ADWG) during the finisher phase and the overall experimental period compared to the vaccinated group. Additionally, average daily feed intake (ADFI) during the post-challenge period (22-29 dpi) was significantly (p ≤ 0.05) reduced in both challenged groups. Alpha diversity decreased in the challenged (p = 0.016) and vaccinated-challenged (p = 0.016) groups compared to control, Accordingly, beta diversity was reduced in groups B and C compared to the control group. This reduction was accompanied by an increased relative abundance of Proteobacteria (18, 71% in Group B and 10, 87% in Group C) and potentially pathogenic genera (Escherichia spp. and Shigella spp. p < 0.05), along with a decline in short-chain fatty acid (SCFA)-producing bacteria (Oscillibacter spp. and Eisenbergiella spp.) in groups B and C, respectively, compared to the control. Predictive functional metagenomics indicated disruptions in amino acid metabolism, nucleotide degradation, and lipid metabolism, potentially affecting gut integrity and nutrient absorption. Additionally, in the vaccinated group, gross lesions in the intestine were reduced in severity and microbial diversity was partially preserved, resulting in a microbiota composition more similar to that of the control group. Overall, these findings support that Eimeria spp. infection alters gut microbiota and function in broiler chicks, underscoring the need for further research into alternative strategies, such as probiotics and phytobiotics, to support gut health and disease resilience in poultry.},
}

@article {pmid40731978,
year = {2025},
author = {Garcia, M and Bruna, P and Duran, P and Abanto, M},
title = {Cyanobacteria and Soil Restoration: Bridging Molecular Insights with Practical Solutions.},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/microorganisms13071468},
pmid = {40731978},
issn = {2076-2607},
abstract = {Soil degradation has been accelerating globally due to climate change, which threatens food production, biodiversity, and ecosystem balance. Traditional soil restoration strategies are often expensive, slow, or unsustainable in the long term. In this context, cyanobacteria have emerged as promising biotechnological alternatives, being the only prokaryotes capable of performing oxygenic photosynthesis. Moreover, they can capture atmospheric carbon and nitrogen, release exopolysaccharides (EPSs) that stabilize the soil, and facilitate the development of biological soil crusts (biocrusts). In recent years, the convergence of multi-omics tools, such as metagenomics, metatranscriptomics, and metabolomics, has advanced our understanding of cyanobacterial dynamics, their metabolic potential, and symbiotic interactions with microbial consortia, as exemplified by the cyanosphere of Microcoleus vaginatus. In addition, recent advances in bioinformatics have enabled high-resolution taxonomic and functional profiling of environmental samples, facilitating the identification and prediction of resilient microorganisms suited to challenging degraded soils. These tools also allow for the prediction of biosynthetic gene clusters and the detection of prophages or cyanophages within microbiomes, offering a novel approach to enhance carbon sequestration in dry and nutrient-poor soils. This review synthesizes the latest findings and proposes a roadmap for the translation of molecular-level knowledge into scalable biotechnological strategies for soil restoration. We discuss approaches ranging from the use of native biocrust strains to the exploration of cyanophages with the potential to enhance cyanobacterial photosynthetic activity. By bridging ecological functions with cutting-edge omics technologies, this study highlights the critical role of cyanobacteria as a nature-based solution for climate-smart soil management in degraded and arid ecosystems.},
}

@article {pmid40731977,
year = {2025},
author = {Li, C and Cong, B and Zhang, W and Lu, T and Guo, N and Zhao, L and Zhang, Z and Liu, S},
title = {Comparative Metagenomics Reveals Microbial Diversity and Biogeochemical Drivers in Deep-Sea Sediments of the Marcus-Wake and Magellan Seamounts.},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/microorganisms13071467},
pmid = {40731977},
issn = {2076-2607},
support = {2023YFC2811402//the National Key Research and Development Program of China/ ; ZR2024QD224//the Shandong Provincial Natural Science Foundation/ ; SD0425017//the Global Deep-Sea Typical Habitat Discovery and Conservation Program/ ; SD0425020//the Global Deep-Sea Typical Habitat Discovery and Conservation Program/ ; },
abstract = {Seamounts are distributed globally across the oceans and are generally considered oases of biomass abundance as well as hotspots of species richness. Diverse microbial communities are essential for biogeochemical cycling, yet their functional partitioning among seamounts with geographic features remains poorly investigated. Through metagenomic sequencing and genome-resolved analysis, we revealed that Proteobacteria (33.18-40.35%) dominated the bacterial communities, while Thaumarchaeota (5.98-10.86%) were the predominant archaea. Metagenome-assembled genomes uncovered 117 medium-quality genomes, 81.91% of which lacked species-level annotation, highlighting uncultured diversity. In the Nazuna seamount, which is located in the Marcus-Wake seamount region, microbiomes exhibited heightened autotrophic potential via the 3-hydroxypropionate cycle and dissimilatory nitrate reduction, whereas in the Magellan seamounts regions, nitrification and organic nitrogen metabolism were prioritized. Sulfur oxidation genes dominated Nazuna seamount microbes, with 33 MAGs coupling denitrification to sulfur redox pathways. Metal resistance genes for tellurium, mercury, and copper were prevalent, alongside habitat-specific iron transport systems. Cross-feeding interactions mediated by manganese, reduced ferredoxin, and sulfur-metal integration suggested adaptive detoxification strategies. This study elucidates how deep-sea microbes partition metabolic roles and evolve metal resilience mechanisms across geographical niches. It also supports the view that microbial community structure and metabolic function across seamount regions are likely influenced by the geomorphological features of the seamounts.},
}

@article {pmid40731966,
year = {2025},
author = {Long, Y and Huang, J and Zheng, S and Bai, S and Liu, Z and Li, X and Gao, W and Ke, X and Tang, Y and Yang, L and Wang, H and Li, G},
title = {Disorders of Gut Microbiota and Plasma Metabolic Profiles May Be Associated with Lymph Node Tuberculosis.},
journal = {Microorganisms},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/microorganisms13071456},
pmid = {40731966},
issn = {2076-2607},
support = {25270G1032， G2022039//the Shenzhen Third People's Hospital Research Fund/ ; 2021YFA1300902//National Key R&D Program of china/ ; G03117K001//High Level Special Funds (Cell Homeostasis and Major Diseases)/ ; },
abstract = {The association of gut microbiota with lymph node tuberculosis (LNTB) remains unexplored. This study employed metagenomic sequencing and plasma metabolomics analyses to investigate the role of gut microbiota in LNTB patients. Significant alterations in gut microbial diversity were observed in LNTB patients, characterized by a notable reduction in bacterial taxa involved in short-chain fatty acid (SCFA) synthesis, including Ruminococcus, Faecalibacterium, Roseburia, and Blautia, compared to healthy individuals. KEGG pathway analysis further revealed that gut dysbiosis could negatively impact SCFA biosynthesis and metabolism. Plasma metabolomics demonstrated disruptions in metabolites associated with SCFA synthesis and inflammation pathways in the LNTB group. Integrated analysis indicated significant correlations between specific gut microbiota (Blautia, Butyricicoccus, Coprococcus, Ruminococcus, Bacteroides, Clostridium) and plasma metabolites, including α-benzylbutyric acid, acetic acid, and succinic acid. Our findings demonstrate that gut microbiota dysbiosis and related metabolic dysfunction significantly reduce SCFA production in LNTB patients, potentially identifying novel therapeutic targets for LNTB management.},
}

@article {pmid40731366,
year = {2025},
author = {Jiménez-González, A and Treitli, SC and Peña-Diaz, P and Janovská, A and Beneš, V and Žáček, P and Hampl, V},
title = {Comprehensive analysis of the microbial consortium in the culture of flagellate Monocercomonoides exilis.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {97},
doi = {10.1186/s40793-025-00758-7},
pmid = {40731366},
issn = {2524-6372},
support = {771592//H2020 European Research Council/ ; 771592//H2020 European Research Council/ ; 771592//H2020 European Research Council/ ; 771592//H2020 European Research Council/ ; 771592//H2020 European Research Council/ ; 771592//H2020 European Research Council/ ; 771592//H2020 European Research Council/ ; CZ.02.1.01/0.0/0.0/16_019/0000759//Centre for Research of Pathogenicity and Virulence of Parasites/ ; CZ.02.1.01/0.0/0.0/16_019/0000759//Centre for Research of Pathogenicity and Virulence of Parasites/ ; CZ.02.1.01/0.0/0.0/16_019/0000759//Centre for Research of Pathogenicity and Virulence of Parasites/ ; CZ.02.1.01/0.0/0.0/16_019/0000759//Centre for Research of Pathogenicity and Virulence of Parasites/ ; CZ.02.1.01/0.0/0.0/16_019/0000759//Centre for Research of Pathogenicity and Virulence of Parasites/ ; CZ.02.1.01/0.0/0.0/16_019/0000759//Centre for Research of Pathogenicity and Virulence of Parasites/ ; CZ.02.1.01/0.0/0.0/16_019/0000759//Centre for Research of Pathogenicity and Virulence of Parasites/ ; },
abstract = {Monocercomonoides exilis is a model species of the amitochondrial eukaryotic group Oxymonadida, which makes it a suitable organism for studying the consequences of mitochondrial loss. Although M. exilis has an endobiotic lifestyle, it can be cultured in vitro in polyxenic conditions alongside an uncharacterized prokaryotic community, while attempts to create axenic cultures have not been successful. In this study, we used metagenomic sequencing, transcriptomics, and metabolomics to characterize the microbial consortium that supports the growth of M. exilis. We assembled genomes for 24 bacterial species and identified at least 30 species in total. M. exilis accounted for less than 1.5% of the DNA reads, while bacterial species dominated the sequence data and shifted in abundance over time. Our metabolic reconstruction and differential gene expression analyses show that the bacterial community relies on organic carbon oxidation, fermentation, and hydrogen production, but does not engage in methanogenesis. We observed rapid depletion of amino acids, nucleotides, glyceraldehyde, lactate, fatty acids, and alcohols in the medium, indicating a reliance on external nutrient recycling. The nitrogen cycle in this community is incomplete, with limited nitrogen fixation and no ammonia oxidation. Despite detailed metabolic profiling, we did not find any direct biochemical connections between M. exilis and the prokaryotes. Several bacterial species produce siderophores to assist themselves and others in the community in acquiring iron. However, M. exilis does not appear to benefit directly from siderophore-mediated iron transport and lacks known iron uptake pathways. This indicates that M. exilis may rely indirectly on the iron metabolism of other bacteria through phagocytosis. Additionally, some bacteria synthesize polyamines like spermidine and phosphatidylcholine, which M. exilis may need but cannot produce on its own. As the culture ages, M. exilis shows changes in gene expression consistent with starvation responses, including the upregulation of carbohydrate storage pathways and processes related to exocytosis. These findings provide new insights into microbial interactions within xenic cultures and emphasize the complex nature of maintaining amitochondriate eukaryotes in vitro.},
}

@article {pmid40731321,
year = {2025},
author = {Rech de Laval, V and Dainat, B and Engel, P and Robinson-Rechavi, M},
title = {The BeeBiome data portal provides easy access to bee microbiome information.},
journal = {BMC bioinformatics},
volume = {26},
number = {1},
pages = {198},
pmid = {40731321},
issn = {1471-2105},
mesh = {Bees/microbiology ; Animals ; *Microbiota/genetics ; Metagenomics/methods ; *Databases, Genetic ; Metagenome ; },
abstract = {Bees can be colonized by a large diversity of microbes, including beneficial gut symbionts and detrimental pathogens, with implications for bee health. Over the last few years, researchers around the world have collected a huge amount of genomic and transcriptomic data about the composition, genomic content, and gene expression of bee-associated microbial communities. While each of these datasets by itself has provided important insights, the integration of such datasets provides an unprecedented opportunity to obtain a global picture of the microbes associated with bees and their link to bee health. The challenge of such an approach is that datasets are difficult to find within large generalist repositories and are often not readily accessible, which hinders integrative analyses. Here we present a publicly-available online resource, the BeeBiome data portal (https://www.beebiome.org), which provides an overview of and easy access to currently available metagenomic datasets involving bee-associated microbes. Currently the data portal contains 33,678 Sequence Read Archive (SRA) experiments for 278 Apoidea hosts. We present the content and functionalities of this portal. By providing access to all bee microbiomes in a single place, with easy filtering on relevant criteria, BeeBiome will allow faster progress of applied and fundamental research on bee biology and health. It should be a useful tool for researchers, academics, funding agencies, and governments, with beneficial impacts for stakeholders.},
}

Bees/microbiology
Animals
*Microbiota/genetics
Metagenomics/methods
*Databases, Genetic
Metagenome

@article {pmid40731267,
year = {2025},
author = {Xu, X and Qin, D and Qin, X and Gao, X and Li, C and Liu, X and Wu, G},
title = {Sustainable management of soil-borne disease: integrating fumigation with Andrographis paniculata residues to rebuild rhizosphere function.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {460},
doi = {10.1186/s12866-025-04188-w},
pmid = {40731267},
issn = {1471-2180},
support = {32060639//the National Natural Science Foundation of China/ ; 202105AC160037, 202205AC160077//the Reserve Talents Project for Yunnan Young and Middle-aged Academic and Technical Leaders/ ; },
mesh = {*Rhizosphere ; *Soil Microbiology ; *Fumigation/methods ; *Andrographis/chemistry ; *Plant Diseases/microbiology/prevention & control ; *Plant Extracts/pharmacology/chemistry ; Metabolomics ; Fusarium/drug effects ; Soil/chemistry ; Microbiota/drug effects ; Metagenomics ; },
abstract = {Continuous pepper cropping induces soil-borne diseases and disrupts rhizosphere microecological balance. This study employed untargeted metabolomics and metagenomics to investigate treatment effects on rhizosphere metabolic reprogramming and microbe-metabolite interactions. Aqueous and ethanolic extracts of Andrographis paniculata residues (TCMR) were rich in flavonoids, terpenoids, and phenolic acids, exhibiting significant inhibition against soil-borne pathogens (Fusarium oxysporum, Fusarium solani, and others; >70% inhibition at high doses). While single fumigation (W1, M1) transiently suppressed pathogens, it disrupted rhizosphere metabolic homeostasis. In contrast, combined fumigation-TCMR treatments (WC, MC) enhanced plant stress resistance, stabilized membrane integrity, and reshaped microbial communities by modulating amino acid, lipid, and phenylpropanoid biosynthesis pathways. Microbe-metabolite network analysis revealed that coupling carbon-nitrogen cycling with redox homeostasis drives soil microecological optimization. This integrated strategy provides a sustainable solution for continuous cropping obstacles through synergistic metabolic reprogramming and microbiome reconstruction.},
}

*Rhizosphere
*Soil Microbiology
*Fumigation/methods
*Andrographis/chemistry
*Plant Diseases/microbiology/prevention & control
*Plant Extracts/pharmacology/chemistry
Metabolomics
Fusarium/drug effects
Soil/chemistry
Microbiota/drug effects
Metagenomics

@article {pmid40730965,
year = {2025},
author = {Clark-Boucher, D and Coull, BA and Reeder, HT and Wang, F and Sun, Q and Starr, JR and Lee, KH},
title = {Group-wise normalization in differential abundance analysis of microbiome samples.},
journal = {BMC bioinformatics},
volume = {26},
number = {1},
pages = {196},
pmid = {40730965},
issn = {1471-2105},
support = {T32GM135117/GM/NIGMS NIH HHS/United States ; R01GM126257/GM/NIGMS NIH HHS/United States ; R01GM126257/GM/NIGMS NIH HHS/United States ; P30ES000002/ES/NIEHS NIH HHS/United States ; R03DE027486/DE/NIDCR NIH HHS/United States ; R03DE027486/DE/NIDCR NIH HHS/United States ; },
mesh = {*Microbiota/genetics ; Metagenome ; Algorithms ; *Metagenomics/methods ; Humans ; },
abstract = {BACKGROUND: A key challenge in differential abundance analysis (DAA) of microbial sequencing data is that the counts for each sample are compositional, resulting in potentially biased comparisons of the absolute abundance across study groups. Normalization-based DAA methods rely on external normalization factors that account for compositionality by standardizing the counts onto a common numerical scale. However, existing normalization methods have struggled to maintain the false discovery rate in settings where the variance or compositional bias is large. This article proposes a novel framework for normalization that can reduce bias in DAA by re-conceptualizing normalization as a group-level task. We present two new normalization methods within the group-wise framework: group-wise relative log expression (G-RLE) and fold-truncated sum scaling (FTSS).

