@article {pmid40560509,
year = {2025},
author = {Andersen, C and Ebsen, TS and Thorup, CA and Reinholdt, KB and Kjaerulff, AMG and Udholm, N and Khalid, V and Madzak, A and Duez, C and Münch, H and Pauli, S and Danstrup, CS and Petersen, NK and Greve, T and Klug, TE},
title = {Next-generation sequencing of the tonsillar microbiome in severe acute tonsillitis: comparison with healthy controls and culture-based findings.},
journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology},
volume = {},
number = {},
pages = {},
pmid = {40560509},
issn = {1435-4373},
abstract = {PURPOSE: Previous culture-based studies suggest three significant pathogens in acute tonsillitis (AT): Streptococcus pyogenes, Fusobacterium necrophorum, and Streptococcus dysgalactiae. Next-generation sequencing (NGS) provides further insights into the human microbiome and may pinpoint additional pathogens in bacterial infections. We aimed to investigate the tonsillar microbiome and identify pathogens associated with AT by applying NGS to tonsillar swabs from patients with severe AT, comparing the findings with both healthy controls and culture-based results.

METHODS: Full-length sequencing of the 16S rRNA gene (16S tNGS) was performed on tonsillar swabs from 64 AT patients and 55 controls, who were prospectively enrolled at two Danish Ear-Nose-Throat Departments between June 2016 and December 2019.

RESULTS: The mean number of detected bacteria was significantly higher in patients analysed with 16S tNGS (36) than with culture methods (6.5, p < 0.001). The alpha diversity was lower in patients compared to controls (p < 0.001) and beta diversity showed separation of the two groups (p = 0.001). S. pyogenes (p = 0.001) and Bifidobacteriaceae (p = 0.002) were significantly more abundant in patients compared to controls. The three suggested pathogens were detected more frequently using 16S tNGS compared to culture: S. pyogenes (38% vs. 27%, p = 0.26), F. necrophorum (19% vs. 11%, p = 0.32), and S. dysgalactiae (14% vs. 11%, p = 0.79).

CONCLUSION: The tonsillar microbiome differed significantly between AT patients and healthy controls. Our findings confirm the role of S. pyogenes in AT, but did not identify additional likely pathogens. The addition of 16S tNGS to cultures increased the collective detection rate of three previously suggested pathogens from 48 to 70%.},
}

@article {pmid40560314,
year = {2025},
author = {Rojas-Chacón, JA and Echeverría-Beirute, F and Jiménez-Madrigal, JP and Varela-Benavides, I and Faggioli, V and Berkelmann, D and Gatica-Arias, A},
title = {Deciphering soil nematode-bacteria-fungi community composition and functional dynamics in coffee agroecosystems under conventional and sustainable management practices in Costa Rica.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {7},
pages = {220},
pmid = {40560314},
issn = {1573-0972},
support = {801-C3-501//UKRI-BBSRC Capacity Building for Bioinformatics in Latin America Network (CABANA-net) grant, between the Chan Zuckerberg Initiative (CZI) and the University of Costa Rica/ ; 801-C3-501//UKRI-BBSRC Capacity Building for Bioinformatics in Latin America Network (CABANA-net) grant, between the Chan Zuckerberg Initiative (CZI) and the University of Costa Rica/ ; 801-C3-501//UKRI-BBSRC Capacity Building for Bioinformatics in Latin America Network (CABANA-net) grant, between the Chan Zuckerberg Initiative (CZI) and the University of Costa Rica/ ; 2022-316296//The Chan Zuckerberg Initiative DAF/ ; 2022-316296//The Chan Zuckerberg Initiative DAF/ ; 2022-316296//The Chan Zuckerberg Initiative DAF/ ; },
mesh = {Costa Rica ; *Soil Microbiology ; Animals ; *Nematoda/classification/genetics/physiology ; Soil/chemistry/parasitology ; *Fungi/classification/genetics/isolation & purification ; *Bacteria/classification/genetics/isolation & purification ; Agriculture/methods ; *Coffee/growth & development ; Coffea/growth & development ; High-Throughput Nucleotide Sequencing ; },
abstract = {Understanding the interactions between soil bacteria, fungi, and nematodes in coffee agroecosystems is crucial for optimizing sustainable agriculture. This study investigated the composition and functional dynamics of these communities under conventional and sustainable management systems. Soil samples were collected from three major coffee-growing regions in Costa Rica, representing different agricultural regimes. Nematode community was analyzed using optical microscopy, while microbial communities were analyzed using high-throughput sequencing. In both cases, bioinformatic tools were used for functional prediction based on taxonomy.. Herbivorous nematodes dominated both systems, while bacterivores (Rhabditidae, Cephalobidae) and fungivores (Aphelenchoidae) were significantly more abundant in soils subject to sustainable practice (p < 0.05). Nematode maturity indices and food web diagnostics showed no significant differences between systems, even though metabolic footprints related to organic matter decomposition varied (p < 0.05). Bacterial communities were dominated by the phyla Proteobacteria, Acidobacteria, and Chloroflexi, while the fungal community was largely composed of Ascomycota (53.21% in both systems). The fungal genus Mortierella was particularly prevalent. Soil pH, along with Ca, Mg, K, and extractable acidity, influenced community composition. Functional profiles revealed higher gene abundances linked to nutrient and energy cycling in sustainable systems, particularly phosphorus and sulfur metabolism. Saprotroph-symbiotroph fungi were more common in sustainable soils, while pathotrophic fungi dominated conventional systems. This is the first comprehensive analysis of bacteria, fungi, and nematodes across different agricultural practices in coffee agroecosystems in Costa Rica.},
}

Costa Rica
*Soil Microbiology
Animals
*Nematoda/classification/genetics/physiology
Soil/chemistry/parasitology
*Fungi/classification/genetics/isolation & purification
*Bacteria/classification/genetics/isolation & purification
Agriculture/methods
*Coffee/growth & development
Coffea/growth & development
High-Throughput Nucleotide Sequencing

@article {pmid40560287,
year = {2025},
author = {Zhuang, Y and Lyu, T and Chen, Y and Li, W and Tang, L and Xian, SP and Yang, PF and Wang, L and Zhang, QQ and Mei, C and Lin, YJ and Yan, Z and Li, Z and He, JZ and Zeng, FM},
title = {Mechanistic insights into endometriosis: roles of Streptococcus agalactiae and L-carnitine in lesion development and angiogenesis.},
journal = {Angiogenesis},
volume = {28},
number = {3},
pages = {38},
pmid = {40560287},
issn = {1573-7209},
support = {202401AY070001-120//Yunnan Province Applied Basic Research Program Kunming Medical University Joint Project/ ; WYYXQN-2021016//the Excellent Young Researchers Program of the Fifth Affiliated Hospital of Sun Yat-sen University/ ; 2023080017//the Excellent Young Researchers Program of the Fifth Affiliated Hospital of Sun Yat-sen University/ ; 82102689//National Natural Science Foundation of China/ ; 2022A1515220187//The Guangdong Basic and Applied Basic Research Foundation/ ; 22qntd3502//Fundamental Research Funds for the Central Universities, Sun Yat-sen University/ ; 2018-016//Project of Guiyang Health and Family Planning Commission/ ; },
mesh = {Female ; Humans ; *Streptococcus agalactiae/metabolism ; Animals ; *Carnitine/metabolism/pharmacology ; *Neovascularization, Pathologic/microbiology/pathology/metabolism ; Mice ; *Endometriosis/microbiology/pathology/metabolism ; Adult ; *Streptococcal Infections/microbiology/pathology ; Cell Movement ; Angiogenesis ; },
abstract = {Retrograde menstruation is a widely recognized etiological factor for endometriosis (EMs); however, it is not the sole cause, as not all affected women develop EMs. Emerging evidence suggests a significant association between the vaginal microbiota and EMs. Nonetheless, the precise mechanisms by which microbial communities influence the pathophysiology and progression of EMs remain unclear. In this study, the cervical mucus from patients with EMs showed significantly greater microbial abundance compared with that of controls, with Streptococcus agalactiae (S. agalactiae) exhibiting the most substantial increase as determined by 16S rRNA gene sequencing. In a murine model, elevated S. agalactiae levels significantly increased the lesion number and colonization, whereas antibiotic treatment reduced lesion formation. Metabolomic analyses showed elevated L-carnitine levels in the cervical secretions and serum of patients with EMs, a finding corroborated in murine tissues. Exogenous L-carnitine administration similarly increased the number and weight of endometriotic lesions. Meanwhile, the inhibition of L-carnitine synthesis suppressed lesion formation induced by S. agalactiae. In vitro, both S. agalactiae and L-carnitine promoted EMs cell proliferation, migration, and invasion. L-carnitine synthesis inhibition attenuated cell motility stimulated by S. agalactiae. Mechanistically, S. agalactiae enhanced angiogenesis through L-carnitine by upregulating vascular endothelial growth factor expression and increasing human umbilical vein endothelial cell motility. These findings identify S. agalactiae as a key cervical microbiome component in EMs development and reveal a microbiota-metabolite-angiogenesis axis that may offer novel therapeutic targets.},
}

Female
Humans
*Streptococcus agalactiae/metabolism
Animals
*Carnitine/metabolism/pharmacology
*Neovascularization, Pathologic/microbiology/pathology/metabolism
Mice
*Endometriosis/microbiology/pathology/metabolism
Adult
*Streptococcal Infections/microbiology/pathology
Cell Movement
Angiogenesis

@article {pmid40560276,
year = {2025},
author = {Sharma, A and Bora, P},
title = {Engineering synthetic microbial communities to restructure the phytobiome for plant health and productivity.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {7},
pages = {228},
pmid = {40560276},
issn = {1573-0972},
mesh = {*Plants/microbiology ; *Microbiota ; Soil Microbiology ; Agriculture/methods ; Bacteria/genetics/metabolism ; *Synthetic Biology/methods ; *Microbial Consortia ; },
abstract = {Global agriculture stands at a critical juncture, facing the dual challenge of sustaining food production for a rapidly growing population while mitigating the environmental consequences of intensive farming. The overuse of chemical fertilizers and pesticides has accelerated soil degradation, biodiversity loss, and ecological imbalances, threatening long-term viability. Synthetic microbial communities (SynComs) have emerged as a promising approach to reshape plant-microbe interactions, offering a precise, scalable, and ecologically sustainable alternative to conventional agrochemicals. Unlike native microbial communities, which form naturally and vary with environmental conditions, SynComs are deliberately assembled consortium of multiple microbial strains selected for their complementary functions, ecological compatibility, and ability to perform targeted roles within a host or environment. By engineering microbes with targeted functional traits, SynComs enhance nutrient assimilation, bolster plant defence, and fortify resilience against biotic and abiotic stresses. The understanding of SynCom design, exploring their composition, functional dynamics, and mechanisms for optimizing plant health is crucial for effective synthesis and application, alongside cutting-edge computational tools and genomic databases that enable precision engineering of microbial communities. Despite their transformative potential, large-scale application of SynComs remains constrained by challenges related to field efficacy, regulatory frameworks, and long-term microbial persistence. Addressing these barriers through interdisciplinary research and policy innovation is imperative. As environmental microbiome moves towards sustainability-driven solutions, SynComs hold the key to revolutionizing farming practices, reducing chemical dependence, and ensuring global food security in an era of mounting environmental stressors.},
}

*Plants/microbiology
*Microbiota
Soil Microbiology
Agriculture/methods
Bacteria/genetics/metabolism
*Synthetic Biology/methods
*Microbial Consortia

@article {pmid40560225,
year = {2025},
author = {Li, T and Tian, Y and Wang, Y and Yang, J and Chen, Z and Li, Y},
title = {Elucidation of novel diagnostic biomarkers and therapeutic targets in colorectal carcinoma: an integrative approach leveraging multi-omics, computational biology, and single-cell sequencing technologies.},
journal = {Mammalian genome : official journal of the International Mammalian Genome Society},
volume = {},
number = {},
pages = {},
pmid = {40560225},
issn = {1432-1777},
support = {82104012, 82202950, 82303681//The National Natural Science Foundation of China/ ; 2021-I2M-1-042//the Chinese Academy of Medical Sciences Innovation Fund for Medical Sciences/ ; 3332022063//the Fundamental Research Funds for the Central Universities/ ; },
abstract = {This study employs a comprehensive, multi-layered analytical approach to comprehensively investigate the pathogenesis, diagnostic methodologies, and potential therapeutic targets of colorectal cancer. Integrating data from the Global Burden of Disease (GBD) database, transcriptomics, proteomics, and single-cell sequencing technologies, this study elucidates both the epidemiological characteristics and molecular mechanisms of colorectal cancer. Our findings indicate that VEGFA, ICAM1, and IL6R play prominent roles in cancer progression. Proteomics analysis has identified multiple potential drug targets, and molecular docking and dynamic simulations have provided a theoretical foundation for developing drugs targeting VEGFA. Multi-omics studies have revealed that colorectal cancer progression involves intricate microbiome-host interactions, metabolic regulation, and immune response mechanisms, with factors such as Clostridia, 4E-BP1, AIFM1, and CXCL5 exhibiting dual roles. These discoveries not only deepen our understanding of colorectal cancer pathogenesis but also offer novel insights for optimizing diagnostic and therapeutic strategies, thereby laying the groundwork for developing personalized treatment regimens. Future research should focus on further validating these findings and exploring their potential clinical applications.},
}

@article {pmid40560060,
year = {2025},
author = {Dinakis, E and Xu, C and Muralitharan, R and Jama, H and Xie, L and Leung, C and Mirabito Colafella, K and McArdle, Z and Salimova, E and Camargo Tavares, L and Snelson, M and Johnson, C and Gaspari, T and Mackay, C and O'Donnell, J and Marques, F},
title = {pH-sensor GPR68 plays a role in how dietary fibre lowers blood pressure in a preclinical model of hypertension.},
journal = {Clinical science (London, England : 1979)},
volume = {},
number = {},
pages = {},
doi = {10.1042/CS20243009},
pmid = {40560060},
issn = {1470-8736},
support = {102927, 105663, 106698//National Heart Foundation of Australia/ ; GTN2017382, GNT2017382, GNT1124288//National Health and Medical Research Council/ ; Not applicable//Sylvia and Charles Viertel Charitable Foundation/ ; },
abstract = {Dietary fibre lowers blood pressure (BP) via short-chain fatty acids, acidic metabolites released from fibre fermentation by bacteria in the large intestine. This acidic microenvironment may activate the pH-sensing receptor GPR68, primarily expressed in immune cells. Here, we aimed to investigate whether GPR68 confers the BP-lowering effects of a high-fibre diet in hypertension by regulating inflammatory responses. Baseline BP parameters were measured using telemetry in C57BL/6J wildtype (WT) and GPR68-deficient (Gpr68-/-) male and female mice. Moreover, male mice were fed a control or high-fibre diet following minipump implantation with saline or Angiotensin II (Ang II), where BP was measured weekly by tail-cuff. Cardiac ultrasounds, histological, flow cytometric and gut microbiome (16S) analyses were performed. No BP differences were detected in untreated male and female mice, irrespective of genotype. Similarly to WT mice, Gpr68-/- male mice were susceptible to Ang II-induced hypertension. High-fibre-fed WT mice exhibited blunted elevations in BP and improved cardiac collagen deposition and aortic elastin content compared to control-fed WT mice. These were not observed in high-fibre-fed Gpr68-/- mice. A high-fibre diet decreased pro-inflammatory renal and aortic immune cell counts independently of GPR68. Dietary fibre, rather than GPR68 or Ang II, was the primary factor influencing differences in the gut microbiota. This study provides novel insight into how the pH-sensing receptor GPR68 may be implicated in the protective effects of a high-fibre diet. However, these effects are likely immune-independent.},
}

@article {pmid40560035,
year = {2025},
author = {Shan, L and Xu, X and Huang, L and Li, D and Deng, Y and Xue, X and Guo, S and Huang, Y and Zhang, X and Yu, Y and Ma, L and Qian, K and Wang, J},
title = {A Novel nor@DHB Matrix for Direct Microbial Analysis in Lung Cancer Tissues.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e04038},
doi = {10.1002/advs.202504038},
pmid = {40560035},
issn = {2198-3844},
support = {2022YFC2406600//National Key Research and Development; and Technology Plan of the Ministry of Science/ ; 82302641//National Natural Science Foundation of China/ ; 82472771//National Natural Science Foundation of China/ ; 23XD1423200//Science and Technology Commission of Shanghai Municipality/ ; 21140902800//Science and Technology Commission of Shanghai Municipality/ ; YG2022ZD024//Shanghai Jiao Tong University STAR Grant/ ; },
abstract = {Dynamic changes occurring in the lung microbiota can impact the initiation, progression, and prognosis of lung cancer (LC). Consequently, the development of suitable intratumoral microbiota analysis methods is crucial. Although matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) involves straightforward operations and provides precise results, the "direct smear method" limits the identification of bacterial subspecies. Furthermore, the issue of inadequate quantification with MALDI MS renders it unsuitable for direct analysis of intratumoral bacteria. To address these challenges, a novel ionic liquid in this study is employed, called norharmane conjugated to 2,5-dihydroxybenzoic acid (Nor@DHB) for the direct detection of intratumoral bacteria using MALDI MS. Because gram-negative bacteria are dominant within cancer cells, lipid A is selected as the chemical fingerprint for bacterial identification. The results demonstrated that using Nor@DHB can enhance the lipid A signal by an order of magnitude and achieved a good linear relationship within a concentration range of 0.01-80 ng mL[-1]. Here, this method is successfully applied to the direct analysis of lipid A in actual clinical samples. Subsequent machine learning and nomogram models further confirmed the correlation between characteristic lipid A ions and LC patient clinicopathological features, which are further validated through both in vitro and in vivo experiments.},
}

@article {pmid40559977,
year = {2025},
author = {Tomuța, RA and Moldovan, AF and Matiș, L and Maris, L and Ghitea, TC and Banica, F},
title = {The Paradox of Clean Eating: Neuroactive Dysbiosis and Pesticide Residues in Fruit- and Vegetable-Based Diets.},
journal = {Toxics},
volume = {13},
number = {6},
pages = {},
doi = {10.3390/toxics13060504},
pmid = {40559977},
issn = {2305-6304},
support = {410068//University of Oradea/ ; },
abstract = {(1) Background: Exposure to pesticide residues through food remains a critical issue in public health, especially given their potential cumulative neurotoxic effects. (2) Methods: This study investigated the presence of pesticide residues in commonly consumed vegetables, fruits, and cereals based on official laboratory reports and evaluated the intestinal microbiome profiles of individuals whose diets consisted of over 50% plant-based foods. (3) Results: Analytical results from accredited laboratories in Romania demonstrated that all tested food samples were compliant with European regulations (Regulation (EC) 396/2005), with either undetectable or below-quantification-limit pesticide residues. However, organophosphates such as chlorpyrifos and diazinon were frequently tested, indicating persistent regulatory concern due to their known neurotoxic potential. A parallel analysis of stool samples revealed significant imbalances in neuroactive gut bacteria, including consistently low levels of Bifidobacterium and Lactobacillus species, and elevated levels of Oscillibacter and Alistipes, which are implicated in modulating GABA and serotonin pathways. Markers of proinflammatory activity, such as LPS-positive bacteria and histamine producers, were also elevated. (4) Conclusions: These findings suggest that even in diets rich in plant-based foods, microbial dysbiosis with neuroactive relevance can occur, potentially linked to environmental or dietary factors. The study underscores the need for a comprehensive evaluation of food safety and microbiome function as interconnected determinants of neurological health.},
}

@article {pmid40559883,
year = {2025},
author = {Jasemi, S and Molicotti, P and Fais, M and Cossu, I and Simula, ER and Sechi, LA},
title = {Biological Mechanisms of Enterotoxigenic Bacteroides fragilis Toxin: Linking Inflammation, Colorectal Cancer, and Clinical Implications.},
journal = {Toxins},
volume = {17},
number = {6},
pages = {},
doi = {10.3390/toxins17060305},
pmid = {40559883},
issn = {2072-6651},
support = {legge 22//Regione Autonoma della Sardegna legger regionale 2022/ ; },
mesh = {Humans ; *Bacterial Toxins/toxicity/metabolism/chemistry ; *Colorectal Neoplasms/microbiology ; *Metalloendopeptidases/toxicity/metabolism/chemistry ; Animals ; *Bacteroides fragilis/pathogenicity/metabolism ; *Inflammation/microbiology ; *Bacteroides Infections/microbiology ; },
abstract = {Enterotoxigenic Bacteroides fragilis (ETBF) has emerged as a gut microbiome pathogen that can promote intestinal inflammation and contribute to colorectal cancer (CRC). Its principal virulence factor, the Bacteroides fragilis toxin (BFT), is a zinc-dependent metalloprotease that disrupts epithelial barrier integrity, initiates inflammatory signaling pathways, and enhances epithelial proliferation. Although growing evidence supports a link between ETBF and CRC, some inconsistencies across studies highlight the need for further investigation into the molecular mechanisms underpinning BFT-mediated pathogenesis. This review examines the biological structure and activity of BFT, with a focus on its role in epithelial injury, inflammatory responses, and tumorigenesis. In addition, we discuss current challenges in the detection and characterization of ETBF and BFT, including technical limitations in clinical diagnostics and methodological variability across studies. Recent advances in multi-omics technologies, molecular diagnostics, nanobody-based detection platforms, and probiotic intervention are also highlighted as promising avenues for improving ETBF identification and therapeutic targeting. Future research integrating systematic molecular profiling with clinical data is essential to enhance diagnostic accuracy, elucidate pathophysiological mechanisms, and develop effective interventions against ETBF-associated diseases.},
}

Humans
*Bacterial Toxins/toxicity/metabolism/chemistry
*Colorectal Neoplasms/microbiology
*Metalloendopeptidases/toxicity/metabolism/chemistry
Animals
*Bacteroides fragilis/pathogenicity/metabolism
*Inflammation/microbiology
*Bacteroides Infections/microbiology

@article {pmid40559850,
year = {2025},
author = {Shi, L and Niu, QJ and Xu, HH and Huang, YX and Zhao, YW and Refaie, A and Sun, LH and Deng, ZC},
title = {Dietary Supplementation of Zinc Oxide Quantum Dots Protective Against Clostridium perfringens Induced Negative Effects in Broilers.},
journal = {Toxins},
volume = {17},
number = {6},
pages = {},
doi = {10.3390/toxins17060272},
pmid = {40559850},
issn = {2072-6651},
support = {2023TZXD038//Key R&D Program of Shandong Province, China/ ; 2662023DKPY002//Fundamental Research Funds for the Central Universities/ ; NA//a research gift from Sichuan Chelota Biotech Corporation Limited/ ; },
mesh = {Animals ; *Zinc Oxide/administration & dosage/pharmacology ; *Chickens/growth & development ; *Quantum Dots/administration & dosage ; *Clostridium perfringens ; *Clostridium Infections/veterinary/microbiology/prevention & control ; *Poultry Diseases/microbiology/prevention & control ; *Dietary Supplements ; Gastrointestinal Microbiome/drug effects ; Intestines/drug effects/microbiology/pathology ; Animal Feed ; },
abstract = {Clostridium perfringens is a major cause of necrotizing enteritis in chickens. This study aimed to investigate the effects of zinc oxide quantum dots (ZnO-QDs) on growth performance, redox status, and gut microbiota in broilers challenged with C. perfringens. A total of 320 1-day-old chicks were divided into five groups: negative control (NC) without treatment; positive control (PC) infected with C. perfringens; and the other three groups (40, 80, and 120 Zn) were given ZnO-QDs at doses of 40, 80, and 120 mg/kg, respectively, under C. perfringens infection, respectively. The results show that, compared to the NC group, the PC group exhibited negative effects on growth performance, intestinal morphology, and antioxidant status in broilers. However, compared to the PC group, 120 mg Zn increased (p < 0.05) the body weight of broilers at 21 days, while 40 mg Zn reduced (p < 0.05) serum diamine oxidase activity. The intestinal macroscopic evaluation showed that the PC group had the highest lesion scores, whereas the 120 mg Zn group exhibited the lowest lesion score. Meanwhile, compared to the PC group, the 40 mg Zn group had higher (p < 0.05) CAT and GPX activities and a lower (p < 0.05) MDA concentration. Moreover, the 40 mg Zn group up-regulated (p < 0.05) the gene expression of Cathelicidin-1, IL-10, Claudin-1, and MLCK in the jejunum. Furthermore, the 120 mg Zn group increased (p < 0.05) the abundance of Blautia, Parasutterella, and Lachnospiraceae FCS020 in the cecum. In conclusion, ZnO-QDs exerted a beneficial effect on improving growth performance and overall health in broilers under C. perfringens infection, potentially by regulating redox balance and gut microbiota.},
}

Animals
*Zinc Oxide/administration & dosage/pharmacology
*Chickens/growth & development
*Quantum Dots/administration & dosage
*Clostridium perfringens
*Clostridium Infections/veterinary/microbiology/prevention & control
*Poultry Diseases/microbiology/prevention & control
*Dietary Supplements
Gastrointestinal Microbiome/drug effects
Intestines/drug effects/microbiology/pathology
Animal Feed