RESULTS: G-RLE and FTSS achieve higher statistical power for identifying differentially abundant taxa than existing methods in model-based and synthetic data simulation settings. The two novel methods also maintain the false discovery rate in challenging scenarios where existing methods suffer. The best results are obtained from using FTSS normalization with the DAA method MetagenomeSeq.

CONCLUSION: Compared with other methods for normalizing compositional sequence count data prior to DAA, the proposed group-level normalization frameworks offer more robust statistical inference. With a solid mathematical foundation, validated performance in numerical studies, and publicly available software, these new methods can help improve rigor and reproducibility in microbiome research.},
}

*Microbiota/genetics
Metagenome
Algorithms
*Metagenomics/methods
Humans

@article {pmid40730483,
year = {2025},
author = {Zhong, H and Song, Y and Hu, S and Zhang, C and Li, L},
title = {Metagenomics-Metabolomics Reveals the Alleviation of Indole-3-Ethanol on Radiation-Induced Enteritis in Mice.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2502037},
doi = {10.4014/jmb.2502.02037},
pmid = {40730483},
issn = {1738-8872},
mesh = {Animals ; *Indoles/pharmacology/metabolism ; *Enteritis/drug therapy/etiology/metabolism/microbiology/pathology ; Mice ; Gastrointestinal Microbiome/drug effects ; Mice, Inbred C57BL ; *Metabolomics/methods ; *Metagenomics/methods ; Male ; *Anti-Inflammatory Agents/pharmacology ; Colon/pathology/drug effects/radiation effects ; Cytokines/metabolism ; Interleukin-17/metabolism ; },
abstract = {Indole-3-ethanol (IEt), a small molecule metabolite from intestinal microbial tryptophan metabolism, has been established to have anti-inflammatory properties. However, its effect on radiation-induced enteritis has not been reported. Here, we aim to explore the effects and potential mechanisms of IEt on radiation enteritis. C57BL/6J mice were orally administered an IEt solution before radiation exposure. Inflammatory factors, including IL-17A, IFN-γ, IL-6 and IL-1β, were detected using enzyme-linked immunosorbent assay. Colonic histopathology was assessed through H&E staining. Subsequently, gut microbiota and its metabolites were analyzed using metagenomics and metabolomics. The results suggested that IEt alleviated radiation-induced enteritis, as evidenced by improved colonic structural integrity, decreased levels of pro-inflammatory factors like IL-17A, and the restoration of intestinal microecological and metabolic balance. IEt enriched the abundance of Lachnospiraceae family members, particularly the genus Roseburia - a known anti-inflammatory commensal. In addition, IEt upregulated the levels of metabolites with anti-inflammatory effects such as indole-3-carbinol, pteridine, and pyropheophorbide-a. Furthermore, Roseburia was significantly positively correlated with indole-3-carbinol and negatively correlated with the pro-inflammatory factor IL-17A. Therefore, IEt may alleviate radiation enteritis through Roseburia-indole-3-carbinol and Roseburia-IL-17A axes. This study revealed the potential mechanisms by which IEt alleviated radiation enteritis, providing a potential protective candidate for radiation enteritis.},
}

Animals
*Indoles/pharmacology/metabolism
*Enteritis/drug therapy/etiology/metabolism/microbiology/pathology
Mice
Gastrointestinal Microbiome/drug effects
Mice, Inbred C57BL
*Metabolomics/methods
*Metagenomics/methods
Male
*Anti-Inflammatory Agents/pharmacology
Colon/pathology/drug effects/radiation effects
Cytokines/metabolism
Interleukin-17/metabolism

@article {pmid40730159,
year = {2025},
author = {Che, Y and Han, J and Harkins, CP and Hou, P and Conlan, S and Deming, C and Amirkhani, A and Bingham, MA and Holmes, CJ and Englander, H and Shen, Z and , and Castelo-Soccio, L and Dimitrova, D and Kanakry, JA and Bergerson, JRE and Notarangelo, LD and Pittaluga, S and Zhao, C and Dell'Orso, S and Pai, SY and Hickstein, DD and Holland, SM and Brownell, I and Nagao, K and Gonzalez, CE and Shah, NN and Freeman, AF and Su, HC and Segre, JA and Kong, HH},
title = {Restoration of the human skin microbiome following immune recovery after hematopoietic stem cell transplantation.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2025.07.002},
pmid = {40730159},
issn = {1934-6069},
abstract = {The human skin microbiome is intricately intertwined with host immunity. While studies have elucidated microbial influences on immunity, understanding how immune alterations modulate this equilibrium remains limited. We investigated the dual impact of immune deficiency and hematopoietic stem cell transplantation (HSCT) on the skin microbiome in 24 patients with dedicator of cytokinesis 8 (DOCK8) deficiency, a rare inborn error of immunity. Analyzing 590 metagenomic and 534 16S rDNA sequencing samples across eight skin sites, we observed disrupted microbiota pre-HSCT (median eukaryotic viruses 67.6% vs. 0.04% in controls), with extremely diverse human papillomaviruses (HPVs) and polyomaviruses-including oncogenic viruses. Specific bacterial species markedly changed, including decreased Staphylococcus aureus post-HSCT. DNA eukaryotic viruses dramatically decreased (79.7% ± 28.3% to 4.9% ± 8.6%; p < 0.01) 12 months post-HSCT. Recovered microbial communities remained relatively stable through 1-year follow-up with clearance of oncogenic HPV and no convergence with transplant donors. These results highlight the immune system's critical role in restoring microbial balance and skin health.},
}

@article {pmid40729914,
year = {2025},
author = {Shen, D and Gao, X and Hui, C and Long, Y and Shentu, J and Lu, L and Qi, S},
title = {Overlooked risk of antibiotic resistance genes in typical landfill plumes and their influencing factors.},
journal = {Ecotoxicology and environmental safety},
volume = {302},
number = {},
pages = {118765},
doi = {10.1016/j.ecoenv.2025.118765},
pmid = {40729914},
issn = {1090-2414},
abstract = {Landfills are one of the primary reservoirs of antibiotic resistance genes (ARGs). Previous studies always focus on the distribution of ARGs in landfill leachate, while the distribution of ARGs in groundwater around the landfill and the corresponding influencing factors are always overlooked. In this study, seven groundwater samples and one leachate sample were collected from a typical landfill in Yueqing, China. Sulfonamide was the most abundant antibiotic in groundwater with its concentration of 1.2-23.1 ng L[-1]. Metagenomic analysis revealed 13 major types and 88 subtypes of antibiotic resistance genes (ARGs) in the leachate and surrounding groundwater. Multidrug (23.2-51.4 %), sulfonamide (2.6-24.1 %), tetracycline (3.0-35.8 %), macrolides-lincosamide-streptogramin (MLS, 1.1-26.3 %) and aminoglycoside (0.9-13.1 %) resistance genes were the top five types in the detected ARGs, while the ARGs abundance in groundwater increased with landfill age. Heavy metals (Ni, Pb, Cr, Cd) were strongly correlated with certain ARG subtypes, while no significant correlations were observed between antibiotics and their corresponding ARGs due to their low concentrations. Through co-occurrence network analysis, it was found that ARGs were tightly correlated with mobile genetic elements (MGEs), while several types of virulence factors such as flmH, cylG and clbF were also tightly correlated with MGEs. Besides, ARGs were also correlated with some denitrification genes such as nirB and norC, showing that the denitrification process would enhance the dissemination of ARGs. This study provides important insights for assessing the risk of ARGs spreading through leachate leakage in groundwater and can help optimize the management strategy of landfill.},
}

@article {pmid40729529,
year = {2025},
author = {Dey, S and Gireesan, S and Solovou, T and Inniss, NL and Satchell, KJF},
title = {High-Throughput Pipeline for Protein Expression and Solubility Profiling Using Synthetically Generated Plasmids.},
journal = {Current protocols},
volume = {5},
number = {7},
pages = {e70188},
doi = {10.1002/cpz1.70188},
pmid = {40729529},
issn = {2691-1299},
mesh = {Solubility ; *Plasmids/genetics ; *High-Throughput Screening Assays/methods ; Cloning, Molecular/methods ; *Recombinant Proteins/genetics/chemistry/isolation & purification ; },
abstract = {High-throughput protein expression and purification can now take advantage of the copious expansion of genes from extensive genomics and metagenomic surveillance programs. This article outlines a pipeline that involves strategic selection of a large repertoire of protein targets for cloning by commercial synthetic services, followed by high-throughput transformation, expression, and solubility screening. This pipeline will be applicable to structural and functional genomics approaches, as well as any project that requires large-scale screening for production of soluble proteins in a time-efficient manner. The protocols involve transformation, protein expression and solubility determination in a high-throughput fashion in a 96-well plate format. Proteins screened in this pipeline are then able to be purified for any assay needed. © 2025 The Author(s). Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Target optimization Basic Protocol 2: High-throughput transformation Basic Protocol 3: High-throughput expression and solubility screening.},
}

Solubility
*Plasmids/genetics
*High-Throughput Screening Assays/methods
Cloning, Molecular/methods
*Recombinant Proteins/genetics/chemistry/isolation & purification

@article {pmid40728669,
year = {2025},
author = {Priyadarsini, M and Dhoble, AS},
title = {Combination of flow cytometry and metagenomics to monitor the effect of raw vs digested manure on microbial diversity in anaerobic digestion of Napier grass.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {8},
pages = {963},
pmid = {40728669},
issn = {1573-2959},
support = {SPARC/2019-2020/P1570/SL//Scheme for Promotion of Academic and Research Collaboration (SPARC)/ ; },
mesh = {*Manure/microbiology ; Flow Cytometry ; Metagenomics ; *Poaceae/microbiology ; Anaerobiosis ; *Microbiota ; Biofuels ; Bacteria ; Archaea ; Animals ; },
abstract = {Microbiomes play a crucial role in anaerobic digestion (AD), by degrading the complex lignocellulosic biomass leading to biomethane production. This study emphasizes the role of microbial diversity and its impact on the digester's performance with raw (CD) and digested manure (ADS) as a source of microbiome and Napier grass (NG) as feedstock. The integration of flow cytometry and metagenomics provides a novel perspective on microbial dynamics during anaerobic digestion. Initially, the inocula (ADS and CD) had 354 bacterial and 8 archaeal genera in common that decreased to 39 bacteria and 1 archaeon at the end of experiment, indicating significant shift in microbial diversity during the process. Metagenome sequencing showed that Clostridium was the most abundant genera in NG digested with ADS, while Prevotella was in NG digested with CD. An approximately 2.45% increase in Clostridium in NG digested with ADS led to VFA accumulation and pH drop, inhibiting methanogens and lower biogas production. Most of the flow cytometric populations showed positive correlation with Prevotella suggesting its key role in breaking down of complex substrate. The population 2, 3, and 5 positively correlated to biogas production. NG digested with CD produced nearly twice biogas yield (1064.33 ± 119.97 mL) compared to ADS (508 ± 20.95 mL) which corresponds to the enhanced microbial activity in CD. These findings suggest that microbiome of CD might be better acclimatized for NG degradation than ADS as NG is often used as cattle fodder.},
}

*Manure/microbiology
Flow Cytometry
Metagenomics
*Poaceae/microbiology
Anaerobiosis
*Microbiota
Biofuels
Bacteria
Archaea
Animals

@article {pmid40728615,
year = {2025},
author = {Zou, J and Yuan, Q and Yang, Y},
title = {An Online Server for Geometry-Aware Protein Function Annotations Through Predicted Structure.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2947},
number = {},
pages = {191-208},
pmid = {40728615},
issn = {1940-6029},
mesh = {*Software ; *Molecular Sequence Annotation/methods ; *Proteins/chemistry/metabolism/genetics ; Databases, Protein ; Internet ; Binding Sites ; *Computational Biology/methods ; Ligands ; Protein Binding ; Protein Conformation ; },
abstract = {Understanding protein functions is critical for metagenomic research, disease mechanism elucidation, and rational drug discovery. Traditional biochemical methods to determine protein functions are often inefficient and costly, leading to a widening gap between the rapid accumulation of protein sequences and their functional annotations. To address this, we introduce GPSFun, a fast and accurate web server that provides comprehensive geometry-aware protein sequence function annotations, including protein-binding sites for multiple ligands, gene ontologies, subcellular locations, and protein solubility. GPSFun's web server can be accessed at https://bio-web1.nscc-gz.cn/app/GPSFun , offering users a result with a rich visualized interface. Additionally, GPSFun was adopted to annotate ligand-binding sites for over 568,000 proteins from Swiss-Prot, leading to a complementary database named GPSiteDB (https://bio-web1.nscc-gz.cn/database/GPSiteDB). In this chapter, we first overview the workflow and results of our method, and then, we provide a step-by-step instruction on the usage of GPSFun and GPSiteDB, along with the detailed interpretations of the corresponding results.},
}

*Software
*Molecular Sequence Annotation/methods
*Proteins/chemistry/metabolism/genetics
Databases, Protein
Internet
Binding Sites
*Computational Biology/methods
Ligands
Protein Binding
Protein Conformation