@article {pmid40559796,
year = {2025},
author = {Popov, IV and Peshkova, DA and Lukbanova, EA and Tsurkova, IS and Emelyantsev, SA and Krikunova, AA and Malinovkin, AV and Chikindas, ML and Ermakov, AM and Popov, IV},
title = {Gut Microbiota Dynamics in Hibernating and Active Nyctalus noctula: Hibernation-Associated Loss of Diversity and Anaerobe Enrichment.},
journal = {Veterinary sciences},
volume = {12},
number = {6},
pages = {},
doi = {10.3390/vetsci12060559},
pmid = {40559796},
issn = {2306-7381},
support = {23-14-00316//Russian Science Foundation/ ; 075-10-2025-017//Ministry of Science and Higher Education of the Russian Federation/ ; },
abstract = {Hibernation in mammals entails profound physiological changes that are known to impact host-associated microbial communities, yet its effects on the gut microbiota of synanthropic bats remain underexplored. In this study, we investigated the gut bacterial composition and diversity of Nyctalus noctula before and during hibernation using high-throughput 16S rRNA amplicon sequencing. Fecal samples from individually banded bats were collected under controlled conditions at a rehabilitation center and analyzed for alpha and beta diversity, as well as differential taxonomic abundance. Hibernation was associated with a marked reduction in microbial diversity according to the Shannon and Simpson indices and a distinct restructuring of gut communities based on the Bray-Curtis dissimilarity index. Active bats exhibited a diverse microbiota enriched in facultative anaerobes, including Lactococcus, Enterococcus, and Escherichia-Shigella, while hibernating individuals were dominated by obligate anaerobes, such as Romboutsia and Paeniclostridium. These findings suggest a contraction and functional specialization of the gut microbiota during torpor, potentially reflecting adaptations to fasting, hypothermia, and reduced gut motility. Our results demonstrate that the bat's gut microbiome is highly responsive to physiological status and underscore the importance of microbial ecology for understanding the host's energy balance and health under seasonal contexts.},
}

@article {pmid40559778,
year = {2025},
author = {Nishigaki, A and Marchesi, JR and Previdelli, RL},
title = {Faecal Microbiota Transplantation as an Adjuvant Treatment for Extraintestinal Disorders: Translating Insights from Human Medicine to Veterinary Practice.},
journal = {Veterinary sciences},
volume = {12},
number = {6},
pages = {},
doi = {10.3390/vetsci12060541},
pmid = {40559778},
issn = {2306-7381},
abstract = {Faecal microbiota transplantation (FMT) has emerged as a transformative therapy in human medicine, particularly for managing recurrent Clostridioides difficile infections and other gastrointestinal (GI) disorders. Beyond the GI tract, FMT has shown potential in addressing extraintestinal conditions in people, including metabolic, immune-mediated, dermatological, neurological, and infectious diseases. Research in people has highlighted its efficacy in decolonising multidrug-resistant organisms in infection, mitigating autoimmune diseases, and improving outcomes in metabolic disorders such as obesity and diabetes. Furthermore, FMT has also been linked to enhanced responses to immunotherapy in cancer and improved management of hepatic and renal conditions. These findings underscore the intricate connections between the gut microbiome and systemic health, opening novel therapeutic avenues. In veterinary medicine, while FMT has demonstrated benefits for GI disorders, its application in extraintestinal diseases remains largely unexplored. Emerging evidence suggests that conditions such as atopic dermatitis, chronic kidney disease, immune-mediated diseases, and behavioural disorders in companion animals could benefit from microbiome-targeted therapies. However, significant gaps in knowledge persist, particularly regarding the long-term safety and efficacy for veterinary applications. This review synthesises findings from human medicine to assess their relevance for veterinary applications and future research.},
}

@article {pmid40559763,
year = {2025},
author = {Sun, N and Xie, L and Chao, J and Xiu, F and Zhai, H and Zhou, Y and Yu, X and Shui, Y},
title = {Study on the Correlation Between Aggressive Behavior and Gut Microbiota and Serum Serotonin (5-HT) in Working Dogs.},
journal = {Veterinary sciences},
volume = {12},
number = {6},
pages = {},
doi = {10.3390/vetsci12060526},
pmid = {40559763},
issn = {2306-7381},
support = {No.D2024005//Fundamental Research Funds for the Central Universities/ ; },
abstract = {Aggressive canine behavior poses a significant threat to public health. Understanding aggressive behavior is crucial for canine socialization and human-dog interactions. This study conducted an exploratory analysis of working dogs to investigate changes in gut microbiota and neurotransmitters associated with aggressive behavior. Notably, it represents the first research to systematically differentiate canine aggression into offensive and defensive subtypes for investigation. In this study, 56 working dogs from three regions of China, comprising different breeds (11 Spaniels, 13 German Shepherds, and 32 Belgian Malinois), aged 4.89 ± 1.54 years, and of both sexes (38 males and 18 females), were assessed and grouped for aggressive behavior using a C-BARQ-based questionnaire. Then, 16S rRNA sequencing and ELISA were employed to compare differences in gut microbiota and serotonin concentrations between aggressive (n = 35) and non-aggressive (n = 21) groups, as well as between offensive (n = 26) and defensive (n = 9) aggression subgroups. β-diversity analysis confirmed no significant correlation between aggressive behavior and gut microbiota composition (p > 0.05), suggesting a limited role of gut microbiota in modulating host behavior. Comparative analysis of gut microbiota composition revealed no significant differences in phylum-level abundance among different aggression types (p > 0.05). Notably, the non-aggressive group exhibited significantly higher relative abundances of Escherichia-Shigella, Erysipelotrichaceae_UCG-003, and Clostridium_sensu_stricto_1 compared to the aggressive group (p < 0.05). Random forest analysis identified Lactobacillus as a biomarker for canine aggressive behavior and Turicibacter as a discriminatory factor between offensive and defensive aggression. The results demonstrated a strong correlation between aggression and 5-HT neurotransmission. Serum serotonin levels were significantly lower in both the defensive (39.92 ± 2.58 ng/mL) and offensive (50.07 ± 3.90 ng/mL) aggression groups compared to the non-aggressive group (59.49 ± 2.76 ng/mL), with the lowest levels found in defensively aggressive dogs. The defensive group showed significantly lower serotonin levels than the offensive group (p < 0.001). The results demonstrate that different behavioral phenotypes in aggressive dogs lead to distinct gut microbiome compositions. This suggests that microbiome analysis may facilitate early diagnosis and preventive intervention before aggressive behavior manifests. As such, 5-HT shows potential as a monitoring tool for diagnosing canine aggression, with significant practical applications in canine behavior management.},
}

@article {pmid40559651,
year = {2025},
author = {Wimmer, BC and Dwan, C and De Medts, J and Duysburgh, C and Rotsaert, C and Marzorati, M},
title = {Undaria pinnatifida Fucoidan Enhances Gut Microbiome, Butyrate Production, and Exerts Anti-Inflammatory Effects in an In Vitro Short-Term SHIME[®] Coupled to a Caco-2/THP-1 Co-Culture Model.},
journal = {Marine drugs},
volume = {23},
number = {6},
pages = {},
doi = {10.3390/md23060242},
pmid = {40559651},
issn = {1660-3397},
support = {n.a.//Marinova Pty Ltd., 249 Kennedy Drive, Cambridge, TAS 7170, Australia/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Polysaccharides/pharmacology/isolation & purification ; *Undaria/chemistry ; *Anti-Inflammatory Agents/pharmacology ; Caco-2 Cells ; Coculture Techniques ; *Butyrates/metabolism ; THP-1 Cells ; Colon/microbiology/drug effects ; Feces/microbiology ; Cytokines/metabolism ; Adult ; Fatty Acids, Volatile/metabolism ; Edible Seaweeds ; },
abstract = {Fucoidans have demonstrated a wide range of bioactivities including immune modulation and benefits in gut health. To gain a deeper understanding on the effects of fucoidan from Undaria pinnatifida (UPF) on the colonic microbiome, the short-term Simulator of the Human Intestinal Microbial Ecosystem[®], a validated in vitro gut model, was applied. Following a three-week intervention period on adult faecal samples from three healthy donors, microbial community activity of the colonic microbiota was assessed by quantifying short-chain fatty acids while composition was analysed utilising 16S-targeted Illumina sequencing. Metagenomic data were used to describe changes in community structure. To assess the secretion of cytokines, co-culture experiments using Caco-2 and THP1-Blue™ cells were performed. UPF supplementation over a three-week period had a profound butyrogenic effect while also enriching colonic microbial diversity, consistently stimulating saccharolytic genera, and reducing genera linked with potentially negative health effects in both regions of the colon. Mild immune modulatory effects of UPF were also observed. Colonic fermentation of UPF showed anti-inflammatory properties by inducing the secretion of the anti-inflammatory cytokines IL-6 and IL-10 in two out of three donors in the proximal and distal colon. In conclusion, UPF supplementation may provide significant gut health benefits.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Polysaccharides/pharmacology/isolation & purification
*Undaria/chemistry
*Anti-Inflammatory Agents/pharmacology
Caco-2 Cells
Coculture Techniques
*Butyrates/metabolism
THP-1 Cells
Colon/microbiology/drug effects
Feces/microbiology
Cytokines/metabolism
Adult
Fatty Acids, Volatile/metabolism
Edible Seaweeds

@article {pmid40559436,
year = {2025},
author = {Domilescu, I and Miutescu, B and Horhat, FG and Popescu, A and Nica, C and Ghiuchici, AM and Gadour, E and Sîrbu, I and Hutanu, D},
title = {Gut-Microbiome Signatures Predicting Response to Neoadjuvant Chemoradiotherapy in Locally Advanced Rectal Cancer: A Systematic Review.},
journal = {Metabolites},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/metabo15060412},
pmid = {40559436},
issn = {2218-1989},
abstract = {BACKGROUND AND OBJECTIVES: Rectal cancer management increasingly relies on watch-and-wait strategies after neoadjuvant chemoradiotherapy (nCRT). Accurate, non-invasive prediction of pathological complete response (pCR) remains elusive. Emerging evidence suggests that gut-microbiome composition modulates radio-chemosensitivity. We systematically reviewed primary studies that correlated baseline or on-treatment gut-microbiome features with nCRT response in locally advanced rectal cancer (LARC).

METHODS: MEDLINE, Embase and PubMed were searched from inception to 30 April 2025. Eligibility required (i) prospective or retrospective human studies of LARC, (ii) faecal or mucosal microbiome profiling by 16S, metagenomics, or metatranscriptomics, and (iii) response assessment using tumour-regression grade or pCR. Narrative synthesis and random-effects proportion meta-analysis were performed where data were homogeneous.

RESULTS: Twelve studies (n = 1354 unique patients, median sample = 73, range 22-735) met inclusion. Four independent machine-learning models achieved an Area Under the Receiver Operating Characteristic curve AUROC ≥ 0.85 for pCR prediction. Consistently enriched taxa in responders included Lachnospiraceae bacterium, Blautia wexlerae, Roseburia spp., and Intestinimonas butyriciproducens. Non-responders showed over-representation of Fusobacterium nucleatum, Bacteroides fragilis, and Prevotella spp. Two studies linked butyrate-producing modules to radiosensitivity, whereas nucleotide-biosynthesis pathways conferred resistance. Pooled pCR rate in patients with a "butyrate-rich" baseline profile was 44% (95% CI 35-54) versus 21% (95% CI 15-29) in controls (I[2] = 18%).

CONCLUSIONS: Despite heterogeneity, convergent functional and taxonomic signals underpin a microbiome-based radiosensitivity axis in LARC. Multi-centre validation cohorts and intervention trials manipulating these taxa, such as prebiotics or live-biotherapeutics, are warranted before clinical deployment.},
}

@article {pmid40559414,
year = {2025},
author = {Moustakli, E and Stavros, S and Katopodis, P and Potiris, A and Drakakis, P and Dafopoulos, S and Zachariou, A and Dafopoulos, K and Zikopoulos, K and Zikopoulos, A},
title = {Gut Microbiome Dysbiosis and Its Impact on Reproductive Health: Mechanisms and Clinical Applications.},
journal = {Metabolites},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/metabo15060390},
pmid = {40559414},
issn = {2218-1989},
abstract = {The human gut microbiome is integral to maintaining systemic physiological balance, with accumulating evidence emphasizing its critical role in reproductive health. This review investigates the bidirectional interactions between the gut microbiota and the female reproductive system, mediated by neuroendocrine, immune, and metabolic pathways, constituting the gut-reproductive axis. Dysbiosis, characterized by microbial imbalance, has been linked to reproductive disorders such as polycystic ovary syndrome (PCOS), endometriosis, infertility, impaired spermatogenesis, and pregnancy complications. These associations can be explained by immunological dysregulation, systemic inflammation, altered sex hormone metabolism, and hypothalamic-pituitary-gonadal (HPG) axis disturbances. This review aims to clarify the molecular and cellular mechanisms underpinning gut-reproductive interactions and to evaluate the feasibility of microbiome-targeted therapies as clinical interventions for improving reproductive outcomes.},
}

@article {pmid40559413,
year = {2025},
author = {Malcangi, G and Marinelli, G and Inchingolo, AD and Trilli, I and Ferrante, L and Casamassima, L and Nardelli, P and Inchingolo, F and Palermo, A and Inchingolo, AM and Dipalma, G},
title = {Salivaomics: New Frontiers in Studying the Relationship Between Periodontal Disease and Alzheimer's Disease.},
journal = {Metabolites},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/metabo15060389},
pmid = {40559413},
issn = {2218-1989},
abstract = {BACKGROUND: This study explores the link between oral biofluids, microbial dysbiosis, and Alzheimer's disease (AD), highlighting saliva and gingival crevicular fluid (GCF) as non-invasive diagnostic sources. AD onset and progression appear to be influenced not only by genetic and environmental factors but also by changes in the oral microbiome and related inflammatory and metabolic alterations. As global populations age, the incidence of AD is projected to rise significantly. Emerging evidence implicates the oral microbiome and salivary metabolites in neurodegenerative pathways, suggesting that oral health may mirror or influence brain pathology.

MATERIALS AND METHODS: A systematic review of recent multi-omics studies was performed, focusing on salivary and GCF analysis in patients with AD, those with mild cognitive impairment (MCI), and cognitively healthy individuals. Databases searched included PubMed, Web of Science, and Scopus, following PRISMA guidelines.

RESULTS: Across the 11 included studies, significant alterations were reported in both the salivary microbiome and metabolome in AD patients. Notable microbial shifts involved increased abundance of Veillonella parvula and Porphyromonas gingivalis, while key metabolites such as L-tyrosine, galactinol, and mannitol were consistently dysregulated. These biomarkers correlated with cognitive performance and systemic inflammation.

CONCLUSIONS: Oral biofluids represent promising, accessible sources of biomarkers for early AD detection. Multi-omics integration reveals the oral-brain axis as a potential target for diagnosis, monitoring, and therapeutic strategies.},
}

@article {pmid40559396,
year = {2025},
author = {Corral-Guerrero, IA and Martínez-Medina, AE and Alvarado-Mata, LY and Chávez, ACF and Muñoz-García, R and Luévanos-Escareño, MP and Sosa-Martínez, JD and Castro-Alonso, MJ and Nimmakayala, P and Reddy, UK and Balagurusamy, N},
title = {Capsaicin as a Microbiome Modulator: Metabolic Interactions and Implications for Host Health.},
journal = {Metabolites},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/metabo15060372},
pmid = {40559396},
issn = {2218-1989},
support = {2025-03710//the United States Department of Agriculture/ ; 2023-09267//National Institute of Food and Agriculture (USDA-NIFA)/ ; 2242771//the National Science Foundation (NSF)/ ; },
abstract = {Background/Objectives: Capsaicin is the principal pungent compound in chili peppers and is increasingly recognized as a multifunctional phytochemical with systemic effects beyond its sensory properties. It has been linked to metabolic regulation, neuroprotection, inflammation control, and cancer modulation. This review aims to provide an integrative synthesis of capsaicin's metabolism, its interaction with the gut microbiome, and its physiological implications across organ systems. Methods: We conducted a critical literature review of recent in vivo and in vitro studies exploring capsaicin's metabolic fate, biotransformation by host enzymes and gut microbes, tissue distribution, and molecular pathways. The literature was analyzed thematically to cover gastrointestinal absorption, hepatic metabolism, microbiota interactions, and systemic cellular responses. Results: Capsaicin undergoes extensive hepatic metabolism, producing hydroxylated and dehydrogenated metabolites that differ in transient receptor potential vanilloid type 1 (TRPV1) receptor affinity and tissue-specific bioactivity. It crosses the blood-brain barrier, alters neurotransmitter levels, and accumulates in brain regions involved in cognition. In addition to its systemic effects, capsaicin appears to undergo microbial transformation and influences gut microbial composition, favoring short-chain fatty acid producers and suppressing pro-inflammatory taxa. These changes contribute to anti-obesity, anti-inflammatory, and potentially anticancer effects. Dose-dependent adverse outcomes, such as epithelial damage or tumor promotion, have also been observed. Conclusions: Capsaicin represents a diet-derived bioactive molecule whose systemic impact is shaped by dynamic interactions between host metabolism and the gut microbiota. Clarifying its biotransformation pathways and context-specific effects is essential for its safe and effective use in metabolic and neurological health strategies.},
}

@article {pmid40559387,
year = {2025},
author = {Zong, J and Wu, H and Hu, X and Yao, A and Zhu, W and Dou, G and Liu, S and Zhu, X and Gu, R and Sun, Y and Wu, Z and Wang, S and Gan, H},
title = {Plasma and Fecal Metabolites Combined with Gut Microbiome Reveal Systemic Metabolic Shifts in [60]Co Gamma-Irradiated Rats.},
journal = {Metabolites},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/metabo15060363},
pmid = {40559387},
issn = {2218-1989},
abstract = {Background: High-dose γ-ray exposure (≥7 Gy) in nuclear emergencies induces life-threatening acute radiation syndrome, characterized by rapid hematopoietic collapse (leukocytes <0.5 × 10[9]/L) and gastrointestinal barrier failure. While clinical biomarkers like leukocyte depletion guide current therapies targeting myelosuppression, the concomitant metabolic disturbances and gut microbiota dysbiosis-critical determinants of delayed mortality-remain insufficiently profiled across the 28-day injury-recovery continuum. Methods: This study investigates the effects of [60]Co γ-ray irradiation on metabolic characteristics and gut microbiota in Sprague Dawley rats using untargeted metabolomics and 16S rRNA sequencing. Meanwhile, body weight and complete blood counts were measured. Results: Body weight exhibited significant fluctuations, with the most pronounced deviation observed at 14 days. Blood counts revealed a rapid decline in white blood cells, red blood cells, and platelets post-irradiation, reaching nadirs at 7-14 days, followed by gradual recovery to near-normal levels by 28 days. Untargeted metabolomics identified 32 upregulated and 33 downregulated plasma metabolites at 14 days post-irradiation, while fecal metabolites showed 47 upregulated and 18 downregulated species at 3 days. Key metabolic pathways impacted included Glycerophospholipid metabolism, alpha-linolenic acid metabolism, and biosynthesis of unsaturated fatty acids. Gut microbiota analysis demonstrated no significant change in α-diversity but significant β-diversity shifts (p < 0.05), indicating a marked alteration in the compositional structure of the intestinal microbial community following radiation exposure. Principal coordinate analysis confirmed distinct clustering between control and irradiated groups, with increased abundance of Bacteroidota and decreased Firmicutes in irradiated rats. These findings highlight dynamic metabolic and microbial disruptions post-irradiation, with recovery patterns suggesting a 28-day restoration cycle. Spearman's rank correlation analysis explored associations between the top 20 fecal metabolites and 50 abundant bacterial taxa. Norank_f_Muribaculaceae, Prevotellaceae_UCG-001, and Bacteroides showed significant correlations with various radiation-altered metabolites, highlighting metabolite-microbiota relationships post-radiation. Conclusions: This study provides insights into potential biomarkers for radiation-induced physiological damage and underscores the interplay between systemic metabolism and gut microbiota in radiation response.},
}

@article {pmid40559197,
year = {2025},
author = {Prisco, SZ and Oliveira, SD and Weir, EK and Thenappan, T and Al Ghouleh, I},
title = {Gut Microbiome in Pulmonary Arterial Hypertension-An Emerging Frontier.},
journal = {Infectious disease reports},
volume = {17},
number = {3},
pages = {},
doi = {10.3390/idr17030066},
pmid = {40559197},
issn = {2036-7430},
support = {5K08HL168166-02A1/NH/NIH HHS/United States ; 5K01HL159037-04A1/NH/NIH HHS/United States ; },
abstract = {Pulmonary arterial hypertension (PAH) is an irreversible disease characterized by vascular and systemic inflammation, ultimately leading to right ventricular failure. There is a great need for adjunctive therapies to extend survival for PAH patients. The gut microbiome influences the host immune system and is a potential novel target for PAH treatment. We review the emerging preclinical and clinical evidence which strongly suggests that there is gut dysbiosis in PAH and that alterations in the gut microbiome may either initiate or facilitate the progression of PAH by modifying systemic immune responses. We also outline approaches to modify the intestinal microbiome and delineate some practical challenges that may impact efforts to translate preclinical microbiome findings to PAH patients. Finally, we briefly describe studies that demonstrate contributions of infections to PAH pathogenesis. We hope that this review will propel further investigations into the mechanisms by which gut dysbiosis impacts PAH and/or right ventricular function, approaches to modify the gut microbiome, and the impact of infections on PAH development or progression.},
}

@article {pmid40559193,
year = {2025},
author = {Anselmo, A and Rizzo, F and Gervasi, E and Corrent, L and Ciammaruconi, A and Fillo, S and Fortunato, A and Marella, AM and Costantini, S and Baldassari, L and Lista, F and Ciervo, A},
title = {Tropheryma whipplei and Giardia intestinalis Co-Infection: Metagenomic Analysis During Infection and the Recovery Follow-Up.},
journal = {Infectious disease reports},
volume = {17},
number = {3},
pages = {},
doi = {10.3390/idr17030062},
pmid = {40559193},
issn = {2036-7430},
support = {B1519 ESM4 GP//Italian General Secretariat of Defense and the National Armaments Directorate within the "Eu-ropean Biodefence Laboratory Network 2 (EBLN2) project",/ ; },
abstract = {BACKGROUND: Whipple's disease (WD) is a rare infection caused by Tropheryma whipplei. Diagnosis is challenging and requires a combination of several data sets, such as patient history, clinical and laboratory investigations, and endoscopy with histology analyses. While persistent diarrhea is a common symptom, WD can affect multiple organs.

CASE DESCRIPTION: We present the case of a 66-year-old immunocompetent patient with WD and a history of Helicobacter pylori infection who developed chronic diarrhea. Colonoscopy and histopathological analysis revealed the presence of foamy macrophages with periodic acid-Schiff-positive particles. Subsequently, molecular methods confirmed the clinical WD diagnosis and metagenomic analyses further identified a co-infection with Giardia intestinalis. The patient fully recovered after 14 months of antibiotic therapy. During pharmacological treatment, clinical and laboratory follow-ups were conducted at 6 and 12 months, and microbiome profiles were also analyzed to identify the most abundant species in the samples.