@article {pmid40728577,
year = {2025},
author = {Raziq, MF and Manzoor, H and Kayani, MUR},
title = {Non-small Cell Lung Cancer, Immunotherapy and the Influence of Gut Microbiome.},
journal = {Current microbiology},
volume = {82},
number = {9},
pages = {419},
pmid = {40728577},
issn = {1432-0991},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Carcinoma, Non-Small-Cell Lung/therapy/microbiology/immunology ; *Immunotherapy/methods ; *Lung Neoplasms/therapy/microbiology/immunology ; Immune Checkpoint Inhibitors/therapeutic use ; Animals ; },
abstract = {Lung cancer remains the second most commonly diagnosed cancer and the leading cause of cancer-related deaths worldwide. Non-small cell lung cancer (NSCLC), accounting for approximately 85% of lung cancer cases, is the most prevalent form. Treatment options for NSCLC include surgery, radiation therapy, chemotherapy, immunotherapy, and targeted drug therapies. Among these, immune checkpoint inhibitors targeting PD-1/PD-L1 have demonstrated significant potential, particularly in improving treatment outcomes. However, their clinical efficacy is impeded by challenges such as toxicity, resistance development, and variable patient responses. Emerging evidence highlights the critical role of the gut microbiome as an important modulator of immune responses in NSCLC, particularly in the context of anti-PD-1/PD-L1 therapies. Specific gut microbes, such as Akkermansia muciniphila, have been associated with improved responses to immunotherapy, suggesting that modulation of the gut microbiome may enhance treatment outcomes. This review discusses the current understanding of the influence of gut microbiome on NSCLC and its potential to improve the clinical efficacy of anti-PD-1/PD-L1 therapies. By integrating microbiome-based insights into personalized treatment strategies, we can overcome the limitations of current immunotherapy approaches and optimize patient outcomes. This review aims to serve as a resource for the scientific community by providing insights into how modulation of gut microbiome may enhance treatment outcomes in NSCLC patients receiving anti-PD-1/PD-L1 immunotherapy.},
}

Humans
*Gastrointestinal Microbiome
*Carcinoma, Non-Small-Cell Lung/therapy/microbiology/immunology
*Immunotherapy/methods
*Lung Neoplasms/therapy/microbiology/immunology
Immune Checkpoint Inhibitors/therapeutic use
Animals

@article {pmid40728316,
year = {2025},
author = {Armitage, DW and Alonso-Sánchez, AG and Coy, SR and Cheng, Z and Hagenbeek, A and López-Martínez, KP and Phua, YH and Sears, AR},
title = {Adaptive pangenomic remodeling in the Azolla cyanobiont amid a transient microbiome.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf154},
pmid = {40728316},
issn = {1751-7370},
abstract = {Plants fix nitrogen in concert with diverse microbial symbionts, often recruiting them from the surrounding environment each generation. Vertical transmission of a microbial symbiont from parent to offspring can produce extreme evolutionary consequences, including metabolic codependence, genome reduction, and synchronized life cycles. One of the few examples of vertical transmission of N-fixing symbionts occurs in Azolla ferns, which maintain an obligate mutualism with the cyanobacterium Trichormus azollae-but the genomic consequences of this interaction, and whether the symbiosis involves other vertically transmitted microbial partners, are currently unknown. We generated high-coverage metagenomes across the genus Azolla and reconstructed metagenome assembled genomes to investigate whether a core microbiome exists within Azolla leaf cavities, and how the genomes of T. azollae diverged from their free-living relatives. Our results suggest that T. azollae is the only consistent symbiont across all Azolla accessions, and that other bacterial groups are transient or facultative associates. Pangenomic analyses of T. azollae indicate extreme pseudogenization and gene loss compared to free-living relatives-especially in defensive, stress-tolerance, and secondary metabolite pathways-yet the key functions of nitrogen fixation and photosynthesis remain intact. Additionally, differential codon bias and intensified positive selection on photosynthesis, intracellular transport, and carbohydrate metabolism genes suggest ongoing evolution in response to the unique conditions within Azolla leaf cavities. These findings highlight how genome erosion and shifting selection pressures jointly drive the evolution of this unique mutualism, while broadening the taxonomic scope of genomic studies on vertically transmitted symbioses.},
}

@article {pmid40726432,
year = {2025},
author = {Hua, R and Ding, N and Hua, Y and Wang, X and Xu, Y and Qiao, X and Shi, X and Bai, T and Xiong, Y and Zhuo, X and Fan, C and Zhou, J and Wu, Y and Liu, J and Yuan, Z and Li, T},
title = {Ligilactobacillus Murinus and Lactobacillus Johnsonii Suppress Macrophage Pyroptosis in Atherosclerosis through Butyrate-GPR109A-GSDMD Axis.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e01707},
doi = {10.1002/advs.202501707},
pmid = {40726432},
issn = {2198-3844},
support = {2021YFA1301201//National Key R&D Program of China/ ; 2021YFA0805400//National Key R&D Program of China/ ; 2024YFA1307004//National Key R&D Program of China/ ; 82000474//National Science Foundation of China/ ; 82370458//National Science Foundation of China/ ; 82370875//National Science Foundation of China/ ; 82430019//National Science Foundation of China/ ; 2021KJXX-04//Innovative Talents Promotion Plan of Shaanxi Province of China/ ; xzy012019093//Xi'an Jiaotong University/ ; 2020JM-383//Natural Science Foundation of Shaanxi Province/ ; },
abstract = {Gut microbiota and their metabolites are remarkable regulators in atherosclerosis. Oral drugs such as aspirin have recently been found to modulate the gut microbiome. However, the roles of drug-microbiota-metabolite interactions in atherosclerosis have not been explored. Herein, two gut probiotics, Ligilactobacillus murinus (L. murinus) and Lactobacillus johnsonii (L. johnsonii), are identified from mouse models and human cohorts, which are positively correlated with aspirin usage. Specifically, the eradication of these two species eliminated aspirin's anti-atherosclerotic effects, while their transplantation exhibited therapeutic effects against atherosclerosis. Integrative analysis of metagenomic and metabolomic data showed that elevated levels of butyrate are associated with these two species. Mechanically, L. murinus and L. johnsonii form symbiotic networks with butyrate-producing bacteria such as Allobaculum. This study confirmed that gut microbes produce butyrate, which helps preserve the gut barrier and prevents the leakage of lipopolysaccharides. By integrating molecular biology and single-cell sequencing data, G protein-coupled receptor 109A (GPR109A) is confirmed as the direct target of butyrate. Through the activation of GPR109A, butyrate produced by L. murinus and L. johnsonii suppressed the expression of Gasdermin D (GSDMD) in the pyroptosis of macrophages during atherosclerosis. These findings offer novel insights into the drug-microbiota axis that can be targeted to improve the treatment of atherosclerosis.},
}

@article {pmid40726156,
year = {2025},
author = {Yang, S and Huang, X and Li, X and Feng, J and Chen, P and Cao, Z and He, L and Li, C and Li, Z and Xie, M},
title = {Aloe vera polysaccharides mitigate high-fat high-cholesterol diet-induced atherosclerosis in ApoE[-/-] mice via regulation of lipid metabolism and gut microbiota.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo01995h},
pmid = {40726156},
issn = {2042-650X},
abstract = {Cardiovascular diseases are leading causes of death globally, often manifesting after years of atherosclerosis (AS) progression. In this study, we investigated the atheroprotective effects of three different sources of glucomannan, Dendrobium officinale polysaccharide, Konjac glucomannan, and Aloe vera polysaccharide (AVP), using an in vitro ox-LDL-induced foam cell model and an in vivo high-fat high-cholesterol diet-fed ApoE[-/-] mouse model. Both settings indicate that AVP exerts the most significant atheroprotective effects. It inhibits lipid absorption and enhances the regulation of lipid homeostasis by the liver X receptor, thereby suppressing the formation of foam cells. It can also alleviate ox-LDL-induced oxidative stress and apoptosis in RAW 264.7 cells. Animal experiments show that AVP can prevent the formation of atherosclerotic plaques and coronary artery fibrosis, while also reducing circulating IL-1β levels. Furthermore, liver transcriptomic analysis shows that AVP inhibits inflammation and promotes bile acid excretion and transport by upregulating the farnesoid X receptor. Additionally, metagenomic analysis indicates that AVP can significantly reverse the microbial alterations associated with AS. Specific gut microbes, such as Prevotella, may partially mediate the effects of AVP through the gut-liver axis. This is the first study to report the atheroprotective effects of AVP, demonstrating that it alleviates atherosclerosis by restoring lipid metabolism homeostasis and modulating the gut microbiome.},
}

@article {pmid40725792,
year = {2025},
author = {Issilbayeva, A and Kozhakhmetov, S and Jarmukhanov, Z and Vinogradova, E and Mukhanbetzhanov, N and Meiramova, A and Rib, Y and Ivanova-Razumova, T and Myrzakhmetova, G and Andossova, S and Zeinoldina, A and Kuantkhan, M and Ainabekova, B and Bekbossynova, M and Kushugulova, A},
title = {Metagenomic Characterization of Gut Microbiota in Individuals with Low Cardiovascular Risk.},
journal = {Journal of clinical medicine},
volume = {14},
number = {14},
pages = {},
pmid = {40725792},
issn = {2077-0383},
support = {АР23487014; BR21881970//The Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; },
abstract = {Background/Objectives: Cardiovascular diseases remain the leading cause of global mortality, with the gut microbiome emerging as a critical factor. This study aimed to characterize gut microbiome composition and metabolic pathways in individuals with low cardiovascular risk (LCR) compared to healthy controls to reveal insights into early disease shifts. Methods: We performed shotgun metagenomic sequencing on fecal samples from 25 LCR individuals and 25 matched healthy controls. Participants underwent a comprehensive cardiovascular evaluation. Taxonomic classification used MetaPhlAn 4, and functional profiling employed HUMAnN 3. Results: Despite similar alpha diversity, significant differences in bacterial community structure were observed between groups (PERMANOVA, p < 0.05). The LCR group showed enrichment of Faecalibacterium prausnitzii (p = 0.035), negatively correlating with atherogenic markers, including ApoB (r = -0.3, p = 0.025). Conversely, Fusicatenibacter saccharivorans positively correlated with ApoB (r = 0.4, p = 0.006). Metabolic pathway analysis revealed upregulation of nucleotide biosynthesis, glycolysis, and sugar degradation pathways in the LCR group, suggesting altered metabolic activity. Conclusions: We identified distinct gut microbiome signatures in LCR individuals that may represent early alterations associated with cardiovascular disease development. The opposing correlations between F. prausnitzii and F. saccharivorans with lipid parameters highlight their potential roles in cardiometabolic health. These findings suggest gut microbiome signatures may serve as indicators of early metabolic dysregulation preceding clinically significant cardiovascular disease.},
}

@article {pmid40725341,
year = {2025},
author = {López-Hernández, MG and Rincón-Rosales, R and Rincón-Molina, CI and Manzano-Gómez, LA and Gen-Jiménez, A and Maldonado-Gómez, JC and Rincón-Molina, FA},
title = {Diversity and Functional Potential of Gut Bacteria Associated with the Insect Arsenura armida (Lepidoptera: Saturniidae).},
journal = {Insects},
volume = {16},
number = {7},
pages = {},
pmid = {40725341},
issn = {2075-4450},
support = {19337.24-P and 19414.24-P//Tecnológico Nacional de México/ ; },
abstract = {Insects are often associated with diverse microorganisms that enhance their metabolism and nutrient assimilation. These microorganisms, residing in the insect's gut, play a crucial role in breaking down complex molecules into simpler compounds essential for the host's growth. This study investigates the diversity and functional potential of symbiotic bacteria in the gut of Arsenura armida (Lepidoptera: Saturniidae) larvae, an edible insect from southeastern Mexico, using culture-dependent and metagenomic approaches. Bacterial strains were isolated from different gut sections (foregut, midgut, and hindgut) and cultured on general-purpose media. Isolates were identified through 16S rRNA gene sequencing and genomic fingerprinting. Metagenomics revealed the bacterial community structure and diversity, along with their functional potential. A total of 96 bacterial strains were isolated, predominantly Gram-negative bacilli. Rapidly growing colonies exhibited enzymatic activity, cellulose degradation, and sugar production. Phylogenetic analysis identified eight genera, including Acinetobacter, Bacillus, Enterobacter, Pseudomonas, and others, with significant cellulose-degrading capabilities. Metagenomics confirmed Bacillota as the most abundant phylum. These complementary methods revealed abundant symbiotic bacteria with key metabolic roles in A. armida, offering promising biotechnological applications in enzymatic bioconversion and cellulose degradation.},
}

@article {pmid40724992,
year = {2025},
author = {Rušanac, A and Škibola, Z and Matijašić, M and Čipčić Paljetak, H and Perić, M},
title = {Microbiome-Based Products: Therapeutic Potential for Inflammatory Skin Diseases.},
journal = {International journal of molecular sciences},
volume = {26},
number = {14},
pages = {},
pmid = {40724992},
issn = {1422-0067},
support = {NPOO.C3.2.R3-I1.04.0240//European Regional Development Fund/ ; KK.01.2.1.02.0137//European Regional Development Fund/ ; IP.1.1.03.0157//European Regional Development Fund/ ; },
mesh = {Humans ; *Microbiota/drug effects ; Probiotics/therapeutic use ; Prebiotics/administration & dosage ; *Skin Diseases/microbiology/therapy ; Dysbiosis/microbiology/therapy ; Skin/microbiology ; Animals ; Psoriasis/microbiology/therapy ; Dermatitis, Atopic/microbiology/therapy ; },
abstract = {Maintaining a balanced skin microbiota is essential for skin health, whereas disruptions in skin microbiota composition, known as dysbiosis, can contribute to the onset and progression of various skin disorders. Microbiota dysbiosis has been associated with several inflammatory skin conditions, including atopic dermatitis, seborrheic dermatitis, acne, psoriasis, and rosacea. Recent advances in high-throughput sequencing and metagenomic analyses have provided a deeper understanding of the skin microbial communities in both health and disease. These discoveries are now being translated into novel therapeutic approaches aimed at restoring microbial balance and promoting skin health through microbiome-based interventions. Unlike conventional therapies that often disrupt the microbiota and lead to side effects or resistance, microbiome-based products offer a more targeted strategy for preventing and managing inflammatory skin diseases. These products, which include probiotics, prebiotics, postbiotics, and live biotherapeutic agents, are designed to modulate the skin ecosystem by enhancing beneficial microbial populations, suppressing pathogenic strains, and enhancing immune tolerance. As a result, they represent a promising class of products with the potential to prevent, manage, and even reverse inflammatory skin conditions. However, realizing the full therapeutic potential of microbiome-based strategies in dermatology will require continued research, robust clinical validation, and clear regulatory frameworks.},
}