CONCLUSION: The metagenomic analyses showed the eradication of the two pathogens and a progressive restoration to a healthy/balanced status after antibiotic therapy.},
}

@article {pmid40559130,
year = {2025},
author = {Chaple-Gil, AM and Santiesteban-Velázquez, M and Urbizo Vélez, JJ},
title = {Association Between Oral Microbiota Dysbiosis and the Risk of Dementia: A Systematic Review.},
journal = {Dentistry journal},
volume = {13},
number = {6},
pages = {},
doi = {10.3390/dj13060227},
pmid = {40559130},
issn = {2304-6767},
abstract = {Background/Objectives: Growing evidence suggests that oral microbiota dysbiosis may contribute to the development of systemic conditions, including neurodegenerative diseases. This dysregulation promotes immunoinflammatory responses that are increasingly associated with dementia. This systematic review aimed to evaluate the association between oral microbiota dysbiosis and the risk of dementia in older adults. Methods: Eligible studies evaluated oral microbial composition using validated methods such as genetic sequencing, bacterial culture, or metagenomic analysis. Following PRISMA guidelines and a PICO framework, the review included cohort, case-control, and cross-sectional studies. Searches were conducted across PubMed, Scopus, Web of Science, Embase, and Cochrane Library. Two independent reviewers screened and selected studies, resolving disagreements through a third evaluator. Results: This systematic review revealed that Tannerella forsythia, Fusobacterium nucleatum, Porphyromonas, Prevotella, Leptotrichia, Fusobacteriota, Peptostreptococcaceae, and Candida spp. were consistently associated with Alzheimer's disease and mild cognitive impairment, indicating their potential role in neurodegeneration. In contrast, Streptococcus gordonii, Gemella haemolysans, Rothia, Neisseria, and Haemophilus were reduced in cognitively impaired individuals, suggesting a link with healthy cognition. Studies also showed decreased microbial diversity in Alzheimer's disease and the possible modifying effect of the APOE4 allele. Oral health interventions improved microbial composition and slowed cognitive decline, supporting the diagnostic and therapeutic potential of oral microbiota modulation. Conclusions: The findings suggest that oral microbiota dysbiosis may not only result from cognitive decline but also contribute to its pathogenesis. Future studies with larger and more diverse cohorts are recommended to validate these associations.},
}

@article {pmid40559033,
year = {2025},
author = {Zhang, X and Cao, Q and Wang, F and Du, Y and Zhao, W and Guo, Y and Rueppell, O},
title = {Diverse Sublethal Effects of a Common Fungicide Impact the Behavior and Physiology of Honey Bees.},
journal = {Insects},
volume = {16},
number = {6},
pages = {},
doi = {10.3390/insects16060603},
pmid = {40559033},
issn = {2075-4450},
support = {RGPIN-2022-03629//Natural Sciences and Engineering Research Council/ ; 202103021223142//Shanxi Provincial Applied Basic Research Plan (Youth) Project/ ; 2021BQ53//Shanxi Agricultural University Doctoral Fund Project/ ; CARS-44-KXJ2//Modern Agro-Industry Technology Research System/ ; 202208140055//China Scholarship Council/ ; NA//Alberta Beekeepers Commission/ ; },
abstract = {Honey bees and other pollinators are key to functioning natural and managed ecosystems. However, their health is threatened by many factors, including pesticides. Spraying fungicides during flowering of fruit trees is widespread even though it directly exposes pollinators to these fungicides. Here, we report a series of experiments designed to understand how the combination of propiconazole and carbendazim, marketed in China as Chunmanchun[®], affects honey bee health. With an acute oral toxicity of 23.8 μg a.i./bee over 24 h in the laboratory, we considered the acute mortality risk from normal Chunmanchun[®] applications as relatively low. However, our comprehensive studies revealed other diverse effects: Chunmanchun[®] reduced memory after classic conditioning by approximately 25% and altered the activity of protective enzymes and the composition of the honey bees' gut microbiota. Specifically, the genus Lactobacillus was decreased by ~13%, and Bartonella and Snodgrassella were increased by ~10% and ~7.5%, respectively. The gut metabolome was also disrupted in diverse ways, possibly as a functional consequence of the microbiome changes. Thus, we demonstrated numerous sublethal effects of the combination of propiconazole and carbendazim, which adds to the growing evidence that agrochemicals and fungicides in particular can harm pollinator health in subtle ways that are not captured in simple mortality assays.},
}

@article {pmid40559017,
year = {2025},
author = {Danmek, K and Praphawilai, P and Ghosh, S and Jung, C and Mohamadzade Namin, S and Aedtem, P and Chuttong, B},
title = {Evaluation of Red Palm Weevils (Rhynchophorus ferrugineus: Curculionidae) for Putative Oxidation of Ingested Polystyrene and Polyurethane and Their Gut Microbiota Response.},
journal = {Insects},
volume = {16},
number = {6},
pages = {},
doi = {10.3390/insects16060587},
pmid = {40559017},
issn = {2075-4450},
support = {208210//National Research Council of Thailand (NRCT)/ ; 2024K2A9A1A06003640//National Research Foundation of Korea/ ; //Chiang Mai University/ ; },
abstract = {This study assessed the growth performance of red palm weevil (RPW) (Rhynchophorus ferrugineus: Curculionidae) larvae on a liquid diet of yeast-enriched potato dextrose broth (control) and on diets with added polystyrene and polyurethane. For 15 days of diet exposure, the growth and survival, plastic degradation, and gut microbiota of larvae were examined. RPWs showed higher survival rates under polystyrene and polyurethane treatments than in the control group. Head diameter showed a higher trend under polyurethane treatment than under the other treatments. Treated plastics were partly degraded after a 15-day exposure. Further analysis of plastic residues from frass revealed significant differences in Fourier Transform Infrared Spectroscopy (FTIR), with decreased intensity of characteristic peaks compared to frass from larvae fed in the control. Gut bacterial communities in the gut of RPW larvae showed that plastic feeding did not significantly alter the presence of key microbial taxa, but members of Firmicutes and Proteobacteria were higher in the plastic treatment, showing preliminary signs of plastic oxidation and degradation. Overall, these findings provide evidence that ingestion of PS and PU by RPW larvae supports their survival and alters their gut microbiota, possibly due to plastic degradation, paving the way for further research into the interactions between RPWs, their microbiome, and key functional activities, with implications for plastic waste management and recycling.},
}

@article {pmid40558984,
year = {2025},
author = {Crane, YM and Crane, CF and Subramanyam, S and Schemerhorn, BJ},
title = {Shotgun Metagenome Analysis of Two Schizaphis graminum Biotypes over Time With and Without Carried Cereal Yellow Dwarf Virus.},
journal = {Insects},
volume = {16},
number = {6},
pages = {},
doi = {10.3390/insects16060554},
pmid = {40558984},
issn = {2075-4450},
support = {5020-21000-000-D//USDA-ARS Research Project/ ; },
abstract = {The greenbug aphid (Schizaphis graminum (Rondani)) is a major pest of wheat and an important vector of wheat viruses. An RNA-seq study was conducted to investigate the microbial effects of two greenbug genotypes, the presence or absence of cereal yellow dwarf virus, and the condition of the wheat host over a 20-day time course of unrestricted greenbug feeding. Messenger RNA reads were mapped to ca. 47,000 bacterial, 1218 archaeal, 14,165 viral, 571 fungal, and 94 protozoan reference or representative genomes, plus greenbug itself and its wheat host. Taxon counts were analyzed with QIIME2 and DESeq2. Distinct early (days 1 through 10) and late (days 15 and 20) communities differed in the abundance of typical enteric genera (Shigella, Escherichia, Citrobacter), which declined in the late community, while the ratio of microbial to greenbug read counts declined 50% and diversity measures increased. The nearly universal aphid endosymbiont, Buchnera aphidicola, accounted for less than 25% of the read counts in both communities. There were 302 differentially expressed (populated) genera with respect to early and late dates, while 25 genera differed between the greenbug genotypes and nine differed between carrier and virus-free greenbugs. The late community was likely responding to starvation as the wheat host succumbed to aphid feeding. Our results add to basic knowledge about aphid microbiomes and offer an attractive alternative method to assess insect microbiomes.},
}

@article {pmid40558498,
year = {2025},
author = {Ahmad, I and Omura, S and Khadka, S and Sato, F and Park, AM and Rimal, S and Tsunoda, I},
title = {Gut Microbiota in a Viral Model of Multiple Sclerosis: Modulation and Pitfalls by Oral Antibiotic Treatment.},
journal = {Cells},
volume = {14},
number = {12},
pages = {},
doi = {10.3390/cells14120871},
pmid = {40558498},
issn = {2073-4409},
support = {JP22K07527//Japan Society for the Promotion of Science/ ; JP23K06493//Japan Society for the Promotion of Science/ ; JP21K07287//Japan Society for the Promotion of Science/ ; JP24K10500//Japan Society for the Promotion of Science/ ; JP22K18378//Japan Society for the Promotion of Science/ ; JP23K08901//Japan Society for the Promotion of Science/ ; JP24K10163//Japan Society for the Promotion of Science/ ; KD2303//2023 Kindai University Research Enhancement Grant/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Anti-Bacterial Agents/pharmacology/administration & dosage/therapeutic use ; *Multiple Sclerosis/microbiology/virology/drug therapy ; Mice ; *Theilovirus ; Administration, Oral ; Disease Models, Animal ; Mice, Inbred C57BL ; Female ; },
abstract = {Viral infections have been associated with multiple sclerosis (MS), an immune-mediated disease in the central nervous system (CNS). Since Theiler's murine encephalomyelitis virus (TMEV) can induce MS-like demyelination, TMEV infection is the most widely used viral model for MS. Although the precise pathophysiology is unknown, altered fecal bacterial populations were associated with distinct immune gene expressions in the CNS. We aimed to determine the role of gut microbiota in TMEV infection by administering an antibiotic cocktail in drinking water before (prophylactic administration) or after (therapeutic administration) TMEV infection. The antibiotic administration reduced total eubacteria, including the phyla Bacillota and Bacteroidota, but increased the phylum Pseudomonadata in feces. Prophylactic administration did not alter TMEV-induced inflammatory demyelination clinically or histologically, without changes in anti-viral IgG1/IgG2c levels or lymphoproliferative responses; therapeutic administration temporarily suppressed the neurological signs. Although antibiotic treatment had minimal effects on TMEV infection, adding metronidazole and ampicillin in drinking water substantially reduced water intake in the antibiotic group of mice, resulting in significant body weight loss. Since dehydration and stress could affect immune responses and gut microbiota, caution should be exercised when planning or evaluating the oral antibiotic cocktail treatment in experimental animals.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Anti-Bacterial Agents/pharmacology/administration & dosage/therapeutic use
*Multiple Sclerosis/microbiology/virology/drug therapy
Mice
*Theilovirus
Administration, Oral
Disease Models, Animal
Mice, Inbred C57BL
Female

@article {pmid40558392,
year = {2025},
author = {Xu, Y and Sha, Y and Chen, X and Chen, Q and Liu, X and He, Y and Huang, W and He, Y and Gao, X},
title = {Interaction Between Rumen Microbiota and Epithelial Mitochondrial Dynamics in Tibetan Sheep: Elucidating the Mechanism of Rumen Epithelial Energy Metabolism.},
journal = {Biotech (Basel (Switzerland))},
volume = {14},
number = {2},
pages = {},
doi = {10.3390/biotech14020043},
pmid = {40558392},
issn = {2673-6284},
support = {32260820//National Natural Science Foundation of China/ ; GAU-XKTD-2022-21//Discipline Team Project of Gansu Agricultural University/ ; GAU-QDFC-2022-06//Gansu Agricultural University Youth Mentor Support Fund project/ ; 2025CXZX-824//Post-graduate Innovation Star Project of Gansu Province/ ; },
abstract = {Investigating the functional interactions between rumen microbial fermentation and epithelial mitochondrial dynamics/energy metabolism in Tibetan sheep at different altitudes, this study examined ultrastructural changes in rumen epithelial tissues, expression levels of mitochondrial dynamics-related genes (fusion: Mfn1, Mfn2, OPA1, Mic60; fission: Drp1, Fis1, MFF), and ketogenesis pathway genes (HMGS2, HMGCL) in Tibetan sheep raised at three altitudes (TS 2500m, TS 3500m, TS 4500m). Correlation analysis was performed between rumen microbiota/metabolites and mitochondrial energy metabolism. Results: Ultrastructural variations were observed across altitudes. With increasing altitude, keratinized layer became more compact; desmosome connections between granular layer cells increased; mitochondrial quantity and distribution in spinous and basal layers increased. Mitochondrial dynamics regulation: Fission genes (FIS1, DRP1, MFF) showed significantly higher expression at TS 4500m (p < 0.01); fusion genes (Mfn1, OPA1) exhibited altitude-dependent upregulation. Energy metabolism markers: Pyruvate (PA) decreased significantly at TS 3500m/TS 4500m (p < 0.01); citrate (CA) increased with altitude; NAD[+] peaked at TS 3500m but decreased significantly at TS 4500m (p < 0.01); Complex II (SDH) and Complex IV (CO) activities decreased at TS 4500m (p < 0.01). Ketogenesis pathway: β-hydroxybutyrate increased significantly with altitude (p < 0.01); acetoacetate peaked at TS 2500 m/TS 4500 m; HMGCS2 expression exceeded HMGCL, showing altitude-dependent upregulation at TS 4500m (p < 0.01). Microbiome-metabolism correlations: Butyrivibrio_2 and Fibrobacter negatively correlated with Mic60 (p < 0.01); Ruminococcaceae_NK4A214_Group positively correlated with Mfn1/OPA1 (p < 0.05); WGCNA identified 17 metabolite modules, with MEturquoise module positively correlated with DRP1/Mfn2/MFF (p < 0.05). Conclusion: Altitude-induced ultrastructural adaptations in rumen epithelium correlate with mitochondrial dynamics stability and ketogenesis upregulation. Mitochondrial fission predominates at extreme altitudes, while microbiota-metabolite interactions suggest compensatory energy regulation mechanisms.},
}

@article {pmid40558199,
year = {2025},
author = {He, M and Kolhoff, F and Mont, MA and Parvizi, J},
title = {Is Osteoarthritis a State of Joint Dysbiosis?.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/antibiotics14060609},
pmid = {40558199},
issn = {2079-6382},
abstract = {Osteoarthritis (OA) has traditionally been defined as a degenerative joint disease driven by mechanical wear, aging, and metabolic disturbances. However, emerging evidence suggests that joint dysbiosis, a dysregulation in the joint microbiome, may play an important role in OA pathogenesis. This review explores the mechanisms linking dysbiosis to OA. We examine the presence and origin of joint dysbiosis, also highlighting the gut-joint and oral-joint axes as potential routes for microbial translocation. However, challenges remain in distinguishing causation from correlation and addressing microbial contaminants in microbiome studies. Future research should prioritize longitudinal studies and multiomics integration to elucidate the complex interplay between microbial communities and joint health.},
}

@article {pmid40558145,
year = {2025},
author = {Kline, A and Cobián Güemes, AG and Yore, J and Ghose, C and Van Tyne, D and Whiteson, K and Pride, DT},
title = {Current Clinical Laboratory Challenges to Widespread Adoption of Phage Therapy in the United States.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/antibiotics14060553},
pmid = {40558145},
issn = {2079-6382},
abstract = {The resurgence of phage therapy in Western societies has been in direct response to recent increases in antimicrobial resistance (AMR) that have ravaged many societies. While phage therapy as a concept has been around for over 100 years, it has largely been replaced by antibiotics due to their relative ease of use and their predictability in spectrum of activity. Now that antibiotics have become less reliable due to greater antibiotic resistance and microbiome disruption, phage therapy has once again become a viable and promising alternative, but it is not without its challenges. Much like the development of antibiotics, with deployment of phage therapeutics there will be a simultaneous need for diagnostics in the clinical laboratory. This review provides an overview of current challenges to widespread adoption of phage therapy with a focus on adoption in the clinical diagnostic laboratory. Current barriers include a lack of standard methodology and quality controls for phage susceptibility testing and selection, the absence of phage-antibiotic synergy testing, and the absence of standard methods to assay phage activity on biofilms. Additionally, there are a number of lab-specific administrative and regulatory barriers to widespread phage therapy adoption including the need for pharmacokinetic (PK) and pharmacodynamic (PD) assays, methods to account for changes in phages after passaging, an absence of regulatory guidance on what will be required for agency approvals of phages and how broad that approval will apply, and the increased need for lab personnel or automation to account for the work of testing large phage libraries against bacteria isolates.},
}

@article {pmid40558084,
year = {2025},
author = {Brumfield, KD and Enke, S and Swan, BK and Carrasquilla, L and Lee, MD and Stern, DB and Gieser, L and Hasan, NA and Usmani, M and Jutla, AS and Huq, A and Caviness, K and Goodrich, JS and Bull, R and Colwell, RR},
title = {Hybridization capture sequencing for Vibrio spp. and associated virulence factors.},
journal = {mBio},
volume = {},
number = {},
pages = {e0051625},
doi = {10.1128/mbio.00516-25},
pmid = {40558084},
issn = {2150-7511},
abstract = {Proliferation of Vibrio spp. in aquatic ecosystems is associated with climate change and, concomitantly, increased incidence of vibriosis. They are autochthonous to aquatic environments globally, but traditional metagenomic methods for detecting and typing pathogenic Vibrio spp. are challenged by their presence in relatively low abundance and ability to persist in a viable but nonculturable state. In the study reported here, hybridization capture sequencing (HCS) was employed to profile low-abundance Vibrio spp. in environmental samples. The HCS panel targeted a family of molecular chaperones (CPN60) specific to 69 Vibrio spp. and 162 Vibrio-specific virulence factors. This approach was evaluated in parallel with traditional whole-community shotgun sequencing in a metagenomic analysis of water and oyster samples collected from the Chesapeake Bay. In addition, Vibrio parahaemolyticus and Vibrio vulnificus strains isolated from the samples were subjected to whole-genome sequencing to determine the genetic characteristics of pathogenic Vibrio spp. circulating in an aquatic environment. HCS, employed to determine the incidence and characterization of specific Vibrio spp., yielded significantly greater metagenomic insight, notably a variety of other Vibrio spp., including detection of Vibrio cholerae, Vibrio fluvialis, and Vibrio aestuarianus, in addition to Vibrio parahaemolyticus and Vibrio vulnificus, and also important virulence factors not detectable using traditional molecular methods. Thus, pathogenic Vibrio spp. in aquatic ecosystems may be far more common than currently understood. It is concluded that environmental surveillance should include HCS, a valuable tool for the detection and characterization of pathogenic agents in aquatic ecosystems, notably vibrios.IMPORTANCEThe increasing prevalence of pathogenic Vibrio spp. in aquatic ecosystems, driven by climate change, is closely linked to a rise in cholera and vibriosis cases, emphasizing the need for improved environmental surveillance. Vibrios are naturally occurring in aquatic environments globally, but traditional metagenomic methods for detecting and typing pathogenic Vibrio spp. are challenged by their presence in relatively low abundance and ability to persist in a viable but nonculturable state. In the study reported here, hybridization capture sequencing was employed to profile low-abundance Vibrio spp. in metagenomic samples, namely water and oysters collected from the Chesapeake Bay. This approach was evaluated in parallel with traditional whole-community shotgun sequencing and whole-genome sequencing of Vibrio parahaemolyticus and Vibrio vulnificus strains isolated from the samples. Results suggest pathogenic Vibrio spp. in aquatic ecosystems may be far more common than currently understood, when multiple methods are considered for environmental surveillance.},
}

@article {pmid40558055,
year = {2025},
author = {Huang, F and Zhou, Y and Chen, D and Lin, H},
title = {Anti-cariogenic activity of mutanocyclin, a secondary metabolite of Streptococcus mutans, in mono- and multispecies biofilms.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0018325},
doi = {10.1128/spectrum.00183-25},
pmid = {40558055},
issn = {2165-0497},
abstract = {UNLABELLED: Streptococcus mutans (S. mutans), a principal cariogenic pathogen responsible for dental caries, alters the oral biofilm ecology through the production of various metabolites. One such metabolite, mutanocyclin (MUC), a recently identified secondary metabolite, may have implications for both caries development and oral microbiome interactions. This study aimed to investigate the properties of MUC and its effects on S. mutans, as well as other oral commensal streptococci in mono- and multispecies biofilms. Our findings revealed that MUC significantly inhibited S. mutans planktonic growth, biofilm formation, lactic acid production, water-insoluble glucan synthesis, and extracellular polysaccharide production. In contrast, at lower concentrations, MUC stimulated the growth of Streptococcus gordonii (S. gordonii) and Streptococcus sanguinis (S. sanguinis). Additionally, MUC reduced the abundance of S. mutans and enhanced the antagonistic activity of S. gordonii and S. sanguinis against S. mutans in multispecies biofilms by upregulating the expression of the H2O2-related gene spxB and stimulating H2O2 production. These results suggest that MUC has potential for anti-cariogenic activity against S. mutans and for modulating oral microbial communities within the cariogenic microenvironment, providing new therapeutic strategies for preventing dental caries.

IMPORTANCE: Dental caries is a major global health concern, affecting millions and contributing to reduced quality of life and economic burdens. Our study investigated the properties of mutanocyclin (MUC), a recently discovered secondary metabolite produced by S. mutans. Our work sheds light on the role of MUC in modulating microbial communities in the oral cavity. We demonstrated that MUC influences the formation and cariogenicity of S. mutans biofilms and its interactions with other beneficial oral bacteria. This research enhances our understanding of newly discovered secondary metabolites of S. mutans and offers a potential novel strategy for managing the microbial imbalances that lead to caries.},
}

@article {pmid40558050,
year = {2025},
author = {Phan, J and Jain, S and Nijkamp, JF and Sasidharan, R and Agarwal, A and Bird, JK and Spooren, A and Wittwer Schegg, J and Ver Loren van Themaat, E and Mak, TN},
title = {Gut health predictive indices linking gut microbiota dysbiosis with healthy state, mild gut discomfort, and inflammatory bowel disease phenotypes using gut microbiome profiling.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0027125},
doi = {10.1128/spectrum.00271-25},
pmid = {40558050},
issn = {2165-0497},
abstract = {Despite the complexity of the gut microbiome, several scores that use taxonomic characteristics exist that attempt to identify a healthy gut or gastrointestinal disease. Two systems in use are the metagenomic aerotolerant predominance index (MAPI) and keystone scores. The aim of this analysis was to compare different gut microbiome scores, specifically MAPI and a keystone species score, on two cross-sectional data sets and to investigate correlations of these scores with self-reported gut discomfort and gastrointestinal disease. The first data set is a commercial data set (Sun Genomics data set) with whole-genome shotgun sequencing samples from 5,372 customers. The second data set is curated from publicly available data (public data set) with 2,415 samples from participants in human studies with gut-related taxonomic profiles. MAPI scores and keystone species scores were calculated using standard methodology. The MAPI score was significantly lower in men for the public data set. There was a graded response for both the MAPI and keystone scores between healthy subjects, subjects with mild gastrointestinal discomfort, and patients with gastrointestinal disease: the MAPI score was higher, and the keystone score was lower in subjects with gastrointestinal discomfort or with inflammatory bowel disease patients. The keystone and MAPI scores have the potential to help identify factors associated with gut microbial dysbiosis and gastrointestinal discomfort or disease. Furthermore, given the functional link of the MAPI score to oxidative stress in the microbiome, the scores can help to identify conditions where oxidative stress is one of the hallmarks of dysbiosis.IMPORTANCEGut bacteria play a role in both mild gastrointestinal discomfort, which includes bloating and constipation, and inflammatory bowel disease. There are many different types of bacteria in the gut, and gut microbiome composition differs greatly between different people. Therefore, it is difficult to predict who has a gut microbiome associated with a healthy gut and who might develop disease or experience gut discomfort. Several scoring systems have been developed to categorize gut health states. This analysis compared two different scoring systems using data from two different sources to see how well they could identify people with gastrointestinal disease, gastrointestinal complaints, or a healthy gut. The scoring systems showed similar trends according to gut health status: groups of people with gut bacteria imbalance or gut disease had a different score than groups of people with healthy gut bacteria.},
}

@article {pmid40558046,
year = {2025},
author = {Wu, S and Luo, G and Jiang, F and Jia, W and Li, J and Huang, T and Zhang, X and Mao, Y and Su, S and Han, W and He, F and Cheng, R},
title = {Early life bifidobacterial mother-infant transmission: greater contribution from the infant gut to human milk revealed by microbiomic and culture-based methods.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0048025},
doi = {10.1128/msystems.00480-25},
pmid = {40558046},
issn = {2379-5077},
abstract = {UNLABELLED: The colonization and development of the gut microbiota during early life, especially Bifidobacterium, may be influenced by maternal bacterial communities, including those of human milk. However, the interaction of bacteria in mother-infant dyads during breastfeeding remains unclear. This study focused primarily on the characteristics and dynamics of the infant gut and human milk microbiota within the first month of life on the basis of a birth cohort and explored the interaction of the microbiota derived from the two niches by sequencing and culture-based methods, especially Bifidobacterium, as the representative dominator in the infant gut. Infant feces and human milk samples from 21 mother-infant dyads were collected on days 0, 7, and 30 postpartum. The bacterial composition was identified by sequencing the 16S rRNA gene, and the contributions of the bacterial communities were estimated via SourceTracker2. Bifidobacterial strains were isolated from infant feces and human milk via culture-based methods. The suspected strains were identified through Sanger sequencing and genotyped via multilocus sequence typing (MLST). The bacterial communities were distinct between infant feces and human milk. Human milk microbes contribute 63.89%-77.61% to the infant's gut within the first month of life, whereas Bifidobacterium in the infant's gut contributes more (80.18%-84.30%) to human milk. A total of 60 bifidobacterial isolates were obtained from 10 pairs of mother-infant samples, 48 isolates from 10 out of 27 infant feces samples, and 12 isolates from 4 out of 27 human milk samples. Among these, 30 isolates were identified as Bifidobacterium breve, and 18 were identified as B. longum subsp. longum. Strains belonging to B. breve from a single mother-infant pair were found to be monophyletic (ST: BRE-1), whereas this strain was found much earlier in infant feces across the three time points (collected on days 0, 7, and 30) than in human milk (collected on day 30). Our data suggest that during very early breastfeeding, human milk contributes a significant proportion of the overall bacterial population to the infant's gut, whereas the infant's gut selectively contributes a greater proportion of Bifidobacterium to human milk. Certain bifidobacterial strains, such as B. breve, are retrogradely transmitted from the infant's gut to the mother's human milk during breastfeeding, implying a potential challenge regarding the reliability of the source when potential probiotics are isolated from human milk.

IMPORTANCE: Understanding how microbes, especially beneficial bacteria such as Bifidobacterium, are shared between mothers and infants during breastfeeding is crucial for promoting infant health. Although most research has focused on transmission from mother to child, our study reveals a novel and significant reverse route: from the infant gut to breast milk. By combining microbiome sequencing with culture-based techniques, we provide evidence that specific strains of Bifidobacterium, especially B. breve, may transmit back to the mother during breastfeeding. This insight reshapes our understanding of microbial exchange within the mother-infant dyad and highlights breastfeeding as a bidirectional process that influences both maternal and infant microbiota. These findings may have important implications for designing probiotics and supporting early-life microbial development through maternal health interventions.},
}

@article {pmid40558044,
year = {2025},
author = {Li, K and Liu, X and Zhong, X and Zeng, H and Liu, T and Lin, B and Chen, P and Xie, B and Zhong, X},
title = {Significant associations between high-risk sexual behaviors and enterotypes of gut microbiome in HIV-negative men who have sex with men.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0023225},
doi = {10.1128/msphere.00232-25},
pmid = {40558044},
issn = {2379-5042},
abstract = {UNLABELLED: Gut microbiome of men who have sex with men (MSM) exhibits distinctive characteristics compared with general populations. The dysbiosis of the gut microbiome in MSM is also associated with the onset and evolution of HIV infection. Enterotype is an important feature of the gut microbiome and remains unaffected by demographic factors. However, the enterotypes of gut microbiome in MSM are unclear. The associations between enterotypes and high-risk sexual behaviors in this population also remain to be elucidated. HIV-negative MSM were recruited in this study. Fecal samples of the participants were collected and subjected to 16S rRNA gene sequencing. Enterotype clusters were determined by Jensen-Shannon divergence based on genus-level relative abundance. Microbial function predictions were conducted by PICRUSt2 software. Univariate and multivariate logistic regression approaches were utilized to analyze the associations of enterotypes with sexual behaviors. A three-category random forest machine learning model was performed to further examine the correlation between abundant microbiome in each enterotype cluster and anal sex roles. Two enterotype clusters were identified in our data sets, primarily driven by genera Phocaeicola and Segatella. The alpha diversity was comparable between the two enterotype clusters. Microbial metabolic functions significantly differed, and multivariate logistic regression indicated a significant association between anal sex role and enterotype. The results of the three-category random forest model indicate that the dominant bacterial communities in gut enterotypes can effectively differentiate MSM who engage exclusively in receptive anal intercourse from those who engage in insertive or versatile anal intercourse (AUC: 0.6400, 0.6929, respectively). We identified two enterotype clusters of gut microbiome in HIV-negative MSM. Enterotypes of MSM were significantly associated with anal sex roles. These findings further highlight the close correlation between the gut microbiome and anal intercourse roles.

IMPORTANCE: Our study's discovery that gut microbiome enterotypes are significantly associated with anal sex roles in HIV-negative MSM opens a new frontier in understanding the complex interplay between microbiology and sexual health. This finding underscores the urgency of delving into the mechanistic connections between the gut microbiome, sexual behaviors, and HIV infection. By identifying modifiable factors influencing gut microbiome composition, we have paved the way for developing personalized preventive strategies that could disrupt the transmission dynamics of HIV within this high-risk population. This research contributes to the fundamental understanding of the gut microbiome's role in the sexual health of MSM, making it a pivotal advancement in the fields of gut microbiome research and sexual health.},
}

@article {pmid40558028,
year = {2025},
author = {Gao, Y and Zhang, H and Chu, D and Ning, K},
title = {Intra-tumor microbiome-based tumor survival indices predict immune interaction and drug sensitivity on pan-cancer scale.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0031225},
doi = {10.1128/msystems.00312-25},
pmid = {40558028},
issn = {2379-5077},
abstract = {UNLABELLED: Growing research evidence indicates a substantial influence of the intra-tumor microbiome on tumor outcome. However, there is currently no consistent criterion for identifying the association of microbes with tumor progression and response to treatment across various types of cancer. In this study, we concentrate on the intra-tumor microbiome and develop the Tumor Microbiome Survival Index (TMSI), a measure indicative of cancer patient survival risk. Our indices revealed notable distinctions between two stratified risk groups for each of the 10 cancer types and could precisely predict patients' overall survival. For each type of cancer, our findings unveiled two distinct gene expression profiles and shed light on the varying patterns of immune and stromal cell enrichment between the two risk groups. Additionally, we noted that the high-TMSI group exhibited substantially elevated IC50 values for a number of drugs, indicating that individuals in the low-TMSI group might experience superior therapeutic effects from chemotherapy. These findings illuminate the complex dynamics between the tumor microbiome, the patient's immune reaction, and medical outcomes, thus shedding light on microbiome-based personalized therapeutic interventions.

IMPORTANCE: This work presents the Tumor Microbiome Survival Index (TMSI), a crucial innovation. It stratifies cancer patients into risk groups across 10 cancer types, accurately predicting survival. By uncovering distinct gene expression and immune/stromal cell patterns, it deepens understanding of tumor complexity. The finding of altered drug sensitivity in different TMSI groups offers insights for personalized chemotherapy. Overall, it paves the way for microbiome-targeted cancer therapies and enhanced patient prognostication.},
}

@article {pmid40557875,
year = {2025},
author = {Ikeda, SI and Lee, D and Chen, J and Fukuda, S and Negishi, K and Tsubota, K and Kurihara, T},
title = {Antibiotics-Induced Gut Microbiome Dysbiosis Affects Susceptibility to Minus Lens-Induced Myopia in Mice.},
journal = {Investigative ophthalmology & visual science},
volume = {66},
number = {6},
pages = {76},
doi = {10.1167/iovs.66.6.76},
pmid = {40557875},
issn = {1552-5783},
mesh = {Animals ; Mice, Inbred C57BL ; *Dysbiosis/chemically induced/microbiology/complications ; *Anti-Bacterial Agents/pharmacology ; Mice ; Male ; *Myopia/etiology/microbiology ; *Gastrointestinal Microbiome/drug effects ; Disease Models, Animal ; Disease Susceptibility ; RNA, Ribosomal, 16S/genetics ; Vancomycin ; },
abstract = {PURPOSE: The prevalence of myopia has increased worldwide in recent decades, shifting the focus in research from genetic to environmental factors. The roles of diet in the development of myopia may be directly associated with gut microbiota composition. Therefore this study evaluated the effects of antibiotic-induced gut dysbiosis on the development of negative lens-induced myopia.

METHODS: We administered several antibiotics (ampicillin, vancomycin, neomycin, or a mixture) to induce gut dysbiosis in male C57BL/6J mice with negative lens-induced myopia. Gut microbiome profiles were analyzed by 16 S rRNA gene sequencing.

RESULTS: Mice administered vancomycin, neomycin, and a mixture of three antibiotics exhibited resistance to lens-induced myopia, unlike control or ampicillin-administered mice. Further analyses revealed no specific trend in the gut microbiota composition and diversity related to myopia resistance, except for an increase in the abundance of Clostridiaceae.

CONCLUSIONS: These findings demonstrate the potential role of the gut microbiome, particularly Clostridiaceae family, in myopia susceptibility. This study offers new insights into the preventive strategies and therapeutic interventions to mitigate myopia development.},
}

Animals
Mice, Inbred C57BL
*Dysbiosis/chemically induced/microbiology/complications
*Anti-Bacterial Agents/pharmacology
Mice
Male
*Myopia/etiology/microbiology
*Gastrointestinal Microbiome/drug effects
Disease Models, Animal
Disease Susceptibility
RNA, Ribosomal, 16S/genetics
Vancomycin

@article {pmid40557534,
year = {2025},
author = {Dong, H and Yang, X and Zhou, Y and Yang, M and Zhang, H and Liu, X and Zhu, W},
title = {Kudzu resistant starch effectively ameliorates non-alcoholic fatty liver disease by protecting the gut microbiota intestinal barrier and suppressing inflammatory responses.},
journal = {Journal of the science of food and agriculture},
volume = {},
number = {},
pages = {},
doi = {10.1002/jsfa.14371},
pmid = {40557534},
issn = {1097-0010},
support = {82260765//National Natural Science Foundation of China/ ; 2017YFC1702905//National Key R&D Program Key Special Project, China/ ; CXTD-22004//Jiangxi University of Chinese Medicine Science and Technology Innovation Team Development Program/ ; },
abstract = {BACKGROUND: Non-alcoholic fatty liver disease (NAFLD), including non-alcoholic steatohepatitis, may lead to a cocktail of disease consequences, for instance, type II diabetes, liver fibrosis, and even hepatocarcinogenesis. The complex pathogenesis of NAFLD results in a shortage of an effective drug for its treatment. Currently, a healthy diet and regular exercise are considered one of the most effective and safe ways to mitigate NAFLD as well as other types of metabolic disorders. Kudzu-resistant starch (KRS) has developed as a potential dietary supplement attributed to its prebiotic properties, particularly its ability to regulate gut microbiota and intestinal barrier function. This study discusses the alleviative effects of KRS on high-fat diet and dextran sulfate sodium induced intestinal barrier dysfunction, inflammation, gut microbial dysbiosis, and liver steatosis.

RESULTS: The results identified KRS has ameliorated intestinal barrier dysfunction by increasing the expression of zonula occludens-1 (ZO-1) and mucin 2 (Muc2). Furthermore, it also down-regulated the gut-derived LPS/TLR4 signaling pathway, dramatically alleviating inflammatory responses, including serum, colon, and liver tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6), and monocyte chemotactic protein-1 (MCP-1) levels. KRS also had attenuating effects on gut microbiota dysbiosis, restored the gut microbiota abundance and diversity, and increased the butyric acid-producing bacteria, such as Coprococcus, Bifidobacterium, and Lactobacillus, and it exhibited positive effects in short-chain fatty acids (SCFAs). KRS attenuated fatty acid-induced lipid accumulation and regulates lipid metabolism via the sterol regulatory element-binding protein 1-c (SREBP-1c), G-protein coupled receptors 43 (GPR43), peroxisome proliferator-activated receptor-γ (PPAR-γ), and CCAAT/enhancer-binding proteins-α (C/EBP-α).

CONCLUSION: The findings reveal that kudzu resistant starch could be a potential supplement for metabolic syndromes, and the efficacy and effectiveness might facilitate the multi-targeting strategy required to mitigate NAFLD. © 2025 Society of Chemical Industry.},
}

@article {pmid40557325,
year = {2025},
author = {Sellers-Porter, C and Lueschow-Guijosa, SR and Santana, JM and Cera, AJ and Bautista, GM and Persiani, M and Good, M and McElroy, SJ},
title = {Modeling pathogen-driven neonatal late-onset sepsis: a modification to the murine cecal slurry.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1589712},
pmid = {40557325},
issn = {2235-2988},
mesh = {Animals ; *Disease Models, Animal ; *Cecum/microbiology/pathology ; Mice ; Animals, Newborn ; *Neonatal Sepsis/microbiology/pathology ; Gastrointestinal Microbiome ; Enterocolitis, Necrotizing/microbiology ; Humans ; Cytokines/blood ; Infant, Newborn ; Mice, Inbred C57BL ; *Sepsis/microbiology ; Female ; },
abstract = {INTRODUCTION: Neonatal sepsis is a major cause of neonatal morbidity and mortality. Reliable animal models are essential to our understanding of late-onset sepsis, but notable limitations exist in the current standard murine cecal slurry model. We sought to refine the existing model by using an injection of known stock slurry ("NEC'teria") cultured from an infant who died of necrotizing enterocolitis to better mimic sepsis following the translocation of neonatal specific bacterial pathogens from the intestine into the peritoneum.

METHODS: To induce sepsis, neonatal mice (P7 and P14 - P16) were given an intraperitoneal injection of varying concentrations of NEC'teria, while sham controls received an injection of PBS. Mice were monitored for survival and tissue samples, serum, and peritoneal washes were collected for further assessment of inflammation, immune response, and intestinal injury. Ceca were collected for microbiome analysis.

RESULTS: While the polymicrobial cecal slurry from adult mice contained common healthy gut microbes, NEC'teria is composed of bacteria, primarily from the Enterobacteriaceae and Enterococcaceae families, that are common causes of late-onset sepsis. NEC'teria exposure significantly increased serum inflammatory cytokines, resulted in intestinal injury, altered the microbiome composition, and induced significant changes in local and systemic immune cell expression. Sepsis-induced mortality, inflammation, and intestinal injury were live-bacteria dependent and could be attenuated by administration of an antibiotic one hour after bacterial injection.

DISCUSSION: Our modification to the cecal slurry neonatal sepsis model resulted in a consistent sepsis-related mortality and phenotypic changes in neonatal mouse pups that resembled the changes that occur in human preterm infants who develop late-onset sepsis. Our pathogenic slurry is highly relevant to neonatal sepsis, as it is comprised of bacterial families found commonly in septic neonates. We expect our model to be highly reproducible between institutions, due to the standardized bacterial dose and characterized stock solution.},
}

Animals
*Disease Models, Animal
*Cecum/microbiology/pathology
Mice
Animals, Newborn
*Neonatal Sepsis/microbiology/pathology
Gastrointestinal Microbiome
Enterocolitis, Necrotizing/microbiology
Humans
Cytokines/blood
Infant, Newborn
Mice, Inbred C57BL
*Sepsis/microbiology
Female

@article {pmid40557322,
year = {2025},
author = {Melvan, E and Allen, AP and Vuckovic, T and Soljic, I and Starcevic, A},
title = {Predicting gut microbiota dynamics in obese individuals from cross-sectional data.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1485791},
pmid = {40557322},
issn = {2235-2988},
mesh = {Humans ; *Obesity/microbiology ; *Gastrointestinal Microbiome ; Cross-Sectional Studies ; RNA, Ribosomal, 16S/genetics ; *Dysbiosis/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Microbial Interactions ; Adult ; Firmicutes/isolation & purification/genetics ; Male ; Bacteroidetes ; Female ; },
abstract = {INTRODUCTION: Obesity affects approximately 39% of adults worldwide. While gut microbiota has been linked to obesity, most research has focused on static taxonomic composition rather than the dynamic interactions between microbial taxa.

METHODS: We applied BEEM-Static, a generalized Lotka-Volterra model, to cross-sectional 16S rRNA gut microbiome data from six public datasets, comprising 2,435 profiles from lean and obese individuals.

RESULTS: A total of 57 significant microbial interactions were identified in obese individuals (79% negative), compared to 37 in lean individuals (92% negative). For example, Bacteroidetes showed a stronger inhibitory effect on Firmicutes in obese individuals (-0.41) than in lean ones (-0.26). Firmicutes and Proteobacteria exhibited consistently higher carrying capacities in obese populations.

DISCUSSION: These findings suggest that microbial interaction networks-not just taxonomic abundance-play a key role in obesity-related dysbiosis. Our approach enables the inference of microbiota dynamics from a single time point, paving the way for tailored dietary interventions, which we refer to as Optibiomics.},
}

Humans
*Obesity/microbiology
*Gastrointestinal Microbiome
Cross-Sectional Studies
RNA, Ribosomal, 16S/genetics
*Dysbiosis/microbiology
*Bacteria/classification/genetics/isolation & purification
*Microbial Interactions
Adult
Firmicutes/isolation & purification/genetics
Male
Bacteroidetes
Female

@article {pmid40557264,
year = {2025},
author = {Radulovic, E and Mehinagic, K and Wüthrich, TM and Hilty, M and Summerfield, A and Ruggli, N and Benarafa, C},
title = {Development of protective immunity against African swine fever depends on host-environment interactions.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1553310},
pmid = {40557264},
issn = {2297-1769},
abstract = {African swine fever virus (ASFV) is a major threat for pig health and meat production in many countries. The development and commercialization of vaccine candidates are complicated by efficacy and safety concerns. Improved vaccine design requires further studies to identify factors that regulate immune responses to vaccines leading to protective immunity against a virulent challenge. In a previous study, we reported that infection with the moderately virulent ASFV field strain Estonia 2014 was less severe in specific pathogen-free (SPF) pigs than in conventional farm pigs, which differ in their gut microbiome and their basal immune activation status. As shown previously using intramuscular infection, SPF pigs were more resilient to oronasal infection with the ASFV Estonia 2014 strain compared to farm pigs, which showed increased fever and clinical signs. All SPF and farm pigs nevertheless survived the infection and remained viremic for approximately 4 months. When all animals had no detectable viremia, both groups were rechallenged with the virulent ASFV Armenia 2008 strain. SPF pigs were fully protected against disease and showed little or no viremia upon re-challenge. In contrast, farm pigs developed high viremia, high proinflammatory cytokine responses, severe clinical signs, and 40% (2 of 5 pigs) reached humane endpoints. Our findings suggest that limited prior immune exposure to other pathogens and/or the microbiome composition of SPF pigs promotes resilience to infection with a moderately virulent strain such as Estonia 2014, and importantly promotes the development of a strong protective immune response against a second challenge with a virulent ASFV strain. In conclusion, testing safety and efficacy of live attenuated vaccine candidates should take into account the specific hygiene conditions and the associated changes of general immune status of pigs in clinical trials.},
}

@article {pmid40557239,
year = {2025},
author = {Hamari, N and Blaak, EE and Canfora, EE},
title = {The impact of butyrate on glycemic control in animals and humans: a comprehensive semi-systemic review.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1603490},
pmid = {40557239},
issn = {2296-861X},
abstract = {The gut microbiome has been identified as a significant factor in host metabolism, playing a key role in the etiology of obesity, type 2 diabetes and cardiometabolic risk. Butyrate, produced by the gut microbiome from indigestible carbohydrates, has been shown to have beneficial effects on body weight control, inflammation, and insulin resistance, primarily evidenced by animal studies and in vitro experiments. However, translating these benefits to humans remains challenging due to variability in mode of butyrate administration or production upon fermentation of dietary fibers, as well as in butyrate absorption, and its metabolism. For instance, oral butyrate supplementation can directly increase circulating butyrate levels, thereby targeting peripheral tissues. In contrast, butyrate produced by the gut microbiome may also influence metabolism through local signaling mechanisms affecting peripheral tissues. Additionally, there may be large heterogeneity in the response of the individuals to butyrate interventions. Future research should aim to better understand butyrate kinetics and dynamics and its mechanisms in regulating intestinal and metabolic health. In human studies, longer-term, placebo-controlled trials are needed to establish the efficacy of either targeting butyrate production or supplementation in individuals with obesity and/or metabolic disturbances. Personalized dietary interventions based on individual microbiota composition and/or function and metabolic profiles may optimize butyrate production and its metabolic benefits. This could pave the way for effective butyrate-based interventions to improve metabolic health and prevent obesity-related complications.},
}

@article {pmid40557154,
year = {2025},
author = {Bai, X and Raju, SC and Knudsen, AD and Thudium, RF and Arentoft, NS and Gelpi, M and Heidari, SL and Kunisaki, KM and Kristiansen, K and Hov, JR and Nielsen, SD and Trøseid, M},
title = {Microbiome profiling reveals gut bacterial species associated with rapid lung function decline in people with HIV.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1555441},
pmid = {40557154},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Female ; *HIV Infections/microbiology/complications/physiopathology ; Middle Aged ; Dysbiosis ; *Lung/physiopathology ; *Bacteria/genetics/classification ; Adult ; *Lung Diseases/microbiology ; Respiratory Function Tests ; Aged ; },
abstract = {BACKGROUND: People with HIV (PWH) have an increased risk of pulmonary comorbidities compared to people without HIV. The gut microbiome regulates host immunity and is altered in PWH. This study aims to determine potential associations between gut microbiome, lung function decline, and airflow limitation in PWH.

METHODS: PWH from the Copenhagen Comorbidity in HIV Infection (COCOMO) Study with available lung function testing and microbiome data were included (n=385). The gut microbiome was characterized using shotgun metagenomic sequencing. Associations between gut microbiome, rapid lung function decline, and airflow limitation were analysed in multivariable logistic regressions adjusted for traditional and HIV-associated risk factors for lung disease.

RESULTS: Several bacterial species were significantly enriched in PWH with rapid lung function decline, including opportunistic pathogenic bacterial species Bacteroides coprophilus, Klebsiella michiganensis, and Clostridium perfringens. A gut microbial dysbiosis index based on compositional changes was associated with rapid lung function decline (adjusted odds ratio (aOR) 1.18, 95% confidence interval (CI) [1.11-1.27], p<0.001), and airflow limitation (aOR 1.16, 95% CI [1.04-1.29], p=0.007) in adjusted multivariable logistic regression analyses.

CONCLUSION: Associations between the gut dysbiosis index and rapid lung function decline and airflow limitation suggest a potential role of certain gut bacterial species in the pathogenesis of pulmonary comorbidities in PWH.},
}

Humans
*Gastrointestinal Microbiome
Male
Female
*HIV Infections/microbiology/complications/physiopathology
Middle Aged
Dysbiosis
*Lung/physiopathology
*Bacteria/genetics/classification
Adult
*Lung Diseases/microbiology
Respiratory Function Tests
Aged

@article {pmid40556945,
year = {2025},
author = {Wang, S and Li, S and Zhang, M and Liu, R and Ye, X and Mao, S and Yu, J and Xie, X and Tan, W},
title = {Unraveling the Role of the Microbiota in Cancer Immunotherapy: A New Frontier.},
journal = {Research (Washington, D.C.)},
volume = {8},
number = {},
pages = {0744},
pmid = {40556945},
issn = {2639-5274},
abstract = {Cancer immunotherapy has greatly changed the therapeutic landscape for metastatic malignancies. Nevertheless, due to immune-related adverse events, drug resistance, and other factors, cancer immunotherapy remains largely untapped. Recent research has shown that the microbiota is crucial in shaping immune function and that its modulation can influence antitumor immunity. However, because of the intricate nature of the microbiome and immune system, a comprehensive mechanistic framework for understanding how the microbiota influences antitumor immune responses is still lacking. In this review, we summarize the mechanisms of the microbiota in antitumor immunity. We also comprehensively outline the methods for measuring the microbiota and their limitations. Additionally, we discuss the key challenges facing the targeting of the microbiota as a regulatory strategy for cancer immunotherapy.},
}

@article {pmid40556896,
year = {2025},
author = {Viquez-Umana, FL and Erickson, MG and Young, JD and Zanton, GI and Wattiaux, MA and Suen, G and Mantovani, HC},
title = {Assessing the impact of oscillating dietary crude protein on the stability of the rumen microbiome in dairy cattle.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1568112},
pmid = {40556896},
issn = {1664-302X},
abstract = {INTRODUCTION: Understanding how the rumen microbiota responds to varying protein levels and feeding patterns is critical for optimizing dairy cattle nutrition. This study investigated the influence of dietary crude protein (CP) levels (13.8% or 15.5% CP of ration dry matter) and CP feeding patterns (constant over time (static) or oscillating by 1.8 percentage units above and below the mean every 48 h) on the composition, diversity, and function of the rumen microbiome.

METHODS: Using a replicated Latin Square design, eight rumen-cannulated Holstein cows were assigned each of the four dietary treatments (structured as a 2 × 2 factorial) in four consecutive 28-day periods (with 24 days of adaptation and 4 days of sampling). Rumen samples were collected 4 h post-feeding, and amplicon libraries of the V4 region of the 16S rRNA gene were sequenced and analyzed to assess changes in microbiome composition. Additionally, volatile fatty acids (VFAs) were measured to evaluate rumen microbial function.

RESULTS: Results indicated that dietary CP level did not alter microbial diversity (p = 0.30), but oscillating diets increased rumen microbial diversity (Shannon index, p = 0.04). The rumen microbiome richness was also affected by CP feeding pattern (p = 0.05), but not dietary CP level (p = 0.27). Furthermore, differential abundance analysis using ANCOM-BC identified CAG- 352 (p = 0.0001) and an unclassified member of the family Acholeplasmataceae (p = 0.0002) as taxa significantly impacted by protein level and feeding pattern, even though their relative abundance was low (below 0.02%). The functional profile of the rumen bacterial communities was not affected by CP level or feeding pattern, and VFA profiles also remained consistent across treatments, with no observable changes in concentration.

DISCUSSION: These findings support the hypothesis that the rumen microbiome remains stable despite variations in the ruminal supply of dietary CP, suggesting that compensatory mechanisms may be involved. Although oscillating dietary CP concentration might alter the rumen microbiome, further research into rumen metabolic processes and host-microbiome interactions is needed to evaluate if the changes observed in our study are biologically relevant for developing new opportunities to enhance protein nutrition in dairy cattle.},
}

@article {pmid40556886,
year = {2025},
author = {Klein, ML and Erikson, CB and McCabe, CJ and Huang, L and Rodrigues, JLM and Mitloehner, FM},
title = {Limited effects of tannin supplementation on the dairy cattle fecal microbiome with modulation of metabolites.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1570127},
pmid = {40556886},
issn = {1664-302X},
abstract = {Tannins are plant secondary metabolites that bind organic carbon (C) and nitrogen (N), potentially altering substrate bioavailability for enteric fermentation in ruminants. This interaction may reduce greenhouse gas (GHG) emissions and influence nitrogen partitioning. Given tannins' resistance to ruminal degradation and persistence through the gastrointestinal tract, this study investigated the effects of a tannin-based feed additive on fecal microbial diversity, fecal chemical composition, and GHG emissions. Twenty-four early- to mid-lactation dairy cows were randomized to receive either a tannin-based feed additive (TRT; containing condensed and hydrolyzable tannins from Schinopsis quebracho-colorado [Schltdl.]) or a control diet (CON) for 64 days. Cows were blocked by parity, dry matter intake, milk yield, body weight, and days in milk. Fecal samples were collected on days 0, 16, 32, and 64 and analyzed using 16S rRNA gene amplicon sequencing. Fecal C, N, and indole-3-lactate were measured, and GHG emissions (N2O, CH4, CO2) were assessed via 14-day laboratory incubation. A total of 1,538 amplicon sequence variants were identified, with Firmicutes as the dominant phylum. Fecal phylogenetic diversity showed a significant treatment × day interaction (p < 0.01), with TRT cows exhibiting reduced microbial diversity from day 16 to 64. Fecal C and N concentrations were significantly lower (p < 0.01) in TRT cows on day 16, while indole-3-lactate levels were higher on day 64 (p = 0.02). GHG emissions did not differ significantly between treatments. The tannin-based feed additive influenced fecal microbial community structure and select chemical parameters but did not significantly affect GHG emissions from feces. These findings suggest that dietary tannins may modulate gut microbial ecology with minimal impact on downstream manure-related emissions.},
}

@article {pmid40556746,
year = {2025},
author = {Urquhart, SA and Christof, M and Coelho-Prabhu, N},
title = {The impact of artificial intelligence on the endoscopic assessment of inflammatory bowel disease-related neoplasia.},
journal = {Therapeutic advances in gastroenterology},
volume = {18},
number = {},
pages = {17562848251348574},
pmid = {40556746},
issn = {1756-283X},
abstract = {Inflammatory bowel disease (IBD) is a group of chronic inflammatory conditions of the gastrointestinal tract resulting from an inappropriate immune response to an altered gut microbiome in genetically predisposed individuals. Endoscopy plays a central role in IBD management, aiding in diagnosis, disease staging, monitoring, and therapeutic guidance. Patients with IBD face an increased risk of colorectal neoplasia due to chronic inflammation. Artificial intelligence (AI)-based systems show promise in detecting and classifying dysplasia and neoplasia during endoscopic evaluation. While there have been several studies on the application of AI to detect and diagnose various types of neoplasia in the non-IBD population, the literature in patients with IBD is limited. We aim to summarize the current evidence on the application of AI technologies to detect IBD-associated neoplasia, highlighting potential benefits, limitations, and future directions. A comprehensive literature search was performed using the PubMed database to identify relevant studies from January 2010 to February 2025. Additional references were identified from the relevant articles' bibliographies. AI-assisted endoscopy, particularly using machine learning and deep learning techniques, has shown promise in improving lesion detection rates and supporting real-time decision-making. Computer-aided detection systems may increase the sensitivity of dysplasia identification, while computer-aided diagnosis tools can aid in lesion characterization. Early studies suggest that AI can reduce interobserver variability, improve targeting of biopsies, and potentially lead to more personalized surveillance strategies. Although clinical data specific to IBD-related neoplasia remain limited compared to sporadic colorectal neoplasia, the integration of AI into endoscopic practice holds significant potential to enhance dysplasia detection and improve patient outcomes. Continued research, validation in IBD-specific cohorts, and integration with clinical workflows are essential to realize the full impact of AI in this setting.},
}

@article {pmid40556628,
year = {2025},
author = {Stoll, ML and Appah, M and Tiwari, HK},
title = {The microbiota in axial spondyloarthritis: what have we learned from Mendelian randomisation studies?.},
journal = {Clinical and experimental rheumatology},
volume = {},
number = {},
pages = {},
doi = {10.55563/clinexprheumatol/rvb37m},
pmid = {40556628},
issn = {0392-856X},
abstract = {OBJECTIVES: It has been postulated that the gut microbiota plays an important role in the pathogenesis of spondyloarthritis (SpA). However, cross-sectional studies are limited in their ability to differentiate disease-driven microbial alterations from causative changes. Mendelian randomisation (MR) studies leverage existing genetic associations to investigate causality, offering insights into microbiota-disease associations.