Humans
*Microbiota/drug effects
Probiotics/therapeutic use
Prebiotics/administration & dosage
*Skin Diseases/microbiology/therapy
Dysbiosis/microbiology/therapy
Skin/microbiology
Animals
Psoriasis/microbiology/therapy
Dermatitis, Atopic/microbiology/therapy

@article {pmid40724243,
year = {2025},
author = {Geng, H and Xu, C and Ma, H and Dai, Y and Jiang, Z and Yang, M and Zhu, D},
title = {In Silico Discovery and Sensory Validation of Umami Peptides in Fermented Sausages: A Study Integrating Deep Learning and Molecular Modeling.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {14},
pages = {},
pmid = {40724243},
issn = {2304-8158},
abstract = {Deep learning has great potential in the field of functional peptide prediction. This study combines metagenomics and deep learning to efficiently discover potential umami peptides in fermented sausages. A candidate peptide library was generated using metagenomic data from fermented sausages, an integrated deep learning model was constructed for prediction, and SHAP (SHapley Additive exPlanations) interpretability analysis was performed to elucidate the key amino acid features and contributions of the model in predicting umami peptides, screening the top ten peptides with the highest predicted probability. Subsequently, molecular docking was performed to assess the binding stability of these peptides with the umami receptor T1R1/T1R3, selecting the three peptides DDSMAATGL, DGEEDASM, and DEEEVDI with the most stable binding for further study. Docking analysis revealed the important roles of the key receptor residues Glu301, Arg277, Lys328, and His71 in hydrogen bond formation. Molecular dynamics simulations validated the robust integrity of the peptide-receptor associations. Finally, sensory evaluation demonstrated that these three peptides possessed significant umami characteristics, with low umami thresholds (0.11, 0.37, and 0.44 mg/mL, respectively). This study, based on metagenomics and deep learning, provides a high-throughput strategy for the discovery and validation of functional peptides.},
}

@article {pmid40723458,
year = {2025},
author = {Penalba-Iglesias, D and Robas-Mora, M and González-Reguero, D and Fernández-Pastrana, VM and Probanza, A and Jiménez-Gómez, PA},
title = {Use of Bacillus pretiosus and Pseudomonas agronomica for the Synthesis of a Valorized Water Waste Treatment Plant Waste as a Biofertilizer Intended for Quercus pyrenaica L. Fertigation.},
journal = {Biology},
volume = {14},
number = {7},
pages = {},
pmid = {40723458},
issn = {2079-7737},
support = {TED2021-132285A-I00//Next Generation Funds/ ; },
abstract = {The loss of hectares of forest areas has become a global issue that has worsened over recent years due to unsustainable human activities. In a context of limited availability of productive land, it is urgent to adopt efficient strategies to recover the affected natural areas. Actions based on a circular economy, such as the use of organic chemical matrices recovered from water waste treatment plant waste, have proven to be effective. In this regard, the addition of plant growth-promoting bacteria (PGPB), such as Bacillus pretiosus and Pseudomonas agronomica, can contribute to the chemical treatment, favoring the recovery of soils, accelerating the recovery of vegetation cover, and inducing an increase in biodiversity. In this research, the effect of bio-fertigation under controlled laboratory conditions in Quercus pyrenaica is evaluated. After a thirty-six-week trial, the biometric and nutritional parameters of the plants were harvested and measured, and the diversity and composition of the metagenomes of their rhizospheres were evaluated. As well, the cenoantibiogram and the metabolic diversity were measured. The results showed that the use of these biofertilizers increased the variables related to plant production, quality of plant composition as an indirect means of their resilience, as well as an increase in rhizospheric microbial diversity and a reduction in their MIC resistance to the most widely used antibiotics. For all these reasons, the use of the biofertilizer result of the combination of WWTP waste, Bacillus pretiosus, and Pseudomonas agronomica is postulated as an environmentally friendly strategy that can contribute to the recovery of potential oak forest areas.},
}

@article {pmid40723410,
year = {2025},
author = {Starska-Kowarska, K},
title = {Salivaomic Biomarkers-An Innovative Approach to the Diagnosis, Treatment, and Prognosis of Oral Cancer.},
journal = {Biology},
volume = {14},
number = {7},
pages = {},
pmid = {40723410},
issn = {2079-7737},
abstract = {(1) Background: Oral cancer (OC) is one of the most frequently diagnosed human cancers and remains a challenge for biologists and clinicians. More than 90% of OC cases are squamous cell carcinomas (OSCCs). Despite the use of modern diagnostic and prognostic methods, the 5-year survival rate remains unsatisfactory due to the late diagnosis of the neoplastic process and its resistance to treatment. This comprehensive review aims to present the latest literature data on the use and effectiveness of saliva as a non-invasive biomarker in patients with oral cancer. (2) Methods: The article reviews the current literature on the use of salivary omics biomarkers as an effective method in diagnosing and modifying treatment in patients with OSCC; the research corpus was acquired from the PubMed/Google/Scopus/Cochrane Library/Web of Science databases in accordance with the Systematic Reviews and Meta-Analyses extension for Scoping Reviews (PRISMA 2020) guidelines. (3) Results: The identification of salivary omics biomarkers involved in carcinogenesis and neoplastic transformation may be a potential alternative to traditional invasive diagnostic methods. Saliva, being both an abundant reservoir of organic and inorganic components derived from epithelial cells as well as a cell-free environment, is becoming an interesting diagnostic material for studies in the field of proteomics, genomics, metagenomics, and metabolomics. (4) Conclusions: Saliva-based analysis is a modern and promising method for the early diagnosis and improvement of treatment outcomes in patients with OSCC and oral potentially malignant disorders (OPMDs), with high diagnostic, therapeutic, and prognostic potential.},
}

@article {pmid40723390,
year = {2025},
author = {Guan, T and Yang, X and Hong, C and Xiao, P and Yang, Y and Zhang, C and He, Z},
title = {Exploring the Efficacy and Potential Mechanisms of Topical Periplaneta americana (L.) Extract in Treating Androgenetic Alopecia in a Mouse Model: A Systems Pharmacology and Skin Microbiome Analysis.},
journal = {Biology},
volume = {14},
number = {7},
pages = {},
pmid = {40723390},
issn = {2079-7737},
support = {82060747，202405AF140044//Peiyun Xiao/ ; },
abstract = {Androgenetic alopecia (AGA), the most prevalent form of hair loss worldwide, faces significant therapeutic challenges due to high costs and limited efficacy of current interventions, necessitating safer and more effective solutions. Periplaneta americana (L.)-derived PA-011, endowed with anti-inflammatory and antioxidant properties, has demonstrated notable hair growth-promoting effects in AGA mouse models. This study employed LC-MS/MS, peptidomics, and network pharmacology to characterize PA-011's chemical composition and predict its potential targets in AGA pathogenesis. Using Western blot and RT-qPCR, PA-011 intervention significantly inhibited inflammatory responses and oxidative stress levels in mouse skin tissues. Concurrently, PA-011 activated the proliferative potential of hair follicle stem cells, as demonstrated by upregulated expression of the cell proliferation marker Ki67, and activated the Wnt/β-catenin signaling pathway in DHT-induced AGA mice. Transcriptomic and metabolomic analyses revealed multi-target effects of PA-011, including modulation of PI3K-Akt/MAPK pathways, pentose phosphate metabolism, and amino acid biosynthesis. 16S rRNA sequencing and metagenomic analysis showed that AGA disrupts skin microbial homeostasis, while PA-011 intervention normalized the microbiota composition. Topical application of PA-011 promoted robust hair regrowth without detectable toxicity in safety assessments. This preclinical study establishes PA-011 as a promising candidate for AGA therapy, warranting further translational investigation.},
}

@article {pmid40722483,
year = {2025},
author = {Dragasevic, S and Nikolic, A and Zgradic, S and Stojkovic Lalosevic, M and Stojkovic, S and Matovic Zaric, V and Lukic, S and Glisic, T and Kmezic, S and Saponjski, D and Popovic, D},
title = {Dysbiosis of Gut Microbiota in Microscopic Colitis: Diagnostic and Therapeutic Implications.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {15},
number = {14},
pages = {},
pmid = {40722483},
issn = {2075-4418},
abstract = {Microscopic colitis (MC) is an idiopathic inflammatory bowel disease characterized by watery, non-bloody diarrhea and histopathological changes but normal endoscopic findings. Increasing evidence now suggests that alterations in the gut microbiota contribute to the pathogenesis of MC. In this narrative review, we summarize evidence from nine case-control studies examining microbial composition using sequencing technology. The research presented here illustrates reduced alpha diversity, high dysbiosis, and pro-inflammatory oral-associated taxa enrichment, such as Veillonella dispar, and loss of protective microbes such as Akkermansia muciniphila and Bacteroides stercoris. These microbial changes have the potential to be non-invasive diagnostic biomarkers that can differentiate MC from other etiologies. In addition, the characterization of gut microbiota in MC can guide personalized therapeutic strategies, such as directed probiotic therapy or fecal microbiota transplantation, to help restore microbial balance. These microbial patterns can be applied to guide the creation of diagnostic biomarkers and personalized therapy. Despite differences in sample types and sequencing methods, general microbial trends highlight the need for further longitudinal and standardized investigations.},
}

@article {pmid40722433,
year = {2025},
author = {Manoharan, RK and Han, KI and Shin, HD and Lee, Y and Baek, S and Moon, E and Park, YB and Cho, J and Srinivasan, S},
title = {Modulation of Gut Microbiota and Antibiotic Resistance Genes by Heat-Killed Enterococcus faecalis EF-2001 in High-Fat Diet-Induced Obesity Mice: A Shotgun Metagenomics Study.},
journal = {Bioengineering (Basel, Switzerland)},
volume = {12},
number = {7},
pages = {},
pmid = {40722433},
issn = {2306-5354},
abstract = {The gut microbiome is vital in maintaining metabolic health, and dietary habits can significantly impact its composition. A high-fat diet (HFD) can disrupt gut microbial balance, contributing to obesity, insulin resistance, and fatty liver disease. This study explores the potential benefits of heat-killed Enterococcus faecalis EF-2001 (EF-2001) in restoring gut balance and improving metabolic health in HFD-fed mice (HFD-mice). HFD mice administered EF-2001 had 18% less body fat, 22% lower triglyceride levels, and significantly reduced liver enzyme markers, including aspartate aminotransferase (AST) by 28% and alanine aminotransferase (ALT) by 31%. Additionally, EF-2001 improved glucose metabolism, increasing glucose tolerance by 20% and insulin sensitivity by 15%, while reducing fat buildup in the liver by 24%, indicating protection against fatty liver disease. These changes correlated with better metabolic health and reduced inflammation. Our results show that EF-2001 supplementation helped counteract HFD-induced gut imbalances by increasing microbial diversity and supporting beneficial bacteria, such as Akkermansia and Ligilactobacillus spp. Our findings highlight the potential of heat-killed EF-2001 as a promising strategy to restore gut balance and mitigate diet-related metabolic issues. Furthermore, analysis of antibiotic resistance genes (ARGs) revealed that HFD mice exhibited an increased abundance of multidrug resistance genes, particularly those associated with antibiotic efflux mechanisms, such as bcrA, cdeA, and msbA. Notably, EF-2001 supplementation mitigated this increase, reducing the relative abundance of the above ARGs and suggesting a protective role in limiting the spread of antibiotic resistance linked to dysbiosis. EF-2001 offers a compelling approach to managing obesity and metabolic disorders, paving the way for microbiome-based health interventions.},
}

@article {pmid40722249,
year = {2025},
author = {Hilberath, J and Busch, A and Schoppmeier, U and Schmauder, K and Oberhettinger, P and Marschal, M and Slavetinsky, C and Sturm, E and Peter, S and D'Alvise, P},
title = {Small intestinal bacterial overgrowth and dysbiosis in children with intestinal failure: A descriptive cohort study.},
journal = {JPEN. Journal of parenteral and enteral nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1002/jpen.2808},
pmid = {40722249},
issn = {1941-2444},
abstract = {BACKGROUND: Small intestinal bacterial overgrowth (SIBO) is a clinical and diagnostic challenge in pediatric intestinal failure. This study aimed to assess SIBO and dysbiosis in children with intestinal failure and to analyze clinical characteristics as well as cultural and metagenomic sequencing results from different sampling methods.

METHODS: Descriptive, single-center cohort study in intestinal failure patients with prospective collection of intraluminal aspirate, epithelial brush swab, mucosal biopsy, and small bowel stoma stool for SIBO diagnosis, defined as ≥10[3] CFU/ml of enteric, colonic-type bacteria, and microbiome analysis via whole-genome sequencing. Statistical testing included receiver operating characteristic analysis, chi-square test, and independent samples t test.

RESULTS: Forty-four children with intestinal failure were analyzed (median age 58 months; female 48%; short bowel syndrome 70%). Sixty-six percent of samples were positive for SIBO. In 93%, all three endoscopic sampling methods showed congruent results. SIBO-positive cases were associated (P < 0.05) with small bowel dilatation, proton pump inhibitor use, intestinal inflammation, elevated direct bilirubin and hepatocellular enzyme levels, and a history of liver fibrosis and central venous catheter infections. Metagenomic sequencing revealed microbial dysbiosis in intestinal failure patients, with SIBO-positive cases showing higher microbial reads, lower alpha diversity, and increased abundance of Enterobacteriaceae and enteric anaerobes.

CONCLUSION: SIBO and dysbiosis are common in children with intestinal failure and associated with liver injury, central line-associated bloodstream infections, and intestinal inflammation. Cultural diagnosis of SIBO using mucosal biopsies or brush swabs are alternatives to small bowel aspirates. Metagenomic sequencing is feasible, and high microbial read numbers are indicative of SIBO.},
}

@article {pmid40722120,
year = {2025},
author = {Alaa, MA and Zhang, H and Duan, H and Zhang, J and Mao, S},
title = {Metagenomic analysis reveals rumen microbiome enrichment and functional genes adjustment in carbohydrate metabolism induced by different sorting behavior in mid-lactation dairy cows.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {82},
pmid = {40722120},
issn = {2524-4671},
support = {32072755//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: This study aimed to investigate differences in the structure and function of the rumen microbiome and its associated changes in rumen fermentation patterns and apparent nutrient digestibility in dairy cattle with different sorting behavior. Twenty-four Holstein cows in mid-lactation were initially enrolled in the experiment. All cows were fed and milked three times daily throughout the entire 28-day experimental period, comprising a 7-day pre-trial and a 21-day main trial. On days 1, 7, 14, and 21 of the main trial, feed sorting behavior was measured, and feed and feces samples were collected to determine apparent nutrient digestibility. Rumen content samples were collected on day 21 to measure pH, volatile fatty acids (VFA), and rumen microbiome structure and function. Based on feed sorting behavior, twelve cows were selected and divided into two groups: six cows that were severely sorted for fine particles-severely rejected long particles (SES; n = 6) and six cows that were slightly sorted for fine particles-slightly rejected long particles (SLS; n = 6).

RESULTS: Comparative analysis revealed significant differences between the groups. The SES group exhibited lower rumen pH values and higher concentrations of total VFA (TVFA) and acetate (P < 0.05) than the SLS group. Data on apparent nutrient digestibility showed that compared to the SLS group, the SES group lowered the digestibility of neutral detergent fiber (NDF) and acid detergent fiber (ADF) (P < 0.05). Differential analysis of rumen microbiota indicated that the SES group had a higher relative abundance of Prevotella, Lactobacillus, Bifidobacterium, Selenomonas, and Acetitomaculum by a lower relative abundance of Fibrobacter, Ruminobacter, Pseudobutyrivibrio, Butyrivibrio, and Ruminococcus. Carbohydrate-active enzyme (CAZyme) annotation revealed that the SES group showed increased abundance of GH13 and GH65 enzymes, while exhibiting decreased abundance of GH1, GH3, GH5, GH6, and GH94. Functional profiling of Kyoto encyclopedia of genes and genomes (KEGG) modules revealed that compared to the SLS group, the rumen microbiota in the SES group upregulated the abundance of carbohydrate metabolism, amino acid metabolism, energy metabolism, and lipid metabolism. In carbohydrate metabolism, the rumen microbiota in the SES group upregulated the abundance of starch and sucrose metabolism, the citrate cycle, and pyruvate metabolism, while downregulating the pentose phosphate pathway. Functional profiling of KEGG Orthology (KO) enzymes revealed that the microbiota in the SES group preferred energy production through increasing glycolysis and supported the metabolism changes toward acetate production and fatty acid biosynthesis.

CONCLUSION: Our findings reveal that feed sorting behavior significantly alters the rumen microbial ecosystem and its metabolic functions, negatively impacting fermentation efficiency, fiber digestibility, and overall nutrient utilization, even when cows are provided a well-balanced, standardized diet. This underscores the importance of early detection and management of feed sorting in dairy farms to promote cows' health and support sustainable dairy production.},
}

@article {pmid40721838,
year = {2025},
author = {Giménez, M and Berenstecher, P and Ligrone, A and Iraola, G and Piñeiro, G},
title = {Soil microbiome analysis of Uruguayan grasslands and croplands reveals losses of microbial diversity and necromass recycling traits.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {96},
doi = {10.1186/s40793-025-00696-4},
pmid = {40721838},
issn = {2524-6372},
abstract = {BACKGROUND: Soil microbiomes are critical regulators of nutrient biogeochemical cycles, contributing significantly to ecosystem services that support plant productivity. In this study, we investigated the effects of agricultural rotations on soil microbial communities in Uruguayan grasslands, comparing cropland soils with native grasslands grazed by livestock. By employing advanced metagenomic techniques, we characterized the diversity and functional potential of the soil microbiome, with particular emphasis on its roles in carbon, nitrogen, and phosphorus cycling. Additionally, we assessed functional genes associated with microbial necromass recycling, a key process for maintaining soil health and fertility.

RESULTS: Our analysis revealed a significant decrease in fungal diversity and a restructuring of the fungal community in agricultural soils, highlighting the profound impact of farming practices on soil biology. In contrast, while we did not observe a similar decline in bacterial diversity, there was a noticeable shift in its composition. Agricultural soils showed a reduced abundance of bacteriophages, which are associated with bacterial necromass formation, as well as a decline in enzymes involved in microbial necromass decomposition. This suggests potential long-term consequences for soil carbon dynamics and crop productivity. Additionally, croplands exhibited a marked decrease in genes and enzymes involved in nitrogen and phosphorus cycling, indicating diminished functionality and resilience for these essential nutrient processes compared to grassland soils.

CONCLUSIONS: Our findings emphasize the need for a sustainable approach to agriculture that preserves microbial diversity and functionality, ensuring the resilience of soil ecosystems. By comparing soil microbiomes across different land use types, this research provides novel insights into the mechanisms through which agriculture alters soil ecosystems and offers guidance for enhancing soil management practices to support environmental sustainability and agricultural productivity.},
}

@article {pmid40721531,
year = {2025},
author = {Edahiro, R and Sato, G and Naito, T and Shirai, Y and Saiki, R and Sonehara, K and Tomofuji, Y and Yamamoto, K and Namba, S and Sasa, N and Nagao, G and Wang, QS and Takahashi, Y and Hasegawa, T and Kishikawa, T and Suzuki, K and Liu, YC and Motooka, D and Takuwa, A and Tanaka, H and Azekawa, S and , and Namkoong, H and Koike, R and Kimura, A and Imoto, S and Miyano, S and Kanai, T and Fukunaga, K and Uemura, M and Morita, T and Kato, Y and Hirata, H and Takeda, Y and Doki, Y and Eguchi, H and Okuzaki, D and Sakakibara, S and Ogawa, S and Kumanogoh, A and Okada, Y},
title = {Deciphering state-dependent immune features from multi-layer omics data at single-cell resolution.},
journal = {Nature genetics},
volume = {},
number = {},
pages = {},
pmid = {40721531},
issn = {1546-1718},
support = {22H00476, 24K02697//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 22gm1810003h0001//Japan Agency for Medical Research and Development (AMED)/ ; },
abstract = {Current molecular quantitative trait locus catalogs are mostly at bulk resolution and centered on Europeans. Here, we constructed an immune cell atlas with single-cell transcriptomics of >1.5 million peripheral blood mononuclear cells, host genetics, plasma proteomics and gut metagenomics from 235 Japanese persons, including patients with coronavirus disease 2019 (COVID-19) and healthy individuals. We mapped germline genetic effects on gene expression within immune cell types and across cell states. We elucidated cell type- and context-specific human leukocyte antigen (HLA) and genome-wide associations with T and B cell receptor repertoires. Colocalization using dynamic genetic regulation provided better understanding of genome-wide association signals. Differential gene and protein expression analyses depicted cell type- and context-specific effects of polygenic risks. Various somatic mutations including mosaic chromosomal alterations, loss of Y chromosome and mitochondrial DNA (mtDNA) heteroplasmy were projected into single-cell resolution. We identified immune features specific to somatically mutated cells. Overall, immune cells are dynamically regulated in a cell state-dependent manner characterized with multiomic profiles.},
}

@article {pmid40721426,
year = {2025},
author = {Yang, Y and Ye, M and Song, Y and Xing, W and Zhao, X and Li, Y and Shen, J and Zhou, J and Arikawa, K and Wu, S and Song, Y and Xu, N},
title = {Gut microbiota and SCFAs improve the treatment efficacy of chemotherapy and immunotherapy in NSCLC.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {146},
doi = {10.1038/s41522-025-00785-9},
pmid = {40721426},
issn = {2055-5008},
support = {2020YFC2003700//National Key R&D Plan/ ; ZD2021CY001//Shanghai Municipal Science and Technology Major Project/ ; 20Z11901000, 20DZ2261200, 20XD1401200, 22Y11900800//Science and Technology Commission of Shanghai Municipality/ ; SHDC2020CR5010-002//Clinical Research Plan of SHDC/ ; shslczdzk02201//Shanghai Municipal Key Clinical Specialty/ ; ZY(2021-2023)-0207-01//Shanghai Municipal Health Commission and Shanghai Municipal Administrator of Traditional Chinese Medicine/ ; 81401877, 82130001, and 82272243//National Natural Science Foundation of China/ ; 81401877, 82130001, and 82272243//National Natural Science Foundation of China/ ; },
mesh = {*Gastrointestinal Microbiome ; Humans ; *Carcinoma, Non-Small-Cell Lung/therapy/microbiology/drug therapy ; *Immunotherapy/methods ; Animals ; *Lung Neoplasms/therapy/microbiology/drug therapy ; Mice ; *Fatty Acids, Volatile/metabolism ; Fecal Microbiota Transplantation ; RNA, Ribosomal, 16S/genetics ; Treatment Outcome ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Female ; Male ; Metagenomics ; Middle Aged ; Aged ; Dysbiosis/microbiology ; Antineoplastic Agents/therapeutic use ; },
abstract = {The role of gut dysbiosis in shaping immunotherapy responses is well-recognized, yet its effect on the therapeutic efficacy of chemotherapy and immunotherapy combinations remains poorly understood. We analyzed gut microbiota in non-small cell lung cancer (NSCLC) patients treated with chemo-immunotherapy, comparing responders and non-responders using 16S rRNA sequencing. Responders showed higher microbial richness and abundance of specific genera like Faecalibacterium and Subdoligranulum, and the phylum Firmicutes. Support vector machine (SVM), a machine learning model based on microbial composition, predicted treatment efficacy with the area under the curve (AUC) values of 0.763 for genera and 0.855 for species. Metagenomic analysis revealed significant differences in metabolic pathways, with responders exhibiting higher short-chain fatty acids (SCFAs) production. Fecal microbiota transplantation (FMT) and SCFAs supplementation in mouse models enhanced treatment efficacy by promoting effector T cell activity in tumors. Our study suggests that gut microbiota, through SCFAs production, regulates chemo-immunotherapy efficacy, offering new strategies to improve NSCLC treatment outcomes.},
}

*Gastrointestinal Microbiome
Humans
*Carcinoma, Non-Small-Cell Lung/therapy/microbiology/drug therapy
*Immunotherapy/methods
Animals
*Lung Neoplasms/therapy/microbiology/drug therapy
Mice
*Fatty Acids, Volatile/metabolism
Fecal Microbiota Transplantation
RNA, Ribosomal, 16S/genetics
Treatment Outcome
*Bacteria/classification/genetics/isolation & purification/metabolism
Female
Male
Metagenomics
Middle Aged
Aged
Dysbiosis/microbiology
Antineoplastic Agents/therapeutic use

@article {pmid40717126,
year = {2025},
author = {Gil, AM and Zegarra-Ruiz, DF and Wu, WJ and Norwood, K and Assie, A and Samuel, BS and Major, AM and Diehl, GE and McAlester, AAH},
title = {Dietary lipids induce PPARd and BCL6 to repress macrophage IL-23 induction after intestinal injury and LPS exposure.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {27344},
doi = {10.1038/s41598-025-12448-y},
pmid = {40717126},
issn = {2045-2322},
support = {R01AI125264/GF/NIH HHS/United States ; K01DK121934/DK/NIDDK NIH HHS/United States ; },
mesh = {Animals ; *Macrophages/metabolism/drug effects/immunology ; Mice ; *Proto-Oncogene Proteins c-bcl-6/metabolism/genetics ; *Lipopolysaccharides ; *PPAR delta/metabolism/genetics ; Diet, High-Fat/adverse effects ; *Dietary Fats/pharmacology ; CD36 Antigens/metabolism/genetics ; *Intestines/pathology/injuries ; Mice, Inbred C57BL ; Oleic Acid/pharmacology ; Inflammatory Bowel Diseases/metabolism/pathology ; *Interleukin-23 Subunit p19/metabolism/genetics ; Male ; *Interleukin-23/metabolism ; Interleukins/metabolism ; },
abstract = {Unresolved tissue damage is a common feature of Inflammatory Bowel Disease (IBD) that facilitates disease progression. Here, we showed that high animal fat diets (HFD), an environmental risk factor associated with IBD pathogenesis, suppress intestinal macrophage production of critical tissue repair responses after damage. This includes reduced IL-23 production, which drives downstream production of IL-22, which is needed for barrier repair. Indicating that dietary lipids interfere with responses to microbial molecules needed to induce barrier protective functions, we found oleic acid could directly suppress macrophage Il23a induction after lipopolysaccharide (LPS) treatment. Deleting the lipid transporter CD36 on macrophages restored the Il23a and Il22 response, reducing intestinal damage in HFD-fed DSS-treated mice. We found that CD36-mediated intracellular lipid accumulation, mainly oleic acid, in macrophages leads to peroxisome proliferator-activated receptor delta (PPARδ) release of the transcriptional repressor protein B-cell lymphoma 6 (BCL6). BCL6 suppresses Il23a transcription in microbe-exposed macrophages. The studies suggest dietary lipid modulation of the macrophage PPARδ/BCL6 transcriptional repressor complex is a key mechanism of fat-associated defects in intestinal damage repair and immune dysregulation. Overall, our findings provide new insights into dietary lipid contribution to intestinal disease progression and identify new potential therapeutic targets to decrease diet-associated risk for IBD.},
}

Animals
*Macrophages/metabolism/drug effects/immunology
Mice
*Proto-Oncogene Proteins c-bcl-6/metabolism/genetics
*Lipopolysaccharides
*PPAR delta/metabolism/genetics
Diet, High-Fat/adverse effects
*Dietary Fats/pharmacology
CD36 Antigens/metabolism/genetics
*Intestines/pathology/injuries
Mice, Inbred C57BL
Oleic Acid/pharmacology
Inflammatory Bowel Diseases/metabolism/pathology
*Interleukin-23 Subunit p19/metabolism/genetics
Male
*Interleukin-23/metabolism
Interleukins/metabolism

@article {pmid40717117,
year = {2025},
author = {Yi, L and Tan, L and Long, Q and Lyu, X and Zeng, H and Peng, Y and Gu, D and Liu, H and Ge, H and Yu, Y and Li, Z and Hu, M},
title = {Comparative diagnostic performance of metagenomic and two targeted sequencing methods in lower respiratory infection.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {27365},
pmid = {40717117},
issn = {2045-2322},
support = {No. 2025JJ60514//Hunan Natural Science Foundation/ ; No. 82102499//National Natural Science Foundation of China/ ; No.202211003513//Scientific Research Project for Hunan Health Commission/ ; },
mesh = {Humans ; *Respiratory Tract Infections/diagnosis/microbiology/virology ; *Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; Male ; Female ; Middle Aged ; Aged ; Adult ; Sensitivity and Specificity ; },
abstract = {Lower respiratory tract infections are characterized by high morbidity and mortality, the latter associated with the low sensitivity and long turnaround time (TAT) of traditional diagnostic methods. Advances in next-generation sequencing (NGS) offers a promising solution, but in the face of so many different NGS products, how to use them appropriately remains a great challenge for clinicians. This study included 205 patients with suspected lower respiratory tract infections from the department of respiratory and critical care medicine, and collected their lower respiratory tract samples for metagenomic NGS (mNGS) and two different targeted NGS (tNGS), amplification-based tNGS and capture-based tNGS. We analyzed their microorganisms reported, and evaluated their detection performance based on the comprehensive clinical diagnosis. Compared to the two tNGS, mNGS showed significant higher cost ($840) and longer TAT (20 h). Conversely, it identified the highest number of species, totaling 80, compared to 71 species identified by capture-based tNGS and 65 species by amplification-based tNGS. When benchmarked against the comprehensive clinical diagnosis, the capture-based tNGS demonstrated significantly higher diagnostic performance than the other two NGS, with an accuracy of 93.17% and a sensitivity of 99.43%. However, it showed lower specificity compared to the amplification-based tNGS in identifying DNA virus (74.78% vs. 98.25%). The amplification-based tNGS exhibited a poor sensitivity for both gram-positive (40.23%) and gram-negative bacteria (71.74%). Moreover, tNGS was able to identify genotypes, antimicrobial resistance genes and virulence factors. In conclusion, mNGS is suited for the detection of rare pathogens; the capture-based tNGS is preferable for routine diagnostic testing; the amplification-based tNGS can be an alternative in situations requiring rapid results and constrained by limited resources.},
}