METHODS: We conducted a systematic review of all MR studies that evaluated the relationship between the microbiota and axial SpA. Eight studies were identified and reviewed. To look for genetic associations with the microbiota, all of them used the MiBioGen microbiota genome-wide association study (GWAS), with one also using the Dutch Microbiome Project. To find associations between the human genome and disease, various data sources were used, including the published GWAS in ankylosing spondylitis (AS), FinnGen, the UK Biobank, and the Integrative Epidemiology Unit (IEU) Open GWAS project.

RESULTS: MR findings revealed predicted increased abundances of Ruminococcaceae NK4A214 and Verrucomicrobia among others, alongside decreased abundances of Lactobacillaceae, and Rikenellaceae families, as well as the Bacteroides genus. These findings largely support the results from cross-sectional studies of the microbiota in patients with SpA. They suggest that bacteria that disrupt gut barrier function may result in an increased risk of SpA, while the opposite may be true with bacteria such as Alistipes and Bacteroides that may have a protective role.

CONCLUSIONS: These results underscore the interplay of genetics, microbiota, and disease. Further research is needed to refine these findings and optimise therapeutic approaches.},
}

@article {pmid40556581,
year = {2025},
author = {Guo, M and Li, B and Li, H and Chen, Y and Yuan, Q and Shui, M and Zhou, H and Hao, W and Wang, S},
title = {Colon-Targeted Natural Polysaccharide-Berberine Armored Hydrogel for the Treatment of Colitis.},
journal = {Advanced healthcare materials},
volume = {},
number = {},
pages = {e2404908},
doi = {10.1002/adhm.202404908},
pmid = {40556581},
issn = {2192-2659},
abstract = {The maintenance of gut immune homeostasis and microbial balance is pivotal in the pathogenesis and progression of ulcerative colitis (UC). Despite advances in therapy, effective UC management remains challenging due to the limited efficacy and significant side effects of conventional treatments. Inspired by the synergistic mechanisms of bioactive compounds in traditional Chinese medicine, a colon-targeted hydrogel integrating rhubarb-derived polysaccharides and berberine-loaded dendrimers is engineered. This hydrogel self-assembles via intermolecular hydrogen bonding and electrostatic interactions, enabling localized accumulation in colonic tissues to suppress aberrant immune activation and remodel the dysbiotic microbiome. Mechanistic studies reveal that the hydrogel potently promotes the polarization of anti-inflammatory M2 macrophages while suppressing pro-inflammatory cytokine secretion, resulting in significant amelioration of colitis symptoms in murine models. Importantly, the therapeutic intervention not only restored gut microbiota composition but also corrected metabolic disturbances, collectively contributing to the re-establishment of intestinal homeostasis. The findings underscore the potential of this polysaccharide-based hydrogel as an effective oral therapeutic strategy for UC while demonstrating the translational value of combining natural bioactive constituents for targeted drug delivery.},
}

@article {pmid40556523,
year = {2025},
author = {Huang, J and Liang, W and Zhang, R and Zhao, Y and Shi, R and Chen, X and Zheng, Y and Li, X and Liu, D and Wang, H and Liu, J and Liao, Y and Zhang, X and Jiang, Z and Fu, C and Huang, T and Shan, X and Wang, W and Bu, J and Peng, T and Shen, E},
title = {Pou2af1 Deficiency Aggravates DSS-Induced Colitis via Impaired Germinal Center Responses and Altered Gut Microbiota.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izaf089},
pmid = {40556523},
issn = {1536-4844},
support = {//The Affiliated Qingyuan Hospital/ ; 202301-316//Guangzhou Medical University/ ; JCXKJS2021C11//Discipline from School of Basic Medicine of Guangzhou Medical University/ ; 2021KTSCX090//Department of Education of Guangdong Province/ ; //Guangzhou Medical University 2022 Student Innovation Ability Improvement Program/ ; },
abstract = {BACKGROUND: Bob1 plays a critical role in immune system regulation, particularly in the function of B cells. Its deficiency in the context of colitis remains underexplored. This study investigates the effects of Bob1 (Pou2af1) deficiency on colitis, particularly focusing on immune responses and gut microbiota alterations in a murine model.

METHODS: In this study, we employed Pou2af1 knockout (KO) and wild-type (WT) mice to investigate the role of Bob1 in dextran sodium sulfate (DSS)-induced colitis. Colitis was induced by administering 2.5% DSS in drinking water for 7 days. Mice were monitored daily for weight loss, stool consistency, and rectal bleeding to calculate the disease activity index (DAI). Colon length was measured, and colon tissues were collected for histological analysis using hematoxylin and eosin (H&E) staining. Flow cytometry was performed to assess germinal center responses as well as the proportion of T helper (Th)1 and Th17 cells in the colonic lamina propria. Metagenomic sequencing was conducted on fecal samples to evaluate gut microbiota composition.

RESULTS: Pou2af1-deficient mice exhibited significantly exacerbated colitis compared to WT mice. This was evidenced by greater weight loss, elevated disease activity index, reduced colon length, and more severe pathological changes. Immune analysis revealed an impaired germinal center response, diminished generation of IgA⁺ plasma cells, and decreased Th17 cells in the colonic lamina propria in Pou2af1-deficient mice. Additionally, microbiota analysis indicated dysbiosis in the Pou2af1-deficient group, with a notable decrease in Bacteroides species and an increase in pro-inflammatory microbes.

DISCUSSION: The findings suggest that Pou2af1 deficiency exacerbates DSS-induced colitis by impairing immune responses, particularly the germinal center reaction, and altering gut microbiota composition. These alterations contribute to increased disease severity, highlighting the importance of Pou2af1 in maintaining intestinal immune homeostasis.},
}

@article {pmid40556416,
year = {2025},
author = {Zeng, Q and Wang, S and Nurxat, N and Min, X and Guo, Y and Chen, F and Tang, W and Yang, Y and Liu, Q and Li, M},
title = {Staphylococcus aureus Promotes Cutaneous Lesions in Patients With Epidermolysis Bullosa.},
journal = {Experimental dermatology},
volume = {34},
number = {6},
pages = {e70129},
doi = {10.1111/exd.70129},
pmid = {40556416},
issn = {1600-0625},
support = {//the Natural Science Foundation of China/ ; //National Key Research and Development Program of China/ ; },
mesh = {Humans ; *Staphylococcus aureus/pathogenicity/genetics/isolation & purification ; *Epidermolysis Bullosa/microbiology/pathology ; Male ; Female ; *Skin/microbiology/pathology ; Child ; Animals ; Microbiota ; Adolescent ; Adult ; Child, Preschool ; Young Adult ; RNA, Ribosomal, 16S ; Dysbiosis/microbiology ; China ; Mice ; },
abstract = {Epidermolysis bullosa (EB) is a group of rare, heterogeneous congenital conditions characterised by epidermal fragility, resulting in blister formation and lesions. Patients with EB are prone to developing cutaneous wounds. However, the composition of the EB skin microbiome in Chinese individuals remains poorly understood. The objective was to investigate the EB skin microbiome in Chinese individuals. The clinical symptoms and laboratory tests were collected for a total of 29 EB patients (23 Recessive Dystrophic EB, 3 EB simplex, 2 Kindler syndrome, and 1 Dominant Dystrophic EB). A total of 120 swabs were collected from 62 lesion sites, 29 non-lesion skin areas, and 29 nostrils. These samples underwent 16S rRNA amplicon sequencing and bacterial culture. The epidemiology of S. aureus was characterised, and its features were analysed using an animal model. Patients with EB exhibited a characteristic inflammatory response, marked by cutaneous lesions and elevated levels of C-reactive protein (CRP) and serum amyloid (SAA). Consistently, skin dysbiosis in EB patients was characterised by a predominance of S. aureus, particularly sequence type (ST) 7. Specifically, the abundance of S. aureus showed a positive correlation with EB severity and activity. Mechanistically, S. aureus isolated from lesional skin exhibited higher virulence due to increased accessory gene regulator (Agr) activity. Our study reported altered bacterial diversity and increased carriage of higher-virulence S. aureus in Chinese EB patients, which may potentially influence disease severity through microbiome alterations. Our findings suggested that maintaining the balance of the microbiome is crucial for optimising patient care.},
}

Humans
*Staphylococcus aureus/pathogenicity/genetics/isolation & purification
*Epidermolysis Bullosa/microbiology/pathology
Male
Female
*Skin/microbiology/pathology
Child
Animals
Microbiota
Adolescent
Adult
Child, Preschool
Young Adult
RNA, Ribosomal, 16S
Dysbiosis/microbiology
China
Mice

@article {pmid40556262,
year = {2025},
author = {Zhang, P and Garg, PP and Liu, L and Zhang, W and Kavanagh, K and Shetty, A and Howard, T and Varshney, N and Sawaya, D and Hawkins, G and Schwartz, DJ and Garg, PM},
title = {Distinct microbiota profiles in non-survivors in preterm infants with surgical necrotizing enterocolitis: Insights from FFPE intestinal tissue analysis.},
journal = {Journal of neonatal-perinatal medicine},
volume = {},
number = {},
pages = {19345798251353777},
doi = {10.1177/19345798251353777},
pmid = {40556262},
issn = {1878-4429},
abstract = {BackgroundThe variant microbiome is associated with necrotizing enterocolitis (NEC). We aimed to analyze remnant formalin fixed paraffin-embedded (FFPE) intestine tissue for microbiome profiling in preterm infants with surgical NEC.MethodsWe analyzed FFPE small intestine tissues from 16 infants with NEC (8 survivors and 8 non-survivors). Extracted DNA from FFPE tissue blocks underwent 16S rRNA sequencing. We compared the microbiota profiles in survivors and non-survivors. Alpha- and beta diversity metrics were calculated using QIIME2. To assess differences in overall microbial community structure, we performed a Permutational Multivariate Analysis of Variance (PERMANOVA). The analysis was performed in MaAsLin2 R package to determine the specific microbial taxa whose relative abundances were significantly associated with survival status in a multivariable linear model.ResultsSequencing of FFPE extracted DNA resulted in high-quality sequence reads in 16 cases.AnalysisAnalysis of microbial communities from 16 cases revealed a significant association between microbiome structure and survival status. Beta diversity analysis demonstrated distinct clustering of microbiome profiles between survivor and non-survivor groups. Alpha diversity metrics further characterized these differences: the non-survivor group exhibited a more complex and even microbiota (Shannon entropy, p = 0.02; Pielou's evenness, p = 0.017), whereas the survivor group's microbiome was significantly richer in observed features (p = 0.004). Notably, this association was specific to survival outcome, as overall community structure did not significantly differ when grouped by histological features of disease severity such as necrosis, inflammation, or hemorrhage. Linear mixed effect models and direct comparisons further identified numerous taxa potentially associated with survival status.ConclusionFFPE intestinal tissue enabled retrospective and spatially relevant microbiota assessment at the disease site. The non-survivors had complex microbiota and had distinct bacterial communities compared to survivors. Our findings suggest that the gut microbiome is a key factor related to prognosis, independent of other measures of NEC severity.},
}

@article {pmid40556049,
year = {2025},
author = {Kuo, CH and El-Omar, E and Kao, CY and Lin, JT and Wu, CY},
title = {Compositional and Metabolomic Shifts of the Gut Microbiome in Alcohol-Related Liver Disease.},
journal = {Journal of gastroenterology and hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jgh.17038},
pmid = {40556049},
issn = {1440-1746},
abstract = {Alcohol-related liver disease (ALD) is a major global health concern characterized by steatosis and liver inflammation due to chronic alcohol consumption. Emerging evidence suggests that ALD is not solely a liver pathology but also involves dysfunction of the gut-liver axis, where alterations in the gut microbiota play a significant role. Although alcohol-associated dysbiosis has been extensively studied, whether these microbial changes contribute to ALD development or are merely a consequence of alcohol exposure remains unclear. To prove causation, it is essential to decipher which specific taxa and their metabolites drive the maladaptation of host-microbiota interactions upon alcohol exposure. In this review, we summarize the compositional changes in the gut microbiome after alcohol exposure, identifying traits of alcohol-induced dysbiosis and distinguishing them from those associated with liver disease. The effects of alcohol-induced dysbiosis on microbial metabolism and host responses are reviewed, focusing on the key classes of microbiota-derived metabolites, notably free fatty acids, tryptophan and its indole derivatives, and secondary bile acids. We discuss how alterations in these metabolites disrupt intestinal barrier function, immune responses, and metabolic signaling pathways, thereby exacerbating alcohol-induced injury. Advanced omics technologies and microbiome modulation strategies will help further investigation into these mechanisms. Detailed mechanistic insights into host-microbiota interactions could unveil novel therapeutic targets, offering potential strategies to prevent or mitigate ALD by modulating the gut microbiome and its metabolites.},
}

@article {pmid40555888,
year = {2025},
author = {Tyagi, A and Kumar, V},
title = {The gut microbiota-bile acid axis: a crucial regulator of immune function and metabolic health.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {7},
pages = {215},
pmid = {40555888},
issn = {1573-0972},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology/physiology ; *Bile Acids and Salts/metabolism/immunology ; Animals ; Dysbiosis/immunology/microbiology ; Signal Transduction ; Metabolic Diseases/microbiology/immunology ; Liver/metabolism ; Receptors, G-Protein-Coupled/metabolism ; Bacteria/metabolism/classification ; Inflammatory Bowel Diseases/microbiology ; },
abstract = {The gut microbiota and bile acid metabolism are intricately linked, playing a crucial role in immune regulation, metabolic processes, and overall health. The gut microbiome, consisting of diverse bacterial genera such as Bacteroides, Clostridium, Lactobacillus, Bifidobacterium, and Eubacterium, facilitates the conversion of primary bile acids into secondary bile acids through enzymatic modifications. Bile acids, synthesized in the liver and modified by gut microbiota, act as signaling molecules that regulate immune responses via bile acid receptors, including the farnesoid X receptor (FXR), G protein-coupled bile acid receptor 1 (GPBAR1), pregnane X receptor (PXR), vitamin D receptor (VDR), and sphingosine-1-phosphate receptor 2 (S1PR2). Dysbiosis-an imbalance in gut microbial composition-disrupts bile acid metabolism, leading to impaired activation of bile acid receptors and contributing to various diseases. These include inflammatory bowel disease, metabolic disorders such as obesity and type 2 diabetes, autoimmune diseases like multiple sclerosis, and liver conditions such as cholestasis and non-alcoholic fatty liver disease. Dysfunctional bile acid receptor signaling further promotes chronic inflammation, metabolic dysregulation, and disturbances in gut-liver-immune homeostasis. Emerging therapeutic strategies targeting bile acid receptors, restoring microbiota balance, and implementing dietary interventions offer promising avenues for disease prevention and management. This review explores the pivotal role of gut microbiota in modulating immune responses through bile acid receptors and highlights their therapeutic potential in improving treatment outcomes.},
}

Humans
*Gastrointestinal Microbiome/immunology/physiology
*Bile Acids and Salts/metabolism/immunology
Animals
Dysbiosis/immunology/microbiology
Signal Transduction
Metabolic Diseases/microbiology/immunology
Liver/metabolism
Receptors, G-Protein-Coupled/metabolism
Bacteria/metabolism/classification
Inflammatory Bowel Diseases/microbiology

@article {pmid40555747,
year = {2025},
author = {Jarman, JB and Torres, PJ and Stromberg, S and Sato, H and Stack, C and Ladrillono, A and Pace, S and Jimenez, NL and Haselbeck, RJ and Insel, R and Van Dien, S and Culler, SJ},
title = {Bifidobacterium deficit in United States infants drives prevalent gut dysbiosis.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {867},
pmid = {40555747},
issn = {2399-3642},
mesh = {Humans ; *Bifidobacterium/isolation & purification/genetics ; *Gastrointestinal Microbiome ; *Dysbiosis/epidemiology/microbiology ; Infant ; United States/epidemiology ; Female ; Male ; Infant, Newborn ; Metagenomics ; },
abstract = {The composition of the infant gut microbiome is critical to immune development and noncommunicable disease (NCD) trajectory. However, a comprehensive evaluation of the infant gut microbiome in the United States is lacking. The My Baby Biome study, designed to address this knowledge gap, evaluated the gut microbiomes of 412 infants (representative of U.S. demographic diversity) using metagenomics and metabolomics. Regardless of birth mode and/or feeding method, widespread Bifidobacterium deficit was observed, with approximately 25% of U.S. infants lacking detectable Bifidobacterium. Bifidobacterium-dominant microbiomes exhibit distinct features when compared to microbiomes with other dominant microbial compositions including reduced antimicrobial resistance and virulence factor genes, altered carbohydrate utilization pathways, and altered metabolic signatures. In C-section birth infants, Bifidobacterium tended to be replaced in the human milk oligosaccharide utilization niche with potentially pathogenic species. Longitudinal health outcomes from these infants suggest that the disappearance of key Bifidobacterium may contribute to the development of atopy.},
}

Humans
*Bifidobacterium/isolation & purification/genetics
*Gastrointestinal Microbiome
*Dysbiosis/epidemiology/microbiology
Infant
United States/epidemiology
Female
Male
Infant, Newborn
Metagenomics

@article {pmid40555497,
year = {2025},
author = {Nei, J and Wu, Y and DU, Y},
title = {[The role of Staphylococcus aureus in the occurrence and development of chronic rhinosinusitis with nasal polyps].},
journal = {Lin chuang er bi yan hou tou jing wai ke za zhi = Journal of clinical otorhinolaryngology head and neck surgery},
volume = {39},
number = {7},
pages = {679-685},
doi = {10.13201/j.issn.2096-7993.2025.07.015},
pmid = {40555497},
issn = {2096-7993},
mesh = {Humans ; *Sinusitis/microbiology ; *Nasal Polyps/microbiology ; *Staphylococcus aureus ; Chronic Disease ; *Rhinitis/microbiology ; *Staphylococcal Infections/microbiology ; Quorum Sensing ; Biofilms ; Rhinosinusitis ; },
abstract = {Chronic rhinosinusitis with nasal polyps（CRSwNP） represents a prevalent inflammatory disorder, which is often accompanied by nasal congestion, mucopurulent discharge, olfactory dysfunction, dizziness, and headache. Staphylococcus aureus（SA）, a predominant opportunistic pathogen within the sinonasal microenvironment, has been implicated in modulating the pathogenesis and progression of CRSwNP through multifaceted mechanisms. The physiological activities of SA-dependent quorum-sensing system and biofilm in the nasal microenvironment, including interactions with host, fungi, viruses, and other bacteria, as well as the effects of important superantigens secreted by SA on the microenvironment and immune barrier, are briefly reviewed in this article. These insights provide theoretical foundations for elucidating CRSwNP mechanisms and advancing clinical therapeutic strategies.},
}

Humans
*Sinusitis/microbiology
*Nasal Polyps/microbiology
*Staphylococcus aureus
Chronic Disease
*Rhinitis/microbiology
*Staphylococcal Infections/microbiology
Quorum Sensing
Biofilms
Rhinosinusitis

@article {pmid40555474,
year = {2025},
author = {Akatsu, T and Souno, H and Fujii, A and Minegishi, Y and Ota, N and Yamashita, Y},
title = {Characteristics of Subgingival Plaque Microbiome in Japanese Older Adults With Healthy Gingiva.},
journal = {Journal of clinical periodontology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jcpe.14192},
pmid = {40555474},
issn = {1600-051X},
support = {//Kao Corporation/ ; },
abstract = {AIM: To elucidate the characteristics of the subgingival plaque microbiome in older adults without gingival inflammation.

MATERIALS AND METHODS: Subgingival plaque from 180 participants was collected and analysed using 16S rRNA sequencing. Based on the clinical parameters at the sampling sites, participants were categorised as healthy (gingival index [GI] = 0, maximum probing pocket depth [PPDmax] ≤ 2.0 and gingival recession [GR] = 0) or non-healthy (GI > 0, or PPDmax > 2.0 or GR > 0). Each group was further stratified by age into younger (< 65 years) and older (≥ 65 years) subgroups. We performed diversity and linear discriminant effect size (LEfSe) analyses to elucidate microbiome characteristics of healthy older adults.

RESULTS: We observed differences in α-diversity and β-diversity between younger and older individuals only in the healthy group. Healthy older individuals showed a lower α-diversity index, indicating a healthy-like profile shift and also a significantly greater difference in β-diversity from the non-healthy group than the healthy younger subgroup. LEfSe analysis indicated that six amplicon sequence variants (ASVs), such as Rothia dentocariosa, Neisseria perflava and Actinomyces sp. HMT-448, were predominant in the healthy older subgroup.

CONCLUSION: Maintaining lower α-diversity, with an abundance of R. dentocariosa and N. perflava, which are possible nitrate-reducing bacteria, may contribute to lifelong healthy gingiva by preventing microbial dysbiosis.},
}

@article {pmid40555367,
year = {2025},
author = {McGrath, AH and Steinberg, PD and Egan, S and Kjelleberg, S and Marzinelli, EM},
title = {Disruption of host-associated and benthic microbiota affects reproductive output and settlement of a habitat-forming macroalga.},
journal = {Proceedings. Biological sciences},
volume = {292},
number = {2049},
pages = {20250729},
doi = {10.1098/rspb.2025.0729},
pmid = {40555367},
issn = {1471-2954},
support = {//University of Sydney/ ; //Australian Research Council/ ; //Ecological Society of Australia/ ; },
mesh = {*Microbiota/drug effects ; Reproduction ; Ecosystem ; *Rhodophyta/microbiology/physiology ; Anti-Bacterial Agents/pharmacology ; },
abstract = {The reproduction and establishment of habitat-forming species are key processes affecting their persistence and associated biodiversity. In marine systems, microbial communities associated with habitat-forming macroalgae can influence various aspects of host performance; however, the role of these microorganisms in influencing macroalgal reproduction and settlement is poorly understood. Using a dominant habitat-forming macroalga on Australian rocky shores, Hormosira banksii, we manipulated host- and benthic-associated microbiota to determine the relative importance of microorganisms to reproductive output (number of viable eggs released) and settlement (settlement and morphogenesis of algal zygotes). Disruption of the host microbiota using antibiotics decreased reproductive output after 2 weeks, with the effect dependent on the type of antibiotic used. Disruption of host- and benthic-associated microbiota, in combination, caused a significant decrease in settlement of H. banksii zygotes, with the combined disruption having the greatest impact on settlement success. Our results demonstrate the importance of host-associated microbiota in macroalgal reproduction and an interactive effect of host- and benthic-associated microbiota on settlement-a key ecological process with important implications for host fitness and potentially ecosystem persistence.},
}

*Microbiota/drug effects
Reproduction
Ecosystem
*Rhodophyta/microbiology/physiology
Anti-Bacterial Agents/pharmacology

@article {pmid40555128,
year = {2025},
author = {Amsalu, A and Alvaro, A and Huang, S and May, A and Antipov, A and Quinn, L and Carney, B and Kopecki, Z},
title = {Risk factors for antimicrobial resistance in paediatric burn infections: Insights from a retrospective cohort study.},
journal = {Burns : journal of the International Society for Burn Injuries},
volume = {51},
number = {6},
pages = {107584},
doi = {10.1016/j.burns.2025.107584},
pmid = {40555128},
issn = {1879-1409},
abstract = {AIM: To define the microbiome, antimicrobial resistance profiles and associated risk factors among paediatric patients with infected burns.

METHODS: A retrospective cohort study was conducted among paediatric patients with infected burns admitted to a tertiary burns service between January 2011 to December 2023. Basic demographic data and burn-related clinical information were extracted from the Burns Unit database and linked with microbiological data.