Humans
*Respiratory Tract Infections/diagnosis/microbiology/virology
*Metagenomics/methods
*High-Throughput Nucleotide Sequencing/methods
Male
Female
Middle Aged
Aged
Adult
Sensitivity and Specificity

@article {pmid40716970,
year = {2025},
author = {Rodriguez-Valera, F and Molina-Pardines, C},
title = {On the biological meaning of the population pangenome.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2025.07.004},
pmid = {40716970},
issn = {1878-4380},
abstract = {The prokaryotic pangenome, the full complement of genes within a species, is strikingly large. To understand how ecological forces shape this diversity, it is useful to examine the variable gene pool within a single population, defined as cells of the same species coexisting in the same time and place. This single-population pangenome reflects the minimal flexible gene repertoire required in a specific environmental context. Recent long-read metagenomic studies of marine prokaryotes show that local population pangenomes remain large, often comprising thousands of genes. Specifically, cells belonging to the same species of the streamlined alfaproteobacterium Pelagibacter, coming from the same sampling site and even sample, contain more than a thousand genes. Many of these genes are related variants that collectively expand the population's metabolic potential, akin to paralogs within a single large genome. We propose for them the name 'metaparalogs' together with the idea that these data reflect cooperative, population-level strategies, where the flexible genome operates as a public good (sensu Samuelson), enhancing both adaptability and ecological resilience. A role for extracellular vesicles in facilitating resource sharing is also suggested.},
}

@article {pmid40716597,
year = {2025},
author = {Wang, P and Zhou, J and Lu, B and Chai, X},
title = {Harnessing metabolic pathway modulation and multiple endogenous driving forces for sustainable nitrogen removal from high-ammonia extremely low C/N ratio wastewater.},
journal = {Environmental research},
volume = {},
number = {},
pages = {122453},
doi = {10.1016/j.envres.2025.122453},
pmid = {40716597},
issn = {1096-0953},
abstract = {The treatment of high-ammonia wastewater with low chemical oxygen demand (COD) to total nitrogen (C/N) ratio faces critical bottlenecks, notably excessive energy consumption and unsustainable external carbon supplementation. In this study, a novel denitrification-dual-stage simultaneous nitrification-anammox-denitrification (DDS) process was pioneered for high-ammonia wastewater with extremely low C/N ratio. DDS system has high nitrogen removal efficiency (98.44 ± 0.14%) for wastewater with 1000 mg/L ammonia and C/N only 1:1, while demonstrating good adaptability at C/N ratios of 1:1-3:1. Its effluent can meet the most stringent level of pollutant discharge standard for municipal wastewater treatment plants (GB18918-2002, TN ≤ 15 mg/L) in China. Mechanistic investigations combining denitrification driving forces analysis and metagenomics revealed that the co-occurrence of partial nitrification-anammox and partial nitrification-denitrification synergistically streamlined nitrogen removal routes. Concurrent multiple endogenous carbon mobilization sustainably mitigated C/N ratio limitations, ensuring system stability without exogenous organic carbon inputs. DDS system has been evaluated to save approximately 50% aeration energy and 100% exogenous carbon feeding compared to conventional processes. Overall, DDS system reduces the treatment difficulty and environmental risk of high-ammonia wastewater, while its lower carbon footprint provides technical support for wastewater treatment plants to meet carbon-neutrality policies and sustainable development goals.},
}

@article {pmid40716139,
year = {2025},
author = {Lemos-Lucumi, CA and Cárdenas-Hernández, V and Toro-Perea, N},
title = {Metagenomic and metatranscriptomic exploration of Avicennia germinans L.: Endophytic microbiome of leaves and roots.},
journal = {Microbiological research},
volume = {300},
number = {},
pages = {128287},
doi = {10.1016/j.micres.2025.128287},
pmid = {40716139},
issn = {1618-0623},
abstract = {Mangroves are productive coastal ecosystems with extreme environmental conditions of temperature, salinity and anthropogenic pollution. Their associated microbiota plays an essential role in plant survival, yet their functional dynamics remain poorly understood. This study characterizes the endophytic microbiome of Avicennia germinans L. in the Buenaventura Bay mangrove ecosystem (Colombia), using a combined metagenomic and metatranscriptomic approach. Distinct microbial communities were observed in leaves and pneumatophores. Root-associated endophytes exhibited higher taxonomic richness and greater transcriptional activity. Functional gene expression revealed enrichment of pathways related to osmotic and oxidative stress responses, hydrocarbon degradation, nitrogen metabolism, and ion homeostasis. The expression of efflux pumps, NADH dehydrogenase, cytochromes, chaperones, H[+]-ATPases, and H[+]/Na[+] antiporters suggest active microbial participation in salinity, heavy metal, xenobiotics and stress resistance. These findings highlight the adaptive versatility of the endophytic microbiome in A. germinans and support its potential for biotechnological applications in stress resistance and bioremediation.},
}

@article {pmid40720842,
year = {2025},
author = {Umair, M and Jamal, Z and Haider, SA and Javed, H and Hakim, R and Ali, Q and Usman, M and Suleman, R and Saeed, MU and Salman, M},
title = {Molecular Epidemiology and Genomic Insights Into Norovirus and Coinfections: A 2023 Tertiary Care Hospital Study on Pediatric Acute Gastroenteritis in Pakistan.},
journal = {The Pediatric infectious disease journal},
volume = {},
number = {},
pages = {},
doi = {10.1097/INF.0000000000004915},
pmid = {40720842},
issn = {1532-0987},
abstract = {BACKGROUND: Acute gastroenteritis remains a leading cause of morbidity in children under 5 in Pakistan, with rotavirus group A as a major pathogen. The contribution of norovirus is less understood.

METHODS: In 2023, we analyzed stool samples from 248 rotavirus group A-negative pediatric patients hospitalized with acute gastroenteritis at a tertiary hospital in Punjab, Pakistan. Viral RNA was extracted and screened using multiplex real-time polymerase chain reaction for norovirus genogroups GI and GII. Positive samples with cycle threshold values <30 were selected for metagenomic sequencing on the Illumina MiSeq platform.

RESULTS: Norovirus was detected in 14% (n = 34) of samples, with GII being the predominant genogroup (71%). Higher prevalence was observed among male children (74%), infants aged 0-10 months (59%) and during October (29%). Fifteen samples were sequenced, yielding near-complete genomes for 7 norovirus strains (GII, n = 5; GI, n = 2). Genotypes identified included GII.3[P25], GII.3[P16], GII.13[P16], GI.3[P3], GII.20[P20] and GII.7[P7]. One GII.7[P7] sample was coinfected with Coxsackievirus A22 and Echovirus E9. Phylogenetic analysis revealed close clustering of Pakistani GII strains with those from Thailand, India and Germany, while GI strains showed similarity to isolates from China, the United States of America and the United Kingdom. The coinfecting Coxsackievirus shared >89% identity with European strains.

CONCLUSIONS: This study highlights norovirus, particularly genogroup GII, as a significant contributor to pediatric gastroenteritis in Pakistan. Genomic surveillance revealed diverse genotypes and coinfections, emphasizing the need for ongoing monitoring to inform public health strategies and clinical management.},
}

@article {pmid40720840,
year = {2025},
author = {Slizovskiy, IB and Gaire, TN and Ferm, PM and Odland, CA and Dee, SA and Nerem, J and Bravo, JE and Kimball, AD and Boucher, C and Noyes, NR},
title = {Reducing skin microbiome exposure impacts through swine farm biosecurity.},
journal = {GigaScience},
volume = {14},
number = {},
pages = {},
doi = {10.1093/gigascience/giaf062},
pmid = {40720840},
issn = {2047-217X},
support = {/NH/NIH HHS/United States ; 1R01AI141810-01//National Institute of Allergy and Infectious Diseases/ ; 5U54OH010170-13A/OH/NIOSH CDC HHS/United States ; },
mesh = {*Microbiota ; *Skin/microbiology ; Animals ; Swine/microbiology ; Humans ; Farms ; *Biosecurity ; *Occupational Exposure ; Female ; Male ; Adult ; Bacteria/genetics/classification/isolation & purification ; Longitudinal Studies ; Animal Husbandry ; Skin Microbiome ; },
abstract = {BACKGROUND: Livestock work is unique due to worker exposure to animal-associated microbiomes within the workplace. Swine workers are a unique cohort within the US livestock labor force, as they have direct daily contact with pigs and undertake mandatory biosecurity interventions. However, investigating this occupational cohort is challenging, particularly within tightly regulated commercial swine operations. Thus, little is known about the impacts of animal exposure and biosecurity protocols on the swine worker microbiome. We obtained unique samples from US swine workers, using a longitudinal study design to investigate temporal microbiome dynamics.

RESULTS: We observed a significant increase in bacterial DNA load on worker skin during the workday, with concurrent changes in the composition and abundance of microbial taxa, resistance genes, and mobile genetic elements. However, mandatory showering at the end of the workday partially returned the skin's microbiome and resistome to their original state.

CONCLUSIONS: These novel results from a human cohort demonstrate that existing biosecurity practices can ameliorate work-associated microbiome impacts.},
}

*Microbiota
*Skin/microbiology
Animals
Swine/microbiology
Humans
Farms
*Biosecurity
*Occupational Exposure
Female
Male
Adult
Bacteria/genetics/classification/isolation & purification
Longitudinal Studies
Animal Husbandry
Skin Microbiome

@article {pmid40720778,
year = {2025},
author = {Li, CN and Blumenthal, JA and Sick-Samuels, AC},
title = {Use and Stewardship of Molecular Testing for Diagnosis of Infectious Diseases: A Cross-Sectional Survey.},
journal = {Journal of the Pediatric Infectious Diseases Society},
volume = {},
number = {},
pages = {},
doi = {10.1093/jpids/piaf065},
pmid = {40720778},
issn = {2048-7207},
abstract = {Untargeted molecular tests are increasingly available for diagnosis of infectious diseases. In this national survey, plasma metagenomic next-generation sequencing had widespread use (89.8%), but disparate frequency from a few times ever (18.4%) to > weekly (9.6%). Respondents offered thoughtful insights into stewardship and future research needs.},
}

@article {pmid40720455,
year = {2025},
author = {Li, Z and Zhu, S and Jiang, J and Wang, Y and Zhou, Y and Lou, L and Xu, S and Li, S},
title = {Applying metagenomic next-generation sequencing to analyze infections in immunosuppressed patients with chronic kidney disease: A single-center retrospective study.},
journal = {Journal of infection in developing countries},
volume = {19},
number = {7},
pages = {1030-1038},
doi = {10.3855/jidc.20713},
pmid = {40720455},
issn = {1972-2680},
abstract = {INTRODUCTION: This retrospective study evaluated the diagnostic value and clinical application of metagenomic next-generation sequencing (mNGS) for detecting infections in immunosuppressed CKD patients.

METHODOLOGY: Data from immunosuppressed CKD patients who were suspected of having an infection and admitted to Jinling Hospital from 2018-2022 were retrospectively analyzed. The patients were divided into the conventional microbiological testing (CMT)-confirmed infection group (Group I), clinically diagnosed infection group (Group II), and exclusion of infection group (Group III), and the efficiencies of microbiological detection with mNGS and CMT were compared.

RESULTS: In the 303 patients included in this study, 2 (1, 3) types of immunosuppressants were used for a median duration of 7 (2, 50) months. In Group I, 38.79% of the mNGS results were completely consistent with the CMT results, 27.88% were partially consistent, and 33.33% were inconsistent. In Group II, 57.69% of the infecting pathogens were detected by mNGS. Furthermore, 2 patients in Group III had positive NGS results. mNGS outperformed CMT in terms of the time to a positive test and the detection of mixed or rare microbial pathogens (p < 0.05). The sensitivity and accuracy of the detection of infectious pathogens were greater for mNGS than for CMT (p = 0.014).

CONCLUSIONS: mNGS can improve the sensitivity and accuracy of infectious pathogen detection in immunosuppressed CKD patients. mNGS is a promising emerging technique for detecting pathogens in CKD patients, with potential benefits in speed and sensitivity, and may provide more diagnostic evidence for the detection of mixed, opportunistic, and rare infectious pathogens.},
}

@article {pmid40719990,
year = {2025},
author = {Naqvi, SAH and Umar, UUD and Rehman, AU},
title = {Beneficial communities from core bacterial microbiota of Oryza sativa L. soil and leaves perform dynamic role in growth promotion and suppression of bacterial leaf blight.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {8},
pages = {285},
pmid = {40719990},
issn = {1573-0972},
mesh = {*Oryza/microbiology/growth & development ; *Soil Microbiology ; *Plant Leaves/microbiology/growth & development ; Xanthomonas/pathogenicity/growth & development ; *Bacteria/classification/genetics/isolation & purification ; *Plant Diseases/microbiology/prevention & control ; *Microbiota/genetics ; Rhizosphere ; RNA, Ribosomal, 16S/genetics ; Pakistan ; Biological Control Agents ; Soil/chemistry ; Metagenomics ; Phylogeny ; },
abstract = {Bacterial leaf blight (BLB), caused by Xanthomonas oryzae pv. oryzae (Xoo), severely threatens global rice production, highlighting the urgent need for sustainable alternatives to chemical pesticides. This study investigates the rhizosphere and phyllosphere microbiomes of Oryza sativa in Punjab, Pakistan, to identify native biocontrol agents (BCAs) with potential to suppress BLB. Using 16S rRNA amplicon sequencing (V3-V9 regions), we analyzed soil and leaf samples from 10 agricultural districts. Microbial diversity, community structure, and functional potential were assessed via bioinformatics tools (QIIME 2, DADA2, PICRUSt2), with a focus on taxa antagonistic to Xoo. Healthy rhizospheres exhibited significantly higher alpha diversity (Shannon index: 6.8 vs. 4.2 in leaves; *p* < 0.001), dominated by copiotrophic taxa (Proteobacteria, Bacteroidetes) linked to organic inputs and root exudates. Diseased soils favored oligotrophic Actinobacteria and Chloroflexi. Functional metagenomics revealed enrichment of siderophore biosynthesis, antibiotic production, and nutrient-cycling genes in healthy soils. Antagonistic genera (Bacillus, Pseudomonas, Streptomyces) demonstrated chitinase and surfactin activity against Xoo, while diseased samples showed elevated Xanthomonas and Erwinia abundances correlating with BLB severity. Native BCAs outperformed non-native strains in colonization and nutrient competition, highlighting their adaptability to local agroecological conditions. Our findings position native BCAs as pivotal tools for BLB suppression and sustainable agriculture, reducing reliance on synthetic chemicals. Field trials confirmed that microbial consortia formulations reduced BLB incidence by 40% and increased yield by 18%. These findings highlight the potential of microbiome-driven strategies to mitigate BLB, reduce chemical reliance, and foster sustainable agricultural practices. Future work should integrate multi-omics approaches to optimize microbial solutions for climate resilience and scale their adoption through policy frameworks.},
}