RESULT: Among a total of 3679 paediatric burn patients admitted, 183 (5 % of overall admitted) were identified as clinically having infected burns. Of the 173 (4.7 % of overall admitted) patients with documented cultures, 152 (87.9 % of suspected clinical infections) had culture-positive burn wound infections (BWIs) and 15 (8.7 % of overall admitted) had developed blood stream infections. The most common microorganisms identified in BWI were Gram-positive bacteria (245 isolates, 63.1 %), with Staphylococcus aureus being the most prevalent (32 %) followed by Streptococcus species (11.9 %). Gram-negative bacteria were identified in 32.5 % of cases, with Pseudomonas aeruginosa being the most common organism (5.7 %). Nineteen (5 %) methicillin-resistant Staphylococcus aureus isolates were detected from 17 (9.8 %) paediatric patients with burns. The highest resistance was reported against ampicillin (100 %) followed by penicillin (91.7 %), and amoxicillin (88.6 %) against S. aureus isolates. P. aeruginosa isolates showed resistance in 58.8 % of cases to ceftazidime, followed by 47 % to piperacillin-tazobactam, and 2 isolates were resistant to imipenem, a carbapenem antibiotic considered a last-resort option. Multivariate logistic regression analysis revealed that burns to the head and neck regions (AOR = 5.2, 95 %CI: 2.20-12.31; p < 0.001), admission to the paediatric intensive care unit (PICU) (AOR = 8.2, 95 %CI: 1.03-64.86; p = 0.047) and previous medical history (AOR = 2.4, 95 %CI: 1.07-5.55; p = 0.033) were independent risk factors associated with antimicrobial-resistant (AMR) burn infections CONCLUSIONS: AMR in paediatric patients with infected burns is common and therefore early culture confirmation could improve treatment outcomes especially for patients with high risk factors.},
}

@article {pmid40555059,
year = {2025},
author = {Faysal, M and Zehravi, M and Amin, MA and Rab, SO and Jahnavi, P and Arjun, UVNV and Gupta, JK and Billah, AAM and Vodeti, R and Prasad, PD and Aseri, SSS and Siddiqui, FA and Bin Emran, T},
title = {Clinical insights into the mechanisms of infectious microbes and microbiota in chronic neurologic and psychiatric diseases.},
journal = {Pathology, research and practice},
volume = {272},
number = {},
pages = {156090},
doi = {10.1016/j.prp.2025.156090},
pmid = {40555059},
issn = {1618-0631},
abstract = {Chronic neurologic and psychiatric diseases such as schizophrenia, depression, Parkinson's, and Alzheimer's are increasingly linked to infectious microorganisms and gut microbiota. This review explores how pathogenic microorganisms and microbial communities impact neuropsychiatric, neurodegenerative, and neuroinflammatory processes, highlighting the gut-brain axis' crucial communication network in influencing behavior and brain function. Infectious agents like bacteria, viruses, and fungi cause disease by causing neurotoxic reactions, disrupting the blood-brain barrier, and activating neuroinflammatory cascades. Gut dysbiosis impacts immunological homeostasis and neural transmission by altering the synthesis of metabolites from microorganisms, such as short-chain fatty acids and neurotransmitter precursors. Neurodegeneration and psychiatric diseases are influenced by molecular mechanisms such as toll-like receptor signaling, microglial activation, and mitochondrial dysfunction. This review highlights the potential of microbiota-targeted treatments such as probiotics, prebiotics, and microbiome transplantation as novel treatments for chronic diseases. Understanding the intricate interactions between infectious microorganisms, microbiota, and the central nervous system enables the formation of precision medicine strategies to challenge the rising incidence of neurologic and psychiatric diseases. Future research should explore causal relationships and identify specific microbial biomarkers to enhance early diagnosis, prevention, and personalized treatment plans.},
}

@article {pmid40554434,
year = {2025},
author = {Chen, H and Gao, Y and Huang, H},
title = {Exploration of the GM-IC-DLBCL Axis: A Mendelian Randomization Analysis of the Gut Microbiota, Immune Cells, and Diffuse Large B-Cell Lymphoma.},
journal = {British journal of hospital medicine (London, England : 2005)},
volume = {86},
number = {6},
pages = {1-17},
doi = {10.12968/hmed.2025.0068},
pmid = {40554434},
issn = {1750-8460},
mesh = {*Lymphoma, Large B-Cell, Diffuse/immunology/genetics/microbiology ; Humans ; *Gastrointestinal Microbiome/immunology/genetics ; Mendelian Randomization Analysis ; Genome-Wide Association Study ; },
abstract = {Aims/Background This study aims to investigate the causal relationship among gut microbiome (GM), immune cells (IC), and diffuse large B-cell lymphoma (DLBCL) using the Mendelian randomization (MR) approach. Methods This analysis included GM data (471 taxa; n = 5959), genome-wide association study (GWAS) data on 731 IC phenotypes, and DLBCL data (1373 cases and 345,118 controls) from the FinnGen Consortium. A two-sample bidirectional MR analysis established causal links between GM, IC phenotypes, and DLBCL, followed by a two-step mediation analysis to assess immune cell mediation. Results Potential causal links were observed among 15 GM taxa, 38 IC phenotypes, and DLBCL. Mediation analysis revealed 14 possible gut microbiota-immune cell-diffuse large B-cell lymphoma (GM-IC-DLBCL) axes, with quantifiable effects in five. The maximum and minimum mediating effects included g__Roseibacillus (odds ratio [OR] = 3.30, 95% confidence interval [CI]: 1.22-8.91, p < 0.05; 10.4% via "CD45RA on naive CD8br cells") and s__Lachnospira rogosae (OR = 1.14, 95% CI: 1.01-1.28, p < 0.05; 5.8% via "CD127 on CD28- CD8br cells"), respectively. Conclusion This study suggests that GM may contribute to DLBCL pathogenesis through IC mechanisms, supporting the potential existence of a GM-IC-DLBCL axis.},
}

*Lymphoma, Large B-Cell, Diffuse/immunology/genetics/microbiology
Humans
*Gastrointestinal Microbiome/immunology/genetics
Mendelian Randomization Analysis
Genome-Wide Association Study

@article {pmid40554345,
year = {2025},
author = {Qi, X and Xu, X and Xu, C and Lv, G and Cai, J and Cheng, Z and Yang, Z and Yin, H},
title = {Pseudomonas plecoglossicida inoculation reshapes rhizosphere microbiome for BDE-47 dissipation in the alfalfa rhizosphere.},
journal = {Journal of hazardous materials},
volume = {495},
number = {},
pages = {138959},
doi = {10.1016/j.jhazmat.2025.138959},
pmid = {40554345},
issn = {1873-3336},
abstract = {Microbe-assisted phytoremediation emerges as a promising strategy for the removal of organic pollutants. In addition to the direct effects on plants and pollutants, the inoculant can induce changes in the rhizosphere microbiome; but its association with the dissipation of organic pollutants and the mechanisms underlying the rebuilding of rhizosphere microbiome remain unclear. Here, we study the effects of Pseudomonas plecoglossicida inoculation on BDE-47 elimination in the alfalfa rhizosphere, as well as the corresponding microbial response mechanisms. Microbial degradation in the rhizosphere, rather than plant extraction, was identified as the primary mechanism responsible for BDE-47 dissipation. Compared to the control without strain inoculation, BDE-47 concentration significantly decreased by 40.8 % with the strain inoculation in rhizosphere soil. The inoculate enriched populations of beneficial bacteria (e.g., Pseudomonas, Sphingomonas, Bacillus, and Lysobacter) known for their roles in promoting plant growth and degrading BDE-47. Furthermore, the inoculate markedly induced the production of root metabolites such as amino acids, carbohydrates, lipids, and terpenoids, which played a pivotal role in recruiting beneficial bacterial communities and enhancing the bioavailability of BDE-47. In conclusion, root metabolites and microbial inoculants collaboratively reshaped the rhizosphere microbiome, thereby supporting plant growth and enhancing the degradation of organic pollutants in the rhizosphere soils.},
}

@article {pmid40554292,
year = {2025},
author = {Li, J and Hu, J and Zhuo, D and Yang, L and Wang, L and Yang, B},
title = {Ginger-processed Magnoliae Officinalis Cortex ameliorates ovalbumin-induced asthma by alleviating inflammation via the gut-lung axis.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {145},
number = {},
pages = {156971},
doi = {10.1016/j.phymed.2025.156971},
pmid = {40554292},
issn = {1618-095X},
abstract = {BACKGROUND: The complex pathophysiology of asthma and the lack of effective therapies have driven research into natural product remedies. Ginger-processed Magnoliae Officinalis Cortex (GMOC), a traditional Chinese medicine, has been used for asthma treatment, but the lack of its potential mechanism of action limits the clinical application of GMOC.

PURPOSE: To investigate the mechanism of action of GMOC in asthmatic mice based on the gut-lung axis.

METHODS: The anti-asthma effects of GMOC were evaluated in an ovalbumin (OVA)-induced mouse model of asthma. The lung and gut microbiota were analysed via 16S rRNA gene sequencing and short-chain fatty acids (SCFAs) were determined using GC/MS. Protein expression was evaluated by western blotting. Additionally, the chemical profile of GMOC was elucidated using LC/MS. Candidate compounds targeting target proteins were screened using in silico analysis, and an in vitro experiment was used to preliminarily verify the results.

RESULTS: GMOC mitigated lung inflammation, mucus hypersecretion, and airway hyperresponsiveness (AHR) in asthmatic mice. It modulated the lung and gut microbiota and increased the levels of SCFAs in the colon, resulting in a reduction in inflammatory responses. In addition, GMOC downregulated transient receptor potential (TRP) channels and key proteins in the PI3K/AKT pathway in the lung and colon. The communication between TRPs and the PI3K/AKT pathway was further investigated in vitro using honokiol, the main compound in GMOC. Further, GMOC upregulated the expression of junction proteins in the lungs and colon to protect the epithelial barrier.

CONCLUSION: Crosstalk between organs (lung-gut-microbiota) and proteins (TRPs, junction proteins, and proteins in the PI3K/AKT pathway) contributes to the anti-inflammatory activities of GMOC in asthmatic mice.},
}

@article {pmid40554148,
year = {2025},
author = {Xiang, J and Zhou, Z and Liu, Z and Ren, C and Xu, Y},
title = {Constructing simplified microbial consortia that couple lactic acid and ethanol utilization to highly produce caproic acid from liquor-making wastewater.},
journal = {Water research},
volume = {284},
number = {},
pages = {123973},
doi = {10.1016/j.watres.2025.123973},
pmid = {40554148},
issn = {1879-2448},
abstract = {Converting biodegradable carbon in wastewater into medium-chain fatty acids (MCFAs) through stable microbiota is highly attractive. In this study, we utilized a top-down approach for constructing MCFA-producing microbial consortia. Specifically, an enrichment and plating-screening strategy employing lactic acid and ethanol as selective carbon sources was applied to isolate simplified caproic acid-producing microbial consortia from liquor-making pit mud. The representative microbial consortium SimpCom3 demonstrated high level of caproic acid production (14.62 ± 0.48 g/L) in a semi-synthetic medium, significantly outperforming consortium SimpCom1 (5.96 ± 0.11 g/L) and consortium SimpCom2 (9.63 ± 0.16 g/L). This performance of microbial consortium SimpCom3 was attributed to its ability to co-utilize lactic acid and ethanol, produce fewer odd-chain fatty acids byproducts, and maintain pH self-regulation between 6.45 and 8.29. Metagenomic analyses revealed the dominance of Clostridium kluyveri (30.69 %-50.46 %), C. butyricum (6.71 %-13.98 %) and C. tyrobutyricum (37.11 %-58.07 %) in consortium SimpCom3, which synergistically converted lactic acid and ethanol to caproic acid via reverse β-oxidation. Stable performance over 56 days of cyclic-batch fermentation processes confirmed the robustness of consortium SimpCom3. When applying consortium SimpCom3 to unsterilized liquor-making wastewater in a fermenter with a fed-batch approach, 22.13 g/L caproic acid was produced with 66.38 % selectivity, and microbial dynamics analysis demonstrated the consortium's high adaptability to real wastewater. Metabolic analysis based on high-quality assembly metagenomes (HQ-MAGs) revealed a novel cooperative metabolism: cross-feeding between Clostridium kluyveri (which utilizes ethanol and produces caproic acid) and lactate-utilizing butyrate producers maintained consortium stability and enhanced caproic acid production. Crucially, the decarboxylation of lactic acid counteracted acidification caused by ethanol-driven caproic acid synthesis, enabling self-regulated pH stability within the simplified microbiome system. Together, this study presents a simplified microbial consortium construction method for caproic acid production from liquor-making wastewater, overcoming the limitations of synthetic co-cultures and enhancing the viability of chain-elongation biorefineries in wastewater treatment.},
}

@article {pmid40554105,
year = {2025},
author = {Yang, SI and Im, H and Kim, Y and Kim, HB and Kim, JH and Yeom, J and Yoo, HJ and Kim, MJ and Seong, HJ and Oh, HY and Park, YJ and Kang, MJ and Lee, SH and Kim, HC and Kwon, SO and Lee, KS and Shin, YJ and Yoon, J and Choi, EJ and Shin, YH and Suh, DI and Park, JS and Kim, KW and Ahn, K and Kim, J and Hong, SJ},
title = {Exposome study for allergic diseases in children: Rationale and design of ECHO-COCOA study.},
journal = {Ecotoxicology and environmental safety},
volume = {302},
number = {},
pages = {118533},
doi = {10.1016/j.ecoenv.2025.118533},
pmid = {40554105},
issn = {1090-2414},
abstract = {BACKGROUND: Comprehensive consideration of the totality of environmental exposures and the resulting endogenous responses plays a crucial role in assessing the effect of early-life exposure on child health.

OBJECTIVES: The Exposome and Child Health with Omics-COhort for Childhood Origin of Asthma and allergic diseases (ECHO-COCOA) study was conducted based on the COCOA birth cohort, a general population-based cohort study that aimed to evaluate multi-omics signatures of environmental exposures and their effect on childhood allergic diseases, obesity and neurodevelopment in Korea.

METHODS: In total, 156 chemical pollutants and multi-omics profiles (methylome, genome, gut microbiome, transcriptome, metabolome, proteome, and multiplex cytokine assay) were investigated in 481 mother-child pairs. Our previous studies using omics analysis revealed the mechanisms of childhood allergic diseases. Studies on the complex interactions between early-life environmental exposures, omics, and various endotypes of childhood allergic diseases using an integrative multi-omics approach are underway. The ECHO-COCOA study will evolve further in the future by increasing its sample size, using advanced exposure measurement methods, integrating different omics technologies, and developing new statistical methods. Collaboration and integration with other birth cohort studies or external validation will aid in advancing the ECHO-COCOA study.

CONCLUSIONS: The findings of this study may enable the development of precision medicine and prevention of allergic diseases, obesity, and neurodevelopment based on harmful exposures, especially during critical periods of life.},
}

@article {pmid40553934,
year = {2025},
author = {Hazani, R and Weller, A and Turjeman, S and Sharon, E and Saleev, N and Moadi, L and Elliott, E and Bartal, IB and Koren, O},
title = {The social microbiome: Eubacterium links gut microbiota to prosocial behavior in stressed and naïve rats, a gut-brain axis study.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bbi.2025.06.023},
pmid = {40553934},
issn = {1090-2139},
abstract = {BACKGROUND: Prosocial behavior is associated with positive health outcomes, but the underlying biological mechanisms remain unclear, especially regarding the role of the gut microbiome.

RESULTS: We used the Helping Behavior Test to assess prosocial tendencies in rats and compared gut microbiome profiles between prosocial and non-social individuals across two experiments. In the first, we linked nucleus accumbens mRNA expression to microbiome composition in naïve rats. Prosocial behavior was associated with enriched Eubacterium species and genes tied to immune and neurotransmitter functions. An in vitro follow-up tested effects of additives on Eubacterium ventriosum. In the second experiment, we studied how early life stress (maternal separation) influenced prosocial behavior and the microbiome. Microbiome differences aligned with social behavior. Different stressors led to distinct microbiome profiles, especially among non-social rats, with variations in Bacillota and Bacteroidota abundance.

CONCLUSIONS: Overall, these detailed analyses provide insights into the behavioral, molecular, and microbial bases of prosocial behavior, highlighting the complex relationships between prosocial behavior, the gut-brain-microbiota axis, and early life experiences.},
}

@article {pmid40553933,
year = {2025},
author = {Kaufhold, CJ and Mani, KK and Akbari, Z and Sohrabji, F},
title = {Sex differences in neurological disorders: Insights from ischemic stroke, Parkinson's disease, and multiple sclerosis.},
journal = {Brain, behavior, and immunity},
volume = {129},
number = {},
pages = {335-347},
doi = {10.1016/j.bbi.2025.06.026},
pmid = {40553933},
issn = {1090-2139},
abstract = {Ischemic stroke, Parkinson's disease (PD), and multiple sclerosis (MS), are neurodegenerative disorders that exhibit significant sex differences in pathophysiology, clinical manifestations, and outcomes. Women are more likely to experience strokes in older age, with estrogen playing dual protective/detrimental roles depending on reproductive age. In PD, men show earlier onset and steadier decline, while women exhibit a protective estrogen-driven advantage and distinct gut-brain axis interactions. MS disproportionately affects women (3:1 ratio), particularly during reproductive years, with sex hormones and X-linked genes modulating autoimmune demyelination. This review synthesizes sex-specific mechanisms across these diseases, emphasizing immune dysregulation, hormonal influences, and emerging roles of the gut microbiome. Key modifiers such as epigenetic factors, microbiome composition, and sex chromosome interactions are discussed to inform personalized therapeutic strategies.},
}

@article {pmid40553921,
year = {2025},
author = {Liu, C and Yin, Z and Liu, X and Wang, X and Luo, J and Zhang, Z and Zhou, Y},
title = {Integrative transcriptomics and microbiomicsto exploring the mechanism of Lonicerae japonicae Flos-alleviated alcoholic liver disease.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107817},
doi = {10.1016/j.micpath.2025.107817},
pmid = {40553921},
issn = {1096-1208},
abstract = {Lonicerae japonicae Flos (LJF) is a well-known medicinal and food homologous (MFH) plant used for the prevention and treatment of liver diseases. Our preliminary study indicated that LJF can intervene in alcoholic liver injury (ALI); however, the relationship between genes and gut microbiota in preventing ALI is less clear in the context of LJF. Therefore, we aimed to elucidate the effects of LJF on inflammation and gut microbiota to prevent ALI using multi-omics analysis. Based on the RNA-Seq, we find that 1689 genes showed differential expression in the LJF group compared to model group. These genes are enriched with functions related to immune response, inflammation, and lipometabolism, such as PPAR signaling pathway, NF-κB signaling pathway, and so on. RNA-seq results showed that LJF may protect the liver from injuries through the PPAR/NF-κB pathway. Interestingly, LJF changed the gut microbiota and composition in ALI rat based on α-diversity and β-diversity, and enriched the Akkermansia, Bifidobacteriaceae, Bacteroides, Blautia, Romboutsia by using 16S rRNA gene sequencing. An integrative analysis revealed that the function of the gut microbiome in ALI is significantly associated with the PPAR signaling pathway and the NF-κB signaling pathway. These findings suggest that LJF exerts a hepatoprotective effect by alleviating inflammation, enhancing antioxidant capacity, and restoring the balance of the gut microbiota.},
}

@article {pmid40553881,
year = {2025},
author = {Paillé, V},
title = {Boosting Fertility Through Tryptophan: Linking Diet, Hormones, and the Gut Microbiome.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tjnut.2025.06.005},
pmid = {40553881},
issn = {1541-6100},
}

@article {pmid40553766,
year = {2025},
author = {Carrillo, MP and Vila-Costa, M and Barata, C},
title = {Micro-Bioplastic Impact on Gut Microbiome, Cephalic transcription and Cognitive Function in the aquatic invertebrate Daphnia magna.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126690},
doi = {10.1016/j.envpol.2025.126690},
pmid = {40553766},
issn = {1873-6424},
abstract = {The role of the gut microbiome-brain axis on contaminant effects in invertebrates is limited by our poor knowledge of gut microbiome neurological regulatory pathways. This study investigates the influence of microplastics on the gut microbiome composition and assess subsequent alterations in the cephalic transcriptome, feeding patterns, and overall behaviour of the organism. D. magna individuals were exposed to low and high levels of bioplastic particles and kaolin natural particles and under starving conditions. Feeding and behavioral effects were assessed using previously well-established assays. Changes in gut microbiome composition, cephalic transcription and their functional interpretation were studied by 16S rRNA gene sequencing and cephalic D magna RNA high-throughput sequencing, respectively, and using appropriate bioinformatic pipelines. Only exposures to high concentrations of bioplastic microparticles inhibited feeding and impacted behavioural responses in D. magna, resembling effects observed under starvation. Microbiome analysis revealed shifts in taxonomic composition and functional profiles across the tested microplastic concentrations, which become more notable at higher ones. Functional changes in the gut microbiome indicated that bioplastics at high concentrations altered to a greater extent short-chain fatty acid biosynthesis and tryptophan and L-glutamate metabolism pathways than at low concentrations. Transcriptomic analyses revealed that microplastics up-regulated neurological pathways, cell turnover, and differentiation. In summary exposure to microplastics resulted in gut dysbiosis and increased biosynthesis of short-chain fatty acid signalling pathways in the gut, altered neurological pathways in the cephalic transcriptome and disrupted behavioural responses, altogether supporting the role of the microbiota-gut-brain crosstalk on neurological disorders.},
}

@article {pmid40553763,
year = {2025},
author = {Villegas, V and Rajarajan, A and Funke, E and Susan, M and Sparmann, S and Perez, JPH and Schupp, B and Wolinska, J},
title = {Nanoplastics diversify and reshape Daphnia microbiomes in parasite-infected and uninfected hosts.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126698},
doi = {10.1016/j.envpol.2025.126698},
pmid = {40553763},
issn = {1873-6424},
abstract = {Nanoplastics (NPs) are emerging contaminants of concern that may interact with natural biotic stressors (such as parasites) to disrupt host-associated microbiomes, which play a crucial role in the health and ecological dynamics of aquatic animals. Here, we investigate the effects of polystyrene NP beads and parasite infection on the microbiome diversity and composition of the model plankton organism Daphnia magna. We exposed D. magna to two NP sizes (50 nm and 100 nm) at two concentrations (1 mg L[-1] and 5 mg L[-1]), both with and without infection by the yeast parasite Metschnikowia bicuspidata and sequenced the microbiomes of gut and body tissues using 16S rRNA gene sequencing. High concentrations of 50 nm NPs significantly increased bacterial richness in both gut and body tissue, with shifts exceeding those induced by parasite infection. In the gut, the relative abundances of Burkholderiales and Chitinophagales decreased, while Caulobacterales, Rhizobiales, and Salinisphaerales increased. In body tissues, Chitinophagales declined, whereas Burkholderiales, Caulobacterales, Rhizobiales, and Salinisphaerales were enriched. NP size, concentration and interaction with infection, significantly influenced gut and body microbiome alpha diversity. Bray-Curtis dissimilarity analysis confirmed that 50 nm NPs drove distinct shifts in bacterial community composition, independent of parasite infection. Overall, NP-size and concentration had a stronger influence on the Daphnia microbiome than parasite infection. Given the critical roles of the Daphnia microbiome in nutritional support and stress tolerance, our findings highlight the potential ecological impacts of NPs on aquatic ecosystems.},
}

@article {pmid40553754,
year = {2025},
author = {Karska, J and Skonieczna-Żydecka, K and Jakubiak, N and Czarnecka, W and Misiak, B},
title = {Short-chain fatty acids in mood and schizophrenia spectrum disorders: Evidence in the field and translational perspectives.},
journal = {Progress in neuro-psychopharmacology & biological psychiatry},
volume = {},
number = {},
pages = {111430},
doi = {10.1016/j.pnpbp.2025.111430},
pmid = {40553754},
issn = {1878-4216},
abstract = {The etiology of mood and schizophrenia spectrum disorders remains largely unknown. In recent years, several studies have focused on the role of the microbiome-gut-brain-axis (MGBA) in its etiology, providing several novel insights. The communication within MGBA involves various pathways leading through the vagus nerve and the bloodstream mediators. The latter are represented by short-chain fatty acids (SCFAs), produced by gut microbiota from dietary fiber. To date, several physiological and pathophysiological roles in the periphery and the central nervous system for SCFAs have been suggested. Studies investigating gut microbiota have consistently reported a decreased abundance of bacteria-producing SCFAs in people with mood and schizophrenia spectrum disorders. Yet, studies investigating faecal and blood levels of SCFAs have provided mixed findings. The present article provides a narrative review of studies examining the physiological roles of SCFAs, along with animal model and human studies addressing the involvement of SCFAs in mood and schizophrenia spectrum disorders, formulates future directions and provides translational perspectives.},
}

@article {pmid40553742,
year = {2025},
author = {Frutkoff, YA and Plotkin, L and Pollak, D and Livovsky, J and Focht, G and Lev-Tzion, R and Ledder, O and Assa, A and Yogev, D and Orlanski-Meyer, E and Broide, E and Kierkuś, J and Kang, B and Weiss, B and Aloi, M and Schwerd, T and Shouval, DS and Bramuzzo, M and Griffiths, AM and Yassour, M and Turner, D},
title = {Whole food diet induces remission in children and young adults with mild-moderate Crohn's disease and is more tolerable than exclusive enteral nutrition: a randomized controlled trial.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2025.06.011},
pmid = {40553742},
issn = {1528-0012},
abstract = {BACKGROUND: Tasty&Healthy (T&H) is a whole-food diet for Crohn's disease (CD), which excludes processed food, gluten, red meat, and dairy, without requiring formula or mandatory ingredients. TASTI-MM was a clinician-blinded, randomized-controlled trial comparing tolerability and effectiveness of T&H vs. exclusive enteral nutrition (EEN).

METHODS: Patients with biologic-naive mild-moderate CD aged 6-25 years were randomized to either T&H or EEN for 8 weeks, receiving weekly dietary support. Tolerability was evaluated by weekly interviews, questionnaires and intake diaries. Other outcomes included symptomatic remission, Mucosal-Inflammation Non-Invasive (MINI) index, calprotectin, C-reactive protein (CRP) and erythrocyte sedimentation rate (ESR). Fecal microbiome was analyzed by metagenomics at baseline, week-4 and week-8. Data were analyzed by the intention-to-treat approach unless specified otherwise.

RESULTS: Among 83 included patients (41 T&H, 42 EEN; mean age 14.5±3.7 years), 88% tolerated T&H vs. 52% for EEN (aOR 7.7 [95%CI 2.4-25]; p<0.001). Calprotectin, CRP and ESR decreased significantly in both groups, with no between-group differences. Symptomatic remission was achieved in 56% of T&H group vs. 38% of the EEN group (aOR 2.5 [0.98-6.3], p=0.1; per-protocol: 67% vs. 76%; p=0.47). Calprotectin <250μg/g was achieved in 34% vs. 33% (aOR 0.97 [0.37-2.6], p=0.84) and MINI<8 in 44% vs. 31% (aOR 1.8 [0.7-4.5]; p=0.33). Microbiome α-diversity improved in the T&H arm and declined in the EEN arm, showing superior species richness at both week-4 and week-8. Species associated with bowel inflammation, such as Ruminococcus gnavus, decreased in T&H and increased in EEN (q<0.001).

CONCLUSIONS: T&H demonstrated better tolerability than EEN for inducing remission in mild-to-moderate CD, while positively affecting the microbiome (TASTI-MM, NCT#04239248).},
}

@article {pmid40553443,
year = {2025},
author = {Wang, T and Xu, Y and Li, S and Du, R and Shi, J and Jiang, C and Wang, R and Zhu, Y},
title = {Novel Small-Molecule miR-124 Inducer Acts as "a Physiological Brake" of Inflammation in Ulcerative Colitis by Targeting the PIK3R2/PI3K/Akt Axis.},
journal = {Journal of medicinal chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jmedchem.5c01398},
pmid = {40553443},
issn = {1520-4804},
abstract = {Ulcerative colitis (UC), a chronic inflammatory bowel disease with limited therapeutic options, necessitates novel treatments targeting its complex pathophysiology. This study identified FHND5032, a novel small-molecule miR-124 inducer, as a potent therapeutic candidate for UC. We found that FHND5032 significantly upregulated miR-124 expression in macrophages, surpassing the clinical-stage comparator ABX464 in vitro and in vivo. Mechanistically, miR-124-5p directly targeted PIK3R2, suppressing the PI3K/Akt pathway and decreasing proinflammatory cytokines while promoting M2 macrophage polarization. In dextran sodium sulfate-induced mouse colitis, FHND5032 markedly reduced the disease activity index, restored colon length, preserved mucosal architecture, and repaired intestinal barrier integrity. Additionally, FHND5032 reversed gut dysbiosis by reducing Proteobacteria and enriching beneficial Firmicutes, outperforming ABX464 in microbiome modulation. Safety assessments confirmed no organ toxicity or biochemical abnormalities. Collectively, FHND5032 exerted multifaceted anticolitis effects by targeting the PIK3R2/PI3K/Akt axis, restoring immune homeostasis, and modulating gut microbiota, positioning it as a promising therapeutic agent for UC.},
}

@article {pmid40553348,
year = {2025},
author = {Ramakrishnan, R and Washington, A and Suveena, S and Rani, JR and Oommen, OV},
title = {From DNA to Big Data: NGS Technologies and Their Applications.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2952},
number = {},
pages = {459-482},
pmid = {40553348},
issn = {1940-6029},
mesh = {*High-Throughput Nucleotide Sequencing/methods ; *Big Data ; Humans ; *COVID-19/virology/epidemiology/genetics ; Genomics/methods ; SARS-CoV-2 ; Computational Biology/methods ; Sequence Analysis, DNA/methods ; *DNA/genetics ; },
abstract = {The last decade has witnessed an explosion in NGS data, which was the gift of advances in NGS technology as well as computing power. Along with AI, NGS is revolutionizing healthcare research. In this chapter, we briefly discuss the contribution of NGS in dealing with the COVID-19 pandemic and mention its application across various fields like oncology, agriculture, archaeogenetics, and space biology, followed by a historical perspective on sequencing, the evolution of NGS technologies and those currently in use. The chapter further outlines various NGS methods and workflows, detailing the key stages and the tools commonly employed for efficient analysis. Additionally, we highlight the surge and complexity of NGS data generated by genomics, transcriptomics, and microbiome studies, challenges and discusses their clinical applications. Toward the end, we explore the future directions of NGS. Given the rapid increase in data volume and complexity, there is an urgent need for efficient big data technologies, state-of-the-art tools, and techniques to manage, analyze, and derive actionable insights from these vast datasets, addressing the demands of the present-day scientific landscape.},
}

*High-Throughput Nucleotide Sequencing/methods
*Big Data
Humans
*COVID-19/virology/epidemiology/genetics
Genomics/methods
SARS-CoV-2
Computational Biology/methods
Sequence Analysis, DNA/methods
*DNA/genetics

@article {pmid40553325,
year = {2025},
author = {Mukhopadhyay, S and Ulaganathan, N and Dumpuri, P and Aich, P},
title = {Integrative AI-Based Approaches to Connect the Multiome to Use Microbiome-Metabolome Interactive Outcome as Precision Medicine.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2952},
number = {},
pages = {15-37},
pmid = {40553325},
issn = {1940-6029},
mesh = {Humans ; *Precision Medicine/methods ; *Metabolomics/methods ; *Metabolome ; Metagenomics/methods ; *Microbiota ; *Artificial Intelligence ; Computational Biology/methods ; Gastrointestinal Microbiome ; },
abstract = {In the era of Genome-Wide Association Studies (GWAS), biologists have unprecedented access to vast datasets, mirrored in the wealth of information from various omics studies, including genomics, transcriptomics, proteomics, metabolomics, and metagenomics. Integrating diverse data sources has emerged as crucial in unravelling the intricacies of biological processes. This chapter delves into our method for merging various omics methodologies, emphasizing metabolomics and metagenomics data. A powerful strategy addresses data processing challenges and opens new avenues for personalized microbiome-based interventions. The combined analysis of host and microbial metabolomics and metagenomics data has significantly advanced our understanding in diagnosing and treating conditions such as inflammatory bowel disease and irritable bowel syndrome. Metabolic signatures in biological fluids and their microbial counterparts serve as indicators, differentiating health from disease. The sheer volume of data demands sophisticated automated tools for processing and interpretation. Recognizing this need, integrating artificial intelligence (AI) and data science has become increasingly prominent. In this chapter, we combine microbiome and metabolome analyses through publicly available models to elucidate the correlations between microbial and metabolic profiles. By harnessing AI models across various omics data sources, this chapter bridges the gap between data acquisition and clinical applications, paving the way for personalized interventions and optimizing individual health.},
}

Humans
*Precision Medicine/methods
*Metabolomics/methods
*Metabolome
Metagenomics/methods
*Microbiota
*Artificial Intelligence
Computational Biology/methods
Gastrointestinal Microbiome

@article {pmid40552988,
year = {2025},
author = {Park, JM and Beckman, I and Delaney, CL},
title = {Narrative review of the association between gut microbiota and peripheral artery disease.},
journal = {Vascular medicine (London, England)},
volume = {},
number = {},
pages = {1358863X251346062},
doi = {10.1177/1358863X251346062},
pmid = {40552988},
issn = {1477-0377},
abstract = {It has been posited that the inflammatory process seen in atherosclerosis is underpinned by gut dysbiosis. Dysbiosis refers to alterations in the function, composition, and diversity of the human gut microbiota, all of which are influenced by endogenous and exogenous stimuli. Currently there is limited literature describing the association between gut microbiota and peripheral artery disease (PAD). This review summarizes the evidence surrounding the role of gut microbiota in the initiation of atherosclerosis (through direct infection of atherosclerotic plaque or systemic immune response to bacterial products and metabolites) and how dysbiosis may influence the various treatment modalities for PAD, including medical therapy (pharmacotherapy, lifestyle changes, and supervised exercise training) and surgery (endovascular and open revascularization). In particular, the role of short chain fatty acids (SCFAs), the effects of exercise on SCFA-producing and lactic acid bacteria (LAB) and, consequently, the lack of targeted research into dietary interventions and supplementation are highlighted in this review. This review highlights the potential for gut microbiota as not only a therapeutic target in patients with PAD, but also as a diagnostic and screening tool. It is imperative that the focus of future research is on the potential for personalized treatment which targets the gut microbiota (such as synbiotics, postbiotics, nicotinamide adenine dinucleotide (NAD) supplementation, selective antibiotics, resistance exercise, senolytics, and fecal microbial transplantation [FMT]) to be utilized as adjuncts to already existing treatment options for PAD. This review also highlights the potential role of biobanks and analysis of atherosclerotic plaques in further advancing knowledge and research in this area.},
}

@article {pmid40552978,
year = {2025},
author = {Oncu, AD and Ozgur, A and Ulgen, KO},
title = {Alterations in Gut Microbiota-Brain Axis in Major Depressive Disorder as Identified by Machine Learning.},
journal = {Omics : a journal of integrative biology},
volume = {},
number = {},
pages = {},
doi = {10.1089/omi.2025.0084},
pmid = {40552978},
issn = {1557-8100},
abstract = {Major depressive disorder (MDD) is a complex mental health condition whose causes may extend beyond purely biological explanations and are increasingly understood within wider ecological and social frameworks. Emerging research on the human gut-brain axis with the help of statistical and artificial intelligence tools aims to elucidate the links between the gut microbiota, diet, environment, and MDD. In this study, we analyzed data from the American Gut Project (AGP), including 361 control and 23 MDD samples, to find potential biomarkers associated with MDD. While alpha and beta diversity analyses revealed no significant differences except for age, multiple differential abundance tools and machine learning (ML) models (Random Forest and XGBoost), whose results were analyzed using Shapley Additive Explanations values, consistently detected a decrease in Bifidobacterium adolescentis and increases in Odoribacter, Ruminococcus, and Adlercreutzia among MDD samples. These four organisms influence inflammation, neurotransmitter balance, gut permeability, and other pathways associated with depression and thus can be recognized as potential biomarkers for MDD. This study highlights the promise of ML to decode the gut-brain axis as a first step in biomarker discovery, thus providing new possibilities for a personalized treatment approach and an improvement in diagnostic tools for MDD.},
}

@article {pmid40552763,
year = {2025},
author = {Claypool, J and Lindved, G and Myers, PN and Ward, T and Nielsen, HB and Blount, KF},
title = {Microbiome compositional changes and clonal engraftment in a phase 3 trial of fecal microbiota, live-jslm for recurrent Clostridioides difficile infection.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2520412},
doi = {10.1080/19490976.2025.2520412},
pmid = {40552763},
issn = {1949-0984},
mesh = {Humans ; *Clostridium Infections/therapy/microbiology ; *Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome ; *Feces/microbiology ; Male ; *Clostridioides difficile/physiology ; Female ; Middle Aged ; *Bacteria/classification/genetics/isolation & purification ; Adult ; Recurrence ; Aged ; },
abstract = {Live microbiota therapies have shown promise in many gastrointestinal diseases, including in the prevention of recurrent Clostridioides difficile infections (rCDI); however, frameworks for their pharmacokinetic and pharmacodynamic analysis are not fully established. Fecal microbiota, live-jslm (RBL) is the first microbiota-based product approved by the US Food and Drug Administration for the prevention of rCDI and was superior to placebo in the PUNCH™ CD3 phase 3 clinical trial (NCT03244644). In this analysis, deep shotgun metagenomic sequencing was used to assess changes in gut microbiome compositions of participants and engraftment of bacterial clonal populations (i.e. strains) from RBL to recipients. Among RBL responders, gut microbiota shifted toward compositions that resembled healthy donors as early as 1 week after RBL administration; the resulting microbiota compositions included clonal populations that engrafted from RBL to recipients. Engraftment was higher in RBL responders compared with non-responders, and many clonally engrafted populations persisted for ≥ 6 months. Bacteroidia species were among the most effectively engrafted species from RBL. This study utilizes data from a large clinical trial to establish a method with high specificity for exploring clonal engraftment from microbiota-based treatments to facilitate future pharmacokinetic and pharmacodynamic analyses.Clinicaltrials Registration: NCT03244644.},
}

Humans
*Clostridium Infections/therapy/microbiology
*Fecal Microbiota Transplantation
*Gastrointestinal Microbiome
*Feces/microbiology
Male
*Clostridioides difficile/physiology
Female
Middle Aged
*Bacteria/classification/genetics/isolation & purification
Adult
Recurrence
Aged

@article {pmid40552387,
year = {2025},
author = {Ozbek, DA and Koc, NS and İnal, N and Kablan, SE and Kaygusuz, Y and Karahan, S and Uyaroğlu, OA and Yildirim, T and Ergunay, K and Nemutlu, E and Akyon, Y and Altun, B},
title = {Interplay of gut microbiome and metabolome in various blood pressure phenotypes based on ambulatory BP monitoring reveal new insights in nondipper patients.},
journal = {Journal of hypertension},
volume = {},
number = {},
pages = {},
doi = {10.1097/HJH.0000000000004086},
pmid = {40552387},
issn = {1473-5598},
abstract = {OBJECTIVE: Accumulating evidence has shown an association between stool microbiome and hypertension. However, gut microbiome and metabolome of nondipping blood pressure (BP), high BP variability and morning BP surge have not been extensively studied. Here, we aimed to investigate the interplay between the gut microbiome, metabolome and 24-h urine sodium (Na) levels in different BP phenotypes.

METHODS: This study included 45 newly diagnosed hypertensive, and healthy participants. Ambulatory BP monitoring was performed in all patients to confirm the diagnosis and determine corresponding BP phenotypes. Gut microbiome and metabolome were determined using 16S ribosomal RNA sequencing and gas chromatography-mass spectrometry, respectively.

RESULTS: Firmicutes/Bacteroides ratio was higher in nondipper than dipper group (P = 0.01). Comparative analyses showed that 23 species, 21 genera and 9 families were significantly differentiated in different BP phenotype subgroups. Functional metabolomic enrichment analysis of nondipper patients showed enrichment of catecholamine biosynthesis and tyrosine metabolism due to noradrenaline, dopamine, 3,4-dihydroxyphenylglycol and 3,4-dihydroxyphenylacetic acid. Spearman analyses between significantly enriched metabolites and organized taxonomic units (OTUs) in nondipper patients showed correlations between 3,4-dihydroxyphenylglycol and Parabacteroides diastonis (rho = -0.33, P = 0.03) and dopamine with Chryseobacterium genus (rho = 0.71, P = 0.02). Enterococcus, Lachnobacterium, Odoribacter and Pseudomonas were positively, whereas Lactobacillus and Clostridium were negatively correlated with urine Na levels.

CONCLUSION: We revealed novel relationships among gut microbiome, metabolome and sodium intake in different BP phenotypes. Enrichment of catecholamine synthesis and correlations between OTUs and metabolites in nondipper patients indicated that sympathetic system activation via gut-brain axis could play a role in the nondipping BP profile.},
}

@article {pmid40552317,
year = {2025},
author = {Jafari, E and Azizian, R and Tabasi, M and Banakar, M and Bagheri Lankarani, K},
title = {Human Gut Bacteriophageome: Insights Into Drug Resistance Mechanisms in Tuberculosis.},
journal = {Interdisciplinary perspectives on infectious diseases},
volume = {2025},
number = {},
pages = {8811027},
pmid = {40552317},
issn = {1687-708X},
abstract = {Tuberculosis (TB), caused by Mycobacterium tuberculosis, remains a major global health burden. The emergence of drug-resistant strains presents a critical challenge in TB management. The recent research has explored the interaction between TB and the human gut bacteriophage community (phageome). The gut phageome plays a crucial role in regulating microbial diversity and functionality, and its composition and function have been linked to various health conditions. Examining the gut phageome through metagenomic analysis provides insights into its composition, role in health, and interactions with the host immune system. Exploring the interaction between the gut phageome and M. tuberculosis may reveal how phages affect the bacterium's pathogenicity, survival, and mechanisms of drug resistance. Understanding the gut phageome's impact on TB drug resistance could inform novel therapeutic strategies, such as phage therapy, and highlight the importance of microbiome-based interventions in combating drug-resistant TB strains. This review explores the role of the gut phageome in influencing drug resistance in TB, focusing on interaction mechanisms and potential therapeutic implications, synthesizing current research findings, and identifying knowledge gaps in this emerging field. This review also synthesizes the current evidence on the gut phageome's role in TB drug resistance, focusing on phage-mediated horizontal gene transfer (e.g., rpoB, katG), immune modulation, and preclinical efficacy of mycobacteriophage therapies. Key findings highlight phage cocktails (e.g., DS6A, D29 LysB) as promising adjuncts to antibiotics, reducing M. tuberculosis burden in murine models. These insights advocate for phage therapy as a complementary strategy against drug-resistant TB, urging clinical validation to bridge the existing knowledge gaps.},
}

@article {pmid40552289,
year = {2025},
author = {Xu, DT and Chen, Q and Yang, JY and Yan, GR and Zhang, LL and Liu, XJ and Wang, PR and Liu, J and Wang, XL},
title = {A noteworthy issue: microbiome data variation depending on sampling methods in skin microecology studies in acne vulgaris patients.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1566786},
pmid = {40552289},
issn = {1664-3224},
mesh = {Humans ; *Acne Vulgaris/microbiology/diagnosis ; *Skin/microbiology/pathology ; *Microbiota ; Female ; Male ; *Specimen Handling/methods ; Young Adult ; Adult ; *Bacteria/genetics/classification/isolation & purification ; Biopsy/methods ; },
abstract = {INTRODUCTION: Skin microecology significantly affects health, with the microbiome being a complex community of microorganisms. Different niche preferences of microorganisms raise concerns about the adequacy of common sampling methods like swabbing and cyanoacrylate biopsy. In this study, we aim to contribute to a more suitable sampling strategy in acne microbiome studies.

METHODS: This study involved ten mild to moderate acne patients. Three sampling methods were used: swab sampling (S1), modified standardized skin surface biopsy (S2), and individual comedo extraction (S3). DNA was extracted and sequenced to analyze the microbiome data.

RESULTS: There were significant differences in the bacterial and fungal microbiome data obtained by the three different sampling methods. Staphylococcus spp. (significantly higher in S3, P<0.05) and Malassezia spp. (higher in S3, P<0.05) were most affected by sampling methods. Bacterial phyla Proteobacteria (abundant in S1) and Bacteroidota (dominant in S2) also showed method-dependent variations.

CONCLUSION: The choice of sampling method significantly impacts microbiome data, highlighting the need for accurate sampling to understand the relationship between the skin microbiome and acne. Standardizing sampling methods in future studies is essential for advancing skin microecology research.

CLINICAL TRIAL REGISTRATION: http://www.chictr.org.cn, identifier ChiCTR-CPC-17012398.},
}

Humans
*Acne Vulgaris/microbiology/diagnosis
*Skin/microbiology/pathology
*Microbiota
Female
Male
*Specimen Handling/methods
Young Adult
Adult
*Bacteria/genetics/classification/isolation & purification
Biopsy/methods

@article {pmid40552287,
year = {2025},
author = {Dong, J and Lv, Y and Zhao, C and Shi, Y and Tang, R and He, L and Fan, R and Jia, X},
title = {Extraction of anthocyanins from purple sweet potato: evaluation of anti-inflammatory effects in a rheumatoid arthritis animal model, mechanistic studies on inflammatory cells, and development of exosome-based delivery for enhanced targeting.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1559874},
pmid = {40552287},
issn = {1664-3224},
mesh = {Animals ; *Anthocyanins/pharmacology/isolation & purification ; *Arthritis, Rheumatoid/drug therapy/immunology/pathology/metabolism ; *Ipomoea batatas/chemistry ; *Exosomes/metabolism ; Rats ; Humans ; *Anti-Inflammatory Agents/pharmacology/isolation & purification ; Disease Models, Animal ; *Arthritis, Experimental/drug therapy/pathology/immunology ; Apoptosis/drug effects ; Male ; Cell Line ; Cytokines/metabolism ; Gastrointestinal Microbiome/drug effects ; },
abstract = {OBJECTIVE: Rheumatoid arthritis (RA) is a chronic autoimmune disease marked by inflammation and joint damage. Anthocyanins, such as those from purple sweet potato are known for their anti-inflammatory effects.

METHODS: This study evaluated purple sweet potato anthocyanins (PSPA) therapeutic potential in RA using Human RA cells (MH7A) and collagen-induced arthritis (CIA) rat models. Rats were divided into control, CIA model, and three PSPA treatment groups (10, 20, 40 mg/kg) for 14 days. Meanwhile, exosomes were extracted from MH7A cells and loaded with PSPA, then co-incubated with inflammatory cells to observe the targeting capability of the drug-loaded exosomes.

RESULTS: PSPA significantly reduced joint swelling and structural damage in CIA rats, with the highest dose (40 mg/kg) reducing tissue hyperplasia and inflammatory infiltration. PSPA also altered the gut microbiota, increasing beneficial bacteria like Akkermansia and Lactobacillus. Molecular analysis showed reduced serum levels of inflammatory cytokines TNF-α, IL-1β, and rheumatoid factor (RF). In MH7A cells, PSPA decreased inflammatory cytokines (IL-1α, IL-6, IL-18), inhibited cell proliferation (IC50 = 1.43 μg/mL), and induced apoptosis by modulating Bcl-2, Bax, Caspase-3, and Caspase-9. PSPA also restored the PI3K/AKT signaling pathway, reversing the suppression seen in CIA models, particularly at 40 mg/kg. Flow cytometry and microscopy confirmed dose-dependent apoptosis and cell cycle modulation. Meanwhile the PSPA-loaded exosomes demonstrated a high targeting capability toward inflammatory cells.

CONCLUSION: These findings indicate that PSPA can alleviate RA symptoms by reducing inflammation, modulating gut microbiota, and promoting apoptosis in synovial fibroblasts, with exosome-encapsulated anthocyanins enhancing its targeting efficiency.},
}

Animals
*Anthocyanins/pharmacology/isolation & purification
*Arthritis, Rheumatoid/drug therapy/immunology/pathology/metabolism
*Ipomoea batatas/chemistry
*Exosomes/metabolism
Rats
Humans
*Anti-Inflammatory Agents/pharmacology/isolation & purification
Disease Models, Animal
*Arthritis, Experimental/drug therapy/pathology/immunology
Apoptosis/drug effects
Male
Cell Line
Cytokines/metabolism
Gastrointestinal Microbiome/drug effects

@article {pmid40552147,
year = {2025},
author = {Tang, L and Dong, W and Liu, D and Zhao, C and Chen, J and Wen, Y and Zeng, J and Dong, T and Yang, W},
title = {Gandouling ameliorates Wilson's disease-associated liver fibrosis in mice with associated faecal microbiome and metabolome remodeling.},
journal = {Frontiers in pharmacology},
volume = {16},
number = {},
pages = {1586171},
pmid = {40552147},
issn = {1663-9812},
abstract = {INTRODUCTION: Individuals with Wilson's disease (WD) exhibit liver fibrosis, a basic pathological change that was recently demonstrated to be dynamic and reversible. The gut microbiota markedly influences the occurrence of WD. Gandouling (GDL), a standardized Chinese herbal formula, has demonstrated an anti-fibrotic effect against WD-associated liver fibrosis. We sought to determine whether GDL may prevent liver fibrosis in toxic milk (TX) mice by assessing its ability to regulate gut microbiota, metabolites, and barrier function.

METHODS: TX male mice aged 6 months were analysed. GDL was administered at varying doses over a 6-week period. The biochemical indexes related to liver function, fibrosis, and inflammation were determined using commercial assay kits. Histological analyses and immunohistochemistry staining, were performed to evaluate the histopathological changes and collagen deposition in mouse liver tissues. Additionally, to detect alterations in the intestinal bacterial composition and metabolites, faecal samples were examined using non-targeted metabolomics and 16S rRNA sequencing.

RESULTS: The administration of GDL demonstrated anti-fibrotic effects on the liver, decreased serum inflammatory markers, ameliorated liver histopathology, and restored ileal permeability in the model group, as compared to the control group. Furthermore, a medium dosage of GDL treatment significantly rebalance microbiota composition and function and modulated lipid and lipid-like molecule levels.

DISCUSSION: Modulating intestinal homeostasis is a promising approach for treating liver fibrosis in patients with WD. Therefore, GDL may serve as a useful agent for treating WD-associated liver fibrosis.},
}

@article {pmid40552117,
year = {2025},
author = {Tong, X and Chen, X and Shen, C and Pan, J and Wang, X and Xu, X and Liu, S},
title = {Integrated analysis of microbiome and host transcriptome revealed correlations between tissue microbiota and tumor progression in early-stage papillary thyroid carcinoma.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1571341},
pmid = {40552117},
issn = {2235-2988},
mesh = {Humans ; *Thyroid Cancer, Papillary/microbiology/pathology/genetics ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Disease Progression ; *Thyroid Neoplasms/microbiology/pathology/genetics ; *Transcriptome ; Tumor Microenvironment/genetics ; Female ; Male ; Bacteria/classification/genetics/isolation & purification ; Middle Aged ; Adult ; },
abstract = {INTRODUCTION: Emerging evidences suggest that microorganisms in the tumor microenvironment play important roles in tumor occurrence and progression. However, the microbial distribution in the papillary thyroid carcinoma (PTC) tissue and its relationship with PTC are unclear.

METHODS: We performed 16S rRNA amplicon sequencing and RNA-Seq to characterize the tissue microbiome and transcriptome between the tumor and paracancerous tissue, respectively. The association analysis between microbes and host gene expression were conducted to screen the potential microbe-gene/cell interactions.

RESULTS: We found that the tumor tissues indeed harbored complex microbial communities, which showed significant differences in microbial and functional composition between the tumor and para-cancerous tissues. A set of differential microbial genera were identified to be significantly associated with the clinical factors, such as Planococcus enriched in tumor tissue, Limnobacter in T1a stage and Cutibacterium in N1b stage. 793 differential expressed genes were also identified, which are mainly enriched with functions related to cell-cell communication and extracellular matrix. In terms of the immune cell composition, 8 differential immune cell types were further identified, suggesting a significant immune response in PTC. Finally, association analysis identified 5 pairs of microbe-gene association and 1 pair of microbe-cell with significance, which were all involved in the tumorigenesis and tumor progression via inflammation-related pathways.