*Oryza/microbiology/growth & development
*Soil Microbiology
*Plant Leaves/microbiology/growth & development
Xanthomonas/pathogenicity/growth & development
*Bacteria/classification/genetics/isolation & purification
*Plant Diseases/microbiology/prevention & control
*Microbiota/genetics
Rhizosphere
RNA, Ribosomal, 16S/genetics
Pakistan
Biological Control Agents
Soil/chemistry
Metagenomics
Phylogeny

@article {pmid40719501,
year = {2025},
author = {Keskey, R and Bluiminck, S and Sangwan, N and Meltzer, R and Lam, A and Thewissen, R and Zaborin, A and van Goor, H and Zaborina, O and Alverdy, J},
title = {Dietary impact on the gut resistome: western diet independently increases the prevalence of antibiotic resistance genes within the gut microbiota.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0276624},
doi = {10.1128/spectrum.02766-24},
pmid = {40719501},
issn = {2165-0497},
abstract = {Approximately half of surgical site infections are caused by pathogens resistant to the antibiotics used for prophylaxis. We recently demonstrated that when mice are fed a western diet (WD) that is high in fat and low in fiber, exposed to antibiotics, and undergo an otherwise recoverable surgery, they develop lethal sepsis associated with dissemination of multi-drug-resistant pathogens. Here, we hypothesized that a WD alone can drive the intestinal microbiome to become populated by antibiotic-resistant bacteria independent of exposure to antibiotics. The cecal microbiota response to antibiotics was determined utilizing Biolog Phenotype Microarrays in the presence of 48 different antibiotics. WD-fed mice had a significant increase in antibiotic resistance within their microbiome compared to mice on a standard low-fat, high-fiber diet (SD) including aminoglycosides, tetracyclines, cephalosporins, fluoroquinolones, and sulfamethoxazole. By metagenomic sequencing, there was an increase in the antibiotic resistance genes (ARGs) within the WD cecal microbiota, including CfxA2, ErmG, TetQ, and LnuC. After just 7 days of WD, the ARGs ErmG and CfxA2 were detectable within the stool. WD independent of antibiotic exposure increases the presence of ARGs within the gut microbiota independent of antibiotic exposure.IMPORTANCEAntibiotic resistance is a major challenge in healthcare and results in significant morbidity and mortality. Currently, half of surgical site infections are caused by pathogens resistant to antibiotics used for prophylaxis. In this study, we demonstrate that a western diet alone has the ability to increase the presence of antibiotic resistance genes within the gut microbiome. By understanding dietary influences on the gut resistome, we may improve our understanding of infections with antibiotic-resistant organisms and one day develop personalized antibiotic regimens based on an individual's gut resistome.},
}

@article {pmid40719460,
year = {2025},
author = {Tang, J and Baker, JL},
title = {The salivary virome during childhood dental caries.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0019825},
doi = {10.1128/msphere.00198-25},
pmid = {40719460},
issn = {2379-5042},
abstract = {While many studies have examined the bacterial taxa associated with dental caries, the most common chronic infectious disease, little is known about the caries-associated virome. In this study, the salivary viromes of 21 children with severe caries (>2 dentin lesions) and 23 children with healthy dentition were examined. A total of 2,485 viral metagenome-assembled genomes (vMAGs) were identified, binned, and quantified from the metagenomic assemblies. These vMAGs were mostly phages and represented 1,865 unique species-level viral operational taxonomic units (vOTUs), of which 478 appear to be novel. The metagenomes were also queried for all 3,858 unique species-level vOTUs of DNA viruses with a human host on NCBI Virus; however, all but Human betaherpesvirus 7 were at very low abundance in the saliva. The oral viromes of the children with caries exhibited significantly different beta diversity compared to the oral virome of the children with healthy dentition; several vOTUs predicted to infect Haemophilus and Neisseria were strongly correlated with health, and five vOTUs predicted to infect Saccharibacteria, Prevotella, and Veillonella were correlated with caries. Co-occurrence analysis indicated that the phage typically co-occurred with both their predicted hosts and with bacteria that were themselves associated with the same disease status. Overall, this study provided the sequences of 35 complete or nearly complete novel oral phages and illustrated the potential significance of the oral virome in the context of dental caries, which has been largely overlooked. This work represents an important step toward the identification and study of phage therapy candidates that treat or prevent caries pathogenesis.IMPORTANCEDental caries is the most common chronic infectious disease worldwide and is caused by dysbiosis of the oral microbiome featuring an increased abundance of acid-tolerant, acid-producing, and biofilm-forming bacteria. The oral microbiome also contains viruses; however, very little is known about the caries-associated virome. In this study, the salivary virome of children with severe caries was compared to the salivary virome of children with healthy dentition. The metagenomes contained a total of 1,865 unique species-level viral operational taxonomic units (vOTUs), of which 478 appeared to be novel. The viromes from the children with caries were significantly different than the viromes from the children with healthy teeth, and several health- and disease-associated vOTUs were identified. This study illustrated the potential importance of the oral virome in the context of dental caries and serves as a step towards a better understanding of oral inter-kingdom interactions and identification of potential phage-based caries therapeutics.},
}

@article {pmid40719366,
year = {2025},
author = {Wang, X and Wang, N and Gao, T and Zhang, Y and Fu, Z and Zhao, Y and Huang, Y and Zheng, X and Gao, X and Lu, L and Yang, L},
title = {Symptom-specific gut microbial and metabolic profiles in ADHD reveal SCFA deficiency as a Key pathogenic mechanism.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2537755},
doi = {10.1080/19490976.2025.2537755},
pmid = {40719366},
issn = {1949-0984},
mesh = {*Gastrointestinal Microbiome/physiology ; *Attention Deficit Disorder with Hyperactivity/microbiology/metabolism ; Animals ; Humans ; Mice ; Male ; Female ; *Fatty Acids, Volatile/metabolism ; Feces/microbiology/chemistry ; Fecal Microbiota Transplantation ; Child ; *Bacteria/classification/metabolism/genetics/isolation & purification ; Metabolome ; Adolescent ; Metabolomics ; },
abstract = {Previous evidence links gut microbiota to attention-deficit/hyperactivity disorder (ADHD) through the gut-brain axis. However, the specific microbiota contributing to symptoms remain unclear. To characterize the gut microbial profile related to different symptoms and explore the mediation mechanism between microbiota alterations and the core ADHD symptoms, we conducted shotgun metagenomic sequencing and fecal metabolomics analysis on 94 ADHD patients and 94 age- and gender-matched controls. Microbial characteristics of three subgroups exhibiting different ADHD core symptom presentations were analyzed. We developed a metabolic model and conducted causal mediation analyses to examine how metabolites connect the microbiota to the symptoms. Fecal microbiota transplantation in mice was employed to validate the findings. The redundancy analysis identified ADHD symptoms as environmental gradients and explained the changes in beta diversity (F = 1.345, pFDR = 0.015). Greater gut microbial alterations were observed in combined presentations (ADHD-C). Several beneficial bacteria involved in short-chain fatty acid synthesis were found to be downregulated, with Lactobacillus sanfranciscensis notably linked to all three core symptoms (p.adj = 1.04E-13; p.adj = 5.07E-07; p.adj = 2.61E-05). Various taxa, functional pathways, and metabolites associated with specific ADHD symptom domains were identified. Imidazoleacetic acid partially mediated the effects between Lactobacillus sanfranciscensis and inattention (p = 0.012). In mice subjected to feces from ADHD patients with a low abundance of Lactobacillus sanfranciscensis, treatment with this strain greatly improved both hyperactivity (t = 2.665, p = 0.0237) and inattention (t = 2.389, p = 0.0380), while acetate supplementation only alleviated inattention (t = 2.362, p = 0.0398). Our findings suggest that different ADHD symptoms were related to common and different gut microbiota and metabolites. Fecal microbiota transplantation in mice validated the hypothesis that gut microbial composition affects ADHD symptoms through metabolic alterations. This study provides more insight into the mechanisms underlying metabolic disturbances in ADHD and elucidates the role of gut microbiota in these processes.},
}

*Gastrointestinal Microbiome/physiology
*Attention Deficit Disorder with Hyperactivity/microbiology/metabolism
Animals
Humans
Mice
Male
Female
*Fatty Acids, Volatile/metabolism
Feces/microbiology/chemistry
Fecal Microbiota Transplantation
Child
*Bacteria/classification/metabolism/genetics/isolation & purification
Metabolome
Adolescent
Metabolomics

@article {pmid40719338,
year = {2025},
author = {Louca, S and Mullin, CE},
title = {Effects of Vacuum-Heat-Assisted Sample Desiccation on Microbiome Surveys.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e70020},
doi = {10.1111/1755-0998.70020},
pmid = {40719338},
issn = {1755-0998},
support = {2243038//US National Science Foundation/ ; },
abstract = {Sample preservation in the field and during transport can be a logistical challenge for microbiome surveys, particularly in remote areas. Sample desiccation eliminates the need for complicated cold chains and dangerous preservatives. However, the effects of desiccation on modern microbiome workflows such as gene-centric metagenomic profiling and metagenome-assembled genome (MAG) binning, remain poorly understood. In addition, most common desiccation tools such as lyophilisation cannot easily be deployed in the field. Here, we describe a proof-of-principle sample desiccator using vacuum and heat, specifically built for deployment in the field and exhibiting low power consumption and cost. We then test the effects of vacuum-heat-assisted sample desiccation followed by storage at room temperature, in comparison to conventional freezing, on multiple soil and animal faecal samples, via metagenomic and 16S rRNA amplicon sequencing. We consider multiple metrics related to the success of DNA extraction, sequencing, contig assembly, OTU clustering, gene annotation and MAG construction, as well as effects on inferred microbial community composition. We find that the impact of drying on considered success metrics was almost always either minor, non-significant or positive. For a subset of source materials we observed moderate but statistically significant differences in terms of inferred microbial taxonomic and genetic composition. We conclude that vacuum- and heat-assisted desiccation can be a useful, practical and cost-effective tool for microbiome field surveys, when a high consistency with frozen samples is not required.},
}

@article {pmid40719154,
year = {2025},
author = {Niitsu, T and Kataoka, T and Fukushima, K and Motooka, D and Shichino, S and Natsume-Kitatani, Y and Kitamura, H and Niwa, T and Baba, T and Okuzaki, D and Kumanogoh, A and Akira, S and Okudela, K and Ogura, T},
title = {Spatial transcriptomics identifies SPARC as a prognostic marker in interstitial lung diseases.},
journal = {The Journal of pathology},
volume = {},
number = {},
pages = {},
doi = {10.1002/path.6451},
pmid = {40719154},
issn = {1096-9896},
support = {JPMH20AC5001//Ministry of Health, Labour and Welfare/ ; //Cabinet Office of Japan Government for the Public/Private R&D Investment Strategic Expansion PrograM/ ; },
abstract = {Interstitial lung diseases (ILDs) encompass a diverse group of pulmonary disorders, with progressive fibrosis leading to poor prognosis. Here we aimed to identify key molecules involved in progressive fibrosis across various ILDs, using spatial transcriptomics (ST). ST analysis (Visium) was performed on lung cryobiopsy specimens from five patients with various ILDs. Two cases, rich in young fibrotic lesions, as defined by fibroblastic foci and destructive alveolar organization, were selected for spatial high-dimensional weighted gene coexpression network analysis (hdWGCNA) to identify key gene networks with biological significance in active fibrosis. We utilized public single-cell RNA sequencing datasets of various ILDs, performed enrichment analysis and trajectory-based differential expression analysis, and quantified cell-cell communication to evaluate the involvement of the spatially extracted module in fibrosis. Immunohistochemical staining of the extracted molecules was performed. Using hdWGCNA, we identified a distinct gene module (the SM2 module) enriched in young fibrotic lesions. The SM2 module was characterized by distinct features of fibroblast activation that were represented across various lesions. Key hub genes within this module, including COL1A2, COL3A1, COL1A1, and SPARC, formed a robust coexpression network. Immunohistochemical staining showed that SPARC, a component of the SM2 module, was highly expressed in young fibrotic lesions, but not in old scarring lesions, across various ILDs. To assess the prognostic significance of SPARC immunohistochemical expression, we extended our analysis to a cohort of 71 patients with unclassifiable ILDs (uILDs), a particularly heterogeneous subtype with unclear pathogenesis and limited treatment options. Higher SPARC levels in the upper, lower, or both lung lobes in uILD were significantly associated with poor overall survival. In summary, an integrated cross-disease approach using ST revealed key gene expression patterns central to active fibrosis and successfully identified SPARC as a potentially beneficial prognostic marker. © 2025 The Author(s). The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.},
}

@article {pmid40718818,
year = {2025},
author = {Luo, L and Chen, B and Zeng, S and Li, Y and Chen, X and Zhang, J and Guo, X and Li, S and Ruan, L and Zhu, S and Gao, C and Zhang, C and Li, T},
title = {Machine learning integrates region-specific microbial signatures to distinguish geographically adjacent populations within a province.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1586195},
pmid = {40718818},
issn = {1664-302X},
}

@article {pmid40718788,
year = {2025},
author = {Naccache, C and Ibrahim, C and Hassen, A and Mezghani Khemakhem, M},
title = {Metagenomics-based analysis of mobile genetic elements and antibiotic/metal resistance genes carried by treated wastewater.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19682},
pmid = {40718788},
issn = {2167-8359},
abstract = {Wastewater treatment plants in Tunisia are recognized as key locations for the spread of antibiotic and heavy metal resistance genes among bacteria. Despite the widespread presence of pollutants in these treatment systems, there is still a significant gap in our understanding of resistance dynamics. This study focused on analyzing the bacterial community and resistome-mobilome profiles of the Charguia wastewater treatment plant (WWTP). Using metagenomics sequencing, six samples from the influent, sludge, and effluent were thoroughly examined. Our research findings indicated the prevalence of Proteobacteria and high levels of Bacteroidota, Firmicutes, Campylobacterota, and Patescibacteria. After conducting a species level analysis, we identified important species such as Pseudomonas psychrophila, Pseudomonas fragi, Pseudomonas lundensis, Acinetobacter johnsonii, and Thiothrix unzii linked to antibiotic resistant genes (ARGs) like mdtA and merR1 and heavy metal resistance genes (MRGs), including czcA and cnrA. Our study illustrated the persistence of specific species in the effluent due to the co-occurrence of ARGs/MRGs and mobile genetic elements (MGE). Notably, IncQ and IncP were found to be associated with mdtA, mexR, arsR1, and merR. The conclusions drawn from our research suggest that the WWTP has been potentially effective in reducing multidrug resistance.},
}

@article {pmid40718417,
year = {2025},
author = {Liang, J and Peng, G and Luo, Y and Tang, J},
title = {Mild encephalitis/encephalopathy with reversible corpus callosum lesion associated with listeria infection with meningoencephalitis: a case report.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1568219},
pmid = {40718417},
issn = {2296-858X},
abstract = {BACKGROUND: Currently, Listeria monocytogenes (LM) meningoencephalitis is rare in immunocompetent individuals, and its association with mild encephalitis/encephalopathy with a reversible splenial lesion (MERS) is even more uncommon.

CASE PRESENTATION: We report a case of an immunocompetent adult female presenting with headache, fever, and vomiting, accompanied by hyponatremia and atypical splenial lesions of the corpus callosum on brain MRI. Both cerebrospinal fluid (CSF) metagenomic next-generation sequencing (mNGS) and culture confirmed LM infection, leading to a diagnosis of LM meningoencephalitis. The patient recovered completely after treatment with meropenem.

CONCLUSION: This case highlights distinct clinical manifestations, laboratory findings, imaging features, and therapeutic responses in immunocompetent patients compared to immunocompromised populations. The atypical radiological presentation and favorable outcome underscore the importance of early pathogen identification via advanced diagnostics like mNGS. Our findings provide valuable insights into the heterogeneity of LM infections and emphasize the need for heightened clinical vigilance even in immunologically normal hosts.},
}

@article {pmid40718415,
year = {2025},
author = {Guo, S and Liu, Q and Yan, J and Wang, J and Zhong, Y and Gao, F and Zhong, Y},
title = {An acute Q fever with vessel vasculitis: case report.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1584216},
pmid = {40718415},
issn = {2296-858X},
abstract = {BACKGROUND: Q fever (QF) is a relatively rare zoonotic infectious disease, and complications such as vasculitis and endocarditis are uncommon but severe. This article reports a case of acute QF complicated by vasculitis.

CASE PRESENTATION: The patient presented with a week of recurrent fever. Upon admission, inflammatory markers and liver transaminases were elevated, and a weak positive result for Chlamydia pneumoniae Immunoglobulin M (IgM) antibodies was detected. After treatment with levofloxacin and doxycycline, the fever persisted. Blood metagenomic next-generation sequencing (mNGS) suggested Coxiella species, raising suspicion for acute QF. The antibiotics were switched to moxifloxacin, but fever continued. Autoimmune tests showed positive antinuclear antibodies, and multiple blood cultures were negative. Further positron emission tomography/computed tomography (PET/CT) revealed inflammatory changes at the bifurcation of the right internal and external carotid arteries, as well as the ascending aorta, pulmonary arteries, and descending aorta, suggesting QF complicated by vasculitis. Treatment with methylprednisolone led to gradual resolution of the fever, and rechecked autoimmune antibodies turned negative. The patient did not experience further fever after discharge.

CONCLUSION: Currently, early recognition and diagnostic techniques for QF still require further improvement. As an infectious disease, timely treatment and vaccination for QF remain key areas of focus for future healthcare professionals.},
}

@article {pmid40715831,
year = {2025},
author = {Paloyan, A and Soghomonyan, T and Karapetyan, M and Grigoryan, H and Krüger, A and Cuskin, F and Marles-Wright, J and Burkhardt, C and Antranikian, G},
title = {A novel acidic laminarinase derived from Jermuk hot spring metagenome.},
journal = {Applied microbiology and biotechnology},
volume = {109},
number = {1},
pages = {172},
pmid = {40715831},
issn = {1432-0614},
support = {24LCG-2I019//State Committee of Higher Education and Science of MESCS RA/ ; 24LCG-2I019//State Committee of Higher Education and Science of MESCS RA/ ; 24LCG-2I019//State Committee of Higher Education and Science of MESCS RA/ ; 24LCG-2I019//State Committee of Higher Education and Science of MESCS RA/ ; 57442043//DAAD, Research Stays for University Academics and Scientists/ ; },
mesh = {*Hot Springs/microbiology ; *Metagenome ; Glucans/metabolism ; Cloning, Molecular ; Substrate Specificity ; Hydrogen-Ion Concentration ; Enzyme Stability ; Temperature ; *Cellulases/genetics/metabolism/chemistry/isolation & purification ; Amino Acid Sequence ; Phylogeny ; Hydrolysis ; *Bacteria/enzymology/genetics/classification ; },
abstract = {Laminarinase, an enzyme with a specific affinity for laminarin-a complex polysaccharide found in the cell walls of brown algae and select marine organisms-was investigated in this study. We cloned and characterized a gene encoding a putative glycoside hydrolase family 16 (GH16) laminarinase derived from the Jermuk hot spring metagenome. The resulting product, named Jermuk-LamM, represents a novel 1,3-β-D-glucanase with 48.1% amino acid sequence similarity to previously characterized GH16 family members catalogued in the NCBI database. To date, this stands as the sole described endo-1,3-β-D-glucanase from the Fidelibacterota phylum, which was recently reclassified from Marinimicrobia. Jermuk-LamM, identified as an acidic laminarinase, exhibits optimal enzymatic activity at pH 5.0 and a temperature of 55 °C, maintaining its function for a duration of at least 7 h. Jermuk-LamM is an enzyme that efficiently hydrolyzes both soluble and insoluble (1,3)-β-D-glucans, as well as (1,3;1,4)-β-D-glucans, with a marked preference for laminarin. This enzymatic activity facilitates the valorization of macroalgal biomass by predominantly producing monosaccharides and disaccharides. These hydrolysis products can subsequently be converted into energy carriers such as alcohol, methane, and hydrogen. The enzyme's specific activities, coupled with its resistance to various additives, render Jermuk-LamM a promising candidate for various industrial applications, encompassing the realms of biofuel and pharmaceutical production. KEY POINTS: • Jermuk hot springs have significant potential as a source of novel enzymes. • Jermuk-LamM has less than 50% amino acid similarity to known enzymes. • It is the first enzyme characterized from the Fidelibacterota phylum.},
}

*Hot Springs/microbiology
*Metagenome
Glucans/metabolism
Cloning, Molecular
Substrate Specificity
Hydrogen-Ion Concentration
Enzyme Stability
Temperature
*Cellulases/genetics/metabolism/chemistry/isolation & purification
Amino Acid Sequence
Phylogeny
Hydrolysis
*Bacteria/enzymology/genetics/classification

@article {pmid40715814,
year = {2025},
author = {Xiong, R and Aiken, E and Caldwell, R and Vernon, SD and Kozhaya, L and Gunter, C and Bateman, L and Unutmaz, D and Oh, J},
title = {AI-driven multi-omics modeling of myalgic encephalomyelitis/chronic fatigue syndrome.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
pmid = {40715814},
issn = {1546-170X},
support = {U54 NS105539/NS/NINDS NIH HHS/United States ; DP2 GM126893-01//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; U54 NS105539/NS/NINDS NIH HHS/United States ; U54 NS105539/NS/NINDS NIH HHS/United States ; U54 NS105539/NS/NINDS NIH HHS/United States ; },
abstract = {Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a chronic illness with a multifactorial etiology and heterogeneous symptomatology, posing major challenges for diagnosis and treatment. Here we present BioMapAI, a supervised deep neural network trained on a 4-year, longitudinal, multi-omics dataset from 249 participants, which integrates gut metagenomics, plasma metabolomics, immune cell profiling, blood laboratory data and detailed clinical symptoms. By simultaneously modeling these diverse data types to predict clinical severity, BioMapAI identifies disease- and symptom-specific biomarkers and classifies ME/CFS in both held-out and independent external cohorts. Using an explainable AI approach, we construct a unique connectivity map spanning the microbiome, immune system and plasma metabolome in health and ME/CFS adjusted for age, gender and additional clinical factors. This map uncovers altered associations between microbial metabolism (for example, short-chain fatty acids, branched-chain amino acids, tryptophan, benzoate), plasma lipids and bile acids, and heightened inflammatory responses in mucosal and inflammatory T cell subsets (MAIT, γδT) secreting IFN-γ and GzA. Overall, BioMapAI provides unprecedented systems-level insights into ME/CFS, refining existing hypotheses and hypothesizing unique mechanisms-specifically, how multi-omics dynamics are associated to the disease's heterogeneous symptoms.},
}

@article {pmid40715790,
year = {2025},
author = {Fortuin, J and den Haan, R},
title = {Identifying promoters to enhance heterologous gene expression in recombinant Saccharomyces cerevisiae strains cultivated on non-native substrates.},
journal = {Applied microbiology and biotechnology},
volume = {109},
number = {1},
pages = {173},
pmid = {40715790},
issn = {1432-0614},
support = {137967//National Research Foundation/ ; 137967//National Research Foundation/ ; },
mesh = {*Saccharomyces cerevisiae/genetics/metabolism/growth & development ; *Promoter Regions, Genetic ; Ethanol/metabolism ; Xylose/metabolism ; Fermentation ; Xylosidases/genetics/metabolism ; Lignin/metabolism ; Xylans/metabolism ; *Gene Expression ; Endo-1,4-beta Xylanases/genetics/metabolism ; Glucose/metabolism ; Metabolic Engineering ; Recombinant Proteins/genetics/metabolism ; Saccharomyces cerevisiae Proteins/genetics/metabolism ; },
abstract = {Efficient bioconversion of lignocellulosic biomass (LCB) to ethanol by Saccharomyces cerevisiae requires its engineering to express heterologous enzymes at titres high enough to make significant impacts on industrial consolidated bioprocessing (CBP). Promoters are required for this purpose, but are reportedly influenced by various environmental factors as well as the protein specific nature of expression, warranting the need for assessment under the conditions for which they are intended. Heterologous xylosidase- and xylanase-encoding genes (xln43_SED1 and xyn2) were individually cloned under transcriptional control of the SED1P and TDH3P promoters, and DIT1T terminator, and integrated into the genome of an a S. cerevisiae strain engineered for xylose utilization. Enzymatic assays were used to quantify the performance of the promoters when strains were cultivated on glucose (aerobically and micro-aerobically) and xylose. Additional strains containing both xln43_SED1 and xyn2 under different promoter combinations were then used to allow direct fermentation of beechwood xylan to ethanol in a CBP. The SED1P/DIT1T and TDH3P/DIT1T combinations significantly outperformed the benchmark ENO1P/T under all of the tested cultivation conditions, as well as with regard to growth trials on non-native substrates (xylo-oligosaccharides/XOS and beechwood xylan) and fermentations of beechwood xylan to ethanol. Overall, TDH3P was the best-performing promoter. This study demonstrates that heterologous metabolic pathways and CBP can be significantly enhanced by employing carefully selected promoters tailored to specific conditions. KEY POINTS: • Promoters are unpredictable and must be tested under their intended conditions. • TDH3P, SED1P, and DIT1T were effective in enhancing heterologous xylanase activity. • Optimized xylanolytic enzyme expression improved CBP of xylan to ethanol.},
}

*Saccharomyces cerevisiae/genetics/metabolism/growth & development
*Promoter Regions, Genetic
Ethanol/metabolism
Xylose/metabolism
Fermentation
Xylosidases/genetics/metabolism
Lignin/metabolism
Xylans/metabolism
*Gene Expression
Endo-1,4-beta Xylanases/genetics/metabolism
Glucose/metabolism
Metabolic Engineering
Recombinant Proteins/genetics/metabolism
Saccharomyces cerevisiae Proteins/genetics/metabolism

@article {pmid40702575,
year = {2025},
author = {Rubio-Garcia, A and E C Luiken, R and Marcelino, I and W A Rossen, J and H van Zeijl, J and A Wagenaar, J and L Zomer, A},
title = {Antimicrobial treatment affects the microbiome and resistome of both treated and untreated rehabilitating harbour seals (Phoca vitulina).},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {77},
pmid = {40702575},
issn = {2524-4671},
support = {202085/WT_/Wellcome Trust/United Kingdom ; 202085/WT_/Wellcome Trust/United Kingdom ; },
abstract = {BACKGROUND: Antimicrobial use has contributed to the alarming rise of antimicrobial resistance (AMR), posing a significant global health threat. Effective AMR control requires a One Health approach. The presence of AMR in the environment can challenge wildlife conservation, as resistance may reduce treatment success. This study investigates the impact of antimicrobial treatment on the gut microbiome and resistome of harbour seals (Phoca vitulina) undergoing rehabilitation at the Sealcentre Pieterburen, the Netherlands. A longitudinal cohort study was conducted with 200 seals, from which 127 were treated with antimicrobials and 73 were not treated. Samples were collected before and during rehabilitation, including before and after treatment and analysed using 16 S rRNA gene sequencing, shotgun metagenomics, and targeted qPCR.

RESULTS: We observed a significant but transient decrease in gut microbiome alpha diversity following antimicrobial treatment, with a recovery observed by the time of release. Beta diversity analysis indicated persistent changes in microbial composition post-treatment. An increase in antimicrobial resistance gene load was observed in treated seals, with some resistance genes remaining high at release. Untreated seals cohabiting with treated seals also exhibited increased resistance gene loads, suggesting exposure through environmental transmission.

CONCLUSIONS: Antimicrobial treatments in rehabilitation settings alter the gut microbiome and enhance AMR gene persistence in seals. The potential risk of antimicrobial resistance transmission among rehabilitating seals suggests the need for antimicrobial stewardship as the risk of antimicrobial resistance contamination by seals returning to the wild is currently unknown.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42523-025-00449-1.},
}

@article {pmid40672468,
year = {2025},
author = {Clark, JR and Tisza, MJ and Hammerquist, AL and Prakash, H and Munoz, JL and Surathu, A and Javornik Cregeen, SJ and Parker, NW and Cortes, MS and Hanson, B and Deegan, J and Boerwinkle, E and Barrozo, ER and Maresso, AW},
title = {Wastewater Parvovirus B19 Signal Amid Rising Maternal Cases.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
pmid = {40672468},
abstract = {We report widespread detection of parvovirus B19 in Texas Wastewater using hybrid-capture virome sequencing across 43 sites. Wastewater signal correlated with clinical cases at institutional, county, and state levels and preceded case surges by one month. Full-genome coverage enabled real-time mutation tracking, highlighting wastewater's utility for epidemiologic surveillance.},
}

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