CONCLUSIONS: In addition to characterizing the tissue microbiome and host gene expression in PTC patients, we further explored the roles of microbe-gene/cell interactions in PTC. The results provide candidate biomarkers for exploring the molecular mechanisms of tissue microbiome in tumorigenesis and tumor progression of PTC.},
}

Humans
*Thyroid Cancer, Papillary/microbiology/pathology/genetics
*Microbiota/genetics
RNA, Ribosomal, 16S/genetics
Disease Progression
*Thyroid Neoplasms/microbiology/pathology/genetics
*Transcriptome
Tumor Microenvironment/genetics
Female
Male
Bacteria/classification/genetics/isolation & purification
Middle Aged
Adult

@article {pmid40552099,
year = {2025},
author = {Shah, SAUR and Tang, B and He, D and Ahmad, M and Nabi, G and Wang, C and Kou, Z and Wang, K and Hao, Y},
title = {Seasonal Breeding Alters Fecal Microbiota and Metabolome in the Male Captive Yangtze Finless Porpoise (Neophocaena asiaeorientalis asiaeorientalis).},
journal = {Ecology and evolution},
volume = {15},
number = {6},
pages = {e71611},
pmid = {40552099},
issn = {2045-7758},
abstract = {The Yangtze finless porpoise (YFP) is a critically endangered freshwater cetacean endemic to China. Understanding seasonal breeding patterns is critical for the effective conservation of critically endangered species. The current study was designed to examine the function and taxonomic characteristics of fecal microbiota and their metabolites in male captive YFPs during both nonbreeding (NB) and breeding (B) seasons, analyzing 20 fecal samples using both UHPLC-MS/MS and 16S rRNA gene sequencing approaches. The present study revealed that Firmicutes were increased in the NB season, while Actinobacteria, Proteobacteria, and Fusobacteriota were increased in the B season at the phylum level. At the genus level, Paeniclostridium, Clostridium_sensu_stricto_13, and Mycobacterium were increased in the NB season, while Romboutsia, Plesiomonas, and Cetobacterium were increased in the B season. LEfSe analysis revealed that Staphylococcus, Comamonas, and Tetrasphaera were significantly increased in the B season, while the genus Terrisporobacter was substantially increased in the NB season. The fecal metabolome undergoes significant changes during the B and NB seasons, altering metabolic pathways such as phenylalanine metabolism, protein digestion, taurine and hypotaurine metabolism, lysine degradation, tryptophan biosynthesis, tyrosine metabolism, and bile secretion. Moreover, there was a significant correlation between the fecal metabolome and microbiome in the captive YFPs in the B and NB seasons. This study explores the impact of seasonal reproduction on gut microbes and their metabolites, providing insights into animal seasonal reproductive behavior and providing a theoretical basis for studying gut microbiota and metabolites in cetaceans, both in captivity and in the wild.},
}

@article {pmid40552080,
year = {2025},
author = {Curso-Almeida, P and Subramaniam, M and Costa, MO and Adolphe, JL and Drew, MD and Loewen, ME and Weber, LP},
title = {Effects of feeding Candida utilis-fermented pea starch on overall, metabolic and intestinal health of dogs and cats.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1542484},
pmid = {40552080},
issn = {2297-1769},
abstract = {Pulse-based pet foods often contain peas or pea starch, which tend to impart a bitter taste. Fermentation increases feed palatability, but also has the potential to improve overall health. Therefore, the current study used the yeast, Candida utilis, to ferment pea starch for use in pet food and assessed health effects, focusing on metabolic and intestinal health in dogs and cats. Whole diets had ~30% starch inclusion of either C. utilis-fermented pea starch, unfermented pea starch, or a control corn diet fed over a 20-day period to beagle dogs and domestic cats. Complete blood count, biochemistry, adipokines, and triglyceride levels were assessed, along with fecal short chain fatty acids, microbial diversity and abundance to measure intestinal health. It was found that pea-based diets (regardless of fermentation) generally resulted in improved metabolic health by both species, indicated by lower plasma triglycerides, cholesterol, and leptin levels compared to the control corn diet. Additionally, the C. utilis-fermented pea starch diet improved dog fecal microbial diversity, while both pea diets increased richness and evenness in the microbial population and a larger Faecalibacterium population compared to dogs fed the corn-based diet. In contrast, cat microbiome could not be quantitatively evaluated due to poor fecal quality. Taken together, inclusion of pea starch improves metabolic and intestinal health after 20 days consumption in dogs, while fermentation of pea starch with C. utilis may provide additional benefit.},
}

@article {pmid40552053,
year = {2025},
author = {Menéndez, E and Brígido, C},
title = {Editorial: Deciphering the root nodule microbiome: implications for legume fitness and stress resilience.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1634838},
pmid = {40552053},
issn = {1664-302X},
}

@article {pmid40552042,
year = {2025},
author = {Mu, YQ and Song, JB and Zhao, M and Ren, P and Liu, HY and Huang, X},
title = {Integrative omics analysis of plant-microbe synergies in petroleum pollution remediation.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19396},
pmid = {40552042},
issn = {2167-8359},
mesh = {Biodegradation, Environmental ; *Medicago sativa/microbiology/metabolism/genetics ; Metabolomics ; *Petroleum Pollution ; *Petroleum/metabolism ; *Soil Pollutants/metabolism ; Rhizosphere ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; Hydrocarbons/metabolism ; Plant Roots/microbiology/metabolism ; Transcriptome ; Multiomics ; },
abstract = {As the petrochemical industry continues to advance, the exacerbation of ecological imbalance and environmental degradation due to petroleum pollution is increasingly pronounced. The synergistic interaction between plants and microorganisms are pivotal in the degradation of petroleum hydrocarbons; however, the underlying degradation mechanisms are not yet fully understood. This study aims to contribute to understanding these mechanisms by employing a multi-omics approach, integrating transcriptomics, 16S rRNA gene sequencing, and metabolomics, to analyze key differential genes, dominant microbial strains, and root-secreted metabolites involved in petroleum hydrocarbon degradation in alfalfa. Our findings revealed that several stress-related genes are upregulated in alfalfa contaminated with petroleum hydrocarbon. Moreover, Pseudomonas, Rhodococcus, and Brevundimonas were identified as dominant species in the rhizosphere microbiome. Metabolomics analysis identified pantothenic acid, malic acid, and ascorbic acid as critical metabolites that enhance hydrocarbon degradation. Application of pantothenic acid in oil-contaminated soil increased the degradation rate by approximately 10% compared to other treatments. These results highlight the potential of alfalfa-based phytoremediation strategies and offer a novel perspective for improving the efficiency of soil decontamination. Further research is needed to validate the scalability of these strategies for practical applications.},
}

Biodegradation, Environmental
*Medicago sativa/microbiology/metabolism/genetics
Metabolomics
*Petroleum Pollution
*Petroleum/metabolism
*Soil Pollutants/metabolism
Rhizosphere
RNA, Ribosomal, 16S/genetics
Soil Microbiology
Hydrocarbons/metabolism
Plant Roots/microbiology/metabolism
Transcriptome
Multiomics

@article {pmid40551757,
year = {2025},
author = {Goel, R and Singh, G and Pepine, CJ},
title = {Potential role of gut microbiota in cardiac arrhythmias.},
journal = {American heart journal plus : cardiology research and practice},
volume = {55},
number = {},
pages = {100557},
pmid = {40551757},
issn = {2666-6022},
}

@article {pmid40551742,
year = {2025},
author = {Jiang, Y and Li, Y},
title = {The role of nutrition and gut microbiome in childhood brain development and behavior.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1590172},
pmid = {40551742},
issn = {2296-861X},
abstract = {The intricate relationship between nutrition, the gut microbiome, and brain development has garnered significant attention in recent years, concerning its implications for child behavior and cognitive function. The gut-brain axis mediates this relationship through microbial modulation of inflammation, neuroactive compounds, and blood-brain barrier integrity, particularly during prenatal and early postnatal periods. Healthy dietary patterns such as whole foods, high-fiber foods, and minimally processed foods play a crucial role in shaping the gut microbiota, promoting microbial diversity and overall gut health. As a result, a balanced and diverse microbiome supports healthy brain function and development. Furthermore, disruptions in gut microbiota composition have been linked to various neurodevelopmental disorders in children, including autism spectrum disorder, attention deficit hyperactivity disorder, and anxiety. By integrating findings from animal models, clinical trials, and epidemiological studies, this review summarizes current advances on how early-life nutrition and gut microbiota interaction influence brain development and childhood behaviors. Ultimately, this paper underscores the potential for dietary interventions to promote optimal neurodevelopmental health and address behavioral issues in children.},
}

@article {pmid40551741,
year = {2025},
author = {Gaskell, C and MacDonald, R and Aleem, E and Bendriss, G},
title = {Obesity and cancer: unravelling the microbiome's hidden role.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1602603},
pmid = {40551741},
issn = {2296-861X},
abstract = {Obesity has been implicated as the driving force of many diseases including cancer through multiple biological mechanisms, including gut microbial imbalances, compromised intestinal barrier integrity, persistent low-grade inflammation, and alterations in energy uptake. As lifestyle factors such as diet, physical activity, and sleep are known to influence disease susceptibility, understanding the role of the gut microbiome in these interactions is critical. A deeper understanding of the intricate connections between gut microbiota, obesity, and various cancers could be used to better inform effective strategies for disease prevention and treatment. Investigating the microbiome's influence on tumor progression and systemic metabolic health may be the way forward for novel diagnostic and therapeutic approaches. It is essential to investigate how lifestyle factors are linked to both obesity and cancer, and what role the microbiome is playing. This review synthesizes current research on the mechanistic role of the gut microbiome in obesity and cancer, highlighting its potential role in early detection, prognosis, and its use as a targeted intervention to restore gut eubiosis.},
}

@article {pmid40551738,
year = {2025},
author = {Singh, R and Toumi, M and Salathé, M},
title = {Personalized glucose prediction using in situ data only.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1539118},
pmid = {40551738},
issn = {2296-861X},
abstract = {The worldwide rise in blood glucose levels is a major health concern, as various metabolic diseases become increasingly common. Diet, a modifiable health behaviour, is a primary target for the preventive management of glucose levels. Recent studies have shown that blood glucose responses after meals (post-prandial glucose responses, PPGR) can vary greatly among individuals, even with identical food consumption, and demonstrated accurate PPGR prediction using various features like microbiome data and blood parameters. Our study addresses whether accurate PPGR prediction can be achieved with a limited and easily obtainable set of data collected in real-world, everyday settings. Here, we show that a machine learning algorithm with such real-world data (RWD) collected from a digital cohort with over 1,000 participants can achieve high accuracy in PPGR prediction. Interestingly, we find that the best PPGR prediction model only required glycemic and temporally resolved diet data. This ability to predict PPGR accurately without the need for biological lab analysis offers a path toward highly scalable personalized nutrition and glucose management strategies.},
}

@article {pmid40551557,
year = {2025},
author = {Han, F and Li, W and Duan, N and Hu, X and Yao, N and Yu, G and Qu, J},
title = {Relationship Between Salt Intake and Cardiovascular Disease.},
journal = {Journal of clinical hypertension (Greenwich, Conn.)},
volume = {27},
number = {6},
pages = {e70078},
doi = {10.1111/jch.70078},
pmid = {40551557},
issn = {1751-7176},
mesh = {Humans ; *Cardiovascular Diseases/epidemiology/etiology/prevention & control ; *Sodium Chloride, Dietary/adverse effects ; Blood Pressure/drug effects/physiology ; Gastrointestinal Microbiome ; Risk Factors ; Hypertension/epidemiology ; Heart Disease Risk Factors ; Feeding Behavior/physiology ; },
abstract = {Cardiovascular disease (CVD) is a predominant global health issue, with dietary salt intake recognized as a crucial modifiable risk factor. This review elucidates the multifaceted relationship between salt consumption and CVD, exploring both its direct and indirect effects. While early research emphasized salt's influence on blood pressure, contemporary studies highlight the combined effects of dietary habits and genetic factors on CVD risk. The paper underscores the complex biological mechanisms linking high salt intake to CVD, including its impact on blood pressure, direct cardiovascular effects, immune responses, the role of prostanoids, epigenetic changes, and gut microbiome. Additionally, the review delves into the concept of salt sensitivity and its genetic underpinnings, emphasizing the heightened CVD risk in salt-sensitive individuals. The potential benefits and challenges of salt substitutes are also discussed. Drawing from various study designs, including epidemiological studies and randomized controlled trials, the review provides a comprehensive understanding of the detrimental effects of excessive salt intake on cardiovascular health, emphasizing the need for refined dietary guidelines and targeted interventions.},
}

Humans
*Cardiovascular Diseases/epidemiology/etiology/prevention & control
*Sodium Chloride, Dietary/adverse effects
Blood Pressure/drug effects/physiology
Gastrointestinal Microbiome
Risk Factors
Hypertension/epidemiology
Heart Disease Risk Factors
Feeding Behavior/physiology

@article {pmid40551374,
year = {2025},
author = {Gould, AAM and Walsh, NP and Tipton, MJ and Zurawlew, MJ and Tayari, O and House, C and Delves, SK and Robson, SC and Shute, JJ and Watts, JEM and Roberts, AJ and Rawcliffe, AJ and Robinson, MR and Corbett, J},
title = {Faecal microbiome, gastrointestinal integrity, inflammation and thermoregulation in recent exertional heat illness patients and matched controls.},
journal = {Experimental physiology},
volume = {},
number = {},
pages = {},
doi = {10.1113/EP092849},
pmid = {40551374},
issn = {1469-445X},
support = {//Army Recruiting and Initial Training Command/ ; },
abstract = {The gastrointestinal (GI) microbiota and GI barrier integrity are hypothesised to contribute to exertional heat illness (EHI) aetiology. We compared the faecal microbiome, GI barrier integrity, inflammation and thermoregulation of 29 recent (∼4 months) EHI patients (a group with elevated EHI risk) and 29 control individuals without prior EHI history, matched for variables influencing thermoregulation and GI microbiota. Participants completed an exercise heat tolerance assessment (HTA), with faecal microbiome assessed by 16S rRNA gene amplicon sequencing of stool samples and blood biomarkers of GI barrier integrity and inflammation measured pre- and post-HTA. With the exception of the Simpson index (patient = 0.97 ± 0.01 vs. control = 0.98 ± 0.00, P = 0.030), there were no between-groups differences in faecal microbiome composition (α-diversity, β-diversity, relative abundance, differential abundance), GI barrier integrity, inflammation or terminal thermoregulatory indices. Individuals were subsequently classified as heat tolerant (n = 46) or intolerant (n = 12) on the basis of the HTA. Heat intolerant individuals demonstrated lower sudomotor response (intolerant = 0.53 (0.17) vs. tolerant = 0.62 (0.20) L m[-2] h[-1], P = 0.011) despite greater thermoregulatory strain (e.g., terminal Trec: intolerant = 39.20 ± 0.31 vs. tolerant = 38.80 ± 0.31°C, P < 0.001), lower Firmicutes:Bacteroidota ratio (intolerant = 3.7 (0.6) vs. tolerant = 4.5 (2.0), P = 0.019) and higher plasma [sCD14] (P = 0.014), but other aspects of faecal microbiome, GI integrity or inflammation did not differ from heat tolerant individuals. In conclusion, the faecal microbiome composition and the GI barrier integrity and inflammatory responses to exercise heat-stress showed limited differences between recent EHI patients and matched controls, or between individuals classified as heat intolerant or heat tolerant and are unlikely to explain elevated EHI risk in recent EHI patients, or heat intolerance.},
}

@article {pmid40551275,
year = {2025},
author = {Zhang, Q and Du, M and Shen, Y and Lu, X and Jin, M and Wang, Y},
title = {Prevotella stercorea increases fat deposition in Jinhua pigs fed alfalfa grass-based diets.},
journal = {Journal of animal science and biotechnology},
volume = {16},
number = {1},
pages = {88},
pmid = {40551275},
issn = {1674-9782},
support = {U21A20249//National Natural Science Foundation of China/ ; CARS-35//National Center of Technology Innovation for Pigs/ ; YFD1300702//National Key R&D Program of China/ ; },
abstract = {BACKGROUND: Fat is a key component of body composition in both humans and animals, with intramuscular fat (IMF) being a critical determinant of pork quality. Higher IMF level enhances meat qualities such as flavor, tenderness, and juiciness, directly influencing consumer preference and market demand. Therefore, identifying microbial biomarkers associated with fat deposition is essential for improving meat quality in livestock and understanding how gut microbiota regulates host metabolism.

RESULTS: In this study, we examined changes in meat quality, fat metabolism, and gut microbiota during the pig life cycle, from weaning to marketing. We found that Jinhua pig exhibited higher IMF content and marbling score, and higher α diversity of colonic microbial communities. Microbiome Multivariate Association with Linear Models was used to identify the core genera associated with age, breed, and feed, and Prevotella was found to respond to both age and breed factors. The correlation analysis of fat deposition indicators with microbial genera revealed that Prevotella was a potential biomarker in response to IMF. In addition, the P. stercorea DSM 18206 (P. stercorea) was identified in porcine sample and administered to pseudo sterile mouse to examine the effect on IMF deposition. We found that the gavage of P. stercorea with alfalfa-enriched diet led to a significant increase in triglyceride (TG) and IMF contents in muscle. Metabolomic analysis further confirmed P. stercorea may potentially regulate fat deposition through the sphingolipid signaling pathway.

CONCLUSIONS: We identified P. stercorea as a potential biomarker linked to higher IMF deposition and validated their role in shaping the gut microbiota and promoting fat accumulation in a mouse model, which correlated with the sphingolipid signaling pathway. These findings provide valuable insights into the role of P. stercorea in regulating fat deposition and metabolic health, offering implications for improving both livestock meat quality and lipid metabolism in humans.},
}

@article {pmid40550997,
year = {2025},
author = {Zhang, Y and Ke, S and Wang, XW and Sun, Y and Weiss, ST and Liu, YY},
title = {Association rule mining of the human gut microbiome.},
journal = {Science China. Life sciences},
volume = {},
number = {},
pages = {},
pmid = {40550997},
issn = {1869-1889},
abstract = {The human gut carries a vast and diverse microbial community that is essential for human health. Understanding the structure of this complex community is a crucial step toward comprehending human-microbiome interactions. Traditional co-occurrence and correlation analyses typically focus on pairwise relationships and ignore higher-order relationships. Association rule mining (ARM) is a well-developed technique in data mining and has been applied to human microbiome data to identify higher-order relationships. Yet, existing attempts suffer from small sample sizes and low taxonomic resolution. We developed an advanced ARM framework and systematically investigated the interactions between microbial species using a public large-scale uniformly processed human microbiome data from the curatedMetagenomicData (CMD) together with ARM. First, we inferred association rules in the gut microbiome samples of healthy individuals (n=2,815) in CMD. Then we compared those rules with those inferred from the individuals with different diseases: inflammatory bowel disease (IBD, n=768), colorectal cancer (CRC, n=368), impaired glucose tolerance (IGT, n=199), and type 2 diabetes (T2D, n=164). Finally, we demonstrated that ARM is an efficient feature selection tool that can improve the performance of microbiome-based disease classification. Together, this study illustrates the higher-order microbial relationships in the human gut microbiome and highlights the critical importance of incorporating association rules in microbiome-based disease classification.},
}

@article {pmid40550754,
year = {2025},
author = {Dubey, VP and Kansagra, JJ and Sureja, VP and Kheni, DB},
title = {Efficacy of a Probiotic Combination on Glycemic Index and Insulin Resistance in Adults: A Systematic Review and Meta-Analysis.},
journal = {Journal of dietary supplements},
volume = {},
number = {},
pages = {1-23},
doi = {10.1080/19390211.2025.2522463},
pmid = {40550754},
issn = {1939-022X},
abstract = {Insulin resistance leads to increased glucose and insulin levels. Probiotics can reduce insulin resistance, but the presence of different probiotic strains and doses prevents the generalization to real-world scenario. The current systematic review and meta-analysis study investigated the efficacy of a triple probiotic combination (Lactobacillus acidophilus, Lactobacillus casei, and Bifidobacterium bifidum) on glycemic index and insulin resistance parameters in adults. Randomized controlled trials evaluating the efficacy of the probiotics combination on glycemic index and insulin resistance parameters were identified. Physiotherapy Evidence Database scale and the Cochrane Risk of Bias tool were used for risk of bias assessment and RevMan for meta-analysis. Fourteen good-quality clinical trials were included in the current study. Low-to-moderate risk of bias was observed. Data from 823 participants were included. Probiotics supplementation significantly reduced insulin resistance (MD: -1.05 HOMA-IR score, p < 0.00001), serum glucose (MD: -3.99 mg/dl, p = 0.0003) and insulin levels (MD: -3.79 µIU/ml, p < 0.00001), while significantly improved insulin sensitivity (MD: +0.02 QUICKI score, p < 0.00001) and pancreatic β-cell functioning (MD: -14.71 HOMA-B score, p < 0.00001) compared to the control group. Significant heterogeneity was observed for all evaluation parameters (except the HOMA-B score) while no significant publication bias was observed. The current study suggests that the probiotic combination of Lactobacillus acidophilus, Lactobacillus casei, and Bifidobacterium bifidum is effective in reducing insulin resistance, improving glycemic index parameters, and improving pancreatic β-cell functioning in adults by improving the gastrointestinal microbiome.},
}

@article {pmid40550680,
year = {2025},
author = {Lin, M and Hu, L and Hao, L and Wang, Z},
title = {[Microbiome and its genetic potential for carbon fixation in small urban wetlands].},
journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology},
volume = {41},
number = {6},
pages = {2415-2431},
doi = {10.13345/j.cjb.240399},
pmid = {40550680},
issn = {1872-2075},
mesh = {*Wetlands ; *Microbiota/genetics ; *Carbon Cycle/genetics ; *Bacteria/genetics/metabolism/classification ; RNA, Ribosomal, 16S/genetics ; China ; Cities ; Geologic Sediments/microbiology ; Archaea/genetics/metabolism/classification ; Metagenomics ; Metagenome ; },
abstract = {Small urban wetlands are widely distributed and susceptible to human activities, serving as important sources and sinks of carbon. Microorganisms play a crucial role in carbon cycle, while limited studies have been conducted on the microbial diversity in small urban wetlands and the functions of microbiome in carbon fixation and metabolism. To probe into the microbiome-driven carbon cycling in small urban wetlands and dissect the composition and functional groups of microbiome, we analyzed the relationships between the microbiome structure, element metabolism pathways, and habitat physicochemical properties in sediment samples across three small wetlands in Huzhou City, and compared them with natural wetlands in the Zoige wetland. High-throughput sequencing of 16S rRNA gene amplicons and metagenomics was employed to determine the species and functional groups. Sixty medium to high-quality metagenome-assembled genomes (MAGs) were constructed, including 55 bacterial and 5 archaeal taxa, and their potential in driving elemental cycles were analyzed, with a focus on carbon fixation. Several bacterial species were found to encode a nearly complete carbon fixation pathway, including the Calvin cycle, the reductive tricarboxylic acid cycle, the Wood-Ljungdahl pathway, and the reductive glycine pathway. There were several potential novel carbon-fixing bacterial members, such as those belonging to Syntrophorhabdus (Desulfobacterota) and UBA4417 (Bacteroidetes), which had high relative abundance in the wetland microbiome. Unveiling the genetic potential of these functional groups to facilitate element cycling is of great scientific importance for enhancing the carbon sequestration capacity of small urban wetlands.},
}

*Wetlands
*Microbiota/genetics
*Carbon Cycle/genetics
*Bacteria/genetics/metabolism/classification
RNA, Ribosomal, 16S/genetics
China
Cities
Geologic Sediments/microbiology
Archaea/genetics/metabolism/classification
Metagenomics
Metagenome

@article {pmid40550667,
year = {2025},
author = {Zhao, X and Jiang, C and Liu, S},
title = {[Synthetic microbiomes: rational design, engineering strategies, and application prospects].},
journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology},
volume = {41},
number = {6},
pages = {2221-2235},
doi = {10.13345/j.cjb.250201},
pmid = {40550667},
issn = {1872-2075},
mesh = {*Microbiota/genetics ; *Synthetic Biology/methods ; Biotechnology/methods ; Biodegradation, Environmental ; Humans ; },
abstract = {Microbiomes in natural environments have diverse functions and harbor vast exploitable potential of modifying the nature and hosts, being significant resources for development. The inherent high complexity and uncontrollability of natural microbiomes, as well as the selection by the nature and hosts, impose significant constraints on practical applications. Synthetic microbiomes, serving as precisely defined engineered microbiomes, demonstrate enhanced functionality, stability, and controllability compared with natural microbiomes. These engineered microbiomes emerge as a prominent research focus and are potentially having applications across various fields including environmental bioremediation and host health management. Nevertheless, substantial challenges persist in both fundamental research and practical application of synthetic microbiomes. This review systematically summarizes three core design principles for synthetic microbiomes, introduces current construction strategies including top-down, bottom-up, and integrated approaches, and comprehensively lists their applications in environmental remediation, agricultural innovation, industrial biotechnology, and healthcare. Furthermore, it critically examines existing technical and conceptual challenges while proposing strategic recommendations, thereby providing theoretical guidance for future advancements in the design, engineering, and application of synthetic microbiomes.},
}

*Microbiota/genetics
*Synthetic Biology/methods
Biotechnology/methods
Biodegradation, Environmental
Humans

@article {pmid40550666,
year = {2025},
author = {Liu, S},
title = {[Preface for special issue on microbiome engineering].},
journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology},
volume = {41},
number = {6},
pages = {1-6},
doi = {10.13345/j.cjb.250476},
pmid = {40550666},
issn = {1872-2075},
mesh = {*Microbiota ; Humans ; *Biotechnology ; *Bioengineering ; },
abstract = {Microbiome engineering is an emerging interdisciplinary field that systematically investigates and applies engineering methods to uncover the functions, structures, and interaction mechanisms of microbial communities with their environments, offering critical insights into global challenges. To showcase the latest advancements and achievements in this field, Chinese Journal of biotechnology has specially organized a special issue, inviting experts and scholars from multiple domestic institutions to elaborate on the practical applications and potential of microbiome engineering in agriculture and industrial production, environmental and ecological restoration, and health and medical treatment, from perspectives of fundamental research, technological innovation, and engineering applications. Additionally, this issue explores future trends in the field, providing valuable references to promote innovation and contribute to the sustainable development of human society.},
}

*Microbiota
Humans
*Biotechnology
*Bioengineering